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Molecular Biology

Program in Molecular Medicine Publications and Presentations

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Articles 1 - 30 of 36

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Trim5alpha Restricts Flavivirus Replication By Targeting The Viral Protease For Proteasomal Degradation, Abhilash I. Chiramel, Nicholas R. Meyerson, Kristin L. Mcnally, Rebecca M. Broeckel, Vanessa R. Montoya, Omayra Mendez-Solis, Shelly J. Robertson, Gail L. Sturdevant, Kirk J. Lubick, Vinod Nair, Brian H. Youseff, Robin M. Ireland, Catharine M. Bosio, Kyusik Kim, Jeremy Luban, Vanessa M. Hirsch, R. Travis Taylor, Fadila Bouamr, Sara L. Sawyer, Sonja M. Best Jun 2019

Trim5alpha Restricts Flavivirus Replication By Targeting The Viral Protease For Proteasomal Degradation, Abhilash I. Chiramel, Nicholas R. Meyerson, Kristin L. Mcnally, Rebecca M. Broeckel, Vanessa R. Montoya, Omayra Mendez-Solis, Shelly J. Robertson, Gail L. Sturdevant, Kirk J. Lubick, Vinod Nair, Brian H. Youseff, Robin M. Ireland, Catharine M. Bosio, Kyusik Kim, Jeremy Luban, Vanessa M. Hirsch, R. Travis Taylor, Fadila Bouamr, Sara L. Sawyer, Sonja M. Best

Program in Molecular Medicine Publications and Presentations

Tripartite motif-containing protein 5alpha (TRIM5alpha) is a cellular antiviral restriction factor that prevents early events in retrovirus replication. The activity of TRIM5alpha is thought to be limited to retroviruses as a result of highly specific interactions with capsid lattices. In contrast to this current understanding, we show that both human and rhesus macaque TRIM5alpha suppress replication of specific flaviviruses. Multiple viruses in the tick-borne encephalitis complex are sensitive to TRIM5alpha-dependent restriction, but mosquito-borne flaviviruses, including yellow fever, dengue, and Zika viruses, are resistant. TRIM5alpha suppresses replication by binding to the viral protease NS2B/3 to promote its K48-linked ubiquitination and ...


Smooth Muscle Cell-Specific Tmem16a Deletion Does Not Alter Ca2+ Signaling, Uterine Contraction, Gestation Length Or Litter Size In Micedagger, Mingzi Qu, Ping Lu, Karl D. Bellve, Kevin E. Fogarty, Lawrence M. Lifshitz, Fangxiong Shi, Ronghua Zhuge Jun 2019

Smooth Muscle Cell-Specific Tmem16a Deletion Does Not Alter Ca2+ Signaling, Uterine Contraction, Gestation Length Or Litter Size In Micedagger, Mingzi Qu, Ping Lu, Karl D. Bellve, Kevin E. Fogarty, Lawrence M. Lifshitz, Fangxiong Shi, Ronghua Zhuge

Program in Molecular Medicine Publications and Presentations

Ion channels in myometrial cells play critical roles in spontaneous and agonist-induced uterine contraction during the menstrual cycle, pregnancy maintenance and parturition; thus identifying the genes of ion channels in these cells and determining their roles are essential to understanding the biology of reproduction. Previous studies with in vitro functional and pharmacological approaches have produced controversial results regarding the presence and role of TMEM16A Ca2+-activated Cl- channels in myometrial cells. To unambiguously determine the function of this channel in these cells, we employed a genetic approach by using smooth muscle cell-specific TMEM16A deletion (i.e. TMEM16ASMKO) mice. We found ...


Yeast Sirtuin Family Members Maintain Transcription Homeostasis To Ensure Genome Stability, Jessica L. Feldman, Craig L. Peterson Jun 2019

Yeast Sirtuin Family Members Maintain Transcription Homeostasis To Ensure Genome Stability, Jessica L. Feldman, Craig L. Peterson

Program in Molecular Medicine Publications and Presentations

The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of ...


Arf Gtpases And Their Gefs And Gaps: Concepts And Challenges, Elizabeth Sztul, Pei-Wen Chen, James E. Casanova, Jacqueline Cherfils, Joel B. Dacks, David G. Lambright, Fang-Jen S. Lee, Paul A. Randazzo, Lorraine C. Santy, Annette Schurmann, Ilka Wilhelmi, Marielle E. Yohe, Richard A. Kahn May 2019

Arf Gtpases And Their Gefs And Gaps: Concepts And Challenges, Elizabeth Sztul, Pei-Wen Chen, James E. Casanova, Jacqueline Cherfils, Joel B. Dacks, David G. Lambright, Fang-Jen S. Lee, Paul A. Randazzo, Lorraine C. Santy, Annette Schurmann, Ilka Wilhelmi, Marielle E. Yohe, Richard A. Kahn

Program in Molecular Medicine Publications and Presentations

Detailed structural, biochemical, cell biological, and genetic studies of any gene/protein are required to develop models of its actions in cells. Studying a protein family in the aggregate yields additional information, as one can include analyses of their coevolution, acquisition or loss of functionalities, structural pliability, and the emergence of shared or variations in molecular mechanisms. An even richer understanding of cell biology can be achieved through evaluating functionally linked protein families. In this review, we summarize current knowledge of three protein families: the ARF GTPases, the guanine nucleotide exchange factors (ARF GEFs) that activate them, and the GTPase-activating ...


Rapid Evolution And Conserved Function Of The Pirna Pathway, Swapnil S. Parhad, William E. Theurkauf Jan 2019

Rapid Evolution And Conserved Function Of The Pirna Pathway, Swapnil S. Parhad, William E. Theurkauf

Program in Molecular Medicine Publications and Presentations

Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host-pathogen arms race, suggesting that transposons and ...


Analysis And Correction Of Inappropriate Image Duplication: The Molecular And Cellular Biology Experience, Elisabeth M. Bik, Ferric C. Fang, Amy L. Kullas, Roger J. Davis, Arturo Casadevall Sep 2018

Analysis And Correction Of Inappropriate Image Duplication: The Molecular And Cellular Biology Experience, Elisabeth M. Bik, Ferric C. Fang, Amy L. Kullas, Roger J. Davis, Arturo Casadevall

Program in Molecular Medicine Publications and Presentations

We analyzed 960 papers published in Molecular and Cellular Biology (MCB) from 2009 to 2016 and found 59 (6.1%) to contain inappropriately duplicated images. The 59 instances of inappropriate image duplication led to 41 corrections, 5 retractions, and 13 instances in which no action was taken. Our experience suggests that the majority of inappropriate image duplications result from errors during figure preparation that can be remedied by correction. Nevertheless, approximately 10% of papers with inappropriate image duplications in MCB were retracted ( approximately 0.5% of total). If this proportion is representative, then as many as 35,000 papers in ...


Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban Apr 2018

Intron-Containing Rna From The Hiv-1 Provirus Activates Type I Interferon And Inflammatory Cytokines, Sean M. Mccauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, Jeremy Luban

Program in Molecular Medicine Publications and Presentations

HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, these individuals have chronic inflammation associated with heightened risk of cardiovascular pathology. HIV-1 establishes proviruses in long-lived CD4+ memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Though the majority of proviruses that persist during antiviral therapy are defective for production of infectious virions, many are expressed, raising the possibility that the HIV-1 provirus or its transcripts contribute to ongoing inflammation. Here we found that the HIV-1 provirus activated innate immune ...


Hiv-1 R5 Macrophage-Tropic Envelope Glycoprotein Trimers Bind Cd4 With High Affinity, While The Cd4 Binding Site On Non-Macrophage-Tropic, T-Tropic R5 Envelopes Is Occluded, Briana Quitadamo, Paul J. Peters, Alexander Repik, Olivia O'Connell, Zhongming Mou, Matthew Koch, Mohan Somasundaran, Robin M. Brody, Katherine Luzuriaga, Aaron Wallace, Shixia Wang, Shan Lu, Sean M. Mccauley, Jeremy Luban, Maria J. Duenas-Decamp, Maria Paz Paz Gonzalez-Perez, Paul R. Clapham Jan 2018

Hiv-1 R5 Macrophage-Tropic Envelope Glycoprotein Trimers Bind Cd4 With High Affinity, While The Cd4 Binding Site On Non-Macrophage-Tropic, T-Tropic R5 Envelopes Is Occluded, Briana Quitadamo, Paul J. Peters, Alexander Repik, Olivia O'Connell, Zhongming Mou, Matthew Koch, Mohan Somasundaran, Robin M. Brody, Katherine Luzuriaga, Aaron Wallace, Shixia Wang, Shan Lu, Sean M. Mccauley, Jeremy Luban, Maria J. Duenas-Decamp, Maria Paz Paz Gonzalez-Perez, Paul R. Clapham

Program in Molecular Medicine Publications and Presentations

HIV-1 R5 variants exploit CCR5 as a coreceptor to infect both T cells and macrophages. R5 viruses that are transmitted or derived from immune tissue and peripheral blood are mainly inefficient at mediating infection of macrophages. In contrast, highly macrophage-tropic (mac-tropic) R5 viruses predominate in brain tissue and can be detected in cerebrospinal fluid but are infrequent in immune tissue or blood even in late disease. These mac-tropic R5 variants carry envelope glycoproteins (Envs) adapted to exploit low levels of CD4 on macrophages to induce infection. However, it is unclear whether this adaptation is conferred by an increased affinity of ...


A Microrna Family Exerts Maternal Control On Sex Determination In C. Elegans, Katherine Mcjunkin, Victor R. Ambros Feb 2017

A Microrna Family Exerts Maternal Control On Sex Determination In C. Elegans, Katherine Mcjunkin, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

Gene expression in early animal embryogenesis is in large part controlled post-transcriptionally. Maternally contributed microRNAs may therefore play important roles in early development. We elucidated a major biological role of the nematode mir-35 family of maternally contributed essential microRNAs. We show that this microRNA family regulates the sex determination pathway at multiple levels, acting both upstream of and downstream from her-1 to prevent aberrantly activated male developmental programs in hermaphrodite embryos. Both of the predicted target genes that act downstream from the mir-35 family in this process, suppressor-26 (sup-26) and NHL (NCL-1, HT2A, and LIN-41 repeat) domain-containing-2 (nhl-2), encode RNA-binding ...


End Sequence Analysis Toolkit (Esat) Expands The Extractable Information From Single-Cell Rna-Seq Data, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David M. Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim N. Artyomov, Manuel Garber Oct 2016

End Sequence Analysis Toolkit (Esat) Expands The Extractable Information From Single-Cell Rna-Seq Data, Alan G. Derr, Chaoxing Yang, Rapolas Zilionis, Alexey Sergushichev, David Blodgett, Sambra D. Redick, Rita Bortell, Jeremy Luban, David M. Harlan, Sebastian Kadener, Dale L. Greiner, Allon Klein, Maxim N. Artyomov, Manuel Garber

Program in Molecular Medicine Publications and Presentations

RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolkit (ESAT). As a test, we first compared end-sequencing and bulk RNA-seq using RNA from dendritic cells stimulated with lipopolysaccharide (LPS). As predicted by the telescripting model for transcriptional bursts, ESAT detected an LPS-stimulated shift to shorter 3'-isoforms that was not evident by conventional computational methods. Then, droplet-based microfluidics was used to generate 1000 ...


Staufen Negatively Modulates Microrna Activity In Caenorhabditis Elegans, Zhiji Ren, Isana Veksler-Lublinsky, David Morrissey, Victor R. Ambros Feb 2016

Staufen Negatively Modulates Microrna Activity In Caenorhabditis Elegans, Zhiji Ren, Isana Veksler-Lublinsky, David Morrissey, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

The double-stranded RNA-binding protein Staufen has been implicated in various post-transcriptional gene regulatory processes. Here we demonstrate that the Caenorhabditis elegans homolog of Staufen, STAU-1, functionally interacts with microRNAs. Loss-of-function mutations of stau-1 significantly suppress phenotypes of let-7 family microRNA mutants, a hypomorphic allele of dicer and a lsy-6 microRNA partial loss-of-function mutant. Furthermore, STAU-1 modulates the activity of lin-14, a target of lin-4 and let-7 family microRNAs, and this modulation is abolished when the 3' untranslated region of lin-14 is removed. Deep sequencing of small RNA cDNA libraries reveals no dramatic change in the levels of microRNAs, or other ...


Tenomodulin Promotes Human Adipocyte Differentiation And Beneficial Visceral Adipose Tissue Expansion, Ozlem Senol-Cosar, Rachel J. Roth Flach, Marina Distefano, Anil K. Chawla, Sarah M. Nicoloro, Juerg R. Straubhaar, Olga T. Hardy, Hye Lim Noh, Jason K. Kim, Martin Wabitsch, Philipp E. Scherer, Michael P. Czech Feb 2016

Tenomodulin Promotes Human Adipocyte Differentiation And Beneficial Visceral Adipose Tissue Expansion, Ozlem Senol-Cosar, Rachel J. Roth Flach, Marina Distefano, Anil K. Chawla, Sarah M. Nicoloro, Juerg R. Straubhaar, Olga T. Hardy, Hye Lim Noh, Jason K. Kim, Martin Wabitsch, Philipp E. Scherer, Michael P. Czech

Program in Molecular Medicine Publications and Presentations

Proper regulation of energy storage in adipose tissue is crucial for maintaining insulin sensitivity and molecules contributing to this process have not been fully revealed. Here we show that type II transmembrane protein tenomodulin (TNMD) is upregulated in adipose tissue of insulin-resistant versus insulin-sensitive individuals, who were matched for body mass index (BMI). TNMD expression increases in human preadipocytes during differentiation, whereas silencing TNMD blocks adipogenesis. Upon high-fat diet feeding, transgenic mice overexpressing Tnmd develop increased epididymal white adipose tissue (eWAT) mass, and preadipocytes derived from Tnmd transgenic mice display greater proliferation, consistent with elevated adipogenesis. In Tnmd transgenic mice ...


Endothelial Protein Kinase Map4k4 Promotes Vascular Inflammation And Atherosclerosis, Rachel J. Roth Flach, Athanasia Skoura, Anouch Matevossian, Laura V. Danai, Wei Zheng, Christian Cortes, Samit K. Bhattacharya, Myriam Aouadi, G. Nana Hagan, Joseph Yawe, Pranitha Vangala, Lorena Garcia Menendez, Marcus P. Cooper, Timothy P. Fitzgibbons, Leonard Buckbinder, Michael P. Czech Dec 2015

Endothelial Protein Kinase Map4k4 Promotes Vascular Inflammation And Atherosclerosis, Rachel J. Roth Flach, Athanasia Skoura, Anouch Matevossian, Laura V. Danai, Wei Zheng, Christian Cortes, Samit K. Bhattacharya, Myriam Aouadi, G. Nana Hagan, Joseph Yawe, Pranitha Vangala, Lorena Garcia Menendez, Marcus P. Cooper, Timothy P. Fitzgibbons, Leonard Buckbinder, Michael P. Czech

Program in Molecular Medicine Publications and Presentations

Signalling pathways that control endothelial cell (EC) permeability, leukocyte adhesion and inflammation are pivotal for atherosclerosis initiation and progression. Here we demonstrate that the Sterile-20-like mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), which has been implicated in inflammation, is abundantly expressed in ECs and in atherosclerotic plaques from mice and humans. On the basis of endothelial-specific MAP4K4 gene silencing and gene ablation experiments in Apoe(-/-) mice, we show that MAP4K4 in ECs markedly promotes Western diet-induced aortic macrophage accumulation and atherosclerotic plaque development. Treatment of Apoe(-/-) and Ldlr(-/-) mice with a selective small-molecule MAP4K4 inhibitor also markedly reduces atherosclerotic ...


Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, Anna Y. Zinovyeva, Isana Veksler-Lublinsky, Ajay A. Vashisht, James A. Wohlschlegel, Victor R. Ambros Sep 2015

Caenorhabditis Elegans Alg-1 Antimorphic Mutations Uncover Functions For Argonaute In Microrna Guide Strand Selection And Passenger Strand Disposal, Anna Y. Zinovyeva, Isana Veksler-Lublinsky, Ajay A. Vashisht, James A. Wohlschlegel, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

MicroRNAs are regulators of gene expression whose functions are critical for normal development and physiology. We have previously characterized mutations in a Caenorhabditis elegans microRNA-specific Argonaute ALG-1 (Argonaute-like gene) that are antimorphic [alg-1(anti)]. alg-1(anti) mutants have dramatically stronger microRNA-related phenotypes than animals with a complete loss of ALG-1. ALG-1(anti) miRISC (microRNA induced silencing complex) fails to undergo a functional transition from microRNA processing to target repression. To better understand this transition, we characterized the small RNA and protein populations associated with ALG-1(anti) complexes in vivo. We extensively characterized proteins associated with wild-type and mutant ALG-1 and ...


Inducible Deletion Of Protein Kinase Map4k4 In Obese Mice Improves Insulin Sensitivity In Liver And Adipose Tissues, Laura V. Danai, Rachel J. Roth Flach, Joseph V Virbasius, Lorena Garcia Menendez, Dae Young Jung, Jong Hun Kim, Jason K. Kim, Michael P. Czech Jul 2015

Inducible Deletion Of Protein Kinase Map4k4 In Obese Mice Improves Insulin Sensitivity In Liver And Adipose Tissues, Laura V. Danai, Rachel J. Roth Flach, Joseph V Virbasius, Lorena Garcia Menendez, Dae Young Jung, Jong Hun Kim, Jason K. Kim, Michael P. Czech

Program in Molecular Medicine Publications and Presentations

Studies in vitro suggest that mitogen-activated protein kinase kinase kinase kinase 4 (Map4k4) attenuates insulin signaling, but confirmation in vivo is lacking since Map4k4 knockout is lethal during embryogenesis. We thus generated mice with floxed Map4k4 alleles and a tamoxifen-inducible Cre/ERT2 recombinase under the control of the ubiquitin C promoter to induce whole-body Map4k4 deletion after these animals reached maturity. Tamoxifen administration to these mice induced Map4k4 deletion in all tissues examined, causing decreased fasting blood glucose concentrations and enhanced insulin signaling to AKT in adipose tissue and liver but not in skeletal muscle. Surprisingly, however, mice generated with ...


Biodistribution And Function Of Extracellular Mirna-155 In Mice, Shashi Bala, Timea Csak, Fatemeh Momen-Heravi, Dora Lippai, Karen Kodys, Donna Catalano, Abhishek Satishchandran, Victor R. Ambros, Gyongyi Szabo May 2015

Biodistribution And Function Of Extracellular Mirna-155 In Mice, Shashi Bala, Timea Csak, Fatemeh Momen-Heravi, Dora Lippai, Karen Kodys, Donna Catalano, Abhishek Satishchandran, Victor R. Ambros, Gyongyi Szabo

Program in Molecular Medicine Publications and Presentations

Circulating miRNAs can be found in extracellular vesicles (EV) and could be involved in intercellular communication. Here, we report the biodistribution of EV associated miR-155 using miR-155 KO mouse model. Administration of exosomes loaded with synthetic miR-155 mimic into miR-155 KO mice resulted in a rapid accumulation and clearance of miR-155 in the plasma with subsequent distribution in the liver, adipose tissue, lung, muscle and kidney (highest to lowest, respectively). miR-155 expression was detected in isolated hepatocytes and liver mononuclear cells of recipient KO mice suggesting its cellular uptake. In vitro, exosome-mediated restoration of miR-155 in Kupffer cells from miR-155 ...


Highly Selective In Vivo Labeling Of Subcutaneous White Adipocyte Precursors With Prx1-Cre, Joan Sanchez-Gurmaches, Wen-Yu Hsiao, David A. Guertin Apr 2015

Highly Selective In Vivo Labeling Of Subcutaneous White Adipocyte Precursors With Prx1-Cre, Joan Sanchez-Gurmaches, Wen-Yu Hsiao, David A. Guertin

Program in Molecular Medicine Publications and Presentations

The origins of individual fat depots are not well understood, and thus, the availability of tools useful for studying depot-specific adipose tissue development and function is limited. Cre drivers that selectively target only brown adipocyte, subcutaneous white adipocyte, or visceral white adipocyte precursors would have significant value because they could be used to selectively study individual depots without impacting the adipocyte precursors or intrinsic metabolic properties of the other depots. Here, we show that the majority of the precursor and mature subcutaneous white adipocytes in adult C57Bl/6 mice are labeled by Prx1-Cre. In sharp contrast, few to no brown ...


The Ino80 Complex Prevents Invasion Of Euchromatin Into Silent Chromatin, Yong Xue, Christopher Van, Suman K. Pradhan, Trent Su, Jason Gehrke, Benjamin G. Kuryan, Tasuku Kitada, Ajay Vashisht, Nancy Tran, James Wohlschlegel, Craig L. Peterson, Siavash K. Kurdistani, Michael F. Carey Feb 2015

The Ino80 Complex Prevents Invasion Of Euchromatin Into Silent Chromatin, Yong Xue, Christopher Van, Suman K. Pradhan, Trent Su, Jason Gehrke, Benjamin G. Kuryan, Tasuku Kitada, Ajay Vashisht, Nancy Tran, James Wohlschlegel, Craig L. Peterson, Siavash K. Kurdistani, Michael F. Carey

Program in Molecular Medicine Publications and Presentations

Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Heterochromatin stimulates the binding of Ino80C in vitro and in vivo. Our data reveal that Ino80C serves as a general silencing complex that restricts transcription to gene units in euchromatin.


Ciliary Proteins Bbs8 And Ift20 Promote Planar Cell Polarity In The Cochlea, Helen L. May-Simera, Ronald S. Petralia, Mireille Montcouquiol, Ya-Xian Wang, Katherine B. Szarama, Yun Liu, Weichun Lin, Michael R. Deans, Gregory J. Pazour, Matthew W. Kelley Feb 2015

Ciliary Proteins Bbs8 And Ift20 Promote Planar Cell Polarity In The Cochlea, Helen L. May-Simera, Ronald S. Petralia, Mireille Montcouquiol, Ya-Xian Wang, Katherine B. Szarama, Yun Liu, Weichun Lin, Michael R. Deans, Gregory J. Pazour, Matthew W. Kelley

Program in Molecular Medicine Publications and Presentations

Primary cilia have been implicated in the generation of planar cell polarity (PCP). However, variations in the severity of polarity defects in different cilia mutants, coupled with recent demonstrations of non-cilia-related actions of some cilia genes, make it difficult to determine the basis of these polarity defects. To address this issue, we evaluated PCP defects in cochlea from a selection of mice with mutations in cilia-related genes. Results indicated notable PCP defects, including mis-oriented hair cell stereociliary bundles, in Bbs8 and Ift20 single mutants that are more severe than in other cilia gene knockouts. In addition, deletion of either Bbs8 ...


An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros Jan 2015

An Efficient And Sensitive Method For Preparing Cdna Libraries From Scarce Biological Samples, Catherine H. Sterling, Isana Veksler-Lublinsky, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate ...


The Embryonic Mir-35 Family Of Micrornas Promotes Multiple Aspects Of Fecundity In Caenorhabditis Elegans, Katherine Mcjunkin, Victor R. Ambros Jul 2014

The Embryonic Mir-35 Family Of Micrornas Promotes Multiple Aspects Of Fecundity In Caenorhabditis Elegans, Katherine Mcjunkin, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

MicroRNAs guide many aspects of development in all metazoan species. Frequently, microRNAs are expressed during a specific developmental stage to perform a temporally defined function. The C. elegans mir-35-42 microRNAs are expressed abundantly in oocytes and early embryos and are essential for embryonic development. Here, we show that these embryonic microRNAs surprisingly also function to control the number of progeny produced by adult hermaphrodites. Using a temperature-sensitive mir-35-42 family mutant (a deletion of the mir-35-41 cluster), we demonstrate three distinct defects in hermaphrodite fecundity. At permissive temperatures, a mild sperm defect partially reduces hermaphrodite fecundity. At restrictive temperatures, somatic gonad ...


Mutations In Conserved Residues Of The C. Elegans Microrna Argonaute Alg-1 Identify Separable Functions In Alg-1 Mirisc Loading And Target Repression, Anna Y. Zinovyeva, Samir Bouasker, Martin J. Simard, Christopher M. Hammell, Victor R. Ambros Apr 2014

Mutations In Conserved Residues Of The C. Elegans Microrna Argonaute Alg-1 Identify Separable Functions In Alg-1 Mirisc Loading And Target Repression, Anna Y. Zinovyeva, Samir Bouasker, Martin J. Simard, Christopher M. Hammell, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

microRNAs function in diverse developmental and physiological processes by regulating target gene expression at the post-transcriptional level. ALG-1 is one of two Caenorhabditis elegans Argonautes (ALG-1 and ALG-2) that together are essential for microRNA biogenesis and function. Here, we report the identification of novel antimorphic (anti) alleles of ALG-1 as suppressors of lin-28(lf) precocious developmental phenotypes. The alg-1(anti) mutations broadly impair the function of many microRNAs and cause dosage-dependent phenotypes that are more severe than the complete loss of ALG-1. ALG-1(anti) mutant proteins are competent for promoting Dicer cleavage of microRNA precursors and for associating with and ...


Epstein-Barr Virus Latent Membrane Protein 1 Genetic Variability In Peripheral Blood B Cells And Oropharyngeal Fluids, Nicholas Renzette, Mohan Somasundaran, Frank E. Brewster, James Coderre, Eric R. Weiss, Margaret M. Mcmanus, Thomas C. Greenough, Barbara Tabak, Manuel Garber, Timothy F. Kowalik, Katherine Ruiz De Luzuriaga Apr 2014

Epstein-Barr Virus Latent Membrane Protein 1 Genetic Variability In Peripheral Blood B Cells And Oropharyngeal Fluids, Nicholas Renzette, Mohan Somasundaran, Frank E. Brewster, James Coderre, Eric R. Weiss, Margaret M. Mcmanus, Thomas C. Greenough, Barbara Tabak, Manuel Garber, Timothy F. Kowalik, Katherine Ruiz De Luzuriaga

Program in Molecular Medicine Publications and Presentations

We report the diversity of latent membrane protein 1 (LMP1) gene founder sequences and the level of Epstein-Barr virus (EBV) genome variability over time and across anatomic compartments by using virus genomes amplified directly from oropharyngeal wash specimens and peripheral blood B cells during acute infection and convalescence. The intrahost nucleotide variability of the founder virus was 0.02% across the region sequences, and diversity increased significantly over time in the oropharyngeal compartment (P = 0.004). The LMP1 region showing the greatest level of variability in both compartments, and over time, was concentrated within the functional carboxyl-terminal activating regions 2 ...


A Kras-Directed Transcriptional Silencing Pathway That Mediates The Cpg Island Methylator Phenotype, Ryan W. Serra, Minggang Fang, Sung Mi Park, Lloyd Hutchinson, Michael R. Green Mar 2014

A Kras-Directed Transcriptional Silencing Pathway That Mediates The Cpg Island Methylator Phenotype, Ryan W. Serra, Minggang Fang, Sung Mi Park, Lloyd Hutchinson, Michael R. Green

Program in Molecular Medicine Publications and Presentations

Approximately 70% of KRAS-positive colorectal cancers (CRCs) have a CpG island methylator phenotype (CIMP) characterized by aberrant DNA hypermethylation and transcriptional silencing of many genes. The factors involved in, and the mechanistic basis of, CIMP is not understood. Among the CIMP genes are the tumor suppressors p14(ARF), p15(INK4B), and p16(INK4A), encoded by the INK4-ARF locus. In this study, we perform an RNA interference screen and identify ZNF304, a zinc-finger DNA-binding protein, as the pivotal factor required for INK4-ARF silencing and CIMP in CRCs containing activated KRAS. In KRAS-positive human CRC cell lines and tumors, ZNF304 is bound ...


Hdac6 Regulates Tip60-P400 Function In Stem Cells, Poshen B. Chen, Jui-Hung Hung, Taylor L. Hickman, Andrew H. Coles, James F. Carey, Zhiping Weng, Feixia Chu, Thomas G. Fazzio Dec 2013

Hdac6 Regulates Tip60-P400 Function In Stem Cells, Poshen B. Chen, Jui-Hung Hung, Taylor L. Hickman, Andrew H. Coles, James F. Carey, Zhiping Weng, Feixia Chu, Thomas G. Fazzio

Program in Molecular Medicine Publications and Presentations

In embryonic stem cells (ESCs), the Tip60 histone acetyltransferase activates genes required for proliferation and silences genes that promote differentiation. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs. Hdac6 is necessary for regulation of most Tip60-p400 target genes, particularly those repressed by the complex. Unlike differentiated cells, where Hdac6 is mainly cytoplasmic, Hdac6 is largely nuclear in ESCs, neural stem cells (NSCs), and some cancer cell lines, and interacts with Tip60-p400 in each. Hdac6 localizes to promoters bound by Tip60-p400 in ESCs, binding downstream of transcription start sites. Surprisingly, Hdac6 does not ...


Diet-Induced Obesity Mediated By The Jnk/Dio2 Signal Transduction Pathway, Santiago Vernia, Julie Cavanagh-Kyros, Tamera Barrett, Dae Young Jung, Jason K. Kim, Roger J. Davis Nov 2013

Diet-Induced Obesity Mediated By The Jnk/Dio2 Signal Transduction Pathway, Santiago Vernia, Julie Cavanagh-Kyros, Tamera Barrett, Dae Young Jung, Jason K. Kim, Roger J. Davis

Program in Molecular Medicine Publications and Presentations

The cJun N-terminal kinase (JNK) signaling pathway is a key mediator of metabolic stress responses caused by consuming a high-fat diet, including the development of obesity. To test the role of JNK, we examined diet-induced obesity in mice with targeted ablation of Jnk genes in the anterior pituitary gland. These mice exhibited an increase in the pituitary expression of thyroid-stimulating hormone (TSH), an increase in the blood concentration of thyroid hormone (T4), increased energy expenditure, and markedly reduced obesity compared with control mice. The increased amount of pituitary TSH was caused by reduced expression of type 2 iodothyronine deiodinase (Dio2 ...


Inductive Asymmetric Cell Division: The Wrm Leads The Way, Takao Ishidate, Soyoung Kim, Craig C. Mello, Masaki Shirayama Oct 2013

Inductive Asymmetric Cell Division: The Wrm Leads The Way, Takao Ishidate, Soyoung Kim, Craig C. Mello, Masaki Shirayama

Program in Molecular Medicine Publications and Presentations

C. elegans, with its invariant cell lineage, provides a powerful model system in which to study signaling-dependent asymmetric cell division. The C. elegans β-catenin-related protein, WRM-1, specifies endoderm at the 4-cell stage during the first cell signaling-induced asymmetric cell division of embryogenesis. During this interaction, Wnt signaling and the cell cycle regulator CDK-1 act together to induce the asymmetric cortical release of WRM-1 at prophase of the EMS cell cycle. Genetic studies suggest that release of WRM-1 unmasks a cortical site that drives EMS spindle rotation onto the polarized axis of the cell, simultaneously making WRM-1 available for nuclear translocation ...


Circulating Cell And Plasma Microrna Profiles Differ Between Non-St-Segment And St-Segment-Elevation Myocardial Infarction, Jeanine Ward, Nada Esa, Rahul Pidikiti, Jane E. Freedman, John F. Keaney, Kahraman Tanriverdi, Olga Vitseva, Victor R. Ambros, Rosalind Lee, David D. Mcmanus Oct 2013

Circulating Cell And Plasma Microrna Profiles Differ Between Non-St-Segment And St-Segment-Elevation Myocardial Infarction, Jeanine Ward, Nada Esa, Rahul Pidikiti, Jane E. Freedman, John F. Keaney, Kahraman Tanriverdi, Olga Vitseva, Victor R. Ambros, Rosalind Lee, David D. Mcmanus

Program in Molecular Medicine Publications and Presentations

BACKGROUND: Differences in plasma and whole blood expression microRNAs (miRNAs) in patients with an acute coronary syndrome (ACS) have been determined in both in vitro and in vivo studies. Although most circulating miRNAs are located in the cellular components of whole blood, little is known about the miRNA profiles of whole blood subcomponents, including plasma, platelets and leukocytes in patients with myocardial ischemia.

METHODS: Thirteen patients with a ST-segment-elevation (STEMI) or non-ST-segment elevation (NSTEMI) myocardial infarction were identified in the University of Massachusetts Medical Center Emergency Department (ED) or cardiac catheterization laboratory between February and June of 2012. Whole blood ...


Victor Ambros: The Broad Scope Of Micrornas. Interview By Caitlin Sedwick, Victor R. Ambros May 2013

Victor Ambros: The Broad Scope Of Micrornas. Interview By Caitlin Sedwick, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

Interview with Victor Ambros, who studies how microRNAs impact development.


Effect Of Life History On Microrna Expression During C. Elegans Development, Xantha Karp, Molly Hammell, Maria C. Ow, Victor R. Ambros Apr 2011

Effect Of Life History On Microrna Expression During C. Elegans Development, Xantha Karp, Molly Hammell, Maria C. Ow, Victor R. Ambros

Program in Molecular Medicine Publications and Presentations

Animals have evolved mechanisms to ensure the robustness of developmental outcomes to changing environments. MicroRNA expression may contribute to developmental robustness because microRNAs are key post-transcriptional regulators of developmental gene expression and can affect the expression of multiple target genes. Caenorhabditis elegans provides an excellent model to study developmental responses to environmental conditions. In favorable environments, C. elegans larvae develop rapidly and continuously through four larval stages. In contrast, in unfavorable conditions, larval development may be interrupted at either of two diapause stages: The L1 diapause occurs when embryos hatch in the absence of food, and the dauer diapause occurs ...