Molecular Biology

Phylogenetics of Pteropodinae. 2006

by M.T. Abdullah, PhD

Phylogenetics of Macroglossinae

by M.T. Abdullah, PhD

Systematics of Malaysian woolly bats (Vespertilionidae: Kerivoula ) inferred from mitochondrial, nuclear, karyotypic. 2010. F AISAL A LI A NWARALI .J.Mammology

by M.T. Abdullah, PhD

Read the paper by Hassan & Abdullah 2011 on morphometrics of Kerivoula. Mammalian Studies

Phylogenetics of Pteropodidae

by M.T. Abdullah, PhD

Phylogenetic Analysis of the Malaysian Rhinolopus and Hipposideros using mtDNA cytochrome b gene. PJTAS 34(2):281-294.

by M.T. Abdullah, PhD

Read Abdullah (2003)

The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and... more The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and Peninsular Malaysia were successfully inferred from the partial mitochondrial DNA (mtDNA) cytochrome (cyt) b sequences. Of the 413 nucleotide positions examined, there were 171 positions (41.4%), of which 164 positions (95.9%) were parsimoniously informative. The phylogenetic trees reconstruction using neighbour-joining (NJ), unweighted maximum parsimony (MP) and maximum likelihood (ML) methods suggest the monophyletic clustering of these families. The interspecific relationships within Rhinolophidae were completely resolved, while those within Hipposideridae were not fully resolved, as supported by the low bootstrap values. Overall, the phylogenetic analysis using partial mtDNA cyt b gene was useful to discriminate these complicated taxa and successfully revealed the misidentification of several specimens before due to their similar morphologies.

Keywords: Cytochrome b, Hipposideros, mitochondrial DNA, phylogenetics, Rhinolophus

Phylogeny and Phylogeography of insect bat Myotis muricola. 2012

by M.T. Abdullah, PhD

http://scholar.google.com.my/citations?hl=en&user=ylnvJSAAAAAJ

Myotis muricola is a widespread species covering the Malay Archipelago through the West and East of Wallace’s Line.... more Myotis muricola is a widespread species covering the Malay Archipelago through the West and East of Wallace’s Line. The genetic analysis, based on partial cytochrome b gene, shows the high genetic variation within M. muricola. The phylogenetic analysis has indicated that M. muricola in the Malay Archipelago are monophyletic. Members of M. muricola Eastern are grouped together independently of M. muricola Western and both groups are distantly related. On the other hand, M. muricola Western and M. muricola Eastern are distinct species and sister taxa to M. mystacinus. Based on the high genetic distance (26.8% to 38.5%) and the Genetic Species Concept (Baker & Bradley, 2006), it can be concluded that M. muricola Western and M. muricola Eastern should be considered as two distinct species. Furthermore, two subgroups within M. muricola Western, namely Sumatra-Asian and Bornean subgroups, are recognised as distinct subspecies (with genetic distance of 5.1% to 10.8%). The evidence from the molecular data indicated M. muricola Eastern as the ancestor of M. muricola species complex in the Malay Archipelago, which had earlier diverged into the western region during the Pliocene. Meanwhile, the geographical conditions during the Pleistocene had given more chances for fauna to diversify. It was predicted that M. muricola diverged in the western part of the Malay Archipelago during the Pleistocene when the sea level dropped and produced some landbridges among the islands in Sundaland. The hypothetical dispersal routes of M. muricola are related to the ancient Sunda River systems that produced gallery forest corridors for migration and which served as Pleistocene
refuges during the migration.

Phylogeny and Phylogeography of insect bat Myotis muricola (Gray, 1846) (Chiroptera: Vespertilionidae) from the West and and East of Wallace's Line Inferred from Partial MtDNA Cytochrome b Gene. Sigit Wiantoro, Ibnu Maryanto and M.T. Abdullah. 2012. Pertanika Journal of Tropical Agricultural Science 35(2): 271-292.

Molecular phylogenetics and systematics of five genera of Malaysian murine rodents (Maxomys, Sundamys, Leopoldamys, Niviventer and Rattus) inferred from partial mitochondrial cytochrome c oxidase subunit I (COI) gene.

by M.T. Abdullah, PhD

Nur Aida Md Tamrin and M. T. Abdullah. 2011. Journal of Science and Technology in the Tropics 7: 75-86. (SCOPUS-indexed).

We genetically analysed 50 specimens of Murinae from Peninsular Malaysia and Sarawak, assigned to 12 species.... more We genetically analysed 50 specimens of Murinae from Peninsular Malaysia and Sarawak, assigned to 12 species. Phylogenetic analyses of partial mitochondrial cytochrome c oxidase subunit I (476 base pairs) using four methods, namely, neighbour-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method resulted in similar statistically supported clades with minimal change in branching order. The analyses discovered that there were intermediate form of Maxomys species within M. whiteheadi and M. ochraceiventer populations. They display same external morphology as M. whiteheadi but genetically closer to M. ochraceiventer. Craniodental measurements showed significant differences between the three populations. Rattus and Sundamys appeared not fully resolved while Leopoldamys and Niviventer were steadily clustered. The intraspecific geographic variation in some species agrees with previous studies on the vicariance scenario and diversification of flora and fauna in Malaysia and Borneo.

Nur Aida Md Tamrin and M. T. Abdullah. 2011. Journal of Science and Technology in the Tropics 7: 75-86. (SCOPUS-indexed).

Biogeography and variation of the Malaysian fruit bat, Cynopterus brachyotis, in Sunda Shelf 2003

by M.T. Abdullah, PhD

Five more studies by BU, UKM & UNIMAS had tested and confirmed similar findings in this 2003 PhD study.

There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the... more There are more then one species in the Malayan fruit bat, Cynopterus brachyotis, species complex based on the mophological and MtDNA cytochorome b analyses. The small form is found in the closed canopy forest while the larger form utilised the open habitat. There is a new species within the C. brachyotis populations yet to be described.

Temporal and spatial patterns in waterborne bacterial communities of an island reef system

by Michael Sweet

The bacterial 16S rRNA gene diversity of waterborne bacterial (WBB) communities was assessed using PCR/DGGE... more The bacterial 16S rRNA gene diversity of waterborne bacterial (WBB) communities was assessed using PCR/DGGE techniques, along with sequence analysis of selected bands. 16S rRNA gene diversity varied between seasons and significant differences were recorded between night and day. However, there were no significant differences detected between low, ebb, flood and high tides when the water body sampled would have originated from completely different areas including those off-reef. These results suggest that changes in productivity and/or vertical diurnal migrations of plankton may have greater effects than large scale water movements effected by tidal flows. These results do not demonstrate a strong link between WBB communities and their underlying benthos. This either suggests a lack of coupling between the benthos and the water column (benthic-pelagic coupling) or that the processes are extremely rapid and efficient with strong mixing. Previous studies at this site have shown cycling between coral reef and lagoon sediments via coral mucus release and tidal transport, supporting the latter. We found a strong seasonality in the abundance and composition of WBB communities, with α-proteobacteria being more prevalent during winter and γ-proteobacteria during summer but quantitative PCR (qPCR) showed no significant differences in vibrios between seasons.

Bacterial assemblages differ between compartments within the coral holobiont

by Michael Sweet

It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are... more It is widely accepted that corals are associated with a diverse and host species-specific microbiota, but how they are organized within their hosts remains poorly understood. Previous sampling techniques (blasted coral tissues, coral swabs and milked mucus) may preferentially sample from different compartments such as mucus, tissue and skeleton, or amalgamate them, making comparisons and generalizations between studies difficult. This study characterized bacterial communities of corals with minimal mechanical disruption and contamination from water, air and sediments from three compartments: surface mucus layer (SML), coral tissue and coral skeleton. A novel apparatus (the ‘snot sucker’) was used to separate the SML from tissues and skeleton, and these three compartments were compared to swab samples and milked mucus along with adjacent environmental samples (water column and sediments). Bacterial 16S rRNA gene diversity was significantly different between the various coral compartments and environmental samples (PERMANOVA, F = 6.9, df = 8, P = 0.001), the only exceptions being the complete crushed coral samples and the coral skeleton, which were similar, because the skeleton represents a proportionally large volume and supports a relatively rich microflora. Milked mucus differed significantly from the SML collected with the ‘snot sucker’ and was contaminated with zooxanthellae, suggesting that it may originate at least partially from the gastrovascular cavity rather than the tissue surface. A common method of sampling the SML, surface swabs, produced a bacterial community profile distinct from the SML sampled using our novel apparatus and also showed contamination from coral tissues. Our results indicate that microbial communities are spatially structured within the coral holobiont, and methods used to describe these need to be standardized to allow comparisons between studies.

Coil-to-helix transitions in intrinsically disordered methyl CpG binding protein 2 and its isolated domains

by Kristopher Hite

Design and Evaluation of Three Pair Primers for Exon 1 Amplification of Hyaluroglucosaminidase-1 Gene

by Arli Parikesit

Co-authored with Usman Sumo Friend Tambunan and Sylvia Sugito

Abstract: Problem statement: Hyaluronidase is an enzyme which catalyze hydrolysis of Hyaluronan (HA). Hyaluronan is... more Abstract: Problem statement: Hyaluronidase is an enzyme which catalyze hydrolysis of Hyaluronan (HA). Hyaluronan is important in cell migration during embryonic development, cellular proliferation and differentiation and has a structural role in connective tissues. Hyaluronidase deficiency is correlated with mucopolysaccharidosis IX. In human, hyaluronidase is encoded by HYAL1 gene. The mutation study of HYAL1 gene was carried out by many researchers, but until now, mutation study of HYAL1 still in progress and limited due to the lack of primer used in amplification of
selected DNA sequence of HYAL1 gene and maximum length limitation imposed by DNA sequencer. Approach: The search for three pairs of primers for human exon 1 segmented amplification of HYAL1 gene was conducted and evaluated. The first step was to acquire HYAL1 gene sequence and then had it aligned with human chromosome 3 genomic contig sequence. Exon 1 of HYAL1 gene was found to be located at nt 201-1711 of the acquired human chromosome 3 genomic contig. Online Primer3 program was used to design three pairs of primers. The selected pairs of primer had been subjected to BLASTn operation for selectivity examination while onlineNetPrimer operation
was carried out for examination of secondary structures. Results: The search for primers to amplify three different fragments of exon 1 of HYAL1 gene yielded three selected pairs of primers, namely forward primer 5’- GACCCCCTACAAAAGCTCA-3’ (20 bp) and reverse primer 5’- AAGTCTCCGATTCCCCCACT-3’ (20 bp) for amplifying nt 1-551 of HYAL1 gene, forward primer 5’- GTCCTGTGGGAGATGGCAGA-3’ (21 bp) and reverse primer 5’- CGGTAAATGTCCTTGGTGTCC-3’ (21 bp) for amplifying nt 355-1053 of HYAL1 gene and forward primer 5’-GCCATACCTGCTCCTGACTT-3’ (20 bp) and reverse primer 5’- ACAAGGTGGGCAGGTTACAG-3’ (20 bp) for amplifying nt 956-1511 of HYAL1 gene. When using these primers, nt 1-46 of amplified product of the first pair of primers and nt 555-584 of amplified product of the third pair of primers must not be considered because those are not part of exon 1 of HYAL1 gene. The results from both operations and trial to real samples using these primers
indicated that all three pairs of primer were satisfactory for use. Conclusion/Recommendations: The three pairs of primers could be used to amplify specified segments of HYAL1 gene.

DNA Fingerprinting

by Nurizzati Mohamad Homidi

Subjects in Biotechnology

by Nurizzati Mohamad Homidi

Mutations in FLVCR2 are associated with proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome (Fowler syndrome)

by Mark Morris

Meyer E, Ricketts C, Morgan NV, Morris MR, Pasha S, Tee LJ, Rahman F, Bazin A, Bessières B, Déchelotte P, Yacoubi MT, Al-Adnani M, Marton T, Tannahill D, Trembath RC, Fallet-Bianco C, Cox P, Williams D, Maher ER.

Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome (PVHH), also known as Fowler syndrome, is an... more Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome (PVHH), also known as Fowler syndrome, is an autosomal-recessively inherited prenatal lethal disorder characterized by hydranencephaly; brain stem, basal ganglia, and spinal cord diffuse clastic ischemic lesions with calcifications; glomeruloid vasculopathy of the central nervous system and retinal vessels; and a fetal akinesia deformation sequence (FADS) with muscular neurogenic atrophy. To identify the molecular basis for Fowler syndrome, we performed autozygosity mapping studies in three consanguineous families. The results of SNP microarrays and microsatellite marker genotyping demonstrated linkage to chromosome 14q24.3. Direct sequencing of candidate genes within the target interval revealed five different germline mutations in FLVCR2 in five families with Fowler syndrome. FLVCR2 encodes a transmembrane transporter of the major facilitator superfamily (MFS) hypothesized to be involved in regulation of growth, calcium exchange, and homeostasis. This is the first gene to be associated with Fowler syndrome, and this finding provides a basis for further studies to elucidate the pathogenetic mechanisms and phenotypic spectrum of associated disorders

Effects of overexpression of X-box binding protein 1 on recombinant protein production in mammalian cells

by Sebastian Ku

Anthracnose disease of switchgrass caused by the novel fungal species Colletotrichum navitas

by Lisa Beirn

Molecular analysis and infectivity of Puccinia species pathogenic to turfgrass

by Lisa Beirn

The Apoplastic Oxidative Burst Peroxidase in Arabidopsis Is a Major Component of Pattern-Triggered Immunity

by Arsalan Daudi

Plant Cell, 2012

Daudi A, Cheng Z, O’Brien JA, Mammarella N, Khan S, Ausubel F, and Bolwell GP (2012) The apoplastic oxidative burst peroxidase in Arabidopsis is a major component of pattern-triggered immunity. Plant Cell (published online January 24th 2012)

Chapter 2: A Phenol-Chloroform Protocol for Extracting DNA from Ancient Samples

by Ross Barnett

Research into ancient DNA began more than 25 years ago with the publication of short mitochondrial DNA sequence... more Research into ancient DNA began more than 25 years ago with the publication of short mitochondrial DNA sequence fragments from the quagga, an extinct relative of the zebra. Ancient DNA research really gained momentum following the invention of PCR, which allowed millions of copies to be made of the few remaining DNA molecules preserved in fossils and museum specimens.  In Ancient DNA: Methods and Protocols expert researchers in the field describe many of the protocols that are now commonly used to study ancient DNA. These include instructions for setting up an ancient DNA laboratory, extraction protocols for a wide range of different substrates, details of laboratory techniques including PCR and NGS library preparation, and suggestions for appropriate analytical approaches to make sense of the sequences obtained. Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.



Authoritative and practical, Ancient DNA: Methods and Protocols seeks to aid scientists in the further study of ancient DNA and the methodological approaches in ancient research.

Content Level » Professional/practitioner

Keywords » NGS - PCR - Pleistocene-age DNA - ancient DNA - ancient bone - bone hydroxyl-apatite - hydroxyl-apatite crystals - mitochondrial genomes - phylogeographic patterns - soft tissue