Microbiology Commons^™

Comparing Models Of Evolution For Ordered And Disordered Proteins, Celeste J. Brown, Audra K. Johnson, Gary W. Daughdrill

Molecular Biosciences Faculty Publications

Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity ( …

The Role Of Cuticle, Fatty Acids, And Lipid Signaling In Plant Defense, Ye Xia

Theses and Dissertations--Plant Pathology

Systemic acquired resistance (SAR) is initiated upon recognition of specific microbial effectors by cognate plant resistance proteins and immunizes distal tissues of plants against secondary infections. SAR involves the generation of a mobile signal at the site of primary infection, which then translocates to and activates defense responses in the distal tissues via some unknown mechanism(s). This study shows that an ACYL CARRIER PROTEIN 4 (ACP4), GLABRA1 (GL1) and ACYL CARRIER BINDING PROTEINS (ACBP) are required for the processing of the mobile SAR signal in distal tissues of Arabidopsis. Although acp4, gl1 and acbp plants generate the mobile signal, …

Subtype-Associated Differences In Hiv-1 Reverse Transcription Affect The Viral Replication, Sergey Iordanskiy, Mackenzie Waltke, Yanjun Feng, Charles Wood

Nebraska Center for Virology: Faculty Publications

Background: The impact of the products of the pol gene, specifically, reverse transcriptase (RT) on HIV-1 replication, evolution, and acquisition of drug resistance has been thoroughly characterized for subtype B. For subtype C, which accounts of almost 60% of HIV cases worldwide, much less is known. It has been reported that subtype C HIV-1 isolates have a lower replication capacity than B; however, the basis of these differences remains unclear.

Results: We analyzed the impact of the pol gene products from HIV-1 B and C subtypes on the maturation of HIV virions, accumulation of reverse transcription products, integration of …

Animal Models Of Alzheimer's Disease, Gemma Casadesus, Gary Arendash, Frank Laferla, Mike Mcdonald

Molecular Biosciences Faculty Publications

No abstract provided.

Analysis Of Bacterial Diversity In Arctic Soil And Sediment Samples From Ny-Alesund, Norway Using Denaturing Gradient Gel Electrophoresis., Yew Wen Chyin

Student Works (2010-2019)

Bacterial diversity in soil and sediment samples from eighteen sites in and around Dasan Station, Ny-Ålesund, Norway was analyzed using Denaturing Gradient Gel Electrophoresis (DGGE), and was correlated with the environmental variables. Samples analysed included terrestrial soils, beach soil, periglacier soils, inland lake bank sediments, melt lake sediments, and marine sediments. Spearman rank order correlation showed significant correlations (P = 0.001) between conductivity (r = 0.470) and pH (r = 0.294) with the bacterial diversity. Soil from the tundra site (sample 17) appeared to have the most diverse bacterial community while inland lake bank sediment from the …

Interactions Of The Cellular Sumoylation System With Influenza A Virus And Its Non-Structural Protein Ns1a (Ns1a), Sangita Pal

Open Access Theses & Dissertations

The most important current anti-influenza weapons, vaccination and antiviral drugs, can be rapidly rendered fully ineffective thanks to the virus's high mutational rate, which produces viruses exhibiting new antigenic properties and structural proteins insensitive to the drug's mechanism of action. One attractive alternative is to develop drugs that modulate the activity of cellular systems either required for viral growth or able to neutralize viral growth. Here we demonstrate that the cellular SUMOylation system, a post-translational modification involving the conjugation of the Small Ubiquitin-like MOdifier (SUMO) to specific protein targets using a Ubiquitin-like enzymatic cascade, interacts closely with influenza virus during …

Plasmid Injection And Application Of Electric Pulses Alter Endogenous Mrna And Protein Expression In B16.F10 Mouse Melanomas, L. C. Heller, Y. L. Cruz, B. Ferraro, H. Yang, R. Heller

Bioelectrics Publications

The application of electric pulses to tissues causes cell membrane destabilization, allowing exogenous molecules to enter the cells. This delivery technique can be used for plasmid gene therapy. Reporter gene expression after plasmid delivery with eight representative published protocols was compared in B16.F10 mouse melanoma tumors. This expression varied significantly based on the pulse parameters utilized for delivery. To observe the possible influence of plasmid injection and/or pulse application on endogenous gene expression, levels of stress-related mRNAs 4 and 24 h after delivery were determined by PCR array. Increases in mRNA levels for several inflammatory chemokines and cytokines were observed …

Bacterial Acquisition In Juveniles Of Several Broadcast Spawning Coral Species, Koty H. Sharp, Kim B. Ritchie

Arts & Sciences Faculty Publications

Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, …

Isolation And Characterization Of Bacteria From Extended Aeration Wastewater Treatment Plants., Randy Chin Kok Fei

Student Works (2010-2019)

In this study, three different wastewater treatment plants (STP1, STP2 and STP3) were sampled in Klang Valley. STP1 exhibited the best activated sludge health with healthy Sludge Volume (SV), Mixed Liquor Suspended Solids (MLSS) and Mixed Liquor Volatile Suspended Solids (MLVSS). STP2 were constantly disrupted by the mechanical failures which caused its dissolved oxygen (DO) to decrease whereas STP3 was troubled by the inadequate alkalinity in its mixed liquor causing acidic condition in aeration tank. The acidic condition resulted in pin-floc problem and contributed to high Total Suspended Solids (TSS) and low SV. Influent at STP3 was also found to …

Coronavirus Replicase Proteins: Multifunctional Mediators Of Replication And Innate Immunity Evasion, Mark Anthony Clementz

Dissertations

Coronaviruses are positive-sense, single-stranded RNA viruses. The majority of the RNA encodes non-structural proteins (nsps) that are translated as a large polyprotein, which is cleaved by the papain-like (PLP) and picornavirus 3C-like (3CLpro) proteases. The nsps modify host membranes to produce double membrane vesicles (DMVs) upon which the replicase-transcriptase assembles and synthesizes viral RNA. nsp3, nsp4, and nsp6 are integral membrane proteins believed to be involved in DMV formation. Work presented here demonstrates that nsp4 is subjected to N-linked glycosylation and mutation of N258 to threonine in nsp4 confers a temperature sensitive phenotype to MHV-A59 infectious clone virus. This virus …

The Immune Response In The Central Nervous System During West Nile Virus Persistence, Barbara Sharon Stewart

Legacy Theses & Dissertations (2009 - 2024)

West Nile virus (WNV) persists in a wide array of hosts ranging from mice to humans. In convalescent humans, WNV RNA persists in urine for up to 6.7 years, and IgM antibody against WNV persists in serum for up to 12 months post-inoculation (p.i.). Previous work using the mouse model demonstrated that WNV persists in central nervous system (CNS) tissues as infectious virus and as RNA for up to 4 months and 6 months p.i., respectively. In this study, we sought to elucidate the mechanism for viral persistence in the CNS using the mouse model. Characterization of the leukocyte infiltrate …

Electric Pulses To Prepare Feeder Cells For Sustaining And Culturing Of Undifferentiated Embryonic Stem Cells, Lauren M. Browning, Tao Huang, Xiao-Hong Nancy Xu

Chemistry & Biochemistry Faculty Publications

Current challenges in embryonic-stem-cell (ESC) research include inability of sustaining and culturing of undifferentiated ESCs over time. Growth-arrested feeder cells are essential to the culture and sustaining of undifferentiated ESCs, and they are currently prepared using gammaradiation and chemical inactivation. Both techniques have severe limitations. In this study, we developed a new, simple and effective technique (pulsed-electric-fields, PEFs) to produce viable growth-arrested cells (RTS34st) and used them as high-quality feeder cells to culture and sustain undifferentiated zebrafish ESCs over time. The cells were exposed to 25 sequential 10- nanosecond-electric-pulses (10nsEPs) of 25, 40 and 150 kV/cm with 1s pulse interval, …

Chloroquine Susceptibility And Reversibility In A Plasmodium Falciparum Genetic Cross, Jigar J. Patel, Drew Thacker, John C. Tan, Perri Pleeter, Lisa Checkley, Joseph M. Gonzales, Bingbing Deng, Paul D. Roepe, Roland A. Cooper, Michael T. Ferdig

Biological Sciences Faculty Publications

Mutations in the Plasmodium falciparum chloroquine (CQ) resistance transporter (PfCRT) are major determinants of verapamil (VP)-reversible CQ resistance (CQR). In the presence of mutant PfCRT, additional genes contribute to the wide range of CQ susceptibilities observed. It is not known if these genes influence mechanisms of chemosensitization by CQR reversal agents. Using quantitative trait locus (QTL) mapping of progeny clones from the HB3 x Dd2 cross, we show that the P. falciparum multidrug resistance gene 1 (pfmdr1) interacts with the South-East Asia-derived mutant pfcrt haplotype to modulate CQR levels. A novel chromosome 7 locus is predicted to contribute …

Microbial Quorum Quenching Activities In Marine Water, Wetland Water, And Rainforest Soil., Wong Cheng Siang

Student Works (2010-2019)

Quorum sensing refers to the bacterial cell-to-cell communication phenomenon that is employed to regulate a wide range of activities in a variety of bacteria. One of the most extensively studied mechanisms is that of Gram-negative bacteria utilizing N-acyl homoserine lactone as the signaling molecule. Quorum quenching on the other hand refers to the interference of quorum sensing, that can be achieved by, inter alia, directly inactivating the signaling molecule, and thus preventing the expression of certain genes, notably those regulating virulence. This study aimed to isolate N-acyl homoserine lactone-degrading microorganisms from Malaysian marine water, wetland water, and rainforest soil using …

Pattern Recognition In Cytopathology For Papanicolaou Screening, Jonathan Blackledge, Dmitriy Dubovitskiy

Conference papers

A unique space oriented filer is presented in order to detect and isolate the cell of a nucleus for applications in cytopathology. A classification method for nuclei is then considered based on the application of a set of features which includes certain fractal parameters. Segmentation algorithms are considered in which a self-adjustable sharpening filter is designed to enhance object location. Although the methods discussed and the algorithms developed have a range of applications, in this work we focus the engineering of a system for automating a Papanicolaou screening test using standard optical images

Process Optimization For The Developmenht Of A Functional Beverage Based On Lactic Acid Fermentation Of Oats, Shilpi Gupta, Sabrina Cox, Nissreen Abu-Ghannam

Articles

Oats (Avena sativa) have received considerable interest for their high content of soluble and insoluble fibre and for their high fermentability upon applying probiotic lactic acid bacteria (LAB). In the present study, Box–Behnken optimization design was used to optimize three different levels of oat, sucrose and starter culture concentration on the final viable cell population of Lactobacillus plantarum for the development of a fermented drink. A second-order polynomial response surface equation was developed indicating the effect of the studied variables on L. plantarum growth. Contour maps generated using the response surface equation showed that the experimental variables significantly affected the …

Humboldt Journal Of Microbiology: Volume 12, Number 1- May 2010, Press Humboldt

Humboldt Journal of Microbiology

No abstract provided.

Response Surface Optimization Of Crystal Violet Decolorization By Pellets Of Pyncnoporus Sanguineus., Siti Suhana Sulaiman

Student Works (2010-2019)

Ligninolytic enzymes of white-rot fungi have broad specificities and have been implicated in transformation and mineralization of organo-pollutant with chemical structure similar to lignin e.g. synthetic dyes. This study was carried out to optimize selected parameters for decolorization of Crystal violet by Pycnoporus sanguineus in shake flasks. The parameters studied were initial dye concentration (ppm), agitation speed (rpm) and process time. They were optimized using response surface methodology (RSM). Subsequent to the optimization, the decolorization process was scaled up in stirred tank reactor (STR). Effect of different geometry of impellers on the decolorization process was studied. Curved blade and angled …

Isolation And Characterization Of Actinobacteria From Soil Samples Of Signy Island, Antarctica., Pan Shing Yi

Student Works (2010-2019)

In this study, ninety five actinobacterial isolates were cultured from seven soils samples collected on Signy Island, maritime Antarctica. Nine different isolation media were used and the isolates plates were incubated at 15ºC for up to four months. SCN agar serves as the better media for the isolation of actinobacteria. Presence of actinobacteria in the soil samples was also detected using PCR with actinobacteria specific primers. The actinobacterial isolates were characterized based on morphology (Gram-stain, coverslip examination, colour grouping), analysis of DAP isomers, antibacterial activities and by molecular methods (ARDRA, analysis of 16S rRNA sequence and detection of NRPS gene). …

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 …