VSGdb: a database for trypanosome variant surface glycoproteins, a large and diverse family of coiled coil proteins

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Background: Trypanosomes are coated with a variant surface glycoprotein (VSG) that is so densely packed that it physically protects underlying proteins from effectors of the host immune system. Periodically cells expressing a distinct VSG arise in a population and thereby evade immunity. The main structural feature of VSGs are two long alpha-helices that form a coiled coil, and sets of relatively unstructured loops that are distal to the plasma membrane and contain most or all of the protective epitopes. The primary structure of different VSGs is highly variable, typically displaying only similar to 20% identity with each other. The genome has nearly 2000 VSG genes, which are located in subtelomeres. Only one VSG gene is expressed at a time, and switching between VSGs primarily involves gene conversion events. The archive of silent VSGs undergoes diversifying evolution rapidly, also involving gene conversion. The VSG family is a paradigm for a helical coiled coil structures, epitope variation and GPI-anchor signals. At the DNA level, the genes are a paradigm for diversifying evolutionary processes and for the role of subtelomeres and recombination mechanisms in generation of diversity in multigene families. To enable ready availability of VSG sequences for addressing these general questions, and trypanosome- specific questions, we have created VSGdb, a database of all known sequences.|Description: VSGdb contains fully annotated VSG sequences from the genome sequencing project, with which it shares all identifiers and annotation, and other available sequences. The database can be queried in various ways. Sequence retrieval, in FASTA format, can deliver protein or nucleotide sequence filtered by chromosomes or contigs, gene type ( functional, pseudogene, etc.), domain and domain sequence family. Retrieved sequences can be stored as a temporary database for BLAST querying, reports from which include hyperlinks to the genome project database ( GeneDB) CDS Info and to individual VSGdb pages for each VSG, containing annotation and sequence data. Queries (text search) with specific annotation terms yield a list of relevant VSGs, displayed as identifiers leading again to individual VSG web pages.|Conclusion: VSGdb http://www.vsgdb.org/is a freely available, web-based platform enabling easy retrieval, via various filters, of sets of VSGs that will enable detailed analysis of a number of general and trypanosome- specific questions, regarding protein structure potential, epitope variability, sequence evolution and recombination events

Glucose Dynamics of Cortical Spreading Depolarization in Acute Brain Injury: A Systematic Review.

Cortical spreading depolarization (CSD) is an emerging mode of secondary neuronal damage in acute brain injury (ABI). Subsequent repolarisation is a metabolic process requiring glucose. Instances of CSD and glucose derangement are both linked to poor neurological outcome, but their causal inter-relationship is not fully defined. This systematic review seeks to evaluate the available human evidence studying CSD and glucose to further understand their dynamic relationship. We conducted a systematic review of studies examining CSD through electrocorticography and cerebral/systemic glucose concentrations in ABI, excluding animal studies. The search yielded 478 articles, of which 13 were eligible. Across 10 manuscripts, 125 patients received simultaneous monitoring, with 1987 CSD episodes observed. Eight of 10 studies observed correlation between CSD and glucose change. Seven of eight studies observed possible cumulative effect of recurrent CSD on glucose derangement and two identified correlation between glycopenia and incidence of CSD. These findings confirm a relationship between CSD and glucose, and suggest it may be cyclical, where CSD causes local glycopenia, which may potentiate further CSD. Positive observations were not common to all studies, likely due to differing methodology or heterogeneity in CSD propensity. Further study is required to delineate the utility of the clinical modulation of serum and cerebral glucose to alter the propensity for CSD following brain injury

9-Oxo-4,5-diaza­fluoren-4-ium tetra­chloridoaurate(III)–4,5-diaza­fluoren-9-one (1/1)

The AuIII atom in the title compound, (C11H7N2O)[AuCl4]·C11H6N2O, is in a nearly square-planar environment defined by four Cl atoms. The protonated 9-oxo-4,5-diaza­fluoren-4-ium cation forms an N—H⋯N hydrogen bond with the neutral 4,5-diaza­fluoren-9-one mol­ecule

Material Versatility Using Replica Molding for Large-Scale Fabrication of High Aspect-Ratio, High Density Arrays of Nano-Pillars

Arrays of high aspect-ratio (AR) nano-pillars have attracted a lot of interest for various applications, such as for use in solar cells, surface acoustic sensors, tissue engineering, bio-inspired adhesives and anti-reflective surfaces. Each application may require a different structural material, which can vary in the required chemical composition and mechanical properties. In this paper, a low cost fabrication procedure is proposed for large scale, high AR and high density arrays of nano-pillars. The proposed method enables the replication of a master with high fidelity, using the subsequent replica molds multiple times, and preparing arrays of nano-pillars in a variety of different materials. As an example applied to bio-inspired dry adhesion, polymeric arrays of nano-pillars are prepared in this work. Thermoset and thermoplastic nano-pillar arrays are examined using an atomic force microscope to assess their adhesion strength and its uniformity. Results indicate the proposed method is robust and can be used to reliably prepare nano-structures with a high AR

Survival of lung cancer patients in a resource-limited country

Aim: Data on lung cancer survival are lacking in developing countries. Our objectives were to describe the survival of our lung cancer patients and to determine independent prognostic factors affecting survival. Method: All patients diagnosed with lung cancer from August 2007 to August 2010 were recruited from a single referral hospital of the state of Pahang, Malaysia. Detailed demographic data, ECOG (Eastern Cooperation Oncology Group) performance status, stage of disease and treatment were recorded. The date of histology or cytology confirmation was used as the date of entry. Survival time was calculated from the date of entry to the date of death. Results: One hundred forty-nine patients were included for survival analysis. The median age was 62 years and patients were predominantly males (78%) and smokers (78%). The majority had non-small cell lung cancer (NSCLC) (94%); only six patients (4%) had small cell lung cancer. All patients presented with stage 3 or stage 4 disease. Overall median survival was 18 weeks. “No definitive treatment” and “ECOG 3–4” were the significant independent predictors of death, with the hazard ratios of 2.1 (95% confidence interval [CI] 1.4, 3.0) and 1.6 (95% CI 1.1, 2.3) times, respectively. Among NSCLC patients on treatment, 1- and 2-year survival rates were 27% and 15%, respectively. Conclusion: The majority of lung cancer patients in Pahang presented with advanced disease. No definitive treatment and ECOG 3–4 were independent poor prognostic factors

Liquid-to-liquid phase transition in pancake vortex systems

We study the thermodynamics of a model of pancake vortices in layered superconductors. The model is based on the effective pair potential for the pancake vortices derived from the London approximation of a version of the Lawrence-Doniach model which is valid for extreme type-II superconductors. Using the hypernetted-chain (HNC) approximation, we find that there is a temperature below which multiple solutions to the HNC equations exist. By explicitly evaluating the free energy for each solution we find that the system undergoes a first-order transition between two vortex liquid phases. The low-temperature phase has larger correlations along the field direction than the high-temperature phase. We discuss the possible relation of this phase transition to the liquid-to-liquid phase transition recently observed in Y-Ba-Cu-O superconductors in high magnetic fields in the presence of disorder.Comment: 7 pages, 6 figure

L-theanine in the adjunctive treatment of generalized anxiety disorder: a double-blind, randomised, placebo-controlled trial

Partial or non-response to antidepressants in Generalized Anxiety Disorder (GAD) is common in clinical settings, and adjunctive biological interventions may be required. Adjunctive herbal and nutraceutical treatments are a novel and promising treatment option. L-theanine is a non-protein amino acid derived most-commonly from tea (Camellia sinensis) leaves, which may be beneficial in the treatment of anxiety and sleep disturbance as suggested by preliminary evidence. We conducted a 10-week study (consisting of an 8-week double-blind placebo-controlled period, and 1-week pre-study and 2-week post-study single-blinded observational periods) involving 46 participants with a DSM-5 diagnosis of GAD. Participants received adjunctive L-theanine (450–900 mg) or matching placebo with their current stable antidepressant treatment, and were assessed on anxiety, sleep quality, and cognition outcomes. Results revealed that adjunctive L-theanine did not outperform placebo for anxiety reduction on the HAMA (p = 0.73) nor insomnia severity on the Insomnia Severity Index (ISI; p = 0.35). However, LT treated participants reported greater self-reported sleep satisfaction than placebo (ISI item 4; p = 0.015). Further, a separation in favour of L-theanine was noted on the ISI in those with non-clinical levels of insomnia symptoms (ISI ≤ 14; p = 0.007). No significant cognitive effects (trail making time and the modified emotional Stroop) were revealed. While this preliminary study did not support the efficacy of L-theanine in the treatment of anxiety symptoms in GAD, further studies to explore the application of L-theanine in sleep disturbance are warranted

A review of the catfish genus Pterocryptis (Siluridae) in Vietnam, with the description of two new species

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73958/1/j.1095-8649.2001.tb02367.x.pd