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Mutagenesis (12):
Recent article
Mutagenesis
Abstract
We examined the effects of aneuploidy on genomic stability. We analyzed 13 budding yeast strains that carry extra copies of single chromosomes and found that all aneuploid strains exhibited one or more forms of genomic instability. Most strains displayed increased chromosome loss and mitotic recombi...
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PMID: 21852501
PDF is available here.
PDF is available here.
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Mutation Research (714)1-2 2011
Abstract
Much early work on environmental stress, including ionizing radiation and environmental toxins, emphasised their action on DNA and subsequent mutagenesis in long term effects including germ cell mutagenesis, carcinogenesis and trans-generational effect. However, recent studies are in...
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PMID: 21784086
PDF is available here.
PDF is available here.
FEBS Journal (278)11 2011
Abstract
We report the overexpression of the ARO10 gene product in Escherichia coli and the first detailed in vitro characterization of this enzyme. The enzyme is shown to be an efficient aromatic 2-keto acid decarboxylase, consistent with it playing a major in vivo role in phenylalanine, tryptophan and poss...
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PMID: 21501384
PDF is available here.
PDF is available here.
Abstract
We investigated the role of cyclic AMP-dependent protein kinase A of F. oxysporum (FoCPKA) in growth, morphology, and root attachment, penetration, and pathogenesis in Arabidopsis thaliana. Affinity of spore attachment to root surfaces of A. thaliana, observed microscopically and measured by atomic...
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PMID: 21261464
PDF is available here.
PDF is available here.
Genetika (Moskva) (47)5 2011
Abstract
The earlier identified gene RAD31 was mapped on the right arm of chromosome II in the region of gene MEC1 localization. Epistatic analysis demonstrated that the rad31 mutation is an allele of the MEC1 gene, which allows further designation of the rad31 mutation as mec1-212. Mutation mec1-212, similar...
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PMID: 21786666
PDF is available here.
PDF is available here.
Abstract
We investigated the role of positively and negatively charged amino acids within the 89-99 region of apolipoprotein A-I (apoA-I), which are highly conserved in mammals, on plasma lipid homeostasis and the biogenesis of HDL. We previously showed that deletion of the 89-99 region of apoA-I increased p...
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PMID: 21504968
PDF is available here.
PDF is available here.
Abstract
We performed a phenotype-driven ENU mutagenesis screen in mice with the aim of identifying novel alleles in an unbiased manner, that are critically required for early craniofacial development. Here we describe 10 new mutant lines, which exhibit phenotypes affecting frontonasal and pharyngeal arch pa...
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PMID: 21305688
PDF is available here.
PDF is available here.
Annales d'Endocrinologie (72)2 2011
Abstract
Goitrogenisis is the consequence of a relative iodine deficiency interacting with a genetic predisposition for maladaptation to iodine deficiency. In the long run, the iodine deficiency induces increased H(2)O(2) production that leads to an increased mutagenesis, resulting in somatic mutations with a...
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PMID: 21511241
PDF is available here.
PDF is available here.
Abstract
To screen Phanerochaete chrysosporium mutants resisting nutritional repression and to characterize laccase produced by the mutants.
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PMID: 21604549
PDF is available here.
PDF is available here.
Abstract
Mutation Research (711)1-2 2011
Abstract
We review the current state of knowledge on the role of ROS-induced oxidative stress in altering the genetic and epigenetic involvement during human carcinogenesis....
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PMID: 21419141
PDF is available here.
PDF is available here.
Abstract
CLC anion transport proteins function as Cl (-) channels and Cl (-) /H (+) exchangers and are found in all major groups of life including archaebacteria. Early electrophysiological studies suggested that CLC anion channels have two pores that are opened and closed independently by a...
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PMID: 21317557
PDF is available here.
PDF is available here.
Abstract
We hypothesized that ranolazine will similarly inhibit the paramyotonia congenita NaV 1.4 gain-of-function mutations, R1448C, R1448H, and R1448P that are associated with repetitive action potential firing. Whole-cell Na (+) current (INa) was recorded from HEK293 cells expressing the hNaV 1.4 WT or R...
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PMID: 21317558
PDF is available here.
PDF is available here.
Abstract
We found that Saccharomyces cerevisiae cells lacking all eight thiol peroxidases were viable and withstood redox stresses. They transcriptionally responded to various redox treatments, but were unable to activate and repress gene expression in response to H(2)O(2). Further studies involving redox tr...
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PMID: 21282621
PDF is available here.
PDF is available here.
Abstract
We examined the relative contributions of Rab/Myo5B interactions with specific pathways using Myo5B mutants lacking binding to either Rab11a or Rab8a. Myo5B Q1300L and Y1307C mutations abolished Rab8a association, whereas Myo5B Y1714E and Q1748R mutations uncoupled association with Rab11a. Expressio...
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PMID: 21282656
PDF is available here.
PDF is available here.
Abstract
We report that HCF-1 proteolysis is a regulated process. We demonstrate that a large proportion of the signaling enzyme O-linked-N-acetylglucosaminyl transferase (OGT) is complexed with HCF-1 and this interaction is essential for HCF-1 cleavage. Moreover, HCF-1 is, in turn, required for stabilizing...
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PMID: 21285374
PDF is available here.
PDF is available here.
Abstract
We show that CSP has two conformational states, an adhesive conformation in which the C-terminal cell-adhesive domain is exposed and a nonadhesive conformation in which the N terminus masks this domain. We demonstrate that the cell-adhesive domain functions in sporozoite development and hepatocyte i...
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PMID: 21262960
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)3 2011
Abstract
We developed a procedure that randomly mutagenizes a specific segment of a gene through error-prone PCR and screens for mutants on the basis of the properties of the holoenzymes reconstituted in vivo (REM-ivrs). Previous work showed that the N-terminal domain includes the valine-binding ACT domain o...
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PMID: 21224018
PDF is available here.
PDF is available here.
Abstract
Pyrazinamidase (PncA) activates the first-line antituberculous drug pyrazinamide into pyrazinoic acid. The crystal structure of the Mycobacterium tuberculosis PncA protein has been determined, showing significant differences in the substrate binding cavity when compared to the pyrazinamidases from Py...
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PMID: 21283666
PDF is available here.
PDF is available here.
Abstract
We employed a series of frameshift reporters to measure mutagenesis associated with BIR in Saccharomyces cerevisiae. We demonstrate that BIR DNA synthesis is intrinsically inaccurate over the entire path of the replication fork, as the rate of frameshift mutagenesis during BIR is up to 2,800-fold hi...
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PMID: 21347245
PDF is available here.
PDF is available here.
Abstract
We aimed to characterize these RNA-helicases in more detail. Here, we demonstrate that UAP56 and URH49 exhibit an intrinsic CRM1-independent nucleocytoplasmic shuttling activity. Extensive mapping studies identified distinct regions within UAP56 or URH49 required for (i) intranuclear localization (U...
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PMID: 21799930
PDF is available here.
PDF is available here.
Abstract
We have developed a strategy for rapid and combinatorial optimization of the hot spot residues of enzymes. After combinatorial randomization of target locations in the Candida antarctica lipase B (CalB) gene, the individual variant genes isolated in the E.coli cells were expressed in the cell-free p...
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PMID: 21312354
PDF is available here.
PDF is available here.
Abstract
These results suggested that bacterial cells sense the accumulation of oxidative DNA damage or absence of DNA repair activity, and signal the information to the transcriptional regulation machinery for an ROS-detoxifying system....
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PMID: 21552516
PDF is available here.
PDF is available here.
Abstract
We experimentally assay-binding affinities for a variety of mutants and determine their relative free energy of binding, ΔΔG, to rank the importance of interface residues to binding. We then compare how accurately, precisely and reliably computational methods for calculating ΔΔG can replicate th...
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PMID: 20656696
PDF is available here.
PDF is available here.
Abstract
We report on two different mutant screens as examples of strategies for identifying mutations that affect biogenic and operational control signalling pathways and processes. We also describe strategies for the analysis and genotyping of the mutants....
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PMID: 20960135
PDF is available here.
PDF is available here.
Abstract
We review the protocols for a yeast-based assay to detect effective ZFNs. Additionally, we detail the procedures for synthesis and injection of ZFN-encoding mRNA into zebrafish embryos, screening of injected embryos for induced mutations in the soma, and recovery of germline mutations....
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PMID: 21805278
PDF is available here.
PDF is available here.
Abstract
Features of phosphate-mobilizing bacteria Bacillus subtilis IMB B-7023 and its streptomycin-resistant strain were investigated. While cultivated in medium with glucose and glycerophosphate, the growth rate of the antibiotic-marked strain was approximately similar to this parameter for Bacillus subtil...
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PMID: 21442916
PDF is available here.
PDF is available here.
Abstract
We engineered a set of mimics of CNG channel pores for both structural and functional analysis. The mimics faithfully represent the CNG channels they are modeled after, permeate Na(+) and K(+) equally well, and exhibit the same Ca(2+) blockage and permeation properties. Their high-resolution structu...
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PMID: 21187429
PDF is available here.
PDF is available here.
Mutation Research (711)1-2 2011
Abstract
A clustered DNA lesion, also known as a multiply damaged site, is defined as ≥2 damages in the DNA within 1-2 helical turns. Only ionizing radiation and certain chemicals introduce DNA damage in the genome in this non-random way. What is now clear is that the lethality of a damaging agent is not ju...
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PMID: 21185841
PDF is available here.
PDF is available here.
Abstract
We report for the first time a soluble PQQ-glucose dehydrogenase that is twice more active than the wild type for glucose oxidation and was obtained by combining site directed mutagenesis, modelling and steady-state kinetics. The observed enhancement is attributed to a better interaction between the...
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PMID: 21036156
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)45 2010
Abstract
We performed a systematic mutational analysis of surfaces on the yeast coronin β-propeller domain, which binds to F-actin and is conserved in all coronin family members. We generated 21 mutant alleles and analyzed their biochemical effects on actin binding and ADF/cofilin activity. Conserved actin-...
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PMID: 20813846
PDF is available here.
PDF is available here.
Mutagenesis (25)6 2010
Abstract
Abstract
Abstract
We harness advances in DNA sequencing to annotate genomic rearrangements in 13 patients with pancreatic cancer and explore clonal relationships among metastases. We find that pancreatic cancer acquires rearrangements indicative of telomere dysfunction and abnormal cell-cycle control, namely dysregul...
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PMID: 20981101
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)43 2010
Abstract
We recently determined the structure of a previously unrecognized pol-prim domain (p68N) that docks on Tag, identified the p68N surface that contacts Tag, and demonstrated its vital role in primosome function. Here, we identify the p68N-docking site on Tag by using structure-guided mutagenesis of th...
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PMID: 20685648
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)43 2010
Abstract
We show a novel actin-nucleating activity in mammalian Tmods. Comparison of Tmod isoforms revealed that Tmod1-3 but not Tmod4 nucleate actin filament assembly. All Tmods bind to monomeric actin, and Tmod3 forms a 1:1 complex with actin. By truncation and mutagenesis studies, we demonstrated that the...
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PMID: 20650902
PDF is available here.
PDF is available here.
Abstract
We showed that in mouse kidney collecting duct cells, claudin-4 functioned as a Cl(-) channel. A positively charged lysine residue at position 65 of claudin-4 was critical for its anion selectivity. Claudin-4 was observed to interact with claudin-8 using several criteria. In the collecting duct cell...
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PMID: 20921420
PDF is available here.
PDF is available here.
New England Journal of Medicine (363)14 2010
Abstract
We studied concordant and discordant monozygous twins with de novo mutations in the sodium channel α1 subunit gene (SCN1A) causing Dravet's syndrome, a severe epileptic encephalopathy. On the basis of our findings and the literature on mosaic cases, we conclude that de novo mutations in SCN1A may o...
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PMID: 20879882
PDF is available here.
PDF is available here.
Abstract
One of the major objectives of the Human Genome Project is to understand the biological function of the gene and genome as well as to develop clinical applications for human diseases. For this purpose, the experimental validations and preclinical trails by using animal models are ind...
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PMID: 20933210
PDF is available here.
PDF is available here.
Abstract
We describe the use of a genetic selection system and encoded library of conformationally pre-organized peptides to perform functional profiling of each regulator revealing specific recognition features that guide the antagonism of Hdm2-p53 and Hdmx-p53 interactions. Structure-activity relationship...
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PMID: 20638853
PDF is available here.
PDF is available here.
Abstract
We perform alanine-scanning mutagenesis to identify residues in NPC2 that are essential for transfer of cholesterol to NPC1(NTD). Transfer requires three residues that form a patch on the surface of NPC2. We previously identified a patch of residues on the surface of NPC1(NTD) that are required for...
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PMID: 20674861
PDF is available here.
PDF is available here.
Abstract
Abstract
We report the identification of a gain-of-function allele of peroxiredoxin (thioredoxin peroxidase, Tsa1p) via whole-genome re-sequencing of a dominantSaccharomyces cerevisiae mutant obtained by chemical mutagenesis. Yeast strain K6001, a screening system for lifespan phenotypes, was treated with et...
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PMID: 20729566
PDF is available here.
PDF is available here.
Developmental Biology (344)1 2010
Abstract
We describe an ENU-induced mouse mutation, nearly headless (nehe), that was identified based on the specific absence of most of the forebrain at midgestation. Positional cloning and genetic analysis show that, unlike other mouse mutants that disrupt specification of the forebrain, the nehe mutation...
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PMID: 20450902
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)30 2010
Abstract
We report the crystal structure of a complex between the Pseudomonas translocator chaperone PcrH and a short region from the minor translocator PopD. PcrH displays a 7-helical tetratricopeptide repeat fold that harbors the PopD peptide within its concave region, originally believed to be involved in...
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PMID: 20385547
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)30 2010
Abstract
We applied DNA shuffling methodology to generate and recombine the mutations of Arabidopsis thaliana vacuolar Na(+)/H(+) antiporter gene AtNHX1. Screening using a large scale yeast complementation system identified AtNHXS1, a novel Na(+)/H(+) antiporter. Expression of AtNHXS1 in yeast showed that th...
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PMID: 20457597
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)30 2010
Abstract
We have previously shown that the mutagenic potential of DinB is regulated by the DNA damage response protein UmuD(2). In the current study, we employ a pre-steady-state fluorescence approach to gain a mechanistic understanding of DinB regulation by UmuD(2). Our results suggest that DinB, like its m...
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PMID: 20467052
PDF is available here.
PDF is available here.
Abstract
Abstract
We report an efficient biocatalytic process to replace a recently implemented rhodium-catalyzed asymmetric enamine hydrogenation for the large-scale manufacture of the antidiabetic compound sitagliptin. Starting from an enzyme that had the catalytic machinery to perform the desired chemistry but lac...
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PMID: 20558668
PDF is available here.
PDF is available here.
Abstract
We describe the de novo computational design and experimental characterization of enzymes catalyzing a bimolecular Diels-Alder reaction with high stereoselectivity and substrate specificity. X-ray crystallography confirms that the structure matches the design for the most active of the enzymes, and...
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PMID: 20647463
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (285)29 2010
Abstract
We present crystallographic and mutagenesis data that reveal the mode of action of BAY 58-2667. The 2.3-A resolution structure of BAY 58-2667 bound to a heme NO and oxygen binding domain (H-NOX) from Nostoc homologous to that of sGC reveals that the trifurcated BAY 58-2667 molecule has displaced the...
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PMID: 20463019
PDF is available here.
PDF is available here.
Abstract
We studied gene conversion in which both strands of DNA are newly synthesized. The mutation rate increases up to 1400 times over spontaneous events, with a significantly different mutation signature. Especially prominent are microhomology-mediated template switches. Recombination-induced mutations a...
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PMID: 20595613
PDF is available here.
PDF is available here.
Current Microbiology (61)1 2010
Abstract
The production of indole-3-acetic acid (IAA), by rhizobacteria, has been associated with plant growth promotion, especially root initiation and elongation. Isolate TO3 selected from 103 fluorescent pseudomonads, identified as Pseudomonas aeruginosa, showed maximum production of IAA. Isolate TO3 havi...
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PMID: 20049597
PDF is available here.
PDF is available here.
Abstract
We failed in our initial effort to purify a prematurely developed Camelid-like E-tagged short scFv-K2 antibody that contained a complete variable region of the heavy chain and partial region of the light chain by using an anti-E-tag affinity column. To expedite the purification of this altered but i...
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PMID: 20060473
PDF is available here.
PDF is available here.
Abstract
We initially explored whether MBP would have the same effect in the methylotrophic yeast Pichia pastoris, a popular eukaryotic host for heterologous protein expression. When MBP was fused as an N-terminal partner to several C-terminal cargo proteins expressed in this yeast, proteolysis occurred betw...
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PMID: 20230898
PDF is available here.
PDF is available here.
DNA and Cell Biology (29)7 2010
Transforming growth factor beta-3 and environmental factors and cleft lip with/without cleft palate.
Abstract
To identify the interactions among two loci (C641A and G15572-) of transforming growth factor beta 3 (TGFbeta3), and exposures in pregnancy with cleft lip with/without cleft palate (CL/P), a hospital-based case-control study was conducted. Associations among offspring polymorphisms of TGFbeta3 C641A...
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PMID: 20408761
PDF is available here.
PDF is available here.
Abstract
We report here a system for the functional expression of a synthetic gene encoding the I-SceI homing endonuclease in several streptomycetes. Using the synthetic sce(a) gene, we were able to create controlled genomic DNA double-strand breaks. A mutagenesis system, based on the homing endonuclease I-S...
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PMID: 20473607
PDF is available here.
PDF is available here.
Biochemistry (Washington) (49)26 2010
Abstract
We describe comprehensive mutagenesis of the light chain complementarity determining regions (CDRs) of HIV-1 antibody D5 (which binds its target, "5-Helix", with a reported K(D) of 50 pM). Combinatorial scanning mutagenesis libraries were prepared in which CDR residues on the D5 light chain were var...
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PMID: 20518570
PDF is available here.
PDF is available here.
Infection and Immunity (78)7 2010
Abstract
We created Bp82 and Bp190, which are DeltapurM derivatives of B. pseudomallei strains 1026b and K96243 that are deficient in adenine and thiamine biosynthesis but replication competent in vitro in rich medium. A series of animal challenge studies was conducted to ensure that these strains were fully...
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PMID: 20404077
PDF is available here.
PDF is available here.
Gene Therapy (17)7 2010
Abstract
We used PCR-based random mutagenesis to construct a large library of human TRIM5alpha variants containing mutations in the PRYSPRY domain. We then applied a functional screen to isolate human cells made resistant to HIV-1 infection by the expression of a mutated TRIM5alpha. This protocol led to the...
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PMID: 20357830
PDF is available here.
PDF is available here.