Isolation of fungi from Sabah that produce Bioactive compounds which effect signal transduction

Filamentous micro-fungal strains were isolated from various environments in Sabah especially from the soil of the rain forest.' Sabah with its unique natural resources provides the means for the discovery of new micro-fungal strains with the potential to produce novel bioactive secondary metabolite compounds which affect signal transduction. This is the main focus of this research. A total of 364 fungal strains were isolated. Extracts from the aerobic liquid fermentation of these fungal strains were screened for inhibitory effect on Signal transduction of both yeast and bacterial strains. In the course of this research, soil samples have been collected in the expeditions that were carried out by this university to remote locations of Sabah. These expeditions include the primary forest of the Imbak Valley, limestone hill forest of Tabin Wildlife Reserve, the the lower montane heath forest forest of Maliau Basin Conservation Area and the montane forest of Mount Trus Madi. The soil samples were mostly collected from leaf litter under trees and other plants that were identified to species or genus level. A number for fungal strains were also isolated from explants and from fungal airborne spores of plates and in around the laboratory. The characteristics of the micro-fungi strains on the PDA agar were observed and this includes colour of the aerial and substrate mycelia, difussed pigmentation and growth rate on the' PDA plates. Microscopic identification was done on the strains which showed activity on screening tests performed. All the micro-fungal strains isolated were grown in aerobic condition in liquid fermentation. It was these extracts that were used for,the screening for specific molecular targets involve in signal transduction, such as, serinelthreonine phosphatase, MAPK Kinase, MAP Kinase phosphatase, Ras/Raf protein interaction, and serinelthreonine,kinase. All the screening systems mention are base on the eukaryotic signalling pathways of yeast except for the serinelthreonine kinase screen which is base on the prokaryotic signalling pathway of Streptomyces griseus which shares high similarity with eukaryotic signalling pathway. In this research, there were fungal strains which showed inhibitory effect to the serinelthreonine phosphatase type 1 homolog, Glc7p especially the strains H9318 and H9307 from Maliau Basin. These two strains were latter found to inhibit dephosphorylation of phosphorylase catalyse by the mammalian serineltheronine phosphatase, Protein Phosphatase type 1 gam a (PP1y) as well. The effect on PP1y as well as Glc7p is not supprising as both these protein shares more than 75% homology in its catalytic domain. Three strains which showed positive activity in the MAPK Kinase screening system are H9013, H9014 and H9019. No fungal strains were found to be affecting the MAP Kinase Phosphatase (MSG 5) and the RaslRaf protein interaction which would indicate a positive result. There were numerous extracts from fungal strains which inhibit the growth of Streptomyces griseus and two strains which showed potential to be inhibitors of serinelthreonine kinase (AfsK) of Streptomyces griseus. These two strains were H9016 and H9123. There were also two fungal strains H9341 and H9346 which showed toxicity in all the screens performed except for the serineltheronine kinase test of S.griseus. This would indicate these strains are toxic to at least Scharomycetes cerevisiae cells. The fungal strains isolated .from soil and from other environment showed some specificity in the types of strains isolated and the secondary metabolites produced. The microfungi from Sabah proved to be prolific producers of diverse secondary metabolites which effect signal transduction and growth of cell

Draft Genome Sequence of a Phytopathogenic Ganoderma sp. Strain That Causes Basal Stem Rot Disease on Oil Palm in Sabah, Malaysia

Basal stem rot (BSR) disease on Elaeis guineens is known to be caused by members of the pathogenic fungal genus Ganoderma, especially the species Ganoderma boninense. This species affects oil palm plantation in Sabah, Malaysia. The genome sequence (52.28 Mbp) will add to the representation of this genus, especially in regard to BSR disease

Molecular characteristics of infection and colonization isolates of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA)

Staphylococcus aureus is a gram-positive coccus that colonizes the skin and mucous membranes, particularly the anterior nares. Recently, community-acquired MRSA (CA-MRSA) has emerged as a cause of skin and soft-tissue infections in healthy individuals. These strains are sensitive to antimicrobials, carry genes for Panton-Valentine leukocidin (PVL) toxin, and feature the staphylococcal cassette chromosome mec (SCCmec) type IV or V. The suspected mode of transmission involves close contact with carriers, leading to skin or nasal colonization that results in subsequent active infection. This study was undertaken to determine the molecular characteristics of CA-MRSA isolates in children presenting with wound infections at Likas Hospital, Sabah, Malaysia, and the possible mode of transmission. The results showed that the majority of CA-MRSA infection isolates were from scalp abscesses (49%) in 1–5-year-old children (70%) in the Filipino (54%) community. The presence of the mec gene was detected in all isolates and the PVL virulence factor was found in 92% of the isolates. SCCmec typing revealed that 57% of the isolates were untypable, 35% harbored the SCCmecIVa element, and one each had SCCmecIVc, SCCmecV, or SCCmecII. Sixteen S. aureus strains were isolated from nasal swabs in 19 family members of index patients. Fourteen of these cultures were positive for catalase, coagulase, and DNAase. All of the colonization isolates carried the mecA gene and only a third were positive for the PVL toxin. SCCmec typing showed that 79% of the isolates were untypable and two had SCCmecIVa element and one had SCCmecV element. When five pairs of infection and colonizing isolates were compared by spa typing, only two pairs showed identical spa type with possible transmission between the patient and family contact. Further studies are necessary to establish CA-MRSA transmission by performing multiple-site cultures multiple times instead of one-time naresonly sample collection

A comparative transcriptomic analysis provides insights into the cold-adaptation mechanisms of a psychrophilic yeast, Glaciozyma antarctica PI12

Glaciozyma antarctica PI12, a psychrophilic yeast from Antarctica, grows well at low temperatures. However, it is not clear how it responds and adapts to cold and freeze stresses. Hence, this project was set out to determine the cold-adaptation strategies and mechanisms of G. antarctica PI12 using a transcriptomic analysis approach. G. antarctica PI12 cells, grown in rich medium at 12 °C, were exposed to freeze stress at 0 and − 12 °C for 6 h and 24 h. Their transcriptomes were sequenced and analyzed. A hundred and sixty-eight genes were differentially expressed. The yeast gene expression patterns were found to be dependent on the severity of the cold with more genes being differentially expressed at − 12 °C than at 0 °C. Glaciozyma antarctica PI12 was found to share some common adaptation strategies with other yeasts, Saccharomyces cerevisiae and Mrakia spp., but at the same time, found to have some of its own unique strategies and mechanisms. Among the unique mechanisms was the production of antifreeze protein to prevent ice-crystallization inside and outside the cell. In addition, several molecular chaperones, detoxifiers of reactive oxygen species (ROS), and transcription and translation genes were constitutively expressed in G. antarctica PI12 to enable the cells to endure the fluctuating freezing temperatures. Interestingly, G. antarctica PI12 used nitrite as an alternative terminal acceptor of electrons when the oxygen level was low to minimize disruption of energy production in the cell. These mechanisms coupled with several other common mechanisms ensured that G. antarctica PI12 adapted well to the cold temperatures

Genetic Relatedness of Indigenous Ethic Groups in Northern Borneo to Neighboring Populations from Southeast Asia, as inferred from Genome-wide SNP Data

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s)

Screening for eukaryotic signal transduction and Mycobacterium isocitrate lyase inhibitor from actinomycetes and fungi of dipterocarp rain forests at Imabak Valey, Sabah, Malaysia

A diversity of actinomycetes and fungi was isolated from various sites during the Imbak Valley Scientific Expedition 2000. A total of 144 soil samples were collected under trees that have been identified to species or genus level. Imbak Valley is a lowland dipterocarp forest, which is interestingly dominated by Dryobalanops beccarii. Isolation of Streptomyces and non-Streptomyces actinomycetes on HV medium and other specific isolation media for non-Streptomyces yielded 203 isolates from 89 soil samples. Morphological characterisation of the isolated actinomycetes was carried out based on aerial mycelium colour, substrate mycelium colour and diffusible pigment production on oatmeal medium. Nine strains of fungi were isolated from the six soil samples plated on PDA medium. All actinomycetes isolates were grown under aerobic condition in liquid culture and extracted with acetone, and used for screening against proteins involved eukaryotic signal transduction. Yeast MAPK kinase and MAP kinase phosphatase were some of the targeted proteins used in this research. MKK1P386 and MKK1P386-MSG5 mutant yeasts were used to screen for these inhibitors, as these yeast kinase and phosphatase have homologous proteins in the MAP kinase signal transduction pathway in human. No inhibitors in the extracts were found in these screenings. Type 1 protein serine/ threonine phosphatase (GLC7) in yeast was used to screen inhibitors against PP1 inhibitors and no inhibitor was found. None of the fungal extracts showed any inhibitory activities in all the screening systems. No Ras/Raf inhibitor was found in the in vivo Ras/Raf interaction with the yeast two-hybrid screening system, which used to screen for inhibitor against Ras/ Raf protein interaction inhibitor. There were 11 actinomycetes extracts that showed toxicity against yeast strain LZ (transformant of Ras/ Raf). H7667, a Streptomycete toxic to yeast is further screened for inhibitors of the GSK3-beta pathway. H7763, a Streptomyces species that showed positive in the primary screen for inhibitor of isocitrate lyase (ICL) which is not itaconic acid (known ICL inhibitor). H7240 showed the strongest susceptibility towards the resin in which the concentration of 5g/l of resin is sufficient to produce growth inhibition of the bacteria

Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data

The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the “North Borneo”-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non–Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non–Austro- Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s)