Microbial bioinformatics 2020

Pallen, Mark J.

doi:10.1111/1751-7915.12389

Cited by 24 publications

(16 citation statements)

References 82 publications

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“…Furthermore, microarrays can identify genomic variations between different strains of bacteria. With the advances seen in recent years, whole genome sequencing will become feasible for practical routine screening to rapidly characterise and identify large numbers of virulence genes (Fratamico et al, (2016;Pallen, 2016). …”

Section: Discussionmentioning

confidence: 99%

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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Avian pathogenic Escherichia coli (APEC) is the causative agent of avian colibacillosis, a localised or systemic infection resulting in clinical diseases such as colisepticemia, chronic respiratory disease and swollen-head syndrome. Globally, avian colibacillosis is the leading cause of morbidity and mortality in poultry, and it has been associated with massive economic losses and welfare problems.This organism is of public health significance as APEC is communicable to humans. The diagnosis of avian colibacillosis relies on clinical signs, typical pathological lesions and culture of E. coli from affected tissue(s). Antimicrobial therapy is often used both for treatment and control. Previous overseas studies have characterised APEC and identified virulence genes (VGs) that can be used as molecular markers for the identification of APEC. Little is known about APEC in broiler chickens in Australia.The aim of this thesis was to gain a better understanding of the epidemiology of APEC in Australian broiler flocks and how factors including presence of VGs and phylogenetic group can improve the identification of this pathotype in Australia. Firstly, three faecal DNA extraction methods were evaluated. Faeces were collected from healthy chickens and chickens with colibacillosis from commercial broiler farms in South East Queensland (SEQ). The extracted DNA was screened by a pentaplex-PCR for five APEC-associated VGs (iroN, iutA, iss, hlyF and ompT). DNA extracted from E. coli isolates cultured from the cloaca and organs of the birds were screened using the same PCR.Repeated bead beating plus column elution was the preferred DNA extraction method, as it yielded good PCR quality and adequate quantity DNA. However, identifying APEC by direct detection of the five VGs from the faecal material was not feasible as all of these genes were also detected in all of the birds. However, the VGs were more commonly detected in E. coli isolates cultured from birds with colibacillosis.A cross-sectional study was performed to estimate APEC farm-level prevalence in healthy broiler chickens in SEQ and to identify potential risk factors associated with the carriage of APEC. At the farm-level, all of the 40 farms sampled were positive for APEC, that is at least one bird per farm carried APEC, while the within-farm prevalence was 63% (95% Confidence Interval: 55.8, 70.2).Higher APEC within-farm bird-level prevalence was significantly associated with the usage of well water as a source of drinking water, failure to disinfect the water line after each flock, farm visitors not showering before entering the shed, distances greater than 20 metres between the car park and the poultry shed and the presence of wild birds within 50 metres of the shed. Chlorinating the drinking water combined with automatic water filtration reduced within-farm bird-level APEC prevalence. Page | 3Therefore, based on the results concluded from the multivariable model, improving biosecurity and water treatments might reduce APEC prevalence, decrease the risk of co...

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Section: Discussionmentioning

confidence: 99%

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Awawdeh¹,

Turni²,

Henning³

et al.

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“…The 21th century was actually the generation of molecular biology and biochemistry. Bioinformatics is a discipline using the methods of applied mathematics, informatics, statistics and computer science to study biology [27], mainly for biological mysteries of large and complex biological data [28]. Accordingly, we conducted our study using bioinformatics.…”

Section: Discussionmentioning

confidence: 99%

GINS1/2/3/4 Upregulation Predicts Poor Prognosis in Human Sarcoma

Chen

et al. 2021

Preprint

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Background: GINS family was reported to be highly expressed in many tumors. However, the association of GINS family with human sarcoma remained unknown. This study was undertaken to explore the expression and prognostic value of GINS family in human sarcoma.Methods: In terms of the expression levels of mRNA for GINS family members, a particular contrast in various cancers, especially human sarcoma, was conducted through ONCOMINE and GEPIA and CCLE databases. Kaplan-Meier Plotter was used to identify the prognostic value of GINS family in sarcoma.Results: We discovered that the mRNA expression levels of GINS1, GINS2, GINS3, and GINS4 were all higher in the majority of tumor tissues than in normal samples, of course, including sarcoma. Through the Cancer Cell Line Encyclopedia (CCLE), all the four members (GINS1, GINS2, GINS3, GINS4) expression were observed in high levels in sarcoma cell lines. In Gene Expression Profiling Analysis (GEPIA) and Kaplan-Meier Plotter, our results indicated that the poor overall survival (OS), disease-free survival (DFS) and relapse free survival (RFS) were tightly associated with the increased expression of GINS genes. Conclusion: The four GINS family members are all the prognostic biomarkers for the prognosis of human sarcoma.

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“…This expanding availability of genomic data in publicly accessible databases can be mined in silico , providing a practically inexhaustible supply of new enzymes by means of sequence homology searches with previously characterized enzymes of known function. , At the same time, the cost of gene synthesis has decreased substantially, although not as dramatically as that of sequencing . Thanks to these two developments, a gene sequence of interest can be identified by (meta)genome mining of public databases and its synthesis ordered online, and a researcher can have a plasmid, ready for cloning in an appropriate microbial host, delivered in 2 weeks or less.…”

Section: Enabling Technology: Molecular Biology and The Dna Revolutionmentioning

confidence: 99%

Streamlining Design, Engineering, and Applications of Enzymes for Sustainable Biocatalysis

Sheldon

Brady

2021

ACS Sustainable Chem. Eng.

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In this Perspective we show how an expansion of the scope and impact of biocatalysis in industrial organic synthesis is enabled by streamlining the underpinning biocatalyst and bioprocess engineering. We begin by discussing how the underlying need for waste reduction and high (enantio)selectivities fostered the introduction of biocatalysis as a sustainable technology for the industrial synthesis of active pharmaceutical ingredients (APIs). We continue by showing how advances in molecular biology, in particular gene sequencing and protein engineering, enabled the development of more and better enzymes, thereby broadening the industrial scope of biocatalysis. Further process improvements are provided through protein engineering for enzyme immobilization and integration of enzyme production with in vivo immobilization. Finally, the use of immobilized enzymes in continuous operation (biocatalysis in flow) facilitates the sequential integration of multi-step reactions into enzymatic or chemo-enzymatic cascade processes, thus enabling the complete, cost-effective, and environmentally attractive production of APIs.

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Microbial bioinformatics 2020

Cited by 24 publications

References 82 publications

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

GINS1/2/3/4 Upregulation Predicts Poor Prognosis in Human Sarcoma

Streamlining Design, Engineering, and Applications of Enzymes for Sustainable Biocatalysis

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Microbial bioinformatics 2020

Cited by 24 publications

References 82 publications

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

Studies on avian pathogenic Escherichia coli in commercial broiler chicken in South East Queensland

GINS1/2/3/4&nbsp;Upregulation Predicts Poor Prognosis in Human Sarcoma

Streamlining Design, Engineering, and Applications of Enzymes for Sustainable Biocatalysis

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GINS1/2/3/4 Upregulation Predicts Poor Prognosis in Human Sarcoma