bluuebunny/crossref_metadata_2025_split huggingface dataset:
The changes in mycolic acid structures caused by hadC mutation have a dramatic effect on the virulence of Mycobacterium tuberculosis
Authors: Slama Nawel , Jamet Stevie , Frigui Wafa , Pawlik Alexandre , Bottai Daria , Laval Françoise , Constant Patricia , Lemassu Anne , Cam Kaymeuang , Daffé Mamadou , Brosch Roland , Eynard Nathalie , Quémard Annaïk 
Published: November 2015

SummaryUnderstanding the molecular strategies used by Mycobacterium tuberculosis to invade and persist within the host is of paramount importance to tackle the tuberculosis pandemic. Comparative genomic surveys have revealed that hadC, encoding a subunit of the HadBC dehydratase, is mutated in the avirulent M. tuberculosis H37Ra strain. We show here that mutation or deletion of hadC affects the biosynthesis of oxygenated mycolic acids, substantially reducing their production level. Additionally, it causes the loss of atypical extra‐long mycolic acids, demonstrating the involvement of HadBC in the late elongation steps of mycolic acid biosynthesis. These events have an impact on the morphotype, cording capacity and biofilm growth of the bacilli as well as on their sensitivity to agents such as rifampicin. Furthermore, deletion of hadC leads to a dramatic loss of virulence: an almost 4‐log drop of the bacterial load in the lungs and spleens of infected immunodeficient mice. Both its unique function and importance for M. tuberculosis virulence make HadBC an attractive therapeutic target for tuberculosis drug development.
Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C‐ring assembly in T3SS
Authors: McDowell Melanie A. , Marcoux Julien , McVicker Gareth , Johnson Steven , Fong Yu Hang , Stevens Rebecca , Bowman Lesley A. H. , Degiacomi Matteo T. , Yan Jun , Wise Adam , Friede Miriam E. , Benesch Justin L. P. , Deane Janet E. , Tang Christoph M. , Robinson Carol V. , Lea Susan M. 
Published: November 2015

SummaryFlagellar type III secretion systems (T3SS) contain an essential cytoplasmic‐ring (C‐ring) largely composed of two proteins FliM and FliN, whereas an analogous substructure for the closely related non‐flagellar (NF) T3SS has not been observed in situ. We show that the spa33 gene encoding the putative NF‐T3SS C‐ring component in Shigella flexneri is alternatively translated to produce both full‐length (Spa33‐FL) and a short variant (Spa33‐C), with both required for secretion. They associate in a 1:2 complex (Spa33‐FL/C2) that further oligomerises into elongated arrays in vitro. The structure of Spa33‐C2 and identification of an unexpected intramolecular pseudodimer in Spa33‐FL reveal a molecular model for their higher order assembly within NF‐T3SS. Spa33‐FL and Spa33‐C are identified as functional counterparts of a FliM–FliN fusion and free FliN respectively. Furthermore, we show that Thermotoga maritima FliM and FliN form a 1:3 complex structurally equivalent to Spa33‐FL/C2, allowing us to propose a unified model for C‐ring assembly by NF‐T3SS and flagellar‐T3SS.
Counterfactuals and Epistemic Basing Relations
Authors: Bondy Patrick 
Published: November 2015

AbstractThis article is about the epistemic basing relation, which is the relation that obtains between beliefs and the reasons for which they are held. We need an adequate account of the basing relation if we want to have a satisfactory account of doxastic justification, which we should want to have. To that end, this article aims to achieve two goals. The first is to show that a plausible account of the basing relation must invoke counterfactual concepts. The second is to set out two related analyses of the basing relation, each of which seems quite plausible.
Phloroglucinol Reduces Photodamage in Hairless Mice via Matrix Metalloproteinase Activity Through MAPK Pathway
Authors: Im A‐Rang , Nam Kung‐Woo , Hyun Jin Won , Chae Sungwook 
Published: November 2015

AbstractWe investigated the photoprotective activity of phloroglucinol on ultraviolet B (UVB)‐induced deleterious effects in hairless mice in vivo. To assess the photoprotective effect of phloroglucinol, phloroglucinol‐treated HR‐1 hairless male mice were exposed to UVB irradiation. The inhibitory activity of phloroglucinol on wrinkle formation was determined by analysis of skin replicas, epidermal thickness based on histological examination and collagen damage. Matrix metalloproteinase‐1 (MMP‐1), matrix metalloproteinase‐9 (MMP‐9) and tissue inhibitor of metalloproteinase (TIMP) mRNA levels were measured by real‐time PCR. UVB induced transcription of proinflammatory cytokines, including interleukin‐1 beta (IL‐1β, IL‐6) and IL‐8 (IL‐8). The protective effects of phloroglucinol on UVB‐induced skin photoaging were examined by measuring protein levels of MMPs and mitogen‐activated protein (MAP) kinases. The results of these experiments suggest that phloroglucinol has a significant beneficial effect on the barrier function of the skin. In hairless mice, signs of photoaging and photodamage, including coarse wrinkle formation, epidermal thickness and elastic fiber degeneration, were reduced in severity by phloroglucinol application. The phloroglucinol‐treated group showed remarkably decreased mRNA levels of MMP‐1, MMP‐9 and inflammatory cytokines in comparison with those of the UVB‐induced group. Oral administration of phloroglucinol attenuated phosphorylation of MAP kinases, including extracellular signal‐regulated kinase, c‐Jun N‐terminal kinase and p38.
Monitoring the outcomes of interventions against Taenia solium: options and suggestions
Authors: Lightowlers M. W. , Garcia H. H. , Gauci C. G. , Donadeu M. , Abela‐Ridder B. 
Published: November 2015

SummaryThere is an increasing interest in reducing the incidence of human neurocysticercosis, caused by infection with the larval stage of Taenia solium. Several intervention trials are currently assessing various options for control of T. solium transmission. A critical aspect of these trials will be the evaluation of whether the interventions have been successful. However, there is no consensus about the most appropriate or valuable methods that should be used. Here, we undertake a critical assessment of the diagnostic tests which are currently available for human T. solium taeniasis and human and porcine cysticercosis, as well as their suitability for evaluation of intervention trial outcomes. Suggestions are made about which of the measures that are available for evaluation of T. solium interventions would be most suitable, and which methodologies are the most appropriate given currently available technologies. Suggestions are also made in relation to the most urgent research needs in order to address deficiencies in current diagnostic methods.
Contested Lands? Dissonance and Common Ground in Stakeholder Views on Forest Values
Authors: Haugen Katarina 
Published: November 2015

ABSTRACTForest lands are used in increasingly plural ways and serve society with numerous benefits. This paper analyses the views of private forest owners and the general public in Sweden on the values of the forest. Two main dimensions were identified: ‘preservation and recreation’ values, reflecting ecological and social aspects; and ‘production’ values, reflecting economic aspects. While the general public emphasised the importance of forest uses which cater to ecological and social forest values more strongly compared to the forest owners, no significant difference was found concerning economic forest values. This suggests that while there is scope for contestation over forest land use, there is also some potential for common ground across stakeholder groups. These findings add to the body of knowledge of the views on the use of forest lands, and can inform forest related planning, management and policy development.
Outcomes of Clostridium difficile infection in pediatric solid organ transplant recipients
Authors: Pant C. , Deshpande A. , Desai M. , Jani B.S. , Sferra T.J. , Gilroy R. , Olyaee M. 
Published: November 2015

AbstractBackgroundThe incidence of Clostridium difficile infection (CDI) is increasing in the pediatric population. Pediatric recipients of solid organ transplantation (SOT) may be at a higher risk for CDI in part because of chemotherapy and prolonged hospitalization.MethodsWe utilized data from the Healthcare Cost and Utilization Project Kids' Inpatient Database to study the incidence and outcomes related to CDI as a complicating factor in pediatric recipients of SOT.ResultsOur results demonstrate that hospitalized children with SOT have increased rates of infection, with the greatest risk for younger children with additional comorbidities and severe illness. The type of transplanted organ affects the risk for CDI, with the lowest incidence observed in renal transplant patients.ConclusionThe occurrence of CDI in the pediatric SOT population contributes to a greater length of stay and higher hospital charges. However, CDI is not an independent predictor of increased in‐ hospital mortality in these patients.
Human papillomavirus detected in viral warts of renal transplant recipients
Authors: Martelli‐Marzagão F. , Santos Junior G.F. , Ogawa M.M. , Enokihara M.M.S.S. , Porro A.M. , Tomimori J. 
Published: November 2015

AbstractObjectivesFew studies have been conducted in South America regarding the detection and genotyping of human papillomavirus (HPV) in viral warts of renal transplant recipients (RTRs). The characterization of the population most susceptible to the development of warts and the knowledge of the main HPV types in this environment prompted this study, which focuses on the detection and typing of HPV in RTRs in Brazil.MethodsFifty‐eight patients with viral warts from the Hospital São Paulo/Federal University of São Paulo were included in this study. HPV was detected by polymerase chain reaction (PCR) using combinations of the following primers: PGMY 09/11, RK 91, CP 65/70, and CP 66/69. Restriction fragment length polymorphism and automated sequencing techniques were used for HPV typing.ResultsHPV was detected by PCR in 89.7% of viral wart samples. The most frequently detected HPV types included 57, 27, 1a, 2a, and 20. Other types of HPV‐epidermodysplasia verruciformis were also detected, including 14, 15, 19, 20, 21, 23, 36, and 38. Rare HPV types were also detected in our environment, including RTR X1, RTR X7, and 100. The time after transplant was correlated with an increased number of lesions and beta papillomavirus genus infection.ConclusionsThe HPV types detected in the RTR population were similar to those described in immunocompetent populations. However, the diversity of the HPV types identified and the number of lesions were increased in the RTR population.
SNAC‐As, stress‐responsive NAC transcription factors, mediate ABA‐inducible leaf senescence
Authors: Takasaki Hironori , Maruyama Kyonoshin , Takahashi Fuminori , Fujita Miki , Yoshida Takuya , Nakashima Kazuo , Myouga Fumiyoshi , Toyooka Kiminori , Yamaguchi‐Shinozaki Kazuko , Shinozaki Kazuo 
Published: October 2015

SummaryLeaf senescence is the terminal phenotype of plant leaf development, and ethylene is a major plant hormone inducing leaf senescence. Recent studies have shown that abscisic acid (ABA) also induces leaf senescence. However, the detailed mechanisms of ABA‐induced leaf senescence remain unclear. We focused on the A subfamily of stress‐responsive NAC (SNAC‐A) transcription factors, the expression of which is induced by abiotic stresses, particularly ABA. Gene expression analysis revealed that seven SNAC‐A genes including ANAC055, ANAC019, ANAC072/RD26, ANAC002/ATAF1, ANAC081/ATAF2, ANAC102 and ANAC032 were induced by long‐term treatment with ABA and/or during age‐dependent senescence. The SNAC‐A septuple mutant clearly showed retardation of ABA‐inducible leaf senescence. Microarray analysis indicated that SNAC‐As induce ABA‐ and senescence‐inducible genes. In addition, comparison of the expression profiles of the downstream genes of SNAC‐As and ABA‐responsive element (ABRE)‐binding protein (AREB)/ABRE‐binding factor (ABF) (AREB/ABFs) indicates that SNAC‐As induce a different set of ABA‐inducible genes from those mediated by AREB/ABFs. These results suggest that SNAC‐As play crucial roles in ABA‐induced leaf senescence signaling. We also discuss the function of SNAC‐As in the transcriptional change of leaf senescence as well as in ABA response under abiotic stress conditions.
The natural behavior of mononuclear phagocytes in HTS formation
Authors: Zhu Zhensen , Ding Jie , Ma Zengshuan , Iwashina Takashi , Tredget Edward E 
Published: October 2015

AbstractHypertrophic scars (HTS) are caused by trauma or burn injuries to the deep dermis and are considered fibrosis in the skin. Monocytes, M1 and M2 macrophages are mononuclear phagocytes. Studies suggest that M2 macrophages are profibrotic and might contribute to HTS formation. Our lab has established a human HTS‐like nude mouse model, in which the grafted human skin develops red, raised, and firm scarring, resembling HTS seen in humans. In this study, we observed the natural behavior of mononuclear phagocyte system in this nude mouse model of dermal fibrosis at multiple time points. Thirty athymic nude mice received human skin grafts and an equal number of mice received mouse skin grafts as controls. The grafted skin and blood were harvested at 1, 2, 3, 4, and 8 weeks. Wound area, thickness, collagen morphology and level, the cell number of myofibroblasts, M1‐ and M2‐like macrophages in the grafted skin, as well as monocyte fraction in the blood were investigated at each time points. Xenografted mice developed contracted and thickened scars grossly. The xenografted skin resembled human HTS tissue based on enhanced thickness, fibrotic orientation of collagen bundles, increased collagen level, and infiltration of myofibroblasts. In the blood, monocytes dramatically decreased at 1 week postgrafting and gradually returned to normal in the following 8 weeks. In the xenografted skin, M1‐like macrophages were found predominantly at 1–2 weeks postgrafting; whereas, M2‐like macrophages were abundant at later time points, 3–4 weeks postgrafting coincident with the development of fibrosis in the human skin tissues. This understanding of the natural behavior of mononuclear phagocytes in vivo in our mouse model provides evidence for the role of M2‐like macrophages in fibrosis of human skin and suggests that macrophage depletion in the subacute phases of wound healing might reduce or prevent HTS formation.
Detection and Molecular Characterization of Salmonella enterica Serovar Eppendorf Circulating in Chicken Farms in Tunisia
Authors: Ben Salem R. , Abbassi M.S. , García V. , García‐Fierro R. , Njoud C. , Messadi L. , Rodicio M. R. 
Published: November 2015

SummarySalmonella enterica subsp. enterica serovar Eppendorf, with antigenic formula 1,4,12,[27]:d:1,5, is an infrequent serovar. However, 14% (20 of 142) of the isolates recovered during June–July 2012 in chicken farms in Tunisia belonged to S. Eppendorf. These isolates were analysed for resistance and virulence profiles. None of them were susceptible to all antimicrobials tested, while 70%, 60%, 50%, 50%, 20% and 5% were resistant to sulphonamides (sul1, sul2 and sul3), streptomycin (aadA1‐like), trimethoprim (dfrA1‐like), nalidixic acid (GyrA Asp87→Asn and not identified), gentamicin (not identified) and ampicillin (blaTEM‐1‐like). About 30% of the isolates showed decreased susceptibility to ciprofloxacin and carried the qnrB gene; 65% of the isolates were multidrug resistant and contained class 1 integrons with sul1 or sul3 in the 3′ conserved segment. The orgA, ssaQ, mgtC, siiD and sopB virulence genes located on SPI1 to SPI5 and the fimbrial bcfC gene were present in all isolates; the sopE1 and sodC1 carried by prophages were variably detected; however, the prophage gipA gene and the spvC gene of serovar‐specific virulence plasmids were absent. Altogether, ten resistance and three virulence profiles were identified. Typing of the isolates with XbaI‐ and BlnI‐PFGE supports a close relationship, although they appear to be evolving under selective pressure probably caused by antimicrobial use in chicken husbandry. As far as we know, this is the first study investigating the molecular bases of antimicrobial drug resistance, the virulence gene content and the PFGE profiles of S. Eppendorf. The epidemiological surveillance of this serovar would be necessary to evaluate its possible impact on human health, particularly in Tunisia and other African countries where it was already reported.
Pentanol and Benzyl Alcohol Attack Bacterial Surface Structures Differently
Authors: Yano Takehisa , Miyahara Yoshiko , Morii Noriyuki , Okano Tetsuya , Kubota Hiromi 
Published: October 2015

ABSTRACT

The genus
Methylobacterium
tolerates hygiene agents like benzalkonium chloride (BAC), and infection with this organism is an important public health issue. Here, we found that the combination of BAC with particular alcohols at nonlethal concentrations in terms of their solitary uses significantly reduced bacterial viability after only 5 min of exposure. Among the alcohols, Raman spectroscopic analyses showed that pentanol (pentyl alcohol [PeA]) and benzyl alcohol (BzA) accelerated the cellular accumulation of BAC. Fluorescence spectroscopic assays and morphological assays with giant vesicles indicated that PeA rarely attacked membrane structures, while BzA increased the membrane fluidity and destabilized the structures. Other fluorescent spectroscopic assays indicated that PeA and BzA inactivate bacterial membrane proteins, including an efflux pump for BAC transportation. These findings suggested that the inactivation of membrane proteins by PeA and BzA led to the cellular accumulation but that only BzA also enhanced BAC penetration by membrane fluidization at nonlethal concentrations.
Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp
Authors: Zhao S. , Tyson G. H. , Chen Y. , Li C. , Mukherjee S. , Young S. , Lam C. , Folster J. P. , Whichard J. M. , McDermott P. F. 
Published: October 2015

ABSTRACT

The objectives of this study were to identify antimicrobial resistance genotypes for
Campylobacter
and to evaluate the correlation between resistance phenotypes and genotypes using
in vitro
antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114
Campylobacter
species isolates (82
C. coli
and 32
C. jejuni
) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including
tet
(O),
bla
OXA-61
,
catA
,
lnu
(C),
aph(2
″
)-Ib
,
aph(2
″
)-Ic
,
aph(2
′
)-If
,
aph(2
″
)-Ig
,
aph(2
″
)-Ih
,
aac(6
′
)-Ie-aph(2
″
)-Ia
,
aac(6
′
)-Ie-aph(2
″
)-If
,
aac(6
′
)-Im
,
aadE
,
sat4
,
ant(6
′
)
,
aad9
,
aph(3
′
)-Ic
, and
aph(3
′
)-IIIa
, and mutations in two housekeeping genes (
gyrA
and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs.
Reciprocal Regulation of GlnR and PhoP in Response to Nitrogen and Phosphate Limitations in Saccharopolyspora erythraea
Authors: Yao Li-li , Ye Bang-Ce 
Published: October 2015

ABSTRACT

Nitrogen and phosphate source sensing, uptake, and assimilation are essential for the growth and development of microorganisms. In this study, we demonstrated that SACE_6965 encodes the phosphate regulator PhoP, which controls the transcription of genes involved in phosphate metabolism in the erythromycin-producing
Saccharopolyspora erythraea
. We found that PhoP and the nitrogen regulator GlnR both regulate the transcription of
glnR
as well as other nitrogen metabolism-related genes. Interestingly, both GlnR- and PhoP-binding sites were identified in the
phoP
promoter region. Unlike the nonreciprocal regulation of GlnR and PhoP observed in
Streptomyces coelicolor
and
Streptomyces lividans
, GlnR negatively controls the transcription of the
phoP
gene in
S. erythraea
. This suggests that GlnR directly affects phosphate metabolism and demonstrates that the cross talk between GlnR and PhoP is reciprocal. Although GlnR and PhoP sites in the
glnR
and
phoP
promoter regions are located in close proximity to one another (separated by only 2 to 4 bp), the binding of both regulators to their respective region was independent and noninterfering. These results indicate that two regulators could separately bind to their respective binding sites and control nitrogen and phosphate metabolism in response to environmental changes. The reciprocal cross talk observed between GlnR and PhoP serves as a foundation for understanding the regulation of complex primary and secondary metabolism in antibiotic-producing actinomycetes.