bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annotation of the Modular Polyketide Synthase and Nonribosomal Peptide Synthetase Gene Clusters in the Genome of Streptomyces tsukubaensis NRRL18488
Authors: Blažič Marko , Starcevic Antonio , Lisfi Mohamed , Baranasic Damir , Goranovič Dušan , Fujs Štefan , Kuščer Enej , Kosec Gregor , Petković Hrvoje , Cullum John , Hranueli Daslav , Zucko Jurica 
Published: September 2012

ABSTRACT

The high G+C content and large genome size make the sequencing and assembly of
Streptomyces
genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of
Streptomyces tsukubaensis
NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed.
HIV-1-Specific Enzyme-Linked Immunosorbent Spot Assay Responses in HIV-1-Exposed Uninfected Partners in Discordant Relationships Compared to Those in Low-Risk Controls
Authors: Guthrie Brandon L. , Lohman-Payne Barbara , Liu Amy Y. , Bosire Rose , Nuvor Samuel Victor , Choi Robert Y. , Mackelprang Romel D. , Kiarie James N. , De Rosa Stephen C. , Richardson Barbra A. , John-Stewart Grace C. , Farquhar Carey 
Published: September 2012

ABSTRACTA number of studies of highly exposed HIV-1-seronegative individuals (HESN) have found HIV-1-specific cellular responses. However, there is limited evidence that responses prevent infection or are linked to HIV-1 exposure. Peripheral blood mononuclear cells (PBMC) were isolated from HESN in HIV-1-discordant relationships and low-risk controls in Nairobi, Kenya. HIV-1-specific responses were detected using gamma interferon (IFN-γ) enzyme-linked immunosorbent spot (ELISpot) assays stimulated by peptide pools spanning the subtype A HIV-1 genome. The HIV-1 incidence in this HESN cohort was 1.5 per 100 person years. Positive ELISpot responses were found in 34 (10%) of 331 HESN and 14 (13%) of 107 low-risk controls (odds ratio [OR] = 0.76;P= 0.476). The median immunodominant response was 18.9 spot-forming units (SFU)/106peripheral blood mononuclear cells (PBMC). Among HESN, increasing age (OR = 1.24 per 5 years;P= 0.026) and longer cohabitation with the HIV-1-infected partner (OR = 5.88 per 5 years;P= 0.003) were associated with responses. These factors were not associated with responses in controls. Other exposure indicators, including the partner's HIV-1 load (OR = 0.99 per log10copy/ml;P= 0.974) and CD4 count (OR = 1.09 per 100 cells/μl;P= 0.238), were not associated with responses in HESN. HIV-1-specific cellular responses may be less relevant to resistance to infection among HESN who are using risk reduction strategies that decrease their direct viral exposure.
Differential Control of the Rate of 5′-End-Dependent mRNA Degradation in Escherichia coli
Authors: Luciano Daniel J. , Hui Monica P. , Deana Atilio , Foley Patricia L. , Belasco Kevin J. , Belasco Joel G. 
Published: September 2012

ABSTRACT

Many
Escherichia coli
mRNAs are degraded by a 5′-end-dependent mechanism in which RppH-catalyzed conversion of the 5′-terminal triphosphate to a monophosphate triggers rapid endonucleolytic cleavage by RNase E. However, little is understood about what governs the decay rates of these transcripts. We investigated the decay of three such messages—
rpsT
P1,
yfcZ
, and
ydfG—
to characterize the rate-determining step in their degradation. The steady-state ratio of monophosphorylated to triphosphorylated
rpsT
P1 and
yfcZ
mRNA indicates that their decay rate is limited by cleavage of the monophosphorylated intermediate, making RNase E critical for their rapid turnover. Conversely, the decay rate of
ydfG
is limited by generation of the monophosphorylated intermediate; therefore, either RNase E or its less abundant paralog RNase G is sufficient for rapid
ydfG
degradation. Although all three transcripts are stabilized when RppH is absent, overproducing RppH does not accelerate their decay, nor does RppH overproduction appear to influence the longevity of most other messages that it targets. The failure of excess RppH to hasten
rpsT
P1 and
yfcZ
degradation despite increasing the percentage of each that is monophosphorylated is consistent with the observation that pyrophosphate removal is not the rate-limiting step in their decay. In contrast, neither the
ydfG
decay rate nor the fraction of
ydfG
transcripts that are monophosphorylated increases when the cellular concentration of RppH is raised, suggesting that, for some RppH targets, the rate of formation of the monophosphorylated intermediate is limited by an ancillary factor or by a step that precedes pyrophosphate removal.
Crystal Structures of Complexes of the Branched-Chain Aminotransferase from Deinococcus radiodurans with α-Ketoisocaproate and
l-
Glutamate Suggest the Radiation Resistance of This Enzyme for Catalysis
Authors: Chen Chung-De , Lin Chih-Hao , Chuankhayan Phimonphan , Huang Yen-Chieh , Hsieh Yin-Cheng , Huang Tien-Feng , Guan Hong-Hsiang , Liu Ming-Yih , Chang Wen-Chang , Chen Chun-Jung 
Published: September 2012

ABSTRACT

Branched-chain aminotransferases (BCAT), which utilize pyridoxal 5′-phosphate (PLP) as a cofactor, reversibly catalyze the transfer of the α-amino groups of three of the most hydrophobic branched-chain amino acids (BCAA), leucine, isoleucine, and valine, to α-ketoglutarate to form the respective branched-chain α-keto acids and glutamate. The BCAT from
Deinococcus radiodurans
(
Dr
BCAT), an extremophile, was cloned and expressed in
Escherichia coli
for structure and functional studies. The crystal structures of the native
Dr
BCAT with PLP and its complexes with
l
-glutamate and α-ketoisocaproate (KIC), respectively, have been determined. The
Dr
BCAT monomer, comprising 358 amino acids, contains large and small domains connected with an interdomain loop. The cofactor PLP is located at the bottom of the active site pocket between two domains and near the dimer interface. The substrate (
l
-glutamate or KIC) is bound with key residues through interactions of the hydrogen bond and the salt bridge near PLP inside the active site pocket. Mutations of some interaction residues, such as Tyr71, Arg145, and Lys202, result in loss of the specific activity of the enzymes. In the interdomain loop, a dynamic loop (Gly173 to Gly179) clearly exhibits open and close conformations in structures of
Dr
BCAT without and with substrates, respectively.
Dr
BCAT shows the highest specific activity both in nature and under ionizing radiation, but with lower thermal stability above 60°C, than either BCAT from
Escherichia coli
(
e
BCAT) or from
Thermus thermophilus
(HB8BCAT). The dimeric molecular packing and the distribution of cysteine residues at the active site and the molecular surface might explain the resistance to radiation but small thermal stability of
Dr
BCAT.
Epidemiology and Genotypic Characteristics of Methicillin-Resistant Staphylococcus aureus Strains of Porcine Origin
Authors: Molla Bayleyegn , Byrne Megan , Abley Melanie , Mathews Jennifer , Jackson Charlene R. , Fedorka-Cray Paula , Sreevatsan Srinand , Wang Ping , Gebreyes Wondwossen A. 
Published: September 2012

ABSTRACT

The main goal of this study was to determine the prevalence of methicillin-resistant
Staphylococcus aureus
(MRSA), particularly livestock-associated MRSA (LA-MRSA) in pigs and pork. The genotypic relatedness of isolates on the farm, at slaughter, and at the retail level was assessed. Paired nasal and perianal swab samples were collected from 10 cohorts of market-age pigs (24 pigs per cohort) and carcasses at slaughterhouse, and pork samples were collected at retail. Staphylococci were isolated using selective enrichment method. Isolates were tested for antimicrobial resistance by broth microdilution. Duplex PCR was used to confirm MRSA using species-specific (
nuc
) and methicillin resistance (
mecA
) genes. The clonal relatedness of isolates was determined using pulsed-field gel electrophoresis (PFGE),
Staphylococcus
protein A (
spa
) typing, multilocus sequence typing (MLST), and staphylococcal cassette chromosome
mec
element (SCC
mec
) typing. MRSA was detected in 5 of the 10 cohorts (50%), with the prevalence ranging from 0% to 12.5% per cohort. Of all the pigs sampled on the farm before they went to market, 3% (7/240) were MRSA positive. A higher prevalence of MRSA was detected at holding pens at the slaughterhouse (11% [27/240]). MRSA was also detected in 2% (4/235) of the carcasses and 4% (5/135) of the retail pork. While the isolates appear predominantly to be highly clonal, PFGE had a relatively higher discriminatory power (discriminatory index [DI] = 0.624). Four genotypic clusters were identified by PFGE; of the four clusters, clonal type B was predominant across the farm-to-retail continuum. MLST findings revealed that sequence type 5 (ST5) was the most predominant subtype (32/50). The livestock-associated MRSA (clonal complex 398 [CC398] or sequence type 398 [ST398]) was the second common type (12/50) and was detected at all stages from farm to retail. Nine of the 50 (18%) MRSA isolates belonged to
spa
type 539/t034 that were of ST398 based on MLST. The results of this study confirm that MRSA, including LA-MRSA, is common in herds of swine in Ohio and hereby shown to persist in the farm to processing and retail continuum.
Production of 2-Aminophenoxazin-3-one by Staphylococcus aureus Causes False-Positive Results in β-Galactosidase Assays
Authors: Tse Herman , Chan Elaine , Lam Ching-Wan , Leung Ka-Fai , Chow Pat , Lee Kim-Chung , Sze Kong-Hung , Cheung Stanley K. K. , Tse Man-Kit , Ho Pak-Leung , Leung Sze-Pui , Lau Susanna K. P. , Woo Patrick C. Y. , Yuen Kwok-Yung 
Published: September 2012

ABSTRACTStaphylococcus aureuscan be distinguished from similar coagulase-positive staphylococci by its absence of β-galactosidase activity. This is commonly tested usingo-nitrophenyl-β-d-galactopyranoside (ONPG) as the substrate. Unexpectedly, 111 and 58 of 123 isolates displayed apparent β-galactosidase activity in the ONPG assay and on the Vitek 2 system, respectively. Compositional analysis showed that the yellow coloration of the positive ONPG assay resulted from production of 2-aminophenoxazin-3-one. Alternative β-galactosidase substrates like X-Gal (5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside) should be used for testing staphylococci.
Rapid Transepithelial Transport of Prions following Inhalation
Authors: Kincaid Anthony E. , Hudson Kathryn F. , Richey Matthew W. , Bartz Jason C. 
Published: September 2012

ABSTRACT

Prion infection and pathogenesis are dependent on the agent crossing an epithelial barrier to gain access to the recipient nervous system. Several routes of infection have been identified, but the mechanism(s) and timing of
in vivo
prion transport across an epithelium have not been determined. The hamster model of nasal cavity infection was used to determine the temporal and spatial parameters of prion-infected brain homogenate uptake following inhalation and to test the hypothesis that prions cross the nasal mucosa via M cells. A small drop of infected or uninfected brain homogenate was placed below each nostril, where it was immediately inhaled into the nasal cavity. Regularly spaced tissue sections through the entire extent of the nasal cavity were processed immunohistochemically to identify brain homogenate and the disease-associated isoform of the prion protein (PrP
d
). Infected or uninfected brain homogenate was identified adhering to M cells, passing between cells of the nasal mucosa, and within lymphatic vessels of the nasal cavity at all time points examined. PrP
d
was identified within a limited number of M cells 15 to 180 min following inoculation, but not in the adjacent nasal mucosa-associated lymphoid tissue (NALT). While these results support M cell transport of prions, larger amounts of infected brain homogenate were transported paracellularly across the respiratory, olfactory, and follicle-associated epithelia of the nasal cavity. These results indicate that prions can immediately cross the nasal mucosa via multiple routes and quickly enter lymphatics, where they can spread systemically via lymph draining the nasal cavity.
A clinical audit of changes in suicide ideas with internet treatment for depression
Authors: Watts Sarah , Newby Jill M , Mewton Louise , Andrews Gavin 
Published: September 2012

ObjectivesTo examine reductions in suicidal ideation among a sample of patients who were prescribed an internet cognitive behavior therapy (iCBT) course for depression.DesignEffectiveness study within a quality assurance framework.SettingPrimary care.Participants299 patients who were prescribed an iCBT course for depression by primary care clinicians.InterventionSix lesson, fully automated cognitive behaviour therapy course delivered over the internet. Primary outcome: suicidal ideation as measured by question 9 on the Patient Health Questionnaire (PHQ-9).ResultsSuicidal ideation was common (54%) among primary care patients prescribed iCBT treatment for depression but dropped to 30% post-treatment despite minimal clinician contact and the absence of an intervention focused on suicidal ideation. This reduction in suicidal ideation was evident regardless of sex and age.ConclusionsThe findings do not support the exclusion of patients with significant suicidal ideation.
Evaluation of a predevelopment service delivery intervention: an application to improve clinical handovers
Authors: Yao Guiqing Lily , Novielli Nicola , Manaseki-Holland Semira , Chen Yen-Fu , van der Klink Marcel , Barach Paul , Chilton Peter J , Lilford Richard J 
Published: September 2012

BackgroundWe developed a method to estimate the expected cost-effectiveness of a service intervention at the design stage and ‘road-tested’ the method on an intervention to improve patient handover of care between hospital and community.MethodThe development of a nine-step evaluation framework:1. Identification of multiple endpoints and arranging them into manageable groups;2. Estimation of baseline overall andpreventablerisk;3. Bayesian elicitation of expected effectiveness of the planned intervention;4. Assigning utilities to groups of endpoints;5. Costing the intervention;6. Estimating health service costs associated with preventable adverse events;7. Calculating health benefits;8. Cost-effectiveness calculation;9. Sensitivity and headroom analysis.Results    Literature review suggested that adverse events follow 19% of patient discharges, and that one-third are preventable by improved handover (ie, 6.3% of all discharges). The intervention to improve handover would reduce the incidence of adverse events by 21% (ie, from 6.3% to 4.7%) according to the elicitation exercise. Potentially preventable adverse events were classified by severity and duration. Utilities were assigned to each category of adverse event. The costs associated with each category of event were obtained from the literature. The unit cost of the intervention was €16.6, which would yield a Quality Adjusted Life Year (QALY) gain per discharge of 0.010. The resulting cost saving was €14.3 per discharge. The intervention is cost-effective at approximately €214 per QALY under the base case, and remains cost-effective while the effectiveness is greater than 1.6%.ConclusionsWe offer a usable framework to assist in ex ante health economic evaluations of health service interventions.
Differential Effects of Polymorphic Alleles of FGF Receptor 4 on Colon Cancer Growth and Metastasis
Authors: Heinzle Christine , Gsur Andrea , Hunjadi Monika , Erdem Zeynep , Gauglhofer Christine , Stättner Stefan , Karner Josef , Klimpfinger Martin , Wrba Friedrich , Reti Andrea , Hegedus Balazs , Baierl Andreas , Grasl-Kraupp Bettina , Holzmann Klaus , Grusch Michael , Berger Walter , Marian Brigitte 
Published: September 2012

Abstract
A gly388arg polymorphism (rs351855) in the transmembrane domain of the fibroblast growth factor receptor (FGFR4) is associated with increased risk, staging, and metastasis in several different types of cancer. To specifically assess the impact of the polymorphic FGFR4 in colorectal cancer (CRC), we engineered CRC cell lines with distinct endogenous expression patterns to overexpress either the FGFR4gly or FGFR4arg alleles. The biologic analyses revealed an oncogenic importance for both polymorphic alleles, but FGFR4gly was the stronger inducer of tumor growth, whereas FGFR4arg was the stronger inducer of migration. An evaluation of clinical specimens revealed that FGFR4 was upregulated in 20/71 patients independent of gly388arg status. There was no correlation between the presence of an FGFR4arg allele and CRC or polyp risk in 3,471 participants of the CORSA study. However, among 182 patients with CRC, FGFR4arg-carriers had a fivefold higher risk of tumors that were stage II or greater. Together, our results established that both allelic forms of FGFR4 exert an oncogenic impact and may serve equally well as therapeutic targets in CRC. One important implication of our findings is that FGFR4arg-carriers are at a higher risk for more aggressive tumors and therefore may profit from early detection measures. Cancer Res; 72(22); 5767–77. ©2012 AACR.
Deficient DNA Damage Signaling Leads to Chemoresistance to Cisplatin in Oral Cancer
Authors: Wang Ling , Mosel Adam J. , Oakley Gregory G. , Peng Aimin 
Published: September 2012

AbstractActivation of the cellular DNA damage response (DDR) is an important determinant of cell sensitivity to cisplatin and other chemotherapeutic drugs that eliminate tumor cells through induction of DNA damage. It is therefore important to investigate whether alterations of the DNA damage-signaling pathway confer chemoresistance in cancer cells and whether pharmacologic manipulation of the DDR pathway can resensitize these cells to cancer therapy. In a panel of oral/laryngeal squamous cell carcinoma (SCC) cell lines, we observed deficiencies in DNA damage signaling in correlation with cisplatin resistance, but not with DNA repair. These deficiencies are consistent with reduced expression of components of the ataxia telangiectasia mutated (ATM)-dependent signaling pathway and, in particular, strong upregulation of Wip1, a negative regulator of the ATM pathway. Wip1 knockdown or inhibition enhanced DNA damage signaling and resensitized oral SCC cells to cisplatin. In contrast to the previously reported involvement of Wip1 in cancer, Wip1 upregulation and function in these SCC cells is independent of p53. Finally, using xenograft tumor models, we showed that Wip1 upregulation promotes tumorigenesis and its inhibition improves the tumor response to cisplatin. Thus, this study reveals that chemoresistance in oral SCCs is partially attributed to deficiencies in DNA damage signaling, and Wip1 is an effective drug target for enhanced cancer therapy. Mol Cancer Ther; 11(11); 2401–9. ©2012 AACR.
Fibroblast Growth Factor-2 Is Required for Vasa Vasorum Plexus Stability in Hypercholesterolemic Mice
Authors: Mollmark Jessica I. , Park Andrew J.-H. , Kim Justin , Wang Thomas Z. , Katzenell Sarah , Shipman Samantha L. , Zagorchev Lyubomir G. , Simons Michael , Mulligan-Kehoe Mary Jo 
Published: September 2012

Objective—

Vasa vasorum are angiogenic in advanced stages of human atherosclerosis and hypercholesterolemic mouse models. Fibroblast growth factor-2 (FGF-2) is the predominant angiogenic growth factor in the adventitia and plaque of hypercholesterolemic low-density lipoprotein receptor–deficient/apolipoprotein B
100/100
mice (DKO). FGF-2 seems to play a role in the formation of a distinct vasa vasorum network. This study examined the vasa vasorum structure and its relationship to FGF-2.

Methods and Results—

DKO mice treated with saline, antiangiogenic recombinant plasminogen activator inhibitor-1
23
(rPAI-1
23
), or soluble FGF receptor 1 were perfused with fluorescein-labeled
Lycopersicon esculentum
lectin. Confocal images of FGF-2–probed descending aorta adventitia show that angiogenic vasa vasorum form a plexus-like network in saline-treated DKO similar to the FGF-2 pattern of distribution. Mice treated with rPAI-1
23
and soluble FGF receptor 1 lack a plexus; FGF-2 and vasa vasorum density and area are significantly reduced. A perlecan/FGF-2 complex is critical for plexus stability. Excess plasmin produced in rPAI-1
23
-treated DKO mice degrades perlecan and destabilizes the plexus. Plasmin activity and plaque size measured in DKO and DKO/plasminogen activator inhibitor-1
−
/−
mice demonstrate that elevated plasmin activity contributes to reduced plaque size.

Conclusion—
An FGF-2/perlecan complex is required for vasa vasorum plexus stability. Elevated plasmin activity plays a significant inhibitory role in vasa vasorum plexus and plaque development.
Biglycan Induces the Expression of Osteogenic Factors in Human Aortic Valve Interstitial Cells via Toll-Like Receptor-2
Authors: Song Rui , Zeng Qingchun , Ao Lihua , Yu Jessica A. , Cleveland Joseph C. , Zhao Ke-seng , Fullerton David A. , Meng Xianzhong 
Published: September 2012

Objective—
Although biglycan (BGN) and oxidized low-density lipoprotein (oxLDL) accumulation has been observed in calcific, stenotic aortic valves, their role in the pathogenesis of calcific aortic valve disease is poorly understood. We hypothesized that soluble BGN induces the osteogenic response in human aortic valve interstitial cells via Toll-like receptor (TLR) 2 and TLR4 and mediates the proosteogenic effect of oxLDL.

Methods and Results—

Aortic valve interstitial cells of stenotic valves express higher levels of BGN. Stimulation of cells from normal valves with BGN increased the expression of bone morphogenetic protein-2 (BMP-2) and alkaline phosphatase (ALP) among the chondrogenic/osteogenic markers examined and caused accumulation of calcium deposits. TLR2 silencing, but not TLR4 silencing, reduced BMP-2 and ALP levels after BGN stimulation although coimmunoprecipitation revealed that BGN interacts with both TLR2 and TLR4. BGN induced the phosphorylation of
extracellular signal-regulated protein kinase
-1/2, p38 mitogen-activated protein kinase and nuclear factor-κB. Inhibition of
extracellular-regulated kinase
-1/2 markedly reduced the upregulation of BMP-2 and ALP expression by BGN whereas inhibition of p38 mitogen-activated protein kinase or nuclear factor-κB had a moderate effect. Stimulation of aortic valve interstitial cells with oxLDL upregulated BGN expression and release. Knockdown and neutralization of BGN reduced the effect of oxLDL on BMP-2 and ALP expression.

Conclusion—
Extracellular soluble BGN induces the expression of BMP-2 and ALP in human aortic valve interstitial cells primarily via TLR2 and contributes to the proosteogenic effect of oxLDL. These findings highlight the potential role of soluble BGN and oxLDL in the development of calcific aortic valve disease.