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Articles 31 - 57 of 57
Full-Text Articles in Life Sciences
Reverse Gyrase Is Not Necessary For Survival Of Hyperthermophilic Archaeon Pyrococcus Furiosus, Farshid Taghizadeh, Michael S. Bartlett
Reverse Gyrase Is Not Necessary For Survival Of Hyperthermophilic Archaeon Pyrococcus Furiosus, Farshid Taghizadeh, Michael S. Bartlett
Student Research Symposium
Reverse gyrase is the only known topoisomerase enzyme with positive supercoiling activity on covalently-closed DNA. This positive supercoiling is required to prevent DNA from denaturation at high temperatures. The gene that codes for this protein is present in all hyperthermophiles and absent from all mesophilic and thermophilic genomes, suggesting that this enzyme is the only hyperthermophile-specific protein. To investigate if this protein is vital for the cells, we knocked out its gene from the genome of living organism Pyrococcus furiosus. Pyrococcus furiosus is a hyperthermophilic archaeon that grows between 70°C to 103°C with an optimum growth temperature of 100°C. …
Ex Vivo Dna Cloning, Adam B. Fisher
Ex Vivo Dna Cloning, Adam B. Fisher
Theses and Dissertations
Genetic engineering of microbes has developed rapidly along with our ability to synthesize DNA de novo. Yet, even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. While technological advances have resulted in powerful techniques for in vitro and in vivo assembly of DNA, each suffers inherent disadvantages. Here, an ex vivo DNA cloning suite using crude cellular lysates derived from E. coli is demonstrated to amplify and assemble DNA containing small sequence homologies. Further, the advantages of an ex vivo approach are …
Dancing Through Life: Allosteric Transitions And Structural Analysis Of Hsp70 And Hsp110 Chaperone Proteins, Gabrielle Stetz, Gennady M. Verkhivker
Dancing Through Life: Allosteric Transitions And Structural Analysis Of Hsp70 And Hsp110 Chaperone Proteins, Gabrielle Stetz, Gennady M. Verkhivker
Student Scholar Symposium Abstracts and Posters
The molecular chaperone protein Hsp70 is centrally involved in cellular homeostasis by assisting in the folding and degradation of protein substrates. Hsp70 is joined by co-chaperones, such as Hsp110, which contribute to specialized tasks of the Hsp70 complex. Imbalances of this heat shock protein system are believed to be involved with the deregulation of cancer pathways and other human diseases. Better understanding of how these heat shock proteins work at the molecular level, which has been investigated using molecular docking tools, will give more clues about biological function. Simulating the formation and function of Hsp70 based chaperone complexes could provide …
Gaip Interacting Protein C-Terminus Regulates Autophagy And Exosome Biogenesis Of Pancreatic Cancer Through Metabolic Pathways, Santanu Bhattacharya, Krishnendu Pal, Anil K. Sharma, Shamit K. Dutta, Julie S. Lau, Irene K. Yan, Enfeng Wang, Ahmed Elkhanany, Khalid M. Alkharfy, Arunik Sanyal, Tushar C. Patel, Suresh T. Chari, Mark R. Spaller, Debabrata Mukhopadhyay
Gaip Interacting Protein C-Terminus Regulates Autophagy And Exosome Biogenesis Of Pancreatic Cancer Through Metabolic Pathways, Santanu Bhattacharya, Krishnendu Pal, Anil K. Sharma, Shamit K. Dutta, Julie S. Lau, Irene K. Yan, Enfeng Wang, Ahmed Elkhanany, Khalid M. Alkharfy, Arunik Sanyal, Tushar C. Patel, Suresh T. Chari, Mark R. Spaller, Debabrata Mukhopadhyay
Dartmouth Scholarship
GAIP interacting protein C terminus (GIPC) is known to play an important role in a variety of physiological and disease states. In the present study, we have identified a novel role for GIPC as a master regulator of autophagy and the exocytotic pathways in cancer. We show that depletion of GIPC-induced autophagy in pancreatic cancer cells, as evident from the upregulation of the autophagy marker LC3II. We further report that GIPC regulates cellular trafficking pathways by modulating the secretion, biogenesis, and molecular composition of exosomes. We also identified the involvement of GIPC on metabolic stress pathways regulating autophagy and microvesicular …
Identification Of Proteins Potentially Involved In The Formation Of Lafora Bodies, A Hallmark Of Lafora Disease, Elham Schokraie, Oliver Kötting, Matthew S. Gentry
Identification Of Proteins Potentially Involved In The Formation Of Lafora Bodies, A Hallmark Of Lafora Disease, Elham Schokraie, Oliver Kötting, Matthew S. Gentry
Molecular and Cellular Biochemistry Presentations
Lafora Disease (LD) is a fatal teenage-onset progressive myoclonus epilepsy. It is characterized by the formation of Lafora bodies (LBs), deposits of abnormally branched, insoluble, hyperphosphorylated glycogen-like polymers that are generally believed to trigger the development of the clinical symptoms of LD. 58% and 35% of the LD cases are caused by mutations in EPM2A (laforin) and EPM2B (malin), respectively. However, little is known about their function in LB formation. Two different mechanisms have been proposed to explain the accumulation of insoluble LBs: first, excessive glycogen phosphorylation and, second, an imbalance between glycogen synthesizing enzymes. The present study aims at …
Biochemistry Of 1, 2-Dehydro-N-Acetyldopamine Derivatives, Adal T. Abebe
Biochemistry Of 1, 2-Dehydro-N-Acetyldopamine Derivatives, Adal T. Abebe
Graduate Doctoral Dissertations
Dehydrodopa/dopamine derivatives form an important group of biomolecules participating in sclerotization of all arthropod cuticles, gluing and cementing mussels and related organisms to solid surfaces, and defense reactions of countless marine and invertebrate organisms. Yet very little information is available on the biochemistry of these highly reactive and unstable molecules. To understand their physiological role, I conducted a thorough biochemical study on three representative compounds that cover the entire plethora of dehydrodopa/dopamine derivatives. Employing diode array UV-visible spectroscopy, HPLC, liquid chromatography-mass spectrometry, and electrospray ionization tandem mass spectrometry, I investigated the oxidation chemistry of 1,2-dehydro-N-acetyldopamine (dehydro NADA), 1,2-dehydro-N-acetyldopa and 1,2-dehydro-N-acetyldopa …
Using Rnai In C. Elegans To Demonstrate Gene Knockdown Phenotypes In The Undergraduate Biology Lab Setting, Nicole M. Roy
Using Rnai In C. Elegans To Demonstrate Gene Knockdown Phenotypes In The Undergraduate Biology Lab Setting, Nicole M. Roy
Biology Faculty Publications
RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using Caenorhabditis elegans (C. elegans) was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However, students struggle conceptually with the molecular biology behind the RNAi technology and find the technology difficult to grasp. To this end, we have provided a simple, streamlined and inexpensive RNAi procedure using C. elegans that can be adopted in upper level biology classes. By using an unknown RNAi-producing bacteria, students perform novel …
Cell Type Difference In Influenza A Viral Mrna Nuclear Export, Sean William Larsen
Cell Type Difference In Influenza A Viral Mrna Nuclear Export, Sean William Larsen
Theses Digitization Project
The focus of this thesis research was to clarify the role of host Nxf1 in influenza viral mRNA nuclear export. This study aims to define the nuclear mRNA export pathways of influenza viral mRNA. If viral mRNAs are discovered to utilize neither known mRNA nuclear export pathway this would indicate the mRNA exports via undefined mRNA nuclear export pathway. This might be an atypical pathway not utilized by many host mRNAs and thus might reveal novel antiviral target. 293T (Human embryonic kidney cells) and A549 (Human lung epithelial) cells were purchased from ATCC American Tissue Culture Collection.
Elucidating The Role Of Dopamine In The Avoidance Response Of Caenorhabditis Elegans Utilizing Microfluidics, Patricia Frances Turturro
Elucidating The Role Of Dopamine In The Avoidance Response Of Caenorhabditis Elegans Utilizing Microfluidics, Patricia Frances Turturro
Theses Digitization Project
This study looks at dopamine modulation of ASH neurons, which are part of the avoidance circuit of C. elegans, and their response to water soluble stimuli. Because nematodes such as Caenorhabditis elegans utilize dopamine at the molecular and cellular level in much the same way as mammals, they offer researchers a unique opportunity to study the mechanisms of dopamine signaling.
Starch Phosphates: A Means To Manipulate Biofuel Production, Travis M. Bridges
Starch Phosphates: A Means To Manipulate Biofuel Production, Travis M. Bridges
Kaleidoscope
No abstract provided.
Fundamentals Of Protein Structure Alignment, Allen Holder, Mark Brandt, Yosi Shibberu
Fundamentals Of Protein Structure Alignment, Allen Holder, Mark Brandt, Yosi Shibberu
Mathematical Sciences Technical Reports (MSTR)
The central dogma of molecular biology asserts a one way transfer of information from a cell’s genetic code to the expression of proteins. Proteins are the functional workhorses of a cell, and studying these molecules is at the foundation of much of computational biology. Our goal here is to present a succinct introduction to the biological, mathematical, and computational aspects of making pairwise comparisons between protein structures. The presentation is intended to be useful for those who are entering this research area. The chapter begins with a brief introduction to the biology of protein comparison, which is followed by a …
Electrosensory Ampullary Organs Are Derived From Lateral Line Placodes In Bony Fishes, Melissa S. Modrell, William E. Benis, R. Glenn Northcutt, Marcus C. Davis, Clare V.H. Baker
Electrosensory Ampullary Organs Are Derived From Lateral Line Placodes In Bony Fishes, Melissa S. Modrell, William E. Benis, R. Glenn Northcutt, Marcus C. Davis, Clare V.H. Baker
Faculty and Research Publications
Electroreception is an ancient subdivision of the lateral line sensory system, found in all major vertebrate groups (though lost in frogs, amniotes and most ray-finned fishes). Electroreception is mediated by 'hair cells' in ampullary organs, distributed in fields flanking lines of mechanosensory hair cell-containing neuromasts that detect local water movement. Neuromasts, and afferent neurons for both neuromasts and ampullary organs, develop from lateral line placodes. Although ampullary organs in the axolotl (a representative of the lobe-finned clade of bony fishes) are lateral line placode-derived, non-placodal origins have been proposed for electroreceptors in other taxa. Here we show morphological and molecular …
Arctic Mustard Flower Color Polymorphism Controlled By Petal-Specific Downregulation At The Threshold Of The Anthocyanin Biosynthetic Pathway, Cynthia A. Dick, Jason Buenrostro, Timothy Butler, Matthew L. Carlson, Daniel J. Kliebenstein, Justen B. Whittall
Arctic Mustard Flower Color Polymorphism Controlled By Petal-Specific Downregulation At The Threshold Of The Anthocyanin Biosynthetic Pathway, Cynthia A. Dick, Jason Buenrostro, Timothy Butler, Matthew L. Carlson, Daniel J. Kliebenstein, Justen B. Whittall
Biology
Intra- and interspecific variation in flower color is a hallmark of angiosperm diversity. The evolutionary forces underlying the variety of flower colors can be nearly as diverse as the colors themselves. In addition to pollinator preferences, non-pollinator agents of selection can have a major influence on the evolution of flower color polymorphisms, especially when the pigments in question are also expressed in vegetative tissues. In such cases, identifying the target(s) of selection starts with determining the biochemical and molecular basis for the flower color variation and examining any pleiotropic effects manifested in vegetative tissues. Herein, we describe a widespread purple-white …
Fast Protein Structure Alignment, Yosi Shibberu, Allen Holder, Kyla Lutz
Fast Protein Structure Alignment, Yosi Shibberu, Allen Holder, Kyla Lutz
Mathematical Sciences Technical Reports (MSTR)
We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst case analysis of the algorithm shows that the solution is bounded by a constant depending only on the data of the problem.
Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal
Core Concepts In Biochemistry And Molecular Biology In An Integrated Mbbs Curriculum, M P. Iqbal
Department of Biological & Biomedical Sciences
No abstract provided.
Cell Modeling, Matthew L. Campbell
Cell Modeling, Matthew L. Campbell
Theses and Dissertations
The Air Force is currently developing new products that incorporate a variety of chemicals which may come in contact with product users. To define which chemicals are dangerous to the user, toxicity studies have been performed. However, analysis of toxicity ultimately requires models of the exposed cellular systems. This thesis provides an introduction of how to model and analyze small and large cellular systems. Understanding the underlying behavior of small models and their relation to large systems will lead to a better understanding of how the Air Force should construct intracellular models to assist in future toxicology studies. Developing analysis …
In Vitro Assessment Of The Toxicity Of Cocaine And Its Metabolites In The Human Umbilical Artery, Tessa L. Long
In Vitro Assessment Of The Toxicity Of Cocaine And Its Metabolites In The Human Umbilical Artery, Tessa L. Long
Electronic Theses and Dissertations
An in vitro model was used to assess the effect of cocaine and its metabolites on the umbilical artery. Objectives were to pharmacologically confirm the presence of adrenergic innervation using tyramine, evaluate the ability of cocaine, benzoylecgonine, norcocaine and cocaethylene to potentiate vasoconstriction by serotonin and norepinephrine, examine the ability of ketanserin to block the enhanced vasoconstriction produced by cocaine, and determine displacement of 3 H-ketanserin by serotonin, norepinephrine, tyramine and mianserin. The vasoconstrictive effect of tyramine (100 μM) was enhanced in the presence of cocaine by 257%. Vasoconstrictive effects of serotonin and norepinephrine were significantly enhanced by cocaine by …
The Influence Of A Human Repetitive Dna On Genome Stability, Eugenia L. Posey
The Influence Of A Human Repetitive Dna On Genome Stability, Eugenia L. Posey
Electronic Theses and Dissertations
A uniquely human interspersed repetitive DNA sequence family, the L2Hs, are highly polymorphic in human genomes. Several features of interspersed repeated DNA may contribute to the instability observed. Certain motifs (direct repeats, palindromes, and inverted repeats) comprising L2Hs elements may adopt unusual secondary structures such as cruciforms or hairpins. These motifs have been associated with features of genome instability in recombination, insertions and deletions. The L2Hs elements also are AT-rich (76%) compared to the bulk of human DNA (52%). That their dynamic nature (i.e. polymorphisms) may arise from recombination, insertions and deletions has led to the hypothesis that the L2Hs …
Endogenous Alkylglycerol Functions As A Mediator Of Protein Kinase C Activity And Cell Proliferation, Fritz G. Buchanan
Endogenous Alkylglycerol Functions As A Mediator Of Protein Kinase C Activity And Cell Proliferation, Fritz G. Buchanan
Electronic Theses and Dissertations
To explore the possibility that 1-O-alkyl-sn-glycerol (alkylglycerol) may serve a regulatory role in the control of cell proliferation or PKC activity, we examined the ability of alkylglycerol to influence PKC activity and subcellular distribution as well as the ability of alkylglycerol to effect cell proliferation. MDCK cells grown to confluence show a loss of PKC activity associated with the membrane, as reported in fibroblasts. Preconfluent cultures of MDCK cells have a high level of PKC activity associated with the membrane. However, treatment of preconfluent cultures with alkylglycerol causes a reduction of PKC activity. A similar inhibition was observed with alkylglycerol …
Moraxella (Branhamella) Catarrhalis: A Molecular Epidemiology Study, Lyndell R. Gill
Moraxella (Branhamella) Catarrhalis: A Molecular Epidemiology Study, Lyndell R. Gill
Electronic Theses and Dissertations
Moraxella (Branhamella) catarrhalis is the third-most-frequently isolated microorganism associated with acute exacerbations of chronic bronchitis in patients during their stay at the Mountain Home VA Medical Center (MHVAMC). In order to develop a practical, epidemiologically-meaningful typing method for M. (B.) catarrhalis, we tested two methods based on analysis of chromosomal DNA for typeability, reproducibility, and ability to differentiate between unrelated strains (discriminatory power, D). M. (B.) catarrhalis isolants from MHVAMC from 7/1/87-6/30/88 were grown overnight in broth and embedded in agarose. DNA was isolated by standard methods. The DNA was subjected to: (1) restriction endonuclease digestion (with either Bgl II …
A Molecular Basis For Erythromycin Sensitivity And Resistance In Escherichia Coli, Harold S. Chittum
A Molecular Basis For Erythromycin Sensitivity And Resistance In Escherichia Coli, Harold S. Chittum
Electronic Theses and Dissertations
The effect of erythromycin on the 50S ribosomal subunit during cell growth has been extensively investigated. Sucrose density gradient analysis of ribosomes formed in the presence and absence of the drug revealed a 50S specific assembly defect is partially responsible for erythromycin's inhibitory effects on wild type cells. Examination of two erythromycin-resistant mutants of E. coli (N281 and N282) revealed that mutant N281 (L22 mutant) but not N282 (L4 mutant) was assembly defective in the presence of the drug, although only at much higher drug concentrations (300 ug/ml vs. 75 ug/ml for wild type cells). The altered genes from each …
Unusual Structure Of A Human Middle Repetitive Dna, Duminda D. Ratnasinghe
Unusual Structure Of A Human Middle Repetitive Dna, Duminda D. Ratnasinghe
Electronic Theses and Dissertations
The L2Hs sequences are a polymorphic, interspersed, middle repetitive DNA family unique to human genomes. Genomic fingerprinting indicates that these DNAs vary from one individual to another and between tissues of the same individual. Sequence analysis reveals that they are AT-rich (76%) and contain many unusual sequence arrangements (palindromes, inverted and direct repeats). These sequence properties confer on the L2Hs elements the potential to fold into non-B-form structures, a characteristic of recombination hot spots. To test this hypothesis carbodiimide, osmium tetroxide and S$\sb1$ nuclease were used as single-strand specific probes to study a recombinant plasmid, pN6.4.39, containing a single L2Hs …
Characterization Of Two Temperature-Sensitive Mutants Of Escherichia Coli Exhibiting An Altered L22 Ribosomal Protein, Bonnie A. Burnette-Vick
Characterization Of Two Temperature-Sensitive Mutants Of Escherichia Coli Exhibiting An Altered L22 Ribosomal Protein, Bonnie A. Burnette-Vick
Electronic Theses and Dissertations
Analysis of E. coli strains SK1047 and SK1048 have shown them to be temperature-sensitive, protein-synthesis deficient. An alteration in ribosomal protein L22 was detected in both strains using two dimensional gel electrophoresis. Protein L22 was purified from both strains by reversed phase high performance liquid chromatography and from two dimensional electrophoretic gels. Purified ribosomal protein L22 was labeled by reductive methylation and used in 23S RNA binding assays with and without ribosomal protein L4. At the permissive temperature, protein L22 from SK1047 bound less efficiently than the control while protein L22 from SK1048 bound as efficiently as the control. At …
Mouse Mast Cell Proteases: Induction, Molecular Cloning, And Characterization, Wei Chu
Mouse Mast Cell Proteases: Induction, Molecular Cloning, And Characterization, Wei Chu
Electronic Theses and Dissertations
Tryptase, a mast cell-specific serine protease with trypsin-like specificity, has been identified in a mouse mast cell line (ABFTL-6) based on it's enzymatic activity, inhibition properties, and cross-reactivity to a human mast cell tryptase antibody. The effects of fibroblast-conditioned medium and sodium butyrate on ABFTL-6 mast cell differentiation and tryptase expression have been examined. ABFTL-6 mouse mast cells undergo phenotypic changes upon culturing in media supplemented with fibroblast-conditioned media at 50% or 1 mM sodium butyrate. The induced cells increased in size, had larger and more metachromatic cytoplasmic granules, and increased their total cellular protein about four-fold. Tryptase activity increased …
A Temperature-Sensitive Mutant Of Escherichia Coli Affected In The Alpha Subunit Of Rna Polymerase, Majid Mehrpouyan
A Temperature-Sensitive Mutant Of Escherichia Coli Affected In The Alpha Subunit Of Rna Polymerase, Majid Mehrpouyan
Electronic Theses and Dissertations
A temperature-sensitive mutant of Escherichia coli affected in the alpha subunit of RNA polymerase has been investigated. Gene mapping and complementation experiments placed the mutation to temperature-sensitivity within the alpha operon at 72 min on the bacterial chromosome. The rate of RNA synthesis in vivo and the accumulation of ribosomal RNA were significantly reduced in the mutant at 44$\sp\circ$C. The thermostability at 44$\sp\circ$C of the purified holoenzyme from mutant cells was about 20% of that of the normal enzyme. Assays with T7 DNA as a template showed that the fraction of active enzyme competent for transcription was reduced as a …
Isolation And Characterization Of Temperature-Sensitive Protein Synthesis Mutants Of Escherichia Coli By Directed Mutagenesis Of The Defective Bacteriophage Lambda Fus2, Kenton L. Lohman
Electronic Theses and Dissertations
Mutagenesis of the defective transducing bacteriophage lambda fus2 was used to isolate a collection of temperature-sensitive mutants of E. coli in the major ribosomal protein gene cluster. Four mutants were examined in detail. Two of the mutants were resistant to the ribosomal antibiotics neamine and spectinomycin. Another mutant was defective in 50S ribosomal subunit assembly at 42(DEGREES)C. The 30S subunit proteins S17 and S19 were changed in two different mutants. Each protein migrated as a more basic species in two-dimensional gels of ribosomal proteins. Ribosomes from each of the four mutants examined showed a temperature-dependent reduction in translational activity in …
Characterization Of Kpni Interspersed, Repetitive Dna Sequence Families And Their Association With The Nuclear Matrix, Joseph A. Chimera
Characterization Of Kpni Interspersed, Repetitive Dna Sequence Families And Their Association With The Nuclear Matrix, Joseph A. Chimera
Electronic Theses and Dissertations
The KpnI, 1.2 and 1.5 kb families of interspersed repetitive DNAs from the African green monkey genome were isolated and characterized. Each family contains three populations of segments based on their sequence lengths and susceptibility to cleavage by the restriction enzymes KpnI and RsaI. The first population contains the smallest segments which are susceptible to both KpnI and RsaI cleavage and have fragment lengths of 1.2 kb (1.2 kb family) and 1.5 kb (1.5 kb family) respectively. The members in this population are referred to as KpnI-sensitive segments. The second population contains longer segments (> 2 kb) which represent fusions …