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Fulltext Emerging strengths in Asia Pacific bioinformatics

Ranganathan S, Hsu WL, Yang UC, Tan TW

BMC Bioinformatics, 2008;9 Suppl 12:S1.
PMID: 19091008 DOI: 10.1186/1471-2105-9-S12-S1

The 2008 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998, was organized as the 7th International Conference on Bioinformatics (InCoB), jointly with the Bioinformatics and Systems Biology in Taiwan (BIT 2008) Conference, Oct. 20-23, 2008 at Taipei, Taiwan. Besides bringing together scientists from the field of bioinformatics in this region, InCoB is actively involving researchers from the area of systems biology, to facilitate greater synergy between these two groups. Marking the 10th Anniversary of APBioNet, this InCoB 2008 meeting followed on from a series of successful annual events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea), New Delhi (India) and Hong Kong. Additionally, tutorials and the Workshop on Education in Bioinformatics and Computational Biology (WEBCB) immediately prior to the 20th Federation of Asian and Oceanian Biochemists and Molecular Biologists (FAOBMB) Taipei Conference provided ample opportunity for inducting mainstream biochemists and molecular biologists from the region into a greater level of awareness of the importance of bioinformatics in their craft. In this editorial, we provide a brief overview of the peer-reviewed manuscripts accepted for publication herein, grouped into thematic areas. As the regional research expertise in bioinformatics matures, the papers fall into thematic areas, illustrating the specific contributions made by APBioNet to global bioinformatics efforts.

Matched MeSH terms: Genomics/organization & administration
Fulltext Bioinformatics research in the Asia Pacific: a 2007 update

Ranganathan S, Gribskov M, Tan TW

BMC Bioinformatics, 2008;9 Suppl 1:S1.
PMID: 18315840 DOI: 10.1186/1471-2105-9-S1-S1

We provide a 2007 update on the bioinformatics research in the Asia-Pacific from the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation set up in 1998. From 2002, APBioNet has organized the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2007 Conference was organized as the 6th annual conference of the Asia-Pacific Bioinformatics Network, on Aug. 27-30, 2007 at Hong Kong, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand), Busan (South Korea) and New Delhi (India). Besides a scientific meeting at Hong Kong, satellite events organized are a pre-conference training workshop at Hanoi, Vietnam and a post-conference workshop at Nansha, China. This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. We have organized the papers into thematic areas, highlighting the growing contribution of research excellence from this region, to global bioinformatics endeavours.

Matched MeSH terms: Genomics/trends*
Fulltext Bioinformatics in Malaysia: hope, initiative, effort, reality, and challenges

Zeti AM, Shamsir MS, Tajul-Arifin K, Merican AF, Mohamed R, Nathan S, et al.

PLoS Comput Biol, 2009 Aug;5(8):e1000457.
PMID: 19714208 DOI: 10.1371/journal.pcbi.1000457
Matched MeSH terms: Genomics/trends
Fulltext The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties

Yap HY, Chooi YH, Firdaus-Raih M, Fung SY, Ng ST, Tan CS, et al.

BMC Genomics, 2014;15:635.
PMID: 25073817 DOI: 10.1186/1471-2164-15-635

The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties.

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 Alternative RNA Extraction Method in Vibrio vulnificus Infected BrownMarbled Grouper, Epinephelus fuscoguttatus

Fahmeeda Mohamad Jazamuddin, Wan Mohd Aizat, Hoe-Han Goh, Chen-Fei Low, Syarul Nataqain Baharum

Trop Life Sci Res, 2019;30(2):2012-209.
MyJurnal

Vibriosis is a prevalent aquatic disease caused by Vibrio species and has led to massive loss of brown-marbled grouper, Epinephelus fuscoguttatus. The complexity of molecular mechanisms associated with immune defence can be studied through transcriptomics analysis. High quality and quantity of total RNAs are crucial for the veracity of RNA sequencing and gene expression analysis. A low quality RNA will compromise downstream analysis, resulting in loss of time and revenue to re-acquire the data again. Thus, a reliable and an efficient RNA isolation method is the first and most important step to obtain high quality RNA for gene expression studies. There are many aspects need to be considered when deciding an extraction method, such as the cost-effectiveness of the protocol, the duration of chemical exposure, the duration required for a complete extraction and the number of sample-transferring. A good RNA extraction protocol must be able to produce high yield and purity of RNA free from enzyme inhibitors, such as nucleases (RNase), phenols, alcohols or other chemicals carryover, apart from protein and genomic DNA contamination, to maintain isolated RNA integrity in storage condition. In this study, TransZolTM Up produced clean and pure RNA samples from control gills only but not from the infected gill and whole-body tissues. Modified conventional CTAB (conventional hexadecyltrimethylammonium bromide) method was then used as an alternative method to isolate RNA from gill and whole-body tissues of Vibrio-infected E. fuscoguttatus. Modified CTAB method produced intact RNA on gel electrophoresis with higher RIN number (>6.5) for infected gill and whole-body tissues, suggesting that this method could also be used to isolate high quality RNA from fish samples. Therefore, this method is potentially suitable to be used to extract RNA from other fish species especially those that have been infected.

Matched MeSH terms: Genomics
Metabolomics and its role in understanding cellular responses in plants

Bhalla R, Narasimhan K, Swarup S

Plant Cell Rep, 2005 Dec;24(10):562-71.
PMID: 16220342

A natural shift is taking place in the approaches being adopted by plant scientists in response to the accessibility of systems-based technology platforms. Metabolomics is one such field, which involves a comprehensive non-biased analysis of metabolites in a given cell at a specific time. This review briefly introduces the emerging field and a range of analytical techniques that are most useful in metabolomics when combined with computational approaches in data analyses. Using cases from Arabidopsis and other selected plant systems, this review highlights how information can be integrated from metabolomics and other functional genomics platforms to obtain a global picture of plant cellular responses. We discuss how metabolomics is enabling large-scale and parallel interrogation of cell states under different stages of development and defined environmental conditions to uncover novel interactions among various pathways. Finally, we discuss selected applications of metabolomics.

Matched MeSH terms: Genomics/methods; Genomics/trends*
Fulltext Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach

Sangal V, Goodfellow M, Blom J, Tan GYA, Klenk HP, Sutcliffe IC

Front Microbiol, 2018;9:2281.
PMID: 30319584 DOI: 10.3389/fmicb.2018.02281

Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.

Matched MeSH terms: Genomics
Neonatal buccal cell collection: a non-invasive strategy to provide a reliable source of DNA for high resolution melting analysis

Cheung, Tian Pei, Rostenberghe, Hans Van, Narazah Mohd Yusoff, Noraida Ramli, Nor Rosidah Ibrahim, Nishio, Hisahide, et al.

Malaysian Journal of Paediatrics and Child Health, 2019;25(2):14-22.
MyJurnal

Background: The low yield and quality of buccal-derived genomic DNA have reduced its applicability in various genetic research. The aim of this study was to assess the quantity, purity and genotyping efficiency of genomic DNA isolated from neonatal buccal swabs. Methods: Paired buccal swabs and whole blood samples were collected from 60 neonates with the mean age 5 days (SD=1.57). The genomic DNA quantity and purity were measured by using Infinite® 200 PRO NanoQuant reader and agarose gel electrophoresis. High-resolution melting (HRM) analysis was used to analyse the sequence variants present in uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1 c.211G>A) and nuclear receptor subfamily 1, group I, member 3 (NR1I3 IVS8+116T>G) genes. Results: Buccal swabs provided lower mean genomic DNA concentration (18.78 ± 8.39 ng/μl versus 40.02 ± 13.03 ng/μl), yield (2.63 ± 1.17 μgversus8.00 ± 2.61 μg). The purity of buccal samples however were inconsistent with 16 samples (26.7%) having A260/280 ratios below 1.8 which indicated protein contamination. Genomic DNA purity for all blood samples were within the ideal range with average absorbance ratios of 1.8−2.0. However, all buccal genomic DNA demonstrated 100% genotype call rates for all variants. A complete genotype concordance was also observed between paired genomic DNA samples. Conclusion: Despite related to a reduced quantity and purity, neonatal buccal genomic DNA could generate reliable HRM genotyping results. Therefore, buccal swab collection is a promising alternative to the invasive blood sampling to provide genomic DNA for genetic analysis involving paediatric population.

Matched MeSH terms: Genomics
Fulltext Recent Understanding of Soil Acidobacteria and Their Ecological Significance: A Critical Review

Kalam S, Basu A, Ahmad I, Sayyed RZ, El-Enshasy HA, Dailin DJ, et al.

Front Microbiol, 2020;11:580024.
PMID: 33193209 DOI: 10.3389/fmicb.2020.580024

Acidobacteria represents an underrepresented soil bacterial phylum whose members are pervasive and copiously distributed across nearly all ecosystems. Acidobacterial sequences are abundant in soils and represent a significant fraction of soil microbial community. Being recalcitrant and difficult-to-cultivate under laboratory conditions, holistic, polyphasic approaches are required to study these refractive bacteria extensively. Acidobacteria possesses an inventory of genes involved in diverse metabolic pathways, as evidenced by their pan-genomic profiles. Because of their preponderance and ubiquity in the soil, speculations have been made regarding their dynamic roles in vital ecological processes viz., regulation of biogeochemical cycles, decomposition of biopolymers, exopolysaccharide secretion, and plant growth promotion. These bacteria are expected to have genes that might help in survival and competitive colonization in the rhizosphere, leading to the establishment of beneficial relationships with plants. Exploration of these genetic attributes and more in-depth insights into the belowground mechanics and dynamics would lead to a better understanding of the functions and ecological significance of this enigmatic phylum in the soil-plant environment. This review is an effort to provide a recent update into the diversity of genes in Acidobacteria useful for characterization, understanding ecological roles, and future biotechnological perspectives.

Matched MeSH terms: Genomics
Analysis of raw meats and fats of pigs using polymerase chain reaction for Halal authentication

Aida AA, Che Man YB, Wong CM, Raha AR, Son R

Meat Sci, 2005 Jan;69(1):47-52.
PMID: 22062638 DOI: 10.1016/j.meatsci.2004.06.020

A method for species identification from pork and lard samples using polymerase chain reaction (PCR) analysis of a conserved region in the mitochondrial (mt) cytochrome b (cyt b) gene has been developed. Genomic DNA of pork and lard were extracted using Qiagen DNeasy(®) Tissue Kits and subjected to PCR amplification targeting the mt cyt b gene. The genomic DNA from lard was found to be of good quality and produced clear PCR products on the amplification of the mt cyt b gene of approximately 360 base pairs. To distinguish between species, the amplified PCR products were cut with restriction enzyme BsaJI resulting in porcine-specific restriction fragment length polymorphisms (RFLP). The cyt b PCR-RFLP species identification assay yielded excellent results for identification of pig species. It is a potentially reliable technique for detection of pig meat and fat from other animals for Halal authentication.

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 Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

Palomo A, Pedersen AG, Fowler SJ, Dechesne A, Sicheritz-Pontén T, Smets BF

ISME J, 2018 06;12(7):1779-1793.
PMID: 29515170 DOI: 10.1038/s41396-018-0083-3

The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss.

Matched MeSH terms: Genomics
Fulltext Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine

Salleh MZ, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, et al.

PLoS One, 2013;8(8):e71554.
PMID: 24009664 DOI: 10.1371/journal.pone.0071554

BACKGROUND: With a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine.
METHODS: Genomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences.
PRINCIPAL FINDINGS: Over 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings.
CONCLUSIONS: The current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.

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 Comparative Genomic Analysis Reveals a Possible Novel Non-Tuberculous Mycobacterium Species with High Pathogenic Potential

Choo SW, Dutta A, Wong GJ, Wee WY, Ang MY, Siow CC

PLoS One, 2016;11(4):e0150413.
PMID: 27035710 DOI: 10.1371/journal.pone.0150413

Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species. Thus, we conclude that this possible novel Mycobacterium species should be tightly monitored for its possible causative role in human infections.

Matched MeSH terms: Genomics
Fulltext Genomic and Phenotypic Comparisons Reveal Distinct Variants of Wolbachia Strain wAlbB

Martinez J, Ross PA, Gu X, Ant TH, Murdochy SM, Tong L, et al.

Appl Environ Microbiol, 2022 Nov 22;88(22):e0141222.
PMID: 36318064 DOI: 10.1128/aem.01412-22

The intracellular bacterium Wolbachia inhibits virus replication and is being harnessed around the world to fight mosquito-borne diseases through releases of mosquitoes carrying the symbiont. Wolbachia strains vary in their ability to invade mosquito populations and suppress viruses in part due to differences in their density within the insect and associated fitness costs. Using whole-genome sequencing, we demonstrate the existence of two variants in wAlbB, a Wolbachia strain being released in natural populations of Aedes aegypti mosquitoes. The two variants display striking differences in genome architecture and gene content. Differences in the presence/absence of 52 genes between variants include genes located in prophage regions and others potentially involved in controlling the symbiont's density. Importantly, we show that these genetic differences correlate with variation in wAlbB density and its tolerance to heat stress, suggesting that different wAlbB variants may be better suited for field deployment depending on local environmental conditions. Finally, we found that the wAlbB genome remained stable following its introduction in a Malaysian mosquito population. Our results highlight the need for further genomic and phenotypic characterization of Wolbachia strains in order to inform ongoing Wolbachia-based programs and improve the selection of optimal strains in future field interventions. IMPORTANCE Dengue is a viral disease transmitted by Aedes mosquitoes that threatens around half of the world population. Recent advances in dengue control involve the introduction of Wolbachia bacterial symbionts with antiviral properties into mosquito populations, which can lead to dramatic decreases in the incidence of the disease. In light of these promising results, there is a crucial need to better understand the factors affecting the success of such strategies, in particular the choice of Wolbachia strain for field releases and the potential for evolutionary changes. Here, we characterized two variants of a Wolbachia strain used for dengue control that differ at the genomic level and in their ability to replicate within the mosquito. We also found no evidence for the evolution of the symbiont within the 2 years following its deployment in Malaysia. Our results have implications for current and future Wolbachia-based health interventions.

Matched MeSH terms: Genomics
Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm

Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, et al.

Plant Sci, 2021 Mar;304:110731.
PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731

Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.

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
DENVirDB: a web portal of dengue virus sequence information on Asian isolates

Asnet MJ, Rubia AG, Ramya G, Nagalakshmi RN, Shenbagarathai R

J Vector Borne Dis, 2014 Jun;51(2):82-5.
PMID: 24947213

DENVirDB is a web portal that provides the sequence information and computationally curated information of dengue viral proteins. The advent of genomic technology has increased the sequences available in the public databases. In order to create relevant concise information on Dengue Virus (DENV), the genomic sequences were collected, analysed with the bioinformatics tools and presented as DENVirDB. It provides the comprehensive information of complete genome sequences of dengue virus isolates of Southeast Asia, viz. India, Bangladesh, Sri Lanka, East Timor, Philippines, Malaysia, Papua New Guinea, Brunei and China. DENVirDB also includes the structural and non-structural protein sequences of DENV. It intends to provide the integrated information on the physicochemical properties, topology, secondary structure, domain and structural properties for each protein sequences. It contains over 99 entries in complete genome sequences and 990 entries in protein sequences, respectively. Therefore, DENVirDB could serve as a user friendly database for researchers in acquiring sequences and proteomic information in one platform.

Matched MeSH terms: Genomics/methods

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