Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles

P.F. Colosimo, K.E. Hosemann, S. Balabhadra, G. Jr Villarreal, M. Dickson, J. Grimwood, J. Schmutz, R.M. Myers, D. Schluter, D.M. Kingsley

10.1126/science.1107239

 

Major phenotypic changes evolve in parallel in nature by molecular mechanisms that are largely unknown. Here, we use positional cloning methods to identify the major chromosome locus controlling armor plate patterning in wild threespine sticklebacks. Mapping, sequencing, and transgenic studies show that the Ectodysplasin (EDA) signaling pathway plays a key role in evolutionary change in natural populations and that parallel evolution of stickleback low-plated phenotypes at most freshwater locations around the world has occurred by repeated selection of Eda alleles derived from an ancestral low-plated haplotype that first appeared more than two million years ago. Members of this clade of low-plated alleles are present at low frequencies in marine fish, which suggests that standing genetic variation can provide a molecular basis for rapid, parallel evolution of dramatic phenotypic change in nature.

 

A Septin Diffusion Barrier at the Base of the Primary Cilium Maintains Ciliary Membrane Protein Distribution

Q. Hu, L. Milenkovic, H. Jin, M.P Scott, M.V. Nachury, E.T. Spiliotis, W.J. Nelson

10.1126/science.1191054

 

In animal cells, the primary cilium transduces extracellular signals through signaling receptors localized in the ciliary membrane, but how these ciliary membrane proteins are retained in the cilium is unknown. We found that ciliary membrane proteins were highly mobile, but their diffusion was impeded at the base of the cilium by a diffusion barrier. Septin 2 (SEPT2), a member of the septin family of guanosine triphosphatases that form a diffusion barrier in budding yeast, localized at the base of the ciliary membrane. SEPT2 depletion resulted in loss of ciliary membrane protein localization and Sonic hedgehog signal transduction, and inhibited ciliogenesis. Thus, SEPT2 is part of a diffusion barrier at the base of the ciliary membrane and is essential for retaining receptor-signaling pathways in the primary cilium.

 

Common SNPs explain a large proportion of the heritability for human height

J. Yang, B. Benyamin, B.P. McEvoy, S. Gordon, A.K. Henders, D.R. Nyholt, P.A. Madden, A.C. Heath, N.G. Martin, G.W. Montgomery, M.E. Goddard, P.M. Visscher

10.1038/ng.608

 

SNPs discovered by genome-wide association studies (GWASs) account for only a small fraction of the genetic variation of complex traits in human populations. Where is the remaining heritability? We estimated the proportion of variance for human height explained by 294,831 SNPs genotyped on 3,925 unrelated individuals using a linear model analysis, and validated the estimation method with simulations based on the observed genotype data. We show that 45% of variance can be explained by considering all SNPs simultaneously. Thus, most of the heritability is not missing but has not previously been detected because the individual effects are too small to pass stringent significance tests. We provide evidence that the remaining heritability is due to incomplete linkage disequilibrium between causal variants and genotyped SNPs, exacerbated by causal variants having lower minor allele frequency than the SNPs explored to date.

 

Genome-wide microarray analysis of tomato roots showed defined responses to iron deficiency

A. Zamboni, L. Zanin, N. Tomasi, M. Pezzotti, R. Pinton, Z. Varanini, S. Cesco

10.1186/1471-2164-13-101

 

Background

Plants react to iron deficiency stress adopting different kind of adaptive responses. Tomato, a Strategy I plant, improves iron uptake through acidification of rhizosphere, reduction of Fe3+ to Fe2+ and transport of Fe2+ into the cells. Large-scale transcriptional analyses of roots under iron deficiency are only available for a very limited number of plant species with particular emphasis for Arabidopsis thaliana. Regarding tomato, an interesting model species for Strategy I plants and an economically important crop, physiological responses to Fe-deficiency have been thoroughly described and molecular analyses have provided evidence for genes involved in iron uptake mechanisms and their regulation. However, no detailed transcriptome analysis has been described so far.

Results

A genome-wide transcriptional analysis, performed with a chip that allows to monitor the expression of more than 25,000 tomato transcripts, identified 97 differentially expressed transcripts by comparing roots of Fe-deficient and Fe-sufficient tomato plants. These transcripts are related to the physiological responses of tomato roots to the nutrient stress resulting in an improved iron uptake, including regulatory aspects, translocation, root morphological modification and adaptation in primary metabolic pathways, such as glycolysis and TCA cycle. Other genes play a role in flavonoid biosynthesis and hormonal metabolism.

Conclusions

The transcriptional characterization confirmed the presence of the previously described mechanisms to adapt to iron starvation in tomato, but also allowed to identify other genes potentially playing a role in this process, thus opening new research perspectives to improve the knowledge on the tomato root response to the nutrient deficiency.

 

Cruciform structures are a common DNA feature important for regulating biological processes

V. Brázda, R.C. Laister, E.B. Jagelská, Ch. Arrowsmith

10.1186/1471-2199-12-33

 

DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others.

Cruciform structures are targets for many architectural and regulatory proteins, such as histones H1 and H5, topoisomerase IIβ, HMG proteins, HU, p53, the proto-oncogene protein DEK and others. A number of DNA-binding proteins, such as the HMGB-box family members, Rad54, BRCA1 protein, as well as PARP-1 polymerase, possess weak sequence specific DNA binding yet bind preferentially to cruciform structures. Some of these proteins are, in fact, capable of inducing the formation of cruciform structures upon DNA binding. In this article, we review the protein families that are involved in interacting with and regulating cruciform structures, including (a) the junction-resolving enzymes, (b) DNA repair proteins and transcription factors, (c) proteins involved in replication and (d) chromatin-associated proteins. The prevalence of cruciform structures and their roles in protein interactions, epigenetic regulation and the maintenance of cell homeostasis are also discussed.

 

Systematic identification of genomic markers of drug sensitivity in cancer cells

M.J. Garnett, E.J. Edelman, S.J. Heidorn, C.D. Greenman, A. Dastur, K.W. Lau, P. Greninger, I.R. Thompson,  X. Luo, J. Soares, Q. Liu, F. Iorio, D. Surdez, L. Chen, R.J. Milano, G.R. Bignell, A.T. Tam, H. Davies, J.A. Stevenson, S. Barthorpe, S.R. Lutz, F. Kogera, K. Lawrence, A. McLaren-Douglas, X. Mitropoulos

10.1038/nature11005

 

Clinical responses to anticancer therapies are often restricted to a subset of patients. In some cases, mutated cancer genes are potent biomarkers for responses to targeted agents. Here, to uncover new biomarkers of sensitivity and resistance to cancer therapeutics, we screened a panel of several hundred cancer cell lines—which represent much of the tissue-type and genetic diversity of human cancers—with 130 drugs under clinical and preclinical investigation. In aggregate, we found that mutated cancer genes were associated with cellular response to most currently available cancer drugs. Classic oncogene addiction paradigms were modified by additional tissue-specific or expression biomarkers, and some frequently mutated genes were associated with sensitivity to a broad range of therapeutic agents. Unexpected relationships were revealed, including the marked sensitivity of Ewing's sarcoma cells harbouring the EWS (also known as EWSR1)-FLI1 gene translocation to poly(ADP-ribose) polymerase (PARP) inhibitors. By linking drug activity to the functional complexity of cancer genomes, systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies.

 

A comparative analysis of the evolution of imperfect mimicry

H.D., Penney, C. Hassall, J.H. Skevington, K.R. Abbott, T.N. Sherratt

10.1038/nature10961

 

Although exceptional examples of adaptation are frequently celebrated, some outcomes of natural selection seem far from perfect. For example, many hoverflies (Diptera: Syrphidae) are harmless (Batesian) mimics of stinging Hymenoptera. However, although some hoverfly species are considered excellent mimics, other species bear only a superficial resemblance to their models and it is unclear why this is so. To evaluate hypotheses that have been put forward to explain interspecific variation in the mimetic fidelity of Palearctic Syrphidae we use a comparative approach. We show that the most plausible explanation is that predators impose less selection for mimetic fidelity on smaller hoverfly species because they are less profitable prey items. In particular, our findings, in combination with previous results, allow us to reject several key hypotheses for imperfect mimicry: first, human ratings of mimetic fidelity are positively correlated with both morphometric measures and avian rankings, indicating that variation in mimetic fidelity is not simply an illusion based on human perception; second, no species of syrphid maps out in multidimensional space as being intermediate in appearance between several different hymenopteran model species, as the multimodel hypothesis requires; and third, we find no evidence for a negative relationship between mimetic fidelity and abundance, which calls into question the kin-selection hypothesis. By contrast, a strong positive relationship between mimetic fidelity and body size supports the relaxed-selection hypothesis, suggesting that reduced predation pressure on less profitable prey species limits the selection for mimetic perfection.

 

 

A Bruce effect in wild geladas

E.K. Roberts, E. Lu, T.J.Bergman, J.C. Beehner

10.1126/science.1213600

 

Female rodents are known to terminate pregnancies after exposure to unfamiliar males ("Bruce effect"). Although laboratory support abounds, direct evidence for a Bruce effect under natural conditions is lacking. Here, we report a strong Bruce effect in a wild primate, the gelada (Theropithecus gelada). Female geladas terminate 80% of pregnancies in the weeks after a dominant male is replaced. Further, data on interbirth intervals suggest that pregnancy termination offers fitness benefits for females whose offspring would otherwise be susceptible to infanticide. Taken together, data support the hypothesis that the Bruce effect can be an adaptive strategy for females.

 

Molecular determinants of scouting behavior in honey bees

Z.S. Liang, T. NguyenH.R. Mattila, S.L. Rodriguez-Zas, T.D. Seeley, G.E. Robinson

10.1126/science.1213962

 

Little is known about the molecular basis of differences in behavior among individuals. Here we report consistent novelty-seeking behavior, across different contexts, among honey bees in their tendency to scout for food sources and nest sites, and we reveal some of the molecular underpinnings of this behavior relative to foragers that do not scout. Food scouts showed extensive differences in brain gene expression relative to other foragers, including differences related to catecholamine, glutamate, and γ-aminobutyric acid signaling. Octopamine and glutamate treatments increased the likelihood of scouting, whereas dopamine antagonist treatment decreased it. These findings demonstrate intriguing similarities in human and insect novelty seeking and suggest that this trait, which presumably evolved independently in these two lineages, may be subserved by conserved molecular components.

 

Sex, drugs and recombination: the wild life of Aspergillus

M.C.  Fisher, D.A. Henk

10.1111/j.1365-294X.2012.05506.x

 

Throughout the eukaryotes, sexual reproduction is an almost universal phenomenon. However, within the Kingdom Fungi, this relationship is not so clear-cut. Fungi exhibit a spectrum of reproductive modes and life-cycles; amongst the better known species, sexual reproduction is often facultative, can be rare, and in over half of the known Ascomycota (the moulds) is unknown (Taylor et al. 1999). However, over the last decade, it has become apparent that many of these asexual mitosporic taxa undergo cryptic recombination viaunobserved mechanisms and that wholly asexual fungi are, in fact, a rarity (Taylor et al. 1999, 2001; Heitman 2010). This revolution in our understanding of fungal sexuality has come about in two ways: Firstly, sexual reproduction leaves an imprint on fungal genomes by maintaining genes required for mating and by generating patterns of mutation and recombination restricted to meiotic processes. Secondly, scientists have become better at catching fungi in flagrante delicto. The genus Aspergillus is one such fungus where a combination of population genetics, genomics and taxonomy has been able to intuit the existence of sex, then to catch the fungus in the act and formally describe their sexual stages. So, why are sexy moulds exciting? One species in particular, Aspergillus flavus, is notorious for its ability to produce a diverse array of secondary metabolites, of which the polyketide aflatoxins (AF) are carcinogenic and others (such as cyclopiazonic acid) are toxigenic. Because of the predilection of A. flavus to grow on crops, such as peanuts, corn and cotton, biocontrol is widely used to mitigate infection by pre-applying nonaflatoxigenic (AF−) strains to competitively exclude the wild-type AF+ strains. However, the eventual fate in nature of these biocontrol strains is not known. In this issue of Molecular Ecology,Olarteet al.(2012)make an important contribution by using laboratory crosses of A. flavus to show that not only is AF highly heritable, but AF− strains can become AF+ via crossing over during meiosis. This observation has raised the spectre of cross-breeding and non-mendelian inheritance of AF between native and biocontrol strains of the fungus, leading to an increase in the natural diversity of the fungus with perhaps unanticipated consequences.

 

Speciation with gene flow and the genetics of habitat transitions

M.E. Cristescu, A. Constantin, D.G.Bock, C.E. Cáceres, R.J. Crease

10.1111/j.1365-294X.2011.05465.x

 

Whether speciation can advance to completion in the face of initially high levels of gene flow is a very controversial topic in evolutionary biology. Extensive gene exchange is generally considered to homogenize populations and counteract divergence. Moreover, the role of introgressive hybridization in evolution remains largely unexplored in animals, particularly in freshwater zooplankton in which allopatric speciation is considered to be the norm. Our work investigates the genetic structure of two young ecological species: the pond species,Daphnia pulex and the lake species, Daphnia pulicaria. Phylogenetic and population genetics analyses were conducted on mitochondrialNADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase (Ldh) gene and 21 nuclear microsatellite markers in 416 individuals from habitats with various degrees of permanence. The strong and consistent phylogenetic discordance between nuclear and mitochondrial markers suggests a complex evolutionary history of multiple independent habitat transition events that involved hybridization and introgression between lake and pond Daphnia. On the other hand, the low level of contemporary gene flow between adjacent populations indicates the presence of effective habitat isolating barriers. The Daphnia system provides strong evidence for a divergence-with-gene flow speciation model that involves multiple habitat transition events.

 

Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes

L.Y. Rutledge, B.R. Patterson, B.N., White

10.1186/1471-2148-10-215

 

Background

Phylogenetic studies of wild Canis species have relied heavily on the mitochondrial DNA control region (mtDNA CR) to infer species relationships and evolutionary lineages. Previous analyses of the CR provided evidence for a North American evolved eastern wolf (C. lycaon), that is more closely related to red wolves (C. rufus) and coyotes (C. latrans) than grey wolves (C. lupus). Eastern wolf origins, however, continue to be questioned. Therefore, we analyzed mtDNA from 89 wolves and coyotes across North America and Eurasia at 347 base pairs (bp) of the CR and 1067 bp that included the ATPase6 and ATPase8 genes. Phylogenies and divergence estimates were used to clarify the evolutionary history of eastern wolves, and regional comparisons of nonsynonomous to synonomous substitutions (dN/dS) at the ATPase6 and ATPase8 genes were used to elucidate the potential role of selection in shaping mtDNA geographic distribution.

Results

We found high concordance across analyses between the mtDNA regions studied. Both had a high percentage of variable sites (CR = 14.6%; ATP = 9.7%) and both phylogenies clustered eastern wolf haplotypes monophyletically within a North American evolved lineage apart from coyotes. Divergence estimates suggest the putative red wolf sequence is more closely related to coyotes (DxyCR = 0.01982 ± 0.00494 SD; DxyATP = 0.00332 ± 0.00097 SD) than the eastern wolf sequences (DxyCR = 0.03047 ± 0.00664 SD; DxyATP = 0.00931 ± 0.00205 SD). Neutrality tests on both genes were indicative of the population expansion of coyotes across eastern North America, and dN/dS ratios suggest a possible role for purifying selection in the evolution of North American lineages. dN/dS ratios were higher in European evolved lineages from northern climates compared to North American evolved lineages from temperate regions, but these differences were not statistically significant.

Conclusions

These results demonstrate high concordance between coding and non-coding regions of mtDNA, and provide further evidence that the eastern wolf possessed distinct mtDNA lineages prior to recent coyote introgression. Purifying selection may have influenced North American evolvedCanis lineages, but detection of adaptive selection in response to climate is limited by the power of current statistical tests. Increased sampling and development of alternative analytical tools will be necessary to disentangle demographic history from processes of natural selection.

 

Is female preference for large sexual ornaments due to a bias to escape predation risk?

Z. Zhen,  K. T. Won, C.J.Chun

10.1186/1471-2148-12-33

 

Background

A female preference for intense sexual visual signals is widespread in animals. Although the preferences for a signal per se and for the intensity of the signal were often regarded to have the identical origin, no study has demonstrated if this is true. It was suggested that the female fiddler crabs prefer males with courtship structures because of direct benefit to escape predation. Here we tested if female preference for both components (i.e. presence and size) of the courtship structure in Uca lactea is from the sensory bias to escape predation. If both components have the identical origin, females should show the same response to different-sized courtship structures regardless of predation risk.

Results

First, we observed responses of mate-searching female U. lactea to courting males with full-sized, half-sized and no semidomes which were experimentally manipulated. Females had a directional preference for males with bigger semidomes within normal variation. Thereafter, we tested the effect of predation risk on the female bias in the non-courtship context. When threatened by an avian mock predator, females preferentially approached burrows with full-sized semidomes regardless of reproductive cycles (i.e. reproductive periods and non-reproductive periods). When the predator cue was absent, however, females preferred burrows with semidomes without discriminating structure size during reproductive periods but did not show any bias during non-reproductive periods.

Conclusions

Results indicate that selection for the size of courtship structures in U. lactea may have an origin in the function to reduce predation risk, but that the preference for males with structures may have evolved by female choice, independent of predation pressure.

 

A novel mutation in the ABCD1 gene of a Korean boy diagnosed with X-linked adrenoleukodystrophy

J.A. Park, K.R. Jun, S.H. Han, G.H. Kim, H.W. Yoo, Y.J. Hur

10.1016/j.gene.2012.01.063

 

X-linked adrenoleukodystrophy (ALD; MIM #300100) is a neurodegenerative disorder caused by mutations in the ABCD1 adrenoleukodystrophy protein gene. The ABCD1 gene mutations have been reported by laboratories in China and Japan, but not in Korea. This case report describes a Korean boy diagnosed with X-ALD. Direct sequencing for the ABCD1 gene in this boy and his mother detected Tyr620His missense mutation, caused by cDNA nucleotide change 1858 T > C in exon 8 (c.1858T > C). This missense variant was novel and predicted to be possibly damaging by the PolyPhen and SIFT prediction software. Moreover, this is the first report in Korean.

 

Acetylation and deacetylation of non-histone proteins

M.A. Glozak, N. Sengupta, X. Zhang, E. Seto

10.1016/j.gene.2005.09.010

 

Since the first report of p53 as a non-histone target of a histone acetyltransferase (HAT), there has been a rapid proliferation in the description of new non-histone targets of HATs. Of these, transcription factors comprise the largest class of new targets. The substrates for HATs extend to cytoskeletal proteins, molecular chaperones and nuclear import factors. Deacetylation of these non-histone proteins by histone deacetylases (HDACs) opens yet another exciting new field of discovery in the role of the dynamic acetylation and deacetylation on cellular function. This review will focus on these non-histone targets of HATs and HDACs and the consequences of their modification.

 

Effects of Follicular Size and FSH on Granulosa Cell Apoptosis and Atresia in Porcinr Antral Follicles

P. Lin, R. Rui

doi:10.1002/mrd.21202

 

The purpose of this study was to establish a culture model for isolated intact porcine antral follicles and investigate the relationship between granulosa cell apoptosis and follicular atresia. Small (<3 mm), medium (3–5 mm) and large (>5 mm) healthy porcine follicles were isolated and cultured in serum-free TCM199 with or without follicular stimulating hormone (FSH). Microscopic identification of healthy follicles was confirmed by histology. A spontaneous onset of apoptotic cell death in granulosa cells was observed from cultured antral follicles. The apoptotic rate of granulosa cells from small follicles cultured for 24 hr was higher than those of large and medium follicles, accompanied with high FasL mRNA abundance in granulosa cells. Supplementation with 3 or 5 IU/ml FSH significantly inhibited the percentage of granulosa cells that became apoptotic. FSH did not significantly alter estradiol secretion from cultured follicles. Progesterone secretion significantly decreased after culture for 48 hr, coinciding with the morphological changes observed. FasL and Fas mRNA were expressed in the healthy, early atretic, and progressed atretic porcine follicles regardless of follicular size. However, FasL but not Fas mRNA levels increased during follicular atresia. Addition of FSH significantly decreased FasL rather than Fas mRNA levels in granulosa cells and could attenuate apoptosis. Small follicles seemed to be more susceptible to atresia as compared to medium and large follicles.

 

Androgen Actions and the Ovary

K.A. Walters, C.M. Allan, D.J. Handelsman

10.1095/biolreprod.107.064089

 

Although androgens and the androgen receptor (AR) have defining roles in male reproductive development and function, previously no role in female reproductive physiology beyond testosterone (T) as the precursor in estradiol (E2) biosynthesis was firmly established. Understanding the role and specific mechanisms of androgen action via the AR in the ovary has been limited by confusion on how to interpret results from pharmacological studies, because many androgens can be metabolized in vivo and in vitro to steroids that can also exert actions via the estrogen receptor (ESR). Recent genetic studies using mouse models with specific disruption of the Ar gene have highlighted the role that AR-mediated actions play in maintaining female fertility through key roles in the regulation of follicle health, development, and ovulation. Furthermore, these genetic studies have revealed that AR-mediated effects influence age-related female fertility, possibly via mechanisms acting predominantly at the hypothalamic-pituitary axis in a dose-dependent manner. This review focuses on combining the findings from pharmacological studies and novel genetic mouse models to unravel the roles of ovarian androgen actions in relation to female fertility and ovarian aging, as well as creating new insights into the role of androgens in androgen-associated reproductive disorders such as polycystic ovarian syndrome.

 

TRIAL-Decoy Receptor-1 Disappears in Granulosa Cells of Atretic Follicles in Porcine Ovaries

S. Wada, N. Manabe, N. Inoue, M. Nakayama T.  Matsui H.  Miyamoto

10.1262/jrd.48.167

 

To reveal the specific regulatory molecules that control granulosa cell apoptosis during follicular atresia, we immunohistochemically examined the localization of tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and its receptors in porcine ovaries. A marked reduction in the expression of decoy receptor-1 (DcR1), which has high affinity for TRAIL, was demonstrated in granulosa cells of atretic follicles, but no marked differences were seen in expression of TRAIL or other TRAIL-receptors (death receptor-4 or death receptor-5) in granulosa cells between healthy and atretic follicles. No positive staining for DcR2 was seen. We presum that TRAIL and its receptors are involved in induction of apoptosis in granulosa cells during atresia, and that DcR1 plays an inhibitory role in granulosa cell apoptosis.

 

Morphological classification of bovine ovarian follicles

R.J. Rodgers, H.F. Irving-Rodgers

10.1530/REP-09-0177

 

Follicle classification is an important aid to the understanding of follicular development and atresia. Some bovine primordial follicles have the classical primordial shape, but ellipsoidal shaped follicles with some cuboidal granulosa cells at the poles are far more common. Preantral follicles have one of two basal lamina phenotypes, either a single aligned layer or one with additional layers. In antral follicles <5 mm diameter, half of the healthy follicles have columnar shaped basal granulosa cells and additional layers of basal lamina, which appear as loops in cross section (‘loopy'). The remainder have aligned single-layered follicular basal laminas with rounded basal cells, and contain better quality oocytes than the loopy/columnar follicles. In sizes >5 mm, only aligned/rounded phenotypes are present. Dominant and subordinate follicles can be identified by ultrasound and/or histological examination of pairs of ovaries. Atretic follicles <5 mm are either basal atretic or antral atretic, named on the basis of the location in the membrana granulosa where cells die first. Basal atretic follicles have considerable biological differences to antral atretic follicles. In follicles >5 mm, only antral atresia is observed. The concentrations of follicular fluid steroid hormones can be used to classify atresia and distinguish some of the different types of atresia; however, this method is unlikely to identify follicles early in atresia, and hence misclassify them as healthy. Other biochemical and histological methods can be used, but since cell death is a part of normal homoeostatis, deciding when a follicle has entered atresia remains somewhat subjective.

 

Mitochondria and Caspases in Induced Apoptosis in Human Luteinized Granulosa Cells

S.M. Khan, L.M. Dauffenbach, J. Yeh

10.1006/bbrc.2000.2321

 

Apoptosis occurs as a physiologic process in the ovarian life cycle. Staurosporine, a protein kinase inhibitor, is reported to induce apoptosis. Here, we hypothesize that staurosporine will induce apoptosis in human luteinized granulosa cells and that mitochondria and the caspase cascade participate in this process. Luteinized granulosa cells isolated from in vitro fertilization patients were treated with staurosporine. Microscopy revealed that staurosporine treatment resulted in cells exhibiting evidence of apoptosis, including cell detachment, loss of cell processes, membrane shrinkage, and formation of apoptotic bodies. In the staurosporine-treated cells, flow cytometry and confocal microscopy showed a decrease in the mitochondrial cardiolipin levels. Western analysis showed cleavage of caspase-9, an initiator caspase, of caspase-3, an executioner caspase, and of a caspase substrate, poly-(ADP-ribose)-polymerase (PARP) in staurosporine-treated cells. These data support our hypothesis and that this is the first demonstration of the involvement of mitochondria and of cleavage of caspases in human luteinized granulosa cell apoptosis. This may serve as a useful model to delineate the mechanism of apoptosis in the ovary, such as corpus luteum regression.

 

Bid and Bax Are Involved in Granulosa Cell Apoptosis During Follicular Atresia in Porcine Ovaries

T. Sai, Y. Goto, R. Yoshioka, A. Maeda, F. Matsuda, M. Sugimoto, K. Wongpanit, H.Z. Jin, J.Y. Li, N. Manabe

10.1262/jrd.11-007H

 

More than 99% of follicles undergo "atresia" during follicular development and growth. Follicular atresia is predominantly regulated by granulosa cell apoptosis. However, the intracellular signaling pathway of apoptosis in granulosa cells has not been revealed. In the present study, we examined changes in the expression of BH3-interacting domain death agonist (Bid) and Bcl-2-associated X protein (Bax), which are considered to promote the cell death ligand/receptor-mediated process in mitochondrion-dependent type II apoptosis, in porcine granulosa cells during atresia. Levels of mRNA and protein of Bid and Bax were determined by the reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting techniques, respectively. Levels of Bid and Bax mRNA and protein were markedly increased in granulosa cells of early atretic follicles compared with those of healthy follicles.In situ hybridization and immunohistochemical staining revealed that mRNA and protein of Bid and Bax were present in the granulosa cells, though only traces were found in healthy follicles; however, strong staining was noted in atretic follicles. These results indicate that Bid and Bax appear to be signal transduction factors in granulosa cells during follicular atresia and appear to play proapoptotic roles and confirm that the porcine granulosa cell is a mitochondrion-dependent type II apoptotic cell.

 

Developmental exposure to environmental endocrine disruptiors: Consequences within the ovary and on female reproductive function

M. Uzumcu, R. Zachow

10.1016/j.reprotox.2006.10.006

 

Female reproductive function depends upon the exquisite control of ovarian steroidogenesis that enables folliculogenesis, ovulation, and pregnancy. These mechanisms are set during fetal and/or neonatal development and undergo phases of differentiation throughout pre- and post-pubescent life. Ovarian development and function are collectively regulated by a host of endogenous growth factors, cytokines, gonadotropins, and steroid hormones as well as exogenous factors such as nutrients and environmental agents. Endocrine disruptors represent one class of environmental agent that can impact female fertility by altering ovarian development and function, purportedly through estrogenic, anti-estrogenic, and/or anti-androgenic effects. This review discusses ovarian development and function and how these processes are affected by some of the known estrogenic and anti-androgenic endocrine disruptors. Recent information suggests not only that exposure to endocrine disruptors during the developmental period causes reproductive abnormalities in adult life but also that these abnormalities are transgenerational. This latter finding adds another level of importance for identifying and understanding the mechanisms of action of these agents.

 

Environmental xenoestrogens, antiandrogens and disorders of male sexual differentiation

C. Sultan, P. Balaguer, B. Terouanne, V. Georget, F. Paris, C. Jeandel, S. Lumbroso, J.C. Nicolas

10.1016/S0303-7207(01)00430-0

 

Over the past 20 years, the documented increase in the disorders of male sexual differentiation, such as hypospadias, cryptorchidism, and micropenis, has led to the suspicion that environmental chemicals are detrimental to normal male genital development in utero. Male sexual differentiation is critically dependent on the normal action of androgens, and unbalanced androgen/estrogen ratios can disturb it. Environmental xenoestrogens (such as herbicides, pesticides, PCBs, plasticizers, and polystyrenes) that mimic estrogens or environmental antiandrogens (such as polyaromatic hydrocarbons, linuron, vinclozolin, and pp′DDE) that disturb endocrine balance, cause demasculinizing effects in the male foetus. These environmental chemicals are often referred to as endocrine disruptors: they are thought to mimic endogenous estrogens by entering the cell, binding to the receptor and activating transcription, they may also antagonize normal androgen action. We have established numerous cell lines to assess the estrogenicity and antiandrogenicity of compounds found in the environment and to identify new products present in wastewater effluents that are able to disrupt endocrine functions. Several cell lines responding to estrogens have been obtained in our group, including cells with different enzymatic equipment and cells expressing chimeric receptor or natural estrogen receptors α and β. These cell lines have proved to be useful for assessing the biological activity of pesticides, fungicides, and chemicals found in plastic or discarded in the environment. In order to generate a powerful tool for the investigation of androgen action and the rapid screening of potential antagonists, we developed a new stable prostatic cell line. The PALM cell line is an original cellular model to characterize the response of hAR, and it provides an easy and rapid bioluminescent test to identify new antagonists. We also developed a model based on a fusion protein between the androgen receptor (AR) and the green fluorescent protein (GFP) to study the intracellular dynamics of AR. The GFP–AR model was applied to define the ability of several xenoestrogens and antiandrogens to inhibit the nuclear transfer of AR. The ubiquitous presence of endocrine disruptors in the environment and the increased incidence of neonatal genital malformation support the hypothesis that disturbed male sexual differentiation may in some cases be caused by increased exposure to environmental xenoestrogens and/or antiandrogens.

 

Apoptosis and ovarian Function

J.L. Tilly

10.1530/ror.0.0010162

 

For decades, the mechanisms responsible for germ cell depletion from the ovary, either directly during the perinatal period or indirectly via follicular atresia during postnatal life, have remained relatively obscure. The recent application of sensitive biochemical techniques for the study of cell death to the analysis of ovarian function has revealed that these two events, as well as a third instance of ovarian cell degeneration (luteolysis), are dependent upon the activation of physiological cell death mechanisms. It is therefore hypothesized that the controlled deletion of ovarian cell populations is accomplished via activation of a 'universal' pathway of cellular suicide involving altered expression of a conserved cohort of genes. The identity of the hormonal and intracellular effectors responsible for the coordination of life and death decisions made by ovarian cells during development as well as the biological and clinical implications of gene-directed cell death in the ovary are explored in this review.

 

Multivariate morphometric study of the Cardamine pratensis group (Cruciferae) in the Carpathian and Pannonian area

K. Marhold

10.1007/BF00984932

 

A multivariate morphometric study of theCardamine pratensis group is presented, based on 84 population samples collected from the Carpathian and Pannonian area in the Czech Republic, Slovakia, Poland, Ukraine, Hungary, and Romania. Among the multivariate methods, principal component analysis, cluster analysis, and classificatory and canonical discriminant analysis were used. The analysis of chromosome numbers from all populations studied showed wide variation. The morphometric study showed that not all groups of populations characterised by their chromosome numbers and geographical criteria are morphologically, and thus taxonomically, distinguishable. Besides the morphologically well characterised speciesCardamine dentata andC. rivularis, the following species were recognised in the area studied:C. matthioli, C. majovskii andC. pratensis. Within the last species, besides the typical populations, two diploid types are provisionally recognised: type ucranica and type rivularis auct.

 

Taxonomic revision of the Calamagrostis epigeios complex with particular reference to China

B. Paszko,  H. Ma

10.1111/j.1759-6831.2011.00140.x

 

Principal component analysis of specimen measurements revealed morphological variation within Chinese Calamagrostis epigeios correlated with differences in geographical distribution. We conducted a morphological examination of specimens from the range of the species, with the goal of developing a treatment for its Chinese members reflecting the global diversity complex. The confusing taxonomy of this complex is clarified with the recognition of three species in China, namely C. epigeios, C. extremiorientalis, and C. macrolepis. Calamagrostis epigeios is an exclusively temperate grass occurring in the northwestern, northern, and northeastern parts of China. It has spikelets 4–7 mm long, glumes equal or subequal, awn arising near the middle of the lemma back, upper leaf surface smooth and with shallow ribs and furrows. Calamagrostis extremiorientalis is a tropical and subtropical grass that occurs in the southwest provinces of China (except Xizang) throughout south central provinces and east to the northeastern parts of China. It is morphologically similar to C. epigeios. However, C. extremiorientalis has the awn arising from the upper one-third of the lemma back, upper leaf surface scabrid because of the presence of short stiff hairs, and with tall ribs and deep furrows. Calamagrostis macrolepis occurs in the northwestern, northern, and northeastern parts of China. It has a robust habit, spikelets 6.5–11 mm long, and glumes unequal, the upper 1–1.5 mm shorter than the lower. New synonyms, descriptions, and citations of representative specimens are provided for each species, along with an identification key.

 

Cellular impact of metal trace elements in terricolous lichen Diploschistes muscorum (scop.) R. Sant. – identification of oxidative stress biomarkers

D. Cuny, C. Van Haluwyn, P. Shirali, F. Zerimech, L. Jérôme, J.M. Haguenoer

10.1023/B:WATE.0000015332.94219.ff

 

The purpose of this research is to present toxic effects of some heavy metals (cadmium, lead and zinc) on lichen physiology. In the North of France, those metals are concentrated for example in industrial polluted soils near metallurgic plants and waste dumps. Our investigations were conducted on Diploschistes muscorum (Scop.) R. Sant, a terricolous lichen growing on previously quoted soils as well as on non-contaminated ones. Different stress parameters were investigated as potassium leakage – which is related to the loss of membrane integrity – and oxidative stress through following parameters: malondialdehyde (MDA), glutathione (GSH) and superoxide dismutase (SOD). It seems, therefore, that heavy metals induce oxidative stress in this lichen, in which we found membrane damage and enhancement of SOD activity and GSH concentrations. With regard to very high concentrations of Cd, Pb and Zn, a resistance involving antioxidant mechanisms limits the expected damage. Those mechanisms involve GSH, SOD as well as secondary metabolites, which have this resistance property. This study is a first step of investigation to use – in the future– physiological parameters as tool for environment assessment.

 

Element accumulation in boreal bryophytes, lichens and vascular plants exposed to heavy metal and sulfur deposition in Finland

M. Salemaaa, J. Deromeb, H.S. Helmisaaria, T. Nieminena, I. Vanha-Majamaaa

10.1016/j.scitotenv.2003.10.025

 

Macronutrient (N, P, K, Mg, S, Ca), heavy metal (Fe, Zn, Mn, Cu, Ni, Cd, Pb) and Al concentrations in understorey bryophytes, lichens and vascular plant species growing in Scots pine forests at four distances from the Harjavalta Cu–Ni smelter (0.5, 2, 4 and 8 km) were compared to those at two background sites in Finland. The aim was to study the relationship between element accumulation and the distribution of the species along a pollution gradient. Elevated sulfur, nitrogen and heavy metal concentrations were found in all species groups near the pollution source. Macronutrient concentrations tended to decrease in the order: vascular plants>bryophytes>lichens, when all the species groups grew on the same plot. Heavy metal concentrations (except Mn) were the highest in bryophytes, followed by lichens, and were the lowest in vascular plants. In general, vascular plants, being capable of restricting the uptake of toxic elements, grew closer to the smelter than lichens, while bryophytes began to increase in the understorey vegetation at further distances from the smelter. A pioneer moss (Pohlia nutans) was an exception, because it accumulated considerably higher amounts of Cu and Ni than the other species and still survived close to the smelter. The abundance of most of the species decreased with increasing Cu and Ni concentrations in their tissues. Cetraria islandica, instead, showed a positive relationship between the abundance and Cu, Ni and S concentrations of the thallus. It is probable that, in addition to heavy metals, sporadically high SO2 emissions have also affected the distribution of the plant species.

 

Distinction of Cladonia rei and C. subulata based on molecular, chemical and morphological characteristics

C. Dolnik, A. Beck, D. Zarabska

10.1017/S0024282910000071

 

Cladonia rei and Cladonia subulata are morphologically similar, but chemically different cup lichens of dry grasslands and nutrient-poor ruderal habitats. Recently, C. rei has been synonymized with C. subulata on the basis of combined morphological and chemical investigations. However, doubts remained due to a molecular divergent North American sample of C. rei compared to European C. subulata. To clarify the situation, using molecular methods, we analysed chemically different European samples of C. rei and C. subulata, as well as other morphologically or chemically similar Cladonia species. Molecular data show that European and North American samples of C. rei belong to the same clade, which is closely related to C. fimbriata and followed by a subclade with C. coniocraea and C. ochrochlora. The subclade of C. subulata appears to be distinct from C. rei. In concordance with molecular data, the presence of homosekikaic acid is the determining chemical feature for C. rei. In addition, C. humilis and C. innominata proved to be molecularly distinct species.

 

A biometric study of Fritillaria Montana Hoppe ex W.D.J. Koch s.l. (Liliaceae) shows a single polymorphic species, with no infraspecific taxa

F. Bartolucci, K.F. Caparelli, L. Peruzzi

10.1080/11263500902722956

 

The large amount of morphological variability within Fritillaria montana Hoppe ex W.D.J. Koch, a southeastern European species described from northeastern Italy, led to the creation of several further taxa: Fritillaria caussolensis Goaty & Pons ex Adoino from southeastern France, Fritillaria orsiniana Parl. from central Italy, Fritillaria intermedia N. Terracc. and Fritillaria pollinensis N. Terracc. from southern Italy. Aiming to test the taxonomic value of these taxa, a biometric study of both herbarium and living specimens of F. montana s.l. is carried out. A total of 22 morphological features were analysed and measured in 417 plants from 46 different localities, including loci classici of all the involved taxa. In addition, typical populations of F. montana, F. caussolensis, F. intermedia, F. orsiniana and F. pollinensis and also several other Italian populations resulted with 2n = 18 chromosomes. We also counted 2n = 27 chromosomes in endotriploid cells of plants from Abruzzo. However, there is no clear‐cut correlation between morphology and karyology. The biometric analysis, together with many observations on fresh material in the field, revealed that F. montana is a single polymorphic species with no infraspecific taxa.

 

A combined morphological and molecular phylogenetic analysis of Parthenocissus (Vitaceae) and taxonomic implications

L. Lu, J. Wen, Z. Chen

10.1111/j.1095-8339.2011.01186.x

 

Parthenocissus (the Virginia creeper genus, Vitaceae) consists of 13 species and shows a disjunct distribution between Asia and North America. We investigated the inflorescence structure, calyx morphology, appendages on the inner side of petals, leaf epidermis, pollen and seed characters throughout the genus. A combined phylogenetic analysis with 27 morphological and 4137 molecular characters was conducted and the result was largely congruent with that of the previous molecular work, but with higher resolution. The combined analysis identified two clades corresponding to the Asian and North American taxa. Parthenocissus feddei was resolved as closely related to the clade containing P. cuspidifera, P. heterophylla and P. semicordata. The four species share synapomorphies of having conspicuously raised veinlets, an obscurely five- (to eight-) lobed calyx, appendages on the inner side of petals covering the entire length of anthers and foveolate pollen exine ornamentation. Within the Old World clade, the pentafoliolate species were weakly supported as more closely related to species with both simple and trifoliolate leaves. Furthermore, the ancestral states of tendril apices, inflorescence structure, appendages on the inner side of petals and exine ornamentation of pollen grains were reconstructed on the molecular strict consensus tree. The appendages on the inner side of petals and exine ornamentation of pollen grains were suggested to be important characters in the taxonomy of Parthenocissus, especially for species with trifoliolate leaves. Finally, the previous classifications of Parthenocissus were evaluated within the phylogenetic framework.

 

Genetic patterns in the Lathyrus pannonicus complex (Fabaceae) reflect ecological differentiation rather than biogeography and traditional subspecific division

M. Schlee, M. Göker, G.W. Grimm, V. Hemleben

10.1111/j.1095-8339.2011.01125.x

 

The endangered European relict species complex Lathyrus pannonicus shows distinct morphological variation, reflected by the number of subspecies recognized, and complicated patterns of genetic variation. The traditionally recognized subspecies appear to possess different ecological preferences and disjunct distributions, particularly in the western range of the species. In this study, L. pannonicus was investigated by the correlation of distance matrices based on phytosociological, ecological, molecular and morphological data. Ecological characteristics of selected stands of L. pannonicus throughout Europe were assessed using ‘Ellenberg values' of all the constituent taxa in phytosociological relevés. Genetic distances were calculated using recently developed methods to analyse high degrees of intra-individual nuclear-encoded internal transcribed spacer variability. We found that the remarkable genetic (and morphological) diversity in L. pannonicus could not be explained solely by the fragmentation of the distributional range. Instead, patterns of morphological and genetic differentiation were a reflection of the moisture regime in the sampled stands. Two major lineages could be identified: (1) a lineage adapted to dry conditions (Ellenberg indicator F-value ≤ 3.5) and (2) a lineage preferring moist conditions (F-value ≥ 4.5). Although both lineages occurred in close proximity in the Pannonian area, they appeared to be reproductively isolated in general. Further data are needed to determine whether these genetically and ecologically defined lineages, or ecospecies, within the L. pannonicus species complex can be formalized as (Linnaean) species or subspecies.

 

Genetic structure of the Anthyllis vulneraria L. s. l. species complex in Estonia based on AFLPs

E. Köster, E. Bitocchi, R. Papa, S. Pihu

10.2478/s11535-008-0033-6

 

Anthyllis vulneraria L. (Fabaceae) s. lato includes many cryptic taxa, ranging from 25 to 60 subspecies according to different authors. The delimitation of intraspecific taxa of A. vulneraria s. lato has always been complicated and inconsistent. Different data sets (multivariate analyses of morphological variation, allozymes, chloroplast SSRs and ITS) have not resolved the existing problem with distinguishing some subspecies. We used the amplified fragment length polymorphism (AFLP) analysis to describe the differentiation in this species complex and to characterize variation on a geographic scale. Some correlation was found between genetic variability and geographic distribution (western-eastern directional variation), but AFLP data analysis did not reveal clear intraspecific structure of the seven analysed taxa. The analysed specimens did not comprise groups correlated with the subspecies.

 

A morphometric study on Anthyllis vulneraria (Fabaceae) from Poland and its taxonomic implications

K. Rola

10.2478/s11756-012-0013-1

 

The paper presents results of morphometric analysis of Anthyllis vulneraria L. in Poland based on 828 herbarium specimens. This study investigates five taxa which have been recognized in Poland: Anthyllis vulneraria L. ssp. vulneraria, Anthyllis vulneraria ssp. polyphylla (DC.) Nyman, A. vulneraria ssp. maritima (Schweigg.) Corb., A. vulneraria ssp. Alpestris Asch. et Graebn. and A. vulneraria ssp. carpatica (Pant.) Nyman as well as three intermediate taxa of presumably hybrid origin. Multivariate statistical analyses of 12 quantitative and 10 qualitative characteristics revealed conspicuous variation within A. vulneraria. Analysis of variance (ANOVA), principal coordinate analysis (PCoA), correspondence analysis (CA) and discriminant analysis (DA) proved the taxonomic usefulness of quantitative characteristics such as number of rosette leaves, calyx length, inflorescence length, the ratio of leaf length/width, bract length as well as qualitative characteristics such as stem hairiness, calyx colour, calyx indumentum, distances between stem leaves and form of rosette leaves. The issues concerning intermediate morphotypes occurring in Poland and their status are discussed. Finally, a key for determination of taxa within A. vulneraria in Poland and distribution maps based on the material examined are provided.

 

Boys and Girls Come Out to Play: The Molecular Biology of Dioecious Plants

C. Ainsworth

10.1006/anbo.2000.1201

 

The majority of the world's flowering plants are hermaphrodite but many of them encourage cross pollination by means of spatial or temporal separation of eggs and pollen, or by genetically-controlled physiological incompatibility. A minority of species has taken the avoidance of self-pollination to its logical conclusion by evolving two distinct and sexually different forms (dioecy). In a very small number of plants, dioecy has been accompanied by the development of sex chromosomes. From the study of the development of male and female flowers of different species it is clear that there is no common underlying mechanism and that sex determination systems leading to dioecy have originated independently many times in evolution. This Botanical Briefing highlights new information from recent molecular approaches in the study of dioecy.

 

Genetic structure of population sample of apomictic dandelions

R.G.M . Van Der Hulst, T.H.M. Mes, M . Falque, P . Stam, J.C.M. Den Nijs, K. Bachmann

10.1038/sj.hdy.6800248

 

In Northern Europe, dandelion populations consist solely of triploid or higher polyploid apomicts. Without a regular sexual cycle or lateral gene transmission, a clonal structure is expected for Taraxacum apomicts, although this was not found by compatibility analysis. In this study, we investigate whether this observation could be suported by performing independent tests based on data from hypervariable microsatellite markers as well as more conservative data based on allozymes and matrilinear cpDNA markers. In addition, population genetic methods were used to test departure from panmictic expectations, which is expected for clonal populations. Results indicated that many data sets, again, did not agree with expectations from clonal evolution because only small groups of genotypes exhibit no marker incompatibility. Population genetic analysis revealed that virtually all genotypes, but not individuals, agreed with random segregation and genotypic equilibria. Exceptions were genotypes with rare allozyme alleles or nearly identical microsatellite genotypes. Consequently, a population sample of apomictic dandelions essentially harbours genotypes that resulted from segregation and/or recombination and only a few genotypes that may have differentiated by somatic mutations.

 

Evolution of adaptive phenotypic traits without positive Darwinian selection

A.L. Hughes

10.1038/hdy.2011.97

 

Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity–relaxation–mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation, as well as recently reported cases of apparent adaptive evolution over ecological time.

 

A genome-wide comparison of recent chimpanzee and human segmental duplications

Z. Cheng, M. Ventura, X. She, P. Khaitovich, T. Graves, T. Osegawa, D. Church, P. De Jong, R.K. Wilson, S. Pääbo, M. Rocchi, E.E. Eichler

10.1038/nature04000

 

We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4–5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post-speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).

 

A genetic method to resolve gender complements investigations on sex ratios in Rumex acetosa

H. Korpelainen

10.1046/j.1365-294X.2002.01593.x

 

The perennial dioecious weed, Rumex acetosa, possesses sex chromosomes (XX in females, XY1Y2 in males). Yet, the operational sex ratios are female-biased. Until now, sex ratio studies in R. acetosa, as in most plants, have relied on data obtained at sexual maturity. To resolve gender among the seeds and nonflowering plants of R. acetosa, a genetic method involving a DNA marker located on both Y chromosomes has now been developed and applied. The results suggest that the sex ratios are about 1 : 1 in the whole seed pool, but that a significant female bias develops by the time of flowering. Since the age of sexually mature plants is two years or more, the time frame during which the female bias present at sexual maturity develops can be several years. It appears that male seeds germinate at a lower rate and males suffer from a greater mortality during the years-long lifespan of R. acetosa. However, there are no considerable sex-related differences in vegetative vigour.

 

Sex chromatin and nucleolar analyses in Rumex acetosa L.

M.  Lengerova,  B. Vyskot

10.1007/BF01283395

 

Rumex acetosa (sorrel) is a dioecious plant with a XX/XY1Y2 sex chromosome system. Both the Y chromosomes are nearly entirely heterochromatic and it has been hypothesised that they can persist as chromocenters in male interphase nuclei. Using specific antibodies against 5-methylcytosine and histone H4 acetylated at terminal lysine 5, global levels of DNA methylation and histone acetylation were studied on the sex chromosomes and autosomes of both sexes. The heterochromatic Y chromosomes did not display a higher methylation level compared to the autosomes. The only prominent hypermethylation signals were found at two nucleolar organising regions located on the autosome pair V, as confirmed by in situ hybridisation with 25S rDNA probe and staining. Immunoanalysis of DNA methylation on female and male interphase nuclei neither revealed any sex-specific differences. Two active (silverpositive) nucleoli and two likely inactive nucleolar organising regions (displaying prominent methylation signals) were found in both sexes. In a fraction of nuclei isolated from leaf cells, two peripheral bodies strongly positive for 4,6-diamidino-2-phenylindole were observed only in males, never in females. These heterochromatin regions were depleted in histone H4 acetylation at terminal lysine 5 and corresponded, according to in situ hybridisation with a Y-chromosome-specific repetitive probe, to the two Y chromosomes. We conclude that the peripheral condensed bodies observed exclusively in male nuclei represent the constitutive heterochromatin of the Y chromosomes which is characterised by a substantial histone H4 underacetylation.

 

Somaclonal variation in rye (Secale cereale L.) analyzed using polymorphic and sequenced AFLP markers

R. De La Puente,  A. González AI, M.L. Ruiz, C. Polanco

10.1007/s11627-008-9152-z

 

Ampl i f i  ed  f r a gme n t  l  e ng t h polymor ph i sm (AFLP) analysis of 24 in vitro regenerated rye plants was performed in order to evaluate the somaclonal variation rate in this species and to identify rye genomic regions where mutations are preferentially promoted by in vitro culture processes. Regenerated plants were obtained from cell lines derived from immature embryos and plants were regenerated by somatic embryogenesis. Twenty-three regenerants showed variation when compared against sibling plants obtained from the same cell line. A total number of 887 AFLP markers were scored, and 8.8% identified the same polymorphism in plants obtained independently from different cell lines, revealing putative mutational hot spots. Using controlled crossings and analysis of the corresponding progenies, we were able to verify the genetic stability in the next generation for only five of these polymorphisms. The nucleotide sequence of the AFLP amplicon of four of the polymorphic markers was obtained, but only the sequence of two markers was clearly identified in the databases. The sequence of marker A1-303 was identified as part of a tandemly repeated sequence, the 120-bp family, which is located at telomeric regions and is widely distributed among rye chromosomes. The marker A5-375 showed high similarity with regions of Angela retrotransposons.

 

Assessment of Somaclonal Variation in Chrysanthemum (Dendranthema grandiflora Kitam.) using RAPD and Morphological Analysis

P. Kengkarj, P. Smitamana, Y. Fujime

10.3329/ptcb.v18i2.3396

 

Novel chrysanthemum (Dendranthema grandiflora Kitam.) somaclones from seven commercial cultivars were obtained through the petal segments culture. Morphological variation of the derived clones observed from the field trials was found to be cultivar specific. The major variants within the same cultivar were found only color and inflorescence shape deviation, whereby leaf and stem characters remained unchanged. Distinct variations were found in the 'Pinkgin' cultivar that color changed from magenta to red. The morphological differences of the tested somaclones showed high correlation with the RAPD patterns analysis.  The morphological differences of the tested somaclones were shown to be highly correlated using RAPD pattern analysis. RAPD markers, using ten primers could better separate each cultivar at 80% similarity value. All the somaclones could be singly separated at 90% similarity. However, the higher level of variability of RAPD patterns in chrysanthemum rendered these RAPD fragments as good candidates for somaclonal and cultivar identification. The results from this study revealed the potential increase in range of floral color and morphological changes of petal segment culture, thus this technique would be effectively used for novel plant production.

 

Reduced Rates of Sequence Evolution of Y-Linked Satellite DNA in Rumex (Polygonaceae)

R. Navajas-Perez, R. de la Herran,  M. Jamilena, R. Lozano, C. Ruiz Rejon, M. Ruiz Rejon, M.A. Garrido-Ramo

10.1007/s00239-004-0199-0

 

In a previous paper [1] we showed that Y-linked satellite-DNA sequences of Rumex (Polygonaceae) present reduced rates of evolution in relation to other autosomal satellite-DNA sequences. In the present paper, we re-analyze the same set of sequences by using the satDNA Analyzer 1.2 software, specifically developed by us for analysis of satellite DNA evolution. We do not only confirm our previous findings but also prove that the satDNA Analyzer 1.2 package constitutes a powerful tool for users interested in evolutionary analysis on satellite-DNA sequences. In fact, we are able to gather more accurate calculations regarding location of Strachan positions and evolutionary rates calculations, among others useful statistics. All results are displayed in a very comprehensive multicoloured graphic representation easy to use as an html file. Furthermore, satDNA Analyzer 1.2 is a time saving feature since every utility is automatized and collected in a single software package, so the user does not need to use different programs. Additionally, it significantly reduces the rate of data miscalculations due to human errors, very prone to occur specially in large files.

 

Can genetic bar-coding be used to identify aquatic Ranunculus L. subgenus Batrachium (DC) A. Gray? A test using some species from the British Isles

A. Telforda, M.T. O'Harea, S. Caversa, N. Holmes

10.1016/j.aquabot.2011.03.004

 

Aquatic Batrachium Ranunculus species are a key component of river macrophyte communities selected for protection under European Union legislation. The group's simplified morphology and variable taxonomic interpretation often makes identification to species level very difficult. A genetic approach was trialled as an alternative, more reliable, means of identification. DNA barcoding using four markers (chloroplast and nuclear) was tested. The chloroplast sequence trnH-psbA worked best and allowed identification of three out of five species while nuclear sequences supported the identification of two hybrids.This method is amenable to simplification through techniques such as PCR-RFLP or RT-PCR. It has the potential to provide easy, rapid and inexpensive identification of Batrachium Ranunculus species.

 

Molecular Analysis of the SCARECROW Gene in Maize Reveals a Common Basis for Radial Patterning in Diverse Meristems

J. Lim, Y. Helariutta, Ch. D. Szpecht, J. Jung, L. Sims, W.B. Bruce, S. Diehl, P.N. Benfeya

10.1105/tpc.12.8.1307

 

Maize and Arabidopsis root apical meristems differ in several aspects of their radial organization and ontogeny. Despite the large evolutionary distance and differences in root radial patterning, analysis of the putative maize ortholog of the Arabidopsis patterning gene SCARECROW (SCR) revealed expression localized to the endodermis, which is similar to its expression in Arabidopsis. Expression in maize extends through the quiescent center, a population of mitotically inactive cells formerly thought to be undifferentiated and to lack radial pattern information. Zea mays SCARECROW (ZmSCR), the putative maize SCR ortholog, was used as a molecular marker to investigate radial patterning during regeneration of the root tip after either whole or partial excision. Analysis of the dynamic expression pattern of ZmSCR as well as other markers indicates the involvement of positional information as a primary determinant in regeneration of the root radial pattern.

 

Comparative chloroplast genomics and phylogenetics of Fagopyrum esculentum ssp. ancestrale – A wild ancestor of cultivated buckwheat

M.D. Logacheva, T.H. Samigullin,A. Dhingra,A.A. Penin

10.1186/1471-2229-8-59

 

Background

Chloroplast genome sequences are extremely informative about speciesinterrelationships owing to its non-meiotic and often uniparental inheritance over generations. The subject of our study, Fagopyrum esculentum, is a member of the family Polygonaceae belonging to the order Caryophyllales. An uncertainty remains regarding the affinity of Caryophyllales and the asterids that could be due to undersampling of the taxa. With that background, having access to the complete chloroplast genome sequence for Fagopyrum becomes quite pertinent.

Results

We report the complete chloroplast genome sequence of a wild ancestor of cultivated buckwheat, Fagopyrum esculentum ssp. ancestrale. The sequence was rapidly determined using a previously described approach that utilized a PCR-based method and employed universal primers, designed on the scaffold of multiple sequence alignment of chloroplast genomes. The gene content and order in buckwheat chloroplast genome is similar to Spinacia oleracea. However, some uniqu structural differences exist: the presence of an intron in the rpl2 gene, a frameshift mutation in the rpl23 gene and extension of the inverted repeat region to include the ycf1 gene. Phylogenetic analysis of 61 protein-coding gene sequences from 44 complete plastid genomes provided strong support for the sister relationships of Caryophyllales (including Polygonaceae) to asterids. Further, our analysis also provided support for Amborella as sister to all other angiosperms, but interestingly, in the bayesian phylogeny inference based on first two codon positions Amborella united with Nymphaeales.

Conclusion

Comparative genomics analyses revealed that the Fagopyrum chloroplast genome harbors the characteristic gene content and organization as has been described for several other chloroplast genomes. However, it has some unique structural features distinct from previously reported complete chloroplast genome sequences. Phylogenetic analysis of the dataset, including this new sequence from non-core Caryophyllales supports the sister relationship between Caryophyllales and asterids.

 

Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome

J.A Irwin, C. Lister, E. Soumpourou, Y. Zhang, E.C. Howell, G. Teakle, C. Dean

10.1186/1471-2229-12-21

 

Background

Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea.

Results

We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana.

Conclusions

We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is not syntenic with A. thaliana FRI due to an ancient recombination event. This has complicated previous association analyses of FRI with variation in life history strategy in the Brassica genus.

 

Construction and EST sequencing of full-length, drought stress cDNA libraries for common beans (Phaseolus vulgaris L.)

M.W. Blair, A.C. Fernandez, M. Ishitani, D. Moreta, M. Seki, S. Ayling, K. Shinozaki

10.1186/1471-2229-11-171

 

Background

Common bean is an important legume crop with only a moderate number of short expressed sequence tags (ESTs) made with traditional methods. The goal of this research was to use full-length cDNA technology to develop ESTs that would overlap with the beginning of open reading frames and therefore be useful for gene annotation of genomic sequences. The library was also constructed to represent genes expressed under drought, low soil phosphorus and high soil aluminum toxicity. We also undertook comparisons of the full-length cDNA library to two previous non-full clone EST sets for common bean.

Results

Two full-length cDNA libraries were constructed: one for the drought tolerant Mesoamerican genotype BAT477 and the other one for the acid-soil tolerant Andean genotype G19833 which has been selected for genome sequencing. Plants were grown in three soil types using deep rooting cylinders subjected to drought and non-drought stress and tissues were collected from both roots and above ground parts. A total of 20,000 clones were selected robotically, half from each library. Then, nearly 10,000 clones from the G19833 library were sequenced with an average read length of 850 nucleotides. A total of 4,219 unigenes were identified consisting of 2,981 contigs and 1,238 singletons. These were functionally annotated with gene ontology terms and placed into KEGG pathways. Compared to other EST sequencing efforts in common bean, about half of the sequences were novel or represented the 5' ends of known genes.

Conclusions

The present full-length cDNA libraries add to the technological toolbox available for common bean and our sequencing of these clones substantially increases the number of unique EST sequences available for the common bean genome. All of this should be useful for both functional gene annotation, analysis of splice site variants and intron/exon boundary determination by comparison to soybean genes or with common bean whole-genome sequences. In addition the library has a large number of transcription factors and will be interesting for discovery and validation of drought or abiotic stress related genes in common bean.

 

Genetic diversity among Texas bluegrass genotypes (Poa arachnifera Torr.) revealed by AFLP and RAPD markers

K. Renganayaki, J.C Read, A.K. Fritz

10.1007/s001220000521

 

Texas bluegrass Poa arachnifera Torr., is a vigorous sod-forming perennial, dioecious grass, tolerant to heat. It is native to the Southern Great Plains. Genetic relationships existing among 28 Texas bluegrass genotypes were investigated using amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD). A total of 3756 AFLP markers were generated on the 28 genotypes of Texas bluegrass. A wide range of polymorphism (23.08–85.33%) was observed among primer combinations with a mean of 64.11%. Among 441 RAPDs assayed, 335 were polymorphic with a mean polymorphic rate of 73.71%. Unweighted pair-group method using an arithmetic average (UPGMA) cluster analysis using AFLP and RAPD data separated the 28 Texas bluegrass accessions into two broad groups. With a few exceptions, the females clustered with females and males with males. These results indicate that, it may be possible to discriminate between males and females using molecular markers. Principal coordinate analysis of AFLP and RAPD data also indicated two distinct groups and revealed genetic variability among and within the groups. Based on their genetic similarity indices, high correlation was observed between AFLP and RAPD markers.

 

An interspecific linkage map of SSR and intronic polymorphism markers in tomato

K. Shirasawa, E. Asamizu, H. Fukuoka, A. Ohyama, S. Sato, Y. Nakamura, S. Tabata, S. Sasamoto, T. Wada, Y. Kishida, H. Tsuruoka, T. Fujishiro, M. Hamada, S. Isobe

10.1007/s00122-010-1344-3

 

Despite the collection and availability of abundant tomato genome sequences, PCR-based markers adapted to large scale analysis have not been developed in tomato species. Therefore, using public genome sequence data in tomato, we developed three types of DNA markers: expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers (TES markers), genome-derived SSR markers (TGS markers) and EST-derived intronic polymorphismmarkers (TEI markers). A total of 2,047 TES, 3,510 TGS and 674 TEI markers were established and used in the polymorphic analysis of a cultivated tomato (Solanum lycopersicum) ‘LA925' and its wild relative Solanum pennellii ‘LA716', parents of the Tomato-EXPEN 2000 mapping population. The polymorphic ratios between parents revealed by the TES, TGS and TEI markers were 37.3, 22.6 and 80.0%, respectively. Those showing polymorphisms were used to genotype the Tomato-EXPEN 2000 mapping population, and a high-density genetic linkage map composed of 1,433 new and 683 existing marker loci was constructed on 12 chromosomes, covering 1,503.1 cM. In the present map, 48% of the mapped TGS loci were located within heterochromatic regions, while 18 and 21% of TES and TEI loci, respectively, were located in heterochromatin. The large number of SSR and SNP markers developed in this study provide easily handling genomic tools for molecular breeding in tomato. Information on the DNA markers developed in this study is available at http://www.kazusa.or.jp/tomato/.

 

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

S. Wicke, G.M. Schneeweiss,C.W. de Pamphilis, K.F. Muller, D. Quandt

10.1007/s11103-011

Discovery of a new family of amphibians from northeast India with ancient links of Africa

R.G. Kamei, D. San Mauro, D.J. Gower, I. Van Bocxlaer, E. Sherratt, A. Thomas, S. Babu, F. Bossuyt, M. Wilkinson, S.D. Biju

10.1098/rspb.2012.0150

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

 

Frequency of independent origins of viviparity among caecilians (Gymnophiona): evidence from the first ‘live-bearing' Asian amphibian

D.J Gower, V. Giri, M.S. Dharne, Y.S. Shouche

10.1111/j.1420-9101.2008.01577.x

 

Viviparity is reported for Gegeneophis seshachari (Gymnophiona: Caeciliidae) from a gravid female containing four oviductal foetuses. The oviducts are highly vascularized and contain patches of thickened, layered tissue similar to foetal gut contents. Gegeneophis seshachari probably resemble other viviparous caecilians in having foetuses that ingest thickened oviduct lining using specialized deciduous teeth. This is the first report of viviparity in Asian amphibians and Indo-Seychellean caeciliids. Gegeneophis is the only caecilian genus known to include oviparous and viviparous species, and G. seshachari is the smallest known viviparous caecilian. Phylogenetic analysis of mitochondrial DNA sequences supports assignment of G. seshachari to a monophyletic Gegeneophis. Character optimization indicates that viviparity has evolved independently at least four times within Gymnophiona--a rate of incidence relative to the number of extant species that is higher than for other vertebrate groups except squamate reptiles. Our findings strengthen the proposal that caecilian reproduction demands further attention.

 

The cells and peripheral representation of sodium taste in mice

J. Chandrashekar, C. Kuhn, Y. Oka, D.A. Yarmolinsky, E. Hummler, N.J.P. Ryba, C.S. Zuker

10.1038/nature08783

 

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

 

Amphibian Decline or Extinction? Current Declines Dwarf Background Extinction Rate

M.L. McCallum

10.1670/0022-1511(2007)41[483:ADOECD]2.0.CO;2

Amphibian declines and extinctions are critical concerns of biologists around the world. The estimated current rate of amphibian extinction is known, but how it compares to the background amphibian extinction rate from the fossil record has not been well studied. I compared current amphibian extinction rates with their reported background extinction rates using standard and fuzzy arithmetic. These calculations suggest that the current extinction rate of amphibians could be 211 times the background amphibian extinction rate. If current estimates of amphibian species in imminent danger of extinction are included in these calculations, then the current amphibian extinction rate may range from 25,039–45,474 times the background extinction rate for amphibians. It is difficult to explain this unprecedented and accelerating rate of extinction as a natural phenomenon.

 

Amphibian Encounter Rates on Roads with Different Amounts of Traffic and Urbanization

R.W. Sutherland, P.R. Dunning, W.M. Baker

10.1111/j.1523-1739.2010.01570.x

 

Although amphibians have relatively high rates of road mortality in urban areas, the conditions under which traffic threatens the survival of local amphibian populations remain unclear. In the Sandhills region of North Carolina (U.S.A.), we counted living and dead amphibians along two transects (total length 165 km) established on roads in areas with varying degrees of urbanization. We found 2665 individuals of 15 species, and amphibian encounter rates declined sharply as traffic and urban development increased. Regression-tree models indicated that 35 amphibians/100 km occurred on roads with <535 vehicles/day, whereas the encounter rate decreased to only 2 amphibians/100 km on roads with >2048 vehicles/day. Although mortality rate peaked at higher traffic levels (47% dead on roads with >5200 vehicles/day), the number of dead amphibians was highest at low levels of traffic. This suggests that areas where amphibian mortality is concentrated may actually contain the largest populations remaining on a given road transect.

 

 

 

Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape

W.J. Palen, D.E. Schindler

10.1073/pnas.0912970107

 

Increasing UV-B radiation (UV-B; 290–320 nm) due to stratospheric ozone depletion has been a leading explanation for the decline in amphibians for nearly 2 decades. Yet, the likelihood that UV-B can influence amphibians at the large spatial scales relevant to population declines has not yet been evaluated. A key limitation has been in relating results from individual sites to the effect of UV-B for populations distributed across heterogeneous landscapes. We measured critical embryonic exposures to UV-B for two species of montane amphibians with contrasting physiological sensitivities, long-toed salamander (Ambystoma macrodactylum) and Cascades frog (Rana cascadae), at field sites spanning a gradient of UV-B attenuation in water. We then used these experimental results to estimate the proportion of embryos exposed to harmful UV-B across a large number of breeding sites. By combining surveys of the incubation timing, incident UV-B, optical transparency of water, and oviposition depth and light exposure of embryos at each site, we present a comprehensive assessment of the risk posed by UV-B for montane amphibians of the Pacific Northwest. We found that only 1.1% of A. macrodactylum and no R. cascadae embryos across a landscape of breeding sites are exposed to UV-B exceeding lethal levels. These results emphasize that accurately estimating the risk posed by environmental stressors requires placing experimental results in a broader ecological context that accounts for the heterogeneity experienced by populations distributed across natural landscapes.

 

 

 

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

A.J. Crawford, K.R. Lips, E. Bermingham

10.1073/pnas.0914115107

 

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis.Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

 

Tropical amphibian populations experience higher disease risk in natural habitats

C.G. Becker, K.R. Zamudio

10.1073/pnas.1014497108

 

Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in amphibian populations in the tropics. At a large spatial scale, increased habitat loss predicted lower disease risk in amphibian populations across Costa Rica and eastern Australia, even after jointly considering the effect of potential biotic and abiotic correlates. Lower host-species richness and suboptimal microclimates forBd in disturbed habitats are potential mechanisms underlying this pattern. Furthermore, we found that anthropogenic deforestation practices biased to lowlands and natural vegetation remaining in inaccessible highlands explain increased Bd occurrence at higher elevations. At a smaller spatial scale, holding constant elevation, latitude, and macroclimate, we also found a negative relationship between habitat loss, and both Bd prevalence and infection intensity in frog populations in two landscapes of the Brazilian Atlantic Forest. Our results indicate that amphibians will be disproportionately affected by emerging diseases in pristine environments, and that, paradoxically, disturbed habitats may act as shelters from disease, but only for the very few species that can tolerate deforestation. Thus, tropical amphibian faunas are threatened both by destruction of natural habitats as well as increased disease in pristine forests. To curb further extinctions and develop effective mitigation and restoration programs we must look to interactions between habitat loss and disease, the two main factors at the root of global amphibian declines.

 

Coincident mass extirpation of neotropical amphibians with the emergence of the infectious fungal pathogen Batrachochytrium dendrobatidis

T.L. Cheng, S.M. Rovito, D.B. Wake, V.T. Vredenburg

10.1073/pnas.1105538108

 

Amphibians highlight the global biodiversity crisis because ∼40% of all amphibian species are currently in decline. Species have disappeared even in protected habitats (e.g., the enigmatic extinction of the golden toad, Bufo periglenes, from Costa Rica). The emergence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been implicated in a number of declines that have occurred in the last decade, but few studies have been able to test retroactively whether Bd emergence was linked to earlier declines and extinctions. We describe a noninvasive PCR sampling technique that detects Bd in formalin-preserved museum specimens. We detected Bd by PCR in 83–90% (n = 38) of samples that were identified as positive by histology. We examined specimens collected before, during, and after major amphibian decline events at established study sites in southern Mexico, Guatemala, and Costa Rica. A pattern of Bd emergence coincident with decline at these localities is revealed—the absence of Bd over multiple years at all localities followed by the concurrent emergence of Bd in various species at each locality during a period of population decline. The geographical and chronological emergence of Bd at these localities also indicates a southbound spread from southern Mexico in the early 1970s to western Guatemala in the 1980s/1990s and to Monteverde, Costa Rica by 1987. We find evidence of a historical "Bd epidemic wave" that began in Mexico and subsequently spread to Central America. We describe a technique that can be used to screen museum specimens from other amphibian decline sites around the world.

Discovery of a new family of amphibians from northeast India with ancient links of Africa

R.G. Kamei, D. San Mauro, D.J. Gower, I. Van Bocxlaer, E. Sherratt, A. Thomas, S. Babu, F. Bossuyt, M. Wilkinson, S.D. Biju

10.1098/rspb.2012.0150

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

 

Frequency of independent origins of viviparity among caecilians (Gymnophiona): evidence from the first ‘live-bearing' Asian amphibian

D.J Gower, V. Giri, M.S. Dharne, Y.S. Shouche

10.1111/j.1420-9101.2008.01577.x

 

Viviparity is reported for Gegeneophis seshachari (Gymnophiona: Caeciliidae) from a gravid female containing four oviductal foetuses. The oviducts are highly vascularized and contain patches of thickened, layered tissue similar to foetal gut contents. Gegeneophis seshachari probably resemble other viviparous caecilians in having foetuses that ingest thickened oviduct lining using specialized deciduous teeth. This is the first report of viviparity in Asian amphibians and Indo-Seychellean caeciliids. Gegeneophis is the only caecilian genus known to include oviparous and viviparous species, and G. seshachari is the smallest known viviparous caecilian. Phylogenetic analysis of mitochondrial DNA sequences supports assignment of G. seshachari to a monophyletic Gegeneophis. Character optimization indicates that viviparity has evolved independently at least four times within Gymnophiona--a rate of incidence relative to the number of extant species that is higher than for other vertebrate groups except squamate reptiles. Our findings strengthen the proposal that caecilian reproduction demands further attention.

 

The cells and peripheral representation of sodium taste in mice

J. Chandrashekar, C. Kuhn, Y. Oka, D.A. Yarmolinsky, E. Hummler, N.J.P. Ryba, C.S. Zuker

10.1038/nature08783

 

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

 

Amphibian Decline or Extinction? Current Declines Dwarf Background Extinction Rate

M.L. McCallum

10.1670/0022-1511(2007)41[483:ADOECD]2.0.CO;2

Amphibian declines and extinctions are critical concerns of biologists around the world. The estimated current rate of amphibian extinction is known, but how it compares to the background amphibian extinction rate from the fossil record has not been well studied. I compared current amphibian extinction rates with their reported background extinction rates using standard and fuzzy arithmetic. These calculations suggest that the current extinction rate of amphibians could be 211 times the background amphibian extinction rate. If current estimates of amphibian species in imminent danger of extinction are included in these calculations, then the current amphibian extinction rate may range from 25,039–45,474 times the background extinction rate for amphibians. It is difficult to explain this unprecedented and accelerating rate of extinction as a natural phenomenon.

 

Amphibian Encounter Rates on Roads with Different Amounts of Traffic and Urbanization

R.W. Sutherland, P.R. Dunning, W.M. Baker

10.1111/j.1523-1739.2010.01570.x

 

Although amphibians have relatively high rates of road mortality in urban areas, the conditions under which traffic threatens the survival of local amphibian populations remain unclear. In the Sandhills region of North Carolina (U.S.A.), we counted living and dead amphibians along two transects (total length 165 km) established on roads in areas with varying degrees of urbanization. We found 2665 individuals of 15 species, and amphibian encounter rates declined sharply as traffic and urban development increased. Regression-tree models indicated that 35 amphibians/100 km occurred on roads with <535 vehicles/day, whereas the encounter rate decreased to only 2 amphibians/100 km on roads with >2048 vehicles/day. Although mortality rate peaked at higher traffic levels (47% dead on roads with >5200 vehicles/day), the number of dead amphibians was highest at low levels of traffic. This suggests that areas where amphibian mortality is concentrated may actually contain the largest populations remaining on a given road transect.

 

 

 

Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape

W.J. Palen, D.E. Schindler

10.1073/pnas.0912970107

 

Increasing UV-B radiation (UV-B; 290–320 nm) due to stratospheric ozone depletion has been a leading explanation for the decline in amphibians for nearly 2 decades. Yet, the likelihood that UV-B can influence amphibians at the large spatial scales relevant to population declines has not yet been evaluated. A key limitation has been in relating results from individual sites to the effect of UV-B for populations distributed across heterogeneous landscapes. We measured critical embryonic exposures to UV-B for two species of montane amphibians with contrasting physiological sensitivities, long-toed salamander (Ambystoma macrodactylum) and Cascades frog (Rana cascadae), at field sites spanning a gradient of UV-B attenuation in water. We then used these experimental results to estimate the proportion of embryos exposed to harmful UV-B across a large number of breeding sites. By combining surveys of the incubation timing, incident UV-B, optical transparency of water, and oviposition depth and light exposure of embryos at each site, we present a comprehensive assessment of the risk posed by UV-B for montane amphibians of the Pacific Northwest. We found that only 1.1% of A. macrodactylum and no R. cascadae embryos across a landscape of breeding sites are exposed to UV-B exceeding lethal levels. These results emphasize that accurately estimating the risk posed by environmental stressors requires placing experimental results in a broader ecological context that accounts for the heterogeneity experienced by populations distributed across natural landscapes.

 

 

 

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

A.J. Crawford, K.R. Lips, E. Bermingham

10.1073/pnas.0914115107

 

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis.Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

 

Tropical amphibian populations experience higher disease risk in natural habitats

C.G. Becker, K.R. Zamudio

10.1073/pnas.1014497108

 

Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in amphibian populations in the tropics. At a large spatial scale, increased habitat loss predicted lower disease risk in amphibian populations across Costa Rica and eastern Australia, even after jointly considering the effect of potential biotic and abiotic correlates. Lower host-species richness and suboptimal microclimates forBd in disturbed habitats are potential mechanisms underlying this pattern. Furthermore, we found that anthropogenic deforestation practices biased to lowlands and natural vegetation remaining in inaccessible highlands explain increased Bd occurrence at higher elevations. At a smaller spatial scale, holding constant elevation, latitude, and macroclimate, we also found a negative relationship between habitat loss, and both Bd prevalence and infection intensity in frog populations in two landscapes of the Brazilian Atlantic Forest. Our results indicate that amphibians will be disproportionately affected by emerging diseases in pristine environments, and that, paradoxically, disturbed habitats may act as shelters from disease, but only for the very few species that can tolerate deforestation. Thus, tropical amphibian faunas are threatened both by destruction of natural habitats as well as increased disease in pristine forests. To curb further extinctions and develop effective mitigation and restoration programs we must look to interactions between habitat loss and disease, the two main factors at the root of global amphibian declines.

 

Coincident mass extirpation of neotropical amphibians with the emergence of the infectious fungal pathogen Batrachochytrium dendrobatidis

T.L. Cheng, S.M. Rovito, D.B. Wake, V.T. Vredenburg

10.1073/pnas.1105538108

 

Amphibians highlight the global biodiversity crisis because ∼40% of all amphibian species are currently in decline. Species have disappeared even in protected habitats (e.g., the enigmatic extinction of the golden toad, Bufo periglenes, from Costa Rica). The emergence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been implicated in a number of declines that have occurred in the last decade, but few studies have been able to test retroactively whether Bd emergence was linked to earlier declines and extinctions. We describe a noninvasive PCR sampling technique that detects Bd in formalin-preserved museum specimens. We detected Bd by PCR in 83–90% (n = 38) of samples that were identified as positive by histology. We examined specimens collected before, during, and after major amphibian decline events at established study sites in southern Mexico, Guatemala, and Costa Rica. A pattern of Bd emergence coincident with decline at these localities is revealed—the absence of Bd over multiple years at all localities followed by the concurrent emergence of Bd in various species at each locality during a period of population decline. The geographical and chronological emergence of Bd at these localities also indicates a southbound spread from southern Mexico in the early 1970s to western Guatemala in the 1980s/1990s and to Monteverde, Costa Rica by 1987. We find evidence of a historical "Bd epidemic wave" that began in Mexico and subsequently spread to Central America. We describe a technique that can be used to screen museum specimens from other amphibian decline sites around the world.

-9762-4

 

This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.

 

Auxin–cytokinin interactions in the control of shoot branching

S. Shimizu-Sato, M. Tanaka, H. Mori

10.1007/s11103-008-9416-3

 

In many plant species, the intact main shoot apex grows predominantly and axillary bud outgrowth is inhibited. This phenomenon is called apical dominance, and has been analyzed for over 70 years. Decapitation of the shoot apex releases the axillary buds from their dormancy and they begin to grow out. Auxin derived from an intact shoot apex suppresses axillary bud outgrowth, whereas cytokinin induced by decapitation of the shoot apex stimulates axillary bud outgrowth. Here we describe the molecular mechanisms of the interactions between auxin and cytokinin in the control of shoot branching.

 

Cortisol inhibits apoptosis in carp neutrophilic granulocytes

F.A. Weyts, G. Flik, B.M. Verburg-van Kemenade

10.1016/S0145-305X(98)00027-5

 

The direct effect of cortisol treatment on carp neutrophil viability was examined in vitro. Cortisol treatment caused an inhibition of neutrophil apoptosis. The effect was blocked by glucocorticoid receptor blocker RU486, showing that rescue from apoptosis was receptor mediated. Using binding studies with radioactive cortisol, a single class of glucocorticoid receptors was detected with high affinity (Kd = 2.6 nM) and low capacity (497 receptors/cell) for cortisol binding. Both in vitro and in vivo cortisol treatment did not affect neutrophil respiratory burst activity. These data indicate that cortisol can augment the supply of functional neutrophilic granulocytes in conditions of acute stress, which may be essential for survival, since phagocytes form the first line of defence against micro-organisms.

 

Stress hormones collaborate to induce lymphocyte apoptosis after high level spinal cord injury

K.M. Lucin, V.M. Sanders, P.G. Popovich

10.1111/j.1471-4159.2009.06232.x

 

Post-traumatic immune suppression renders individuals with spinal cord injury (SCI) susceptible to infection. Normally, proper immune function is regulated by collaboration between the sympathetic nervous system (SNS) and hypothalamic-pituitary-adrenal (HPA) axis and involves the controlled release of glucocorticoids (GCs) and norepinephrine (NE). Recently, we showed that after high thoracic (T3) SCI, aberrant levels of GCs and NE accumulate in the blood and spleen, respectively. These changes are associated with splenic atrophy, splenic leucopenia, increased intrasplenic caspase 3 levels, and suppressed B lymphocyte function. As GCs boost SNS function, in part by increasing the expression and affinity of beta2 adrenergic receptors (beta2ARs) while simultaneously preventing beta2AR down-regulation, we predicted that surges in stress hormones (i.e., GCs and NE) in the blood and spleen of mice with high-level SCI would act concurrently to adversely affect lymphocyte function and survival. Here, we show that post-SCI concentrations of GCs enhance the sensitivity of lymphocytes to beta2AR stimulation causing an increase in intracellular Bcl-2 interacting mediator of cell death (Bim) and subsequent apoptosis. In vivo, the combined antagonism of GC receptors and beta2ARs significantly diminished lymphocyte Bim levels and SCI-induced splenic lymphopenia. Together, these data suggest that pharmacological antagonists of the HPA/SNS axes should be considered as adjunct therapies for ameliorating post-traumatic immune suppression in quadriplegics and high paraplegics.

 

Study of NADPH oxidase-activated sites in human neutrophils

H. Seguchi , T. Kobayashi

10.1093/jmicro/51.2.87

 

Neutrophils represent the first line of defence against invading microorganisms. An important part of this defence mechanism is the generation of superoxide (O2*-) and its reactive derivatives after stimulation by a variety of agents. This oxidant production is linked to the activation of NADPH oxidase, which is composed of cytosolic components (p47-phox and p67-phox) and membrane components (p22-phox and gp91-phox). Previous studies have shown that NADPH oxidase resides in the plasma membrane and the traditional view holds that cytoplasmic components of NADPH oxidase are brought into the neighbourhood of the plasma membrane and then conjugated with its membrane components upon stimulation. This review focuses on the evaluation of NADPH oxidase-activated sites in human neutrophils. Based on electron microscopic analysis, O2*- is first generated upon stimulation with certain stimulants, such as phorbol myristate acetate, within a specialized intracellular compartment containing alkaline phosphatase, and not on the plasma membrane, as previously thought. In addition, the cytosolic component of NADPH oxidase, p47-phox, accumulates at the juxtaposition of intracellular compartments but not of the plasma membrane. These results demonstrate that initial O2*- production occurs in an intracellular pool in human neutrophils. The oxidant-producing granules then bind directly to the plasma membrane or fuse to form larger structures that eventually become to be associated with the plasma membrane, and O2*- is released extracellularly from the neutrophils.

 

Effect of melatonin and pineal grafting on thymocyte apoptosis in aging mice

M. Provinciali , G. Di Stefano, D. Bulian , A. Tibaldi , N. Fabris

10.1016/0047-6374(96)01746-0

 

We have evaluated the effect of chronic melatonin (MEL) treatment or pineal grafting (PG) in old mice on the apoptosis of both thymocytes and spleen lymphocytes under conditions of either serum deprivation or glucocorticoid or zinc administration. The apoptosis was correlated with the modulation of thymus and adrenal weight and corticosterone and zinc plasma levels induced by MEL treatment or PG in old mice. Balb/c mice (17-18 months old) were given supplements of MEL (40-50 micrograms/day/mouse) or grafted with a young pineal gland and then sacrificed after 8 months. Both the MEL treatment and PG partially prevented thymic involution in very old mice. Both treatments protected the thymic and spleen lymphocytes in old mice from the apoptosis induced by serum deprivation and recovered the reduced thymocyte sensitivity to the apoptosis induced by dexamethasone (DEX), present in old untreated animals, to the values found in young mice. DEX caused a bigger loss of G D /G 1 phase cells in MEL treated mice than in old untreated mice. The protective action of MEL treatment or PG on serum deprivation induced apoptosis was correlated with increased thymus weight, reduced adrenal weight and corticosterone levels and increased zinc plasma levels. The greater DEX-induced apoptosis found in MEL treated and PG mice was correlated with reduced adrenal weight and function. In vitro MEL did not affect thymocyte apoptosis in young or old mice. These results suggest that MEL treatment or PG prevent age-related thymus involution through regulation of thymocyte apoptosis which, in turn, occurs through modulation of the pituitary-adrenal axis and zinc turnover determined by the pineal hormone.

 

Apoptotic cells can deliver chemotherapeutics to engulfing macrophages and suppress inflammatory cytokine production

B. Perez, N. Paquette, H. Païdassi, B. Zhai , K. White, R. Skvirsky , A. Lacy-Hulbert , L.M. Stuart

10.1074/jbc.M112.340489

 

Immune suppression via cell-cell contact with apoptotic cells is a well-studied immunological phenomenon. Although the original reports of immune repression used primary cells that undergo spontaneous cell death or apoptosis in response to irradiation, more recent studies have relied on chemotherapeutic agents to induce apoptosis in cell lines. In this work we demonstrate that Jurkat cells induced to die with actinomycin D suppress inflammatory cytokine production by macrophages, whereas cells treated with etoposide do not. This immune repression mediated by actinomycin D-treated cells does not require phagocytosis or cell-cell contact and thus occurs through a different mechanism to that seen with primary apoptotic neutrophils. Moreover, cells induced to die with etoposide and then treated for a short time with actinomycin D also suppressed macrophage responses, indicating that suppression was mediated by actinomycin D independent of the mechanism of cell death. Finally, phagocytosis of actinomycin D-treated cells caused apoptosis in macrophages and suppression can be blocked by inhibition of caspase activity in the target macrophage. Together, these data indicate that apoptotic cells act as Trojan Horses delivering actinomycin D to engulfing macrophages. Suppression of cytokine production by macrophages is therefore due to exposure to actinomycin D from apoptotic cells and is not the result of cell receptor interactions. These data suggest that druginduced death may not be an appropriate surrogate for the immuno-suppressive activity of apoptotic cells. Furthermore, these effects of cytotoxic drugs on infiltrating immune phagocytes may have clinical ramifications for their use as antitumor therapies.

 

Extracellular Superoxide Dismutase Inhibits Innate Immune Responses and Clearance of an Intracellular Bacterial Infection

T.J. Break, S. Jun , M. Indramohan , K.D. Carr , A.N.Sieve , L. Dory, R.E. Berg

10.4049/jimmunol.1102341

 

Reactive oxygen species and reactive nitrogen species play important roles during immune responses to bacterial pathogens. Extracellular superoxide dismutase (ecSOD) regulates extracellular concentrations of reactive oxygen species and reactive nitrogen species and contributes to tissue protection during inflammatory insults. The participation of ecSOD in immune responses seems therefore intuitive, yet is poorly understood. In the current study, we used mice with varying levels of ecSOD activity to investigate the involvement of this enzyme in immune responses against Listeria monocytogenes. Surprisingly, our data demonstrate that despite enhanced neutrophil recruitment to the liver, ecSOD activity negatively affected host survival and bacterial clearance. Increased ecSOD activity was accompanied by decreased colocalization of neutrophils with bacteria, as well as increased neutrophil apoptosis, which reduced overall and neutrophil-specific TNF-α production. Liver leukocytes from mice lacking ecSOD produced equivalent NO· compared with liver leukocytes from mice expressing ecSOD. However, during infection, there were higher levels of peroxynitrite (NO(3)·(-)) in livers from mice lacking ecSOD compared with livers from mice expressing ecSOD. Neutrophil depletion studies revealed that high levels of ecSOD activity resulted in neutrophils with limited protective capacity, whereas neutrophils from mice lacking ecSOD provided superior protection compared with neutrophils from wild-type mice. Taken together, our data demonstrate that ecSOD activity reduces innate immune responses during bacterial infection and provides a potential target for therapeutic intervention.

 

Effects of heparin and related drugs on neutrophil function

R.A. Brown, E. Leung , H. Kankaanranta , E. Moilanen, C.P. Page

10.1016/j.pupt.2012.01.006

 

We have previously demonstrated that heparin inhibits neutrophil activation, but the precise mechanism of action remains to be elucidated. The current aim was to further investigate the effects of heparin at inducing apoptosis of neutrophils and whether this was related to antagonism at IP(3) receptors. Furthermore, we investigated the ability of heparin and related molecules to inhibit acute neutrophil-induced injury to human bronchial epithelial cells (HBECs) in vitro. Neutrophils were isolated from human peripheral venous blood. Expression of annexin-V was determined in neutrophils following incubation with LMWH. The effects of LMWH and related molecules upon thapsigargin or m-3M3FBS (phospholipase C activator) induced neutrophil elastase (NE) release were also investigated. The cytotoxic effects of fMLP-activated neutrophils following co-incubation with HBECs were quantified through counting adherent cells before and after incubation. There was no detectable increase in annexin-V positive neutrophils following pre-incubation with LMWH at 30 min, 60 min or 16 h, but an increase was observed with Fas-activating antibody at 16 h. LMWH significantly inhibited NE release induced by either m-3M3FBS (73.4 ± 6.1%, 100 IU ml(-1), P < 0.01) or thapsigargin (62.4 ± 6.9%, 100 IU ml(-1), P < 0.01) in a sulphate-dependent manner. LMWH and related sulphated molecules all abrogated the cytotoxic effects of fMLP-activated neutrophils upon HBECs. In conclusion we were not able to demonstrate that heparin induces apoptosis and we did not find any evidence for heparin acting as an IP(3) receptor antagonist in neutrophils. Nonetheless, the potent inhibitory effects of heparin and related molecules upon neutrophil-induced injury to HBECs provide further evidence of the therapeutic potential of heparin and related molecules in the treatment of chronic inflammatory diseases.

 

Myeloperoxidase Exacerbates Secondary Injury by Generating Highly Reactive Oxygen Species and Mediating Neutrophil Recruitment in Experimental Spinal Cord Injury

K. Kubota, H. Saiwai , H. Kumamaru , T. Maeda , Y. Ohkawa , Y. Aratani , T. Nagano, Y. Iwamoto , S. Okada

10.1097/BRS.0b013e31824b9e77

 

Study Design. An animal study using myeloperoxidase-knockout (MPO-KO) mice to examine the in vivo role of myeloperoxidase (MPO) in spinal cord injury (SCI).Objective. To clarify the influence of MPO on inflammatory cell infiltration, tissue damage, and functional recovery after SCI.Summary of Background Data. MPO is considered to be important in spreading tissue damage after SCI because it generates strong neurotoxic oxidant hypochlorite acid (HOCl). However, the direct involvement of MPO in the pathophysiology of SCI remains to be elucidated.Methods. To compare the inflammatory reaction, tissue damage, and neurological recovery after SCI, a moderate contusion injury was created at the 9 thoracic level in MPO-KO mice and wild-type mice. A HOCl-specific probe solution was injected into the lesion epicenter to assess the spatiotemporal production of MPO-derived HOCl. Inflammatory reactions were quantified by flow cytometry and quantitative real time PCR, and tissue damage was evaluated by an immunohistochemical analysis. The motor function recovery was assessed by the open-field locomotor score.Results. Prominent production of HOCl was observed during the hyper-acute phase of SCI at the lesion site in the wild type mice, however, little expression was observed in the MPO-KO mice. In this phase, the number of infiltrated neutrophils was significantly reduced in the MPO-KO mice compared to the wild-type mice. In addition, significant differences were observed in the expression levels of pro-inflammatory cytokines and apoptosis-related genes between two groups. In the histological sections, fewer TUNEL-positive apoptotic cells and more spared myelin were observed at the lesion site in MPO-KO mice. Consistent with these results, better functional recovery was observed in the MPO-KO mice than in the wild-type mice after SCI.Conclusion. These results clearly indicated that MPO exacerbated secondary injury and impaired the functional recovery by not only generating strong oxidant HOCl.

 

Discovery of a new family of amphibians from northeast India with ancient links of Africa

R.G. Kamei, D. San Mauro, D.J. Gower, I. Van Bocxlaer, E. Sherratt, A. Thomas, S. Babu, F. Bossuyt, M. Wilkinson, S.D. Biju

10.1098/rspb.2012.0150

 

The limbless, primarily soil-dwelling and tropical caecilian amphibians (Gymnophiona) comprise the least known order of tetrapods. On the basis of unprecedented extensive fieldwork, we report the discovery of a previously overlooked, ancient lineage and radiation of caecilians from threatened habitats in the underexplored states of northeast India. Molecular phylogenetic analyses of mitogenomic and nuclear DNA sequences, and comparative cranial anatomy indicate an unexpected sister-group relationship with the exclusively African family Herpelidae. Relaxed molecular clock analyses indicate that these lineages diverged in the Early Cretaceous, about 140 Ma. The discovery adds a major branch to the amphibian tree of life and sheds light on both the evolution and biogeography of caecilians and the biotic history of northeast India—an area generally interpreted as a gateway between biodiversity hotspots rather than a distinct biogeographic unit with its own ancient endemics. Because of its distinctive morphology, inferred age and phylogenetic relationships, we recognize the newly discovered caecilian radiation as a new family of modern amphibians.

 

Frequency of independent origins of viviparity among caecilians (Gymnophiona): evidence from the first ‘live-bearing' Asian amphibian

D.J Gower, V. Giri, M.S. Dharne, Y.S. Shouche

10.1111/j.1420-9101.2008.01577.x

 

Viviparity is reported for Gegeneophis seshachari (Gymnophiona: Caeciliidae) from a gravid female containing four oviductal foetuses. The oviducts are highly vascularized and contain patches of thickened, layered tissue similar to foetal gut contents. Gegeneophis seshachari probably resemble other viviparous caecilians in having foetuses that ingest thickened oviduct lining using specialized deciduous teeth. This is the first report of viviparity in Asian amphibians and Indo-Seychellean caeciliids. Gegeneophis is the only caecilian genus known to include oviparous and viviparous species, and G. seshachari is the smallest known viviparous caecilian. Phylogenetic analysis of mitochondrial DNA sequences supports assignment of G. seshachari to a monophyletic Gegeneophis. Character optimization indicates that viviparity has evolved independently at least four times within Gymnophiona--a rate of incidence relative to the number of extant species that is higher than for other vertebrate groups except squamate reptiles. Our findings strengthen the proposal that caecilian reproduction demands further attention.

 

The cells and peripheral representation of sodium taste in mice

J. Chandrashekar, C. Kuhn, Y. Oka, D.A. Yarmolinsky, E. Hummler, N.J.P. Ryba, C.S. Zuker

10.1038/nature08783

 

Salt taste in mammals can trigger two divergent behavioural responses. In general, concentrated saline solutions elicit robust behavioural aversion, whereas low concentrations of NaCl are typically attractive, particularly after sodium depletion. Notably, the attractive salt pathway is selectively responsive to sodium and inhibited by amiloride, whereas the aversive one functions as a non-selective detector for a wide range of salts. Because amiloride is a potent inhibitor of the epithelial sodium channel (ENaC), ENaC has been proposed to function as a component of the salt-taste-receptor system. Previously, we showed that four of the five basic taste qualities-sweet, sour, bitter and umami-are mediated by separate taste-receptor cells (TRCs) each tuned to a single taste modality, and wired to elicit stereotypical behavioural responses. Here we show that sodium sensing is also mediated by a dedicated population of TRCs. These taste cells express the epithelial sodium channel ENaC, and mediate behavioural attraction to NaCl. We genetically engineered mice lacking ENaCalpha in TRCs, and produced animals exhibiting a complete loss of salt attraction and sodium taste responses. Together, these studies substantiate independent cellular substrates for all five basic taste qualities, and validate the essential role of ENaC for sodium taste in mice.

 

Amphibian Decline or Extinction? Current Declines Dwarf Background Extinction Rate

M.L. McCallum

10.1670/0022-1511(2007)41[483:ADOECD]2.0.CO;2

Amphibian declines and extinctions are critical concerns of biologists around the world. The estimated current rate of amphibian extinction is known, but how it compares to the background amphibian extinction rate from the fossil record has not been well studied. I compared current amphibian extinction rates with their reported background extinction rates using standard and fuzzy arithmetic. These calculations suggest that the current extinction rate of amphibians could be 211 times the background amphibian extinction rate. If current estimates of amphibian species in imminent danger of extinction are included in these calculations, then the current amphibian extinction rate may range from 25,039–45,474 times the background extinction rate for amphibians. It is difficult to explain this unprecedented and accelerating rate of extinction as a natural phenomenon.

 

Amphibian Encounter Rates on Roads with Different Amounts of Traffic and Urbanization

R.W. Sutherland, P.R. Dunning, W.M. Baker

10.1111/j.1523-1739.2010.01570.x

 

Although amphibians have relatively high rates of road mortality in urban areas, the conditions under which traffic threatens the survival of local amphibian populations remain unclear. In the Sandhills region of North Carolina (U.S.A.), we counted living and dead amphibians along two transects (total length 165 km) established on roads in areas with varying degrees of urbanization. We found 2665 individuals of 15 species, and amphibian encounter rates declined sharply as traffic and urban development increased. Regression-tree models indicated that 35 amphibians/100 km occurred on roads with <535 vehicles/day, whereas the encounter rate decreased to only 2 amphibians/100 km on roads with >2048 vehicles/day. Although mortality rate peaked at higher traffic levels (47% dead on roads with >5200 vehicles/day), the number of dead amphibians was highest at low levels of traffic. This suggests that areas where amphibian mortality is concentrated may actually contain the largest populations remaining on a given road transect.

 

Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape

W.J. Palen, D.E. Schindler

10.1073/pnas.0912970107

 

Increasing UV-B radiation (UV-B; 290–320 nm) due to stratospheric ozone depletion has been a leading explanation for the decline in amphibians for nearly 2 decades. Yet, the likelihood that UV-B can influence amphibians at the large spatial scales relevant to population declines has not yet been evaluated. A key limitation has been in relating results from individual sites to the effect of UV-B for populations distributed across heterogeneous landscapes. We measured critical embryonic exposures to UV-B for two species of montane amphibians with contrasting physiological sensitivities, long-toed salamander (Ambystoma macrodactylum) and Cascades frog (Rana cascadae), at field sites spanning a gradient of UV-B attenuation in water. We then used these experimental results to estimate the proportion of embryos exposed to harmful UV-B across a large number of breeding sites. By combining surveys of the incubation timing, incident UV-B, optical transparency of water, and oviposition depth and light exposure of embryos at each site, we present a comprehensive assessment of the risk posed by UV-B for montane amphibians of the Pacific Northwest. We found that only 1.1% of A. macrodactylum and no R. cascadae embryos across a landscape of breeding sites are exposed to UV-B exceeding lethal levels. These results emphasize that accurately estimating the risk posed by environmental stressors requires placing experimental results in a broader ecological context that accounts for the heterogeneity experienced by populations distributed across natural landscapes.

 

Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama

A.J. Crawford, K.R. Lips, E. Bermingham

10.1073/pnas.0914115107

 

Amphibian populations around the world are experiencing unprecedented declines attributed to a chytrid fungal pathogen, Batrachochytrium dendrobatidis.Despite the severity of the crisis, quantitative analyses of the effects of the epidemic on amphibian abundance and diversity have been unavailable as a result of the lack of equivalent data collected before and following disease outbreak. We present a community-level assessment combining long-term field surveys and DNA barcode data describing changes in abundance and evolutionary diversity within the amphibian community of El Copé, Panama, following a disease epidemic and mass-mortality event. The epidemic reduced taxonomic, lineage, and phylogenetic diversity similarly. We discovered that 30 species were lost, including five undescribed species, representing 41% of total amphibian lineage diversity in El Copé. These extirpations represented 33% of the evolutionary history of amphibians within the community, and variation in the degree of population loss and decline among species was random with respect to the community phylogeny. Our approach provides a fast, economical, and informative analysis of loss in a community whether measured by species or phylogenetic diversity.

 

Tropical amphibian populations experience higher disease risk in natural habitats

C.G. Becker, K.R. Zamudio

10.1073/pnas.1014497108

 

Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in amphibian populations in the tropics. At a large spatial scale, increased habitat loss predicted lower disease risk in amphibian populations across Costa Rica and eastern Australia, even after jointly considering the effect of potential biotic and abiotic correlates. Lower host-species richness and suboptimal microclimates forBd in disturbed habitats are potential mechanisms underlying this pattern. Furthermore, we found that anthropogenic deforestation practices biased to lowlands and natural vegetation remaining in inaccessible highlands explain increased Bd occurrence at higher elevations. At a smaller spatial scale, holding constant elevation, latitude, and macroclimate, we also found a negative relationship between habitat loss, and both Bd prevalence and infection intensity in frog populations in two landscapes of the Brazilian Atlantic Forest. Our results indicate that amphibians will be disproportionately affected by emerging diseases in pristine environments, and that, paradoxically, disturbed habitats may act as shelters from disease, but only for the very few species that can tolerate deforestation. Thus, tropical amphibian faunas are threatened both by destruction of natural habitats as well as increased disease in pristine forests. To curb further extinctions and develop effective mitigation and restoration programs we must look to interactions between habitat loss and disease, the two main factors at the root of global amphibian declines.

 

The genomic basis of adaptive evolution in threespine sticklebacks

F.C. Jones, M.G. Grabherr, Y.F. Chan, P. Russell, E. Mauceli, J. Johnson, R. Swofford, M. Pirun, M.C. Zody, S. White, E. Birney, S. Searle, J. Schmutz, J. Grimwood, M.C. Dickson, R.M. Myers, C.T. Miller, B.R. Summers, A.K. Knecht, S.D. Brady, H. Zhang, A.A. Pollen, T. Howes, C. Amemiya, J. Baldwin, T. Bloom, D.B. Jaffe, R. Nicol, J. Wilkinson, E.S. Lander, F. Di Palma, K. Lindblad-Toh, D.M. Kingsley

10.1038/nature10944


Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of twenty additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine–freshwater divergence. Our results indicate that reuse of globally shared standing genetic variation, including chromosomal inversions, has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine–freshwater evolution, but regulatory changes appear to predominate in this well known example of repeated adaptive evolution in nature.
 

Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species

B. Tschirren, M. Andersson , K. Scherman, H. Westerdahl, L. Råberg

10.1111/j.1558-5646.2011.01473.x


Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defense may be evolutionarily more dynamic than has previously been appreciated.

 

Sequencing our way towards understanding global eukaryotic biodiversity

H.M. Bik, D.L. Porazinska, S. Creer, J.G. Caporaso, R. Knight, W.K. Thomas

10.1016/j.tree.2011.11.010

 

Microscopic eukaryotes are abundant, diverse and fill critical ecological roles across every ecosystem on Earth, yet there is a well-recognized gap in understanding of their global biodiversity. Fundamental advances in DNA sequencing and bioinformatics now allow accurate en masse biodiversity assessments of microscopic eukaryotes from environmental samples. Despite a promising outlook, the field of eukaryotic marker gene surveys faces significant challenges: how to generate data that are most useful to the community, especially in the face of evolving sequencing technologies and bioinformatics pipelines, and how to incorporate an expanding number of target genes.

 

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

R.W. Ness, M. Siol, S.CH. Barrett

doi:10.1186/1471-2164-12-298

 

Background

The shift from cross-fertilization to predominant self-fertilization is among the most common evolutionary transitions in the reproductive biology of flowering plants. Increased inbreeding has important consequences for floral morphology, population genetic structure and genome evolution. The transition to selfing is usually characterized by a marked reduction in flower size and the loss of traits involved in pollinator attraction and the avoidance of self-fertilization. Here, we use short-read sequencing to assemble, de novo, the floral transcriptomes of three genotypes of Eichhornia paniculata, including an outcrosser and two genotypes from independently derived selfers, and a single genotype of the sister species E. paradoxa. By sequencing mRNA from tissues sampled at various stages of flower development, our goal was to sequence and assemble the floral transcriptome and identify differential patterns of gene expression.

Results

Our 24 Mbp assembly resulted in ~27,000 contigs that averaged ~900 bp in length. All four genotypes had highly correlated gene expression, but the three E. paniculata genotypes were more correlated with one another than each was to E. paradoxa. Our analysis identified 269 genes associated with floral development, 22 of which were differentially expressed in selfing lineages relative to the outcrosser. Many of the differentially expressed genes affect floral traits commonly altered in selfing plants and these represent a set of potential candidate genes for investigating the evolution of the selfing syndrome.

Conclusions

Our study is among the first to demonstrate the use of Illumina short read sequencing for de novotranscriptome assembly in non-model species, and the first to implement this technology for comparing floral transcriptomes in outcrossing and selfing plants.

 

Running with the Red Queen: Host-Parasite Coevolution Selects for Biparental Sex

L.T. Morran, O.G. Schmidt, I.A. Gelarden, R.C. Parrish II, C.M. Lively

10.1126/science.1206360

 

Most organisms reproduce through outcrossing, even though it comes with substantial costs. The Red Queen hypothesis proposes that selection from coevolving pathogens facilitates the persistence of outcrossing despite these costs. We used experimental coevolution to test the Red Queen hypothesis and found that coevolution with a bacterial pathogen (Serratia marcescens) resulted in significantly more outcrossing in mixed mating experimental populations of the nematode Caenorhabditis elegans. Furthermore, we found that coevolution with the pathogen rapidly drove obligately selfing populations to extinction, whereas outcrossing populations persisted through reciprocal coevolution. Thus, consistent with the Red Queen hypothesis, coevolving pathogens can select for biparental sex.

 

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

G.H. Perry, P. Melsted, J.C. Marioni, Y .Wang, R. Bainer, J.K. Pickrell, K. Michelini, S. Zehr, A.D. Yoder, M. Stephens, J.K. Pritchard, Y. Gilad

10.1101/gr.130468.111

 

Comparative genomic studies in primates have yielded important insights into the evolutionary forces that shape genetic diversity and revealed the likely genetic basis for certain species-specific adaptations. To date, however, these studies have focused on only a small number of species. For the majority of nonhuman primates, including some of the most critically endangered, genome-level data are not yet available. In this study, we have taken the first steps toward addressing this gap by sequencing RNA from the livers of multiple individuals from each of 16 mammalian species, including humans and 11 nonhuman primates. Of the nonhuman primate species, five are lemurs and two are lorisoids, for which little or no genomic data were previously available. To analyze these data, we developed a method for de novo assembly and alignment of orthologous gene sequences across species. We assembled an average of 5721 gene sequences per species and characterized diversity and divergence of both gene sequences and gene expression levels. We identified patterns of variation that are consistent with the action of positive or directional selection, including an 18-fold enrichment of peroxisomal genes among genes whose regulation likely evolved under directional selection in the ancestral primate lineage. Importantly, we found no relationship between genetic diversity and endangered status, with the two most endangered species in our study, the black and white ruffed lemur and the Coquerel's sifaka, having the highest genetic diversity among all primates. Our observations imply that many endangered lemur populations still harbor considerable genetic variation. Timely efforts to conserve these species alongside their habitats have, therefore, strong potential to achieve long-term success.

 

Calling SNPs without a reference sequence

A. Ratan, Y. Zhang, V.M. Hayes, S.C. Schuster, W. Miller

10.1186/1471-2105-11-130

 

Background

The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies.

Results

We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences.

Conclusions

DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available athttp://www.bx.psu.edu/miller_lab/ webcite.

 

Optimization of de novo transcriptome assembly from next-generation sequencing data

Y.S. Groba, J.I. Montoya-Burgos

10.1101/gr.103846.109

 

Transcriptome analysis has important applications in many biological fields. However, assembling a transcriptome without a known reference remains a challenging task requiring algorithmic improvements. We present two methods for substantially improving transcriptome de novo assembly. The first method relies on the observation that the use of a single k-mer length by current de novo assemblers is suboptimal to assemble transcriptomes where the sequence coverage of transcripts is highly heterogeneous. We present the Multiple-k method in which various k-mer lengths are used for de novo transcriptome assembly. We demonstrate its good performance by assembling de novo a published next-generation transcriptome sequence data set of Aedes aegypti, using the existing genome to check the accuracy of our method. The second method relies on the use of a reference proteome to improve the de novo assembly. We developed the Scaffolding using Translation Mapping (STM) method that uses mapping against the closest available reference proteome for scaffolding contigs that map onto the same protein. In a controlled experiment using simulated data, we show that the STM method considerably improves the assembly, with few errors. We applied these two methods to assemble the transcriptome of the non-model catfish Loricaria gr. cataphracta. Using the Multiple-k and STM methods, the assembly increases in contiguity and in gene identification, showing that our methods clearly improve quality and can be widely used. The new methods were used to assemble successfully the transcripts of the core set of genes regulating tooth development in vertebrates, while classic de novo assembly failed.

 

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

C.E. Ellison, C. Hall, D. Kowbel, J. Welch, R.B. Brem, N.L. Glass, J.W. Taylor

10.1073/pnas.1014971108

 

Elucidating the connection between genotype, phenotype, and adaptation in wild populations is fundamental to the study of evolutionary biology, yet it remains an elusive goal, particularly for microscopic taxa, which comprise the majority of life. Even for microbes that can be reliably found in the wild, defining the boundaries of their populations and discovering ecologically relevant phenotypes has proved extremely difficult. Here, we have circumvented these issues in the microbial eukaryote Neurospora crassa by using a "reverse-ecology" population genomic approach that is free of a priori assumptions about candidate adaptive alleles. We performed Illumina whole-transcriptome sequencing of 48 individuals to identify single nucleotide polymorphisms. From these data, we discovered two cryptic and recently diverged populations, one in the tropical Caribbean basin and the other endemic to subtropical Louisiana. We conducted high-resolution scans for chromosomal regions of extreme divergence between these populations and found two such genomic "islands." Through growth-rate assays, we found that the subtropical Louisiana population has a higher fitness at low temperature (10 °C) and that several of the genes within these distinct regions have functions related to the response to cold temperature. These results suggest the divergence islands may be the result of local adaptation to the 9 °C difference in average yearly minimum temperature between these two populations. Remarkably, another of the genes identified using this unbiased, whole-genome approach is the well-known circadian oscillator frequency, suggesting that the 2.4°-10.6° difference in latitude between the populations may be another important environmental parameter.

 

Next-generation transcriptome assembly

M. Jeffrey, W. Zhong

10.1038/nrg3068

 

Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalogue of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches — reference-based, de novo and combined strategies — along with some perspectives on transcriptome assembly in the near future.