bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional activation of the Listeria monocytogenes hemolysin gene in Bacillus subtilis
Authors: Freitag N E , Youngman P , Portnoy D A
Published: November 2016

The prfA gene of Listeria monocytogenes was recently reported to be required for expression of hly, which encodes a pore-forming hemolysin essential for pathogenicity (M. Leimeister-Wachter, C. Haffner, E. Domann, W. Goebel, and T. Chakraborty, Proc. Natl. Acad. Sci. USA 87:8336-8340, 1990). We demonstrate here that a hly-lacZ fusion introduced into Bacillus subtilis is strongly activated when the prfA gene product is supplied in trans under the control of an isopropyl-beta-D-thiogalactopyranoside-inducible promoter, Pspac. Moreover, the PrfA-dependent activation of hly is abolished by point mutations in a 14-bp DNA palindromic sequence present in the 5' upstream region of hly. This indicates that PrfA is both necessary and sufficient for hly transcriptional activation and establishes the palindrome as the likely target sequence for PrfA interaction. The presence of a palindrome in the upstream regions of three additional L. monocytogenes genes clustered near hly suggests that PrfA may serve as a transcriptional activator for a major virulence regulon of L. monocytogenes. In addition, the ability of PrfA to activate its target promoters effectively in B. subtilis suggests that further analysis of this regulon and perhaps other aspects of L. monocytogenes gene regulation might be carried out in part through reconstruction experiments in B. subtilis.
Malate dehydrogenase from Chlorobium vibrioforme, Chlorobium tepidum, and Heliobacterium gestii: purification, characterization, and investigation of dinucleotide binding by dehydrogenases by use of empirical methods of protein sequence analysis
Authors: Charnock C , Refseth U H , Sirevåg R
Published: November 2016

Malate dehydrogenase (MDH; EC 1.1.1.37) from strain NCIB 8327 of the green sulfur bacterium Chlorobium vibrioforme was purified to homogeneity by triazine dye affinity chromatography followed by gel filtration. Purification of MDH gave an approximately 1,000-fold increase in specific activity and recoveries of typically 15 to 20%. The criteria of purity were single bands on sodium dodecyl sulfate (SDS) and nondenaturing polyacrylamide electrophoresis (PAGE) and the detection of a single N terminus in an Edman degradation analysis. MDH activity was detected in purified preparations by activity staining of gels in the direction of malate oxidation. PAGE and gel filtration (Sephadex G-100) analyses showed the native enzyme to be a dimer composed of identical subunits both at room temperature and at 4 degrees C. The molecular weight of the native enzyme as estimated by gel filtration was 77,000 and by gradient PAGE was 74,000. The subunit molecular weight as estimated by SDS-gradient PAGE was 37,500. N-terminal sequences of MDHs from C. vibrioforme, Chlorobium tepidum, and Heliobacterium gestii are presented. There are obvious key sequence similarities in MDHs from the phototrophic green bacteria. The sequences presented probably possess a stretch of amino acids involved in dinucleotide binding which is similar to that of Chloroflexus aurantiacus MDH and other classes of dehydrogenase enzymes but unique among MDHs.
Role of the two-component leader sequence and mature amino acid sequences in extracellular export of endoglucanase EGL from Pseudomonas solanacearum
Authors: Huang J Z , Schell M A
Published: November 2016

The egl gene of Pseudomonas solanacearum encodes a 43-kDa extracellular endoglucanase (mEGL) involved in wilt disease caused by this phytopathogen. Egl is initially translated with a 45-residue, two-part leader sequence. The first 19 residues are apparently removed by signal peptidase II during export of Egl across the inner membrane (IM); the remaining residues of the leader sequence (modified with palmitate) are removed during export across the outer membrane (OM). Localization of Egl-PhoA fusion proteins showed that the first 26 residues of the Egl leader sequence are required and sufficient to direct lipid modification, processing, and export of Egl or PhoA across the IM but not the OM. Fusions of the complete 45-residue leader sequence or of the leader and increasing portions of mEgl sequences to PhoA did not cause its export across the OM. In-frame deletion of portions of mEGL-coding sequences blocked export of the truncated polypeptides across the OM without affecting export across the IM. These results indicate that the first part of the leader sequence functions independently to direct export of Egl across the IM while the second part and sequences and structures in mEGL are involved in export across the OM. Computer analysis of the mEgl amino acid sequence obtained from its nucleotide sequence identified a region of mEGL similar in amino acid sequence to regions in other prokaryotic endoglucanases.
DNA sequence of IS91 and identification of the transposase gene
Authors: Mendiola M V , Jubete Y , de la Cruz F
Published: November 2016

IS91 is a 1,830-bp insertion sequence that inserts specifically at the sequence CAAG or GAAC of the target and does not duplicate any sequence upon insertion (23). By transposon mutagenesis, we have identified open reading frame 426 (ORF426; bp 454 to 1731) as the putative ORF for the transposase. It displays a cysteine-rich, potential metal-binding domain in its N-terminal region. Adjacent to ORF426, there is an ORF (ORF121) which precedes and terminally overlaps ORF426 by one amino acid. Tn1732 insertions in ORF121 do not affect the transposition frequency. IS91 has sequence similarities to IS801 from Pseudomonas syringae. Their putative transposases are 36% identical, including conservation of the cysteine-rich cluster. The information concerning IS801 insertion specificity and target duplication has been reevaluated in the light of our results.
Cloning and sequencing of the gene coding for alcohol dehydrogenase of Bacillus stearothermophilus and rational shift of the optimum pH
Authors: Sakoda H , Imanaka T
Published: November 2016

Using Bacillus subtilis as a host and pTB524 as a vector plasmid, we cloned the thermostable alcohol dehydrogenase (ADH-T) gene (adhT) from Bacillus stearothermophilus NCA1503 and determined its nucleotide sequence. The deduced amino acid sequence (337 amino acids) was compared with the sequences of ADHs from four different origins. The amino acid residues responsible for the catalytic activity of horse liver ADH had been clarified on the basis of three-dimensional structure. Since those catalytic amino acid residues were fairly conserved in ADH-T and other ADHs, ADH-T was inferred to have basically the same proton release system as horse liver ADH. The putative proton release system of ADH-T was elucidated by introducing point mutations at the catalytic amino acid residues, Cys-38 (cysteine at position 38), Thr-40, and His-43, with site-directed mutagenesis. The mutant enzyme Thr-40-Ser (Thr-40 was replaced by serine) showed a little lower level of activity than wild-type ADH-T did. The result indicates that the OH group of serine instead of threonine can also be used for the catalytic activity. To change the pKa value of the putative system, His-43 was replaced by the more basic amino acid arginine. As a result, the optimum pH of the mutant enzyme His-43-Arg was shifted from 7.8 (wild-type enzyme) to 9.0. His-43-Arg exhibited a higher level of activity than wild-type enzyme at the optimum pH.
Membrane-derived oligosaccharides affect porin osmoregulation only in media of low ionic strength
Authors: Geiger O , Russo F D , Silhavy T J , Kennedy E P
Published: November 2016

Gram-negative bacteria grown under conditions of low osmolarity accumulate significant amounts of periplasmic glucans, membrane-derived oligosaccharides (MDO) in Escherichia coli and cyclic glucans in members of the family Rhizobiaceae. It was reported previously (W. Fiedlder and H. Rotering, J. Biol. Chem. 263:14684-14689, 1988) that mdoA mutants unable to synthesize MDO show a number of altered phenotypes, among them a decreased expression of OmpF and an increased expression of OmpC, when grown in a Bacto Peptone medium of low osmolarity and low ionic strength. Although we confirm the findings of Fiedler and Rotering, we find that the regulation of OmpF and OmpC expression in mdoA mutants is normal in cells grown on other low-osmolarity media, eliminating the possibility that MDO itself might control porin expression. Our data suggest that a certain minimal ionic strength in the periplasm is needed for normal porin regulation. In media containing very low levels of salt, this may be contributed by anionic MDO.
The subtilin gene of Bacillus subtilis ATCC 6633 is encoded in an operon that contains a homolog of the hemolysin B transport protein
Authors: Chung Y J , Steen M T , Hansen J N
Published: November 2016

Sequence analysis upstream from the subtilin structural gene (spaS) in Bacillus subtilis ATCC 6633 revealed several open reading frames, SpaB, SpaC, and SpaD. SpaB, consisting of 599 amino acid residues, shows excellent homology with a variety of membrane translocator proteins, such as HlyB from Escherichia coli and some mammalian multidrug resistance proteins. When the spaB gene was interrupted by integration of a chloramphenicol acetyltransferase gene, the ability of the cell to produce subtilin, as determined by a halo assay, was lost. The homology of SpaB to translocator proteins, including transmembrane and ATP-binding regions, suggests that SpaB may play a role in subtilin secretion. The SpaB open reading frame overlaps with another open reading frame called SpaC, and the possibility that the SpaB and SpaC proteins become fused by frameshifting is considered. Regions of homology between SpaD (177 residues) and HlyD were also found, suggesting that SpaD may participate with SpaB in translocation of subtilin through the membrane. Although no readily interpretable homologies to SpaC (442 residues) were found, its sequence suggests that it is membrane associated. The absence of rho-independent transcription terminators between these open reading frames suggests that they are all part of the same operon.
Identification of intrinsic high-level resistance to rare-earth oxides and oxyanions in members of the class Proteobacteria: characterization of tellurite, selenite, and rhodium sesquioxide reduction in Rhodobacter sphaeroides
Authors: Moore M D , Kaplan S
Published: November 2016

We have identified intrinsic high-level resistance (HLR) to tellurite, selenite, and at least 15 other rare-earth oxides and oxyanions in the facultative photoheterotroph Rhodobacter sphaeroides grown either chemoheterotrophically or photoheterotrophically. Other members of the class Proteobacteria, including members of the alpha-2 and alpha-3 phylogenetic subgroups, were also shown to effect the reduction of many of these compounds, although genera from the alpha-1, beta-1, and gamma-3 subgroups did not express HLR to the oxyanions examined. Detailed analyses employing R. sphaeroides have shown that HLR to at least one class of these oxyanions, the tellurite class (e.g., tellurate, tellurite, selenate, selenite, and rhodium sesquioxide), occurred via intracellular oxyanion reduction and resulted in deposition of metal in the cytoplasmic membrane. The concomitant evolution of hydrogen gas from cells grown photoheterotrophically in the presence of these oxyanions was also observed. HLR to tellurite class oxyanions in R. sphaeroides was not affected by exogenous methionine or phosphate but was reduced 40-fold by the addition of cysteine to growth media. In contrast HLR to the periodate class oxyanions (e.g., periodate, siliconate, and siliconite) was inhibited by extracellular PO4(3-) but did not result in metal deposition or gas evolution. Finally, we observed that HLR to arsenate class oxyanions (e.g., arsenate, molybdate, and tungstate) occurred by a third, distinct mechanism, as evidenced by the lack of intracellular metal deposition and hydrogen gas evolution and an insensitivity to extracellular PO4(3-) or cysteine. Examination of a number of R. sphaeroides mutants has determined the obligate requirement for an intact CO2 fixation pathway and the presence of a functional photosynthetic electron transport chain to effect HLR to K2TeO3 under photosynthetic growth conditions, whereas functional cytochromes bc1 and c2 were required under aerobic growth conditions to facilitate HLR. Finally, a purification scheme to recover metals from intact bacterial cells was developed.
Evidence for a new, oxygen-regulated biosynthetic pathway for the pyrimidine moiety of thiamine in Salmonella typhimurium
Authors: Downs D M
Published: November 2016

The synthesis of the pyrimidine moiety of thiamine (vitamin B1) shares five reactions with the de novo purine biosynthetic pathway. Aminoimidazole ribotide (AIR) is the last common intermediate before the two pathways diverge. Evidence for the existence of a new pathway to the pyrimidine which bypasses the de novo purine biosynthetic pathway is reported here. This pathway is only expressed under anaerobic growth conditions and is denoted alternative pyrimidine biosynthesis or APB. Labeling studies are consistent with pantothenate being a precursor to the pyrimidine moiety of thiamine that is synthesized by the APB pathway. The APB pathway is independent of the alternative purF function which was proposed previously (D. M. Downs and J. R. Roth, J. Bacteriol. 173:6597-6604, 1991). The alternative purF function is shown here to be affected by temperature and exogenous pantothenate. Although the evidence suggests that the APB pathway is separate from the alternative purF function, the relationship between this function and the APB pathway is not yet clear.
Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon
Authors: Takiff H E , Baker T , Copeland T , Chen S M , Court D L
Published: November 2016

The mini-Tn10 transposon (delta 16 delta 17Tn10) confers tetracycline resistance. When inserted between a gene and its promoter, it blocks transcription and prevents expression of that gene. Tetracycline in the medium induces divergent transcription of the tetA and tetR genes within the transposon, and this transcription extends beyond the transposon in both directions into the bacterial genes. If the mini-Tn10 inserts between an essential bacterial gene and its promoter, the insertion mutation can cause conditional growth which is dependent on the presence of tetracycline. Two essential genes in adjacent operons of Escherichia coli have been detected by screening for tetracycline dependence among tetracycline-resistant insertion mutants. These essential genes are the era gene in the rnc operon and the dpj gene in the adjacent pdxJ operon. The pdxJ operon has not been described previously. It consists of two genes, pdxJ and dpj. Whereas the dpj gene is essential for E. coli growth in all media tested, pdxJ is not essential. The pdxJ gene encodes a protein required in the biosynthesis of pyridoxine (vitamin B6).
A BlnI restriction map of the Salmonella typhimurium LT2 genome
Authors: Wong K K , McClelland M
Published: November 2016

BlnI or AvrII (5'-CCTAGG) sites are very rare in the Salmonella typhimurium LT2 genome. BlnI was used to construct a physical map which was correlated with the genetic map by using three methods. First, Tn10 carries BlnI sites, and the extra restriction sites produced by 34 genetically mapped Tn10 insertions were physically mapped by using pulsed-field gel electrophoresis. Second, six genetically mapped Mud-P22 prophage insertions were used to assign BlnI fragments. Integration of Mud-P22 introduces 30 kb of DNA that can easily be detected by a "shift up" in all but the largest BlnI fragments. Finally, induced Mud-P22 insertions package more than 100 kb of genomic DNA adjacent to one side of the insertion. Some of the smaller BlnI fragments were localized by hybridization to a dot blot array of 52 lysates from induced Mud-P22 insertions. Of the 10 BlnI sites mapped, 6 probably occur in or near the 16S rRNA genes at about 55, 71, 83, 86, 88.5, and 89.5 min. There is one BlnI site in the 90-kb pSLT plasmid. Two additional BlnI fragments of about 7 and 4 kb have not been localized. The size of the genome was estimated as 4.78 Mb (+/- 0.1 Mb) excluding pSLT but including prophages Fels-1 and Fels-2. One BlnI fragment that maps between 55 and 59 min showed a 40-kb reduction in size in a strain cured of the approximately 40-kb Fels-2 prophage.
Rapid mapping in Salmonella typhimurium with Mud-P22 prophages
Authors: Benson N R , Goldman B S
Published: November 2016

A new method for mapping mutations in the Salmonella typhimurium chromosome is described and applied to the localization of novel regulatory mutations affecting expression of the nirB (nitrite reductase) gene. The mapping technique is also illustrated by the mapping of mutations in genes affecting carbohydrate catabolism and biosynthetic pathways. The new mapping method involves use of the hybrid phage MudP and MudQ (together referred to as Mud-P22), originally constructed by Youderian et al. (Genetics 118:581-592, 1988). This report describes a set of Mud-P22 lysogens, each member of the set containing a different Mud-P22 insertion. The insertions are scattered along the entire Salmonella genome. These lysogens, when induced by mitomycin C, generate transducing lysates that are enriched (45- to 1,400-fold over the background, generalized transducing particle population) for transducing particles containing bacterial DNA that flanks one side of the insertion. We demonstrate that within the set of lysogens there can be found at least one Mud-P22 insertion that enriches for any particular region of the Salmonella chromosome and that, therefore, all regions of the chromosome are discretely enriched and represented by the collection as a whole. We describe a technique that allows the rapid and facile determination of which lysate contains enriched sequences for the repair of a mutant locus, thereby allowing the determination of the map position of the locus. This technique is applicable to those mutations for which the wild-type allele is selectable. We also describe a procedure whereby any Tn10 insertion can be mapped by selecting for the loss of Tetr.
Identification of the pheS5 mutation, which causes thermosensitivity of Escherichia coli mutant NP37
Authors: Kast P , Keller B , Hennecke H
Published: November 2016

The pheS5 mutation responsible for the thermosensitive phenylalanyl-tRNA synthetase of the classical Escherichia coli NP37 was cloned by a recombination event and identified by DNA sequence analysis. The mutation was subsequently verified by direct sequencing of amplified NP37 DNA generated by an asymmetric polymerase chain reaction. The resulting amino acid exchange, Gly-98 to Asp-98 in the phenylalanyl-tRNA synthetase alpha subunit, might cause subunit disaggregation due to electrostatic repulsion.
Isolation and sequence analysis of dacB, which encodes a sporulation-specific penicillin-binding protein in Bacillus subtilis
Authors: Buchanan C E , Ling M L
Published: November 2016

A novel penicillin-binding protein (PBP 5*) with D,D-carboxypeptidase activity is synthesized by Bacillus subtilis, beginning at about stage III of sporulation. The complete gene (dacB) for this protein was cloned by immunoscreening of an expression vector library and then sequenced. The identity of dacB was verified not only by the size and cross-reactivity of its product but also by the presence of the nucleotide sequence that coded for the independently determined NH2 terminus of PBP 5*. Analysis of its complete amino acid sequence confirmed the hypothesis that this PBP is related to other active-site serine D,D-peptidases involved in bacterial cell wall metabolism. PBP 5* had the active-site domains common to all PBPs, as well as a cleavable amino-terminal signal peptide and a carboxy-terminal membrane anchor that are typical features of low-molecular-weight PBPs. Mature PBP 5* was 355 amino acids long, and its mass was calculated to be 40,057 daltons. What is unique about this PBP is that it is developmentally regulated. Analysis of the sequence provided support for the hypothesis that the sporulation specificity and mother cell-specific expression of dacB can be attributed to recognition of the gene by a sporulation-specific sigma factor. There was a good match of the putative promoter of dacB with the sequence recognized by sigma factor E (sigma E), the subunit of RNA polymerase that is responsible for early mother cell-specific gene expression during sporulation. Analysis of PBP 5* production by various spo mutants also suggested that dacB expression is on a sigma E-dependent pathway.
Streptococcus pneumoniae DNA polymerase I lacks 3'-to-5' exonuclease activity: localization of the 5'-to-3' exonucleolytic domain
Authors: Diaz A , Pons M E , Lacks S A , Lopez P
Published: November 2016

The Streptococcus pneumoniae polA gene was altered at various positions by deletions and insertions. The polypeptides encoded by these mutant polA genes were identified in S. pneumoniae. Three of them were enzymatically active. One was a fused protein containing the first 11 amino acid residues of gene 10 from coliphage T7 and the carboxyl-terminal two-thirds of pneumococcal DNA polymerase I; it possessed only polymerase activity. The other two enzymatically active proteins, which contained 620 and 351 amino acid residues from the amino terminus, respectively, lacked polymerase activity and showed only exonuclease activity. These two polymerase-deficient proteins and the wild-type protein were hyperproduced in Escherichia coli and purified. In contrast to the DNA polymerase I of Escherichia coli but similar to the corresponding enzyme of Thermus aquaticus, the pneumococcal enzyme appeared to lack 3'-to-5' exonuclease activity. The 5'-to-3' exonuclease domain was located in the amino-terminal region of the wild-type pneumococcal protein. This exonuclease activity excised deoxyribonucleoside 5'-monophosphate from both double- and single-stranded DNAs. It degraded oligonucleotide substrates to a decameric final product.
Identification of two iron-repressed periplasmic proteins in Haemophilus influenzae
Authors: Harkness R E , Chong P , Klein M H
Published: November 2016

Protein expression by Haemophilus influenzae under iron-limiting growth conditions was examined. The five type b strains and four nontypeable strains studied all expressed a new protein of about 40 kDa when deprived of iron during growth. Most strains also expressed a protein of about 31 kDa under the same growth conditions. Both the 40- and 31-kDa proteins were not expressed by cells grown in iron-replete medium. The 40- and 31-kDa proteins were not expressed in iron-deficient medium to which an excess of ferric nitrate had been added, and therefore it was concluded that their expression was iron regulated. These iron-repressed proteins were localized to the periplasmic space. The amino-terminal sequences of both proteins were determined. The N-terminal sequence of the 40-kDa protein had 81% similarity to the N terminus of Fbp, the major iron-binding protein of Neisseria gonorrhoeae and N. meningitidis. The 31-kDa protein sequence showed no homology with any known protein sequence. As no plasmids were found in the strains, it was concluded that these proteins were chromosomally encoded.
Role of the rfaG and rfaP genes in determining the lipopolysaccharide core structure and cell surface properties of Escherichia coli K-12
Authors: Parker C T , Kloser A W , Schnaitman C A , Stein M A , Gottesman S , Gibson B W
Published: November 2016

Deletions which removed rfa genes involved in lipopolysaccharide (LPS) core synthesis were constructed in vitro and inserted into the chromosome by linear transformation. The deletion delta rfa1, which removed rfaGPBI, resulted in a truncated LPS core containing two heptose residues but no hexose and a deep rought phenotype including decreased expression of major outer membrane proteins, hypersensitivity to novobiocin, and resistance to phage U3. In addition, delta rfa1 resulted in the loss of flagella and pili and a mucoid colony morphology. Measurement of the synthesis of beta-galactosidase from a cps-lacZ fusion showed that the mucoid phenotype was due to rcsC-dependent induction of colanic acid capsular polysaccharide synthesis. Complementation of delta rfa1 with rfaG+ DNA fragments resulted in a larger core and restored the synthesis of flagella and pili but did not reverse the deep rough phenotype or the induction of cps-lacZ, while complementation with a fragment carrying only rfaP+ reversed the deep rough phenotype but not the loss of flagella and pili. A longer deletion which removed rfaQGPBIJ was also constructed, and complementation studies with this deletion showed that the product of rfaQ was not required for the functions of rfaG and rfaP. Thus, the function of rfaQ remains unknown. Tandem mass spectrometric analysis of LPS core oligosaccharides from complemented delta rfa1 strains indicated that rfaP+ was necessary for the addition of either phosphoryl (P) or pyrophosphorylethanolamine (PPEA) substituents to the heptose I residue, as well as for the partial branch substitution of heptose II by heptose III. The substitution of heptose II is independent of the type of P substituent present on heptose I, and this results in four different core structures. A model is presented which relates the deep rough phenotype to the loss of heptose-linked P and PPEA.
Production of a conserved adhesin by the human gastroduodenal pathogen Helicobacter pylori
Authors: Doig P , Austin J W , Kostrzynska M , Trust T J
Published: November 2016

An adhesin protein with an approximate subunit molecular weight of 19,600 has been purified from the gastric pathogen Helicobacter pylori. The protein was loosely associated with the cell surface and was removed by gentle stirring or shearing. Released aggregates of the 19.6-kDa protein were removed from suspension by ultracentrifugation and separated from contaminating membranes by washing in 1.0% sodium dodecyl sulfate (SDS). The SDS-insoluble protein was purified further by Mono Q anion-exchange column chromatography. Electron microscopy of the purified adhesin demonstrated that it formed amorphous aggregates similar to the material attached to the bacterial cells and that the aggregates were morphologically distinct from typical fimbriae. Western blot (immunoblot) analysis with antiserum raised against the purified protein from one strain reacted with a protein with a similar subunit molecular weight present in all nine strains of H. pylori examined, but the protein was not present in other Helicobacter species examined. The N-terminal sequences of the 19.6-kDa protein purified from three different strains of H. pylori were identical for the first 28 amino acids, with the 10 amino-terminal residues showing limited sequence homology with the TcpA pilus protein of Vibrio cholerae. The H. pylori 19.6-kDa protein associated both with human and rabbit erythrocytes and with human buccal epithelial cells. Polystyrene microspheres coated with the protein agglutinated human, horse, and rabbit erythrocytes, suggesting that this protein species could mediate adhesion between H. pylori and eucaryotic cells. This ability to act as an adhesin may make this protein an important virulence factor for H. pylori and hence a potential target for a vaccine and therapy.
Ty insertions upstream and downstream of native DUR1,2 promoter elements generate different patterns of DUR1,2 expression in Saccharomyces cerevisiae
Authors: Chisholm G E , Cooper T G
Published: November 2016

Expression of allantoin pathway genes is subject to induction and nitrogen catabolite repression. Two classes of cis-dominant mutations (DUR80 and DUR1,2-Oh) result in overproduction of DUR1,2 mRNA. In DUR80 mutants, DUR1,2 expression remained inducible, nitrogen catabolite repression sensitive, and unresponsive to cell ploidy, i.e., overproduction was superimposed on normal gene regulation. DUR1,2-Oh mutations, in contrast, generated a pattern of DUR1,2 expression similar to that often reported when a Ty element inserts upstream of a gene, the ROAM phenotype. We analyzed four independent DUR80 and DUR1,2-Oh alleles. The DUR1,2-Oh mutation was, as expected, a Ty insertion at -445 3' of the native DUR1,2 upstream activation sequences (UASs). All three DUR80 alleles were also Ty insertions between -644 and -653 immediately 5' of the native DUR1,2 USASs. We suggest that the difference in DUR1,2-Oh and DUR80 phenotypes depends on whether the native cis-acting elements and transcription factors associated with them can operate. If they can, enhancement of normally regulated DUR1,2 expression is observed. This is a novel phenotype for Ty insertions. If the native DUR1,2 cis-acting elements are not present, the case when Ty insertion occurs 3' of them, a ROAM phenotype is generated. Nitrogen-regulated upstream activation sequence (UASNTR)-homologous sequences present in the Ty delta elements rather than cis-acting elements required for Ty transcription are the most likely candidates to serve as the cis-acting elements mediating the DUR80 phenotype.
Characterization of enzymatic synthesis of sphingolipid long-chain bases in Saccharomyces cerevisiae: mutant strains exhibiting long-chain-base auxotrophy are deficient in serine palmitoyltransferase activity
Authors: Pinto W J , Wells G W , Lester R L
Published: November 2016

We have begun a biochemical-genetic analysis of the synthesis of sphingolipid long-chain bases in Saccharomyces cerevisiae and found evidence for the occurrence of serine palmitoyltransferase (SPT) and 3-ketosphinganine reductase, enzymes that catalyze the initial steps of the pathway in other organisms. SPT activity was demonstrated in vitro with crude membrane preparations from S. cerevisiae as judged by the formation of radiolabeled 3-ketosphinganine from the condensation of palmitoyl-coenzyme A (CoA) with radiolabeled serine. Shorter (C12 and C14) and longer (C18) acyl-CoAs sustain significant SPT activity, a result consistent with the finding of both C18 and C20 long-chain bases in the organism. Three products of the long-chain-base synthetic pathway, 3-ketosphinganine, erythrosphinganine, and phytosphingosine, neither directly inhibited the reaction in vitro nor affected the specific activity of the enzyme when these bases were included in the culture medium of wild-type cells. Thus, no evidence for either feedback inhibition or repression of enzyme synthesis could be found with these putative effectors. Mutant strains of S. cerevisiae that require a sphingolipid long-chain base for growth fall into two genetic complementation groups, LCB1 and LCB2. Membrane preparations from both lcb1 and lcb2 mutant strains exhibited negligible SPT activity when tested in vitro. Step 2 of the long-chain-base synthetic pathway was demonstrated by the stereospecific NADPH-dependent reduction of 3-ketosphinganine to erythrosphinganine. Membranes isolated from wild-type cells and from an lcb1 mutant exhibited substantial 3-ketosphinganine reductase activity. We conclude that the Lcb- phenotype of these mutants results from a missing or defective SPT, an activity controlled by both the LCB1 and LCB2 genes. These results and earlier work from this laboratory establish that SPT plays an essential role in sphingolipid synthesis in S. cerevisiae.
Sequence analysis and complementation studies of the argJ gene encoding ornithine acetyltransferase from Neisseria gonorrhoeae
Authors: Martin P R , Mulks M H
Published: November 2016

Clinical isolates of Neisseria gonorrhoeae frequently are deficient in arginine biosynthesis. These auxotrophs often have defects in the fifth step of the arginine biosynthetic pathway, the conversion of acetylornithine to ornithine. This reaction is catalyzed by the enzyme ornithine acetyltransferase, which is a product of the argJ gene. We have cloned and sequenced the gonococcal argJ gene and found that it contains an open reading frame of 1,218 nucleotides and encodes a peptide with a deduced Mr of 42,879. This predicted size was supported by minicell analysis. This gene was capable of complementing both Escherichia coli argE and argA mutations and of transforming an ArgJ- strain of N. gonorrhoeae to Arg+. Southern blots were able to detect bands that specifically hybridized to the gonococcal argJ gene in genomic DNA from Pseudomonas aeruginosa but not E. coli, a result that reflects the divergent nature of the arginine biosynthetic pathway in these organisms.
The ntrA gene of Agrobacterium tumefaciens: identification, cloning, and phenotype of a site-directed mutant
Authors: Wu Z L , Charles T C , Wang H , Nester E W
Published: November 2016

A 3.6-kb EcoRI fragment containing the ntrA gene of Agrobacterium tumefaciens was cloned by using the homologous ntrA gene of Rhizobium meliloti as a probe. Construction of an ntrA mutant of A. tumefaciens by site-directed insertional mutagenesis demonstrated the requirement of the ntrA gene for nitrate utilization and C4-dicarboxylate transport but not for vir gene expression or tumorigenesis.
Purification of the DNA-dependent RNA polymerase from the myxobacterium Stigmatella aurantiaca
Authors: Heidelbach M , Skladny H , Schairer H U
Published: November 2016

The DNA-dependent RNA polymerase (EC 2.7.7.6) of the myxobacterium Stigmatella aurantiaca has been purified. It shows three main polypeptide bands with apparent molecular weights of 146,000, 105,000, and 40,000 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. beta and beta' subunits of the S. aurantiaca polymerase were shown to migrate in the 146,000-molecular-weight polypeptide band and the main sigma factor was shown to migrate in the 105,000-molecular-weight band by using heterologous antisera.
Biologically Active Secondary Metabolites from the Fungi
Authors: Bills Gerald F. , Gloer James B.
Published: November 2016

Many Fungi have a well-developed secondary metabolism. The diversity of fungal species and the diversification of biosynthetic gene clusters underscores a nearly limitless potential for metabolic variation and an untapped resource for drug discovery and synthetic biology. Much of the ecological success of the filamentous fungi in colonizing the planet is owed to their ability to deploy their secondary metabolites in concert with their penetrative and absorptive mode of life. Fungal secondary metabolites exhibit biological activities that have been developed into life-saving medicines and agrochemicals. Toxic metabolites, known as mycotoxins, contaminate human and livestock food and indoor environments. Secondary metabolites are determinants of fungal diseases of humans, animals, and plants. Secondary metabolites exhibit a staggering variation in chemical structures and biological activities, yet their biosynthetic pathways share a number of key characteristics. The genes encoding cooperative steps of a biosynthetic pathway tend to be located contiguously on the chromosome in coregulated gene clusters. Advances in genome sequencing, computational tools, and analytical chemistry are enabling the rapid connection of gene clusters with their metabolic products. At least three fungal drug precursors, penicillin K and V, mycophenolic acid, and pleuromutilin, have been produced by synthetic reconstruction and expression of respective gene clusters in heterologous hosts. This review summarizes general aspects of fungal secondary metabolism and recent developments in our understanding of how and why fungi make secondary metabolites, how these molecules are produced, and how their biosynthetic genes are distributed across the Fungi. The breadth of fungal secondary metabolite diversity is highlighted by recent information on the biosynthesis of important fungus-derived metabolites that have contributed to human health and agriculture and that have negatively impacted crops, food distribution, and human environments.
Complement Receptors in Myeloid Cell Adhesion and Phagocytosis
Authors: Dustin Michael L.
Published: November 2016

Myeloid cells make extensive use of the complement system in the context of recruitment, phagocytosis, and other effector functions. There are several types of complement receptors on myeloid cells, including G protein-coupled receptors for localizing the source of complement activation, and three sets of type I transmembrane proteins that link complement to phagocytosis: complement receptor 1, having an extracellular domain with tandem complement regulatory repeats; complement receptors 3 and 4, which are integrin family receptors comprising heterodimers of type I transmembrane subunits; and VSIG4, a member of the Ig superfamily. This review will focus on the role of the different classes of complement receptors and how their activities are integrated in the setting of immune tolerance and inflammatory responses.
ImmunoglobuliNin theTreatment ofEncephalitis (IgNiTE): protocol for a multicentre randomised controlled trial
Authors: Iro M A , Sadarangani M , Absoud M , Chong W K , Clark C A , Easton A , Gray V , Kneen R , Lim M , Pike M , Solomon T , Vincent A , Willis L , Yu L-M , Pollard A J
Published: November 2016

Introduction

Infectious and immune-mediated encephalitides are important but under-recognised causes of morbidity and mortality in childhood, with a 7% death rate and up to 50% morbidity after prolonged follow-up. There is a theoretical basis for ameliorating the immune response with intravenous immunoglobulin (IVIG), which is supported by empirical evidence of a beneficial response following its use in the treatment of viral and autoimmune encephalitis. In immune-mediated encephalitis, IVIG is often used after a delay (by weeks in some cases), while diagnosis is confirmed. Wider use of IVIG in infectious encephalitis and earlier use in immune-mediated encephalitis could improve outcomes for these conditions. We describe the protocol for the first ever randomised control trial of IVIG treatment for children with all-cause encephalitis.

Methods and analysis

308 children (6 months to 16 years) with a diagnosis of acute/subacute encephalitis will be recruited in ∼30 UK hospitals and randomised to receive 2 doses (1 g/kg/dose) of either IVIG or matching placebo, in addition to standard treatment. Recruitment will be over a 42-month period and follow-up of each participant will be for 12 months post randomisation. The primary outcome is ‘good recovery’ (score of 2 or lower on the Glasgow Outcome Score Extended—paediatric version), at 12 months after randomisation. Additional secondary neurological measures will be collected at 4–6 weeks after discharge from acute care and at 6 and 12 months after randomisation. Safety, radiological, other autoimmune and tertiary outcomes will also be assessed.

Ethics and dissemination

This trial has been approved by the UK National Research Ethics committee (South Central—Oxford A; REC 14/SC/1416). Current protocol: V4.0 (10/03/2016). The findings will be presented at national and international meetings and conferences and published in peer-reviewed journals.

Trial registration numbers

NCT02308982, EudraCT201400299735 andISRCTN15791925; Pre-results.
Which cuff should I use? Indirect blood pressure measurement for the diagnosis of hypertension in patients with obesity: a diagnostic accuracy review
Authors: Irving Greg , Holden John , Stevens Richard , McManus Richard J
Published: November 2016

Objective

To determine the diagnostic accuracy of different methods of blood pressure (BP) measurement compared with reference standards for the diagnosis of hypertension in patients with obesity with a large arm circumference.

Design

Systematic review with meta-analysis with hierarchical summary receiver operating characteristic models. Bland-Altman analyses where individual patient data were available. Methodological quality appraised using Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS2) criteria.

Data sources

MEDLINE, EMBASE, Cochrane, DARE, Medion and Trip databases were searched.

Eligibility criteria

Cross-sectional, randomised and cohort studies of diagnostic test accuracy that compared any non-invasive BP tests (upper arm, forearm, wrist, finger) with an appropriate reference standard (invasive BP, correctly fitting upper arm cuff, ambulatory BP monitoring) in primary care were included.

Results

4037 potentially relevant papers were identified. 20 studies involving 26 different comparisons met the inclusion criteria. Individual patient data were available from 4 studies. No studies satisfied all QUADAS2 criteria. Compared with the reference test of invasive BP, a correctly fitting upper arm BP cuff had a sensitivity of 0.87 (0.79 to 0.93) and a specificity of 0.85 (0.64 to 0.95); insufficient evidence was available for other comparisons to invasive BP. Compared with the reference test of a correctly fitting upper arm cuff, BP measurement at the wrist had a sensitivity of 0.92 (0.64 to 0.99) and a specificity of 0.92 (0.85 to 0.87). Measurement with an incorrectly fitting standard cuff had a sensitivity of 0.73 (0.67 to 0.78) and a specificity of 0.76 (0.69 to 0.82). Measurement at the forearm had a sensitivity of 0.84 (0.71 to 0.92) and a specificity 0.75 of (0.66 to 0.83). Bland-Altman analysis of individual patient data from 3 studies comparing wrist and upper arm BP showed a mean difference of 0.46 mm Hg for systolic BP measurement and 2.2 mm Hg for diastolic BP measurement.

Conclusions

BP measurement with a correctly fitting upper arm cuff is sufficiently sensitive and specific to diagnose hypertension in patients with obesity with a large upper arm circumference. If a correctly fitting upper arm cuff cannot be applied, an incorrectly fitting standard size cuff should not be used and BP measurement at the wrist should be considered.
Using a simple point-prevalence survey to define appropriate antibiotic prescribing in hospitalised children across the UK
Authors: Gharbi Myriam , Doerholt Katja , Vergnano Stefania , Bielicki Julia Anna , Paulus Stéphane , Menson Esse , Riordan Andrew , Lyall Hermione , Patel Sanjay Valabh , Bernatoniene Jolanta , Versporten Ann , Heginbothom Maggie , Goossens Herman , Sharland Mike
Published: November 2016

Background

The National Health Service England, Commissioning for Quality and Innovation for Antimicrobial Resistance (CQUIN AMR) aims to reduce the total antibiotic consumption and the use of certain broad-spectrum antibiotics in secondary care. However, robust baseline antibiotic use data are lacking for hospitalised children. In this study, we aim to describe, compare and explain the prescription patterns of antibiotics within and between paediatric units in the UK and to provide a baseline for antibiotic prescribing for future improvement using CQUIN AMR guidance.

Methods

We conducted a cross-sectional study using a point prevalence survey (PPS) in 61 paediatric units across the UK. The standardised study protocol from the Antibiotic Resistance and Prescribing in European Children (ARPEC) project was used. All inpatients under 18 years of age present in the participating hospital on the day of the study were included except neonates.

Results

A total of 1247 (40.9%) of 3047 children hospitalised on the day of the PPS were on antibiotics. The proportion of children receiving antibiotics showed a wide variation between both district general and tertiary hospitals, with 36.4% ( 95% CI 33.4% to 39.4%) and 43.0% (95% CI 40.9% to 45.1%) of children prescribed antibiotics, respectively. About a quarter of children on antibiotic therapy received either a medical or surgical prophylaxis with parenteral administration being the main prescribed route for antibiotics (>60% of the prescriptions for both types of hospitals). General paediatrics units were surprisingly high prescribers of critical broad-spectrum antibiotics, that is, carbapenems and piperacillin-tazobactam.

Conclusions

We provide a robust baseline for antibiotic prescribing in hospitalised children in relation to current national stewardship efforts in the UK. Repeated PPS with further linkage to resistance data needs to be part of the antibiotic stewardship strategy to tackle the issue of suboptimal antibiotic use in hospitalised children.
Beam–beam and electron cloud effects in CEPC/FCC-ee
Authors: Ohmi Kazuhito
Published: November 2016

We discuss beam dynamics issues in CEPC/FCC-ee, especially focusing on the beam–beam and electron cloud effects. Beamstrahlung is strong in extreme high energy collision such as Higgs and top factory. Beam–beam simulations considering beamstrahlung are now ready. Several points of beam–beam effects for FCC-ee are presented. Electron cloud effects are serious for high current positron machine, especially in Z factory that many bunches are stored. Analytical estimate for threshold of electron density and electron build-up for CEPC are presented.
CEPC partial double ring scheme and crab-waist parameters
Authors: Wang Dou , Gao Jie , Su Feng , Zhang Yuan , Zhai Jiyuan , Wang Yiwei , Bai Sha , Geng Huiping , Bian Tianjian , Cui Xiaohao , Wang Na , Duan Zhe , Guo Yuanyuan , Qin Qing
Published: November 2016

In order to avoid the pretzel orbit, CEPC is proposed to use partial double ring scheme in CDR. In this paper, a general method of how to make an consistent machine parameter design of CEPC with crab-waist by using analytical expression of maximum beam–beam tune shift and beamstrahlung beam lifetime started from given IP vertical beta, beam power and other technical limitations were developed. FFS with crab sextupoles will be developed and the arc lattice will be redesigned to acheive the lower emittance for crab-waist scheme.
Design Exploration of mm-Wave Integrated Transceivers for Short-Range Mobile Communications Towards 5G
Authors: Saponara Sergio , Giannetti Filippo , Neri Bruno
Published: November 2016

This paper presents a design exploration, at both system and circuit levels, of integrated transceivers for the upcoming fifth generation (5G) of wireless communications. First, a system level model for 5G communications is carried out to derive transceiver design specifications. Being 5G still in pre-standardization phase, a few currently used standards (ECMA-387, IEEE 802.15.3c, and LTE-A) are taken into account as the reference for the signal format. Following a top-down flow, this work presents the design in 65[Formula: see text]nm CMOS SOI and bulk technologies of the key blocks of a fully integrated transceiver: low noise amplifier (LNA), power amplifier (PA) and on-chip antenna. Different circuit topologies are presented and compared allowing for different trade-offs between gain, power consumption, noise figure, output power, linearity, integration cost and link performance. The best configuration of antenna and LNA co-design results in a peak gain higher than 27[Formula: see text]dB, a noise figure below 5[Formula: see text]dB and a power consumption of 35[Formula: see text]mW. A linear PA design is presented to face the high Peak to Average Power Ratio (PAPR) of multi-carrier transmissions envisaged for 5G, featuring a 1[Formula: see text]dB compression point output power (OP1dB) of 8.2[Formula: see text]dBm. The delivered output power in the linear region can be increased up to 13.2[Formula: see text]dBm by combining four basic PA blocks through a Wilkinson power combiner/divider circuit. The proposed circuits are shown to enable future 5G connections, operating in a mm-wave spectrum range (spanning 9[Formula: see text]GHz, from 57[Formula: see text]GHz to 66[Formula: see text]GHz), with a data-rate of several Gb/s in a short-range scenario, spanning from few centimeters to tens of meters.