Bacillus subtilis SbcC protein plays an important role in DNA inter-strand cross-link repair

Background  

Several distinct pathways for the repair of damaged DNA exist in all cells. DNA modifications are repaired by base excision or nucleotide excision repair, while DNA double strand breaks (DSBs) can be repaired through direct joining of broken ends (non homologous end joining, NHEJ) or through recombination with the non broken sister chromosome (homologous recombination, HR). Rad50 protein plays an important role in repair of DNA damage in eukaryotic cells, and forms a complex with the Mre11 nuclease. The prokaryotic ortholog of Rad50, SbcC, also forms a complex with a nuclease, SbcD, in Escherichia coli, and has been implicated in the removal of hairpin structures that can arise during DNA replication. Ku protein is a component of the NHEJ pathway in pro- and eukaryotic cells.     

Bayesian variable selection for the analysis of microarray data with censored outcomes

MOTIVATION: A common task in microarray data analysis consists of identifying genes associated with a phenotype. When the outcomes of interest are censored time-to-event data, standard approaches assess the effect of genes by fitting univariate survival models. In this paper, we propose a Bayesian variable selection approach, which allows the identification of relevant markers by jointly assessing sets of genes. We consider accelerated failure time (AFT) models with log-normal and log-t distributional assumptions. A data augmentation approach is used to impute the failure times of censored observations and mixture priors are used for the regression coefficients to identify promising subsets of variables. The proposed method provides a unified procedure for the selection of relevant genes and the prediction of survivor functions. RESULTS: We demonstrate the performance of the method on simulated examples and on several microarray datasets. For the simulation study, we consider scenarios with large number of noisy variables and different degrees of correlation between the relevant and non-relevant (noisy) variables. We are able to identify the correct covariates and obtain good prediction of the survivor functions. For the microarray applications, some of our selected genes are known to be related to the diseases under study and a few are in agreement with findings from other researchers. AVAILABILITY: The Matlab code for implementing the Bayesian variable selection method may be obtained from the corresponding author. CONTACT: mvannucci@stat.tamu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Maternal Mortality in Rural South Ethiopia: Outcomes of Community-Based Birth Registration by Health Extension Workers

Introduction

Rural communities in low-income countries lack vital registrations to track birth outcomes. We aimed to examine the feasibility of community-based birth registration and measure maternal mortality ratio (MMR) in rural south Ethiopia.

Methods

In 2010, health extension workers (HEWs) registered births and maternal deaths among 421,639 people in three districts (Derashe, Bonke, and Arba Minch Zuria). One nurse-supervisor per district provided administrative and technical support to HEWs. The primary outcomes were the feasibility of registration of a high proportion of births and measuring MMR. The secondary outcome was the proportion of skilled birth attendance. We validated the completeness of the registry and the MMR by conducting a house-to-house survey in 15 randomly selected villages in Bonke.

Results

We registered 10,987 births (81·4% of expected 13,492 births) with annual crude birth rate of 32 per 1,000 population. The validation study showed that, of 2,401 births occurred in the surveyed households within eight months of the initiation of the registry, 71·6% (1,718) were registered with similar MMRs (474 vs. 439) between the registered and unregistered births. Overall, we recorded 53 maternal deaths; MMR was 489 per 100,000 live births and 83% (44 of 53 maternal deaths) occurred at home. Ninety percent (9,863 births) were at home, 4% (430) at health posts, 2·5% (282) at health centres, and 3·5% (412) in hospitals. MMR increased if: the male partners were illiterate (609 vs. 346; p= 0·051) and the villages had no road access (946 vs. 410; p= 0·039). The validation helped to increase the registration coverage by 10% through feedback discussions.

Conclusion

It is possible to obtain a high-coverage birth registration and measure MMR in rural communities where a functional system of community health workers exists. The MMR was high in rural south Ethiopia and most births and maternal deaths occurred at home.     

A Venue-Based Survey of Malaria,Anemia and Mobility Patterns among Migrant Farm Workers in Amhara Region,Ethiopia

Background

Mobile populations present unique challenges to malaria control and elimination efforts. Each year, a large number of individuals travel to northwest Amhara Region, Ethiopia to seek seasonal employment on large-scale farms. Agricultural areas typically report the heaviest malaria burden within Amhara thereby placing migrants at high risk of infection. Yet little is known about these seasonal migrants and their malaria-related risk factors.

Methods and Findings

In July 2013, a venue-based survey of 605 migrant laborers 18 years or older was conducted in two districts of North Gondar zone, Amhara. The study population was predominantly male (97.7%) and young (mean age 22.8 years). Plasmodium prevalence by rapid diagnostic test (RDT) was 12.0%; One quarter (28.3%) of individuals were anemic (hemoglobin <13 g/dl). Nearly all participants (95.6%) originated from within Amhara Region, with half (51.6%) coming from within North Gondar zone. Around half (51.2%) slept in temporary shelters, while 20.5% regularly slept outside. Only 11.9% of participants had access to a long lasting insecticidal net (LLIN). Reported net use the previous night was 8.8% overall but 74.6% among those with LLIN access. Nearly one-third (30.1%) reported having fever within the past two weeks, of whom 31.3% sought care. Cost and distance were the main reported barriers to seeking care. LLIN access (odds ratio [OR] = 0.30, P = 0.04) and malaria knowledge (OR = 0.50, P = 0.02) were significantly associated with reduced Plasmodium infection among migrants, with a similar but non-significant trend observed for reported net use the previous night (OR = 0.16, P = 0.14).

Conclusions

High prevalence of malaria and anemia were observed among a young population that originated from relatively proximate areas. Low access to care and low IRS and LLIN coverage likely place migrant workers at significant risk of malaria in this area and their return home may facilitate parasite transport to other areas. Strategies specifically tailored to migrant farm workers are needed to support malaria control and elimination activities in Ethiopia.     

Epilation for Minor Trachomatous Trichiasis: Four-Year Results of a Randomised Controlled Trial

BackgroundTrachomatous trichiasis (TT) needs to be managed to reduce the risk of vision loss. The long-term impact of epilation (a common traditional practice of repeated plucking of lashes touching the eye) in preventing visual impairment and corneal opacity from TT is unknown. We conducted a randomized controlled trial of epilation versus surgery for the management of minor TT (fewer than six lashes touching the eye) in Ethiopia. Here we report the four-year outcome and the effect on vision and corneal opacity.

Methodology/ Principal Findings

1300 individuals with minor TT were recruited and randomly assigned to quality trichiasis surgery or repeated epilation using high quality epilation forceps by a trained person with good near vision. Participants were examined six-monthly for two-years, and then at four-years after randomisation. At two-years all epilation arm participants were offered free surgery. At four-years 1151 (88.5%) were re-examined: 572 (88%) and 579 (89%) from epilation and surgery arms, respectively. At that time, 21.1% of the surgery arm participants had recurrent TT; 189/572 (33%) of the epilation arm had received surgery, while 383 (67%) declined surgery and had continued epilating (“epilation-only”). Among the epilation-only group, 207 (54.1%) fully controlled their TT, 166 (43.3%) had minor TT and 10 (2.6%) had major TT (&gt;5 lashes). There were no differences between participants in the epilation-only, epilation-to-surgery and surgery arm participants in changes in visual acuity and corneal opacity between baseline and four-years.

Conclusions/ Significance

Most minor TT participants randomised to the epilation arm continued epilating and controlled their TT. Change in vision and corneal opacity was comparable between surgery and epilation-only participants. This suggests that good quality epilation with regular follow-up is a reasonable second-line alternative to surgery for minor TT for individuals who either decline surgery or do not have immediate access to surgical treatment.     

Diet overlap of non‐native common carp and native Nile tilapia: A potential cause for population reduction of Nile tilapia stock in Lake Ziway,Ethiopia

Lake Ziway harbours indigenous and exotic fish species including Nile tilapia (Oreochromis niloticus) and common carp (Cyprinus carpio). Nile tilapia was the dominant and preferred fish. However, its contribution to total catch has dramatically declined from 89.3% in 1994 to 27% in 2014 while the introduced common carp has increased from 0% before 2012 to 25% in 2014. Common carp potentially compete with Nile tilapia for available resources and could be a cause for the decline. Thus, the study explored the dietary overlap of the two species from April to August 2017. Schoener's overlap index (α) revealed significant dietary overlap between the two species (α = 0.84, between juveniles and α = 0.63, between adults). Juveniles fed mainly on animal origin (zooplankton and insects), while adult Nile tilapia have consumed plant origin (macrophyte and phytoplankton), and adult common carp fed on macrophytes and detritus. The presence of significant dietary overlap between the two species, particularly due to intense competition among juveniles, might cause the reduction of Nile tilapia stock because the native species has shown a competitive disadvantage for food in the presence of common carp. This study provides baseline information to researchers and decision makers working towards the sustainable resource utilisation of the system.