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Fulltext Platelet Transcriptome-based approaches in the fight against dengue and other diseases

Suppiah, J., Sakinah, S., Chan, S.Y., Wong, Y.P., Subbiah, S.K., Chee, H.Y., et al.

Pertanika Journal of Science & Technology, 2018;26(3):933-946.
MyJurnal

Human platelets are anucleate cells that lack in deoxyribonucleic acid (DNA), thus hampering genomic study on them. However, the presence of their own messenger ribonucleic acid (mRNA) transcript allows functional study via the transcriptome approach. Transcriptome not only allows profiling of platelet but also aids in studying gene regulation in virus infections and other diseases that have an impact on platelets. Some viruses are known to affect the platelet either by causing a reduction or destruction. Dengue virus is one of the most postulated virus having such effect and frequently linked to platelet reduction. The transcriptome approach has a pivotal role in providing a deeper insight to link certain diseases and their effect on platelets. This review critically discusses role of platelet in dengue and other viral diseases of public health relevance, with a specific focus on the methods currently used in platelet transcriptome profiling.

Matched MeSH terms: Genomics
Fulltext Phylogeography, Transmission, and Viral Proteins of Nipah Virus

Sun B, Jia L, Liang B, Chen Q, Liu D

Virol Sin, 2018 Oct;33(5):385-393.
PMID: 30311101 DOI: 10.1007/s12250-018-0050-1

Nipah virus (NiV), a zoonotic paramyxovirus belonging to the genus Henipavirus, is classified as a Biosafety Level-4 pathogen based on its high pathogenicity in humans and the lack of available vaccines or therapeutics. Since its initial emergence in 1998 in Malaysia, this virus has become a great threat to domestic animals and humans. Sporadic outbreaks and person-to-person transmission over the past two decades have resulted in hundreds of human fatalities. Epidemiological surveys have shown that NiV is distributed in Asia, Africa, and the South Pacific Ocean, and is transmitted by its natural reservoir, Pteropid bats. Numerous efforts have been made to analyze viral protein function and structure to develop feasible strategies for drug design. Increasing surveillance and preventative measures for the viral infectious disease are urgently needed.

Matched MeSH terms: Genomics
Fulltext What We Know about the Molecular Genetics of Central Nervous System (CNS) Tumours in Malaysia

Sulong S, Yusoff AA, Zainuddin N, Abdullah JM, Pannatil JG, Jaafar H, et al.

Malays J Med Sci, 2004 Jan;11(1):37-43.
PMID: 22977358 MyJurnal

The new millennium has been regarded as a genomic era. A lot of researchers and pathologists are beginning to understand the scientific basis of molecular genetics and relates with the progression of the diseases. Central nervous system (CNS) tumours are among the most rapidly fatal of all cancers. It has been proposed that the progression of malignant tumours may result from multi-step of genetic alterations, including activation of oncogenes, inactivation of tumour suppressor genes and also the presence of certain molecular marker such as telomerase activity. In this paper, we review some recent data from the literature, including our own studies, on the molecular genetics analysis in CNS tumours. Our studies have shown that two types of tumour suppressor genes, p53 and PTEN were involved in the development of these tumours but not in p16 gene among the patients from Hospital Universiti Sains Malaysia (HUSM). Telomerase activity also has been detected in various types of CNS tumours. Thus, it is important to assemble all data which related to this study and may provide as a vital information in a new approach to neuro-oncology studies in Malaysia.

Matched MeSH terms: Genomics
Fulltext Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

Strijk JS, Binh HT, Ngoc NV, Pereira JT, Slik JWF, Sukri RS, et al.

PLoS One, 2020;15(5):e0232936.
PMID: 32442164 DOI: 10.1371/journal.pone.0232936

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.

Matched MeSH terms: Genomics/methods*
Fulltext Molecular Detection of Methicillin-Resistant Staphylococcus aureus by Non-Protein Coding RNA-Mediated Monoplex Polymerase Chain Reaction

Soo Yean CY, Selva Raju K, Xavier R, Subramaniam S, Gopinath SC, Chinni SV

PLoS One, 2016;11(7):e0158736.
PMID: 27367909 DOI: 10.1371/journal.pone.0158736

Non-protein coding RNA (npcRNA) is a functional RNA molecule that is not translated into a protein. Bacterial npcRNAs are structurally diversified molecules, typically 50-200 nucleotides in length. They play a crucial physiological role in cellular networking, including stress responses, replication and bacterial virulence. In this study, by using an identified npcRNA gene (Sau-02) in Methicillin-resistant Staphylococcus aureus (MRSA), we identified the Gram-positive bacteria S. aureus. A Sau-02-mediated monoplex Polymerase Chain Reaction (PCR) assay was designed that displayed high sensitivity and specificity. Fourteen different bacteria and 18 S. aureus strains were tested, and the results showed that the Sau-02 gene is specific to S. aureus. The detection limit was tested against genomic DNA from MRSA and was found to be ~10 genome copies. Further, the detection was extended to whole-cell MRSA detection, and we reached the detection limit with two bacteria. The monoplex PCR assay demonstrated in this study is a novel detection method that can replicate other npcRNA-mediated detection assays.

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 Isolation, Purification, and Characterization of Heparinase from Streptomyces variabilis MTCC 12266

Singh V, Haque S, Kumari V, El-Enshasy HA, Mishra BN, Somvanshi P, et al.

Sci Rep, 2019 04 24;9(1):6482.
PMID: 31019210 DOI: 10.1038/s41598-019-42740-7

Arterial/venous thrombosis is the major cardiovascular disorder accountable for substantial mortality; and the current demand for antithrombotic agents is extensive. Heparinases depolymerize unfractionated heparin (UFH) for the production of low molecular-weight heparins (LMWHs; used as anticoagulants against thrombosis). A microbial strain of Streptomyces sp. showing antithrombotic activity was isolated from the soil sample collected from north India. The strain was characterized by using 16S rRNA homology technique and identified as Streptomyces variabilis MTCC 12266 capable of producing heparinase enzyme. This is the very first communication reporting Streptomyces genus as the producer of heparinase. It was observed that the production of intracellular heparinase was [63.8 U/mg protein (specific activity)] 1.58 folds higher compared to extracellular heparinase [40.28 U/mg protein]. DEAE-Sephadex A-50 column followed by Sepharose-6B column purification of the crude protein resulted 19.18 folds purified heparinase. SDS-PAGE analysis of heparinase resulted an estimated molecular-weight of 42 kDa. It was also found that intracellular heparinase has the ability to depolymerize heparin to generate LMWHs. Further studies related to the mechanistic action, structural details, and genomics involved in heparinase production from Streptomyces variabilis are warranted for large scale production/purification optimization of heparinase for antithrombotic applications.

Matched MeSH terms: Genomics
Fulltext Small Interfering RNA (siRNA) and Clustered regularly interspaced short palindromic repeats (CRISPR): emerging molecular tools for genetic manipulation

Simon I. Okekpa, Rabiatul Basria S.M.N. Mydin, Munirah Mohd Nor, Emmanuel Jairaj Moses

Malaysian Journal of Medicine and Health Sciences, 2020;16(3):300-308.
MyJurnal

Gene manipulation tools have transformed biomedical research and improved the possibilities of their uses for therapeutic purposes. These tools have aided effective genomic modification in many organisms and have been successfully applied in biomedical engineering, biotechnology and biomedicine. They also shown a potential for therapeutic applications to alleviate genetic and non-genetic diseases. Small interfering RNA (siRNA) and clustered regularly inter-spaced short-palindromic repeat/associated-protein system (CRISPR/Cas) are two of the tools applied in genetic manipulation. This review aims to evaluate the molecular influence of siRNA and CRISPR/Cas as novel tools for genetic manipulations. This review discusses the molecular mechanism of siRNA and CRISPR/Cas, and the advantages and disadvantages of siRNA and CRISPR/Cas. This review also presents comparison between siRNA and CRISPR/Cas as potential tools for gene therapy. siRNA therapeutic applications occur through protein knockout with- out causing damage to cells. siRNA knocks down gene expression at the mRNA level, whereas CRISPR/Cas knocks out gene permanently at the DNA level. Inconclusion, gene manipulation tools have potential for applications that improve therapeutic strategies and plant-derived products, but ethical standards must be established before the clin- ical application of gene editing.

Matched MeSH terms: Genomics
Fulltext Behavioural, genomics and proteomic approach to examine Alzheimer's disease in zebrafish

Siddiqui A, Abidin SAZ, Shah ZA, Othman I, Kumari Y

Comp Biochem Physiol C Toxicol Pharmacol, 2023 Sep;271:109636.
PMID: 37100105 DOI: 10.1016/j.cbpc.2023.109636

Globally around 24 million elderly population are dealing with dementia, and this pathological characteristic is commonly seen in people suffering from Alzheimer's disease (AD). Despite having multiple treatment options that can mitigate AD symptoms, there is an imperative call to advance our understanding of the disease pathogenesis to unfold disease-modifying treatments/therapies. To explore the driving mechanisms of AD development, we stretch out further to study time-dependant changes after Okadaic acid (OKA)-induced AD-like conditions in zebrafish. We evaluated the pharmacodynamics of OKA at two-time points, i.e., after 4-days and 10-days exposure to zebrafish. T-Maze was utilized to observe the learning and cognitive behaviour, and inflammatory gene expressions such as 5-Lox, Gfap, Actin, APP, and Mapt were performed in zebrafish brains. To scoop everything out from the brain tissue, protein profiling was performed using LCMS/MS. Both time course OKA-induced AD models have shown significant memory impairment, as evident from T-Maze. Gene expression studies of both groups have reported an overexpression of 5-Lox, GFAP, Actin, APP, and OKA 10D group has shown remarkable upregulation of Mapt in zebrafish brains. In the case of protein expression, the heatmap suggested an important role of some common proteins identified in both groups, which can be explored further to investigate their mechanism in OKA-induced AD pathology. Presently, the preclinical models available to understand AD-like conditions are not completely understood. Hence, utilizing OKA in the zebrafish model can be of great importance in understanding the pathology of AD progression and as a screening tool for drug discovery.

Matched MeSH terms: Genomics
Fulltext Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome

Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, et al.

Hum Mol Genet, 2019 Aug 15;28(16):2785-2798.
PMID: 31108506 DOI: 10.1093/hmg/ddz101

Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10-3 (95% CI 1.94 × 10-3 to 2.48 × 10-3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.

Matched MeSH terms: Genomics/methods
Fulltext Tracking the source and origin of H5N1 avian influenza viruses in Malaysia

Sharifah, S .H., Suriani, M. N., Hassuzana, K., Aini, I.

Buletin Persatuan Genetik Malaysia, 2006;12(1):1-3.
MyJurnal

Malaysia, experienced two epidemic waves of HPAI; its fi rst outbreak of HP H5N1 in August 2004 that occurred in the state of Kelantan and the second and subsequent outbreaks in February–March 2006 in three states on the west coast of Malaysia namely Wilayah Persekutuan
Kuala Lumpur, Perak and Penang. Five outbreaks occurred in village chickens and one in a multi-species enclosure of birds in a bird park resort facility. Molecular epidemiological studies by genomic sequencing and phylogenetic analyses of the viruses isolated showed that the
virus isolated from WP Kuala Lumpur is of the V-genotype and it originated from Hunan China, two viruses were found to be similar to the Fujian/Hunan strains and other viruses were similar to the Vietnam/ Thailand strains.

Matched MeSH terms: Genomics
A more elaborative way to check codon quality: an open source program

Shardiwal RK, Sohrab SS

Int J Bioinform Res Appl, 2010;6(3):223-9.
PMID: 20615831

Relative Synonymous Codon Usage (RSCU) and Relative Adaptiveness of a Codon (RAC) table bias importance in gene expression are well documented in the literature. However, to improve the gene expression we need to figure out which codons are optimal for the expression in order to synthesise an appropriate DNA sequence. An alternative to the manual approach, which is obviously a tedious task, is to set up software on your computer to perform this. Though such kinds of programs are available on the internet, none of them are open-source libraries. Here, one can use our Perl program to do his or her task more easily and efficiently. It is free for everyone.

Matched MeSH terms: Genomics/methods*
Fulltext The identification of copy number variation of CNV ESV27061 among young adults with hypertension: preliminary findings. [Abstract]

Shaik Alaudeen SR, Mohd Shah AS, Abdul Talib N, Abdullah A

International Medical Journal Malaysia, 2017;16(11):31.
MyJurnal

Introduction: Hypertension related morbidities and mortalities around the world show a gradual increase and early detection and prevention are advocated. The Database of Genomic Variants (DGV) has associated variation in DNA sequences called copy number variation (CNV) with susceptibility to common diseases. However, little is known about CNV role in essential hypertension. Thus, this study aimed to characterize the CNV esv27061 among prehypertensive and hypertensive young adults in Malaysia. Materials and method: In this comparative cross-sectional study, 104 subjects living in Kuantan who gave voluntary consent to participate are recruited and divided into three groups; control (43 subjects), prehypertensive (38 subjects) and mild hypertensive (23 subjects). An optimized droplet digital polymerase chain reaction (ddPCR) was used in the determination of CNV esv27061 in this study. Results: All subjects in the control (n=38; 88.4% gain), prehypertensive (n=33; 86.8% gain) and mild hypertensive (n=21; 91.3% gain) groups had CNV gain (copy number > 2) while 11.6% of control, 13.2% of prehypertensive and 8.7% of mild hypertensive subjects exhibited normal copies (copy number = 2). Conclusion: The present preliminary finding was consistent with the Database of Genomic Variants (DGV) which stated that CNV esv27061 showed more gain than loss.

Matched MeSH terms: Genomics
Fulltext Construction and validation of a mammalian expression vector for in utero electroporation study of mir-3099 in the Mouse Neocortex

Shahidee Zainal Abidin, Han-Chung Lee, Sze-Zheng Fam, Syahril Abdullah, Norshariza Nordin, Pike-See Cheah, et al.

Malaysian Journal of Medicine and Health Sciences, 2018;14(101):20-29.
MyJurnal

Introduction: MiR-3099 was reported to play a role in neuronal cell differentiation/function in the brain during late embryonic and early neonatal development. To further explore its potential regulatory effects on embryonic brain development, this study aims to construct and validate an expression vector of miR-3099 for future gain-of-function and loss-of-function studies. Methods: pCAG-eGFP vector was modified to include IRES2 and miR-3099 with 150bp upstream and downstream genomic sequences. The newly constructed vector, pCAG-miR-3099-IRES2-eGFP, consists of CAG promoter. The in vitro expression level of miR-3099 was measured using stem-loop RT-qPCR after it was transfected into 293FT cell. Later, the vector was electroporated into the embryonic brain at E15.5. Three days later, the E18.5 embryonic brain was harvested and cryopreserved. Immunohistochemistry was performed by using antibody against eGFP to validate the in utero expression of the transgene in the neocortex of the brain. Results: Our finding showed that, the expression level of miR-3099 was significantly upregulated (p

Matched MeSH terms: Genomics
Reviewing the molecular mechanisms which increase endometrial cancer (EC) risk in women with polycystic ovarian syndrome (PCOS): time for paradigm shift?

Shafiee MN, Chapman C, Barrett D, Abu J, Atiomo W

Gynecol Oncol, 2013 Nov;131(2):489-92.
PMID: 23822891 DOI: 10.1016/j.ygyno.2013.06.032

Endometrial cancer (EC) is the commonest gynaecological cancer in North American and European women. Even though it has been shown that women with polycystic ovary syndrome (PCOS) have a three-fold increase in the risk of developing EC compared to women without PCOS, the precise molecular mechanisms which increase EC risk in women with PCOS remain unclear. Clinical strategies to prevent EC in PCOS are therefore not well researched and understood. Although raised estrogen levels, hyperinsulinaemia and, reduced apoptosis have been suggested as potential mechanisms, there is a lack of clarity about how these factors and other factors may interact to increase EC risk in PCOS. This article reviews the literature, on the potential molecular links between PCOS and EC but argues for a paradigm shift, to a systems biology-based approach in future research into the molecular links between PCOS and EC. The potential challenges of a systems biology-based approach are outlined but not considered insurmountable.

Matched MeSH terms: Genomics
Fulltext Economic evaluations of personalized medicine: existing challenges and current developments

Shabaruddin FH, Fleeman ND, Payne K

Pharmgenomics Pers Med, 2015;8:115-26.
PMID: 26309416 DOI: 10.2147/PGPM.S35063

Personalized medicine, with the aim of safely, effectively, and cost-effectively targeting treatment to a prespecified patient population, has always been a long-time goal within health care. It is often argued that personalizing treatment will inevitably improve clinical outcomes for patients and help achieve more effective use of health care resources. Demand is increasing for demonstrable evidence of clinical and cost-effectiveness to support the use of personalized medicine in health care. This paper begins with an overview of the existing challenges in conducting economic evaluations of genetics- and genomics-targeted technologies, as an example of personalized medicine. Our paper illustrates the complexity of the challenges faced by these technologies by highlighting the variations in the issues faced by diagnostic tests for somatic variations, generally referring to genetic variation in a tumor, and germline variations, generally referring to inherited genetic variation in enzymes involved in drug metabolic pathways. These tests are typically aimed at stratifying patient populations into subgroups on the basis of clinical effectiveness (response) or safety (avoidance of adverse events). The paper summarizes the data requirements for economic evaluations of genetics and genomics-based technologies while outlining that the main challenges relating to data requirements revolve around the availability and quality of existing data. We conclude by discussing current developments aimed to address the challenges of assessing the cost-effectiveness of genetics and genomics-based technologies, which revolve around two central issues that are interlinked: the need to adapt available evaluation methods and identifying who is responsible for generating evidence for these technologies.

Matched MeSH terms: Genomics
Fulltext Comprehensive proteomics data on whole rice grain of selected pigmented and non-pigmented rice varieties using SWATH-MS approach

Sew YS, Aizat WM, Razak MSFA, Zainal-Abidin RA, Simoh S, Abu-Bakar N

Data Brief, 2020 Aug;31:105927.
PMID: 32642524 DOI: 10.1016/j.dib.2020.105927

The proteome data of whole rice grain is considerably limited particularly for rice with pigmentations such as black and red rice. Hence, we performed proteome analysis of two black rice varieties (BALI and Pulut Hitam 9), two red rice varieties (MRM16 and MRQ100) and two white rice varieties (MR297 and MRQ76) using label-free liquid chromatography Triple TOF 6600 tandem mass spectrometry (LC-MS/MS). Our aim was to profile and identify proteins related to nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits based on peptide-centric scoring from the Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH-MS) approach. Both information dependent acquisition (IDA) and SWATH-MS run were performed in this analysis. Raw data was then processed using ProteinPilot software to identify and compare proteins from the six different varieties. In future, this proteomics data will be integrated with previously obtained genomics [1] and transcriptomics [2] data focusing on the above nutritional and quality traits, with an ultimate aim to develop a panel of functional biomarkers related to those traits for future rice breeding programme. The raw MS data of the pigmented and non-pigmented rice varieties have been deposited to ProteomeXchange database with accession number PXD018338.

Matched MeSH terms: Genomics
Fulltext Quantitative magnetic resonance imaging and radiogenomic biomarkers for glioma characterisation: a systematic review

Seow P, Wong JHD, Ahmad-Annuar A, Mahajan A, Abdullah NA, Ramli N

Br J Radiol, 2018 Dec;91(1092):20170930.
PMID: 29902076 DOI: 10.1259/bjr.20170930

OBJECTIVE:: The diversity of tumour characteristics among glioma patients, even within same tumour grade, is a big challenge for disease outcome prediction. A possible approach for improved radiological imaging could come from combining information obtained at the molecular level. This review assembles recent evidence highlighting the value of using radiogenomic biomarkers to infer the underlying biology of gliomas and its correlation with imaging features.
METHODS:: A literature search was done for articles published between 2002 and 2017 on Medline electronic databases. Of 249 titles identified, 38 fulfilled the inclusion criteria, with 14 articles related to quantifiable imaging parameters (heterogeneity, vascularity, diffusion, cell density, infiltrations, perfusion, and metabolite changes) and 24 articles relevant to molecular biomarkers linked to imaging.
RESULTS:: Genes found to correlate with various imaging phenotypes were EGFR, MGMT, IDH1, VEGF, PDGF, TP53, and Ki-67. EGFR is the most studied gene related to imaging characteristics in the studies reviewed (41.7%), followed by MGMT (20.8%) and IDH1 (16.7%). A summary of the relationship amongst glioma morphology, gene expressions, imaging characteristics, prognosis and therapeutic response are presented.
CONCLUSION:: The use of radiogenomics can provide insights to understanding tumour biology and the underlying molecular pathways. Certain MRI characteristics that show strong correlations with EGFR, MGMT and IDH1 could be used as imaging biomarkers. Knowing the pathways involved in tumour progression and their associated imaging patterns may assist in diagnosis, prognosis and treatment management, while facilitating personalised medicine.
ADVANCES IN KNOWLEDGE:: Radiogenomics can offer clinicians better insight into diagnosis, prognosis, and prediction of therapeutic responses of glioma.

Matched MeSH terms: Genomics
Genomic surveillance of omicron B.1.1.529 SARS-CoV-2 and its variants between December 2021 and March 2023 in Tamil Nadu, India-A state-wide prospective longitudinal study

Selvavinayagam ST, Suvaithenamudhan S, Yong YK, Hemashree K, Rajeshkumar M, Kumaresan A, et al.

J Med Virol, 2024 Feb;96(2):e29456.
PMID: 38329187 DOI: 10.1002/jmv.29456

A state-wide prospective longitudinal investigation of the genomic surveillance of the omicron B.1.1.529 SARS-CoV-2 variant and its sublineages in Tamil Nadu, India, was conducted between December 2021 and March 2023. The study aimed to elucidate their mutational patterns and their genetic interrelationship in the Indian population. The study identified several unique mutations at different time-points, which likely could attribute to the changing disease characteristics, transmission, and pathogenicity attributes of omicron variants. The study found that the omicron variant is highly competent in its mutating potentials, and that it continues to evolve in the general population, likely escaping from natural as well as vaccine-induced immune responses. Our findings suggest that continuous surveillance of viral variants at the global scenario is warranted to undertake intervention measures against potentially precarious SARS-CoV-2 variants and their evolution.

Matched MeSH terms: Genomics
Fulltext Genome organization of Eschrichia phage YD-2008.s: a new entry to siphoviridae family

Sellvam, Dharmela, Yahya Mat Arip, Nyok, Sean Lau

Trop Life Sci Res, 2018;29(1):37-50.
MyJurnal

Malaysia is one of the countries that are loaded with mega biodiversity which
includes microbial communities. Phages constitute the major component in the microbial
communities and yet the numbers of discovered phages are just a minute fraction of
its population in the biosphere. Taking into account of a huge numbers of waiting to be
discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s
was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile
flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae
family under the order of Caudovirales. Genomic sequence analyses revealed phage
YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content.
Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome,
using bioinformatics annotation software; Rapid Annotation using Subsystem Technology
(RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are
classified as hypothetical proteins and there are two unidentified proteins. Even though
majority of the coded putative proteins have high amino acids similarities to phages from the
genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own
distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the
growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.

Matched MeSH terms: Genomics

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