Life Sciences Commons^™

Population Responses Of Wood Frog (Rana Sylvatica) Tadpoles To Overwintered Bullfrog (Rana Catesbeiana) Tadpoles, Leroy J. Walston, Stephen J. Mullin

Faculty Publications

A fundamental goal in ecology is to understand how environmental variation influences the distribution of individuals within a population. In this study, we used laboratory experiments to examine the population responses of sympatric Wood Frog (Rana sylvatica) tadpoles to native overwintered Bullfrog (Rana catesbeiana) tadpoles. For periods of up to two weeks, we measured growth, activity, and refuge use of Wood Frog tadpoles in small mesocosms with and without an overwintered Bullfrog tadpole present. Bullfrog tadpoles had a negative effect on the growth of Wood Frog tadpoles allotopic (naive) to Bullfrogs, whereas the presence of Bullfrogs had no effect on …

Appropriate Physical Education Service For All Students, Ron French, Lisa Silliman-French, Deborah Buswell

Faculty Publications

All students, including those with disabilities, deserve appropriate, safe, and meaningful physical education instructional programs as identified by Texas Education Agency (2006) and that are reflected in the National Association for Sport and Physical Education (NASPE, 2005) standards.

Perceived Benefits Of Students' Service-Learning Experiences With Hippotherapy, Deborah Buswell, Filitsa Leriou

Faculty Publications

The term hippotherapy has its roots in the Greek language, and is translated as treatment with the help of the horse (Glasow, 2003). Using horseback tiding as a form of natural exercise dates back to Hippocrates (460-377 B.C.). Although therapeutic riding and hippotherapy are both used as forms of treatment for persons with disabilities, they are not synonymous. Hippotherapy is prescribed by a physician and utilizes equine movement as part of a treatment strategy and is used by physical, occupational, and speech therapists "as part of an integrated treatment program to achieve functional outcomes" (American Hippotherapy Association, 2003, What is …

Phenotypic Plasticity May Facilitate Invasion By Aegilops Triuncialis, Andrew R. Dyer

Faculty Publications

One great obstacle to understanding the invasion of nonnative species into native ecosystems is the lack of information on the population biology of the invading species. In particular, morphological and physiological adaptations and potential for phenotypic plasticity will strongly influence a species’ ability to persist and spread in newly invaded ecosystems. Phenotypic plasticity can buffer populations from selection thereby allowing them to survive the establishment phase of the invasion. The annual grass Aegilops triuncialis (Poaceae, Triticeae) has become highly invasive in California (USA) and provides an opportunity to investigate the importance of phenotypic plasticity to persistence and spread in new …

Structure And Function Predictions Of The Msa Protein In Staphylococcus Aureus, Vijayaraj Nagarajan, Mohamed O. Elasri

Faculty Publications

Background

Staphylococcus aureus is a human pathogen that causes a wide variety of life-threatening infections using a large number of virulence factors. One of the major global regulators used by S. aureus is the staphylococcal accessory regulator (sarA). We have identified and characterized a new gene (modulator of sarA: msa) that modulates the expression of sarA. Genetic and functional analysis shows that msa has a global effect on gene expression in S. aureus. However, the mechanism of Msa function is still unknown. Function predictions of Msa are complicated by the fact that it does …

A Comparative Study Of Different Machine Learning Methods On Microarray Gene Expression Data, Mehdi Pirooznia, Jack Y. Yang, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Several classification and feature selection methods have been studied for the identification of differentially expressed genes in microarray data. Classification methods such as SVM, RBF Neural Nets, MLP Neural Nets, Bayesian, Decision Tree and Random Forrest methods have been used in recent studies. The accuracy of these methods has been calculated with validation methods such as v-fold validation. However there is lack of comparison between these methods to find a better framework for classification, clustering and analysis of microarray gene expression results.

Results

In this study, we compared the efficiency of the classification methods including; SVM, RBF Neural Nets, …

A Hybrid Machine Learning-Based Method For Classifying The Cushing's Syndrome With Comorbid Adrenocortical Lesions, Jack Y. Yang, Mary Qu Yang, Zuojie Lao, Yan Ma, Jianling Li, Youping Deng, Xudong Huang

Faculty Publications

Background

The prognosis for many cancers could be improved dramatically if they could be detected while still at the microscopic disease stage. It follows from a comprehensive statistical analysis that a number of antigens such as hTERT, PCNA and Ki-67 can be considered as cancer markers, while another set of antigens such as P27KIP1 and FHIT are possible markers for normal tissue. Because more than one marker must be considered to obtain a classification of cancer or no cancer, and if cancer, to classify it as malignant, borderline, or benign, we must develop an intelligent decision system that can fullfill …

Improving Prediction Accuracy Of Tumor Classification By Reusing Genes Discarded During Gene Selection, Jack Y. Yang, Guo-Zheng Li, Hao-Hua Meng, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Since the high dimensionality of gene expression microarray data sets degrades the generalization performance of classifiers, feature selection, which selects relevant features and discards irrelevant and redundant features, has been widely used in the bioinformatics field. Multi-task learning is a novel technique to improve prediction accuracy of tumor classification by using information contained in such discarded redundant features, but which features should be discarded or used as input or output remains an open issue.

Results

We demonstrate a framework for automatically selecting features to be input, output, and discarded by using a genetic algorithm, and propose two algorithms: GA-MTL …

Promoting Synergistic Research And Education In Genomics And Bioinformatics, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.

High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to …

Iloop - A Web Application For Two-Channel Microarray Interwoven Loop Design, Mehdi Pirooznia, Ping Gong, Jack Y. Yang, Mary Qu Yang, Edward J. Perkins, Youping Deng

Faculty Publications

Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available from http://mcbc.usm.edu/iloop …

Batch Blast Extractor: An Automated Blastx Parser Application, Mehdi Pirooznia, Edward J. Perkins, Youping Deng

Faculty Publications

Motivation

BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs.

Results

We have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further …

Are Botanists Becoming The Dinosaurs Of Biology In The 21st Century?, Dennis W. Woodland

Faculty Publications

The number of botany students, botany classes, botany departments in universities and botanists attending conventions has been declining over many years in North America. This is part of a general trend throughout the field of organismal biology, not just botany. The history leading up to the situation today in North America, is discussed and reasons are given for this trend over the last century of time. Seven ways to keep botany a viable occupation are discussed otherwise botany, in the 21st century, may go the way of the dinosaur. © 2007.

Genomics, Molecular Imaging, Bioinformatics, And Bio-Nano-Info Integration Are Synergistic Components Of Translational Medicine And Personalized Healthcare Research, Jack Y. Yang, Mary Qu Yang, Hamid R. Arabnia, Youping Deng

Faculty Publications

Supported by National Science Foundation (NSF), International Society of Intelligent Biological Medicine (ISIBM), International Journal of Computational Biology and Drug Design and International Journal of Functional Informatics and Personalized Medicine, IEEE 7th Bioinformatics and Bioengineering attracted more than 600 papers and 500 researchers and medical doctors. It was the only synergistic inter/multidisciplinary IEEE conference with 24 Keynote Lectures, 7 Tutorials, 5 Cutting-Edge Research Workshops and 32 Scientific Sessions including 11 Special Research Interest Sessions that were designed dynamically at Harvard in response to the current research trends and advances. The committee was very grateful for the IEEE Plenary Keynote Lectures …

Observations On The Diets Of An Anuran And Eight Lizard Taxa From Sonora, Chihuahua, And Coahuila, Mexico, With Some Notes On Clutch Sizes, Geoffrey R. Smith, J. A. Lemos-Espinal, Christopher B. Dibble, Megan E. Ogle, Joshua J. Schulte, Andrew J. Terlecky, Allison Boyd

Faculty Publications

No abstract provided.

Multiple Mixed-Type Attractors In A Competition Model, J. M. Cushing, Shandelle M. Henson, Chantel C. Blackburn

Faculty Publications

We show that a discrete-time, two-species competition model with Ricker (exponential) nonlinearities can exhibit multiple mixed-type attractors. By this is meant dynamic scenarios in which there are simultaneously present both coexistence attractors (in which both species are present) and exclusion attractors (in which one species is absent). Recent studies have investigated the inclusion of life-cycle stages in competition models as a casual mechanism for the existence of these kinds of multiple attractors. In this paper we investigate the role of nonlinearities in competition models without life-cycle stages. © 2007 Taylor & Francis Group, LLC.

Genetic Diversity And Low Reproductive Success In Isolated Populations Of Utah Juniper (Juniperus Osteosperma, Cupressaceae), Loreen Allphin, Val J. Anderson, Amy F. Hunt

Faculty Publications

Utah juniper (Juniperus osteosperma) has greatly expanded its historical range in the western United States. Management plans for the species have focused on curtailing its encroachment into sagebrush and grassland communities. These plans often include burning or other methods of elimination. These methods may result in subdivision or fragmentation of existing juniper stands. We initiated a study at Dugway Proving Ground, a U.S. Army facility, to examine the effects of fragmentation on the reproductive success of Utah juniper in isolated populations. We used enzyme electrophoresis to quantify genetic variability in isolated populations. We also determined population reproductive success by examining …

Analyzing Adjuvant Radiotherapy Suggests A Non Monotonic Radio-Sensitivity Over Tumor Volumes, Jack Y. Yang, Andrzej Niemierko, Mary Qu Yang, Youping Deng

Faculty Publications

Background: Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics have been used extensively to validate clinical data. Results: We found that Poisson statistics on RT is actually derived from bacterial cells despite of many validations from clinical data. However cancerous cells do have abnormal cellular communications and use chemical messengers to signal both surrounding normal and cancerous cells to develop new blood vessels …

Transcriptomic Analysis Of Rdx And Tnt Interactive Sublethal Effects In The Earthworm Eisenia Fetida, Ping Gong, Xin Guan, Laura S. Anouye, Youping Deng, Mehdi Pirooznia, Edward J. Perkins

Faculty Publications

Background

Explosive compounds such as TNT and RDX are recalcitrant contaminants often found co-existing in the environment. In order to understand the joint effects of TNT and RDX on earthworms, an important ecological and bioindicator species at the molecular level, we sampled worms (Eisenia fetida) exposed singly or jointly to TNT (50 mg/kg soil) and RDX (30 mg/kg soil) for 28 days and profiled gene expression in an interwoven loop designed microarray experiment using a 4k-cDNA array. Lethality, growth and reproductive endpoints were measured.

Results

Sublethal doses of TNT and RDX had no significant effects on the survival …

Investigation Of Transmembrane Proteins Using A Computational Approach, Jack Y. Yang, Mary Qu Yang, Keith A. Dunker, Youping Deng, Xudong Huang

Faculty Publications

Background

An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmembrane segments. The difficulty of inferring the secondary or tertiary structure of transmembrane proteins using experimental techniques has led to a surge of interest in applying techniques from machine learning and bioinformatics to infer secondary structure from primary structure in these proteins. We are therefore interested in determining which physicochemical properties are most useful for discriminating transmembrane …

Supervised Learning Method For The Prediction Of Subcellular Localization Of Proteins Using Amino Acid And Amino Acid Pair Composition, Tanwir Habib, Chaoyang Zhang, Jack Y. Yang, Mary Qu Yang, Youping Deng

Faculty Publications

Background

Occurrence of protein in the cell is an important step in understanding its function. It is highly desirable to predict a protein's subcellular locations automatically from its sequence. Most studied methods for prediction of subcellular localization of proteins are signal peptides, the location by sequence homology, and the correlation between the total amino acid compositions of proteins. Taking amino-acid composition and amino acid pair composition into consideration helps improving the prediction accuracy.

Results

We constructed a dataset of protein sequences from SWISS-PROT database and segmented them into 12 classes based on their subcellular locations. SVM modules were trained to …

Transcriptome Profiling Of Saccharomyces Cerevisiae Mutants Lacking C2h2 Zinc Finger Proteins, Jinghe Mao, Tanwir Habib, Ming Shenwu, Baobin Kang, Wilbur Allen, Lashonda Robertson, Jack Y. Yang, Youping Deng

Faculty Publications

Background

The budding yeast Saccharomyces cerevisiae is a eukaryotic organism with extensive genetic redundancy. Large-scale gene deletion analysis has shown that over 80% of the ~6200 predicted genes are nonessential and that the functions of 30% of all ORFs remain unclassified, implying that yeast cells can tolerate deletion of a substantial number of individual genes. For example, a class of zinc finger proteins containing C2H2 zinc fingers in tandem arrays of two or three is predicted to be transcription factors; however, seven of the thirty-one predicted genes of this class are nonessential, and their functions are poorly understood. In this …

Whole Genome Duplications And Contracted Breakpoint Graphs, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

The genome halving problem, motivated by the whole genome duplication events in molecular evolution, was solved by El-Mabrouk and Sankoff in the pioneering paper [SIAM J. Comput., 32 (2003), pp. 754–792]. The El-Mabrouk–Sankoff algorithm is rather complex, inspiring a quest for a simpler solution. An alternative approach to the genome halving problem based on the notion of the contracted breakpoint graph was recently proposed in [M. A. Alekseyev and P. A. Pevzner, IEEE/ACM Trans. Comput. Biol. Bioinformatics, 4 (2007), pp. 98–107]. This new technique reveals that while the El-Mabrouk–Sankoff result is correct in most cases, it does not hold in …

Colored De Bruijn Graphs And The Genome Halving Problem, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based …

Threatened Fishes Of The World: Percilia Irwini (Eigenmann 1927) (Perciliidae), Evelyn Habit, Mark C. Belk

Faculty Publications

Common name: Carmelita de Concepcion (Spanish).

Biological Status Of Leatherside Chub: A Framework For Conservation Of Western Freshwater Fishes, Mark C. Belk, Jerald B. Johnson

Faculty Publications

Outside of anadromous salmonids and a few endangered species, biology of native freshwater fishes of western North America is poorly known. What do we need to know to effectively manage native species and avoid decline and extinction? A recent analysis of the role of science in the Pacific salmon controversy outlines a clear framework for biological evaluation and management of native species. This framework has three components: (1) determine status of populations based on genetic and ecological variation, (2) identify and quantify threats to populations, and (3) determine actions to alleviate threats and promote conservation of populations. We use our …

Solar Dryer Construction And Use Manual Version 2.0 2007, Jonathan P. Rowe, Jonathan K. Russon, Frost M. Steele

Faculty Publications

In less time than it took to develop this solar dryer and manual, the Pacific Island area has experienced several typhoons and tropical depressions followed by significant flooding and destruction of homes, properties and crops. It is in the interest of all people to become more self-reliant in times of need and to have the basic necessities available at a moment’s notice to sustain life until transportation, commerce, health care, agriculture, water, etc. can be restored to a more normal state. This work was done to enable the people of the Pacific islands to meet some of their food requirements …

Acute Stretch Perception Alteration Contributes To The Success Of The Pnf "Contract-Relax" Stretch, J. Brent Feland, Sterling C. Hilton, J. Ty Hopkins, Iain Hunter, Ulrike H. Mitchell, J. William Myrer

Faculty Publications

Context: Some researchers have suggested that an alteration of stretch perception could be responsible for the success of the contract-relax (CR) stretch, a stretch technique derived from proprioceptive neuromuscular facilitation (PNF). Objective: This study was conducted to determine if the alteration of the stretch perception is a possible explanation for the range of motion (ROM) gains of the CR stretch. Participants: Eighteen subjects performed two stretches in randomized order: the slow stretch and the CR stretch. Main Outcome Measure: The stretch intensity was controlled. The stretch force was measured and compared between the slow stretch and CR stretch. Results: There …