bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene
Authors: Salmon Jemma , Ward Sally P. , Hanley Steven J. , Leyser Ottoline , Karp Angela 
Published: January 2014

SummaryWillows (Salix spp.) are important biomass crops due to their ability to grow rapidly with low fertilizer inputs and ease of cultivation in short‐rotation coppice cycles. They are relatively undomesticated and highly diverse, but functional testing to identify useful allelic variation is time‐consuming in trees and transformation is not yet possible in willow. Arabidopsis is heralded as a model plant from which knowledge can be transferred to advance the improvement of less tractable species. Here, knowledge and methodologies from Arabidopsis were successfully used to identify a gene influencing stem number in coppiced willows, a complex trait of key biological and industrial relevance. The strigolactone‐related More AXillary growth (MAX) genes were considered candidates due to their role in shoot branching. We previously demonstrated that willow and Arabidopsis show similar response to strigolactone and that transformation rescue of Arabidopsis max mutants with willow genes could be used to detect allelic differences. Here, this approach was used to screen 45 SxMAX1, SxMAX2, SxMAX3 and SxMAX4 alleles cloned from 15 parents of 11 mapping populations varying in shoot‐branching traits. Single‐nucleotide polymorphism (SNP) frequencies were locus dependent, ranging from 29.2 to 74.3 polymorphic sites per kb. SxMAX alleles were 98%–99% conserved at the amino acid level, but different protein products varying in their ability to rescue Arabidopsis max mutants were identified. One poor rescuing allele, SxMAX4D, segregated in a willow mapping population where its presence was associated with increased shoot resprouting after coppicing and colocated with a QTL for this trait.
Plant signalling in acute ozone exposure
Authors: VAINONEN JULIA P. , KANGASJÄRVI JAAKKO 
Published: January 2014

AbstractExposure of plants to high ozone concentrations causes lesion formation in sensitive plants. Plant responses to ozone involve fast and massive changes in protein activities, gene expression and metabolism even before any tissue damage can be detected. Degradation of ozone and subsequent accumulation of reactive oxygen species (ROS) in the extracellular space activates several signalling cascades, which are integrated inside the cell into a fine‐balanced network of ROS signalling. Reversible protein phosphorylation and degradation plays an important role in the regulation of signalling mechanisms in a complex crosstalk with plant hormones and calcium, an essential second messenger. In this review, we discuss the recent advances in understanding the molecular mechanisms of ozone uptake, perception and signalling pathways activated during the early steps of ozone response, and discuss the use of ozone as a tool to study the function of apoplastic ROS in signalling.
Effects of NAD kinase 2 overexpression on primary metabolite profiles in rice leaves under elevated carbon dioxide
Authors: Onda Y. , Miyagi A. , Takahara K. , Uchimiya H. , Kawai‐Yamada M. 
Published: January 2014

AbstractThe concentration of carbon dioxide (CO2) in the atmosphere is projected to double by the end of the 21st century. In C3 plants, elevated CO2 concentrations promote photosynthesis but inhibit the assimilation of nitrate into organic nitrogen compounds. Several steps of nitrate assimilation depend on the availability of ATP and sources of reducing power, such as nicotinamide adenine dinucleotide phosphate (NADPH). Plastid‐localised NAD kinase 2 (NADK2) plays key roles in increasing the ATP/ADP and NADP(H)/NAD(H) ratios. Here we examined the effects of NADK2 overexpression on primary metabolism in rice (Oryza sativa) leaves in response to elevated CO2. By using capillary electrophoresis mass spectrometry, we showed that the primary metabolite profile of NADK2‐overexpressing plants clearly differed from that of wild‐type plants under ambient and elevated CO2. In NADK2‐overexpressing leaves, expression of the genes encoding glutamine synthetase and glutamate synthase was up‐regulated, and the levels of Asn, Gln, Arg, and Lys increased in response to elevated CO2. The present study suggests that overexpression of NADK2 promotes the biosynthesis of nitrogen‐rich amino acids under elevated CO2.
High density FTA plates serve as efficient long‐term sample storage for HLA genotyping
Authors: Lange V. , Arndt K. , Schwarzelt C. , Boehme I. , Giani A. S. , Schmidt A. H. , Ehninger G. , Wassmuth R. 
Published: January 2014

AbstractStorage of dried blood spots (DBS) on high‐density FTA® plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high‐resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high‐quality DNA for reliable high‐resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high‐density FTA® plates is suitable for high‐resolution HLA sequencing, provided that appropriate extraction protocols are employed.
The Myth of Cognitive Decline: Non‐Linear Dynamics of Lifelong Learning
Authors: Ramscar Michael , Hendrix Peter , Shaoul Cyrus , Milin Petar , Baayen Harald 
Published: January 2014

AbstractAs adults age, their performance on many psychometric tests changes systematically, a finding that is widely taken to reveal that cognitive information‐processing capacities decline across adulthood. Contrary to this, we suggest that older adults' changing performance reflects memory search demands, which escalate as experience grows. A series of simulations show how the performance patterns observed across adulthood emerge naturally in learning models as they acquire knowledge. The simulations correctly identify greater variation in the cognitive performance of older adults, and successfully predict that older adults will show greater sensitivity to fine‐grained differences in the properties of test stimuli than younger adults. Our results indicate that older adults' performance on cognitive tests reflects the predictable consequences of learning on information‐processing, and not cognitive decline. We consider the implications of this for our scientific and cultural understanding of aging.
In vivoconfocal microscopy of corneal microscopic foreign bodies in horses
Authors: Ledbetter Eric C. , Irby Nita L. , Schaefer Deanna M. W. 
Published: January 2014

AbstractObjectiveTo describein vivocorneal confocal microscopy of horses with microscopic corneal foreign bodies and to correlate findings with clinical, cytological, and histopathologic evaluations of clinical cases and foreign body morphologies observedin vitrowith the confocal microscope.Animal studiedFive horses with microscopic corneal foreign bodies.ProceduresSedated and anesthetized horses were examined with a modifiedHeidelbergRetinaTomographIIandRostockCorneaModule. Confocal microscopy images were compared with images from cytologic and histopathologic corneal samples. To establish microscopic morphologic features, confocal microscopy images of burdock pappus bristles and surgical glove powder were obtained byin vitroexamination.ResultsHorses were examined byin vivoconfocal microscopy to assist in identifying corneal opacities detected by slit‐lamp biomicroscopy, to determine the etiology of clinically idiopathic keratitis, or to localize corneal opacities presumed to be foreign bodies for surgical planning. Corneal foreign bodies presumptively identified by confocal microscopy included burdock pappus bristles, other plant foreign materials, and surgical glove powder. The corneal foreign bodies appeared as moderately or hyper‐reflective linear, circular, or oval structures by confocal microscopy and did not resemble any normal anatomic structures. The confocal microscopic identification of the foreign bodies was corroborated by cytologic and histopathologic findings in some horses. Thein vivoconfocal microscopic appearance of the foreign bodies was consistent with morphologies observed during examination of foreign bodiesin vitro.ConclusionsIn vivocorneal confocal microscopy provides a noninvasive method for the detection, characterization, and localization of microscopic foreign bodies in the equine cornea.
Low‐Z linac targets for low‐MV gold nanoparticle radiation therapy
Authors: Tsiamas P. , Mishra P. , Cifter F. , Berbeco R. I. , Marcus K. , Sajo E. , Zygmanski P. 
Published: January 2014

Purpose:To investigate the potential of low‐Z/low‐MV (low‐Z) linac targets for gold nanoparticle radiotherapy (GNPT) and to determine the microscopic dose enhancement ratio (DER) due to GNP for the alternative beamlines. In addition, to evaluate the degradation of dose enhancement arising from the increased attenuation of x rays and larger skin dose in water for the low‐MV beams compared to the standard linac.Methods:Monte Carlo simulations were used to compute dose and DER for various flattening‐filter‐free beams (2.5, 4, 6.5 MV). Target materials were beryllium, diamond, and tungsten‐copper high‐Z target. Target thicknesses were selected based on 20%, 60%, 70%, and 80% of the continuous slowing down approximation electron ranges for a given target material and energy. Evaluation of the microscopic DER was carried out for 100 nm GNP including the degradation factors due to beam attenuation.Results:The greatest increase in DER compared to the standard 6.5 MV linac was for a 2.5 MV Be‐target (factor of ∼2). Skin dose ranged from ∼10% (Be, 6.5 MV‐80%) to ∼85% (Be, 2.5 MV‐20%) depending on the target case. Attenuation of 2.5 MV beams at 22 cm was higher by ∼75% compared with the standard beam. Taking into account the attenuation at 22 cm depth, the effective dose enhancement was up to ∼60% above the DER of the high‐Z target. For these cases the effective DER ranged between ∼1.6 and 6 compared with the standard linac.Conclusions:Low‐Z (2.5 MV) GNPT is possible even after accounting for greater beam attenuation for deep‐seated tumors (22 cm) and the increased skin dose. Further, it can lead to significant sparing of normal tissue while simultaneously escalating the dose in the tumor cells.
SmeOP-TolC
Sm
Efflux Pump Contributes to the Multidrug Resistance of Stenotrophomonas maltophilia
Authors: Lin Cheng-Wen , Huang Yi-Wei , Hu Rouh-Mei , Yang Tsuey-Ching 
Published: January 2014

ABSTRACT

A five-gene cluster,

tolC
Sm
-pcm-smeRo-smeO-smeP

, of
Stenotrophomonas maltophilia
was characterized. The presence of
smeOP
and

smeRo-pcm-tolC
Sm

operons was verified by reverse transcription (RT)-PCR. Both operons were negatively regulated by the TetR-type transcriptional regulator SmeRo, as demonstrated by quantitative RT-PCR and a promoter-fusion assay. SmeO and SmeP were associated with TolC
Sm
(the TolC protein of
S. maltophilia
) for the assembly of a resistance-nodulation-cell-division (RND)-type pump. The compounds extruded by SmeOP-TolC
Sm
mainly included nalidixic acid, doxycycline, amikacin, gentamicin, erythromycin, leucomycin, carbonyl cyanide 3-chlorophenylhydrazone, crystal violet, sodium dodecyl sulfate, and tetrachlorosalicylanilide.
Low or High Doses of Cefquinome Targeting Low or High Bacterial Inocula Cure Klebsiella pneumoniae Lung Infections but Differentially Impact the Levels of Antibiotic Resistance in Fecal Flora
Authors: Vasseur Maleck V. , Laurentie Michel , Rolland Jean-Guy , Perrin-Guyomard Agnès , Henri Jérôme , Ferran Aude A. , Toutain Pierre-Louis , Bousquet-Mélou Alain 
Published: January 2014

ABSTRACT

The combination of efficacious treatment against bacterial infections and mitigation of antibiotic resistance amplification in gut microbiota is a major challenge for antimicrobial therapy in food-producing animals. In rats, we evaluated the impact of cefquinome, a fourth-generation cephalosporin, on both
Klebsiella pneumoniae
lung infection and intestinal flora harboring CTX-M-producing
Enterobacteriaceae
. Germfree rats received a fecal flora specimen from specific-pathogen-free pigs, to which a CTX-M-producing
Escherichia coli
strain had been added.
K. pneumoniae
cells were inoculated in the lungs of these gnotobiotic rats by using either a low (10
5
CFU) or a high (10
9
CFU) inoculum. Without treatment, all animals infected with the low or high
K. pneumoniae
inoculum developed pneumonia and died before 120 h postchallenge. In the treated groups, the low-inoculum rats received a 4-day treatment of 5 mg/kg of body weight cefquinome beginning at 24 h postchallenge (prepatent phase of the disease), and the high-inoculum rats received a 4-day treatment of 50 mg/kg cefquinome beginning when the animals expressed clinical signs of infection (patent phase of the disease). The dose of 50 mg/kg targeting the high
K. pneumoniae
inoculum cured all the treated rats and resulted in a massive amplification of CTX-M-producing
Enterobacteriaceae
. A dose of 5 mg/kg targeting the low
K. pneumoniae
inoculum cured all the rats and averted an outbreak of clinical disease, all without any amplification of CTX-M-producing
Enterobacteriaceae
. These findings might have implications for the development of new antimicrobial treatment strategies that ensure a cure for bacterial infections while avoiding the amplification of resistance genes of human concern in the gut microbiota of food-producing animals.
Peptidoglycan Cross-Linking in Glycopeptide-Resistant Actinomycetales
Authors: Hugonnet Jean-Emmanuel , Haddache Nabila , Veckerlé Carole , Dubost Lionel , Marie Arul , Shikura Noriyasu , Mainardi Jean-Luc , Rice Louis B. , Arthur Michel 
Published: January 2014

ABSTRACT

Synthesis of peptidoglycan precursors ending in
d
-lactate (
d
-Lac) is thought to be responsible for glycopeptide resistance in members of the order
Actinomycetales
that produce these drugs and in related soil bacteria. More recently, the peptidoglycan of several members of the order
Actinomycetales
was shown to be cross-linked by
l
,
d
-transpeptidases that use tetrapeptide acyl donors devoid of the target of glycopeptides. To evaluate the contribution of these resistance mechanisms, we have determined the peptidoglycan structure of
Streptomyces coelicolor
A(3)2, which harbors a
vanHAX
gene cluster for the production of precursors ending in
d
-Lac, and
Nonomuraea
sp. strain ATCC 39727, which is devoid of
vanHAX
and produces the glycopeptide A40296. Vancomycin retained residual activity against
S. coelicolor
A(3)2 despite efficient incorporation of
d
-Lac into cytoplasmic precursors. This was due to a
d
,
d
-transpeptidase-catalyzed reaction that generated a stem pentapeptide recognized by glycopeptides by the exchange of
d
-Lac for
d
-Ala and Gly. The contribution of
l
,
d
-transpeptidases to resistance was limited by the supply of tetrapeptide acyl donors, which are essential for the formation of peptidoglycan cross-links by these enzymes. In the absence of a cytoplasmic metallo-
d
,
d
-carboxypeptidase, the tetrapeptide substrate was generated by hydrolysis of the C-terminal
d
-Lac residue of the stem pentadepsipeptide in the periplasm in competition with the exchange reaction catalyzed by
d
,
d
-transpeptidases. In
Nonomuraea
sp. strain ATCC 39727, the contribution of
l
,
d
-transpeptidases to glycopeptide resistance was limited by the incomplete conversion of pentapeptides into tetrapeptides despite the production of a cytoplasmic metallo-
d
,
d
-carboxypeptidase. Since the level of drug production exceeds the level of resistance, we propose that
l
,
d
-transpeptidases merely act as a tolerance mechanism in this bacterium.
Gingerol Fraction from Zingiber officinale Protects against Gentamicin-Induced Nephrotoxicity
Authors: Rodrigues Francisco A. P. , Prata Mara M. G. , Oliveira Iris C. M. , Alves Natacha T. Q. , Freitas Rosa E. M. , Monteiro Helena S. A. , Silva Jame's A. , Vieira Paulo C. , Viana Daniel A. , Libório Alexandre B. , Havt Alexandre 
Published: January 2014

ABSTRACTNephrotoxicity is the main complication of gentamicin (GM) treatment. GM induces renal damage by overproduction of reactive oxygen species and inflammation in proximal tubular cells. Phenolic compounds from ginger, called gingerols, have been demonstrated to have antioxidant and anti-inflammatory effects. We investigated if oral treatment with an enriched solution of gingerols (GF) would promote a nephroprotective effect in an animal nephropathy model. The following six groups of male Wistar rats were studied: (i) control group (CT group); (ii) gingerol solution control group (GF group); (iii) gentamicin treatment group (GM group), receiving 100 mg/kg of body weight intraperitoneally (i.p.); and (iv to vi) gentamicin groups also receiving GF, at doses of 6.25, 12.5, and 25 mg/kg, respectively (GM+GF groups). Animals from the GM group had a significant decrease in creatinine clearance and higher levels of urinary protein excretion. This was associated with markers of oxidative stress and nitric oxide production. Also, there were increases of the mRNA levels for proinflammatory cytokines (tumor necrosis factor alpha [TNF-α], interleukin-1β [IL-1β], IL-2, and gamma interferon [IFN-γ]). Histopathological findings of tubular degeneration and inflammatory cell infiltration reinforced GM-induced nephrotoxicity. All these alterations were attenuated by previous oral treatment with GF. Animals from the GM+GF groups showed amelioration in renal function parameters and reduced lipid peroxidation and nitrosative stress, in addition to an increment in the levels of glutathione (GSH) and superoxide dismutase (SOD) activity. Gingerols also promoted significant reductions in mRNA transcription for TNF-α, IL-2, and IFN-γ. These effects were dose dependent. These results demonstrate that GF promotes a nephroprotective effect on GM-mediated nephropathy by oxidative stress, inflammatory processes, and renal dysfunction.
The Complete Nucleotide Sequence of the Carbapenem Resistance-Conferring Conjugative Plasmid pLD209 from a Pseudomonas putida Clinical Strain Reveals a Chimeric Design Formed by Modules Derived from Both Environmental and Clinical Bacteria
Authors: Marchiaro Patricia M. , Brambilla Luciano , Morán-Barrio Jorgelina , Revale Santiago , Pasteran Fernando , Vila Alejandro J. , Viale Alejandro M. , Limansky Adriana S. 
Published: January 2014

ABSTRACT

The complete sequence of the carbapenem-resistance-conferring conjugative plasmid pLD209 from a
Pseudomonas putida
clinical strain is presented. pLD209 is formed by 3 well-defined regions: an adaptability module encompassing a Tn
402
-like class 1 integron of clinical origin containing
bla
VIM-2
and
aacA4
gene cassettes, partitioning and transfer modules, and a replication module derived from plasmids of environmental bacteria. pLD209 is thus a mosaic of modules originating in both the clinical and environmental (nonclinical) microbiota.
Outcomes of a specialist weight management programme in the UK National Health Service: prospective study of 1838 patients
Authors: Logue Jennifer , Allardice Gwen , Gillies Michelle , Forde Lorna , Morrison David S 
Published: January 2014

ObjectivesThere is limited evidence on the effectiveness of weight management programmes provided within routine healthcare and inconsistent use of outcome measures. Our aim was to evaluate a large National Health Service (NHS) weight management service and report absolute and proportional weight losses over 12 months.DesignProspective observational study.SettingGlasgow and Clyde Weight Management Service (GCWMS), which provides care for residents of NHS Greater Glasgow and Clyde area (population 1.2 million).ParticipantsAll patients who began GCWMS between 1 October 2008 and 30 September 2009.InterventionsStructured educational lifestyle programme employing cognitive behavioural therapy, 600 kcal deficit diet, physical activity advice, lower calorie diet and pharmacotherapy.Primary and secondary outcomes measuresBaseline observation carried forward (BOCF), last observation carried forward (LOCF) and changes in programme completers reported using outcomes of absolute 5 kg and 5% weight losses and mean weight changes at a variety of time points.Results6505 referrals were made to GCWMS, 5637 were eligible, 3460 opted in and 1916 (34%) attended a first session. 78 patients were excluded from our analysis on 1838 patients. 72.9% of patients were women, mean age of all patients at baseline was 49.1 years, 43.3% lived in highly socioeconomically deprived areas and mean weights and body mass indices at baseline were 118.1 kg and 43.3 kg/m2, respectively. 26% lost ≥5 kg by the end of phase 1, 30% by the end of phase 2 and 28% by the end of phase 3 (all LOCF). Weight loss was more successful among men, particularly those ≤29 years old.ConclusionsRoutine NHS weight management services may achieve moderate weight losses through a comprehensive evidence-based dietary, activity and behavioural approach including psychological care. Weight losses should be reported using a range of outcome measures so that the effectiveness of different services can be compared.
RsaI but notDraI polymorphism inCYP2E1gene increases the risk of gastrointestinal cancer in Malaysians: a case–control study
Authors: Chong Eric Tzyy Jiann , Lee Chong Cin , Chua Kek Heng , Chuah Jitt Aun , Lee Ping-Chin 
Published: January 2014

ObjectivesOur study aimed to investigate the association ofCYP2E1C-1019TRsaI and T7678ADraI polymorphisms and factors such as age, gender and ethnicity to the risk of gastrointestinal cancer (GIC) in Malaysians.DesignCase–control study.SettingMalaysia.Participants520 consented healthy blood donors with no previous GIC record and 175 patients with GIC.MeasurementsC-1019TRsaI and T7678ADraI genotyping ofCYP2E1gene; direct sequencing.ResultsThis study reveals that the variantc2allele and carrier with at least onec2allele of C-1019T single nucleotide polymorphism (SNP) significantly increased the risk of GIC but no significant association was found between T7678A SNP and combined analysis of C-1019T and T7678A SNPs to risk of GIC. The Malaysian Chinese had greater risk of GIC compared with the Malays, Indians and KadazanDusun. An increased risk of GIC was observed in individuals aged >40 years and women had a 2.22-fold and 1.58-fold increased risk of stomach and colorectal cancers, respectively, when compared with men.LimitationsThe future research should be conducted with a larger sample population and including the gene–gene and gene–environmental interactions.ConclusionsOur study suggests that the rarec2allele and carrier with at least onec2allele ofCYP2E1 RsaI polymorphism significantly elevated the risk of GIC and may be used as a genetic biomarker for early screening of GIC in Malaysians. The risk age-group has been shifted to a younger age at 40s and women showed a significant greater risk of stomach and colorectal cancers than men.