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The Plant Structure Ontology, A Unified Vocabulary Of Anatomy And Morphology Of A Flowering Plant, Katica Ilic, Elizabeth A. Kellogg, Pankaj Jaiswal, Felipe Zapata, Peter F. Stevens, Leszek P. Vincent, Shulamit Avraham, Leonore Reiser, Anuradha Pujar, Martin M. Sachs, Noah T. Whitman, Susan R. Mccouch, Mary L. Schaeffer, Doreen H. Ware, Lincoln D. Stein, Seung Y. Rhee

Peter Stevens

Cadherin-2 Participates In The Morphogenesis Of The Zebrafish Inner Ear, Sherry Babb-Clendenon, Yu-Chi Shen, Qin Liu, Katharyn E. Turner, M. Susan Mills, Greg W. Cook, Caroline A. Miller, Vincent H. Gattone Ii, Kate F. Barald, James A. Marrs

Qin Liu

Molecular mechanisms that control inner ear morphogenesis from the placode to the three-dimensional functional organ are not well understood. We hypothesize that cell-cell adhesion, mediated by cadherin molecules, contributes significantly to various stages of inner ear formation. Cadherin-2 (Cdh2) function during otic vesicle morphogenesis was investigated by examining morpholino antisense oligonucleotide knockdown and glass onion (glo) ( Cdh2 mutant) zebrafish embryos. Placode formation, vesicle cavitation and specification occurred normally, but morphogenesis of the otic vesicle was affected by Cdh2 deficiency: semicircular canals were reduced or absent. Phalloidin staining of the hair cell stereocillia demonstrated that cadherin-2 (cdh2) loss-of-function did not …

Possible Nonconductive Role Of Geobacter Sulfurreducens Pilus Nanowires In Biofilm Formation, Gemma Reguera, Rachael B. Pollina, Julie S. Nicoll, Derek Lovley

Derek Lovley

Geobacter sulfurreducens required expression of electrically conductive pili to form biofilms on Fe(III) oxide surfaces, but pili were also essential for biofilm development on plain glass when fumarate was the sole electron acceptor. Furthermore, pili were needed for cell aggregation in agglutination studies. These results suggest that the pili of G. sulfurreducens also have a structural role in biofilm formation.

Wavelet-Based Functional Mixed Models To Characterize Population Heterogeneity In Accelerometer Profiles: A Case Study. , Jeffrey S. Morris, Cassandra Arroyo, Brent A. Coull, Louise M. Ryan, Steven L. Gortmaker

Jeffrey S. Morris

We present a case study illustrating the challenges of analyzing accelerometer data taken from a sample of children participating in an intervention study designed to increase physical activity. An accelerometer is a small device worn on the hip that records the minute-by-minute activity levels of the child throughout the day for each day it is worn. The resulting data are irregular functions characterized by many peaks representing short bursts of intense activity. We model these data using the wavelet-based functional mixed model. This approach incorporates multiple fixed effects and random effect functions of arbitrary form, the estimates of which are …

Alternative Probeset Definitions For Combining Microarray Data Across Studies Using Different Versions Of Affymetrix Oligonucleotide Arrays, Jeffrey S. Morris, Chunlei Wu, Kevin R. Coombes, Keith A. Baggerly, Jing Wang, Li Zhang

Jeffrey S. Morris

Many published microarray studies have small to moderate sample sizes, and thus have low statistical power to detect significant relationships between gene expression levels and outcomes of interest. By pooling data across multiple studies, however, we can gain power, enabling us to detect new relationships. This type of pooling is complicated by the fact that gene expression measurements from different microarray platforms are not directly comparable. In this chapter, we discuss two methods for combining information across different versions of Affymetrix oligonucleotide arrays. Each involves a new approach for combining probes on the array into probesets. The first approach involves …

Raphidophyceae [Chadefaud Ex Silva] Systematics And Rapid Identification: Sequence Analyses And Real–Time Pcr Assays, Torstein Tengs

Dr. Torstein Tengs

Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for …

Equal Performance Of Taqman, Mgb, Molecular Beacon, And Sybr Green-Based Detection Assays In Detection And Quantification Of Roundup Ready Soybean, Torstein Tengs

Dr. Torstein Tengs

We have tested and compared the performance of 12 different assays representing four different real-time polymerase chain reaction (PCR) chemistries in the context of genetically modified organism detection. Several different molecular beacon, SYBR Green, TaqMan, and MGB assays were designed for the event specific detection and quantification of the 3' integration junction of GTS 40-3-2 (Roundup Ready) soybean. Sensitivity as well as robustness in the presence of background DNA were tested. None of the PCR-based approaches appeared to be significantly better than any of the other, but the molecular beacon assays had the lowest efficiency and also seemed more sensitive …

High-Level Resistance To Bacillus Thuringiensis Toxin Cry1ac And Cadherin Genotype In Pink Bollworm, Aaron J. Gassmann, Robert W. Biggs, Jeffrey A. Fabrick, Bruce E. Tabashnick, Timothy J. Dennehy, Yves Carriere, Shai Morin

Aaron J. Gassmann

Resistance to transgenic cotton, Gossypium hirsutum L., producing Bacillus thuringiensis (Bt) toxin Cry1Ac is linked with three recessive alleles of a cadherin gene in laboratory-selected strains of pink bollworm, Pectinophora gossypiella (Saunders), a major cotton pest. Here, we analyzed a strain (MOV97-R) with a high frequency of cadherin resistance alleles, a high frequency of resistance to 10 μg of Cry1Ac per milliliter of diet, and an intermediate frequency of resistance to 1,000 μg of Cry1Ac per ml of diet. We selected two strains for increased resistance by exposing larvae from MOV97-R to diet with 1,000 μg of Cry1Ac per ml …

A Brief History Of Oyster Aquaculture In Rhode Island, Michael Rice

Michael A Rice

Passive Stiffness In Drosophila Indirect Flight Muscle Reduced By Disrupting Paramyosin Phosphorylation, But Not By Embryonic Myosin S2 Hinge Substitution, Yudong Hao, Mark S. Miller, Douglas M. Swank, Hongjun Liu, Sanford I. Bernstein, David W. Maughan, Gerald H. Pollack

Mark S. Miller

High passive stiffness is one of the characteristic properties of the asynchronous indirect flight muscle (IFM) found in many insects like Drosophila. To evaluate the effects of two thick filament protein domains on passive sarcomeric stiffness, and to investigate their correlation with IFM function, we used microfabricated cantilevers and a high resolution imaging system to study the passive IFM myofibril stiffness of two groups of transgenic Drosophila lines. One group (hinge-switch mutants) had a portion of the endogenous S2 hinge region replaced by an embryonic version; the other group (paramyosin mutants) had one or more putative phosphorylation sites near the …

Bmc Infectious Diseases, Frances Cirino, Wilmore C. Webley, Corrie West, Nancy L. Croteau, Chester Andrzejewski Jr, Elizabeth S. Stuart

Wilmore C Webley

No abstract provided.

Prepms: Tof Ms Data Graphical Preprocessing Tool, Yuliya V. Karpievitch, Elizabeth G. Hill, Adam J. Smolka, Jeffrey S. Morris, Kevin R. Coombes, Keith A. Baggerly, Jonas S. Almeida

Jeffrey S. Morris

We introduce a simple-to-use graphical tool that enables researchers to easily prepare time-of-flight mass spectrometry data for analysis. For ease of use, the graphical executable provides default parameter settings experimentally determined to work well in most situations. These values can be changed by the user if desired. PrepMS is a stand-alone application made freely available (open source), and is under the General Public License (GPL). Its graphical user interface, default parameter settings, and display plots allow PrepMS to be used effectively for data preprocessing, peak detection, and visual data quality assessment.

Qim Method Scores Quality, Shelf Life Of Pangasius Fillets, Huynh Nguyen Duy Bao

Huynh Nguyen Duy Bao

A Quality Index Method developed to assess the freshness of Pangasius hypophthalmus fillets stored on ice showed a high correlation between the index score and storage time. With cross referencing of total viable microbial count and ammonia content analysis, the shelf life of iced fillets was estimated at 12 days based on evaluation of eight sensory parameters.

A Genomic Approach To Identify Regulatory Nodes In The Transcriptional Network Of Systemic Acquired Resistance In Plants, Dong Wang, Nita Amornsiripanitch, Xinnian Dong

Dong Wang

Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR) is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor) fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able …

An Anaerobic Methane Oxidizing Community Of Anme-1b Archaea In Hypersaline Gulf Of Mexico Sediments, Karen Lloyd, Laura Lapham, Andreas Teske

Karen Lloyd

Sediments overlying a brine pool methane seep in the Gulf of Mexico (Green Canyon 205) were analyzed using molecular and geochemical approaches to identify geochemical controls on microbial community composition and stratification. 16S rRNA gene and rRNA clone libraries, as well as mcrA gene clone libraries, showed that the archaeal community consists predominantly of ANME-1b methane oxidizers; no archaea of other ANME subgroups were found with general and group-specific PCR primers. The ANME-1b community was found in the sulfate-methane interface, where undersaturated methane concentrations of ca. 100 to 250 _M coexist with sulfate concentrations around 10 mM. Clone libraries of …

Age-Related Dystrophin–Glycoprotein Complex Structure And Function In The Rat Extensor Digitorum Longus And Soleus Muscle, Kevin M. Rice, Deborah L. Preston, David Neff, Michael L. Norton, Eric R. Blough

Eric Blough

Age-Related Dystrophin–Glycoprotein Complex Structure And Function In The Rat Extensor Digitorum Longus And Soleus Muscle, Kevin M. Rice, Deborah L. Preston, David Neff, Michael L. Norton, Eric R. Blough

Kevin M Rice

Age-Related Dystrophin–Glycoprotein Complex Structure And Function In The Rat Extensor Digitorum Longus And Soleus Muscle, Kevin M. Rice, Deborah L. Preston, David Neff, Michael L. Norton, Eric R. Blough

Deborah L Preston

Postexercise Insulin Action In African-American Women, Rebecca E. Hasson, Patty S. Freedson, Barry Braun

Barry Braun

African Americans are more insulin resistant than Caucasians. A single bout of moderate-intensity exercise reduces insulin resistance in sedentary Caucasian individuals. The impact of a single bout of exercise on insulin resistance has never been studied in African Americans. The purpose of this experiment was to evaluate the impact of a single bout of exercise on insulin resistance in African-American women. DESIGN: Insulin resistance was assessed in 10 sedentary, over-weight or obese African-American women during a sedentary and exercise condition over a two-day period. During the sedentary condition, participants fasted overnight and sat quietly in the laboratory for 75 minutes. …

Nonparametric Pathway-Based Regression Models For Analysis Of Genomic Data, Zhi Wei, Hongzhe Li

Hongzhe Li

High-throughout genomic data provide an opportunity for identifying pathways and genes that are related to various clinical phenotypes. Besides these genomic data, another valuable source of data is the biological knowledge about genes and pathways that might be related to the phenotypes of many complex diseases. Databases of such knowledge are often called the metadata. In microarray data analysis, such metadata are currently explored in post hoc ways by gene set enrichment analysis but have hardly been utilized in the modeling step. We propose to develop and evaluate a pathway-based gradient descent boosting procedure for nonparametric pathways-based regression(NPR) analysis to …

Group Additive Regression Models For Genomic Data Analysis, Yihui Luan, Hongzhe Li

Hongzhe Li

One important problem in genomic research is to identify genomic features such as gene expression data or DNA single nucleotide polymorphisms (SNPs) that are related to clinical phenotypes. Often these genomic data can be naturally divided into biologically meaningful groups such as genes belonging to the same pathways or SNPs within genes. In this paper, we propose group additive regression models and a group gradient descent boosting procedure for identifying groups of genomic features that are related to clinical phenotypes. Our simulation results show that by dividing the variables into appropriate groups, we can obtain better identification of the group …

Reconstitution Of Protein Targeting To The Inner Envelope Membrane Of Chloroplasts, Ming Li, Danny Schnell

Danny Schnell

The chloroplast envelope plays critical roles in the synthesis and regulated transport of key metabolites, including intermediates in photosynthesis and lipid metabolism. Despite this importance, the biogenesis of the envelope membranes has not been investigated in detail. To identify the determinants of protein targeting to the inner envelope membrane (IM), we investigated the targeting of the nucleus-encoded integral IM protein, atTic40. We found that pre-atTic40 is imported into chloroplasts and processed to an intermediate size (int-atTic40) before insertion into the IM. Int-atTic40 is soluble and inserts into the IM from the internal stromal compartment. We also show that atTic40 and …

The Importance Of Emerging Biobased Industries To Engineering And Technology, Kurt A. Rosentrater, R. Balamuralikrishma

Kurt A. Rosentrater

Our society has developed an insatiable demand for energy and material goods. Historically, these needs have been met primarily by fossil fuels and other non-renewable raw materials. As environmental concerns grow, however, renewable resources are gaining increased attention. This paper examines the emergence and importance that biobased industries are increasingly beginning to play. A biobased enterprise, similar in concept to a traditional refinery or factory, utilizes conversion technologies to produce various products. These operations are rapidly increasing both in number as well as in capacity throughout this country, and are poised to add significantly to the nation’s energy and material …

Analytical And Experimental Studies Of Properties Of Ethanol Coproduct-Filled Plastics, Robert Tatara, Andrew Otieno, Srikrishna Suraparaju, Kurt A. Rosentrater

Kurt A. Rosentrater

As the renewable fuels industry continues to grow, the quantity of resulting byproducts has expanded in tandem. Currently, these materials are primarily used for animal feed, but at some point will saturate the animal feeds market. Thus, it is necessary to investigate alternative methods and applications by which these coproducts can be utilized. One potential application for these process residues involves plastics manufacturing. Due, in part, to the increasing cost of resins and conventional fillers, alternate fillers have been increasingly sought. Many of these include biological materials such as grasses, bamboo, starch, chicken feathers, soy protein, and cellulose. Not only …

A New Species Of Emballonura (Chiroptera: Emballonuridae) From The Dry Regions Of Madagascar, Steven M. Goodman, Scott G. Cardiff, Julie Ranivo, Amy L. Russell, Anne D. Yoder

Amy L. Russell

Role Of Red Gsu In Stress Response And Fe(Iii) Reduction In Geobacter Sulfurreducens, Laurie N. Didonato, Sara A. Sullivan, Barbara A. Methѐ, Kelly P. Nevin, Reg England, Derek Lovley

Kelly Nevin

Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated relGsu, which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3′,5′-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of RelGsu in G. sulfurreducens, a relGsu mutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type and relGsu mutant strains. In the wild-type …

Role Of Red Gsu In Stress Response And Fe(Iii) Reduction In Geobacter Sulfurreducens, Laurie N. Didonato, Sara A. Sullivan, Barbara A. Methѐ, Kelly P. Nevin, Reg England, Derek Lovley

Derek Lovley

Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated relGsu, which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3′,5′-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of RelGsu in G. sulfurreducens, a relGsu mutant was constructed and characterized, and ppGpp levels were monitored under various conditions in both the wild-type and relGsu mutant strains. In the wild-type …

). Clonal Micropropagation Of Indian Gooseberry (Emblica Officinalis Gaertn)., Rajesh Pati

Rajesh Pati

No abstract provided.

Adding Ecological Considerations To Environmental Accounting, David A. Bainbridge

David A Bainbridge

Environmental accounting has often neglected ecological costs. These are essential to complete a true cost accounting. Ecological costs are often very large and long term and if they are ignored the costs/benefits of projects are incorrectly calculated.

Implicating An Introduced Generalist Parasitoid In The Invasive Browntail Moth's Enigmatic Demise, Joseph Elkinton, D. Parry, G. Boettner

Joseph Elkinton

Recent attention has focused on the harmful effects of introduced biological control agents on nontarget species. The parasitoid Compsilura concinnata is a notable example of such biological control gone wrong. Introduced in 1906 primarily for control of gypsy moth, Lymantria dispar, this tachinid fly now attacks more than 180 species of native Lepidoptera in North America. While it did not prevent outbreaks or spread of gypsy moth, we present reanalyzed historical data and experimental findings suggesting that parasitism by C. concinnata is the cause of the enigmatic near-extirpation of another of North America's most successful invaders, the browntail moth (Euproctis …