A5034224412- Immune Cell Function and Interaction
- HIV Research and Treatment
- T-cell and B-cell Immunology
- SARS-CoV-2 and COVID-19 Research
- Drug-Induced Adverse Reactions
- Animal Virus Infections Studies
- Immunotherapy and Immune Responses
- Cytomegalovirus and herpesvirus research
- HIV/AIDS Research and Interventions
- vaccines and immunoinformatics approaches
- Viral gastroenteritis research and epidemiology
- Genomics and Phylogenetic Studies
- HIV/AIDS drug development and treatment
- HIV-related health complications and treatments
- CRISPR and Genetic Engineering
- Diabetes and associated disorders
- Herpesvirus Infections and Treatments
- Helicobacter pylori-related gastroenterology studies
- Monoclonal and Polyclonal Antibodies Research
- Advanced biosensing and bioanalysis techniques
- Cancer Immunotherapy and Biomarkers
- Allergic Rhinitis and Sensitization
- SARS-CoV-2 detection and testing
- Cell Image Analysis Techniques
- Polyomavirus and related diseases
Murdoch University
2015-2023
Genetic variations across the SARS-CoV-2 genome may influence transmissibility of virus and host's anti-viral immune response, in turn affecting frequency variants over time. In this study, we examined adjacent amino acid polymorphisms nucleocapsid (R203K/G204R) that arose on background spike D614G change describe how strains harboring these changes became dominant circulating globally.Deep-sequencing data from public databases clinical samples were analyzed to identify map genetic...
Assessing the location and frequency of HIV integration sites in latently infected cells can potentially inform our understanding how persists during combination antiretroviral therapy. We developed a novel high throughput sequencing method to evaluate cell lines determine whether there was virus replication or clonal expansion these observed as multiple events at same position.We modified previously reported using random DNA shearing PCR allow for robotic processing identify site lines....
We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation genome most open reading frames (ORFs) occurs via intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream ORF start codons that TRS-L, is located 5' UTR. TRS-L immediately preceded by leader sequence. This therefore...
Abstract SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result in modest reductions antibody neutralization. subgenomic RNA (sgRNA) is produced by discontinuous transcription of the genome a crucial step life cycle. Applying our tool (periscope) ARTIC Network Oxford Nanopore genomic sequencing data from 4400 positive samples, we show that normalised sgRNA expression profiles significantly increased infections (n=879). This increase seen...
B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions antibody neutralization. Subgenomic RNA (sgRNA) produced by discontinuous transcription of the genome. Applying our tool (periscope) ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 positive samples, we show that normalised sgRNA significantly increased (alpha) infections (n = 879). This increase seen over previous dominant UK, B.1.177 943), which...
Abstract Background Genetic variations across the SARS-CoV-2 genome may influence transmissibility of virus and host’s anti-viral immune response, in turn affecting frequency variants over-time. In this study, we examined adjacent amino acid polymorphisms nucleocapsid (R203K/G204R) that arose on background spike D614G change describe how strains harboring these changes became dominant circulating globally. Methods Deep sequencing data from public databases clinical samples were analyzed to...
Persons with HIV are at increased risk for diabetes mellitus compared individuals without HIV. Adipose tissue is an important regulator of glucose and lipid metabolism, adipose T cells modulate local inflammatory responses and, by extension, adipocyte function. have a high proportion CX3CR1+ GPR56+ CD57+ (C-G-C+) CD4+ in tissue, subset which cytomegalovirus specific, whereas but predominantly CD69+ cells. C-G-C+ cell subsets demonstrate higher receptor clonality the same blood, potentially...
A key to improving cancer immunotherapy will be the identification of tumor-specific "neoantigens" that arise from mutations and augment resultant host immune response. In this study we identified single nucleotide variants (SNVs) by RNA sequencing asbestos-induced murine mesothelioma cell lines AB1 AB1-HA. Using NetMHCpan 2.8 algorithm, theoretical binding affinity predicted peptides arising high-confidence, exonic, non-synonymous SNVs was determined for BALB/c strain. The immunoreactivity...
Objective Helicobacter pylori is the strongest risk factor for gastric cancer; however, majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, two dietary factors linked with cancer iron deficiency high salt. We hypothesised that prolonged adaptation H. to in vivo carcinogenic microenvironments results genetic modification important Design Whole genome sequencing genetically...
Type B adverse drug reactions (ADRs) are iatrogenic immune-mediated syndromes with mechanistic etiologies that remain incompletely understood. Some of the most severe ADRs, including delayed hypersensitivity reactions, T-cell mediated, restricted by specific human leukocyte antigen risk alleles and sometimes public or oligoclonal receptors (TCRs), central to immunopathogenesis tissue-damaging response. However, cellular signatures effector, regulatory, accessory immune populations mediate...
Human immunodeficiency virus (HIV) can adapt to an individual's T cell immune response via genomic mutations that affect antigen recognition and impact disease outcome. These viral adaptations are specific the host's human leucocyte (HLA) alleles, as these molecules determine which peptides presented cells. As HLA highly polymorphic at population level, horizontal transmission events most commonly between HLA-mismatched donor/recipient pairs, representing new selection environments for...
Neoantigens present unique and specific targets for personalized cancer immunotherapy strategies. Given the low mutational burden yet responsiveness of malignant mesothelioma (MM) when compared to other carcinogen-induced malignancies, identifying candidate neoantigens T cells that recognize them has been a challenge. We used pleural effusions gain access MM tumor as well immune in order characterize tumor-immune interface MM. characterized landscape potential from SNVs identified 27...
Background Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as dominant allele. In this study, we have utilised standard and next-generation sequencing techniques investigate EBNA-1...
Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. adaptation in the Mongolian gerbil model. This model is particular interest because -infected gerbils develop a high level inflammation often adenocarcinoma or ulceration. We whole genome sequences strains cultured from experimentally infected gerbils, comparison sequence input strain. The mean annualized single nucleotide...
Human cytomegalovirus (HCMV) is a beta-herpesvirus carried by ~80% of adults worldwide. Acute infections are often asymptomatic in healthy individuals but generate diverse syndromes neonates, renal transplant recipients (RTR), and people with HIV (PWH). The HCMV gene UL111a encodes homolog human interleukin-10 (IL-10) that interacts the IL-10 receptor. Deep sequencing technologies were used to sequence directly from 59 clinical samples Indonesian PWH Australian RTR, adults, neonates....
Loss of T cell immunogenicity due to mutations in virally encoded epitopes is a well-described adaptation strategy limit host anti-viral immunity. Another described, but less understood, involves the selection within that retain immune recognition, suggesting benefit for virus despite continued pressure (termed non-classical adaptation). To understand this strategy, we utilized single transcriptomic approach identify features HIV-specific CD8 + responses targeting non-adapted (NAE) and...
Adaptation to human leukocyte antigen (HLA)-associated immune pressure represents a major driver of immunodeficiency virus (HIV) evolution at both the individual and population level. To date, there has been limited exploration impact initial cellular response in driving viral adaptation, dynamics these changes during infection their effect on circulating transmitting viruses Capturing detailed virological immunological data from acute early HIV is challenging as this commonly precedes...
Abstract We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation genome most open reading frames (ORFs) occurs via intermediates termed “sub-genomic RNAs”. sgRNAs are produced through discontinuous transcription which relies on homology between regulatory sequences (TRS-B) upstream ORF start codons that TRS-L is located 5’ UTR. immediately preceded by leader sequence. This therefore found at end...
Cellular immune responses to Gag correlate with improved HIV viral control. The full extent of cellular comprise both the number epitopes recognized by CD4+ and CD8+ T cells, as well diversity cell receptor (TCR) repertoire directed against each epitope. optimal responsive TCR is unclear. Therefore, we evaluated cells responding HIV-1 determine if correlates clinical or virologic metrics. Previous studies repertoires have been limited primarily a small well-characterized restricted specific...