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2015

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Articles 1 - 30 of 1038

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

Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap Dec 2015

Alternative Use Of Dna Binding Domains By The Neurospora White Collar Complex Dictates Circadian Regulation And Light Responses, Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap

Open Dartmouth: Faculty Open Access Scholarship

In the Neurospora circadian system, the White Collar complex (WCC) of WC-1 and WC-2 drives transcription of the circadian pacemaker gene frequency (frq), whose gene product, FRQ, as a part of the FRQ-FRH complex (FFC), inhibits its own expression. The WCC is also the principal Neurospora photoreceptor; WCC-mediated light induction of frq resets the clock, and all acute light induction is triggered by WCC binding to promoters of light-induced genes. However, not all acutely light-induced genes are also clock regulated, and conversely, not all clock-regulated direct targets of WCC are light induced; the structural determinants governing the shift from WCC ...


Amyloid Proteins Structure, Dynamics, Interactions And Early Stages Of Self-Assembly, Yuliang Zhang Dec 2015

Amyloid Proteins Structure, Dynamics, Interactions And Early Stages Of Self-Assembly, Yuliang Zhang

Theses & Dissertations

The self-assembly and aggregation of amyloid protein are associated with several neurodegenerative diseases. The evidence indicates that the oligomeric intermediates, formed prior to the final fibrillary product, are the primary culprits of neurotoxicity. Although tremendous efforts have been dedicated for the characterization of structures, dynamics and toxic-related hallmarks of the oligomers, to date, yet the mechanism of such assembly from disordered monomers and their structure remain elusive.

In this dissertation, I focused on understanding the dimerization process of amyloid proteins and peptides of different sizes and I combined experimental studies with high-power computer simulations. The AFM force spectroscopy experiments showed ...


Period-1 Encodes An Atp-Dependent Rna Helicase That Influences Nutritional Compensation Of The Neurospora Circadian Clock, Jillian M. Emerson, Bradley M. Bartholomai, Carol S. Ringelberg, Scott E. Baker, Jennifer Loros, Jay Dunlap Dec 2015

Period-1 Encodes An Atp-Dependent Rna Helicase That Influences Nutritional Compensation Of The Neurospora Circadian Clock, Jillian M. Emerson, Bradley M. Bartholomai, Carol S. Ringelberg, Scott E. Baker, Jennifer Loros, Jay Dunlap

Open Dartmouth: Faculty Open Access Scholarship

Mutants in the period-1 (prd-1) gene, characterized by a recessive allele, display a reduced growth rate and period lengthening of the developmental cycle controlled by the circadian clock. We refined the genetic location of prd-1 and used whole genome sequencing to find the mutation defining it, confirming the identity of prd-1 by rescuing the mutant circadian phenotype via transformation. PRD-1 is an RNA helicase whose orthologs, DDX5 [DEAD (Asp-Glu-Ala-Asp) Box Helicase 5] and DDX17 in humans and DBP2 (Dead Box Protein 2) in yeast, are implicated in various processes, including transcriptional regulation, elongation, and termination, ribosome biogenesis, and mRNA decay ...


Mechanism Of Lignin Inhibition Of Enzymatic Biomass Deconstruction, Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy C. Smith Dec 2015

Mechanism Of Lignin Inhibition Of Enzymatic Biomass Deconstruction, Josh V. Vermaas, Loukas Petridis, Xianghong Qi, Roland Schulz, Benjamin Lindner, Jeremy C. Smith

Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology

Background

The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process.

Results

By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical ...


Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault Dec 2015

Characterization Of Cytidylyltransferase Enzyme Activity Through High Performance Liquid Chromatography, James Brault

Theses and Dissertations

The cytidylyltransferases are a family of enzymes that utilize cytidine 5â?? triphosphate (CTP) to synthesize molecules that are precursors to membrane phospholipids. There are four well known enzymes: CTP: phosphoethanolamine cytidylyltransferase (ECT), CTP: glycerol-3-phosphate cytidylyltransferase (GCT), 2-C-methyl-D-erythritol-4-phosphate cytidylyltransferase synthetase (CMS), and CTP: phosphocholine cytidylyltransferase (CCT). Previously, a radioisotope tagging method was employed to study cytidylyltransferase catalysis. Using CCT as a model, a method utilizing high performance liquid chromatography (HPLC) was developed to replace the radioisotope scintillation technique. The development of this new HPLC method is cheaper, more efficient, and more accurate than the previously established method.

The targets of separation ...


In Vivo Single-Particle Imaging Of Nuclear Mrna Export In Budding Yeast Demonstrates An Essential Role For Mex67p, Carlas Smith, Azra Lari, Carina Patrizia. Derrer, Anette Ouwehand, Ammeret Rossouw, Maximiliaan Huisman, Thomas Dange, Mark Hopman, Aviva Joseph, Daniel Zenklusen, Karsten Weis, David Grünwald, Ben Montpetit Dec 2015

In Vivo Single-Particle Imaging Of Nuclear Mrna Export In Budding Yeast Demonstrates An Essential Role For Mex67p, Carlas Smith, Azra Lari, Carina Patrizia. Derrer, Anette Ouwehand, Ammeret Rossouw, Maximiliaan Huisman, Thomas Dange, Mark Hopman, Aviva Joseph, Daniel Zenklusen, Karsten Weis, David Grünwald, Ben Montpetit

RNA Therapeutics Institute Publications

Many messenger RNA export proteins have been identified; yet the spatial and temporal activities of these proteins and how they determine directionality of messenger ribonucleoprotein (mRNP) complex export from the nucleus remain largely undefined. Here, the bacteriophage PP7 RNA-labeling system was used in Saccharomyces cerevisiae to follow single-particle mRNP export events with high spatial precision and temporal resolution. These data reveal that mRNP export, consisting of nuclear docking, transport, and cytoplasmic release from a nuclear pore complex (NPC), is fast ( approximately 200 ms) and that upon arrival in the cytoplasm, mRNPs are frequently confined near the nuclear envelope. Mex67p functions ...


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 ...


Crispr Interference And Priming Varies With Individual Spacer Sequences, Chaoyou Xue, Arun S. Seetharam, Olga Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew J. Severin, Dipali G. Sashital Dec 2015

Crispr Interference And Priming Varies With Individual Spacer Sequences, Chaoyou Xue, Arun S. Seetharam, Olga Musharova, Konstantin Severinov, Stan J. J. Brouns, Andrew J. Severin, Dipali G. Sashital

Biochemistry, Biophysics and Molecular Biology Publications

CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed ...


Control Of The Basal Recycling And Surface Expression Of Epidermal Growth Factor Receptor By The Endocytic Recycling Regulator Ehd1 Utilizing A Pathway Shared By Rusc2, Eric Tom Dec 2015

Control Of The Basal Recycling And Surface Expression Of Epidermal Growth Factor Receptor By The Endocytic Recycling Regulator Ehd1 Utilizing A Pathway Shared By Rusc2, Eric Tom

Theses & Dissertations

The epidermal growth factor receptor (EGFR) is a prototype receptor tyrosine kinase (RTK) and oncogene aberrantly expressed or mutated in solid tumors. Its surface expression is dynamically regulated. Display of an activation-competent pool is essential for response to ligands. Internalization and degradation of EGFR following stimulation has received the most attention, fewer studies have characterized the recycling arm of EGFR transit, basal traffic and surface display are poorly understood. Thus, we evaluated the endocytic recycling of EGFR for its therapeutic potential in EGFR driven cancers. The C-Terminal Eps15 homology (EH) domain-containing proteins have emerged as regulators of surface receptor recycling ...


Regulation Of The Transmembrane Mucin Muc4 By Wnt/Β-Catenin In Gastrointestinal Cancers, Priya Pai Dec 2015

Regulation Of The Transmembrane Mucin Muc4 By Wnt/Β-Catenin In Gastrointestinal Cancers, Priya Pai

Theses & Dissertations

The transmembrane mucin MUC4 is a high molecular weight glycoprotein that is expressed de novo in pancreatic ductal adenocarcinoma (PDAC). MUC4 has been shown to play a tumor-promoting role in malignancies such as PDAC, ovarian cancer and breast cancer. Unlike the normal pancreas, MUC4 is ordinarily expressed by goblet and absorptive cells in the normal colonic epithelium. However, its expression/role in colorectal cancer (CRC) is not well studied.

In this dissertation, the goal was to identify factor(s) that may differentially regulate MUC4 in these two disparate malignancies. Furthermore, in light of its pro-tumorigenic role in other malignancies, we ...


A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage Dec 2015

A Novel Transcription Factor In Arabidopsis Thaliana Abiotic Stress Response, Achira S. Weerathunga Arachchilage

University of New Orleans Theses and Dissertations

Plants respond to environmental stress by altering their gene expression. Under stress conditions some genes are activated and some genes are repressed. Even though a lot of work has been done to understand mechanisms of gene activation under abiotic stress very little information is available on how stress responsive genes are kept repressed under normal growth conditions. Recent work has revealed that plants use transcriptional repression as common mechanism of gene repression. Transcriptional repression is achieved by recruitment co-repressor complexes to the target genes. Recent studies have revealed that the co-repressor LUH complexes with SLK1 and SLK2 to silence Arabidopsis ...


The Exocyst Subunit Sec6 Interacts With Assembled Exocytic Snare Complexes: A Dissertation, Michelle L. Dubuke Dec 2015

The Exocyst Subunit Sec6 Interacts With Assembled Exocytic Snare Complexes: A Dissertation, Michelle L. Dubuke

GSBS Dissertations and Theses

In eukaryotic cells, membrane-bound vesicles carry cargo between intracellular compartments, to and from the cell surface, and to the extracellular environment. Many conserved families of proteins are required for properly localized vesicle fusion, including the multi-subunit tethering complexes and the SNARE complexes. These protein complexes work together to promote proper vesicle fusion in other trafficking pathways. Contrary to these other pathways, our lab previously suggested that the exocyst subunit Sec6, a component of the exocytosis-specific tethering complex, inhibited Sec9:Sso1 SNARE complex assembly due to interactions in vitro with the SNARE protein Sec9 (Sivaram et al., 2005).

My goal for ...


Ubiquitin Goes Green, Zhihua Hua, Richard D. Vierstra Dec 2015

Ubiquitin Goes Green, Zhihua Hua, Richard D. Vierstra

Biology Faculty Publications & Presentations

Chloroplasts depend on the nucleus for much of their proteome. Consequently, strong transcriptional coordination exists between the genomes, which is attuned to the developmental and physiological needs of the organelle. Recent studies highlight that the post-translational modifier ubiquitin adds another layer to plastid homeostasis and even helps eliminate damaged chloroplasts.


Systematic Dissection Of Roles For Chromatin Regulators In Dynamics Of Transcriptional Response To Stress In Yeast: A Dissertation, Hsiuyi V. Chen Dec 2015

Systematic Dissection Of Roles For Chromatin Regulators In Dynamics Of Transcriptional Response To Stress In Yeast: A Dissertation, Hsiuyi V. Chen

GSBS Dissertations and Theses

The following work demonstrates that chromatin regulators play far more pronounced roles in dynamic gene expression than they do in steady-state. Histone modifications have been associated with transcription activity. However, previous analyses of gene expression in mutants affecting histone modifications show limited alteration. I systematically dissected the effects of 83 histone mutants and 119 gene deletion mutants on gene induction/repression in response to diamide stress in yeast. Importantly, I observed far more changes in gene induction/repression than changes in steady-state gene expression. The extensive dynamic gene expression profile of histone mutants and gene deletion mutants also allowed me ...


Population Density Of The Florida Scrub Lizard (Sceloporus Woodi) In Managed Sand Pine Scrub And Longleaf Pine Sandhill Habitats, Matthew D. Kaunert, Lance D. Mcbrayer Dec 2015

Population Density Of The Florida Scrub Lizard (Sceloporus Woodi) In Managed Sand Pine Scrub And Longleaf Pine Sandhill Habitats, Matthew D. Kaunert, Lance D. Mcbrayer

Biology Faculty Publications

Studies investigating managed landscapes are of increasing importance, as fragmentation is a known cause of biodiversity loss. From June to September 2012, we sampled populations of the rare, endemic Florida Scrub Lizard (Sceloporus woodi) across the Ocala National Forest (ONF) to compare lizard density across two managed habitat types. Florida Scrub habitat in the ONF is clearcut and roller-chopped, whereas Longleaf Pine habitat is managed via prescribed burning. We sampled 10 stands of Florida Scrub (2–3 y post disturbance) and 10 stands of Longleaf Pine (1 y post-disturbance) for lizards. We compared lizard density between the interior of each ...


Aggregation Characterization Of Wild-Type P53 And Six Common P53 Mutants, Taylor A. Arhar Dec 2015

Aggregation Characterization Of Wild-Type P53 And Six Common P53 Mutants, Taylor A. Arhar

Honors Thesis

P53 is a tumor suppressor protein, which functions in maintaining the cell cycle. When p53 loses its function, cells may multiply at an uncontrolled rate and form tumors. This loss of function is linked to over fifty percent of human cancers. This investigation aims to explore the possible link between p53 aggregation and tumorigenesis. There is a possibility that p53, especially in mutant form, will aggregate beyond its normal tetrameric conformation and lose its function, leading to tumor formation. Wild-type p53 and six mutants, R175H, R175C, R248Q, R248W, R273C, and R273H (six of the most common mutations found in human ...


Microsolvation Of Anions By Molecules Forming Ch∙∙X- Hydrogen Bonds, Steve Scheiner, Binod Nepal Dec 2015

Microsolvation Of Anions By Molecules Forming Ch∙∙X- Hydrogen Bonds, Steve Scheiner, Binod Nepal

Chemistry and Biochemistry Faculty Publications

Various anions were surrounded by n molecules of CF3H, which was used as a prototype CH donor solvent, and the structures and energies studied by M06-2X calculations with a 6-31+G∗∗ basis set. Anions considered included the halides F-, Cl-, Br- and I-, as well as those with multiple proton acceptor sites: CN-, NO3 -, HCOO-, CH3COO-, HSO4 -, H2PO4 -, and anions with higher charges SO4 2-, HPO4 2- and PO4 3-. Well structured cages were formed and the average H-bond energy decreases steadily as the number of surrounding solvent ...


The Role Of Bone Sialoprotein In Periodontal Tissue Development And Bone Repair, Yohannes Soenjaya Dec 2015

The Role Of Bone Sialoprotein In Periodontal Tissue Development And Bone Repair, Yohannes Soenjaya

Electronic Thesis and Dissertation Repository

Bone development and repair involve complex processes that include interaction between cells and their surrounding matrix. In the body, bone sialoprotein (BSP) expression is up-regulated at the onset of mineralization. BSP is a multifunctional acidic phosphoprotein with collagen-binding, hydroxyapatite nucleating, and integrin recognition (RGD sequence, which is important for cell-attachment and signaling) regions. Mice lacking BSP expression (Bsp-/-), exhibit a bone phenotype with reductions in bone mineral density, bone length, osteoclast activation, and impaired bone healing. This thesis examined the role of BSP in tooth development and also its potential use as a therapeutic reagent for bone repair. MicroCT and ...


The Role Of Thymine Dna Glycosylase (Tdg) And Dna Demethylation In Tgf Beta Signaling, Matthew E.R. Maitland Dec 2015

The Role Of Thymine Dna Glycosylase (Tdg) And Dna Demethylation In Tgf Beta Signaling, Matthew E.R. Maitland

Electronic Thesis and Dissertation Repository

Prompted by findings that TGFβ stimulates thymine DNA glycosylase (TDG) dependent rapid DNA demethylation and activation of the CDKN2B gene, I investigated the global role of TDG and DNA demethylation in TGFβ signaling in HaCaT cells. Using dot blot analysis, I show that TGFβ treatment increases the global levels of 5-formylcytosine, an intermediate metabolite of active DNA demethylation. Characterization of genomic regions that undergo DNA demethylation and recruitment of TDG indicate that they are both frequent events, but only overlap at 11 genomic locations. I identified 440 TGFβ upregulated genes, 40 of which were bound by TDG and 169 that ...


The Rational Design And Evaluation Of Ck2alpha Mutants Bearing Inhibitor-Refractory Amino Acid Substitutions, Sam Reid Fess Dec 2015

The Rational Design And Evaluation Of Ck2alpha Mutants Bearing Inhibitor-Refractory Amino Acid Substitutions, Sam Reid Fess

Electronic Thesis and Dissertation Repository

CK2 is a ubiquitously expressed and constitutively active serine/threonine protein kinase that is implicated in many cellular functions. Previous studies have indicated that the generation of mutants that are less sensitive to inhibition can be advantageous when studying protein kinases. Importantly, studies have demonstrated that mutants of CK2 rendered less sensitive to inhibition are attainable. To extend these observations, mutants of CK2α were designed and evaluated to test their effect on the inhibition of CK2 by CX-4945 using in vitro enzymatic assays followed by the development of inducible cell lines. CX-4945 is a CK2 inhibitor that has demonstrated anti-tumor ...


The Preparation And Characterization Of Cyclodextrin:Sterol Inclusion Complexes As Anti-Tumor Therapeutics, Janet V. Cowins Dec 2015

The Preparation And Characterization Of Cyclodextrin:Sterol Inclusion Complexes As Anti-Tumor Therapeutics, Janet V. Cowins

Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University

An inclusion complex between β-cyclodextrin and insoluble guest compounds has been reported by several researchers. The main purpose of forming an inclusion complex between β-CD and sparingly soluble guests is to enhance the guest’s solubility and mask its undesirable properties. Preliminary studies have shown that when conjugated with target-specific moieties, these inclusion complexes can be used in pharmaceutical applications for drug delivery. β-Sitosterol, a plant sterol, has been well documented to reduce tumor cell growth and migration as well as exhibit apoptotic characteristics. An issue with this plant sterol and most pharmaceutical compounds is their lack of solubility. In ...


Hepatitis C Virus: Structural Insights Into Protease Inhibitor Efficacy And Drug Resistance: A Dissertation, Djade I. Soumana Dec 2015

Hepatitis C Virus: Structural Insights Into Protease Inhibitor Efficacy And Drug Resistance: A Dissertation, Djade I. Soumana

GSBS Dissertations and Theses

The Hepatitis C Virus (HCV) is a global health problem as it afflicts an estimated 170 million people worldwide and is the major cause of viral hepatitis, cirrhosis and liver cancer. HCV is a rapidly evolving virus, with 6 major genotypes and multiple subtypes. Over the past 20 years, HCV therapeutic efforts have focused on identifying the best-in-class direct acting antiviral (DAA) targeting crucial components of the viral lifecycle, The NS3/4A protease is responsible for processing the viral polyprotein, a crucial step in viral maturation, and for cleaving host factors involved in activating immunity. Thus targeting the NS3/4A ...


Hd2d Is A Regulator Of Abscisic Acid Responses In Arabidopsis, Joshua A. Farhi Dec 2015

Hd2d Is A Regulator Of Abscisic Acid Responses In Arabidopsis, Joshua A. Farhi

Electronic Thesis and Dissertation Repository

Histone deacetylases have important roles in development and stress response in plants. To further investigate their function, the HD2D gene, of the plant specific HD2 family, was studied. An hd2d-1 mutant and two HD2D overexpression lines were used in this study. Germination was delayed in hd2d-1 and HD2D overexpression seeds only in the presence of ABA. HD2D was found to positively regulate the expression of members of the ABA-response pathway (ABI1, ABI5, and RD29A) leading to increased resistance to drought and salinity treatments. Furthermore, HD2D expression delayed flowering by positively regulating FLC expression. Using bimolecular fluorescence complementation, the HD2D protein ...


Genetic And Acute Cpeb1 Depletion Ameliorate Fragile X Pathophysiology, Tsuyoshi Udagawa, Natalie Farny, Mira Jakovcevski, Hanoch Kaphzan, Juan Alarcon, Shobha Anilkumar, Maria Ivshina, Jessica Hurt, Kentaro Nagaoka, Vijayalaxmi Nalavadi, Lori Lorenz, Gary Bassell, Schahram Akbarian, Sumantra Chattarji, Eric Klann, Joel Richter Dec 2015

Genetic And Acute Cpeb1 Depletion Ameliorate Fragile X Pathophysiology, Tsuyoshi Udagawa, Natalie Farny, Mira Jakovcevski, Hanoch Kaphzan, Juan Alarcon, Shobha Anilkumar, Maria Ivshina, Jessica Hurt, Kentaro Nagaoka, Vijayalaxmi Nalavadi, Lori Lorenz, Gary Bassell, Schahram Akbarian, Sumantra Chattarji, Eric Klann, Joel Richter

Natalie G. Farny

Fragile X syndrome (FXS), the most common cause of inherited mental retardation and autism, is caused by transcriptional silencing of FMR1, which encodes the translational repressor fragile X mental retardation protein (FMRP). FMRP and cytoplasmic polyadenylation element-binding protein (CPEB), an activator of translation, are present in neuronal dendrites, are predicted to bind many of the same mRNAs and may mediate a translational homeostasis that, when imbalanced, results in FXS. Consistent with this possibility, Fmr1(-/y); Cpeb1(-/-) double-knockout mice displayed amelioration of biochemical, morphological, electrophysiological and behavioral phenotypes associated with FXS. Acute depletion of CPEB1 in the hippocampus of adult Fmr1 ...


Characterization And Structure Of A Zn2+ And [2fe-2s]-Containing Copper Chaperone From Archaeoglobus Fulgidus, Matthew Sazinsky, Benjamin Lemoine, Maria Orofino, Roman Davydov, Krisztina Bencze, Timothy Stemmler, Brian Hoffman, José Argüello, Amy Rosenzweig Dec 2015

Characterization And Structure Of A Zn2+ And [2fe-2s]-Containing Copper Chaperone From Archaeoglobus Fulgidus, Matthew Sazinsky, Benjamin Lemoine, Maria Orofino, Roman Davydov, Krisztina Bencze, Timothy Stemmler, Brian Hoffman, José Argüello, Amy Rosenzweig

José M. Argüello

Bacterial CopZ proteins deliver copper to P1B-type Cu+-ATPases that are homologous to the human Wilson and Menkes disease proteins. The genome of the hyperthermophile Archaeoglobus fulgidus encodes a putative CopZ copper chaperone that contains an unusual cysteine rich N-terminal domain of 130 amino acids in addition to a C-terminal copper-binding domain with a conserved CXXC motif. The N-terminal domain (CopZ-NT) is homologous to proteins found only in extremophiles and is the only such protein that is fused to a copper chaperone. Surprisingly, optical, electron paramagnetic resonance, and X-ray absorption spectroscopic data indicate the presence of a [2Fe-2S] cluster in ...


Correlations Between Oxygen Affinity And Sequence Classifications Of Plant Hemoglobins, Benoit Smagghe, Julie Hoy, Ryan Percifield, Suman Kundu, Mark Hargrove, Gautam Sarath, Jean-Louis Hilbert, Richard Watts, Elizabeth Dennis, W. James Peacock, Sylvia Dewilde, Luc Moens, George Blouin, John Olson, Cyril Appleby Dec 2015

Correlations Between Oxygen Affinity And Sequence Classifications Of Plant Hemoglobins, Benoit Smagghe, Julie Hoy, Ryan Percifield, Suman Kundu, Mark Hargrove, Gautam Sarath, Jean-Louis Hilbert, Richard Watts, Elizabeth Dennis, W. James Peacock, Sylvia Dewilde, Luc Moens, George Blouin, John Olson, Cyril Appleby

John Olson

Plants express three phylogenetic classes of hemoglobins (Hb) based on sequence analyses. Class 1 and 2 Hbs are full-length globins with the classical eight helix Mb-like fold, whereas Class 3 plant Hbs resemble the truncated globins found in bacteria. With the exception of the specialized leghemoglobins, the physiological functions of these plant hemoglobins remain unknown. We have reviewed and, in some cases, measured new oxygen binding properties of a large number of Class 1 and 2 plant nonsymbiotic Hbs and leghemoglobins. We found that sequence classification correlates with distinct extents of hexacoordination with the distal histidine and markedly different overall ...


Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, Christoph Kreutz, T. Kwaku Dayle Dec 2015

Chemo-Enzymatic Synthesis Of Site-Specific Isotopically Labeled Nucleotides For Use In Nmr Resonance Assignment, Dynamics And Structural Characterizations, Andrew P. Longhini, Regan M. Leblanc, Owen Becette, Carolina Salguero, Christoph H. Wunderlich, Bruce A. Johnson, Victoria M. D'Souza, Christoph Kreutz, T. Kwaku Dayle

Advanced Science Research Center

Stable isotope labeling is central to NMR studies of nucleic acids. Development of methods that incorporate labels at specific atomic positions within each nucleotide promises to expand the size range of RNAs that can be studied by NMR. Using recombinantly expressed enzymes and chemically synthesized ribose and nucleobase, we have developed an inexpensive, rapid chemo-enzymatic method to label ATP and GTP site specifically and in high yields of up to 90%.We incorporated these nucleotides into RNAs with sizes ranging from 27 to 59 nucleotides using in vitro transcription: A-Site (27 nt), the iron responsive elements (29 nt), a fluoride ...


Linker Histone H1 And H3k56 Acetylation Are Antagonistic Regulators Of Nucleosome Dynamics, Morgan Bernier, Yi Luo, Kingsley C. Nwokelo, Michelle Goodwin, Sarah J. Dreher, Pei Zhang, Mark R. Parthun, Yvonne N. Fondufe-Mittendorf, Jennifer J. Ottesen, Michael G. Poirier Dec 2015

Linker Histone H1 And H3k56 Acetylation Are Antagonistic Regulators Of Nucleosome Dynamics, Morgan Bernier, Yi Luo, Kingsley C. Nwokelo, Michelle Goodwin, Sarah J. Dreher, Pei Zhang, Mark R. Parthun, Yvonne N. Fondufe-Mittendorf, Jennifer J. Ottesen, Michael G. Poirier

Molecular and Cellular Biochemistry Faculty Publications

H1 linker histones are highly abundant proteins that compact nucleosomes and chromatin to regulate DNA accessibility and transcription. However, the mechanisms that target H1 regulation to specific regions of eukaryotic genomes are unknown. Here we report fluorescence measurements of human H1 regulation of nucleosome dynamics and transcription factor (TF) binding within nucleosomes. H1 does not block TF binding, instead it suppresses nucleosome unwrapping to reduce DNA accessibility within H1-bound nucleosomes. We then investigated H1 regulation by H3K56 and H3K122 acetylation, two transcriptional activating histone post translational modifications (PTMs). Only H3K56 acetylation, which increases nucleosome unwrapping, abolishes H1.0 reduction of ...


Near-Infrared Photoactivatable Control Of Ca Signaling And Optogenetic Immunomodulation, Lian He, Yuanwei Zhang, Guolin Ma, Peng Tan, Zhan Jun Li, Shengbing Zhang, Xiang Wu, Ji Jing, Shaohai Fang, Lijuan Zhou, Youjun Wang, Yun Huang, Patrick Hogan, Gang Han, Yubin Zhou Dec 2015

Near-Infrared Photoactivatable Control Of Ca Signaling And Optogenetic Immunomodulation, Lian He, Yuanwei Zhang, Guolin Ma, Peng Tan, Zhan Jun Li, Shengbing Zhang, Xiang Wu, Ji Jing, Shaohai Fang, Lijuan Zhou, Youjun Wang, Yun Huang, Patrick Hogan, Gang Han, Yubin Zhou

Open Access Articles

The application of current channelrhodopsin-based optogenetic tools is limited by the lack of strict ion selectivity and the inability to extend the spectra sensitivity into the near-infrared (NIR) tissue transmissible range. Here we present an NIR-stimulable optogenetic platform (termed "Opto-CRAC") that selectively and remotely controls Ca2+ oscillations and Ca2+-responsive gene expression to regulate the function of non-excitable cells, including T lymphocytes, macrophages and dendritic cells. When coupled to upconversion nanoparticles, the optogenetic operation window is shifted from the visible range to NIR wavelengths to enable wireless photoactivation of Ca2+-dependent signaling and optogenetic modulation of immunoinflammatory responses. In a ...


A 4d View On Mrna, Carlas Smith, Li-Chun Tu, David Grünwald Dec 2015

A 4d View On Mrna, Carlas Smith, Li-Chun Tu, David Grünwald

David Grünwald

Imaging single molecules in live cells in 4+ D (space, time and colors) is crucial for studying various biological processes, especially for observing the behavior of RNA molecules within the nuclear landscape [1]. RNA molecules are known to serve a multitude of tasks such as being templates for protein translation or to act as enzymes for regulating countless reactions in the nucleus [1]. Studying RNA kinetics in living cells can provide new information on RNA function or even human diseases, for instance caused by viruses such as the human immunodeficiency virus (HIV) [2]. A challenge to imaging nuclear RNA function ...