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The Prediction Of B-Cell Epitope Via Biostatistical And Bioinformatic Methodology And Applications, Bo Yao 2014 University of Nebraska - Lincoln

The Prediction Of B-Cell Epitope Via Biostatistical And Bioinformatic Methodology And Applications, Bo Yao

Dissertations and Theses in Biological Sciences

By creating antibodies against antigens, B-cells, also named B-lymphocytes, play an important role in the immune system to fight against foreign invasion to the host body. Within the antigen specific to a certain B-cell antibody, the sections recognized and bound by antibody are called B-cell epitopes. As antigenic determinants, B-cell epitope identification is of vital importance in many immunological processes, such as vaccine design, immunodiagnostic tests, and antibody production. Towards this goal, biologists and immunologists have applied a variety of methods to identify B-cell epitopes through both experiments and bioinformatic predictions.

There are two kinds of B-cell epitopes: linear (continuous ...


Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz 2014 University of Massachusetts Medical School

Calmodulation Meta-Analysis: Predicting Calmodulin Binding Via Canonical Motif Clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, William R. Kobertz

Biochemistry and Molecular Pharmacology Publications and Presentations

The calcium-binding protein calmodulin (CaM) directly binds to membrane transport proteins to modulate their function in response to changes in intracellular calcium concentrations. Because CaM recognizes and binds to a wide variety of target sequences, identifying CaM-binding sites is difficult, requiring intensive sequence gazing and extensive biochemical analysis. Here, we describe a straightforward computational script that rapidly identifies canonical CaM-binding motifs within an amino acid sequence. Analysis of the target sequences from high resolution CaM-peptide structures using this script revealed that CaM often binds to sequences that have multiple overlapping canonical CaM-binding motifs. The addition of a positive charge discriminator ...


Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian 2014 SelectedWorks

Alternative Tools For Mining The Biomedical Literature, Rolando Garcia-Milian

Rolando Garcia-Milian

The rapid growth of experimental and computational biomedical data is being accompanied by an increase in the number of biomedical publications discussing these results. This makes retrieving relevant scientific information and identifying connections between findings, a challenging task. New literature-mining tools (e.g. KNALIJ, Quertle, NextBio, iHOP, SemMed, GoPubMed, etc) may be of help when sorting through this abundance of literature, as discovery and hypothesis generating tools. This workshop provides an introduction on how to use some of these literature-mining tools when answering research questions.


An Examination Of The Phylogenetic Diversity Of Green Algae (Chlorophyceae) That Symbiose With Spotted Salamanders (Ambystoma Maculatum) In The Egg Stage., Crystal Xue 2014 University of Connecticut

An Examination Of The Phylogenetic Diversity Of Green Algae (Chlorophyceae) That Symbiose With Spotted Salamanders (Ambystoma Maculatum) In The Egg Stage., Crystal Xue

Honors Scholar Theses

In 1909, the species Oophila amblystomatis Lambert ex Wille was described for green algae that symbiose with salamanders in the egg stage (Wille). There are two hypotheses about the source of algae: 1) that algae enter from the surrounding water once the egg clutch is laid in a pond, and 2) that they are acquired from the maternal reproductive tract. We developed a third hypothesis developed to account for the salamander reproductive cycle. Male salamanders lay spermatophores, which are protein-filled capsules, on plant matter in and around ponds. Spermatophores are exposed to the environment before use by females in internal ...


Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko 2014 Seton Hall University

Transcriptome Analysis Of Sea Lamprey Embryogenesis, Zakary Ilya Yermolenko

Seton Hall University Dissertations and Theses (ETDs)

The sea lamprey (Petromyzon marinus) has survived throughout evolution for hundreds of millions of years. It is considered an invasive species to the Great Lakes that has caused dramatic changes in the ecosystem for fish communities resulting in the collapse of a fishing industry that was previously valued at billions of dollars. Successful management of the sea lamprey is essential to a sustainable fishing industry and biodiversity. Therefore sea lamprey embryos were studied at various stages of development by growing them in a simulated habitat. RNAs from adult female ovaries and embryos at different time points during embryogenesis were extracted ...


The Association Between The Il-1 Pathway, Isaac C. Wun 2014 Texas Medical Center Library

The Association Between The Il-1 Pathway, Isaac C. Wun

UT GSBS Dissertations and Theses (Open Access)

Cutaneous malignant melanoma (CMM) is a potentially lethal malignancy that warrants attention and further research, as it is known to that there is an increasing rate of incidence in theUnited States, and it is also known that exposure to UV light is its most crucial risk factor, and family history of melanoma is also an important risk factor. Melanoma is an aggressive and lethal cancer in humans. There are an estimated new 132,000 melanoma cases annually worldwide, and the trend has doubled in the past 20 years. However, attempts to treat melanoma have encountered considerable resistance and remained ineffective ...


Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton 2014 University of Connecticut

Numerical Assessment Of Sequence Conservation In Flu-Virus Hemagglutinin, Scott S. Norton

Honors Scholar Theses

The flu virus was investigated to find a common recognition domain to which an antibody against human-infected viruses can bind. If such a target site is structurally and electrostaticly conserved or invariant, only a single antibody would be required to attack the virus in all cases. The sequence of one of the viral surface proteins contains 24 amino acids that do not vary through mutation. However, these amino acids are neither contiguous in sequence or in space, and the ones that are associated with each other are not readily accessible to an antibody. They do provide a first impression of ...


Mining Contrast Subspaces, Lei Duan, Guanting Tang, Jian Pei, James Bailey, Guozhu Dong, Akiko Campbell, Changjie Tang 2014 Wright State University

Mining Contrast Subspaces, Lei Duan, Guanting Tang, Jian Pei, James Bailey, Guozhu Dong, Akiko Campbell, Changjie Tang

Kno.e.sis Publications

In this paper, we tackle a novel problem of mining contrast subspaces. Given a set of multidimensional objects in two classes C  +  and C  − and a query object o, we want to find top-ksubspaces S that maximize the ratio of likelihood of o in C  +  against that in C  −. We demonstrate that this problem has important applications, and at the same time, is very challenging. It even does not allow polynomial time approximation. We present CSMiner, a mining method with various pruning techniques. CSMiner is substantially faster than the baseline method. Our experimental results on real data sets ...


Isolation & Characterization Of The Novel Bacteriophage Gaius, Rohan Khazanchi, John A. Nahon, Anna M. Kolasa, Elisa S. De Togni 2014 Washington University in St. Louis

Isolation & Characterization Of The Novel Bacteriophage Gaius, Rohan Khazanchi, John A. Nahon, Anna M. Kolasa, Elisa S. De Togni

Undergraduate Research Symposium Posters & Abstracts

There are an estimated 1031 species of bacteriophages in the Earth’s biome. As a result, understanding the immense diversity of bacteriophages is a topic of great interest. We isolated a novel mycobacteriophage, called Gaius, from soil collected near the Watershed Nature Center in Edwardsville, IL. We enriched our soil sample using Mycobacterium smegmatis, and after purification, its plaque morphology was characteristic of a temperate phage. Following purification, we used electron microscope imaging to find Gaius’ physical structure to be similar to other members of the A4 subcluster. We sequenced Gaius’ genome using the Pacific Biosystems Sequencing technique, making ...


Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, ENCODE Project Consortium 2014 University of Massachusetts Medical School

Defining Functional Dna Elements In The Human Genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, Encode Project Consortium

Program in Systems Biology Publications and Presentations

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily ...


Bioinformatic Analysis Of Plant-Like Vacuole (Plv) Proteins In Toxoplasma Gondii, Javier A. Tovar 2014 Georgia State University

Bioinformatic Analysis Of Plant-Like Vacuole (Plv) Proteins In Toxoplasma Gondii, Javier A. Tovar

Georgia State Undergraduate Research Conference

No abstract provided.


Statistical Analysis Of Enhanced Ctl Killing Activity Against Irradiated Tumor Cells, Catannian Sanogo 2014 Georgia State University

Statistical Analysis Of Enhanced Ctl Killing Activity Against Irradiated Tumor Cells, Catannian Sanogo

Georgia State Undergraduate Research Conference

No abstract provided.


Statistical Phylogenetic Models For The Inference Of Functionally Important Regions In Proteins, Yifei Huang 2014 McMaster University

Statistical Phylogenetic Models For The Inference Of Functionally Important Regions In Proteins, Yifei Huang

Open Access Dissertations and Theses

An important question in biology is the identification of functionally important sites and regions in proteins. A variety of statistical phylogenetic models have been developed to predict functionally important protein sites, e.g. ligand binding sites or protein-protein interaction interfaces, by comparing sequences from different species. However, most of the existing methods ignore the spatial clustering of functionally important sites in protein tertiary/primary structures, which significantly reduces their power to identify functionally important regions in proteins. In this thesis, we present several new statistical phylogenetic models for inferring functionally important protein regions in which Gaussian processes or hidden Markov ...


Stream Crossing Barrier Prioritization Methods For Increasing Eastern Brook Trout Habitat In The Little Androscoggin River Watershed, Michele Windsor 2014 University of Southern Maine

Stream Crossing Barrier Prioritization Methods For Increasing Eastern Brook Trout Habitat In The Little Androscoggin River Watershed, Michele Windsor

Thinking Matters

Eastern Brook Trout (Salvelinas fontanalis) are an important cold water fishery in the state of Maine. While populations in Maine are relatively abundant there has been decline in some parts of its range due in part to loss of habitat connectivity. Brook trout require access to specific types of stream habitat for spawning, feeding, and seasonal thermal refuges. Stream crossing structures such as undersized, poorly installed, or blocked culverts, as well as small remnant dams, can create barriers to accessing important stream habitat for brook trout. A recent Fish Barrier/Culvert Survey in the Little Androscoggin River Watershed provided data ...


New Statistical Methods For Analysis Of Historical Data From Wildlife Populations, Trevor Hefley 2014 University of Nebraska - Lincoln

New Statistical Methods For Analysis Of Historical Data From Wildlife Populations, Trevor Hefley

Dissertations and Theses in Statistics

Wildlife biologists, many times with the help of ordinary citizens, have developed and maintained long-term datasets for monitoring the status of wildlife populations. These datasets can range from a collection of citizen-reported sightings of a rare species, to datasets collected by biologists using standardized methods. The commonality is that these datasets span a temporal and spatial scale that is beyond the scope of most scientific studies. Ensuring the continued persistence of wildlife populations requires predictions of the impact of human actions. Regardless if the predictions are quantitative or qualitative, the best we can do is use the past data to ...


Computational Model For Survey And Trend Analysis Of Patients With Endometriosis : A Decision Aid Tool For Ebm, Salvo Reina, Vito Reina, Franco Ameglio, Mauro Costa, Alessandro Fasciani 2014 COBRA

Computational Model For Survey And Trend Analysis Of Patients With Endometriosis : A Decision Aid Tool For Ebm, Salvo Reina, Vito Reina, Franco Ameglio, Mauro Costa, Alessandro Fasciani

COBRA Preprint Series

Endometriosis is increasingly collecting worldwide attention due to its medical complexity and social impact. The European community has identified this as a “social disease”. A large amount of information comes from scientists, yet several aspects of this pathology and staging criteria need to be clearly defined on a suitable number of individuals. In fact, available studies on endometriosis are not easily comparable due to a lack of standardized criteria to collect patients’ informations and scarce definitions of symptoms. Currently, only retrospective surgical stadiation is used to measure pathology intensity, while the Evidence Based Medicine (EBM) requires shareable methods and correct ...


Comparative Modeling And Functional Characterization Of Two Enzymes Of The Cyclooxygenase Pathway In Drosophila Melanogaster, Yan Qi 2014 The Graduate Center, CUNY

Comparative Modeling And Functional Characterization Of Two Enzymes Of The Cyclooxygenase Pathway In Drosophila Melanogaster, Yan Qi

Dissertations and Theses, 2014-Present

Eicosanoids are biologically active molecules oxygenated from twenty carbon polyunsaturated fatty acids. Natural eicosanoids exert potent biological effects in humans, and a great deal of pharmaceutical research has led to the discovery of compounds for selective inhibition of specific enzymes in eicosanoid biosynthesis. Coupled with different receptors, eicosanoids mediate various physiological and pathophysiological processes, including fever generation, pain response, vasoconstriction, vasodilation, platelet aggregation, platelet declumping, body temperature maintenance and sleep-wake cycle regulation. In mammals, the eicosanoid biosynthesis has three pathways: the cyclooxygenase (COX) pathway, the lipoxygenase (LOX) pathway and the epoxygenase pathway. The COX pathway synthesizes prostanoids, which are important ...


Time Series Data For 3b Image Processing, George McNamara 2014 The University of Texas

Time Series Data For 3b Image Processing, George Mcnamara

George McNamara

Time series data for 3B image processing

Four time series data sets of Stellaris single molecules RNA FISH (fluorescence in situ hybridization). All four datasets are 301 imaqe planes. FISH probes are to TOP1 mRNA (Topoisomerase I)in Saos osterosarcoma cells.

One dataset is 10 millisecond exposures (very dim), acquired in Streaming acquisition mode (no hardware overhead).

The other three datasets are a three consecutive planes of the same XY field of view.

I have included image processing results for:

PiMP - a fast method developed by Sebastian Munck et al 2012, http://www.ncbi.nlm.nih.gov/pubmed/?term=22357945 ...


The Atp2c2 Gene As Transcribed From A Novel Transcriptional Start Site In Pancreatic Acinar Cells, Caitlin M. Sullivan 2014 Western University

The Atp2c2 Gene As Transcribed From A Novel Transcriptional Start Site In Pancreatic Acinar Cells, Caitlin M. Sullivan

University of Western Ontario - Electronic Thesis and Dissertation Repository

Strict regulation of cytosolic Ca2+ is essential to regulated exocytosis and proper pancreatic acinar cell function, controlled in part by pumps that shuttle Ca2+ out of the cytosol. Our laboratory identified a novel isoform of Secretory Ca2+ ATPase 2 (SPCA2) containing only the carboxy terminus. Pancreatic SPCA2, is an approximately 17-20 kDa, protein encoded by the Atp2c2 gene and is completely absent in Mist1-/- acini.. The focus of this thesis was to understand transcriptional regulation of Atp2c2 in the pancreas. Pancreatic Atp2c2 appears to be transcribed from an alternative transcriptional start site (TSS) and is regulated by ...


Software To Accompany "A Kernel Machine Approach For Differential Expression Analysis Of Mass Spectrometry-Based Metabolomics Data", Debashis Ghosh 2014 SelectedWorks

Software To Accompany "A Kernel Machine Approach For Differential Expression Analysis Of Mass Spectrometry-Based Metabolomics Data", Debashis Ghosh

Debashis Ghosh

No abstract provided.


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