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Fulltext A Comprehensive Review on Phytochemistry and Pharmacological Activities of Clinacanthus nutans (Burm.f.) Lindau

Khoo LW, Audrey Kow S, Lee MT, Tan CP, Shaari K, Tham CL, et al.

Evid Based Complement Alternat Med, 2018;2018:9276260.
PMID: 30105077 DOI: 10.1155/2018/9276260

Clinacanthus nutans (Burm.f.) Lindau (Acanthaceae), commonly known as Sabah snake grass, is a vegetable and a well-known herb that is considered an alternative medicine for insect bites, skin rashes, herpes infection, inflammation, and cancer and for health benefits. Current review aims to provide a well-tabulated repository of the phytochemical screening, identification and quantification, and the pharmacological information of C. nutans according to the experimental design and the plant preparation methods which make it outstanding compared to existing reviews. This review has documented valuable data obtained from all accessible library databases and electronic searches. For the first time we analyzed the presence of flavonoids, triterpenoids, steroids, phytosterols, and glycosides in C. nutans based on the results from phytochemical screening which are then further confirmed by conventional phytochemical isolation methods and advanced spectroscopic techniques. Phytochemical quantification further illustrated that C. nutans is a good source of phenolics and flavonoids. Pharmacological studies on C. nutans revealed that its polar extract could be a promising anti-inflammation, antiviral, anticancer, immune and neuromodulating, and plasmid DNA protective agent; that its semipolar extract could be a promising antiviral, anticancer, and wound healing agent; and that its nonpolar extract could be an excellent anticancer agent.

Matched MeSH terms: Libraries
A Novel Liquid Chromatography Tandem Mass Spectrometry Technique using Multi-Period-Multi-Experiment of MRM-EPI-MRM3 with Library Matching for Simultaneous Determination of Amphetamine Type Stimulants Related Drugs in Whole Blood, Urine and Dried Blood Stain (DBS)-Application to Forensic Toxicology Cases in Malaysia

Zubaidi FA, Choo YM, Tan GH, Hamid HA, Choy YK

J Anal Toxicol, 2019 Aug 23;43(7):528-535.
PMID: 31141150 DOI: 10.1093/jat/bkz017

A novel mass spectrometry detection technique based on a multi-period and multi- experiment (MRM-EPI-MRM3) with library matching in a single run for fast and rapid screening and identification of amphetamine type stimulants (ATS) related drugs in whole blood, urine and dried blood stain was developed and validated. The ATS-related drugs analyzed in this study include ephedrine, pseudoephedrine, amphetamine, methamphetamine, MDMA (3,4-Methylenedioxymethamphetamine), MDA (3,4-Methylenedioxyamphetamine), MDEA (3,4-Methylenedioxy-N-ethylamphetamine) and phentermine. The relative standard deviation for inter and intraday was less than 15% while recoveries ranged from 80% to 120% for all three matrices, i.e., whole blood, urine and dried blood stain. All compounds gave library matching percentage of more than 85% based on the purity. This method was proven to be simple and robust, and provide high confident results complemented with library matching confirmation.

Matched MeSH terms: Libraries
Fulltext A review of pharmacist-led interventions on diabetes outcomes: an observational analysis to explore diabetes care opportunities for pharmacists

Iqbal MZ, Khan AH, Iqbal MS, Syed Sulaiman SA

J Pharm Bioallied Sci, 2019 10 18;11(4):299-309.
PMID: 31619911 DOI: 10.4103/jpbs.JPBS_138_19

A strict and adherence treatment is required by the patient with diabetes mellitus and it demands a proper self-medication by the patient. Pharmacists are involved in providing self-management support to the patients. This review evaluates the interventions of pharmacist for patients to improve self-management with diabetes mellitus and also to improve the clinical outcomes of diabetes mellitus. A comprehensive literature search was performed by using different keywords "pharmacist-led intervention," "diabetes," "effect of pharmacist on outcome of diabetes," and "self-management of diabetes" with the help of various electronic databases such as PubMed, Science Direct, Embase, Web of Science, and the Cochrane Library from the beginning of the database through September 2018. The primary outcome was glycated hemoglobin (HbA1c), whereas the secondary outcomes were blood glucose level, blood pressure (BP) measure, body mass index, lipids, adherence to medication, and quality of life. Twenty-five studies comprising 2997 diabetic patients were included in the analysis. Pharmacist-led intervention was involved in all included studies in the form of education on diabetes and its complications, medication adherence, lifestyle, and education about self-management skills. Pharmacist-led interventions are able to reduce HbA1c levels with a mean of 0.75%. Most studies do not expose the material and methods used in pharmacist-led intervention. The variation in the reduction of HbA1c, fasting blood sugar, BP, and lipid profile was due to the lack of this standardization. The included studies indicated that pharmacist-led interventions in diabetes mellitus can significantly improve the outcomes of diabetes mellitus and its complication later on. Hence, these long-term improvements in outcomes added more value of pharmacists in health-care system of the world.

Matched MeSH terms: Libraries
A review of the Australian healthcare system: A policy perspective

Dixit SK, Sambasivan M

SAGE Open Med, 2018;6:2050312118769211.
PMID: 29686869 DOI: 10.1177/2050312118769211

This article seeks to review the Australian healthcare system and compare it to similar systems in other countries to highlight the main issues and problems. A literature search for articles relating to the Australian and other developed countries' healthcare systems was conducted by using Google and the library of Victoria University, Melbourne. Data from the websites of the Commonwealth of Australia, the Australian Institute of Health and Welfare, the Australian Productivity Commission, the Organisation for Economic Co-operation and Development and the World Bank have also been used. Although care within the Australian healthcare system is among the best in the world, there is a need to change the paradigm currently being used to measure the outcomes and allocate resources. The Australian healthcare system is potentially dealing with two main problems: (a) resource allocation, and (b) performance and patient outcomes improvements. An interdisciplinary research approach in the areas of performance measurement, quality and patient outcomes improvement could be adopted to discover new insights, by using the policy implementation error/efficiency and bureaucratic capacity. Hospital managers, executives and healthcare management practitioners could use an interdisciplinary approach to design new performance measurement models, in which financial performance, quality, healthcare and patient outcomes are blended in, for resource allocation and performance improvement. This article recommends that public policy implementation error and the bureaucratic capacity models be applied to healthcare to optimise the outcomes for the healthcare system in Australia. In addition, it highlights the need for evaluation of the current reimbursement method, freedom of choice to patients and a regular scrutiny of the appropriateness of care.

Matched MeSH terms: Libraries
Fulltext A systematic review of automated pre-processing, feature extraction and classification of cardiotocography

Al-Yousif S, Jaenul A, Al-Dayyeni W, Alamoodi A, Jabori I, Md Tahir N, et al.

PeerJ Comput Sci, 2021;7:e452.
PMID: 33987454 DOI: 10.7717/peerj-cs.452

Context: The interpretations of cardiotocography (CTG) tracings are indeed vital to monitor fetal well-being both during pregnancy and childbirth. Currently, many studies are focusing on feature extraction and CTG classification using computer vision approach in determining the most accurate diagnosis as well as monitoring the fetal well-being during pregnancy. Additionally, a fetal monitoring system would be able to perform detection and precise quantification of fetal heart rate patterns.
Objective: This study aimed to perform a systematic review to describe the achievements made by the researchers, summarizing findings that have been found by previous researchers in feature extraction and CTG classification, to determine criteria and evaluation methods to the taxonomies of the proposed literature in the CTG field and to distinguish aspects from relevant research in the field of CTG.
Methods: Article search was done systematically using three databases: IEEE Xplore digital library, Science Direct, and Web of Science over a period of 5 years. The literature in the medical sciences and engineering was included in the search selection to provide a broader understanding for researchers.
Results: After screening 372 articles, and based on our protocol of exclusion and inclusion criteria, for the final set of articles, 50 articles were obtained. The research literature taxonomy was divided into four stages. The first stage discussed the proposed method which presented steps and algorithms in the pre-processing stage, feature extraction and classification as well as their use in CTG (20/50 papers). The second stage included the development of a system specifically on automatic feature extraction and CTG classification (7/50 papers). The third stage consisted of reviews and survey articles on automatic feature extraction and CTG classification (3/50 papers). The last stage discussed evaluation and comparative studies to determine the best method for extracting and classifying features with comparisons based on a set of criteria (20/50 articles).
Discussion: This study focused more on literature compared to techniques or methods. Also, this study conducts research and identification of various types of datasets used in surveys from publicly available, private, and commercial datasets. To analyze the results, researchers evaluated independent datasets using different techniques.
Conclusions: This systematic review contributes to understand and have insight into the relevant research in the field of CTG by surveying and classifying pertinent research efforts. This review will help to address the current research opportunities, problems and challenges, motivations, recommendations related to feature extraction and CTG classification, as well as the measurement of various performance and various data sets used by other researchers.

Matched MeSH terms: Libraries, Digital
Advances in the Generation of Functional β-cells from Induced Pluripotent Stem Cells As a Cure for Diabetes Mellitus

Kalra K, Chandrabose ST, Ramasamy TS, Kasim NHBA

Curr Drug Targets, 2018;19(13):1463-1477.
PMID: 29874998 DOI: 10.2174/1389450119666180605112917

Diabetes mellitus is one of the leading causes of death worldwide. Loss and functional failure of pancreatic β-cells, the parenchyma cells in the islets of Langerhans, progress diabetes mellitus. The increasing incidence of this metabolic disorder necessitates efficient strategies to produce functional β-cells for treating diabetes mellitus. Human induced Pluripotent Stem Cells (hiPSC), hold potential for treating diabetes ownig to their self-renewal capacity and the ability to differentiate into β- cells. iPSC technology also provides unlimited starting material to generate differentiated cells for regenerative applications. Progress has also been made in establishing in-vitro culture protocols to yield definitive endoderm, pancreatic endoderm progenitor cells and β-cells via different reprogramming strategies and growth factor supplementation. However, these generated β-cells are still immature, lack functional characteristics and exhibit lower capability in reversing the diseases conditions. Current methods employed to generate mature and functional β-cells include; use of small and large molecules to enhance the reprogramming and differentiation efficiency, 3D culture systems to improve the functional properties and heterogeneity of differentiated cells. This review details recent advancements in the generation of mature β-cells by reprogramming stem cells into iPSCs that are further programmed to β-cells. It also provides deeper insight into current reprogramming protocols and their efficacy, focusing on the underlying mechanism of chemical-based approach to generate iPSCs. Furthermore, we have highlighted the recent differentiation strategies both in-vitro and in-vivo to date and the future prospects in the generation of mature β-cells.

Matched MeSH terms: Small Molecule Libraries/pharmacology
Fulltext Alkyl-Resorcinol Derivatives as Inhibitors of GDP-Mannose Pyrophosphorylase with Antileishmanial Activities

Levaique H, Pamlard O, Apel C, Bignon J, Arriola M, Kuhner R, et al.

Molecules, 2021 Mar 11;26(6).
PMID: 33799883 DOI: 10.3390/molecules26061551

Leishmaniasis is a vector-borne disease caused by the protozoan parasite Leishmania found in tropical and sub-tropical areas, affecting 12 million people around the world. Only few treatments are available against this disease and all of them present issues of toxicity and/or resistance. In this context, the development of new antileishmanial drugs specifically directed against a therapeutic target appears to be a promising strategy. The GDP-Mannose Pyrophosphorylase (GDP-MP) has been previously shown to be an attractive therapeutic target in Leishmania. In this study, a chemical library of 5000 compounds was screened on both L. infantum (LiGDP-MP) and human (hGDP-MP) GDP-MPs. From this screening, oncostemonol D was found to be active on both GDP-MPs at the micromolar level. Ten alkyl-resorcinol derivatives, of which oncostemonols E and J (2 and 3) were described for the first time from nature, were then evaluated on both enzymes as well as on L. infantum axenic and intramacrophage amastigotes. From this evaluation, compounds 1 and 3 inhibited both GDP-MPs at the micromolar level, and compound 9 displayed a three-times lower IC50 on LiGDP-MP, at 11 µM, than on hGDP-MP. As they displayed mild activities on the parasite, these compounds need to be further pharmacomodulated in order to improve their affinity and specificity to the target as well as their antileishmanial activity.

Matched MeSH terms: Small Molecule Libraries
Fulltext Biomedical and health sciences publication productivity from Malaysia

Zainal H, Zainab AN

Health Info Libr J, 2011 Sep;28(3):216-25.
PMID: 21831221 DOI: 10.1111/j.1471-1842.2011.00943.x

BACKGROUND: The aim of this study was to examine Malaysian contributions in the field of biomedical and health sciences.
METHODS: In this study, 3697 publications affiliated to Malaysian addresses from the sci database between 1990 and 2005 were sampled. This study also explored publication productivity trends, authorship and collaboration pattern, core journals used, and citations obtained.
RESULTS: Main contributions were journal articles (73.3%). Most authors (63.7%) contributed only one article and 16.1% produced over 30-68 publications. Multi-authored works were the norm. The productive authors were named either first or second in publications. There were active collaborations with authors from Asia-Pacific countries (35%) and Europe (30%). The majority of publications were contributed by institutions of higher learning (87%). Core journals used follow quite close to Bradford's zonal ratios of 44:152:581. The active research areas were identified. About 71.3% of publications received citations especially those published from 1995 to 1999.
CONCLUSION: This study helped librarians identify active researchers, active research areas and journals relevant to biomedical and health sciences researchers and useful when producing reports to university management and planning medical collection policies and deciding on journal subscriptions and cancellations.

Matched MeSH terms: Libraries, Medical
Fulltext Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS

Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC, Pain A, et al.

Front Microbiol, 2016;7:1288.
PMID: 27597847 DOI: 10.3389/fmicb.2016.01288

Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.

Matched MeSH terms: Libraries
Fulltext Cell-Based High-Throughput Screening Protocol for Discovering Antiviral Inhibitors Against SARS-COV-2 Main Protease (3CLpro)

Rothan HA, Teoh TC

Mol Biotechnol, 2021 Mar;63(3):240-248.
PMID: 33464543 DOI: 10.1007/s12033-021-00299-7

The global public health has been compromised since the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) emerged in late December 2019. There are no specific antiviral drugs available to combat SARS-CoV-2 infection. Besides the rapid dissemination of SARS-CoV-2, several variants have been identified with a potential epidemiologic and pathogenic variation. This fact has forced antiviral drug development strategies to stay innovative, including new drug discovery protocols, combining drugs, and establishing new drug classes. Thus, developing novel screening methods and direct-targeting viral enzymes could be an attractive strategy to combat SARS-CoV-2 infection. In this study, we designed, optimized, and validated a cell-based assay protocol for high-throughput screening (HTS) antiviral drug inhibitors against main viral protease (3CLpro). We applied the split-GFP complementation to develop GFP-split-3CLpro HTS system. The system consists of GFP-based reporters that become fluorescent upon cleavage by SARS-CoV-2 protease 3CLpro. We generated a stable GFP-split-3CLpro HTS system valid to screen large drug libraries for inhibitors to SARS-CoV-2 main protease in the bio-safety level 2 laboratory, providing real-time antiviral activity of the tested compounds. Using this assay, we identified a new class of viral protease inhibitors derived from quinazoline compounds that worth further in vitro and in vivo validation.

Matched MeSH terms: Small Molecule Libraries
Fulltext Comparison of Fluorinated and Nonfluorinated Lipids in Self-Adjuvanting Delivery Systems for Peptide-Based Vaccines

Hussein WM, Mukaida S, Azmi F, Bartlett S, Olivier C, Batzloff MR, et al.

ACS Med Chem Lett, 2017 Feb 09;8(2):227-232.
PMID: 28197317 DOI: 10.1021/acsmedchemlett.6b00453

Safe immunostimulants (adjuvants) are essential for the development of highly potent peptide-based vaccines. This study examined for the first time whether fluorinated lipids could stimulate humoral immunity in vivo when conjugated to peptide antigen. The impact of fluorination on humoral immunity was tested using a library of peptide-based vaccine candidates against the group A streptococcus (GAS). The fluorinated constructs stimulated similar mouse IgG titers to those elicited by complete Freund's adjuvant (CFA) and were higher than those produced in mice that received the nonfluorinated constructs.

Matched MeSH terms: Libraries
Controversies in the vascular theory of glaucomatous optic nerve degeneration

Ahmad SS

Taiwan J Ophthalmol, 2016 Oct-Dec;6(4):182-186.
PMID: 29018738 DOI: 10.1016/j.tjo.2016.05.009

An understanding of the pathogenesis of glaucoma is one of the foundations in glaucoma management. A number of theories have been presented to explain glaucomatous neural degeneration. The vascular theory attempts to explain the causation of glaucoma on the basis of vasogenic factors and altered he-modynamics in the body; however, this theory remains controversial. There are proponents for and against the role played by vascular factors in the development of glaucomatous optic nerve degeneration. This review aims to analyze the various studies performed to provide evidence for and against the vascular theory of glaucoma. It also affirms the need to undertake further studies regarding the path-ogenesis of glaucoma and integrate them into our management strategies. The literature search for this systemic analysis was performed using search engines, such as PubMed, The Virtual Library of the Ministry of Health Malaysia, Google Scholar, and ClinicalKey.

Matched MeSH terms: Libraries, Digital
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: Libraries
Dataset on LC-Q-TOF/MS tentative identification of phytochemicals in the extract of Vernonia amygdalina leaf through positive ionization

Alara OR, Abdurahman NH, Ukaegbu CI, Hassan Z, Kabbashi NA

Data Brief, 2018 Dec;21:1686-1689.
PMID: 30505901 DOI: 10.1016/j.dib.2018.10.159

The tentative identification of bioactive compounds in the extract of Vernonia amygdalina leaf was carried out using positive ionization of Liquid chromatography-mass spectrometry quadrupole time of flight (LC-Q-TOF/MS). The positive ionization is associated with the presence of saponins, flavonoids, alkaloids, terpenoids, and glycosides. Tentative assignments of the secondary metabolites were performed by comparing the MS fragmentation patterns with Waters® UNIFY library which allows positive identification of the compounds based on the spectral match. All the metabolites compounds were estimated and presented in a BPI (Base peak intensity) plot. These data are the unpublished supplementary materials related to "Ethanolic extraction of bioactive compounds from V. amygdalina leaf using response surface methodology as an optimization tool" (Alara et al., 2018).

Matched MeSH terms: Libraries
De novo whole genome sequencing data of two mangrove-isolated microalgae from Terengganu coastal waters

Teh KY, Afifudeen CLW, Aziz A, Wong LL, Loh SH, Cha TS

Data Brief, 2019 Dec;27:104680.
PMID: 31720332 DOI: 10.1016/j.dib.2019.104680

Interest in harvesting potential benefits from microalgae renders it necessary to have the many ecological niches of a single species to be investigated. This dataset comprises de novo whole genome assembly of two mangrove-isolated microalgae (from division Chlorophyta); Chlorella vulgaris UMT-M1 and Messastrum gracile SE-MC4 from Universiti Malaysia Terengganu, Malaysia. Library runs were carried out with 2 × 150 base paired-ends reads, whereas sequencing was conducted using Illumina Novaseq 2500 platform. Sequencing yielded raw reads amounting to ∼11 Gb in total bases for both species and was further assembled de novo. Genome assembly resulted in a 50.15 Mbp and 60.83 Mbp genome size for UMT-M1 and SE-MC4, respectively. All filtered and assembled genomic data sequences have been submitted to National Centre for Biotechnology Information (NCBI) and can be located at DDBJ/ENA/GenBank under the accession of VJNP00000000 (UMT-M1) and VIYE00000000 (SE-MC4).

Matched MeSH terms: Libraries
Development of a video tampering dataset for forensic investigation

Ismael Al-Sanjary O, Ahmed AA, Sulong G

Forensic Sci Int, 2016 Sep;266:565-572.
PMID: 27574113 DOI: 10.1016/j.forsciint.2016.07.013

Forgery is an act of modifying a document, product, image or video, among other media. Video tampering detection research requires an inclusive database of video modification. This paper aims to discuss a comprehensive proposal to create a dataset composed of modified videos for forensic investigation, in order to standardize existing techniques for detecting video tampering. The primary purpose of developing and designing this new video library is for usage in video forensics, which can be consciously associated with reliable verification using dynamic and static camera recognition. To the best of the author's knowledge, there exists no similar library among the research community. Videos were sourced from YouTube and by exploring social networking sites extensively by observing posted videos and rating their feedback. The video tampering dataset (VTD) comprises a total of 33 videos, divided among three categories in video tampering: (1) copy-move, (2) splicing, and (3) swapping-frames. Compared to existing datasets, this is a higher number of tampered videos, and with longer durations. The duration of every video is 16s, with a 1280×720 resolution, and a frame rate of 30 frames per second. Moreover, all videos possess the same formatting quality (720p(HD).avi). Both temporal and spatial video features were considered carefully during selection of the videos, and there exists complete information related to the doctored regions in every modified video in the VTD dataset. This database has been made publically available for research on splicing, Swapping frames, and copy-move tampering, and, as such, various video tampering detection issues with ground truth. The database has been utilised by many international researchers and groups of researchers.

Matched MeSH terms: Libraries
Development of small molecule inhibitors targeting TGF-β ligand and receptor: Structures, mechanism, preclinical studies and clinical usage

Wang H, Chen M, Sang X, You X, Wang Y, Paterson IC, et al.

Eur J Med Chem, 2020 Apr 01;191:112154.
PMID: 32092587 DOI: 10.1016/j.ejmech.2020.112154

Transforming growth factor-β (TGF-β) is a member of a superfamily of pleiotropic proteins that regulate multiple cellular processes such as growth, development and differentiation. Following binding to type I and II TGF-β serine/threonine kinase receptors, TGF-β activates downstream signaling cascades involving both SMAD-dependent and -independent pathways. Aberrant TGF-β signaling is associated with a variety of diseases, such as fibrosis, cardiovascular disease and cancer. Hence, the TGF-β signaling pathway is recognized as a potential drug target. Various organic molecules have been designed and developed as TGF-β signaling pathway inhibitors and they function by either down-regulating the expression of TGF-β or by inhibiting the kinase activities of the TGF-β receptors. In this review, we discuss the current status of research regarding organic molecules as TGF-β inhibitors, focusing on the biological functions and the binding poses of compounds that are in the market or in the clinical or pre-clinical phases of development.

Matched MeSH terms: Small Molecule Libraries/chemical synthesis; Small Molecule Libraries/pharmacology*; Small Molecule Libraries/chemistry
Fulltext Draft genome sequencing data of a pathogenic Pantoea stewartii subspecies stewartii strain SQT1 causing bronzing disease of jackfruit in Malaysia

Ibrahim R, Ismail-Suhaimy NW, Shu-Qing T, Ismail SI, Ina-Salwany MY, Yusof MT, et al.

Data Brief, 2020 Jun;30:105634.
PMID: 32395592 DOI: 10.1016/j.dib.2020.105634

A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 bp with a G+C content of 53.7%. A total protein of 4,671 was identified including virulence factors, resistance factors and secretion systems. Pantoea stewartii subsp. stewartii strain DC283 (NCBI accession no. CP017581.1) was used as a reference genome, where the query hit 72% coverage and average sequencing depth of 68. In total, 28,717 nucleotide polymorphisms, 520 small insertion/deletions and 142 structure variants were identified. The complete genome was deposited at the European Nucleotide Archive under the sample accession number ERP119356 and study accession number PRJEB36196.

Matched MeSH terms: Libraries
Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Lee PS, Gan HM, Clements GR, Wilson JJ

Genome, 2016 May 11.
PMID: 27696907

Mammal diversity assessments based on DNA derived from invertebrates have been suggested as alternatives to assessments based on traditional methods; however, no study has field-tested both approaches simultaneously. In Peninsular Malaysia, we calibrated the performance of mammal DNA derived from blowflies (Diptera: Calliphoridae) against traditional methods used to detect species. We first compared five methods (cage trapping, mist netting, hair trapping, scat collection, and blowfly-derived DNA) in a forest reserve with no recent reports of megafauna. Blowfly-derived DNA and mist netting detected the joint highest number of species (n = 6). Only one species was detected by multiple methods. Compared to the other methods, blowfly-derived DNA detected both volant and non-volant species. In another forest reserve, rich in megafauna, we calibrated blowfly-derived DNA against camera traps. Blowfly-derived DNA detected more species (n = 11) than camera traps (n = 9), with only one species detected by both methods. The rarefaction curve indicated that blowfly-derived DNA would continue to detect more species with greater sampling effort. With further calibration, blowfly-derived DNA may join the list of traditional field methods. Areas for further investigation include blowfly feeding and dispersal biology, primer biases, and the assembly of a comprehensive and taxonomically-consistent DNA barcode reference library.

Matched MeSH terms: Libraries
Flurbiprofen derivatives as novel α-amylase inhibitors: Biology-oriented drug synthesis (BIODS), in vitro, and in silico evaluation

Khan M, Alam A, Khan KM, Salar U, Chigurupati S, Wadood A, et al.

Bioorg Chem, 2018 12;81:157-167.
PMID: 30125730 DOI: 10.1016/j.bioorg.2018.07.038

Novel derivatives of flurbiprofen 1-18 including flurbiprofen hydrazide 1, substituted aroyl hydrazides 2-9, 2-mercapto oxadiazole derivative 10, phenacyl substituted 2-mercapto oxadiazole derivatives 11-15, and benzyl substituted 2-mercapto oxadiazole derivatives 16-18 were synthesized and characterized by EI-MS, 1H and 13C NMR spectroscopic techniques. All derivatives 1-18 were screened for α-amylase inhibitory activity and demonstrated a varying degree of potential ranging from IC50 = 1.04 ± 0.3 to 2.41 ± 0.09 µM as compared to the standard acarbose (IC50 = 0.9 ± 0.04 µM). Out of eighteen compounds, derivatives 2 (IC50 = 1.69 ± 0.1 µM), 3 (IC50 = 1.04 ± 0.3 µM), 9 (IC50 = 1.25 ± 1.05 µM), and 13 (IC50 = 1.6 ± 0.18 µM) found to be excellent inhibitors while rest of the compounds demonstrated comparable inhibition potential. A limited structure-activity relationship (SAR) was established by looking at the varying structural features of the library. In addition to that, in silico study was conducted to understand the binding interactions of the compounds (ligands) with the active site of α-amylase enzyme.

Matched MeSH terms: Libraries

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