Molecular Genetics Commons^™

Structural Dynamics And Signaling Roles Of The Aer Pas And F1 Regions, Asharie J. Campbell

Loma Linda University Electronic Theses, Dissertations & Projects

The Aer aerotaxis receptor in Escherichia coli mounts such a rapid response to redox that E. coli changes its swimming behavior within 100 ms after an oxygen pulse. This receptor is a membrane-bound homodimer, and it monitors internal energy (redox) via an FAD cofactor bound to a cytoplasmic N-terminal PAS domain. Understanding PAS sensing is important, as PAS domains comprise a superfamily of more than 25,000 members from all kingdoms. This study focused on the Aer N-terminal PAS sensor, as well as the region tethering it to the membrane anchor, known as the F1. Previous genetic studies on these regions …

Proteomic Analysis Of Iron Acquisition, Metabolic And Regulatory Responses Of Yersinia Pestis To Iron Starvation, Rembert Pieper, Shih-Ting Huang, Prashanth P. Parmar, David J. Clark, Hamid Alami, Robert D. Fleischmann, Robert D. Perry, Scott N. Peterson

Microbiology, Immunology, and Molecular Genetics Faculty Publications

BACKGROUND: The Gram-negative bacterium Yersinia pestis is the causative agent of the bubonic plague. Efficient iron acquisition systems are critical to the ability of Y. pestis to infect, spread and grow in mammalian hosts, because iron is sequestered and is considered part of the innate host immune defence against invading pathogens. We used a proteomic approach to determine expression changes of iron uptake systems and intracellular consequences of iron deficiency in the Y. pestis strain KIM6+ at two physiologically relevant temperatures (26°C and 37°C).

RESULTS: Differential protein display was performed for three Y. pestis subcellular fractions. Five characterized Y. pestis …

Implications Of The Plastid Genome Sequence Of Typha (Typhaceae, Poales) For Understanding Genome Evolution In Poaceae, Mary M. Guisinger, Timothy W. Chumley, Jennifer V. Kuehl, Jeffrey L. Boore, Robert K. Jansen

All Faculty Scholarship for the College of the Sciences

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including …

Development Of Protocols For Tissue Culture And Mutagenesis In Two Variegated Sansevieria Sp., Irmawati Akma Abdul Hapiz

Student Works (2010-2019)

Studies were conducted to develop the tissue culture protocol and mutagenesis through Gamma ray irradiation for two variegated Sansevieria species known as Sansevieria trifasciata var. Laurentii (goldband Sansevieria) and Sansevieria trifasciata var. Hahnii (birdnest Sansevieria). Seven combinations of BAP and NAA were chosen which are represented by letter A= 1.00 mg/I BAP, B = 1.00 mg/I BAP + 0.25 mg/I NAA, C = 2.00 mg/I BAP + 0.50 mg/I NAA, D = 2.00 mg/I BAP + 1.00 mg/I NAA, E = 3.00 mg/I BAP + 1.00 mg/I NAA, F = 4.00 mg/I BAP + 1.00 mg/I NAA and G = …

Molecular Characterization And Expression Analysis Of Putative Rpk1 And Putative Clv1 In Malaysian Indica Rice (Oryza Sativa L.) Cv.Mr219 And Malaysian Wild Rice (Oryza Rufipogon) Irgc105491., Law Yee Song

Student Works (2010-2019)

Two candidate yield-related genes, putative Receptor-like Protein Kinase 1 (putative RPK1) and putative CLAVATA1 Receptor Kinase (putative CLV1), were selected for molecular characterization and expression analysis. This was carried out using in four rice lines comprising the parents and two BC₂F₇ lines from a local rice breeding program, with Malaysian rice variety, Oryza sativa ssp. indica cv. MR219 as recurrent parent, and Oryza rufipogon (IRGC105491) as donor parent. Approximately 2.8 kb and 2.6 kb putative RPK1 cDNA nucleotide sequences were obtained from Oryza rufipogon and Oryza sativa ssp. indica cv. MR219 respectively. However, only 402 …

Characterization Of Microrna172 And Its Potential Target In Oil Palm (Elaeis Guineensis Jaq.), Fatemeh Mehrpooyan

Student Works (2010-2019)

Oil palm (Elaeis guineensis) is the world’s major perennial monocot crop and contributes highly to the economies of South East Asia. As the oil palm fruit is the source of the main economic output for this crop, floral development is a critical process related to oil palm productivity. miR172 has been shown to be an important regulator of the AP2 family transcription factors involved in floral timing in a number of plants and belongs to a group of highly conserved miRNA that can be identified based on sequence homology. Six oil palm miR172 paralogs, representing two distinct mature miR172 sequences, …

Phylogeographical Patterns Of Neobalanocarpus Heimii (Dipterocarpaceae) For The Evolutionary History And Chain Of Custody Certification., Tnah Lee Hong

Student Works (2010-2019)

Tectonic movement and climatic oscillations during the Cenozoic have had dramatic effect on the biota of the tropical rain forest. This study aims to reveal the phylogeography and evolutionary history of a Peninsular Malaysian endemic tropical timber, Neobalanocarpus heimii (Dipterocarpaceae), based on chloroplast DNA (cpDNA) variation. Fifteen haplotypes were identified from 10 intraspecific variable sites of five non-coding cpDNA regions: trnL intron, trnS-trnG spacer, trnG intron, trnK intron and psbK-trnS spacer. Two major genealogical cpDNA lineages of N. heimii were elucidated: a widespread southern and a northern region. The species is predicted to survive in multiple refugia during climatic oscillation: …

Enterobacterial Repetitive Intergenic Consensus-Pcr (Eric-Pcr) Analysis Among Raw Vegetables Isolates Of Campylobacter Jejuni., Tuan Suraya Tuan Soh

Student Works (2010-2019)

A total of 20 (n=20) raw vegetable isolates of Campylobacter jejuni were examined for the presence of virulence genes and genetic diversity using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) analysis. All C. jejuni isolates were obtained from the laboratory of Food Science and Biotechnology, University Putra Malaysia, Serdang, Selangor. When specific PCR amplification were determined, all raw vegetables isolates of Campylobacter jejuni contained cadF and ceuE genes. Whereas, 12 (12/20) isolates were positive cdtB and 6 (6/20) were positive cdtC. None of the C. jejuni isolates was cdtA positive. Using ERIC-PCR analysis, all 20 isolates of C. jejuni were …

Biolistic Transformation Of Oil Palm Using The Phosphomannose Isomerase (Pmi) Gene As The Positive Selectable Marker., Bahariah Bohari

Student Works (2010-2019)

The selectable marker system based on the Escherichia coli phosphomannose isomerase (pmi) gene was adapted for genetic transformation of oil palm. This system makes use of the pmi gene that encodes phosphomannose isomerase, which converts mannose-6-phosphate to fructose-6-phosphate and uses mannose as the selection agent. This is to anticipate the future requirement of using non-antibiotic resistance genes for the commercialization of transgenic oil palm. The use of antibiotic or herbicide-based selection systems has caused much public concern due to inadequate knowledge of the agents’ impact on the environment and on human health. In this study, four transformation vectors, namely pMI3, …

A Systematic Study Of Fagraea Sensu Lato And A Revision Of The Peninsular Malaysian Taxa., Sugumaran Manickam

Student Works (2010-2019)

systematic study of the Peninsular Malaysian species of Fagraea sensu lato was undertaken. This was done in the light of recent revisionary work done for Borneo that documented 20 new species and demonstrated that previous species concepts for Fagraea were too broad. Parallel to this the distinction of the subgeneric groups recognised as sections, i.e., Cyrtophyllum, Fagraea and Racemosae, were investigated with molecular phylogenetic methods. Representative taxa from the Malay Peninsula and Borneo augmented by sequences from other taxa in the same subtribe and tribe were used in the molecular analysis. Gene sequences from ITS, trnL–F (trnL intron + trnL–F …

Computational Identification Of Micro Rna In Musa Sp Est Sequences., Tan Yew Seong

Student Works (2010-2019)

MicroRNAs (miRNAs) are small single-stranded non-protein-coding RNAs of about 22 nucleotides that play an important role in post-transcriptional gene regulation in animals and plants by targeting mRNAs for direct cleavage of mRNAs or repression of mRNA translation. In this study, a homology search based approach has been used for identifying the novel miRNA genes of Musa sp. using the BLAST program with a total of 42,978 Musa sp. expressed sequence tags (EST) were compared to a total of 959 previously known plant miRNA sequences. Forty-seven candidate miRNA with homology to previously known miRNAs were identified. By using the mFold3.1 program, …

Isolation And Development Of Microsatellite Markers Of Channa Striata., Faiza Omar

Student Works (2010-2019)

Channa striata, locally known as haruan has long been regarded as a valuable edible fish and it is also consumed for its putative effects on wound healing. The main objective of the project was to develop microsatellite markers for use in the study of genetic diversity of the wild Channa striata populations in Malaysia. In this study, seven new microsatellite loci were isolated from Channa striata using a Random Amplified Microsatellite (RAMs) based technique which was an efficient and reliable method. Ten primers were used in population genetic studies of Channa striata.Sixty sets of microsatellite primer pairs were used in …

Molecular Identification Of Arowana Species Based On Cytochrome B And Cytochrome C Oxidase I (Coi) / Maryam Zahedi Fard, Maryam Zahedi Fard

Student Works (2010-2019)

Mitochondrial DNA (mtDNA) markers has been widely used to better resolve the taxonomic identification as well as display the genetic relatedness of different species and closely related fish. The highly cost ornamental fish, Asian arowana (Scleropages formosus) of family Osteoglossidae has different colored strains that are geographically distributed in different regions around Southeast Asia. The taxonomic classification of these different strains still remains unclear and disputable. The partial sequences of the cytochrome b and the DNA barcoding gene, cytochrome C oxidase were analyzed and assessed for molecular identification; to differentiate the colored varieties of this species. The results of this …

High-Density Screening Reveals A Different Spectrum Of Genomic Aberrations In Chronic Lymphocytic Leukemia Patients With ‘Stereotyped’ Ighv3-21 And Ighv4-34 B-Cell Receptors, Millaray Marincevic, Nicola Cahill, Rebeqa Gunnarsson, Anders Isaksson, Mahmoud Mansouri, Hanna Göransson, Markus Rasmussen, Mattias Jansson, Fergus Ryan, Karin Karlsson, Hans-Olov Adami, Fred Davi, Jesper Jurlander, Gunnar Juliusson, Kostas Stamatopoulos, Richard Rosenquist

Articles

Background The existence of multiple subsets of chronic lymphocytic leukemia expressing ‘stereotyped’ Bcell receptors implies the involvement of antigen(s) in leukemogenesis. Studies also indicate that ‘stereotypy’ may influence the clinical course of patients with chronic lymphocytic leukemia, for example, in subsets with stereotyped IGHV3-21 and IGHV4-34 B-cell receptors; however, little is known regarding the genomic profile of patients in these subsets. Design and Methods We applied 250K single nucleotide polymorphism-arrays to study copy-number aberrations and copy-number neutral loss-of-heterozygosity in patients with stereotyped IGHV3-21 (subset #2, n=29), stereotyped IGHV4-34 (subset #4, n=17; subset #16, n=8) and non-subset #2 IGHV3-21 (n=13) and …