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Fulltext Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia

Baddam R, Kumar N, Shaik S, Suma T, Ngoi ST, Thong KL, et al.

Gut Pathog, 2012;4(1):20.
PMID: 23234298 DOI: 10.1186/1757-4749-4-20

Salmonella Typhi is a human restricted pathogen with a significant number of individuals as asymptomatic carriers of the bacterium. Salmonella infection can be effectively controlled if a reliable method for identification of these carriers is developed. In this context, the availability of whole genomes of carrier strains through high- throughput sequencing and further downstream analysis by comparative genomics approaches is very promising. Herein we describe the genome sequence of a Salmonella Typhi isolate representing an asymptomatic carrier individual during a prolonged outbreak of typhoid fever in Kelantan, Malaysia. Putative genomic coordinates relevant in pathogenesis and persistence of this carrier strain are identified and discussed.

Matched MeSH terms: Genomics
Fulltext Comparative Study between Covid-19, SARS and MERS

Sohayla M. Attalla, Kavitha Ashok Kumar, Sakinah Ruhi, Saw Aung, Fazna Saleem, Hassan O. Ads, et al.

Journal of Optometry, Eye and Health Research, 2020;2(1):19-27.
MyJurnal

Coronaviruses were discovered in the mid-1960s then at 2002 in Foshan, China a new virus discovered to cause a Severe Acute Respiratory Syndrome (SARS-CoV) then at 2012 another strain was identified in Saudi Arabia causing the Middle East Respiratory Syndrome (MERS). In December 2019 in Wuhan, Hubei, SARS-CoV-2 (COVID-19) emerged to spread as pandemic. Being a series of the same family, the current research aimed to compare the characteristics of COVID-19 in relation to SARS and MERS regarding the origin and genomic structure, mode of transmission, distribution of cases along the world countries, infectivity and mortality rates together with the clinical presentation, diagnosis and treatment.

Matched MeSH terms: Genomics
Fulltext Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4

Gan HM, Lee MVL, Savka MA

PeerJ, 2019;7:e6366.
PMID: 30775173 DOI: 10.7717/peerj.6366

The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.

Matched MeSH terms: Genomics
Fulltext Draft Genome Sequence of Lactarius deliciosus Strain CBS 582.63 from the CBS-KNAW Culture Collection

Goh JE, Rahman AY, Hari R, Lim MP, Najimudin N, Yap WS, et al.

Microbiol Resour Announc, 2020 May 21;9(21).
PMID: 32439681 DOI: 10.1128/MRA.01485-19

A type strain of Lactarius deliciosus was obtained from the CBS-KNAW culture collection. The mycelium was cultured using potato dextrose agar, and the extracted genomic DNA was subjected to PacBio genome sequencing. Upon assembly and annotation, the genome size was estimated to be 54 Mbp, with 12,753 genes.

Matched MeSH terms: Genomics
Fulltext Global agricultural intensification during climate change: a role for genomics

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, et al.

Plant Biotechnol J, 2016 Apr;14(4):1095-8.
PMID: 26360509 DOI: 10.1111/pbi.12467

Agriculture is now facing the 'perfect storm' of climate change, increasing costs of fertilizer and rising food demands from a larger and wealthier human population. These factors point to a global food deficit unless the efficiency and resilience of crop production is increased. The intensification of agriculture has focused on improving production under optimized conditions, with significant agronomic inputs. Furthermore, the intensive cultivation of a limited number of crops has drastically narrowed the number of plant species humans rely on. A new agricultural paradigm is required, reducing dependence on high inputs and increasing crop diversity, yield stability and environmental resilience. Genomics offers unprecedented opportunities to increase crop yield, quality and stability of production through advanced breeding strategies, enhancing the resilience of major crops to climate variability, and increasing the productivity and range of minor crops to diversify the food supply. Here we review the state of the art of genomic-assisted breeding for the most important staples that feed the world, and how to use and adapt such genomic tools to accelerate development of both major and minor crops with desired traits that enhance adaptation to, or mitigate the effects of climate change.

Matched MeSH terms: Genomics
Fulltext Prediction of hub genes of Alzheimer's disease using a protein interaction network and functional enrichment analysis

Wee JJ, Kumar S

Genomics Inform, 2020 Dec;18(4):e39.
PMID: 33412755 DOI: 10.5808/GI.2020.18.4.e39

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

Matched MeSH terms: Genomics
Complete genome sequence of Serratia fonticola DSM 4576 T, a potential plant growth promoting bacterium

Lim YL, Yong D, Ee R, Krishnan T, Tee KK, Yin WF, et al.

J Biotechnol, 2015 Nov 20;214:43-4.
PMID: 26376471 DOI: 10.1016/j.jbiotec.2015.09.005

Here, we present the first complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting (PGP) bacterium which confers solubilization of inorganic phosphate, indole-3-acetic acid production, hydrogen cyanideproduction, siderophore production and assimilation of ammonia through the glutamate synthase (GS/GOGAT) pathway. This genome sequence is valuable for functional genomics and ecological studies which are related to PGP and biocontrol activities.

Matched MeSH terms: Genomics
Fulltext Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solos

Wengert PC, Wong NH, Barton HA, Gan HM, Hudson AO, Savka MA

BMC Res Notes, 2021 May 08;14(1):175.
PMID: 33964980 DOI: 10.1186/s13104-021-05589-6

OBJECTIVES: To characterize the bacterial community of Wind Cave's Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems.
RESULTS: Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.

Matched MeSH terms: Genomics
Fulltext Psychrophilic lipase from arctic bacterium

Zakiah Ramle, Rashidah Abdul Rahim

Trop Life Sci Res, 2016;27(11):151-157.
MyJurnal

A lipase producer psychrophilic microorganism isolated from Arctic sample was
studied. The genomic DNA of the isolate was extracted using modified CTAB method.
Identification of the isolate by morphological and 16S rRNA sequence analysis revealed
that the isolate is closely related to Arthrobacter gangotriensis (97% similarity).
A. gangotriensis was determined as positive lipase producer based on the plate screening
using specific and sensitive plate assay of Rhodamine B. The PCR result using
Arthrobacter sp.’s full lipase gene sequence as the template primers emphasised a
possible lipase gene at 900 bp band size. The gene is further cloned in a suitable vector
system for expression of lipase.

Matched MeSH terms: Genomics
Fulltext Efficient and High-Quality RNA Isolation from Metabolite-Rich Tissues of Stevia rebaudiana, an Important Commercial Crop

Leh TY, Yong CSY, Nulit R, Abdullah JO

Trop Life Sci Res, 2019 Jan;30(1):149-159.
PMID: 30847038 MyJurnal DOI: 10.21315/tlsr2019.30.1.9

Stevia rebaudiana, a perennial herb native to northeastern Paraguay, has gained immense attention globally over the recent decades due to the natural sweetness of its leaves. Like in most plants, this particular species contains high amount of secondary metabolites, thus rendering the isolation of high quality and quantity RNA extract for molecular applications rather challenging. An effective, high-yield and high-quality RNA isolation protocol for this economically important plant species was devised here based on the cetyltrimethylammonium bromide (CTAB) extraction method, with an additional genomic DNA (gDNA) removal step. DNA and other contaminants that may affect downstream applications were effectively removed. Our results exhibited that RNA samples isolated from the leaves and stems of Stevia rebaudiana using this improvised method are high in integrity and quality with RNA integrity number (RIN) of more than 8 and low in contaminants.

Matched MeSH terms: Genomics
von Willebrand disease: Diagnosis and treatment, treatment of women, and genomic approach to diagnosis

Laffan M, Sathar J, Johnsen JM

Haemophilia, 2021 Feb;27 Suppl 3:66-74.
PMID: 32578345 DOI: 10.1111/hae.14050

von Willebrand disease (VWD) is the most common inherited bleeding disorder. VWD is caused by deficiencies in von Willebrand factor (VWF), a critical adhesive haemostatic protein. This review provides an overview of VWD diagnosis and treatment, special considerations in treating women with VWD, and current genomic approaches to VWD. For diagnosis and treatment in VWD, an accurate diagnosis is critical to providing effective treatments, determining appropriate laboratory monitoring and for counselling the patient and family. Diagnosis of VWD begins with the clinical assessment for the bleeding phenotype, which is usually characterized by mucocutaneous and provoked bleeding. The diagnosis of VWD is then made by laboratory investigation. Multiple assays are used to assess VWF levels and functions. The mainstays of VWD treatment are tailored by VWD type and symptoms, and can include antifibrinolytic treatment, desmopressin and VWF replacement treatment. Women with VWD are also at risk for excessive uterine bleeding, such as with menses and childbirth. In addition to standard VWD treatments, heavy menstrual bleeding can be treated with hormones. Interdisciplinary management of childbirth and prophylaxis in the postpartum period are needed to reduce the risk of postpartum haemorrhage. Genomic approaches to VWD can inform VWD diagnosis, treatment, test assay selection, reproductive planning and family counselling. Most VWD patients have an identifiable VWF gene DNA variant. Next-generation sequencing is rapidly being adopted to provide more comprehensive VWF sequence information for patients with known or suspected VWD.

Matched MeSH terms: Genomics
Fulltext Biological impact of mutually exclusive exon switching

Lam SD, Babu MM, Lees J, Orengo CA

PLoS Comput Biol, 2021 03;17(3):e1008708.
PMID: 33651795 DOI: 10.1371/journal.pcbi.1008708

Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem.ucl.ac.uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.

Matched MeSH terms: Genomics
Fulltext Isolation and optimization of inter-simple sequence repeat (issr) technique for pleurotus sajor caju towards enviromental study in support of the country’s nuclear power programme

Rosnani Abdul Rashid, Azhar Mohamad, Mat Rasol Awang, Hassan Hamdani Mutaat, Shaiful Azuar Mohamad, Affrida Abu Hasan, et al.

Jurnal Sains Nuklear Malaysia, 2013;25(1):1-18.
MyJurnal

Mushroom can be used as a biological indicator in assessing radiological impact on the
environment. Radiological effect would be reflected through morphological changes as well as
those changes at molecular level. For this purpose, a preliminary work was conducted, which
included DNA isolation, optimization of PCR parameters for Inter-Simple Sequence Repeat (ISSR)
and primers screening on Pleurotus sajor caju mushroom strains from Nuclear Malaysia’s
Sterifeed Mushrooms Collection Centre. In this work, DNA isolation technique from cap and stalk
of fruit body were optimized and quantified. It was found that stalk produced highest amount of
genomic DNA at 304.01ng/µl and cap at 149.00ng/µl. A total of 100 ISSR primers were tested and
51 primers were successfully amplified. These primers will be used further for dose response
evaluation and molecular profiling in mushroom species.

Matched MeSH terms: Genomics
Fulltext Rapid isolation of genomic DNA from Asian green-lipped mussel (Perna viridis) for random amplified microsatellite polymorphism

Chai, L.C., Fatimah, C.A., Norhisyam, M.S., Rozila, A., Nadzirah, A.S., Natasha, L.H.Y.

International Food Research Journal, 2009;16(1):113-118.
MyJurnal

The objective of the present study was to develop a rapid, reliable and yet inexpensive protocol for genomic DNA extraction from frozen and ethanol-preserved Asian green-lipped mussels for random amplified microsatelite (RAM) analysis. The procedure comprised of three major steps: (1) Tissue degradation by boiling in 6% Chelex 100 resin in TE buffer; (2) Protein digestion by Proteinase K; and (3) DNA precipitation by adding 2 volumes of cold absolute ethanol. The entire procedure can be completed within two hours. The resulting RAM profiles were clear and reproducible. Our results demonstrate that the combined protocol of Chelex 100-Proteinase K-ethanol precipitation is a powerful yet economical DNA isolation method for population genetic studies involving a large sample size.

Matched MeSH terms: Genomics
Development of Diversity Arrays Technology markers as a tool for rapid genomic assessment in Nile tilapia, Oreochromis niloticus

Lind CE, Kilian A, Benzie JAH

Anim. Genet., 2017 Jun;48(3):362-364.
PMID: 28094451 DOI: 10.1111/age.12536

The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.

Matched MeSH terms: Genomics
Fulltext Genomic diversity of cholera outbreak strains in East Malaysia

Bilung, Lesley Maurice, Yong, Sy Fuh, Linang, Velnetti, Benjamin, Adam, Vincent, Micky, Apun, Kasing, et al.

Malaysian Journal of Medicine and Health Sciences, 2014;10(2):19-26.
MyJurnal

Thirty one Vibrio cholera isolates recovered from cholera outbreak in Bintulu, Sarawak (Malaysia) were detected with the presence of ctx gene by using specific PCR. These isolates were further characterized and differentiated by using the Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR) and BOX-PCR to determine their genomic fingerprints. The specific PCR result confirmed the identities of 27 isolates out of 31 as pathogenic V. cholerae. The ERIC-PCR generated several genetic profiles consisting of 4-6 bands with sizes in the range of 100 to 600 bp, while the BOX-PCR produced profiles numbering 2-7 bands in the sizes between 200 to 1000 bp. Based on the dendrogram generated from the DNA fingerprinting profiles (ERIC-PCR and BOX-PCR), all of the isolates can be divided into 2 main clusters that is further divided into 2 sub-clusters. The low genetic diversity of the isolates indicated the outbreak of V. cholerae in the study area was due to the contamination from a single or few sources of V. cholerae.

Matched MeSH terms: Genomics
Fulltext Molecular markers for eurycoma longifolia and orthosiphon stamineus

Rodrigues, K. F., Tam, H. K.

Buletin Persatuan Genetik Malaysia, 2009;15(1):4-6.
MyJurnal

This paper describes the first reported attempt to isolate DNA sequences containing repeat motifs in Eurycoma longifolia and Orthosiphon stamineus. A library enriched for genomic repeat motifs was developed using novel oligonucleotides designed with inosine residues incorporated at predetermined positions. A total of eight and twelve specific molecular markers were developed for O. stamineus and E. longifolia respectively. These markers have a potential application in estimating population diversity levels and QTL mapping in these two medicinal plants, which are widely used in the Malaysian herbal industry.

Matched MeSH terms: Genomics
Fulltext Genes, medicine and society: from paediatrics to genetic counselling and beyond

Thong MK

JUMMEC, 2012;15(2):1-8.
MyJurnal

The story of clinical genetics is a relatively new one, first spearheaded by paediatrics but increasingly, has taken root in all branches of medicine leading to ‘personalised medicine’. There are expectations that this revolution in genetics will pave the way to genomic medicine and a cure for all inherited disorders. The development of the field of Clinical Genetics and genetic counselling in Malaysia is still in its infancy. Using evidence-based data on genetic disorders such as birth defects, inborn errors of metabolism, genetic syndromes, neurological disorders and hereditary cancers, that hitherto have not been well documented in Malaysia, this review article will focus on findings and issues that will present a unique insight and opportunity to understanding the complex genetic counselling issues related to clinical genetics in Malaysia.

Matched MeSH terms: Genomics
Fulltext A new paradigm in medicine: genome wide association studies

S, MARAN, LEE, Y. Y., ZILFALIL BA, NOORIZAN AM

Buletin Persatuan Genetik Malaysia, 2011;18(1):3-6.
MyJurnal

Genome Wide Association (GWA) Studies of complex diseases represents a new paradigm in the
post-genomic era. Since then, the eld of human genetics has been revolutionized by the GWA Studies approach (Yang and Hibberd 2009). Adding to this, the completion of human genome sequence had enabled a systemic identi cation of genetic loci that determines
the etiology of complex diseases.

Matched MeSH terms: Genomics
Acanthamoeba keratitis: current status and urgent research priorities

Khan NA, Anwar A, Siddiqui R

Curr Med Chem, 2018 May 10.
PMID: 29745319 DOI: 10.2174/0929867325666180510125633

BACKGROUND: First discovered in the early 1970s, Acanthamoeba keratitis has remained a major eye infection and presents a significant threat to the public health, especially in developing countries. The aim is to present a timely review of our current understanding of the advances made in this field in a comprehensible manner and includes novel concepts and provides clear directions for immediate research priorities.
METHOD: We undertook a search of bibliographic databases for peer-reviewed research literature and also summarized our published results in this field.
RESULTS: The present review focuses on novel diagnostic and therapeutic strategies in details which can provide access to management and treatment of Acanthamoeba keratitis. This coupled with the recently available genome sequence information together with high throughput genomics technology and innovative approaches should stimulate interest in the rational design of preventative and therapeutic measures. Current treatment of Acanthamoeba keratitis is problematic and often leads to infection recurrence. Better understanding of diagnosis, pathogenesis, pathophysiology and therapeutic regimens, would lead to novel strategies in treatment and prophylaxis.

Matched MeSH terms: Genomics

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