ORCID Profile
0000-0002-3751-3921
Current Organisation
Murdoch University
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Publisher: Springer International Publishing
Date: 2018
DOI: 10.1007/82_2017_48
Abstract: The 'colonic' spirochetes assigned to the genus Brachyspira are slow-growing anaerobic bacteria. The genus includes both pathogenic and non-pathogenic species, and these variously colonise the large intestines of different species of birds and animals, including humans. Scientific understanding of the physiology and molecular biology of Brachyspira spp. remains very limited compared with that of other pathogenic spirochetes, and there are few descriptions of successful genetic manipulations undertaken to investigate gene function. An important boost to knowledge occurred in 2009 when, for the first time, the whole genome sequence of a Brachyspira strain (Brachyspira hyodysenteriae strain WA1) was obtained. The genomics analysis provided a significant increase in knowledge: for ex le, a previously unknown ~36 Kb plasmid was discovered and metabolic pathways were constructed. The study also revealed likely acquisition of genes involved in transport and central metabolic functions from other enteric bacterial species. Four subsequent publications have provided a similarly detailed analysis of other Brachyspira genomes, but of these only two included more than one strain of a species (20 strains of B. hyodysenteriae in one and three strains of B. pilosicoli in the other). Since then, more Brachyspira genomes have been made publicly available, with the sequences of at least one representative of each of the nine officially recognised species deposited at public genome repositories. All species have a single circular chromosome varying in size from ~2.5 to 3.3 Mb, with a C + G content of around 27%. In this chapter, we summarise the current knowledge and present a preliminary comparative genomic analysis conducted on 56 strains covering the official Brachyspira species. Besides providing detailed genetic maps of the bacteria, this analysis has revealed gene island rearrangements, putative phenotypes (including antimicrobial drug resistance) and genetic mutation mechanisms that enable brachyspires to evolve and respond to stress. The application of Next-Generation Sequencing (NGS) to generate genomic data from many more Brachyspira species and strains increasing will improve our understanding of these enigmatic spirochetes.
Publisher: MDPI AG
Date: 13-01-2020
Abstract: The aim of this study was to investigate the occurrence and distribution of Salmonella in commercial layer farming environments of 26 flocks belonging to seven egg businesses (free-range and barn-laid) in Western Australia (WA). Between November 2017 and June 2018, a total of 265 environmental s les of dust, feed, water, pooled feces, and boot swabs were tested for detection of Salmonella according to standard culture-based methods. Isolates were assayed for serovar and subtyped by multilocus sequence typing (MLST). Salmonella spp. were recovered from 35% (93/265) of all tested s les. Dust (53.8%, 28/52) and pooled fecal (54.5%, 18/33) s les provided the highest Salmonella recovery rates. Nine different Salmonella serovars were characterized across the positive (n = 93) environmental s les, of which S. Typhimurium (60/93, 64.5%) and S. Infantis (21/93, 22.5%) were the most prevalent. MLST revealed that all S. Typhimurium isolates were of sequence type ST-19. Microbiological screening of Salmonella was not routinely practiced in any of the surveyed egg businesses. Some of the egg businesses exhibited variable levels of compliance with basic biosecurity measures as well as high-risk egg handling practices. Egg businesses in WA should be encouraged to adopt a voluntary program of environmental s ling and verification testing for Salmonella. Such voluntary programs will aid in supporting solutions for the management of this pathogen in the human food chain.
Publisher: Elsevier BV
Date: 02-2021
Publisher: Springer Science and Business Media LLC
Date: 19-10-2018
DOI: 10.1007/S00122-017-2997-Y
Abstract: An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F
Publisher: Public Library of Science (PLoS)
Date: 18-11-2014
Publisher: Springer Science and Business Media LLC
Date: 17-06-2020
DOI: 10.1038/S41598-020-66619-0
Abstract: The central nervous system regulates the immune system through the secretion of hormones from the pituitary gland and other endocrine organs, while the peripheral nervous system (PNS) communicates with the immune system through local nerve-immune cell interactions, including sympathetic arasympathetic (efferent) and sensory (afferent) innervation to lymphoid tissue/organs. However, the precise mechanisms of this bi-directional crosstalk of the PNS and immune system remain mysterious. To study this kind of bi-directional crosstalk, we performed immunofluorescent staining of neurofilament and confocal microscopy to reveal the distribution of nerve fibers and nerve-immune cell associations inside mouse spleen. Our study demonstrates (i) extensive nerve fibers in all splenic compartments including the splenic nodules, periarteriolar lymphoid sheath, marginal zones, trabeculae, and red pulp (ii) close associations of nerve fibers with blood vessels (including central arteries, marginal sinuses, penicillar arterioles, and splenic sinuses) (iii) close associations of nerve fibers with various subsets of dendritic cells, macrophages (Mac1 + and F4/80 + ), and lymphocytes (B cells, T helper cells, and cytotoxic T cells). Our data concerning the extensive splenic innervation and nerve-immune cell communication will enrich our knowledge of the mechanisms through which the PNS affects the cellular- and humoral-mediated immune responses in healthy and infectious/non-infectious states.
Publisher: IEEE
Date: 12-2013
Publisher: Elsevier BV
Date: 06-2020
Publisher: Springer Science and Business Media LLC
Date: 12-2016
Publisher: IEEE
Date: 2006
Publisher: IEEE
Date: 04-2013
Publisher: Proceedings of the National Academy of Sciences
Date: 12-10-2016
Abstract: Integrative and conjugative elements (ICEs) are one of the most prevalent but least-characterized families of mobile genetic elements in bacteria. We identified a family of ICEs that exists as three separate parts integrated within the single chromosomes of symbiotic mesorhizobia. These “tripartite ICEs,” through a series of chromosomal recombinations mediated by integrase proteins, assemble into a single circular ICE. Following transfer to nonsymbiotic mesorhizobia, tripartite ICEs integrate and disassemble into three parts in the recipient genome and exconjugant mesorhizobia gain the ability to form a symbiosis with legumes. These discoveries expand our appreciation of the potential for gene transfer in bacteria and demonstrate how mobile genetic elements can dramatically manipulate the bacterial genome.
Publisher: Wiley
Date: 09-03-2021
DOI: 10.1111/TPJ.15173
Publisher: IEEE
Date: 2007
Publisher: Springer Science and Business Media LLC
Date: 25-11-2020
DOI: 10.1038/S41586-020-2947-8
Abstract: Genetic ersity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence ersity of a crop species (known as the ‘pan-genome’ 1 ). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley ( Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions 2 . Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley ersity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
Publisher: MDPI AG
Date: 14-07-2020
DOI: 10.3390/ANI10071192
Abstract: Non-typhoidal Salmonella is a major zoonotic pathogen that plays a significant role in foodborne human salmonellosis worldwide through the consumption of contaminated foods, particularly those of animal origin. Despite a considerable reduction in human salmonellosis outbreaks in developed countries, Australia is experiencing a continuous rise of such outbreaks in humans. This review of the literature highlights the reported non-typhoidal Salmonella outbreaks in humans as well as the occurrence of the pathogen in foods from animal sources throughout Australia. Non-typhoidal Salmonella infections from food animals are more often associated with at-risk people, such as immunocompromised and aged people or children. Although several animal-sourced foods were recognised as the catalysts for salmonellosis outbreaks in Australia, egg and egg-based products remained the most implicated foods in the reported outbreaks. This review further highlights the antimicrobial resistance trends of non-typhoidal Salmonella isolates at the human–food interface, with a focus on clinically important antimicrobials in humans, by collating evidence from previous investigations in Australia. The rise in antimicrobial-resistant Salmonella, especially to antimicrobials commonly prescribed to treat human salmonellosis, has become a significant global public health concern. However, the overall prevalence of antimicrobial resistance in Australia is considerably lower than in other parts of the world, particularly in terms of critically important antimicrobials for the treatment of human salmonellosis. The present review adds to our understanding of the global epidemiology of non-typhoidal Salmonella with emphasis on the past few decades in Australia.
Publisher: Oxford University Press (OUP)
Date: 2020
Abstract: Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at 146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: 146.118.64.11/BarleyVar
Publisher: MDPI AG
Date: 03-02-2019
Abstract: Cold treatment at 0.0 °C with different exposure durations (0–12 days) was applied to the Mediterranean fruit fly Ceratitis capitata (Wiedemann) fed on a lab diet. The examined developmental stages were early eggs ( h), late eggs ( h), first instar, second instar and third instar larvae. Pupation, adult emergence and sex ratios of survived flies were investigated to study the C. capitata responses to this low temperature treatment. Our results showed that exposure time at low temperature has a clear effect on pupation and adult emergence. Based on pupation ratios, the first and third instar are the most cold tolerant stages, with LT99 = 7.3 for both of them. Cold tolerance at both stages are very close and no significant differences were detected. There were no significant differences on C. capitata sex ratios among different stages after treatment. This study improves our understanding of C. capitata responses to cold treatment, which may assist in the improvement of the current treatment strategies to control this destructive horticulture pest species.
Publisher: Springer Science and Business Media LLC
Date: 04-2017
DOI: 10.1038/NATURE22043
Abstract: Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Publisher: Springer Science and Business Media LLC
Date: 17-07-2020
Publisher: Wiley
Date: 03-2020
DOI: 10.1111/TPJ.14557
Abstract: Functional ergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional ergence for plant ersity and environmental adaptation.
Publisher: Wiley
Date: 14-02-2017
DOI: 10.1111/VCO.12292
Abstract: Sterile haemorrhagic cystitis (SHC) is a known risk of cyclophosphamide treatment. Diuresis using furosemide is effective in canines when maximally tolerated dosed cyclophosphamide is administered. This retrospective study aimed to determine whether orally administered furosemide decreased the incidence of SHC. Secondary aims were to identify predisposing factors for SHC. One-hundred and fifteen dogs treated with metronomic cyclophosphamide were analysed retrospectively. Populations were not randomized. 25 dogs (21.7%) developed SHC. Furosemide administration significantly reduced the likelihood of SHC development (P = 0.010, where SHC was diagnosed in 30.3% of dogs administered cyclophosphamide without furosemide, and 10.2% of dogs administered cyclophosphamide with furosemide). Age, gender, breed, bodyweight, number of cyclophosphamide treatments, piroxicam use and previous or pre-existing disease were not found to be associated with SHC development. This study demonstrates furosemide is effective in the prevention of SHC and its use may be considered when implementing metronomic cyclophosphamide therapy.
Publisher: IEEE
Date: 05-2013
Publisher: American Society for Microbiology
Date: 26-10-2017
Abstract: We report here the complete genome sequence of Mesorhizobium sophorae ICMP 19535 T . This strain was isolated from Sophora microphylla root nodules and can nodulate and fix nitrogen with this host and also with Sophora prostrata , Sophora longicarinata , and Clianthus puniceus . The genome consists of 8.05 Mb.
Publisher: American Society for Microbiology
Date: 30-06-2016
Abstract: We report the complete genome sequence of Mesorhizobium ciceri bv. biserrulae strain WSM1284, a nitrogen-fixing microsymbiont of the pasture legume Biserrula pelecinus . The genome consists of 6.88 Mb distributed between a single chromosome (6.33 Mb) and a single plasmid (0.55 Mb).
Publisher: MDPI AG
Date: 21-05-2023
DOI: 10.3390/IJMS24109059
Abstract: The quality and maturation of an oocyte not only play decisive roles in fertilization and embryo success, but also have long-term impacts on the later growth and development of the fetus. Female fertility declines with age, reflecting a decline in oocyte quantity. However, the meiosis of oocytes involves a complex and orderly regulatory process whose mechanisms have not yet been fully elucidated. This review therefore mainly focuses on the regulation mechanism of oocyte maturation, including folliculogenesis, oogenesis, and the interactions between granulosa cells and oocytes, plus in vitro technology and nuclear/cytoplasm maturation in oocytes. Additionally, we have reviewed advances made in the single-cell mRNA sequencing technology related to oocyte maturation in order to improve our understanding of the mechanism of oocyte maturation and to provide a theoretical basis for subsequent research into oocyte maturation.
Publisher: Wiley
Date: 16-12-2014
Publisher: SAGE Publications Ltd
Publisher: Springer Science and Business Media LLC
Date: 06-02-2018
DOI: 10.1038/S41598-018-20935-8
Abstract: Wheat ( Triticum aestivum ) quality is mainly determined by grain storage protein compositions. Sulphur availability is essential for the biosynthesis of the main wheat storage proteins. In this study, the impact of different sulphur fertilizer regimes on a range of agronomically important traits and associated gene networks was studied. High-performance liquid chromatography was used to analyse the protein compositions of grains grown under four different sulphur treatments. Results revealed that sulphur supplementation had a significant effect on grain yield, harvest index, and storage protein compositions. Consequently, two comparative sulphur fertilizer treatments (0 and 30 kg ha −1 sulphur, with 50 kg ha −1 nitrogen) at seven days post-anthesis were selected for a transcriptomics analysis to screen for differentially expressed genes (DEGs) involved in the regulation of sulphur metabolic pathways. The International Wheat Genome Sequencing Consortium chromosome survey sequence was used as reference. Higher sulphur supply led to one up-regulated DEG and sixty-three down-regulated DEGs. Gene ontology enrichment showed that four down-regulated DEGs were significantly enriched in nitrogen metabolic pathway related annotation, three of which were annotated as glutamine synthetase. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment identified three significantly enriched pathways involved in nitrogen and amino acid metabolism.
Publisher: No publisher found
Date: 2015
DOI: 10.1038/NCOMMS6882
Abstract: Transcription of the vernalization1 gene (VRN1) is induced by prolonged cold (vernalization) to trigger flowering of cereal crops, such as wheat and barley. VRN1 encodes a MADS box transcription factor that promotes flowering by regulating the expression of other genes. Here we use transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to identify direct targets of VRN1. Over 500 genomic regions were identified as potential VRN1-binding targets by ChIP-seq. VRN1 binds the promoter of flowering locus T-like 1, a promoter of flowering in vernalized plants. VRN1 also targets vernalization2 and ODDSOC2, repressors of flowering that are downregulated in vernalized plants. RNA-seq identified additional VRN1 targets that might play roles in triggering flowering. Other targets of VRN1 include genes that play central roles in low-temperature-induced freezing tolerance, spike architecture and hormone metabolism. This provides evidence for direct regulatory links between the vernalization response pathway and other important traits in cereal crops.
Publisher: Wiley
Date: 14-08-2014
DOI: 10.1111/PCMR.12290
Publisher: Inderscience Publishers
Date: 2010
Publisher: MDPI AG
Date: 27-04-2020
Abstract: Non-typhoidal Salmonella serovars are recognized as zoonotic pathogens. Although human salmonellosis is frequently associated with ingestion of contaminated foods of animal origin, contact with animals may also be a significant source of Salmonella infection, especially contact with turtles, which have shown to be an important reservoir of Salmonella, specifically through their intestinal tracts. Turtles are among the most common reptiles kept as house pets that may pose a public health risk associated with Salmonella exposure, especially among infants and young children. This review discusses the literature reporting the link between turtles and Salmonella as well as turtle-associated human salmonellosis in the last ten years. In most outbreaks, a high proportion of patients are children under five years of age, which indicates that children are at the greatest risk of turtle-associated salmonellosis. Therefore, turtles should not be preferred as recommended pets for children under five years of age. Reducing turtle stress to minimise Salmonella shedding as well as providing client education handouts at the points of sale of these animals may reduce the risk of transmitting such significant pathogen to humans. Further studies are required to investigate the role of both direct contact with turtles as well as indirect contact through cross-contamination in the transmission of turtles-associated Salmonella to humans.
Publisher: American Chemical Society (ACS)
Date: 05-06-2017
DOI: 10.1021/ACS.JPROTEOME.6B00882
Abstract: Tandem mass spectrometry is one of the most popular techniques for quantitation of proteomes. There exists a large variety of options in each stage of data preprocessing that impact the bias and variance of the summarized protein-level values. Using a newly released data set satisfying a replicated Latin squares design, a erse set of performance metrics has been developed and implemented in a web-based application, Quantitative Performance Evaluator for Proteomics (QPEP). QPEP has the flexibility to allow users to apply their own method to preprocess this data set and share the results, allowing direct and straightforward comparison of new methodologies. Application of these new metrics to three case studies highlights that (i) the summarization of peptides to proteins is robust to the choice of peptide summary used, (ii) the differences between iTRAQ labels are stronger than the differences between experimental runs, and (iii) the commercial software ProteinPilot performs equivalently well at between-s le normalization to more complicated methods developed by academics. Importantly, finding (ii) underscores the benefits of using the principles of randomization and blocking to avoid the experimental measurements being confounded by technical factors. Data are available via ProteomeXchange with identifier PXD003608.
Publisher: Springer Science and Business Media LLC
Date: 2013
Publisher: Springer Science and Business Media LLC
Date: 12-05-2015
Publisher: Public Library of Science (PLoS)
Date: 25-07-2017
Publisher: Oxford University Press (OUP)
Date: 29-03-2012
DOI: 10.1093/BIOINFORMATICS/BTS150
Abstract: Motivation: Mass spectrometry-based iTRAQ protein quantification is a high-throughput assay for determining relative protein expressions and identifying disease biomarkers. Processing and analysis of these large and complex data involves a number of distinct components and it is desirable to have a pipeline to efficiently integrate these together. To date, there are limited public available comprehensive analysis pipelines for iTRAQ data and many of these existing pipelines have limited visualization tools and no convenient interfaces with downstream analyses. We have developed a new open source comprehensive iTRAQ analysis pipeline, OCAP, integrating a wavelet-based preprocessing algorithm which provides better peak picking, a new quantification algorithm and a suite of visualizsation tools. OCAP is mainly developed in C++ and is provided as a standalone version (OCAP_standalone) as well as an R package. The R package (OCAP) provides the necessary interfaces with downstream statistical analysis. Availability: OCAP is freely available and can be downloaded at www.maths.usyd.edu.au/u enghao Contact: penghao.wang@sydney.edu.au
Publisher: MDPI AG
Date: 31-10-2023
DOI: 10.3390/V15112198
Publisher: Association for Research in Vision and Ophthalmology (ARVO)
Date: 27-03-2013
Abstract: Müller cells, the principal glial cells in the mammalian retina, play an important role in the maintenance of retinal homeostasis. Recent reports suggest that Müller-cell dysfunction may contribute to the pathogenesis of retinal diseases such as idiopathic macular telangiectasia type 2. In the present study, we used microarray to compare retinae isolated from transgenic mice in which the Müller cells of adult mice retinae can be selectively ablated with control mice. Retinae were isolated 1 week, 1 month, and 3 months after tamoxifen-induced selective Müller-cell ablation and microarray were performed with Affymatrix microarrays. Differentially expressed (DE) genes, temporal trends of DE genes, and pathway analysis were conducted. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate the results. Strong upregulation of mRNA of proteins involved in gliosis, apoptosis, and neurotrophism was found 1 week after ablation and their related pathways such as the apoptotic and Jak/Stat pathways were identified. Three months after induced Müller-cell ablation, Müller-cell metabolic pathways and vasculopathy-related pathways such as genes involved in glycolysis and tight junctions were downregulated. qRT-PCR analysis showed consistent expression trends of selected genes. The results were generally consistent with the previous morphologic findings in this model, in which photoreceptor degeneration soon after Müller-cell ablation, accompanied by blood-retinal barrier breakdown and subsequent retinal neovascularization were reported. These results are consistent with a significant contribution of Müller-cell dysfunction on retinal neuronal injury and vascular pathology at the mRNA level.
Publisher: Canadian Science Publishing
Date: 03-2017
Abstract: Gene loss during the formation of hexaploid bread wheat has been repeatedly reported. However, our knowledge on genome-wide analysis of the genes present on a single subgenome (SSG) in bread wheat is still limited. In this study, by analysing the ‘Chinese Spring’ chromosome arm shotgun sequences together with high-confidence gene models, we detected 433 genes on a SSG. Greater gene loss was observed in A and D subgenomes compared with B subgenome. More than 79% of the orthologs for these SSG genes were detected in diploid and tetraploid relatives of hexaploid wheat. Unexpectedly, no bias in expression breadth or in the distribution patterns of GO (gene ontology) terms for these genes was detected among the high-confidence genes. Further, network and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses indicated that most of these genes were not functionally related to each other. Interestingly, 30.7% of these SSG genes were most highly expressed in root, showing biased distribution given the distribution of the whole high-confidence genes. Collectively, these results facilitate our understanding of the loss of the genes that were retained in a SSG during the formation of hexaploid wheat.
Publisher: IEEE
Date: 2006
Publisher: IEEE
Date: 2004
Publisher: Wiley
Date: 11-01-2021
DOI: 10.1111/TPJ.15100
Publisher: Oxford University Press (OUP)
Date: 13-07-2010
DOI: 10.1093/BIOINFORMATICS/BTQ403
Abstract: Motivation: Mass spectrometry (MS)-based proteomics is one of the most commonly used research techniques for identifying and characterizing proteins in biological and medical research. The identification of a protein is the critical first step in elucidating its biological function. Successful protein identification depends on various interrelated factors, including effective analysis of MS data generated in a proteomic experiment. This analysis comprises several stages, often combined in a pipeline or workflow. The first component of the analysis is known as spectra pre-processing. In this component, the raw data generated by the mass spectrometer is processed to eliminate noise and identify the mass-to-charge ratio (m/z) and intensity for the peaks in the spectrum corresponding to the presence of certain peptides or peptide fragments. Since all downstream analyses depend on the pre-processed data, effective pre-processing is critical to protein identification and characterization. There is a critical need for more robust pre-processing algorithms that perform well on tandem mass spectra under a variety of different conditions and can be easily integrated into sophisticated data analysis pipelines for practical wet-lab applications. Result: We have developed a new pre-processing algorithm. Based on wavelet theory, our method uses a dynamic peak model to identify peaks. It is designed to be easily integrated into a complete proteomic analysis workflow. We compared the method with other available algorithms using a reference library of raw MS and tandem MS spectra with known protein composition information. Our pre-processing algorithm results in the identification of significantly more peptides and proteins in the downstream analysis for a given false discovery rate. Availability: Software available at: www.maths.usyd.edu.au/u enghao/index.html Contact: penghao.wang@sydney.edu.au
Publisher: American Society for Microbiology
Date: 30-06-2016
Abstract: We report the complete genome sequence of Mesorhizobium ciceri strain CC1192, an efficient nitrogen-fixing microsymbiont of Cicer arietinum (chickpea). The genome consists of 6.94 Mb distributed between a single chromosome (6.29 Mb) and a plasmid (0.65 Mb).
Publisher: PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO.
Date: 2007
Publisher: Springer Berlin Heidelberg
Date: 2005
DOI: 10.1007/11552413_175
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 09-2012
DOI: 10.1109/TCBB.2012.86
Publisher: Frontiers Media SA
Date: 19-08-2016
Publisher: Springer Berlin Heidelberg
Date: 2005
DOI: 10.1007/11552413_170
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.IJFOODMICRO.2019.108305
Abstract: In recent years, the number of human salmonellosis cases in Western Australia (WA) has increased more dramatically than in any other Australian state. In 2017, the number of cases in WA was more than double the five-year average, and eggs had emerged as the key culprit for several Salmonella foodborne disease outbreaks. To better understand such an epidemiologically intriguing situation, our research goal was to investigate the prevalence, serovar ersity, multilocus sequence types, and antimicrobial resistance of non-typhoidal Salmonella contamination in retail eggs produced and sold in WA. A total of 200 visually clean and intact retail egg s les (each containing a dozen eggs) were purchased for one year (2017-2018) from supermarkets in metropolitan Perth, the capital of WA. For each s le, the contents and shells of the 12 eggs were separately pooled and cultured according to standard methods. Overall, Salmonella was detected in 11.5% (23/200) of the tested egg s les. Salmonella was isolated from 4.5% (9/200) and 3% (6/200) of eggshells and egg contents, respectively. In 4% (8/200) of the s les, Salmonella was recovered from both eggshell and egg contents. Isolates from positive retail egg s les were serotyped as either S. Typhimurium (52.2% [12/23]) or S. Infantis (39.1% [9/23]). Both serotypes were concurrently recovered from two different retail egg s les. We retained a set of both S. Typhimurium (n = 29) and S. Infantis (n = 12) isolates from all Salmonella-positive retail packs (n = 23) for further characterization. Only two (S. Typhimurium) isolates showed resistance to icillin, of which one carried β-lactamase resistance gene bla
No related grants have been discovered for Penghao Wang.