bluuebunny/crossref_metadata_2025 huggingface dataset:
The yeast MOT2 gene encodes a putative zinc finger protein that serves as a global negative regulator affecting expression of several categories of genes, including mating-pheromone-responsive genes.
Authors: Irie K , Yamaguchi K , Kawase K , Matsumoto K
Published: October 2015

The STE4 gene encodes the beta subunit of a heterotrimeric G protein that is an essential component of the pheromone signal transduction pathway. To identify downstream component(s) of Ste4, we sought pseudo-revertants that restored mating competence to ste4 mutants. The suppressor mot2 was isolated as a recessive mutation that restored conjugational competence to a temperature-sensitive ste4 mutant and simultaneously conferred a temperature-sensitive growth phenotype. The MOT2 gene encodes a putative zinc finger protein, the deletion of which resulted in temperature-sensitive growth, increased expression of FUS1 in the absence of pheromones, and suppression of a deletion of the alpha-factor receptor. On the other hand, sterility resulting from deletion of STE4 was not suppressed by the mot2 deletion. These phenotypes are similar to those associated with temperature-sensitive mutations in CDC36 and CDC39, which are proposed to encode general negative regulators of transcription rather than factors involved in the pheromone response pathway. Deletion of MOT2 also caused increased transcription of unrelated genes such as GAL7 and PHO84. Overexpression of MOT2 suppresses the growth defect of temperature-sensitive mutations in CDC36 and CDC39. These observations suggest that Mot2 functions as a general negative regulator of transcription in the same processes as Cdc36 and Cdc39.
The Glc7 type 1 protein phosphatase of Saccharomyces cerevisiae is required for cell cycle progression in G2/M.
Authors: Hisamoto N , Sugimoto K , Matsumoto K
Published: October 2015

We isolated a mutant carrying a conditional mutation in the GLC7 gene, encoding the catalytic subunit of a type 1 protein phosphatase, by selection of suppressors that restored the growth defect of cdc24 mutants at high temperature and simultaneously conferred cold-sensitive growth. This cold sensitivity for growth is caused by a single mutation (glc7Y-170) at position 170 of the Glc7 protein, resulting in replacement of cysteine with tyrosine. Genetic analysis suggested that the glc7Y-170 allele is associated with a recessive negative phenotype, reducing the activity of Glc7 in the cell. The glc7Y-170 mutant missegregated chromosome III at the permissive temperature, arrested growth as large-budded cells at the restrictive temperature, exhibited a significant increase in the number of nuclei at or in the neck, and had a short spindle. Furthermore, the glc7Y-170 mutant exhibited a high level of CDC28-dependent protein kinase activity when incubated at the restrictive temperature. These findings suggest that the glc7Y-170 mutation is defective in the G2/M phase of the cell cycle. Thus, type 1 protein phosphatase in Saccharomyces cerevisiae is essential for the G2/M transition.
The transcription factors Elk-1 and serum response factor interact by direct protein-protein contacts mediated by a short region of Elk-1.
Authors: Shore P , Sharrocks A D
Published: October 2015

Transcriptional induction of the c-fos gene in response to epidermal growth factor stimulation is mediated in part by a ternary nucleoprotein complex within the promoter consisting of serum response factor (SRF), p62TCF/Elk-1 and the serum response element (SRE). Both SRF and p62TCF/Elk-1 contact the DNA and bind in a cooperative manner to the SRE. In this study, we demonstrate that SRF and Elk-1 interact directly in the absence of the SRE. A 30-amino-acid peptide from Elk-1 (B-box) is both necessary and sufficient to mediate protein-protein contacts with SRF. Moreover, the Elk-1 B-box is necessary to enable SRF-dependent binding of an alternative ETS domain (from the transcription factor PU.1) to the c-fos SRE. Mutations in either the Elk-1 B-box or the C-terminal half of the SRF DNA-binding domain (coreSRF) which show reduced ability to form ternary complexes also show greatly reduced protein-protein interactions in the absence of the SRE. Our results clearly demonstrate that direct protein-protein interactions between the transcription factors Elk-1 and SRF, in addition to DNA contacts, contribute to the formation of a ternary complex on the c-fos SRE. We discuss the wider applicability of our results in describing specific protein-protein interactions between short well-defined transcription factor domains.
Mutations in XRS2 and RAD50 delay but do not prevent mating-type switching in Saccharomyces cerevisiae.
Authors: Ivanov E L , Sugawara N , White C I , Fabre F , Haber J E
Published: October 2015

In Saccharomyces cerevisiae, a large number of genes in the RAD52 epistasis group has been implicated in the repair of chromosomal double-strand breaks and in both mitotic and meiotic homologous recombination. While most of these genes are essential for yeast mating-type (MAT) gene switching, neither RAD50 nor XRS2 is required to complete this specialized mitotic gene conversion process. Using a galactose-inducible HO endonuclease gene to initiate MAT switching, we have examined the effect of null mutations of RAD50 and of XRS2 on intermediate steps of this recombination event. Both rad50 and xrs2 mutants exhibit a marked delay in the completion of switching. Both mutations reduce the extent of 5'-to-3' degradation from the end of the HO-created double-strand break. The steps of initial strand invasion and new DNA synthesis are delayed by approximately 30 min in mutant cells. However, later events are still further delayed, suggesting that XRS2 and RAD50 affect more than one step in the process. In the rad50 xrs2 double mutant, the completion of MAT switching is delayed more than in either single mutant, without reducing the overall efficiency of the process. The XRS2 gene encodes an 854-amino-acid protein with no obvious similarity to the Rad50 protein or to any other protein in the database. Overexpression of RAD50 does not complement the defects in xrs2 or vice versa.
Novel muscle-specific enhancer sequences upstream of the cardiac actin gene.
Authors: Biben C , Kirschbaum B J , Garner I , Buckingham M
Published: October 2015

A DNase I-hypersensitive site analysis of the 5'-flanking region of the mouse alpha-cardiac actin gene with muscle cell lines derived from C3H mice shows the presence of two such sites, at about -5 and -7 kb. When tested for activity in cultured cells with homologous and heterologous promoters, both sequences act as muscle-specific enhancers. Transcription from the proximal promoter of the alpha-cardiac actin gene is increased 100-fold with either enhancer. The activity of the distal enhancer in C2/7 myotubes is confined to an 800-bp fragment, which contains multiple E boxes. In transfection assays, this sequence does not give detectable transactivation by any of the myogenic factors even though one of the E boxes is functionally important. Bandshift assays showed that MyoD and myogenin can bind to this E box. However, additional sequences are also required for activity. We conclude that in the case of this muscle enhancer, myogenic factors alone are not sufficient to activate transcription either directly via an E box or indirectly through activation of genes encoding other muscle factors. In BALB/c mice, in which cardiac actin mRNA levels are 8- to 10-fold lower, the alpha-cardiac actin locus is perturbed by a 9.5-kb insertion (I. Garner, A. J. Minty, S. Alonso, P. J. Barton, and M. E. Buckingham, EMBO J. 5:2559-2567, 1986). This is located at -6.5 kb, between the two enhancers. The insertion therefore distances the distal enhancer from the promoter and from the proximal enhancer of the bona fide cardiac actin gene, probably thus perturbing transcriptional activity.
A novel developmental regulatory motif required for stage-specific activation of the epsilon-globin gene and nuclear factor binding in embryonic erythroid cells.
Authors: Trepicchio W L , Dyer M A , Baron M H
Published: October 2015

Members of the human beta-globin gene family are expressed at discrete stages of development and therefore provide an important model system for examining mechanisms of temporal gene regulation. We have previously shown that expression of the embryonic beta-like globin gene (epsilon) is mediated by a complex array of positive and negative upstream control elements. Correct developmental stage- and tissue-specific gene expression is conferred by synergistic interactions between a positive regulatory element (termed epsilon-PRE II) which is active only in embryonic erythroid cells and at least two other regulatory domains upstream of the epsilon-globin gene promoter. A nuclear factor highly enriched in cultured embryonic erythroid cells and in mouse embryonic yolk sac binds to a novel, evolutionarily conserved sequence within epsilon-PRE II. We show here that binding of this factor to the conserved element within epsilon-PRE II is critical for transcriptional activity. Point mutations that interfere with protein binding to epsilon-PRE II abolish transcriptional activation of the constitutive epsilon-globin promoter. Adult erythroid nuclei (from cultured cells or adult mouse liver) also contain a factor that binds to this region, but the complex formed migrates more rapidly during nondenaturing electrophoresis, suggesting either that distinct proteins bind to epsilon-PRE II or that a single protein is differentially modified in these cells in a way that modulates its activity. Several lines of evidence suggest that the binding factors in embryonic and adult erythroid cells are distinguished by posttranscriptional differences.
Fine-resolution mapping of spontaneous and double-strand break-induced gene conversion tracts in Saccharomyces cerevisiae reveals reversible mitotic conversion polarity.
Authors: Sweetser D B , Hough H , Whelden J F , Arbuckle M , Nickoloff J A
Published: October 2015

Spontaneous and double-strand break (DSB)-induced gene conversion was examined in alleles of the Saccharomyces cerevisiae ura3 gene containing nine phenotypically silent markers and an HO nuclease recognition site. Conversions of these alleles, carried on ARS1/CEN4 plasmids, involved interactions with heteroalleles on chromosome V and were stimulated by DSBs created at HO sites. Crossovers that integrate plasmids into chromosomes were not detected since the resultant dicentric chromosomes would be lethal. Converted alleles in shuttle plasmids were easily transferred to Escherichia coli and analyzed for marker conversion, facilitating the characterization of more than 400 independent products from five crosses. This analysis revealed several new features of gene conversions. The average length of DSB-induced conversion tracts was 200 to 300 bp, although about 20% were very short (less than 53 bp). About 20% of spontaneous tracts also were also less than 53 bp, but spontaneous tracts were on average about 40% longer than DSB-induced tracts. Most tracts were continuous, but 3% had discontinuous conversion patterns, indicating that extensive heteroduplex DNA is formed during at least this fraction of events. Mismatches in heteroduplex DNA were repaired in both directions, and repair tracts as short as 44 bp were observed. Surprisingly, most DSB-induced gene conversion tracts were unidirectional and exhibited a reversible polarity that depended on the locations of DSBs and frameshift mutations in recipient and donor alleles.
Erythroid expression of the heme-regulated eIF-2 alpha kinase.
Authors: Crosby J S , Lee K , London I M , Chen J J
Published: October 2015

The role of heme-regulated eIF-2 alpha kinase (HRI) in the regulation of protein synthesis in rabbit reticulocytes is well documented. Inhibitors of protein synthesis with properties similar to those of HRI have been described in some nonerythroid cell types, but it has not yet been determined whether these eIF-2 alpha kinase activities are mediated by HRI or one or more as yet uncharacterized kinases. We have studied the expression of mRNA, polypeptide, and kinase activities of HRI in various tissues from both nonanemic and anemic rabbits. Our results indicate that HRI is expressed in an erythroid cell-specific manner. HRI is present in the bone marrow and peripheral blood of both nonanemic and anemic rabbits but not in any of the other tissues tested. HRI mRNA is present at low levels in uninduced mouse erythroleukemic (MEL) cells and human K562 cells and accumulates to higher levels upon induction. The accumulation of HRI mRNA in differentiating MEL cells is dependent upon the presence of heme. The addition of 3-amino-1,2,4-triazole (AT), an inhibitor of heme biosynthesis, to the induction medium markedly reduced HRI mRNA accumulation. Simultaneous addition of hemin and AT to the dimethyl sulfoxide induction medium largely prevented the inhibition of HRI mRNA induction by AT. These findings indicate that HRI is expressed in an erythroid cell-specific manner and that the major physiologic role of HRI is in adjusting the synthesis of globins to the availability of heme.
A human Alu RNA-binding protein whose expression is associated with accumulation of small cytoplasmic Alu RNA.
Authors: Chang D Y , Nelson B , Bilyeu T , Hsu K , Darlington G J , Maraia R J
Published: October 2015

Human Alu sequences are short interspersed DNA elements which have been greatly amplified by retrotransposition. Although initially derived from the 7SL RNA component of signal recognition particle (SRP), the Alu sequence has evolved into a dominant transposon while retaining a specific secondary structure found in 7SL RNA. We previously characterized a set of Alu sequences which are expressed as small cytoplasmic RNAs and isolated a protein that binds to these transcripts. Here we report that biochemical purification of this protein revealed it as the human homolog of the SRP 14 polypeptide which binds the Alu-homologous region of 7SL RNA. The human cDNA predicts an alanine-rich C-terminal tail translated from a trinucleotide repeat not found in the rodent homolog, which accounts for why the human protein-RNA complex migrates more slowly than its rodent counterpart in RNA mobility shift assays. The human Alu RNA-binding protein (RBP) is expressed after transfection of this cDNA into mouse cells. Expression of human RBP in rodent x human somatic cell hybrids is associated with substantial increase in endogenous small cytoplasmic Alu and scB1 transcripts but not other small RNAs. These studies provide evidence that this RBP associates with Alu transcripts in vivo and affects their metabolism and suggests a role for Alu transcripts in translation in an SRP-like manner. Analysis of hybrid lines indicated that the Alu RBP gene maps to human chromosome 15q22, which was confirmed by Southern blotting. The possibility that the primate-specific structure of this protein may have contributed to Alu evolution is considered.
A novel basic helix-loop-helix protein is expressed in muscle attachment sites of the Drosophila epidermis.
Authors: Armand P , Knapp A C , Hirsch A J , Wieschaus E F , Cole M D
Published: October 2015

We have found that a novel basic helix-loop-helix (bHLH) protein is expressed almost exclusively in the epidermal attachments sites for the somatic muscles of Drosophila melanogaster. A Drosophila cDNA library was screened with radioactively labeled E12 protein, which can dimerize with many HLH proteins. One clone that emerged from this screen encoded a previously unknown protein of 360 amino acids, named delilah, that contains both basic and HLH domains, similar to a group of cellular transcription factors implicated in cell type determination. Delilah protein formed heterodimers with E12 that bind to the muscle creatine kinase promoter. In situ hybridization with the delilah cDNA localized the expression of the gene to a subset of cells in the epidermis which form a distinct pattern involving both the segmental boundaries and intrasegmental clusters. This pattern was coincident with the known sites of attachment of the somatic muscles to tendon cells in the epidermis. delilah expression persists in snail mutant embryos which lack mesoderm, indicating that expression of the gene was not induced by attachment of the underlying muscles. The similarity of this gene to other bHLH genes suggests that it plays an important role in the differentiation of epidermal cells into muscle attachment sites.
Apoptosis in erythroid progenitors deprived of erythropoietin occurs during the G1 and S phases of the cell cycle without growth arrest or stabilization of wild-type p53.
Authors: Kelley L L , Green W F , Hicks G G , Bondurant M C , Koury M J , Ruley H E
Published: October 2015

Erythropoietin (Epo) inhibits apoptosis in murine proerythroblasts infected with the anemia-inducing strain of Friend virus (FVA cells). We have shown that the apoptotic process in FVA cell populations deprived of Epo is asynchronous as a result of a heterogeneity in Epo dependence among individual cells. Here we investigated whether apoptosis in FVA cells correlated with cell cycle phase or stabilization of p53 tumor suppressor protein. DNA analysis in nonapoptotic FVA cell subpopulations cultured without Epo demonstrated little change in the percentages of cells in G1,S, and G2/M phases over time. Analysis of the apoptotic subpopulation revealed high percentages of cells in G1 and S, with few cells in G2/M at any time. When cells were sorted from G1 and S phases prior to culture without Epo, apoptotic cells appeared at the same rate in both populations, indicating that no prior commitment step had occurred in either G1 or S phase. Steady-state wild-type p53 protein levels were very low in FVA cells compared with control cell lines and did not accumulate in Epo-deprived cultures; however, p53 protein did accumulate when FVA cells were treated with the DNA-damaging agent actinomycin D. These data indicate that erythroblast apoptosis caused by Epo deprivation (i) occurs throughout G1 and S phases and does not require cell cycle arrest, (ii) does not have a commitment event related to cell cycle phase, and (iii) is not associated with conformational changes or stabilization of wild-type p53 protein.
sir2 mutants of Kluyveromyces lactis are hypersensitive to DNA-targeting drugs.
Authors: Chen X J , Clark-Walker G D
Published: October 2015

A Kluyveromyces lactis mutant, hypersensitive to the DNA-targeting drugs ethidium bromide (EtBr), berenil, and HOE15030, can be complemented by a wild-type gene with homology to SIR2 of Saccharomyces cerevisiae (ScSIR2). The deduced amino acid sequence of the K. lactis Sir2 protein has 53% identity with ScSir2 protein but is 108 residues longer. K. lactis sir2 mutants show decreased mating efficiency, deficiency in sporulation, an increase in recombination at the ribosomal DNA locus, and EtBr-induced death. Some functional equivalence between the Sir2 proteins of K. lactis and S. cerevisiae has been demonstrated by introduction of ScSIR2 into a sir2 mutant of K. lactis. Expression of ScSIR2 on a multicopy plasmid restores resistance to EtBr and complements sporulation deficiency. Similarly, mating efficiency of a sir2 mutant of S. cerevisiae is partially restored by K. lactis SIR2 on a multicopy plasmid. Although these observations suggest that there has been some conservation of Sir2 protein function, a striking difference is that sir2 mutants of S. cerevisiae, unlike their K. lactis counterparts, are not hypersensitive to DNA-targeting drugs.
T7 RNA polymerase-dependent expression of COXII in yeast mitochondria.
Authors: Pinkham J L , Dudley A M , Mason T L
Published: October 2015

An in vivo expression system has been developed for controlling the transcription of individual genes in the mitochondrial genome of Saccharomyces cerevisiae. The bacteriophage T7 RNA polymerase (T7Pol), fused to the COXIV mitchondrial import peptide and expressed under the control of either the GAL1 or the ADH1 promoter, efficiently transcribes a target gene, T7-COX2, in the mitochondrial genome. Cells bearing the T7-COX2 gene, but lacking wild-type COX2, require T7Pol for respiration. Functional expression of T7-COX2 is completely dependent on the COX2-specific translational activator Pet111p, despite additional nucleotides at the 5' end of the T7-COX2 transcript. Expression of mitochondrion-targeted T7Pol at high levels from the GAL1 promoter has no detectable effect on mitochondrial function in rho+ cells lacking the T7-COX2 target gene, but in cells with T7-COX2 integrated into the mitochondrial genome, an equivalent level of T7Pol expression causes severe respiratory deficiency. In comparison with wild-type COX2 expression, steady-state levels of T7-COX2 mRNA increase fivefold when transcription is driven by T7Pol expressed from the ADH1 promoter, yet COXII protein levels and cellular respiration rates decrease by about 50%. This discoordinate expression of mRNA and protein provides additional evidence for posttranscriptional control of COX2 expression.
Scaffold attachment regions stimulate HSP70.1 expression in mouse preimplantation embryos but not in differentiated tissues.
Authors: Thompson E M , Christians E , Stinnakre M G , Renard J P
Published: October 2015

Eukaryotic interphase chromatin is thought to be organized into topologically discrete, independent domains acting as units upon which differential patterns of gene expression are established. Sequences which attach chromatin to in vitro preparations of a nucleoprotein matrix (scaffold attachment regions [SARs]) may act as domain boundaries, but their role remains poorly defined compared with those of other elements such as locus control regions. We have produced mice homozygous for a transgene which is transcribed as early as the activation of the embryonic genome at the two-cell stage and which is expressed ubiquitously in a number of differentiated tissues. Transgenic lines were generated in the presence or absence of flanking SAR sequences, creating an original model which enabled us to examine the effects of these elements at different developmental stages. In the preimplantation mouse embryo, flanking SARs stimulated transgene expression in a copy-dependent manner. In contrast, in the differentiated tissues of newborn and adult mice, no significant SAR-dependent increase in transgene expression was found, correlation with copy number was lost, and position effects were observed. These results suggest a limited capacity of SARs to act as insulating elements but are consistent with a proposed model of SAR-mediated chromatin opening and closing.
Structural and functional conservation of the human homolog of the Schizosaccharomyces pombe rad2 gene, which is required for chromosome segregation and recovery from DNA damage.
Authors: Murray J M , Tavassoli M , al-Harithy R , Sheldrick K S , Lehmann A R , Carr A M , Watts F Z
Published: October 2015

The rad2 mutant of Schizosaccharomyces pombe is sensitive to UV irradiation and deficient in the repair of UV damage. In addition, it has a very high degree of chromosome loss and/or nondisjunction. We have cloned the rad2 gene and have shown it to be a member of the Saccharomyces cerevisiae RAD2/S. pombe rad13/human XPG family. Using degenerate PCR, we have cloned the human homolog of the rad2 gene. Human cDNA has 55% amino acid sequence identity to the rad2 gene and is able to complement the UV sensitivity of the rad2 null mutant. We have thus isolated a novel human gene which is likely to be involved both in controlling the fidelity of chromosome segregation and in the repair of UV-induced DNA damage. Its involvement in two fundamental processes for maintaining chromosomal integrity suggests that it is likely to be an important component of cancer avoidance mechanisms.
Mapping initiation sites for simian virus 40 DNA synthesis events in vitro.
Authors: Bullock P A , Tevosian S , Jones C , Denis D
Published: October 2015

Primer RNA-DNA, a small (approximately 30-nucleotide) RNA-DNA hybrid molecule, was identified in recent studies of simian virus 40 DNA synthesis in vitro. The available evidence indicates that primer RNA-DNA is the product of the polymerase alpha-primase complex. Primer RNA-DNA is formed exclusively on lagging-strand DNA templates; it is synthesized initially in the vicinity of the simian virus 40 origin and at later times at sites progressively distal to the origin. To further characterize initiation events, template sequences encoding the 5' ends of both primer RNA and primer DNA, formed during a 5-s pulse, have been determined. Analyses of these sequences demonstrate the existence of an initiation signal for lagging-strand synthesis. At any given position, the initiation signal is located within those template sequences encoding primer RNA, situated proximal to the nucleotide encoding the 5' end of the RNA primer. In most instances, the sequence 5'-TTN-3' (where N encodes the nucleotide at the 5' end of the primer) is a feature of the initiation signal. Initiation signals are present, on average, once every 19 nucleotides. These results are discussed in terms of the mechanism of Okazaki fragment formation and possible links between prokaryotic and eukaryotic initiation events.
Developmental characterization of a Drosophila RNA-binding protein homologous to the human systemic lupus erythematosus-associated La/SS-B autoantigen.
Authors: Bai C , Li Z , Tolias P P
Published: October 2015

Patients with humoral autoimmune diseases such as systemic lupus erythematosus and Sjögren's syndrome contain antibodies in their sera directed against certain normal cellular components such as the La/SS-B autoantigen, an RNA-binding protein believed to function as a putative processor of RNA polymerase III precursor transcripts. We have identified cDNA clones from the fruit fly Drosophila melanogaster that encode a protein displaying significant sequence homology with human La/SS-B. The fly protein (which we refer to as D-La) contains a putative ribonucleoprotein 1 (RNP1) and RNP2 RNA-binding domain. D-La also possesses a leucine zipper motif, suggesting that it may interact with itself or other proteins. Using gel retardation analysis, we show that D-La can bind RNA; in addition, we demonstrate the first reported DNA-binding activity associated with a La protein. Northern (RNA) blot analysis revealed a single 1,600-nucleotide transcript expressed throughout embryonic, larval, pupal, and adult development. Surprisingly, whole-mount in situ hybridization experiments revealed that D-La transcripts are not present in all ovarian tissues. In addition, early expression throughout the embryo is followed by a restricted pattern of mesodermal expression that is later confined to the visceral mesoderm, gonads, gut, and salivary glands. These results suggest that D-La may play a more specialized role during fly development as opposed to a rather general role inferred by its homology to La proteins from other organisms.
Chromatin structure modulation in Saccharomyces cerevisiae by centromere and promoter factor 1.
Authors: Kent N A , Tsang J S , Crowther D J , Mellor J
Published: October 2015

CPF1 is an abundant basic-helix-loop-helix-ZIP protein that binds to the CDEI motif in Saccharomyces cerevisiae centromeres and in the promoters of numerous genes, including those encoding enzymes of the methionine biosynthetic pathway. Strains lacking CPF1 are methionine auxotrophs, and it has been proposed that CPF1 might positively influence transcription at the MET25 and MET16 genes by modulating promoter chromatin structure. We test this hypothesis and show that the regions surrounding the CDEI motifs in the MET25 and MET16 promoters are maintained in a nucleosome-free state and that this requires the entire CPF1 protein. However, the chromatin structure around the CDEI motifs does not change on derepression of transcription and does not correlate with the methionine phenotype of the cell. An intact CDEI motif but not CPF1 is required for transcriptional activation from a region of the MET25 upstream activation sequence. Our results suggest that CPF1 functions to modulate chromatin structure around the CDEI motif but that these changes at the MET25 and MET16 promoters do not explain how CPF1 functions to maintain methionine-independent growth. The presence of CPF1-dependent chromatin structures at these promoters leads to a weak repression of transcription.
The 5' leader of a chloroplast mRNA mediates the translational requirements for two nucleus-encoded functions in Chlamydomonas reinhardtii.
Authors: Zerges W , Rochaix J D
Published: October 2015

In the green alga Chlamydomonas reinhardtii, the nuclear mutations F34 and F64 have been previously shown to abolish the synthesis of the photosystem II core polypeptide subunit P6, which is encoded by the chloroplast psbC gene. In this report the functions encoded by F34 and F64 are shown to be required for translation of the psbC mRNA, on the basis of the finding that the expression of a heterologous reporter gene fused to the psbC 5' nontranslated leader sequence requires wild-type F34 and F64 alleles in vivo. Moreover, a point mutation in the psbC 5' nontranslated leader sequence suppresses this requirement for wild-type F34 function. In vitro RNA-protein cross-linking studies reveal that chloroplast protein extracts from strains carrying the F64 mutation contain an approximately 46-kDa RNA-binding protein. The absence of the RNA-binding activity of this protein in chloroplast extracts of wild-type strains suggests that it is related to the role of the F64-encoded function for psbC mRNA translation. The binding specificity of this protein appears to be for an AU-rich RNA sequence motif.
E-box- and MEF-2-independent muscle-specific expression, positive autoregulation, and cross-activation of the chicken MyoD (CMD1) promoter reveal an indirect regulatory pathway.
Authors: Dechesne C A , Wei Q , Eldridge J , Gannoun-Zaki L , Millasseau P , Bougueleret L , Caterina D , Paterson B M
Published: October 2015

Members of the MyoD family of gene-regulatory proteins (MyoD, myogenin, myf5, and MRF4) have all been shown not only to regulate the transcription of numerous muscle-specific genes but also to positively autoregulate and cross activate each other's transcription. In the case of muscle-specific genes, this transcriptional regulation can often be correlated with the presence of a DNA consensus in the regulatory region CANNTG, known as an E box. Little is known about the regulatory interactions of the myogenic factors themselves; however, these interactions are thought to be important for the activation and maintenance of the muscle phenotype. We have identified the minimal region in the chicken MyoD (CMD1) promoter necessary for muscle-specific transcription in primary cultures of embryonic chicken skeletal muscle. The CMD1 promoter is silent in primary chick fibroblast cultures and in muscle cell cultures treated with the thymidine analog bromodeoxyuridine. However, CMD1 and chicken myogenin, as well as, to a lesser degree, chicken Myf5 and MRF4, expressed in trans can activate transcription from the minimal CMD1 promoter in these primary fibroblast cultures. Here we show that the CMD1 promoter contains numerous E-box binding sites for CMD1 and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific and the other myogenic factors, as well as a MEF-2 binding site. Surprisingly, neither muscle-specific expression, autoregulation, or cross activation depends upon the presence of of these E-box or MEF-2 binding sites in the CMD1 promoter. These results demonstrate that the autoregulation and cross activation of the chicken MyoD promoter through the putative direct binding of the myogenic basic helix-loop-helix regulatory factors is mediated through an indirect pathway that involves unidentified regulatory elements and/or ancillary factors.
Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant.
Authors: Finley D , Sadis S , Monia B P , Boucher P , Ecker D J , Crooke S T , Chau V
Published: October 2015

The degradation of many proteins requires their prior attachment to ubiquitin. Proteolytic substrates are characteristically multiubiquitinated through the formation of ubiquitin-ubiquitin linkages. Lys-48 of ubiquitin can serve as a linkage site in the formation of such chains and is required for the degradation of some substrates of this pathway in vitro. We have characterized the recessive and dominant effects of a Lys-48-to-Arg mutant of ubiquitin (UbK48R) in Saccharomyces cerevisiae. Although UbK48R is expected to terminate the growth of Lys-48 multiubiquitin chains and thus to exert a dominant negative effect on protein turnover, overproduction of UbK48R in wild-type cells results in only a weak inhibition of protein turnover, apparently because the mutant ubiquitin can be removed from multiubiquitin chains. Surprisingly, expression of UbK48R complements several phenotypes of polyubiquitin gene (UB14) deletion mutants. However, UbK48R cannot serve as a sole source of ubiquitin in S. cerevisiae, as evidenced by its inability to rescue the growth of ubi1 ubi2 ubi3 ubi4 quadruple mutants. When provided solely with UbK48R, cells undergo cell cycle arrest with a terminal phenotype characterized by replicated DNA, mitotic spindles, and two-lobed nuclei. Under these conditions, degradation of amino acid analog-containing proteins is severely inhibited. Thus, multiubiquitin chains containing Lys-48 linkages play a critical role in protein degradation in vivo.
An unusual inguinoscrotal hernia with renal involvement
Authors: Osmani Humza Tariq , Boulton Richard , Wyatt Harry , Saunders Stephen Michael
Published: October 2015

We present a case of a 74-year-old man who, while in intensive treatment unit for an upper gastrointestinal bleed, decompensated cardiac failure and concurrent pneumonia, was found to have a large right hydronephrotic pelvic kidney and bladder within the hernia. After discharge, he was medically optimised for 7 months before undergoing an elective open mesh repair of his hernia. During the procedure, drainage of a large hydrocoele was performed to facilitate reduction of the hernia. Postoperatively, he underwent ureteric stenting due to a persistent hydronephrosis with impairment of his renal function. He subsequently made a good recovery and was discharged home with outpatient follow-up planned.
A systematic review protocol for reporting deficiencies within surgical case series
Authors: Agha Riaz , Fowler Alexander J , Lee Seon-Young , Gundogan Buket , Whitehurst Katharine , Sagoo Hakiran , Jeong Kyung Jin Lee , Altman Douglas G , Orgill Dennis P
Published: October 2015

Introduction

Case series are an important and common study type in surgical literature. There is evidence that key data are excluded from published case series, and currently no reporting guideline exists for case series. There is, therefore, the potential to change practices and improve the reporting of case series. Reporting guidelines have been shown to be efficacious in raising the bar for reporting quality. We present our protocol for the first stage of guideline development—a systematic review of previously identified deficiencies in how surgical case series are reported.

Methods and analysis

Electronic searches will be conducted on MEDLINE, EMBASE, Cochrane Methods Register, Science Citation Index and Conference Proceedings Citation Index, from the start of indexing until 5 November 2014. The electronic search strategy was developed with an information specialist. Two independent researchers will identify articles for inclusion, specifically those that describe reporting deficiencies within surgical case series. Data will be extracted to specifically focus on the deficiencies of reporting. These will be categorised according to their type, and other identified issues will also be presented. Data will be presented with descriptive statistics to determine frequently missing types of data, and the commonest reporting issues tabulated.

Ethics and dissemination

The authors hope to disseminate the findings as widely as possible, irrespective of results, as these will add to the wider corpora of information on this subject. The systematic review will be published in a peer-reviewed journal and will be presented at a wide range of national and international conferences. Ultimately, this will inform a Delphi process for the development of a surgical case series reporting guideline.

Protocol registration

CRD42015016145.
Willingness to pay per quality-adjusted life year for life-saving treatments in Thailand
Authors: Nimdet Khachapon , Ngorsuraches Surachat
Published: October 2015

Objective

To estimate the willingness to pay (WTP) per quality-adjusted life year (QALY) value for life-saving treatments and to determine factors affecting the WTP per QALY value.

Design

A cross-sectional survey with multistage sampling and face-to-face interviews.

Setting

General population in the southern part of Thailand.

Participants

A total of 600 individuals were included in the study. Only 554 (92.3%) responses were usable for data analyses.

Outcome measure

Participants were asked for the maximum amount of WTP value for life-saving treatments by an open-ended question. EQ-5D-3L and visual analogue scale (VAS) were used to estimate additional QALY.

Results

The amount of WTP values varied from 0 to 720 000 Baht/year (approximately 32 Baht=US$1). The averages of additional QALY obtained from VAS and EQ-5D-3L were only slightly different (0.872 and 0.853, respectively). The averages of WTP per QALY obtained from VAS and EQ-5D-3L were 244720 and 243120 Baht/QALY, respectively. As compared to male participants, female participants were more likely to pay less for an additional QALY (p=0.007). In addition, participants with higher household incomes tended to have higher WTP per QALY values (p<0.001).

Conclusions

Our study added another WTP per QALY value specifically for life-saving treatments, which would complement the current cost-effectiveness threshold used in Thailand and optimise patient access to innovative treatments or technologies.
Association between COX-2 gene polymorphisms and risk of hepatocellular carcinoma development: a meta-analysis
Authors: Lu Si-Cong , Zhong Jian-Hong , Tan Jun-Tao , Tang Hua-Lin , Liu Xiao-Guang , Xiang Bang-De , Li Le-Qun , Peng Tao
Published: October 2015

Objective

To investigate the association between cyclo-oxygenase-2 (COX-2) polymorphism and the risk of hepatocellular carcinoma (HCC) development.

Design

Systematic review and meta-analysis of COX-2 polymorphism and risk of HCC development among people with or without HCC.

Data sources

EMBASE, PubMed, Public Library of Science, SCOPUS, Web of Knowledge and Chinese National Knowledge Infrastructure were searched for all clinical and experimental case–control studies of COX-2 polymorphism and HCC risk. Studies published up to March 2015 were included.

Review method

Ten studies were included for data extraction, which were mainly from Asian countries.

Results

2538 people with HCC and 3714 without HCC were found to satisfy the inclusion criteria and included in the review. The associations of specific genotypes in the eight polymorphic variants of COX-2 and the risk of HCC development were analysed. GG genotype at the A-1195G polymorphism may be associated with a reduced risk of HCC development: the OR across all studies was 0.87 (95% CI 0.75 to 1.02) for the G allele versus the A allele, 0.72 (0.53 to 0.97) for GG versus AA, 0.72 (0.57 to 0.92) for GG versus GA+AA and 1.05 (0.77 to 1.44) for AA versus GA+GG. Similar results were found when the meta-analysis was repeated separately for the Chinese subgroup. However, more reliable data are needed to demonstrate associations between variants in G-765C, T+8473C, A-1290G, G-899C and introns 1, 5 and 6 polymorphisms and the risk of HCC development.

Conclusions

Only the COX-2 A-1195G gene polymorphism may be associated with a decreased risk of HCC development. These conclusions should be verified in further studies.
Commutative rings whose proper ideals are direct sum of completely cyclic modules
Authors: Behboodi M. , Heidari S. , Roointan-Isfahani S.
Published: October 2015

By two results of Köthe and Cohen–Kaplansky we obtain that “a commutative ring [Formula: see text] has the property that every [Formula: see text]-module is a direct sum of (completely) cyclic modules if and only if [Formula: see text] is an Artinian principal ideal ring” (an [Formula: see text]-module [Formula: see text] is called completely cyclic if each submodule of [Formula: see text] is cyclic). In this paper, we describe and study commutative rings whose proper ideals are direct sum of completely cyclic modules. It is shown that every proper ideal of a commutative ring [Formula: see text] is a direct sum of completely cyclic [Formula: see text]-modules if and only if [Formula: see text] is a principal ideal ring or [Formula: see text] is a local ring with maximal ideal [Formula: see text] such that there is an index set [Formula: see text] and a set of elements [Formula: see text] such that [Formula: see text] with each [Formula: see text] a simple [Formula: see text]-module and [Formula: see text] a principal ideal ring.
QM/MM description of periodic systems
Authors: Doll K. , Jacob T.
Published: October 2015

A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.
Reconstruction of inverted sedimentary basins from syn-tectonic remagnetizations. A methodological proposal
Authors: Villalaín Juan J. , Casas-Sainz Antonio M. , Soto Ruth
Published: October 2015

Syn-tectonic remagnetizations related to burial processes that occurred during their extensional stage are frequently recognized in inverted sedimentary basins. The incremental fold test is the main analytical tool used to detect these syn-tectonic remagnetizations. However this test gives spurious results when asymmetrical folding occurs (i.e. both limbs were not tilted simultaneously at the same rate). Asymmetrical folding is very common in sedimentary basins, especially at their margins, during the basinal stage and subsequent tectonic inversion. To correctly analyse syn-tectonic remagnetizations in these scenarios, we propose a method to restore palaeomagnetic vectors, which allows determining the tilting of beds at the remagnetization stage and therefore gives some hints on the geometry of sedimentary basins and/or folds at the overprint acquisition time. In this paper we consider the analysis of syn-tectonic remagnetization directions for basin reconstruction in two end-member basin models (i.e. syncline vs roll-over geometry). Finally, we compare the results obtained with several northern Iberian examples (Cameros basin in the Iberian Chain, Cabuérniga and Polientes Basin in the Pyrenées), formed during the Mesozoic as extensional basins and subsequently inverted during the Cenozoic compression. From these examples we propose generalizations for the application of syn-tectonic remagnetizations to constrain the geometry of sedimentary basins.
Mesoscale Transport in Magnetite Electrodes for Lithium-Ion Batteries
Authors: Knehr Kevin William , Brady Nicholas W , Lininger Christianna Naomi , Cama Christina A , Bock David C , Lin Zhou , Marschilok Amy C , Takeuchi Kenneth J , Takeuchi Esther S , West Alan C
Published: October 2015

The mass transport processes occurring within magnetite electrodes during discharge and voltage recovery are investigated using a combined experimental and modeling approach. Voltage recovery data are analyzed through a comparison of the mass transport time-constants associated with different length-scales within the electrode. The long voltage recovery times can be hypothesized to result from the relaxation of concentration profiles on the mesoscale, which consists of the agglomerate and crystallite length-scales. The hypothesis was tested through the development of a multi-scale mathematical model, which showed good agreement with experimental data.
Multiphysics Simulation of the Bromine Cathode: Cell Architecture and Electrode Optimization
Authors: Kok Matthew D. R. , Gostick Jeff T.
Published: October 2015

A multiphysics model of a flow battery fibrous cathode was designed in COMSOL. A seven level parametric study was performed to determine the effect of a variety of physical and chemical parameters on overall cell performance. It was found that kinetic factors dominate the operation and performance however certain morphological properties, such as fiber diameter, porosity and anisotropy, could be modified to optimize cell performance. It was also found that further optimization could be performed on engineering parameters such as the electrode thickness and design of the flow distributor. Due to the strong dependence on porosity, future studies will take into account membrane compression.
Study of the Impedance Growth and Capacity Fade of High Power Lithium-Iron Phosphate, Valve Regulated Lead Acid, and Nickel Metal Hydride Batteries When Cycled in High Rated Pulsed Profiles
Authors: Williams Christopher , Martin Matthew Jene , Wetz David Alan , Gnegy-Davidson Clint Gerhard
Published: October 2015

Electrochemical energy storage has become more power and energy dense in recent years. Many applications demanding energy storage operate in a pulsed manner. The most common chemistries considered for use in these applications include valve regulated lead acid (VRLA), nickel metal hydride (NiMH), and lithium-ion (LI). The University of Texas at Arlington’s (UTA’s) Pulsed Power and Energy Laboratory (PPEL) has assembled three batteries, one of each chemistry, with ~60 V open circuit potentials (OCPs) and is in the process of experimentally characterizing their capacity fade and impedance growth when they are used to drive a high current pulsed load in a 5 seconds on / 5 seconds off pulsed profile. All of the batteries are being discharged and recharged at rates much higher than thier 1C rating. Using standard voltage, current, and thermal diagnostics as well as periodic electrochemical impedance spectroscopy (EIS) measurements, the capacity fade and impedance growth of each chemistry is being studied to understand how the high rate pulsed profile ages the cells. Empirical and lumped element models of the impedance rise will be developed to better understand what is aging internally and how it impacts the usable life of the batteries compared with manufacturers rated life predictions. The experimental and modeling efforts will be summarized and conclusions will be drawn to provide the audience with a better understanding of how each of these technologies ages when used in high rate, pulsed applications.
Discovery of New Anode SEI Forming Additives Using an in silico Evolutionary Approach
Authors: Murdock Stuart E. , Hughes Thomas F. , Kwak Shaun H. , Goldberg Alexander , Giesen David J , Cao Yixiang , Sanders Jeffrey , Gavartin Jacob , Dathar G. K. Phani , Halls Mathew D.
Published: October 2015

To improve the performance of lithium ion batteries, functional additives are included in electrolyte formulations. To reduce damage to the electrolyte when a cell is charged, sacrificial anode SEI forming additives are used, requiring high reduction potential and high reactivity. Previously, high throughput quantum chemical screening of structure libraries has been demonstrated for electrolyte component discovery, but this can be a time consuming and highly curated procedure. An alternative approach involves the automated evolution of a set of input structures toward target property characteristics. This requires less user management and enables knowledge creation rather than knowledge implementation. In this work, a quantum chemistry based genetic optimization framework is applied to battery electrolyte components for the first time, seeking to simultaneously maximize reduction potential and minimize oxidation potential for evolved candidate anode SEI additives.