Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

Selective pressures at the DNA level shape genes into pro les consisting of patterns of rapidly evolving sites and sites withstanding change. These pro les remain detectable even when protein sequences become extensively diverged. It has been hypothesised that these patterns can be used as gene identi ers. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. The problem is that the algorithm produces numerous false positives when highly conserved datasets are aligned. To increase the sensitivity of the algorithm, the evolutionary rate based approach was reimplemented and coupled with a conventional BLOSUM substitution matrix to produce a new implementation called BLOSUM-FIRE. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. Analysis of quality of alignments produced, revealed that the new implementation of the FIRE algorithm performs as well as conventional algorithms. In addition, the Evolutionary rate Database (EvoDB), which is a compilation of evolutionary rate pro les of all the members of the PFAM-A protein domain database has been developed. The EvoDB database can be queried using FIRE to infer protein domain functions. The utility of this algorithm and database was tested by inferring the domain functions of the Hepatitis B X protein. Results show that the BLOSUM-FIRE algorithm was able to accurately identify the domain function of HBx as a trans-activation protein using EvoDB. The biological relevance of these results was not validated and requires further interrogation; however, these proteins share vital roles in viral replication. This study demonstrates the utility of an evolutionary rate based approach and demonstrates that such an approach is robust when coupled with an amino acid substitution matrix yielding results comparable to conventional algorithms. EvoDB is a catalogue of the evolutionary rate pro les and provides the corresponding phylogenetic trees, PFAM-A alignments and annotated accession identi er data. The BLOSUM-FIRE software and user manual including the EvoDB at le database and release notes have been made freely available at www.bioinf.wits.ac.za/software/fire. The BLOSUM-FIRE algorithm and EvoDB database present a tier of information untapped by current databases and tools.A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in ful lment of the requirements of the degree of Master of Science (Medicine)

Programmed cell death as a black queen in microbial communities

Programmed cell death (PCD) in unicellular organisms is in some instances an altruistic trait. When the beneficiaries are clones or close kin, kin selection theory may be used to explain the evolution of the trait, and when the trait evolves in groups of distantly related individuals, group or multilevel selection theory is invoked. In mixed microbial communities, the benefits are also available to unrelated taxa. But the evolutionary ecology of PCD in communities is poorly understood. Few hypotheses have been offered concerning the community role of PCD despite its far-reaching effects. The hypothesis we consider here is that PCD is a black queen. The Black Queen Hypothesis (BQH) outlines how public goods arising from a leaky function are exploited by other taxa in the community. Black Queen (BQ) traits are essential for community survival, but only some members bear the cost of possessing them, while others lose the trait In addition, BQ traits have been defined in terms of adaptive gene loss, and it is unknown whether this has occurred for PCD. Our conclusion is that PCD fulfils the two most important criteria of a BQ (leakiness and costliness), but that more empirical data are needed for assessing the remaining two criteria. In addition, we hold that for viewing PCD as a BQ, the original BQH needs to include social traits. Thus, despite some empirical and conceptual shortcomings, the BQH provides a helpful avenue for investigating PCD in microbial communities

Reproductive health services in KwaZulu Natal, South Africa: A situation analysis study focusing on HIV/AIDS services

This Horizons report examines the readiness of reproductive health services in South Africa, which are primarily geared to women, to deliver HIV and AIDS treatment, care, and prevention services. The goal of the study was to obtain information from a representative sample of provincial health care facilities offering reproductive health services in KwaZulu Natal to meet the growing demand for HIV/AIDS-related services. Ninety-eight hospitals, community health centers, and clinics participated in the situation analysis that identified gaps in service delivery and determined priorities for service integration. Results of the study were presented to a large audience of Department of Health, NGO, and donor agency staff with the hope that this workshop would set a trend for feedback and the use of research for service improvement

Early Adherence to Antiretroviral Medication as a Predictor of Long-Term HIV Virological Suppression: Five-Year Follow Up of an Observational Cohort

OBJECTIVE: Previous studies have demonstrated a cross-sectional relationship between antiretroviral adherence and HIV virological suppression. We assessed the predictive value of baseline adherence in determining long-term virological failure. DESIGN: We assessed baseline adherence via an adherence questionnaire between administered to all consenting patients attending antiretroviral clinics in Khayelitsha township, South Africa, between May 2002 and March 2004. Virological status was ascertained after five years of follow up and multivariate analysis used to model associations of baseline variables and medication adherence with time to viral suppression or failure. RESULTS: Our adherence cohort comprised 207 patients, among whom 72% were female. Median age was 30 years and median CD4 count at initiation was 55 cells/mm(3). We found no statistically significant differences between baseline characteristics and early adherence groups. Multivariate analysis adjusting for baseline CD4 and age found that patients with suboptimal baseline adherence had a hazard ratio of 2.82 (95% CI 1.19-6.66, p = 0.018) for progression to virological failure compared to those whose baseline adherence was considered optimal. CONCLUSIONS: Our longitudinal study provides further confirmation of adherence as a primary determinant of subsequent confirmed virological failure, and serves as a reminder of the importance of initial early investments in adherence counseling and support as an effective way to maximize long-term treatment success

The Situation Analysis Approach to Assessing Family Planning and Reproductive Health Services: A Handbook

Good family planning service delivery emphasizing both access and quality is key to the related goals of satisfying individual needs and achieving programmatic success. Situation Analysis (SA) provides a needed link between the manager and the client he or she is trying to serve. The data marshaled for SA offer a representative picture of how subsystems are working and provide a way to “see” the client’s experience. Situation Analyses assist managers in achieving the broadest management goal—that of efficient administration of a vital health care service while keeping in view the ultimate goal—providing good care for those who seek it. “The Situation Analysis Approach to Assessing Family Planning and Reproductive Health Services” handbook is a tool to help implement SA studies. Some of the sections are more valuable for policymakers and program planners, others for researchers, and still others for field interviewers. The handbook consists of four chapters: The Situation Analysis Study Methodology; Conducting the Study; Instruments and Question-by-Question Guides; and Data Analysis and Reporting

Provision of HIV viral load testing services in Zimbabwe: Secondary data analyses using data from health facilities using the electronic Patient Monitoring System

Introduction Routine viral load (VL) testing among persons living with Human Immunodeficiency Virus (PLHIV) enables earlier detection of sub-optimal antiretroviral therapy (ART) adherence and for appropriate management of treatment failure. Since adoption of this policy by Zimbabwe in 2016, the extent of implementation is unclear. Therefore we set out to determine among PLHIV ever enrolled on ART from 2004-2017 and in ART care for ≥12 months at health facilities providing ART in Zimbabwe: numbers (proportions) with VL testing uptake, VL suppression and subsequently switched to 2nd-line ART following confirmed virologic failure. Materials and methods We used retrospective data from the electronic Patient Monitoring System (ePMS) in which PLHIV on ART are registered at 525 public and 4 private health facilities. Results Among the 392,832 PLHIV in ART care for ≥12 months, 99,721 (25.4%) had an initial VL test done and results available of whom 81,932 (82%) were virally suppressed. Among those with a VL>1000 copies/mL; 6,689 (37.2%) had a follow-up VL test and 4,086 (61%) had unsuppressed VLs of whom only 1,749 (42.8%) were switched to 2nd-line ART. Lower age particularly adolescents (10-19 years) were more likely (ARR 1.34; 95%CI: 1.25-1.44) to have virologic failure. Conclusion: The study findings provide insights to implementation gaps including limitations in VL testing; low identification of high- risk PLHIV in care and lack of prompt utilization of test results. The use of electronic patient-level data has demonstrated its usefulness in assessing the performance of the national VL testing program. By end of 2017 implementation of VL testing was sub-optimal, and virological failure was relatively common, particularly among adolescents. Of concern is evidence of failure to act on VL test results that were received. A quality improvement initiative has been planned in response to these findings and its effect on patient management will be monitored

Multi-antigen Vaccination With Simultaneous Engagement of the OX40 Receptor Delays Malignant Mesothelioma Growth and Increases Survival in Animal Models

Malignant Mesothelioma (MM) is a rare and highly aggressive cancer that develops from mesothelial cells lining the pleura and other internal cavities, and is often associated with asbestos exposure. To date, no effective treatments have been made available for this pathology. Herein, we propose a novel immunotherapeutic approach based on a unique vaccine targeting a series of antigens that we found expressed in different MM tumors, but largely undetectable in normal tissues. This vaccine, that we term p-Tvax, is comprised of a series of immunogenic peptides presented by both MHC-I and -II to generate robust immune responses. The peptides were designed using in silico algorithms that discriminate between highly immunogenic T cell epitopes and other harmful epitopes, such as suppressive regulatory T cell epitopes and autoimmune epitopes. Vaccination of mice with p-Tvax led to antigen-specific immune responses that involved both CD8+ and CD4+ T cells, which exhibited cytolytic activity against MM cells in vitro. In mice carrying MM tumors, p-Tvax increased tumor infiltration of CD4+ T cells. Moreover, combining p-Tvax with an OX40 agonist led to decreased tumor growth and increased survival. Mice treated with this combination immunotherapy displayed higher numbers of tumor-infiltrating CD8+ and CD4+ T cells and reduced T regulatory cells in tumors. Collectively, these data suggest that the combination of p-Tvax with an OX40 agonist could be an effective strategy for MM treatment

Age-Related Expansion of Tim-3 Expressing T Cells in Vertically HIV-1 Infected Children

As perinatally HIV-1-infected children grow into adolescents and young adults, they are increasingly burdened with the long-term consequences of chronic HIV-1 infection, with long-term morbidity due to inadequate immunity. In progressive HIV-1 infection in horizontally infected adults, inflammation, T cell activation, and perturbed T cell differentiation lead to an "immune exhaustion'', with decline in T cell effector functions. T effector cells develop an increased expression of CD57 and loss of CD28, with an increase in co-inhibitory receptors such as PD-1 and Tim-3. Very little is known about HIV-1 induced T cell dysfunction in vertical infection. In two perinatally antiretroviral drug treated HIV-1-infected groups with median ages of 11.2 yr and 18.5 yr, matched for viral load, we found no difference in the proportion of senescent CD28(-)CD57(+)CD8(+) T cells between the groups. However, the frequency of Tim-3(+)CD8(+) and Tim-3(+)CD4(+) exhausted T cells, but not PD-1(+) T cells, was significantly increased in the adolescents with longer duration of infection compared to the children with shorter duration of HIV-1 infection. PD-1(+)CD8(+) T cells were directly associated with T cell immune activation in children. The frequency of Tim-3(+)CD8(+) T cells positively correlated with HIV-1 plasma viral load in the adolescents but not in the children. These data suggest that Tim-3 upregulation was driven by both HIV-1 viral replication and increased age, whereas PD-1 expression is associated with immune activation. These findings also suggest that the Tim-3 immune exhaustion phenotype rather than PD-1 or senescent cells plays an important role in age-related T cell dysfunction in perinatal HIV-1 infection. Targeting Tim-3 may serve as a novel therapeutic approach to improve immune control of virus replication and mitigate age related T cell exhaustion.National Institute of Allergy and Infectious DiseasesNational Institute of Allergy and Infectious Diseases [R56AI083112]National Institutes of Health grant [AI60397]National Institutes of Health gran

Regulatory T Cells Expanded from Hiv-1-Infected Individuals Maintain Phenotype, Tcr Repertoire and Suppressive Capacity

While modulation of regulatory T cell (Treg) function and adoptive Treg transfer are being explored as therapeutic modalities in the context of autoimmune diseases, transplantation and cancer, their role in HIV-1 pathogenesis remains less well defined. Controversy persists regarding their beneficial or detrimental effects in HIV-1 disease, which warrants further detailed exploration. Our objectives were to investigate if functional CD4+ Tregs can be isolated and expanded from HIV-1-infected individuals for experimental or potential future therapeutic use and to determine phenotype and suppressive capacity of expanded Tregs from HIV-1 positive blood and tissue. Tregs and conventional T cell controls were isolated from blood and gut-associated lymphoid tissue of individuals with HIV-1 infection and healthy donors using flow-based cell-sorting. The phenotype of expanded Tregs was assessed by flow-cytometry and quantitative PCR. T-cell receptor ß-chain (TCR-β) repertoire diversity was investigated by deep sequencing. Flow-based T-cell proliferation and chromium release cytotoxicity assays were used to determine Treg suppressive function. Tregs from HIV-1 positive individuals, including infants, were successfully expanded from PBMC and GALT. Expanded Tregs expressed high levels of FOXP3, CTLA4, CD39 and HELIOS and exhibited a highly demethylated TSDR (Treg-specific demethylated region), characteristic of Treg lineage. The TCRß repertoire was maintained following Treg expansion and expanded Tregs remained highly suppressive in vitro. Our data demonstrate that Tregs can be expanded from blood and tissue compartments of HIV-1+ donors with preservation of Treg phenotype, function and TCR repertoire. These results are highly relevant for the investigation of potential future therapeutic use, as currently investigated for other disease states and hold great promise for detailed studies on the role of Tregs in HIV-1 infection.Elizabeth Glaser Pediatric AIDS Foundation (Pediatric HIV Vaccine Program Award MV-00-9-900-1429-0-00)Massachusetts General Hospital. Executive Committee on Research (MGH/ECOR Physician Scientist Development Award)National Institutes of Health (U.S.) (NIH NIAID (KO8 AI074405))National Institutes of Health (U.S.) (NIH NIAID AI074405-03S1)Massachusetts General Hospital (William F. Milton Fund)Harvard University. Center for AIDS Research (CFAR Scholar Award)Massachusetts General Hospital. Center for the Study Inflammatory Bowel Disease (P30DK043351)Harvard University. Center for AIDS Research (NIH funded program (5P30AI060354-09

Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix

BACKGROUND: Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algorithm with an amino acid substitution matrix in a dynamic scoring function. The enigmatic hepatitis B virus X protein was used as a test case for BLOSUM-FIRE and its associated database EvoDB. RESULTS: The evolutionary rate based approach was coupled with a conventional BLOSUM substitution matrix. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. The dynamic scoring function is based on a coupled additive approach that scores aligned sites based on the level of conservation inferred from the ω values. Evaluation of the accuracy of this new implementation, BLOSUM-FIRE, using MAFFT alignment as reference alignments has shown that it is more accurate than its predecessor FIRE. Comparison of the alignment quality with widely used algorithms (MUSCLE, T-COFFEE, and CLUSTAL Omega) revealed that the BLOSUM-FIRE algorithm performs as well as conventional algorithms. Its main strength lies in that it provides greater potential for aligning divergent sequences and addresses the problem of low specificity inherent in the original FIRE algorithm. The utility of this algorithm is demonstrated using the Hepatitis B virus X (HBx) protein, a protein of unknown function, as a test case. CONCLUSION: This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62 amino acid substitution matrix in inferring protein domain function. We demonstrate that such an approach is robust and performs as well as an array of conventional algorithms.This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at [email protected]