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Molecular biology

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Articles 1 - 30 of 55

Full-Text Articles in Molecular Biology

Basic Cell And Molecular Biology 3e: What We Know And How We Found Out, Gerald Bergtrom Sep 2018

Basic Cell And Molecular Biology 3e: What We Know And How We Found Out, Gerald Bergtrom

Cell and Molecular Biology 3e: What We Know and How We Found Out - All Versions

No abstract provided.


Llc Tumor Cells-Derivated Factors Reduces Adipogenesis In Co-Culture System, Magno Alves Lopes, Felipe Oliveira Franco, Felipe Henriques, Sidney Barnabe Peres, Miguel Luiz Batista Jr. Jul 2018

Llc Tumor Cells-Derivated Factors Reduces Adipogenesis In Co-Culture System, Magno Alves Lopes, Felipe Oliveira Franco, Felipe Henriques, Sidney Barnabe Peres, Miguel Luiz Batista Jr.

Open Access Articles

Cancer cachexia (CC) is a multifactorial syndrome with an unknown etiology. The primary symptom is the progressive reduction of the body weight. Recently, down-regulation of adipogenic and lipogenic genes were demonstrated to be early affected during cachexia progression in adipose tissue (AT), resulting in AT remodeling. Thus, this study aimed to evaluate in a co-culture system the influence of the Lewis Lung Carcinoma (LLC) tumor cells (c/c-LLC) in an established pre-adipocyte cell line 3T3-L1 adipogenic capacity. c/c-LLC in the presence of 3T3-L1 caused a reduction in lipids accumulation, suggesting that secretory tumor cells products may affect adipogenesis. Interestingly ...


Annotated Cell And Molecular Biology 3e: What We Know And How We Found Out, Gerald Bergtrom Jul 2018

Annotated Cell And Molecular Biology 3e: What We Know And How We Found Out, Gerald Bergtrom

Cell and Molecular Biology 3e: What We Know and How We Found Out - All Versions

No abstract provided.


Nmecas9 Is An Intrinsically High-Fidelity Genome Editing Platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer May 2018

Nmecas9 Is An Intrinsically High-Fidelity Genome Editing Platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

Background: The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild-type SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large (e.g. mammalian) genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively ...


Small Rnas Gained During Epididymal Transit Of Sperm Are Essential For Embryonic Development In Mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, Oliver J. Rando Apr 2018

Small Rnas Gained During Epididymal Transit Of Sperm Are Essential For Embryonic Development In Mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, Oliver J. Rando

University of Massachusetts Medical School Faculty Publications

The small RNA payload of mammalian sperm undergoes dramatic remodeling during development, as several waves of microRNAs and tRNA fragments are shipped to sperm during post-testicular maturation in the epididymis. Here, we take advantage of this developmental process to probe the function of the sperm RNA payload in preimplantation development. We generated zygotes via intracytoplasmic sperm injection (ICSI) using sperm obtained from the proximal (caput) vs. distal (cauda) epididymis, then characterized development of the resulting embryos. Embryos generated using caput sperm significantly overexpress multiple regulatory factors throughout preimplantation development, and subsequently implant inefficiently and fail soon after implantation. Remarkably, microinjection ...


A Single Mechanism Of Biogenesis, Initiated And Directed By Piwi Proteins, Explains Pirna Production In Most Animals, Phillip D. Zamore, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini Apr 2018

A Single Mechanism Of Biogenesis, Initiated And Directed By Piwi Proteins, Explains Pirna Production In Most Animals, Phillip D. Zamore, Ildar Gainetdinov, Cansu Colpan, Katharine Cecchini

University of Massachusetts Medical School Faculty Publications

In animals, piRNAs guide PIWI-proteins to silence transposons and regulate gene expression. The mechanisms for making piRNAs have been proposed to differ among cell types, tissues, and animals. Our data instead suggest a single model that explains piRNA production in most animals. piRNAs initiate piRNA production by guiding PIWI proteins to slice precursor transcripts. Next, PIWI proteins direct the stepwise fragmentation of the sliced precursor transcripts, yielding tail-to-head strings of phased pre-piRNAs. Our analyses detect evidence for this piRNA biogenesis strategy across an evolutionarily broad range of animals including humans. Thus, PIWI proteins initiate and sustain piRNA biogenesis by the ...


A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, Nathan S. Winter Apr 2018

A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis, Nathan S. Winter

Chemistry Faculty Publications

This paper describes a series of experiments involving handling and manipulating the DNA coding for Green Fluorescent Protein (GFP) including the subcloning of this gene, and mutating the DNA so that Cyan Fluorescent Protein (CFP) or Blue Fluorescent protein (BFP) are expressed. The primers needed for the PCR based subcloning of GFP are presented, as are those needed to mutate the GFP to either CFP or BFP.


A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis., Nathan S. Winter Apr 2018

A Multisession, Undergraduate Molecular Biology Lab Experiment Using Green Fluorescent Protein Including Subcloning And Color Changing Mutagenesis., Nathan S. Winter

Library Faculty Publications

This paper describes a series of experiments involving handling and manipulating the DNA coding for Green Fluorescent Protein (GFP) including the subcloning of this gene, and mutating the DNA so that Cyan Fluorescent Protein (CFP) or Blue Fluorescent protein (BFP) are expressed. The primers needed for the PCR based subcloning of GFP are presented, as are those needed to mutate the GFP to either CFP or BFP.


Primate Immunodeficiency Virus Vpx And Vpr Counteract Transcriptional Repression Of Proviruses By The Hush Complex, Leonid Yurkovetskiy, Mehmet Hakan Guney, Kyusik Kim, Shih Lin Goh, Sean M. Mccauley, Ann Dauphin, William E. Diehl, Jeremy Luban Apr 2018

Primate Immunodeficiency Virus Vpx And Vpr Counteract Transcriptional Repression Of Proviruses By The Hush Complex, Leonid Yurkovetskiy, Mehmet Hakan Guney, Kyusik Kim, Shih Lin Goh, Sean M. Mccauley, Ann Dauphin, William E. Diehl, Jeremy Luban

University of Massachusetts Medical School Faculty Publications

Drugs that inhibit HIV-1 replication and prevent progression to AIDS do not eliminate HIV-1 proviruses from the chromosomes of long-lived CD4+ memory T cells. To escape eradication by these antiviral drugs, or by the host immune system, HIV-1 exploits poorly defined host factors that silence provirus transcription. These same factors, though, must be overcome by all retroviruses, including HIV-1 and other primate immunodeficiency viruses, in order to activate provirus transcription and produce new virus. Here we show that Vpx and Vpr, proteins from a wide range of primate immunodeficiency viruses, activate provirus transcription in human CD4+ T cells. Provirus activation ...


Higher-Order Organization Principles Of Pre-Translational Mrnps, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, Melissa J. Moore Mar 2018

Higher-Order Organization Principles Of Pre-Translational Mrnps, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, Melissa J. Moore

University of Massachusetts Medical School Faculty Publications

Compared to noncoding RNAs (ncRNAs) such as rRNAs and ribozymes, for which high resolution structures abound, little is known about the tertiary structures of mRNAs. In eukaryotic cells, newly made mRNAs are packaged with proteins in highly compacted mRNPs, but the manner of this mRNA compaction is unknown. Here we developed and implemented RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), a transcriptome-wide method for probing the 3D conformations of RNAs stably-associated with defined proteins, in this case exon junction complex (EJC) core factors. EJCs multimerize with other mRNP components to form megadalton sized complexes that protect large swaths of ...


Herpes Icp8 Protein Stimulates Homologous Recombination In Human Cells, Melvys Valledor, Richard S. Myers, Paul C. Schiller Feb 2018

Herpes Icp8 Protein Stimulates Homologous Recombination In Human Cells, Melvys Valledor, Richard S. Myers, Paul C. Schiller

University of Massachusetts Medical School Faculty Publications

Recombineering has transformed functional genomic analysis. Genome modification by recombineering using the phage lambda Red SynExo homologous recombination proteins Beta in Escherichia coli has approached 100% efficiency. While highly efficient in E. coli, recombineering using the Red SynExo in other organisms declines in efficiency roughly correlating with phylogenetic distance from E. coli. SynExo recombinases are common to double-stranded DNA viruses infecting a variety of organisms, including humans. Human Herpes virus Type 1 (HHV1) encodes a SynExo comprised of ICP8 synaptase and UL12 exonuclease. In a previous study, the Herpes SynExo was reconstituted in vitro and shown to catalyze a model ...


Regulation Of Atm And Atr By Smarcal1 And Brg1, Ramesh Sethy, Radhakrishnan Rakesh, Ketki Patne, Vijendra Arya, Tapan Sharma, Dominic T. Haokip, Reshma Kumari, Rohini Muthuswami Feb 2018

Regulation Of Atm And Atr By Smarcal1 And Brg1, Ramesh Sethy, Radhakrishnan Rakesh, Ketki Patne, Vijendra Arya, Tapan Sharma, Dominic T. Haokip, Reshma Kumari, Rohini Muthuswami

University of Massachusetts Medical School Faculty Publications

The G2/M checkpoint is activated on DNA damage by the ATM and ATR kinases that are regulated by post-translational modifications. In this paper, the transcriptional co-regulation of ATM and ATR by SMARCAL1 and BRG1, both members of the ATP-dependent chromatin remodeling protein family, is described. SMARCAL1 and BRG1 co-localize on the promoters of ATM and ATR; downregulation of SMARCAL1/BRG1 results in transcriptional repression of ATM/ATR and therefore, overriding of the G2/M checkpoint leading to mitotic abnormalities. On doxorubicin-induced DNA damage, SMARCAL1 and BRG1 are upregulated and in turn, upregulate the expression of ATM/ATR. Phosphorylation of ...


C-Berst: Defining Subnuclear Proteomic Landscapes At Genomic Elements With Dcas9-Apex2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer Jan 2018

C-Berst: Defining Subnuclear Proteomic Landscapes At Genomic Elements With Dcas9-Apex2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

Mapping proteomic composition at distinct genomic loci and subnuclear landmarks in living cells has been a long-standing challenge. Here we report that dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging (C-BERST) allows the rapid, unbiased mapping of proteomes near defined genomic loci, as demonstrated for telomeres and centromeres. By combining the spatially restricted enzymatic tagging enabled by APEX2 with programmable DNA targeting by dCas9, C-BERST has successfully identified nearly 50% of known telomere-associated factors and many known centromere-associated factors. We also identified and validated SLX4IP and RPA3 as telomeric factors, confirming C-BERST ...


Flt1 And Transcriptome-Wide Polyadenylation Site (Pas) Analysis In Preeclampsia, Ami Ashar-Patel, Yasin Kaymaz, Augustine Rajakumar, Jeffrey A. Bailey, S. Ananth Karumanchi, Melissa J. Moore Sep 2017

Flt1 And Transcriptome-Wide Polyadenylation Site (Pas) Analysis In Preeclampsia, Ami Ashar-Patel, Yasin Kaymaz, Augustine Rajakumar, Jeffrey A. Bailey, S. Ananth Karumanchi, Melissa J. Moore

Open Access Articles

Maternal symptoms of preeclampsia (PE) are primarily driven by excess anti-angiogenic factors originating from the placenta. Chief among these are soluble Flt1 proteins (sFlt1s) produced from alternatively polyadenylated mRNA isoforms. Here we used polyadenylation site sequencing (PAS-Seq) of RNA from normal and PE human placentae to interrogate transcriptome-wide gene expression and alternative polyadenylation signatures associated with early-onset PE (EO-PE; symptom onset < 34 weeks) and late-onset PE (LO-PE; symptom onset > 34 weeks) cohorts. While we observed no general shift in alternative polyadenylation associated with PE, the EO-PE and LO-PE cohorts do exhibit gene expression profiles distinct from both each other and from normal placentae. The only two genes upregulated ...


A Synthetic Biology Approach To Probing Nucleosome Symmetry, Yuichi Ichikawa, Yuanyuan Chen, Vineeta Bajaj, Caitlin M. Connolly, Hsin-Jung Chou, Upasna Sharma, Hsiuyi V. Chen, Daniel N. Bolon, Oliver J. Rando, Paul D. Kaufman Sep 2017

A Synthetic Biology Approach To Probing Nucleosome Symmetry, Yuichi Ichikawa, Yuanyuan Chen, Vineeta Bajaj, Caitlin M. Connolly, Hsin-Jung Chou, Upasna Sharma, Hsiuyi V. Chen, Daniel N. Bolon, Oliver J. Rando, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this ...


Heterogeneity And Intrinsic Variation In Spatial Genome Organization, Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, Tom Misteli Aug 2017

Heterogeneity And Intrinsic Variation In Spatial Genome Organization, Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, Tom Misteli

University of Massachusetts Medical School Faculty Publications

The genome is hierarchically organized in 3D space and its architecture is altered in differentiation, development and disease. Some of the general principles that determine global 3D genome organization have been established. However, the extent and nature of cell-to-cell and cell-intrinsic variability in genome architecture are poorly characterized. Here, we systematically probe the heterogeneity in genome organization in human fibroblasts by combining high-resolution Hi-C datasets and high-throughput genome imaging. Optical mapping of several hundred genome interaction pairs at the single cell level demonstrates low steady-state frequencies of colocalization in the population and independent behavior of individual alleles in single nuclei ...


Ki-67 Contributes To Normal Cell Cycle Progression And Inactive X Heterochromatin In P21 Checkpoint-Proficient Human Cells, Xiaoming Sun, Aizhan Bizhanova, Timothy D. Matheson, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman May 2017

Ki-67 Contributes To Normal Cell Cycle Progression And Inactive X Heterochromatin In P21 Checkpoint-Proficient Human Cells, Xiaoming Sun, Aizhan Bizhanova, Timothy D. Matheson, Jun Yu, Lihua Julie Zhu, Paul D. Kaufman

University of Massachusetts Medical School Faculty Publications

Ki-67 protein is widely used as a tumor proliferation marker. However, whether Ki-67 affects cell cycle progression has been controversial. Here, we demonstrate that depletion of Ki-67 in human hTERT-RPE1, WI-38, IMR90, hTERT-BJ cell lines and primary fibroblast cells slowed entry into S phase and coordinately downregulated genes related to DNA replication. Some gene expression changes were partially relieved in Ki-67-depleted hTERT-RPE1 cells by co-depletion of the Rb checkpoint protein, but more thorough suppression of the transcriptional and cell cycle defects was observed upon depletion of cell cycle inhibitor p21. Notably, induction of p21 upon depletion of Ki-67 was a ...


Melatonin And Its Metabolites Protect Human Melanocytes Against Uvb-Induced Damage: Involvement Of Nrf2-Mediated Pathways, Zorica Janjetovic, Stuart G. Jarrett, Elizabeth F. Lee, Cory Duprey, Russel J. Reiter, Andrzej T. Slominski Apr 2017

Melatonin And Its Metabolites Protect Human Melanocytes Against Uvb-Induced Damage: Involvement Of Nrf2-Mediated Pathways, Zorica Janjetovic, Stuart G. Jarrett, Elizabeth F. Lee, Cory Duprey, Russel J. Reiter, Andrzej T. Slominski

Toxicology and Cancer Biology Faculty Publications

Ultraviolet light (UV) is an inducer of reactive oxygen species (ROS) as well as 6-4-photoproducts and cyclobutane pyrimidine dimers (CPD) in the skin, which further cause damage to the skin cells. Irradiation of cultured human melanocytes with UVB stimulated ROS production, which was reduced in cells treated with melatonin or its metabolites: 6-hydroxymelatonin (6-OHM), N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK), N-acetylserotonin (NAS), and 5-methoxytryptamine (5-MT). Melatonin and its derivatives also stimulated the expression of NRF2 (nuclear factor erythroid 2 [NF-E2]-related factor 2) and its target enzymes and proteins that play an important role in cell protection from different damaging factors including UVB ...


Prima: A Gene-Centered, Rna-To-Protein Method For Mapping Rna-Protein Interactions, Alex M. Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D. Holdorf, Sean P. Ryder, Albertha J. M. Walhout Sep 2016

Prima: A Gene-Centered, Rna-To-Protein Method For Mapping Rna-Protein Interactions, Alex M. Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D. Holdorf, Sean P. Ryder, Albertha J. M. Walhout

University of Massachusetts Medical School Faculty Publications

Interactions between RNA binding protein (RBP) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher ...


Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre Feb 2016

Clinical Light Exposure, Photoreceptor Degeneration, And Ap-1 Activation: A Cell Death Or Cell Survival Signal In The Rhodopsin Mutant Retina?, Danian Gu, William Beltran, Zexiao Li, Gregory M. Acland, Gustavo D. Aguirre

Gustavo D. Aguirre, VMD, PhD

PURPOSE. The T4R RHO mutant dog retina shows retinal degeneration with exposures to light comparable to those used in clinical eye examinations of patients. To define the molecular mechanisms of the degeneration, AP-1 DNA-binding activity, composition, posttranslational modification of the protein complex, and modulation of ERK/MAPK signaling pathways were examined in light-exposed mutant retinas. METHODS. Dark-adapted retinas were exposed to short-duration light flashes from a retinal camera used clinically for retinal photography and were collected at different time points after exposure. Electrophoretic mobility shift assay (EMSA), supershift EMSA, Western blot analysis, and immunocytochemistry were used to examine AP-1 signaling ...


Bestrophin Gene Mutations Cause Canine Multifocal Retinopathy: A Novel Animal Model For Best Disease, Karina E. Guziewicz, Barbara Zangerl, Sarah J. Lindauer, Robert F. Mullins, Lynne S. Sandmeyer, Bruce H. Grahn, Edwin M. Stone, Gregory M. Acland, Gustavo D. Aguirre Feb 2016

Bestrophin Gene Mutations Cause Canine Multifocal Retinopathy: A Novel Animal Model For Best Disease, Karina E. Guziewicz, Barbara Zangerl, Sarah J. Lindauer, Robert F. Mullins, Lynne S. Sandmeyer, Bruce H. Grahn, Edwin M. Stone, Gregory M. Acland, Gustavo D. Aguirre

Gustavo D. Aguirre, VMD, PhD

PURPOSE. Canine multifocal retinopathy (cmr) is an autosomal recessive disorder of multiple dog breeds. The disease shares a number of clinical and pathologic similarities with Best macular dystrophy (BMD), and cmr is proposed as a new large animal model for Best disease. METHODS. cmr was characterized by ophthalmoscopy and histopathology and compared with BMD-affected patients. BEST1 (alias VMD2), the bestrophin gene causally associated with BMD, was evaluated in the dog. Canine ortholog cDNA sequence was cloned and verified using RPE/choroid 5′- and 3′-RACE. Expression of the canine gene transcripts and protein was analyzed by Northern and Western blotting ...


Analysis Of Alternative Storage Conditions For Dna Recovery From Field Samples, Alison Schutt, Emily Stricklin, Britta Ten Haken, Joseph Tolsma, Laurie Furlong, Sara S. Tolsma Jan 2016

Analysis Of Alternative Storage Conditions For Dna Recovery From Field Samples, Alison Schutt, Emily Stricklin, Britta Ten Haken, Joseph Tolsma, Laurie Furlong, Sara S. Tolsma

Northwestern Review

As ecologists increasingly employ molecular methods, they find that tried and true preservation solutions (e.g. ethanol or formalin) may not be optimal when samples are targeted for genetic analyses. Before traveling to remote sample sites, researchers need to consider which preservation methods are likely to yield the largest quantity and highest quality of DNA based on their travel times and field conditions. They also need to consider whether they will have access to preservatives at remote sites and whether those preservatives can be safely transported. To determine which preservation methods would most reliably preserve tissue for genetic analysis under ...


On The Molecular Biology And Evolution Of Plant Parasitism By Nematodes, Jason Brett Noon Jan 2016

On The Molecular Biology And Evolution Of Plant Parasitism By Nematodes, Jason Brett Noon

Graduate Theses and Dissertations

Plant-parasitic nematodes (PPN) are among the most devastating plant pathogens. However, our understanding of how nematodes adapted to plant parasitism, and the molecular mechanisms that PPN use during infection is limited. Among the most important genomic changes that occurred in the free-living nematode ancestors of PPN were multiple horizontal gene transfer (HGT) events from bacteria. Though it is clear that HGT helped shape the genomes of many PPN, how this process occurred is unknown. Also, it is evident that successful parasitism occurs from the delivery of proteinaceous effectors into plant roots to hijack and modify host cellular processes.

The research ...


Electrosensory Ampullary Organs Are Derived From Lateral Line Placodes In Bony Fishes, Melissa S. Modrell, William E. Benis, R. Glenn Northcutt, Marcus C. Davis, Clare V.H. Baker Oct 2015

Electrosensory Ampullary Organs Are Derived From Lateral Line Placodes In Bony Fishes, Melissa S. Modrell, William E. Benis, R. Glenn Northcutt, Marcus C. Davis, Clare V.H. Baker

Marcus C Davis

Electroreception is an ancient subdivision of the lateral line sensory system, found in all major vertebrate groups (though lost in frogs, amniotes and most ray-finned fishes). Electroreception is mediated by 'hair cells' in ampullary organs, distributed in fields flanking lines of mechanosensory hair cell-containing neuromasts that detect local water movement. Neuromasts, and afferent neurons for both neuromasts and ampullary organs, develop from lateral line placodes. Although ampullary organs in the axolotl (a representative of the lobe-finned clade of bony fishes) are lateral line placode-derived, non-placodal origins have been proposed for electroreceptors in other taxa. Here we show morphological and molecular ...


Smad3 Deficiency Promotes Vessel Wall Remodeling, Collagen Fiber Reorganization And Leukocyte Infiltration In An Inflammatory Abdominal Aortic Aneurysm Mouse Model, Xiaohua Dai, Jianbin Shen, Neeraja Priyanka Annam, Hong Jiang, Edi Levi, Charles M. Schworer, Gerard Tromp, Anandita Arora, Mary Higgins, Xiao-Fan Wang, Maozhou Yang, Hui J. Li, Kezhong Zhang, Helena Kuivaniemi, Li Li May 2015

Smad3 Deficiency Promotes Vessel Wall Remodeling, Collagen Fiber Reorganization And Leukocyte Infiltration In An Inflammatory Abdominal Aortic Aneurysm Mouse Model, Xiaohua Dai, Jianbin Shen, Neeraja Priyanka Annam, Hong Jiang, Edi Levi, Charles M. Schworer, Gerard Tromp, Anandita Arora, Mary Higgins, Xiao-Fan Wang, Maozhou Yang, Hui J. Li, Kezhong Zhang, Helena Kuivaniemi, Li Li

Open Access Articles

TGF-beta signaling plays critical roles in the pathogenesis of aneurysms; however, it is still unclear whether its role is protective or destructive. In this study, we investigate the role of SMAD3 in the pathogenesis of calcium chloride (CaCl2)-induced abdominal aortic aneurysms (AAA) in Smad3(-/-), Smad3(+/-) and Smad3(+/+) mice. We find that loss of SMAD3 drastically increases wall thickening of the abdominal aorta. Histological analyses show significant vessel wall remodeling with elastic fiber fragmentation. Remarkably, under polarized light, collagen fibers in the hyperplastic adventitia of Smad3(-/-) mice show extensive reorganization accompanied by loosely packed thin and radial collagen fibers. The ...


Reverse Gyrase Is Not Necessary For Survival Of Hyperthermophilic Archaeon Pyrococcus Furiosus, Farshid Taghizadeh, Michael S. Bartlett May 2015

Reverse Gyrase Is Not Necessary For Survival Of Hyperthermophilic Archaeon Pyrococcus Furiosus, Farshid Taghizadeh, Michael S. Bartlett

Student Research Symposium

Reverse gyrase is the only known topoisomerase enzyme with positive supercoiling activity on covalently-closed DNA. This positive supercoiling is required to prevent DNA from denaturation at high temperatures. The gene that codes for this protein is present in all hyperthermophiles and absent from all mesophilic and thermophilic genomes, suggesting that this enzyme is the only hyperthermophile-specific protein. To investigate if this protein is vital for the cells, we knocked out its gene from the genome of living organism Pyrococcus furiosus. Pyrococcus furiosus is a hyperthermophilic archaeon that grows between 70°C to 103°C with an optimum growth temperature of ...


Ex Vivo Dna Cloning, Adam B. Fisher Jan 2015

Ex Vivo Dna Cloning, Adam B. Fisher

Theses and Dissertations

Genetic engineering of microbes has developed rapidly along with our ability to synthesize DNA de novo. Yet, even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. While technological advances have resulted in powerful techniques for in vitro and in vivo assembly of DNA, each suffers inherent disadvantages. Here, an ex vivo DNA cloning suite using crude cellular lysates derived from E. coli is demonstrated to amplify and assemble DNA containing small sequence homologies. Further, the advantages of an ex vivo approach are leveraged ...


Dancing Through Life: Allosteric Transitions And Structural Analysis Of Hsp70 And Hsp110 Chaperone Proteins, Gabrielle Stetz, Gennady M. Verkhivker Dec 2014

Dancing Through Life: Allosteric Transitions And Structural Analysis Of Hsp70 And Hsp110 Chaperone Proteins, Gabrielle Stetz, Gennady M. Verkhivker

Student Scholar Symposium Abstracts and Posters

The molecular chaperone protein Hsp70 is centrally involved in cellular homeostasis by assisting in the folding and degradation of protein substrates. Hsp70 is joined by co-chaperones, such as Hsp110, which contribute to specialized tasks of the Hsp70 complex. Imbalances of this heat shock protein system are believed to be involved with the deregulation of cancer pathways and other human diseases. Better understanding of how these heat shock proteins work at the molecular level, which has been investigated using molecular docking tools, will give more clues about biological function. Simulating the formation and function of Hsp70 based chaperone complexes could provide ...


Gaip Interacting Protein C-Terminus Regulates Autophagy And Exosome Biogenesis Of Pancreatic Cancer Through Metabolic Pathways, Santanu Bhattacharya, Krishnendu Pal, Anil K. Sharma, Shamit K. Dutta, Julie S. Lau, Irene K. Yan, Enfeng Wang, Ahmed Elkhanany, Khalid M. Alkharfy, Arunik Sanyal, Tushar C. Patel, Suresh T. Chari, Mark R. Spaller, Debabrata Mukhopadhyay Dec 2014

Gaip Interacting Protein C-Terminus Regulates Autophagy And Exosome Biogenesis Of Pancreatic Cancer Through Metabolic Pathways, Santanu Bhattacharya, Krishnendu Pal, Anil K. Sharma, Shamit K. Dutta, Julie S. Lau, Irene K. Yan, Enfeng Wang, Ahmed Elkhanany, Khalid M. Alkharfy, Arunik Sanyal, Tushar C. Patel, Suresh T. Chari, Mark R. Spaller, Debabrata Mukhopadhyay

Open Dartmouth: Faculty Open Access Articles

GAIP interacting protein C terminus (GIPC) is known to play an important role in a variety of physiological and disease states. In the present study, we have identified a novel role for GIPC as a master regulator of autophagy and the exocytotic pathways in cancer. We show that depletion of GIPC-induced autophagy in pancreatic cancer cells, as evident from the upregulation of the autophagy marker LC3II. We further report that GIPC regulates cellular trafficking pathways by modulating the secretion, biogenesis, and molecular composition of exosomes. We also identified the involvement of GIPC on metabolic stress pathways regulating autophagy and microvesicular ...


Identification Of Proteins Potentially Involved In The Formation Of Lafora Bodies, A Hallmark Of Lafora Disease, Elham Schokraie, Oliver Kötting, Matthew S. Gentry Sep 2013

Identification Of Proteins Potentially Involved In The Formation Of Lafora Bodies, A Hallmark Of Lafora Disease, Elham Schokraie, Oliver Kötting, Matthew S. Gentry

Molecular and Cellular Biochemistry Presentations

Lafora Disease (LD) is a fatal teenage-onset progressive myoclonus epilepsy. It is characterized by the formation of Lafora bodies (LBs), deposits of abnormally branched, insoluble, hyperphosphorylated glycogen-like polymers that are generally believed to trigger the development of the clinical symptoms of LD. 58% and 35% of the LD cases are caused by mutations in EPM2A (laforin) and EPM2B (malin), respectively. However, little is known about their function in LB formation. Two different mechanisms have been proposed to explain the accumulation of insoluble LBs: first, excessive glycogen phosphorylation and, second, an imbalance between glycogen synthesizing enzymes. The present study aims at ...