Complete genome sequence of Ferroglobus placidus AEDII12DO

Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.     

No association between Angiotensin Converting Enzyme (ACE) gene variation and endurance athlete status in Kenyans

East African runners are continually successful in international distance running. The extent to which genetic factors influence this phenomenon is unknown. The insertion (I) rather than deletion (D) of a 287 bp fragment in the human angiotensin converting enzyme (ACE) gene is associated with lower circulating and tissue ACE activity and with endurance performance amongst Caucasians. To assess the association between ACE gene variation and elite endurance athlete status in an African population successful in distance running, DNA samples were obtained from 221 national Kenyan athletes (N), 70 international Kenyan athletes (I), and 85 members of the general Kenyan population (C). Blood samples were obtained from C and assayed for circulating ACE activity. ACE I/D (rs????--from NCBI SNPdb first time poly mentioned) genotype was determined, as was genotype at A22982GD (rs????--from NCBI SNPdb first time poly mentioned) which has been shown to associate more closely with ACE levels in African subjects than the I/D polymorphism. ACE I/D and A22982G genotypes explained 13 and 24% of variation in circulating ACE activity levels (P = 0.034 and <0.001 respectively). I/D genotype was not associated with elite endurance athlete status (df = 4, chi(2) = 4.1, P=0.39). In addition, genotype at 22982 was not associated with elite endurance athlete status (df = 4, chi(2) = 5.7, P = 0.23). Nor was the A allele at 22982, which is associated with lower ACE activity, more prevalent in N (0.52) or I (0.41) relative to C (0.53). We conclude that ACE I/D and A22982G polymorphisms are not strongly associated with elite endurance athlete status amongst Kenyans.     

Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20

Desulfovibrio alaskensis G20 (formerly Desulfovibrio desulfuricans G20) is a Gram-negative mesophilic sulfate-reducing bacterium (SRB), known to corrode ferrous metals and to reduce toxic radionuclides and metals such as uranium and chromium to sparingly soluble and less toxic forms. We present the 3.7-Mb genome sequence to provide insights into its physiology.     

Recognition of the neural chemoattractant Netrin-1 by integrins alpha6beta4 and alpha3beta1 regulates epithelial cell adhesion and migration

Netrins, axon guidance cues in the CNS, have also been detected in epithelial tissues. In this study, using the embryonic pancreas as a model system, we show that Netrin-1 is expressed in a discrete population of epithelial cells, localizes to basal membranes, and specifically associates with elements of the extracellular matrix. We demonstrate that alpha6beta4 integrin mediates pancreatic epithelial cell adhesion to Netrin-1, whereas recruitment of alpha6beta4 and alpha3beta1 regulate the migration of CK19+/PDX1+ putative pancreatic progenitors on Netrin-1. These results provide evidence for the activation of epithelial cell adhesion and migration by a neural chemoattractant, and identify Netrin-1/integrin interactions as adhesive/guidance cues for epithelial cells.     

Reef reconstruction after extinction events of the latest ordovician in the Yangtze platform,South China

Summary Early Silurian reef reconstruction on the Yangtze Platform, in the northern part of the South China Block, is preceded by a combination of regional and global processes. During most of Ashgill time (Late Ordovician), the area was dominated by Wufeng Formation deep water graptolitic black shales. Reefs largely disappeard in the middle of the Ashgill Stage, from the northwestern margin of Cathaysian Land (southeastern South China Block), in advance of the Late Ordovician glaciation and mass extinction, due to regional sea-level changes and regional uplift, unrelated to the mass extinction itselt. Late Ordovician microbial mudmound occurrence is also found in the western margin of the Yangtze Platform, its age corresponding to theDicellograptus complexus graptolite biozone of pre-extinction time. On the Yangtze Platform, a thin, non-reef-bearing carbonate, the Kuanyinchiao Formation (=Nancheng Formation in some sites), thickness generally no more than 1m, occurs near several landmasses as a result of Hirnantian regression. Reappearance of the earliest Silurian carbonates consisting of rare skeletal lenses in the upper part of Lungmachi Formation, are correlated to theacensus graptolite biozone, early Rhuddanian of Shiqian, northeastern Guizhou, near Qianzhong Land. Carbonate sediments gradually developed into beds rich in brachiopods and crinoids in the lower part of Xiangshuyuan Formation, middle Rhuddanian. In the middle part of Xiangshuyan Formation, biostromes, containing abundant and high diversity benthic faunas such as corals, crinoids and brachiopods, show beginnings of reconstruction of reef facies. Substantial reef recovery occurred in the upper part of Xiangshuyuan Formation, lower Aeronian, as small patch reefs and biostromes. During the late Aeronian, carbonate sediments, especially reefs and reef-related facies, expanded on the upper Yangtze Platform, and radiation of reefs occurred in Ningqiang Formation, upper Telychian. The long period of reef recovery, taking several million years, remains difficult to explain, because redistribution of any refugia faunas would be expected to take place soon after the extinction. Reefs and reef-related facies subsequently declined after Telychian time due to regional uplift of the major portion of the Yangtze Platform. Carbonate facies are therefore uncommon in South China during the rest of Silurian time.     

Systems analysis of primary Sjögren's syndrome pathogenesis in salivary glands identifies shared pathways in human and a mouse model

Bone tissue has an exceptional quality to regenerate to native tissue in response to injury. However, the fracture repair process requires mechanical stability or a viable biological microenvironment or both to ensure successful healing to native tissue. An improved understanding of the molecular and cellular events that occur during bone repair and remodeling has led to the development of biologic agents that can augment the biological microenvironment and enhance bone repair. Orthobiologics, including stem cells, osteoinductive growth factors, osteoconductive matrices, and anabolic agents, are available clinically for accelerating fracture repair and treatment of compromised bone repair situations like delayed unions and nonunions. Preclinical and clinical studies using biologic agents like recombinant bone morphogenetic proteins have demonstrated an efficacy similar or better than that of autologous bone graft in acute fracture healing. A lack of standardized outcome measures for comparison of biologic agents in clinical fracture repair trials, frequent off-label use, and a limited understanding of the biological activity of these agents at the bone repair site have limited their efficacy in clinical applications.     

Effects of thermal history on the responses to thermal stress of a large benthic foraminifera,Calcarina gaudichaudii

Marine ecosystems, particularly coastal environments, are rapidly changing due to anthropogenic impacts resulting in increased global climate change (ocean warming), ocean acidification, hypoxia, and eutrophication. On coral reefs, symbiont-bearing large benthic foraminifera (LBFs) can play a key role as reef constituents and carbonate producers, contributing up to 5% of reef-scale carbonate budgets. However, projected climate change, particularly ocean warming, has the potential to significantly alter the conditions in which marine organisms persist. While the response of LBFs to elevated thermal stress is well documented in laboratory studies, the potential influence of adaptation or acclimatization through prior environmental thermal history on this response remains largely unknown. In this study, specimens of Calcarina gaudichaudii, an LBF from the Penghu Islands, Taiwan, were collected from thermally variable intertidal and thermally stable subtidal (~ 6 m depth) environments representing thermal history. LBFs were then acclimated to laboratory conditions at ambient (25 °C) and elevated (28 °C) temperatures for three weeks, and subsequently exposed to control and heat stress treatments (25 °C, 28 °C, 30 °C, 33 °C) for an additional one week. Photosynthetic rates (determined through oxygen flux measurements) of C. gaudichaudii significantly decreased in specimens collected at subtidal depths acclimated at 25 °C when compared to those acclimated at 28 °C, whereas there was no effect of thermal history on respiration, indicating that symbiont and holobiont responses may differ in LBFs. Additionally, maximum photochemical efficiency (Fv/Fm) significantly decreased as a result of heat stress, although bleaching was not visually observed after one week. These results highlight the plastic responses of the algal microbiome and indicate that thermal history, acclimatization temperature, and heat stress interact to affect the physiological status of C. gaudichaudii. This study adds to the growing literature which highlights the larger implications of understanding thermal history as an important factor to consider to better understand how ecosystem processes (e.g., carbonate production) are altered on modern coral reefs.

     

Congruent responses to weather variability in high arctic herbivores

Assessing the role of weather in the dynamics of wildlife populations is a pressing task in the face of rapid environmental change. Rodents and ruminants are abundant herbivore species in most Arctic ecosystems, many of which are experiencing particularly rapid climate change. Their different life-history characteristics, with the exception of their trophic position, suggest that they should show different responses to environmental variation. Here we show that the only mammalian herbivores on the Arctic islands of Svalbard, reindeer (Rangifer tarandus) and sibling voles (Microtus levis), exhibit strong synchrony in population parameters. This synchrony is due to rain-on-snow events that cause ground ice and demonstrates that climate impacts can be similarly integrated and expressed in species with highly contrasting life histories. The finding suggests that responses of wildlife populations to climate variability and change might be more consistent in Polar regions than elsewhere owing to the strength of the climate impact and the simplicity of the ecosystem.     

Analysis of gene expression in a human cell line stably transduced with herpesvirus saimiri

Herpesvirus saimiri (HVS) is the prototype gamma-2 herpesvirus; it has significant homology to the human gammaherpesviruses Kaposi's sarcoma-associated virus and Epstein-Barr virus and the murine gammaherpesvirus murine herpesvirus 68. HVS causes a persistent asymptomatic infection in its natural host, the squirrel monkey. Both subgroups A and C possess the ability to immortalize common marmoset T lymphocytes to interleukin-2-independent proliferation. However, only subgroup C is capable of transforming human, rabbit, and rhesus monkey lymphocytes in vitro. In addition, HVS can stably transduce a variety of human cell lines where the virus persists as a nonintegrating circular episome. In this study, we have developed a system in which the HVS DNA is stably maintained as a nonintegrated circular episome in the human lung carcinoma cell line A549. Virus production can be reactivated using chemical inducing agents, including tetradecanoyl phorbol acetate and n-butyrate, suggesting that the infection in human A549 cells is latent. To analyze virus gene expression in these stably transduced cells, Northern blot analysis was performed using a series of probes produced from restriction fragments spanning the entire coding region of the HVS genome. This demonstrated that an adjacent set of genes containing open reading frames (ORFs) 71 to 73 are expressed in this stably transduced cell line. Moreover, these genes are transcribed as a polycistronic mRNA species produced from a common promoter upstream of ORF 73. This model may serve as a useful tool in the further analysis of the role of ORFs 71 to 73 in gamma-2 herpesvirus latency.     

Olfactory Bulbectomy Leads to the Development of Epilepsy in Mice

There is a clear link between epilepsy and depression. Clinical data demonstrate a 30–35% lifetime prevalence of depression in patients with epilepsy, and patients diagnosed with depression have a three to sevenfold higher risk of developing epilepsy. Traditional epilepsy models partially replicate the clinical observations, with the demonstration of depressive traits in epileptic animals. Studies assessing pro-epileptogenic changes in models of depression, however, are more limited. Here, we examined whether a traditional rodent depression model—bilateral olfactory bulbectomy—predisposes the animals towards the development of epilepsy. Past studies have demonstrated increased neuronal excitability after bulbectomy, but continuous seizure monitoring had not been conducted. For the present study, we monitored control and bulbectomized animals by video-EEG 24/7 for approximately two weeks following the surgery to determine whether they develop spontaneous seizures. All seven bulbectomized mice exhibited seizures during the monitoring period. Seizures began about one week after surgery, and occurred in clusters with severity increasing over the monitoring period. These results suggest that olfactory bulbectomy could be a useful model of TBI-induced epilepsy, with advantages of relatively rapid seizure onset and a high number of individuals developing the disease. The model may also be useful for investigating the mechanisms underlying the bidirectional relationship between epilepsy and depression.