bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Streptococcus mutans Aminotransferase Encoded by
ilvE
Is Regulated by CodY and CcpA
Authors: Santiago Brendaliz , Marek Maksym , Faustoferri Roberta C. , Quivey Robert G. 
Published: June 2013

ABSTRACT

The aminotransferase IlvE was implicated in the acid tolerance response of
Streptococcus mutans
when a mutation in its gene resulted in an acid-sensitive phenotype (B. Santiago, M. MacGilvray, R. C. Faustoferri, and R. G. Quivey, Jr., J. Bacteriol. 194:2010–2019, 2012). The phenotype suggested that amino acid metabolism is important for acid adaptation, as turnover of branched-chain amino acids (bcAAs) could provide important signals to modulate expression of genes involved in the adaptive process. Previous studies have demonstrated that
ilvE
is regulated in response to the external pH, though the mechanism is not yet established. CodY and CcpA have been shown to regulate expression of branched-chain amino acid biosynthetic genes, suggesting that the ability to sense carbon flow and the nutritional state of the cell also plays a role in the regulation of
ilvE
. Electrophoretic mobility shift assays using the
ilvE
promoter and a purified recombinant CodY protein provided evidence of the physical interaction between CodY and
ilvE
. In order to elucidate the signals that contribute to
ilvE
regulation,
cat
reporter fusions were utilized. Transcriptional assays demonstrated that bcAAs are signaling molecules involved in the repression of
ilvE
through regulation of CodY. In a
codY
deletion background,
ilvE
transcription was elevated, indicating that CodY acts a repressor of
ilvE
transcription. Conversely, in a
ccpA
deletion background,
ilvE
transcription was reduced, showing that CcpA activated
ilvE
transcription. The effects of both regulators were directly relevant for transcription of
ilvE
under conditions of acid stress, demonstrating that both regulators play a role in acid adaptation.
Chemoreceptor Gene Loss and Acquisition via Horizontal Gene Transfer in Escherichia coli
Authors: Borziak Kirill , Fleetwood Aaron D. , Zhulin Igor B. 
Published: June 2013

ABSTRACT

Chemotaxis allows bacteria to more efficiently colonize optimal microhabitats within their larger environment. Chemotaxis in
Escherichia coli
is the best-studied model system, and a large number of
E. coli
strains have been sequenced. The
Escherichia/Shigella
genus encompasses a great variety of commensal and pathogenic strains, but the role of chemotaxis in their association with the host remains poorly understood. Here we show that the core chemotaxis genes are lost in many, but not all, nonmotile strains but are well preserved in all motile strains. The genes encoding the Tar, Tsr, and Aer chemoreceptors, which mediate chemotaxis to a broad spectrum of chemical and physical cues, are also nearly uniformly conserved in motile strains. In contrast, the clade of extraintestinal pathogenic
E. coli
strains apparently underwent an ancestral loss of Trg and Tap chemoreceptors, which sense sugars, dipeptides, and pyrimidines. The broad range of time estimated for the loss of these genes (1 to 3 million years ago) corresponds to the appearance of the genus
Homo
.
In the Absence of RidA, Endogenous 2-Aminoacrylate Inactivates Alanine Racemases by Modifying the Pyridoxal 5′-Phosphate Cofactor
Authors: Flynn Jeffrey M. , Downs Diana M. 
Published: June 2013

ABSTRACT

Members of the RidA (YjgF/YER057c/UK114) protein family are broadly conserved across the domains of life.
In vitro
, these proteins deaminate 3- or 4-carbon enamines that are generated as mechanistic intermediates of pyridoxal 5′-phosphate (PLP)-dependent serine/threonine dehydratases. The three-carbon enamine 2-aminoacrylate can inactivate some enzymes by forming a covalent adduct via a mechanism that has been well characterized
in vitro
. The biochemical activity of RidA suggested that the phenotypes of
ridA
mutant strains were caused by the accumulation of reactive enamine metabolites. The data herein show that in
ridA
mutant strains of
Salmonella enterica
, a stable 2-aminoacrylate (2-AA)/PLP adduct forms on the biosynthetic alanine racemase, Alr, indicating the presence of 2-aminoacrylate
in vivo
. This study confirms the deleterious effect of 2-aminoacrylate generated by metabolic enzymes and emphasizes the need for RidA to quench this reactive metabolite.
The Sinorhizobium meliloti Essential Porin RopA1 Is a Target for Numerous Bacteriophages
Authors: Crook Matthew B. , Draper Alicia L. , Guillory R. Jordan , Griffitts Joel S. 
Published: June 2013

ABSTRACT

The symbiotic nitrogen-fixing bacterium
Sinorhizobium meliloti
harbors a gene,
SMc02396
, which encodes a predicted outer membrane porin that is conserved in many symbiotic and pathogenic bacteria in the order
Rhizobiales
. Here, this gene (renamed
ropA1
) is shown to be required for infection by two commonly utilized transducing bacteriophages (ΦM12 and N3). Mapping of
S. meliloti
mutations conferring resistance to ΦM12, N3, or both phages simultaneously revealed diverse mutations mapping within the
ropA1
open reading frame. Subsequent tests determined that RopA1, lipopolysaccharide, or both are required for infection by all of a larger collection of
Sinorhizobium
-specific phages. Failed attempts to disrupt or delete
ropA1
suggest that this gene is essential for viability. Phylogenetic analysis reveals that
ropA1
homologs in many
Rhizobiales
species are often found as two genetically linked copies and that the intraspecies duplicates are always more closely related to each other than to homologs in other species, suggesting multiple independent duplication events.
Functional Consequences of Substitution Mutations in MepR, a Repressor of the Staphylococcus aureus
mepA
Multidrug Efflux Pump Gene
Authors: Schindler Bryan D. , Seo Susan M. , Jacinto Pauline L. , Kumaraswami Muthiah , Birukou Ivan , Brennan Richard G. , Kaatz Glenn W. 
Published: June 2013

ABSTRACT

The expression of
mepA
, encoding the
Staphylococcus aureus
MepA multidrug efflux protein, is repressed by the MarR homologue MepR. MepR dimers bind differently to operators upstream of
mepR
and
mepA
, with affinity being greatest at the
mepA
operator. MepR substitution mutations may result in
mepA
overexpression, with A103V most common in clinical strains. Evaluation of the functional consequences of this and other MepR substitutions using a
lacZ
reporter gene assay revealed markedly reduced repressor activity in the presence of Q18P, F27L, G97E, and A103V substitutions. Reporter data were generally supported by susceptibility and efflux assays, and electrophoretic mobility shift assays (EMSAs) confirmed compromised affinities of MepR F27L and A103V for the
mepR
and
mepA
operators. One mutant protein contained two substitutions (T94P and T132M); T132M compensated for the functional defect incurred by T94P and also rescued that of A103V but not F27L, establishing it as a limited-range suppressor. The function of another derivative with 10 substitutions was minimally affected, and this may be an extreme example of suppression involving interactions among several residues. Structural correlations for the observed functional effects were ascertained by modeling mutations onto apo-MepR. It is likely that F27L and A103V affect the protein-DNA interaction by repositioning of DNA recognition helices. Negative functional consequences of MepR substitution mutations may result from interference with structural plasticity, alteration of helical arrangements, reduced protein-cognate DNA affinity, or possibly association of MepR protomers. Structural determinations will provide further insight into the consequences of these and other mutations that affect MepR function, especially the T132M suppressor.
How can clinical practice guidelines be adapted to facilitate shared decision making? A qualitative key-informant study
Authors: van der Weijden Trudy , Pieterse Arwen H , Koelewijn-van Loon Marije S , Knaapen Loes , Légaré France , Boivin Antoine , Burgers Jako S , Stiggelbout Anne M , Faber Marjan , Elwyn Glyn 
Published: June 2013

BackgroundTo explore how clinical practice guidelines can be adapted to facilitate shared decision making.MethodsThis was a qualitative key-informant study with group discussions and semi-structured interviews. First, 75 experts in guideline development or shared decision making participated in group discussions at two international conferences. Next, health professionals known as experts in depression or breast cancer, experts on clinical practice guidelines and/or shared decision making, and patient representatives were interviewed (N=20). Using illustrative treatment decisions on depression or breast cancer, we asked the interviewees to indicate as specifically as they could how guidelines could be used to facilitate shared decision making.ResultsInterviewees suggested some generic strategies, namely to include a separate chapter on the importance of shared decision making, to use language that encourages patient involvement, and to develop patient versions of guidelines. Recommendation-specific strategies, related to specific decision points in the guideline, were also suggested: These include structuring the presentation of healthcare options to increase professionals' option awareness; structuring the deliberation process between professionals and patients; and providing relevant patient support tools embedded at important decision points in the guideline.ConclusionsThis study resulted in an overview of strategies to adapt clinical practice guidelines to facilitate shared decision making. Some strategies seemed more contentious than others. Future research should assess the feasibility and impact of these strategies to make clinical practice guidelines more conducive to facilitate shared decision making.
The changing pattern of amputations
Authors: Brown Kate V , Clasper J C 
Published: June 2013

IntroductionConflict in the Middle East over the past 10 years has seen a change in warfare tactics from the use of ballistic missiles to blast weapons, which has resulted in a well-documented change in wounding patterns. Due to the severity of these injuries, there have been large numbers of amputations, both as life and limb saving procedures. The purpose of this paper is to retrospectively review all UK service personnel who have undergone limb amputation in the last 8 years of conflict and compare those from the early years with the more recent.MethodsAll UK service personnel scoring more than 1 on the extremity score of the Abbreviated Injury Score were identified from the UK Joint Theatre Trauma Registry and separated into two temporal cohorts (August 2003–February 2008 and August 2008–July 2010). Intheatre medical facility and Role 4 hospital notes from the Queen Elizabeth Hospital Birmingham were examined for details of mechanisms of injury, number of limbs injured, associated injuries, method of amputation, microbiology of contaminating organisms and outcome.ResultsThere were significant differences in the nature of the amputations, the number of multiple amputations and soft tissue perineal wounds, as well as a significantly higher Injury Severity Score in the later time period. There were also significant differences in the surgical techniques, with more guillotine amputations in the early group, and mechanism of injury, with more blast injuries in the late group.ConclusionsThis study has confirmed the clinical impression that there has been a significant change in the limb trauma from the Iraq conflict to Afghanistan. These injury patterns have significantly different logistic implications and this must be considered when planning the required medical assets in future conflicts.
Intradural spinal tumours and their mimics: a review of radiographic features
Authors: Wein Sara , Gaillard Francesco 
Published: June 2013

Abstract
Intradural spinal tumours, although relatively uncommon, can be diagnostically challenging, and often result in significant morbidity. They can be subdivided according to their cell of origin and whether they are within the cord (intramedullary) or intradural but extramedullary in location. The differential diagnosis for masses of the cauda equina region is often considered separately. Additionally, some inflammatory processes, cysts, benign tumour-like masses and vascular malformations may mimic intradural tumours. Although in many instances, a precise preoperative diagnosis is not possible as many of the imaging findings overlap, some features may strongly suggest one diagnosis over others. This article reviews the range of intradural spinal tumours in the adult and paediatric populations, with an emphasis on pertinent imaging characteristics. An approach is provided for distinguishing tumours from lesions that mimic tumours and for narrowing the differential diagnosis according to imaging findings.
eIF4B Phosphorylation by Pim Kinases Plays a Critical Role in Cellular Transformation byAblOncogenes
Authors: Yang Jianling , Wang Jun , Chen Ke , Guo Guijie , Xi Ruijiao , Rothman Paul B. , Whitten Douglas , Zhang Lianfeng , Huang Shile , Chen Ji-Long 
Published: June 2013

AbstractAlterations in translation occur in cancer cells, but the precise pathogenic processes and mechanistic underpinnings are not well understood. In this study, we report that interactions between Pim family kinases and the translation initiation factor eIF4B are critical for Abl oncogenicity. Pim kinases, Pim-1 and Pim-2, both directly phosphorylated eIF4B on Ser406 and Ser422. Phosphorylation of eIF4B on Ser422 was highly sensitive to pharmacologic or RNA interference-mediated inhibition of Pim kinases. Expression and phosphorylation of eIF4B relied upon Abl kinase activity in both v-Abl- and Bcr-Abl–expressing leukemic cells based on their blockade by the Abl kinase inhibitor imatinib. Ectopic expression of phosphomimetic mutants of eIF4B conferred resistance to apoptosis by the Pim kinase inhibitor SMI-4a in Abl-transformed cells. In contrast, silencing eIF4B sensitized Abl-transformed cells to imatinib-induced apoptosis and also inhibited their growth as engrafted tumors in nude mice. Extending these observations, we found that primary bone marrow cells derived from eIF4B-knockdown transgenic mice were less susceptible to Abl transformation, relative to cells from wild-type mice. Taken together, our results identify eIF4B as a critical substrate of Pim kinases in mediating the activity of Abl oncogenes, and they highlight eIF4B as a candidate therapeutic target for treatment of Abl-induced cancers. Cancer Res; 73(15); 4898–908. ©2013 AACR.
Plasma Sphingolipids and Lung Cancer: A Population-Based, Nested Case–Control Study
Authors: Alberg Anthony J. , Armeson Kent , Pierce Jason S. , Bielawski Jacek , Bielawska Alicja , Visvanathan Kala , Hill Elizabeth G. , Ogretmen Besim 
Published: June 2013

Abstract
Background: Sphingosine-1-phosphate (S1P) and ceramides are bioactive signaling sphingolipids that regulate pathways that are central to cancer pathogenesis.
Methods: A nested case–control study was implemented to test whether prediagnostic circulating concentrations of S1P and ceramides were associated with future lung cancer risk. In the community-based CLUE II cohort study in Washington County, Maryland, the study consisted of 100 incident lung cancer cases, each matched to two cancer-free controls on age, sex, race, and cigarette smoking status. Plasma stored at −70°C at the beginning of follow-up in 1989 was assayed for sphingolipids using liquid chromatography/tandem mass spectrometry methodology (LC/MS-MS).
Results: Compared with controls, geometric mean plasma concentrations of S1P and total ceramides were 2.9% (P = 0.10) and 5.1% (P = 0.02), respectively, greater in lung cancer cases. For S1P, the ORs and 95% confidence intervals (CI) for lung cancer risk were 2.7 (1.2–5.9), 2.7 (1.1–6.4), and 1.9 (0.8–4.5) for the second, third, and highest fourth, respectively, compared with the lowest fourth (overall P = 0.006). Compared with those with total ceramide concentrations in the lowest fourth, the ORs (and 95% CI) for lung cancer risk were 1.6 (0.7–3.3), 1.5 (0.7–3.4), and 2.1 (0.9–4.7) for the second, third, and highest fourth, respectively (Ptrend = 0.01).
Conclusions: Higher concentrations of S1P and total ceramide in plasma were associated with increased future risk of lung cancer.
Impact: These novel findings suggest that perturbation of sphingolipid metabolism and S1P generation may either contribute to the etiology of lung cancer or be a marker of latent lung cancer. Cancer Epidemiol Biomarkers Prev; 22(8); 1374–82. ©2013 AACR.
Molecular Pathways: PI3K Pathway Targets in Triple-Negative Breast Cancers
Authors: Gordon Vallerie , Banerji Shantanu 
Published: June 2013

Abstract
The triple-negative breast cancer (TNBC) subtype, defined clinically by the lack of estrogen, progesterone, and Her2 receptor expression, accounts for 10% to 15% of annual breast cancer diagnoses. Currently, limited therapeutic options have shown clinical benefit beyond cytotoxic chemotherapy. Defining this clinical cohort and identifying subtype-specific molecular targets remain critical for new therapeutic development. The current era of high-throughput molecular analysis has revealed new insights into these targets and confirmed the phosphoinositide 3-kinase (PI3K) as a key player in pathogenesis. The improved knowledge of the molecular basis of TNBC in parallel with efforts to develop new PI3K pathway–specific inhibitors may finally produce the therapeutic breakthrough that is desperately needed. Clin Cancer Res; 19(14); 3738–44. ©2013 AACR.
USP8 Is a Novel Target for Overcoming Gefitinib Resistance in Lung Cancer
Authors: Byun Sanguine , Lee Sung-Young , Lee Jihoon , Jeong Chul-Ho , Farrand Lee , Lim Semi , Reddy Kanamata , Kim Ji Young , Lee Mee-Hyun , Lee Hyong Joo , Bode Ann M. , Won Lee Ki , Dong Zigang 
Published: June 2013

Abstract
Purpose: Common treatment modalities for non–small cell lung cancer (NSCLC) involve the EGF receptor-tyrosine kinase inhibitors (EGFR-TKIs) like gefitinib and erlotinib. However, the vast majority of treated patients acquire resistance to EGFR-TKIs, due, in large part, to secondary mutations in EGFR or amplification of the MET gene. Our purpose was to test ubiquitin-specific peptidase 8 (USP8) as a potential therapeutic target for gefitinib-resistant and -sensitive non–small cell lung cancer (NSCLC).
Experimental Design: Testing the effect of knockdown of USP8 and use of a synthetic USP8 inhibitor to selectively kill gefitinib-resistant (or -sensitive) NSCLCs with little effect on normal cells in cell culture and a xenograft mouse model.
Results: Knockdown of ubiquitin-specific peptidase 8 (USP8) selectively kills gefitinib-resistant NSCLCs while having little toxicity toward normal cells. Genetic silencing of USP8 led to the downregulation of several receptor tyrosine kinases (RTK) including EGFR, ERBB2, ERBB3, and MET. We also determined that a synthetic USP8 inhibitor markedly decreased the viability of gefitinib-resistant and -sensitive NSCLC cells by decreasing RTK expression while having no effect on normal cells. Moreover, treatment with a USP8 inhibitor led to significant reductions in tumor size in a mouse xenograft model using gefitinib-resistant and -sensitive NSCLC cells.
Conclusions: Our results show for the first time that the inhibition of USP8 activity or reduction in USP8 expression can selectively kill NSCLC cells. We propose USP8 as a potential therapeutic target for gefitinib-resistant and -sensitive NSCLC cells. Clin Cancer Res; 19(14); 3894–904. ©2013 AACR.
Increased Incidence of Esophageal Thermal Lesions Using the Second-Generation 28-mm Cryoballoon
Authors: Metzner Andreas , Burchard Andre , Wohlmuth Peter , Rausch Peter , Bardyszewski Alexander , Gienapp Christina , Tilz Roland Richard , Rillig Andreas , Mathew Shibu , Deiss Sebastian , Makimoto Hisaki , Ouyang Feifan , Kuck Karl-Heinz , Wissner Erik 
Published: June 2013

Background—
Pulmonary vein isolation is an established treatment option for atrial fibrillation. To date, the incidence and quality of ablation-induced esophageal thermal lesions (ETLs) using the recently introduced second-generation cryoballoon (CB, ArcticFront Advance, Medtronic) is unknown.

Methods and Results—
In patients with drug-refractory paroxysmal atrial fibrillation or short-standing persistent atrial fibrillation, pulmonary vein (PV) isolation was performed using the second-generation CB. The endoluminal esophageal temperature was monitored via a temperature probe. After PV isolation, esophagogastroduodenoscopy (EGD) was performed to assess the incidence of ETLs. In 50 patients (18 women; age, 61±11 years; left atrial diameter, 43±5 mm), successful CB-based PV isolation was performed. Lowest median balloon temperature and esophageal temperature for the right superior PV were −51°C and 35.8°C, −47°C and 35°C for the right inferior PV, −51°C and 34.4°C for the left superior PV, −48°C and 34.6°C for the left inferior PV, and −54°C and 34.5°C for the left common PV, respectively. EGD performed 2±1 days post ablation demonstrated superficial thermal lesions and thermal ulcerations in 1 of 50 (2%) and 5 of 50 (10%) patients, respectively. In patients with ETLs, during ≥1 freeze cycle the endoluminal esophageal temperature measured <3.0°C. All thermal lesions were in the healing process on repeat EGD 4±2 days after initial endoscopy.

Conclusions—
Using the second-generation 28-mm CB, ETLs were detected in 6 of 50 (12%) patients. All ETLs were in the healing process on repeat EGD. An esophageal temperature safety cutoff may prove valuable in the prevention of ETLs and requires further evaluation.
Progression of Atrial Fibrillation After a Failed Initial Ablation Procedure in Patients With Paroxysmal Atrial Fibrillation
Authors: Pokushalov Evgeny , Romanov Alexander , De Melis Mirko , Artyomenko Sergey , Baranova Vera , Losik Denis , Bairamova Sevda , Karaskov Alexander , Mittal Suneet , Steinberg Jonathan S. 
Published: June 2013

Background—
The aim of this prospective randomized study was to assess whether an early reablation was superior to antiarrhythmic drug (AAD) therapy in patients with previous failed pulmonary vein isolation.

Methods and Results—

Patients with paroxysmal atrial fibrillation (AF) eligible for AAD therapy or reablation after a previously failed initial pulmonary vein isolation procedure were eligible for this study and were followed up for 3 years to assess rhythm by means of an implanted cardiac monitor. After the blanking period postablation, 154 patients had symptomatic AF recurrences and were randomized to AAD (n=77) or repulmonary vein isolation (n=77). At the end of follow-up, 61 (79%) patients in the AAD group and 19 (25%) patients in the reablation group demonstrated AF% progression (
P
<0.01). The AF% at 36 months was significantly greater in the AAD group compared with patients in the reablation group (18.8±11.4% versus 5.6±9.5%, respectively;
P
<0.01). In addition, 18 (23%) patients in the AAD group and 3 (4%) patients in the reablation group progressed to persistent AF (
P
<0.01). Furthermore, 45 (58%) of the 77 reablation group patients were free of AF/atrial tachycardia on no AADs; in contrast, in the AAD group, only 9 (12%) of the 77 patients were free of AF/atrial tachycardia (
P
<0.01) throughout follow-up.

Conclusions—
Redo AF ablation was substantially more effective than AAD in reducing the progression and prevalence of AF after the failure of an initial ablation.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT01709682.