bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spontaneous Excision of the
Salmonella enterica
Serovar Enteritidis-Specific Defective Prophage-Like Element φSE14
Authors: Santiviago Carlos A. , Blondel Carlos J. , Quezada Carolina P. , Silva Cecilia A. , Tobar Pia M. , Porwollik Steffen , McClelland Michael , Andrews-Polymenis Helene L. , Toro Cecilia S. , Zaldívar Mercedes , Contreras Inés 
Published: February 2010

ABSTRACT

Salmonella enterica
serovar Enteritidis has emerged as a major health problem worldwide in the last few decades. DNA loci unique to
S
. Enteritidis can provide markers for detection of this pathogen and may reveal pathogenic mechanisms restricted to this serovar. An
in silico
comparison of 16
Salmonella
genomic sequences revealed the presence of an ∼12.5-kb genomic island (GEI) specific to the sequenced
S
. Enteritidis strain NCTC13349. The GEI is inserted at the 5′ end of gene
ydaO
(
SEN1377
), is flanked by 308-bp imperfect direct repeats (
attL
and
attR
), and includes 21 open reading frames (
SEN1378
to
SEN1398
), encoding primarily phage-related proteins. Accordingly, this GEI has been annotated as the defective prophage SE14 in the genome of strain NCTC13349. The genetic structure and location of φSE14 are conserved in 99 of 103 wild-type strains of
S
. Enteritidis studied here, including reference strains NCTC13349 and LK5. Notably, an extrachromosomal circular form of φSE14 was detected in every strain carrying this island. The presence of
attP
sites in the circular forms detected in NCTC13349 and LK5 was confirmed. In addition, we observed spontaneous loss of a
tetRA
-tagged version of φSE14, leaving an empty
attB
site in the genome of strain NCTC13349. Collectively, these results demonstrate that φSE14 is an unstable genetic element that undergoes spontaneous excision under standard growth conditions. An internal fragment of φSE14 designated Sdf I has been used as a serovar-specific genetic marker in PCR-based detection systems and as a tool to determine
S
. Enteritidis levels in experimental infections. The instability of this region may require a reassessment of its suitability for such applications.
The Nonmevalonate Pathway of Isoprenoid Biosynthesis in
Mycobacterium tuberculosis
Is Essential and Transcriptionally Regulated by Dxs
Authors: Brown Amanda C. , Eberl Matthias , Crick Dean C. , Jomaa Hassan , Parish Tanya 
Published: February 2010

ABSTRACT

Mycobacterium tuberculosis
synthesizes isoprenoids via the nonmevalonate or DOXP pathway. Previous work demonstrated that three enzymes in the pathway (Dxr, IspD, and IspF) are all required for growth
in vitro
. We demonstrate the essentiality of the key genes
dxs1
and
gcpE
, confirming that the pathway is of central importance and that the second homolog of the synthase (
dxs2
) cannot compensate for the loss of
dxs1
. We looked at the effect of overexpression of Dxr, Dxs1, Dxs2, and GcpE on viability and on growth in
M. tuberculosis
. Overexpression of
dxs1
or
dxs2
was inhibitory to growth, whereas overexpression of
dxr
or
gcpE
was not. Toxicity is likely to be, at least partially, due to depletion of pyruvate from the cells. Overexpression of
dxs1
or
gcpE
resulted in increased flux through the pathway, as measured by accumulation of the metabolite 4-hydroxy-3-methyl-but-2-enyl pyrophosphate. We identified the functional translational start site and promoter region for
dxr
and demonstrated that it is expressed as part of a polycistronic mRNA with
gcpE
and two other genes. Increased expression of this operon was seen in cells overexpressing Dxs1, indicating that transcriptional control is effected by the first enzyme of the pathway via an unknown regulator.
In theStaphylococcus aureusTwo-Component Systemsae, the Response Regulator SaeR Binds to a Direct Repeat Sequence and DNA Binding Requires Phosphorylation by the Sensor Kinase SaeS
Authors: Sun Fei , Li Chunling , Jeong Dowon , Sohn Changmo , He Chuan , Bae Taeok 
Published: February 2010

ABSTRACTStaphylococcus aureususes the SaeRS two-component system to control the expression of many virulence factors such as alpha-hemolysin and coagulase; however, the molecular mechanism of this signaling has not yet been elucidated. Here, using the P1 promoter of thesaeoperon as a model target DNA, we demonstrated that the unphosphorylated response regulator SaeR does not bind to the P1 promoter DNA, while its C-terminal DNA binding domain alone does. The DNA binding activity of full-length SaeR could be restored by sensor kinase SaeS-induced phosphorylation. Phosphorylated SaeR is more resistant to digestion by trypsin, suggesting conformational changes. DNase I footprinting assays revealed that the SaeR protection region in the P1 promoter contains a direct repeat sequence (GTTAAN6GTTAA [where N is any nucleotide]). This sequence is critical to the binding of phosphorylated SaeR. Mutational changes in the repeat sequence greatly reduced both thein vitrobinding of SaeR and thein vivofunction of the P1 promoter. From these results, we concluded that SaeR recognizes the direct repeat sequence as a binding site and that binding requires phosphorylation by SaeS.
Genomic Content ofNeisseriaSpecies
Authors: Tobiason Deborah M. , Seifert H. Steven 
Published: February 2010

ABSTRACTThe physical properties of most bacterial genomes are largely unexplored. We have previously demonstrated that the strict human pathogenNeisseria gonorrhoeaeis polyploid, carrying an average of three chromosome copies per cell and only maintaining one pair of replication forks per chromosome (D. M. Tobiason and H. S. Seifert, PLos Biol. 4:1069-1078, 2006). We are following up this initial report to test several predictions of the polyploidy model of gonococcal chromosome organization. We demonstrate that theN. gonorrhoeaechromosomes exist solely as monomers and not covalently linked dimers, and in agreement with the monomer status, we show that distinct nucleoid regions can be detected by electron microscopy. Two different approaches to isolate heterozygousN. gonorrhoeaeresulted in the formation of merodiploids, showing that even with more than one chromosome copy, these bacteria are genetically haploid. We show that the closely related bacteriumNeisseria meningitidisis also polyploid, while the commensal organismNeisseria lactamicamaintains chromosomes in single copy. We conclude that the pathogenicNeisseriastrains are homozygous diploids.
Comparable biocompatibility of Phisio- and Bioline-coated cardiopulmonary bypass circuits indicated by the inflammatory response
Authors: Thiara AS , Andersen VY , Videm V. , Mollnes TE , Svennevig K. , Hoel TN , Fiane AE 
Published: February 2010

Background: The biocompatibility of cardiopulmonary bypass surfaces has been improved by heparin and polymer surface modifications. The present study compared the effect of two such coatings on the inflammatory reactions after open heart surgery. Methods:Thirty patients undergoing elective heart surgery were randomly assigned to receive one of two types of coated circuits: Bioline (n=15) or phosphorylcholine (Phisio, n=15). The platelet and leukocyte counts, neutrophil activation (myeloperoxidase), complement activation (C3a and TCC), concentrations of lactate dehydrogenase, 27 cytokines (including interleukins, chemokines and growth factors), thrombin-antithrombin complexes, and the endothelial cell marker syndecan-1 were analyzed at five predetermined time points until 24 hrs post operatively. Results: Most measurements were comparable in both groups. However, myeloperoxidase was significantly higher in the Bioline group (p < 0.001). Postoperative lactate dehydrogenase concentrations were significantly higher in the Phisio group (p<0.01) and the maximal concentration of thrombin-antithrombin complexes 2 hours postoperatively tended to be higher in the Phisio group (p=0.08), consistent with a longer aortic cross-clamp and cardiopulmonary bypass time. Conclusions: The two circuits exhibited a comparable degree of in vivo biocompatibility.
Alternative modes of GM-CSF receptor activation revealed using activated mutants of the common β-subunit
Authors: Perugini Michelle , Brown Anna L. , Salerno Diana G. , Booker Grant W. , Stojkoski Cvetan , Hercus Timothy R. , Lopez Angel F. , Hibbs Margaret L. , Gonda Thomas J. , D'Andrea Richard J. 
Published: February 2010

AbstractGranulocyte/macrophage colony-stimulating factor promotes growth, survival, differentiation, and activation of normal myeloid cells and plays an important role in myeloid leukemias. The GM-CSF receptor (GMR) shares a signaling subunit, βc, with interleukin-3 and interleukin-5 receptors and has recently been shown to induce activation of Janus kinase 2 (JAK2) and downstream signaling via formation of a unique dodecameric receptor complex. In this study we use 2 activated βc mutants that display distinct signaling capacity and have differential requirements for the GMR α-subunit (GMR-α) to dissect the signaling pathways associated with the GM-CSF response. The V449E transmembrane mutant selectively activates JAK2/signal transducer and activator of transcription 5 and extracellular signal-regulated kinase (ERK) pathways, resulting in a high level of sensitivity to JAK and ERK inhibitors, whereas the extracellular mutant (FIΔ) selectively activates the phosphoinositide 3-kinase/Akt and IκKβ/nuclear factorκB pathways. We also demonstrate a novel and direct interaction between the SH3 domains of Lyn and Src with a conserved proline-rich motif in GMR-α and show a selective requirement for Src family kinases by the FIΔ mutant. We relate the nonoverlapping nature of signaling by the activated mutants to the structure of the unique GMR complex and propose alternative modes of receptor activation acting synergistically in the mature liganded receptor complex.
X-linked thrombocytopenia (XLT) due to WAS mutations: clinical characteristics, long-term outcome, and treatment options
Authors: Albert Michael H. , Bittner Tanja C. , Nonoyama Shigeaki , Notarangelo Lucia Dora , Burns Siobhan , Imai Kohsuke , Espanol Teresa , Fasth Anders , Pellier Isabelle , Strauss Gabriele , Morio Tomohiro , Gathmann Benjamin , Noordzij Jeroen G. , Fillat Cristina , Hoenig Manfred , Nathrath Michaela , Meindl Alfons , Pagel Philipp , Wintergerst Uwe , Fischer Alain , Thrasher Adrian J. , Belohradsky Bernd H. , Ochs Hans D. 
Published: February 2010

AbstractA large proportion of patients with mutations in the Wiskott-Aldrich syndrome (WAS) protein gene exhibit the milder phenotype termed X-linked thrombocytopenia (XLT). Whereas stem cell transplantation at an early age is the treatment of choice for patients with WAS, therapeutic options for patients with XLT are controversial. In a retrospective multicenter study we defined the clinical phenotype of XLT and determined the probability of severe disease-related complications in patients older than 2 years with documented WAS gene mutations and mild-to-moderate eczema or mild, infrequent infections. Enrolled were 173 patients (median age, 11.5 years) from 12 countries spanning 2830 patient-years. Serious bleeding episodes occurred in 13.9%, life-threatening infections in 6.9%, autoimmunity in 12.1%, and malignancy in 5.2% of patients. Overall and event-free survival probabilities were not significantly influenced by the type of mutation or intravenous immunoglobulin or antibiotic prophylaxis. Splenectomy resulted in increased risk of severe infections. This analysis of the clinical outcome and molecular basis of patients with XLT shows excellent long-term survival but also a high probability of severe disease-related complications. These observations will allow better decision making when considering treatment options for individual patients with XLT.
Structural alphabets derived from attractors in conformational space
Authors: Pandini Alessandro , Fornili Arianna , Kleinjung Jens 
Published: February 2010

AbstractBackgroundThe hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.ResultsA Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.ConclusionsThe density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics.
Surveillance of febrile patients in a district and evaluation of their spatiotemporal associations: a pilot study
Authors: Choi Kin-wing , Wong Ngai-sze , Lee Lap-yip , Lee Shui-shan 
Published: February 2010

AbstractBackgroundFever is an undifferentiated clinical feature that may enhance the sensitivity of syndromic surveillance systems. By studying the spatiotemporal associations of febrile patients, it may allow early detection of case clustering that indicates imminent threat of infectious disease outbreaks in the community.MethodsWe captured consecutive emergency department visits that led to hospitalization in a district hospital in Hong Kong during the period of 12 Sep 2005 to 14 Oct 2005. We recorded demographic data, provisional diagnoses, temperature on presentation and residential location for each patient-episode, and geocoded the residential addresses. We applied Geographical Information System technology to study the geographical distribution these cases, and their associations within a 50-m buffer zone spatially. A case cluster was defined by three or more spatially associated febrile patients within each three consecutive days.ResultsOne thousand and sixty six patient-episodes were eligible for analysis; 42% of them had fever (>37°C; oral temperature) on presentation. Two hundred and four patient-episodes (19.1%) came from residential care homes for elderly (RCHE). We detected a total of 40 case clusters during the study period. Clustered cases were of older age; 57 (33.3%) were residents of RCHE. We found a median of 3 patients (range: 3 - 8) and time span of 3 days (range: 2 - 8 days) in each cluster. Twenty five clusters had 2 or more patients living in the same building block; 18 of them were from RCHE.ConclusionsIt is technically feasible to perform surveillance on febrile patients and studying their spatiotemporal associations. The information is potentially useful for early detection of impending infectious disease threats.
Transmembrane potential induced on the internal organelle by a time-varying magnetic field: a model study
Authors: Ye Hui , Cotic Marija , Kang Eunji E , Fehlings Michael G , Carlen Peter L 
Published: February 2010

Abstract
Background
When a cell is exposed to a time-varying magnetic field, this leads to an induced voltage on the cytoplasmic membrane, as well as on the membranes of the internal organelles, such as mitochondria. These potential changes in the organelles could have a significant impact on their functionality. However, a quantitative analysis on the magnetically-induced membrane potential on the internal organelles has not been performed.

Methods
Using a two-shell model, we provided the first analytical solution for the transmembrane potential in the organelle membrane induced by a time-varying magnetic field. We then analyzed factors that impact on the polarization of the organelle, including the frequency of the magnetic field, the presence of the outer cytoplasmic membrane, and electrical and geometrical parameters of the cytoplasmic membrane and the organelle membrane.

Results
The amount of polarization in the organelle was less than its counterpart in the cytoplasmic membrane. This was largely due to the presence of the cell membrane, which "shielded" the internal organelle from excessive polarization by the field. Organelle polarization was largely dependent on the frequency of the magnetic field, and its polarization was not significant under the low frequency band used for transcranial magnetic stimulation (TMS). Both the properties of the cytoplasmic and the organelle membranes affect the polarization of the internal organelle in a frequency-dependent manner.

Conclusions
The work provided a theoretical framework and insights into factors affecting mitochondrial function under time-varying magnetic stimulation, and provided evidence that TMS does not affect normal mitochondrial functionality by altering its membrane potential.
17β-Hydroxysteroid Dehydrogenase Type 1 Stimulates Breast Cancer by Dihydrotestosterone Inactivation in Addition to Estradiol Production
Authors: Aka Juliette A. , Mazumdar Mausumi , Chen Chang-Qing , Poirier Donald , Lin Sheng-Xiang 
Published: February 2010

AbstractThe active estrogen estradiol (E2) stimulates breast cancer cell (BCC) growth, whereas the androgen dihydrotestosterone (DHT) has shown an antiproliferative effect. The principal product synthesized by the 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1) is E2, although we have demonstrated that the purified enzyme also inactivates DHT. However, the direct roles of 17β-HSD1 in sex-hormone regulation and BCC proliferation have not been completely established. Here, we show that 17β-HSD1 inhibition suppresses DHT catabolism by 19%, whereas knockdown of the gene expression increases the concentration of DHT by 41% in the T47D BCC line. The 17β-HSD1/DHT complex crystal structure reveals that DHT binds in both normal and reverse modes, but the latter mode leading to O3 reduction is preferred with stronger interactions. Using RNA interference and an inhibitor of 17β-HSD1, we demonstrate that 17β-HSD1 expression is negatively correlated to DHT levels in BCC but positively correlated to estrone reduction, E2 levels, and cell proliferation. 17β-HSD1 inhibition reduces DHT inactivation, increasing the antiproliferative effect by DHT in T47D cells after 8 d treatment. Thus, 17β-HSD1 up-regulates BCC growth by a dual action on estradiol synthesis and DHT inactivation. We have further demonstrated that 17β-HSD1 can enhance the E2-induced expression of the endogenous estrogen-responsive gene pS2, providing an important information regarding the modulation of the estrogen responsiveness by 17β-HSD1 that may also contribute to BCC growth. These results strongly support the rationale for inhibiting 17β-HSD1 in breast cancer therapy to eliminate estrogen activation via the sulfatase pathway while avoiding the deprivation of DHT.
Evaluation of five routine glucose methods on an Olympus AU5400 analyzer using the CDC hexokinase reference method
Authors: Jia Ke-ke , Zhang Jie 
Published: February 2010

Abstract

Background: In China, two common methods are used to detect serum glucose, glucose oxidase (GOD) and hexokinase (HK) methods. We evaluated five commercially available glucose reagent kits with the Center of Disease Control (CDC) HK reference method.

Methods: Five routine methods were compared with the HK reference method according to Clinical and Laboratory Standards Institute (CLSI) guideline (EP9-A2). These five routine methods were performed on an “open channel” Olympus 5400 analyzer.

Results: All five evaluated methods were closely correlated to the reference method (r>0.9998). Compared to the HK reference method, the Olympus-HK method and Roche-GOD method showed a very small positive bias (mean±SD: 0.08±0.09 mmol/L and 0.03±0.08 mmol/L); while the Biosino-HK method, Osborne-GOD method and Baiding-GOD method showed a very small negative bias (mean±SD: –0.07±0.06 mmol/L, –0.09±0.07 mmol/L and –0.01±0.04 mmol/L).

Conclusions: All five reagents we evaluated using matching calibrators showed good correlation to the reference method and small bias. These five glucose reagents are acceptable for use in clinical laboratories.
Clin Chem Lab Med 2010;48:361–4.
The underestimated problem of using serum magnesium measurements to exclude magnesium deficiency in adults; a health warning is needed for “normal” results
Authors: Ismail Yasmin , Ismail Abbas A. , Ismail Adel A.A. 
Published: February 2010

Abstract

Background: A major use of serum magnesium measurements in clinical practice is to identify patients with deficiency. However, numerous studies have shown that magnesium deficiency is common and may be present in over 10% of hospitalized patients, as well as in the general population. An important cause for under diagnosis of deficiency is that serum magnesium, the most commonly used test, can be normal despite negative body stores. This article focuses on the limitations of “normal” magnesium results and highlights the importance of lifestyle or “modus vivendi” as a pragmatic means of identifying those individuals potentially at risk for negative body magnesium stores.

Methods: Researched peer reviewed articles on magnesium published between 1990 and 2008 in MEDLINE and EMBASE, using database keywords “magnesium, deficiency, diagnosis, treatment and hypomagnesaemia”. Bibliographies of retrieved articles have been searched and followed. We have also performed a manual search of each individual issue in which most of these reports have appeared.

Results: In 183 peer reviewed studies published from 1990 to 2008, magnesium deficiency was associated with increased prevalence and risk in 11 major conditions. Similarly, in 68 studies performed over the same period, magnesium deficiency was found to predict adverse events and a decreased risk of pathology was noted when supplementation or treatment was instituted.

Conclusions: The perception that “normal” serum magnesium excludes deficiency is common among clinicians. This perception is probably enforced by the common laboratory practice of highlighting only abnormal results. A health warning is therefore warranted regarding potential misuse of “normal” serum magnesium because restoration of magnesium stores in deficient patients is simple, tolerable, inexpensive and can be clinically beneficial.
Clin Chem Lab Med 2010;48:323–7.