Independent Origins of New Sex-Linked Chromosomes in the <Emphasis Type="Italic">melanica</Emphasis> and <Emphasis Type="Italic">robusta</Emphasis> Species Groups of <Emphasis Type="Italic">Drosophila</Emphasis>

Background  

Recent translocations of autosomal regions to the sex chromosomes represent important systems for identifying the evolutionary forces affecting convergent patterns of sex-chromosome heteromorphism. Additions to the sex chromosomes have been reported in the melanica and robusta species groups, two sister clades of Drosophila. The close relationship between these two species groups and the similarity of their rearranged karyotypes motivates this test of alternative hypotheses; the rearranged sex chromosomes in both groups are derived through a common origin, or the rearrangements are derived through at least two independent origins. Here we examine chromosomal arrangement in representatives of the melanica and the robusta species groups and test these alternative hypotheses using a phylogenetic approach.     

Viable nonsense mutants for the essential gene <Emphasis Type="Italic">SUP45</Emphasis> of <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Background  

Termination of protein synthesis in eukaryotes involves at least two polypeptide release factors (eRFs) – eRF1 and eRF3. The highly conserved translation termination factor eRF1 in Saccharomyces cerevisiae is encoded by the essential gene SUP45.     

Phylogenetic assessment and biogeographic analyses of tribe <Emphasis Type="Italic">Peracarpeae</Emphasis> (Campanulaceae)

Peracarpeae is a small tribe consisting of three genera: Homocodon, Heterocodon and Peracarpa, with a disjunct distribution between eastern Asia and western North America. Homocodon is endemic to southwestern China and was previously placed in the western North American genus Heterocodon. Our phylogenetic analysis using four plastid markers (matK, atpB, rbcL and trnL-F) suggests the polyphyly of Peracarpeae. Homocodon is sister to a clade consisting of the eastern Asian Adenophora, Hanabusaya and species of Campanula from the Mediterranean region and North America, rather than forming a clade with Heterocodon. Homocodon and its Eurasia relatives are estimated to have diverged in the early Miocene (16.84 mya, 95% HPD 13.35–21.45 mya). The eastern Asian Peracarpa constitutes a clade with the North American Heterocodon, Githopsis and three species of Campanula, supporting a disjunction between eastern Asia and North America in Campanulaceae. The Asian-North American disjunct lineages diverged in the early Miocene (16.17 mya, 95% HPD 13.12–20.9 mya). The biogeographic analyses suggest that Homocodon may be a relict of an early radiation in eastern Asia, and that Peracarpa and its closest North American relatives most likely originated from a Eurasian ancestor.     

Analysis of the human <Emphasis Type="Italic">Alu</Emphasis> Ye lineage

Background  

Alu elements are short (~300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30–50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation.     

Specific and sensitive detection of the conifer pathogen <Emphasis Type="Italic">Gremmeniella abietina</Emphasis> by nested PCR

Background  

Gremmeniella abietina (Lagerb.) Morelet is an ascomycete fungus that causes stem canker and shoot dieback in many conifer species. The fungus is widespread and causes severe damage to forest plantations in Europe, North America and Asia. To facilitate early diagnosis and improve measures to control the spread of the disease, rapid, specific and sensitive detection methods for G. abietina in conifer hosts are needed.     

<Emphasis Type="Italic">Gdt</Emphasis>2 regulates the transition of <Emphasis Type="Italic">Dictyostelium</Emphasis>cells from growth to differentiation

Background  

Dictyostelium life cycle consists of two distinct phases – growth and development. The control of growth-differentiation transition in Dictyostelium is not completely understood, and only few genes involved in this process are known.     

Late Quaternary loss of genetic diversity in muskox (<Emphasis Type="Italic">Ovibos</Emphasis>)

Background  

The modern wildherd of the tundra muskox (Ovibos moschatus) is native only to the New World (northern North America and Greenland), and its genetic diversity is notably low. However, like several other megafaunal mammals, muskoxen enjoyed a holarctic distribution during the late Pleistocene. To investigate whether collapse in range and loss of diversity might be correlated, we collected mitochondrial sequence data (hypervariable region and cytochrome b) from muskox fossil material recovered from localities in northeastern Asia and the Arctic Archipelago of northern North America, dating from late Pleistocene to late Holocene, and compared our results to existing databases for modern muskoxen.     

A polymorphism in <Emphasis Type="Italic">PTPN2</Emphasis> gene is associated with an earlier onset of type 1 diabetes

The Wellcome Trust Case Control Consortium (WTCCC) genome-wide study found association of PTPN2 with three autoimmune diseases, among them is type 1 diabetes (T1D). This result was confirmed by a follow-up study that pointed to new independent signals within the region. However, both studies were performed in patients with an early-onset T1D. We aimed at replicating the previous results and studying the influence of these polymorphisms in the age at T1D debut. We genotyped 439 T1D Spanish subjects (age at onset, 1 to 65 years) and 861 controls for two PTPN2 single nucleotide polymorphisms (SNPs), rs2542151 and rs478582, and studied the effect of both polymorphisms in age at onset through stratified and continuous analyses. The frequency of rs2542151*G carriers was significantly higher in the early-onset group compared with late-onset patients (p = 0.023) and with controls (OR = 1.61 [1.14–2.26]; p = 0.005). No significant differences were found between controls and late-onset patients. The log-rank chi-square test for the Kaplan–Meier plots (carriers of susceptibility allele vs non carriers) was statistically significant (χ _1df² = 4.485; p = 0.034), yielding an earlier disease debut for G carriers. The analysis of the SNP rs478582 did not reach statistical significance. In summary, we replicate the association detected by the WTCCC and propose that the rs2542151*G allele confers risk to an earlier onset of T1D.     

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

Background  

Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to contextualize within broader Pleistocene paleoecology and biogeography. Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing.     

Recovery of a <Emphasis Type="Italic">Burkholderia thailandensis</Emphasis>-like isolate from an Australian water source

Background  

Burkholderia thailandensis, a close relative of Burkholderia pseudomallei, has previously been reported only from Southeast Asia and North America. It is biochemically differentiated from B. pseudomallei by the ability to utilize arabinose. During the course of environmental sampling for B. pseudomallei in the Northern Territory of Australia, an isolate, MSMB 43, was recovered that is arabinose positive.     

Sibship reconstruction for inferring mating systems,dispersal and effective population size in headwater brook trout (<Emphasis Type="Italic">Salvelinus fontinalis</Emphasis>) populations

Brook trout Salvelinus fontinalis populations have declined in much of the native range in eastern North America and populations are typically relegated to small headwater streams in Connecticut, USA. We used sibship reconstruction to infer mating systems, dispersal and effective population size of resident (non-anadromous) brook trout in two headwater stream channel networks in Connecticut. Brook trout were captured via backpack electrofishing using spatially continuous sampling in the two headwaters (channel network lengths of 4.4 and 7.7 km). Eight microsatellite loci were genotyped in a total of 740 individuals (80–140 mm) subsampled in a stratified random design from all 50 m-reaches in which trout were captured. Sibship reconstruction indicated that males and females were both mostly polygamous although single pair matings were also inferred. Breeder sex ratio was inferred to be nearly 1:1. Few large-sized fullsib families (>3 individuals) were inferred and the majority of individuals were inferred to have no fullsibs among those fish genotyped (family size = 1). The median stream channel distance between pairs of individuals belonging to the same large-sized fullsib families (>3 individuals) was 100 m (range: 0–1,850 m) and 250 m (range: 0–2,350 m) in the two study sites, indicating limited dispersal at least for the size class of individuals analyzed. Using a sibship assignment method, the effective population size for the two streams was estimated at 91 (95%CI: 67–123) and 210 (95%CI: 172–259), corresponding to the ratio of effective-to-census population size of 0.06 and 0.12, respectively. Both-sex polygamy, low variation in reproductive success, and a balanced sex ratio may help maintain genetic diversity of brook trout populations with small breeder sizes persisting in headwater channel networks.     

Old divergences in a boreal bird supports long-term survival through the Ice Ages

Background  

Unlike northern Europe and most of northern North America, the Eastern Palearctic and the northwesternmost tip of North America are believed to have been almost unglaciated during the Quarternary glacial periods. This could have facilitated long-term survival of many organisms in that area. To evaluate this, we studied the phylogeography in east Asia and Alaska of a boreal migratory passerine bird, the Arctic Warbler Phylloscopus borealis, and compared our results with published data on especially North American species.     

Frequency distribution of XbaIG > T and HaeIIIT > C <Emphasis Type="Italic">GLUT1</Emphasis> polymorphisms among different Brazilian ethnic groups

GLUT is the major glucose transporter in mammalian cells. Single nucleotide polymorphisms (SNP) at GLUT1 promoter and regulatory regions have been associated to the risk of developing nephropathy in different type 1 and type 2 diabetic populations. It has been demonstrated that differences in allelic and genotypic frequencies of GLUT1 gene (SLC2A1) polymorphisms occur among different populations. Therefore, ethnic differences in distribution of GLUT1 gene polymorphisms may be an important factor in determining gene-disease association. In this study, we investigated the XbaIG > T and HaeIIIT > C polymorphisms in six different Brazilian populations: 102 individuals from Salvador population (Northern Brazil), 56 European descendants from Joinville (South Brazil), 85 Indians from Tiryió tribe (North Brazil) and 127 samples from Southern Brazil: 44 from European descendants, 42 from African descendants and 41 from Japanese descendants. Genotype frequencies from both sites did not differ significantly from those expected under the Hardy–Weinberg equilibrium. We verified that the allele frequencies of both polymorphisms were heterogeneous in these six Brazilian ethnic groups.     

A high-throughput <Emphasis Type="Italic">de novo</Emphasis> sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry

Background  

High-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as LTQ-Orbitrap and LTQ-FT, in high-throughput shotgun proteomics workflows. The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms.     

A proteomic approach analysing the <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis> response to virulent and avirulent <Emphasis Type="Italic">Pseudomonas syringae</Emphasis> strains

The present work is directed at studying changes at the proteome level in Arabidopsis thaliana leaves in response to Pseudomonas syringae virulent (Pst) and avirulent (Pst avrRpt2) strains. Arabidopsis leaves were sampled from challenged plants at 4, 8 and 24 h post inoculation. Proteins were TCA–acetone–phenol extracted and subjected to 2-DE (5–8 pH range) and MS/MS (MALDI–TOF–TOF) analysis. Out of 800 matched spots on each of the 36 gels analysed, 147 spots were either absent in at least one of the conditions studied (time or treatments; qualitative variable spots) or differentially accumulated between time and treatments (quantitative variable spots). Out of the 24 proteins successfully identified over TAIR10 database, 23 have not been reported previously in similar proteomics studies of the Arabidopsis thaliana–Pseudomonas syringae interaction. The exhaustive statistical analysis performed, including principal component and heat map, showed that 24 h post inoculation can clearly discriminate the challenged plants from the control. The protein change occurred early (4 h post inoculation) following the virulent pathogen infection, whereas the change occurred later (24 h post inoculation) following the avirulent pathogen inoculation. Concerning the variable proteins, three behavioural groups can be observed: group 1 (common protein changes in response to virulent and avirulent pathogen infection), group 2 (protein changes in response to virulent pathogen infection) and group 3 (protein changes in response to avirulent pathogen infection). Differential identified proteins following the pathogen infection belonged to different groups including those of oxidative stress defence, enzymes of metabolic pathways and molecular chaperones.     

The functional <Emphasis Type="Italic">SLC11A1</Emphasis> gene polymorphisms are associated with sarcoidosis in Turkish population

Sarcoidosis (SA) is an immune-mediated multisystemic disorder of unknown etiology characterized by the accumulation of lymphocytes, mononuclear phagocytes and epithelioid cell granulomas involved in different organs and tissues. The belief that genetics contribute to SA etiology is supported by twin studies, disease clustering in families and racial differences in incidence rates. Involvements of SLC11A1 in macrophage function and activation, makes it an attractive candidate gene for immune-mediated and infectious diseases. We investigated the association between SA and four polymorphisms of the SLC11A1 gene, including a single nucleotide change in intron 4 (INT4); a nonconservative single-base substitution at codon 543 (D543N); a TGTG deletion in the 3′ untranslated region; and the functional (GT)_n repeat polymorphism in the 5′ region, in 95 Turkish SA patients and 150 healthy controls, by using amplification refractory mutation system–polymerase chain reaction and sequencing. We found significant association between SA and INT4 G/C allele frequency (P = 0.0000; odds ratio 2.75; 95% confidence interval 1.68–4.52) and 5′(GT)_n allele 2/3 frequency (P = 0.0000; odds ratio 2.69; 95% confidence interval 1.61–4.47) suggesting that SLC11A1 might be a plausible candidate gene for SA.     

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

Background  

Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeographic relationships within this lineage at a global scale have been largely unknown. In this study, we obtained DNA sequences from a nearly complete taxon sampling of known species from Europe, Central America and North America. We inferred intra- and interspecific phylogenetic relationships as well as major morphological evolutionary trends within section Calochroi based on 576 ITS sequences, 230 ITS + 5.8S + D1/D2 sequences, and a combined dataset of ITS + 5.8S + D1/D2 and RPB1 sequences of a representative subsampling of 58 species.     

Filamin repeat segments required for photosensory signalling in <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>

Background  

Filamin is an actin binding protein which is ubiquitous in eukaryotes and its basic structure is well conserved – an N-terminal actin binding domain followed by a series of repeated segments which vary in number in different organisms. D. discoideum is a well established model organism for the study of signalling pathways and the actin cytoskeleton and as such makes an excellent organism in which to study filamin. Ddfilamin plays a putative role as a scaffolding protein in a photosensory signalling pathway and this role is thought to be mediated by the unusual repeat segments in the rod domain.     

A new anchovy, <Emphasis Type="Italic">Stolephorus teguhi</Emphasis> (Clupeiformes: Engraulidae), from North Sulawesi,Indonesia

Stolephorus teguhi sp. nov. is described from the holotype and 14 paratypes, 49–77 mm in standard length, collected from North Sulawesi, Indonesia. The species is characterized by having numerous gill rakers (31–35 + 41–46 = 72–82) and a short upper jaw, its posterior tip reaching to or extending slightly beyond the anterior margin of the preopercle. Stolephorus pacificus and S. multibranchus also have relatively numerous gill rakers for species of this genus (21–27 + 29–36 = 53–61 and 21–28 + 30–35 = 54–60, respectively), but counts for S. teguhi exceed those for the two species. Although S. advenus also has a short upper jaw similar to that of S. teguhi, the former has far fewer gill rakers (19 + 24 = 43) than the latter.     

Population genetics and symbiont assemblages support opposing invasion scenarios for the red turpentine beetle (Dendroctonus valens)

Exotic forest insects and their symbionts pose an increasing threat to forest health. This is apparently true for the red turpentine beetle (Dendroctonus valens), which was unintentionally introduced to China, where the beetle has killed millions of healthy native pine trees. Previous population genetics studies that used cytochrome oxidase I as a marker concluded that the source of D. valens in China was western North America. In contrast, surveys of fungi associated with D. valens demonstrated that more fungal species are shared between China and eastern North America than between China and western North America, suggesting that the source population of D. valens could be eastern North America. In this study, we used microsatellite markers to determine population structure of D. valens in North America as well as the source population of the beetle in China. The analyses revealed that four genetically distinct populations (herein named the West, Central, Northeast and Mexico) represent the native range of D. valens. Clustering analyses and a simulation‐based approximate Bayesian computation (ABC) approach supported the hypothesis that western North America is the source of the invasive D. valens population. This study provides a demonstration of non‐congruence between patterns inferred by studies on population genetics and symbiont assemblages in an invasive bark beetle.