Life Sciences Commons^™

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Photocycloaddition Of Allenes, Crystal Ward

Theses and Dissertations

For the past ten years the Fleming research group has been involved in the research of allene compounds. We have explored the synthesis of allenes as well as several reactions involving allenes, such as oxidation and nitrene addition. Recently, we have explored the synthesis and photochemistry of allenic alcohols tethered to silicon. There are literature examples using allenes in synthesis, but very few examples exist using allenes in photochemical cycloaddition reactions. We have found that a diisopropylallenyloxy(cinnamyloxy)silane derivative undergoes [2+2] photochemical cycloaddition to produce a cyclobutylsilane product when irradiated for 60-75 minutes.

The Evolutionary Dynamics Of The Lion Panthera Leo Revealed By Host And Viral Population Genomics, Agostinho Antunes, Jennifer L. Troyer, Melody E. Roelke, Jill Pecon-Slattery, Craig Packer, Christiaan Winterbach, Graham Hemson, Laurence G. Frank, Philip Stander, Ludwig Siefert, Margaret Driciru, Paul J. Funston, Kathy A. Alexander, Katherine C. Prager, Gus Mills, David E. Wildt, Mitch E. Bush, Stephen J. O'Brien, Warren E. Johnson

Biology Faculty Articles

The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV_Ple), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, …

The Role Of P44/42 Activation In Tributyltin-Induced Inhibition Of Human Natural Killer Cells: Effects Of Mek Inhibitors, Abraham B. Abraha, Margaret M. Whalen

Chemistry Faculty Research

Destruction of tumor cells is a key function of natural killer (NK) cells. Previous studies have shown that tributyltin (TBT) can significantly reduce the lytic function of the human NK cells with accompanying increases in the phosphorylation (activation) states of the mitogen activated protein kinases (MAPKs), p44/42. The current studies examine the role of p44/42 activation in the TBT-induced reduction of NK-lytic function, by using MAPK kinase (MEK) inhibitors, PD98059 and U0126. A 1 h treatment with PD98059 or U0126 or both decreased the ability of NK cells to lyse K562 tumor cells. PD98059, U0126 or a combination of both …

The Future Of Generic Biologics: Should The United States “Follow-On” The European Pathway?, Ingrid Kaldre

Duke Law & Technology Review

The United States is embarking on a biotechnology drug revolution. In the last few decades, biotech drugs have saved millions of lives, and the market for these miracle cures continues to grow at an astronomical rate. Unfortunately, as the market for biotech drugs is skyrocketing, drug prices are following suit. As Congress strives to make these new drugs more affordable, it must not ignore significant safety concerns unique to these revolutionary therapies. Congress should follow the lead of the European Union to create an accessible pathway for generic forms of biotech drugs that includes strict regulatory measures to ensure drug …

Professor Bruce Criley To Retire, Rachel Hatch

News and Events (Discontinued Series)

No abstract provided.

Crileys Reflect On Years With Illinois Wesleyan, Rachel Hatch

News and Events (Discontinued Series)

No abstract provided.

2008 Oregon Harvest Report, Oregon Wine Board

Oregon Wine Board Documents

This harvest report for the Oregon wine industry from 2008 discusses how a cool growing season led to a dry and mild harvest. According to the report, the late harvest and lower yields brought about mature and complex flavors, translating to a vintage with good potential for high quality. The report also includes four-region comparative data prepared by climatologist Dr. Greg Jones.

Evolution Acts On Enhancer Organization To Fine-Tune Gradient Threshold Readouts, Justin Crocker, Yoichiro Tamori, Albert Erives

Dartmouth Scholarship

The elucidation of principles governing evolution of gene regulatory sequence is critical to the study of metazoan diversification. We are therefore exploring the structure and organizational constraints of regulatory sequences by studying functionally equivalent cis-regulatory modules (CRMs) that have been evolving in parallel across several loci. Such an independent dataset allows a multi-locus study that is not hampered by nonfunctional or constrained homology. The neurogenic ectoderm enhancers (NEEs) of Drosophila melanogaster are one such class of coordinately regulated CRMs. The NEEs share a common organization of binding sites and as a set would be useful to study the relationship …

Eelgrass Distribution In The Great Bay Estuary 2007, Frederick T. Short

PREP Reports & Publications

Eelgrass has now, in 2007, almost totally disappeared from Little Bay and the Piscataqua River. Despite these critical losses in mid-estuary, eelgrass distribution in the Great Bay Estuary (GBE) as a whole between 2006 and 2007 experienced an overall loss of 3% in area because of the areal dominance of Great Bay itself, where most of the eelgrass that remains in the GBE is found. Eelgrass area in Great Bay itself remained about the same between 2006 and 2007, with an increase in biomass due to some of the remaining beds becoming more dense. However, Little Bay and the Piscataqua …

The Strength Of Statistical Evidence For Composite Hypotheses With An Application To Multiple Comparisons, David R. Bickel

COBRA Preprint Series

The strength of the statistical evidence in a sample of data that favors one composite hypothesis over another may be quantified by the likelihood ratio using the parameter value consistent with each hypothesis that maximizes the likelihood function. Unlike the p-value and the Bayes factor, this measure of evidence is coherent in the sense that it cannot support a hypothesis over any hypothesis that it entails. Further, when comparing the hypothesis that the parameter lies outside a non-trivial interval to the hypotheses that it lies within the interval, the proposed measure of evidence almost always asymptotically favors the correct hypothesis …

Smokejumper Obituary: Weber, William P. (Missoula 1945), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Alternative Cereal Processing Technologies [Conference Program And Proceedings] (Lobatse, Botswana, November 4-6, 2008), Martin Kebakile, Kemelo Ookeditse

INTSORMIL Presentations

Objectives of the workshop:

To review the current status of local cereals production and processing explore opportunities for growing the cereal industry.

To promote diversification of cereal processing by sensitizing all players and stakeholders in the cereals industry about readily available alternative cereals processing technologies which have commercial potential.

To promote and strengthen collaboration between local and international researchers, as well as fostering strategic partnerships between researchers and users of technologies to develop customer tailored processing technologies.

Polymer Supported Optical Biosensors, Ignacio Joseph Garcia

Electronic Theses and Dissertations

The use of various polymer supports adhering phospholipid multibilayers to an internal reflection element have been investigated. The polymer supports studied range from polystyrene (PS), and 100 nm wide PS nanospheres to triethylaminated poly(vinyl benzyl chloride) (PVBC). The PS nanospheres showed the most promise as an adhesion layer since they appear to be the most robust with repeated washings. They also appear to stabilize their adjacent phospholipid multibilayer by increasing the lipid melting temperature. The triethylaminated DVBC also provided an increase of lipid melting temperature, but not quite to the same degree as the PS nanospheres. The cooperativity of such …

Kentucky Warbler (Vol. 84, No. 4), Kentucky Library Research Collections

The Kentucky Warbler

No abstract provided.

Distributional Ecology Of The Anemone Shrimp Periclimenes Rathbunae Associating With The Sea Anemone Stichodactyla Helianthus At Tobago, Neville A. Trimm, Floyd E. Hayes

Faculty Works

We studied the distributional ecology of the anemone shrimp Periclimenes rathbunae associating with the anemone Stichodactyla helianthus in Tobago, West Indies. The shrimps occupied 83.1% of the anemones (n = 83), with mean densities of 2.8 shrimps per anemone in the population and 3.4 shrimps per occupied anemone, and up to 11 inhabiting a single anemone. Shrimp density was significantly correlated with anemone size. Because the density of shrimps was not significantly correlated with the distance to the nearest neighboring anemone or the number of anemones in a cluster, colonization appears to be related to chance or some unknown factor …

Neuroendocrine Peptides Neuropeptide-Y (Npy) And Peptide-Yy (Pyy) Suppress Cl- Secretion And K+ Secretion In Guinea Pig Distal Colon Through Action At Y2-Receptors, Susan T. Halm, Jin Zhang, Dan R. Halm

Neuroscience, Cell Biology & Physiology Faculty Publications

Electrogenic Cl^– and K⁺ secretion in isolated mucosa from guinea pig distal colon measured as short-circuit current (I_sc) and transepithelial conductance (G_t) were stimulated by epinephrine (epi), prostaglandin-E₂ (PGE₂) and carbachol (CCh). neuropeptide-Y (NPY) and peptide-YY (PYY) inhibited by 60% Cl^– secretion activated by either PGE₂ or PGE₂+CCh with EC₅₀’s of 16nM and 6nM, respectively. Neither peptide markedly inhibited the transient component of the PGE₂+CCh response. Immunoreactivity (IR) for NPY was present in enteric ganglia and in proximity with crypts. Basolateral membranes of …

It's In Your Nature: A Pluralistic Folk Psychology, Kristin Andrews

Sentience Collection

I suggest a pluralistic account of folk psychology according to which not all predictions or explanations rely on the attribution of mental states, and not all intentional actions are explained by mental states. This view of folk psychology is supported by research in developmental and social psychology. It is well known that people use personality traits to predict behavior. I argue that trait attribution is not shorthand for mental state attributions, since traits are not identical to beliefs or desires, and an understanding of belief or desire is not necessary for using trait attributions. In addition, we sometimes predict and …

Behavioural Analysis Of A Nociceptive Event In Fish: Comparisons Between Three Species Demonstrate Specific Responses, Siobhan C. Reilly, John P. Quinn, Andrew R. Cossins, Lynne U. Sneddon

Sentience Collection

Nociception is the sensory mechanism by which potentially harmful stimuli are detected in animals and humans. The behavioural responses to noxious stimulation have been studied in two fish species thus far. However, since species-specific differences are seen in mammals, more species need to be examined to determine whether nociceptive responses are generic in fish. The present study investigated the behavioural and respiratory response to an acute noxious or potentially painful stimulus in common carp (Cyprinus carpio), zebrafish (Danio rerio) and rainbow trout (Oncorhynchus mykiss). Behavioural parameters such as frequency of swimming, use of cover and any anomalous behaviour were measured …

Ph-Induced Activation Of Arenavirus Membrane Fusion Is Antagonized By Small-Molecule Inhibitors, Joanne York, Dongcheng Dai, Sean M. Amberg, Jack H. Nunberg

Biological Sciences Faculty Publications

The arenavirus envelope glycoprotein (GPC) mediates viral entry through pH-induced membrane fusion in the endosome. This crucial process in the viral life cycle can be specifically inhibited in the New World arenaviruses by the small-molecule compound ST-294. Here, we show that ST-294 interferes with GPC-mediated membrane fusion by targeting the interaction of the G2 fusion subunit with the stable signal peptide (SSP). We demonstrate that amino acid substitutions at lysine-33 of the Junin virus SSP confer resistance to ST-294 and engender de novo sensitivity to ST-161, a chemically distinct inhibitor of the Old World Lassa fever virus. These compounds, as …

North Shore Bays Benthic Mapping: Groundtruth Studies., Robert M. Cerrato, Lee Holt

School of Marine & Atmospheric Sciences Faculty Publications

We combined high-resolution remote sensing techniques with detailed study of the physical and faunal characteristics at point locations in different seafloor environments within the Oyster Bay- Cold Spring Harbor Complex, the Huntington-Northport Bay Complex, and Port Jefferson Harbor, including Conscience Bay. High-resolution backscatter and bathymetric maps created by side scan and multibeam sonar surveys were used to classify the sea bed into provinces. Samples for macrofauna and sediment properties were collected within each province to provide "ground truth" for the acoustic maps. Oyster Bay, Huntington Harbor, and Port Jefferson Harbor were sampled at 40, 38, and 50 locations, respectively, with …

North Shore Bays Benthic Mapping: Groundtruth Studies Gis Data, Robert M. Cerrato, Lee Holt

SoMAS Research Data

We combined high-resolution remote sensing techniques with detailed study of the physical and faunal characteristics at point locations in different seafloor environments within the Oyster Bay- Cold Spring Harbor Complex, the Huntington-Northport Bay Complex, and Port Jefferson Harbor, including Conscience Bay. High-resolution backscatter and bathymetric maps created by side scan and multibeam sonar surveys were used to classify the seabed into provinces. Samples for macrofauna and sediment properties were collected within each province to provide "ground truth" for the acoustic maps. Oyster Bay, Huntington Harbor, and Port Jefferson Harbor were sampled at 40, 38, and 50 locations, respectively, with two …

Tethering Polypeptides Through Bifunctional Peg Cross-Linking Agents To Probe Protein Function: Application To Atp Synthase., Daniel J Cipriano, Stanley D Dunn

Biochemistry Publications

Chemical crosslinking mediated by short bifunctional reagents has been widely used for determining physical relationships among polypeptides in multisubunit proteins, but less often for functional studies. Here we introduce the approach of tethering polypeptides by using bifunctional reagents containing a lengthy, flexible PEG linker as a form of crosslinking especially suited to functional analyses. The rotary molecular motor ATP synthase was used as a model subject. Single cysteine residues were introduced into selected positions of ATP synthase epsilon subunit, a component of the rotor subcomplex of the enzyme, and the unrelated maltose binding protein (MBP), then the two purified recombinant …

Jointed Goatgrass Management With Imazamox-Resistant Cultivars In A Winter Wheat–Fallow Rotation, Andrew R. Kniss, Drew J. Lyon, Stephen D. Miller

Panhandle Research and Extension Center

Jointed goatgrass (Aegilops cylindrica Host) is an economically important weed in winter wheat (Triticum aestivum L.)–fallow production regions of the United States. Few options exist for management of jointed goatgrass in winter wheat due to the close genetic relationship between the two species. This research evaluated use of imazamox herbicide (2-[(RS)-4-isopropyl-4- methyl-5-oxo-2-imidazolin-2-yl]-5-methoxymethylnicotinic acid) in an imazamox-resistant (IR) winter wheat–fallow rotation over 6 yr when grown continuously or in rotation with a conventional winter wheat cultivar. The objectives of this study were to compare use patterns of IR technology in winter wheat with respect to jointed goatgrass density and …

Induction Of Plant Defense Gene Expression By Plant Activators And Pseudomonas Syringae Pv. Tomato In Greenhouse-Grown Tomatoes, Maryann Herman, J. K. Davidson, C. D. Smart

Biology Faculty/Staff Publications

Plant activators provide an appealing management option for bacterial diseases of greenhouse-grown tomatoes. Two types of plant activators, one that induces systemic acquired resistance (SAR) and a second that activates induced systemic resistance (ISR), were evaluated for control of Pseudomonas syringae pv. tomato and effect on plant defense gene activation. Benzothiadiazole (BTH, SAR-inducing compound) effectively reduced bacterial speck incidence and severity, both alone and in combination with the ISR-inducing product. Application of BTH also led to elevated activation of salicylic acid and ethylene-mediated responses, based on real-time polymerase chain reaction analysis of marker gene expression levels. In contrast, the ISR-inducing …

Live Release Of A Bigeye Sand Tiger Odontaspis Noronhai (Elasmobranchii: Lamniformes) In The Western North Atlantic Ocean, David W. Kerstetter, Mae Taylor

Marine & Environmental Sciences Faculty Articles

No abstract provided.

Blood Pressure Lowering And Vasomodulator Effects Of Piperine, Syed Intasar Husain Taqvi, Abdul Jabbar Shah, Anwar Gilani

Department of Biological & Biomedical Sciences

This study was aimed to explore underlying mechanism(s) of cardiovascular effects of piperine. Intravenous administration of piperine caused a dose-dependent (1 to 10 mg/kg) decrease in mean arterial pressure (MAP) in normotensive anesthetized rats, the next higher dose (30 mg/kg) did not cause any further change in MAP. The fall in blood pressure (BP) was followed by small increase in MAP after each dose. In Langendorrf's rabbit heart preparation, piperine caused partial inhibition and verapamil caused complete inhibition of force and rate of ventricular contractions and coronary flow. In rabbit aortic rings, piperine inhibited high K(+) (80 mM) precontractions and …

Genetic Change Following Fire In Populations Of A Seed-Banking Perennial Plant, Rebecca W. Dolan, Pedro F. Quintana-Ascencio, Eric S. Menges

Scholarship and Professional Work - LAS

Disturbances such as fire have the potential to remove genetic variation, but seed banks may counter this loss by restoring alleles through a reservoir effect. We used allozyme analysis to characterize genetic change in two populations of the perennial Hypericum cumulicola, an endemic of the fire-prone Florida scrub. We assessed genetic variation before and 1, 2, and 3 years after fire that killed nearly all aboveground plants. Populations increased in size following fire, with most seedlings likely recruited from a persistent seed bank. Four of five loci were variable. Most alleles were present in low frequencies, but our large sample …

An Inositolphosphorylceramide Synthase Is Involved In Regulation Of Plant Programmed Cell Death Associated With Defense In Arabidopsis, Wenming Wang, Xiaohua Yang, Samantha Tangchiaburana, Roland Ndeh, Jennifer E. Markham, Yoseph Tsegaye, Teresa M. Dunn, Guo-Liang Wang, Maria Bellizzi, James F. Parsons, Danielle Morrissey, Janis E. Bravo, Daniel V. Lynch, Shunyuan Xiao

Department of Biochemistry: Faculty Publications

The Arabidopsis thaliana resistance gene RPW8 triggers the hypersensitive response (HR) to restrict powdery mildew infection via the salicylic acid–dependent signaling pathway. To further understand how RPW8 signaling is regulated, we have conducted a genetic screen to identify mutations enhancing RPW8-mediated HR-like cell death (designated erh). Here, we report the isolation and characterization of the Arabidopsis erh1 mutant, in which the At2g37940 locus is knocked out by a T-DNA insertion. Loss of function of ERH1 results in salicylic acid accumulation, enhanced transcription of RPW8 and RPW8-dependent spontaneous HR-like cell death in leaf tissues, and reduction in plant stature. …

Sustained Attention In Children With Two Etiologies Of Early Hydrocephalus, Maegan D. Swartwout, Paul T. Cirino, Amy W. Hampson, Jack M. Fletcher, Michael E. Brandt, Maureen Dennis

Faculty, Staff and Student Publications

Several studies have shown that children with spina bifida meningomyelocele (SBM) and hydrocephalus have attention problems on parent ratings and difficulties in stimulus orienting associated with a posterior brain attention system. Less is known about response control and inhibition associated with an anterior brain attention system. Using the Gordon Vigilance Task (Gordon, 1983), we studied error rate, reaction time, and performance over time for sustained attention, a key anterior attention function, in 101 children with SBM, 17 with aqueductal stenosis (AS; another condition involving congenital hydrocephalus), and 40 typically developing controls (NC). In SBM, we investigated the relation between cognitive …