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The histone H3K9 methylation and RNAi pathways regulate normalnucleolar and repeated DNA organization by inhibiting formation ofextrachromosomal DNAs

Description: In order to identify regulators of nuclear organization, Drosophila mutants in the Su(var)3-9 histone H3K9 methyltransferase, RNAi pathway components, and other regulators of heterochromatin-mediated gene silencing were examined for altered nucleoli and positioning of repeated DNAs. Animals lacking components of the H3K9 methylation and RNAi pathways contained disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared to wild type. We also observed a substantial increase in extrachromosomal repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 (Lig4), and ecc DNA formation is not induced by removal of cohesin. We conclude that H3K9 methylation of rDNA and satellites, maintained by Su(var)3-9, HP1, and the RNAi pathway, is necessary for the structural stability of repeated DNAs, which is mediated through suppression of non-homologous end joining (NHEJ). These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.
Date: June 15, 2006
Creator: Peng, Jamy C. & Karpen, Gary H.
Partner: UNT Libraries Government Documents Department

Telomere dysfunction and cell survival: Roles for distinct TIN2-containing complexes

Description: Telomeres are maintained by three DNA binding proteins (TRF1, TRF2 and POT1), and several associated factors. One factor, TIN2, binds TRF1 and TRF2 directly and POT1 indirectly. Along with two other proteins, TPP1 and hRap1, these form a soluble complex that may be the core telomere maintenance complex. It is not clear whether sub-complexes also exist in vivo. We provide evidence for two TIN2 sub-complexes with distinct functions in human cells. We isolated these two TIN2 sub-complexes from nuclear lysates of unperturbed cells and cells expressing TIN2 mutants TIN2-13, TIN2-15C, which cannot bind TRF2 or TRF1, respectively. In cells with wild-type p53 function, TIN2-15C was more potent than TIN2-13 in causing telomere uncapping and eventual growth arrest. In cells lacking p53 function, TIN2-15C was more potent than TIN2-13 in causing telomere dysfunction and cell death. Our findings suggest that distinct TIN2 complexes exist, and that TIN2-15C-sensitive subcomplexes are particularly important for cell survival in the absence of functional p53.
Date: October 2, 2007
Creator: Kim, Sahn-ho; Davalos, Albert R.; Heo, Seok-Jin; Rodier, Francis; Zou, Ying; Beausejour, Christian et al.
Partner: UNT Libraries Government Documents Department

Impact of phenolic substrate and growth temperature on the arthrobacter chlorophenolicus proteome

Description: We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol or phenol at 5 C and 28 C; both for the wild type and a mutant strain with mass spectrometry based proteomics. A label free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.
Date: February 15, 2009
Creator: Unell, Maria; Abraham, Paul E.; Shah, Manesh; Zhang, Bing; Ruckert, Christian; VerBerkmoes, Nathan C. et al.
Partner: UNT Libraries Government Documents Department

Porphyrin Interactions with Wild Type and Mutant Mouse Ferrochelatase

Description: Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the heme biosynthetic pathway, catalyzes Fe<sup>2+</sup> chelation into protoporphyrin IX. Resonance Raman and W-visible absorbance spectroscopes of wild type and engineered variants of murine ferrochelatase were used to examine the proposed structural mechanism for iron insertion into protoporphyrin by ferrochelatase. The recombinant variants (i.e., H207N and E287Q) are enzymes in which the conserved amino acids histidine-207 and glutamate-287 of murine ferrochelatase were substituted with asparagine and glutamine, respectively. Both of these residues are at the active site of the enzyme as deduced from the Bacillus subtilis ferrochelatase three-dimensional structure. Addition of free base or metalated porphyrins to wild type ferrochelatase and H207N variant yields a quasi 1:1 complex, possibly a monomeric protein-bound species. In contrast, the addition of porphyrin (either free base or metalated) to E287Q is sub-stoichiometric, as this variant retains bound porphyrin in the active site during isolation and purification. The specificity of porphyrin binding is confirmed by the narrowing of the structure-sensitive resonance Raman lines and the vinyl vibrational mode. Resonance Raman spectra of free base and metalated porphyrins bound to the wild type ferrochelatase indicate a nonplanar distortion of the porphyrin macrocycle, although the magnitude of the distortion cannot be determined without first defining the specific type of deformation. Significantly, the extent of the nonplanar distortion varies in the case of H207N- and E287Q-bound porphyrins. In fact, resonance Raman spectral decomposition indicates a homogeneous ruffled distortion for the nickel protoporphyrin bound to the wild type ferrochelatase, whereas both a planar and ruffled conformations are present for the H207N-bound porphyrin. Perhaps more revealing is the unusual resonance , 3 Raman spectrum of the endogenous E287Q-bound porphyrin, which has the structure-sensitive lines greatly upshifted relative to those of the free base protoporphyrin in solution. This could be interpreted as an equilibrium ...
Date: May 19, 1999
Creator: Ferreira, Gloria C.; Franco, Ricardo; Lu, Yi; Ma, Jian-Guo & Shelnutt, John A.
Partner: UNT Libraries Government Documents Department

The Evolutionary Dynamics of Cancer

Description: We hypothesized that a subset of the mutations observed in the progression to cancer confer beneficial selective effects on the cell. Our aim was to identify these selective mutations and to infer the interactions between the mutant clones in Barrett's esophagus (BE) that eventually lead to the development of esophageal adenocarcinoma. The results were to be a set of predictions about the roles of specific mutations in the progression to cancer.
Date: August 29, 2000
Creator: Maley, Carlo C.
Partner: UNT Libraries Government Documents Department

Partially redundant functions of two SET-domain polycomb-group proteins in controlling initiation of seed development in Arabidopsis

Description: In Arabidopsis, a complex of Polycomb-group (PcG) proteins functions in the female gametophyte to control the initiation of seed development. Mutations in the PcG genes, including MEDEA (MEA) and FERTILIZATION-INDEPENDENT SEED 2 (FIS2), produce autonomous seeds where endosperm proliferation occurs in the absence of fertilization. By using a yeast two-hybrid screen, we identified MEA and a related protein, SWINGER (SWN), as SET-domain partners of FIS2. Localization data indicated that all three proteins are present in the female gametophyte. Although single-mutant swn plants did not show any defects, swn mutations enhanced the mea mutant phenotype in producing autonomous seeds. Thus, MEA and SWN perform partially redundant functions in controlling the initiation of endosperm development before fertilization in Arabidopsis.
Date: August 29, 2006
Creator: Wang, Dongfang; Tyson, Mark D.; Jackson, Shawn S. & Yadegari, Ramin
Partner: UNT Libraries Government Documents Department

Three Frontiers in the Thermodynamics of Protein Solutions

Description: Three examples illustrate the versatility and usefulness of biothermodynamics. The first example concerns calculation of a phase diagram for aqueous lysozyme with a new potential of mean force that takes the Hofmeister effect into account; such calculations may be useful for design of a separation process where addition of a salt to an aqueous protein mixture precipitates a target protein. The second example concerns thermodynamic studies to elucidate the effect of an organic cosolvent on the mechanism of crystallizing aqueous insulin. The final example concerns a thermodynamic contribution to mitigating the AIDS epidemic; it indicates how isothermal-titration-calorimetry studies are helpful for choosing an optimum inhibitor that is effective not only for the wild-type HIV protease but also for at least some of its mutants.
Date: August 30, 2006
Creator: Prausnitz, John & Hagar, Loddie
Partner: UNT Libraries Government Documents Department

Rapid identification of causative insertions underlying Medicago truncatula Tnt1 mutants defective in symbiotic nitrogen fixation from a forward genetic screen by whole genome sequencing

Description: This article demonstrates that whole genome sequencing is an efficient approach for identification of causative genes underlying symbiotic nitrogen fixation defective phenotypes in Medicago truncatula Tnt1 insertion mutants obtained via forward genetic screens.
Date: February 27, 2016
Creator: Veerappan, Vijaykumar; Jani, Mehul; Kadel, Khem; Troiani, Taylor; Gale, Ronny; Mayes, Tyler et al.
Partner: UNT College of Arts and Sciences

Hereditary Spherocytosis and Hereditary Elliptocytosis: Aberrant Protein Sorting during Erythroblast Enucleation

Description: During erythroblast enucleation, membrane proteins distribute between extruded nuclei and reticulocytes. In hereditary spherocytosis (HS) and hereditary elliptocytosis (HE), deficiencies of membrane proteins, in addition to those encoded by the mutant gene, occur. Elliptocytes, resulting from protein 4.1R gene mutations, lack not only 4.1R but also glycophorin C, which links the cytoskeleton and bilayer. In HS resulting from ankyrin-1 mutations, band 3, Rh-associated antigen, and glycophorin A are deficient. The current study was undertaken to explore whether aberrant protein sorting, during enucleation, creates these membrane-spanning protein deficiencies. We found that although glycophorin C sorts to reticulocytes normally, it distributes to nuclei in 4.1R-deficient HE cells. Further, glycophorin A and Rh-associated antigen, which normally partition predominantly to reticulocytes, distribute to both nuclei and reticulocytes in an ankyrin-1-deficient murine model of HS. We conclude that aberrant protein sorting is one mechanistic basis for protein deficiencies in HE and HS.
Date: February 8, 2010
Creator: Salomao, Marcela; Chen, Ke; Villalobos, Jonathan; Mohandas, Narla; An, Xiuli & Chasis, Joel Anne
Partner: UNT Libraries Government Documents Department

Determining mutant spectra of three RNA viral samples using ultra-deep sequencing

Description: RNA viruses have extremely high mutation rates that enable the virus to adapt to new host environments and even jump from one species to another. As part of a viral transmission study, three viral samples collected from naturally infected animals were sequenced using Illumina paired-end technology at ultra-deep coverage. In order to determine the mutant spectra within the viral quasispecies, it is critical to understand the sequencing error rates and control for false positive calls of viral variants (point mutantations). I will estimate the sequencing error rate from two control sequences and characterize the mutant spectra in the natural samples with this error rate.
Date: June 6, 2012
Creator: Chen, H
Partner: UNT Libraries Government Documents Department

Expanded breadth of the T-cell response to mosaic HIV-1 envelope DNA vaccination

Description: An effective AIDS vaccine must control highly diverse circulating strains of HIV-1. Among HIV -I gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV -I Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential Tcell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likely to elicit strain-specific responses. DNA vaccines were evaluated using intracellular cytokine staining (ICS) in inbred mice with a standardized panel of highly conserved 15-mer PTE peptides. I, 2 and 3 mosaic sets were developed that increased theoretical epitope coverage. The breadth and magnitude ofT-cell immunity stimulated by these vaccines were compared to natural strain Env's; additional comparisons were performed on mutant Env's, including gpl60 or gpl45 with or without V regions and gp41 deletions. Among them, the 2 or 3 mosaic Env sets elicited the optimal CD4 and CD8 responses. These responses were most evident in CD8 T cells; the 3 mosaic set elicited responses to an average of 8 peptide pools compared to 2 pools for a set of3 natural Env's. Synthetic mosaic HIV -I antigens can therefore induce T-cell responses with expanded breadth and may facilitate the development of effective T -cell-based HIV -1 vaccines.
Date: January 1, 2009
Creator: Korber, Bette; Fischer, William & Wallstrom, Timothy
Partner: UNT Libraries Government Documents Department

Invariability of Central Metabolic Flux Distribution in Shewanella oneidensis MR-1 Under Environmental or Genetic Perturbations

Description: An environmentally important bacterium with versatile respiration, Shewanella oneidensis MR-1, displayed significantly different growth rates under three culture conditions: minimal medium (doubling time {approx} 3 hrs), salt stressed minimal medium (doubling time {approx} 6 hrs), and minimal medium with amino acid supplementation (doubling time {approx}1.5 hrs). {sup 13}C-based metabolic flux analysis indicated that fluxes of central metabolic reactions remained relatively constant under the three growth conditions, which is in stark contrast to the reported significant changes in the transcript and metabolite profiles under various growth conditions. Furthermore, ten transposon mutants of S. oneidensis MR-1 were randomly chosen from a transposon library and their flux distributions through central metabolic pathways were revealed to be identical, even though such mutational processes altered the secondary metabolism, for example, glycine and C1 (5,10-Me-THF) metabolism.
Date: April 21, 2009
Creator: Tang, Yinjie; Martin, Hector Garcia; Deutschbauer, Adam; Feng, Xueyang; Huang, Rick; Llora, Xavier et al.
Partner: UNT Libraries Government Documents Department

Analysis of a Ferric Uptake Regulator (Fur) Mutant ofDesulfovibrio vulgaris Hildenborough

Description: Previous experiments examining the transcriptional profileof the anaerobe Desulfovibrio vulgaris demonstrated up-regulation of theFur regulon in response to various environmental stressors. To test theinvolvement of Fur in the growth response and transcriptional regulationof D. vulgaris, a targeted mutagenesis procedure was used for deletingthe fur gene. Growth of the resulting ?fur mutant (JW707) was notaffected by iron availability, but the mutant did exhibit increasedsensitivity to nitrite and osmotic stresses compared to the wild type.Transcriptional profiling of JW707 indicated that iron-bound Fur acts asa traditional repressor for ferrous iron uptake genes (feoAB) and othergenes containing a predicted Fur binding site within their promoter.Despite the apparent lack of siderophore biosynthesis genes within the D.vulgaris genome, a large 12-gene operon encoding orthologs to TonB andTolQR also appeared to be repressed by iron-bound Fur. While other genespredicted to be involved in iron homeostasis were unaffected by thepresence or absence of Fur, alternative expression patterns that could beinterpreted as repression or activation by iron-free Fur were observed.Both the physiological and transcriptional data implicate a globalregulatory role for Fur in the sulfate-reducing bacterium D.vulgaris.
Date: September 21, 2007
Creator: Bender, Kelly S.; Yen, Huei-Che Bill; Hemme, Christopher L.; Yang, Zamin K.; He, Zhili; He, Qiang et al.
Partner: UNT Libraries Government Documents Department

Disparate requirements for the Walker A and B ATPase motifs ofhuman RAD51D in homologous recombination

Description: In vertebrates, homologous recombinational repair (HRR) requires RAD51 and five RAD51 paralogs (XRCC2, XRCC3, RAD51B, RAD51C, and RAD51D) that all contain conserved Walker A and B ATPase motifs. In human RAD51D we examined the requirement for these motifs in interactions with XRCC2 and RAD51C, and for survival of cells in response to DNA interstrand crosslinks. Ectopic expression of wild type human RAD51D or mutants having a non-functional A or B motif was used to test for complementation of a rad51d knockout hamster CHO cell line. Although A-motif mutants complement very efficiently, B-motif mutants do not. Consistent with these results, experiments using the yeast two- and three-hybrid systems show that the interactions between RAD51D and its XRCC2 and RAD51C partners also require a functional RAD51D B motif, but not motif A. Similarly, hamster Xrcc2 is unable to bind to the non-complementing human RAD51D B-motif mutants in co-immunoprecipitation assays. We conclude that a functional Walker B motif, but not A motif, is necessary for RAD51D's interactions with other paralogs and for efficient HRR. We present a model in which ATPase sites are formed in a bipartite manner between RAD51D and other RAD51 paralogs.
Date: April 21, 2006
Creator: Wiese, Claudia; Hinz, John M.; Tebbs, Robert S.; Nham, Peter B.; Urbin, Salustra S.; Collins, David W. et al.
Partner: UNT Libraries Government Documents Department

Drosophila by the dozen

Description: This year's conference on Drosophila research illustratedwell the current focus of Drosophila genomics on the comprehensiveidentification of functional elements in the genome sequence, includingmRNA transcripts arising from multiple alternative start sites and splicesites, a multiplicity of noncoding transcripts and small RNAs,identification of binding sites for transcription factors, sequenceconservation in related species and sequence variation within species.Resources and technologies for genetics and functional genomics aresteadily being improved, including the building of collections oftransposon insertion mutants and hairpin constructs for RNA interference(RNAi). The conference also highlighted progress in the use of genomicinformation by many laboratories to study diverse aspects of biology andmodels of human disease. Here we will review a few highlights of especialinterest to readers of Genome Biology.
Date: July 13, 2007
Creator: Celniker, Susan E. & Hoskins, Roger A.
Partner: UNT Libraries Government Documents Department

GROWTH REGULATION IN ROUS SARCOMA VIRUS INFECTED CHICKEN EMBRYO FIBROBLASTS: THE ROLE OF THE src GENE

Description: We report here a study of the mechanisms leading to loss of growth control in chicken embryo fibroblasts transformed by Rous sarcoma virus (RSV). We have been particularly concerned with the role of the src gene in this process, and have used RSV mutants temperature sensitive (ts) for transformation to investigate the nature of the growth regulatory lesion. The two principal findings were (1) the stationary phase of the cell cycle (G{sub 1}) in chick embryo fibroblasts seems to have two distinct regulatory compartments (using the terminology of Brooks et al. we refer to these as 'Q' and 'A' states). When rendered stationary at 41.5 C by serum deprivation, normal cells enter a Q state, but cells infected with the ts-mutant occupy an A state. (2) Whereas normal cells can occupy either state depending on culture conditions, the ts-infected cells, at 41.5 C, do not seem to enter Q even though a known src gene product, a kinase, is reported to be inactive at this temperature. We discuss the possibility that viral factors other than the active src protein kinase influence growth control in infected cultures.
Date: July 1, 1980
Creator: Parry, G.; Bartholomew, J.A. & Blssell, M.J.
Partner: UNT Libraries Government Documents Department

Telomere dysfunction and cell survival: roles for distinctTIN2-containing complexes

Description: Telomeres are maintained by three DNA binding proteins, TRF1, TRF2 and POT1, and several associated factors. One factor, TIN2, binds TRF1 and TRF2 directly and POT1 indirectly. These and two other proteins form a soluble complex that may be the core telomere-maintenance complex. It is not clear whether subcomplexes exist or function in vivo. Here, we provide evidence for two TIN2 subcomplexes with distinct functions in human cells. TIN2 ablation by RNA interference caused telomere uncapping and p53-independent cell death in all cells tested. However, we isolated two TIN2 complexes from cell lysates, each selectively sensitive to a TIN2 mutant (TIN2-13, TIN2-15C). In cells with wild-type p53 function, TIN2-15C was more potent than TIN2-13 in causing telomere uncapping and eventual growth arrest. In cells lacking p53 function, TIN215C more than TIN2-13 caused genomic instability and cell death. Thus, TIN2 subcomplexes likely have distinct functions in telomere maintenance, and may provide selective targets for eliminating cells with mutant p53.
Date: November 7, 2006
Creator: Kim, Sahn-Ho; Davalos, Albert R.; Heo, Seok-Jin; Rodier, Francis; Beausejour, Christian; Kaminker, Patrick et al.
Partner: UNT Libraries Government Documents Department

Structural mechanisms of nonplanar hemes in proteins

Description: The objective is to assess the occurrence of nonplanar distortions of hemes and other tetrapyrroles in proteins and to determine the biological function of these distortions. Recently, these distortions were found by us to be conserved among proteins belonging to a functional class. Conservation of the conformation of the heme indicates a possible functional role. Researchers have suggested possible mechanisms by which heme distortions might influence biological properties; however, no heme distortion has yet been shown conclusively to participate in a structural mechanism of hemoprotein function. The specific aims of the proposed work are: (1) to characterize and quantify the distortions of the hemes in all of the more than 300 hemoprotein X-ray crystal structures in terms of displacements along the lowest-frequency normal coordinates, (2) to determine the structural features of the protein component that generate and control these nonplanar distortions by using spectroscopic studies and molecular-mechanics calculations for the native proteins, their mutants and heme-peptide fragments, and model porphyrins, (3) to determine spectroscopic markers for the various types of distortion, and, finally, (4) to discover the functional significance of the nonplanar distortions by correlating function with porphyrin conformation for proteins and model porphyrins.
Date: May 1, 1997
Creator: Shelnutt, J.A.
Partner: UNT Libraries Government Documents Department

Health hazards associated with the use of di-(2-ethylhexyl) phthalate (commonly referred to as DOP) in HEPA filter test

Description: Di-(2-ethylhexyl) phthalate (DEHP), commonly referred to as di-octyl phthalate, is an important production chemical in the US. In addition to its major use as an additive in plastics, DEHP is widely used to evaluate the effectiveness of high efficiency particulate air (HEPA) filters. Historically, DEHP was also used in quantitative fit testing for respirators. Evaluations of this compound a decade ago showed that it can induce hepatocellular carcinomas in laboratory animals. Although most Department of Energy (DOE) facilities have since discontinued using DEHP in respirator fit testing, DEHP continues to be used for evaluating HEPA filters. This report summarizes available information on the toxicity, mutagenicity, carcinogenicity, and other hazards and problems posed by DEHP, specifically with reference to HEPA filter testing. Information on work practice improvements as well as the availability and suitability of DEHP substitutes are also presented. This material should assist the DOE in the safe use of this material.
Date: January 1, 1995
Partner: UNT Libraries Government Documents Department

Surface plasmon enhanced interfacial electron transfer and resonance Raman, surface-enhanced resonance Raman studies of cytochrome C mutants

Description: Surface plasmon resonance was utilized to enhance the electron transfer at silver/solution interfaces. Photoelectrochemical reductions of nitrite, nitrate, and CO{sub 2} were studied on electrochemically roughened silver electrode surfaces. The dependence of the photocurrent on photon energy, applied potential and concentration of nitrite demonstrates that the photoelectrochemical reduction proceeds via photoemission process followed by the capture of hydrated electrons. The excitation of plasmon resonances in nanosized metal structures resulted in the enhancement of the photoemission process. In the case of photoelectrocatalytic reduction of CO{sub 2}, large photoelectrocatalytic effect for the reduction of CO{sub 2} was observed in the presence of surface adsorbed methylviologen, which functions as a mediator for the photoexcited electron transfer from silver metal to CO{sub 2} in solution. Photoinduced reduction of microperoxidase-11 adsorbed on roughened silver electrode was also observed and attributed to the direct photoejection of free electrons of silver metal. Surface plasmon assisted electron transfer at nanostructured silver particle surfaces was further determined by EPR method.
Date: November 8, 1999
Creator: Zheng, Junwei
Partner: UNT Libraries Government Documents Department

The iojap gene in maize

Description: The classical maize mutant iojap (Iodent japonica) has variegated green and white leaves. Green sectors have cells with normal chloroplasts whereas white sectors have cells where plastids fail to differentiate. These mutant plastids, when transmitted through the female gametophyte, do not recover in the presence of wild type Iojap. We cloned the Ij locus, and we have investigated the mechanism of epigenetic inheritance and phenotypic expression. More recently, a modifier of this type of variegation, ''Inhibitor of striate'', has also been cloned. Both the iojap and inhibitor of striate proteins have homologs in bacteria and are members of ancient conserved families found in multiple species. These tools can be used to address fundamental questions of inheritance and variegation associated with this classical conundrum of maize genetics. Since the work of Rhoades there has been considerable speculation concerning the nature of the Iojap gene product, the origin of leaf variegation and the mechanism behind the material inheritance of defective plastids. This has made Iojap a textbook paradigm for cytoplasmic inheritance and nuclear-organellar interaction for almost 50 years. Cloning of the Iojap gene in maize, and homologs in other plants and bacteria, provides a new means to address the origin of heteroplastidity, variegation and cytoplasmic inheritance in higher plants.
Date: December 1, 2001
Creator: Martienssen, Robert
Partner: UNT Libraries Government Documents Department