bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expression of Fluorescent Proteins in Bifidobacteria for Analysis of Host-Microbe Interactions
Authors: Grimm Verena , Gleinser Marita , Neu Caroline , Zhurina Daria , Riedel Christian U. 
Published: March 2014

ABSTRACT

Bifidobacteria are an important component of the human gastrointestinal microbiota and are frequently used as probiotics. The genetic inaccessibility and lack of molecular tools commonly used in other bacteria have hampered a detailed analysis of the genetic determinants of bifidobacteria involved in their adaptation to, colonization of, and interaction with the host. In the present study, a range of molecular tools were developed that will allow the closing of some of the gaps in functional analysis of bifidobacteria. A number of promoters were tested for transcriptional activity in
Bifidobacterium bifidum
S17 using pMDY23, a previously published promoter probe vector. The promoter of the
gap
gene (P

gap

) of
B. bifidum
S17 yielded the highest promoter activity among the promoters tested. Thus, this promoter and the pMDY23 backbone were used to construct a range of vectors for expression of different fluorescent proteins (FPs). Successful expression of cyan fluorescent protein (CFP), green fluorescent protein (GFP), yellow fluorescent protein (YFP), and mCherry could be shown for three strains representing three different
Bifidobacterium
spp. The red fluorescent
B. bifidum
S17/pVG-mCherry was further used to demonstrate application of fluorescent bifidobacteria for adhesion assays and detection in primary human macrophages cultured
in vitro
. Furthermore, pMGC-mCherry was cloned by combining a chloramphenicol resistance marker and expression of the FP mCherry under the control of P

gap

. The chloramphenicol resistance marker of pMGC-mCherry was successfully used to determine gastrointestinal transit time of
B. bifidum
S17. Moreover,
B. bifidum
S17/pMGC-mCherry could be detected in fecal samples of mice after oral administration.
Purification and Characterization of Phosphonoglycans from Glycomyces sp. Strain NRRL B-16210 and Stackebrandtia nassauensis NRRL B-16338
Authors: Yu Xiaomin , Price Neil P. J. , Evans Bradley S. , Metcalf William W. 
Published: March 2014

ABSTRACT

Two related actinomycetes,
Glycomyces
sp. strain NRRL B-16210 and
Stackebrandtia nassauensis
NRRL B-16338, were identified as potential phosphonic acid producers by screening for the gene encoding phosphoenolpyruvate (PEP) mutase, which is required for the biosynthesis of most phosphonates. Using a variety of analytical techniques, both strains were subsequently shown to produce phosphonate-containing exopolysaccharides (EPS), also known as phosphonoglycans. The phosphonoglycans were purified by sequential organic solvent extractions, methanol precipitation, and ultrafiltration. The EPS from the
Glycomyces
strain has a mass of 40 to 50 kDa and is composed of galactose, xylose, and five distinct partially
O
-methylated galactose residues. Per-deutero-methylation analysis indicated that galactosyl residues in the polysaccharide backbone are 3,4-linked Gal, 2,4-linked 3-MeGal, 2,3-linked Gal, 3,6-linked 2-MeGal, and 4,6-linked 2,3-diMeGal. The EPS from the
Stackebrandtia
strain is comprised of glucose, galactose, xylose, and four partially
O
-methylated galactose residues. Isotopic labeling indicated that the
O
-methyl groups in the
Stackebrandtia
phosphonoglycan arise from
S
-adenosylmethionine. The phosphonate moiety in both phosphonoglycans was shown to be 2-hydroxyethylphosphonate (2-HEP) by
31
P nuclear magnetic resonance (NMR) and mass spectrometry following strong acid hydrolysis of the purified molecules. Partial acid hydrolysis of the purified EPS from
Glycomyces
yielded 2-HEP in ester linkage to the
O
-5 or
O
-6 position of a hexose and a 2-HEP mono(2,3-dihydroxypropyl)ester. Partial acid hydrolysis of
Stackebrandtia
EPS also revealed the presence of 2-HEP mono(2,3-dihydroxypropyl)ester. Examination of the genome sequences of the two strains revealed similar
pepM
-containing gene clusters that are likely to be required for phosphonoglycan synthesis.
Mycobacterium tuberculosis Latin American-Mediterranean Family and Its Sublineages in the Light of Robust Evolutionary Markers
Authors: Mokrousov Igor , Vyazovaya Anna , Narvskaya Olga 
Published: March 2014

ABSTRACT

Mycobacterium tuberculosis
has a clonal population structure, and the Latin American-Mediterranean (LAM) family is one of the largest and most widespread within this species, showing evidence for remarkable pathobiology and a confusing phylogeny. Here, we applied robust phylogenetic markers to study the evolution of the LAM family and its major sublineages circulating in Russia and neighboring countries. A total of 250
M. tuberculosis
isolates were confirmed to belong to the LAM family based on the analysis of the LAM-specific single-nucleotide polymorphisms (SNPs) in the
Rv3062
and
Rv0129c
genes. At this stage, the family status was rectified for 121 isolates misleadingly assigned by CRISPR spoligotyping to non-LAM families (T1- or T5-RUS1). Consequently, the reestimated LAM prevalence rate increased 2-fold in Russia and Kazakhstan and 4-fold in Belarus. The majority (91.8 to 98.7%) of the LAM isolates from all three countries belonged to the LAM-RUS sublineage. In contrast, the Ibero-American LAM RD-Rio sublineage was identified in only 7 Russian isolates. Taken together, our findings and further analyses suggest a monophyletic origin of LAM-RUS: at a historically distant time, in Russia, in a small founding bacterial/human population. Its dissemination pattern and high prevalence rate in Northern Eurasia may indicate a long-term coexistence of the LAM-RUS sublineage and local human populations hypothetically leading to coadaptation and reduced pathogenicity of the relatively more ancient clones, such as spoligotype international type 254 (SIT254), compared to the more recent SIT252 and SIT266 clones. In contrast, rare LAM RD-Rio isolates were likely brought to Russia through occasional human contact. The spread of RD-Rio strains is not as global as commonly claimed and is determined largely by human migration flows (rather than by pathobiological properties of these strains). Consequently, a host population factor appears to play a major role in shaping the
in situ
dissemination pattern of the imported strains in an autochthonous population.
Structure of Bacterial Transcription Factor SpoIIID and Evidence for a Novel Mode of DNA Binding
Authors: Chen Bin , Himes Paul , Liu Yu , Zhang Yang , Lu Zhenwei , Liu Aizhuo , Yan Honggao , Kroos Lee 
Published: March 2014

ABSTRACT

SpoIIID is evolutionarily conserved in endospore-forming bacteria, and it activates or represses many genes during sporulation of
Bacillus subtilis
. An SpoIIID monomer binds DNA with high affinity and moderate sequence specificity. In addition to a predicted helix-turn-helix motif, SpoIIID has a C-terminal basic region that contributes to DNA binding. The nuclear magnetic resonance (NMR) solution structure of SpoIIID in complex with DNA revealed that SpoIIID does indeed have a helix-turn-helix domain and that it has a novel C-terminal helical extension. Residues in both of these regions interact with DNA, based on the NMR data and on the effects on DNA binding
in vitro
of SpoIIID with single-alanine substitutions. These data, as well as sequence conservation in SpoIIID binding sites, were used for information-driven docking to model the SpoIIID-DNA complex. The modeling resulted in a single cluster of models in which the recognition helix of the helix-turn-helix domain interacts with the major groove of DNA, as expected. Interestingly, the C-terminal extension, which includes two helices connected by a kink, interacts with the adjacent minor groove of DNA in the models. This predicted novel mode of binding is proposed to explain how a monomer of SpoIIID achieves high-affinity DNA binding. Since SpoIIID is conserved only in endospore-forming bacteria, which include important pathogenic
Bacilli
and
Clostridia
, whose ability to sporulate contributes to their environmental persistence, the interaction of the C-terminal extension of SpoIIID with DNA is a potential target for development of sporulation inhibitors.
The association of the ‘additional height index’ with atopic diseases, non-atopic asthma, ischaemic heart disease and mortality: a population-based study
Authors: Fenger R V , Vidal C , Gonzalez-Quintela A , Husemoen L L N , Skaaby T , Aadahl M , Linneberg A 
Published: March 2014

ObjectiveIntrauterine growth has been associated with atopic conditions. Growth and adult height have been associated with cardiovascular disease, cancers and mortality but are highly genetic traits. The objectives of the study were as follows: first, to define a height measure indicating an individual's height below or above that which could be expected based on parental height (genetic inheritance) and growth charts. It was named ‘the additional height index’ (AHI), defined as (attained—expected) height; second, to investigate possible associations of AHI with atopic versus non-atopic health outcomes and with ischaemic heart disease (IHD) and IHD mortality.DesignGeneral population-based study.SettingResearch centre.ParticipantsA random sample of 2656 men and women living in greater Copenhagen took part in the MONICA10 study (the Danish monitoring trends and determinants of cardiovascular disease). In total, 1900 participants with information of parental height were selected.Outcome measuresAtopic sensitisation (serum IgE), questionnaire information of atopic dermatitis, rhinoconjunctivitis, asthma or wheezing, and registry-based diagnoses of IHD/IHD mortality from National Registries.ResultsIncreasing levels of AHI were inversely associated with non-atopic asthma, non-atopic wheezing, IHD and IHD mortality (IHD-all). For one SD increase of AHI, the OR or HR with CI in adjusted analyses was non-atopic asthma OR=0.52 (0.36 to 0.74), non-atopic wheezing OR=0.67 (0.51 to 0.89), and IHD-all HR=0.89 (0.78 to 1.01). The level of AHI was higher among individuals with atopic dermatitis, allergic rhinoconjunctivitis and atopic sensitisation (all p values <0.001) compared with individuals without those conditions; however, the associations were not confirmed in adjusted analyses.ConclusionsIndividuals with childhood conditions that led them to attain tallness higher than expected from their parents’ height may be at lower risk of non-atopic asthma/wheeze and IHD/IHD mortality but possibly at higher risk of atopic conditions. The measure of tallness below or above the expected height could be a sensitive alternative to normal height in epidemiological analyses.
Changing community health service delivery in economically less-developed rural areas in China: impact on service use and satisfaction
Authors: Liu Yong , Yuan Zhaokang , Liu Yuxi , Jayasinghe Upali W , Harris Mark F 
Published: March 2014

ObjectiveTo evaluate the impact of a model of rural community health service (CHS) on the use and acceptability of primary healthcare services.DesignQuasi-experimental.SettingTwo adjacent rural counties in China.Participants5842 residents in 2009 and 3807 in 2010 from 980 households in 7 intervention townships and 49 villages; 2232 residents in 2009 and 2315 in 2010 from 628 households in 3 comparison townships and 9 villages. All residents were approached to participate, with no significant differences in age or sex between groups.InterventionMultilevel intervention in 2009 including training rural practitioners, encouraging clinic improvements, providing clinical guidelines, standards and subsidies.Data collectionSurveys of community members from randomly sampled households in 2009 and 2010.Primary outcome measuresSatisfaction with and utilisation of outpatient and public health services.AnalysisFactor analysis confirmed two components of satisfaction. Univariate and multilevel analysis was used.ResultsSatisfaction scores for intervention county respondents increased from 21.4 (95% CI 21.1 to 21.7) to 22.1 (95% CI 21.7 to 22.4) with no change in comparison area. In multilevel analysis, satisfaction with patient-centred care was associated with chronic disease, shorter waiting times and county. Satisfaction with clinic environment and cost was associated with female gender, shorter waiting times but not county. The proportion of children receiving immunisation in intervention village clinics increased from 42.5% (95% CI 27.9% to 47.1%) to 59.2% (95% CI 53.8% to 64.6%) whereas this decreased in comparison villages (16.5%; 95% CI 10.3% to 22.7% to 6.0%; 95% CI 1.3% to 10.7%). Antenatal visits increased in intervention villages (from 69.0%, 95% CI 65.8% to 73.1% to 75.8%, 95% CI 72.2% to 79.4%) with no change in comparison villages.ConclusionsIntroduction of a CHS model adapted to economically less-developed rural areas was associated with some improvements in satisfaction with care and use of some village-based public health services. Further research is needed to determine its public health impact and application to other areas.
Chlamydia trachomatisIgG seroprevalence in the general population of the Netherlands in 1996 and in 2007: differential changes by gender and age
Authors: van Aar F , de Moraes M , Morré S A , van Bergen J E A M , van der Klis F R M , Land J A , van der Sande M A B , van den Broek I V F 
Published: March 2014

ObjectivesChlamydia trachomatis(CT) reporting rates from sexually transmitted infection clinics and general practitioners have shown a rising trend in the Netherlands. It is unknown to what extent this reflects increased CT transmission or improved case finding. To achieve more insight into the CT epidemic, we explored the CT IgG seroprevalence (a marker of past CT infection) in the general population of the Netherlands in 1996 and in 2007.MethodsFrom two population-based studies in 1996 and 2007, serum samples, demographic and sexual behaviour outcomes were examined, including 1246 men and 1930 women aged 15–39 years. Serum CT IgG antibodies were analysed using the Medac CT IgG ELISA test. Multivariate logistic regression analyses explored the seroprevalence and determinants over time.ResultsThe CT IgG seroprevalence was higher in women than in men (10% vs 6%). Among women aged 25–39 years the seroprevalence was lower in 2007 (9%) than in 1996 (14%; adjusted OR (aOR) 0.6, 95% CI 0.4 to 0.8). There was no statistical evidence of a difference in seroprevalence within birth cohorts. Factors associated with seropositivity were male gender (aOR 0.4, 95% CI 0.3 to 0.7), a self-reported history of CT infection (aOR 5.1, 95% CI 2.6 to 10.0), age 25–39 years (aOR 1.7, 95% CI 1.1 to 2.7), non-Western ethnicity (aOR 2.2, 95% CI 1.4 to 3.3) and ≥2 recent sexual partners (aOR 2.2, 95% CI 1.3 to 3.5).ConclusionsBetween 1996 and 2007 the proportion of individuals in the general population with CT IgG antibodies was lower among women aged 25–39 years, but remained similar among younger women and men.
The release and persistence of radioactive anthropogenic nuclides
Authors: Hancock Gary J. , Tims Stephen G. , Fifield L. Keith , Webster Ian T. 
Published: March 2014

Abstract

Atmospheric testing of nuclear weapons during the period 1945–1980 ushered in the ‘atomic age’ and released large quantities of anthropogenic radiogenic nuclides into the atmosphere. These radionuclides were subsequently deposited as fallout to the entire surface of the planet. While many have decayed to negligible levels, long-lived radionuclides persist and will do so for thousands of years. Isotopes of plutonium,
239
Pu (half-life 24 100 years) and
240
Pu (half-life 6563 years), provide the best chronological markers for the onset of this anthropogenic event both now and into the future due to their long half-lives, particle-reactivity, and the fact that they were present in negligible quantities prior to anthropogenic production and release. Chronostratigraphic markers established by distinct Pu concentration profiles and Pu isotope changes in sediment sequences and ice and coral cores can provide high-resolution dating over the last 60 years. However, even though fallout has ceased, it is found that the Pu inventory currently held in surface soil layers and the oceans will continue to supply Pu to sediment deposition zones for millennia and centuries, respectively. The delivery of this Pu will depend on soil erosion and bioturbation rates, and the rate of removal of dissolved Pu from the ocean.
Basement exploration, West of Shetlands: progress in opening a new play on the UKCS
Authors: Trice Robert 
Published: March 2014

Abstract
Commercial production of hydrocarbon from fractured crystalline basement is well documented, with petroleum basins across the globe hosting fractured basement fields. The UK is an anomaly within this global phenomenon as, despite numerous serendipitous discoveries of basement oil in the North Sea and the West of Shetlands, there is currently no commercial field on the United Kingdom Continental Shelf (UKCS) that is reliant on oil production from fractured basement. Recognizing that this situation presented an exploration niche, Hurricane Energy plc (Hurricane) was formed to focus on UKCS basement exploration and concentrated its efforts in acquiring exploration acreage in the West of Shetlands. In 2009 Hurricane drilled the first well designed to explore the basement play on the UKCS, leading to the Lancaster Discovery with a contingent resource range (1C–3C) of 62–456 million barrels of oil equivalent (MMboe). The Lancaster Discovery is presented to summarize the challenges and processes that have been applied in the exploration and evaluation of the West of Shetlands basement play. Conclusions from this work indicate that basement hydrocarbon resource potential is of such significance that it may represent a strategic resource for the UK, with over 1154 MMboe of 2C and mean unrisked prospective resources so far identified.
Sedimentation model of piggyback basins: Cenozoic examples of San Juan Precordillera, Argentina
Authors: Suriano J. , Limarino C. O. , Tedesco A. M. , Alonso M. S. 
Published: March 2014

Abstract
Piggyback basins are one of the most important sediment storage systems for foredeep basins within foreland basin systems, so understanding the dynamics of sediment accumulation and allocyclic changes is essential. Three alluvial systems are proposed here to depict sediment movement along the piggyback basin: piedmont, axial and transference systems. We propose differentiation between open continental piggyback basins that include a transference system that is able to deliver sediment to the foredeep and closed piggyback basins that are isolated. Two idealized models of sedimentation in piggyback basins are proposed. For open piggyback basins we identify four stages: (a) the incision stage; (b) the confined low accommodation system tract; (c) the high accommodation system tract; and (d) the unconfined low accommodation system tract. Meanwhile two stages are proposed for closed ones: (a) the high accommodation system tract; and (b) the low accommodation system tract. To test these models, Quaternary deposits and a Miocene unit are analysed. The first one is controlled by climatic changes, and the second is related to tectonic activity in the Precordillera.
Preclinical and Early Clinical Evaluation of the Oral AKT Inhibitor, MK-2206, for the Treatment of Acute Myelogenous Leukemia
Authors: Konopleva Marina Y. , Walter Roland B. , Faderl Stefan H. , Jabbour Elias J. , Zeng Zhihong , Borthakur Gautam , Huang Xuelin , Kadia Tapan M. , Ruvolo Peter P. , Feliu Jennie B. , Lu Hongbo , Debose LaKiesha , Burger Jan A. , Andreeff Michael , Liu Wenbin , Baggerly Keith A. , Kornblau Steven M. , Doyle L. Austin , Estey Elihu H. , Kantarjian Hagop M. 
Published: March 2014

AbstractPurpose: Recent studies suggested that AKT activation might confer poor prognosis in acute myelogenous leukemia (AML), providing the rationale for therapeutic targeting of this signaling pathway. We, therefore, explored the preclinical and clinical anti-AML activity of an oral AKT inhibitor, MK-2206.Experimental Methods: We first studied the effects of MK-2206 in human AML cell lines and primary AML specimens in vitro. Subsequently, we conducted a phase II trial of MK-2206 (200 mg weekly) in adults requiring second salvage therapy for relapsed/refractory AML, and assessed target inhibition via reverse phase protein array (RPPA).Results: In preclinical studies, MK-2206 dose-dependently inhibited growth and induced apoptosis in AML cell lines and primary AML blasts. We then treated 19 patients with MK-2206 but, among 18 evaluable participants, observed only 1 (95% confidence interval, 0%–17%) response (complete remission with incomplete platelet count recovery), leading to early study termination. The most common grade 3/4 drug-related toxicity was a pruritic rash in 6 of 18 patients. Nevertheless, despite the use of MK-2206 at maximum tolerated doses, RPPA analyses indicated only modest decreases in Ser473 AKT (median 28%; range, 12%–45%) and limited inhibition of downstream targets.Conclusions: Although preclinical activity of MK-2206 can be demonstrated, this inhibitor has insufficient clinical antileukemia activity when given alone at tolerated doses, and alternative approaches to block AKT signaling should be explored. Clin Cancer Res; 20(8); 2226–35. ©2014 AACR.
Phase I Safety, Pharmacokinetic, and Pharmacodynamic Study of SAR245409 (XL765), a Novel, Orally Administered PI3K/mTOR Inhibitor in Patients with Advanced Solid Tumors
Authors: Papadopoulos Kyriakos P. , Tabernero Josep , Markman Ben , Patnaik Amita , Tolcher Anthony W. , Baselga José , Shi Weiliang , Egile Coumaran , Ruiz-Soto Rodrigo , Laird A. Douglas , Miles Dale , LoRusso Patricia M. 
Published: March 2014

Abstract
Purpose: This phase I, first-in-human study evaluated the safety, maximum-tolerated dose (MTD), pharmacokinetics, pharmacodynamics, and preliminary efficacy of SAR245409, an inhibitor of pan-Class I phosphoinositide 3-kinase (PI3K) and mTOR, administered orally once or twice daily in patients with advanced solid tumors.
Experimental Design: Eighty-three patients received SAR245409. Doses ranged from 15 to 120 mg twice daily, and 70 to 100 mg once daily. A 3+3 dose-escalation design was used to determine the MTD. Patients were evaluated for adverse events and response. Assessments included pharmacokinetic, pharmacodynamic impact of SAR245409 on PI3K pathway signaling in hair sheath cells, skin and tumor, and characterization of tumor molecular alterations.
Results: The MTDs were 50 mg twice daily and 90 mg once daily. The most frequent treatment-related adverse events were nausea (36.1%), diarrhea (21.7%), vomiting (19.3%), and decreased appetite (16.9%). The most frequent treatment-related grade 3/4 adverse events were increases in alanine aminotransferase (6.0%) and aspartate aminotransferase (4.8%). SAR245409 had a relatively short plasma half-life (2.96–7.52 hours). At MTDs, once- and twice-daily regimens yielded similar mean steady-state plasma exposure. A reduction in PI3K and mTORC1/mTORC2 pathway signaling was observed in serial hair sheath cells, skin, and tumor samples. Best response was stable disease in 48% of evaluable patients; seven patients had minor tumor regression. Twelve patients with stable disease were treated for ≥16 weeks. No trend was observed correlating tumor molecular alteration with antitumor activity.
Conclusion: SAR245409 had a manageable safety profile, demonstrated reduced PI3K and mTORC1/mTORC2 pathway signaling and was associated with clinically relevant stable disease. Clin Cancer Res; 20(9); 2445–56. ©2014 AACR.