Draft Genome Sequences of Two Benthic Cyanobacteria, Oscillatoriales USR 001 and Nostoc sp. MBR 210, Isolated from Tropical Freshwater Lakes

Genomes of two filamentous benthic cyanobacteria were obtained from cocultures obtained from two freshwater lakes. The cultures were obtained by first growing cyanobacterial trichome on solid medium, followed by subculturing in freshwater media. Subsequent shotgun sequencing, de novo assembly, and genomic binning yielded almost complete genomes of Oscillatoriales USR 001 and Nostoc sp. MBR 210.Singapore. National Research FoundationSingapore-MIT Alliance for Research and Technology. Center for Environmental Sensing and Modelin

Draft Genome Sequence of a Tropical Freshwater Cyanobacterium, Limnothrix sp. Strain P13C2

A nonaxenic unialgal culture of Limnothrix sp. strain P13C2 was obtained through multiple subculturing of an inoculum obtained from a tropical freshwater lake. Here, we report the genome of P13C2 of 4.6 Mbp, extracted from the metagenome of this coculture.Singapore-MIT Alliance for Research and Technology (SMART)Singapore. National Research Foundation (NRF, 1102-IRIS-14-02

Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production

A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium, Hapalosiphon strain MRB 220, was obtained from a benthic freshwater algal mat through multiple transfers following growth in sterile media. Physiological characterization demonstrated the culture was capable of nitrogen-fixation and production of the off flavor compound 2-methylisoborneol (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq and de novo assembled into contigs. The genome of MRB 220 was separated from co-occurring heterotrophic bacteria using sequence homology and compositional approaches, and its purity was confirmed based on best BLAST hit classification and principle component analysis of the tetranucleotide frequencies of fragmented contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of these having functional prediction including predicted pathways for biosynthesis of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole genome sequence average nucleotide identity indicated close relatedness of MRB 220 to the genera Hapalosiphon and Fischerella within the order Stigonematales. Microscopic examination showed that MRB 220 formed heterocystous branched filaments, thereby supporting identification of strain MRB 220 as a morphospecies of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220 enables future work to elucidate the pathway and dynamics for biosynthesis of 2-MIB and other secondary metabolites and understand the ecology and physiology of Stigonematales cyanobacteria in tropical freshwaters.Singapore. National Research Foundation (under its Environmental & Water Technologies Strategic Research Programme and administered by the Environment & Water Industry Programme Office (EWI) of the PUB (Grant number: 1102-IRIS-14-02))Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology’s (SMART) Center for Environmental Sensing and Modeling (CENSAM) research program

A Protective Role for Complement C3 Protein during Pandemic 2009 H1N1 and H5N1 Influenza A Virus Infection

Highly pathogenic H5N1 influenza infections are associated with enhanced inflammatory and cytokine responses, severe lung damage, and an overall dysregulation of innate immunity. C3, a member of the complement system of serum proteins, is a major component of the innate immune and inflammatory responses. However, the role of this protein in the pathogenesis of H5N1 infection is unknown. Here we demonstrate that H5N1 influenza virus infected mice had increased levels of C5a and C3 activation byproducts as compared to mice infected with either seasonal or pandemic 2009 H1N1 influenza viruses. We hypothesized that the increased complement was associated with the enhanced disease associated with the H5N1 infection. However, studies in knockout mice demonstrated that C3 was required for protection from influenza infection, proper viral clearance, and associated with changes in cellular infiltration. These studies suggest that although the levels of complement activation may differ depending on the influenza virus subtype, complement is an important host defense mechanism

Semen characteristics of Bornean sun bear (Helarctos malayanus euryspilus)

The Bornean sun bear (Helarctos malayanus euryspilus), endemic to Borneo Island, is the subspecies of the Malayan sun bear. The species is at risk, not just because of anthropogenic threats, but also slow reproduction in the wild. In captivity, due to poor reproductive performance, assisted reproductive technology is deemed a fundamental tool to propagate the depleting numbers of the Bornean sun bear. This is a pioneer study that presents the semen characteristics of the Bornean sun bear via conventional semen evaluation methods. Forty-two semen samples from ten sun bears were collected via electroejaculation and evaluated. The electro ejaculator probe (2.5 cm in diameter and 7.0 cm in length) was inserted rectally and positioned dorsal to the prostate gland. The optimum voltage used to obtain semen differed with each individual, but all showed hindlegs contraction and penile erection before ejaculation. The average combined testes volume in the Bornean sun bear was 23.37 ± 5.09 cm³. The mean semen volume was 617.30 µL, with sperm concentration of 1034.40 × 10⁶ sperm/mL and pH 7.79. Sperm viability was 80.19% with a general motility of 79.13% and progressive movement of 70.20%. There were high sperm abnormalities at 70.67%. Sun bear sperm length was 61.28 ± 2.46 µm and consisted of an oval head, midpiece, and tail. From this study, good semen donors were identified from the captive Bornean sun bear population in Sabah, Malaysia. The fresh semen baseline data established in this study will provide crucial reference for assisted reproduction programs in the Bornean sun bear

The Peripheral Blood Transcriptome Identifies the Presence and Extent of Disease in Idiopathic Pulmonary Fibrosis

<div><h3>Rationale</h3><p>Peripheral blood biomarkers are needed to identify and determine the extent of idiopathic pulmonary fibrosis (IPF). Current physiologic and radiographic prognostic indicators diagnose IPF too late in the course of disease. We hypothesize that peripheral blood biomarkers will identify disease in its early stages, and facilitate monitoring for disease progression.</p> <h3>Methods</h3><p>Gene expression profiles of peripheral blood RNA from 130 IPF patients were collected on Agilent microarrays. Significance analysis of microarrays (SAM) with a false discovery rate (FDR) of 1% was utilized to identify genes that were differentially-expressed in samples categorized based on percent predicted D_LCO and FVC.</p> <h3>Main Measurements and Results</h3><p>At 1% FDR, 1428 genes were differentially-expressed in mild IPF (D_LCO >65%) compared to controls and 2790 transcripts were differentially- expressed in severe IPF (D_LCO >35%) compared to controls. When categorized by percent predicted D_LCO, SAM demonstrated 13 differentially-expressed transcripts between mild and severe IPF (< 5% FDR). These include CAMP, CEACAM6, CTSG, DEFA3 and A4, OLFM4, HLTF, PACSIN1, GABBR1, IGHM, and 3 unknown genes. Principal component analysis (PCA) was performed to determine outliers based on severity of disease, and demonstrated 1 mild case to be clinically misclassified as a severe case of IPF. No differentially-expressed transcripts were identified between mild and severe IPF when categorized by percent predicted FVC.</p> <h3>Conclusions</h3><p>These results demonstrate that the peripheral blood transcriptome has the potential to distinguish normal individuals from patients with IPF, as well as extent of disease when samples were classified by percent predicted D_LCO, but not FVC.</p> </div

NIPTRIC:an online tool for clinical interpretation of non-invasive prenatal testing (NIPT) results

To properly interpret the result of a pregnant woman's non-invasive prenatal test (NIPT), her a priori risk must be taken into account in order to obtain her personalised a posteriori risk (PPR), which more accurately expresses her true likelihood of carrying a foetus with trisomy. Our aim was to develop a tool for laboratories and clinicians to calculate easily the PPR for genome-wide NIPT results, using diploid samples as a control group. The tool takes the a priori risk and Z-score into account. Foetal DNA percentage and coefficient of variation can be given default settings, but actual values should be used if known. We tested the tool on 209 samples from pregnant women undergoing NIPT. For Z-scores <5, the PPR is considerably higher at a high a priori risk than at a low a priori risk, for NIPT results with the same Z-score, foetal DNA percentage and coefficient of variation. However, the PPR is effectively independent under all conditions for Z-scores above 6. A high PPR for low a priori risks can only be reached at Z-scores > 5. Our online tool can assist clinicians in understanding NIPT results and conveying their true clinical implication to pregnant women, because the PPR is crucial for individual counselling and decision-making

Individual, family and offence characteristics of high risk childhood offenders: comparing non-offending, one-time offending and re-offending Dutch-Moroccan migrant children in the Netherlands

<p>Abstract</p> <p>Background</p> <p>Childhood offenders are at an increased risk for developing mental health, social and educational problems later in life. An early onset of offending is a strong predictor for future persistent offending. Childhood offenders from ethnic minority groups are a vulnerable at-risk group. However, up until now, no studies have focused on them.</p> <p>Aims</p> <p>To investigate which risk factors are associated with (re-)offending of childhood offenders from an ethnic minority.</p> <p>Method</p> <p>Dutch-Moroccan boys, who were registered by the police in the year 2006-2007, and their parents as well as a control group (n = 40) were interviewed regarding their individual and family characteristics. Two years later a follow-up analysis of police data was conducted to identify one-time offenders (n = 65) and re-offenders (n = 35).</p> <p>Results</p> <p>All groups, including the controls, showed substantial problems. Single parenthood (OR 6.0) and financial problems (OR 3.9) distinguished one-time offenders from controls. Reading problems (OR 3.8), having an older brother (OR 5.5) and a parent having Dutch friends (OR 4.3) distinguished re-offenders from one-time offenders. First offence characteristics were not predictive for re-offending. The control group reported high levels of emotional problems (33.3%). Parents reported not needing help for their children but half of the re-offender's families were known to the Child Welfare Agency, mostly in a juridical framework.</p> <p>Conclusion</p> <p>The Moroccan subgroup of childhood offenders has substantial problems that might hamper healthy development. Interventions should focus on reaching these families tailored to their needs and expectations using a multi-system approach.</p

Effects of dopaminergic modulation on electrophysiological brain response to affective stimuli

Introduction: Several theoretical accounts of the role of dopamine suggest that dopamine has an influence on the processing of affective stimuli. There is some indirect evidence for this from studies showing an association between the treatment with dopaminergic agents and self-reported affect. Materials and methods: We addressed this issue directly by examining the electrophysiological correlates of affective picture processing during a single-dose treatment with a dopamine D2 agonist (bromocriptine), a dopamine D2 antagonist (haloperidol), and a placebo. We compared early and late event-related brain potentials (ERPs) that have been associated with affective processing in the three medication treatment conditions in a randomized double-blind crossover design amongst healthy males. In each treatment condition, subjects attentively watched neutral, pleasant, and unpleasant pictures while ERPs were recorded. Results: Results indicate that neither bromocriptine nor haloperidol has a selective effect on electrophysiological indices of affective processing. In concordance with this, no effects of dopaminergic modulation on self-reported positive or negative affect was observed. In contrast, bromocriptine decreased overall processing of all stimulus categories regardless of their affective content. Discussion: The results indicate that dopaminergic D2 receptors do not seem to play a crucial role in the selective processing of affective visual stimuli