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Combination Of 16s Rrna Variable Regions Provides A Detailed Analysis Of Bacterial Community Dynamics In The Lungs Of Cystic Fibrosis Patients, Melissa S. Doud, Michael Light, Gisela Gonzalez, Giri Narasimhan, Kalai Mathee 2015 Florida International University, Department of Biological Sciences

Combination Of 16s Rrna Variable Regions Provides A Detailed Analysis Of Bacterial Community Dynamics In The Lungs Of Cystic Fibrosis Patients, Melissa S. Doud, Michael Light, Gisela Gonzalez, Giri Narasimhan, Kalai Mathee

Kalai Mathee

Chronic bronchopulmonary bacterial infections remain the most common cause of morbidity and mortality among patients with cystic fibrosis (CF). Recent community sequencing work has now shown that the bacterial community in the CF lung is polymicrobial. Identifying bacteria in the CF lung through sequencing can be costly and is not practical for many laboratories. Molecular techniques such as terminal restriction fragment length polymorphism or amplicon length heterogeneity-polymerase chain reaction (LH-PCR) can provide many laboratories with the ability to study CF bacterial communities without costly sequencing. The aim of this study was to determine if the use of LH-PCR with multiple ...


Splicing Regulation In Spinal Muscular Atrophy By An Rna Structure Formed By Long‐Distance Interactions, Natalia N. Singh, Brian M. Lee, Ravindra N. Singh 2015 Iowa State University

Splicing Regulation In Spinal Muscular Atrophy By An Rna Structure Formed By Long‐Distance Interactions, Natalia N. Singh, Brian M. Lee, Ravindra N. Singh

Biomedical Sciences Publications

Humans carry two copies of the survival motor neuron gene: SMN1 and SMN2. Loss of SMN1 coupled with skipping of SMN2 exon 7 causes spinal muscular atrophy (SMA), a leading genetic disease associated with infant mortality. Our discovery of intronic splicing silencer N1 (ISS‐N1) is a promising target, currently in a phase III clinical trial, for an antisense oligonucleotide–mediated splicing correction in SMA. We have recently shown that the first residue of ISS‐N1 is locked in a unique RNA structure that we term ISTL1 (internal stem through long‐distance interaction–1). Complementary strands of ISTL1 are separated ...


Codex: A Normalization And Copy Number Variation Detection Method For Whole Exome Sequencing, Yuchao Jiang, Derek A. Oldridge, Sharon J. Diskin, Nancy R. Zhang 2015 University of Pennsylvania

Codex: A Normalization And Copy Number Variation Detection Method For Whole Exome Sequencing, Yuchao Jiang, Derek A. Oldridge, Sharon J. Diskin, Nancy R. Zhang

Statistics Papers

High-throughput sequencing of DNA coding regions has become a common way of assaying genomic variation in the study of human diseases. Copy number variation (CNV) is an important type of genomic variation, but detecting and characterizing CNV from exome sequencing is challenging due to the high level of biases and artifacts. We propose CODEX, a normalization and CNV calling procedure for whole exome sequencing data. The Poisson latent factor model in CODEX includes terms that specifically remove biases due to GC content, exon capture and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure ...


Deletion Of Shank1 Has Minimal Effects On The Molecular Composition And Function Of Glutamatergic Afferent Postsynapses In The Mouse Inner Ear, Jeremy P. Braude, Sarath Vijayakumar, Katherine Baumgarner, Rebecca Laurine, Timothy A. Jones, Sherri M. Jones, Sonya J. Pyott 2015 University of North Carolina - Wilmington

Deletion Of Shank1 Has Minimal Effects On The Molecular Composition And Function Of Glutamatergic Afferent Postsynapses In The Mouse Inner Ear, Jeremy P. Braude, Sarath Vijayakumar, Katherine Baumgarner, Rebecca Laurine, Timothy A. Jones, Sherri M. Jones, Sonya J. Pyott

Special Education and Communication Disorders Faculty Publications

Abstract

Shank proteins (1-3) are considered the master organizers of glutamatergic postsynaptic densities in the central nervous system, and the genetic deletion of either Shank1, 2, or 3 results in altered composition, form, and strength of glutamatergic postsynapses. To investigate the contribution of Shank proteins to glutamatergic afferent synapses of the inner ear and especially cochlea, we used immunofluorescence and quantitative real time PCR to determine the expression of Shank1, 2, and 3 in the cochlea. Because we found evidence for expression of Shank1 but not 2 and 3, we investigated the morphology, composition, and function of afferent postsynaptic densities ...


Investigation Of Ultrasound Targeted Microbubbles As A Therapeutic Gene Delivery System For Prostate Cancer, Rounak Paramjeet Nande 2015 Marshall University

Investigation Of Ultrasound Targeted Microbubbles As A Therapeutic Gene Delivery System For Prostate Cancer, Rounak Paramjeet Nande

Theses, Dissertations and Capstones

A major challenge for effective gene therapy is systemic delivery of viruses carrying therapeutic genes into affected tissue. The immunogenic nature of human adenoviruses (Ads) limits their use for intratumoral (IT) injection in gene therapy. Ads transfection is further hampered by the fluctuating presence of Coxsackie and Adenovirus Receptor (CAR) and integrins on the cells’ surface. To circumvent these limitations we developed a novel approach wherein Ads are encapsulated inside the shell of lyophilized, lipid-encapsulated, perfluorocarbon microbubbles (MBs)/ultrasound (US) contrast agents, which act as delivery vehicles for a sitespecific gene transfer system.

We performed infection studies with Ad.GFP ...


Engineered Plga Nanoparticles For Delivery Of Sirna In Mcf-7 Breast Cancer Cells, Sydney Pong, Samit Shah, Vivek Gupta 2014 Chapman University

Engineered Plga Nanoparticles For Delivery Of Sirna In Mcf-7 Breast Cancer Cells, Sydney Pong, Samit Shah, Vivek Gupta

Student Scholar Symposium Abstracts and Posters

Small interfering RNAs have been an emerging medical treatment for molecular based diseases as they are capable of gene-specific knockdown. Appropriate and efficient delivery remains one of the biggest challenges in the development of siRNA as an anti-cancer treatment. Nanoparticles containing siRNA were characterized and the efficacy of various peptides in the transfection of the nanoparticles were tested. A gene silencing assay was developed in order to determine the effect of siRNA therapeutics on gene functionality in breast cancer cells.


Genetic Genealogy: What Every Librarian Should Know, Katherine A. Pennavaria, Rosemary L. Meszaros 2014 Western Kentucky University Libraries

Genetic Genealogy: What Every Librarian Should Know, Katherine A. Pennavaria, Rosemary L. Meszaros

Rosemary L. Meszaros

The past few years television, podcasts, and blogs across the Internet promoted the role of DNA testing in genealogy. But what do you really get, and is it worth the price? We discuss the logistics of DNA testing as it relates to genealogy and take a hard look at the legal issues involved in genealogy’s hottest topic.


Lineage-Specific Interface Proteins Match Up The Cell Cycle And Differentiation In Embryo Stem Cells, Angela Re, Christopher T. Workman, Levi Waldron, Alessandro Quattrone, Søren Brunak 2014 University of Trento

Lineage-Specific Interface Proteins Match Up The Cell Cycle And Differentiation In Embryo Stem Cells, Angela Re, Christopher T. Workman, Levi Waldron, Alessandro Quattrone, Søren Brunak

Publications and Research

The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We analyzed germ layer specific gene expression changes during the cell cycle and ESC differentiation by combining four human cell cycle transcriptome profiles with thirteen in vitro human ESC differentiation studies. To detect cross-talk mechanisms we then integrated the transcriptome data that displayed differential regulation with protein interaction data. A new class of non-transcriptionally regulated genes was identified, encoding proteins which interact ...


Cryptorchidism And Infertility In Rats With Targeted Disruption Of The Adamts16 Locus, Shakila Abdul-Majeed, Blair Mell, Surya M. Nauli, Bina Joe 2014 University of Toledo

Cryptorchidism And Infertility In Rats With Targeted Disruption Of The Adamts16 Locus, Shakila Abdul-Majeed, Blair Mell, Surya M. Nauli, Bina Joe

Pharmacy Faculty Articles and Research

A Disintegrin And Metalloproteinase with ThromboSpondin motifs16 (ADAMTS-16) is a member of a family of metalloproteinases. Using a novel zinc-finger nuclease based gene-edited rat model harboring a targeted mutation of the Adamts16 locus, we previously reported this gene to be linked to blood pressure regulation. Here we document our observation with this model that Adamts16 is essential for normal development of the testis. Absence of Adamts16 in the homozygous Adamts16(mutant) males resulted in cryptorchidism and male sterility. Heterozygous Adamts16(mutant) males were normal, indicating that this is a recessive trait. Testes of homozygous Adamts16(mutant) males were significantly smaller ...


Truncation Of Type Iv Pilin Induces Mucoidy In Pseudomonas Aeruginosa Strain Pao579, T. Ryan Withers, F. Heath Damron, Yeshi Yin, Hongwei D. Yu 2014 Marshall University

Truncation Of Type Iv Pilin Induces Mucoidy In Pseudomonas Aeruginosa Strain Pao579, T. Ryan Withers, F. Heath Damron, Yeshi Yin, Hongwei D. Yu

Hongwei Yu

Pseudomonas aeruginosa is a Gram negative, opportunistic pathogen that uses the overproduction of alginate, a surface polysaccharide, to form biofilms in vivo. Overproduction of alginate, also known as mucoidy, affords the bacterium protection from the host's defenses and facilitates the establishment of chronic lung infections in individuals with cystic fibrosis. Expression of the alginate biosynthetic operon is primarily controlled by the alternative sigma factor AlgU (AlgT/σ22). In a nonmucoid strain, AlgU is sequestered by the transmembrane antisigma factor MucA to the cytoplasmic membrane. AlgU can be released from MucA via regulated intramembrane proteolysis by proteases AlgW and MucP ...


Gene Expression Profiles Identify Features Common To Lobular And Ductal Premalignant Breast Lesions, Amy L. Roberts, D. Joseph Jerry, Kelly J. Gauger, Sallie S. Schneider, Giovanna M. Crisi, Grace Makari-Judson, Ashraf Khan, Karl Simin 2014 University of Massachusetts Amherst

Gene Expression Profiles Identify Features Common To Lobular And Ductal Premalignant Breast Lesions, Amy L. Roberts, D. Joseph Jerry, Kelly J. Gauger, Sallie S. Schneider, Giovanna M. Crisi, Grace Makari-Judson, Ashraf Khan, Karl Simin

UMass Center for Clinical and Translational Science Research Retreat

Premalignant lesions have been identified in both the ductal and lobular units of the breast epithelium. These lesions have a 4-fold increase in risk of progression to invasive breast cancer, but 80% will remain indolent. This may be due, in part, to the uncertainty of diagnoses as inter-observer reproducibility is poor. When treated with prophylactic hormone therapies blocking the estrogen receptor, up to 40% of women still develop tumors. Therefore the challenge is to develop diagnostic tests that identify the subset of high-risk lesions and provide appropriate prophylactic therapies. We undertook genome-wide expression studies to define sets of genes that ...


Pillow Talk: The Epigenetic And Physiological Effects Of Sleep Deprivation, Jennifer D. Cotter 2014 University of Southern Maine

Pillow Talk: The Epigenetic And Physiological Effects Of Sleep Deprivation, Jennifer D. Cotter

Thinking Matters Symposium Archive

Circadian rhythms, or the 24-hour biological cycles of living cells, function as the body’s internal clock. Although circadian rhythms and sleep are very different processes, they are closely related to one another as these cycles play an important role in sleeping and waking patterns. Recent studies have shown that lack of sleep or sleep of poor quality can disrupt circadian rhythms and may actually cause cognitive disorders and memory loss, facilitate false memory production, and even alter gene expression in humans. This literature review is focused on identifying the epigenetic and physiological effects of disruptions and desynchronization in circadian ...


Estudo De Associação Entre Os Polimorfismos De Um Único Nucleotídeo Em Genes De Citocinas E A Doença Renal Policística Autossômica Dominante Em Uma População Brasileira, Everton Fernando Alves 2014 Universidade Estadual de Maringá

Estudo De Associação Entre Os Polimorfismos De Um Único Nucleotídeo Em Genes De Citocinas E A Doença Renal Policística Autossômica Dominante Em Uma População Brasileira, Everton Fernando Alves

Everton Fernando Alves

A doença Renal Policística Autossômica Dominante (DRPAD) é causada por mutações em um de dois genes, PKD1 ou PKD2, que resultam em acúmulos de cistos nos rins. O objetivo deste trabalho foi verificar a existência de possíveis associações entre variantes em genes de citocinas e em receptores de citocinas para as posições IL1A-889 (rs1800587), IL1B-511, +3962 (rs16944, rs1143634), IL1R1970 (rs2234650), IL1RA11100 (rs315952), IL4RA+1902 (rs1801275), IL12-1188 (rs3212227), IFNG+874 (rs2430561), TGFB1códon 10, códon 25 (rs1982073, rs1800471), TNF-308, -238 (rs1800629, rs361525), IL2-330, +166 (rs2069762, rs2069763), IL4-1098, -590, -33 (rs2243248, rs2243250, rs2070874), IL6-174, nt565 (rs1800795, rs1800797) e IL10-1082,-819,-592 (rs1800896, rs1800871 ...


Retinoic Acid Regulation Of Thyroid Hormone Action In Bone Cells, Anjali Babbar 2014 Loma Linda University

Retinoic Acid Regulation Of Thyroid Hormone Action In Bone Cells, Anjali Babbar

Loma Linda University Electronic Theses, Dissertations & Projects

Retinoic acid and thyroid hormone are known to play key roles in the regulation of endochondral ossification. However, the issue of whether these two hormones interact with each other to regulate bone functions remains to be established. We investigated how thyroid hormone and retinoic acid interact to regulate cells involved in endochondral bone formation. We demonstrate that thyroid hormone treatment stimulates differentiation of ATDC5 chondrocytes and promotes formation of mineralized nodules while retinoic acid treatment at high dose inhibits chondrocyte differentiation and formation of mineralized nodules. Furthermore, thyroid hormone induced mineralized nodule formation is inhibited by co-treatment with retinoic acid ...


Mapping Genes With Longitudinal Phenotypes Via Bayesian Posterior Probabilities, Anthony Musolf, Alejandro Q. Nato Jr., Douglas Londono, Lisheng Zhou, Tara C. Matise, Derek Gordon 2014 Marshall University

Mapping Genes With Longitudinal Phenotypes Via Bayesian Posterior Probabilities, Anthony Musolf, Alejandro Q. Nato Jr., Douglas Londono, Lisheng Zhou, Tara C. Matise, Derek Gordon

Biochemistry and Microbiology

Most association studies focus on disease risk, with less attention paid to disease progression or severity. These phenotypes require longitudinal data. This paper presents a new method for analyzing longitudinal data to map genes in both population-based and family-based studies. Using simulated systolic blood pressure measurements obtained from Genetic Analysis Workshop 18, we cluster the phenotype data into trajectory subgroups. We then use the Bayesian posterior probability of being in the high subgroup as a quantitative trait in an association analysis with genotype data. This method maintains high power (>80%) in locating genes known to affect the simulated phenotype for ...


The Clinical Utility Of The Halosperm Assay And The Development Of A Simplified Method Of Human Semen Storage For The Testing Of Sperm Dna Fragmentation, Ashleigh Cavell McEvoy 2014 Edith Cowan University

The Clinical Utility Of The Halosperm Assay And The Development Of A Simplified Method Of Human Semen Storage For The Testing Of Sperm Dna Fragmentation, Ashleigh Cavell Mcevoy

Theses: Doctorates and Masters

Male infertility is typically diagnosed upon routine semen analysis following the World Health Organisation’s (WHO) semen analysis manual. Recent editions of the manual have essentially changed the diagnosis of a semen sample, prompting debate between experts as to which edition should be followed. Deoxyribonucleic Acid (DNA) integrity analysis is proving to be a useful adjunct to semen analysis as 15% of infertile men have a normal semen analysis but they have an increased DNA fragmentation level (DFL) which has been associated with increased disease incidence in any resultant offspring. However, such tests are not endorsed by the WHO, possibly ...


Cocaine Enhances Hiv-1 Infectivity In Monocyte Derived Dendritic Cells By Suppressing Microrna-155, Jessica Napuri, Sudheesh Pilakka-Kanthikeel, Andrea Raymond, Marisela Agudelo, Adriana Yndart-Arias, Madhavan Nair, Shailendra K. Saxena 2013 Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida

Cocaine Enhances Hiv-1 Infectivity In Monocyte Derived Dendritic Cells By Suppressing Microrna-155, Jessica Napuri, Sudheesh Pilakka-Kanthikeel, Andrea Raymond, Marisela Agudelo, Adriana Yndart-Arias, Madhavan Nair, Shailendra K. Saxena

HWCOM Faculty Publications

Cocaine and other drugs of abuse increase HIV-induced immunopathogenesis; and neurobiological mechanisms of cocaine addiction implicate a key role for microRNAs (miRNAs), single-stranded non-coding RNAs that regulate gene expression and defend against viruses. In fact, HIV defends against miRNAs by actively suppressing the expression of polycistronic miRNA cluster miRNA-17/92, which encodes miRNAs including miR-20a. IFN-g production by natural killer cells is regulated by miR-155 and this miRNA is also critical to dendritic cell (DC) maturation. However, the impact of cocaine on miR-155 expression and subsequent HIV replication is unknown. We examined the impact of cocaine on two miRNAs, miR-20a ...


Novel Ceramic Bone Replacement Material Ceraball® Seeded With Human Mesenchymal Stem Cells, Timothy Douglas, Qin Liu, Andreas Humpe, Jörg Wiltfang, Sureshan Sivananthan, Patrick Warnke 2013 University of Kiel

Novel Ceramic Bone Replacement Material Ceraball® Seeded With Human Mesenchymal Stem Cells, Timothy Douglas, Qin Liu, Andreas Humpe, Jörg Wiltfang, Sureshan Sivananthan, Patrick Warnke

Qin Liu

Objectives: Hydroxyapatite (HA) and tricalcium phosphate (TCP) are two very common ceramic materials for bone replacement. A recently developed material for bone replacement is CeraBall®, which is a mixed HA-TCP scaffold available as porous spherical scaffolds of diameter 4 and 6 mm. Before their use as bone replacement materials in vivo, in vitro testing of these scaffolds is necessary. The goal of this study was to characterise 4 and 6 mm CeraBall® scaffolds in vitro with a view to their future use as bone replacement materials. Materials and methods: The proliferation of human mesenchymal stromal cells (hMSCs) seeded on CeraBall ...


Genetic Background And Climatic Droplet Keratopathy Incidence In A Mapuche Population From Argentina, Theodore G. Schurr, Matthew C. Dulik, Thamara A. Cafaro, María F. Suarez, Julio A. Urrets-Zavalia, Horacio M. Serra 2013 University of Pennsylvania

Genetic Background And Climatic Droplet Keratopathy Incidence In A Mapuche Population From Argentina, Theodore G. Schurr, Matthew C. Dulik, Thamara A. Cafaro, María F. Suarez, Julio A. Urrets-Zavalia, Horacio M. Serra

Department of Anthropology Papers

Purpose

To determine whether the incidence of and susceptibility to climatic droplet keratopathy (CDK), an acquired, often bilateral degenerative corneal disease, is influenced by the genetic background of the individuals who exhibit the disorder.

Methods

To determine whether the disease expression was influenced by the genetic ancestry of CDK cases in native Mapuche of the northwest area of Patagonia in Argentina, we examined mitochondrial DNA and Y-chromosome variation in 53 unrelated individuals. Twenty-nine of them were part of the CDK (patient) population, while 24 were part of the control group. The analysis revealed the maternal and paternal lineages that were ...


Maternal Genital Tract Colonisation By Group-B Streptococcus: A Hospital Based Study, Nida Najmi, Rozina Sikandar, Nadeem F. Zuberi, Imtiaz Jehan 2013 Aga Khan University

Maternal Genital Tract Colonisation By Group-B Streptococcus: A Hospital Based Study, Nida Najmi, Rozina Sikandar, Nadeem F. Zuberi, Imtiaz Jehan

Department of Obstetrics & Gynaecology

Objectives: To determine the prevalence of Group B Streptococcus genital tract infection in pregnant women and to determine the risk factors for its colonisation.
Methods: The cross-sectional study was conducted at the Aga Khan University Hospital, Karachi and Sobhraj Hospital, Karachi, from May to August 2007. Pregnant women at 35-37 weeks gestation attending antenatal clinic at these hospitals constituted the study population. Based on stratified sampling, 405 patients were recruited. High vaginal swabs of these patients were taken in order to calculate the prevalence of infection at each hospital. Logistic regression was used to evaluate the risk factor association. SPSS ...


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