Urinary Proteomic Shifts over Time and Their Associations with eGFR Decline in Chronic Kidney Disease.

Chronic kidney disease (CKD) is a progressive condition characterized by declining renal function, with limited biomarkers to predict its progression. The early identification of prognostic biomarkers is crucial for improving patient care and therapeutic strategies. This follow-up study investigated urinary proteomics and clinical outcomes in 18 CKD patients (stages 1-3) and 15 healthy controls using liquid chromatography-mass spectrometry and Mascot-SwissProt for protein identification.

Analysis of seroprevalence and risk factors for syphilis and HIV among female sex workers and transgender individuals in different cities of Sindh, Pakistan.

Introduction: Co-infections of syphilis and HIV have been found to exacerbate the impact on sexual and reproductive health, especially among key population groups such as Female Sex Workers (FSWs) and Transgender Individuals (TGs). The data on the prevalence and determinants of syphilis and HIV in Pakistan, particularly in Sindh province, is limited. This prospective cross-sectional study aimed to determine the seroprevalence and risk factors for HIV and syphilis infections among FSWs and TGs in different cities of Sindh, Pakistan.

Prevalence of resistance-associated substitutions (RAS) in hepatitis C virus in the Former Soviet Union countries.

Objective: The emergence of resistance-associated substitutions (RASs) poses a significant challenge to the effective treatment of hepatitis C virus (HCV) infection using direct-acting antivirals. This study's objective was to observe the prevalence of HCV genotypes and RAS within the Former Soviet Union (FSU) countries.

Methods: We analysed 60 NS3, 313 NS5A and 1119 NS5B sequences of HCV deposited in open-access databases from 11 FSU countries for the prevalence of genotypes and the presence of RAS using the Geno2Pheno software.

Comparison of baseline global gene expression profiles of prostate cancer cell lines LNCaP and DU145.

Introduction: DU145 and LNCaP are classic prostate cancer cell lines. Characterizing their baseline transcriptomics profiles (without any intervention) can offer insights into baseline genetic features and oncogenic pathways that should be considered while interpreting findings after various experimental interventions such as exogenous gene transfection or drug treatment.

Methods: LNCaP and DU145 cell lines were cultured under normal conditions, followed by RNA extraction, cDNA conversion, library preparation, and RNA sequencing using the Illumina NovaSeq platform.

Correction: IgG antibodies to SARS-CoV-2 in asymptomatic blood donors at two time points in Karachi.

[This corrects the article DOI: 10.1371/journal.pone.

Candidate protein biomarkers in chronic kidney disease: a proteomics study.

Proteinuria poses a substantial risk for the progression of chronic kidney disease (CKD) and its related complications. Kidneys excrete hundreds of individual proteins, some with a potential impact on CKD progression or as a marker of the disease. However, the available data on specific urinary proteins and their relationship with CKD severity remain limited.

Evaluation of the Training Program to Train HIV Treatment Center Staff in Pakistan.

Introduction In Pakistan, HIV training programs, especially for health professionals working in HIV treatment centers, are limited. Consequently, there is little data about HIV awareness among physicians and allied health workers and how it may affect their care for people living with HIV (PLWH). Recently, the Global Fund to Fight AIDS, Tuberculosis, and Malaria (GFATM) grant Principal Recipient UNDP engaged an NGO experienced in HIV/AIDS training, on a competitive basis, to develop a training manual and conduct training of all categories of HIV treatment centers staff.

Identification of a novel first-generation HIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan.

Unlabelled: The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiency virus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them.

Differential analysis of histopathological and genetic markers of cancer aggressiveness, and survival difference in EBV-positive and EBV-negative prostate carcinoma.

Several studies have shown an association between prostate carcinoma (PCa) and Epstein-Barr virus (EBV); however, none of the studies so far have identified the histopathological and genetic markers of cancer aggressiveness associated with EBV in PCa tissues. In this study, we used previously characterized EBV-PCR-positive (n = 39) and EBV-negative (n = 60) PCa tissues to perform an IHC-based assessment of key histopathological and molecular markers of PCa aggressiveness (EMT markers, AR expression, perineural invasion, and lymphocytic infiltration characterization). Additionally, we investigated the differential expression of key oncogenes, EMT-associated genes, and PCa-specific oncomiRs, in EBV-positive and -negative tissues, using the qPCR array.

Humoral and T cell responses to SARS-CoV-2 reveal insights into immunity during the early pandemic period in Pakistan.

Background: Protection against SARS-CoV-2 is mediated by humoral and T cell responses. Pakistan faced relatively low morbidity and mortality from COVID-19 through the pandemic. To examine the role of prior immunity in the population, we studied IgG antibody response levels, virus neutralizing activity and T cell reactivity to Spike protein in a healthy control group (HG) as compared with COVID-19 cases and individuals from the pre-pandemic period (PP).

Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan.

Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants.

Association of Interferon Lambda 3 and 4 Gene SNPs and Their Expression with COVID-19 Disease Severity: A Cross-Sectional Study.

Introduction: Expression and certain SNPs of interferon lambda 3 and 4 (IFNL3 and 4) have been associated with variable outcomes in COVID-19 patients in different regions, suggesting population-specific differences in the disease outcome. This study examined the association of INFL3 and INFL4 SNPs (rs12979860 and rs368234815, respectively) and nasopharyngeal expression with COVID-19 disease severity in Pakistani patients.

Methods: For this study, 117 retrospectively collected nasopharyngeal swab samples were used from individuals with mild and severe COVID-19 disease.

Genetic and antiretroviral drug resistance mutations analysis of reverse transcriptase and protease gene from Pakistani people living with HIV-1.

Background: Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor.

Origin and evolution of subtype B variants in the former Soviet Union countries.

Contrary to the global trend, between 2010 and 2020, an increase of 43% new HIV infections was recorded in Eastern Europe and Central Asia. Analyses of phylogenetic relationship, and routes and modes of transmission of the HIV-1 subtype B across the former Soviet Union (FSU) region are currently lacking. The objective of this analysis was to investigate the origin and transmission routes of HIV subtype B in FSU countries.

Analysis of differential gene expression of pro-inflammatory cytokines in the nasopharyngeal milieu of mild & severe COVID-19 cases.

Introduction: A subset of individuals with COVID-19 can suffer from a severe form of the disease requiring breathing support for respiratory failure and even death due to disease complications. COVID-19 disease severity can be attributed to numerous factors, where several studies have associated changes in the expression of serum pro-inflammatory cytokines with disease severity. However, very few studies have associated the changes in expression of pro-inflammatory changes in the nasopharyngeal milieu with disease severity.

Interactions of Apigenin and Safranal with the 5HT1A and 5HT2A Receptors and Behavioral Effects in Depression and Anxiety: A Molecular Docking, Lipid-Mediated Molecular Dynamics, and In Vivo Analysis.

Background: The current study utilizes in silico molecular docking/molecular dynamics to evaluate the binding affinity of apigenin and safranal with 5HT1AR/5HT2AR, followed by assessment of in vivo effects of these compounds on depressive and anxious behavior.

Methods: The docking between apigenin and safranal and the 5HT1A and 5HT2A receptors was performed utilizing AutoDock Vina software, while MD and protein-lipid molecular dynamics simulations were executed by AMBER16 software. For in vivo analysis, healthy control (HC), disease control (DC), fluoxetine-, and apigenin-safranal-treated rats were tested for changes in depression and anxiety using the forced swim test (FST) and the elevated plus-maze test (EPMT), respectively.

Molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase.

It is of an interest to document the molecular docking analysis of fluoroquinolones and other natural and synthetic compounds with the HCV NS3 helicase. Data shows that three fluoroquinolones interacted with the NS3 helicase in the catalytic region, targeting some of the amino acids known to play a crucial role in NS3 helicase activity. Similarly, binding energy shows that the fluoroquinolones were comparable to the thiazolpiperazinyl derivatives, while superior to several of the synthetic and natural derivatives.

Phylogenetic Characterization of HIV-1 Sub-Subtype A1 in Karachi, Pakistan.

(1) Background: HIV-1 sub-subtype A1 is common in parts of Africa, Russia, former Soviet Union countries, and Eastern Europe. In Pakistan, sub-subtype A1 is the predominant HIV-1 subtype. Preliminary evidence suggests that distinct strains of HIV-1 sub-subtype A1 are circulating in Pakistan; however, an in-depth molecular phylogenetic characterization of HIV-1 sub-subtype A1 strains in Pakistan have not been presented.

Analysis of the Antimicrobial and Anti-Biofilm Activity of Natural Compounds and Their Analogues against Isolates.

(1) Background: Staphylococcus aureus (S. aureus) is one of the most frequent causes of biofilm-associated infections. With the emergence of antibiotic-resistant, especially methicillin-resistant S.

Biobutanol production from sustainable biomass process of anaerobic ABE fermentation for industrial applications.

The growing population increases the need to develop advanced biological methods for utilizing renewable and sustainable resources to produce environmentally friendly biofuels. Currently, energy resources are limited for global demand and are constantly depleting and creating environmental problems. Some higher chain alcohols, like butanol and ethanol, processing similar properties to gasoline, can be alternate sources of biofuel.

Phylogenetic and drug- and vaccine-resistance profiles of Hepatitis B Virus among children with HIV co-infection in Pakistan.

Introduction: HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection.

CMV and EBV Co-Infection in HIV-Infected Children: Infection Rates and Analysis of Differential Expression of Cytokines in HIV Mono- and HIV-CMV-EBV Co-Infected Groups.

(1) Background: CMV and EBV co-infections can affect the HIV disease progression by modulating the immune system. The disease dynamics can differ in HIV-positive adults and children. In Pakistan, HIV is rapidly expanding, especially in children; however, the prevalence of CMV and EBV co-infection and the effect on immune modulation in HIV-positive children are not known.

IgG antibodies to SARS-CoV-2 in asymptomatic blood donors at two time points in Karachi.

Introduction: An estimated 1.5 million cases were reported in Pakistan until 23 March, 2022. However, SARS-CoV-2 PCR testing capacity has been limited and the incidence of COVID-19 infections is unknown.