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Fulltext Preliminary study on the occurrence of pten and PIK3CA gene mutations in endometrial cancer among Malaysian women

Subramaniam, K.S., Wong, M.S., Woo, Y.L., Mat Adenan, N.A., Mohamed, Z., Chung, I., et al.

JUMMEC, 2013;16(1):1-5.
MyJurnal

Genetic mutations in endometrial cancer (EC) have been extensively studied in the Western population but not much in Asian cohorts. This study has demonstrated that PTEN and PIK3CA mutations are commonly found in EC among Malaysian women. Following RNA extraction from 20 cancerous and 18 non-cancerous tissues, the presence of mutations in 9 exons of PTEN and 3 exons of PIK3CA genes were detected using real-time PCR, accompanied by High Resolution Melt (HRM) analysis. Sequencing confirmed specificity of each PCR product. The mutations for both genes were detected in the samples with varying frequencies. Notably, all samples expressed mutation of PTEN at exon 7 but none in exon 4. Further analysis demonstrated that strong concurrent mutations occurred between exons 7 of PTEN with exon 20 region 1 of PIK3CA gene (90%). Our data showed mutations are present in EC and not the non-cancerous tissues. Larger samples are being collected to validate this observation.

Matched MeSH terms: RNA
Carbon nanotubes (CNTs) based advanced dermal therapeutics: current trends and future potential

Kuche K, Maheshwari R, Tambe V, Mak KK, Jogi H, Raval N, et al.

Nanoscale, 2018 May 17;10(19):8911-8937.
PMID: 29722421 DOI: 10.1039/c8nr01383g

The search for effective and non-invasive delivery modules to transport therapeutic molecules across skin has led to the discovery of a number of nanocarriers (viz.: liposomes, ethosomes, dendrimers, etc.) in the last few decades. However, available literature suggests that these delivery modules face several issues including poor stability, low encapsulation efficiency, and scale-up hurdles. Recently, carbon nanotubes (CNTs) emerged as a versatile tool to deliver therapeutics across skin. Superior stability, high loading capacity, well-developed synthesis protocol as well as ease of scale-up are some of the reason for growing interest in CNTs. CNTs have a unique physical architecture and a large surface area with unique surface chemistry that can be tailored for vivid biomedical applications. CNTs have been thus largely engaged in the development of transdermal systems such as tuneable hydrogels, programmable nonporous membranes, electroresponsive skin modalities, protein channel mimetic platforms, reverse iontophoresis, microneedles, and dermal buckypapers. In addition, CNTs were also employed in the development of RNA interference (RNAi) based therapeutics for correcting defective dermal genes. This review expounds the state-of-art synthesis methodologies, skin penetration mechanism, drug liberation profile, loading potential, characterization techniques, and transdermal applications along with a summary on patent/regulatory status and future scope of CNT based skin therapeutics.

Matched MeSH terms: RNA Interference
Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community

How SW, Lim SY, Lim PB, Aris AM, Ngoh GC, Curtis TP, et al.

Water Sci Technol, 2018 May;77(9-10):2274-2283.
PMID: 29757179 DOI: 10.2166/wst.2018.143

Intensive aeration for nitrification is a major energy consumer in sewage treatment plants (STPs). Low-dissolved-oxygen (low-DO) nitrification has the potential to lower the aeration demand. However, the applicability of low-DO nitrification in the tropical climate is not well-understood. In this study, the potential of low-DO nitrification in tropical setting was first examined using batch kinetic experiments. Subsequently, the performance of low-DO nitrification was investigated in a laboratory-scale sequential batch reactor (SBR) for 42 days using real tropical sewage. The batch kinetic experiments showed that the seed sludge has a relatively high oxygen affinity. Thus, the rate of nitrification was not significantly reduced at low DO concentrations (0.5 mg/L). During the operation of the low-DO nitrification SBR, 90% of NH4-N was removed. The active low-DO nitrification was mainly attributed to the limited biodegradable organics in the sewage. Fluorescence in-situ hybridisation and 16S rRNA amplicon sequencing revealed the nitrifiers were related to Nitrospira genus and Nitrosomonadaceae family. Phylogenetic analysis suggests 47% of the operational taxonomic units in Nitrospira genus are closely related to a comammox bacteria. This study has demonstrated active low-DO nitrification in tropical setting, which is a more sustainable process that could significantly reduce the energy footprint of STPs.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext 16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows

Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Jamal R

Front Microbiol, 2018;9:767.
PMID: 29755427 DOI: 10.3389/fmicb.2018.00767

The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Morphometric and morphological study of mental foramen in the Malaysian population: anatomy and forensic implications

Aspalilah Alias, AbdelNasser Ibrahim, Siti Noorain Abu Bakar, Mohamed Swarhib Shafie, Faridah Mohd Nor, Srijit Das

International Medical Journal Malaysia, 2017;16(2):47-53.
MyJurnal

Introduction: The mental foramen is present on either side of the body of the mandible bone. This foramen
transmits mental vessels and nerves. In forensic anthropology, mental foramen may be important for
differentiating sex, estimating age and identifying various races based on morphology. The main aim of the
present study was to determine the position, shape and diameter of the mental foramen according to sex,
age and race by postmortem computed tomography in the Malaysian population.

Materials and Methods: A total of 79 dentulous patients (48 males, 31 females) from 3 age groups (18-30 years, 31– 50 years, 51-74
years) were selected for this study, and ten parameters were observed for each mandible. The parameters
were divided into two morphological and eight morphometric parameters. The morphometric parameters
were measured by using Osirix MD Software 3D Volume Rendering.

Results: Results showed that mandibular
body length and height were significantly greater in males than in females by independent t-test. (p< 0.05).
However, the mandibular body height was found to decrease significantly with age in both sexes by one-way
Anova. It was observed that the shape of mental foramen was 45.6% oval and 54.4% rounded. About 44.3% of
them were in line with the longitudinal axis of the second premolar tooth.

Conclusion: It was concluded that
mental foramen may be used for identification purposes, particularly for sex, age and race determination.

Matched MeSH terms: RNA-Binding Proteins
Fulltext Characterization of Occult Hepatitis C Virus (HCV) infection among Hemodialysis patient

Siti Nurul Fazlin Abdul Rahman, Hairul Aini Hamzah, Mohammed Imad Mustafa, Mohamed Hadzri Hasmoni

International Medical Journal Malaysia, 2017;16(11):22-22.
MyJurnal

The existence of new entity called occult hepatitis C virus (HCV) has
become a raising and escalating concern among healthcare professionals worldwide. It
is defined by the presence of viral RNA in liver and/or peripheral blood mononuclear
cells (PBMCs) within non HCV-infected patients. Previous study had shown the occult
HCV is infectious and capable of transmitting the virus to another host. Till today, HCV
infection remains common among hemodialysis patients despite having the best
preventive plans. Because of this, there is a significant concern about the source of viral
transmission. The aim of the study was to identify and characterize occult HCV infection
in PBMC sample of hemodialysis patients. This was an observational and cross sectional
study. (Copied from article).

Matched MeSH terms: RNA, Viral
Fulltext Linkage and retention in HCV care for HIV-infected populations: early data from the DAA era

Sacks-Davis R, Doyle JS, Rauch A, Beguelin C, Pedrana AE, Matthews GV, et al.

J Int AIDS Soc, 2018 04;21 Suppl 2:e25051.
PMID: 29633559 DOI: 10.1002/jia2.25051

INTRODUCTION: There is currently no published data on the effectiveness of DAA treatment for elimination of HCV infection in HIV-infected populations at a population level. However, a number of relevant studies and initiatives are emerging. This research aims to report cascade of care data for emerging HCV elimination initiatives and studies that are currently being evaluated in HIV/HCV co-infected populations in the context of implementation science theory.
METHODS: HCV elimination initiatives and studies in HIV co-infected populations that are currently underway were identified. Context, intervention characteristics and cascade of care data were synthesized in the context of implementation science frameworks.
RESULTS: Seven HCV elimination initiatives and studies were identified in HIV co-infected populations, mainly operating in high-income countries. Four were focused mainly on HCV elimination in HIV-infected gay and bisexual men (GBM), and three included a combination of people who inject drugs (PWID), GBM and other HIV-infected populations. None were evaluating treatment delivery in incarcerated populations. Overall, HCV RNA was detected in 4894 HIV-infected participants (range within studies: 297 to 994): 48% of these initiated HCV treatment (range: 21% to 85%; within studies from a period where DAAs were broadly available the total is 57%, range: 36% to 74%). Among studies with treatment completion data, 96% of 1109 initiating treatment completed treatment (range: 94% to 99%). Among those who could be assessed for sustained virological response at 12 weeks (SVR12), 1631 of 1757 attained SVR12 (93%, range: 86% to 98%).
CONCLUSIONS: Early results from emerging research on HCV elimination in HIV-infected populations suggest that HCV treatment uptake is higher than reported levels prior to DAA treatment availability, but approximately half of patients remain untreated. These results are among diagnosed populations and additional effort is required to increase diagnosis rates. Among those who have initiated treatment, completion and SVR rates are promising. More data are required in order to evaluate the effectiveness of these elimination programmes in the long term, assess which intervention components are effective, and whether they need to be tailored to particular population groups.

Matched MeSH terms: RNA
Fulltext Transcriptome analysis of reproductive tissue differentiation in Jatropha curcas Linn

Govender N, Senan S, Mohamed-Hussein ZA, Ratnam W

Genom Data, 2017 Sep;13:11-14.
PMID: 28626637 DOI: 10.1016/j.gdata.2017.05.008

Shoot and inflorescence are central physiological and developmental tissues of plants. Flowering is one of the most important agronomic traits for improvement of crop yield. To analyze the vegetative to reproductive tissue transition in Jatropha curcas, gene expression profiles were generated from shoot and inflorescence tissues. RNA isolated from both tissues was sequenced using the Ilumina HiSeq 2500 platform. Differential gene expression analysis identified key biological processes associated with vegetative to reproductive tissue transition. The present data for J. curcas may inform the design of breeding strategies particularly with respect to reproductive tissue transition. The raw data of this study has been deposited in the NCBI's Sequence Read Archive (SRA) database with the accession number SRP090662.

Matched MeSH terms: RNA
Fulltext In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas

Tran PN, Savka MA, Gan HM

Front Microbiol, 2017;8:1296.
PMID: 28747902 DOI: 10.3389/fmicb.2017.01296

The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans-P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Flexural and morphological properties of newly developed glass ionomer cement (GIC) with the incorporation of 3-acetylcoumarin

Azlisham, N.A.F., Abdul Rahman, F.S., Mohamad, D.

Malaysian Journal of Microscopy, 2015;11(1):11-15.
MyJurnal

The objective of the present study is to evaluate the effect of incorporation of 3- acetylcoumarin (3-AC), an antibacterial agent, on the mechanical and surface morphology of glass ionomer cement (GIC). A conventional GIC, Fuji II LC, was used as a control. 3-AC was incorporated into GIC during its manipulation at percentage of 2% and 5% (wt/wt). Flexural strength of the specimens were analysed using Shimadzu AGX-Plus while morphological evaluation of the specimens were observed using Scanning Electron Microscope (SEM). Oneway analysis (ANOVA) with post-hoc Bonferroni multiple-range test was used to determine the significant differences among the groups. Statistically, the incorporation of 2% (wt/wt) of 3-AC into GIC showed a significantly lower flexural strength (p

Matched MeSH terms: RNA-Binding Proteins
Fulltext RNA sequencing analysis of human podocytes reveals glucocorticoid regulated gene networks targeting non-immune pathways

Jiang L, Hindmarch CC, Rogers M, Campbell C, Waterfall C, Coghill J, et al.

Sci Rep, 2016 10 24;6:35671.
PMID: 27774996 DOI: 10.1038/srep35671

Glucocorticoids are steroids that reduce inflammation and are used as immunosuppressive drugs for many diseases. They are also the mainstay for the treatment of minimal change nephropathy (MCN), which is characterised by an absence of inflammation. Their mechanisms of action remain elusive. Evidence suggests that immunomodulatory drugs can directly act on glomerular epithelial cells or 'podocytes', the cell type which is the main target of injury in MCN. To understand the nature of glucocorticoid effects on non-immune cell functions, we generated RNA sequencing data from human podocyte cell lines and identified the genes that are significantly regulated in dexamethasone-treated podocytes compared to vehicle-treated cells. The upregulated genes are of functional relevance to cytoskeleton-related processes, whereas the downregulated genes mostly encode pro-inflammatory cytokines and growth factors. We observed a tendency for dexamethasone-upregulated genes to be downregulated in MCN patients. Integrative analysis revealed gene networks composed of critical signaling pathways that are likely targeted by dexamethasone in podocytes.

Matched MeSH terms: RNA/genetics*; Sequence Analysis, RNA/methods
Fulltext Data of the first de novo transcriptome assembly of the inflorescence of Curcuma alismatifolia

Taheri S, Abdullah TL, Noor YM, Padil HM, Sahebi M, Azizi P

Data Brief, 2018 Aug;19:2452-2454.
PMID: 30246104 DOI: 10.1016/j.dib.2018.07.038

Curcuma alismatifolia, is an Asian crop from Zingiberaceae family, popularly used as ornamental plant in floriculture industry of Thailand and Cambodia. Different varieties with a wide range of colors can be found in species. Until now, few breeding programs have been done on this species and most commercially important cultivars are hybrids that are propagated vegetatively. In spite of other flowering plants, there is still lack of transcriptomic-based data on the functions of genes related to flower color in C. alismatifolia. The raw data presented in this article provides information on new original transcriptome data of two cultivars of C. alismatifolia by Illumina Hiseq. 4000 RNA-Seq technology which is the first ever report about this plant. The data is accessible via European Nucleotide Archive (ENA) under project number PRJEB18956.

Matched MeSH terms: RNA
Fulltext Data on degradome sequencing and analysis from mock-inoculated and Fusarium oxysporum treated leaves samples in Persicaria minor

Samad AFA, Sajad M, Jani J, Murad AMA, Ismail I

Data Brief, 2018 Oct;20:555-557.
PMID: 30197911 DOI: 10.1016/j.dib.2018.08.034

Degradome sequencing referred as parallel analysis of RNA ends (PARE) by modifying 5'-rapid amplification of cDNA ends (RACE) with deep sequencing method. Deep sequencing of 5' products allow the determination of cleavage sites through the mapping of degradome fragments against small RNAs (miRNA or siRNA) on a large scale. Here, we carried out degradome sequencing in medicinal plant, Persicaria minor, to identify cleavage sites in small RNA libraries in control (mock-inoculated) and Fusarium oxysporum treated plants. The degradome library consisted of both control and treated samples which were pooled together during library preparation and named as D4. The D4 dataset have been deposited at GenBank under accession number SRX3921398, https://www.ncbi.nlm.nih.gov/sra/SRX3921398.

Matched MeSH terms: RNA, Small Interfering
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: RNA, Messenger
Fulltext Online shopping practices and factors influencing

Farhan Mat Arisah, Shamsul Azahari Zainal Badari, Ahmad Hariza Hashim

Malaysian Journal of Social Sciences and Humanities, 2016;1(3):111-123.
MyJurnal

Online shopping has been preferred over the conventional shopping methods as the results of hectic
lifestyles nowadays. It is a convenient way to get groceries without having to queue at the counters.
The objective of this research is to study the online shopping practices and the factors that affect it.
Apart from that, it is also to identify the difference in online shopping behaviour among selected
background factors (sex, social status, generation, ethnic, household income, education level and zone).
The populations of this research include consumers of 17 years old and above whose chosen by
convenience through mall intercept method. T-test result shows there is significant difference (t=-
3.156, p=0.001) for online shopping practice between men and women. Meanwhile, based on ANOVA result, it shows that there is significant difference between mean scores of different generation [F(3,
1298)= 3.475, p = 0.016], ethnics [F(4, 1291)= 3.678, p = 0.006] and household income [F (4, 1227)=
6.935, p = 0.000]. However, there is no significant difference among mean scores for education level,
zones and stratum (p>0.05). Apart from that, the result also indicates that only five factors taken into
consideration before a particular customer does the online shopping which are safety, products offered,
risk, trustworthy and customers experience. Thus, the sellers should approach their customers in
different ways in order to meet the demand, hence expanding their bussiness.

Matched MeSH terms: RNA-Binding Proteins
Fulltext A quantitative reverse transcription-polymerase chain reaction for detection of Getah virus

Sam SS, Teoh BT, Chee CM, Mohamed-Romai-Noor NA, Abd-Jamil J, Loong SK, et al.

Sci Rep, 2018 12 05;8(1):17632.
PMID: 30518924 DOI: 10.1038/s41598-018-36043-6

Getah virus (GETV), a mosquito-borne alphavirus, is an emerging animal pathogen causing outbreaks among racehorses and pigs. Early detection of the GETV infection is essential for timely implementation of disease prevention and control interventions. Thus, a rapid and accurate nucleic acid detection method for GETV is highly needed. Here, two TaqMan minor groove binding (MGB) probe-based quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays were developed. The qRT-PCR primers and TaqMan MGB probe were designed based on the conserved region of nsP1 and nsP2 genes of 23 GETV genome sequences retrieved from GenBank. Only the qRT-PCR assay using nsP2-specific primers and probe detected all two Malaysia GETV strains (MM2021 and B254) without cross-reacting with other closely related arboviruses. The qRT-PCR assay detected as few as 10 copies of GETV RNA, but its detection limit at the 95% probability level was 63.25 GETV genome copies (probit analysis, P ≤ 0.05). Further validation of the qRT-PCR assay using 16 spiked simulated clinical specimens showed 100% for both sensitivity and specificity. In conclusion, the qRT-PCR assay developed in this study is useful for rapid, sensitive and specific detection and quantification of GETV.

Matched MeSH terms: RNA, Viral/analysis; RNA, Viral/blood; RNA, Viral/genetics
Discovery of the westernmost population of the genus Ansonia Stoliczka (Anura, Bufonidae) with the description of a new species from the Shan Plateau of eastern Myanmar

Quah ESH, Grismer LL, Wood PLJ, Thura MK, Oaks JR, Lin A

Zootaxa, 2019 Aug 14;4656(3):zootaxa.4656.3.11.
PMID: 31716818 DOI: 10.11646/zootaxa.4656.3.11

A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but differs from it and other congeners by at least a 5.0% sequence divergence. It is further differentiated by the following combination of morphological characters: (1) maximum SVL 24 mm in males and females; (2) first finger shorter than second; (3) absence of interorbital and tarsal ridges; (4) presence of light-coloured interscapular spot; (5) presence of yellow rictal tubercle; (6) absence of wide, light-coloured patch below eye; (7) presence of large, discrete, bright-yellow submandibular spots along the underside of lower jaw; (8) iris yellow-gold; (9) presence of markings on the snout consisting of streaks below the eye to the lip, and on the canthus rostralis to the nostril; (10) dorsum grey-brown with orange-beige spots, a dark-brown X-shaped marking on the back surrounding the interscapular spot, and dark-coloured markings on rump; (11) fore- and hind limbs with orange-beige cross-bars; and (12) venter light-gray with yellow spotting, especially near flanks and underside of hind limbs. Ansonia kyaiktiyoensis sp. nov. is the westernmost known record for the genus and the only species west of the Salween Basin. Its discovery echoes the increasing number of herpetological discoveries being made in upland regions fringing the Ayeyarwady and Salween Basins.

Matched MeSH terms: RNA, Ribosomal, 16S
Tumbuhan etnoperubatan sebagai perumah aktinomiset endofit yang bersifat bioaktif

Nurul ‘Izzah Mohd Sarmin, Noraziah M. Zin, Nik Marzuki Sidik, Franco CM, Ng KT, Kaewkla O

Sains Malaysiana, 2012;41:547-551.

Sembilan aktinomiset endofit telah berjaya dipencilkan daripada pokok yang mempunyai nilai ubatan dari beberapa tempat di Semenanjung Malaysia. Pencilan tersebut telah dikenalpasti melalui pemerhatian morfologi, amplifikasi gen 16S rRNA dan analisis penjujukan 16S rRNA. Saringan awal terhadap aktiviti antimikrob telah dilakukan dengan menggunakan teknik calitan plat. Pembentukan miselium substrat dan aerial, warna jisim spora, pigmen larut dan morfologi rantai spora pada semua pencilan menyerupai Streptomyces sp. dan Microbispora sp. Analisis filogenetik jujukan separa 16S rRNA mendapati pencilan SUK 08, SUK 10 dan SUK 15 saling berkaitan dengan Streptomyceseurythermus ATCC 14975T. Walau bagaimanapun pencilan ini telah dipencilkan dari tumbuhan yang berbeza. Pencilan ini didapati mempunyai aktiviti antimikrob terhadap bakteria dan kulat kajian. Empat pencilan aktif iaitu SUK 08, SUK10, SUK 12 dan SUK 15 berupaya untuk membunuh dan merencat sehingga 100% satu atau lebih organisma patogen seperti Bacillus subtilis, Aspergillus fumigatus, Aspergillus niger, Fusarium solani, Rhizoctonia solani dan Trichoderma viride. Kajian ini mengesahkan bahawa tumbuhan etnoperubatan adalah sumber pencarian aktinomiset endofit bioaktif yang berupaya menjadi sumber novel dalam pencarian agen antibakteria dan antimikotik.

Matched MeSH terms: RNA, Ribosomal, 16S
Molecular characterization of Malaysian marine fish species using partial sequence of mitochondrial DNA 12S and 16S rRNA markers

Nur Haslindawaty Abd Rashid, Siti Farah Quraisha, Sundararajulu Panneerchelvam, Zafarina Zainuddin

Sains Malaysiana, 2015;44:1119-1123.

This study was conducted to characterize the selected marine fish species using partial sequence of mtDNA 12S and 16S rRNA gene. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 350 and 440 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Two reference species have been used namely Gobio gobio (AB239596 and EF112528) and Pentapodus caninus (DQ533268 and DQ532933). Based on the result obtained, mtDNA 12S and 16S rRNA were found to be useful as molecular markers for fish species identification. These markers will provide correct identification of fish species when considered along with morphological characteristics.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext The Whole Genome Sequence and mRNA Transcriptome of the Tropical Cyclopoid Copepod Apocyclops royi

Jørgensen TS, Nielsen BLH, Petersen B, Browne PD, Hansen BW, Hansen LH

G3 (Bethesda), 2019 05 07;9(5):1295-1302.
PMID: 30923136 DOI: 10.1534/g3.119.400085

Copepoda is one of the most ecologically important animal groups on Earth, yet very few genetic resources are available for this Subclass. Here, we present the first whole genome sequence (WGS, acc. UYDY01) and the first mRNA transcriptome assembly (TSA, Acc. GHAJ01) for the tropical cyclopoid copepod species Apocyclops royi Until now, only the 18S small subunit of ribosomal RNA gene and the COI gene has been available from A. royi, and WGS resources was only available from one other cyclopoid copepod species. Overall, the provided resources are the 8th copepod species to have WGS resources available and the 19th copepod species with TSA information available. We analyze the length and GC content of the provided WGS scaffolds as well as the coverage and gene content of both the WGS and the TSA assembly. Finally, we place the resources within the copepod order Cyclopoida as a member of the Apocyclops genus. We estimate the total genome size of A. royi to 450 Mb, with 181 Mb assembled nonrepetitive sequence, 76 Mb assembled repeats and 193 Mb unassembled sequence. The TSA assembly consists of 29,737 genes and an additional 45,756 isoforms. In the WGS and TSA assemblies, >80% and >95% of core genes can be found, though many in fragmented versions. The provided resources will allow researchers to conduct physiological experiments on A. royi, and also increase the possibilities for copepod gene set analysis, as it adds substantially to the copepod datasets available.

Matched MeSH terms: RNA, Messenger

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