AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators

Protein families evolve functional variation by accumulating point mutations at functionally important amino acid positions. Homologs in the LacI/GalR family of transcription regulators have evolved to bind diverse DNA sequences and allosteric regulatory molecules. In addition to playing key roles in bacterial metabolism, these proteins have been widely used as a model family for benchmarking structural and functional prediction algorithms. We have collected manually curated sequence alignments for >ﾠ3000 sequences, in vivo phenotypic and biochemical data for >ﾠ5750 LacI/GalR mutational variants, and noncovalent residue contact networks for 65 LacI/GalR homolog structures. Using this rich data resource, we compared the noncovalent residue contact networks of the LacI/GalR subfamilies to design and experimentally validate an allosteric mutant of a synthetic LacI/GalR repressor for use in biotechnology. The AlloRep database (freely available at www.AlloRep.org) is a key resource for future evolutionary studies of LacI/GalR homologs and for benchmarking computational predictions of functional change

Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, "AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators" (Sousa et al., 2016) [1]

Vasectomy by ligation and excision, with or without fascial interposition: a randomized controlled trial [ISRCTN77781689]

BACKGROUND: Randomized controlled trials comparing different vasectomy occlusion techniques are lacking. Thus, this multicenter randomized trial was conducted to compare the probability of the success of ligation and excision vasectomy with, versus without, fascial interposition (i.e. placing a layer of the vas sheath between two cut ends of the vas). METHODS: The trial was conducted between December 1999 and June 2002 with a single planned interim analysis. Men requesting vasectomies at eight outpatient clinics in seven countries in North America, Latin America, and Asia were included in the study. The men were randomized to receive vasectomy with versus without fascial interposition. All surgeons performed the vasectomies using the no-scalpel approach to the vas. Participants had a semen analysis two weeks after vasectomy and then every four weeks up to 34 weeks. The primary outcome measure was time to azoospermia. Additional outcome measures were time to severe oligozoospermia (<100 000 sperm/mL) and vasectomy failure based on semen analyses. RESULTS: We halted recruitment after the planned interim analysis, when 841 men had been enrolled. Fascial interposition decreased time to azoospermia (hazard ratio [HR], 1.35; P < 0.0001) and time to severe oligozoospermia (HR, 1.32; P < 0.0001) and reduced failures based on semen analysis by about half, from 12.7% (95% confidence interval [CI], 9.7 to 16.3) to 5.9% (95% CI, 3.8 to 8.6) (P < 0.0001). Older men benefited less from fascial interposition than younger men in terms of the speed of achieving azoospermia. However, the number of vasectomy failures was reduced to a similar degree in all age groups. Slightly more adverse events occurred in the fascial interposition group, but the difference was not significant. These failure rates may appear high to practitioners in countries such as the USA, but they are similar to results from other careful studies of ligation and excision techniques. CONCLUSION: Fascial interposition significantly improves vasectomy success when ligation and excision is the method of vas occlusion. A limitation of this study is that the correlation between postvasectomy sperm concentrations and risk of pregnancy is not well quantified

Potential Cost-Effectiveness of Universal Access to Modern Contraceptives in Uganda

<div><h3>Background</h3><p>Over two thirds of women who need contraception in Uganda lack access to modern effective methods. This study was conducted to estimate the potential cost-effectiveness of achieving universal access to modern contraceptives in Uganda by implementing a hypothetical new contraceptive program (NCP) from both societal and governmental (Ministry of Health (MoH)) perspectives.</p> <h3>Methodology/Principal Findings</h3><p>A Markov model was developed to compare the NCP to the status quo or current contraceptive program (CCP). The model followed a hypothetical cohort of 15-year old girls over a lifetime horizon. Data were obtained from the Uganda National Demographic and Health Survey and from published and unpublished sources. Costs, life expectancy, disability-adjusted life expectancy, pregnancies, fertility and incremental cost-effectiveness measured as cost per life-year (LY) gained, cost per disability-adjusted life-year (DALY) averted, cost per pregnancy averted and cost per unit of fertility reduction were calculated. Univariate and probabilistic sensitivity analyses were performed to examine the robustness of results. Mean discounted life expectancy and disability-adjusted life expectancy (DALE) were higher under the NCP vs. CCP (28.74 vs. 28.65 years and 27.38 vs. 27.01 respectively). Mean pregnancies and live births per woman were lower under the NCP (9.51 vs. 7.90 and 6.92 vs. 5.79 respectively). Mean lifetime societal costs per woman were lower for the NCP from the societal perspective ($1,949 vs.$1,987) and the MoH perspective ($636 vs.$685). In the incremental analysis, the NCP dominated the CCP, i.e. it was both less costly and more effective. The results were robust to univariate and probabilistic sensitivity analysis.</p> <h3>Conclusion/Significance</h3><p>Universal access to modern contraceptives in Uganda appears to be highly cost-effective. Increasing contraceptive coverage should be considered among Uganda's public health priorities.</p> </div

Woman-centered research on access to safe abortion services and implications for behavioral change communication interventions: a cross-sectional study of women in Bihar and Jharkhand, India

<p>Abstract</p> <p>Background</p> <p>Unsafe abortion in India leads to significant morbidity and mortality. Abortion has been legal in India since 1971, and the availability of safe abortion services has increased. However, service availability has not led to a significant reduction in unsafe abortion. This study aimed to understand the gap between safe abortion availability and use of services in Bihar and Jharkhand, India by examining accessibility from the perspective of rural, Indian women.</p> <p>Methods</p> <p>Two-stage stratified random sampling was used to identify and enroll 1411 married women of reproductive age in four rural districts in Bihar and Jharkhand, India. Data were collected on women's socio-demographic characteristics; exposure to mass media and other information sources; and abortion-related knowledge, perceptions and practices. Multiple linear regression models were used to explore the association between knowledge and perceptions about abortion.</p> <p>Results</p> <p>Most women were poor, had never attended school, and had limited exposure to mass media. Instead, they relied on community health workers, family and friends for health information. Women who had knowledge about abortion, such as knowing an abortion method, were more likely to perceive that services are available (β = 0.079; p < 0.05) and have positive attitudes toward abortion (β = 0.070; p < 0.05). In addition, women who reported exposure to abortion messages were more likely to have favorable attitudes toward abortion (β = 0.182; p < 0.05).</p> <p>Conclusions</p> <p>Behavior change communication (BCC) interventions, which address negative perceptions by improving community knowledge about abortion and support local availability of safe abortion services, are needed to increase enabling resources for women and improve potential access to services. Implementing BCC interventions is challenging in settings such as Bihar and Jharkhand where women may be difficult to reach directly, but interventions can target individuals in the community to transfer information to the women who need this information most. Interpersonal approaches that engage community leaders and influencers may also counteract negative social norms regarding abortion and associated stigma. Collaborative actions of government, NGOs and private partners should capitalize on this potential power of communities to reduce the impact of unsafe abortion on rural women.</p

Identification of a covert evolutionary pathway between two protein folds

Abstract Although homologous protein sequences are expected to adopt similar structures, some amino acid substitutions can interconvert α-helices and β-sheets. Such fold switching may have occurred over evolutionary history, but supporting evidence has been limited by the: (1) abundance and diversity of sequenced genes, (2) quantity of experimentally determined protein structures, and (3) assumptions underlying the statistical methods used to infer homology. Here, we overcome these barriers by applying multiple statistical methods to a family of ~600,000 bacterial response regulator proteins. We find that their homologous DNA-binding subunits assume divergent structures: helix-turn-helix versus α-helix + β-sheet (winged helix). Phylogenetic analyses, ancestral sequence reconstruction, and AlphaFold2 models indicate that amino acid substitutions facilitated a switch from helix-turn-helix into winged helix. This structural transformation likely expanded DNA-binding specificity. Our approach uncovers an evolutionary pathway between two protein folds and provides a methodology to identify secondary structure switching in other protein families