Control of pyrene fluorescence intensity by in situ addition of CO(2) to an amidine/amine mixture or CO(2) removal from an amidinium carbamate ionic liquid

Addition of CO(2) to an equimolar amidine/amine mixture leads to formation of a switchable ionic liquid, an amidinium carbamate, and appearance of strong fluorescence by a solute, pyrene. Passing a 'displacement gas', N(2), through the ionic liquid or heating it regenerates the amidine/amine mixture and quenches the fluorescence almost totally. No switching or appreciable fluorescence is found when an amidinium dithiocarbamate is the medium.     

The relationship between fire history and an exotic fungal disease in a deciduous forest

Exotic diseases have fundamentally altered the structure and function of forest ecosystems. Controlling exotic diseases across large expanses of forest has proven difficult, but fire may reduce the levels of diseases that are sensitive to environmental conditions. We examined Cornus florida populations in burned and unburned Quercus–Carya stands to determine if burning prior to anthracnose infection has reduced the impacts of an exotic fungal disease, dogwood anthracnose, caused by Discula destructiva. We hypothesized that fire has altered stand structure and created open conditions less conducive to dogwood anthracnose. We compared C. florida density, C. florida health, and species composition and density among four sampling categories: unburned stands, and stands that had burned once, twice, and 3 times over a 20-year period (late 1960s to late 1980s). Double burn stands contained the greatest density of C. florida stems (770 stems ha⁻¹) followed by triple burn stands (233 stems ha⁻¹), single burn stands (225 stems ha⁻¹) and unburned stands (70 stems ha⁻¹; P < 0.01). We observed less crown dieback in small C. florida trees (<5 cm diameter at breast height) in burned stands than in unburned stands (P < 0.05). Indicator species analysis showed that burning favored species historically associated with Quercus–Carya forests and excluded species associated with secondary succession following nearly a century of fire suppression. Our results suggest that fire may mitigate the decline of C. florida populations under attack by an exotic pathogen by altering forest structure and composition. Further, our results suggest that the burns we sampled have had an overall restorative effect on forest communities and were within the fire return interval of the historic fire regime. Consequently, prescribed fire may offer a management tool to reduce the impacts of fungal disease in forest ecosystems that developed under historic burning regimes.     

The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples

Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS) revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral sequences within microbial fractions, the prevalence of genes among viral sequences that encode microbial physiological function and their distinct phylogenetic distribution lend strong support to the notion that viral-mediated gene acquisition is a common and ongoing mechanism for generating microbial diversity in the marine environment.     

Compensatory mechanisms of central U.S. hardwood forest communities in a changing environment

Although it is known that forest productivity is highly correlated with canopy leaf area, the influence of environmental gradients within a forest on leaf area-productivity relationships has not been well-documented, particularly for mixed-species forests. The present study was conducted to define the mechanisms by which Central Hardwood forest communities respond to changes in environment. Ecological Land Type Phases (ELTPs) of the Central Hardwood region, delineated by soils, topography, and indicator vegetation, provided a framework to examine the impacts of environmental gradients on leaf area-productivity relationships at a landscape level. Three ELTPs- (1) Quercus prinus / Carex picta-Vaccinium, Dry slope, (2) Quercus alba-Acer saccharum / Parthenocissus, Dry-Mesic Slope, and (3) Fagus-Acer saccharum / Arisaema, Mesic Slope- were selected and stratified into three slope positions viz. the upper edge of the community, the middle or center of the community on the slope, and the lower edge of the community. Circular plots of 0.02 ha in size were established for sampling. Standing stock (basal area, volume, and biomass), annual production, leaf area index, and growth efficiency were determined for each slope position and examined to determine the mechanisms and trends for community change across slope positions. Among the three communities studied, dry slopes compensated for drier conditions through both a shift in species composition and reduced annual production. Dry-mesic slopes exhibited adaptation only through changing species composition whereas mesic slopes compensated for drier conditions primarily through reduction in annual production. These results indicate that mixed-species forest communities adjust to environmental gradients through several mechanisms and that the relative importance of these mechanisms changes with community type.     

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly

Background

Metagenomics is a cultivation-independent approach that enables the study of the genomic composition of microbes present in an environment. Metagenomic samples are routinely sequenced using next-generation sequencing technologies that generate short nucleotide reads. Proteins identified from these reads are mostly of partial length. On the other hand, de novo assembly of a large metagenomic dataset is computationally demanding and the assembled contigs are often fragmented, resulting in the identification of protein sequences that are also of partial length and incomplete. Annotation of an incomplete protein sequence often proceeds by identifying its homologs in a database of reference sequences. Identifying the homologs of incomplete sequences is a challenge and can result in substandard annotation of proteins from metagenomic datasets. To address this problem, we recently developed a homology detection algorithm named GRASP (Guided Reference-based Assembly of Short Peptides) that identifies the homologs of a given reference protein sequence in a database of short peptide metagenomic sequences. GRASP was developed to implement a simultaneous alignment and assembly algorithm for annotation of short peptides identified on metagenomic reads. The program achieves significantly improved recall rate at the cost of computational efficiency. In this article, we adopted three techniques to speed up the original version of GRASP, including the pre-construction of extension links, local assembly of individual seeds, and the implementation of query-level parallelism.

Results

The resulting new program, GRASPx, achieves >30X speedup compared to its predecessor GRASP. At the same time, we show that the performance of GRASPx is consistent with that of GRASP, and that both of them significantly outperform other popular homology-search tools including the BLAST and FASTA suites. GRASPx was also applied to a human saliva metagenome dataset and shows superior performance for both recall and precision rates.

Conclusions

In this article we present GRASPx, a fast and accurate homology-search program implementing a simultaneous alignment and assembly framework. GRASPx can be used for more comprehensive and accurate annotation of short peptides. GRASPx is freely available at http://graspx.sourceforge.net/.

     

Outcome of Tuberculosis Treatment in Patients with Diabetes Mellitus Treated in the Revised National Tuberculosis Control Programme in Malappuram District,Kerala, India

Settings

Kerala State, India has reported the greatest dual burden of Tuberculosis (TB) and Diabetes Mellitus (DM). Malappuram district in Kerala has monitored and recorded DM status and its control from 2010 under Revised National Tuberculosis Control Program (RNTCP).

Objectives

To assess, under programme conditions, comprehensiveness of recording DM status among TB cases and the TB treatment outcomes among DM patients (disaggregated by glycemic control) and compare with-non DM patients.

Design

This retrospective record review included 3,116TB patients from April 2010 to September 2011.DM was defined as per international guidelines and TB treatment outcomes were categorized as favourable(cured and treatment completed) and unfavourable(death, default, failure and transfer out). Relative Risk (RR) and 95% confidence intervals(CI) were calculated to assess the risk of unfavourable outcomes.

Results

DM status was recorded in 90% of TB cases and 667 (24%) had DM. 17% of DM patients and 23% of patients with unknown DM status had unfavourable outcomes but this difference was not statistically significant. Unadjusted RR for poor glycemic control or unknown control status for unfavourable outcome were (2.00; 95% CI 0.97–4.13) and (2.14; 95% CI 1.11–4.13).

Conclusion

This study could not confirm an adverse association between DM or its control during treatment and the course of response to TB treatment.DM screening in TB cases and recording of DM care needs to be improved to enable more conclusive evidence.     

Protein acyltransferase function of purified calreticulin: the exclusive role of P-domain in mediating protein acylation utilizing acyloxycoumarins and acetyl CoA as the acyl group donors

The distinct biochemical function of endoplasmic reticulum (ER) protein Calreticulin (CR) catalyzing the transfer of acyl group from acyloxycoumarin to a receptor protein was termed calreticulin transacylase (CRTAase). The present study, unlike the previous reports of others utilizing CR-deficient cells alone, dealt with the recombinant CR domains of Heamonchus contortus (rhCRTAase) in order to examine their CRTAase activity. P-domain of rhCR unlike N- and C-domains was found to be endowed with CRTAase function. We have also observed for the first time acetyl CoA, as a substrate for rhCRTAase/P-domain mediated acetylation of recombinant Schistosoma japonicum glutathione S-transferase (rGST). rhCRTAase/P-domain were also found to undergo autoacylation by acyloxycoumarins. Also, the isolated autoacylated rhCRTAase/P-domain in non-denatured form alone exhibited the ability to transfer acyl group to rGST indicating the stable intermediate nature of acylated CR. P-domain catalyzed acetylation of rGST by 7,8-Diacetoxy-4-methylcoumarin or acetyl CoA resulted in the modification of several lysine residues in common was evidenced by LC-MS/MS analysis. The putative site of the binding of acyloxycoumarins with CR was predicted by computational blind docking studies. The results showed the involvement of two lysine residues Lys-173 and Lys-174 present in P-domain for binding acyloxycoumarins and acetyl CoA thus highlighting that the active site for the CRTAase activity would reside in the P-domain of CR. Certain ER proteins are known to undergo acetylation under the physiological conditions involving acetyl CoA. These results demonstrating CRTAase mediated protein acetylation by acetyl CoA may hint at CR as the possible protein acetyltransferase of the ER lumen.     

Invasion success of cogongrass,an alien C<Subscript>4</Subscript> perennial grass,in the southeastern United States: exploration of the ecological basis

Cogongrass (Imperata cylindrica) is considered one of the worst invasive species in the world. The species is readily adaptable to a wide range of environmental conditions and upon invasion reduces forest productivity, alters nutrient cycling, and threatens native species biodiversity. This paper explores seven major ecological hypotheses (Propagule Pressure Hypothesis, Natural Enemies or Enemy Release Hypothesis, Empty Niche Hypothesis, Invasional Meltdown Hypothesis, Evolution of Increased Competitive Ability Hypothesis/Superior Competitor Hypothesis, Novel Weapons Hypothesis, and Diversity—Invasibility (Elton’s) Hypothesis) that explain the invasiveness of cogongrass in the southeastern United States. Information gathered from this review can be used to reduce the spread of cogongrass and is applicable for control of other invasive species as well.     

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)

As metagenomic studies continue to increase in their number, sequence volume and complexity, the scalability of biological analysis frameworks has become a rate-limiting factor to meaningful data interpretation. To address this issue, we have developed JCVI Metagenomics Reports (METAREP) as an open source tool to query, browse, and compare extremely large volumes of metagenomic annotations. Here we present improvements to this software including the implementation of a dynamic weighting of taxonomic and functional annotation, support for distributed searches, advanced clustering routines, and integration of additional annotation input formats. The utility of these improvements to data interpretation are demonstrated through the application of multiple comparative analysis strategies to shotgun metagenomic data produced by the National Institutes of Health Roadmap for Biomedical Research Human Microbiome Project (HMP) (http://nihroadmap.nih.gov). Specifically, the scalability of the dynamic weighting feature is evaluated and established by its application to the analysis of over 400 million weighted gene annotations derived from 14 billion short reads as predicted by the HMP Unified Metabolic Analysis Network (HUMAnN) pipeline. Further, the capacity of METAREP to facilitate the identification and simultaneous comparison of taxonomic and functional annotations including biological pathway and individual enzyme abundances from hundreds of community samples is demonstrated by providing scenarios that describe how these data can be mined to answer biological questions related to the human microbiome. These strategies provide users with a reference of how to conduct similar large-scale metagenomic analyses using METAREP with their own sequence data, while in this study they reveal insights into the nature and extent of variation in taxonomic and functional profiles across body habitats and individuals. Over one thousand HMP WGS datasets and the latest open source code are available at http://www.jcvi.org/hmp-metarep.     

High Diabetes Prevalence among Tuberculosis Cases in Kerala,India

Background

While diabetes mellitus (DM) is a known risk factor for tuberculosis, the prevalence among TB patients in India is unknown. Routine screening of TB patients for DM may be an opportunity for its early diagnosis and improved management and might improve TB treatment outcomes. We conducted a cross-sectional survey of TB patients registered from June–July 2011 in the state of Kerala, India, to determine the prevalence of DM.

Methodology/Principal Findings

A state-wide representative sample of TB patients in Kerala was interviewed and screened for DM using glycosylated hemoglobin (HbA1c); patients self-reporting a history of DM or those with HbA1c ≥6.5% were defined as diabetic. Among 552 TB patients screened, 243(44%) had DM – 128(23%) had previously known DM and 115(21%) were newly diagnosed - with higher prevalence among males and those aged >50years. The number needed to screen(NNS) to find one newly diagnosed case of DM was just four. Of 128 TB patients with previously known DM, 107(84%) had HbA1c ≥7% indicating poor glycemic control.

Conclusions/Significance

Nearly half of TB patients in Kerala have DM, and approximately half of these patients were newly-diagnosed during this survey. Routine screening of TB patients for DM using HbA1c yielded a large number of DM cases and offered earlier management opportunities which may improve TB and DM outcomes. However, the most cost-effective ways of DM screening need to be established by futher operational research.