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Application Of Cyclic Voltammetry To Investigate Enhanced Catalytic Current Generation By Biofilm-Modified Anodes Of Geobacter Sulfurreducens Strain Dl1 Vs. Variant Strain Kn400, Sarah M. Strycharz, Anthony P. Malanoski, Rachel M. Snider, Hana Yi, Derek Lovley, Leonard M. Tender

Derek Lovley

A biofilm of Geobacter sulfurreducens will grow on an anode surface and catalyze the generation of an electrical current by oxidizing acetate and utilizing the anode as its metabolic terminal electron acceptor. Here we report qualitative analysis of cyclic voltammetry of anodes modified with biofilms of G. sulfurreducens strains DL1 and KN400 to predict possible rate-limiting steps in current generation. Strain KN400 generates approximately 2 to 8-fold greater current than strain DL1 depending upon the electrode material, enabling comparative electrochemical analysis to study the mechanism of current generation. This analysis is based on our recently reported electrochemical model for biofilm-catalyzed …

Fairmount Greenway - A Community Initative, Leah H. Bamberger, Liliana Carvajal, Mary F. Dehais, Yuanfang Gong, John E. Hulsey, Eric C. Kells, Kimberley Klosterman, Pamela Jo Landi, Adam G. Monroy, Seth A. Morrow, Bryan O'Bara, Jie Su, Arianna Thompson, Owen M. White

Landscape Architecture & Regional Planning Studio and Student Research and Creative Activity

This studio was based on the Fairmount Greenway that was developed through a series of public meetings with the neighborhood community and with consultants from the firm Crosby, Schlessinger and Smallridge (CSS). The Fairmount Greenway, while drawing its identity from the traditional greenway model is in fact a reinterpretation of an urban greenway. The greenway path follows along both primary and secondary city streets because of the lack of space along the rail right-of-way. The Fairmount Greenway begins at what will be a new station stop at New Market South Bay near Upham’s Corner in northern Dorchester. The greenway follows …

Ecological Boundary Detection Using Bayesian Areal Wombling, Joseph Elkinton, M. C. Fitzpatrick, E. L. Preisser, A. H. Porter, L. A. Wallwe, B. P. Carlin, A. M. Ellison

Joseph Elkinton

The study of ecological boundaries and their dynamics is of fundamental importance to much of ecology, biogeography, and evolution. Over the past two decades, boundary analysis (of which wombling is a subfield) has received considerable research attention, resulting in multiple approaches for the quantification of ecological boundaries. Nonetheless, few methods have been developed that can simultaneously (1) analyze spatially homogenized data sets (i.e., areal data in the form of polygons rather than point-reference data); (2) account for spatial structure in these data and uncertainty associated with them; and (3) objectively assign probabilities to boundaries once detected. Here we describe the …

Bioinformatic Analysis Of Gene Regulation In The Metal-Reducing Bacteria Family, Derek Lovley, Julia Krushkal, Ronald M. Adkins, Yanhua Qu, Jeanette Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D. Young, Toshiyuki Ueki, Katy Juarez

Derek Lovley

Knowledge of how structural genome differences among microorganisms lead to variation in gene regulation is fundamentally important for our understanding of the functioning of gene regulatory pathways and their individual components. This knowledge is also necessary for our better understanding of the genomic changes leading to adaptation to diverse and changing environments. Our research focuses on Geobacteraceae, a metal-reducing family of delta-Proteobacteria, which are capable of harvesting electricity from organic matter and environmental bioremediation of organic and metal pollutants. We are investigating molecular mechanisms which allow these species to adapt and regulate their responses to environmental stimuli, which result in …

Feronia Receptor-Like Kinase Regulates Rho Gtpase Signaling Of Root Hair Development, Q. Duan, D. Kita, C. Li, Alice Cheung, H. M. Wu

Alice Cheung

Plant RHO GTPases (RAC/ROPs) mediate multiple extracellular signals ranging from hormone to stress and regulate diverse cellular processes important for polarized cell growth, differentiation, development, reproduction, and responses to the environment. They shuttle between the GDP-bound inactive state and the GTP-bound activated state and their activation is predominantly mediated by a family of guanine nucleotide exchange factors (GEFs) referred to as ROPGEFs. Using the Arabidopsis ROPGEF1 as bait, we identified members of a receptor-like kinase (RLK) family as potential upstream regulators for RAC/ROP signaling. NADPH oxidase-derived reactive oxygen species (ROS) are emerging as important regulators for growth and development and …

Essential Genes For Astroglial Development And Axon Pathfinding During Zebrafish Embryogenesis, Michael J.F. Barresi, Sean Burton, Kristina Dipietrantonio, Adam Amsterdam, Nancy Hopkins, Rolf O. Karlstrom

Rolf O Karlstrom

The formation of the central nervous system depends on the coordinated development of neural and glial cell types that arise from a common precursor. Using an existing group of zebrafish mutants generated by viral insertion, we performed a “shelf-screen” to identify genes necessary for astroglial development and axon scaffold formation. We screened 274 of 315 viral insertion lines using antibodies that label axons (anti-Acetylated Tubulin) and astroglia (anti-Gfap) and identified 25 mutants with defects in gliogenesis, glial patterning, neurogenesis, and axon guidance. We also identified a novel class of mutants affecting radial glial cell numbers. Defects in astroglial patterning were …

The Land Institute, Madeleine K. Charney

Madeleine K. Charney

An overview of the mission and current projects of The Land Institute in Salinas, Kansas. This organization strives to develop an agricultural system with the ecological stability of the prairie and a grain yield comparable to that from annual crops.

An Interdomain Sector Mediating Allostery In Hsp70 Molecular Chaperones, Robert G. Smock, Olivier Rivoire, William P. Russ, Joanna F. Swain, Stanislas Leibler, Rama Ranganathan, Lila Gierasch

Lila Gierasch

Allosteric coupling between protein domains is fundamental to many cellular processes. For example, Hsp70 molecular chaperones use ATP binding by their actin-like N-terminal ATPase domain to control substrate interactions in their C-terminal substrate-binding domain, a reaction that is critical for protein folding in cells. Here, we generalize the statistical coupling analysis to simultaneously evaluate co-evolution between protein residues and functional divergence between sequences in protein sub-families. Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co-evolving residues called a ‘sector’, which is an attribute of the allosteric Hsp70 sub-family that links the …

Smoking During Pregnancy And Risk Of Abnormal Glucose Tolerance: A Prospective Cohort Study, Amy E. Haskins, Elizabeth R. Bertone-Johnson, Penelope Pekow, Elena T. Carbone, Renée T. Fortner, Lisa Chasan-Taber

Elena T Carbone

Background: Disturbances in glucose metabolism during pregnancy are associated with negative sequalae for both mother and infant. The association between smoking and abnormal glucose tolerance (AGT) remains controversial. Therefore, the aim of this study was to examine the relationship between smoking prior to and during pregnancy and risk of AGT. Methods: We utilized data from a prospective cohort of 1,006 Hispanic (predominantly Puerto Rican) prenatal care patients in Western Massachusetts. Women reported pre- and early pregnancy smoking at recruitment (mean = 15 weeks) and mid pregnancy smoking at a second interview (mean = 28 weeks). AGT was defined as > 135 …

Role Of Hsp70 Atpase Domain Intrinsic Dynamics And Sequence Evolution In Enabling Its Functional Interactions With Nefs, Ying Liu, Lila Gierasch, Ivet Bahar

Lila Gierasch

12 Hide Figures Abstract Author Summary Introduction Materials and Methods Results Discussion Supporting Information Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract Catalysis of ADP-ATP exchange by nucleotide exchange factors (NEFs) is central to the activity of Hsp70 molecular chaperones. Yet, the mechanism of interaction of this family of chaperones with NEFs is not well understood in the context of the sequence evolution and structural dynamics of Hsp70 ATPase domains. We studied the interactions of Hsp70 ATPase domains with four different NEFs on the basis of the evolutionary trace and co-evolution of the ATPase domain sequence, combined with elastic …

Muscle Weakness In Persons With Multiple Sclerosis, Linda Haiwon Chung

Open Access Dissertations

Skeletal muscle weakness is a problem for people living with Multiple Sclerosis (MS). Alterations in the central nervous system may be the primary source of muscle weakness because of the pathophysiology of MS. However, changes in peripheral mediators of force production may also contribute to muscle weakness in persons with MS. The main objective of the dissertation was to systematically identify key neural (motor unit discharge rates, spasticity) and muscular (muscle size, contractile function) mechanisms of force production that may explain lower isometric strength and dynamic power in persons with MS compared with age-matched controls. The knee extensor muscles of …

Reproduction In The Wild: The Effect Of Individual Life History Strategies On Population Dynamics And Persistence, Jason Asa Coombs

Open Access Dissertations

For a sexually reproducing species, the two major decisions facing all individuals are when and with whom to reproduce. When scaled to the population level, the outcome from all individual decisions determines reproductive variance, and age-class contribution to population growth rate. Both of these attributes determine a population‟s effective size (Ne), which is directly correlated with its fitness, persistence probability, and adaptability. The questions of when and with whom to reproduce, and their subsequent effects on Ne and age-at-maturity were assessed for wild brook trout (Salvelinus fontinalis) populations. Mating pairs were significantly size-assortative, with individual length accounting for 37% of …

Examining The Development Of Handedness In Rhesus Monkey And Human Infants Using Behavioral And Kinematic Measures, Eliza Lynn Nelson

Open Access Dissertations

Handedness is a widely studied behavioral asymmetry that is commonly measured as a preference for using one hand over the other. Right hand preference in humans occurs at a ratio of 9:1, whereas left hand preference in rhesus monkeys has been estimated at 2:1. Despite differences in the direction and degree of hand preference, this dissertation investigated whether primates share common underlying factors for the development of handedness. Previous work in human infants has identified a predictive relationship between rightward supine head orientation and later right hand preference. Experiment 1 examined the relationship between neonatal head orientation and later hand …

Growth Of Atlantic Salmon (Salmo Salar) In Freshwater, Douglas Bradlee Sigourney

Open Access Dissertations

Growth plays a key role in regulating ecological and population dynamics. Life history characteristics such as age at maturity, fecundity and age and size at migration are tightly linked to growth rate. In addition, size can often determine survival and individual breeding success. To fully understand the process of growth it is important to understand the mechanisms that drive growth rates. In Atlantic salmon, growth is critical in determining life history pathways. Models to estimate growth could be useful in the broader context of predicting population dynamics. In this dissertation I investigate the growth process in juvenile Atlantic salmon (Salmo …

Role Of Sulfate-Reducing Bacteria In The Attenuation Of Acid Mine Drainage Through Sulfate And Iron Reduction, Caryl Ann Becerra

Open Access Dissertations

Acid mine drainage (AMD) is an acidic, iron-rich leachate that causes the dissolution of metals. It constitutes a worldwide problem of environmental contamination detrimental to aquatic life and water quality. AMD, however, is naturally attenuated at Davis Mine in Rowe, Massachusetts. We hypothesize that sulfate-reducing bacteria (SRB) are attenuating AMD. To elucidate the mechanisms by which SRB attenuate AMD, three research projects were conducted using a suite of molecular and geochemical techniques. First we established biological influence on the attenuation of AMD by comparing the microbial community and geochemical trends of microcosms of two contrasting areas within the site: AMD …

Conservation While Under Invasion: Insights From A Rare Hemiparasitic Plant, Swamp Lousewort (Pedicularis Lanceolata Michx.), Sydne Record

Open Access Dissertations

with non-native invasive species is considered a major threat to many rare native species. As such, invasives removals are a common management strategy. Rare native species that interact uniquely with other organisms in their community (e.g., hemiparasitic plants) may be adversely affected by removing invasives. A management plan for a regionally rare hemiparasitic plant in Massachusetts, Pedicularis lanceolata Michx., identified invasives as a threat, but more quantitative evidence is needed to determine how P. lanceolata‟s persistence is influenced by its co-occurrence with native or invasive hosts. This research asks how P. lanceolata is affected by growth with native versus invasive …

Novel Regulatory Cascades Controlling Expression Of Nitrogen Fixation Genes, Toshiyuki Ueki, Derek Lovley

Derek Lovley

Geobacter species often play an important role in bioremediation of environments contaminated with metals or organics and show promise for harvesting electricity from waste organic matter in microbial fuel cells. The ability of Geobacter species to fix atmospheric nitrogen is an important metabolic feature for these applications. We identified novel regulatory cascades controlling nitrogen-fixation gene expression in Geobacter sulfurreducens. Unlike the regulatory mechanisms known in other nitrogen-fixing microorganisms, nitrogen-fixation gene regulation in G. sulfurreducens is controlled by two two-component His-Asp phosphorelay systems. One of these systems appears to be the master regulatory system that activates transcription of the majority of …

Species-Specific Differences In The Activity And Nuclear Localizatoin Of Murine And Bovine Phospholipase C Zeta 1, Rafael Fissore, M.A. Cooney, C. Malcuit, B. Cheon, M.K. Holland, N.T. D'Cruz

Rafael Fissore

Injection of mammalian sperm extracts or cRNA of the sperm-specific phospholipase C zeta 1 (PLCZ1) has been shown to trigger repetitive oscillations in the concentration of free calcium ([Ca(2+)](i)), leading to oocyte activation and embryo development in all mammals studied to date. While PLCZ1 has cross-species activity, it has also been observed that species-specific differences may exist in the frequency and pattern of the resulting [Ca(2+)](i) oscillations following PLCZ1 cRNA injection into oocytes of different species. Accordingly, we used a crossover design strategy to directly investigate the activity of murine and bovine PLCZ1 in both murine and bovine oocytes. In …

Electrodic Voltages Accompanying Stimulated Bioremediation Of A Uranium-Contaminated Aquifer, Kenneth H. Williams, A. Lucie N'Guessan, Jennifer Druhan, Philip E. Long, Susan S. Hubbard, Derek Lovley, Jillian F. Banfield

Derek Lovley

The inability to track the products of subsurface microbial activity during stimulated bioremediation has limited its implementation. We used spatiotemporal changes in electrodic potentials (EP) to track the onset and persistence of stimulated sulfate-reducing bacteria in a uranium-contaminated aquifer undergoing acetate amendment. Following acetate injection, anomalous voltages approaching −900 mV were measured between copper electrodes within the aquifer sediments and a single reference electrode at the ground surface. Onset of EP anomalies correlated in time with both the accumulation of dissolved sulfide and the removal of uranium from groundwater. The anomalies persisted for 45 days after halting acetate injection. Current-voltage …

Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie Thurber, Brian Gross, Kenneth Olsen, Yulin Jia, Ana Caicedo

Biology Department Faculty Publication Series

Background: Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results: We find greater population structure than has been previously reported for …

Evolution Of The Cd163 Family And Its Relationship To The Bovine Gamma Delta T Cell Co-Receptor Wc1, Carolyn T. A. Herzig, Ray W. Walters, Cynthia L. Baldwin, Janice T. Telfer

Janice C. Telfer

Background

The scavenger receptor cysteine rich (SRCR) domain is an ancient and conserved protein domain. CD163 and WC1 molecules are classed together as group B SRCR superfamily members, along with Spα, CD5 and CD6, all of which are expressed by immune system cells. There are three known types of CD163 molecules in mammals, CD163A (M130, coded for by CD163), CD163b (M160, coded for by CD163L1) and CD163c-α (CD163L1 or SCART), while their nearest relative, WC1, is encoded by a multigene family so far identified in the artiodactyl species of cattle, sheep, and pigs. Results

We annotated the bovine genome and …

Evolution Of The Cd163 Family And Its Relationship To The Bovine Gamma Delta T Cell Co-Receptor Wc1, Carolyn Ta Herzig, Ray W. Waters, Cynthia Baldwin, Janice C. Telfer

Cynthia Baldwin

Background: The scavenger receptor cysteine rich (SRCR) domain is an ancient and conserved protein domain. CD163 and WC1 molecules are classed together as group B SRCR superfamily members, along with Spα, CD5 and CD6, all of which are expressed by immune system cells. There are three known types of CD163 molecules in mammals, CD163A (M130, coded for by CD163), CD163b (M160, coded for by CD163L1) and CD163c-α (CD163L1 or SCART), while their nearest relative, WC1, is encoded by a multigene family so far identified in the artiodactyl species of cattle, sheep, and pigs. Results: We annotated the bovine genome and …

Genomic Patterns Of Nucleotide Diversity In Divergent Populations Of U.S. Weedy Rice, Michael Reagon, Carrie S. Thurber, Brian L. Gross, Kenneth M. Olsen, Yulin Jia, Ana Lucia Caicedo

Ana Lucia Caicedo

Background: Weedy rice (red rice), a conspecific weed of cultivated rice (Oryza sativa L.), is a significant problem throughout the world and an emerging threat in regions where it was previously absent. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We use genome-wide patterns of single nucleotide polymorphism (SNP) variation in a broad geographic sample of weedy, domesticated, and wild Oryza samples to infer the origin and demographic processes influencing U.S. weedy rice evolution. Results: We find greater population structure than has been previously reported for …

Mammary Epithelial Transplant Procedure, Karen A. Dunphy, Luwei Tao, D. Joseph Jerry

D. Joseph Jerry

This article describes and compares the fat pad clearance procedure developed by DeOme KB et al.1 and the sparing procedure developed by Brill B et al.2, followed by the mammary epithelial transplant procedure. The mammary transplant procedure is widely used by mammary biologists because it takes advantage of the fact that significant development of the mammary epithelium doesn't occur until after puberty. At 3 weeks of age, growth of the mammary epithelial tree is confined to the vicinity of the nipple and the fat pad is largely devoid of mammary epithelium, but by 7 weeks of age the epithelial ductal …

Molecular Basis For Distinct Pathways For Protein Import Into Arabidopsis Chloroplasts, Danny Schnell, C. Rounds, H. Inoue

Danny Schnell

The translocons at the outer envelope membrane of chloroplasts (TOCs) initiate the import of thousands of nucleus-encoded proteins into the organelle. The identification of structurally and functionally distinct TOC complexes has led to the hypothesis that the translocons constitute different import pathways that are required to coordinate the import of sets of proteins whose expression varies in response to organelle biogenesis and physiological adaptation. To test this hypothesis, we examined the molecular basis for distinct TOC pathways by analyzing the functional diversification among the Toc159 family of TOC receptors. We demonstrate that the N-terminal A-domains of the Toc159 receptors regulate …

Gravitropism Of Arabidopsis Thaliana Roots Requires The Polarization Of Pin2 Toward The Root Tip In Meristematic Cortical Cells, Abidur Rahman, Maho Takahashi, Kyohei Shibasaki, Shuang Wu, Takehito Inaba, Seiji Tsurumi, Tobias Baskin

Tobias Baskin

In the root, the transport of auxin from the tip to the elongation zone, referred to here as shootward, governs gravitropic bending. Shootward polar auxin transport, and hence gravitropism, depends on the polar deployment of the PIN-FORMED auxin efflux carrier PIN2. In Arabidopsis thaliana, PIN2 has the expected shootward localization in epidermis and lateral root cap; however, this carrier is localized toward the root tip (rootward) in cortical cells of the meristem, a deployment whose function is enigmatic. We use pharmacological and genetic tools to cause a shootward relocation of PIN2 in meristematic cortical cells without detectably altering PIN2 polarization …

Notch 1 Mediated Inhibition Of Nur77-Induced Apoptosis: Implications For T-Cell Leukemia, Jonathan George Rud

Open Access Dissertations

It is widely accepted that activating mutations of genes encoding the Notch family of transmembrane receptors, specifically Notch1, are associated with oncogenic transformation. Previous data from our lab has shown that an active form of Notch1 (NICD) provides protection against apoptosis in D011.10 T cells; and that this effect may be attributed to NICD binding the pro-apoptotic protein Nur77. Nur77 is an immediate early gene that is upregulated during both negative selection of thymocytes and activation-induced apoptosis in D011.10 T cells. Nur77 upregulation is tightly regulated and requires MEF2D, NFAT, and the transcriptional co-activator, p300, to effectively respond to apoptotic …

Identifying Critical Fish Habitat And Long-Term Trends In Fish Abundances In The Hudson River Estuary, Megan Patricia O'Connor

Open Access Dissertations

The Hudson River estuary (HRE) is a well monitored aquatic resource and much secondary data exist for this system. We developed two objectives based on accessible HRE aquatic data. The first objective was to determine if changes in HRE fish community over the time period (1974 to 2005) years are correlated to local and regional climate. We addressed this objective by employing a multivariate statistical approach. We confirmed that the HRE fish community structure has changed over the time period (1974 to 2005). These changes are correlated with local hydrology (freshwater flow and water temperature) and regional climate (Atlantic Multidecadal …

Fire Regime Dynamics Following The Mid-Holocene Hemlock Decline In Eastern North America, Kennedy Helm Clark

Open Access Dissertations

Approximately 5,000 years ago, eastern hemlock (Tsuga canadensis) experienced a sudden, rapid, range-wide decline most probably due to pest, disease, or climate change. An aphid-like defoliating insect, the hemlock woolly adelgid (Adelges tsugae), recently (1950’s) introduced to eastern North America has been spreading across the eastern United States. The adelgid attacks all size and age classes of hemlocks causing up to 95% mortality in affected stands. The potential for another range-wide hemlock decline has raised a number of concerns including the increased threat of wildfire. Altered fuel loadings in modern adelgid-affected stands and the effects of presumably similar changes in …

From Mouse Mammary Tumor Model To New Therapeutic Method ---Mammary Tumor Development In Balb/C-Trp53+/- Mice And Magnetic Nanoparticle Induced Heating For Cancer Treatment, Haoheng Yan

Open Access Dissertations

Mutation and loss of p53 function are common features among human breast cancers. We use BALB/c-Trp53+/- mice as a model to examine the sequence of events leading to mammary tumors. Mammary epithelium proliferation rates were similar in both BALB/c-Trp53+/- mice and wild type controls. Among the 28 mammary tumors collected from BALB/c-Trp53+/- mice, loss of heterozygosity for Trp53 was detected in more than 90% of invasive mammary tumors. Transplantation of Trp53+/- ductal hyperplasias indicated an association between loss of the wild type allele of Trp53 and progression to invasive carcinomas. Expression of biomarkers such as ERα, PR, Her2/Neu and activated …