Genetics and Genomics Commons^™

Identifying Gene Network Patterns And Associated Cellular Immune Responses In Children With Or Without Nut Allergy, Khui Hung Lee, Anthony Bosco, Michael O'Sullivan, Yong Song, Jessica Metcalfe, Kan Yu, Benjamin J. Mullins, Richard Loh, Guicheng Zhang

Research outputs 2022 to 2026

Background: Although evidence suggests that the immune system plays a key role in the pathophysiology of nut allergy, the precise immunological mechanisms of nut allergy have not been systematically investigated. The aim of the present study was to identify gene network patterns and associated cellular immune responses in children with or without nut allergy. Methods: Transcriptome profiling of whole blood cells was compared between children with and without nut allergy. Three genes were selected to be validated on a larger cohort of samples (n = 86) by reverse transcription-polymerase chain reactions (RT-qPCR). The composition of immune cells was inferred from …

Population-Based Case-Control Study Revealed Metabolomic Biomarkers Of Suboptimal Health Status In Chinese Population—Potential Utility For Innovative Approach By Predictive, Preventive, And Personalized Medicine, Hao Wang, Qiuyue Tian, Jie Zhang, Hongqi Liu, Xiaoyu Zhang, Weijie Cao, Jinxia Zhang, Enoch Odame Anto, Xingang Li, Xueqing Wang, Di Liu, Yulu Zheng, Zheng Guo, Lijuan Wu, Manshu Song, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

Background: Suboptimal health status (SHS) is a subclinical stage of chronic diseases, and the identification of SHS provides an opportunity for the predictive, preventive, and personalized medicine (PPPM) of chronic diseases. Previous studies have reported the associations between metabolic signatures and early signs of chronic diseases. Methods: This study aimed to detect the metabolic biomarkers for the identification of SHS in a case-control study. SHS questionnaire-25 (SHSQ-25) was used in a population-based health survey to measure the SHS levels of participants. The liquid chromatography-mass spectrometry-based untargeted metabolomics analysis was conducted on plasma samples collected from 50 SHS participants and 50 …

Conospermum Undulatum: Insights Into Population Genetics And Pollination Ecology Of A Threatened Species, Nicola Delnevo

Theses: Doctorates and Masters

Fragmentation of natural vegetation is currently one of the largest threats to biodiversity. Within the southwest Australia global biodiversity hotspot, the Swan Coastal Plain was historically cleared for agriculture and forestry and is now experiencing extensive land clearing for urbanisation. The wavy-leaved smokebush Conospermum undulatum is a rare species endemic to the Swan Coastal Plain, and its future persistence is threatened by urban expansion.

Throughout this research, I investigated the pollination ecology of this species and found a specific association between C. undulatum and native bees for pollination. I also demonstrated that C. undulatum has evolved pollen with resistance to …

Heritability Enrichment Of Immunoglobulin G N-Glycosylation Relevant Genes In Specific Tissues, Xingang Li

Theses: Doctorates and Masters

Genome-wide association studies (GWAS) have identified over 60 genetic loci associated with IgG N-glycosylation; however, the causal genes and their abundance in relevant tissues are uncertain. In this study, firstly, I leveraged data from GWAS summary statistics for 8,090 Europeans, and large-scale expression quantitative trait loci (eQTL) data from the genotype-tissue expression of 53 types of tissues (GTEx v7), to derive a linkage disequilibrium score for the specific expression of genes (LDSC-SEG) and conduct a transcriptome-wide association study (TWAS). I identified 55 genes whose predicted levels of expression were significantly associated with IgG Nglycosylation in 14 tissues with regard to …

A Comparative Evaluation Of The Generalised Predictive Ability Of Eight Machine Learning Algorithms Across Ten Clinical Metabolomics Data Sets For Binary Classification, Kevin M. Mendez, Stacey N. Reinke, David I. Broadhurst

Research outputs 2014 to 2021

Introduction:

Metabolomics is increasingly being used in the clinical setting for disease diagnosis, prognosis and risk prediction. Machine learning algorithms are particularly important in the construction of multivariate metabolite prediction. Historically, partial least squares (PLS) regression has been the gold standard for binary classification. Nonlinear machine learning methods such as random forests (RF), kernel support vector machines (SVM) and artificial neural networks (ANN) may be more suited to modelling possible nonlinear metabolite covariance, and thus provide better predictive models.

Objectives:

We hypothesise that for binary classification using metabolomics data, non-linear machine learning methods will provide superior generalised predictive ability when …

Causes And Possible Consequences Of Hybridisation In Angelfishes At Christmas Island, Federico Vitelli

Theses: Doctorates and Masters

The angelfishes (family Pomacanthidae) have the greatest proportion (~30%) of hybridising species, compared to other families of reef fishes, with 26 species implicated in hybridisation. However, very little is known about hybridisation in angelfish, especially in terms of fitness of the hybrids and possible ecological consequences. Hybrids between three species (C. flavissima, C. eibli and C. vroliki) in the genus Centropyge have previously been reported from Christmas island, where these have been observed in heterospecific harems and interbreeding. This provides the unique opportunity to examine the breakdown in assortative mating in marine fishes. The broad aim of this …

Increased Fxyd1 And Pgc-1Α Mrna After Blood Flow-Restricted Running Is Related To Fibre Type-Specific Ampk Signalling And Oxidative Stress In Human Muscle, Danny Christiansen, Robyn M. Murphy, Christos G. Stathis, David Bishop

Research outputs 2014 to 2021

Aim: This study explored the effects of blood flow restriction (BFR) on mRNA responses of PGC-1α (total, 1α1, and 1α4) and Na+,K+-ATPase isoforms (NKA; α1-3, β1-3, and FXYD1) to an interval running session and determined whether these effects were related to increased oxidative stress, hypoxia, and fibre type-specific AMPK and CaMKII signalling, in human skeletal muscle. Methods: In a randomized, crossover fashion, 8 healthy men (26 ± 5 year and 57.4 ± 6.3 mL kg−1 min−1) completed 3 exercise sessions: without (CON) or with blood flow restriction (BFR), or in systemic hypoxia (HYP, ~3250 m). A muscle sample was collected …

Adverse Pregnancy Outcomes And Imbalance In Angiogenic Growth Mediators And Oxidative Stress Biomarkers Is Associated With Advanced Maternal Age Births: A Prospective Cohort Study In Ghana, Enoch Odame Anto, William K. Owiredu, Samuel A. Sakyi, Cornelius A. Turpin, Richard K. Ephraim, Linda A. Fondjo, Christian Obirikorang, Eric Adua, Emmanuel Acheampong

Research outputs 2014 to 2021

Background Advanced maternal age (AMA) has been associated with negative pregnancy outcomes. Oxidative stress (OS) and defective placental dysfunction are contributing factors. This study determined the association between AMA and adverse pregnancy outcomes, OS biomarkers and angiogenic growth mediators (AGMs) in normal pregnancies. Methods This prospective cohort study conducted at the Obstetrics and Gynaecology (O&G) Department of the Komfo Anokye Teaching Hospital (KATH) finally included 175 normal pregnant women comprising, 58 AMA (35–45 years), 55 (30–34 years) and 62 optimal childbearing age (20–29 years). Venous blood samples were collected at 28–32 weeks for soluble fms-like tyrosine kinase-1 (sFlt-1), placental growth …

Manipulating Graded Exercise Test Variables Affects The Validity Of The Lactate Threshold And Vo2peak, Nicholas A. Jamnick, Javier Botella, David B. Pyne, David Bishop

Research outputs 2014 to 2021

Background To determine the validity of the lactate threshold (LT) and maximal oxygen uptake (V_ O2max) determined during graded exercise test (GXT) of different durations and using different LT calculations. Trained male cyclists (n = 17) completed five GXTs of varying stage length (1, 3, 4, 7 and 10 min) to establish the LT, and a series of 30-min constant power bouts to establish the maximal lactate steady state (MLSS). V_ O2 was assessed during each GXT and a subsequent verification exhaustive bout (VEB), and 14 different LTs were calculated from four of the GXTs (3, 4, 7 and 10 …

Identification Of The Cftr C.1666a > G Mutation In Hereditary Inclusion Body Myopathy Using Next-Generation Sequencing Analysis, Yan Lu, Yuwei Da, Yong B. Zhang, Xingang Li, Min Wang, Li Di, Mi Pang, Lin Lei

Research outputs 2014 to 2021

Hereditary inclusion body myopathy (HIBM) is a rare autosomal recessive adult onset muscle disease which affects one to three individuals per million worldwide. This disease is autosomal dominant and occurs in adulthood. Our previous study reported a new subtype of HIBM linked to the susceptibility locus at 7q22.1-31.1. The present study is aimed to identify the candidate gene responsible for the phenotype in HIBM pedigree. After multipoint linkage analysis, we performed targeted capture sequencing on 16 members and whole-exome sequencing (WES) on 5 members. Bioinformatics filtering was performed to prioritize the candidate pathogenic gene variants, which were further genotyped by …

Genome Analysis Of Clostridium Difficile Pcr Ribotype 014 Lineage In Australian Pigs And Humans Reveals A Diverse Genetic Repertoire And Signatures Of Long-Range Interspecies Transmission, Daniel R. Knight, Michael M. Squire, Deirdre A. Collins, Thomas V. Riley

Research outputs 2014 to 2021

Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42 % of human strains showed …

Biodiversity Monitoring Using Environmental Dna: Can It Detect All Fish Species In A Waterbody And Is It Cost Effective For Routine Monitoring?, Lia Smith

Theses: Doctorates and Masters

The challenges associated with environmental monitoring such as the impact on the environment and the financial costs are problems we face when trying to conserve freshwater systems around the world. The need for precise and accurate results that are cost effective is important so that we can achieve our conservation goals.

The overall aim of this study was to explore Next-Generation - metabarcoding for the detection of feral and native freshwater fish species based on the DNA shed by individual organisms into the water column. Cytochrome c oxidase I (COI) primers were developed for this study using DNA from six …

Association Between Igf2bp2 Polymorphisms And Type 2 Diabetes Mellitus: A Case-Control Study And Meta-Analysis, Ping Rao, Hao Wang, Honghong Fang, Qing Gao, Jie Zhang, Manshu Song, Yong Zhou, Youxin Wang, Wei Wang

Research outputs 2014 to 2021

Background:

Genome-wide association studies (GWAS) found that IGF2BP2 rs4402960 and rs1470579 polymorphisms were associated with type 2 diabetes mellitus (T2DM) risk. Many studies have replicated this association, but yielded inconsistent results.

Materials and Methods:

A case-control study consisting of 461 T2DM patients and 434 health controls was conducted to detect the genetic susceptibility of IGF2BP2 in a northern Han Chinese population. A meta-analysis was to evaluate the association more precisely in Asians.

Results:

In the case-control study, the carriers of TT genotype at rs4402960 had a higher T2DM risk than the G carriers (TG + GG) (adjusted …

The Uyghur Population And Genetic Susceptibility To Type 2 Diabetes: Potential Role For Variants In Capn10, Apm1 And Fut6 Genes, Feifei Zhao, Dolikun Mamatyusupu, Youxin Wang, Honghong Fang, Hao Wang, Qing Gao, Hao Dong, Siqi Ge, Xinwei Yu, Jie Zhang, Lijuan Wu, Manshu Song, Wei Wang

Research outputs 2014 to 2021

Genome-wide association studies have successfully identified over 70 loci associated with the risk of type 2 diabetes mellitus (T2DM) in multiple populations of European ancestry. However, the risk attributable to an individual variant is modest and does not yet provide convincing evidence for clinical utility. Association between these established genetic variants and T2DM in general populations is hitherto understudied in the isolated populations, such as the Uyghurs, resident in Hetian, far southern Xinjiang Uyghur Autonomous Region, China. In this case–control study, we genotyped 13 single-nucleotide polymorphisms (SNPs) at 10 genes associated with diabetes in 130 cases with T2DM and 135 …

Gene Flow And Genetic Structure Of The Seagrass Thalassia Hemprichii In The Indo-Australian Archipelago, Udhi Eko Hernawan

Theses: Doctorates and Masters

How genetic variation is distributed across space (genetic structure) and what factors influence the spatial genetic structuring is one of the primary questions in population genetics. The interaction between species biology (e.g. life-history traits) and physical processes operating in the seascape over time, including palaeo-historical events (e.g. sea level fluctuations) and contemporary processes (e.g. ocean currents), have been predicted to influence the extent of gene flow and the spatial genetic structuring in marine organisms. However, the relative contribution of each factor in governing the genetic pattern remains unclear. This study examined the pattern of genetic structure and the factors influencing …

Postmitotic Expression Of Sod1g93a Gene Affects The Identity Of Myogenic Cells And Inhibits Myoblasts Differentiation, M. Martini, G. Dobrowolny, M. Aucello, Antonio Musaro

Research outputs 2014 to 2021

To determine the role of mutant SOD1 gene (SOD1G93A) on muscle cell differentiation, we derived C2C12 muscle cell lines carrying a stably transfected SOD1G93A gene under the control of a myosin light chain (MLC) promoter-enhancer cassette. Expression of MLC/SOD1G93A in C2C12 cells resulted in dramatic inhibition of myoblast differentiation. Transfected SOD1G93A gene expression in postmitotic skeletal myocytes downregulated the expression of relevant markers of committed and differentiated myoblasts such as MyoD, Myogenin, MRF4, and the muscle specific miRNA expression. The inhibitory effects of SOD1G93A gene on myogenic program perturbed Akt/p70 and MAPK signaling pathways which promote differentiation cascade. Of note, …

Erratum To: Hclp46 Increases Smad3 Protein Stability Via Inhibiting Its Ubiquitin-Proteasomal Degradation, Yingying Xing, Qiaoyun Chu, Run Feng, Wei Wang, Lixin Lu

Research outputs 2014 to 2021

No abstract provided.

Delivering Genetic Education And Genetic Counseling For Rare Diseases In Rural Brazil, A.X. Acosta, K Abe-Sandes, R Giugliani, Alan H. Bittles

Research outputs 2013

Brazil is the largest country in Latin America, with an ethnically diverse, Portuguese-speaking and predominantly Roman Catholic population of some 194 million. Universal health care is provided under the Federal Unified Health System (Sistema Único de Saúde) but, as in many other middle and low income countries, access to medical genetics services is limited in rural and remote regions of the country. Since there is no formally recognized Genetic Counseling profession, genetic counseling is provided by physicians, trained either in medical genetics or a related clinical discipline. A comprehensive medical genetics program has been established in Monte Santo, an inland …

Genome Sequence Of Strain Himb30, A Novel Member Of The Marine Gammaproteobacteria, Megan Huggett, Michael Rappe

Research outputs 2012

Strain HIMB30 was isolated from coastal Hawaii seawater by extinction culturing in seawater-based oligotrophic medium. It is a phylogenetically unique member of the class Gammaproteobacteria that is only distantly related to its closest cultured relatives. Here we present the genome sequence of strain HIMB30, including genes for proteorhodopsin-based phototrophy and the Calvin-Benson-Bassham cycle.

Genome Sequence Of Strain Himb624, A Cultured Representative From The Om43 Clade Of Marine Betaproteobacteria, Megan Huggett, Darren Hayakawa, Michael Rappe

Research outputs 2012

Strain HIMB624 is a planktonic marine bacterium within the family Methylophilaceae of the class Betaproteobacteria isolated from coastal seawater of Oahu, Hawaii. This strain is of interest because it is one of few known isolates from an abundant clade of Betaproteobacteria found in cultivation-independent studies of coastal seawater and freshwater environments around the globe, known as OM43. Here we describe some preliminary features of the organism, draft genome sequence and annotation, and comparative genomic analysis with one other sequenced member of this clade (strain HTCC2181). The 1,333,209 bp genome of strain HIMB624 is arranged in a single scaffold containing four …

Genome Sequence Of Strain Himb55, A Novel Marine Gammaproteobacterium Of The Om60/Nor5 Clade, Megan Huggett, Michael Rappe

Research outputs 2012

Strain HIMB55 is a phylogenetically unique member of the OM60/NOR5 clade of the Gammaproteobacteria isolated from coastal seawater of Kaneohe Bay on the northeastern shore of Oahu, Hawaii, by extinction culturing in seawater-based oligotrophic medium. Here we present the genome sequence of strain HIMB55, including genes for bacteriochlorophyll-based phototrophy.

Interleukin 6 And 8 Gene Expression Responses To Resistance Exercise And The Correlation To Muscle Mass, Vivien Massie

Theses : Honours

The post exercise inflammatory response is a key signalling mechanism regulating muscle protein synthesis. The purpose of this research was firstly to determine whether muscle mass in non-strength trained individuals was associated with the inflammatory muscle gene response after a single bout of eccentric muscle loading. Secondly, to determine whether changes in muscle cross-sectional area after a chronic increase in muscle loading (resistance training) is related to the inflammatory gene response to a single bout of muscle loading. Eleven male participants (21.6 ± 4.1 years) volunteered for this study. Each participant completed a preliminary testing session that consisted of two …

Neural Induction And Differentiation Of Stem Cells Using The Developmental Gene Pax7, Vijesh G. Vaghjiani

Theses : Honours

Neurodegenerative disorders are conditions that mainly affect the brain and the central nervous system (CNS). Each disease type is characterised by loss of function which results from death of a particular region. Interestingly enough, most of the time disease pathology is due to loss of specific cell types in the CNS. These pathological conditions have both high economic costs and social implications for society. To treat such conditions, either the lost cells must be replaced or the cells surrounding the damaged tissue must be induced to undergo repair to replace the lost cells. The former looks more achievable whereas the …

The Functional Significance Of Multiple Pax7 Isoforms, Chantel L. Burchill

Theses : Honours

The Pax7 gene is critical for specification of both neurons in the mid-brain and skeletal muscle satellite cells. Several alternate transcripts are transcribed from the single gene. Previous studies have shown that the resultant alternate Pax7 isoforms differ in the structure of their paired domain (a DNA-binding domain that influences target gene selection), yet the functional significance of each isoform for specification of neurogenic and myogenic cell types remains unknown. Although previous studies have identified the presence of multiple alternate Pax7 transcripts in both neurogenic and myogenic cell lines, more research is necessary to understand the functional significance of the …

Is The Ability To Regenerate Damaged Skeletal Muscle Genetically Determined? : Can Allelic Variation In The Gene, Pax7, Explain Observed Differences In Recovery Of Force Following Damage By Eccentric Exercise?, Zoran Groznica

Theses : Honours

High force eccentric muscle actions, during forcibly lengthening contracting muscle, have been found to produce pronounced muscle damage, especially if exercise is unaccustomed. A cascade of events is initiated in order to repair damaged skeletal muscle tissue including degeneration and regeneration processes. For the duration of muscle regeneration, satellite cells are the primary source of new myoblasts in adult muscle. This process requires activation of quiescent mononucleated satellite cells which proliferate, differentiate and fuse together to form fully functional muscle fibres. The satellite cells are specified by the gene, Pax7, during development. Experimental studies of Pax7 null mice that lack …

Genetic Diversity In The Bo'an, Salar, And Dongxiang : Co-Resident Muslim Populations In Gansu Province, P.R. China, Thomas Baric

Theses : Honours

Patterns s of genetic diversity within and between three co-resident Muslim populations from Gansu Provence in the Peoples Republic of China were examined and the results contrasted with historical information. This study of members of the Bo'an, Salar and Dongxiang communities will contribute to a clearer understanding of the origins and migratory patterns of Muslims in PR China, and more generally the effect of population subdivision on gene pool structure and composition. Ten autosomal and live Y-chromosome microsatellite loci were genotyped to determine allele distribution patterns. Subsequently, the D-loop region of mitochondrial DNA was sequenced to complement the autosomal and …

Analysis Of The Population Genetics Of The Han And Hui Of Liaoning Province, Peoples Republic Of China, Michael L. Black

Theses: Doctorates and Masters

Throughout recorded Chinese history, regions of the country populated by persons of non-Han ancestry often fluctuated significantly in population numbers and in their political and commercial influence. However, at all times they were considered as important contributors to the nation. Many of these peoples had moved from their homelands, settled in China and had intermarried with Han Chinese. Over the generations they became accepted as fully-fledged Chinese citizens although, in many instances, they retained their traditional customs and religious practices, and frequently their own language. The Hui Muslims are a good example of this process of integration, and today they …

A Study Of The Effects Of Consanguinity At The Genomic Level In Two Pakistani Bradaris, Sheena Sullivan

Theses : Honours

The purpose of the project was to assess the effects of inbreeding on the genetic constitution of two Pakistani bradaris (literally defined as brotherhoods). Both bradaris contain children born to consanguineous (first cousin) and nonconsanguineous marriages. DNA samples have been supplied by Dr Subaib Ahmed of the Armed Forces Institute of Pathology in Rawalpindi, for a total of 91 individuals. The specific allele frequencies, and levels of homozygosity of each bradari, were determined using twenty fluorescence-labelled microsatellite markers for chromosomes 13 and 15. Amplification of the DNA was performed using the polymerase chain reaction (PCR). The PCR products were separated …

Homozygosity Levels In Consanguineous Populations: A Study Of The Sankethi Community, Karnataka, India, Janet Cahill

Theses : Honours

The project has studied the inheritance of microsatellite alleles across four chromosomes within two multi-generation families from a highly endogamous community, the Sankethi of Karnataka, India. The two families each have members from four generations participating in the study. Finger prick blood samples and detailed pedigree information were collected from subjects in India. DNA was extracted from the blood spot samples using a phenol-chloroform technique, and analysed by spectrophotometry to determine DNA concentrations. Fluorescent markers from chromosomes 15, 16, 17 & 18 were amplified using polymerase chain reaction (PCR) techniques on a Perkin Elmer 96 well thermocycler. The PCR products …

Localisation Of The Gene For A Novel Form Of Charcot-Marie-Tooth Disease In An Isolated Population, Kaite Honeyman

Theses : Honours

Localising the gene for a previously undescribed autosomal recessive form of CMT involved the use of a relatively new approach to rapid genome screening based on the identification of segments which are inherited identical by descent (IBD) from common founding ancestors. It is most feasible for populations which have been founded relatively recently (say less than 25 generations) and which have remained relatively isolated either geographically or culturally. The method is not suitable for highly inbred populations, that is with first and second cousin matings, as many segments will be inherited by chance. It appears to be a suitable screening …