Cymbidium mosaic virus and odontoglossum ringspot tobamovirus genes cloned from infected Oncidium orchids (Gen-gen cymbidium mosaic virus dan odontoglossum ringspot tobamovirus yang diklon daripada orkid Oncidium yang terinfeksi)

Abstract Several recombinant phages were picked at random from the cDNA library of Oncidium (Oncidium Goldiana x Oncidium Flexuosum) flowers, converted into plasmids by in vivo excision and sequenced. Two of the clones named CyMV1 and CyMV2, showed very high DNA and protein sequence homology to those of the cymbidium mosaic virus (CyMV) in the genebank database. CyMV1, 1,186 bp in size, contained within it the entire sequence for coat protein (CP) gene, movement protein (MP)3 gene and an almost complete sequence for MP2 gene. CyMV2, which is 626 bp in size, only contained the extreme 3' end sequence of the RNA polymerase gene. The percentage of homology of the isolated CyMV1 gene was 97% to the Taiwanese strain (AY571289), 96% to the Korean type 2 CyMV complete genome (AF016914) and to the Singaporean CyMV complete genome (CMU62963) in the CP and MP regions of the genome. CyMV2 showed 95% homology to the Korean type 2 CyMV complete genome (AF016914) and to the Singaporean CyMV complete genome (CMU62963) but in the RNA polymerase region. Another clone named ORSV1, 728 bp in size, isolated by RT-PCR method was a partial fragment of odontoglossum ringspot virus (ORSV) RNA replicase gene. This partial gene sequence of ORSV1 showed 98% homology to the ORSV gene isolated from United States (Accession nos. ORU89894), Taiwan (Accession nos. AY571290) and Korea (Accession nos. X82130). All of these genes could be used in developing Oncidium orchids resistant to CyMV or ORSV through the transgenic approach

Phylogenetic classification of the world's tropical forests

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.</p

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Malaxis inexpectata and Habenaria paradiseoides (Orchidaceae), new records for Peninsular Malaysia

Volume: 57Start Page: 263End Page: 26

The Evidence of Non n-glycan Linked Mannose in Exochitinase 42kDa, from Trichoderma harzianum BIO10671 Glycosylation

Chitinase 42 kDa produced by Trichoderma harzianum has been proven as a prime compound to be excreted onto the hyphae of the pathogen causing localised cell wall lysis at the point of interaction. Later it will initiate the process of the host cell becomes empty of cytoplasm, disintegrates and shows a rapid collapse. This study investigates the existence of N-glycan linked mannose in chitinase 42 kDa produced by the Malaysian T. harzianum strain BIO10671. The chitinase 42 kDa from T. harzianum BIO10671 was initially purified using anion exchange chromatography prior to a series of experiments such as immunoblotting against the chitinase 42 kDa antibody, lectin staining for detecting any terminal linked mannose, and galactofuranose detection to determine the presence of galatofuranase components in glycoproteins. The enzyme purification harvested about 12-fold of chitinase 42 kDa from T. harzianum BIO10671 with strong indication of the chitinase 42 kDa presence on SDS-Page. This was confirmed by immunoblotting with a strong response around 42 kDa after overnight incubation in chitinase 42 kDa antibody suggesting that the gene for chitinase 42 kDa was greatly expressed in this strain. There are no intervation of galatofuranose on any of the terminal mannose in chitinase 42 kDa as shown by negative results on samples treated with or without endoglycosidase-H and lectin staining. Therefore, it can be concludeed that glycosylation occurred in the chitinase 42 kDa from T. harzianum 42 kDa was not in the form of N-glycan linked mannose as expected

Antidiabetic and antioxidants activities of Clinacanthus nutans(Burm F.) Lindau leaves extracts

Clinacanthus nutans (Acanthaceae) is a local plant consumed as tisane in Indonesia and ‘ulam’ in Malaysia. This plant has been claimed for its ability to prevent many diseases including diabetes. However, the scientific proof on this claim is still lacking. Therefore, the present work study was designed to evaluate the antidiabetic potential and antioxidant capacity of C. nutans leaves extracts using in vitro bioassay tests. The 80% methanolic crude extract of this plant was further partitioned using different polarity solvents namely hexane, hexane:ethyl acetate (1:1, v/v), ethyl acetate, ethyl acetate:methanol (1:1, v/v), and methanol. All the sub-fractions were analysed for antioxidant effect via 2, 2-diphenyl-2-picrylhydrazil (DPPH) scavenging activity, ferric reducing power (FRAP) and xanthine oxidase (XO) assays followed by antidiabetic evaluation via α-glucosidase and dipeptidyl peptidase-IV (DPP-IV) inhibitory assays and glucose uptake experiment. The ethyl acetate fraction showed a good antioxidant potential while the hexane fraction exhibited high α-glucosidase and DPP-IV enzyme inhibition. The hexane fraction also improved glucose uptake in a dose-dependent manner. The present work thus provides an informative data on the potential of C. nutans to be developed as a functional food in preventing diabetes

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe