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Inflammatory Muscle Diseases., Marinos C Dalakas Apr 2015

Inflammatory Muscle Diseases., Marinos C Dalakas

Department of Neurology Faculty Papers

No abstract provided.


Evidence For Patterns Of Selective Urban Migration In The Greater Indus Valley (2600-1900 Bc): A Lead And Strontium Isotope Mortuary Analysis, Benjamin Valentine, George D. Kamenov, Jonathan Mark Kenoyer, Vasant Shinde, Veena Mushrif-Tripathy, Erik Otarola-Castillo, John Krigbaum Apr 2015

Evidence For Patterns Of Selective Urban Migration In The Greater Indus Valley (2600-1900 Bc): A Lead And Strontium Isotope Mortuary Analysis, Benjamin Valentine, George D. Kamenov, Jonathan Mark Kenoyer, Vasant Shinde, Veena Mushrif-Tripathy, Erik Otarola-Castillo, John Krigbaum

Dartmouth Scholarship

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people’s movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a …


Can Polychlorinated Biphenyl (Pcb) Signatures And Enantiomer Fractions Be Used For Source Identification And To Age Date Occupational Exposure?, David Megson, Jean Françios Focant, Donald G. Patterson, Matthew Robson, Maeve C. Lohan, Paul J. Worsfold, Sean Comber, Robert Kalin, Eric Reiner, Gwen O'Sullivan Apr 2015

Can Polychlorinated Biphenyl (Pcb) Signatures And Enantiomer Fractions Be Used For Source Identification And To Age Date Occupational Exposure?, David Megson, Jean Françios Focant, Donald G. Patterson, Matthew Robson, Maeve C. Lohan, Paul J. Worsfold, Sean Comber, Robert Kalin, Eric Reiner, Gwen O'Sullivan

School of Geography, Earth and Environmental Sciences

Detailed polychlorinated biphenyl (PCB) signatures and chiral Enantiomer Fractions (EFs) of CB-95, CB-136 and CB-149 were measured for 30 workers at a transformer dismantling plant. This was undertaken to identify sources of exposure and investigate changes to the PCB signature and EFs over different exposure periods. Approximately 1.5 g of serum was extracted and PCB signatures were created through analysis by comprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC×GC-TOFMS) and EFs calculated following analysis by gas chromatography with high resolution mass spectrometry (GC-HRMS). A total of 84 PCBs were identified in the serum samples with concentrations of the 7 …


Translation Initiation Complex Eif4f Is A Therapeutic Target For Dual Mtor Kinase Inhibitors In Non-Hodgkin Lymphoma., Christos Demosthenous, Jing Jing Han, Mary J Stenson, Matthew J Maurer, Linda E Wellik, Brian Link, Kristen Hege, Ahmet Dogan, Eduardo Sotomayor, Thomas Witzig, Mamta Gupta Apr 2015

Translation Initiation Complex Eif4f Is A Therapeutic Target For Dual Mtor Kinase Inhibitors In Non-Hodgkin Lymphoma., Christos Demosthenous, Jing Jing Han, Mary J Stenson, Matthew J Maurer, Linda E Wellik, Brian Link, Kristen Hege, Ahmet Dogan, Eduardo Sotomayor, Thomas Witzig, Mamta Gupta

Medicine Faculty Publications

Deregulated mRNA translation has been implicated in disease development and in part is controlled by a eukaryotic initiation complex eIF4F (composed of eIF4E, eIF4G and eIF4A). We demonstrate here that the cap bound fraction from lymphoma cells was enriched with eIF4G and eIF4E indicating that lymphoma cells exist in an activated translational state. Moreover, 77% (110/142) of diffuse large B cell lymphoma tumors expressed eIF4E and this was associated with an inferior event free survival. Over-expression of wild-type eIF4E (eIF4E(WT)) but not cap-mutant eIF4E (eIF4E(cap mutant)) increased the activation of the eIF4F complex. Treatment with the active-site dual mTOR inhibitor …


Loregic: A Method To Characterize The Cooperative Logic Of Regulatory Factors, Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel Rozowsky, William Meyerson, Mark B. Gerstein Apr 2015

Loregic: A Method To Characterize The Cooperative Logic Of Regulatory Factors, Daifeng Wang, Koon-Kiu Yan, Cristina Sisu, Chao Cheng, Joel Rozowsky, William Meyerson, Mark B. Gerstein

Dartmouth Scholarship

The topology of the gene-regulatory network has been extensively analyzed. Now, given the large amount of available functional genomic data, it is possible to go beyond this and systematically study regulatory circuits in terms of logic elements. To this end, we present Loregic, a computational method integrating gene expression and regulatory network data, to characterize the cooperativity of regulatory factors. Loregic uses all 16 possible two-input-one-output logic gates (e.g. AND or XOR) to describe triplets of two factors regulating a common target. We attempt to find the gate that best matches each triplet’s observed gene expression pattern across many conditions. …


Targeting Human Central Nervous System Protein Kinases: An Isoform Selective P38Αmapk Inhibitor That Attenuates Disease Progression In Alzheimer's Disease Mouse Models, Saktimayee M. Roy, Valerie L. Grum-Tokars, James P. Schavocky, Faisal Saeed, Agnieszka Staniszewski, Andrew F. Teich, Ottavio Arancio, Adam D. Bachstetter, Scott J. Webster, Linda J. Van Eldik, George Minasov, Wayne F. Anderson, Jeffrey C. Pelletier, D. Martin Watterson Apr 2015

Targeting Human Central Nervous System Protein Kinases: An Isoform Selective P38Αmapk Inhibitor That Attenuates Disease Progression In Alzheimer's Disease Mouse Models, Saktimayee M. Roy, Valerie L. Grum-Tokars, James P. Schavocky, Faisal Saeed, Agnieszka Staniszewski, Andrew F. Teich, Ottavio Arancio, Adam D. Bachstetter, Scott J. Webster, Linda J. Van Eldik, George Minasov, Wayne F. Anderson, Jeffrey C. Pelletier, D. Martin Watterson

Spinal Cord and Brain Injury Research Center Faculty Publications

The first kinase inhibitor drug approval in 2001 initiated a remarkable decade of tyrosine kinase inhibitor drugs for oncology indications, but a void exists for serine/threonine protein kinase inhibitor drugs and central nervous system indications. Stress kinases are of special interest in neurological and neuropsychiatric disorders due to their involvement in synaptic dysfunction and complex disease susceptibility. Clinical and preclinical evidence implicates the stress related kinase p38αMAPK as a potential neurotherapeutic target, but isoform selective p38αMAPK inhibitor candidates are lacking and the mixed kinase inhibitor drugs that are promising in peripheral tissue disease indications have limitations for neurologic indications. Therefore, …


Chaperone Hsp47 Drives Malignant Growth And Invasion By Modulating An Ecm Gene Network, Jieqing Zhu, Gaofeng Xiong, Hanjiang Fu, B. Mark Evers, Binhua P. Zhou, Ren Xu Apr 2015

Chaperone Hsp47 Drives Malignant Growth And Invasion By Modulating An Ecm Gene Network, Jieqing Zhu, Gaofeng Xiong, Hanjiang Fu, B. Mark Evers, Binhua P. Zhou, Ren Xu

Markey Cancer Center Faculty Publications

The extracellular matrix (ECM) is a determining factor in the tumor microenvironment that restrains or promotes malignant growth. In this report, we show how the molecular chaperone protein Hsp47 functions as a nodal hub in regulating an ECM gene transcription network. A transcription network analysis showed that Hsp47 expression was activated during breast cancer development and progression. Hsp47 silencing reprogrammed human breast cancer cells to form growth-arrested and/or noninvasive structures in 3D cultures, and to limit tumor growth in xenograft assays by reducing deposition of collagen and fibronectin. Coexpression network analysis also showed that levels of microRNA(miR)-29b and -29c were …


Implementing A Patient-Initiated Review System In Rheumatoid Arthritis: A Qualitative Evaluation., Sue Child, Victoria A. Goodwin, Mark G. Perry, Christian A. Gericke, Richard Byng Apr 2015

Implementing A Patient-Initiated Review System In Rheumatoid Arthritis: A Qualitative Evaluation., Sue Child, Victoria A. Goodwin, Mark G. Perry, Christian A. Gericke, Richard Byng

Peninsula Medical School

BACKGROUND: The management of Rheumatoid Arthritis (RA), a chronic relapsing condition primarily affecting joints usually entails regular hospital reviews with a specialist. These reviews can occur when the patient is well. This study forms part of a service evaluation of a system wide implementation of a patient initiated review appointment system which we have called Direct Access (DA). The aim was to explore the experiences of patients and staff of a DA system in order to understand the process of the implementation and to identify potential improvements. METHODS: Twenty-three patients with RA that had completed one year of follow-up on …


Machine Learning Methods Enable Predictive Modeling Of Antibody Feature:Function Relationships In Rv144 Vaccinees, Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayapha, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg Apr 2015

Machine Learning Methods Enable Predictive Modeling Of Antibody Feature:Function Relationships In Rv144 Vaccinees, Ickwon Choi, Amy W. Chung, Todd J. Suscovich, Supachai Rerks-Ngarm, Punnee Pitisuttithum, Sorachai Nitayapha, Jaranit Kaewkungwal, Robert J. O'Connell, Donald Francis, Merlin L. Robb, Nelson L. Michael, Jerome H. Kim, Galit Alter, Margaret E. Ackerman, Chris Bailey-Kellogg

Dartmouth Scholarship

The adaptive immune response to vaccination or infection can lead to the production of specific antibodies to neutralize the pathogen or recruit innate immune effector cells for help. The non-neutralizing role of antibodies in stimulating effector cell responses may have been a key mechanism of the protection observed in the RV144 HIV vaccine trial. In an extensive investigation of a rich set of data collected from RV144 vaccine recipients, we here employ machine learning methods to identify and model associations between antibody features (IgG subclass and antigen specificity) and effector function activities (antibody dependent cellular phagocytosis, cellular cytotoxicity, and cytokine …


Transcriptional Activity Of The Islet Β Cell Factor Pdx1 Is Augmented By Lysine Methylation Catalyzed By The Methyltransferase Set7/9, Aarthi V. Maganti, Bernhard Maier, Sarah A. Tersey, Megan L. Sampley, Amber L. Mosley, Sabire Özcan, Boobalan Pachaiyappan, Patrick M. Woster, Chad S. Hunter, Roland Stein, Raghavendra G. Mirmira Apr 2015

Transcriptional Activity Of The Islet Β Cell Factor Pdx1 Is Augmented By Lysine Methylation Catalyzed By The Methyltransferase Set7/9, Aarthi V. Maganti, Bernhard Maier, Sarah A. Tersey, Megan L. Sampley, Amber L. Mosley, Sabire Özcan, Boobalan Pachaiyappan, Patrick M. Woster, Chad S. Hunter, Roland Stein, Raghavendra G. Mirmira

Molecular and Cellular Biochemistry Faculty Publications

The transcription factor Pdx1 is crucial to islet β cell function and regulates target genes in part through interaction with coregulatory factors. Set7/9 is a Lys methyltransferase that interacts with Pdx1. Here we tested the hypothesis that Lys methylation of Pdx1 by Set7/9 augments Pdx1 transcriptional activity. Using mass spectrometry and mutational analysis of purified proteins, we found that Set7/9 methylates the N-terminal residues Lys-123 and Lys-131 of Pdx1. Methylation of these residues occurred only in the context of intact, full-length Pdx1, suggesting a specific requirement of secondary and/or tertiary structural elements for catalysis by Set7/9. Immunoprecipitation assays and mass …


Targeted Single Molecule Sequencing Methodology For Ovarian Hyperstimulation Syndrome., Funda Orkunoglu-Suer, Arthur F. Harralson, David Frankfurter, Paul Gindoff, Travis J. O'Brien Apr 2015

Targeted Single Molecule Sequencing Methodology For Ovarian Hyperstimulation Syndrome., Funda Orkunoglu-Suer, Arthur F. Harralson, David Frankfurter, Paul Gindoff, Travis J. O'Brien

Genomics and Precision Medicine Faculty Publications

BACKGROUND: One of the most significant issues surrounding next generation sequencing is the cost and the difficulty assembling short read lengths. Targeted capture enrichment of longer fragments using single molecule sequencing (SMS) is expected to improve both sequence assembly and base-call accuracy but, at present, there are very few examples of successful application of these technologic advances in translational research and clinical testing. We developed a targeted single molecule sequencing (T-SMS) panel for genes implicated in ovarian response to controlled ovarian hyperstimulation (COH) for infertility.

RESULTS: Target enrichment was carried out using droplet-base multiplex polymerase chain reaction (PCR) technology (RainDance®) …


Molecular Effects Of Cancer-Associated Somatic Mutations On The Structural And Target Recognition Properties Of Keap1., Halema Khan, Ryan C Killoran, Anne Brickenden, Jingsong Fan, Daiwen Yang, Wing-Yiu Choy Apr 2015

Molecular Effects Of Cancer-Associated Somatic Mutations On The Structural And Target Recognition Properties Of Keap1., Halema Khan, Ryan C Killoran, Anne Brickenden, Jingsong Fan, Daiwen Yang, Wing-Yiu Choy

Biochemistry Publications

Kelch-like ECH-associated protein 1 (Keap1) plays an important regulatory role in the nuclear factor erythroid 2-related factor 2 (Nrf2)-dependent oxidative stress response pathway. It functions as a repressor of Nrf2, a key transcription factor that initiates the expression of cytoprotective enzymes during oxidative stress to protect cells from damage caused by reactive oxygen species. Recent studies show that mutations of Keap1 can lead to aberrant activation of the antioxidant pathway, which is associated with different types of cancers. To gain a mechanistic understanding of the links between Keap1 mutations and cancer pathogenesis, we have investigated the molecular effects of a …


The Human Motor System Alters Its Reaching Movement Plan For Task-Irrelevant, Positional Forces., Joshua G A Cashaback, Heather R Mcgregor, Paul L Gribble Apr 2015

The Human Motor System Alters Its Reaching Movement Plan For Task-Irrelevant, Positional Forces., Joshua G A Cashaback, Heather R Mcgregor, Paul L Gribble

Brain and Mind Institute Researchers' Publications

The minimum intervention principle and the uncontrolled manifold hypothesis state that our nervous system only responds to force perturbations and sensorimotor noise if they affect task success. This idea has been tested in muscle and joint coordinate frames and more recently using workspace redundancy (e.g., reaching to large targets). However, reaching studies typically involve spatial and or temporal constraints. Constrained reaches represent a small proportion of movements we perform daily and may limit the emergence of natural behavior. Using more relaxed constraints, we conducted two reaching experiments to test the hypothesis that humans respond to task-relevant forces and ignore task-irrelevant …


Antibody-Mediated Targeting Of Iron Oxide Nanoparticles To The Folate Receptor Alpha Increases Tumor Cell Association In Vitro And In Vivo, Christian Ndong, Seiko Toraya-Brown, Katsiaryna Kekalo, Ian Baker, Tillman U. Gerngross, Steven N. Fiering, Karl E. Griswold Apr 2015

Antibody-Mediated Targeting Of Iron Oxide Nanoparticles To The Folate Receptor Alpha Increases Tumor Cell Association In Vitro And In Vivo, Christian Ndong, Seiko Toraya-Brown, Katsiaryna Kekalo, Ian Baker, Tillman U. Gerngross, Steven N. Fiering, Karl E. Griswold

Dartmouth Scholarship

Active molecular targeting has become an important aspect of nanoparticle development for oncology indications. Here, we describe molecular targeting of iron oxide nanoparticles (IONPs) to the folate receptor alpha (FOLRα) using an engineered antibody fragment (Ffab). Compared to control nanoparticles targeting the non-relevant botulinum toxin, the Ffab-IONP constructs selectively accumulated on FOLRα-overexpressing cancer cells in vitro, where they exhibited the capacity to internalize into intracellular vesicles. Similarly, Ffab-IONPs homed to FOLRα-positive tumors upon intraperitoneal administration in an orthotopic murine xenograft model of ovarian cancer, whereas negative control particles showed no detectable tumor accumulation. Interestingly, Ffab-IONPs built with custom 120 nm …


An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein Mar 2015

An Approach For Determining And Measuring Network Hierarchy Applied To Comparing The Phosphorylome And The Regulome, Chao Cheng, Erik Andrews, Koon-Kiu Yan, Matthew Ung, Daifeng Wang, Mark Gerstein

Dartmouth Scholarship

Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.


Focused Ultrasound For Treatment Of Bone Tumours., Dario B. Rodrigues, Paul R. Stauffer, David Vrba, Mark Hurwitz, Md Mar 2015

Focused Ultrasound For Treatment Of Bone Tumours., Dario B. Rodrigues, Paul R. Stauffer, David Vrba, Mark Hurwitz, Md

Department of Radiation Oncology Faculty Papers

PURPOSE: Focused ultrasound (FUS) is a modality with rapidly expanding applications across the field of medicine. Treatment of bone lesions with FUS including both benign and malignant tumours has been an active area of investigation. Recently, as a result of a successful phase III trial, magnetic resonance-guided FUS is now a standardised option for treatment of painful bone metastases. This report reviews the clinical applications amenable to treatment with FUS and provides background on FUS and image guidance techniques, results of clinical studies, and future directions.

METHODS: A comprehensive literature search and review of abstracts presented at the recently completed …


G9a Is Essential For Emt-Mediated Metastasis And Maintenance Of Cancer Stem Cell-Like Characters In Head And Neck Squamous Cell Carcinoma, Shuli Liu, Dongxia Ye, Wenzheng Guo, Wenwen Yu, Yue He, Jingzhou Hu, Yanan Wang, Ling Zhang, Yueling Liao, Hongyong Song, Shuangshuang Zhong, Dongliang Xu, Huijing Yin, Beibei Sun, Xiaofei Wang, Jingyi Liu, Yadi Wu, Binhua P. Zhou, Zhiyuan Zhang, Jiong Deng Mar 2015

G9a Is Essential For Emt-Mediated Metastasis And Maintenance Of Cancer Stem Cell-Like Characters In Head And Neck Squamous Cell Carcinoma, Shuli Liu, Dongxia Ye, Wenzheng Guo, Wenwen Yu, Yue He, Jingzhou Hu, Yanan Wang, Ling Zhang, Yueling Liao, Hongyong Song, Shuangshuang Zhong, Dongliang Xu, Huijing Yin, Beibei Sun, Xiaofei Wang, Jingyi Liu, Yadi Wu, Binhua P. Zhou, Zhiyuan Zhang, Jiong Deng

Markey Cancer Center Faculty Publications

Head and neck squamous cell carcinoma (HNSCC) is a particularly aggressive cancer with poor prognosis, largely due to lymph node metastasis and local recurrence. Emerging evidence suggests that epithelial-to-mesenchymal transition (EMT) is important for cancer metastasis, and correlated with increased cancer stem cells (CSCs) characteristics. However, the mechanisms underlying metastasis to lymph nodes in HNSCC is poorly defined. In this study, we show that E-cadherin repression correlates with cancer metastasis and poor prognosis in HNSCC. We found that G9a, a histone methyltransferase, interacts with Snail and mediates Snail-induced transcriptional repression of E-cadherin and EMT, through methylation of histone H3 lysine-9 …


Effects Of Periodontal Therapy On White Blood Cell Count And Levels Of Transforming Growth Factor Beta In Serum Of Subjects With Severe Periodontitis, A. C. E. Leite, V. M. A. Carneiro, Ana Carolina Morandini, Erivan Schnaider Ramos-Junior, M. C. M. Guimarães Mar 2015

Effects Of Periodontal Therapy On White Blood Cell Count And Levels Of Transforming Growth Factor Beta In Serum Of Subjects With Severe Periodontitis, A. C. E. Leite, V. M. A. Carneiro, Ana Carolina Morandini, Erivan Schnaider Ramos-Junior, M. C. M. Guimarães

All Dugoni School of Dentistry Faculty Articles

This study aimed to investigate the effects of nonsurgical periodontal therapy on white blood cell (WBC) count and levels of transforming growth factor beta (TGF—β) in serum from subjects with severe periodontitis. Serum from 28 subjects with periodontitis (mean age: 34.36±6.24; 32% men) and 27 healthy controls (mean age: 33.18±6.42; 33% men) were collected prior to therapy. Blood samples were obtained from 23 subjects who completed therapy (9—12 months). A well—controlled periodontal treatment protocol was established in three stages: mechanical periodontal therapy (scaling and root planning), reinstrumentation of dental sites, and supportive periodontal therapy. Periodontal and systemic parameters such as …


Review Of Nanomaterials In Dentistry: Interactions With The Oral Microenvironment, Clinical Applications, Hazards, And Benefits., Alexandros Besinis, Peralta T De, Christopher J. Tredwin, Richard D. Handy Mar 2015

Review Of Nanomaterials In Dentistry: Interactions With The Oral Microenvironment, Clinical Applications, Hazards, And Benefits., Alexandros Besinis, Peralta T De, Christopher J. Tredwin, Richard D. Handy

School of Engineering, Computing and Mathematics

Interest in the use of engineered nanomaterials (ENMs) as either nanomedicines or dental materials/devices in clinical dentistry is growing. This review aims to detail the ultrafine structure, chemical composition, and reactivity of dental tissues in the context of interactions with ENMs, including the saliva, pellicle layer, and oral biofilm; then describes the applications of ENMs in dentistry in context with beneficial clinical outcomes versus potential risks. The flow rate and quality of saliva are likely to influence the behavior of ENMs in the oral cavity, but how the protein corona formed on the ENMs will alter bioavailability, or interact with …


Kalkitoxin Inhibits Angiogenesis, Disrupts Cellular Hypoxic Signaling, And Blocks Mitochondrial Electron Transport In Tumor Cells, J B. Morgan, Yang Liu, Veena Coothankandaswamy, Fakhri Mahdi, Mika B. Jekabsons, William H. Gerwick, Frederick A. Valeriote, Yu-Dong Zhou, Dale G. Nagle Mar 2015

Kalkitoxin Inhibits Angiogenesis, Disrupts Cellular Hypoxic Signaling, And Blocks Mitochondrial Electron Transport In Tumor Cells, J B. Morgan, Yang Liu, Veena Coothankandaswamy, Fakhri Mahdi, Mika B. Jekabsons, William H. Gerwick, Frederick A. Valeriote, Yu-Dong Zhou, Dale G. Nagle

Hematology/Oncology Articles

The biologically active lipopeptide kalkitoxin was previously isolated from the marine cyanobacterium Moorea producens (Lyngbya majuscula). Kalkitoxin exhibited N-methyl-D-aspartate (NMDA)-mediated neurotoxicity and acted as an inhibitory ligand for voltage-sensitive sodium channels in cultured rat cerebellar granule neurons. Subsequent studies revealed that kalkitoxin generated a delayed form of colon tumor cell cytotoxicity in 7-day clonogenic cell survival assays. Cell line- and exposure time-dependent cytostatic/cytotoxic effects were previously observed with mitochondria-targeted inhibitors of hypoxia-inducible factor-1 (HIF-1). The transcription factor HIF-1 functions as a key regulator of oxygen homeostasis. Therefore, we investigated the ability of kalkitoxin to inhibit hypoxic signaling in human tumor …


Predicted Protein-Protein Interactions In The Moss Physcomitrella Patens: A New Bioinformatic Resource., Scott Schuette, Brian Piatkowski, Aaron Corley, Daniel Lang, Matt Geisler Mar 2015

Predicted Protein-Protein Interactions In The Moss Physcomitrella Patens: A New Bioinformatic Resource., Scott Schuette, Brian Piatkowski, Aaron Corley, Daniel Lang, Matt Geisler

Publications

BACKGROUND: Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants.

RESULTS: The first predicted protein-protein interactome for a bryophyte …


Sparcoc: A New Framework For Molecular Pattern Discovery And Cancer Gene Identification, Shiqian Ma, Daniel Johnson, Cody Ashby, Donghai Xiong, Carole L. Cramer, Jason H. Moore, Shuzhong Zhang, Xiuzhen Huang Mar 2015

Sparcoc: A New Framework For Molecular Pattern Discovery And Cancer Gene Identification, Shiqian Ma, Daniel Johnson, Cody Ashby, Donghai Xiong, Carole L. Cramer, Jason H. Moore, Shuzhong Zhang, Xiuzhen Huang

Dartmouth Scholarship

It is challenging to cluster cancer patients of a certain histopathological type into molecular subtypes of clinical importance and identify gene signatures directly relevant to the subtypes. Current clustering approaches have inherent limitations, which prevent them from gauging the subtle heterogeneity of the molecular subtypes. In this paper we present a new framework: SPARCoC (Sparse-CoClust), which is based on a novel Common-background and Sparse-foreground Decomposition (CSD) model and the Maximum Block Improvement (MBI) co-clustering technique. SPARCoC has clear advantages compared with widely-used alternative approaches: hierarchical clustering (Hclust) and nonnegative matrix factorization (NMF). We apply SPARCoC to the study of lung …


Microscale Magnetic Field Modulation For Enhanced Capture And Distribution Of Rare Circulating Tumor Cells, Peng Chen, Yu-Yen Huang, Kazunori Hoshino, John X.J Zhang Mar 2015

Microscale Magnetic Field Modulation For Enhanced Capture And Distribution Of Rare Circulating Tumor Cells, Peng Chen, Yu-Yen Huang, Kazunori Hoshino, John X.J Zhang

Dartmouth Scholarship

Immunomagnetic assay combines the powers of the magnetic separation and biomarker recognition and has been an effective tool to perform rare Circulating Tumor Cells detection. Key factors associated with immunomagnetic assay include the capture rate, which indicates the sensitivity of the system, and distributions of target cells after capture, which impact the cell integrity and other biological properties that are critical to downstream analyses. Here we present a theoretical framework and technical approach to implement a microscale magnetic immunoassay through modulating local magnetic field towards enhanced capture and distribution of rare cancer cells. Through the design of a two-dimensional micromagnet …


Unlocking The Mysteries Of Tdp-43, Keith A. Josephs, Peter T. Nelson Mar 2015

Unlocking The Mysteries Of Tdp-43, Keith A. Josephs, Peter T. Nelson

Sanders-Brown Center on Aging Faculty Publications

No abstract provided.


Metabolic Reprogramming Of Cancer-Associated Fibroblasts By Idh3Α Downregulation, Daoxiang Zhang, Yongbin Wang, Zhimin Shi, Jingyi Liu, Pan Sun, Xiaodan Hou, Jian Zhang, Shimin Zhao, Binhua P. Zhou, Jun Mi Mar 2015

Metabolic Reprogramming Of Cancer-Associated Fibroblasts By Idh3Α Downregulation, Daoxiang Zhang, Yongbin Wang, Zhimin Shi, Jingyi Liu, Pan Sun, Xiaodan Hou, Jian Zhang, Shimin Zhao, Binhua P. Zhou, Jun Mi

Markey Cancer Center Faculty Publications

Cancer-associated fibroblasts (CAFs) provide critical metabolites for tumor growth and undergo metabolic reprogramming to support glycolysis. However, the molecular mechanisms responsible for this change remain unclear. Here, we report that TGF-β1- or PDGF-induced CAFs switch from oxidative phosphorylation to aerobic glycolysis. We identify downregulation of isocitrate dehydrogenase 3α (IDH3α) as a marker for this switch. Furthermore, miR-424 downregulates IDH3α during CAF formation. Downregulation of IDH3α decreases the effective level of α-ketoglutarate (α-KG) by reducing the ratio of α-KG to fumarate and succinate, resulting in PHD2 inhibition and HIF-1α protein stabilization. The accumulation of HIF-1α, in turn, promotes glycolysis by increasing …


Identification Of A Family Of Fatty Acid-Speciated Sonic Hedgehog Proteins, Whose Members Display Differential Biological Properties, Jun Long, Robert Tokhunts, William M. Old, Stephane Houel, Jezabel Rodgriguez-Blanco, Samer Singh, Neal Schilling, Anthony J. Capobianco, Natalie G. Ahn, David J. Robbins Mar 2015

Identification Of A Family Of Fatty Acid-Speciated Sonic Hedgehog Proteins, Whose Members Display Differential Biological Properties, Jun Long, Robert Tokhunts, William M. Old, Stephane Houel, Jezabel Rodgriguez-Blanco, Samer Singh, Neal Schilling, Anthony J. Capobianco, Natalie G. Ahn, David J. Robbins

Dartmouth Scholarship

Hedgehog (HH) proteins are proteolytically processed into a biologically active form that is covalently modified by cholesterol and palmitate. However, most studies of HH biogenesis have characterized protein from cells in which HH is overexpressed. We purified Sonic Hedgehog (SHH) from cells expressing physiologically relevant levels and showed that it was more potent than SHH isolated from overexpressing cells. Furthermore, the SHH in our preparations was modified with a diverse spectrum of fatty acids on its amino termini, and this spectrum of fatty acids varied dramatically depending on the growth conditions of the cells. The fatty acid composition of SHH …


Spectral Gene Set Enrichment (Sgse), H Robert Frost, Zhigang Li, Jason H. Moore Mar 2015

Spectral Gene Set Enrichment (Sgse), H Robert Frost, Zhigang Li, Jason H. Moore

Dartmouth Scholarship

Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes …


Overexpression Of Mir‑145 In U87 Cells Reduces Glioma Cell Malignant Phenotype And Promotes Survival After In Vivo Implantation, Yong Lu, Michael Chopp, Xuguang Zheng, Mark Katakowski, Ding Wang, Elise Fraser, Monique Nguyen, Feng Jiang Mar 2015

Overexpression Of Mir‑145 In U87 Cells Reduces Glioma Cell Malignant Phenotype And Promotes Survival After In Vivo Implantation, Yong Lu, Michael Chopp, Xuguang Zheng, Mark Katakowski, Ding Wang, Elise Fraser, Monique Nguyen, Feng Jiang

Neurology Articles

In the present study, we sought to elucidate the effect of miR‑145 on glioma cell progression and its mechanisms of action. We examined the effects of miR‑145 on proliferation and invasion of U87 glioma cells and on capillary tube formation. Our data show that restoration of miR‑145 in U87 glioma cells significantly reduced their in vitro proliferation, invasion and angiogenesis. However, decreased miR‑145 expression promoted U87 glioma cell proliferation, invasion and angiogenesis, and reduced-expression of miR‑145 increased ADAM17 and EGFR expression in U87 cells. Overexpression of miR‑145 reduced ADAM17 and EGFR expression. VEGF secretion and VEGF expression were decreased by …


Clinical Outcomes Of Splenectomy In Children: Report Of The Splenectomy In Congenital Hemolytic Anemia Registry., Henry E. Rice, Brian R. Englum, Jennifer Rothman, Sarah Leonard, Audra Reiter, Courtney Thornburg, Mary Brindle, Nicola Wright, Matthew M. Heeney, Charles Smithers, Rebeccah L. Brown, Theodosia Kalfa, Jacob C. Langer, Michaela Cada, Keith T. Oldham, J Paul Scott, Shawn D. St Peter, Mukta Sharma, Andrew M. Davidoff, Kerri Nottage, Kathryn Bernabe, David B. Wilson, Sanjeev Dutta, Bertil Glader, Shelley E. Crary, Melvin S. Dassinger, Levette Dunbar, Saleem Islam, Manjusha Kumar, Fred Rescorla, Steve Bruch, Andrew Campbell, Mary Austin, Robert Sidonio, Martin L Blakely, Splenectomy In Congenital Hemolytic Anemia (Sicha) Consortium Mar 2015

Clinical Outcomes Of Splenectomy In Children: Report Of The Splenectomy In Congenital Hemolytic Anemia Registry., Henry E. Rice, Brian R. Englum, Jennifer Rothman, Sarah Leonard, Audra Reiter, Courtney Thornburg, Mary Brindle, Nicola Wright, Matthew M. Heeney, Charles Smithers, Rebeccah L. Brown, Theodosia Kalfa, Jacob C. Langer, Michaela Cada, Keith T. Oldham, J Paul Scott, Shawn D. St Peter, Mukta Sharma, Andrew M. Davidoff, Kerri Nottage, Kathryn Bernabe, David B. Wilson, Sanjeev Dutta, Bertil Glader, Shelley E. Crary, Melvin S. Dassinger, Levette Dunbar, Saleem Islam, Manjusha Kumar, Fred Rescorla, Steve Bruch, Andrew Campbell, Mary Austin, Robert Sidonio, Martin L Blakely, Splenectomy In Congenital Hemolytic Anemia (Sicha) Consortium

Manuscripts, Articles, Book Chapters and Other Papers

The outcomes of children with congenital hemolytic anemia (CHA) undergoing total splenectomy (TS) or partial splenectomy (PS) remain unclear. In this study, we collected data from 100 children with CHA who underwent TS or PS from 2005 to 2013 at 16 sites in the Splenectomy in Congenital Hemolytic Anemia (SICHA) consortium using a patient registry. We analyzed demographics and baseline clinical status, operative details, and outcomes at 4, 24, and 52 weeks after surgery. Results were summarized as hematologic outcomes, short-term adverse events (AEs) (≤30 days after surgery), and long-term AEs (31-365 days after surgery). For children with hereditary spherocytosis, …


Cosmetics For The Matrix: An Attractive New Style For Matrix Biology., Renato V. Iozzo, Thomas Neill Mar 2015

Cosmetics For The Matrix: An Attractive New Style For Matrix Biology., Renato V. Iozzo, Thomas Neill

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

No abstract provided.