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Ph-Dependent Substrate Preference Of Pig Heart Lipoamide Dehydrogenase Varies With Oligomeric State: Response To Mitochondrial Matrix Acidification, Natalia L. Klyachko, Valentina A. Shchedrina, Alexander V. Efimov, Sergey V. Kazakov, Irina G. Gazaryan, Bruce S. Kristal, Abraham M. Brown

Department of Biochemistry: Faculty Publications

Cycling of intracellular pH has recently been shown to play a critical role in ischemia-reperfusion injury. Ischemia-reperfusion also leads to mitochondrial matrix acidification and dysfunction. However, the mechanism by which matrix acidification contributes to mitochondrial dysfunction, oxidative stress, and the resultant cellular injury has not been elucidated. We observe pH-dependent equilibria between monomeric, dimeric, and a previously undescribed tetrameric form of pig heart lipoamide dehydrogenase (LADH), a mitochondrial matrix enzyme. Dynamic light scattering studies of native LADH in aqueous solution indicate that lowering pH favors a shift in average molecular mass from higher oligomeric states to monomer. Sedimentation velocity of …

Regulation Of Enteric Endophytic Bacterial Colonization By Plant Defenses, A. Leonardo Iniguez, Yuemei Dong, Heather D. Carter, Brian M. M. Ahmer, Julie M. Stone, Eric W. Triplett

Department of Biochemistry: Faculty Publications

Bacterial endophytes reside within the interior of plants without causing disease or forming symbiotic structures. Some endophytes, such as Klebsiella pneumoniae 342 (Kp342), enhance plant growth and nutrition. Others, such as Salmonella enterica serovar Typhimurium (S. typhimurium), are human pathogens that contaminate raw produce. Several lines of evidence are presented here to support the hypothesis that plant defense response pathways regulate colonization by endophytic bacteria. An ethyleneinsensitive mutant of Medicago truncatula is hypercolonized by Kp342 compared to the parent genotype. Addition of ethylene, a signal molecule for induced systemic resistance in plants, decreased endophytic colonization in Medicago spp. …

Phylogenetic Engineering At An Interface Between Large And Small Subunits Imparts Land-Plant Kinetic Properties To Algal Rubisco, Robert J. Spreitzer, Srinivasa R. Peddi, Sriram Satagopan

Department of Biochemistry: Faculty Publications

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) catalyzes the rate-limiting step of photosynthetic CO₂ fixation and, thus, limits agricultural productivity. However, Rubisco enzymes from different species have different catalytic constants. If the structural basis for such differences were known, a rationale could be developed for genetically engineering an improved enzyme. Residues at the bottom of the large-subunit α/β-barrel active site of Rubisco from the green alga Chlamydomonas reinhardtii (methyl-Cys-256, Lys-258, and Ile-265) were previously changed through directed mutagenesis and chloroplast transformation to residues characteristic of land-plant Rubisco (Phe-256, Arg-258, and Val-265). The resultant enzyme has decreases in carboxylation efficiency and CO₂/O …

Roles For Nutrients In Epigenetic Events, Anna M. Oommen, Jacob B. Griffin, Gautam Sarath, Janos Zempleni

Gautam Sarath Publications

The field of epigenetics is the study of modifications of DNA and DNA-binding proteins that alter the structure of chromatin without altering the nucleotide sequence of DNA; some of these modifications may be associated with heritable changes in gene function. Nutrients play essential roles in the following epigenetic events. First, folate participates in the generation of S-adenosylmethionine, which acts as a methyl donor in the methylation of cytosines in DNA; methylation of cytosines is associated with gene silencing. Second, covalent attachment of biotin to histones (DNA-binding proteins) plays a role in gene silencing and in the cellular response to DNA …

Homologous And Heterologous Reconstitution Of Golgi To Chloroplast Transport And Protein Import Into The Complex Chloroplasts Of Euglena, Silvia Sláviková, Rostislav Vacula, Zhiwei Fang, Tomoko Ehara, Tetsuaki Osafune, Steven D. Schwartzbach

School of Biological Sciences: Faculty Publications

Euglena complex chloroplasts evolved through secondary endosymbiosis between a phagotrophic trypanosome host and eukaryotic algal endosymbiont. Cytoplasmically synthesized chloroplast proteins are transported in vesicles as integral membrane proteins from the ER to the Golgi apparatus to the Euglena chloroplast. Euglena chloroplast preprotein pre-sequences contain a functional N-terminal ER-targeting signal peptide and a domain having characteristics of a higher plant chloroplast targeting transit peptide, which contains a hydrophobic stop-transfer membrane anchor sequence that anchors the precursor in the vesicle membrane. Pulse-chase subcellular fractionation studies showed that ³⁵S-labeled precursor to the light harvesting chlorophyll a/b binding protein accumulated in the Golgi …

Indirect Interaction Between Two Native Thistles Mediated By An Invasive Exotic Floral Herbivore, F. Leland Russell, Svata M. Louda

School of Biological Sciences: Faculty Publications

Spatial and temporal variation in insect floral herbivory is common and often important. Yet, the determinants of such variation remain incompletely understood. Using 12 years of flowering data and 4 years of biweekly insect counts, we evaluated four hypotheses to explain variation in damage by the Eurasian flower head weevil, Rhinocyllus conicus, to the native North American wavyleaf thistle, Cirsium undulatum. The four factors hypothesized to influence weevil impact were variations in climate, weevil abundance, phenological synchrony, and number of flower heads available, either on wavyleaf thistle or on the other co-occurring, acquired native host plant (Platte thistle, Cirsium …

First Record Of Drosophila Parthenogenetica And D. Neomorpha, Cardini Group, Heed, 1962 (Drosophila, Drosophilidae), In Brazil, Daniela Cristina De Toni, Jennifer A. Brisson, Paulo R. P. Hofmann, Marlucia Martins, Hope Hollocher

School of Biological Sciences: Faculty Publications

The cardini group of the Quinaria section of the genus Drosophila is composed of 16 Neotropical species. The two focal species of this report, Drosophila parthenogenetica and D. neomorpha, are included in this group, and are placed in the cardini subgroup with seven other species: D. polymorpha, D. cardinoides, D. cardini, D. neocardini, D. acutilabella, D. bedicheki and D. procardinoides (Heed and Krishnamurthy, 1959; Heed, 1962; Heed and Russell, 1971; Wilder et al., 2003). The group is characterized by medium-sized flies with a shiny thorax (Vilela et al., 2002). Different species of the group display different abdominal pigmentation patterns …

Abdominal Pigmentation Variation In Drosophila Polymorpha: Geographic Variation In The Trait, And Underlying Phylogeography, Jennifer A. Brisson, Daniela Cristina De Toni, Ian Duncan, Alan R. Templeton

School of Biological Sciences: Faculty Publications

Drosophila polymorpha is a widespread species that exhibits abdominal pigmentation variation throughout its range. To gain insight into this variation we combined phenotypic and genotypic data to test a series of nested hypotheses. First, we tested the null hypothesis that geographic variation in pigmentation is due to neutral factors. We used nested clade analysis to examine the distribution of haplotypes from a nuclear and a mitochrondrial locus. Restricted gene flow via isolation by distance, the primary inference of this phylogeographic analysis, was then used to generate and test the hypothesis of increasing average abdominal pigmentation difference with increasing geographic distance. …

Evaluation Of Ecological Risk To Populations Of A Threatened Plant From An Invasive Biocontrol Insect, Svata M. Louda, Tatyana A. Rand, Amy E. Arnett, A. S. Mcclay, K. Shea, A. Kathryn Mceachern

School of Biological Sciences: Faculty Publications

Controversy exists over estimation of ecological risk in biological control. At present, the risk to the rare, federally listed Pitcher’s thistle (Cirsium pitcheri) in North America from Rhinocyllus conicus, a biological control weevil now feeding on many native thistles, is unknown. We hypothesized that quantification of host specificity and potential phenological overlap between insect and plant would improve assessment of the magnitude of risk. In laboratory host specificity tests, we found no significant difference in R. conicus feeding or oviposition preference between the rare C. pitcheri and the targeted exotic weed (Carduus nutans) or between …

Microsatellite Dna Analysis Shows That Greater Sage Grouse Leks Are Not Kin Groups, Robert M. Gibson, Debra Pires, Kathleen S. Delaney, Robert K. Wayne

School of Biological Sciences: Faculty Publications

The spectacular social courtship displays of lekking birds are thought to evolve via sexual selection, but this view does not easily explain the participation of many males that apparently fail to mate. One of several proposed solutions to this ‘lek skew paradox’ is that kin selection favors low-ranking males joining leks to increase the fitness of closely related breeders. We investigated the potential for kin selection to operate in leks of the greater sage grouse, Centrocercus urophasianus, by estimating relatedness between lekking males using microsatellite DNA markers. We also calibrated these estimates using data from known families. Mean relatedness within …

Web-Based Toolkits For Topology Prediction Of Transmembrane Helical Proteins, Fold Recognition, Structure And Binding Scoring, Folding-Kinetics Analysis And Comparative Analysis Of Domain Combinations, Hongyi Zhou, Chi Zhang, Song Liu, Yaoqi Zhou

School of Biological Sciences: Faculty Publications

We have developed the following web servers for protein structural modeling and analysis at http:// theory.med.buffalo.edu: THUMBUP, UMDHMM^TMHP and TUPS, predictors of trans-membrane helical protein topology based on a mean-burial-propensity scale of amino acid residues (THUMBUP), hidden Markov model (UMDHMM^TMHP) and their combinations (TUPS); SPARKS 2.0 and SP3, two profile– profile alignment methods, that match input query sequence(s) to structural templates by integrating sequence profile with knowledge-based structural score (SPARKS 2.0) and structure-derived profile (SP³); DFIRE, a knowledge-based potential for scoring free energy of monomers (DMONOMER), loop conformations (DLOOP), mutant stability (DMUTANT) and binding affinity …

Linking Seed Fate To Natural Dispersal Patterns: Factors Affecting Predation And Scatter-Hoarding Of Virola Calophylla Seeds In Peru, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Natural seed deposition patterns and their effects on post-dispersal seed fate are critical in tropical tree recruitment. Previous research showed that the key dispersal agent of the neotropical tree, Virola calophylla, is the spider monkey (Ateles paniscus). Spider monkeys generate a heterogeneous seed deposition pattern because they scatter-disperse seeds diurnally, whereas they clump-disperse seeds at their sleeping sites. The recruitment consequences of this pattern were investigated using manipulative experiments and observations. Scatter-hoarding by spiny rats (Proechimys spp.) caused little rearrangement of the initial seed deposition pattern because they moved seeds only short distances. Seed survival to …

Terrestrial Behavior Of Ateles Spp., Christina J. Campbell, Filippo Aureli, Colin A. Chapman, Gabriel Ramos-Fernández, Kim Matthews, Sabrina E. Russo, Scott Suarez, Laura Vick

School of Biological Sciences: Faculty Publications

Spider monkeys (Ateles spp.) are well known for their highly arboreal lifestyle, spending much of their time in the highest levels of the canopy and rarely venturing to the ground. To investigate terrestriality by Ateles and to illuminate the conditions under which spider monkeys venture to the ground, we analyzed ad libitum data from 5 study sites, covering 2 species and 5 subspecies. Three of the sites are in Central/North America: Barro Colorado Island (BCI), Panama (Ateles geoffroyi panamensis), Santa Rosa National Park, Costa Rica (A. g. frontatus), and Punta Laguna, Mexico (A. g. yucatanensis). The 2 remaining sites are …

Soil-Related Performance Variation And Distributions Of Tree Species In A Bornean Rain Forest, Sabrina E. Russo, Stuart J. Davies, David A. King, Sylvester Tan

School of Biological Sciences: Faculty Publications

1. Spatial distributions of tropical trees often correlate with environmental variation, suggesting that ecological sorting caused by niche differentiation may be important for maintaining species diversity.

2. Four soil types have been identified in a 52-ha forest dynamics plot in Bornean mixed dipterocarp forest (ranked by increasing fertility and moisture: sandy loam, loam, fine loam, and clay). The distributions of 73% of tree species in the plot are significantly aggregated on one of these soil types. We tested the hypothesis that variation in performance (growth and mortality) underlies these edaphically biased species distributions.

3. Annual growth and mortality rates over …

Methylation Patterns Of Histone H3 Lys 4, Lys 9 And Lys 27 In Transcriptionally Active And Inactive Arabidopsis Genes And In Atx1 Mutants, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

Covalent modifications of histone-tail amino acid residues communicate information via a specific ‘histone code’. Here, we report histone H3-tail lysine methylation profiles of several Arabidopsis genes in correlation with their transcriptional activity and the input of the epigenetic factor ARABIDOPSIS HOMOLOGOF TRITHORAX (ATX1) at ATX1-regulated loci. By chromatin immunoprecipitation (ChIP) assays, we compared modification patterns of a constitutively expressed housekeeping gene, of a tissue-specific gene, and among genes that differed in degrees of transcriptional activity. Our results suggest that the di-methylated isoform of histone H3-lysine4 (m²K4/H3) provide a general mark for gene-related sequences distinguishing them from non-transcribed …

Gene Set Coregulated By The Saccharomyces Cerevisiae Nonsense-Mediated Mrna Decay Pathway, Rachel Taylor, Bessie Wanja Kebaara, Tara Nazarenus, Ashley Jones, Rena Yamanaka, Rachel Uhrenholdt, Jason P. Wendler, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

The nonsense-mediated mRNA decay (NMD) pathway has historically been thought of as an RNA surveillance system that degrades mRNAs with premature translation termination codons, but the NMD pathway of Saccharomyces cerevisiae has a second role regulating the decay of some wild-type mRNAs. In S. cerevisiae, a significant number of wild-type mRNAs are affected when NMD is inactivated. These mRNAs are either wild-type NMD substrates or mRNAs whose abundance increases as an indirect consequence of NMD. A current challenge is to sort the mRNAs that accumulate when NMD is inactivated into direct and indirect targets. We have developed a …

Characterization Of Different Crystal Forms Of The Α-Glucosidase Mala From Sulfolobus Solfataricus, Heidi Asschenfeldt Ernst, Martin Willemoës, Leila Lo Leggio, Gordon Leonard, Paul H. Blum, Sine Larsen

School of Biological Sciences: Faculty Publications

MalA is an _-glucosidase from the hyperthermophilic archaeon Sulfolobus

solfataricus. It belongs to glycoside hydrolase family 31, which includes several

medically interesting α-glucosidases. MalA and its selenomethionine derivative

have been overproduced in Escherichia coli and crystallized in four different

crystal forms. Microseeding was essential for the formation of good-quality

crystals of forms 2 and 4. For three of the crystal forms (2, 3 and 4) full data sets

could be collected. The most suitable crystals for structure determination are the

monoclinic form 4 crystals, belonging to space group P21, from which data sets

extending to 2.5 Å resolution …

Insulin Signaling Is Necessary For Vitellogenesis In Drosophila Melanogaster Independent Of The Roles Of Juvenile Hormone And Ecdysteroids: Female Sterility Of The Chico1 Insulin Signaling Mutation Is Autonomous To The Ovary, David S. Richard, Robert Rybczynski, Thomas G. Wilson, Yue Wang, Marta L. Wayne, You Zhou, Linda Partridge, Lawrence G. Harshman

Lawrence G. Harshman Publications

It has been suggested that insulin signaling mutations of Drosophila melanogaster are sterile and long-lived because of juvenile hormone (JH) and ecdysteroid deficiency. However, female sterility of an insulin/IGF-like signaling mutant (chico¹) of D. melanogaster is not mediated by downstream systemic signaling in terms of major alterations in JH or ecdysteroid levels. chico¹ is a null mutation in the insulin substrate protein (CHICO) gene of D. melanogaster. Homozygous chico1 females are sterile and their oocytes do not mature beyond the last previtellogenic stage. Homozygous chico1 females exhibit approximately wild-type rates of JH biosynthesis, ovarian release …

Quantitative Trait Loci For Lipid Content In Drosophila Melanogaster, Mei-Hui Wang, Lawrence G. Harshman, Sergey V. Nuzhdin

Lawrence G. Harshman Publications

Recombinant inbred lines derived from a natural population were used to investigate natural genetic variation for lipid abundance, protein abundance, and weight of Drosophila melanogaster. Females were heavier and contained more lipid and soluble protein than males. Lipid and protein abundance were genetically correlated with female weight, but male weight was not correlated with lipid or protein. Lipid and protein abundance were genetically correlated in males but not in females. Quan-titative trait loci (QTLs) for weight and protein abundance were predominantly on the X chromo-some, whereas QTLs for lipid abundance were found on the second and third chromosomes. QTLs …

Complex Signal Function: Developing A Framework Of Testable Hypotheses, Eileen Hebets, Daniel R. Papaj

Eileen Hebets Publications

The basic building blocks of communication are signals, assembled in various sequences and combinations, and used in virtually all inter- and intra-specific interactions. While signal evolution has long been a focus of study, there has been a recent resurgence of interest and research in the complexity of animal displays. Much past research on signal evolution has focused on sensory specialists, or on single signals in isolation, but many animal displays involve complex signaling, or the combination of more than one signal or related component, often serially and overlapping, frequently across multiple sensory modalities. Here, we build a framework of functional …

Upf1p, A Highly Conserved Protein Required For Nonsense-Mediated Mrna Decay, Interacts With The Nuclear Pore Proteins Nup100p And Nup116p, Tara Nazarenus, Rebecca Cedarberg, Ryan Bell, Joseph Cheatle, Amanda Forch, Alexis Haifley, Ann Hou, Bessie Wanja Kebaara, Christina Shields, Kate Stoysich, Rachel Taylor, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

Saccharomyces cerevisiae Upf1p is a 971-amino-acid protein that is required for the nonsense-mediated mRNA decay (NMD) pathway, a pathway that degrades mRNAs with premature translational termination codons. We have identified a two-hybrid interaction between Upf1p and the nuclear pore (Nup) proteins, Nup100p and Nup116p. Both nucleoporins predominantly localize to the cytoplasmic side of the nuclear pore and participate in mRNA transport. The two-hybrid interaction between Upf1p and the nuclear pore proteins, Nup100p and Nup116p, is dependent on the presence of the C-terminal 158 amino acids of Upf1p. Nup100p and Nup116p can be coimmunoprecipitated from whole-cell extracts with Upf1p, confirming in …

Potential Roles Of Follicular Dendritic Cell–Associated Osteopontin In Lymphoid Follicle Pathology And Repair And In B Cell Regulation In Hiv-1 And Siv Infection, Qingsheng Li, Jeffrey D. Lifson, Lijie Duan, Timothy Schacker, Cavan Reilly, John V. Carlis, Jacob D. Estes, Ashley T. Haase

Qingsheng Li Publications

Osteopontin is a multifunctional protein with known roles in bone remodeling, wound healing, and normal and pathological immune responses. We showed in microarray studies that osteopontin gene expression is increased in human immunodeficiency virus type 1 (HIV-1)–infected lymphatic tissues after treatment, and we undertook mapping experiments to study osteopontin’s possible functions in this context. We discovered species-specific colocalization of osteopontin with the follicular dendritic cell (FDC) network in lymphatic tissues in HIV-1 and simian immunodeficiency virus infections, and we found that changes in FDC-associated osteopontin covary with changes in lymphoid follicles during acute and late stages of infection and in …

Modeling Sediment Trapping In A Vegetative Filter Accounting For Converging Overland Flow, M. J. Helmers, D. E. Eisenhauer, Thomas G. Franti, Michael G. Dosskey

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Vegetative filters (VF) are used to remove sediment and other pollutants from overland flow. When modeling the hydrology of VF, it is often assumed that overland flow is planar, but our research indicates that it can be two-dimensional with converging and diverging pathways. Our hypothesis is that flow convergence will negatively influence the sediment trapping capability of VF. The objectives were to develop a two-dimensional modeling approach for estimating sediment trapping in VF and to investigate the impact of converging overland flow on sediment trapping by VF. In this study, the performance of a VF that has field-scale flow path …

Ll.M, In Taxation 2005 Course Listing Announcement, New York Law School

NYLS Bulletins and Catalogs

No abstract provided.

Evaluation Of Ecological Risk To Populations Of A Threatened Plant From An Invasive Biocontrol Insect, Svata M. Louda, Tatyana A. Rand, A. E. Arnett, A. S. Mcclay, K. Shea, K. Mceachern

Svata M. Louda Publications

Controversy exists over estimation of ecological risk in biological control. At present, the risk to the rare, federally listed Pitcher’s thistle (Cirsium pitcheri) in North America from Rhinocyllus conicus, a biological control weevil now feeding on many native thistles, is unknown. We hypothesized that quantification of host specificity and potential phenological overlap between insect and plant would improve assessment of the magnitude of risk. In laboratory host specificity tests, we found no significant difference in R. conicus feeding or oviposition preference between the rare C. pitcheri and the targeted exotic weed (Carduus nutans) or between …

Using Molt Limits To Age Western Bluebirds, Daizaburo Shizuka, Janis L. Dickinson

Papers in Ornithology

Using data on the extent of prebasic molt in known-aged adult and first-winter Western Bluebirds (Sialia mexicana), we assessed the accuracy of the molt limit as a tool for ageing birds. Sixty-nine known-aged birds were examined over the winter 2002–2003 in upper Carmel Valley, California. We also examined 29 breeding males in spring 2004 to assess the accuracy of this method for ageing birds during the breeding season. All birds were aged correctly using molt limit as the defining characteristic. We found that all first-winter birds had replaced 2–8 greater secondary coverts, while adults had replaced all wing …

Imposed Constraints On The Smith-Waterman Alignment Algorithm For Enhanced Modeling Of A Single-Molecule Dna Sequencer, Patrick G. Humphrey, Gregory R. Bashford

Biomedical Imaging and Biosignal Analysis Laboratory

An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection …

Bibliography Of Studies In Electron Transmission Spectroscopy, Paul Burrow

Paul Burrow Publications

A variety of techniques can be used to locate temporary negative ion states in atoms and molecules. One of the most efficient methods passes an electron beam through a gas cell and observes structure appearing in the attenuated “transmitted” electron current as a function of the electron energy. In 1971 L. Sanche and G.J. Schulz introduced a scheme whereby the derivative with respect to energy of the transmitted current was measured. Combining this with the trochoidal electron monochromator devised by A. Stamatovic and G.J. Schulz in 1968 produced a compact, sensitive and easily used apparatus for the detection of short-lived …

Dynamics Of Filament Formation In A Kerr Medium (With Erratum), Martin Centurion, Ye Pu, Mankei Tsang, Demetri Psaltis

Martin Centurion Publications

We have studied the large-scale beam breakup and filamentation of femtosecond pulses in a Kerr medium. We have experimentally monitored the formation of stable light filaments, conical emission, and interactions between filaments. Three major stages lead to the formation of stable light filaments: First the beam breaks up into a pattern of connected lines (constellation), then filaments form on the constellations, and finally the filaments release a fraction of their energy through conical emission. We observed a phase transition to a faster filamentation rate at the onset of conical emission. We attribute this to the interaction of conical emissions with …

Switching In One Monolayer Of The Ferroelectric Polymer, Vladimir Fridkin, A. Ievlev, K. Verkhovskaya, G. Vizdrik, S. Yudin, Stephen Ducharme

Stephen Ducharme Publications

The switching in one monolayer of ferroelectric vinylidene fluoride-trifluoroethylene copolymer P[VDF-TrFE] is observed. The kinetics of switching is well described by Landau- Khalatnikov (LK) equation.

The paper is devoted to the 75th anniversary of Prof. Lemanov’s birthday.