Widespread Antisense Transcription in Escherichia coli

The vast majority of annotated transcripts in bacteria are mRNAs. Here we identify ~1,000 antisense transcripts in the model bacterium Escherichia coli. We propose that these transcripts are generated by promiscuous transcription initiation within genes and that many of them regulate expression of the overlapping gene

Identification of Novel sRNAs in Mycobacterial Species

Bacterial small RNAs (sRNAs) are short transcripts that typically do not encode proteins and often act as regulators of gene expression through a variety of mechanisms. Regulatory sRNAs have been identified in many species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. Here, we use a computational algorithm to predict sRNA candidates in the mycobacterial species M. smegmatis and M. bovis BCG and confirmed the expression of many sRNAs using Northern blotting. Thus, we have identified 17 and 23 novel sRNAs in M. smegmatis and M. bovis BCG, respectively. We have also applied a high-throughput technique (Deep-RACE) to map the 5′ and 3′ ends of many of these sRNAs and identified potential regulators of sRNAs by analysis of existing ChIP-seq datasets. The sRNAs identified in this work likely contribute to the unique biology of mycobacteria

Transcriptional profiling of C57 and DBA strains of mice in the absence and presence of morphine

BACKGROUND: The mouse C57BL/6 (C57) and DBA/2J (DBA) inbred strains differ substantially in many aspects of their response to drugs of abuse. The development of microarray analyses represents a genome-wide method for measuring differences across strains, focusing on expression differences. In the current study, we carried out microarray analysis in C57 and DBA mice in the nucleus accumbens of drug-naïve and morphine-treated animals. RESULTS: We identified mRNAs with altered expression between the two strains. We validated the mRNA expression changes of several such mRNAs, including Gnb1, which has been observed to be regulated by several drugs of abuse. In addition, we validated alterations in the enzyme activity of one mRNA product, catechol-O-methyltransferase (Comt). Data mining of expression and behavioral data indicates that both Gnb1 and Comt expression correlate with aspects of drug response in C57/DBA recombinant inbred strains. Pathway analysis was carried out to identify pathways showing significant alterations as a result of treatment and/or due to strain differences. These analyses identified axon guidance genes, particularly the semaphorins, as showing altered expression in the presence of morphine, and plasticity genes as showing altered expression across strains. Pathway analysis of genes showing strain by treatment interaction suggest that the phosphatidylinositol signaling pathway may represent an important difference between the strains as related to morphine exposure. CONCLUSION: mRNAs with differing expression between the two strains could potentially contribute to strain-specific responses to drugs of abuse. One such mRNA is Comt and we hypothesize that altered expression of Comt may represent a potential mechanism for regulating the effect of, and response to, multiple substances of abuse. Similarly, a role for Gnb1 in responses to multiple drugs of abuse is supported by expression data from our study and from other studies. Finally, the data support a role for semaphorin signaling in morphine effects, and indicate that altered expression of genes involved in phosphatidylinositol signaling and plasticity might also affect the altered drug responses in the two strains

Decacationic Pillar[5]arene: A New Scaffold for the Development of 129Xe MRI Imaging Agents

A decacationic water-soluble pillar[5]arene possessing a nonsolvated hydrophobic core has been designed and synthesized. This supramolecular host is capable of binding xenon, as evidenced by hyperCEST depletion experiments. Fluorescence-based studies also demonstrate that xenon binds into the cavity of the pillararene with an association constant of 4.6 × 103 M−1. These data indicate that the water-soluble pillararene is a potential scaffold for building contrast agents that can be detected by xenon-129 magnetic resonance imaging

Research review: young people leaving care

This paper reviews the international research on young people leaving care. Set in the context of a social exclusion framework, it explores young people's accelerated and compressed transitions to adulthood, and discusses the development and classification of leaving care services in responding to their needs. It then considers the evidence from outcome studies and argues that adopting a resilience framework suggests that young people leaving care may fall into three groups: young people 'moving on', 'survivors' and 'victims'. In concluding, it argues that these three pathways are associated with the quality of care young people receive, their transitions from care and the support they receive after care

Global Assessment of the SMAP Level-4 Surface and Root-Zone Soil Moisture Product Using Assimilation Diagnostics

The Soil Moisture Active Passive (SMAP) mission Level-4 Soil Moisture (L4_SM) product provides 3-hourly, 9-km resolution, global estimates of surface (0-5 cm) and root-zone (0-100 cm) soil moisture and related land surface variables from 31 March 2015 to present with ~2.5-day latency. The ensemble-based L4_SM algorithm assimilates SMAP brightness temperature (Tb) observations into the Catchment land surface model. This study describes the spatially distributed L4_SM analysis and assesses the observation-minus-forecast (O-F) Tb residuals and the soil moisture and temperature analysis increments. Owing to the climatological rescaling of the Tb observations prior to assimilation, the analysis is essentially unbiased, with global mean values of ~0.37 K for the O-F Tb residuals and practically zero for the soil moisture and temperature increments. There are, however, modest regional (absolute) biases in the O-F residuals (under ~3 K), the soil moisture increments (under ~0.01 cu.m/cu.m), and the surface soil temperature increments (under ~1 K). Typical instantaneous values are ~6 K for O-F residuals, ~0.01 (~0.003) cu.m/cu.m for surface (root-zone) soil moisture increments, and ~0.6 K for surface soil temperature increments. The O-F diagnostics indicate that the actual errors in the system are overestimated in deserts and densely vegetated regions and underestimated in agricultural regions and transition zones between dry and wet climates. The O-F auto-correlations suggest that the SMAP observations are used efficiently in western North America, the Sahel, and Australia, but not in many forested regions and the high northern latitudes. A case study in Australia demonstrates that assimilating SMAP observations successfully corrects short-term errors in the L4_SM rainfall forcing

High HIV Prevalence Among Men Who have Sex with Men in Soweto, South Africa: Results from the Soweto Men’s Study

The Soweto Men’s Study assessed HIV prevalence and associated risk factors among MSM in Soweto, South Africa. Using respondent driven sampling (RDS) recruitment methods, we recruited 378 MSM (including 15 seeds) over 30 weeks in 2008. All results were adjusted for RDS sampling design. Overall HIV prevalence was estimated at 13.2% (95% confidence interval 12.4–13.9%), with 33.9% among gay-identified men, 6.4% among bisexual-identified men, and 10.1% among straight-identified MSM. In multivariable analysis, HIV infection was associated with being older than 25 (adjusted odds ratio (AOR) 3.8, 95% CI 3.2–4.6), gay self-identification (AOR 2.3, 95% CI 1.8–3.0), monthly income less than ZAR500 (AOR 1.4, 95% CI 1.2–1.7), purchasing alcohol or drugs in exchange for sex with another man (AOR 3.9, 95% CI 3.2–4.7), reporting any URAI (AOR 4.4, 95% CI 3.5–5.7), reporting between six and nine partners in the prior 6 months (AOR 5.7, 95% CI 4.0–8.2), circumcision, (AOR 0.2, 95% CI 0.1–0.2), a regular female partner (AOR 0.2, 95% CI 0.2–0.3), smoking marijuana in the last 6 months (AOR 0.6, 95% CI 0.5–0.8), unprotected vaginal intercourse in the last 6 months (AOR 0.5, 95% CI 0.4–0.6), and STI symptoms in the last year (AOR 0.7, 95% CI 0.5–0.8). The results of the Soweto Men’s Study confirm that MSM are at high risk for HIV infection, with gay men at highest risk. HIV prevention and treatment for MSM are urgently needed