SULAM 2023 Pelajar UMP berkongsi teknologi penjujukan di MRSM Kuantan

Seramai 21 orang pelajar BSB3703 Microbial Genomics telah turun menyantuni pelajar tingkatan 4 MRSM Kuantan pada baru-baru ini bagi menjayakan projek SULAM 2023 yang diselia oleh Ts Dr Hajar Fauzan Bin Ahmad dan para pendidik program Bioteknologi Industri, Fakulti Sains dan Teknologi Industri, Universiti Malaysia Pahang

Isolation and genome sequencing of bacillus megaterium found from the gut sea cucumber (Holithuria Leucospilota)

Bacillus megaterium is a bacterium that is widely used in the application of biotechnology. Often its popularity is due to its ability to represent a suitable host to generate compounds such as cobalamin and perform biosynthesis production of smaller biological molecules. The bacterium can also be found in a wide variety of habitats including sea water. The interest towards sea cucumbers have skyrocketed to a point of extinction in certain species. This popularity could be due to the uniqueness associated to the gut microbiome observed within sea cucumber or just the organism itself. However, the presence of B.megaterium within the gut of Holithuria leucospilota could prove an answer to the previous statement. In this study, isolation of an unknown bacterium (which was B.Megaterium), identification and genomic analysis of the bacterium which was obtained from the gut of H.leucospilota was carried out. DNA was extracted using commercial kits, and later quantified using a NanoDrop Biophotometer. The V3-V4 region of the 16s RNA was used as specific primers for PCR amplification. Quality of DNA and PCR results were verified using agarose gel electrophoresis. Identification was carried out by performing sanger sequencing towards the PCR products obtained. The study identified and reported a complete genome of B.megaterium compromising of 5,323,711 bp genome size with a GC content of 37.9%. The annotated genome was submitted to the NCBI database. Overall, this study revealed the complete genome of B.megaterium and would serve to potentially explain its association towards the gut microbiome found within H.leucospilota

Phylogeny of holothuria leucospilota (echinodermata: holothuroidea) as inferred from cytochrome c oxidase i mtDNA gene sequences

This study aimed to generate the genetic profile of Holothuria (Mertensiothuria) leucospilota (Brandt 1835) from Intan Besar Island, Langkawi, Kedah Darul Aman, Malaysia and then to determine the phylogenetic relationship between H. leucospilota and other members of genus Holothuria available in the GenBank using partial sequences of cytochrome c oxidase I (COI) mitochondrial DNA (mtDNA) gene. In this study, tree topologies of neighbour joining, maximum parsimony and maximum likelihood show that H. leucospilota has its own monophyletic clade clearly distinct from the other species and it is genetically closer to Holothuria (Acanthotrapeza) coluber Semper 1868

Tensile properties of jute-polypropylene composites

This paper describes the tensile behaviour of jute-polypropylene fibre composites with different fibre volume fractions. Here, the composite laminates consisting of weaving jute fibres, with the fibre volume percent in the range of 20 to 80 % and polypropylene plies were prepared using hand lamination. The composite laminates were subjected to tensile testing as per ASTM D3039. The experimental results suggested that fibre-to-resin contents have a strong influence on the tensile properties of the composites. There is an increase in the tensile strength and Young's Modulus of the composites with increasing fibre volume fraction. However, upon reaching 60 % of the fibre contents, the tensile properties of the laminate showed a sudden decrease due to stress concentration of the fibre in the laminates. Theoretical models including Rule of Mixture, Halpin-Tsai, Hirsch, and Einstein-Guth models were used to predict the tensile strength of the composites. It was found that the experimental result attained is in close agreement with the values predicted using the rule of mixture model

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs

<div><p>Polyphenols are a class of bioactive plant secondary metabolites that are thought to have beneficial effects on gut health, such as modulation of mucosal immune and inflammatory responses and regulation of parasite burdens. Here, we examined the interactions between a polyphenol-rich diet supplement and infection with the enteric nematode <i>Ascaris suum</i> in pigs. Pigs were fed either a basal diet or the same diet supplemented with grape pomace (GP), an industrial by-product rich in polyphenols such as oligomeric proanthocyanidins. Half of the animals in each group were then inoculated with <i>A</i>. <i>suum</i> for 14 days to assess parasite establishment, acquisition of local and systemic immune responses and effects on the gut microbiome. Despite <i>in vitro</i> anthelmintic activity of GP-extracts, numbers of parasite larvae in the intestine were not altered by GP-supplementation. However, the bioactive diet significantly increased numbers of eosinophils induced by <i>A</i>. <i>suum</i> infection in the duodenum, jejunum and ileum, and modulated gene expression in the jejunal mucosa of infected pigs. Both GP-supplementation and <i>A</i>. <i>suum</i> infection induced significant and apparently similar changes in the composition of the prokaryotic gut microbiota, and both also decreased concentrations of isobutyric and isovaleric acid (branched-chain short chain fatty acids) in the colon. Our results demonstrate that while a polyphenol-enriched diet in pigs may not directly influence <i>A</i>. <i>suum</i> establishment, it significantly modulates the subsequent host response to helminth infection. Our results suggest an influence of diet on immune function which may potentially be exploited to enhance immunity to helminths.</p></div

Near-complete whole-genome sequence of Paenibacillus sp. nov. Strain J5C2022, a sucretolerant and endospore-forming bacterium isolated from highly concentrated sugar brine

Here, we present a 7.62-Mbp genome sequence of Paenibacillus sp. nov. strain J5C2022, a Gram-positive facultatively anaerobic bacterium that was isolated from 4-month-old fruit pickle brine and sequenced using the Illumina platform

Whole genome sequencing of Priestia megaterium isolated from the gut of sea cucumber (Holothuria leucospilota)

Priestia megatrium represents a bacterium of interest in a wide application of the field of biotechnology. Often it is sought after for its ability that boasts great rate for biosynthesis production of smaller biological molecules while also representing a suitable host to generate compounds such as cobalamin. The bacterium can also be found in a wide variety of habitats including sea water. Sea cucumbers have begun to be quite popular to a point of extinction in certain species. This interest could be associated to the uniqueness attributed to its gut microbiome or just the organism itself. Nevertheless, the presence of Priestia megaterium within the gut of Holothuria leucospilota might serve as rationale to the previous statement. Here, we describe a detailed genomic analysis of Priestia megaterium isolated from the gut of Holothuria leucospilota. Genomic DNA was extracted from nutrient broths which were incubated with pure cultures of Priestia megatrium which were previously isolated from the sea cucumber. Whole genome sequencing was carried out using an Oxford Nanopore Technology platform which used a long-read protocol. The study reported a complete genome of Priestia megatrium compromising of 5,323,711Â bp genome size with a GC content of 37.9Â . Finally, the annotated genome was submitted to the NCBI database. Overall, this study revealed the complete genome of Priestia megatrium and would serve to potentially explain its association towards the gut microbiome found within Holothuria leucospilota

Whole genome sequencing analysis of Komagataeibacter nataicola reveals its potential in food waste valorisation for cellulose production

Background: Komagataeibacter nataicola (K. nataicola) is a gram-negative acetic acid bacterium that produces natural bacterial cellulose (BC) as a fermentation product under acidic conditions. The goal of this work was to study the complete genome of K. nataicola and gain insight into the functional genes in K. nataicola that are responsible for BC synthesis in acidic environments. Methods and result; The pure culture of K. nataicola was obtained from yeast-glucose-calcium carbonate (YGC) agar, followed by genomic DNA extraction, and subjected to whole genome sequencing on a Nanopore flongle flow cell. The genome of K. nataicola consists of a 3,767,936 bp chromosome with six contigs and 4,557 protein coding sequences. The maximum likelihood phylogenetic tree and average nucleotide identity analysis confirmed that the bacterial isolate was K. nataicola. The gene annotation via RAST server discovered the presence of cellulose synthase, along with three genes associated with lactate utilization and eight genes involved in lactate fermentation that could potentially contribute to the increase in acid concentration during BC synthesis. Conclusion: A more comprehensive genome study of K. nataicola may shed light into biological pathway in BC productivity as well as benefit the analysis of metabolites generated and understanding of biological and chemical interactions in BC production later

Phylogenetic analysis of Macroglossus Sobrinus from Peninsular Malaysia

A study on the phylogeneticso f Mocroglossuss obrinus( GreaterL ong-nosedF ruit Bat)from Peninsular Malaysia was done using partial cytochrome b (cyt-b) mitochondrial DNA (mtDNA)g ene.T he specimenso f M. sobrinusw ere collectedf rom Kedah( WengU lu Muda ForestR eserve)P, erak( BintangF orestR eserve)s, elangor( Ulu Langat),M elaka (Asahan Catchment Area), Johor (Gunung Ledang), Kelantan (Gua Musang), and pahang (Krau WildlifeR eserve)T. hirty ninec yt-bs equencesin cludinge ighteens equenceso f M. sobrinus, twenty sequenceso f M. minimust aken from the GenBanka, nd a sequenceo f Penthetor /ucosi( Lucas'sS hort-nosedF ruit Bat) as an outgroup were incorporatedi n the analyses. Three main methods namely neighbourj oining (NJ) ,m aximum parsimony( Mp) , and maximuml ikelihood( ML) were usedi n the phylogenetictr ees reconstructionfo llowed by the consensusp hylogenetictr ee to summarizet he overallf indings.T he four trees were reconstructedto determinet he geneticr elationshipb etweenM . sobrinusa ndM . minimus. Generallyt,h e trees indicatedg eneticd ivergenceb etweenp opulationso f M. sobrinus.The resultw as fur,thers upportedb y very low geneticd istancesb asedo n Kimura2 -parameter distance( 1980)c alculationT. herew as an individuaol f M. sobrinus( GuaM usang,K elantan) 55 clusteredw ith the M. minimus individualst,h us indicatingo f possiblem isidentification. Apart from that, M. sobrinusf rom Kelantang avet he highestn ucleotided iversity,P 1(J ukes & Cantor1 969)w ith 0,65%,f ollowed by Perak( 0.36%),K edah( 0.27%)S, elangor( 0.78%1, and finally Pahang and Melaka with no nucleotide diversity. Overall, the nucleotide diversityo f M. sobrinusi n PeninsularM alaysiaw as 0.29%i ndicatingl ow level of genetic diversity. However, the sample size is too small to relate the results with the phylogeography and population genetic views. Therefore, more extensive studies incorporatingo ther mtDNAg enesw ith higherr ate of evolutions ucha s control regiong ene are highlyr ecommendedin the futures tud