Displaying publications 21 - 36 of 36 in total

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  1. Fulltext Genome Sequence ofSerratia marcescenssubsp.sakuensisStrain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis)
    Cheng TH, Saidin J, Danish-Daniel M, Gan HM, Mat Isa MN, Abu Bakar MF, et al.
    Genome Announc, 2018 Feb 08;6(6).
    PMID: 29439033 DOI: 10.1128/genomeA.00022-18
    Serratia marcescens
    subsp.sakuensisstrain K27 was isolated from sponge (Haliclona amboinensis). The genome of this strain consists of 5,325,727 bp, with 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for the production of amylases, lipases, and proteases. Gene clusters for the biosynthesis of nonribosomal peptides and thiopeptide were also identified.
  2. Fulltext Cyst viability and stress tolerance upon heat shock protein 70 knockdown in the brine shrimp Artemia franciscana
    Iryani MTM, Sorgeloos P, Danish-Daniel M, Tan MP, Wong LL, Mok WJ, et al.
    Cell Stress Chaperones, 2020 Nov;25(6):1099-1103.
    PMID: 32383141 DOI: 10.1007/s12192-020-01113-0
    Females of the brine shrimp Artemia franciscana produce either free-swimming nauplii via ovoviviparous pathway of reproduction or encysted embryos, known as cysts, via oviparous pathway, in which biological processes are arrested. While previous study has shown a crucial role of ATP-dependent molecular chaperone, heat shock protein 70 (Hsp70) in protecting A. franciscana nauplii against various abiotic and abiotic stressors, the function of this protein in diapausing embryos and cyst development, however, remains unknown. RNA interference (RNAi) was applied in this study to examine the role of Hsp70 in cyst development and stress tolerance, with the latter performed by desiccation and freezing, a common method used for diapause termination in Artemia cysts. Hsp70 knockdown was apparent in cysts released from females that were injected with Hsp70 dsRNA. The loss of Hsp70 affected neither the development nor morphology of the cysts. The time between fertilization and cyst release from Artemia females injected with Hsp70 dsRNA was delayed slightly, but the differences were not significant when compared to the controls. However, the hatching percentage of cysts which lacks Hsp70 were reduced following desiccation and freezing. Taken together, these results indicated that Hsp70 possibly plays a role in the stress tolerance but not in the development of diapause-destined embryos of Artemia. This research makes fundamental contributions to our understanding of the role molecular chaperone Hsp70 plays in Artemia, an excellent model organism for diapause studies of the crustaceans.
  3. Fulltext Knowledge mapping analysis of the global seaweed research using CiteSpace
    Segaran TC, Azra MN, Mohd Noor MI, Danish-Daniel M, Burlakovs J, Lananan F, et al.
    Heliyon, 2024 Apr 15;10(7):e28418.
    PMID: 38560172 DOI: 10.1016/j.heliyon.2024.e28418
    Seaweed research has gained substantial momentum in recent years, attracting the attention of researchers, academic institutions, industries, policymakers, and philanthropists to explore its potential applications and benefits. Despite the growing body of literature, there is a paucity of comprehensive scientometric analyses, highlighting the need for an in-depth investigation. In this study, we utilized CiteSpace to examine the global seaweed research landscape through the Web of Science Core Collection database, assessing publication trends, collaboration patterns, network structures, and co-citation analyses across 48,278 original works published since 1975. Our results demonstrate a diverse and active research community, with a multitude of authors and journals contributing to the advancement of seaweed science. Thematic co-citation cluster analysis identified three primary research areas: "Coral reef," "Solar radiation," and "Mycosporine-like amino acid," emphasizing the multidisciplinary nature of seaweed research. The increasing prominence of "Chemical composition" and "Antioxidant" keywords indicates a burgeoning interest in characterizing the nutritional value and health-promoting properties of seaweed. Timeline co-citation analysis unveils that recent research priorities have emerged around the themes of coral reefs, ocean acidification, and antioxidants, underlining the evolving focus and interdisciplinary approach of the field. Moreover, our analysis highlights the potential of seaweed as a functional food product, poised to contribute significantly to addressing global food security and sustainability challenges. This study underscores the importance of bibliometric analysis in elucidating the global seaweed research landscape and emphasizes the need for sustained knowledge exchange and collaboration to drive the field forward. By revealing key findings and emerging trends, our research offers valuable insights for academics and stakeholders, fostering a more profound understanding of seaweed's potential and informing future research endeavors in this promising domain.
  4. Pandanus tectorius fruit extract promotes Hsp70 accumulation, immune-related genes expression and Vibrio parahaemolyticus tolerance in the white-leg shrimp Penaeus vannamei
    Anirudhan A, Okomoda VT, Mimi Iryani MT, Andriani Y, Abd Wahid ME, Tan MP, et al.
    Fish Shellfish Immunol, 2021 Feb;109:97-105.
    PMID: 33352338 DOI: 10.1016/j.fsi.2020.12.011
    Plants and herbal extracts are indispensable for controlling the spread of disease-causing bacteria, including those that infect aquatic organisms used in aquaculture. The use of plant or herbal extract is expected to be safe for aquatic animals and less harmful to the environment, as opposed to conventional therapeutic alternatives such as antibiotics that promote the occurrence of potential antibiotic-resistant bacteria when used improperly. The efficacy of Pandanus tectorius fruit extract in the regulation of Hsp70 expression, pro-phenoloxidase (ProPO), peroxinectin, penaeidin, crustin and transglutaminase, all immune peptides essential for Vibrio tolerance in white leg shrimp, Penaeus vannamei, was investigated in this study, which included the determination of the safety levels of the extract. Tolerance of shrimp against Vibrio parahaemolyticus, a pathogenic bacteria that causes Acute Hepatopancreas Necrosis Disease (AHPND), was assessed on the basis of median lethal dose challenge survival (LD50 = 106 cells/ml). Mortality was not observed 24 h after exposure of 0.5-6 g/L of the fruit extract, indicating that P. tectorius was not toxic to shrimp at these concentrations. A 24-h incubation of 2-6 g/L of the fruit extract increased shrimp tolerance to V. parahaemolyticus, with survival doubled when the maximum dose tested in this study was used. Concomitant with a rise in survival was the increase in immune-related proteins, with Hsp70, ProPO, peroxinectin, penaeidin, crustin and transglutaminase increased 10, 11, 11, 0.4, 8 and 13-fold respectively. Histological examination of the hepatopancreas and muscle tissues of Vibrio-infected shrimp primed with P. tectorius extract revealed reduced signs of histopathological degeneration, possibly due to the accumulation of Hsp70, a molecular chaperone crucial to cellular protein folding, tissue repair and immune response of living organisms, including Penaeid shrimp.
  5. Fulltext Applications of Next-Generation Sequencing Technologies and Computational Tools in Molecular Evolution and Aquatic Animals Conservation Studies: A Short Review
    Tan MP, Wong LL, Razali SA, Afiqah-Aleng N, Mohd Nor SA, Sung YY, et al.
    Evol Bioinform Online, 2019;15:1176934319892284.
    PMID: 31839703 DOI: 10.1177/1176934319892284
    Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.
  6. Fulltext Recent population expansion of longtail tuna Thunnus tonggol (Bleeker, 1851) inferred from the mitochondrial DNA markers
    Syahida Kasim N, Mat Jaafar TNA, Mat Piah R, Mohd Arshaad W, Mohd Nor SA, Habib A, et al.
    PeerJ, 2020;8:e9679.
    PMID: 32844067 DOI: 10.7717/peerj.9679
    The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison ФST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989-1.000; ND5 = 0.848-0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019-0.025; ND5 = 0.0017-0.003), "star-like" haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.
  7. Hsp70 Knockdown in the Brine Shrimp Artemia franciscana: Implication on Reproduction, Immune Response and Embryonic Cuticular Structure
    Tiong IKR, Lau CC, Sorgeloos P, Mat Taib MI, Muhammad TST, Danish-Daniel M, et al.
    Mar Biotechnol (NY), 2024 Apr 29.
    PMID: 38683457 DOI: 10.1007/s10126-024-10318-8
    The potential functional role(s) of heat shock protein 70 (Hsp70) in the brine shrimp, Artemia franciscana, a crucial crustacean species for aquaculture and stress response studies, was investigated in this study. Though we have previously reported that Hsp70 knockdown may have little or no impact on Artemia development, the gestational survival and number of offspring released by adult females were impaired by obscuring Hsp70 synthesis. Transcriptomic analysis revealed that several cuticle and chitin synthetic genes were downregulated, and carbohydrate metabolic genes were differentially expressed in Hsp70-knockdown individuals. A more comprehensive microscopic examination performed in this study revealed exoskeleton structural destruction and abnormal eye lenses featured in Hsp70-deficient adult females 48 h after Hsp70 dsRNA injection. Cysts produced by these Hsp70-deficient broods, instead, had a defective shell and were smaller in size, whereas nauplii had shorter first antennae and a rougher body epicuticle surface. Changes in carbohydrate metabolism caused by Hsp70 knockdown affected glycogen levels in adult Artemia females, as well as trehalose in cysts released from these broods, indicating that Hsp70 may play a role in energy storage preservation. Outcomes from this work provided novel insights into the roles of Hsp70 in Artemia reproduction performance, cyst formation, and exoskeleton structure preservation. The findings also support our previous observation that Hsp70 knockdown reduced Artemia nauplius tolerance to bacterial pathogens, which could be explained by the fact that loss of Hsp70 downregulated several Toll receptor genes (NT1 and Spaetzle) and reduced the integrity of the exoskeleton, allowing pathogens to enter and cause infection, ultimately resulting in mortality.
  8. Fulltext Phylogenomics of the genus Tursiops and closely related Delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers
    Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, et al.
    Mol Phylogenet Evol, 2020 05;146:106756.
    PMID: 32028032 DOI: 10.1016/j.ympev.2020.106756
    Phylogeographic inference has provided extensive insight into the relative roles of geographical isolation and ecological processes during evolutionary radiations. However, the importance of cross-lineage admixture in facilitating adaptive radiations is increasingly being recognised, and suggested as a main cause of phylogenetic uncertainty. In this study, we used a double digest RADseq protocol to provide a high resolution (~4 Million bp) nuclear phylogeny of the Delphininae. Phylogenetic resolution of this group has been especially intractable, likely because it has experienced a recent species radiation. We carried out cross-lineage reticulation analyses, and tested for several sources of potential bias in determining phylogenies from genome sampling data. We assessed the divergence time and historical demography of T. truncatus and T. aduncus by sequencing the T. aduncus genome and comparing it with the T. truncatus reference genome. Our results suggest monophyly for the genus Tursiops, with the recently proposed T. australis species falling within the T. aduncus lineage. We also show the presence of extensive cross-lineage gene flow between pelagic and European coastal ecotypes of T. truncatus, as well as in the early stages of diversification between spotted (Stenella frontalis; Stenella attenuata), spinner (Stenella longirostris), striped (Stenella coeruleoalba), common (Delphinus delphis), and Fraser's (Lagenodelphis hosei) dolphins. Our study suggests that cross-lineage gene flow in this group has been more extensive and complex than previously thought. In the context of biogeography and local habitat dependence, these results improve our understanding of the evolutionary processes determining the history of this lineage.
  9. Corrigendum to "Phylogenomics of the genus Tursiops and closely related delphininae reveals extensive reticulation among lineages and provides inference about eco-evolutionary drivers" [Mol. Phylogenet. Evol. 146 (2020) 106756]
    Moura AE, Shreves K, Pilot M, Andrews KR, Moore DM, Kishida T, et al.
    Mol Phylogenet Evol, 2021 Jan 08.
    PMID: 33431184 DOI: 10.1016/j.ympev.2020.107047
  10. Fulltext Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)
    Mohd Yusoff NIS, Mat Jaafar TNA, Vilasri V, Mohd Nor SA, Seah YG, Habib A, et al.
    Sci Rep, 2021 Jun 25;11(1):13357.
    PMID: 34172804 DOI: 10.1038/s41598-021-92905-6
    Benthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490-0.900, nucleotide diversity, π = 0.0010-0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118-0.216; π = 0.0004-0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.
  11. STROCSS 2019 Guideline: Strengthening the reporting of cohort studies in surgery
    Agha R, Abdall-Razak A, Crossley E, Dowlut N, Iosifidis C, Mathew G, et al.
    Int J Surg, 2019 Nov 06;72:156-165.
    PMID: 31704426 DOI: 10.1016/j.ijsu.2019.11.002
    INTRODUCTION: The STROCSS guideline was developed in 2017 to improve the reporting quality of observational studies in surgery. Building on its impact and usefulness, we sought to update the guidelines two years after its publication.

    METHODS: A steering group was formed to review the existing guideline and propose amendments to the 17-item checklist. A Delphi consensus exercise was utilised to determine agreement across a list of proposed modifications to the STROCSS 2017 guideline. An expert panel of 46 surgeons were invited to assess the proposed updates via Google Forms.

    RESULTS: The response rate was 91% (n = 42/46). High agreement was reached across all the items and the guideline was finalised in the first round. The checklist maintained 17-items, with modifications primarily considered to improve content and readability.

    CONCLUSIONS: The STROCSS 2019 guideline is hereby presented as a considered update to improve reporting of cohort, cross-sectional and case-control studies in surgery.

  12. Fulltext Somatic mutations of GNA11 and GNAQ in CTNNB1-mutant aldosterone-producing adenomas presenting in puberty, pregnancy or menopause
    Zhou J, Azizan EAB, Cabrera CP, Fernandes-Rosa FL, Boulkroun S, Argentesi G, et al.
    Nat Genet, 2021 Sep;53(9):1360-1372.
    PMID: 34385710 DOI: 10.1038/s41588-021-00906-y
    Most aldosterone-producing adenomas (APAs) have gain-of-function somatic mutations of ion channels or transporters. However, their frequency in aldosterone-producing cell clusters of normal adrenal gland suggests a requirement for codriver mutations in APAs. Here we identified gain-of-function mutations in both CTNNB1 and GNA11 by whole-exome sequencing of 3/41 APAs. Further sequencing of known CTNNB1-mutant APAs led to a total of 16 of 27 (59%) with a somatic p.Gln209His, p.Gln209Pro or p.Gln209Leu mutation of GNA11 or GNAQ. Solitary GNA11 mutations were found in hyperplastic zona glomerulosa adjacent to double-mutant APAs. Nine of ten patients in our UK/Irish cohort presented in puberty, pregnancy or menopause. Among multiple transcripts upregulated more than tenfold in double-mutant APAs was LHCGR, the receptor for luteinizing or pregnancy hormone (human chorionic gonadotropin). Transfections of adrenocortical cells demonstrated additive effects of GNA11 and CTNNB1 mutations on aldosterone secretion and expression of genes upregulated in double-mutant APAs. In adrenal cortex, GNA11/Q mutations appear clinically silent without a codriver mutation of CTNNB1.
  13. Fulltext An estimate of the number of tropical tree species
    Slik JW, Arroyo-Rodríguez V, Aiba S, Alvarez-Loayza P, Alves LF, Ashton P, et al.
    Proc Natl Acad Sci U S A, 2015 Jun 16;112(24):7472-7.
    PMID: 26034279 DOI: 10.1073/pnas.1423147112
    The high species richness of tropical forests has long been recognized, yet there remains substantial uncertainty regarding the actual number of tropical tree species. Using a pantropical tree inventory database from closed canopy forests, consisting of 657,630 trees belonging to 11,371 species, we use a fitted value of Fisher's alpha and an approximate pantropical stem total to estimate the minimum number of tropical forest tree species to fall between ∼ 40,000 and ∼ 53,000, i.e., at the high end of previous estimates. Contrary to common assumption, the Indo-Pacific region was found to be as species-rich as the Neotropics, with both regions having a minimum of ∼ 19,000-25,000 tree species. Continental Africa is relatively depauperate with a minimum of ∼ 4,500-6,000 tree species. Very few species are shared among the African, American, and the Indo-Pacific regions. We provide a methodological framework for estimating species richness in trees that may help refine species richness estimates of tree-dependent taxa.
  14. Fulltext Phylogenetic classification of the world's tropical forests
    Slik JWF, Franklin J, Arroyo-Rodríguez V, Field R, Aguilar S, Aguirre N, et al.
    Proc Natl Acad Sci U S A, 2018 02 20;115(8):1837-1842.
    PMID: 29432167 DOI: 10.1073/pnas.1714977115
    Knowledge about the biogeographic affinities of the world's tropical forests helps to better understand regional differences in forest structure, diversity, composition, and dynamics. Such understanding will enable anticipation of region-specific responses to global environmental change. Modern phylogenies, in combination with broad coverage of species inventory data, now allow for global biogeographic analyses that take species evolutionary distance into account. Here we present a classification of the world's tropical forests based on their phylogenetic similarity. We identify five principal floristic regions and their floristic relationships: (i) Indo-Pacific, (ii) Subtropical, (iii) African, (iv) American, and (v) Dry forests. Our results do not support the traditional neo- versus paleotropical forest division but instead separate the combined American and African forests from their Indo-Pacific counterparts. We also find indications for the existence of a global dry forest region, with representatives in America, Africa, Madagascar, and India. Additionally, a northern-hemisphere Subtropical forest region was identified with representatives in Asia and America, providing support for a link between Asian and American northern-hemisphere forests.
  15. The ChoCO-W prospective observational global study: Does COVID-19 increase gangrenous cholecystitis?
    De Simone B, Abu-Zidan FM, Chouillard E, Di Saverio S, Sartelli M, Podda M, et al.
    World J Emerg Surg, 2022 Dec 16;17(1):61.
    PMID: 36527038 DOI: 10.1186/s13017-022-00466-4
    BACKGROUND: The incidence of the highly morbid and potentially lethal gangrenous cholecystitis was reportedly increased during the COVID-19 pandemic. The aim of the ChoCO-W study was to compare the clinical findings and outcomes of acute cholecystitis in patients who had COVID-19 disease with those who did not.

    METHODS: Data were prospectively collected over 6 months (October 1, 2020, to April 30, 2021) with 1-month follow-up. In October 2020, Delta variant of SARS CoV-2 was isolated for the first time. Demographic and clinical data were analyzed and reported according to the STROBE guidelines. Baseline characteristics and clinical outcomes of patients who had COVID-19 were compared with those who did not.

    RESULTS: A total of 2893 patients, from 42 countries, 218 centers, involved, with a median age of 61.3 (SD: 17.39) years were prospectively enrolled in this study; 1481 (51%) patients were males. One hundred and eighty (6.9%) patients were COVID-19 positive, while 2412 (93.1%) were negative. Concomitant preexisting diseases including cardiovascular diseases (p 

  16. Goodbye Hartmann trial: a prospective, international, multicenter, observational study on the current use of a surgical procedure developed a century ago
    Perrone G, Giuffrida M, Abu-Zidan F, Kruger VF, Livrini M, Petracca GL, et al.
    World J Emerg Surg, 2024 Apr 16;19(1):14.
    PMID: 38627831 DOI: 10.1186/s13017-024-00543-w
    BACKGROUND: Literature suggests colonic resection and primary anastomosis (RPA) instead of Hartmann's procedure (HP) for the treatment of left-sided colonic emergencies. We aim to evaluate the surgical options globally used to treat patients with acute left-sided colonic emergencies and the factors that leading to the choice of treatment, comparing HP and RPA.

    METHODS: This is a prospective, international, multicenter, observational study registered on ClinicalTrials.gov. A total 1215 patients with left-sided colonic emergencies who required surgery were included from 204 centers during the period of March 1, 2020, to May 31, 2020. with a 1-year follow-up.

    RESULTS: 564 patients (43.1%) were females. The mean age was 65.9 ± 15.6 years. HP was performed in 697 (57.3%) patients and RPA in 384 (31.6%) cases. Complicated acute diverticulitis was the most common cause of left-sided colonic emergencies (40.2%), followed by colorectal malignancy (36.6%). Severe complications (Clavien-Dindo ≥ 3b) were higher in the HP group (P 

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