bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of context preexposure and delay until anxiety retrieval on generalization of contextual anxiety
Authors: Andreatta Marta , Neueder Dorothea , Glotzbach-Schoon Evelyn , Mühlberger Andreas , Pauli Paul
Published: December 2016

Animal studies suggest that time delay between acquisition and retrieval of contextual anxiety increases generalization. Moreover, such generalization is prevented by preexposure to the context (CTX), presumably due to an improved representation of such context. We investigated whether preexposure and time-passing modulate generalization of contextual anxiety, in humans. On Day 1, 42 participants (preexposure group) explored two virtual offices, while 41 participants (no-preexposure group) explored a virtual stadium. On Day 2 (24 h later), all participants learned to associate one office (CTX+) with unpredictable unconditioned stimuli (USs), and another office (CTX−) with safety. On Day 3, either 24 h (recent test) or 2 wk (remote test) later, participants revisited CTX− and CTX+ without USs, as well as a generalization context (G-CTX). Results revealed successfully conditioned anxiety and anxiety generalization for ratings (G-CTX was as aversive as CTX+ was), while safety generalization was found for startle responses (G-CTX elicited startle attenuation as CTX− did). Time between learning and testing enhanced generalization as reflected by comparable startle responses to all three offices in the remote test. Contextual preexposure facilitated extinction of explicit conditioned anxiety assessed with ratings. These results suggest that memory trace of a context degrades with passage of time in humans like in animals and, consequently, anxiety generalization enhances. After context preexposure, high cognitive processes seem to be crucially involved in facilitating extinction (or safety) learning.
A novel, potentially targetable TMEM106B-BRAF fusion in pleomorphic xanthoastrocytoma
Authors: Hsiao Susan J. , Karajannis Matthias A. , Diolaiti Daniel , Mansukhani Mahesh M. , Bender Julia Glade , Kung Andrew L. , Garvin James H.
Published: December 2016

Pleomorphic xanthoastrocytoma (PXA) is a World Health Organization (WHO) Grade II glioma occurring primarily in children and young adults. Most PXAs harbor the known activating mutation BRAF V600E. We report a case of locally recurrent PXA with anaplastic features in a 10-yr-old female. The PXA was negative by immunohistochemical (IHC) staining for BRAF V600E mutation. Whole-exome and transcriptome sequencing of the tumor confirmed the absence of BRAF V600E, but identified copy-number alterations (including loss of the tumor suppressor CDKN2A) and a novel TMEM106B-BRAF fusion. Based on similar BRAF fusion proteins, this novel fusion is predicted to result in activation of BRAF signaling. Demonstration of positive IHC for phospho-ERK1/2 and phospho-MEK1/2 supported this prediction, and implicated MEK inhibitors as a potential therapeutic strategy.
Uridine as a new scavenger for synchrotron-based structural biology techniques
Authors: Crosas Eva , Castellvi Albert , Crespo Isidro , Fulla Daniel , Gil-Ortiz Fernando , Fuertes Gustavo , Kamma-Lorger Christina S. , Malfois Marc , Aranda Miguel A. G. , Juanhuix Jordi
Published: December 2016

Macromolecular crystallography (MX) and small-angle X-ray scattering (SAXS) studies on proteins at synchrotron light sources are commonly limited by the structural damage produced by the intense X-ray beam. Several effects, such as aggregation in protein solutions and global and site-specific damage in crystals, reduce the data quality or even introduce artefacts that can result in a biologically misguiding structure. One strategy to reduce these negative effects is the inclusion of an additive in the buffer solution to act as a free radical scavenger. Here the properties of uridine as a scavenger for both SAXS and MX experiments on lysozyme at room temperature are examined. In MX experiments, upon addition of uridine at 1 M, the critical dose D
1/2 is increased by a factor of ∼1.7, a value similar to that obtained in the presence of the most commonly used scavengers such as ascorbate and sodium nitrate. Other figures of merit to assess radiation damage show a similar trend. In SAXS experiments, the scavenging effect of 40 mM uridine is similar to that of 5% v/v glycerol, and greater than 2 mM DTT and 1 mM ascorbic acid. In all cases, the protective effect of uridine is proportional to its concentration.
Crystal structure ofmeso-di-μ-chlorido-bis[bis(2,2′-bipyridine)cadmium] bis(1,1,3,3-tetracyano-2-ethoxypropenide) 0.81-hydrate
Authors: Setifi Fatima , Morgenstern Bernd , Hegetschweiler Kaspar , Setifi Zouaoui , Touzani Rachid , Glidewell Christopher
Published: December 2016

The hydrated title salt, [Cd2Cl2(C10H8N2)4](C9H5N4O)2·0.81H2O, was obtained from the hydrothermal reaction between 2,2′-bipyridine, cadmium(II) chloride and potassium 1,1,3,3-tetracyano-2-ethoxypropenide. The binuclear cation lies across a centre of inversion in the space groupP21/c, with the other components in general positions. The cation has approximate, but non-crystallographic 2/msymmetry and each of the CdIIatoms is a stereogenic centre, one having the Δ configuration and the other the Λ configuration. In the anion, one of the C(CN)2units is disordered over two sets of atomic sites having occupancies 0.75 (2) and 0.25 (2). The cations are linked by two independent C—H...Cl hydrogen bonds to form a sheet ofR22(14) andR42(24) rings.
1,4-Bis{5-[bis(propan-2-yloxy)phosphoryl]thiophen-2-yl}-2,5-dipropoxybenzene
Authors: Detert Heiner , Schollmeyer Dieter
Published: December 2016

The title compound, C32H48O8P2S2, was prepared by the nickel-catalyzed reaction of bis(5-bromothienyl)dipropoxybenzene and triisopropyl phosphite. The thiophene rings are inclined to the benzene ring by 14.6 (2) and 25.3 (3)°. One propyloxy group is disordered. Four hydrogen bonds connect the molecules, which are arranged in ribbons parallel to thebcplane.
Tris(6-tert-butyl-4-methylpyridazine-3-thiolato-κ2N,S)aluminium
Authors: Holler Stefan , Belaj Ferdinand , Mösch-Zanetti Nadia C.
Published: December 2016

The title complex, [Al(C9H13N2S)3], is composed of an aluminium atom coordinated by three bidentate thiopyridazine ligands in an octahedral environment. It has approximateC3symmetry, with Al—N distances in the range 1.9732 (17)–1.9794 (17) Å and three Al—S distances in the range 2.3961 (8)–2.4354 (8) Å. In the crystal, there are no significant intermolecular interactions present.
Estimation of a growth factor for achieve scalability in ad hoc networks
Authors: Ospina Juan Pablo , Ortiz Triviño Jorge Eduardo
Published: December 2016

Given the fact that the ad hoc networks with flat architectures are not scalable, this study focuses on determining the conditions to guarantee the scalability in a hierarchical architecture based on the resources availability in the different layers of the network. A model based on the truncated geometric distribution that allows to characterize the available resources in an ad hoc network was proposed. Starting by this characterization, the concept of growth factor j was introduced as a constant value that represents the appropriate relationship among the available resources in two successive layers of the network to ensure scalability. Simulation scenarios were explored to develop the estimation process of the growth factor j in ad hoc networks of two and three-layer hierarchical architectures in the software ns-3. The results showed that the growth of resources between layers in an ad hoc network can be expressed through a linear model. Also, a relation was found between the estimated value of j and the golden ratio as a way to inspire the design of artificial system based on the attributes that can be found in nature. 
Review Article: Recommended reading list of early publications on atomic layer deposition—Outcome of the “Virtual Project on the History of ALD”
Authors: Ahvenniemi Esko , Akbashev Andrew R. , Ali Saima , Bechelany Mikhael , Berdova Maria , Boyadjiev Stefan , Cameron David C. , Chen Rong , Chubarov Mikhail , Cremers Veronique , Devi Anjana , Drozd Viktor , Elnikova Liliya , Gottardi Gloria , Grigoras Kestutis , Hausmann Dennis M. , Hwang Cheol Seong , Jen Shih-Hui , Kallio Tanja , Kanervo Jaana , Khmelnitskiy Ivan , Kim Do Han , Klibanov Lev , Koshtyal Yury , Krause A. Outi I. , Kuhs Jakob , Kärkkänen Irina , Kääriäinen Marja-Leena , Kääriäinen Tommi , Lamagna Luca , Łapicki Adam A. , Leskelä Markku , Lipsanen Harri , Lyytinen Jussi , Malkov Anatoly , Malygin Anatoly , Mennad Abdelkader , Militzer Christian , Molarius Jyrki , Norek Małgorzata , Özgit-Akgün Çağla , Panov Mikhail , Pedersen Henrik , Piallat Fabien , Popov Georgi , Puurunen Riikka L. , Rampelberg Geert , Ras Robin H. A. , Rauwel Erwan , Roozeboom Fred , Sajavaara Timo , Salami Hossein , Savin Hele , Schneider Nathanaelle , Seidel Thomas E. , Sundqvist Jonas , Suyatin Dmitry B. , Törndahl Tobias , van Ommen J. Ruud , Wiemer Claudia , Ylivaara Oili M. E. , Yurkevich Oksana
Published: December 2016

Atomic layer deposition (ALD), a gas-phase thin film deposition technique based on repeated, self-terminating gas–solid reactions, has become the method of choice in semiconductor manufacturing and many other technological areas for depositing thin conformal inorganic material layers for various applications. ALD has been discovered and developed independently, at least twice, under different names: atomic layer epitaxy (ALE) and molecular layering. ALE, dating back to 1974 in Finland, has been commonly known as the origin of ALD, while work done since the 1960s in the Soviet Union under the name “molecular layering” (and sometimes other names) has remained much less known. The virtual project on the history of ALD (VPHA) is a volunteer-based effort with open participation, set up to make the early days of ALD more transparent. In VPHA, started in July 2013, the target is to list, read and comment on all early ALD academic and patent literature up to 1986. VPHA has resulted in two essays and several presentations at international conferences. This paper, based on a poster presentation at the 16th International Conference on Atomic Layer Deposition in Dublin, Ireland, 2016, presents a recommended reading list of early ALD publications, created collectively by the VPHA participants through voting. The list contains 22 publications from Finland, Japan, Soviet Union, United Kingdom, and United States. Up to now, a balanced overview regarding the early history of ALD has been missing; the current list is an attempt to remedy this deficiency.
Microstructure-dependent thermoelectric properties of polycrystalline InGaO3(ZnO)2 superlattice films
Authors: Cho Sung Woon , Baek Seung Ki , Kim Da Eun , Kim Yunseok , Cho Hyung Koun
Published: December 2016

The authors fabricated polycrystalline InGaO3(ZnO)m superlattices with different degrees of c-axis-preferred orientation and grain sizes using atomic layer deposition (ALD)-grown zinc oxide (ZnO) buffer layers to introduce nanometer-scale grains and modulate the thermoelectric properties. The ALD-grown ZnO buffer layer facilitates crystallization of solution-processed amorphous indium gallium zinc oxide (InGaZnO) films into an InGaO3(ZnO)2 superlattice film, acting as a preferential seed layer to reduce the lattice mismatch between InGaO3(ZnO)2 nuclei and the sapphire substrate. Thus, the preferential orientation of the ZnO buffer layer dramatically influenced the final microstructure of the polycrystalline InGaO3(ZnO)m superlattice films. The c-axis-preferred orientation and grain size in the ALD-grown polycrystalline ZnO buffer layer can be easily controlled by varying the growth temperature. The ZnO buffer layer with a superior c-axis-preferred orientation produced a polycrystalline InGaO3(ZnO)2 film consisting of InGaO3(ZnO)2 grains with a strong c-axis-preferred orientation. Interestingly, it showed dramatically reduced thermal conductivity (0.61 W/m K) compared to randomly oriented poly- and single-crystalline InGaO3(ZnO)2 films (>1 W/m K) owing to effective phonon–interface and phonon–grain boundary scattering by the well-ordered alternating stacking structure and introduced grain boundaries.
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
Authors: Liu S. John , Horlbeck Max A. , Cho Seung Woo , Birk Harjus S. , Malatesta Martina , He Daniel , Attenello Frank J. , Villalta Jacqueline E. , Cho Min Y. , Chen Yuwen , Mandegar Mohammad A. , Olvera Michael P. , Gilbert Luke A. , Conklin Bruce R. , Chang Howard Y. , Weissman Jonathan S. , Lim Daniel A.
Published: December 2016

A very focused function for lncRNAs

The human genome generates many thousands of long noncoding RNAs (lncRNAs). A very small number of lncRNAs have been shown to be functional. Liu
et al.
carried out a large-scale CRISPR-based screen to assess the function of ∼17,000 lncRNAs in seven different human cell lines. A considerable number (∼500) of the tested lncRNAs influenced cell growth, suggesting biological function. In almost all cases, though, the function was highly cell type—specific, often limited to just one cell type.

Science
, this issue p.
10.1126/science.aah7111
Purification of nitrogen regulator II, the product of the glnL (ntrB) gene of Escherichia coli
Authors: Ninfa A J , Ueno-Nishio S , Hunt T P , Robustell B , Magasanik B
Published: December 2016

We purified the product of glnL (ntrB), NRII, and the product of a mutant glnL allele, NRII2302. In vitro transcription of the nitrogen-regulated promoter glnAp2 by purified components of Escherichia coli required NRII or NRII2302 when the template DNA was linear.
Partition functions of unit-copy plasmids can stabilize the maintenance of plasmid pBR322 at low copy number
Authors: Austin S , Friedman S , Ludtke D
Published: December 2016

The maintenance of plasmid pBR322 is highly unstable in a polA12 strain of Escherichia coli at 29 degrees C due to severely reduced copy number. Under these conditions, introduction of the par (partition) locus of plasmid P1 or the par (sop) region of F into pBR322 stabilizes it. A region with similar activity was detected in the P7 plasmid. The activity of the P1 par locus was dependent on the P1 parA gene product and was sensitive to par-specified incompatibility.
Translational coupling in Escherichia coli of a heterologous Bacillus subtilis-Escherichia coli gene fusion
Authors: Zaghloul T I , Doi R H
Published: December 2016

The efficient expression in Escherichia coli of the Tn9-derived chloramphenicol acetyltransferase (EC 2.3.1.28) gene fused distal to the promoter and N terminus of the Bacillus subtilis aprA gene was dependent on the initiation of translation from the ribosome-binding site in the aprA gene.
DNA replication termination in Escherichia coli parB (a dnaG allele), parA, and gyrB mutants affected in DNA distribution
Authors: Norris V , Alliotte T , Jaffé A , D'Ari R
Published: December 2016

We investigated the Escherichia coli mutants carrying the parB, parA, and gyrB mutations, all of which display faulty chromosome partitioning at the nonpermissive temperature, to see whether their phenotype reflected a defect in the termination of DNA replication. In the parB strain DNA synthesis slowed down at 42 degrees C and the SOS response was induced, whereas in the parA strain DNA synthesis continued normally for 120 min and there was no SOS induction. To see whether replication forks accumulated in the vicinity of terC at the nonpermissive temperature, the mutants were incubated for 60 min at 42 degrees C and then returned to low temperature and pulse-labeled with [3H]thymidine. In all cases the restriction pattern of the labeled DNA was incompatible with that of the terC region, suggesting that replication termination was normal. In the parA mutant no DNA sequences were preferentially labeled, whereas in the parB and gyrB strains there was specific labeling of sequences whose restriction pattern resembled that of oriC. In the case of parB this was confirmed by DNA-DNA hybridization with appropriate probes. This test further revealed that the parB mutant over initiates at oriC after the return to the permissive temperature. Like dna(Ts) strains, the parB mutant formed filaments at 42 degrees C in the absence of SOS-associated division inhibition, accompanied by the appearance of anucleate cells of nearly normal size (28% of the population after 3 h), as revealed by autoradiography. The DNA in the filaments was either centrally located or distributed throughout. The parB mutation lies at 67 min, and the ParB- phenotype is corrected by a cloned dnaG gene or by a plasmid primase, strongly suggesting that parB is an allele of dnaG, the structural gene of the E. coli primase. It is thus likely that the parB mutant possesses an altered primase which does not affect replication termination but causes a partial defect in replication initiation and elongation and in chromosome distribution.
New locus (ttr) in Escherichia coli K-12 affecting sensitivity to bacteriophage T2 and growth on oleate as the sole carbon source
Authors: Morona R , Henning U
Published: December 2016

The nature of resistance to phage T2 in Escherichia coli K-12 was investigated by analyzing a known phage T2-resistant mutant and by isolating new T2-resistant mutants. It was found that mutational alterations at two loci, ompF (encoding the outer membrane protein OmpF) and ttr (T-two resistance), are needed to give full resistance to phage T2. A ttr::Tn10 mutation was isolated and was mapped between aroC and dsdA, where the fadL gene (required for long-chain fatty acid transport) is located. The receptor affected by ttr was the major receptor used by phage T2 and was located in the outer membrane. Phage T2 was thus able to use two outer membrane proteins as receptors. All strains having a ttr::Tn10 allele and most of the independently isolated phage T2-resistant mutants were unable to grow on oleate as the sole carbon and energy source, i.e., they had the phenotype of fadL mutants. The gene fadL is known to encode an inner membrane protein. The most likely explanation is that fadL and ttr are in an operon and that ttr encodes an outer membrane protein which functions in translocating long-chain fatty acids across the outer membrane and also as a receptor for phage T2.
Characterization of a manganese-containing catalase from the obligate thermophile Thermoleophilum album
Authors: Allgood G S , Perry J J
Published: December 2016

A manganese-containing catalase has been characterized from Thermoleophilum album NM, a gram-negative aerobic bacterium obligate for thermophily and n-alkane substrates. The level of catalase in cells was increased about ninefold by growth in the presence of paraquat (2.5 microM), a superoxide-generating toxicant. Superoxide dismutase levels were unaffected by this compound. The enzyme was purified from cultures grown in the presence of paraquat to greater than 95% homogeneity and had an Mr of 141,000. The enzyme was composed of four subunits, and each had an Mr of 34,000. There were 1.4 +/- 0.4 atoms of manganese present per subunit. The catalase had a Km for hydrogen peroxide of 15 mM and a Vmax of 11 mM/mg. Peroxidase activity, as measured with p-phenylenediamine, copurified with the catalase. Inhibitors of heme-catalase were weak inhibitors of the T. album enzyme. The optimum pH for catalase activity was 8 to 9. The enzyme was stable from pH 6.5 to 11 and retained activity at assay temperatures from 25 to 80 degrees C. The catalase was stable for 24 h of incubation at 60 degrees C.
Extracellular RNase produced by Yarrowia lipolytica
Authors: Cheng S C , Ogrydziak D M
Published: December 2016

Production of extracellular RNase(s) by Yarrowia lipolytica CX161-1B was examined in media between pHs 5 and 7. RNase production occurred during the exponential growth phase. High-molecular-weight nitrogen compounds supported the highest levels of RNase production. Several RNases were detected in the supernatant medium. Based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the RNases had estimated molecular weights of 45,000, 43,000, and 34,000. It was found that Y. lipolytica secretes only one RNase (the 45,000-molecular-weight RNase) and that the 43,000 and 34,000-molecular-weight RNases are degradation products of this RNase. The alkaline extracellular protease secreted by Y. lipolytica was shown to have a major role in the 45,000- to 43,000-molecular-weight conversion, and it was demonstrated that the 45,000-molecular-weight RNase could be purified from a mutant which does not produce the alkaline extracellular protease. Purification of the RNase from a wild-type strain resulted in purification of the 43,000-molecular-weight RNase. This RNase was a glycoprotein with a molecular weight of 44,000 as estimated by gel filtration, an isoelectric point of pH 4.8, and a pH optimum between 6.5 and 7.0.
Structure of two pectate lyase genes from Erwinia chrysanthemi EC16 and their high-level expression in Escherichia coli
Authors: Keen N T , Tamaki S
Published: December 2016

The pelB and pelE genes from Erwinia chrysanthemi EC16, which encode different pectate lyase enzymes, were sequenced and expressed at a high level in Escherichia coli. The genes possessed little similarity to each other in 5' signal regions, signal peptide sequences, coding sequences, or 3' noncoding regions. Both genes contained their own promoters as well as sequences 3' to the coding regions with considerable secondary structure which may function as rho-independent transcriptional termination signals. High-level expression plasmids were constructed with both genes, which led to 20% or more of E. coli cellular protein. The pectate lyases were secreted efficiently to the periplasm and, to a lesser extent, the culture medium. The mature proteins in E. coli periplasmic fractions were obtained in milligram amounts and high purity with a single-column affinity purification method. E. coli cells which produced high amounts of the pelE protein macerated potato tuber tissue as efficiently as E. chrysanthemi EC16 cells but cells producing high amounts of the pelB protein were less effective. Thus, the pelE gene product is an important pathogenicity factor which solely enables E. coli to cause a soft-rot disease on potato tuber tissue under laboratory conditions.
Cloning and regulation of Erwinia herbicola pigment genes
Authors: Perry K L , Simonitch T A , Harrison-Lavoie K J , Liu S T
Published: December 2016

The genes coding for yellow pigment production in Erwinia herbicola Eho10 (ATCC 39368) were cloned and localized to a 12.4-kilobase (kb) chromosomal fragment. A 2.3-kb AvaI deletion in the cloned fragment resulted in the production of a pink-yellow pigment, a possible precursor of the yellow pigment. Production of yellow pigment in both E. herbicola Eho10 and pigmented Escherichia coli clones was inhibited by glucose. When the pigment genes were transformed into a cya (adenylate cyclase) E. coli mutant, no expression was observed unless exogenous cyclic AMP was provided, which suggests that cyclic AMP is involved in the regulation of pigment gene expression. In E. coli minicells, the 12.4-kb fragment specified the synthesis of at least seven polypeptides. The 2.3-kb AvaI deletion resulted in the loss of a 37K polypeptide and the appearance of a polypeptide of 40 kilodaltons (40K polypeptide). The synthesis of the 37K polypeptide, which appears to be required for yellow pigment production, was not repressed by the presence of glucose in the culture medium, as was the synthesis of other polypeptides specified by the 12.4-kb fragment, suggesting that there are at least two types of gene regulation involved in yellow pigment synthesis. DNA hybridization studies indicated that different yellow pigment genes exist among different E. herbicola strains. None of six pigmented plant pathogenic bacteria examined, Agrobacterium tumefaciens C58, Cornyebacterium flaccumfaciens 1D2, Erwinia rubrifaciens 6D364, Pseudomonas syringae ATCC 19310, Xanthomonas campestris 25D11, and "Xanthomonas oryzae" 17D54, exhibited homology with the cloned pigment genes.
Molecular cloning of virulence genes from Erwinia stewartii
Authors: Coplin D L , Frederick R D , Majerczak D R , Haas E S
Published: December 2016

A library of Erwinia stewartii DNA was constructed in cosmid pVK100 and used to complement spontaneous and Mu pf7701-induced (designated by the prefix MU) avirulent mutants. Plasmid pES4507 restored water-soaking ability and extracellular polysaccharide (EPS) synthesis to mutants MU14110 and MU2B70 (group I); pES1044 restored water-soaking ability to MU43, MU51, MU136, MU141, and RDF6011 (group II); and pES2144 complemented four spontaneous EPS- mutants (group III). Hybridization of labeled plasmid DNA to Southern blots of genomic DNA from the mutants revealed that a Mu pf7701 insertion was associated with the respective cloned region in all mutants except MU2B70 and MU223. In these strains, the plasmid may be suppressing the avirulent phenotype rather than complementing the mutation.
Heat production by ruminal bacteria in continuous culture and its relationship to maintenance energy
Authors: Russell J B
Published: December 2016

Selenomonas ruminantium HD4 and Bacteroides ruminicola B(1)4 were grown in continuous culture with glucose as the energy source, and heat production was measured continuously with a microcalorimeter. Because the bacteria were grown under steady-state conditions, it was possible to calculate complete energy balances for substrate utilization and product formation (cells, fermentation acids, and heat). As the dilution rate increased from 0.04 to 0.60 per h, the heat of fermentation declined from 19 to 2% and from 34 to 8% for S. ruminantium and B. ruminicola, respectively. At slow dilution rates the specific rate of heat production remained relatively constant (135 mW/g [dry weight] or 190 mW/g of protein for S. ruminantium and 247 mW/g [dry weight] or 467 mW/g of protein for B. ruminicola). Since the heat due to growth-related functions was small compared to maintenance expenditures, total heat production provided a reasonable estimate of maintenance under glucose-limiting conditions. As the dilution rate was increased, glucose eventually accumulated in the chemostat vessel and the specific rates of heat production increased more than twofold. Pulses of glucose added to glucose-limited cultures (0.167 per h) caused an immediate doubling of heat production and little increase in cell protein. These experiments indicate that bacterial maintenance energy is not necessarily a constant and that energy source accumulation was associated with an increase in heat production.
Biosynthesis of enterobacterial common antigen requires dTDPglucose pyrophosphorylase determined by a Salmonella typhimurium rfb gene and a Salmonella montevideo rfe gene
Authors: Lew H C , Mäkelä P H , Kuhn H M , Mayer H , Nikaido H
Published: December 2016

In group C1 salmonellae, rfe and rff genes linked to the ilv locus specify the synthesis of a glycolipid called the enterobacterial common antigen. In contrast, in group B salmonellae the synthesis requires in addition some of the genes in the rfb cluster, the main genetic determinant of the O side chains of lipopolysaccharide. In an effort to define the biochemical functions of these rfb genes, we looked in Salmonella typhimurium LT2 (group B) for rfb mutants in which the synthesis of both enterobacterial common antigen and the O side chains would be blocked in a manner suppressible by the wild-type rfe cluster of S. montevideo, of group C1. We found one mutant with these characteristics. This rfb mutation affected the activity of dTDPglucose pyrophosphorylase (glucose-1-phosphate thymidylyltransferase, EC 2.7.7.24). Whereas the rfe cluster of S. montevideo contained a gene producing this enzyme activity, there was no evidence for the presence of such a gene in the rfe cluster of group B strains. These results also showed that the synthesis of dTDP-glucose is necessary for the biosynthesis of enterobacterial common antigen; this conclusion fits with the recent demonstration of 4-acetamido-4,6-dideoxy-D-galactose as a component of enterobacterial common antigen (Lugowski et al., Carbohydr. Res. 118:173-181, 1983), because the biosynthesis of the donor of this sugar, dTDP-4-acetamido-4,6-dideoxy-D-galactose, requires dTDPglucose pyrophosphorylase.
Transport and hydrolysis of disaccharides by Trichosporon cutaneum
Authors: Mörtberg M , Neujahr H Y
Published: December 2016

Trichosporon cutaneum is shown to utilize six disaccharides, cellobiose, maltose, lactose, sucrose, melibiose, and trehalose. T. cutaneum can thus be counted with the rather restricted group of yeasts (11 to 12% of all investigated) which can utilize lactose and melibiose. The half-saturation constants for uptake were 10 +/- 3 mM sucrose or lactose and 5 +/- 1 mM maltose, which is of the same order of magnitude as those reported for Saccharomyces cerevisiae. Our results indicate that maltose shares a common transport system with sucrose and that there may be some interaction between the uptake systems for lactose, cellobiose, and glucose. Lactose, cellobiose, and melibiose are hydrolyzed by cell wall-bound glycosidase(s), suggesting hydrolysis before or in connection with uptake. In contrast, maltose, sucrose, and trehalose seem to be taken up as such. The uptake of sucrose and lactose is dependent on a proton gradient across the cell membrane. In contrast, there were no indications of the involvement of gradients of H+, K+, or Na+ in the uptake of maltose. The uptake of lactose is to a large extent inducible, as is the corresponding glycosidase. Also the glycosidases for cellobiose, trehalose, and melibiose are inducible. In contrast, the uptake of sucrose and maltose and the corresponding glycosidases is constitutive.
Location of epitopes on Campylobacter jejuni flagella
Authors: Logan S M , Trust T J
Published: December 2016

Flagella were isolated from strains of Campylobacter jejuni belonging to different heat-labile serogroups and from a strain of Campylobacter fetus, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed that the flagellin molecular weights (Mr) were approximately 62,000. The flagellins were cleaved by hydrolysis with cyanogen bromide, and sodium dodecyl sulfate-urea peptide gel electrophoresis showed that the C. jejuni flagellins were structurally similar, and differed from C. fetus flagellin. Immunochemical analysis by Western blotting, enzyme-linked immunosorbent assay, immune electron microscopy, and immunoprecipitation with polyclonal and monoclonal antibodies revealed the presence of both internal and surface-exposed epitopes. The internal epitopes were antigenically cross-reactive and linear, and in the case of C. jejuni flagellin were located on cyanogen bromide peptides of apparent Mr 22,400 and 11,000. Antigenically cross-reactive epitopes were also present on an Mr 43,000 cyanogen bromide peptide of C. fetus flagellin. The Mr 22,400 peptide of C. jejuni VC74 flagellin also carried closely positioned internal linear epitopes for two monoclonal antibodies. One epitope was strain specific, while the other was shared by some but not all Campylobacter flagellins. The flagella of C. jejuni VC74 also displayed both surface-exposed antigenically cross-reactive and surface-exposed serospecific epitopes. Both linear and conformational epitopes contributed to the serospecificity of C. jejuni VC74 flagella, and a linear serospecific epitope was located on a cyanogen bromide peptide of apparent Mr 4,000.
Mapping and cloning of a fla-che region of the Rhizobium meliloti chromosome
Authors: Ziegler R J , Peirce C , Bergman K
Published: December 2016

We constructed a genetic map of the fla-che region of the Rhizobium meliloti chromosome using cotransduction with bacteriophage phi M12. Several other chromosomal markers located in the general area are included in the map. We isolated plasmids carrying wild-type DNA inserts that complement the mapped mutations from a genomic library carried in the broad-host-range vector pLAFR1. The complementation data obtained from the clones confirmed the contransduction map and clarified the exact order of several of the behavioral genes. A restriction map of this area was developed by using the cloned DNA. One of the five individual EcoRI fragments subcloned from the original clones complemented two of the behavioral mutations.
Colonial heterogeneity of Thiobacillus versutus
Authors: Claassen P A , Kortstee G J , Oosterveld-van Vliet W M , van Neerven A R
Published: December 2016

In acetate-limited chemostat cultures started with single-colony cultures of Thiobacillus versutus, a mutant appeared after approximately 85 volume changes. The inhomogeneity of the culture was detected by the development of two different types of colonies on agar plates. When a pure culture of the mutant was grown in a chemostat, parent colonies appeared after almost the same period of time. Electron micrographs of the mutant grown on butyrate showed the presence of fibrils surrounding the cells. The cells of the parent strain were bald when grown under the same conditions. The growth kinetics of the parent and the mutant were investigated in batch cultures with a variety of substrates and were found to be identical. Major differences between the two strains were observed during growth on mannitol; the mutant attained a lower yield and excreted large amounts of extracellular polysaccharides.
Effects of nucleotides on ATP-dependent protein translocation into Escherichia coli membrane vesicles
Authors: Chen L , Tai P C
Published: December 2016

We have shown previously that Escherichia coli can translocate the same protein either co- or posttranslationally and that ATP hydrolysis is essential for the posttranslational translocation of the precursors of alkaline phosphatase and OmpA protein into inverted E. coli membrane vesicles. ATP-dependent protein translocation has now been further characterized. In the absence of exogenous Mg2+, dATP, formycin A-5'-triphosphate, ATP-alpha-S, and N1-oxide-ATP could replace ATP, but many other nucleotides were not only ineffective but inhibited ATP-dependent translocation. The inhibitors included nonhydrolyzable ATP analogs, ATP-gamma-S, 8-azido-ATP, AMP, ADP, cyclic AMP, PPi, and tripolyphosphate. On the other hand, adenosine, adenosine 5'-tetraphosphate, and N1,N6-etheno-ATP neither supported nor inhibited translocation. Moreover, photoaffinity labeling of azido-adenine nucleotides rendered membranes inactive for subsequent ATP-dependent protein translocation. These results suggest that protein translocation involves at least an ATP-binding site in the membrane and hydrolysis of ATP and that both the adenosine and phosphate moieties of ATP play a role.
Characterization of a cloned Bacillus subtilis gene that inhibits sporulation in multiple copies
Authors: Gaur N K , Dubnau E , Smith I
Published: December 2016

We have isolated a 1.0-kilobase fragment of the Bacillus subtilis chromosome which, when present in high-copy-number plasmids, caused a sporulation-proficient strain to become phenotypically sporulation deficient. This is referred to as the sporulation inhibition (Sin) phenotype. This DNA fragment, in multicopy, also inhibited the production of extracellular protease activity, which normally appears at the beginning of stationary growth. The origin of the fragment was mapped between the dnaE and spo0A genes on the B. subtilis chromosome, and its complete DNA sequence has been determined. By analysis of various deletions and a spontaneous mutant the Sin function was localized to an open reading frame (ORF) predicted from the DNA sequence. Inactivation of this ORF in the chromosome did not affect the ability of cells to sporulate. However, the late-growth-associated production of proteases and alpha-amylase was elevated in these cells. The predicted amino acid sequence of the protein encoded by this ORF had a DNA-binding domain, typically present in several regulatory proteins. We propose that the sin ORF encodes a regulatory protein that is involved in the transition from vegetative growth to sporulation.
Location of functional regions of the Escherichia coli RecA protein by DNA sequence analysis of RecA protease-constitutive mutants
Authors: Wang W B , Tessman E S
Published: December 2016

In previous work (E. S. Tessman and P. K. Peterson, J. Bacteriol. 163:677-687 and 688-695, 1985), we isolated many novel protease-constitutive (Prtc) recA mutants, i.e., mutants in which the RecA protein was always in the protease state without the usual need for DNA damage to activate it. Most Prtc mutants were recombinase positive and were designated Prtc Rec+; only a few Prtc mutants were recombinase negative, and those were designated Prtc Rec-. We report changes in DNA sequence of the recA gene for several of these mutants. The mutational changes clustered at three regions on the linear RecA polypeptide. Region 1 includes amino acid residues 25 through 39, region 2 includes amino acid residues 157 through 184, and region 3 includes amino acid residues 298 through 301. The in vivo response of these Prtc mutants to different effectors suggests that the RecA effector-binding sites have been altered. In particular we propose that the mutations may define single-stranded DNA- and nucleoside triphosphate-binding domains of RecA, that polypeptide regions 1 and 3 comprise part of the single-stranded DNA-binding domain, and that polypeptide regions 2 and 3 comprise part of the nucleoside triphosphate-binding domain. The overlapping of single-stranded DNA- and nucleoside triphosphate-binding domains in region 3 can explain previously known complex allosteric effects. Each of four Prtc Rec- mutants sequenced was found to contain a single amino acid change, showing that the change of just one amino acid can affect both the protease and recombinase activities and indicating that the functional domains for these two activities of RecA overlap. A recA promoter-down mutation was isolated by its ability to suppress the RecA protease activity of one of our strong Prtc mutants.
Isolation of a Fusarium solani mutant reduced in cutinase activity and virulence
Authors: Dantzig A H , Zuckerman S H , Andonov-Roland M M
Published: December 2016

Fusarium solani isolate T-8 produces an extracellular enzyme, cutinase, which catalyzes the degradation of cutin in the plant cuticle. Cutinase activity can be measured by the hydrolysis of either the artifical substrate, p-nitrophenylbutyrate (PNB), or radioactive cutin containing [14C]palmitic acid. In the present study, the culture filtrate contained basal levels of cutinase when T-8 was grown on acetate as a sole source of carbon. After mutagenesis, a cutinase-defective mutant (PNB-1) was identified by screening acetate-grown colonies for a loss of PNBase activity. The mutant possessed an 80 to 90% reduction in cutinase activity when grown for 3 to 5 days on acetate- or cutin-containing medium. Induction of cutinase by cutin or hydrolyzed cutin after growth on glucose medium was similarly reduced. Kinetic analysis indicated that cutinase from the mutant possessed a near normal Km for PNB and a 92% reduction in Vmax. Fluorography and Western blotting of 15% sodium dodecyl sulfate-polyacrylamide gels of separated 35S-labeled proteins from cutin induction medium revealed that in the mutant the 22,000-molecular-weight band corresponding to cutinase was reduced approximately 85%. The virulence of the mutant in a pea stem bioassay was decreased by 55% and was restored to nearly the parental level by the addition of purified cutinase. The data suggest that the mutant synthesizes reduced quantities of a functional and immunoreactive cutinase enzyme and that cutinase plays a critical role in infection. The PNB1 mutation may be within a regulatory gene or a promoter for cutinase.
Glucose represses formation of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine and isopenicillin N synthase but not penicillin acyltransferase in Penicillium chrysogenum
Authors: Revilla G , Ramos F R , López-Nieto M J , Alvarez E , Martín J F
Published: December 2016

The content of alpha-aminoadipyl-cysteinyl-valine, the first intermediate of the penicillin biosynthetic pathway, decreased when Penicillium chrysogenum was grown in a high concentration of glucose. Glucose repressed the incorporation of [14C]valine into alpha-aminoadipyl-cysteinyl-[14C]valine in vivo. The pool of alpha-aminoadipic acid increased sevenfold in control (lactose-grown) penicillin-producing cultures, coinciding with the phase of rapid penicillin biosynthesis, but this increase was very small in glucose-grown cultures. Glucose stimulated homocitrate synthase and saccharopine dehydrogenase activities in vivo and increased the incorporation of lysine into proteins. These results suggest that glucose stimulates the flux through the lysine biosynthetic pathway, thus preventing alpha-aminoadipic acid accumulation. The repression of alpha-aminoadipyl-cysteinyl-valine synthesis by glucose was not reversed by the addition of alpha-aminoadipic acid, cysteine, or valine. Glucose also repressed isopenicillin N synthase, which converts alpha-aminoadipyl-cysteinyl-valine into isopenicillin N, but did not affect penicillin acyltransferase, the last enzyme of the penicillin biosynthetic pathway.
Association between Dietary Inflammatory Index (DII) and risk of prediabetes: a case-control study
Authors: Vahid Farhad , Shivappa Nitin , Karamati Mohsen , Naeini Alireza Jafari , Hebert James R. , Davoodi Sayed Hossein
Published: December 2016

The possible relationship between diet-related inflammation and the risk of prediabetes requires further investigation, especially in non-Western populations. We examined the ability of the dietary inflammatory index (DII) to predict the risk of prediabetes in a case-control study conducted at specialized centers in Esfahan, Iran. A total of 214 incident cases of prediabetes were selected with the nonrandom sampling procedure, and the 200 controls randomly selected from the same clinics were frequency-matched on age (±5 years) and sex. DII scores were computed based on dietary intake assessed using a validated and reproducible 168-item food-frequency questionnaire. Linear and logistic regression models were used to estimate multivariable beta estimates and odds ratios (ORs). Subjects in tertile 3 versus tertile 1 (T3VS1) of DII had significantly higher fasting plasma glucose (DIIT3VS1: b = 4.49; 95% CI 1.89, 7.09), oral glucose tolerance (DIIT3VS1: b = 8.76; 95% CI 1.78, 15.73), HbA1c (DIIT3VS1: b = 0.30; 95% CI 0.17, 0.42), low-density lipoprotein (DIIT3VS1: b = 16.37; 95% CI 11.04, 21.69), triglyceride (DIIT3VS1: b = 21.01; 95% CI 8.61, 33.42) and body fat (DIIT3VS1: b = 2.41; 95% CI 0.56, 4.26) and lower high-density lipoprotein (DIIT3VS1: b = −3.39; 95% CI −5.94, −0.84) and lean body mass (DIIT3VS1: b = −3.11; 95% CI −4.83, −1.39). After multivariate adjustment, subjects in the most pro-inflammatory DII group had 19 times higher odds of developing prediabetes compared with subjects in tertile 1 (DIIT3VS1: OR = 18.88; 95% CI 7.02, 50.82). Similar results were observed when DII was used as a continuous variable, (DIIcontinuous: OR = 3.62; 95% CI 2.50, 5.22). Subjects who consumed a more pro-inflammatory diet were at increased risk of prediabetes compared with those who consumed a more anti-inflammatory diet.
Protective effects of essential oil of Citrus limon against aspirin-induced toxicity in IEC-6 cells
Authors: Bouzenna Hafsia , Hfaiedh Najla , Giroux-Metges Marie-Agnès , Elfeki Abdelfattah , Talarmin Hélène
Published: December 2016

Aspirin, one of the widely used nonsteroidal anti-inflammatory drugs, is the most highly consumed pharmaceutical product in the world. However, it has several side effects in cells. This study was designed to investigate the antioxidative activity and cytoprotective effects of essential oil of Citrus limon (EOC) extracted from leaves against aspirin-induced damages in the rat small intestine epithelial cells (IEC-6). Biochemical indicators were used to assess cytotoxicity and oxidative damages caused by aspirin treatment on IEC-6. Our results showed that the chemical characterization of EOC identified 25 compounds representing 98.19% of the total oil. The major compounds from this oil were z-citral (53.21%), neryl acetate (13.06%), geranyl acetate (10.33%), and limonene (4.23%). Aspirin induced a decrease in cell viability as well as an increase in superoxide dismutase (SOD) and catalase (CAT) activities. Contrariwise, the co-exposure of cells to aspirin and EOC alleviated every above syndrome by an increase in cell survival and decrease in SOD and CAT activities. In conclusion, the essential oil of C. limon has a potent cytoprotective effect against aspirin-induced toxicity in IEC-6 cells.
Automatic Business Process Test Case Selection: Coverage Metrics, Algorithms, and Performance Optimizations
Authors: Böhmer Kristof , Rinderle-Ma Stefanie
Published: December 2016

Business processes describe and implement the business logic of companies, control human interaction, and invoke heterogeneous services during runtime. Therefore, ensuring the correct execution of processes is crucial. Existing work is addressing this challenge through process verification. However, the highly dynamic aspects of the current processes and the deep integration and frequent invocation of third party services limit the use of static verification approaches. Today, one frequently utilized approach to address this limitation is to apply process tests. However, the complexity of process models is steadily increasing. So, more and more test cases are required to assure process model correctness and stability during design and maintenance. But executing hundreds or even thousands of process model test cases lead to excessive test suite execution times and, therefore, high costs. Hence, this paper presents novel coverage metrics along with a genetic test case selection algorithm. Both enable the incorporation of user-driven test case selection requirements and the integration of different knowledge sources. In addition, techniques for test case selection computation performance optimization are provided and evaluated. The effectiveness of the presented genetic test case selection algorithm is evaluated against five alternative test case selection algorithms.
Nonlinear Dynamic Thermal Buckling of Sandwich Spherical and Conical Shells with CNT Reinforced Facesheets
Authors: Sankar A. , Natarajan S. , Merzouki T. , Ganapathi M.
Published: December 2016

Owing to their superior mechanical and thermal properties, carbon nanotube (CNT) reinforced composite materials have wide range of applications in various technical areas such as aerospace, automobile, chemical, structural and energy. In this paper, the nonlinear axisymmetric dynamic behavior of sandwich spherical and conical shells made up of CNT reinforced facesheets is studied. The shell is subjected to thermal loads and discretized with three-noded axisymmetric curved shell element based on field consistency approach. The in-plane and the rotary inertia effects are included within the transverse shear deformation theory in the element formulation. The present model is validated with the available analytical solutions from the literature. A detailed parametric study is carried out to showcase the effects of the shell geometry, the volume fraction of the CNT, the core-to-face sheet thickness and the environment temperature on the dynamic buckling thermal load of spherical caps.
Protocols for quantum binary voting
Authors: Thapliyal Kishore , Sharma Rishi Dutt , Pathak Anirban
Published: December 2016

Two new protocols for quantum binary voting are proposed. One of the proposed protocols is designed using a standard scheme for controlled deterministic secure quantum communication (CDSQC), and the other one is designed using the idea of quantum cryptographic switch, which uses a technique known as permutation of particles. A few possible alternative approaches to accomplish the same task (quantum binary voting) have also been discussed. Security of the proposed protocols is analyzed. Further, the efficiencies of the proposed protocols are computed, and are compared with that of the existing protocols. The comparison has established that the proposed protocols are more efficient than the existing protocols.