bluuebunny/crossref_metadata_2025_split huggingface dataset:
A phytochrome/phototropin chimeric photoreceptor of fern functions as a blue/far‐red light‐dependent photoreceptor for phototropism in Arabidopsis
Authors: Kanegae Takeshi , Kimura Izumi 
Published: June 2015

SummaryIn the fern Adiantum capillus‐veneris, the phototropic response of the protonemal cells is induced by blue light and partially inhibited by subsequent irradiation with far‐red light. This observation strongly suggests the existence of a phytochrome that mediates this blue/far‐red reversible response; however, the phytochrome responsible for this response has not been identified. PHY3/NEO1, one of the three phytochrome genes identified in Adiantum, encodes a chimeric photoreceptor composed of both a phytochrome and a phototropin domain. It was demonstrated that phy3 mediates the red light‐dependent phototropic response of Adiantum, and that phy3 potentially functions as a phototropin. These findings suggest that phy3 is the phytochrome that mediates the blue/far‐red response in Adiantum protonemata. In the present study, we expressed Adiantum phy3 in a phot1 phot2 phototropin‐deficient Arabidopsis line, and investigated the ability of phy3 to induce phototropic responses under various light conditions. Blue light irradiation clearly induced a phototropic response in the phy3‐expressing transgenic seedlings, and this effect was fully inhibited by simultaneous irradiation with far‐red light. In addition, experiments using amino acid‐substituted phy3 indicated that FMN‐cysteinyl adduct formation in the light, oxygen, voltage (LOV) domain was not necessary for the induction of blue light‐dependent phototropism by phy3. We thus demonstrate that phy3 is the phytochrome that mediates the blue/far‐red reversible phototropic response in Adiantum. Furthermore, our results imply that phy3 can function as a phototropin, but that it acts principally as a phytochrome that mediates both the red/far‐red and blue/far‐red light responses.
Ectopic expression of snapdragon transcription factors facilitates the identification of genes encoding enzymes of anthocyanin decoration in tomato
Authors: Tohge Takayuki , Zhang Yang , Peterek Silke , Matros Andrea , Rallapalli Ghanasyam , Tandrón Yudelsy A. , Butelli Eugenio , Kallam Kalyani , Hertkorn Norbert , Mock Hans‐Peter , Martin Cathie , Fernie Alisdair R. 
Published: June 2015

SummaryGiven the potential health benefits of polyphenolic compounds in the diet, there is a growing interest in the generation of food crops enriched with health‐protective flavonoids. We undertook a series of metabolite analyses of tomatoes ectopically expressing the Delila and Rosea1 transcription factor genes from snapdragon (Antirrhinum majus), paying particular attention to changes in phenylpropanoids compared to controls. These analyses revealed multiple changes, including depletion of rutin and naringenin chalcone, and enhanced levels of anthocyanins and phenylacylated flavonol derivatives. We isolated and characterized the chemical structures of the two most abundant anthocyanins, which were shown by NMR spectroscopy to be delphinidin‐3–(4′′′–O‐trans‐p–coumaroyl)‐rutinoside‐5–O–glucoside and petunidin‐3–(4′′′–O‐trans‐p‐coumaroyl)‐rutinoside‐5–O–glucoside. By performing RNA sequencing on both purple fruit and wild‐type fruit, we obtained important information concerning the relative expression of both structural and transcription factor genes. Integrative analysis of the transcript and metabolite datasets provided compelling evidence of the nature of all anthocyanin biosynthetic genes, including those encoding species‐specific anthocyanin decoration enzymes. One gene, SlFdAT1 (Solyc12g088170), predicted to encode a flavonoid‐3–O‐rutinoside‐4′′′–phenylacyltransferase, was characterized by assays of recombinant protein and over‐expression assays in tobacco. The combined data are discussed in the context of both our current understanding of phenylpropanoid metabolism in Solanaceous species, and evolution of flavonoid decorating enzymes and their transcriptional networks in various plant species.
Mucocutaneous lupus erythematosus in dogs (21 cases)
Authors: Olivry Thierry , Rossi Michael A. , Banovic Frane , Linder Keith E. 
Published: June 2015

BackgroundThe diagnosis of dogs with chronic juxtamucosal erosive lesions and histopathology typical of cutaneous lupus erythematosus (CLE) is unclear.Hypothesis/ObjectivesWe report herein 21 dogs with mucocutaneous erosive lesions and lupus‐specific histopathology that we propose to be affected with mucocutaneous lupus erythematosus (MCLE), another variant of chronic CLE.MethodsInclusion criteria were the presence of the following: (i) a >2 month history of chronic or recurrent skin lesions; (ii) erosions or ulcers predominating at mucosae or mucocutaneous junctions; (iii) microscopic lesions of CLE (i.e. a lymphocyte‐rich interface dermatitis with basal keratinocyte damage); and (iv) a lack of complete remission following antimicrobials. Clinical questionnaires and skin biopsies were reviewed. Direct immunofluorescence and antinuclear antibody serology were performed whenever possible.ResultsMore than half of the 21 dogs were German shepherds or their crosses. The disease affected mostly dogs in their mid‐adulthood and there was an over‐representation of females. Erosions and ulcers predominated at genital/perigenital and anal/perianal areas, with a lower frequency of involvement of periocular, perioral and perinasal regions. In these dogs, there were no clinical signs suggestive of an associated systemic lupus erythematosus. Microscopic lesions were specific for CLE, but they were patchy and often infected with bacteria. The most common immunological finding was focal IgG deposition at the basement membrane zone. Lesions responded to varying interventions, but oral glucocorticoids led to a shorter time to complete remission. Relapses were common upon treatment tapering.Conclusions and clinical importanceThese observations support MCLE being another variant of canine CLE.
Generalized severe junctional epidermolysis bullosa with congenital absence of skin in churra lambs
Authors: Benavides Julio , Suárez‐Vega Aroa , Gutiérrez Jorge , de la Hera Sandra , Fuertes Miguel , Delgado Laetitia , Fernández Miguel , Ferreras María del Carmen , Arranz Juan José , Pérez Valentín 
Published: June 2015

BackgroundUp to 0.5% of churra lambs from two genetically related flocks showed congenital skin lesions of variable severity, jeopardizing the life of the lambs in the most severe cases.Hypothesis/ObjectivesThe primary objective of this study was to classify the type of congenital epithelial disease suffered by these animals, based on the description of the macroscopic skin defects, the histological and ultrastructural changes and the hereditary nature of the condition.AnimalsThirty affected newborn lambs from two genetically related flocks were studied. Three additional lambs acquired from two other flocks, which had no grossly apparent skin lesions and had died of infectious diseases, were studied as unaffected control animals.MethodsHistological and ultrastructural examinations of skin and oral mucosa samples were performed. Pedigree analyses were used to investigate genealogical relationships.ResultsGeneralized severe junctional epidermolysis bullosa with congenital absence of skin was described in all lambs studied and an autosomal recessive mode of inheritance was identified.Conclusions and clinical importanceThe pathological findings and mode of inheritance in these lambs are similar to an inherited epidermolysis bullosa subtype of humans, which has not been reported previously in veterinary medicine.
The Short Questionnaire to Assess Health-Enhancing (SQUASH) Physical Activity in Adolescents: A Validation Using Doubly Labeled Water
Authors: Campbell Nerissa , Gaston Anca , Gray Casey , Rush Elaine , Maddison Ralph , Prapavessis Harry 
Published: June 2015

Background:Accurate assessment of physical activity energy expenditure (PAEE) among adolescents is important for surveillance, evaluating interventions, and understanding the relation between energy balance and normal physiological and behavioral growth and development. The purpose of this study was to examine the validity of the Short Questionnaire to Assess Health-Enhancing Physical Activity (SQUASH)13 for measuring PAEE among adolescents.Methods:The participants were seventeen adolescents (9 females; Mean age = 17.53; SD = 0.62). Energy expenditure was measured during a 9-day period with doubly labeled water (DLW). The SQUASH was self-administered on the morning of the 10th day and assessed commuting activities, leisure time activities, household activities, and activities at work and school over the previous 9 days.Results:A Bland-Altman plot indicated that the SQUASH underestimated PAEE compared with DLW by a mean difference of 126 kcal·d−1 (95% limits of agreement: –1,207 to 1,459 kcal·d−1), representative of a 10% underestimation. The Spearman rank order correlation coefficient showed there was a significant association between the SQUASH and DLW (r = .50, P = .04), for estimating PAEE.Conclusion:When using a sample of highly active adolescents, the SQUASH is a valid self-report tool for measuring PAEE at the group and individual rank order level.
Transcription Factor ADS-4 Regulates Adaptive Responses and Resistance to Antifungal Azole Stress
Authors: Wang Kangji , Zhang Zhenying , Chen Xi , Sun Xianyun , Jin Cheng , Liu Hongwei , Li Shaojie 
Published: June 2015

ABSTRACT

Azoles are commonly used as antifungal drugs or pesticides to control fungal infections in medicine and agriculture. Fungi adapt to azole stress by rapidly activating the transcription of a number of genes, and transcriptional increases in some azole-responsive genes can elevate azole resistance. The regulatory mechanisms that control transcriptional responses to azole stress in filamentous fungi are not well understood. This study identified a bZIP transcription factor, ADS-4 (
a
ntifungal
d
rug
s
ensitive-4), as a new regulator of adaptive responses and resistance to antifungal azoles. Transcription of
ads-4
in
Neurospora crassa
cells increased when they were subjected to ketoconazole treatment, whereas the deletion of
ads-4
resulted in hypersensitivity to ketoconazole and fluconazole. In contrast, the overexpression of
ads-4
increased resistance to fluconazole and ketoconazole in
N. crassa
. Transcriptome sequencing (RNA-seq) analysis, followed by quantitative reverse transcription (qRT)-PCR confirmation, showed that ADS-4 positively regulated the transcriptional responses of at least six genes to ketoconazole stress in
N. crassa
. The gene products of four ADS-4-regulated genes are known contributors to azole resistance, including the major efflux pump CDR4 (Pdr5p ortholog), an ABC multidrug transporter (NcAbcB), sterol C-22 desaturase (ERG5), and a lipid transporter (NcRTA2) that is involved in calcineurin-mediated azole resistance. Deletion of the
ads-4
-homologous gene Af
ads-4
in
Aspergillus fumigatus
caused hypersensitivity to itraconazole and ketoconazole, which suggested that ADS-4 is a functionally conserved regulator of adaptive responses to azoles. This study provides important information on a new azole resistance factor that could be targeted by a new range of antifungal pesticides and drugs.
A Novel Point Mutation Promotes Growth Phase-Dependent Daptomycin Tolerance in Staphylococcus aureus
Authors: Mechler Lukas , Herbig Alexander , Paprotka Kerstin , Fraunholz Martin , Nieselt Kay , Bertram Ralph 
Published: June 2015

ABSTRACT

Recalcitrance of genetically susceptible bacteria to antibiotic killing is a hallmark of bacterial drug tolerance. This phenomenon is prevalent in biofilms, persisters, and also planktonic cells and is associated with chronic or relapsing infections with pathogens such as
Staphylococcus aureus
. Here we report the
in vitro
evolution of an
S. aureus
strain that exhibits a high degree of nonsusceptibility to daptomycin as a result of cyclic challenges with bactericidal concentrations of the drug. This phenotype was attributed to stationary growth phase-dependent drug tolerance and was clearly distinguished from resistance. The underlying genetic basis was revealed to be an adaptive point mutation in the putative inorganic phosphate (P
i
) transporter gene
pitA
. Drug tolerance caused by this allele, termed
pitA6
, was abrogated when the upstream gene
pitR
was inactivated. Enhanced tolerance toward daptomycin, as well as the acyldepsipeptide antibiotic ADEP4 and various combinations of other drugs, was accompanied by elevated intracellular concentrations of P
i
and polyphosphate, which may reversibly interfere with critical cellular functions. The evolved strain displayed increased rates of survival within human endothelial cells, demonstrating the correlation of intracellular persistence and drug tolerance. These findings will be useful for further investigations of
S. aureus
drug tolerance, toward the development of additional antipersister compounds and strategies.
In Vitro
Selection of Ceftazidime-Avibactam Resistance in Enterobacteriaceae with KPC-3 Carbapenemase
Authors: Livermore David M. , Warner Marina , Jamrozy Dorota , Mushtaq Shazad , Nichols Wright W. , Mustafa Nazim , Woodford Neil 
Published: June 2015

ABSTRACT

Ceftazidime-avibactam is active against most
Enterobacteriaceae
isolates with KPC carbapenemases. We investigated whether this activity could be compromised by mutation. Single-step and multistep selections were attempted using ceftazidime-avibactam (avibactam fixed at 1 or 4 μg/ml)
versus
two strains each of
Enterobacter cloacae
and
Klebsiella pneumoniae
, all with the KPC-3 enzyme. Mutant
bla
KPC
alleles were sequenced, and their parentage was confirmed by typing. Ceftazidime-avibactam selected mutants at up to 16× MIC, with frequencies of ca. 10
−9
. This contrasted with previous experience for ceftaroline-avibactam, where mutant frequencies under similar conditions were <10
−9
. The MICs of ceftazidime with 1 μg/ml avibactam for the ceftazidime-avibactam-selected mutants rose from 1 to 8 μg/ml to 16 to >256 μg/ml and those of ceftazidime with 4 μg/ml avibactam from 0.25 to 1 μg/ml to 4 to 128 μg/ml; ceftaroline-avibactam MICs rose less, typically from 0.5 to 1 μg/ml to 1 to 8 μg/ml. The MICs of carbapenems and cephalosporins except ceftazidime and piperacillin-tazobactam were reduced for many mutants. Sequencing of

bla
KPC

revealed point and insertion changes in 12/13 mutants investigated, representing all four parents; one mutant lacked
bla
KPC
changes and possibly had reduced permeability. Amino acid changes commonly involved Ω loop alterations or 1 to 6 amino acid insertions immediately C-terminal to this loop. The most frequent change, seen in four mutants from three strains, was Asp179Tyr, replacing a residue that ordinarily forms a salt bridge to stabilize the Ω loop. Since ceftaroline-avibactam was less affected than ceftazidime-avibactam, we postulate that these mutations increase ceftazidimase specificity rather than conferring avibactam resistance. The clinical relevance remains uncertain.
In Vitro
Activities of a Wide Panel of Antifungal Drugs against Various Scopulariopsis and Microascus Species
Authors: Skóra Magdalena , Bulanda Małgorzata , Jagielski Tomasz 
Published: June 2015

ABSTRACT

The
in vitro
activities of 11 antifungal drugs against 68
Scopulariopsis
and
Microascus
strains were investigated. Amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, ketoconazole, miconazole, posaconazole, voriconazole, and ciclopirox showed no or poor antifungal effect. The best activities were exhibited by terbinafine and caspofungin, where the MIC and MEC (minimal effective concentration) ranges were 0.0313 to >16 μg/ml and 0.125 to 16 μg/ml, respectively. The MIC and MEC modes were both 1 µg/ml for terbinafine and caspofungin; the MIC
50
and MEC
50
were 1 µg/ml for both drugs, whereas the MIC
90
and MEC
90
were 4 µg/ml and 16 µg/ml, respectively.
Genome Sequences of Mycobacteriophages Luchador and Nerujay
Authors: Pope Welkin H. , Ahmed Taha , Drobitch Marissa K. , Early David R. , Eljamri Soukaina , Kasturiarachi Naomi S. , Klonicki Emily F. , Manjooran Daniel T. , Ní Chochlain Aífe N. , Puglionesi Andrew O. , Rajakumar Vinod , Shindle Katherine A. , Tran Mai T. , Brown Bryony R. , Churilla Bryce M. , Cohen Karen L. , Wilkes Kellyn E. , Grubb Sarah R. , Warner Marcie H. , Bowman Charles A. , Russell Daniel A. , Hatfull Graham F. 
Published: June 2015

ABSTRACT

Luchador and Nerujay are two newly isolated mycobacteriophages recovered from soil samples using
Mycobacterium smegmatis
. Their genomes are 53,387 bp and 53,455 bp long and have 96 and 97 predicted open reading frames, respectively. Nerujay is related to subcluster A1 phages, and Luchador represents a new subcluster, A14.
Genome Sequence of Mycobacteriophage Momo
Authors: Pope Welkin H. , Bina Elizabeth A. , Brahme Indraneel S. , Hill Amy B. , Himmelstein Philip H. , Hunsicker Sara M. , Ish Amanda R. , Le Tinh S. , Martin Mary M. , Moscinski Catherine N. , Shetty Sameer A. , Swierzewski Tomasz , Iyengar Varun B. , Kim Hannah , Schafer Claire E. , Grubb Sarah R. , Warner Marcie H. , Bowman Charles A. , Russell Daniel A. , Hatfull Graham F. 
Published: June 2015

ABSTRACT

Momo is a newly discovered phage of
Mycobacterium smegmatis
mc
2
155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages.
Draft Genome Sequences of Bacillus anthracis Strains Stored for Several Decades in Japan
Authors: Okutani Akiko , Osaki Makoto , Takamatsu Daisuke , Kaku Yoshihiro , Inoue Satoshi , Morikawa Shigeru 
Published: June 2015

ABSTRACTWe report the draft genome sequences ofBacillus anthracisstrains Shikan-NIID, 52-40-NIAH, and 44-NIAH stored in Japan and belonging to the A3 cluster.
Molecular Characterization of the First Ebola Virus Isolated in Italy, from a Health Care Worker Repatriated from Sierra Leone
Authors: Castilletti Concetta , Carletti Fabrizio , Gruber Cesare E. M. , Bordi Licia , Lalle Eleonora , Quartu Serena , Meschi Silvia , Lapa Daniele , Colavita Francesca , Chiappini Roberta , Mazzarelli Antonio , Marsella Patrizia , Petrosillo Nicola , Nicastri Emanuele , Chillemi Giovanni , Valentini Alessio , Desideri Alessandro , Di Caro Antonino , Ippolito Giuseppe , Capobianchi Maria R. 
Published: June 2015

ABSTRACT
Here, we report the complete genome sequence of an Ebola virus (EBOV) isolated from a health worker repatriated from Sierra Leone to Italy in November 2014. The sequence, clustering in clade 3 of the Sierra Leone sequences, was analyzed with respect to mutations possibly affecting diagnostic and therapeutic targets as well as virulence.
Complete Genome Sequence of a Recent Panzootic Virulent Newcastle Disease Virus from Pakistan
Authors: Wajid Abdul , Wasim Muhammad , Rehmani Shafqat F. , Bibi Tasra , Ahmed Nazir , Afonso Claudio L. 
Published: June 2015

ABSTRACT
The genome sequence of a new strain of Newcastle disease virus (NDV) (chicken/Pak/Quality Operations Lab/SFR-611/13) is reported here. The strain was isolated from a vaccinated chicken flock in Pakistan in 2013 and has panzootic features. The genome is 15,192 nucleotides in length and is classified in subgenotype VIIi of genotype VII, class II.
Manipulation of Autophagy in Phagocytes Facilitates Staphylococcus aureus Bloodstream Infection
Authors: O'Keeffe Kate M. , Wilk Mieszko M. , Leech John M. , Murphy Alison G. , Laabei Maisem , Monk Ian R. , Massey Ruth C. , Lindsay Jodi A. , Foster Timothy J. , Geoghegan Joan A. , McLoughlin Rachel M. 
Published: June 2015

ABSTRACT

The capacity for intracellular survival within phagocytes is likely a critical factor facilitating the dissemination of
Staphylococcus aureus
in the host. To date, the majority of work on
S. aureus
-phagocyte interactions has focused on neutrophils and, to a lesser extent, macrophages, yet we understand little about the role played by dendritic cells (DCs) in the direct killing of this bacterium. Using bone marrow-derived DCs (BMDCs), we demonstrate for the first time that DCs can effectively kill
S. aureus
but that certain strains of
S. aureus
have the capacity to evade DC (and macrophage) killing by manipulation of autophagic pathways. Strains with high levels of Agr activity were capable of causing autophagosome accumulation, were not killed by BMDCs, and subsequently escaped from the phagocyte, exerting significant cytotoxic effects. Conversely, strains that exhibited low levels of Agr activity failed to accumulate autophagosomes and were killed by BMDCs. Inhibition of the autophagic pathway by treatment with 3-methyladenine restored the bactericidal effects of BMDCs. Using an
in vivo
model of systemic infection, we demonstrated that the ability of
S. aureus
strains to evade phagocytic cell killing and to survive temporarily within phagocytes correlated with persistence in the periphery and that this effect is critically Agr dependent. Taken together, our data suggest that strains of
S. aureus
exhibiting high levels of Agr activity are capable of blocking autophagic flux, leading to the accumulation of autophagosomes. Within these autophagosomes, the bacteria are protected from phagocytic killing, thus providing an intracellular survival niche within professional phagocytes, which ultimately facilitates dissemination.
Protection against Shiga-Toxigenic Escherichia coli by Non-Genetically Modified Organism Receptor Mimic Bacterial Ghosts
Authors: Paton Adrienne W. , Chen Austen Y. , Wang Hui , McAllister Lauren J. , Höggerl Florian , Mayr Ulrike Beate , Shewell Lucy K. , Jennings Michael P. , Morona Renato , Lubitz Werner , Paton James C. 
Published: June 2015

ABSTRACT

Shiga-toxigenic
Escherichia coli
(STEC) causes severe gastrointestinal infections in humans that may lead to life-threatening systemic sequelae, such as the hemolytic uremic syndrome (HUS). Rapid diagnosis of STEC infection early in the course of disease opens a window of opportunity for therapeutic intervention, for example, by administration of agents that neutralize Shiga toxin (Stx) in the gut lumen. We previously developed a recombinant bacterium that expresses a mimic of the Stx receptor globotriaosyl ceramide (Gb3) on its surface through modification of the lipopolysaccharide (A. W. Paton, R. Morona, and J. C. Paton, Nat Med
6:
265–270, 2000,
http://dx.doi.org/10.1038/73111
). This construct was highly efficacious
in vivo
, protecting mice from otherwise fatal STEC disease, but the fact that it is a genetically modified organism (GMO) has been a barrier to clinical development. In the present study, we have overcome this issue by development of Gb3 receptor mimic bacterial ghosts (BGs) that are not classified as GMOs. Gb3-BGs neutralized Stx1 and Stx2
in vitro
with high efficiency, whereas alternative Gb3-expressing non-GMO subbacterial particles (minicells and outer membrane blebs) were ineffective. Gb3-BGs were highly efficacious in a murine model of STEC disease. All mice (10/10) treated with Gb3-BGs survived challenge with a highly virulent O113:H21 STEC strain and showed no pathological signs of renal injury. In contrast, 6/10 mice treated with control BGs succumbed to STEC challenge, and survivors exhibited significant weight loss, neutrophilia, and histopathological evidence of renal damage. Thus, Gb3-BGs offer a non-GMO approach to treatment of STEC infection in humans, particularly in an outbreak setting.