Digital Commons Network^™

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.

Investigation Of Ferroelectricity In Newly Synthesized Nitrile Polymer Systems, Matt Poulsen, Stephen Ducharme, Alexander V. Sorokin, Sahadeva Reddy, James M. Takacs, Y. Wen, Jihee Kim, Shireen Adenwalla

Stephen Ducharme Publications

The ferroelectric and piezoelectric properties of newly synthesized polymer systems have been studied. To date PVDF and its copolymers P(VDF-TrFE) have provided the bulk of the knowledge pertaining to ferroelectricity in polymers. Recently, ultrathin ferroelectric films of P(VDF-TrFE) 70:30 have been fabricated using the Langmuir-Blodgett technique [4]. In this study, various new polymers have been synthesized by chemically altering the PVDF structure. This alteration was performed in order to enhance the amphiphilic nature of the polymer and thus improve the LB film quality and control. Various chemical groups have been used to replace the electropositive hydrogen and electronegative fluorine found …

Faunal Survey Of Streblid Flies (Diptera: Streblidae) Associated With Bats In Paraguay, Carl W. Dick, Donald Gettinger

Harold W. Manter Laboratory of Parasitology: Faculty Publications

An extensive survey of the ectoparasites infesting bats in Paraguay provides information regarding the taxonomy and host distribution of streblid bat flies at a geographic interface between subtropical and temperate habitats. Five families of bats representing 45 species, including Molossidae (5 genera and 15 species), Natalidae (1 genus and 1 species), Phyllostomidae (11 genera and 15 species), Noctilionidae (1 genus and 2 species), and Vespertilionidae (4 genera and 12 species) were collected from 24 localities across Paraguay and sampled for ectoparasites. In total, 2,467 bat flies were collected, representing 11 genera and 31 nominal species of Streblidae, of which 6 …

Hesperoctenes Fumarius (Hemiptera: Polyctenidae) Infesting Molossus Rufus (Chiroptera: Molossidae) In Southeastern Brazil, Carlos E. L. Esbérard, Andrea C. Jesus, Adarene G. Motta, Helena G. Bergallo, Donald Gettinger

Harold W. Manter Laboratory of Parasitology: Faculty Publications

We analyzed the prevalence. intensity. and medium density of parasitism of Hesperoctenes fumarius infesting Molossus rufus in natural (hollow trees) and anthropogenic roosts (attics) in southeastern Brazil. The prevalence and intensity of infestations were higher in the hollow trees than in the attic roosts. We also noted a relationship between the amount of space available within the roost and the infestation levels of H. fumarius. One advantage of roosting in larger. often manmade. refuges may be the reduction in ectoparasite infestations.

Laelapine Mites (Acari: Laelapidae) Associated With Small Mammals From Amazonas, Brazil, Including A New Species From Marsupials, Donald Gettinger, Fernanda Martins-Hetano, Marcela Lareschi, Jay R. Malcolm

Harold W. Manter Laboratory of Parasitology: Faculty Publications

An intensive survey of ectoparasitic arthropods associated with small mammals in upland forests near Manaus, Brazil, provides information on the taxonomy and host distribution of laelapine mites in the Amazonian Region. We identified 5 genera and 21 species of these mites by comparisonw ith representativem useum specimens, the taxonomic literature, and, when possible, the original type specimens. These mites are host specific, with associations ranging from strict monoxeny (18 species) to oligoxeny (1 species) and pleioxeny (2 species). Marsupials were infested with species of Androlaelaps, echimyid rodents with Tur, and sigmodontine rodents with Gigantolaelaps, Laelaps, and Mysolaelaps. Androlaelaps bergalloi …

A New Species Of Skrjabingylus Petrov, 1927 (Nematoda: Metastrongyloidea) From The Frontal Sinuses Of The Hooded Skunk, Mephitis Macroura (Mustelidae), Ramon A. Carreno, Kathryn E. Reif, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Skrjabingylus santaceciliae n. sp. is described based on specimens from the frontal sinuses of a hooded skunk, Mephitis macroura, collected from the Area de Conservación Guanacaste, Costa Rica. Skrjabingylus santaceciliae n. sp. differs from the other 5 species in the genus in having pointed spicule tips that lack a rounded or lobed formation and by lacking a prominent distal projection at the tail tip. Morphometric comparisons show that S. santaceciliae n. sp. is much smaller than the only other valid species from Mephitis, Skrjabingylus chitwoodorum Hill, 1939. Likewise, morphometric comparisons also distinguish S. santaceciliae n. sp. from other described Skrjabingylus …

Phylogenetic Relationships Of Palaeacanthocephala (Acanthocephala) Inferred From Ssu And Lsu Rdna Gene Sequences, Martín García-Varela, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The Palaeacanthocephala is traditionally represented by 2 orders, Echinorhynchida and Polymorphida, with 10 and 3 families, respectively. To test the monophyly of the class, these 2 orders, and certain families, phylogenies were inferred using nuclear small-subunit (SSU) and large-subunit (LSU) ribosomal DNA sequences obtained for 29 species representing 10 families, 2 other classes of acanthocephalans, and 3 rotifer outgroups. Phylogenetic relationships were inferred by analyzing combined SSU and LSU sequences using maximum parsimony (MP) and maximum likelihood (ML) methods. Parsimony and ML trees inferred from combined analysis of these rDNA data strongly supported monophyly of Palaeacanthocephala and provided good resolution …

Are Dispositions Causally Relevant?, Jennifer Mckitrick

Department of Philosophy: Faculty Publications

To determine whether dispositions are causally relevant, we have to get clear about what causal relevance is. Several characteristics of causal relevance have been suggested, including Explanatory Power, Counterfactual Dependence, Lawfulness, Exclusion, Independence, and Minimal Sufficiency. Different accounts will yield different answers about the causal relevance of dispositions. However, accounts of causal relevance that are the most plausible, for independent reasons, render the verdict that dispositions are causally relevant.

Coevolution And Biogeography Among Nematodirinae (Nematoda: Trichostrongylina) Lagomorpha And Artiodactyla (Mammalia): Exploring Determinants Of History And Structure For The Northern Fauna Across The Holarctic, Eric P. Hoberg

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Nematodes of the subfamily Nematodirinae are characteristic components of a Holarctic fauna. the topology of a generic-level phylogenetic hypothesis, patterns of diversity, and geographic distributions for respective nematode taxa in conjunction with data for host occurrence are consistent with primary distributions determined across Beringia for species of Murielus, Rauschia, Nematodirus, and Nematodirella. Ancestral ghosts are represented by Lagomorpha, with evidence for a minimum of 1 host-switching-event and subsequent radiation in the Artiodactyla. Diversification may reflect vicariance of respective faunas along with episodic or cyclical range expansion and isolation across Beringia during the late Tertiary and Quaternary. Secondarily, species …

Pseudostertagia Bullosa (Nematoda: Trichostrongyloidea) In Artiodactyl Hosts From North America: Redescription And Comments On Systematics, Eric P. Hoberg, A. Abrams

Harold W. Manter Laboratory of Parasitology: Faculty Publications

A relationship for Pseudostertagia bullosa within the trichostrongyloids has been enigmatic or unresolved. Studies of the synlophe in males and females of P. bullosa revealed a tapering system anterior to the deirids and a pattern of parallel ridges extending to near the caudal extremity in both lateral and median fields. Structurally, the synlophe differs considerably from that seen among the Cooperiinae and exhibits homoplasy with respect to ridge systems among some Ostertagiinae. Other structural characters due to symplesiomorphy, homoplasy or because they represent autapomorphies do not serve to reveal the putative relationships for P. bullosa with other trichostrongyloids. Although somewhat …

Book Review: Gideon Yaffee, Manifest Activity: Thomas Reid’S Theory Of Action, Jennifer Mckitrick

Department of Philosophy: Faculty Publications

Gideon Yaffee’s Manifest Activity is an important contribution to both the studies of Thomas Reid’s views and action theory. Reid is known as an early advocate of an agent-causal view of free will; more recent advocates include Roderick Chisholm. Manifest Activity is a well-appreciated effort at bringing Reid’s particular version of agent-causalism and his arguments for it into the contemporary discussion. Manifest Activity should be of interest to Reid scholars, action theorists, and anyone who wants to explore a focused, critical analysis of a fascinating thinker.

Yaffee’s writing is clear and readable, yet rigorous and detailed. Yaffee’s aim in each …

Boron-Rich Semiconducting Boron Carbide Neutron Detector, Andrew D. Harken, Ellen E. Day, Brian W. Robertson, Shireen Adenwalla

Shireen Adenwalla Papers

Data on the neutron detection capabilities of a variety of boron carbide/Si heterojunction diodes is presented. The pulse height spectra are compared with previously measured conversion layer devices and the variations in shape and position of the peaks are discussed.

Possible Recent Range Expansion Of Alcataenia Longicervica (Eucestoda: Dilepididae) Parasitic In Murres Uria Spp. (Alcidae) Into The North Atlantic [Short Communications], Sabir B. Muzaffar, Eric P. Hoberg, Ian L. Jones

Harold W. Manter Laboratory of Parasitology: Faculty Publications

A wide range of helminths has been recorded from murres Uria spp. (Threlfall 1971, reviewed by Hoberg 1984a, Muzaffar & Jones 2004). Of the cyclophyllidean cestodes that parasitize murres, the genus Alcataenia Spasskaya 1971 (Dilepididae) is represented by ten species, eight of which are restricted and specific to the auks; the other two species occur in gulls (Laridae). The intermediate hosts of Alcataenia are euphausiid crustaceans such as species of Thysanoessa (Shimazu 1975), which also form an important dietary component of breeding and wintering murres, particularly Thick-billed Murres Uria lomvia (Gaston & Noble 1985, Birkhead & Nettleship 1987, Elliot et …