Complete genome sequence of Meiothermus ruber type strain (21)

Meiothermus ruber (Loginova et al. 1984) Nobre et al. 1996 is the type species of the genus Meiothermus. This thermophilic genus is of special interest, as its members share relatively low degrees of 16S rRNA gene sequence similarity and constitute a separate evolutionary lineage from members of the genus Thermus, from which they can generally be distinguished by their slightly lower temperature optima. The temperature related split is in accordance with the chemotaxonomic feature of the polar lipids. M. ruber is a representative of the low-temperature group. This is the first completed genome sequence of the genus Meiothermus and only the third genome sequence to be published from a member of the family Thermaceae. The 3,097,457 bp long genome with its 3,052 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Haloterrigena turkmenica type strain (4k)

Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847)

Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is currently the only genus in the corynebacterial family Segniliparaceae. This family is of large interest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300)

Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

The aftermath of an invasion: Structure and composition of Central Appalachian hemlock forests following establishment of the hemlock woolly adelgid, <Emphasis Type="Italic">Adelges tsugae</Emphasis>

As the highly invasive hemlock woolly adelgid, Adelges tsugae, continues to expand its distribution in eastern North America, affected forests will incur drastic changes in composition and structure. While these changes have been well-studied in dense hemlock forests in the Northeast, relatively little work is known about the effects of the adelgid at the western edge of the range of eastern hemlock, Tsuga canadensis. We evaluated the nature and extent of these changes using vegetation assessments coupled with growth simulations. The woody plant community was assessed in three strata (upper, mid- and lower) and was used to predict forest succession. Using the Forest Vegetation Simulator (FVS), we then projected the growth of hemlock forests 20 years into the future with and without the effects of the adelgid. In forest simulations lacking adelgid invasion, little change in composition or structure is forecast. In contrast, our projections predict a near complete loss of the hemlock forest type within 20 years of adelgid establishment, with widespread conversion to hardwood forest types, most notably white oak-red oak-hickory, chestnut oak-black oak-scarlet oak, and yellow poplar-white oak-red oak. Hemlock loss will result in denser deciduous forests with thinner canopies and multiple gaps, and significant alterations to terrestrial and aquatic wildlife habitat.     

Cardiac function adaptations in hibernating grizzly bears (Ursus arctos horribilis)

Research on the cardiovascular physiology of hibernating mammals may provide insight into evolutionary adaptations; however, anesthesia used to handle wild animals may affect the cardiovascular parameters of interest. To overcome these potential biases, we investigated the functional cardiac phenotype of the hibernating grizzly bear (Ursus arctos horribilis) during the active, transitional and hibernating phases over a 4 year period in conscious rather than anesthetized bears. The bears were captive born and serially studied from the age of 5 months to 4 years. Heart rate was significantly different from active (82.6 ± 7.7 beats/min) to hibernating states (17.8 ± 2.8 beats/min). There was no difference from the active to the hibernating state in diastolic and stroke volume parameters or in left atrial area. Left ventricular volume:mass was significantly increased during hibernation indicating decreased ventricular mass. Ejection fraction of the left ventricle was not different between active and hibernating states. In contrast, total left atrial emptying fraction was significantly reduced during hibernation (17.8 ± 2.8%) as compared to the active state (40.8 ± 1.9%). Reduced atrial chamber function was also supported by reduced atrial contraction blood flow velocities and atrial contraction ejection fraction during hibernation; 7.1 ± 2.8% as compared to 20.7 ± 3% during the active state. Changes in the diastolic cardiac filling cycle, especially atrial chamber contribution to ventricular filling, appear to be the most prominent macroscopic functional change during hibernation. Thus, we propose that these changes in atrial chamber function constitute a major adaptation during hibernation which allows the myocardium to conserve energy, avoid chamber dilation and remain healthy during a period of extremely low heart rates. These findings will aid in rational approaches to identifying underlying molecular mechanisms.     

Web orientation and prey resources for web-building spiders in eastern hemlock

We examined the arthropod community on eastern hemlock, Tsuga canadensis (L.) Carr, in the context of its role in providing potential prey items for hemlock-associated web-weaving spiders. Using sticky traps simulating spider webs, we evaluated what prey items are available to web-weaving spiders in eastern hemlock based on web orientation (horizontal versus vertical) and cardinal direction. We found that the overwhelming majority (>70%) of prey items available to spiders in hemlock canopies were Diptera. Psocoptera, Hymenoptera, and Hemiptera comprised most of the remaining potential prey. A significant direction × orientation interaction, and greater trap capture in some direction-orientation combinations, suggests that spiders might locate their webs in eastern hemlock canopies for thermoregulatory purposes, ultimately optimizing prey capture. We also evaluated these findings in the context of hemlock infestation by the invasive hemlock woolly adelgid, Adelges tsugae Annand. The adelgid is a sedentary insect with a mobile crawler stage that provides a readily available, easily obtained food source for predators in hemlock canopies. However, an abundance of alternative prey will affect within canopy spider distribution and the potential intensity with which spiders consume these prey. Understanding the response of spiders to potential prey availability is essential to understanding the trophic interactions involving these predators and their potential for influencing herbivore populations.     

Evaluation of virulence factor profiling in the characterization of veterinary Escherichia coli isolates

Escherichia coli has been used as an indicator organism for fecal contamination of water and other environments and is often a commensal organism in healthy animals, yet a number of strains can cause disease in young or immunocompromised animals. In this study, 281 E. coli isolates from bovine, porcine, chicken, canine, equine, feline, and other veterinary sources were analyzed by BOXA1R PCR and by virulence factor profiling of 35 factors to determine whether they had utility in identifying the animal source of the isolates. The results of BOXA1R PCR analysis demonstrated a high degree of diversity; less than half of the isolates fell into one of 27 clusters with at least three isolates (based on 90% similarity). Nearly 60% of these clusters contained isolates from more than one animal source. Conversely, the results of virulence factor profiling demonstrated clustering by animal source. Three clusters, named Bovine, Chicken, and Porcine, based on discriminant components analysis, were represented by 90% or more of the respective isolates. A fourth group, termed Companion, was the most diverse, containing at least 84% of isolates from canine, feline, equine, and other animal sources. Based on these results, it appears that virulence factor profiling may have utility, helping identify the likely animal host species sources of certain E. coli isolates.     

Overlapping genetic susceptibility variants between three autoimmune disorders: rheumatoid arthritis, type 1 diabetes and coeliac disease

Introduction

Genome wide association studies, replicated by numerous well powered validation studies, have revealed a large number of loci likely to play a role in susceptibility to many multifactorial diseases. It is now well established that some of these loci are shared between diseases with similar aetiology. For example, a number of autoimmune diseases have been associated with variants in the PTPN22, TNFAIP3 and CTLA4 genes. Here we have attempted to define overlapping genetic variants between rheumatoid arthritis (RA), type 1 diabetes (T1D) and coeliac disease (CeD).

Methods

We selected eight SNPs previously identified as being associated with CeD and six T1D-associated SNPs for validation in a sample of 3,962 RA patients and 3,531 controls. Genotyping was performed using the Sequenom MassArray platform and comparison of genotype and allele frequencies between cases and controls was undertaken. A trend test P-value < 0.004 was regarded as significant.

Results

We found statistically significant evidence for association of the TAGAP locus with RA (P = 5.0 × 10^-4). A marker at one other locus, C1QTNF6, previously associated with T1D, showed nominal association with RA in the current study but did not remain statistically significant at the corrected threshold.

Conclusions

In exploring the overlap between T1D, CeD and RA, there is strong evidence that variation within the TAGAP gene is associated with all three autoimmune diseases. Interestingly a number of loci appear to be specific to one of the three diseases currently studied suggesting that they may play a role in determining the particular autoimmune phenotype at presentation.     

Regulation of Microtubule Dynamics by Bim1 and Bik1, the Budding Yeast Members of the EB1 and CLIP-170 Families of Plus-End Tracking Proteins

Microtubule dynamics are regulated by plus-end tracking proteins (+TIPs), which bind microtubule ends and influence their polymerization properties. In addition to binding microtubules, most +TIPs physically associate with other +TIPs, creating a complex web of interactions. To fully understand how +TIPs regulate microtubule dynamics, it is essential to know the intrinsic biochemical activities of each +TIP and how +TIP interactions affect these activities. Here, we describe the activities of Bim1 and Bik1, two +TIP proteins from budding yeast and members of the EB1 and CLIP-170 families, respectively. We find that purified Bim1 and Bik1 form homodimers that interact with each other to form a tetramer. Bim1 binds along the microtubule lattice but with highest affinity for the microtubule end; however, Bik1 requires Bim1 for localization to the microtubule lattice and end. In vitro microtubule polymerization assays show that Bim1 promotes microtubule assembly, primarily by decreasing the frequency of catastrophes. In contrast, Bik1 inhibits microtubule assembly by slowing growth and, consequently, promoting catastrophes. Interestingly, the Bim1-Bik1 complex affects microtubule dynamics in much the same way as Bim1 alone. These studies reveal new activities for EB1 and CLIP-170 family members and demonstrate how interactions between two +TIP proteins influence their activities.