Faecal microbial transfer and complex carbohydrates mediate protection against COPD

OBJECTIVE

Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear.

DESIGN

Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation.

RESULTS

FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes.

CONCLUSION

The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.

Uncovering domain motif interactions using high-throughput protein-protein interaction detection methods

Protein-protein interactions (PPIs) are often mediated by short linear motifs (SLiMs) in one protein and domain in another, known as domain-motif interactions (DMIs). During the past decade, SLiMs have been studied to find their role in cellular functions such as post-translational modifications, regulatory processes, protein scaffolding, cell cycle progression, cell adhesion, cell signalling and substrate selection for proteasomal degradation. This review provides a comprehensive overview of the current PPI detection techniques and resources, focusing on their relevance to capturing interactions mediated by SLiMs. We also address the challenges associated with capturing DMIs. Moreover, a case study analysing the BioGrid database as a source of DMI prediction revealed significant known DMI enrichment in different PPI detection methods. Overall, it can be said that current high-throughput PPI detection methods can be a reliable source for predicting DMIs.

Prediction of virus-host interactions and identification of hot spot residues of DENV-2 and SH3 domain interactions

Dengue virus, particularly serotype 2 (DENV-2), poses a significant global health threat, and understanding the molecular basis of its interactions with host cell proteins is imperative for developing targeted therapeutic strategies. This study elucidated the interactions between proline-enriched motifs and Src homology 3 (SH3) domain. The SH3 domain is pivotal in mediating protein-protein interactions, particularly by recognizing and binding to proline-rich regions in partner proteins. Through a computational pipeline, we analyzed the interactions and binding modes of proline-enriched motifs with SH3 domains, identified new potential DENV-2 interactions with the SH3 domain, and revealed potential hot spot residues, underscoring their significance in the viral life cycle. This comprehensive analysis provides crucial insights into the molecular basis of DENV-2 infection, highlighting conserved and serotype-specific interactions. The identified hot spot residues offer potential targets for therapeutic intervention, laying the foundation for developing antiviral strategies against Dengue virus infection. These findings contribute to the broader understanding of viral-host interactions and provide a roadmap for future research on Dengue virus pathogenesis and treatment.

Digital Knowledge Translation Tools for Disseminating Sexual and Reproductive Health Information to Adolescents: Protocol for an Evidence Gap Map Review

BACKGROUND

Digital or eHealth knowledge translation (KT) interventions have been identified as useful public health tools, particularly to advance sexual and reproductive health (SRH) among adolescents. Existing literature reviews on digital health interventions for adolescents' SRH demonstrate limitations, including shortcomings in reporting and comprehensiveness that limit the utility and trustworthiness of findings. However, there is a lack of evidence synthesis on the effectiveness of available digital or mobile health KT tools to promote SRH interventions for adolescents.

OBJECTIVE

We aim to identify, map, and describe existing empirical evidence on the digital KT tools developed to improve adolescent SRH outcomes globally.

METHODS

This study will be conducted using an evidence gap map (EGM) approach to address the objectives, including reviewing relevant literature and a landscape analysis of the outcomes of interest. The following electronic databases will be searched for retrieval of literature: MEDLINE (1946-present), Embase (1974-present), and Global Health (1910-present) via OVID; CINAHL (1936-present) via EBSCOhost; Scopus (1976-present); and Cochrane Library (1993-present) via Wiley. We will include only those studies that focused on adolescents aged 10-19 years and addressed SRH outcomes. We will include experimental studies (randomized or cluster randomized and nonrandomized controlled trials, including quasi-randomized, controlled before-after, and interruptive time series) and observational studies, that is, including prospective cohort and case-control studies. The experimental and observational studies will only be included in the presence of control or comparison arms. Studies with a historical control arm will be excluded. The systematic review software, Covidence (Ventas Health Innovation), will be used to screen and select the studies. Further, 2 independent reviewers will complete the first and second levels of screening of studies and any conflicts arising will be resolved by consensus between the 2 reviewers or by involving the third reviewer. We will conduct the quality assessment of all included studies using the Risk of Bias tool for randomized controlled trials and nonrandomized controlled trials, and AMSTAR2 for systematic reviews.

RESULTS

Papers screening, data extraction, and synthesis will be completed by March 2024. We will use EPPI-Mapper (The International Public Policy Observatory) software to generate an online evidence map and to produce the tables and figures for the descriptive report. This EGM review will identify areas with high-quality, evidence-based digital KT tools (for immediate scale and spread) and areas where few or no KT tools exist (for targeted KT tool development and research or policy prioritization).

CONCLUSIONS

This protocol focused on mapping eHealth KT tools that have been used in the literature to address SRH among adolescents. This will be the first EGM exercise to map digital KT tools to promote adolescents' SRH and will incorporate a range of published sources.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

DERR1-10.2196/55081.

Prediction of motif-mediated viral mimicry through the integration of host-pathogen interactions

One of the mechanisms viruses use in hijacking host cellular machinery is mimicking Short Linear Motifs (SLiMs) in host proteins to maintain their life cycle inside host cells. In the face of the escalating volume of virus-host protein-protein interactions (vhPPIs) documented in databases; the accurate prediction of molecular mimicry remains a formidable challenge due to the inherent degeneracy of SLiMs. Consequently, there is a pressing need for computational methodologies to predict new instances of viral mimicry. Our present study introduces a DMI-de-novo pipeline, revealing that vhPPIs catalogued in the VirHostNet3.0 database effectively capture domain-motif interactions (DMIs). Notably, both affinity purification coupled mass spectrometry and yeast two-hybrid assays emerged as good approaches for delineating DMIs. Furthermore, we have identified new vhPPIs mediated by SLiMs across different viruses. Importantly, the de-novo prediction strategy facilitated the recognition of several potential mimicry candidates implicated in the subversion of host cellular proteins. The insights gleaned from this research not only enhance our comprehension of the mechanisms by which viruses co-opt host cellular machinery but also pave the way for the development of novel therapeutic interventions.

Bioinformatics prediction and screening of viral mimicry candidates through integrating known and predicted DMI data

Domain-motif interactions (DMIs) represent transient bonds formed when a Short Linear Motif (SLiM) engages a globular domain via a compact contact interface. Understanding the mechanics of DMIs is critical for maintaining diverse regulatory processes and deciphering how various viruses hijack host cellular machinery. However, identifying DMIs through traditional in vitro and in vivo experiments is challenging due to their degenerate nature and small contact areas. Predictions often carry a high rate of false positives, necessitating rigorous in-silico validation before embarking on experimental work. This study assessed the binding energy changes in predicted SLiM instances through in-silico peptide exchange experiment, elucidating how they interact with known 3D DMI complexes. We identified a subset of potential mimicry candidates that exhibited effective binding affinities with native DMI structures, suggesting their potential to be true mimicry candidates. The identified viral SLiMs can be potential targets in developing therapeutics, opening new opportunities for innovative treatments that can be finely tuned to address the complex molecular underpinnings of various diseases. To gain a comprehensive understanding of identified DMIs, it is imperative to conduct further validation through experimental approaches.

TLR7 promotes smoke-induced experimental lung damage through the activity of mast cell tryptase

Toll-like receptor 7 (TLR7) is known for eliciting immunity against single-stranded RNA viruses, and is increased in both human and cigarette smoke (CS)-induced, experimental chronic obstructive pulmonary disease (COPD). Here we show that the severity of CS-induced emphysema and COPD is reduced in TLR7-deficient mice, while inhalation of imiquimod, a TLR7-agonist, induces emphysema without CS exposure. This imiquimod-induced emphysema is reduced in mice deficient in mast cell protease-6, or when wild-type mice are treated with the mast cell stabilizer, cromolyn. Furthermore, therapeutic treatment with anti-TLR7 monoclonal antibody suppresses CS-induced emphysema, experimental COPD and accumulation of pulmonary mast cells in mice. Lastly, TLR7 mRNA is increased in pre-existing datasets from patients with COPD, while TLR7+ mast cells are increased in COPD lungs and associated with severity of COPD. Our results thus support roles for TLR7 in mediating emphysema and COPD through mast cell activity, and may implicate TLR7 as a potential therapeutic target.

How different viruses perturb host cellular machinery via short linear motifs

The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.

CRISPR single base-editing: in silico predictions to variant clonal cell lines

Engineering single base edits using CRISPR technology including specific deaminases and single-guide RNA (sgRNA) is a rapidly evolving field. Different types of base edits can be constructed, with cytidine base editors (CBEs) facilitating transition of C-to-T variants, adenine base editors (ABEs) enabling transition of A-to-G variants, C-to-G transversion base editors (CGBEs) and recently adenine transversion editors (AYBE) that create A-to-C and A-to-T variants. The base-editing machine learning algorithm BE-Hive predicts which sgRNA and base editor combinations have the strongest likelihood of achieving desired base edits. We have used BE-Hive and TP53 mutation data from The Cancer Genome Atlas (TCGA) ovarian cancer cohort to predict which mutations can be engineered, or reverted to wild-type (WT) sequence, using CBEs, ABEs or CGBEs. We have developed and automated a ranking system to assist in selecting optimally designed sgRNA that considers the presence of a suitable protospacer adjacent motif (PAM), the frequency of predicted bystander edits, editing efficiency and target base change. We have generated single constructs containing ABE or CBE editing machinery, an sgRNA cloning backbone and an enhanced green fluorescent protein tag (EGFP), removing the need for co-transfection of multiple plasmids. We have tested our ranking system and new plasmid constructs to engineer the p53 mutants Y220C, R282W and R248Q into WT p53 cells and shown that these mutants cannot activate four p53 target genes, mimicking the behaviour of endogenous p53 mutations. This field will continue to rapidly progress, requiring new strategies such as we propose to ensure desired base-editing outcomes.

Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation

Introduction

The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss.

Results

RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression.

Discussion

Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.

Digital health education and training for undergraduate and graduate nursing students: a scoping review protocol

OBJECTIVE

The objective of this review is to collate and analyze literature reporting on digital health education and training courses, or other pedagogical interventions, for nursing students at the undergraduate and graduate level to identify gaps and inform the development of future educational interventions.

INTRODUCTION

In this era of technology-driven health care, upskilling and/or reskilling the nursing workforce is urgently needed for nurses to lead the digital health future and improve patient care. While informatics competency frameworks serve to inform nursing education and practice, they do not address the entire digital health spectrum.

INCLUSION CRITERIA

This review will include research studies, theoretical/discussion papers, and reports, as well as gray literature from relevant sources published in the last 10 years. Opinion pieces, editorials, conference proceedings, and papers published in languages other than English will be excluded.

METHODS

The JBI methodology for scoping reviews will be followed. Searches will be conducted in Embase, CINAHL, ERIC, MEDLINE, Scopus, and Education Research Complete to retrieve potentially relevant studies. Hand searches of reference lists of included studies will be completed. Two reviewers will independently screen records against predefined eligibility criteria and consult a third reviewer if conflicts arise. Decisions will be documented using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) flow diagram. Quantitative data will be analyzed using descriptive statistics. Content analysis will be applied to qualitative data to identify categories and themes. Findings will be synthesized and reported in tables and narrative format.

SCOPING REVIEW REGISTRATION

Open Science Framework osf.io/42eug.

RIPK1 kinase-dependent inflammation and cell death contribute to the pathogenesis of COPD

RATIONALE

Receptor-interacting protein kinase 1 (RIPK1) is a key mediator of regulated cell death (including apoptosis and necroptosis) and inflammation, both drivers of chronic obstructive pulmonary disease (COPD) pathogenesis.

OBJECTIVE

We aimed to define the contribution of RIPK1 kinase-dependent cell death and inflammation in the pathogenesis of COPD.

METHODS

We assessed RIPK1 expression in single-cell RNA-sequencing data from human and mouse lungs and validated RIPK1 levels in lung tissue of COPD patients via immunohistochemistry. Next, we assessed the consequences of genetic and pharmacological inhibition of RIPK1 kinase activity in experimental COPD, using Ripk1^{S25D /S25D} kinase deficient mice and the RIPK1 kinase inhibitor GSK'547.

MEASUREMENTS AND MAIN RESULTS

RIPK1 expression increased in alveolar type I (AT1), AT2, ciliated and neuroendocrine cells in human COPD. RIPK1 protein levels were significantly increased in airway epithelium of COPD patients, compared to never smokers and smokers without airflow limitation. In mice, exposure to cigarette smoke (CS) increased Ripk1 expression similarly in AT2 cells, and further in alveolar macrophages and T cells. Genetic and/or pharmacological inhibition of RIPK1 kinase activity significantly attenuated airway inflammation upon acute and subacute CS-exposure, as well as airway remodeling, emphysema and apoptotic and necroptotic cell death upon chronic CS-exposure. Similarly, pharmacological RIPK1 kinase inhibition significantly attenuated elastase-induced emphysema and lung function decline. Finally, RNA-sequencing on lung tissue of CS-exposed mice revealed downregulation of cell death and inflammatory pathways upon pharmacological RIPK1 kinase inhibition.

CONCLUSIONS

RIPK1 kinase inhibition is protective in experimental models of COPD and may represent a novel promising therapeutic approach.

Rapid separation of bacteria from primary nasal samples using inertial microfluidics

Microbial populations play a crucial role in human health and the development of many diseases. These diseases often arise from the explosive proliferation of opportunistic bacteria, such as those in the nasal cavity. Recently, there have been increases in the prevalence of these opportunistic pathogens displaying antibiotic resistance. Thus, the study of the nasal microbiota and its bacterial diversity is critical in understanding pathogenesis and developing microbial-based therapies for well-known and emerging diseases. However, the isolation and analysis of these populations for clinical study complicates the already challenging task of identifying and profiling potentially harmful bacteria. Existing methods are limited by low sample throughput, expensive labeling, and low recovery of bacteria with ineffective removal of cells and debris. In this study, we propose a novel microfluidic channel with a zigzag configuration for enhanced isolation and detection of bacteria from human clinical nasal swabs. This microfluidic zigzag channel separates the bacteria from epithelial cells and debris by size differential focusing. As such, pure bacterial cell fractions devoid of large contaminating debris or epithelial cells are obtained. DNA sequencing performed on the separated bacteria defines the diversity and species present. This novel method of bacterial separation is simple, robust, rapid, and cost-effective and has the potential to be used for the rapid identification of bacterial cell populations from clinical samples.

Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing

Rationale: Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. Objectives: To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. Methods: We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. Measurements and Main Results: Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (TMPRSS2 and CTSB) were increased, and protease inhibitors (serpins) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. Conclusions: COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic interventions suppress SARS-CoV-2 replication and consequent inflammation.

Understanding the sexual and reproductive health needs of immigrant adolescents in Canada: A qualitative study

Background

Literature suggests that immigrant adolescents receive limited sexual and reproductive health (SRH) education and rarely utilize SRH services in Canada. This study sought to explore the SRH information needs of immigrant adolescents in the province of Alberta.

Methods

A qualitative descriptive methodology was undertaken to conduct 21 individual interviews with immigrant adolescents in Alberta.

Results

A total of four themes emerged from the interviews: (1) Barriers to SRH; (2) needs of adolescents regarding SRH; (3) sources of knowledge; and (4) strategies to improve SRH. Our findings document the conflicting needs and preferences between adolescents and their parents regarding access to SRH resources and services.

Discussion

Adolescents often felt unprepared to deal with their SRH issues due to socio-cultural barriers and conflicts with their parents' conservative attitude toward SRH concerns. Structural barriers to accessing SRH resources and services were also reported, including the location and cost of services. As a result, the majority of adolescents relied on digital methods to receive SRH information.

Conclusion

This study highlights that future research and SRH service provider efforts need to remain cognizant of the positionality of immigrant adolescents and explore innovative ways to deliver SRH resources and services that meet their unique needs.

Racism and the mental health of East Asian diasporas in North America: a scoping review

BACKGROUND

The COVID-19 pandemic heightened anti-Asian racism towards East Asian diasporas in North America. Experiences of racism encountered by East Asian communities have been documented to negatively impact their mental health.

METHODS

A scoping review was undertaken following Arksey and O'Malley's (2005) methodology to (a) map the foci of literature on racism and the mental health of East Asian diasporas in North America and (b) identify gaps in the current literature.

RESULTS

A total of 1309 articles were identified in May 2021. Based on the inclusion criteria, 35 records were included. Two distinct mental health foci were found: mental health outcomes and mental healthcare access and utilization. The majority (n = 22) of the articles focused on racism at the interpersonal level. Six articles provided anti-racism solutions at the individual level, such as overcoming biases. Five articles targeted anti-racism solutions from both the individual and institutional levels, while 1 article addressed barriers at the institutional level, such as dismantling sanctioned power hierarchies.

CONCLUSION

The expanding knowledge base on COVID-19-related racial discrimination is reminiscent of previous literature examining the history of anti-Asian racism in North America. Greater attention is needed to navigate impactful anti-racism solutions for East Asian populations' mental health in North America.

SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions

Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiM-Enrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiM-Enrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiM-Enrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiM-Enrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.

In silico analysis of five missense mutations in CYP1B1 gene in Pakistani families affected with primary congenital glaucoma

PURPOSE

The purpose of this study was to characterize the five missense mutations in CYP1B1 gene identified in Pakistani families affected with primary congenital glaucoma (PCG) using various bioinformatics and protein modeling tools.

METHODS

We previously reported four novel missense mutations in CYP1B1 gene segregating in consanguineous Pakistani families. These mutations were identified by direct sequencing of all coding exons, the exon-intron boundaries and the 5' untranslated region of CYP1B1 using genomic DNA from affected and unaffected family members. In order to understand the effect of CYP1B1 mutations on protein structure and function, we used bioinformatics tools to investigate five mutations including four novels (W434R, D374E, L487P and L177R) and one known (E229K) mutation previously reported by our group in four Pakistani PCG-affected families.

RESULTS

In silico analysis of the missense mutations using the computational algorithms SNAP, I-Mutant 2.0 IUPred, PrDOS and PASTA predicted pathogenic effects on stability and function of protein.

CONCLUSION

In silico analysis of identified mutations confirmed their molecular pathogenicity. Similar analysis will be helpful in understanding of the biological role of CYP1B1 and the effect of mutations on the regulatory and enzymatic functions of CYP1B1 that result in PCG.

Determination of substrate specificities against β-glucosidase A (BglA) from Thermotoga maritime: a molecular docking approach

Thermostable enzymes derived from Thermotoga maritima have attracted worldwide interest for their potential industrial applications. Structural analysis and docking studies were preformed on T. maritima β-glucosidase enzyme with cellobiose and pNP-linked substrates. The 3D structure of the thermostable β-glucosidase was downloaded from the Protein Data Bank database. Substrates were downloaded from the PubCehm database and were minimized using MOE software. Docking of BglA and substrates was carried out using MOE software. After analyzing docked enzyme/substrate complexes, it was found that Glu residues were mainly involved in the reaction, and other important residues such as Asn, Ser, Tyr, Trp, and His were involved in hydrogen bonding with pNP-linked substrates. By determining the substrate recognition pattern, a more suitable β-glucosidase enzyme could be developed, enhancing its industrial potential.

Missense mutation in SLC4A11 in two Pakistani families affected with congenital hereditary endothelial dystrophy (CHED2)

BACKGROUND

Autosomal recessive congenital hereditary endothelial dystrophy (CHED2) is a recessively inherited eye disorder that is more common in consanguineous populations.

METHODS

Two families affected with CHED2 were recruited from the Punjab province of Pakistan to identify the underlying genetic defect. Blood samples from both the families, designated as CH01 and CH02, were collected. Genomic DNA was isolated. Initially, linkage analysis using microsatellite markers was carried out to confirm the linkage to the SLC4A11 gene, previously reported to be implicated in the pathology of the disease. Later on, sequencing was carried out to find the pathogenic mutation in the enrolled families. Identified variation was further confirmed by typing 50 ethnically matched normal control samples.

RESULTS

The results of linkage analysis indicated the putative linkage to SLAC4A11 gene, located at the CHED2 locus on chromosome 20p13-p12 in both families. Mutational analysis revealed an unidentified homozygous mutation c.2024A>C (p.E675A) in the affected members of both the families. Haplotype analysis of both the families showed that the affected members carry the same haplotype, thereby indicating a possibility of a common ancestral mutation. Use of bioinformatic tools including PolyPhen and SIFT suggested that a single amino acid change of E to A at position 675 affected the function of the protein.

CONCLUSION

This study reports a newly identified mutation (c.2024A>C) in the SLC4A11 gene segregating with the diseased haplotype in two consanguineous Pakistani families.

Medicinal plants against hepatitis C virus

Hepatitis C virus (HCV) is a global health concern which is responsible for most of the liver diseases. Currently, there is no vaccine available for prevention of HCV infection due to the high degree of strain variation. The current standard of care is a combination of pegylated interferon α with ribavirin and boceprevir/telaprevir. This treatment was partially effective and had significant side effects. Hence, there is a need to develop new antiviral agents that interfere with different stages of the HCV life cycle. Recent advances in the understanding of both the cellular and molecular mechanisms of HCV replication have provided the basis for novel therapeutic strategies. Several hundred plant species and their phyto-constituents have been isolated for screening against HCV, and some have been shown to have great medicinal value in preventing and/or ameliorating viral diseases in pre-clinical and clinical trials. This review summarizes medicinal plants and their phytochemicals which inhibit different stages of HCV life cycle and discuss their potential use in HCV therapy.

Computer Aided Screening of Phytochemicals from Garcinia against the Dengue NS2B/NS3 Protease

Dengue virus NS2/NS3 protease because of its ability to cleave viral proteins is considered as an attractive target to screen antiviral agents. Medicinal plants contain a variety of phytochemicals that can be used as drug against different diseases and infections. Therefore, this study was designed to uncover possible phytochemical of different classes (Aromatic, Carbohydrates, Lignin, Saponins, Steroids, Tannins, Terpenoids, Xanthones) that could be used as inhibitors against the NS2B/NS3 protease of DENV. With the help of molecular docking, Garcinia phytochemicals found to be bound deeply inside the active site of DENV NS2B/NS3 protease among all tested phytochemicals and had interactions with catalytic triad (His51, Asp75, Ser135). Thus, it can be concluded from the study that these Gracinia phytochemicals could serve as important inhibitors to inhibit the viral replication inside the host cell. Further in-vitro investigations require confirming their efficacy.

Molecular screening of phytochemicals from Amelanchier Alnifolia against HCV NS3 protease/helicase using computational docking techniques

Hepatitis C is serious health concern worldwide caused by HCV. It causes liver cirrhosis and hepato-cellular carcinoma. Development of prevention solutions is under progress. Meanwhile, the treatment of the viral disease using compounds isolated from natural medicinal plants is promising. The traditional use of photo-chemicals from medicinal plants like Amelanchier alnifolia for viral treatment is hopeful. Therefore, it is of interest to screen for flavonoids from Amelanchier alnifolia against protein targets of HCV. Hence, we assessed the binding of flavonoids to HCV NS3/4A protease and helicase proteins. Results show that Quercitin 3- galactoside and 3-glucosideshowed good binding score with protease and helicase respectively. Their interaction/binding sites are documented in this report. This data provide insights for the consideration of flavonoids as potential inhibitors of HCV/NS3/4A protease and helicase.

Global consensus sequence development and analysis of dengue NS3 conserved domains

The dengue virus (DENV) genome encodes 10 different genes including the NS3 gene, which has a protease and helicase domain used in virus replication. This domain is a potential target for antiviral agents against dengue. Due to a high mutation rate, DENV is classified into four major serotypes (DENV1–DENV4). This study was designed to perform conservancy analysis of all four serotypes by drawing a consensus sequence for each serotype and then drawing a global consensus sequence to study conserved residues in all four serotypes. A total of 127 NS3 sequences belonging to all four serotypes were retrieved and aligned using multiple alignment feature of CLC Workbench and were subjected to phylogenetic tree construction. Conservancy analysis of NS3 revealed conserved peptides with active site residues that can be important in developing antiviral agents against dengue virus. Among conserved residues, residues G142, Ser144, and G145 (catalytic pocket residues), A219, D220, and D221 (divalent cations binding residues), and His56, Asp79, Ser144, 146 were highly conserved among all the serotypes. Residues from L138 to L149 and from L226 to L245 were also considerably conserved in all serotypes, while lysine141 mutated to serine in serotype 3. A total of 14 peptides from the conserved regions of DENV NS3 protein were identified, which may be helpful to develop peptide inhibitors. The DENV NS3 phylogenetic tree showed the evolutionary relationship among all four serotypes, and all serotypes of dengue were found to have evolved from the dengue 4 serotype. Because of its high variability, DENV has become a global health concern. It is important to study residues that are present in protease, helicase, the catalytic pocket Mg²⁺ binding site, and the AAA domain. This study revealed peptides with active site residues that are highly conserved among all four serotypes. These regions of the NS3 sequence may be helpful in developing antiviral agents.

Computer aided screening of Accacia nilotica phytochemicals against HCV NS3/4a

Background: HCV has become a leading cause of liver cirrhosis and hepatocellular carcinoma and is a major health concern worldwide. To date, there is no vaccine available in the market to tackle this disease, therefore there is a strong need to develop antiviral compounds that can target all genotypes of HCV with the same efficiency. Medicinal plants have low cost and are less toxic therefore, extracts of medicinal plants can serve as important antiviral agents against HCV. This study was designed to screen phytochemicals of Accacia nilotica to find a potent drug candidate that can inhibit HCV infection effectively.

Results: Docking of NS3/4A protease and Flavonoids of Accacia nilotica revealed that most of the flavonoids bound deeply with the active site of NS3/4A protease. Compound 01 showed a high ranking on docking score. All other compounds also showed reliable docking scores and had interactions with the binding cavity of NS3/4A protease, suggesting them as a potent drug candidate to block HCV replication.

Conclusion: To recognize binding interactions of Accacia nilotica phytochemicals with NS3/4A protease, molecular docking was performed to find potential inhibitor against NS3/4A protease of HCV. After post docking analysis, important interactions were found between active compounds and active site of NS3/4A protease. It can be concluded from the study that phytochemicals of Accacia nilotica may serve as a potential drug candidate with relatively simple structural changes against HCV NS3/4A protease.

HCV Envelope protein 2 sequence comparison of Pakistani isolate and In-silico prediction of conserved epitopes for vaccine development

BACKGROUND

HCV is causing hundreds of cases yearly in Pakistan and has become a threat for Pakistani population. HCV E2 protein is a transmembrane protein involved in viral attachment and thus can serve as an important target for vaccine development but because of its variability, vaccine development against it has become a challenge. Therefore, this study was designed to isolate the HCV E2 gene from Pakistani HCV infected patients of 3a genotype, to perform In-silico analysis of HCV E2 isolated in Pakistan and to analyze HCV E2 protein sequence in comparison with other E2 proteins belonging to 3a and 1a genotypes to find potential conserved B-cells and T-cell epitopes that can be important in designing novel inhibitory compounds and peptide vaccine against genotype 3a and 1a.

PATIENTS AND METHODS

Patients were selected on the basis of elevated serum ALT and AST levels at least for six months, histological examination, and detection of serum HCV RNA anti-HCV antibodies (3rd generation ELISA). RNA isolation, cDNA synthesis, amplification, cloning and sequencing was performed from 4 patient's serum samples in order to get the HCV E2 sequence. HCV E2 protein of Pakistani origin was analyzed using various bioinformatics tools including sequence and structure tools.

RESULTS

HCV E1 protein modeling was performed with I-TASSER online server and quality of the model was assessed with ramchandran plot and Z-score. A total of 3 B-cell and 3 T-cell epitopes were found to be highly conserved among HCV 3a and 1a genotype.

CONCLUSION

The present study revealed potential conserved B-cell and T-cell epitopes of the HCV E2 protein along with 3D protein modeling. These conserved B-cell and T-cell epitopes can be helpful in developing effective vaccines against HCV and thus limiting threats of HCV infection in Pakistan.

Structural analysis and epitope prediction of HCV E1 protein isolated in Pakistan: an in-silico approach

Background

HCV infection is a major health problem causing acute and chronic hepatitis. HCV E1 protein is a transmembrane protein that is involved in viral attachment and therefore, can serve as an important target for vaccine development. Consequently, this study was designed to analyze the HCV E1 protein sequence isolated in Pakistan to find potential conserved epitopes/antigenic determinants.

Results

HCV E1 protein isolated in Pakistan was analyzed using various bio-informatics and immuno-informatics tools including sequence and structure tools. A total of four antigenic B cell epitopes, 5 MHC class I binding peptides and 5 MHC class II binding peptides were predicted. Best designed epitopes were subjected to conservation analyses with other countries.

Conclusion

The study was conducted to predict antigenic determinants/epitopes of HCV E1 protein of genotype 3a along with the 3D protein modeling. The study revealed potential B-cell and T-cell epitopes that can raise the desired immune response against HCV E1 protein isolated in Pakistan. Conservation analysis can be helpful in developing effective vaccines against HCV and thus limiting threats of HCV infection in Pakistan.

Development of global consensus sequence of HCV glycoproteins involved in viral entry

Background

HCV affects >170 million people worldwide and is a leading cause of liver diseases such as hepatocellular carcinoma. Each year, Pakistan reports hundreds of cases and now it has become a serious health issue. HCV has two transmembrane glycoproteins (E1 and E2) that are involved in virus entry through viral attachment, but because of their hypervariable nature they have become difficult targets for vaccine development.

Methods

A total of 150 protein sequences of E1 and E2 belonging to genotypes 3a and 1a were retrieved from the NCBI protein database and were subjected to conservation and variation analysis using the multiple sequence alignment feature of the CLC workbench. A consensus sequence of each genotype of E1 and E2 was obtained and these consensus sequences were further analyzed to construct a global consensus sequence, which was used to design potentially conserved peptides.

Results

From the sequence conservation analysis, highly conserved residues were identified and were used to design peptides. Only two peptides were found to be conserved in the E1 protein of genotypes 3a and 1a and a total of nine conserved peptides were designed for the HCV E2 protein of those genotypes. These designed peptides could serve as useful targets in developing new inhibitory compounds.

Conclusion

This study was designed to perform conservation and variability analysis of HCV glycoproteins and to find potentially conserved peptides among genotypes 3a and 1a (the most prevalent genotypes in Pakistan) that could serve as useful targets in the development of novel inhibitory compounds, thus reducing the threat of HCV infection in Pakistan.

The effect of opioids and their antagonists on the nocifensive response of Caenorhabditis elegans to noxious thermal stimuli

Opiates modulate nociception in vertebrates. This has also been demonstrated in a number of invertebrate models. Herein, the effect of the opiate morphine and opioid neuropeptides Endomorphin 1 and 2 on the thermal avoidance (Tav) behavior of Caenorhabditis elegans is explored. Adult wild-type C. elegans N2 were collected from NGM plates using M9 buffer and exposed to morphine and endomorphine 1 and 2 in concentrations between 10(-8) and 10(-4) M (2.5 pmol/mg to 25 nmol/mg) for 30 min and tested for Tav. The opioid receptor antagonists Naloxone and CTOP were tested in combination with the drugs. Forty-seven percentage of the morphine exposed worms exhibited a class I response versus 76% of the control group (P < 0.001). Endomorphin 1 and 2 also caused a statistically significant reduction in class I responses, 36 and 39%, respectively. These effects were reversed with Naloxone and CTOP. Thermonocifensive behavior in C. elegans is modulated by opioids.