Molecular analysis of bacterial community succession during prolonged compost curing

The compost environment consists of complex organic materials that form a habitat for a rich and diverse microbial community. The aim of this research was to study the dynamics of microbial communities during the compost-curing phase. Three different methods based on 16S rRNA gene sequence were applied to monitor changes in the microbial communities: (1) denaturing gradient gel electrophoresis of PCR-generated rRNA gene fragments; (2) partial rRNA gene clone libraries; and (3) a microarray of oligonucleotide probes targeting rRNA gene sequences. All three methods indicated distinctive community shifts during curing and the dominant species prevailing during the different curing stages were identified. We found a successional transition of different bacterial phylogenetic groups during compost curing. The Proteobacteria were the most abundant phylum in all cases. The Bacteroidetes and the Gammaproteobacteria were ubiquitous. During the midcuring stage, Actinobacteria were dominant. Different members of nitrifying bacteria and cellulose and macromolecule-degrading bacteria were found throughout the curing process. In contrast, pathogens were not detected. In the cured compost, bacterial population shifts were still observed after the compost organic matter and other biochemical properties had seemingly stabilized.     

Filling the Knowledge Gap: Measuring HIV Prevalence and Risk Factors among Men Who Have Sex with Men and Female Sex Workers in Tripoli,Libya

Background

Publications on Libya’s HIV epidemic mostly examined the victims of the tragic nosocomial HIV outbreak in the 1990s and the related dispute about the detention of foreign medical workers. The dispute resolution in 2003 included an agreement with the European Union on humanitarian cooperation and the development of Libya’s first National HIV Strategy. As part of this we conducted Libya’s first bio-behavioural survey among men having sex with men (MSM) and female sex workers (FSW).

Methods

Using respondent-driven sampling, we conducted a cross-sectional study to estimate the prevalence of HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), and related risk factors among 227 MSM and 69 FSW in Tripoli (FSW recruitment ended prematurely due to the political events in 2011).

Results

For MSM we estimated an HIV prevalence of 3.1%, HBV prevalence of 2.9%, and HCV prevalence of 7.3%, and for FSW an HIV prevalence of 15.7%, HBV prevalence of 0%, and HCV prevalence of 5.2%. We detected high levels of risk behaviours, poor HIV-related knowledge, high stigma and lack of prevention programmes. These results must be interpreted in the context of the political situation which prohibited reaching an ideal sample size for FSW.

Conclusion

There is urgent need to implement an effective National HIV Strategy informed by the results of this research. The risk of transmission within different risk groups and to the general population may be high given the recent military events that led to increased violence, migration, and the disruption of essential HIV-related services.     

Cytogenetic and Molecular Analyses Reveal a Divergence between Acromyrmex striatus (Roger, 1863) and Other Congeneric Species: Taxonomic Implications

The leafcutter ants, which consist of Acromyrmex and Atta genera, are restricted to the New World and they are considered the main herbivores in the neotropics. Cytogenetic studies of leafcutter ants are available for five species of Atta and 14 species of Acromyrmex, both including subspecies. These two ant genera have a constant karyotype with a diploid number of 22 and 38 chromosomes, respectively. The most distinct Acromyrmex species from Brazil is A. striatus, which is restricted to the southern states of Santa Catarina and Rio Grande do Sul. Several cytogenetic and phylogenetic studies have been conducted with ants, but the karyotypic characterization and phylogenetic position of this species relative to leafcutter ants remains unknown. In this study, we report a diploid number of 22 chromosomes for A. striatus. The phylogenetic relationship between A. striatus and other leafcutter ants was estimated based on the four nuclear genes. A. striatus shared the same chromosome number as Atta species and the majority of metacentric chromosomes. Nuclear data generated a phylogenetic tree with a well-supported cluster, where A. striatus formed a different clade from other Acromyrmex spp. This combination of cytogenetic and molecular approaches provided interesting insights into the phylogenetic position of A. striatus among the leafcutter ants and the tribe Attini.     

Using bleach-chase to measure protein half-lives in living cells

Protein removal has a central role in numerous cellular processes. Obtaining systematic measurements of multiple protein removal rates is necessary to understand the principles that govern these processes, but it is currently a major technical challenge. To address this, we developed 'bleach-chase', a noninvasive method for measuring the half-lives of multiple proteins at high temporal resolution in living cells. The method uses a library of annotated human reporter cell clones, each with a unique fluorescently tagged protein expressed from its native chromosomal location. In this protocol, we detail a simple procedure that bleaches the cells and uses time-lapse fluorescence microscopy and automated image analysis to systematically measure the half-life dynamics of multiple proteins. The duration of the protocol is 4-5 d. The method may be applicable to a wide range of fluorescently tagged proteins and cell lines.