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Genome-Wide Gene Regulation Of Biosynthesis And Energy Generation By A Novel Transcriptional Repressor In Geobacter Species, Derek Lovley, Toshiyuki Ueki 2010 University of Massachusetts - Amherst

Genome-Wide Gene Regulation Of Biosynthesis And Energy Generation By A Novel Transcriptional Repressor In Geobacter Species, Derek Lovley, Toshiyuki Ueki

Derek Lovley

Geobacter species play important roles in bioremediation of contaminated environments and in electricity production from waste organic matter in microbial fuel cells. To better understand physiology of Geobacter species, expression and function of citrate synthase, a key enzyme in the TCA cycle that is important for organic acid oxidation in Geobacter species, was investigated. Geobacter sulfurreducens did not require citrate synthase for growth with hydrogen as the electron donor and fumarate as the electron acceptor. Expression of the citrate synthase gene, gltA, was repressed by a transcription factor under this growth condition. Functional and comparative genomics approaches, coupled with genetic ...


The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land, Derek Lovley 2010 University of Massachusetts - Amherst

The Genome Of Geobacter Bemidjiensis, Exemplar For The Subsurface Clade Of Geobacter Species That Predominate In Fe(Iii)-Reducing Subsurface Enviorments, Muktak Aklujkar, Nealson D. Young, Dawn Holmes, Milind Chavan, Carla Risso, Hajnalka E. Kiss, Cliff S. Han, Miriam L. Land, Derek Lovley

Derek Lovley

BACKGROUND: Geobacter species in a phylogenetic cluster known as subsurface clade 1 are often the predominant microorganisms in subsurface environments in which Fe(III) reduction is the primary electron-accepting process. Geobacter bemidjiensis, a member of this clade, was isolated from hydrocarbon-contaminated subsurface sediments in Bemidji, Minnesota, and is closely related to Geobacter species found to be abundant at other subsurface sites. This study examines whether there are significant differences in the metabolism and physiology of G. bemidjiensis compared to non-subsurface Geobacter species. RESULTS: Annotation of the genome sequence of G. bemidjiensis indicates several differences in metabolism compared to previously sequenced ...


Unbalanced Nature, Unbounded Bodies, And Unlimited Technology: Ecocriticism And Karen Traviss’S Wess’Har Series, Heather I. Sullivan 2010 Trinity University

Unbalanced Nature, Unbounded Bodies, And Unlimited Technology: Ecocriticism And Karen Traviss’S Wess’Har Series, Heather I. Sullivan

Modern Languages and Literatures Faculty Research

While nature is often claimed to be a space of harmonized balance or an antidote to the chaos of the modern world, we need a more grounded assessment of nature as endlessly changing and much less predictable than we like to assume. In this essay, I explore Karen Traviss’ provocative exploration of unbalanced nature and unbounded bodies in her wess’har series with the guidance of two ecocritics who reject the concept of balanced nature, Dana Phillips and Ursula Heise. Additionally, I turn to the environmental philosopher Val Plumwood for insights regarding Traviss’ spurious yet rather standard vision of an ...


Interleukin-6 Increases Expression And Secretion Of Cathepsin B By Breast Tumor-Associated Monocytes., Mona M. Mohamed, Dora Cavallo-Medved, Deborah Rudy, Arulselvi Anbalagan, Bonnie F. Sloane, Kamir Moin 2010 University of Windsor

Interleukin-6 Increases Expression And Secretion Of Cathepsin B By Breast Tumor-Associated Monocytes., Mona M. Mohamed, Dora Cavallo-Medved, Deborah Rudy, Arulselvi Anbalagan, Bonnie F. Sloane, Kamir Moin

Biological Sciences Publications

In the tumor microenvironment, monocytes respond to paracrine stimuli from breast cancer cells by secreting molecules that participate in breast cancer growth, invasion, intravasation and metastasis. Here we examined the effects of media conditioned by MDA-MB-231 human breast carcinoma cells (231-CM) on expression and secretion of proteases and secretion of cytokines by U937 human monocytes. We found that 231-CM increased U937: 1) proliferation; 2) expression, activity and secretion of the cysteine protease cathepsin B (CTSB); 3) secretion of matrix metalloproteinases (MMP)-2 and -9; and 4) secretion of interleukin-6 (IL-6) and insulin-like growth factor binding protein-1 (IGFBP-1). We further demonstrated ...


Probing Local Structural Fluctuations In Myoglobin By Size-Dependent Thiol-Disulfide Exchange, Margaret M. Stratton, S N. Loh, T A. Cutler, J H. Ha 2010 University of Massachusetts Amherst

Probing Local Structural Fluctuations In Myoglobin By Size-Dependent Thiol-Disulfide Exchange, Margaret M. Stratton, S N. Loh, T A. Cutler, J H. Ha

Biochemistry & Molecular Biology Department Faculty Publication Series

All proteins undergo local structural fluctuations (LSFs) or breathing motions. These motions are likely to be important for function but are poorly understood. LSFs were initially defined by amide hydrogen exchange (HX) experiments as opening events, which expose a small number of backbone amides to (1)H/(2)H exchange, but whose exchange rates are independent of denaturant concentration. Here, we use size-dependent thiol-disulfide exchange (SX) to characterize LSFs in single cysteine-containing variants of myoglobin (Mb). SX complements HX by providing information on motions that disrupt side chain packing interactions. Most importantly, probe reagents of different sizes and chemical properties ...


Environmental And Endogenous Factors Influencing Emigration In Juvenile Anadromous Alewives, Benjamin I. Gahagan, Eric T. Schultz, Katie E. Gherard 2010 University of Connecticut - Storrs

Environmental And Endogenous Factors Influencing Emigration In Juvenile Anadromous Alewives, Benjamin I. Gahagan, Eric T. Schultz, Katie E. Gherard

EEB Articles

We analyzed juvenile anadromous alewife migration at Bride Lake, a coastal lake in Connecticut, during summer 2006 and found that migration on 24-hour and seasonal timescales was influenced by conditions of the environment and characteristics of the individual. To identify environmental cues of juvenile migration, we continuously video recorded fish at the lake outflow and employed information-theoretic model selection to identify the best predictors of daily migration rate. More than 80% of the approximately 320,000 juveniles that migrated from mid-June to mid-August departed in three pulses lasting one or two days. Pulses of migration were associated with precipitation events ...


Dietary Patterns And Markers For The Metabolic Syndrome In Australian Adolescents, Gina L. Ambrosini, Rae-Chi Huang, Trevor A. Mori, Beth P. Hands, Therese O'Sullivan, Nicholas H. de Klerk, Lawrence J. Beilin, Wendy H. Oddy 2010 Curtin University of Technology

Dietary Patterns And Markers For The Metabolic Syndrome In Australian Adolescents, Gina L. Ambrosini, Rae-Chi Huang, Trevor A. Mori, Beth P. Hands, Therese O'Sullivan, Nicholas H. De Klerk, Lawrence J. Beilin, Wendy H. Oddy

Health Sciences Papers and Journal Articles

Background and Aims: Overweight and other risk factors for cardiovascular disease (CVD) as well as their clustering, or the metabolic syndrome, are increasingly prevalent among children and adolescents. We examined dietary patterns, CVD risk factors, and the clustering of these risk factors, in 1139 14 year olds living in Western Australia.

Methods and Results: Usual dietary intake was assessed with a food frequency questionnaire. Two dietary patterns, ‘Western’ and ‘Healthy’, were identified using factor analysis. Associations between these dietary patterns and BMI, waist circumference, systolic blood pressure, fasting levels of serum glucose, insulin, total cholesterol, HDL C, LDL C, triglycerides ...


A Quantitative Description Of The Vocalizations And Vocal Activity Of The Barred Owl, Karan J. Odom, Daniel J. Mennill 2010 University of Windsor

A Quantitative Description Of The Vocalizations And Vocal Activity Of The Barred Owl, Karan J. Odom, Daniel J. Mennill

Biological Sciences Publications

Barred Owls (Strix varia) are highly vocal and perform a diverse array of vocalizations. They are often monitored by acoustic surveys, yet Barred Owl vocalizations and vocal behavior are poorly described. We present a detailed analysis of Barred Owl vocal behavior with four goals: (1) to provide a quantitative description of Barred Owl vocalizations, including those given within duets, (2) to examine diel variation in vocal output for multiple vocalizations, (3) to explore the use of vocalizations inside and outside of duets, and (4) to identify sex-specific vocal characteristics and discuss their utility in identifying an owl's sex. Adult ...


A Novel Neural Substrate For The Transformation Of Olfactory Inputs Into Motor Output, Dominique Derjean, Aimen Moussaddy, Elias Atallah, Melissa St-Pierre, François Auclair, Steven Chang, Xiang Ren, Barbara Zielinski, Réjean Dubuc 2010 University of Windsor

A Novel Neural Substrate For The Transformation Of Olfactory Inputs Into Motor Output, Dominique Derjean, Aimen Moussaddy, Elias Atallah, Melissa St-Pierre, François Auclair, Steven Chang, Xiang Ren, Barbara Zielinski, Réjean Dubuc

Biological Sciences Publications

Anatomical and physiological experiments in the lamprey reveal the neural circuit involved in transforming olfactory inputs into motor outputs, which was previously unknown in a vertebrate.


Changes In Light Levels With Loss Of Eastern Hemlock (Tsuga Canadensis) At A Southern Appalachian Headwater Stream: Implications For Brook Trout (Salvelinus Fontinalis), L. A. Siderhurst, Heather P. Griscom, M. Hudy, Z. J. Bortolot 2010 James Madison University

Changes In Light Levels With Loss Of Eastern Hemlock (Tsuga Canadensis) At A Southern Appalachian Headwater Stream: Implications For Brook Trout (Salvelinus Fontinalis), L. A. Siderhurst, Heather P. Griscom, M. Hudy, Z. J. Bortolot

Heather P. Griscom

No abstract provided.


Proteome-Wide Prediction Of Acetylation Substrates, Amrita Basu 2010 Rockefeller University

Proteome-Wide Prediction Of Acetylation Substrates, Amrita Basu

Student Theses and Dissertations

Eukaryotic DNA is found packaged with proteins and RNA, which forms a substance called chromatin. This packaging is dynamic and regulates access to DNA for essential cellular processes such as transcription, replication, and repair. In recent years, studies have shown that regulated changes in the chemical and physical properties of chromatin often lead to dynamic changes in multiple cellular processes by affecting the accessibility of the DNA. These changes can be brought about in part through posttranslational modifications of histone proteins, which are involved in disrupting chromatin contacts or by recruiting effector proteins to chromatin. Acetylation is one of the ...


Synaptic Specificity In The Zebrafish Lateral Line, Aaron Nagiel 2010 Rockefeller University

Synaptic Specificity In The Zebrafish Lateral Line, Aaron Nagiel

Student Theses and Dissertations

The proper wiring of the vertebrate brain represents an extraordinary developmental challenge, requiring billions of neurons to select their appropriate synaptic targets. In view of this complexity, simple vertebrate systems provide necessary models for understanding how synaptic specificity arises. The posterior lateral-line organ of larval zebrafish consists of polarized hair cells organized in discrete clusters known as neuromasts. Here I show that each afferent neuron of the posterior lateral line establishes specific contacts with hair cells of the same hair-bundle polarity. I quantify this specificity by modeling the neuron as a biased selector of hair-cell polarity and find evidence for ...


Genome-Scale Genetics: Lessons From Founder Populations, Eimear Elizabeth Kenny 2010 Rockefeller University

Genome-Scale Genetics: Lessons From Founder Populations, Eimear Elizabeth Kenny

Student Theses and Dissertations

The potential benefits of using population isolates in genetic mapping due to reduced genetic and environmental heterogeneity are offset by the challenges posed by these populations for traditional association methods. Population isolates often contain large amounts of direct and cryptic relatedness that confound baseline assumptions of independence among genotypes and phenotypes and require specialized approaches to account for this sample structure. We examined three such approaches for association testing: (i) scoring allele transmission to offspring within families (ii) incorporating a permutation-based association score between families into the test statistic and finally (iii) incorporation of a kinship matrix to capture the ...


Mechanisms For Maintaining Cell Identity In C.Elegans Olfactory Neurons, Bluma J. Lesch 2010 Rockefeller University

Mechanisms For Maintaining Cell Identity In C.Elegans Olfactory Neurons, Bluma J. Lesch

Student Theses and Dissertations

Maintenance of cell identity is a complex process that depends on developmentally determined transcriptional states and on environmental input. In neurons, which are both highly differentiated and highly sensitive to external stimuli, maintenance of identity is especially challenging. In this thesis, I describe the isolation and characterization of several genes involved in maintaining the identities of two olfactory neuron subtypes, AWCON and AWCOFF, in the nematode Caenorhabditis elegans. The AWCON and AWCOFF identities are specified by a stochastic decision during embryogenesis, but several of the genes involved in this embryonic decision are subsequently downregulated. Additional mechanisms must therefore act to ...


Characterization Of The Functional Role Of The Intracellular Cholesterol Transporter Stard4 In Knockout Mice, And Investigation Of Epigenetic Modulation Of Apoa-I Transcription, Joshua Riegelhaupt 2010 Rockefeller University

Characterization Of The Functional Role Of The Intracellular Cholesterol Transporter Stard4 In Knockout Mice, And Investigation Of Epigenetic Modulation Of Apoa-I Transcription, Joshua Riegelhaupt

Student Theses and Dissertations

Cholesterol is crucial for mammalian survival by playing important roles, such as regulating membrane fluidity and as a precursor for the synthesis of steroid and sex hormones, bile acids, and Vitamin D. In addition, cellular and organismal regulation of cholesterol is important for health. For example, increased levels of plasma LDL cholesterol are a risk factor for coronary heart disease and stroke. Intracellular cholesterol levels are regulated by a variety of mechanisms, but numerous studies indicate a very important role for transcriptional regulation by Sterol Regulatory Binding Proteins (SREBPs), Liver X Receptors (LXRs) and Unfolded Protein Response (UPR) or ER ...


Dissecting The Contribution Of The Carboxyl-Terminal Domain And Tail Of Hiv-1 Integrase To Viral Dynamics And Enzymatic Function, Kevin Dominic Mohammed 2010 Rockefeller University

Dissecting The Contribution Of The Carboxyl-Terminal Domain And Tail Of Hiv-1 Integrase To Viral Dynamics And Enzymatic Function, Kevin Dominic Mohammed

Student Theses and Dissertations

The Human Immunodeficiency Virus Type-1 (HIV-1) is the causative agent of the Acquired Immune Deficiency Syndrome (AIDS). Combination antiviral therapy has proven to be particularly effective at suppressing viral replication, yet complete eradication of the virus from an infected individual remains elusive. Recently, a new class of antiviral drugs targeting the viral integrase (IN) has been added to the HAART (high active antiretroviral therapy) regimen. This novel drug class exerts its inhibitory effect by targeting one aspect of the dual-staged integration reaction. In contrast to the other two viral targets of HAART, the reverse transcriptase (RT) and protease (PR) enzymes ...


Structural And Molecular Correlates Of Individual Differences In Anxiety Behavior And The Stress Response, Melinda Miller 2010 Rockefeller University

Structural And Molecular Correlates Of Individual Differences In Anxiety Behavior And The Stress Response, Melinda Miller

Student Theses and Dissertations

Although many people are exposed to stressful experiences during their lifetime, only 5-35% will be diagnosed with Post-Traumatic Stress Disorder (PTSD). While most animal models of stress are effective at producing behavioral changes in an entire group of animals, they fail to account for individual differences in the human stress response or for the variability in baseline anxiety. Animal models of acute and chronic stress increase anxiety behavior and induce structural and neurochemical changes in brain regions necessary for learning, memory, fear responses, and executive function; the hippocampus, amygdala and medial prefrontal cortex (mPFC). In the following experiments, we measured ...


Variability And Dynamics Of Apoptotic Events In Single Cells, Patrick Bhola 2010 Rockefeller University

Variability And Dynamics Of Apoptotic Events In Single Cells, Patrick Bhola

Student Theses and Dissertations

Apoptosis is a form of programmed cell death that is necessary for development and organism homeostasis. The early stages of apoptosis are marked by the permeabilization of the mitochondrial outer membrane, the release of cytochrome c and Smac from mitochondria, and the activation of the caspase family of proteases. The permeabilization of the mitochondria outer membrane is thought to represent the commitment of a cell to an apoptotic fate, and the subsequent release of mitochondrial proteins is an “all or none” phenomenon that is completed in an individual cell within minutes. Although the cellular decision to commit to apoptosis ...


Mechanisms Of Controlled Proteolysis During Drosophila Spermatogenesis: Coordinate Action Of Apoptotic Caspases And The Ubiquitin-Proteasome System, Maya Bader 2010 Rockefeller University

Mechanisms Of Controlled Proteolysis During Drosophila Spermatogenesis: Coordinate Action Of Apoptotic Caspases And The Ubiquitin-Proteasome System, Maya Bader

Student Theses and Dissertations

The regulation of apoptosis, or programmed cell death has been the subject of a vast body of research because of its implication in normal development, tissue homeostasis and a wide range of diseases. The major point of focus for understanding apoptosis regulation is the activation of its primary executioner: the caspase. This family of proteolytic enzymes has been shown to be tightly controlled, as many different proteins govern their transcription, stability, activation, and activity. Consequently, caspase regulation is extremely complex, and is further complicated by a discrepancy between different cell types and paradigms. Caspases have also been shown to have ...


Regulation Of Surface Proteins Assembly On The Wall Of Gram-Positive Bacteria, Assaf Raz 2010 Rockefeller University

Regulation Of Surface Proteins Assembly On The Wall Of Gram-Positive Bacteria, Assaf Raz

Student Theses and Dissertations

Cell wall peptidoglycan-anchored surface proteins are essential virulence factors in many Gram-positive bacteria. Attachment of these proteins to the peptidoglycan is achieved through a transpeptidation reaction, whereby sortase cleaves a conserved Cterminal LPXTG motif and attaches the protein to the peptidoglycan precursor lipid II. This thesis deals with the spatial regulation of the sorting reaction, and the role sortase localization plays in the correct distribution of surface proteins. We have introduced a new immunofluorescence procedure to study the distribution of sub-surface antigens in Streptococcus pyogenes, which utilizes the phage lysin PlyC to permeabilize the cell wall of to antibodies. We ...


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