bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitrate/oxygen co‐sensing by an NreA/NreB sensor complex of Staphylococcus carnosus
Authors: Nilkens Stephanie , Koch‐Singenstreu Mareike , Niemann Volker , Götz Friedrich , Stehle Thilo , Unden Gottfried 
Published: November 2013

SummaryIn Staphylococci maximal induction of nitrate reductase (narGHJI genes) requires anaerobic conditions, the presence of nitrate, and the NreABC regulatory system. Aerobic regulation is effected by the NreB/NreC two‐component system. The role of the nitrate receptor NreA in nitrate induction and its relation to aerobic regulation was analysed in Staphylococcus carnosus. Nitrate induction of a narG‐lip reporter gene required presence of NreB/NreC. When nreA was deleted, nitrate was no longer required for maximal induction, suggesting that NreA is a nitrate regulated inhibitor of NreB/NreC. In vitro, NreA and mutant NreA(Y95A) decreased NreB phosphorylation in part or completely, which was due to the inhibition of the autophosphorylating activity rather than an increase of phosphatase activity. Inhibition of phosphorylation was relieved completely when the nitrate‐bound NreA was used instead of the nitrate‐free form. In the bacterial two‐hybrid BACTH system and HPINE interaction assays, NreA interacted with NreB, but not with NreC, and the interaction was diminished by nitrate. In summary, NreA interacts with NreB and controls its phosphorylation level in a nitrate dependent manner. In this way nitrate and NreA modulate the function of the oxygen sensor NreB, resulting in nitrate/oxygen co‐sensing by an NreA/NreB sensor unit as part of the NreABC‐system.
Biological and molecular variation of Cherry leaf roll virus isolates from Malus domestica, Ribes rubrum, Rubus idaeus, Rumex obtusifolius and Vaccinium darrowii
Authors: Woo E. N. Y. , Pearson M. N. 
Published: November 2013

Cherry leaf roll virus (CLRV) isolates from Malus domestica, Ribes rubrum, Rubus idaeus, Rumex obtusifolius and Vaccinium darrowii were characterized based on nucleotide sequences of a 371 bp fragment of the 3′ untranslated region (UTR) of their genomic RNAs, symptoms in the herbaceous hosts, Chenopodium amaranticolor, Chenopodium quinoa, Nicotiana benthamiana, Nicotiana occidentalis and Nicotiana tabacum, and seed transmission in N. occidentalis. The different isolates induced a range of localized and systemic disease symptoms, of varying severity, in the herbaceous hosts. The isolates from M. domestica, R. rubrum, R. obtusifolius and V. darrowii all showed greater than 80% seed transmission in N. occidentalis, but no seed transmission was observed for the R. idaeus isolate. Based on symptoms and seed transmission, the isolates appear to be biologically distinct strains of CLRV. Phylogenetic analysis of the nucleotide sequences from the 3′ UTR, commonly used to detect CLRV, showed that four isolates from M. domestica, R. rubrum, R. idaeus and V. darrowii were almost identical but an isolate from R. obtusifolius exhibited a pairwise nucleotide difference of up to 5·4% when compared to these isolates. There was no obvious correlation between sequence differences and symptomatology.
IL‐10 promoter polymorphisms influence susceptibility to aGvHD and are associated with proportions of CD4+FoxP3+ lymphocytes in blood after hematopoietic stem cell transplantation
Authors: Jaskula E. , Lange A. , Dlubek D. , Kyrcz‐Krzemień S. , Markiewicz M. , Dzierzak‐Mietla M. , Jedrzejczak W. W. , Gronkowska A. , Nowak J. , Warzocha K. , Hellmann A. , Kowalczyk J. , Drabko K. , Goździk J. , Mizia S. ,   on behalf of the Polish Donor‐Recipient Matching Group
Published: November 2013

AbstractFour hundred and ninety‐five patients (390 and 105 grafted from unrelated and sibling (SIB) donors, respectively) and their donors were analyzed for the impact of interleukin‐10 (IL‐10) promoter genotype [rs18000896 (−1082 G/A), rs18000871 (−819 C/T) and rs18000872 (−592 C/A)] on the outcome of hematopoietic stem cell transplantation (HSCT). Patients having ACC haplotype were at a lower risk of acute graft versus host disease (aGvHD, grade > I) if transplanted from human leukocyte antigen (HLA) well‐matched (10/10) unrelated donors (20/135 vs 39/117, P < 0.001, Pcorr = 0.002), which was not seen if patients were transplanted from either sibling (SIB) or poorly matched (<10/10) unrelated donors (MUD). In addition, GCC haplotype positive recipients of unrelated donor transplants tended to be more susceptible to aGvHD (68/199 vs 39/169, P = 0.019, Pcorr = 0.057). Multivariate logistic regression analysis in the MUD transplanted group showed that donor–recipient human leukocyte antigen (HLA) mismatch [odds ratio (OR) = 3.937, P = 0.001] and a lack of ACC haplotype in recipients (OR = 0.417, P = 0.013) played a significant role as independent risk factors of aGvHD grade > I. ACC carriers had higher proportions of FoxP3+ lymphocytes gated in CD4+ lymphocytes as compared with patients with other IL‐10 haplotypes. It was seen at the time of hematological recovery (mean ± SEM: 3.80 ± 0.91% vs 2.06 ± 0.98%, P = 0.012) and 2 weeks later (5.32 ± 0.87% vs 2.50 ± 0.83%, P = 0.013); −592 C/A polymorphism was separately analyzed and it was found that AA homozygotes tended to have a higher incidence of aGvHD (8/15 vs 116/456, P = 0.034) and low proportions of FoxP3 CD4+ lymphocytes in blood (0.43 ± 0.22% vs 4.32 ± 0.71%, P = 0.051) measured 2 weeks after hematological recovery. Functional IL‐10 polymorphism associated features influenced the risk of aGvHD with a positive effect of ACC on the pool of Treg in blood.
Influence of KIR genes and their HLA ligands in susceptibility to dengue in a population from southern Brazil
Authors: Beltrame L. M. , Sell A. M. , Moliterno R. A. , Clementino S. L. , Cardozo D. M. , Dalalio M. M. , Fonzar U. J. , Visentainer J. E. 
Published: November 2013

AbstractKiller cell immunoglobulin‐like receptors (KIR) form a group of regulatory molecules that specifically recognise human leukocyte antigen (HLA) class I molecules, modulating the cytolytic activity of natural killer cells. The purpose of this study was to investigate the influence of KIR genes and their class I HLA ligands in susceptibility to dengue fever in a population from southern Brazil through a case–control study. One hundred four subjects with confirmed diagnoses of dengue participated in this study, along with a control group of 172 individuals from the same geographic area. HLA and KIR genotyping was performed by polymerase chain reaction with sequence‐specific oligonucleotide probes (PCR‐SSOP) and with sequence‐specific primer (PCR‐SSP) techniques, respectively. Data analysis showed significant differences for the KIR2DS1 (54.8% vs 40.7%, P = 0.03), KIR2DS5 (50.0% vs 36.0%, P = 0.03) and KIR2DL5 (76.0% vs 56.4%, P = 0.001) genes. With regard to KIR‐ligand pairs, positive associations with dengue were observed in KIR3DS1‐Bw4 (45.2% vs 29.7%, P = 0.01), KIR3DL1‐Bw4 (80.7% vs 65.1%, P < 0.001), KIR2DL1‐C2 (75.0% vs 62.2%, P = 0.03) and KIR2DS1‐C2 (40.4% vs 25.6%, P = 0.01) interactions, and a negative association in KIR2DL3‐C1/C1 (18.2% vs 33.1%, P = 0.01). Furthermore, the analysis of KIR haplogroups showed a possible protective factor against dengue fever in individuals with the AA genotype. Taken together, these results suggest the existence of genetic predisposition to dengue fever in the population from southern Brazil.
Finding new agents in medicinal plants to act on the myometrium
Authors: Kupittayanant Sajeera , Munglue Phukphon , Lijuan Wanwisa , Promprom Wilawan , Budhaklala Nopparat , Wray Susan 
Published: November 2013

New Findings
What is the topic of this review?
How do medicinal plants act on the myometrium? What are the underlying mechanisms whereby medicinal plants exert their effects?
What advances does it highlight?
We show that medicinal plants can affect uterine contraction at many loci. These studies give us a better understanding of how medicinal plants work on the uterus and can be applied in other areas of smooth muscle physiology, as well as pharmacy and medicine. This knowledge is also useful for developing new agents with potential to improve women's reproductive and gynaecological heath.
This report summarizes work investigating the effects of some medicinal plants on uterine contraction. As there is a clinical need to find better drugs to help control uterine activity, and novel compounds are sought, the mechanisms whereby the medicinal plants exert their effects, as well as their major compounds, are discussed. By identifying the plants, major constituents and mechanisms, this review also illustrates the potential for development of new drugs, so that better ways to treat uterine disorders will be available to women worldwide.
Dependence with air density of the response of the PTW SourceCheck ionization chamber for low energy brachytherapy sources
Authors: Tornero‐López Ana M. , Guirado Damián , Perez‐Calatayud Jose , Ruiz‐Arrebola Samuel , Simancas Fernando , Gazdic‐Santic Maja , Lallena Antonio M. 
Published: November 2013

Purpose:Air‐communicating well ionization chambers are commonly used to assess air kerma strength of sources used in brachytherapy. The signal produced is supposed to be proportional to the air density within the chamber and, therefore, a density‐independent air kerma strength is obtained when the measurement is corrected to standard atmospheric conditions using the usual temperature and pressure correction factor. Nevertheless, when assessing low energy sources, the ionization chambers may not fulfill that condition and a residual density dependence still remains after correction. In this work, the authors examined the behavior of the PTW 34051 SourceCheck ionization chamber when measuring the air kerma strength of125I seeds.Methods:Four different SourceCheck chambers were analyzed. With each one of them, two series of measurements of the air kerma strength for125I selectSeedTM brachytherapy sources were performed inside a pressure chamber and varying the pressure in a range from 747 to 1040 hPa (560 to 780 mm Hg). The temperature and relative humidity were kept basically constant. An analogous experiment was performed by taking measurements at different altitudes above sea level.Results:Contrary to other well‐known ionization chambers, like the HDR1000 PLUS, in which the temperature‐pressure correction factor overcorrects the measurements, in the SourceCheck ionization chamber they are undercorrected. At a typical atmospheric situation of 933 hPa (700 mm Hg) and 20 °C, this undercorrection turns out to be 1.5%. Corrected measurements show a residual linear dependence on the density and, as a consequence, an additional density dependent correction must be applied. The slope of this residual linear density dependence is different for each SourceCheck chamber investigated. The results obtained by taking measurements at different altitudes are compatible with those obtained with the pressure chamber.Conclusions:Variations of the altitude and changes in the weather conditions may produce significant density corrections, and that effect should be taken into account. This effect is chamber‐dependent, indicating that a specific calibration is necessary for each particular chamber. To our knowledge, this correction has not been considered so far for SourceCheck ionization chambers, but its magnitude cannot be neglected in clinical practice. The atmospheric pressure and temperature at which the chamber was calibrated need to be taken into account, and they should be reported in the calibration certificate. In addition, each institution should analyze the particular response of its SourceCheck ionization chamber and compute the adequate correction factors. In the absence of a suitable pressure chamber, a possibility for this assessment is to take measurements at different altitudes, spanning a wide enough air density range.
Novel Highly Thermostable Endolysin from Thermus scotoductus MAT2119 Bacteriophage Ph2119 with Amino Acid Sequence Similarity to Eukaryotic Peptidoglycan Recognition Proteins
Authors: Plotka Magdalena , Kaczorowska Anna-Karina , Stefanska Aleksandra , Morzywolek Agnieszka , Fridjonsson Olafur H. , Dunin-Horkawicz Stanislaw , Kozlowski Lukasz , Hreggvidsson Gudmundur O. , Kristjansson Jakob K. , Dabrowski Slawomir , Bujnicki Janusz M. , Kaczorowski Tadeusz 
Published: November 2013

ABSTRACT

In this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage Ph2119 infecting
Thermus
strain MAT2119 isolated from geothermal areas in Iceland. Nucleotide sequence analysis of the 16S rRNA gene affiliated the strain with the species
Thermus scotoductus
. Bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an
M
r
of 17,555. Ph2119 endolysin does not resemble any known thermophilic phage lytic enzymes. Instead, it has conserved amino acid residues (His
30
, Tyr
58
, His
132
, and Cys
140
) that form a Zn
2+
binding site characteristic of T3 and T7 lysozymes, as well as eukaryotic peptidoglycan recognition proteins, which directly bind to, but also may destroy, bacterial peptidoglycan. The purified enzyme shows high lytic activity toward thermophiles, i.e.,
T. scotoductus
(100%),
Thermus thermophilus
(100%), and
Thermus flavus
(99%), and also, to a lesser extent, toward mesophilic Gram-negative bacteria, i.e.,
Escherichia coli
(34%),
Serratia marcescens
(28%),
Pseudomonas fluorescens
(13%), and
Salmonella enterica
serovar Panama (10%). The enzyme has shown no activity against a number of Gram-positive bacteria analyzed, with the exception of
Deinococcus radiodurans
(25%) and
Bacillus cereus
(15%). Ph2119 endolysin was found to be highly thermostable: it retains approximately 87% of its lytic activity after 6 h of incubation at 95°C. The optimum temperature range for the enzyme activity is 50°C to 78°C. The enzyme exhibits lytic activity in the pH range of 6 to 10 (maximum at pH 7.5 to 8.0) and is also active in the presence of up to 500 mM NaCl.
Modification of Gene Expression and Virulence Traits in Streptococcus mutans in Response to Carbohydrate Availability
Authors: Moye Zachary D. , Zeng Lin , Burne Robert A. 
Published: November 2013

ABSTRACT

The genetic and phenotypic responses of
Streptococcus mutans
, an organism that is strongly associated with the development of dental caries, to changes in carbohydrate availability were investigated.
S. mutans
UA159 or a derivative of UA159 lacking ManL, which is the EIIAB component (EIIAB
Man
) of a glucose/mannose permease of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) and a dominant effector of catabolite repression, was grown in continuous culture to steady state under conditions of excess (100 mM) or limiting (10 mM) glucose. Microarrays using RNA from
S. mutans
UA159 revealed that 174 genes were differentially expressed in response to changes in carbohydrate availability (
P
< 0.001). Glucose-limited cells possessed higher PTS activity, could acidify the environment more rapidly and to a greater extent, and produced more ManL protein than cultures grown with excess glucose. Loss of ManL adversely affected carbohydrate transport and acid tolerance. Comparison of the histidine protein (HPr) in
S. mutans
UA159 and the
manL
deletion strain indicated that the differences in the behaviors of the strains were not due to major differences in HPr pools or HPr phosphorylation status. Therefore, carbohydrate availability alone can dramatically influence the expression of physiologic and biochemical pathways that contribute directly to the virulence of
S. mutans
, and ManL has a profound influence on this behavior.
Genome Sequences of an H5N1 Highly Pathogenic Avian Influenza Virus Isolated from Vaccinated Layers in China in 2012
Authors: Liu Hualei , Wang Xiaoliang , Wang Jingjing , Zhao Yunling , Zheng Dongxia , Chen Jiming , Huang Baoxu , Wang Zhiliang 
Published: November 2013

ABSTRACT
An H5N1 virus was isolated from vaccinated layers during an outbreak of highly pathogenic avian influenza (HPAI) in Ningxia, China, in 2012. Phylogenetic analysis revealed that the virus is a novel variant in clade 7.2, and the outbreak likely resulted from mutations in the viral hemagglutinin (HA) gene.
Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds
Authors: Kong Chunlei , Wang Lijuan , Li Pengpeng , Qu Yuanyuan , Tang Hongzhi , Wang Jingwei , Zhou Hao , Ma Qiao , Zhou Jiti , Xu Ping 
Published: November 2013

ABSTRACT

Dyella ginsengisoli
strain LA-4 can efficiently degrade environmental pollutants such as biphenyl and azo dyes. Here, we present a 4.55-Mb draft genome sequence of strain LA-4, which may provide further insights into the molecular mechanism in environmental pollution remediation.
Genome Sequences of Clinical Vibrio cholerae Isolates from an Oyster-Borne Cholera Outbreak in Florida
Authors: Haley Bradd J. , Choi Seon Young , Hasan Nur A. , Abdullah Abdul Shakur H. , Cebula Thomas A. , Huq Anwar , Colwell Rita R. 
Published: November 2013

ABSTRACT

Between November 2010 and April 2011, 11 cases of cholera were identified and associated with the consumption of raw oysters harvested from Apalachicola Bay, Florida. The etiological agent was the
ctxAB
-positive
Vibrio cholerae
serogroup O75. The genome sequences of the isolates provide useful information and are deposited in the public genome databases.
Draft Genome Sequence of Lactobacillus plantarum Strain Lp91, a Promising Indian Probiotic Isolate of Human Gut Origin
Authors: Grover Sunita , Sharma Vineet K. , Mallapa Rashmi H. , Batish Virender K. 
Published: November 2013

ABSTRACT

Lactobacillus plantarum
is a highly versatile species among lactic acid bacteria that has been widely isolated from highly diversified ecological niches, including the gastrointestinal tract. Here, we report the first draft genome sequence of an Indian isolate of the probiotic strain
L. plantarum
Lp91, isolated from human gut.
An Unorthodox Sensory Adaptation Site in the Escherichia coli Serine Chemoreceptor
Authors: Han Xue-Sheng , Parkinson John S. 
Published: November 2013

ABSTRACT

The serine chemoreceptor of
Escherichia coli
contains four canonical methylation sites for sensory adaptation that lie near intersubunit helix interfaces of the Tsr homodimer. An unexplored fifth methylation site, E502, lies at an intrasubunit helix interface closest to the HAMP domain that controls input-output signaling in methyl-accepting chemotaxis proteins. We analyzed, with
in vivo
Förster resonance energy transfer (FRET) kinase assays, the serine thresholds and response cooperativities of Tsr receptors with different mutationally imposed modifications at sites 1 to 4 and/or at site 5. Tsr variants carrying E or Q at residue 502, in combination with unmodifiable D and N replacements at adaptation sites 1 to 4, underwent both methylation and demethylation/deamidation, although detection of the latter modifications required elevated intracellular levels of CheB. These Tsr variants could not mediate a chemotactic response to serine spatial gradients, demonstrating that adaptational modifications at E502 alone are not sufficient for Tsr function. Moreover, E502 is not critical for Tsr function, because only two amino acid replacements at this residue abrogated serine chemotaxis: Tsr-E502P had extreme kinase-off output and Tsr-E502I had extreme kinase-on output. These large threshold shifts are probably due to the unique HAMP-proximal location of methylation site 5. However, a methylation-mimicking glutamine at any Tsr modification site raised the serine response threshold, suggesting that all sites influence signaling by the same general mechanism, presumably through changes in packing stability of the methylation helix bundle. These findings are consistent with control of input-output signaling in Tsr through dynamic interplay of the structural stabilities of the HAMP and methylation bundles.
Quality of reporting of studies evaluating time to diagnosis: a systematic review in paediatrics
Authors: Launay Elise , Morfouace Michele , Deneux-Tharaux Catherine , Gras le-Guen Christèle , Ravaud Philippe , Chalumeau Martin 
Published: November 2013

ObjectiveAn ever-increasing number of studies analyses the distribution, determinants and consequences of time to diagnosis and delays. Weaknesses in their reporting can impede the assessment of the risks of bias and variation and thus create a risk of invalid conclusions and counterproductive clinical and public health efforts. This study sought to assess systematically the quality of reporting of articles about time to diagnosis in paediatrics.DesignTwo authors identified and analysed the quality of reporting of 50 consecutive articles assessing these intervals published from 2005 through October 2011, according to a checklist we developed of 35 items potentially associated with risks of bias and variation.Main outcome measureFrequency of articles reporting each item.ResultsSymptoms that should trigger a diagnostic procedure were reported in 28% of the articles; only two articles reported whether all patients with these symptoms underwent that procedure. Only 44% of the articles defined the beginning of the illness, 46% the date of diagnosis and 60% the distribution of time to diagnosis. Two studies met the criteria for all 11 items considered essential for assessing the risks of bias and variation in this type of study.InterpretationThis study identified many weaknesses in the quality of reporting of studies of time to diagnosis in paediatrics, especially for items potentially related to risks of bias and variation. This finding underlines the need for the development of new (or the refinement of existing) guidelines for reporting this type of study.
Occult bladder injury after laparoscopic appendicectomy
Authors: Lad Meher , Duncan Sarah , Patten Darren K 
Published: November 2013

Minimally invasive procedures have revolutionised surgery by reducing pain and the length of hospital stay for patients. These are not simple procedures and training in laparoscopic surgery is an arduous process. Meticulous preparation prior to surgery is paramount to prevent complications.We report a rare complication involving a 35-year-old patient who underwent a laparoscopic appendicectomy for a perforated appendix. Two days after surgery the patient experienced redness and swelling in the lower abdominal region and oliguria. A delayed computer tomography (CT) scan revealed contrast leakage around the bladder spreading within the peritoneal cavity consistent with an intraperitoneal bladder perforation. She underwent urinary catheterisation for 6 days. A follow-up CT cystogram showed no evidence of leakage into the peritoneal cavity. This case highlights the need for thorough preparation prior to laparoscopic surgery and careful manipulation of instruments during routine procedures to minimise the risk of serious patient complications such as the aforementioned.