Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid phosphatidic acid accumulation in response to low temperature stress in Arabidopsis is generated through diacylglycerol kinase

Phosphatidic acid (PtdOH) is emerging as an important signaling lipid in abiotic stress responses in plants. The effect of cold stress was monitored using 32P-labeled seedlings and leaf discs of Arabidopsis thaliana. Low, non-freezing temperatures were found to trigger a very rapid 32P-PtdOH increase, peaking within 2 and 5 min, respectively. In principle, PtdOH can be generated through three different pathways, i.e., (1) via de novo phospholipid biosynthesis (through acylation of lyso-PtdOH), (2) via phospholipase D hydrolysis of structural phospholipids, or (3) via phosphorylation of diacylglycerol (DAG) by DAG kinase (DGK). Using a differential 32P-labeling protocol and a PLD-transphosphatidylation assay, evidence is provided that the rapid 32P-PtdOH response was primarily generated through DGK. A simultaneous decrease in the levels of 32P-PtdInsP, correlating in time, temperature dependency, and magnitude with the increase in 32P-PtdOH, suggested that a PtdInsP-hydrolyzing PLC generated the DAG in this reaction. Testing T-DNA insertion lines available for the seven DGK genes, revealed no clear changes in 32P-PtdOH responses, suggesting functional redundancy. Similarly, known cold-stress mutants were analyzed to investigate whether the PtdOH response acted downstream of the respective gene products. The hos1, los1, and fry1 mutants were found to exhibit normal PtdOH responses. Slight changes were found for ice1, snow1, and the overexpression line Super-ICE1, however, this was not cold-specific and likely due to pleiotropic effects. A tentative model illustrating direct cold effects on phospholipid metabolism is presented.
Continuous expression of genes for xylem cysteine peptidases in long-lived ray parenchyma cells in Populus

XYLEM CYSTEINE PEPTIDASE 1 (XCP1) and XCP2 are key autolytic enzymes in programmed cell death of short-lived tracheary elements in plants. However, the patterns of expression of XCP genes remain to be clarified in long-lived ray parenchyma cells, which survive for several years after the completion of secondary wall formation. We isolated full-length cDNAs that encoded three XCPs (PsgXCP1, PsgXCP2A and PsgXCP2B) of Populus. The deduced amino acid sequences of the XCPs revealed three conserved catalytic residues, namely, cysteine (Cys), histidine (His) and asparagine (Asn), indicating that PsgXCP1, PsgXCP2A and PsgXCP2B might function as papain-like cysteine proteases. Ray parenchyma cells in hybrid poplar remained alive for several years, with continuous expression of XCP genes even after obvious secondary wall thickenings. Levels of expression of XCP genes were lower in the innermost annual ring of sapwood than in one and/or two outer annual rings from beyond the innermost sapwood. This result implies that autolysis of ray parenchyma cells might not be fully explained by dramatically enhanced expression of XCP genes just before their programmed death. In addition, the expression of PtaSND1-A1, PtaVND6-A1 and PtaMYB003 genes was detected in all annual ring in sapwood. Our observations suggest that the expression of genes associated with xylem differentiation such as secondary wall formation and cell death continues for several years in long-lived ray parenchyma cells before their death.
Molecular Methods for Detecting and Discriminating Shigella Associated with Foods and Human Clinical Infections — A Review

There are four species of the genus Shigella: S. dysenteriae, S. flexneri, S. sonneii, and S. boydii. It is extremely difficult if not impossible to utilize the PCR for distinguishing between shigellae and the five diarrheagenic pathotypes of Escherichia coli—enterohemolytic (EHEC), enteropathogenic (EPEC), engteroinvasive (EIEC), enterotoxigenic (ETEC), and enteroaggresive (EAEC)—due to the extremely close genetic relationship between Shigella spp. and E. coli. This problem is magnified by the presence of common virulence plasmids in these two microbial groups with virulence genes of extremely high homology. Although gastrointestinal infections by shigellae and EICC occur most frequently in developing nations, the responsible E. coli strains are indistinguishable from shigellae by PCR. In addition, with the exception of S. boydii, the other three species of Shigella are completely indistinguishable from one another by the PCR. The most fruitful approach to date in attempting to use the PCR for distinguishing the four species of Shigella from one another has been to first use immuno-capture based on somatic O antigenicity immediately prior to the use of the PCR to impart species selectivity to a coupled ELISA-PCR assay system. Most PCR assays involving the detection of shigellae have been designed to detect shigellae plus the E. coli pathotype EIEC as a collective and indistinguishable group of enteroinvasive organisms or to distinguish Shigella from pathogenic members of other pathogenic genera.
A comparison of biological, molecular and enzymatic markers to investigate variability within Microdochium nivale (Fries) Samuels and Hallett

Comparaison de marqueurs biologiques, moleculaires et enzymatiques pour l'analyse de la variabilite chez Microdochium nivale. Les variations au sein d'une collection de souches europeennes de Microdochium nivale isolees de plusieurs hotes sont etudiees sur la base de la morphologie des conidies, des profils d'esterases et de RFLP de la region des ITS de l'ADN ribosomique, de l'agressivite sur des plantules de ble et de la capacite a produire des peritheces in vitro. Un groupe homogene est differencie a la fois par les profils d'esterases et les RFLP des ITS de l'ADN-r. Les isolats de ce groupe possedent des profils d'ITS identiques aux isolats de reference de la variete majus utilises par d'autres auteurs et sont, par consequent, assignes a la variete majus. Les isolats a l'interieur du groupe homogene majus ont ete collectes a travers l'Europe, ce qui demontre que ce groupe n'est pas restreint au Royaume-Uni. Parallelement, 19 profils d'esterases et 2 profils d'ITS sont observes parmi le reste des isolats, ce qui suggere que ce groupe pourrait etre constitue de plusieurs autres sous-groupes. Les resultats demontrent que les 2 types d'isolats coexistent dans un meme lieu et que l'agressivite sur plantules de ble n'est liee a aucun autre caractere etudie.
V‐ AND P‐TYPE Ca2+‐STIMULATED ATPases IN A CALCIFYING STRAIN OF PLEUROCHRYSIS SP. (HAPTOPHYCEAE)

Coccolithophorids are marine unicellular algae characterized by their ability to carry out controlled, subcellular calcification. The biochemical and kinetic features of membrane‐bound Ca2+‐stimulated ATPases have been examined. Membranes and organelles from axenic cultures of Pleurochrysis sp. (CCMP299) were isolated by means of sucrose density centrifugation. High levels of Ca2+‐stimulated ATPase were detected in chloroplasts, Golgi apparatus, plasma membrane, and coccolith vesicles. The sensitivity of the enzyme activity in the organelles and membranes was assessed with pharmacologic agents that are known to be specific for the several isoforms of Ca2+‐stimulated ATPase. The Ca2+‐stimulated ATPase activity in the Golgi and coccolith vesicle preparations was sensitive to nitrate, thiocyanate, and sodium azide and insensitive to vanadate, cyclopiazonic acid, and thapsigargin. ATP‐dependent H+ movement, but not 45Ca2+ transport, across the coccolith vesicle was demonstrated. The Ca2+‐stimulated ATPase in the plasma membrane preparation was sensitive to vanadate. ATP‐dependent, vanadate‐sensitive efflux of 45Ca2+ was demonstrated for microsomal material derived from gradient‐isolated plasma membrane. Polypeptides from isolated Golgi and coccolith vesicle preparations cross‐reacted to an antibody raised against a subunit of the oat root proton pump, whereas polypeptides from the chloroplast preparations did not cross‐react. These findings show that a V‐type Ca2+‐stimulated ATPase is located on the coccolith vesicle membrane and a P‐type Ca2+‐stimulated ATPase is located on the plasma membrane.
A taxonomic revision of the genus Pastinaca L. (Umbelliferae).

A taxonomic revision of the genus Pastinaca L. was carried out with respect to fruitmacro- and micro-morphology, anatomy, palynology, and phytochemistry. The study covers the world distribution of the genus, confined to Europe and Asia, except for Pastinaca sativa L. subsp. sativa (parsnip) cultivated all over the world. Pollen studies showed that the pollen of the genus could be described as cerebroid. Three flavonoid compounds were detected in the genus. Pastinaca is represented with eight species and four subspecies in the world. P. latifolia DC. is regarded as a subspecies of P. sativa.
A trait dataset for Taiwan's breeding birds

Abstract Background Species traits affect how a species interacts with the environment and other species and thus determine the role of the species in an ecosystem. They affect not only population dynamics of a species across space and over time, but also community structure and function through their key role in the community assembly processes. Information on species traits is also highly relevant for conservation planning as they determine the adaptive ability of a species in the face of environmental changes. However, information on species traits is usually scarce and sparsely distributed amongst diverse types of literature and sources. Difficulty in accessing comprehensive information on species traits has formed an essential knowledge gap, limiting our understanding of biodiversity patterns and ecosystem functioning and preventing effective conservation. Even for birds, a well-studied taxon, comprehensive trait information is still unavailable or distributed across different sources for many species. New information In this study, we compiled information from a variety of sources on 23 traits for all breeding birds, including 157 resident and 14 summer visiting species, in Taiwan and surrounding islands. The 23 traits include those related to the movement patterns, morphology, geographic distributions, activity patterns, feeding behaviour, habitat use, and breeding behaviour and strategies of the species. The trait information was obtained, not only from published literature and datasets, but also from unpublished banding records and specimen measurements. The dataset also contains derived traits, including the elevation and temperature boundaries of species distribution ranges in Taiwan. In addition, structured information on nest characters, which is seldom compiled in trait datasets, has been made available, for the first time, for the breeding birds in Taiwan. Therefore, the most comprehensive trait dataset to date on breeding birds in Taiwan will allow trait-based research and applications in diverse topics and thus enhance our understanding of the patterns and dynamics of breeding bird diversity and its functions in Taiwan.
A new species of freshwater crab of the genus Qianguimon Huang, 2018 (Decapoda: Brachyura: Potamidae) from Guangxi, Southern China

A new species of freshwater crab of the genus Qianguimon Huang, 2018, is described from Guangxi Zhuang Autonomous Region, southern China. It can be distinguished from congeners by the following characters: male first gonopods bent inward at about 45° at base of terminal segment, carapace regions distinct and rugged and the female vulva opening inwards and downwards. In addition, molecular evidence derived from the 16S rRNA gene supported the species described in this study as a new species of Qianguimon.
Aggregation and coexistence of dung beetles in montane rain forest and deforested sites in central Peru

The ‘aggregation model of coexistence’ predicts that a strong and independent aggregation of species across ephemeral resource patches promotes species coexistence and maintains diversity. This study examines the role of aggregation in maintaining tropical dung beetle diversity and the effects of deforestation on aggregation patterns and diversity loss. Using clusters of pitfall traps, dung beetle aggregation was quantified in natural and disturbed habitat at nested temporal and spatial scales in central Peru. The results indicate that dung was colonized by a greater number of species, many of which were large, leading to a higher total beetle biomass in forest habitat than in deforested, farm habitat. Beetles were intraspecifically aggregated at each spatial scale examined. Habitat-type (forest/deforested) had no effect on the intensity of intra- or interspecific aggregation. Analyses of aggregation patterns revealed that dung beetle assemblages in forest habitat were generally saturated whereas in deforested habitat they were unsaturated. In general, interspecific aggregation was too weak relative to intraspecific aggregation to explain the high diversity of species in forest habitat. Other mechanisms, including resource partitioning are likely to play a greater role in maintaining the diversity of dung beetle assemblages in the region. These results also indicate that the loss of species from disturbed habitat has not been due to a breakdown in the aggregation mechanism.
Statistical Tests and Retention of Terms in the Additive Main Effects and Multiplicative Interaction Model for Cultivar Trials

The additive main effects and multiplicative interaction (AMMI) model has been recommended for cultivar trials repeated across lo. cations and/or years. Previous studies, using approximate F-tests introduced by Gollob, have declared more AMMI interaction principal components (PCs) significant than cross validation could show to be predictively useful. This study used Monte Carlo simulation to investigate whether such a result in an international maize (Zea mays L.) yield trial of nine cultivars in 20 environments could be wholly or partially explained by liberality of the Gollob tests and also to compare properties of Gollob tests and several more conservative procedures. Gollob tests were found extremely liberal (Type I error rate as high as 66% when the first interaction PC in a 9 by 20 table is null) and AMMI users are warned not to rely on them. Tests known as F(GH1) and F(GH2) were essentially equivalent and effectively controlled Type I error rates at or below the intended level, but were conservative for any component for which the previous component was small. Simulation tests and iterated simulation tests with greater power than F(GH1) and F(GH2), but apparently with adequate control of Type I error rates, were developed. Simulation results suggest that or F(GH2) could usually be used to choose a predictive model with only a small loss in accuracy, and sometimes a gain, as compared to the expected model choice by cross validation with half of the data used for modeling and the other half for validation. In some cases cross validation is likely to choose a model with fewer PCs than the optimal truncated model obtainable from the full data set. If cross validation is used to choose a model, it is recommended that all but one replication should be used for modeling and only one for validation.
Agreement between the GAITRite® System and the Wearable Sensor BTS G-Walk® for measurement of gait parameters in healthy adults and Parkinson’s disease patients

Background Nowadays, the most widely used types of wearable sensors in gait analysis are inertial sensors. The aim of the study was to assess the agreement between two different systems for measuring gait parameters (inertial sensor vs. electronic walkway) on healthy control subjects (HC) and patients with Parkinson’s disease (PD). Methods Forty healthy volunteers (26 men, 14 women, mean age 58.7 ± 7.7 years) participated in the study and 24 PD patients (19 men, five women, mean age 62.7 ± 9.8 years). Each participant walked across an electronic walkway, GAITRite, with embedded pressure sensors at their preferred walking speed. Concurrently a G-Walk sensor was attached with a semi-elastic belt to the L5 spinal segment of the subject. Walking speed, cadence, stride duration, stride length, stance, swing, single support and double support phase values were compared between both systems. Results The Passing-Bablock regression slope line manifested the values closest to 1.00 for cadence and stride duration (0.99 ≤ 1.00) in both groups. The slope of other parameters varied between 0.26 (double support duration in PD) and 1.74 (duration of single support for HC). The mean square error confirmed the best fit of the regression line for speed, stride duration and stride length. The y-intercepts showed higher systematic error in PD than HC for speed, stance, swing, and single support phases. Conclusions The final results of this study indicate that the G-Walk system can be used for evaluating the gait characteristics of the healthy subjects as well as the PD patients. However, the duration of the gait cycle phases should be used with caution due to the presence of a systematic error.
Movements and Habitat Use by Fledgling Wood Storks (Mycteria Americana) Prior to Dispersal from the Natal Colony

Abstract. Activity patterns of fledgling storks (Ciconiidae) during the parental-dependency period are poorly understood for many species, including the Wood Stork (Mycteria americana). Satellite telemetry was used to track the movements of fledgling Wood Storks ( n = 50) from the time they attained minimum flight capabilities until dispersal from the natal colony. Distances traveled, range size, and habitat use by fledgling Wood Storks were quantified for early (prior to the final week before dispersal) and late (the final week before dispersal) predispersal periods and for the entire predis-persal period as a whole. Metrics were compared among three colonies and between two years at a single colony using nonparametric tests. For the entire predispersal period, the mean daily maximum distance of juvenile Wood Storks from their nest was 1.39 ± 0.2 km (median = 0.18 and maximum = 103.13) and the mean cumulative distance moved per day was 2.38 ± 0.28 km (median = 0.45 and maximum = 110.58). Movement distances differed among colonies and between years, while core and total ranges were similar regardless of location. The majority of locations (84%) occurred within colony boundaries, 95% occurred within 1.0 km of the colony and 98% occurred within 3.5 km of the colony. Flight distances did not increase linearly with time and instead followed a Poisson distribution, increasing sharply during the final week before dispersal. Habitat management recommendations for juvenile Wood Storks are to preserve wetland features within a 1.0–3.5 km zone around a colony.
Novel functional variants in the MC4R gene among severely obese children from Iberian population

Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Portugal Unit of Genetic Paediatrics, Maternal and Child, Badajoz, Spain Department of Dietician, Endocrinologist Service, Infanta Cristina Hospital, Badajoz Genetics Unit, Infanta Cristina Hospital, Badajoz, Spain Department of Medical & Surgical Therapeutics, Medical School, University of Extremadura, Badajoz, Spain Nephrology Service, Infanta Cristina Hospital, Badajoz, Spain Center for Neurosciences & Cell Biology, University of Coimbra, Portugal
Atmospheric Nanoparticles

Atmospheric nanoparticles are of growing interest to many investigators for two main reasons. First, nanoparticles are important precursors for the formation of larger particles, which are known to strongly influence global climate, atmospheric chemistry, visibility, and the regional and global transport of pollutants and biological nutrients. Second, atmospheric nanoparticles may play critical roles in the deleterious human health effects associated with air pollution. In addition to these two well-recognized roles, nanoparticles may also significantly influence the chemistry of the atmosphere. Because their composition and reactivity can be quite different from larger particles, the presence of nanoparticles may open novel chemical transformation pathways in the atmosphere. There is possibly also an important role for nanostructures within larger particles, which often contain nanoscale features such as mineral grain agglomerates, soot spherules, or layer coatings of sulfates and nitrates. These complex morphological features likely influence a number of properties. For example, nanostructures probably affect water uptake via capillary condensation and nanoscale aqueous surface films may provide a medium for heterogeneous chemistry. In addition, nanoscale active sites on surfaces may influence particle phase transitions through heterogeneous nucleation. However, with a few notable exceptions, the potential roles and implications in atmospheric chemistry for nanoparticles and nanostructures have not been quantitatively examined.
Hybrid-Dependent Effect of Lactic Acid on Corn Starch Yields

ABSTRACT The effect of lactic acid on starch yields of different corn hybrids was determined by wet-milling 18 commercial corn hybrids at three levels of lactic acid. All 18 hybrid samples tested had higher starch yields when lactic acid was added to the steep solution, although the magnitude of the increased starch yields varied between 2.9 and 12.0%. The optimal lactic acid concentration for maximum starch recovery was found to be between 0.55 and 1.67% lactic acid, by wet-milling nine of the same 18 corn hybrids with seven levels of added lactic acid. Between 0.83 and 1.67% lactic acid, the starch yields of eight of the nine hybrids were constant (within ±0.5%). Results showed that the average starch yield across all hybrids decreased with a lactic acid concentration 1.67%.
Genome-Wide Association Study Reveals the Genetic Architecture of Stripe Rust Resistance at the Adult Plant Stage in Chinese Endemic Wheat

Chinese endemic wheat, comprising Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum), Yunnan hulled wheat (T. aestivum ssp. yunnanense), and Xinjiang rice wheat (T. petropavlovskyi), are genetically and morphologically unique. To examine the adult plant resistance to stripe rust among Chinese endemic wheat germplasms, a panel of 213 accessions was inoculated with mixed virulent races of wheat stripe rust (Puccinia striiformis f. sp. tritici) in four different field environments. Four traits associated with stripe rust resistance, infection type, final disease severity, disease index, and area under the disease progress curve, were used to evaluate the accessions. The phenotypic datasets were used for 55K single-nucleotide polymorphism (SNP) array-based genome-wide association studies to identify effective resistance loci. Eighty-nine accessions with stable resistance were identified in at least three of the four environments by phenotypic evaluation. Eleven markers located on chromosomes 1A, 2B, 5A, 5D, 7B, and 7D by the genome-wide association studies analysis showed significant associations with at least two resistance-associated traits in two of the environments. These loci, corresponding to seven genomic regions based on linkage disequilibrium decay distance, explained 9.3 to 26.0% of the total phenotypic variation. Five quantitative trait loci (QTLs) on chromosomes 1A, 2B, 7B, and 7D overlapped or were in close proximity to previously reported QTLs based on the consensus and physical maps using the reference sequence of bread wheat (IWGSC RefSeq v1.0). The other two QTLs were potential novel QTLs given their physical positions. Haplotype variants of QTL QYr.sicau-2BS showed subspecies-specific inheritance of the stripe rust resistance locus. Resistant loci among Chinese endemic wheat germplasms could be introduced into common wheat cultivars, and the high-confidence SNP markers will aid in marker-assisted selection in breeding for stripe rust disease resistance.