bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenoscope: an automated large‐scale phenotyping platform offering high spatial homogeneity
Authors: Tisné Sébastien , Serrand Yann , Bach Liên , Gilbault Elodie , Ben Ameur Rachid , Balasse Hervé , Voisin Roger , Bouchez David , Durand‐Tardif Mylène , Guerche Philippe , Chareyron Gaël , Da Rugna Jérôme , Camilleri Christine , Loudet Olivier 
Published: March 2013

SummaryIncreased phenotyping accuracy and throughput are necessary to improve our understanding of quantitative variation and to be able to deconstruct complex traits such as those involved in growth responses to the environment. Still, only a few facilities are known to handle individual plants of small stature for non‐destructive, real‐time phenotype acquisition from plants grown in precisely adjusted and variable experimental conditions. Here, we describe Phenoscope, a high‐throughput phenotyping platform that has the unique feature of continuously rotating 735 individual pots over a table. It automatically adjusts watering and is equipped with a zenithal imaging system to monitor rosette size and expansion rate during the vegetative stage, with automatic image analysis allowing manual correction. When applied to Arabidopsis thaliana, we show that rotating the pots strongly reduced micro‐environmental disparity: heterogeneity in evaporation was cut by a factor of 2.5 and the number of replicates needed to detect a specific mild genotypic effect was reduced by a factor of 3. In addition, by controlling a large proportion of the micro‐environmental variance, other tangible sources of variance become noticeable. Overall, Phenoscope makes it possible to perform large‐scale experiments that would not be possible or reproducible by hand. When applied to a typical quantitative trait loci (QTL) mapping experiment, we show that mapping power is more limited by genetic complexity than phenotyping accuracy. This will help to draw a more general picture as to how genetic diversity shapes phenotypic variation.
Deployment of the Burkholderia glumae type III secretion system as an efficient tool for translocating pathogen effectors to monocot cells
Authors: Sharma Shailendra , Sharma Shiveta , Hirabuchi Akiko , Yoshida Kentaro , Fujisaki Koki , Ito Akiko , Uemura Aiko , Terauchi Ryohei , Kamoun Sophien , Sohn Kee Hoon , Jones Jonathan D. G. , Saitoh Hiromasa 
Published: March 2013

SummaryGenome sequences of plant fungal pathogens have enabled the identification of effectors that cooperatively modulate the cellular environment for successful fungal growth and suppress host defense. Identification and characterization of novel effector proteins are crucial for understanding pathogen virulence and host‐plant defense mechanisms. Previous reports indicate that the Pseudomonas syringae pv. tomato DC3000 type III secretion system (T3SS) can be used to study how non‐bacterial effectors manipulate dicot plant cell function using the effector detector vector (pEDV) system. Here we report a pEDV‐based effector delivery system in which the T3SS of Burkholderia glumae, an emerging rice pathogen, is used to translocate the AVR‐Pik and AVR‐Pii effectors of the fungal pathogen Magnaporthe oryzae to rice cytoplasm. The translocated AVR‐Pik and AVR‐Pii showed avirulence activity when tested in rice cultivars containing the cognate R genes. AVR‐Pik reduced and delayed the hypersensitive response triggered by B. glumae in the non‐host plant Nicotiana benthamiana, indicative of an immunosuppressive virulence activity. AVR proteins fused with fluorescent protein and nuclear localization signal were delivered by B. glumae T3SS and observed in the nuclei of infected cells in rice, wheat, barley and N. benthamiana. Our bacterial T3SS‐enabled eukaryotic effector delivery and subcellular localization assays provide a useful method for identifying and studying effector functions in monocot plants.
A Myb transcription factor regulates genes of the phenylalanine pathway in maritime pine
Authors: Craven‐Bartle Blanca , Pascual Mª Belen , Cánovas Francisco M. , Ávila Concepción 
Published: March 2013

SummaryDuring the life cycles of conifer trees, such as maritime pine (Pinus pinaster Ait.), large quantities of carbon skeletons are irreversibly immobilized in the wood. In energetic terms this is an expensive process, in which carbon from photosynthesis is channelled through the shikimate pathway for the biosynthesis of phenylpropanoids. This crucial metabolic pathway is finely regulated, primarily through transcriptional control, and because phenylalanine is the precursor for phenylpropanoid biosynthesis, the precise regulation of phenylalanine synthesis and use should occur simultaneously. The promoters of three genes encoding the enzymes prephenate aminotransferase (PAT), phenylalanine ammonia lyase (PAL) and glutamine synthetase (GS1b) contain AC elements involved in the transcriptional activation mediated by R2R3‐Myb factors. We have examined the capacity of the R2R3‐Myb transcription factors Myb1, Myb4 and Myb8 to co‐regulate the expression of PAT, PAL and GS1b. Only Myb8 was able to activate the transcription of the three genes. Moreover, the expression of this transcription factor is higher in lignified tissues, in which a high demand for phenylpropanoids exits. In a gain‐of‐function experiment, we have shown that Myb8 can specifically bind a well‐conserved eight‐nucleotide‐long AC‐II element in the promoter regions of PAT, PAL and GS1b, thereby activating their expression. Our results show that Myb8 regulates the expression of these genes involved in phenylalanine metabolism, which is required for channelling photosynthetic carbon to promote wood formation. The co‐localization of PAT, PAL, GS1b and MYB8 transcripts in vascular cells further supports this conclusion.
The microtubule‐associated kinase‐like protein RUNKEL functions in somatic and syncytial cytokinesis
Authors: Krupnova Tamara , Stierhof York‐Dieter , Hiller Ulrike , Strompen Georg , Müller Sabine 
Published: March 2013

SummaryThe microtubule (MT)‐associated putative kinase RUNKEL (RUK) is an important component of the phragmoplast machinery involved in cell plate formation in Arabidopsis somatic cytokinesis. Since loss‐of‐function ruk mutants display seedling lethality, it was previously not known whether RUK functions in mature sporophytes or during gametophyte development. In this study we utilized RUK proteins that lack the N‐terminal kinase domain to further examine biological processes related to RUK function. Truncated RUK proteins when expressed in wild‐type Arabidopsis plants cause cellularization defects not only in seedlings and adult tissues but also during male meiocyte development, resulting in abnormal pollen and reduced fertility. Ultrastructural analysis of male tetrads revealed irregular and incomplete or absent intersporal cell walls, caused by disorganized radial MT arrays. Moreover, in ruk mutants endosperm cellularization defects were also caused by disorganized radial MT arrays. Intriguingly, in seedlings expressing truncated RUK proteins, the kinesin HINKEL, which is required for the activation of a mitogen‐activated protein kinase signaling pathway regulating phragmoplast expansion, was mislocalized. Together, these observations support a common role for RUK in both phragmoplast‐based cytokinesis in somatic cells and syncytial cytokinesis in reproductive cells.
Pharmacodynamics of Ceftaroline against Staphylococcus aureus Studied in an
In Vitro
Pharmacokinetic Model of Infection
Authors: MacGowan Alasdair P. , Noel Alan R. , Tomaselli Sharon , Bowker Karen E. 
Published: March 2013

ABSTRACT

An
in vitro
single-compartment dilutional pharmacokinetic model was used to study the pharmacodynamics of ceftaroline against
Staphylococcus aureus
(both methicillin-susceptible
S. aureus
[MSSA] and methicillin-resistant
S. aureus
[MRSA]). Mean serum free concentrations of ceftaroline (the active metabolite of the prodrug ceftaroline fosamil) dosed in humans at 600 mg every 12 h (q12h) were simulated, and activities against 12
S. aureus
strains (3 MSSA strains and 9 MRSA strains, 3 of which had a vancomycin-intermediate phenotype) were determined. Ceftaroline produced 2.5- to 4.0-log
10
-unit reductions in viable counts by 24 h with all strains and a 0.5- to 4.0-log-unit drop in counts at 96 h. The antibacterial effect could not be related to the strain MIC across the ceftaroline MIC range from 0.12 to 2.0 μg/ml. In dose-ranging studies, the cumulative percentage of a 24-h period that the free drug concentration exceeded the MIC under steady-state pharmacokinetic conditions (
fT
MIC
) of 24.5% ± 8.9% was associated with a 24-h bacteriostatic effect, one of 27.8% ± 9.5% was associated with a −1-log-unit drop, and one of 32.1% ± 8.1% was associated with a −2-log-unit drop. The MSSA and MRSA strains had similar
fT
MIC
values.
fT
MIC
values increased with increasing duration of exposure up to 96 h. Changes in ceftaroline population analysis profiles were related to
fT
MIC
.
fT
MIC
s of <50% were associated with growth on 4× MIC recovery plates at 96 h of drug exposure. These data support the use of ceftaroline fosamil at doses of 600 mg q12h to treat
S. aureus
strains with MICs of ≤2 μg/ml. An
fT
MIC
of 25 to 30% would make a suitable pharmacodynamic index target, but
fT
MIC
values of ≥50% are needed to suppress the emergence of resistance and require clinical evaluation.
Coproduction of 16S rRNA Methyltransferase RmtD or RmtG with KPC-2 and CTX-M Group Extended-Spectrum β-Lactamases in Klebsiella pneumoniae
Authors: Bueno Maria Fernanda C. , Francisco Gabriela R. , O'Hara Jessica A. , de Oliveira Garcia Doroti , Doi Yohei 
Published: March 2013

ABSTRACT

Eight
Klebsiella pneumoniae
clinical strains with high-level aminoglycoside resistance were collected from eight hospitals in São Paulo State, Brazil, in 2010 and 2011. Three of them produced an RmtD group 16S rRNA methyltransferase, RmtD1 or RmtD2. Five strains were found to produce a novel 16S rRNA methyltransferase, designated RmtG, which shared 57 to 58% amino acid identity with RmtD1 and RmtD2. Seven strains coproduced KPC-2 with or without various CTX-M group extended-spectrum β-lactamases, while the remaining strain coproduced CTX-M-2.
Cytosporone B, an Inhibitor of the Type III Secretion System of Salmonella enterica Serovar Typhimurium
Authors: Li Jianfang , Lv Chao , Sun Weiyang , Li Zhenyu , Han Xiaowei , Li Yaoyao , Shen Yuemao 
Published: March 2013

ABSTRACT

Bacterial virulence factors have been increasingly regarded as attractive targets for development of novel antibacterial agents. Virulence inhibitors are less likely to generate bacterial resistance, which makes them superior to traditional antibiotics that target bacterial viability.
Salmonella enterica
serovar Typhimurium, an important food-borne human pathogen, has type III secretion system (T3SS) as its major virulence factor. T3SS secretes effector proteins to facilitate invasion into host cells. In this study, we identified several analogs of cytosporone B (Csn-B) that strongly block the secretion of
Salmonella
pathogenicity island 1 (SPI-1)-associated effector proteins, without affecting the secretion of flagellar protein FliC
in vitro
. Csn-B and two other derivatives exhibited a strong inhibitory effect on SPI-1-mediated invasion to HeLa cells, while no significant toxicity to bacteria was observed. Nucleoid proteins Hha and H-NS bind to the promoters of SPI-1 regulator genes
hilD
,
hilC
, and
rtsA
to repress their expression and consequently regulate the expression of SPI-1 apparatus and effector genes. We found that Csn-B upregulated the transcription of
hha
and
hns
, implying that Csn-B probably affected the secretion of effectors through the Hha–H-NS regulatory pathway. In summary, this study presented an effective SPI-1 inhibitor, Csn-B, which may have potential in drug development against antibiotic-resistant
Salmonella
.
Ruminant Rhombencephalitis-Associated Listeria monocytogenes Strains Constitute a Genetically Homogeneous Group Related to Human Outbreak Strains
Authors: Rocha Paulo Ricardo Dell'Armelina , Lomonaco Sara , Bottero Maria Teresa , Dalmasso Alessandra , Dondo Alessandro , Grattarola Carla , Zuccon Fabio , Iulini Barbara , Knabel Stephen John , Capucchio Maria Teresa , Casalone Cristina 
Published: March 2013

ABSTRACTListeriosis is a disease that causes significant economic losses at the farm level because of high morbidity and mortality in ruminants. This study was performed to investigate the role of ruminants in the epidemiology of listeriosis in northern Italy and the possible association of animal-adapted strains ofListeria monocytogeneswith strains associated with human disease. Twenty ruminant rhombencephalitis isolates previously confirmed asL. monocytogenesby bacteriology and PCR were characterized by serotyping, pulsed-field gel electrophoresis, multi-virulence-locus sequence typing (MVLST), and multiplex single nucleotide polymorphism (mSNP) typing for the detection of epidemic clones. Subtyping results were subsequently compared with those obtained from human, food, and environmental isolates ofL. monocytogenes, including 311 isolates from the University of Turin, Grugliasco, Italy, and 165 isolates representing major human listeriosis outbreaks worldwide, in addition to other unrelated isolates. Both mSNP typing and MVLST showed that 60% of the isolates analyzed belonged to epidemic clone I (ECI), which has been epidemiologically linked to several human outbreaks of listeriosis. In particular, the 1981 Canada outbreak was linked to the use of sheep manure and the 1985 California outbreak was linked to the use of raw cow's milk. In our study, ECI isolates were collected from different ruminant species on geographically and temporally distinct occasions for the last 13 years. Our results support the hypothesis that ruminants represent possible natural reservoirs ofL. monocytogenesstrains capable of causing epidemics of listeriosis in humans.
Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model
Authors: Lira Felipe , Perez Pedro S. , Baranauskas José A. , Nozawa Sérgio R. 
Published: March 2013

ABSTRACT

Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created
in silico
by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 μg/ml against
Staphylococcus aureus
and
Escherichia coli
. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools.
The Carboxyl Terminus of Rtt109 Functions in Chaperone Control of Histone Acetylation
Authors: Radovani Ernest , Cadorin Matthew , Shams Tahireh , El-Rass Suzan , Karsou Abdel R. , Kim Hyun-Soo , Kurat Christoph F. , Keogh Michael-Christopher , Greenblatt Jack F. , Fillingham Jeffrey S. 
Published: March 2013

ABSTRACT

Rtt109 is a fungal histone acetyltransferase (HAT) that catalyzes histone H3 acetylation functionally associated with chromatin assembly. Rtt109-mediated H3 acetylation involves two histone chaperones, Asf1 and Vps75.
In vivo
, Rtt109 requires both chaperones for histone H3 lysine 9 acetylation (H3K9ac) but only Asf1 for full H3K56ac.
In vitro
, Rtt109-Vps75 catalyzes both H3K9ac and H3K56ac, whereas Rtt109-Asf1 catalyzes only H3K56ac. In this study, we extend the
in vitro
chaperone-associated substrate specificity of Rtt109 by showing that it acetylates vertebrate linker histone in the presence of Vps75 but not Asf1. In addition, we demonstrate that in
Saccharomyces cerevisiae
a short basic sequence at the carboxyl terminus of Rtt109 (Rtt109C) is required for H3K9ac
in vivo
. Furthermore, through
in vitro
and
in vivo
studies, we demonstrate that Rtt109C is required for optimal H3K56ac by the HAT in the presence of full-length Asf1. When Rtt109C is absent, Vps75 becomes important for H3K56ac by Rtt109
in vivo
. In addition, we show that lysine 290 (K290) in Rtt109 is required
in vivo
for Vps75 to enhance the activity of the HAT. This is the first
in vivo
evidence for a role for Vps75 in H3K56ac. Taken together, our results contribute to a better understanding of chaperone control of Rtt109-mediated H3 acetylation.
FtsZ Ring Stability: of Bundles, Tubules, Crosslinks, and Curves
Authors: Huang Kuo-Hsiang , Durand-Heredia Jorge , Janakiraman Anuradha 
Published: March 2013

ABSTRACTThe first step in bacterial cytokinesis is the assembly of a stable but dynamic cytokinetic ring made up of the essential tubulin homolog FtsZ at the future site of division. Although FtsZ and its role in cytokinesis have been studied extensively, the precise architecture of thein vivomedial FtsZ ring (Z ring) is not well understood. Recent advances in superresolution imaging suggest that the Z ring comprises short, discontinuous, and loosely bundled FtsZ polymers, some of which are tethered to the membrane. A diverse array of regulatory proteins modulate the assembly, stability, and disassembly of the Z ring via direct interactions with FtsZ. Negative regulators of FtsZ play a critical role in ensuring the accurate positioning of FtsZ at the future site of division and in maintaining Z ring dynamics by controlling FtsZ polymer assembly/disassembly processes. Positive regulators of FtsZ are essential for tethering FtsZ polymers to the membrane and promoting the formation of stabilizing lateral interactions, permitting assembly of a mature Z ring. The past decade has seen the identification of several factors that promote FtsZ assembly, presumably through a variety of distinct molecular mechanisms. While a few of these proteins are broadly conserved, many positive regulators of FtsZ assembly are limited to small groups of closely related organisms, suggesting that FtsZ assembly is differentially modulated across bacterial species. In this review, we focus on the roles of positive regulators in Z ring assembly and in maintaining the integrity of the cytokinetic ring during the early stages of division.
Synchronous sclerosing haemangiomas of the lung: an unusual presentation of a rare tumour
Authors: Chu Michael , Kumari Hemlata , Salmah Nor , Sachithanandan Anand 
Published: March 2013

Pulmonary sclerosing haemangioma is a rare lung tumour with a preponderance for Asian oriental women. Typically a well-circumscribed, solitary lesion with benign characteristics, there are concerns of malignant potential including regional lymph node metastases. Four histological subtypes exist. Diagnosis can be challenging as patients are usually asymptomatic and radiological findings are non-specific. Surgical resection alone is diagnostic and therapeutic. We present a case of this rare tumour with an uncommon presentation as two synchronous tumours initially misdiagnosed as a pulmonary adenocarcinoma.
Does childhood adversity account for poorer mental and physical health in second-generation Irish people living in Britain? Birth cohort study from Britain (NCDS)
Authors: Das-Munshi Jayati , Clark Charlotte , Dewey Michael E , Leavey Gerard , Stansfeld Stephen A , Prince Martin J 
Published: March 2013

ObjectivesWorldwide, the Irish diaspora experience elevated mortality and morbidity across generations, not accounted for through socioeconomic position. The main objective of the present study was to assess if childhood disadvantage accounts for poorer mental and physical health in adulthood, in second-generation Irish people.DesignAnalysis of prospectively collected birth cohort data, with participants followed to midlife.SettingEngland, Scotland and Wales.ParticipantsApproximately 17 000 babies born in a single week in 1958. Six per cent of the cohort were of second-generation Irish descent.OutcomesPrimary outcomes were common mental disorders assessed at age 44/45 and self-rated health at age 42. Secondary outcomes were those assessed at ages 23 and 33.ResultsRelative to the rest of the cohort, second-generation Irish children grew up in marked material and social disadvantage, which tracked into early adulthood. By midlife, parity was reached between second-generation Irish cohort members and the rest of the sample on most disadvantage indicators. At age 23, Irish cohort members were more likely to screen positive for common mental disorders (OR 1.44; 95% CI 1.06 to 1.94). This had reduced slightly by midlife (OR 1.27; 95% CI 0.96 to 1.69). Although at age 23 second-generation cohort members were just as likely to report poorer self-rated health (OR 1.06; 95% CI 0.79 to 1.43), by midlife this difference had increased (OR 1.25; 95% CI 0.98 to 1.60). Adjustment for childhood and early adulthood adversity fully attenuated differences in adult health disadvantages.ConclusionsSocial and material disadvantage experienced in childhood continues to have long-range adverse effects on physical and mental health at midlife, in second-generation Irish cohort members. This suggests important mechanisms over the life-course, which may have important policy implications in the settlement of migrant families.
Initiation rites at menarche and self-reported dysmenorrhoea among indigenous women of the Colombian Amazon: a cross-sectional study
Authors: Zuluaga Germán , Andersson Neil 
Published: March 2013

ObjectivesTo investigate the association between self-reported dysmenorrhoea and patterns of female initiation rites at menarche among Amazonian indigenous peoples of Vaupés in Colombia.DesignA cross-sectional study of all women in seven indigenous communities. Questionnaire administered in local language documented female initiation rites and experience of dysmenorrhoea. Analysis examined 10 initiation components separately, then together, comparing women who underwent all rites, some rites and no rites.SettingsSeven indigenous communities belonging to the Tukano language group in the Great Eastern Reservation of Vaupés (Colombia) in 2008.ParticipantsAll women over the age of 13 years living in the seven communities in Vaupés, who had experienced at least two menstruations (n=185), aged 13–88 years (mean 32.5; SD 15.6).Primary and secondary outcome measuresThe analysis rested on pelvic pain to define dysmenorrhoea as the main outcome. Women were also asked about other disorders present during menstruation or the precedent days, and about the interval between two menstruations and duration of each one.ResultsOnly 17.3% (32/185) completed all initiation rites and 52.4% (97/185) reported dysmenorrhoea. Women not completing the rites were more likely to report dysmenorrhoea than those who did so (p=0.01 Fisher exact), taking into account age, education, community, parity and use of family planning. Women who completed less than the full complement of rites had higher risk than those who completed all rites. Those who did not complete all rites reported increased severity of dysmenorrhoea (p=0.00014).ConclusionsOur results are compatible with an association between traditional practices and women's health. We could exclude indirect associations with age, education, parity and use of family planning as explanations for the association. The study indicates feasibility, possible utility and limits of intercultural epidemiology in small groups.