Browse publications by year: 2018

  1. Vikashini B, Shanthi A, Ghosh Dasgupta M
    Gene, 2018 Nov 15;676:37-46.
    PMID: 30201104 DOI: 10.1016/j.gene.2018.07.012
    Casuarina equisetifolia L. is an important multi-purpose, fast growing and widely planted tree species native to tropical and subtropical coastlines of Australia, Southeast Asia, Malaysia, Melanesia, Polynesia and New Caledonia. It is a nitrogen-fixing tree mainly used for charcoal making, construction poles, landscaping, timber, pulp, firewood, windbreaks, shelterbelts, soil erosion and sand dune stabilization. Casuarina wood is presently used for paper and pulp production. Raw material with reduced lignin is highly preferred to increase the pulp yield. Hence, understanding the molecular regulation of wood formation in this tree species is vital for selecting industrially suitable phenotypes for breeding programs. The lignin biosynthetic pathway has been extensively studied in tree species like Eucalypts, poplars, pines, Picea, Betula and Acacia sp. However, studies on wood formation at molecular level is presently lacking in casuarinas. Hence, in the present study, the transcriptome of the developing secondary tissues of 15 years old Casuarina equiseitfolia subsp. equisetifolia was sequenced, de novo assembled, annotated and mapped to functional pathways. Transcriptome sequencing generated a total of 26,985 transcripts mapped to 31 pathways. Mining of the annotated data identified nine genes involved in lignin biosynthesis pathway and relative expression of the transcripts in four tissues including scale-like leaves, needle-like brachlets, wood and root were documented. The expression of CeCCR1 and CeF5H were found to be significantly high in wood tissues, while maximum expression of CeHCT was documented in stem. Additionally, CeTUBA and CeH2A were identified as the most stable reference transcript for normalization of qRT-PCR data in C. equisetifolia. The present study is the first wood genomic resource in C. equisetifolia, which will be valuable for functional genomics research in this genus.
    MeSH terms: Plant Breeding; Base Sequence; Lignin/biosynthesis*; Lignin/genetics*; Trees/genetics; Wood; Gene Expression Regulation, Plant/genetics; Gene Expression Profiling/methods; Pinus/genetics*; Pinus/metabolism; Transcriptome/genetics; Gene Ontology
  2. Mukheem A, Muthoosamy K, Manickam S, Sudesh K, Shahabuddin S, Saidur R, et al.
    Materials (Basel), 2018 Sep 10;11(9).
    PMID: 30201852 DOI: 10.3390/ma11091673
    Many wounds are unresponsive to currently available treatment techniques and therefore there is an immense need to explore suitable materials, including biomaterials, which could be considered as the crucial factor to accelerate the healing cascade. In this study, we fabricated polyhydroxyalkanoate-based antibacterial mats via an electrospinning technique. One-pot green synthesized graphene-decorated silver nanoparticles (GAg) were incorporated into the fibres of poly-3 hydroxybutarate-co-12 mol.% hydroxyhexanoate (P3HB-co-12 mol.% HHx), a co-polymer of the polyhydroxyalkanoate (PHA) family which is highly biocompatible, biodegradable, and flexible in nature. The synthesized PHA/GAg biomaterial has been characterized by field emission scanning electron microscopy (FESEM), elemental mapping, thermogravimetric analysis (TGA), UV-visible spectroscopy (UV-vis), and Fourier transform infrared spectroscopy (FTIR). An in vitro antibacterial analysis was performed to investigate the efficacy of PHA/GAg against gram-positive Staphylococcus aureus (S. aureus) strain 12,600 ATCC and gram-negative Escherichia coli (E. coli) strain 8739 ATCC. The results indicated that the PHA/GAg demonstrated significant reduction of S. aureus and E. coli as compared to bare PHA or PHA- reduced graphene oxide (rGO) in 2 h of time. The p value (p < 0.05) was obtained by using a two-sample t-test distribution.
    MeSH terms: Anti-Bacterial Agents; Biocompatible Materials; Escherichia coli; Graphite; Microscopy, Electron, Scanning; Oxides; Silver; Spectrophotometry, Ultraviolet; Staphylococcal Infections; Staphylococcus aureus; Thermogravimetry; Spectroscopy, Fourier Transform Infrared; Metal Nanoparticles; Polyhydroxyalkanoates
  3. Almoudi MM, Hussein AS, Abu Hassan MI, Mohamad Zain N
    Saudi Dent J, 2018 Oct;30(4):283-291.
    PMID: 30202164 DOI: 10.1016/j.sdentj.2018.06.003
    OBJECTIVES: The aim of this study was to systematically review the growth inhibition effectiveness of zinc against Streptococcus mutans. The main question was, "Does the zinc inhibit the growth of oral Streptococcus mutans in vitro?

    METHODS: Literature search on PubMed, Medline, and science direct databases was carried out for in vitro studies published in English from 1990 to 2016, and the reported outcomes of minimum inhibitory concentration (MIC), minimum bactericidal concentrations (MBC), zone of inhibition (ZOI) and bacterial count method using colony forming unit (CFU) were used to assess the antibacterial effectiveness of zinc.

    RESULTS: Seventeen studies were included in this review. Seven studies reported MIC and MBC. Four studies reported ZOI, and eight studies reported CFU. MIC values using zinc chloride and zinc oxide nanoparticles were ranged from 0.025 to 0.2 mM and 0.390 to 500 ± 306.18 µg/ml respectively. MBC values using zinc oxide nanoparticles have ranged from 3.125 to 500 µg/ml. ZOI ranged from no inhibition zone to 21 ± 1.4 mm using 23.1% zinc oxide. A considerable reduction in the bacterial count was reported after adding zinc. However, only two studies have reported no inhibitory effect of zinc.

    CONCLUSION: This review indicated a significant growth inhibition effectiveness of zinc even at lower concentrations which indicate it's safely to be used in oral health products.

  4. Nassir AM, Shahzad N, Ibrahim IAA, Ahmad I, Md S, Ain MR
    Saudi Pharm J, 2018 Sep;26(6):876-885.
    PMID: 30202231 DOI: 10.1016/j.jsps.2018.03.009
    Resveratrol (RL), a natural polyphenol, is known for its diverse biological effects against various human cancer cell lines. But low aqueous solubility, poor bioavailability, and stability limit its efficacy against prostate cancer. In this study polymeric nanoparticles encapsulating resveratrol (RLPLGA) were designed and their cytotoxic and mode of apoptotic cells death against prostate cancer cell line (LNCaP) was determined. Nanoparticles were prepared by solvent displacement method and characterized for particle size, TEM, entrapment efficiency, DSC and drug release study. RLPLGA exhibited a significant decrease in cell viability with 50% and 90% inhibitory concentration (IC50 and IC90) of 15.6 ± 1.49 and 41.1 ± 2.19 μM respectively against the LNCaP cells. This effect was mediated by apoptosis as confirmed by cell cycle arrest at G1-S transition phase, externalization of phosphatidylserine, DNA nicking, loss of mitochondrial membrane potential and reactive oxygen species generation in LNCaP cells. Furthermore, significantly greater cytotoxicity to LNCaP cells was observed with nanoparticles as compared to that of free RL at all tested concentrations. RLPLGA nanoparticles presented no adverse cytotoxic effects on murine macrophages even at 200 μM. Our findings support the potential use of developed resveratrol loaded nanoparticle for the prostate cancer chemoprevention/ chemotherapy with no adverse effect on normal cells.
    MeSH terms: Animals; Biological Availability; Cell Survival; Humans; Male; Particle Size; Phosphatidylserines; Prostatic Neoplasms; Solubility; Apoptosis; Reactive Oxygen Species; Inhibitory Concentration 50; Mice; Membrane Potential, Mitochondrial; Nanoparticles; Cell Cycle Checkpoints; Polyphenols; Drug Liberation
  5. Ibrahim IA, Ting HN, Moghavvemi M
    Int J Health Sci (Qassim), 2018 9 12;12(5):25-34.
    PMID: 30202405
    Objectives: The hearing process in the brain is very complicated and hard to solve. However, an understanding of the hearing process is an essential issue and needed in many rehabilitation or treatment applications. This study investigates and compares the effects of simple and complex sounds on latency and amplitude of various event-related potential (ERP) components to male ethnic Malay adults. Comparisons were made with previous studies.

    Materials and Methods: Simple and complex sounds were used (pure tones and the naturally produced Malay consonant-vowels [CVs]) to evoke the cortical auditory-evoked potential (CAEP) signals. Moreover, this study analyzed the influence of related CAEP components that are distinct to the selected population and determined which of the ERP components among (CAEP) components is most affected by the two distinct stimuli. Moreover, the study used classification algorithms to discover the ability of the brain in distinguishing CAEP evoked by stimuli contrasts.

    Results: The results showed some resemblance between our results and ERP waveforms outlined in previous studies conducted on native speakers of English. On the other hand, it was also observed that the P1 and N2 had a significant effect in amplitude due to different stimulus.

    Conclusion: The results show high classification accuracy for the brain to distinguish auditory stimuli. Moreover, the results indicated some resemblance to previous studies conducted on native English speakers using similar tones and English CV stimuli. However, the amplitudes and latencies of the P1 were found to have a significant difference due to stimuli complexity.

    MeSH terms: Adult; Algorithms; Biological Products; Brain; Evoked Potentials; Evoked Potentials, Auditory; Hearing; Humans; Malaysia; Male; Sound
  6. Al-Namnam NM, Hariri F, Thong MK, Rahman ZA
    J Oral Biol Craniofac Res, 2018 08 29;9(1):37-39.
    PMID: 30202723 DOI: 10.1016/j.jobcr.2018.08.007
    Crouzon syndrome exhibits considerable phenotypic heterogeneity, in the aetiology of which genetics play an important role. FGFR2 mediates extracellular signals into cells and the mutations in the FGFR2 gene cause this syndrome occurrence. Activated FGFs/FGFR2 signaling disrupts the balance of differentiation, cell proliferation, and apoptosis via its downstream signal pathways. However, very little is known about the cellular and molecular factors leading to severity of this phenotype. Revealing the molecular pathology of craniosynostosis will be a great value for genetic counselling, diagnosis, prognosis and early intervention programs. This mini-review summarizes the fundamental and recent scientific literature on genetic disorder of Crouzon syndrome and presents a graduated strategy for the genetic approach, diagnosis and the management of this complex craniofacial defect.
    MeSH terms: Cell Differentiation; Craniofacial Dysostosis; Craniosynostoses; Genetic Counseling; Humans; Mutation; Phenotype; Prognosis; Signal Transduction; Apoptosis; Early Intervention (Education); Cell Proliferation; Receptor, Fibroblast Growth Factor, Type 2; Pathology, Molecular
  7. Nagappan J, Chin CF, Angel LPL, Cooper RM, May ST, Low EL
    Biotechnol Lett, 2018 Dec;40(11-12):1541-1550.
    PMID: 30203158 DOI: 10.1007/s10529-018-2603-7
    The first and most crucial step of all molecular techniques is to isolate high quality and intact nucleic acids. However, DNA and RNA isolation from fungal samples are usually difficult due to the cell walls that are relatively unsusceptible to lysis and often resistant to traditional extraction procedures. Although there are many extraction protocols for Ganoderma species, different extraction protocols have been applied to different species to obtain high yields of good quality nucleic acids, especially for genome and transcriptome sequencing. Ganoderma species, mainly G. boninense causes the basal stem rot disease, a devastating disease that plagues the oil palm industry. Here, we describe modified DNA extraction protocols for G. boninense, G. miniatocinctum and G. tornatum, and an RNA extraction protocol for G. boninense. The modified salting out DNA extraction protocol is suitable for G. boninense and G. miniatocinctum while the modified high salt and low pH protocol is suitable for G. tornatum. The modified DNA and RNA extraction protocols were able to produce high quality genomic DNA and total RNA of ~ 140 to 160 µg/g and ~ 80 µg/g of mycelia respectively, for Single Molecule Real Time (PacBio Sequel® System) and Illumina sequencing. These protocols will benefit those studying the oil palm pathogens at nucleotide level.
    MeSH terms: Cell Wall; DNA; Hydrogen-Ion Concentration; Nucleic Acids; Nucleotides; Plague; RNA; Causality; Genomics; Mycelium; Ganoderma; High-Throughput Nucleotide Sequencing; Transcriptome
  8. Wu Q, Miao G, Li X, Liu W, Ikhwanuddin M, Ma H
    Mol Biol Rep, 2018 Dec;45(6):1913-1918.
    PMID: 30203240 DOI: 10.1007/s11033-018-4339-9
    The blue swimming crab (Portunus pelagicus) is a valuable marine fishery resource in Indo-West Pacific Ocean. So far, rare genetic resource of this species is available. In this report, the restriction-site associated DNA (RAD) approach was employed to mine the genomic information and identify molecular markers in P. pelagicus. A total of 0.82 Gbp clean data were generated from the genome of individual "X2A". De novo assembly produced 85,796 contigs with an average length of 339 bp. A total of 45,464 putative SNPs and 17,983 microsatellite loci were identified from the genomes of ten individuals. Furthermore, 31 pairs of primers were successfully designed, with 16 of them exhibiting polymorphism in a wild population. For these polymorphic loci, the expected and observed alleles per locus ranged from 1.064 to 7.314 and from 2 to 11, respectively. The expected and observed heterozygosity per locus ranged from 0.0615 to 0.819 and from 0.0626 to 1.000, respectively. Nine loci showed high informative with polymorphism information content (PIC) > 0.5. Five loci significantly deviated from Hardy-Weinberg equilibrium in the samples analyzed. No linkage disequilibrium was found among the 16 polymorphic microsatellite loci. This study provided massive genetic resource and polymorphic molecular markers that should be helpful for studies on conservation genetics, population dynamics and genetic diversity of P. pelagicus and related crab species.
    MeSH terms: Alleles; Animals; Brachyura/genetics*; DNA; Gene Frequency/genetics; Genetics, Population/methods; Pacific Ocean; Polymorphism, Genetic/genetics; Genetic Variation; Restriction Mapping/methods*; Linkage Disequilibrium/genetics; Sequence Analysis, DNA/methods; Microsatellite Repeats/genetics; Polymorphism, Single Nucleotide/genetics; Genetic Loci/genetics
  9. Khasri A, Ahmad MA
    Environ Sci Pollut Res Int, 2018 Nov;25(31):31508-31519.
    PMID: 30203351 DOI: 10.1007/s11356-018-3046-3
    The adsorption behavior of basic, methylene blue (MB), and reactive, remazol brilliant violet 5R (RBV), dyes from aqueous solution onto Intsia bijuga sawdust-based activated carbon (IBSAC) was executed via batch and column studies. The produced activated carbon was characterized through Brunauer-Emmett-Teller (BET) surface area and pore structural analysis, proximate and ultimate, scanning electron microscopy (SEM), and Fourier transform infrared spectroscopy (FTIR). Batch studies were performed to investigate the effects of contact time, initial concentration, and solution pH. The equilibrium data for both MB and RBV adsorption better fits Langmuir model with maximum adsorption capacity of 434.78 and 212.77 mg/g, respectively. Kinetic studies for both MB and RBV dyes showed that the adsorption process followed a pseudo-second-order and intraparticle diffusion kinetic models. For column mode, the breakthrough curves were plotted by varying the flow rate, bed height, and initial concentration and the breakthrough data were best correlated with the Yoon-Nelson model compared to Thomas and Adams-Bohart model. The adsorption activity of IBSAC shows good stability even after four consecutive cycles.
    MeSH terms: Adsorption; Carbon Dioxide/chemistry; Charcoal/chemistry*; Diffusion; Coloring Agents/isolation & purification*; Coloring Agents/chemistry; Kinetics; Fabaceae/chemistry*; Methylene Blue/isolation & purification; Methylene Blue/chemistry; Microscopy, Electron, Scanning; Microwaves; Naphthalenesulfonates/isolation & purification; Naphthalenesulfonates/chemistry; Water/chemistry; Water Pollutants, Chemical/isolation & purification*; Water Pollutants, Chemical/chemistry; Wood/chemistry; Spectroscopy, Fourier Transform Infrared; Water Purification/methods
  10. Chen Y, Ge D, Zhang J, Chu R, Zheng J, Wu C, et al.
    Nanoscale, 2018 Sep 20;10(36):17378-17387.
    PMID: 30203824 DOI: 10.1039/c8nr01195h
    Tin-based materials have been intensively studied as attractive candidates for high-capacity and long-cycle-life anodes in Li-ion batteries (LIBs) owing to their low cost and high energy density. However, they all suffer from severe structural decay during the lithium ion insertion/extraction process, which results in deterioration in the overall performance of the batteries. To mitigate this problem, we have synthesized a Mo-doped SnO2 nanostructure via a facile hydrothermal method, which then fragmented into ultrafine particles after dozens of cycles. The fracture-resistant size and ample contact with Super-P and Li2O greatly improved the electrochemical kinetics and cyclability to deliver a reversible capacity of 670 mA h g-1 after 700 cycles, which demonstrated the potential suitability of Mo-doped SnO2 nanoparticles as a long-cycle-life anode material. Then, the compounds were uniformly dispersed in carbon nanofibers and reduced in situ to prepare a free-standing anode via electrospinning and carbonization. When used directly as an anode in LIBs (without a polymeric binder or conductive agent, as well as a current collector), the nanofiber membrane anode delivered comparable cycling performance and capacity to that of a slurry-coated electrode.
  11. Lonsdale KA, Abadi FH
    Med Probl Perform Art, 2018 09;33(3):191-197.
    PMID: 30204825 DOI: 10.21091/mppa.2018.3027
    While numerous studies have investigated associations between Ramadan fasting and sports performance, as well as general health, little is known about the experiences of musicians who play while fasting. This exploratory case study aimed to gain a better understanding of the experiences of tertiary-level woodwind players who practice, rehearse, and perform while fasting. Sixteen undergraduate woodwind players from two Malaysian university music faculties completed an 11-item questionnaire, as well as a 7-day food and playing diary, which formed the basis for a semi-structured interview. Their experiences were compared with previous studies of fasting athletes. Many participants stated that practicing from noon to 3:00 pm was difficult due to feeling thirsty, hungry, tired, and exhausted, with some experiencing a dry mouth and/or lips. By 3:00 to 6:00 pm, some had difficulty focusing and felt tired, dizzy, or lacked energy to practice. Many felt more comfortable playing after breaking the fast or after eating sahur. The majority experienced positive impacts such as increased focus and efficiency while practicing. This study suggests that fasting woodwind players would benefit from practicing in the morning and after sunset, limiting their practice time in the afternoon, not skipping sahur, and ensuring adequate hydration during sunset and sunrise.
    MeSH terms: Adaptation, Physiological; Fasting*; Fatigue/physiopathology*; Female; Holidays/statistics & numerical data*; Humans; Islam*; Malaysia; Male; Music*; Surveys and Questionnaires; Young Adult
  12. Nna VU, Bakar ABA, Mohamed M
    Life Sci, 2018 Oct 15;211:40-50.
    PMID: 30205096 DOI: 10.1016/j.lfs.2018.09.018
    AIMS: Hepatic oxidative stress and weak antioxidant defence system resulting in hepatic lesion, has been reported in diabetic rats. The present study investigated the possible hepatoprotective effects of Malaysian propolis (MP) in diabetic rats, on the background that MP has been reported to have anti-hyperglycemic, antioxidant and anti-inflammatory effects.

    MATERIALS AND METHODS: Sprague-Dawley rats were randomly divided into 5 groups, namely: normal control (NC), diabetic control (DC), diabetic on 300 mg/kg b.w. MP, diabetic on 300 mg/kg b.w. metformin, and diabetic on MP and metformin combined therapy. Treatment was done orally for 4 weeks, and NC and DC groups received distilled water as vehicle.

    KEY FINDINGS: Results showed increased fasting blood glucose and serum markers of hepatic lesion (aspartate aminotransferase, alkaline phosphatase, alanine aminotransferase and gamma-glutamyl transferase), increased hepatic lactate dehydrogenase activity, decreased hepatic superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase and glutathione reductase activities, increased immunoexpressions of nuclear factor kappa B, tumor necrosis factor-α, interleukin(IL)-1β and caspase-3, and decreased immunoexpressions of IL-10 and proliferating cell nuclear antigen in the liver of DC group. Histopathology of the liver revealed numerous hepatocytes with pyknotic nuclei and inflammatory infiltration, while periodic acid-schiff staining decreased in the liver of DC group. Treatment with MP attenuated these negative effects and was comparable to metformin. Furthermore, these effects were better attenuated in the combined therapy-treated diabetic rats.

    SIGNIFICANCE: Malaysian propolis attenuates hepatic lesion in DM and exerts a synergistic protective effect with the anti-hyperglycemic medication, metformin.

    MeSH terms: Animals; Anti-Infective Agents/therapeutic use; Anti-Inflammatory Agents/therapeutic use; Diabetes Mellitus, Experimental/drug therapy*; Diabetes Mellitus, Experimental/metabolism; Diabetes Mellitus, Experimental/pathology; Drug Combinations; Hypoglycemic Agents/therapeutic use; Liver/drug effects*; Liver/metabolism; Liver/pathology; Malaysia; Male; Metformin/therapeutic use*; Propolis/therapeutic use*; Rats, Sprague-Dawley; Oxidative Stress/drug effects; Protective Agents/therapeutic use*; Hepatocytes/drug effects*; Hepatocytes/metabolism; Hepatocytes/pathology; Rats
  13. Alim S, Vejayan J, Yusoff MM, Kafi AKM
    Biosens Bioelectron, 2018 Dec 15;121:125-136.
    PMID: 30205246 DOI: 10.1016/j.bios.2018.08.051
    The innovation of nanoparticles assumes a critical part of encouraging and giving open doors and conceivable outcomes to the headway of new era devices utilized as a part of biosensing. The focused on the quick and legitimate detecting of specific biomolecules using functionalized gold nanoparticles (Au NPs), and carbon nanotubes (CNTs) has turned into a noteworthy research enthusiasm for the most recent decade. Sensors created with gold nanoparticles or carbon nanotubes or in some cases by utilizing both are relied upon to change the very establishments of detecting and distinguishing various analytes. In this review, we will examine the current utilization of functionalized AuNPs and CNTs with other synthetic mixes for the creation of biosensor prompting to the location of particular analytes with low discovery cutoff and quick reaction.
    MeSH terms: Electrochemistry/trends*; Gold/chemistry*; Biosensing Techniques/instrumentation; Biosensing Techniques/methods*; Biosensing Techniques/trends*; Nanotubes, Carbon/chemistry*; Metal Nanoparticles/chemistry*
  14. Syahir Habib, Siti Aqlima Ahmad, Mohd Yunus Abd Shukor, Nur Adeela Yasid, Wan Lutfi Wan Johari
    MyJurnal
    The increase of anthropogenic activities and growth of technology in Antarctica is fuelled by the high demand for petroleum hydrocarbons needed for daily activities. Oil and fuel spills that occur during explorations have caused hydrocarbon pollution in this region, prompting concern for the environment by polar communities and the larger world community. Crude oil and petroleum hydrocarbon products contain a wide variety of lethal components with high toxicity and low biodegradability. Hydrocarbon persistence in the Antarctic environment only worsens the issues stemming from environmental pollution as they can be long-term. Numerous efforts to lower the contamination level caused by these pollutants have been conducted mainly in bioremediation, an economical and degrading-wise method. Bioremediation mainly functions on conversion of complex toxic compounds to simpler organic compounds due to the consumption of hydrocarbons by microorganisms as their energy source. This review presents a summary of the collective understanding on bioremediation of petroleum hydrocarbons by microorganisms indigenous to the Antarctic region from past decades to current knowledge.
    MeSH terms: Antarctic Regions; Biodegradation, Environmental; Biological Phenomena; Hydrocarbons; Petroleum
  15. Yong HL, Mustapa NI, Lee LK, Lim ZF, Tan TH, Usup G, et al.
    Harmful Algae, 2018 09;78:56-68.
    PMID: 30196925 DOI: 10.1016/j.hal.2018.07.009
    Few studies have investigated the effect of fine-scale habitat differences on the dynamics of benthic harmful dinoflagellate assemblages. To determine how these microhabitat differences affect the distribution and abundance of the major benthic harmful dinoflagellate genera in a tropical coral reef ecosystem, a field study was undertaken between April-September 2015 and January 2016 on the shallow reef flat of the fringing reef of Rawa Island, Terengganu, Malaysia. Sampling of benthic dinoflagellates was carried out using an artificial substrate sampling method (fiberglass screens). Benthic microhabitats surrounding the sampling screens were characterized simultaneously from photographs of a 0.25-m2 quadrat based on categories of bottom substrate types. Five taxonomic groups of benthic dinoflagellates, Ostreopsis, Gambierdiscus, Prorocentrum, Amphidinium, and Coolia were identified, and cells were enumerated using a light microscope. The results showed Gambierdiscus was less abundant than other genera throughout the study period, with maximum abundance of 1.2 × 103 cells 100 cm-2. While most taxa were present on reefs with high coral cover, higher cell abundances were observed in reefs with high turf algal cover and coral rubble, with the exception of Ostreopsis, where the abundance reached a maximum of 3.4 × 104 cells 100 cm-2 in habitats with high coral cover. Microhabitat heterogeneity was identified as a key factor governing the benthic harmful dinoflagellate assemblages and may account for much of the observed variability in dominant taxa. This finding has significant implications for the role of variability in the benthic harmful algal bloom (BHAB) outbreaks and the potential in identifying BHAB-related toxin transfer pathways and the key vectors in the food webs.
  16. Loeliger KB, Altice FL, Ciarleglio MM, Rich KM, Chandra DK, Gallagher C, et al.
    Lancet HIV, 2018 11;5(11):e617-e628.
    PMID: 30197101 DOI: 10.1016/S2352-3018(18)30175-9
    BACKGROUND: People transitioning from prisons or jails have high mortality, but data are scarce for people with HIV and no studies have integrated data from both criminal justice and community settings. We aimed to assess all-cause mortality in people with HIV released from an integrated system of prisons and jails in Connecticut, USA.

    METHODS: We linked pharmacy, custodial, death, case management, and HIV surveillance data from Connecticut Departments of Correction and Public Health to create a retrospective cohort of all adults with HIV released from jails and prisons in Connecticut between 2007 and 2014. We compared the mortality rate of adults with HIV released from incarceration with the general US and Connecticut populations, and modelled time-to-death from any cause after prison release with Cox proportional hazard models.

    FINDINGS: We identified 1350 people with HIV who were released after 24 h or more of incarceration between 2007 and 2014, of whom 184 (14%) died after index release; median age was 45 years (IQR 39-50) and median follow-up was 5·2 years (IQR 3·0-6·7) after index release. The crude mortality rate for people with HIV released from incarceration was 2868 deaths per 100 000 person-years, and the standardised mortality ratio showed that mortality was higher for this cohort than the general US population (6·97, 95% CI 5·96-7·97) and population of Connecticut (8·47, 7·25-9·69). Primary cause of death was reported for 170 individuals; the most common causes were HIV/AIDS (78 [46%]), drug overdose (26 [15%]), liver disease (17 [10%]), cardiovascular disease (16 [9%]), and accidental injury or suicide (13 [8%]). Black race (adjusted hazard ratio [HR] 0·52, 95% CI 0·34-0·80), having health insurance (0·09, 0·05-0·17), being re-incarcerated at least once for 365 days or longer (0·41, 0·22-0·76), and having a high percentage of re-incarcerations in which antiretroviral therapy was prescribed (0·08, 0·03-0·21) were protective against mortality. Positive predictors of time-to-death were age (≥50 years; adjusted HR 3·65, 95% CI 1·21-11·08), lower CD4 count (200-499 cells per μL, 2·54, 1·50-4·31; <200 cells per μL, 3·44, 1·90-6·20), a high number of comorbidities (1·86, 95% CI 1·23-2·82), virological failure (2·76, 1·94-3·92), and unmonitored viral load (2·13, 1·09-4·18).

    INTERPRETATION: To reduce mortality after release from incarceration in people with HIV, resources are needed to identify and treat HIV, in addition to medical comorbidities, psychiatric disorders, and substance use disorders, during and following incarceration. Policies that reduce incarceration and support integrated systems of care between prisons and communities could have a substantial effect on the survival of people with HIV.

    FUNDING: US National Institutes of Health.

    MeSH terms: Adult; Cause of Death; Connecticut; Female; Humans; Male; Middle Aged; Prisoners/psychology; Prisoners/statistics & numerical data*; Prisons*; Retrospective Studies; Risk Factors; HIV Infections/mortality*; Proportional Hazards Models
  17. Jayusman PA, Mohamed IN, Shuid AN
    Int J Endocrinol Metab, 2018 Jul;16(3):e64038.
    PMID: 30197659 DOI: 10.5812/ijem.64038
    Background: Gonadotropin releasing hormone (GnRH) antagonists may cause chemical castration in males by suppressing the pituitary-gonadal axis, hence reducing testosterone level. There are limited data on the effects of degarelix, a newer series of potent and long acting GnRH antagonist on bone.

    Objectives: The current study aimed at determining the effects of degarelix on bone turnover, bone densitometry, and bone mechanical strength in male rats.

    Methods: Eighteen male Sprague-Dawley rats were randomly divided into sham (SHAM), orchidectomized (ORX), and degarelix-induced (DGX) groups. Chemical castration was performed by subcutaneous degarelix injection (2 mg/kg) at the scapular region. The rats were scanned for baseline bone mineral area (BMA), bone mineral content (BMC), and bone mineral density (BMD) using dual-energy x-ray absorptiometry (DXA). Following six weeks of experimental period, BMA, BMC, and BMD were measured again with DXA and blood was collected for testosterone and bone biomarkers (osteocalcin and C-terminal of type I collagen crosslink (CTX-1)) measurements. The rats were euthanized and femora were dissected for bone biomechanical strength analysis.

    Results: Bilateral orchidectomy and degarelix administration significantly lowered serum testosterone level, decreased whole body BMC, femoral BMA, femoral BMC, and femoral BMD (P < 0.05) compared with the SHAM group. However, no significant changes were observed in bone biochemical markers and bone mechanical strength in all experimental groups.

    Conclusions: In conclusion, degarelix administration had comparable effects on bone as bilateral orchidectomy. Administration of degarelix provides an alternative method of inducing testosterone deficient-osteopenia in male rats without need for removing the testes.

    MeSH terms: Animals; Bone Diseases, Metabolic; Femur; Humans; Gonadotropin-Releasing Hormone; Male; Minerals; Orchiectomy; Testis; Testosterone; Biomarkers; Absorptiometry, Photon; Bone Density; Osteocalcin; Bone Remodeling; Rats, Sprague-Dawley; Collagen Type I; Rats
  18. 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.
    MeSH terms: Fusarium; Libraries; Plants, Medicinal; Gene Library; DNA, Complementary; Databases, Nucleic Acid; RNA, Small Interfering; MicroRNAs; High-Throughput Nucleotide Sequencing
  19. Mat Jalaluddin NS, Othman RY, Harikrishna JA
    Crit Rev Biotechnol, 2018 Sep 09.
    PMID: 30198341 DOI: 10.1080/07388551.2018.1496064
    It has only been about 20 years since the first Nobel Prize-winning work on RNA interference (RNAi) in Caenorhabditis elegans was published in the journal Nature. Fast forward to today, and the use of RNA molecules as gene-silencing elements in crops has helped scientists to unveil possible solutions to the global problems of agricultural losses due to pests, viruses, pathogens, and to other abiotic and biotic stresses. The recent proliferation of publications suggests that the technology has gained significant attention and received ample funding support. In this article, an attempt has been made to visualize recent trends in Research & Development (R&D) investment in this field by analyzing top cited scholarly articles, patent trends, and commercialization activity. The publication and citation analysis identified that the development of RNAi-based crops conferring resistance against viruses, fungi, and pests are at the forefront of RNAi research and that Chinese and US institutions are the leaders in this field. The patent landscape analysis for RNAi technology over all aspects related to RNAi-derived crops provides an overview of patenting activity from a geographical, organizational, and legal perspective. Such an exercise is pivotal to industry players and public institutions aiming at creating intellectual property that is commercially appealing. An upswing in commercial interests in this technology in recent years is reflected by a consistent number of patent filings in US, European, and Chinese patent offices, with multinational giant firms as the most prolific patent filers. The expanding RNAi commercialization landscape is supported by a series of strategic partnerships, licensing agreements, and acquisitions created between agribusinesses, public research institutions, and startup companies. From key observations, we would like to highlight that such investments have very positive impacts on the development of RNAi technology. Nonetheless, the success of this technology is dependent on several factors, such as financial requirements, the complexity, and timeframe of the entire development process, as well as stringent regulations imposed by the relevant authorities. In most countries, RNAi-based transgenic crops are still considered as a genetically modified (GM) product, which necessitates the crops to undergo rigorous evaluation before approval is granted. Recent advancements in exogenous RNAi-derived biopesticides have provided a nontransgenic alternative to GM crops. However, challenges still remain in the form of technical hurdles and regulatory ambiguities surrounding this emerging technology. Its full potential remains to be realized.
    MeSH terms: Agriculture; Animals; Attention; Filing; Fungi; Nobel Prize; Research; RNA; Viruses; Caenorhabditis elegans; Crops, Agricultural; Intellectual Property; Gene Silencing; RNA Interference; Silencer Elements, Transcriptional; Cell Proliferation; Biological Control Agents
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