bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper accumulation, subcellular partitioning and physiological and molecular responses in relation to different copper tolerance in apple rootstocks
Authors: Wan Huixue , Du Jiayi , He Jiali , Lyu Deguo , Li Huifeng 
Published: April 2019

Abstract
To unravel the physiological and molecular regulation mechanisms underlying the variation in copper (Cu)accumulation, translocation and tolerance among five apple rootstocks, seedlings were exposed to either basal or excess Cu. Excess Cu suppressed plant biomass and root architecture, which was less pronounced in Malus prunifolia Borkh., indicating its relatively higher Cu tolerance. Among the five apple rootstocks, M. prunifolia exhibited the highest Cu concentration and bio-concentration factor in roots but the lowest translocation factor, indicating its greater ability to immobilize Cu and restrict translocation to the aerial parts. Higher Cu concentration in cell wall fraction but lower Cu proportion in membrane-containing and organelle-rich fractions were found in M. prunifolia. Compared with the other four apple rootstocks under excess Cu conditions, M. prunifolia had a lower increment of hydrogen peroxide in roots and leaves and malondialdehyde in roots, but higher concentrations of carbohydrates and enhanced antioxidants. Transcript levels of genes involved in Cu uptake, transport and detoxification revealed species-specific differences that are probably related to alterations in Cu tolerance. M. prunifolia had relatively higher gene transcript levels including copper transporters 2 (COPT2), COPT6 and zinc/iron-regulated transporter-related protein 2 (ZIP2), which probably took part in Cu uptake, and C-type ATP-binding cassette transporter 2 (ABCC2), copper chaperone for Cu/Zn superoxide dismutase (CCS), Cu/Zn superoxide dismutase 1 (CSD1) and metallothionein 2 (MT2) probably implicated in Cu detoxification, and relatively lower mRNA levels of yellow stripe-like transporter 3 (YSL3) and heavy metal ATPase 5 (HMA5) involved in transport of Cu to aerial parts. These results suggest that M. prunifolia is more tolerant to excess Cu than the other four apple rootstocks under the current experimental conditions, which is probably attributed to more Cu retention in roots, subcellular partitioning, well-coordinated antioxidant defense mechanisms and transcriptional expression of genes involved in Cu uptake, translocation and detoxification.
Carbon-use strategies in stem radial growth of two oak species, one Temperate deciduous and one Mediterranean evergreen: what can be inferred from seasonal variations in the δ13C of the current year ring?
Authors: Vincent-Barbaroux Cécile , Berveiller Daniel , Lelarge-Trouverie Caroline , Maia Rodrigo , Máguas Cristina , Pereira João , Chaves Manuela M , Damesin Claire 
Published: April 2019

Abstract
Tree ring synthesis is a key process in wood production; however, little is known of the origin and fate of the carbon involved. We used natural 13C abundance to investigate the carbon-use process for the ring development in a temperate deciduous (Quercus petraea (Matt.) Liebl.) and a Mediterranean evergreen (Quercus ilex L.) oak. The sapwood carbon reserves, phloem sucrose contents, stem respired CO2 efflux and their respective carbon isotope compositions (δ13C) were recorded over 1 year, in the native area of each species. The seasonal δ13C variation of the current year ring was determined in the total ring throughout the seasons, as well as in slices from the fully mature ring after the growth season (intra-ring pattern). Although the budburst dates of the two oaks were similar, the growth of Quercus ilex began 50 days later. Both species exhibited growth cessation during the hot and dry summer but only Q. ilex resumed in the autumn. In the deciduous oak, xylem starch storage showed clear variations during the radial growth. The intra-ring δ13C variations of the two species exhibited similar ranges, but contrasting patterns, with an early increase for Q. petraea. Comparison between δ13C of starch and total ring suggested that Q. petraea (but not Q. ilex) builds its rings using reserves during the first month of growth. Shifts in ring and soluble sugars δ13C suggested an interspecific difference in either the phloem unloading or the use of fresh assimilate inside the ring. A decrease in ring δ13C for both oaks between the end of the radial growth and the winter is attributed to a lignification of ring cell walls after stem increment. This study highlighted the differences in carbon-use during ring growth for evergreen and deciduous oaks, as well as the benefits of exploring the process using natural 13C abundance.
Prediction of temperate broadleaf tree species mortality in arid limestone habitats with stomatal safety margins
Authors: Chen Zhicheng , Li Shan , Luan Junwei , Zhang Yongtao , Zhu Shidan , Wan Xianchong , Liu Shirong 
Published: April 2019

AbstractA growing body of evidence highlights the occurrence of increased widespread tree mortality during climate change-associated severe droughts; however, in situ long-term drought experiments with multispecies communities for the prediction of tree mortality and exploration of related mechanisms are rather limited in natural environments. We conducted a 7-year afforestation trial with 20 drought-resistant broadleaf tree species in an arid limestone habitat in northern China, where the species displayed a broad range of survival rates. The stomatal and xylem hydraulic traits of all the species were measured. We found that species’ stomatal closure points were strongly related to their xylem embolism resistance and xylem minimum water potential but not to their survival rates. Hydraulic failure of the vascular system appeared to be the main cause of tree mortality, and the stomatal safety margin was a better predictor of tree mortality than the traditionally considered xylem embolism resistance and hydraulic safety margin. We recommend the stomatal safety margin as the indicator for predicting drought-induced tree mortality and for selecting tree species in future forest restorations in arid regions.
Malachite: A Gene Enrichment Meta-Analysis (GEM) Tool for ToppGene
Authors: Gershkowitz Gregory R. , Abrams Zachary B. , Coombes Caitlin E. , Coombes Kevin R. 
Published: April 2019

AbstractBackgroundResearchers commonly use online tools such as ToppGene to conduct enrichment analyses on gene expression data. This process does not easily allow multiple gene data sets to be analyzed and compared at once. ToppGene requires the user to manually enter gene symbols or other gene identifiers into a text box and to manually sift through forms with many adjustable parameters in order to obtain a downloadable text file of results. This process makes the analysis of multiple sets of genes tedious, time-consuming, and error prone. To address this problem, we developed Malachite, a Python package that enables researchers to perform gene enrichment analyses on multiple gene lists and concatenate the resulting enrichment statistics. In this way, Malachite enables meta-enrichment analyses across multiple data sets.ResultsTo illustrate its use, we applied Malachite to three data sets from the Gene Expression Omnibus comparing gene expression in the large airways of smokers and non-smokers. Biological processes enriched in all three data sets were related to xenobiotic stimulus; molecular functions typically involved nicotinamide adenine dinucleotide phosphate (NADP) activity.ConclusionMalachite enables researchers to automate gene enrichment metaanalyses using ToppGene. Malachite also enhances ToppGene’s gene set analysis of drug-gene relationships by further filtering for FDA approved drugs.
Co-culture ofSaccharomyces cerevisiae(VS3) andPichia stipitis(NCIM 3498) for bioethanol production using concentratedProsopis julifloraacid hydrolysate
Authors: Naseeruddin Shaik , Desai Suseelendra , Rao L Venkateswar 
Published: April 2019

AbstractBioethanol production from lignocellulosic biomass is a viable option for improving energy security and reducing green house emissions. In the present studyProsopis juliflora, an invasive tree found through out India, with total carbohydrate content of 67.4 +/- 6% was selected as lignocellulosic feedstock for bioethanol production. The hydrolysate obtained after biphasic dilute acid hydrolysis contained initial sugar concentration of 18.70 +/- 0.16 g/L and hence to increase the ethanol yield it was concentrated to 33.59 +/- 0.52 g/L (about two-folds) by vacuum distillation. The concentration of sugars, phenols and furans was analyzed before and after concentration process. The concentrated hydrolysate was further detoxified by over liming, neutralization and charcoal treatment and later used for ethanol fermentation by mono- and co culture method. Monoculture ofSaccharomyces cerevisiae(VS3) andPichia stipitis(NCIM 3498) produced 8.52 +/- 0.43 and 4.52 +/- 0.23 g/L of ethanol with 66.21 +/- 3.26% and 60.46 +/- 3.02% of fermentation efficiency, 0.33 +/- 0.02 and 0.31 +/- 0.02 g/g of ethanol yield and 0.24 +/- 0.01 and 0.13 +/- 0.01 g/L/h of productivity, respectively. The co-culture ofS. cerevisiae(VS3) andP. stipitis(NCIM 3498) helped to improve all parameters i.e. 10.94 +/- 0.53 g/L of ethanol with fermentation efficiency, ethanol yield and productivity of 83.11 +/- 0.42%, 0.420 +/- 0.01 g/g and 0.30 +/- 0.01 g/L/h, respectively.
Proteome analysis of xylose metabolism inRhodotorula toruloidesduring lipid production
Authors: Tiukova Ievgeniia A. , Brandenburg Jule , Blomqvist Johanna , Samples Sabine , Mikkelsen Nils , Skaugen Morten , Øverlie Arntzen Magnus , Nielsen Jens , Sandgren Mats , Kerkhoven Eduard J. 
Published: April 2019

AbstractBackgroundRhodotorula toruloidesis a promising platform organism for production of lipids from lignocellulosic substrates. Little is known about the metabolic aspects of lipid production from the lignocellolosic sugar xylose by oleaginous yeasts in general andR. toruloidesin particular. This study presents the first proteome analysis of the metabolism ofR. toruloidesduring conversion of xylose to lipids.ResultsR. toruloidescultivated on either glucose or xylose was subjected to comparative analysis of its growth dynamics, lipid composition, fatty acid profiles and proteome. The maximum growth and sugar uptake rate of glucose-grownR. toruloidescells were almost twice that of xylose-grown cells. Cultivation on xylose medium resulted in a lower final biomass yield although final cellular lipid content was similar between glucose- and xylose-grown cells. Analysis of lipid classes revealed the presence of monoacylglycerol in the early exponential growth phase as well as a high proportion of free fatty acids. Carbon source-specific changes in lipid profiles were only observed at early exponential growth phase, where C18 fatty acids were more saturated in xylose-grown cells. Proteins involved in sugar transport, initial steps of xylose assimilation and NADPH regeneration were among the proteins whose levels increased the most in xylose-grown cells across all time points. The levels of enzymes involved in the mevalonate pathway, phospholipid biosynthesis and amino acids biosynthesis differed in response to carbon source. In addition, xylose-grown cells contained higher levels of enzymes involved in peroxisomal beta-oxidation and oxidative stress response compared to cells cultivated on glucose.ConclusionsThe results obtained in the present study suggest that sugar import is the limiting step during xylose conversion byR. toruloidesinto lipids. NADPH appeared to be regenerated primarily through pentose phosphate pathway although it may also involve malic enzyme as well as alcohol and aldehyde dehydrogenases. Increases in enzyme levels of both fatty acid biosynthesis and beta-oxidation in xylose-grown cells was predicted to result in a futile cycle. The results presented here are valuable for the development of lipid production processes employingR. toruloideson xylose-containing substrates.
Ancestral role of Fat-like cadherins in planar cell polarity
Authors: Brooun Maria , Klimovich Alexander , Bashkurov Mikhail , Pearson Bret J. , Steele Robert E. , McNeill Helen 
Published: April 2019

ABSTRACTFat family cadherins are enormous proteins that regulate planar cell polarity (PCP) and cell adhesion in bilaterian animals. Their evolutionary origin can be traced back to prebilaterian species, but their ancestral function(s) are unknown. We identified Fat-like and Dachsous cadherins inHydra, a member of the early-diverging metazoan phylum Cnidaria.Hydrahas a simple body plan with only two epithelial layers and radial symmetry. We find thatHydrahomologues of Fat-like (HyFat) and Dachsous (HyDs) co-localize at the apico-lateral membrane of ectodermal epithelial cells. Remarkably, HyFat is planar polarized perpendicular to the oral-aboral axis of the animal. Using knockdown approaches we found that HyFat is involved in the regulation of local cell alignment, but is dispensable for the global alignment of ectodermal myonemes along the oral-aboral axis. The intracellular domain (ICD) of HyFat is involved in the morphogenesis of ectodermal myonemes. Thus, Fat family cadherins have ancient, prebilaterian functions in cell adhesion, tissue organization and planar polarity.
Zinc Solubilizing Plant Growth Promoting Microbes Produce Zinc Nanoparticles
Authors: Sultana Uzma , Desai Suseelendra , Reddy Gopal , Prasad TNVKV 
Published: April 2019

AbstractStrains of Pseudomonas, Bacillus and Azospirillum with plant growth promoting ability were checked for their zinc solubilizing ability. Efficient zinc solubilizers were checked for their ability to produce nano-scale zinc particles. The nanoparticles from the cell-free culture filtrates obtained from these strains were characterized for particle size, Zeta potential and functional groups. Presence of Zn nanoparticles in the bacterial culture filtrate was confirmed by particle distribution and Scanning electron microscope (SEM) analysis. Most properties of nanoparticles are size dependent. Zinc nanoparticles were observed to be spherical in shape and size ranged from 52.0 to 106.0 nm. Zeta potential of the Zn nanoparticles was estimated to understand the stability of the particles. The measured zeta potentials varied from −14.5mV to +179.10 mV indicating high stability and dispersion of the zinc nanoparticles. FTIR peaks at different wave numbers depicted the role of functional groups of proteins in the biosynthesis of Zn nanoparticles. This finding opens a new area of research focusing on microbe-microbe interactions in rhizosphere and plant-microbe interactions at rhizosphere apart from biosynthesis of nanoparticles, which has major applications. To our knowledge, this is the first report of production of nanoparticles as part of nutrient mobilization by plant growth promoting rhizobacteria.
Development of specific molecular markers to distinguish and quantify broomrape species in a soil sample from infected field
Authors: Aly Radi , Bari Vinay K. , Londner Avishai , Nassar Jackline Abu , Taha-Salaime Leena , Hanan Eizenberg , Lati Ran 
Published: April 2019

AbstractBroomrapes (OrobancheandPhelipanche) are obligate holoparasites that cause heavy damage to numerous crops, reducing the yield and its quality. The parasite develops in the soil and exerts the greatest damage prior to its emergence; therefore the majority of field loss may occur before diagnosis of infection. Because of the parasite tiny seed size (200 to 300 μm) and dormancy for several decades in the field, it is very difficult to diagnose the parasite by conventional methods. Therefore, to restrict the parasite seeds spread and contamination to other commercial fields, development of DNA-based molecular markers to identify and quantify broomrape species in a soil sample is much needed. In this study, we developed a specific molecular marker (RbcL-M) based onrbcL(large subunit of the ribulose-bisphosphate carboxylase) gene fromOrobanche crenatato differentiate betweenOrobanche crenataandOrobanche cumana.Likewise, a specific marker (ITS100) based upon unique sequences in the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA ofPhelipanche aegyptiacato quantify three species of the parasite (P. aegyptiaca, O. crenataandO. cumana) in a soil sample was developed. Genomic DNA was extracted from soil samples artificially infested with broomrape seeds or tissue ofP. aegyptiaca, O. cumanaandO. crenataand subjected to PCR analysis. RbcL-M marker successfully amplified a PCR product (1300bp) whenO. crenataseeds or tissues (collected from several locations in Israel) were added to the soil samples. The same marker amplified a PCR product (1000bp) whenO. cumanaseeds or tissues were added to the soil samples. RbcL-M marker did not amplify soil samples with seeds or tissues ofP. aegyptiacaor any soil-borne DNA. Furthermore, using ITS-100 marker and Real-Time PCR analysis, allowed quantitative diagnostic of the parasite in a soil sample from infected sunflower field. As expected the universal internal control primer (UCP-555) amplified a PCR product (555bp) when genomic DNA extracted from soil samples with or without broomrape tissues. The development of an efficient, simple and robust molecular marker to detect and distinguish between broomrape species, has a significant insights on assessment the level of infestation and planning eradication program to the parasite in a field crop.
Differential nanoscale organisation of LFA-1 modulates T cell migration
Authors: Shannon Michael J. , Pineau Judith , Griffié Juliette , Aaron Jesse , Peel Tamlyn , Williamson David J. , Zamoyska Rose , Cope Andrew P. , Cornish Georgina H. , Owen Dylan M. 
Published: April 2019

AbstractEffector T-cells rely on integrins to drive adhesion and migration to facilitate their immune function. Heterodimeric transmembrane integrin LFA-1 (αLβ2) regulates adhesion and migration through linkage of the extracellular matrix with the intracellular actin treadmill machinery. We quantitated the velocity and direction of F-actin flow in migrating T-cells alongside single molecule localisation of transmembrane and intracellular LFA-1. Our results show that retrograde actin flow positively correlated and immobile actin negatively correlated with T-cell velocity. Plasma membrane localised LFA-1 forms unique nano-clustering patterns in the leading edge, compared to the mid-focal zone, in migrating T-cells. Deleting the cytosolic phosphatase PTPN22, a negative regulator of integrin signaling, increased T-cell velocity, and leading-edge cluster co-localisation of pY397 FAK, pY416 Src family kinases and LFA-1. These data suggest that differential nanoclustering patterns of LFA-1 in migrating T-cells can instruct intracellular signalling linked with the actin treadmill. Our data presents a paradigm where T cells modulate the nanoscale organisation of adhesion and signalling molecules to fine tune their migration speed. This has implications for the regulation of immune and inflammatory responses.
Potential of on-scalp MEG: Robust detection of human visual gamma-band responses
Authors: Iivanainen Joonas , Zetter Rasmus , Parkkonen Lauri 
Published: April 2019

AbstractElectrophysiological signals recorded intracranially show rich frequency content spanning from near-DC to hundreds of hertz. Noninvasive electromagnetic signals measured with electroencephalography (EEG) or magnetoencephalography (MEG) typically contain less signal power in high frequencies than invasive recordings. Particularly, noninvasive detection of gamma-band activity (> 30 Hz) is challenging since coherently active source areas are small at such frequencies and the available imaging methods have limited spatial resolution. Compared to EEG and conventional SQUID-based MEG, on-scalp MEG should provide substantially improved spatial resolution, making it an attractive method for detecting gamma-band activity.Using an on-scalp array comprised of eight optically-pumped magnetometers (OPMs) and a conventional whole-head SQUID array, we measured responses to a dynamic visual stimulus known to elicit strong gamma-band responses. OPMs had substantially higher signal power than SQUIDs, and had a slightly larger relative gamma-power increase over the baseline. With only eight OPMs, we could obtain gamma-activity source estimates comparable to those of SQUIDs at the group level.Our results show the feasibility of OPMs to measure gamma-band activity. To further facilitate the noninvasive detection of gamma-band activity, the on-scalp OPM arrays should be optimized with respect to sensor noise, the number of sensors and inter-sensor spacing.
WASP restricts active Rac to maintain cells’ front-rear polarisation
Authors: Amato Clelia , Thomason Peter , Davidson Andrew , Swaminathan Karthic , Ismail Shehab , Machesky Laura , Insall Robert 
Published: April 2019

SummaryEfficient motility requires polarised cells, with anterior pseudopods and a retracting rear. This polarisation requires that the pseudopod catalyst Rac is restricted to the front. Here we show that the Arp2/3 complex regulator WASP is important for maintaining front–rear polarity, using a mechanism that limits where active Rac localises. Dictyostelium cells lacking WASP inappropriately activate Rac and SCAR/WAVE at their rears, leading to reduced cell speed. WASP facilitates the internalisation of clathrin-coated pits, and its Rac-binding CRIB motif is considered essential for its localisation and activity. However, WASP mutants with deleted CRIB domains, or harbouring a new mutation that prevents Rac binding, localise normally, recruit Arp2/3 complex, and drive actin polymerisation. Similarly, Rac inhibitors do not block WASP localisation or activation. Despite this, WASP CRIB mutants cannot restore polarisation of active Rac. Thus, WASP’s interaction with Rac regulates Rac activity and cell polarity, but is dispensable for activating actin polymerization.
MuGVRE. A virtual research environment for 3D/4D genomics
Authors: Codó Laia , Bayarri Genís , Cid-Fuentes Javier Alvarez , Conejero Javier ,   Adam Hospital, Royo Romina , Repchevsky Dmitry , Pasi Marco , Meletiou Athina , McDowall Mark D. , Reham Fatima , Alcantara José A. , Jimenez-Garcia Brian , Walther Jürgen , Illa Ricard , Serra François , Goodstadt Michael , Castillo David , Sati Satish , Buitrago Diana , Brun-Heath Isabelle , Fernandez-Recio Juan , Cavalli Giacomo , Marti-Renom Marc , Yates Andrew , Laughton Charles A. , Badia Rosa M. , Orozco Modesto , Gelpí Josep Ll. 
Published: April 2019

ABSTRACTMultiscale Genomics (MuG) Virtual Research Environment (MuGVRE) is a cloud-based computational infrastructure created to support the deployment of software tools addressing the various levels of analysis in 3D/4D genomics. Integrated tools tackle needs ranging from high computationally demanding applications (e.g. molecular dynamics simulations) to high-throughput data analysis applications (like the processing of next generation sequencing). The MuG Infrastructure is based on openNebula cloud systems implemented at the Institute for research in Biomedicine, and the Barcelona Supercomputing Center, and has specific interfaces for users and developers. Interoperability of the tools included in MuGVRE is maintained through a rich set of metadata allowing the system to associate tools and data in a transparent manner. Execution scheduling is based in a traditional queueing system to handle demand peaks in applications of fixed needs, and an elastic and multi-scale programming model (pyCOMPSs, controlled by the PMES scheduler), for complex workflows requiring distributed or multi-scale executions schemes. MuGVRE is available athttps://vre.multiscalegenomics.euand documentation and general information athttps://www.multiscalegenomics.eu. The infrastructure is open and freely accessible.