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Molecular identification of Eimeria hestermani and Eimeria prionotemni from a red-necked wallaby (Macropodidae; Macropus rufogriseus) in Japan

Ekawasti F, Kitagawa K, Domae H, Wardhana AH, Shibahara T, Uni S, et al.

Parasitol Res, 2020 Apr;119(4):1271-1279.
PMID: 32072327 DOI: 10.1007/s00436-020-06618-2

To date, more than 50 Eimeria spp. have been isolated from marsupials of the family Macropodidae. Although 18 species of Eimeria have been previously detected from multiple animal species belonging to the genus Macropus of the family, limited genetic analyses of the parasites are available, and their pathogenicity remains unclear. Here, we report the isolation of Eimeria spp. from a zoo specimen of red-necked wallaby (Macropodidae; Macropus rufogriseus). Specifically, two distinct types of Eimeria oocysts were recovered, one from the feces before treatment with an anthelmintic and the second from the intestinal contents after death of the animal. The oocysts obtained from the two sources were morphologically identified as E. hestermani and E. prionotemni, respectively. We successfully determined partial gene sequences from the two isolates, including segments of the 18S rRNA genes, and for the first time have used phylogenetic analyses of these sequences to assign the species to distinct clades. In combination with further genetic data, these results are expected to help elucidate the pathogenicity and host ranges of Eimeria spp. within the respective family and genus.

Matched MeSH terms: RNA, Ribosomal, 18S
Fulltext The first dataset of de novo transcriptome assembly of Heterotrigona itama (Apidae, Meliponinae) queen larva

Tamizi AA, Nazaruddin NH, Yeong WC, Mohd Radzi MF, Jaafar MA, Sekeli R

Data Brief, 2020 Apr;29:105235.
PMID: 32071998 DOI: 10.1016/j.dib.2020.105235

Heterotrigona itama is a species of stingless bee recently domesticated (or reared) for honey production in a few Southeast Asian countries namely Malaysia and Indonesia. Being categorized in the clade Corbiculata together with the honeybees (Apis spp.) and bumble bees (Bombus spp.), the stingless bees are highly social in which the colony members are subjected to labor division where a queen functions as the reproductive caste. In this data article, we provide a resource encompassing a transcriptome profile (de novo assembled) from H. itama queen larva - the first report of transcriptome assembly for this species. The generated data is pivotal for the characterization of important genes and biological pathways in order to further improve our understanding on the developmental biology, behavior, social structure and ecological needs of this eusocial hymenopteran insect from the molecular aspect. The raw RNA sequencing data is available at NCBI Sequence Read Archive (SAR) under the accession number SRP230250 and the assembled reads are deposited at DDBJ/EMBL/Genbank as Transcriptome Shotgun Assembly (TSA) under the accession GIIH00000000.

Matched MeSH terms: Sequence Analysis, RNA
Characterization of Aquimarina hainanensis isolated from diseased mud crab Scylla serrata larvae in a hatchery

Midorikawa Y, Shimizu T, Sanda T, Hamasaki K, Dan S, Lal MTBM, et al.

J Fish Dis, 2020 May;43(5):541-549.
PMID: 32147853 DOI: 10.1111/jfd.13151

Mass mortality due to necrosis signs occurred in hatchery-reared zoea stage larvae of the mud crab Scylla serrata in Okinawa, Japan, and a causative bacterium was isolated. In this study, we identified and characterized the bacterium by genome analysis, biochemical properties and pathogenicity. The bacterium was a Gram-negative, non-motile, long rod, forming yellow colonies on a marine agar plate. It grew at 20-33°C (not at 37°C) and degraded chitin and gelatin. Phylogenetic analysis of the 16S rRNA gene sequence identified the bacterium as Aquimarina hainanensis. Genome sequence data obtained from Illumina MiSeq generated 29 contigs with 3.56 Mbp in total length and a G + C content of 32.5%. The predicted 16 chitinase genes, as putative virulence factors, had certain homologies with those of genus Aquimarina. Experimental infection with the bacterium conducted on larvae of four crustacean species, brine shrimp Artemia franciscana, freshwater shrimp Caridina multidentata, swimming crab Portunus trituberculatus and mud crab S. serrata, revealed that this bacterium was highly virulent to these species. The present study suggests that the bacterium caused mass mortality in mud crab seed production was A. hainanensis and can be widely pathogenic to crustaceans.

Matched MeSH terms: RNA, Ribosomal, 16S
MicroRNAomic Transcriptomic Analysis Reveal Deregulation of Clustered Cellular Functions in Human Mesenchymal Stem Cells During in Vitro Passaging

Aung SW, Abu Kasim NH, Shamsuddin SAA, Ramasamy TS

Stem Cell Rev Rep, 2020 02;16(1):222-238.
PMID: 31848878 DOI: 10.1007/s12015-019-09924-0

Clinical trials using human mesenchymal stem/stromal cells (hMSCs) for cell replacement therapy showed varied outcomes, where cells' efficacy has been perceived as the limiting factor. In particular, the quality and number of the expanded cells in vitro. In this study, we aimed to determine molecular signatures of hMSCs derived from the pulp of extracted deciduous teeth (SHED) and Wharton's jelly (WJSCs) that associated with cellular ageing during in vitro passaging. We observed distinct phenotypic changes resembling proliferation reduction, cell enlargement, an increase cell population in G2/M phase, and differentially expressed of tumor suppressor p53 in passage (P) 6 as compared to P3, which indicating in vitro cell senescence. The subsequent molecular analysis showed a set of diverse differentially expressed miRNAs and mRNAs involved in maintaining cell proliferation and stemness properties. Considering the signaling pathway related to G2/M DNA damage regulation is widely recognized as part of anti-proliferation mechanism controlled by p53, we explored possible miRNA-mRNA interaction in this regulatory pathway based on genomic coordinates retrieved from miRanda. Our work reveals the potential reason for SHED underwent proliferation arrest due to the direct impinge on the expression of CKS1 by miRNAs specifically miR-22 and miR-485-5p which lead to down regulation of CDK1 and Cyclin B. It is intended that our study will contribute to the understanding of these miRNA/mRNA driving the biological process and regulating different stages of cell cycle is beneficial in developing effective rejuvenation strategies in order to obtain quality stem cells for transplantation.

Matched MeSH terms: RNA, Messenger
First Report of Cabbage Soft Rot Caused by Pectobacterium carotovorum subsp. carotovorum in Malaysia

Nazerian E, Sijam K, Mior Ahmad ZA, Vadamalai G

Plant Dis, 2011 Apr;95(4):491.
PMID: 30743350 DOI: 10.1094/PDIS-09-10-0683

Cabbage (Brassica oleracea L. var. capitata L.) is one of the most important vegetables cultivated in Pahang and Kelantan, Malaysia. Pectobacterium carotovorum can cause soft rot on a wide range of crops worldwide, especially in countries with warm and humid climates such as Malaysia. Cabbage with symptoms of soft rot from commercial fields were sampled and brought to the laboratory during the winter of 2010. Disease symptoms were a gray to pale brown discoloration and expanding water-soaked lesions on leaves. Several cabbage fields producing white cultivars were investigated and 27 samples were collected. Small pieces of leaf samples were immersed in 5 ml of saline solution (0.80% NaCl) for 20 min to disperse the bacterial cells. Fifty microliters of the resulting suspension was spread on nutrient agar (NA) and King's B medium and incubated at 30°C for 48 h. Purification of cultures was repeated twice on these media. Biochemical and phenotypical tests gave these results: gram negative, rod shaped, ability to grow under liquid paraffin (facultative anaerobe); oxidase negative; phosphatase negative; positive degradation of pectate; sensitive to erythromycin; negative to Keto-methyl glucoside utilization, indole production and reduction sugars from sucrose were negative; acid production from sorbitol and arabitol was negative and from melibiose, citrate, and raffinose was positive. Hypersensitivity reaction on tobacco leaf with the injection of 106 CFU/ml of bacterial suspension for all strains was positive. Four representative strains were able to cause soft rot using cabbage slices (three replications) inoculated with a bacterial suspension at 106 CFU/ml. Inoculated cabbage slices were incubated in a moist chamber at 80% relative humidity and disease symptoms occurred after 24 h. Cabbage slices inoculated with water as a control remained healthy. The bacteria reisolated from rotted cabbage slices on NA had P. carotovorum cultural characteristics and could cause soft rot in subsequent tests. PCR amplification with Y1 and Y2 primers (1), which are specific for P. carotovorum, produced a 434-bp band with 15 strains. PCR amplification of the 16S-23S rRNA intergenic transcribed spacer region (ITS) using G1 and L1 primers gave two main bands approximately 535 and 580 bp and one faint band approximately 740 bp when electrophoresed through a 1.5% agarose gel. The ITS-PCR products were digested with RsaI restriction enzyme. According to biochemical and physiological characterictics (2), PCR-based pel gene (1), and analysis by ITS-PCR and ITS-restriction fragment length polymorphism (3), all isolates were identified as P. carotovorum subsp. carotovorum. This pathogen has been reported from Thailand, Indonesia, and Singapore with whom Malaysia shares its boundaries. To our knowledge, this is the first report of P. carotovorum subsp. carotovorum in cabbage from Malaysia. References: (1) A. Darraas et al. Appl. Environ. Microbiol. 60:1437, 1994. (2) N. W. Schaad et al. Laboratory Guide for the Identification of Plant Pathogenic Bacteria. 3rd ed. The American Phytopathological Society, St. Paul, 2001. (3) I. K. Toth et al. Appl. Environ. Microbiol. 67:4070, 2001.

Matched MeSH terms: RNA, Ribosomal, 23S
Fulltext A 23 bp cyp51A Promoter Deletion Associated With Voriconazole Resistance in Clinical and Environmental Isolates of Neocosmospora keratoplastica

James JE, Lamping E, Santhanam J, Milne TJ, Abd Razak MF, Zakaria L, et al.

Front Microbiol, 2020;11:272.
PMID: 32296397 DOI: 10.3389/fmicb.2020.00272

In the fungal pathogen Aspergillus fumigatus, resistance to azole antifungals is often linked to mutations in CYP51A, a gene that encodes the azole antifungal drug target lanosterol 14α-demethylase. The aim of this study was to investigate whether similar changes could be associated with azole resistance in a Malaysian Fusarium solani species complex (FSSC) isolate collection. Most (11 of 15) clinical FSSC isolates were Neocosmospora keratoplastica and the majority (6 of 10) of environmental isolates were Neocosmospora suttoniana strains. All 25 FSSC isolates had high minimum inhibitory concentrations (MICs) for itraconazole and posaconazole, low MICs for amphotericin B, and various (1 to >32 mg/l) voriconazole susceptibilities. There was a tight association between a 23 bp CYP51A promoter deletion and high (>32 mg/l) voriconazole MICs; of 19 FSSC strains sequenced, nine isolates had voriconazole MICs > 32 mg/l, and they all contained the 23 bp CYP51A promoter deletion, although it was absent in the ten remaining isolates with low (≤12 mg/l) voriconazole MICs. Surprisingly, this association between voriconazole resistance and the 23 bp CYP51A promoter deletion held true across species boundaries. It was randomly distributed within and across species boundaries and both types of FSSC isolates were found among environmental and clinical isolates. Three randomly selected N. keratoplastica isolates with low (≤8 mg/l) voriconazole MICs had significantly lower (1.3-7.5 times) CYP51A mRNA expression levels than three randomly selected N. keratoplastica isolates with high (>32 mg/l) voriconazole MICs. CYP51A expression levels, however, were equally strongly induced (~6,500-fold) by voriconazole in two representative strains reaching levels, after 80 min of induction, that were comparable to those of CYP51B. Our results suggest that FSSC isolates with high voriconazole MICs have a 23 bp CYP51A promoter deletion that provides a potentially useful marker for voriconazole resistance in FSSC isolates. Early detection of possible voriconazole resistance is critical for choosing the correct treatment option for patients with invasive fusariosis.

Matched MeSH terms: RNA, Messenger
Fulltext RNA-seq data from whole rice grains of pigmented and non-pigmented Malaysian rice varieties

Zainal-Abidin RA, Zainal Z, Mohamed-Hussein ZA, Abu-Bakar N, Ab Razak MSF, Simoh S, et al.

Data Brief, 2020 Jun;30:105432.
PMID: 32280737 DOI: 10.1016/j.dib.2020.105432

Pigmented rice is enriched with antioxidants, macro- and micronutrients. A comprehensive investigation of the gene expression patterns among the pigmented rice varieties would help to understand the cellular mechanism and biological processes of rice grain pigmentation. Hence, we performed RNA sequencing and analysis on the whole grain of dehusked mature seeds of selected six Malaysian rice varieties with varying grain pigmentations. These varieties were black rice (BALI and Pulut Hitam 9), red rice (MRM16 and MRQ100) and white rice (MR297 and MRQ76). Illumina HiSeq™ 4000 sequencer was used to generate total raw nucleotides of approximately 53 Gb in size. From 353,937,212 total paired-end raw reads, 340,131,496 total clean reads were obtained. The raw reads were deposited into European Nucleotide Archive (ENA) database and can be accessed via accession number PRJEB34340. This dataset allows us to identify and profile all expressed genes with functions related to nutritional traits (i.e. antioxidants, folate and amylose content) and quality trait (i.e. aroma) across both pigmented and non-pigmented rice varieties. In addition, the transcriptome data obtained will be valuable for discovery of potential gene markers and functional SNPs related to functional traits to assist in rice breeding programme.

Matched MeSH terms: Sequence Analysis, RNA
Effects of different doses of fertilizers on growth and yield components of biodiesel plant (jatropha curcas l.)

Inam Ali Shah, Sultan Mehmod Wazir, Rahmat Ali Khan

Sains Malaysiana, 2017;46:117-122.

Effects of different doses of fertilizers on growth and yield components of biodiesel plant (Jatropha curcas L.), was
made in the prevailing environment of University of Science and Technology Bannu. The experiment was carried out in
randomized complete block design (RCBD) with three replications. Nitrogen, phosphorus and potassium were applied
in the form of urea, single super phosphate and potash in the shape of combined NPK, respectively, during sprouting
of leaves and thereafter with each irrigation in split doses. The analysis of variance for number of branches per plant
showed significant results indicated in ANOVA. Significantly the number of primary branches per plant 8.07 was recorded
in T4 with the application of dose of (N P K: 2507.5 gm: 1091.5 gm: 501.5 gm). Maximum No. of secondary branches
per plant (9.100) were recorded in T1 especially at both plots. Flower per inflorescence showed that maximum value
(122.810) was recorded in T5 of especially at both plots. Inflorescence plant-1 showed that maximum value (39.477) were
recorded in T1 and minimum value were noted as (12.733) at T3 on both the flats. The data for fruits per plant showed
that maximum value (143.300) was recorded in T1. The seed index, which was the output of the aim of this research work,
reflects highly significant differences in mean value observed for both subplots. Mean values showed that maximum seeds
weight 45.86 was recorded in T1 of especially at both plots while low seed index was noted as 22.84 at T5 (N: 3400 gm,
P: 1480 gm, K: 680 gm) at both the subplots.

Matched MeSH terms: RNA-Binding Proteins
Dual panel multiplex PCR assay for rapid detection of medically important fungi and resistant species of candida and aspergillus

Jacinta Santhanam, Mohd Hanif Jainlabdin, Ang LC, Tzar Mohd Nizam

Sains Malaysiana, 2018;47:489-498.

Invasive fungal infections (IFIs) have risen dramatically in recent years among high risk immunocompromised patients.
Rapid detection of fungal pathogens is crucial to timely and accurate antifungal therapy. Two multiplex polymerase
chain reaction (PCR) assays were developed to detect major fungal species that cause invasive infections and identify
resistant species. Genus specific primers for Candida, Aspergillus, Fusarium and species specific primers for Candida
glabrata, Candida krusei and Aspergillus terreus which are known to be clinically resistant species, were designed from
the internal transcribed spacer (ITS) regions of ribosomal ribonucleic acid (rRNA) gene complex. Both assays were
performed simultaneously to promote rapid detection of fungal isolates based on distinct amplicon sizes. Inclusion of the
universal fungal primers ITS 1 and ITS 4 in the genus specific assay produced a second amplicon for each isolate which
served to confirm the detection of a fungal target. The limit of detection for the genus specific assay was 1 nanogram
(ng) deoxyribonucleic acid (DNA) for Aspergillus fumigatus and Candida albicans, 0.1 ng DNA for Fusarium solani, while
the species-specific assay detected 0.1 ng DNA of A. terreus and 10 picogram (pg) DNA of C. krusei and C. glabrata. The
multiplex PCR assays, apart from universal detection of any fungal target, are able to detect clinically important fungi
and differentiate resistant species rapidly and accurately, which can contribute to timely implementation of effective
antifungal regime.

Matched MeSH terms: RNA
Fulltext Discovery of novel genic-SSR markers from transcriptome dataset of an important non-human primate, Macaca fascicularis

Chang W, Ee-Uli J, Ng WL, Rovie-Ryan JJ, Tan SG, Yong CSY

Sci Rep, 2019 06 11;9(1):8504.
PMID: 31186469 DOI: 10.1038/s41598-019-44870-4

Macaca fascicularis, also known as the cynomolgus macaque, is an important non-human primate animal model used in biomedical research. It is an Old-World primate widely distributed in Southeast Asia and is one of the most abundant macaque species in Malaysia. However, the genetic structure of wild cynomolgus macaque populations in Malaysia has not been thoroughly elucidated. In this study, we developed genic-simple sequence repeat (genic-SSR) markers from an in-house transcriptome dataset generated from the Malaysian cynomolgus macaque via RNA sequencing, and applied these markers on 26 cynomolgus macaque individuals. A collection of 14,751 genic-SSRs were identified, where 13,709 were perfect SSRs. Dinucleotide repeats were the most common repeat motifs with a frequency of 65.05%, followed by trinucleotide repeats (20.55%). Subsequently, we designed 300 pairs of primers based on perfect di- and trinucleotide SSRs, in which 105 SSRs were associated with functional genes. A subset of 30 SSR markers were randomly selected and validated, yielding 19 polymorphic markers with an average polymorphism information content value of 0.431. The development of genic-SSR markers in this study is indeed timely to provide useful markers for functional and population genetic studies of the cynomolgus macaque and other related non-human primate species.

Matched MeSH terms: Sequence Analysis, RNA
Fulltext Purification and kinetics of the PHB depolymerase of Microbacterium paraoxydans RZS6 isolated from a dumping yard

Sayyed RZ, Wani SJ, Alyousef AA, Alqasim A, Syed A, El-Enshasy HA

PLoS One, 2019;14(6):e0212324.
PMID: 31211775 DOI: 10.1371/journal.pone.0212324

Poly-β-hydroxybutyrate (PHB) depolymerase is known to decompose PHB, biodegradable polymers and therefore has great commercial significance in the bioplastic sector. However, reports on PHB depolymerases from isolates obtained from plastic-contaminated sites that reflect the potential of the source organism is scarce. In this study, we evaluated the production of extracellular PHB depolymerase from Microbacterium paraoxydans RZS6 isolated from the plastic-contaminated site in the municipal area of Shahada, Maharashtra, India, for the first time. The isolate was identified using 16S rRNA gene sequencing, gas chromatographic analysis of fatty acid methyl esters (GC-FAME), and BIOLOG method. Ithydrolyzed PHB on minimal salt medium (MSM) containing PHB as the only source of carbon. The isolate produced PHB depolymerase at 45°C during 48 h of incubation. The enzyme was purified most efficiently using octyl-sepharose CL-4B column, with the highest purification yield of 6.675 Umg-1mL-1. The activity of the enzyme was enhanced in the presence of Ca2+ and Mg2+ ions but inhibited by Fe2+ (1 mM) ions and mercaptoethanol (1000 rpm). the nzyme kinetic analysis revealed that the enzyme was a metalloenzyme; requiring Mg2+ ions, that showed optimum enzyme activity at 30°C (mesophilic) and under neutrophilic (pH 7) conditions. Scale-up from the shake-flask level to a laboratory-scale bioreactor further enhanced the enzyme yield by 0.809 UmL-1. The molecular weight of the enzyme (40 kDa), as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, closely resembled the PHB depolymerase of Aureobacterium saperdae. Our findings highlighted the applicability of M. paraoxydans as a producer of extracellular PHB depolymerase having potential of degrading PHB under diverse conditions.

Matched MeSH terms: RNA, Ribosomal, 16S
Scale morphologies of freshwater fishes at Tembat Forest Reserve, Terengganu, Malaysia

Farah Ayuni Farinordin, Wan Seribani Wan Nilam, Shahril Mod Husin, Abdullah Samat, Shukor Md. Nor

Sains Malaysiana, 2017;46:1429-1439.

Scales are calcium carbonate and collagen-contained structures embedded within the fish epidermis and useful for
species identification. This study aimed to describe morphological characteristics of scales and use the differences to
prepare keys to species. Fishes were sampled from selected rivers of Tembat Forest Reserve, Hulu Terengganu. Specimens
caught were from 3 families (Cyprinidae, Channidae, Nandidae) and 17 species. Each species was represented by ten
individuals (size ranges 2.5 - 50 cm TL). The scales were removed, soaked in H2
O2
(0.5%), NH3 (0.3%), DH2
O and
mounted between a pair of glass slides for digital photographing. The morphological descriptions were based on types
of scales, distinctiveness of radii arrangement at the anterior field, radii cover, radii distribution, overall shape, focus
position and focus pattern. Keys to species were constructed based on these scale morphological characters described.
Measurements of scale total length (L), total width (W), rostral field length (L1) and caudal field length (L2) of the scales
were taken using Image J software. The inter-specific variation among scales was indicated by L1/L, L2/L, L1/L2 and
W/L indices through multiple comparison tests (ANOVA). It was found that all 17 species showed significant differences
with at least one other species in all four indices. Pristolepis grootii (Bleeker 1852) was the only one that significantly
different (p<0.05) from other 16 species in the first three indices. Species that showed the least significant differences
among species was Probarbus jullieni (Sauvage 1880). The differences among the scales were primarily due to the
different types of scale that was either ctenoid or cycloid.

Matched MeSH terms: RNA-Binding Proteins
Molecular and physiological responses during thermal acclimation of leaf photosynthesis and respiration in rice

Rashid FAA, Crisp PA, Zhang Y, Berkowitz O, Pogson BJ, Day DA, et al.

Plant Cell Environ, 2020 03;43(3):594-610.
PMID: 31860752 DOI: 10.1111/pce.13706

To further our understanding of how sustained changes in temperature affect the carbon economy of rice (Oryza sativa), hydroponically grown plants of the IR64 cultivar were developed at 30°C/25°C (day/night) before being shifted to 25/20°C or 40/35°C. Leaf messenger RNA and protein abundance, sugar and starch concentrations, and gas-exchange and elongation rates were measured on preexisting leaves (PE) already developed at 30/25°C or leaves newly developed (ND) subsequent to temperature transfer. Following a shift in growth temperature, there was a transient adjustment in metabolic gene transcript abundance of PE leaves before homoeostasis was reached within 24 hr, aligning with Rdark (leaf dark respiratory CO2 release) and An (net CO2 assimilation) changes. With longer exposure, the central respiratory protein cytochrome c oxidase (COX) declined in abundance at 40/35°C. In contrast to Rdark , An was maintained across the three growth temperatures in ND leaves. Soluble sugars did not differ significantly with growth temperature, and growth was fastest with extended exposure at 40/35°C. The results highlight that acclimation of photosynthesis and respiration is asynchronous in rice, with heat-acclimated plants exhibiting a striking ability to maintain net carbon gain and growth when exposed to heat-wave temperatures, even while reducing investment in energy-conserving respiratory pathways.

Matched MeSH terms: RNA, Messenger
Short communication: Genetic variants of Sarcocystis cruzi in infected Malaysian cattle based on 18S rDNA

Ng YH, Fong MY, Subramaniam V, Shahari S, Lau YL

Res Vet Sci, 2015 Dec;103:201-4.
PMID: 26679818 DOI: 10.1016/j.rvsc.2015.10.009

Sarcocystis species are pathogenic parasites that infect a wide range of animals, including cattle. A high prevalence of cattle sarcocystosis has been reported worldwide, but its status is unknown in Malaysia. This study focused on utilizing 18S rDNA to identify Sarcocystis species in Malaysian cattle and to determine their genetic variants. In this study, only Sarcocystis cruzi was detected in Malaysian cattle. The intra-species S. cruzi phylogenetic tree analysis and principal coordinate analysis (PCoA), respectively displayed two minor groups among the parasite isolates. This finding was supported by high Wright FST value (FST=0.647). The definitive hosts (dogs) may play a fundamental role in the development of S. cruzi genetic variants. Additionally, the existence of microheterogeneity within the S. cruzi merozoites and/or distinct genetic variants arisen from independent merozoites in mature sarcocysts, possibly contributed to the existence of intra-species variations within the population.

Matched MeSH terms: RNA, Ribosomal, 18S
Isolation and Pathogenicity of Streptococcus iniae in Cultured Red Hybrid Tilapia in Malaysia

Rahmatullah M, Ariff M, Kahieshesfandiari M, Daud HM, Zamri-Saad M, Sabri MY, et al.

J Aquat Anim Health, 2017 Dec;29(4):208-213.
PMID: 28787246 DOI: 10.1080/08997659.2017.1360411

This study describes the isolation and pathogenicity of Streptococcus iniae in cultured red hybrid tilapia (Nile Tilapia Oreochromis niloticus × Mozambique Tilapia O. mossambicus) in Malaysia. The isolated gram-positive S. iniae appeared punctiform, transparently white, catalase and oxidase negative and produced complete β-hemolysis on blood agar, while a PCR assay resulted in the amplification of the 16 S rRNA gene and lactate oxidase encoded genes. The isolate was sensitive to tetracycline, vancomycin, and bacitracin but was resistant to streptomycin, ampicillin, penicillin, and erythromycin. Pathogenicity trials conducted in local red hybrid tilapia (mean ± SE = 20.00 ± 0.45 g) showed 90.0, 96.7, and 100.0% mortality within 14 d postinfection following intraperitoneal exposure to 104, 106, and 108 CFU/mL of the pathogen, respectively. The clinical signs included erratic swimming, lethargy, and inappetance at 6 h postinfection, while mortality was recorded at less than 24 h postinfection in all infected groups. The LD50-336 h of S. iniae against the red hybrid tilapia was 102 CFU/mL. The post mortem examinations revealed congested livers, kidneys, and spleens of the infected fish. This is the first report of S. iniae experimental infection in cultured red hybrid tilapia in Malaysia. Received January 20, 2017; accepted July 16, 2017.

Matched MeSH terms: RNA, Bacterial/genetics; RNA, Ribosomal, 16S/genetics
Fulltext NFIX as a Master Regulator for Lung Cancer Progression

Rahman NIA, Abdul Murad NA, Mollah MM, Jamal R, Harun R

Front Pharmacol, 2017;8:540.
PMID: 28871224 DOI: 10.3389/fphar.2017.00540

About 40% of lung cancer cases globally are diagnosed at the advanced stage. Lung cancer has a high mortality and overall survival in stage I disease is only 70%. This study was aimed at finding a candidate of transcription regulator that initiates the mechanism for metastasis by integrating computational and functional studies. The genes involved in lung cancer were retrieved using in silico software. 10 kb promoter sequences upstream were scanned for the master regulator. Transient transfection of shRNA NFIXs were conducted against A549 and NCI-H1299 cell lines. qRT-PCR and functional assays for cell proliferation, migration and invasion were carried out to validate the involvement of NFIX in metastasis. Genome-wide gene expression microarray using a HumanHT-12v4.0 Expression BeadChip Kit was performed to identify differentially expressed genes and construct a new regulatory network. The in silico analysis identified NFIX as a master regulator and is strongly associated with 17 genes involved in the migration and invasion pathways including IL6ST, TIMP1 and ITGB1. Silencing of NFIX showed reduced expression of IL6ST, TIMP1 and ITGB1 as well as the cellular proliferation, migration and invasion processes. The data was integrated with the in silico analyses to find the differentially expressed genes. Microarray analysis showed that 18 genes were expressed differentially in both cell lines after statistical analyses integration between t-test, LIMMA and ANOVA with Benjamini-Hochberg adjustment at p-value < 0.05. A transcriptional regulatory network was created using all 18 genes, the existing regulated genes including the new genes PTCH1, NFAT5 and GGCX that were found highly associated with NFIX, the master regulator of metastasis. This study suggests that NFIX is a promising target for therapeutic intervention that is expected to inhibit metastatic recurrence and improve survival rate.

Matched MeSH terms: RNA, Small Interfering
Fulltext Advances in the study of nodavirus

Yong CY, Yeap SK, Omar AR, Tan WS

PeerJ, 2017;5:e3841.
PMID: 28970971 DOI: 10.7717/peerj.3841

Nodaviruses are small bipartite RNA viruses which belong to the family of Nodaviridae. They are categorized into alpha-nodavirus, which infects insects, and beta-nodavirus, which infects fishes. Another distinct group of nodavirus infects shrimps and prawns, which has been proposed to be categorized as gamma-nodavirus. Our current review focuses mainly on recent studies performed on nodaviruses. Nodavirus can be transmitted vertically and horizontally. Recent outbreaks have been reported in China, Indonesia, Singapore and India, affecting the aquaculture industry. It also decreased mullet stock in the Caspian Sea. Histopathology and transmission electron microscopy (TEM) are used to examine the presence of nodaviruses in infected fishes and prawns. For classification, virus isolation followed by nucleotide sequencing are required. In contrast to partial sequence identification, profiling the whole transcriptome using next generation sequencing (NGS) offers a more comprehensive comparison and characterization of the virus. For rapid diagnosis of nodavirus, assays targeting the viral RNA based on reverse-transcription PCR (RT-PCR) such as microfluidic chips, reverse-transcription loop-mediated isothermal amplification (RT-LAMP) and RT-LAMP coupled with lateral flow dipstick (RT-LAMP-LFD) have been developed. Besides viral RNA detections, diagnosis based on immunological assays such as enzyme-linked immunosorbent assay (ELISA), immunodot and Western blotting have also been reported. In addition, immune responses of fish and prawn are also discussed. Overall, in fish, innate immunity, cellular type I interferon immunity and humoral immunity cooperatively prevent nodavirus infections, whereas prawns and shrimps adopt different immune mechanisms against nodavirus infections, through upregulation of superoxide anion, prophenoloxidase, superoxide dismutase (SOD), crustin, peroxinectin, anti-lipopolysaccharides and heat shock proteins (HSP). Potential vaccines for fishes and prawns based on inactivated viruses, recombinant proteins or DNA, either delivered through injection, oral feeding or immersion, are also discussed in detail. Lastly, a comprehensive review on nodavirus virus-like particles (VLPs) is presented. In recent years, studies on prawn nodavirus are mainly focused on Macrobrachium rosenbergii nodavirus (MrNV). Recombinant MrNV VLPs have been produced in prokaryotic and eukaryotic expression systems. Their roles as a nucleic acid delivery vehicle, a platform for vaccine development, a molecular tool for mechanism study and in solving the structures of MrNV are intensively discussed.

Matched MeSH terms: RNA, Viral
Fulltext The complete genome sequence of Ensifer meliloti strain CCMM B554 (FSM-MA), a highly effective nitrogen-fixing microsymbiont of Medicago truncatula Gaertn

Nagymihály M, Vásarhelyi BM, Barrière Q, Chong TM, Bálint B, Bihari P, et al.

Stand Genomic Sci, 2017;12:75.
PMID: 29255570 DOI: 10.1186/s40793-017-0298-3

Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is exceptional because it is a highly effective symbiotic partner of the two most widely used accessions, A17 and R108, of the model legume Medicago truncatula Gaertn. Based on 16S rRNA gene sequence, multilocus sequence and average nucleotide identity analyses, FSM-MA is identified as a new Ensifer meliloti strain. The genome is 6,70 Mbp and is comprised of the chromosome (3,64 Mbp) harboring 3574 predicted genes and two megaplasmids, pSymA (1,42 Mbp) and pSymB (1,64 Mbp) with respectively 1481 and 1595 predicted genes. The average GC content of the genome is 61.93%. The FSM-MA genome structure is highly similar and co-linear to other E. meliloti strains in the chromosome and the pSymB megaplasmid while, in contrast, it shows high variability in the pSymA plasmid. The large number of strain-specific sequences in pSymA as well as strain-specific genes on pSymB involved in the biosynthesis of the lipopolysaccharide and capsular polysaccharide surface polysaccharides may encode novel symbiotic functions explaining the high symbiotic performance of FSM-MA.

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Streptomyces colonosanans sp. nov., A Novel Actinobacterium Isolated from Malaysia Mangrove Soil Exhibiting Antioxidative Activity and Cytotoxic Potential against Human Colon Cancer Cell Lines

Law JW, Ser HL, Duangjai A, Saokaew S, Bukhari SI, Khan TM, et al.

Front Microbiol, 2017;8:877.
PMID: 28559892 DOI: 10.3389/fmicb.2017.00877

Streptomyces colonosanans MUSC 93JT, a novel strain isolated from mangrove forest soil located at Sarawak, Malaysia. The bacterium was noted to be Gram-positive and to form light yellow aerial and vivid yellow substrate mycelium on ISP 2 agar. The polyphasic approach was used to determine the taxonomy of strain MUSC 93JT and the strain showed a range of phylogenetic and chemotaxonomic properties consistent with those of the members of the genus Streptomyces. Phylogenetic and 16S rRNA gene sequence analysis indicated that closely related strains include Streptomyces malachitofuscus NBRC 13059T (99.2% sequence similarity), Streptomyces misionensis NBRC 13063T (99.1%), and Streptomyces phaeoluteichromatogenes NRRL 5799T (99.1%). The DNA-DNA relatedness values between MUSC 93JT and closely related type strains ranged from 14.4 ± 0.1 to 46.2 ± 0.4%. The comparison of BOX-PCR fingerprints indicated MUSC 93JT exhibits a unique DNA profile. The genome of MUSC 93JT consists of 7,015,076 bp. The DNA G + C content was determined to be 69.90 mol%. The extract of strain MUSC 93JT was demonstrated to exhibit potent antioxidant activity via ABTS, metal chelating, and SOD assays. This extract also exhibited anticancer activity against human colon cancer cell lines without significant cytotoxic effect against human normal colon cells. Furthermore, the chemical analysis of the extract further emphasizes the strain is producing chemo-preventive related metabolites. Based on this polyphasic study of MUSC 93JT, it is concluded that this strain represents a novel species, for which the name Streptomyces colonosanans sp. nov. is proposed. The type strain is MUSC 93JT (= DSM 102042T = MCCC 1K02298T).

Matched MeSH terms: RNA, Ribosomal, 16S
Fulltext Effectiveness of chemotherapy counselling on self-esteem and psychological affects among cancer patients in Malaysia: Randomized controlled trial

Mohd-Sidik S, Akhtari-Zavare M, Periasamy U, Rampal L, Fadhilah SI, Mahmud R

Patient Educ Couns, 2018 05;101(5):862-871.
PMID: 29336859 DOI: 10.1016/j.pec.2018.01.004

OBJECTIVES: The aim of this study was to implement and evaluate the outcomes of chemotherapy counselling based on the "Managing Patients on Chemotherapy" module on self-esteem and psychological affect (anxiety, depression) of cancer patients by pharmacists in ten selected government hospitals in Peninsular Malaysia.
METHODS: A randomized control trial was conducted among 2120 cancer patients from April 2016 to January 2017 in ten selected government hospitals in Peninsular Malaysia. Cancer patients were randomly assigned to intervention and control groups. The intervention group received chemotherapy counselling by pharmacists based on the "Managing Patients on Chemotherapy" module. The outcomes were assessed at baseline, 1st, 2nd and 3rd follow-ups after counselling. In the course of data analysis; independent sample t-test, chi-square and two-way repeated measures ANOVA were conducted.
RESULTS: Mean scores of self-esteem in the intervention group had significant difference in comparison with those of the control group in the 1st, 2nd and 3rd follow-ups after counselling (P 

Matched MeSH terms: RNA-Binding Proteins

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