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Superresolution Imaging Identifies That Conventional Trafficking Pathways Are Not Essential For Endoplasmic Reticulum To Outer Mitochondrial Membrane Protein Transport., Kyle Salka, Shivaprasad Bhuvanendran, Kassandra Wilson, Petros Bozidis, Mansi Mehta, Kristin Rainey, Hiromi Sesaki, George H Patterson, Jyoti K. Jaiswal, Anamaris M. Colberg-Poley 2017 George Washington University

Superresolution Imaging Identifies That Conventional Trafficking Pathways Are Not Essential For Endoplasmic Reticulum To Outer Mitochondrial Membrane Protein Transport., Kyle Salka, Shivaprasad Bhuvanendran, Kassandra Wilson, Petros Bozidis, Mansi Mehta, Kristin Rainey, Hiromi Sesaki, George H Patterson, Jyoti K. Jaiswal, Anamaris M. Colberg-Poley

Integrative Systems Biology Faculty Publications

Most nuclear-encoded mitochondrial proteins traffic from the cytosol to mitochondria. Some of these proteins localize at mitochondria-associated membranes (MAM), where mitochondria are closely apposed with the endoplasmic reticulum (ER). We have previously shown that the human cytomegalovirus signal-anchored protein known as viral mitochondria-localized inhibitor of apoptosis (vMIA) traffics from the ER to mitochondria and clusters at the outer mitochondrial membrane (OMM). Here, we have examined the host pathways by which vMIA traffics from the ER to mitochondria and clusters at the OMM. By disruption of phosphofurin acidic cluster sorting protein 2 (PACS-2), mitofusins (Mfn1/2), and dynamin related protein 1 ...


Evolutionary Adaptations Of Biofilms Infecting Cystic Fibrosis Lungs Promote Mechanical Toughness By Adjusting Polysaccharide Production, Kristin Kovach, Megan Davis-Fields, Yasuhiko Irie, Kanishk Jain, Shashvat Doorwar, Katherine Vuong, Numa Dhamani, Kishore Mohanty, Ahmed Touhami, Vernita D. Gordon 2017 University of Texas at Austin

Evolutionary Adaptations Of Biofilms Infecting Cystic Fibrosis Lungs Promote Mechanical Toughness By Adjusting Polysaccharide Production, Kristin Kovach, Megan Davis-Fields, Yasuhiko Irie, Kanishk Jain, Shashvat Doorwar, Katherine Vuong, Numa Dhamani, Kishore Mohanty, Ahmed Touhami, Vernita D. Gordon

Yasuhiko Irie

Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances, largely polysaccharides. Multiple types of extracellular polymeric substances can be produced by a single bacterial strain. The distinct polymer components of biofilms are known to provide chemical protection, but little is known about how distinct extracellular polysaccharides may also protect biofilms against mechanical stresses such as shear or phagocytic engulfment. Decades-long infections of Pseudomonas. aeruginosa biofilms in the lungs of cystic fibrosis patients are natural models for studies of biofilm fitness under pressure from antibiotics and the immune system. In cystic fibrosis infections, production of the extracellular ...


Homppi: A Class Of Sequence Homology Based Protein-Protein Interface Prediction Methods, Li C. Xue, Drena Dobbs, Vasant Honavar 2017 Iowa State University

Homppi: A Class Of Sequence Homology Based Protein-Protein Interface Prediction Methods, Li C. Xue, Drena Dobbs, Vasant Honavar

Drena Dobbs

Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i) NPS-HomPPI (Non partner-specific HomPPI), which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii) PS-HomPPI (Partner-specific HomPPI), which can be used ...


Pridb: A Protein–Rna Interface Database, Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, Drena Dobbs 2017 Iowa State University

Pridb: A Protein–Rna Interface Database, Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, Drena Dobbs

Drena Dobbs

The Protein–RNA Interface Database (PRIDB) is a comprehensive database of protein–RNA interfaces extracted from complexes in the Protein Data Bank (PDB). It is designed to facilitate detailed analyses of individual protein–RNA complexes and their interfaces, in addition to automated generation of user-defined data sets of protein–RNA interfaces for statistical analyses and machine learning applications. For any chosen PDB complex or list of complexes, PRIDB rapidly displays interfacial amino acids and ribonucleotides within the primary sequences of the interacting protein and RNA chains. PRIDB also identifies ProSite motifs in protein chains and FR3D motifs in RNA chains ...


Zfngenome: A Comprehensive Resource For Locating Zinc Finger Nuclease Target Sites In Model Organisms, Deepak Reyon, Jessica R. Kirkpatrick, Jeffry D. Sander, Feng Zhang, Daniel F. Voytas, J Keith Joung, Drena Dobbs, Clark R. Coffman 2017 Iowa State University

Zfngenome: A Comprehensive Resource For Locating Zinc Finger Nuclease Target Sites In Model Organisms, Deepak Reyon, Jessica R. Kirkpatrick, Jeffry D. Sander, Feng Zhang, Daniel F. Voytas, J Keith Joung, Drena Dobbs, Clark R. Coffman

Drena Dobbs

Background: Zinc Finger Nucleases (ZFNs) have tremendous potential as tools to facilitate genomic modifications, such as precise gene knockouts or gene replacements by homologous recombination. ZFNs can be used to advance both basic research and clinical applications, including gene therapy. Recently, the ability to engineer ZFNs that target any desired genomic DNA sequence with high fidelity has improved significantly with the introduction of rapid, robust, and publicly available techniques for ZFN design such as the Oligomerized Pool ENgineering (OPEN) method. The motivation for this study is to make resources for genome modifications using OPEN-generated ZFNs more accessible to researchers by ...


Computational Modeling Suggests Dimerization Of Equine Infectious Anemia Virus Rev Is Required For Rna Binding, Chijioke N. Umunnakwe, Hyelee Loyd, Kinsey Cornick, Jerald R. Chavez, Drena Dobbs, Susan Carpenter 2017 Iowa State University

Computational Modeling Suggests Dimerization Of Equine Infectious Anemia Virus Rev Is Required For Rna Binding, Chijioke N. Umunnakwe, Hyelee Loyd, Kinsey Cornick, Jerald R. Chavez, Drena Dobbs, Susan Carpenter

Drena Dobbs

Background The lentiviral Rev protein mediates nuclear export of intron-containing viral RNAs that encode structural proteins or serve as the viral genome. Following translation, HIV-1 Rev localizes to the nucleus and binds its cognate sequence, termed the Rev-responsive element (RRE), in incompletely spliced viral RNA. Rev subsequently multimerizes along the viral RNA and associates with the cellular Crm1 export machinery to translocate the RNA-protein complex to the cytoplasm. Equine infectious anemia virus (EIAV) Rev is functionally homologous to HIV-1 Rev, but shares very little sequence similarity and differs in domain organization. EIAV Rev also contains a bipartite RNA binding domain ...


Metastatic Biomarkers In Synovial Sarcoma, Rosalia de Necochea-Campion, Lee M. Zuckerman, Hamid R. Mirshahidi, Shahrzad Khosrowpour, Chien-Shing Chen, Saied Mirshahidi 2017 Loma Linda University

Metastatic Biomarkers In Synovial Sarcoma, Rosalia De Necochea-Campion, Lee M. Zuckerman, Hamid R. Mirshahidi, Shahrzad Khosrowpour, Chien-Shing Chen, Saied Mirshahidi

Library Articles and Research

Synovial sarcoma (SS) is an aggressive soft tissue sarcoma (STS) that typically occurs in the extremities near a joint. Metastatic disease is common and usually occurs in the lungs and lymph nodes. Surgical management is the mainstay of treatment with chemotherapy and radiation typically used as adjuvant treatment. Although chemotherapy has a positive impact on survival, the prognosis is poor if metastatic disease occurs. The biology of sarcoma invasion and metastasis remain poorly understood. Chromosomal translocation with fusion of the SYT and SSX genes has been described and is currently used as a diagnostic marker, although the full impact of ...


Differentiation And Containment Of Derived Pancreatic Beta Cells, Caden Duffy, Alonzo Cook Ph.D. 2017 Brigham Young University - Provo

Differentiation And Containment Of Derived Pancreatic Beta Cells, Caden Duffy, Alonzo Cook Ph.D.

Biomedical Engineering Western Regional Conference

Currently, the only permanent cure for Type 1 Diabetes is a pancreatic or islet transplant. With the shortage of donors, we are progressing research towards alternative therapies by differentiating induced pluripotent stem cells into derived pancreatic β-cells that can be transplanted and used as treatment for Type 1 Diabetes. We are investigating methods to increase the yield of fully derived, insulin producing pancreatic β-cells and are additionally researching the use of hydrophilized expanded polytetrafluoroethylene for use in cell containment devices. These devices could offer a future alternative for islet transplantation in human patients.


Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows 2017 Oregon State University

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.


Chimeric Antigen Receptor (Cars) For Thymidine Kinase 1 (Tk1): A Novel Immunotherapy Approach To Fight Cancer., Edwin Jesus Velazquez, Kiara Vaden, Michelle H. Townsend, Evita G. Weagel, Scott Weber, Richard A. Robison, Kim L. O'Neill 2017 Brigham Young University - Provo

Chimeric Antigen Receptor (Cars) For Thymidine Kinase 1 (Tk1): A Novel Immunotherapy Approach To Fight Cancer., Edwin Jesus Velazquez, Kiara Vaden, Michelle H. Townsend, Evita G. Weagel, Scott Weber, Richard A. Robison, Kim L. O'Neill

Biomedical Engineering Western Regional Conference

We have found the expression of Thymidine Kinase 1 (TK1) on the cell membrane of multiple cancer cell lines. We propose TK1 as a novel potential target for immune cell recognition in different cancer cell lines. Our research explores the use of these new targets in Chimeric antigen receptor (CAR) T-cell therapy.


Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, Mihai Hajdu 2017 The Graduate Center, City University of New York

Transcriptional And Post-Transcriptional Regulation Of Histone Variant H2a.Z During Sea Urchin Development, Mihai Hajdu

All Graduate Works by Year: Dissertations, Theses, and Capstone Projects

Histone variant H2A.Z promotes chromatin accessibility at transcriptional regulatory elements and is developmentally regulated in metazoans. We characterize the transcriptional and post-transcriptional regulation of H2A.Z in the purple sea urchin Strongylocentrotus purpuratus. H2A.Z depletion by antisense translation-blocking morpholino oligonucleotides during early development causes developmental collapse, in agreement with its previously demonstrated general role in transcriptional multipotency. During H2A.Z peak expression in 24-h embryos, endogenous H2A.Z 3’ UTR sequences stabilize GFP mRNAs relative to those with SV40 3’ UTR sequences, although the 3’UTR of H2A.Z does not determine the spatial distribution of H2A.Z ...


Analysis For Science Librarians Of The 2016 Nobel Prize In Physiology Or Medicine: The Life And Work Of Yoshinori Ohsumi, Neyda Gilman 2017 Binghamton University

Analysis For Science Librarians Of The 2016 Nobel Prize In Physiology Or Medicine: The Life And Work Of Yoshinori Ohsumi, Neyda Gilman

Library Scholarship

Autophagy is a cellular process of destruction and recycling. Cellular materials are broken down and recycled as needed, providing the body a way to remove unwanted material while also providing the means to create new needed items. The importance of this process and its possible role in numerous diseases is why Yoshinori Ohsumi has been awarded a 2016 Noble Prize. Ohsumi has been awarded the 2016 Nobel in Physiology or Medicine for his “discoveries of mechanisms for autophagy and thus paving the way for the exciting field of autophagy research” (Nobelprize.org “Press release: The 2016 Nobel Prize in Physiology ...


Mt1-Mmp Mediates The Migratory And Tumourigenic Potential Of Breast Cancer Cells Via Non-Proteolytic Mechanisms, Mario Cepeda 2017 The University of Western Ontario

Mt1-Mmp Mediates The Migratory And Tumourigenic Potential Of Breast Cancer Cells Via Non-Proteolytic Mechanisms, Mario Cepeda

Electronic Thesis and Dissertation Repository

Membrane Type-1 Matrix Metalloproteinase (MT1-MMP) is a multifunctional protease that affects cell function via proteolytic and non-proteolytic mechanisms such as promoting degradation of the extracellular matrix (ECM) or augmentation of cell migration and viability, respectively. MT1-MMP has been implicated in metastatic progression ostensibly due to its ability to degrade ECM components and to allow migration of cells through the basement membrane. Despite in vitro studies demonstrating this principle, this knowledge has not translated into the use of MMP inhibitors (MMPi) that inhibit substrate catalysis as effective cancer therapeutics, or been corroborated by evidence of in vivo ECM degradation mediated by ...


The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila 2017 University of California, Irvine School of Law

The Subject Librarian Newsletter, Biology, Spring 2017, Sandy Avila

Libraries' Newsletters

No abstract provided.


Evolutionary Adaptations Of Biofilms Infecting Cystic Fibrosis Lungs Promote Mechanical Toughness By Adjusting Polysaccharide Production, Kristin Kovach, Megan Davis-Fields, Yasuhiko Irie, Kanishk Jain, Shashvat Doorwar, Katherine Vuong, Numa Dhamani, Kishore Mohanty, Ahmed Touhami, Vernita D. Gordon 2017 University of Texas at Austin

Evolutionary Adaptations Of Biofilms Infecting Cystic Fibrosis Lungs Promote Mechanical Toughness By Adjusting Polysaccharide Production, Kristin Kovach, Megan Davis-Fields, Yasuhiko Irie, Kanishk Jain, Shashvat Doorwar, Katherine Vuong, Numa Dhamani, Kishore Mohanty, Ahmed Touhami, Vernita D. Gordon

Biology Faculty Publications

Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances, largely polysaccharides. Multiple types of extracellular polymeric substances can be produced by a single bacterial strain. The distinct polymer components of biofilms are known to provide chemical protection, but little is known about how distinct extracellular polysaccharides may also protect biofilms against mechanical stresses such as shear or phagocytic engulfment. Decades-long infections of Pseudomonas. aeruginosa biofilms in the lungs of cystic fibrosis patients are natural models for studies of biofilm fitness under pressure from antibiotics and the immune system. In cystic fibrosis infections, production of the extracellular ...


Chloroquine-Inducible Par-4 Secretion Is Essential For Tumor Cell Apoptosis And Inhibition Of Metastasis, Ravshan Burikhanov, Nikhil Hebbar, Sunil K. Noothi, Nidhi Shukla, James Sledziona, Nathália Araujo, Meghana Kudrimoti, Qing Jun Wang, David S. Watt, Danny R. Welch, Jodi Maranchie, Akihiro Harada, Vivek M. Rangnekar 2017 University of Kentucky

Chloroquine-Inducible Par-4 Secretion Is Essential For Tumor Cell Apoptosis And Inhibition Of Metastasis, Ravshan Burikhanov, Nikhil Hebbar, Sunil K. Noothi, Nidhi Shukla, James Sledziona, Nathália Araujo, Meghana Kudrimoti, Qing Jun Wang, David S. Watt, Danny R. Welch, Jodi Maranchie, Akihiro Harada, Vivek M. Rangnekar

Radiation Medicine Faculty Publications

The induction of tumor suppressor proteins capable of cancer cell apoptosis represents an attractive option for the re-purposing of existing drugs. We report that the anti-malarial drug, chloroquine (CQ), is a robust inducer of Par-4 secretion from normal cells in mice and cancer patients in a clinical trial. CQ-inducible Par-4 secretion triggers paracrine apoptosis of cancer cells and also inhibits metastatic tumor growth. CQ induces Par-4 secretion via the classical secretory pathway that requires the activation of p53. Mechanistically, p53 directly induces Rab8b, a GTPase essential for vesicle transport of Par-4 to the plasma membrane prior to secretion. Our findings ...


Caf-1 P150 And Ki-67 Regulate Nuclear Structure Throughout The Human Cell Cycle, Timothy D. Matheson 2017 University of Massachusetts Medical School

Caf-1 P150 And Ki-67 Regulate Nuclear Structure Throughout The Human Cell Cycle, Timothy D. Matheson

GSBS Dissertations and Theses

The three-dimensional organization of the human genome is non-random in interphase cells. Heterochromatin is highly clustered at the nuclear periphery, adjacent to nucleoli, and near centromeres. These localizations are reshuffled during mitosis when the chromosomes are condensed, nucleoli disassembled, and the nuclear envelope broken down. After cytokinesis, heterochromatin is re-localized to the domains described above. However, the mechanisms by which this localization is coordinated are not well understood. This dissertation will present evidence showing that both CAF-1 p150 and Ki-67 regulate nuclear structure throughout the human cell cycle.

Chromatin Assembly Factor 1 (CAF-1) is a highly conserved three-subunit protein complex ...


Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Susan Starling 2017 Trivedi Global Inc

Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Susan Starling

Susan Elizabeth Starling

With the increasing popularity of herbomineral preparations in healthcare, a new proprietary herbomineral formulation was formulated with ashwagandha root extract and three minerals viz. zinc, magnesium, and selenium. The aim of the study was to evaluate the immunomodulatory potential of Biofield Energy Healing (The Trivedi Effect®) on the herbomineral formulation using murine splenocyte cells. The test formulation was divided into two parts. One was the control without the Biofield Energy Treatment. The other part was labelled the Biofield Energy Treated sample, which received the Biofield Energy Healing Treatment remotely by twenty renowned Biofield Energy Healers. Through MTT assay, all the ...


Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Peter Surguy 2017 Trivedi Global Inc

Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Peter Surguy

Peter Lynwood Surguy

With the increasing popularity of herbomineral preparations in healthcare, a new proprietary herbomineral formulation was formulated with ashwagandha root extract and three minerals viz. zinc, magnesium, and selenium. The aim of the study was to evaluate the immunomodulatory potential of Biofield Energy Healing (The Trivedi Effect®) on the herbomineral formulation using murine splenocyte cells. The test formulation was divided into two parts. One was the control without the Biofield Energy Treatment. The other part was labelled the Biofield Energy Treated sample, which received the Biofield Energy Healing Treatment remotely by twenty renowned Biofield Energy Healers. Through MTT assay, all the ...


Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Susan Allen 2017 Trivedi Global Inc.

Modulation Of Pro-Inflammatory Cytokines Expression Of The Biofield Energy Healing (The Trivedi Effect®) Based Herbomineral Formulation In Mouse Splenocytes, Susan Allen

Susan Mardis Allen

With the increasing popularity of herbomineral preparations in healthcare, a new proprietary herbomineral formulation was formulated with ashwagandha root extract and three minerals viz. zinc, magnesium, and selenium. The aim of the study was to evaluate the immunomodulatory potential of Biofield Energy Healing (The Trivedi Effect®) on the herbomineral formulation using murine splenocyte cells. The test formulation was divided into two parts. One was the control without the Biofield Energy Treatment. The other part was labelled the Biofield Energy Treated sample, which received the Biofield Energy Healing Treatment remotely by twenty renowned Biofield Energy Healers. Through MTT assay, all the ...


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