bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bacterial sugar utilization gives rise to distinct single‐cell behaviours
Authors: Afroz Taliman , Biliouris Konstantinos , Kaznessis Yiannis , Beisel Chase L. 
Published: June 2014

SummaryInducible utilization pathways reflect widespread microbial strategies to uptake and consume sugars from the environment. Despite their broad importance and extensive characterization, little is known how these pathways naturally respond to their inducing sugar in individual cells. Here, we performed single‐cell analyses to probe the behaviour of representative pathways in the model bacterium Escherichia coli. We observed diverse single‐cell behaviours, including uniform responses (d‐lactose, d‐galactose, N‐acetylglucosamine, N‐acetylneuraminic acid), ‘all‐or‐none’ responses (d‐xylose, l‐rhamnose) and complex combinations thereof (l‐arabinose, d‐gluconate). Mathematical modelling and probing of genetically modified pathways revealed that the simple framework underlying these pathways – inducible transport and inducible catabolism – could give rise to most of these behaviours. Sugar catabolism was also an important feature, as disruption of catabolism eliminated tunable induction as well as enhanced memory of previous conditions. For instance, disruption of catabolism in pathways that respond to endogenously synthesized sugars led to full pathway induction even in the absence of exogenous sugar. Our findings demonstrate the remarkable flexibility of this simple biological framework, with direct implications for environmental adaptation and the engineering of synthetic utilization pathways as titratable expression systems and for metabolic engineering.
Understanding the formation of Mediterranean–African–Asian disjunctions: evidence for Miocene climate‐driven vicariance and recent long‐distance dispersal in the Tertiary relict Smilax aspera (Smilacaceae)
Authors: Chen Chen , Qi Zhe‐Chen , Xu Xi‐Hui , Comes Hans Peter , Koch Marcus A. , Jin Xin‐Jie , Fu Cheng‐Xin , Qiu Ying‐Xiong 
Published: June 2014

Summary

Tethyan plant disjunctions, including Mediterranean–African–Asian disjunctions, are thought to be vicariant, but their temporal origin and underlying causes remain largely unknown. To address this issue, we reconstructed the evolutionary history of Smilax aspera, a hypothesized component of the European Tertiary laurel forest flora.

Thirty‐eight populations and herbarium specimens representing 57 locations across the species range were sequenced at seven plastid regions and the nuclear ribosomal internal transcribed spacer region. Time‐calibrated phylogenetic and phylogeographic inferences were used to trace ancestral areas and biogeographical events.

The deep intraspecific split between Mediterranean and African–Asian lineages is attributable to range fragmentation of a southern Tethyan ancestor, as colder and more arid climates developed shortly after the mid‐Miocene. In the Mediterranean, climate‐induced vicariance has shaped regional population structure since the Late Miocene/Early Pliocene. At around the same time, East African and South Asian lineages split by vicariance, with one shared haplotype reflecting long‐distance dispersal.

Our results support the idea that geographic range formation and divergence of Tertiary relict species are more or less gradual (mostly vicariant) processes over long time spans, rather than point events in history. They also highlight the importance of the Mediterranean Basin as a centre of intraspecific divergence for Tertiary relict plants.
Development of a real‐time PCR method for the detection of the dagger nematodes Xiphinema index, X. diversicaudatum, X. vuittenezi and X. italiae, and for the quantification of X. index numbers
Authors: Van Ghelder C. , Reid A. , Kenyon D. , Esmenjaud D. 
Published: June 2014

The ectoparasitic dagger nematodes Xiphinema index and Xiphinema diversicaudatum, often at low numbers in the soil, are vectors of grapevine nepoviruses, which cause huge agronomical problems for the vineyard industry. This study reports a method, based on real‐time PCR, for the specific detection of these species and of the closely related non‐vector species Xiphinema vuittenezi and Xiphinema italiae. Specific primers and TaqMan probes were designed from the ribosomal DNA internal transcribed spacer 1 (ITS1), enabling the specific detection of single individuals of each of the X. index, X. diversicaudatum, X. italiae and X. vuittenezi species whatever the nematode population. The specificity of detection and absence of false positive reaction were confirmed in samples of each species mixed with the three other Xiphinema species or mixed with nematodes representative from other genera (non‐plant‐parasitic Dorylaimida, Longidorus sp., Meloidogyne spp., Globodera spp. and Pratylenchus sp.). The method was shown to be valid for the relative quantification of X. index numbers through its use, from crude nematode extracts of soil samples, in a greenhouse assay of grapevine accessions ranging from highly susceptible to resistant. As an alternative to time‐consuming microscopic identification and counting, this real‐time PCR method will provide a fast, sensitive and reliable diagnostic and relative quantification technique for X. index nematodes extracted from fields or controlled conditions.
In search of a reliable electrophysiological marker of oculomotor inhibition of return
Authors: Satel Jason , Hilchey Matthew D. , Wang Zhiguo , Reiss Caroline S. , Klein Raymond M. 
Published: June 2014

AbstractInhibition of return (IOR) operationalizes a behavioral phenomenon characterized by slower responding to cued, relative to uncued, targets. Two independent forms of IOR have been theorized: input‐based IOR occurs when the oculomotor system is quiescent, while output‐based IOR occurs when the oculomotor system is engaged. EEG studies forbidding eye movements have demonstrated that reductions of target‐elicited P1 components are correlated with IOR magnitude, but when eye movements occur, P1 effects bear no relationship to behavior. We expand on this work by adapting the cueing paradigm and recording event‐related potentials: IOR is caused by oculomotor responses to central arrows or peripheral onsets and measured by key presses to peripheral targets. Behavioral IOR is observed in both conditions, but P1 reductions are absent in the central arrow condition. By contrast, arrow and peripheral cues enhance Nd, especially over contralateral electrode sites.
Diagnostic properties of the methacholine and mannitol bronchial challenge tests: A comparison study
Authors: Kim Min‐Hye , Song Woo‐Jung , Kim Tae‐Wan , Jin Hyun‐Jung , Sin You‐Seob , Ye Young‐Min , Kim Sang‐Heon , Park Heung‐Woo , Lee Byung‐Jae , Park Hae‐Sim , Yoon Ho‐Joo , Choi Dong‐Chull , Min Kyung‐Up , Cho Sang‐Heon 
Published: June 2014

AbstractBackground and objectiveAirway hyperresponsiveness is a common feature of asthma. Methacholine and mannitol are two representative agonists for bronchial challenge. They have theoretically different mechanisms of action, and may have different diagnostic properties. However, their difference has not been directly evaluated among Korean adults. In this study, we compare the diagnostic properties of methacholine and mannitol bronchial provocation tests.MethodsAsthmatic patients and non‐asthmatic controls were recruited prospectively from four referral hospitals in Korea. Participants were challenged with each of methacholine and mannitol inhalation on different days. Their diagnostic utility was evaluated by calculating their sensitivity and specificity for asthma diagnosis. Response–dose ratio was also compared.ResultsA total of 50 asthmatic adults and 54 controls were enrolled (mean age 43.8 years). The sensitivity and specificity of mannitol challenge (defined by a PD15 of <635 mg) were 48.0% and 92.6%, respectively, whereas those of methacholine (defined by a PC20 of <16 mg/mL) were 42.0% and 98.1%, respectively. Twenty asthmatic participants (24%) showed positive response to a single agonist only. In the receiver operating curve analyses using response–dose ratio values, area under the curve was 0.77 (95% confidence interval (CI): 0.68–0.86) for mannitol, and 0.89 (95% CI: 0.83–0.95) for methacholine. The correlations between log‐ transformed mannitol and methacholine response–dose ratios were significant but moderate (r = 0.683, P < 0.001).ConclusionsThe present study demonstrated overall similar diagnostic properties of two diagnostic tests, but also suggested their intercomplementary roles for asthma.The clinical trial registration number at ClinicalTrial.gov is NCT02104284.
A Multigrid PGD‐based Algorithm for Volumetric Displacement Fields Measurements
Authors: Gomes Perini L. A. , Passieux J.‐C. , Périé J.‐N. 
Published: June 2014

ABSTRACTThe use of a finite elements‐based Digital Volume Correlation (FE‐DVC) leads to lower measurement uncertainties in comparison to subset‐based approaches. However, the associated computing time may become prohibitive when dealing with high‐resolution measurements. To overcome this limitation, a Proper Generalised Decomposition solver was recently applied to 2D digital image correlation. In this paper, this method is extended to measure volumetric displacements from 3D digital images. In addition, a multigrid Proper Generalised Decomposition algorithm is developed, which allows to use different discretisations in each term of the decomposition. Associated to a coarse graining of the digital images, this allows to avoid local minima, especially in presence of large displacements. Synthetic and practical cases are analysed with the present approach, and measurement uncertainties are compared with standard FE‐DVC. Results show that such an approach reduces the computational cost (when compared to FE‐DVC) whilst maintaining lower measurement uncertainties than standard subset‐based DVC.
A massif‐type (~1.86 Ga) anorthosite complex in the Yeongnam Massif, Korea: late‐orogenic emplacement associated with the mantle delamination in the North China Craton
Authors: Lee Yuyoung , Cho Moonsup , Cheong Wonseok , Yi Keewook 
Published: June 2014

AbstractTo unravel the petrogenesis of a massif‐type anorthosite in terms of the crust‐mantle geodynamics, we dated zircons separated from six samples from the Sancheong‐Hadong (SH) complex, Korea, using a sensitive high‐resolution ion microprobe. The weighted mean 207Pb/206Pb age of two anorthosites is 1862 ± 2 Ma, whereas the ages of the hornblende gabbro and granitic gneiss are 1873 ± 4 Ma and 1875 ± 5 Ma respectively. Zircon rims from mafic granulite and migmatitic gneiss yielded ages of 1860 ± 5 Ma and 1858 ± 4 Ma, respectively, implying that the granulite facies metamorphism and anatexis are associated with anorthosite emplacement. Our results, together with available Re–Os data, are compatible with the ~1.9–1.86 Ga collisional orogeny prevalent in the North China Craton and the Korean Peninsula, and suggest that orogenesis was accompanied by mantle delamination beneath the craton. It is thus likely that the SH anorthositic rocks are a product of late‐orogenic magmatism during the post‐collisional extension‐dominated phase of orogeny.
Rapid construction and screening of artificial microRNA systems in Chlamydomonas reinhardtii
Authors: Hu Jinlu , Deng Xuan , Shao Ning , Wang Gaohong , Huang Kaiyao 
Published: June 2014

SummaryThe unicellular green algae Chlamydomonas reinhardtii is a classic model for the study of flagella/cilia and photosynthesis, and it has recently been exploited for producing biopharmaceuticals and biofuel. Due to the low frequency of homologous recombination, reverse genetic manipulation in Chlamydomonas relies mainly on miRNA‐ and siRNA‐based knockdown methods. However, the difficulty in constructing artificial miRNA vectors, laborious screening of knockdown transformants, and undesired epigenetic silencing of exogenous miRNA constructs limit their application. We have established a one‐step procedure to construct an artificial miRNA precursor by annealing eight oligonucleotides of approximately 40 nucleotides. In the final construct, the Gaussia princeps luciferase gene (G‐Luc) is positioned between the promoter and the artificial miRNA precursor so that knockdown strains may quickly be screened by visualizing luciferase luminescence using a photon‐counting camera. Furthermore, the luciferase activity of transformants correlates with the knockdown level of two test target proteins: the chloroplast protein VIPP1 (vesicle inducing protein in plastids 1) and the flagellar protein CDPK3 (calcium‐dependent protein kinase 3). Adding an intron from RBCS2 (ribulose bisphosphate carboxylase/oxygenase small subunit 2) to the miRNA construct enhanced both the luciferase activity and the miRNA knockdown efficiency. A second miRNA vector incorporated the promoter of the nitrate reductase gene to allow inducible expression of the artificial miRNA. These vectors will facilitate application of the artificial miRNA and provide tools for studying the mechanism of epigenetics in Chlamydomonas, and may also be adapted for use in other model organisms.
VEGFR‐2 expression in malignant tumours of the canine mammary gland: a prospective survival study
Authors: Santos A. , Lopes C. , Gärtner F. , Matos A. J. F. 
Published: June 2014

AbstractVascular endothelial growth factor receptor‐2 (VEGFR‐2) is the main receptor activated by vascular endothelial growth factor ‐A (VEGF‐A) to promote tumour angiogenesis. Its clinical prognostic value has not been studied in canine mammary tumours (CMTs). Dogs with mammary cancer were enrolled in a survival study and the immunohistochemical expressions of VEGFR‐2 and VEGF‐A were analysed and associated with clinicopathological features. VEGFR‐2 expression was associated with VEGF immunoreactivity in cancer cells, supporting the presence of an autocrine loop that may be involved in CMTs growth and survival. VEGFR‐2 was also expressed by endothelial cells from tumour vasculature and positively associated with stromal matrix metalloproteinase‐9 (MMP‐9), suggesting the existence of a link between endothelial cells activation and up‐regulation of matrix degrading proteins. Carcinosarcomas exhibited high VEGFR‐2 expression suggesting that it may be one of the activated molecular pathways in this aggressive histological type and that VEGFR‐2 inhibitors may constitute a potential treatment to improve the prognosis of these patients. Both VEGF and VEGFR‐2 immunoreactivities were independent of patients' overall survival (OS) and disease‐free survival (DFS).
Negative interference of icteric serum on a bichromatic biuret total protein assay
Authors: Gupta Aradhana , Stockham Steven L. 
Published: June 2014

BackgroundBilirubin is stated to be a negative interferent in some biuret assays and thus could contribute to pseudohypoproteinemia in icteric samples.ObjectiveThe purpose of the study was to evaluate the magnitude of and reason for a falsely low total protein concentration in icteric serum when the protein concentration is measured with a bichromatic spectrophotometric biuret assay.MethodsCommercially available bilirubin was dissolved in 0.1 M NaOH and mixed with sera from 2 dogs to achieve various bilirubin concentrations of up to 40 mg/dL (first set of samples) and 35 mg/dL (second set of samples, for confirmation of first set of results and to explore the interference). Biuret total protein and bilirubin concentrations were determined with a chemistry analyzer (Cobas 6000 with c501 module). Line graphs were drawn to illustrate the effects of increasing bilirubin concentrations on the total protein concentrations. Specific spectrophotometric absorbance readings were examined to identify the reason for the negative interference.ResultsHigh bilirubin concentrations created a negative interference in the Cobas biuret assay. The detectable interference occurred with a spiked bilirubin concentration of 10.7 mg/dL in one set of samples, 20.8 mg/dL in a second set. The interference was due to a greater secondary‐absorbance reading at the second measuring point in the samples spiked with bilirubin, which possibly had converted to biliverdin.ConclusionMarked hyperbilirubinemia is associated with a falsely low serum total protein concentration when measured with a bichromatic spectrophotometric biuret assay. This can result in pseudohypoproteinemia and pseudohypoglobulinemia in icteric serum.
Relationships between cerebrospinal fluid characteristics, injury severity, and functional outcome in dogs with and without intervertebral disk herniation
Authors: Levine Gwendolyn J. , Cook Jennifer R. , Kerwin Sharon C. , Mankin Joseph , Griffin John F. , Fosgate Geoffrey T. , Levine Jonathan M. 
Published: June 2014

BackgroundCerebrospinal fluid (CSF) is commonly acquired in dogs with intervertebral disk herniation (IVDH) and is a common method to assess inflammatory responses following spinal cord injury (SCI).ObjectivesThe purpose of the study was to describe relationships between cisternalCSFcharacteristics, behavioral measures ofSCI, T2‐ weighted (T2W) hyperintensity on magnetic resonance imaging (MRI), and long‐term outcome in dogs withIVDH. Diagnostic accuracy ofCSFfor differentiatingIVDHfrom other myelopathies was also assessed.MethodsThe retrospective case series included 727 dogs, 443 with thoracolumbarIVDH, 103 with cervicalIVDH, and 181 with other spinal cord diseases. Signalment, initial neurologic function, ambulatory function at long‐term follow‐up, T2WMRI, andCSFvariables were recorded for dogs withIVDH. Signalment, etiology, andCSFdata were retrieved for dogs with other myelopathies. Associations betweenCSFpredictors, diagnosis, and outcomes were assessed.ResultsCSFtotal nucleated cell count (TNCC) increased withSCIseverity (rho −0.256,P < .001) in dogs withIVDH,TNCCwas significantly higher in the presence of T2W hyperintensity (P = .001) in dogs with thoracolumbarIVDH, butTNCC,RBCcount, microprotein, and percent neutrophils decreased with increasing injury duration (rho −0.253,P < .001; rho −0.269,P < .001; rho −0.141,P = .004, and rho −0.356,P < .001, respectively).CSFcharacteristics were not accurate for differentiatingIVDHfrom other spinal cord diseases.ConclusionsIn dogs withIVDH,CSF TNCC,RBCcount, microprotein, and percent neutrophils are correlated with clinical aspects ofSCIsuch as injury severity and duration, but cannot differentiateIVDHfrom other etiologies.
Platelet vacuoles in a dog with severe nonregenerative anemia: evidence of platelet autophagy
Authors: Pieczarka Emily M. , Yamaguchi Mamoru , Wellman Maxey L. , Judith Radin M. 
Published: June 2014

AbstractA 13‐year‐old neutered male English Springer Spaniel was presented to The Ohio State University Veterinary Medical Center for evaluation of severe anemia. Upon blood smear review, approximately 50% of the platelets contained single to multiple variably sized clear vacuoles. Transmission electron microscopy of the platelets revealed hallmark features of autophagy, including membrane‐lined vesicles and vacuoles containing membrane whorls and degrading organelles. While autophagy has been demonstrated in a wide range of eukaryotic cells for decades, reports of platelet autophagy are lacking. This case report illustrates atypical platelet vacuolation with electron microscopic features characteristic of autophagy.
Addition of sialidase or p38 MAPK inhibitors does not ameliorate decrements in platelet in vitro storage properties caused by 4 °C storage
Authors: Skripchenko A. , Thompson‐Montgomery D. , Awatefe H. , Turgeon A. , Wagner S. J. 
Published: June 2014

Background and ObjectivesBacterial proliferation is inhibited in platelets (PLTs) stored at refrigerated temperatures, but also dramatically decreases PLT in vivo survival. Recent studies have demonstrated that cold temperature (CT) stored PLTs secrete sialidases upon re‐warming, removing sialic acid from the PLT surface, which may be responsible for clustering of GPIbα and PLT clearance from circulation. In this study, the influence of a sialidase inhibitor or a p38 MAP kinase inhibitor was evaluated in units stored at 4 °C.Materials and MethodsAfter collection of a single Trima apheresis unit (n = 12), PLTs were aliquoted into four 60‐ml CLX storage bags. One bag was stored at 20–24 °C (RT) with continuous agitation; a second bag was stored at 4 °C without agitation; a third bag was held at 4 °C without agitation with sialidase inhibitor, a fourth bag was incubated at 4 °C with a p38 MAPK inhibitor without agitation.ResultsBeginning from Day 1, all in vitro PLT parameters were adversely affected by CT compared to those of RT. Similar in vitro storage properties were observed in CT PLT in the presence or absence of sialidase or p38 MAPK inhibitors. P38 MAPK phosphorylation inhibition was not observed at CT. Decrease of sialidase activity was observed for 2 days in PLTs stored in additive solution but not in plasma.ConclusionAddition of either sialidase or p38 MAPK inhibitors do not improve any in vitro parameters of PLTs stored at 4 °C in 100% plasma.
Unweaving hippolytoid systematics (Crustacea, Decapoda, Hippolytidae): resurrection of several families
Authors: De Grave Sammy , Li Chi Pang , Tsang Ling Ming , Chu Ka Hou , Chan Tin‐Yam 
Published: June 2014

The Hippolytidae is the fourth largest family within the Caridea, currently containing over 330 described species in 37 genera, and the classification of this family has been rather controversial. In this study, sequences of two nuclear protein‐coding genes, enolase and sodium‐potassium ATPase α‐subunit, and the mitochondrial 16S rRNA gene (totalling 1405 bp) from 29 hippolytid species in 20 genera plus 17 species from eight other caridean families were used to examine the phylogenetic status of Hippolytidae sensu lato. Our results clearly reject the monophyly of Hippolytidae and support the recognition of the Lysmatidae Dana, 1852, Thoridae Kingsley, 1879, Bythocarididae Christoffersen and Merguiidae Christoffersen .
Thermohaline circulation crisis and impacts during the mid-Pleistocene transition
Authors: Pena Leopoldo D. , Goldstein Steven L. 
Published: June 2014

Circulating between different cycles
Around a million years ago, large-scale ocean circulation changed dramatically during the switch from ∼41,000- to ∼100,000-year long glacial cycles. Pena and Goldstein analyzed the isotopic composition of neodymium in marine sediments from the South Atlantic. The results suggest how the contributions of deep water from northern and southern sources varied across the transition. The boundary between the two glacial states appears to have been marked by a dramatic weakening, perhaps even a shutdown, of deep-water currents.

Science
, this issue p.
318
Genome Sequence of
Pseudomonas
sp. Strain P482, a Tomato Rhizosphere Isolate with Broad-Spectrum Antimicrobial Activity
Authors: Krzyzanowska Dorota M. , Ossowicki Adam , Jafra Sylwia 
Published: June 2014

ABSTRACT

The tomato rhizosphere isolate
Pseudomonas
sp. strain P482 is a member of a diverse group of fluorescent pseudomonads. P482 produces a yet unidentified broad-spectrum antimicrobial compound(s), active
inter alia
(i.a.) against
Dickeya
spp. Here, we present a nearly complete genome of P482 obtained by a hybrid assembly of Illumina and PacBio sequencing data.
Full Genome Sequence of a Bovine Enterovirus Isolated in China
Authors: Peng Xiao-wei , Dong Hao , Wu Qing-min , Lu Yan-li 
Published: June 2014

ABSTRACT
We report the full genome sequence of an isolate of bovine enterovirus type B from China. The virus (BEV-BJ001) was isolated from Beijing, China, from fecal swabs of cattle suffering from severe diarrhea. This genome sequence will give useful insight for future molecular epidemiological studies in China.