A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better known roles as antibiotics. To date, close to five hundred bacteriocins have been identified and classified. Recent discoveries have shown that bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel bacteriocins due to their vast sequence and structural diversity. Many bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as \textit{context genes} in this study. Although bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species. Using this knowledge, we set out to identify new candidates for context genes which may clarify how bacteriocins are synthesized, and identify new candidates for bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones. We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: https://github.com/idoerg/BOAComment: Accepted for publication in BMC Bioinformatic

Evaluation Of Acupuncture Therapy For Chronic Prostatitis/Chronic Pelvic Pain Syndrome

Penyakit prostatitis kronikl sindrom sakit pelvis kronik merupakan sejenis sindrom yang mengecewakan, mengelirukan dan kerap ditemui. Chronic prostatitis/ chronic pelvic pain syndrome is a frustrating, confusing and prevalent syndrome

Evaluation Of Acupuncture Therapy For Chronic Prostatitis/Chronic Pelvic Pain Syndrome [RM184. L481 2007 F Rb].

Penyakit prostatitis kronik/ sindrom sakit pelvis kronik merupakan sejenis sindrom yang mengecewakan, mengelirukan dan kerap ditemui. Sebanyak 2 juta orang dirawat untuk penyakit ini di Amerika Syarikat dan di Malaysia, penyakit ini dihidapi oleh 8.7% kaum lelaki. Hanya sejak 1995 penyakit ini mendapat perhatian perkhidmatan kesihatan di serata dunia. Chronic prostatitis/ chronic pelvic pain syndrome is a frustrating, confusing and prevalent syndrome. It accounts for nearly 2 million visits to the physicians annually in US, and in Malaysia, is known to affect the lives of approximately 8.7% of the male population. As recent as 1995, only did this syndrome gain the attention of healthcare providers worldwide

Expression and purification of an adenylation domain from a eukaryotic nonribosomal peptide synthetase: Using structural genomics tools for a challenging target

Nonribosomal peptide synthetases (NRPSs) are large multimodular and multidomain enzymes that are involved in synthesising an array of molecules that are important in human and animal health. NRPSs are found in both bacteria and fungi but most of the research to date has focused on the bacterial enzymes. This is largely due to the technical challenges in producing active fungal NRPSs, which stem from their large size and multidomain nature. In order to target fungal NRPS domains for biochemical and structural characterisation, we tackled this challenge by using the cloning and expression tools of structural genomics to screen the many variables that can influence the expression and purification of proteins. Using these tools we have screened 32 constructs containing 16 different fungal NRPS domains or domain combinations for expression and solubility. Two of these yielded soluble protein with one, the third adenylation domain of the SidN NRPS (SidNA3) from the grass endophyte Neotyphodium lolii, being tractable for purification using Ni-affinity resin. The initial purified protein exhibited poor solution behaviour but optimisation of the expression construct and the buffer conditions used for purification, resulted in stable recombinant protein suitable for biochemical characterisation, crystallisation and structure determination

Second-generation PLINK: rising to the challenge of larger and richer datasets

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a strong need for even faster and more scalable implementations of key functions. In addition, GWAS and population-genetic data now frequently contain probabilistic calls, phase information, and/or multiallelic variants, none of which can be represented by PLINK 1's primary data format. To address these issues, we are developing a second-generation codebase for PLINK. The first major release from this codebase, PLINK 1.9, introduces extensive use of bit-level parallelism, O(sqrt(n))-time/constant-space Hardy-Weinberg equilibrium and Fisher's exact tests, and many other algorithmic improvements. In combination, these changes accelerate most operations by 1-4 orders of magnitude, and allow the program to handle datasets too large to fit in RAM. This will be followed by PLINK 2.0, which will introduce (a) a new data format capable of efficiently representing probabilities, phase, and multiallelic variants, and (b) extensions of many functions to account for the new types of information. The second-generation versions of PLINK will offer dramatic improvements in performance and compatibility. For the first time, users without access to high-end computing resources can perform several essential analyses of the feature-rich and very large genetic datasets coming into use.Comment: 2 figures, 1 additional fil

Perovskite-polymer composite cross-linker approach for highly-stable and efficient perovskite solar cells.

Manipulation of grain boundaries in polycrystalline perovskite is an essential consideration for both the optoelectronic properties and environmental stability of solar cells as the solution-processing of perovskite films inevitably introduces many defects at grain boundaries. Though small molecule-based additives have proven to be effective defect passivating agents, their high volatility and diffusivity cannot render perovskite films robust enough against harsh environments. Here we suggest design rules for effective molecules by considering their molecular structure. From these, we introduce a strategy to form macromolecular intermediate phases using long chain polymers, which leads to the formation of a polymer-perovskite composite cross-linker. The cross-linker functions to bridge the perovskite grains, minimizing grain-to-grain electrical decoupling and yielding excellent environmental stability against moisture, light, and heat, which has not been attainable with small molecule defect passivating agents. Consequently, all photovoltaic parameters are significantly enhanced in the solar cells and the devices also show excellent stability

Construction of a gridded energy analyzer for measurements of ion energy distribution in the versatile toroidal facility

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Nuclear Engineering, 1998.Includes bibliographical references (p. 80-82).The Versatile Toroidal Facility (VTF) at MIT's Plasma Science and Fusion Center provides a laboratory environment for studying ionospheric plasmas. Various plasma diagnostic devices have been created and used to study the VTF plasma since 1991. An accurate method for measuring VTF's ion characteristics has never been designed or installed in the laboratory facility. Gridded Energy Analyzers (GEA) are useful diagnostic tools for determining plasma ion energy distributions and ion temperature. Research was done on the theory behind Gridded Energy Analyzers and their applicability for use in the Versatile Toroidal Facility. A design and method for constructing a miniaturized GEA for VTF was developed and documented. The construction method covers material selection, machining, and assembly of VTF's miniature GEA. The miniature GEA is a non-perturbing probe used in VTF's plasma, which is approximately 3 cm in diameter. The GEA was constructed and preliminary experimental data was obtained. From this data VTF's ion temperature was found to be approximately 8eV and an ion distribution function was determined to be roughly Maxwellian in nature.by Shaun L. Meredith.S.M

Factors Associated with HIV Infection and Condom Use in the Armed Forces of the Democratic Republic of the Congo

Background: HIV infection has been shown to be high among military personnel in sub-Saharan Africa. Furthermore, research has shown inconsistent condom use is common in African military populations. In an effort to determine the prevalence of HIV, quantify condom use, and investigate correlates of condom use, a cross-sectional seroprevalence study was implemented in the Armed Forces of the Democratic Republic of the Congo (FARDC). Recent condom use behaviors and correlates of low condom use were also assessed.Methods: From October 2013-April 2014, 2,701 sexually-active FARDC soldiers, aged 19-83, participated in the study. Participants from 30 military sites were administered a survey via personal interview by a trained FARDC counselor. The survey collected information on demographics, military characteristics, and HIV risk behaviors such as condom use.Results: The seroprevalence of HIV was 3.5%. After adjustment, primary risk factors associated with HIV infection included: not being married, multiple regular partners in the past 12 months, screening positive for PTSD, and testing positive for active syphilis infection (p<0.05). After stratification by region, participants in the Eastern region were found to have the highest HIV prevalence at 5.1%. HIV testing frequency was also found to be associated with HIV infection, with participants who reported ≤1 test since joining the military being more than three times more likely to test positive. Furthermore, 85% of male participants reported rarely/never using condoms. Lower condom use was associated with condom accessibility, reduced sexual pleasure, trust issues with condoms, negative attitudes towards condoms, and lower knowledge of HIV prevention and transmission.Conclusions: The HIV prevalence in the FARDC is about three times higher than the general population, indicating a concentrated epidemic. HIV prevention interventions aimed at increasing condom use in the FARDC should address issues of accessibility and trust. The FARDC should consider providing scented condoms and reinforce the importance of correct and consistent condom use. Results suggest that a mental health program focused on PTSD and a syphilis awareness and treatment campaign would be beneficial to the FARDC. Routine HIV testing should also be implemented in the FARDC

Comparative effectiveness of telemedicine strategies on type 2 diabetes management: A systematic review and network meta-analysis

The effects of telemedicine strategies on the management of diabetes is not clear. This study aimed to investigate the impact of different telemedicine strategies on glycaemic control management of type 2 diabetes patients. A search was performed in 6 databases from inception until September 2016 for randomized controlled studies that examined the use of telemedicine in adults with type 2 diabetes. Studies were independently extracted and classified according to the following telemedicine strategies: teleeducation, telemonitoring, telecase-management, telementoring and teleconsultation. Traditional and network meta-analysis were performed to estimate the relative treatment effects. A total of 107 studies involving 20,501 participants were included. Over a median of 6 months follow-up, telemedicine reduced haemoglobin A1c (HbA1c) by a mean of 0.43% (95% CI: −0.64% to −0.21%). Network meta-analysis showed that all telemedicine strategies were effective in reducing HbA1c significantly compared to usual care except for telecase-management and telementoring, with mean difference ranging from 0.37% and 0.71%. Ranking indicated that teleconsultation was the most effective telemedicine strategy, followed by telecase-management plus telemonitoring, and finally teleeducation plus telecase-management. The review indicates that most telemedicine strategies can be useful, either as an adjunct or to replace usual care, leading to clinically meaningful reduction in HbA1c