Miracle-dz/UniFAR-FTUs huggingface dataset:
In Situ Visualization of the Dynamics in Xylem Embolism Formation and Removal in the Absence of Root Pressure: A Study on Excised Grapevine Stems1[OPEN]

In excised grapevine stems, temporal changes in xylem embolism formation and removal are driven by vessel-associated tissue. Gas embolisms formed during drought can disrupt long-distance water transport through plant xylem vessels, but some species have the ability to remove these blockages. Despite evidence suggesting that embolism removal is linked to the presence of vessel-associated parenchyma, the underlying mechanism remains controversial and is thought to involve positive pressure generated by roots. Here, we used in situ x-ray microtomography on excised grapevine stems to determine if embolism removal is possible without root pressure, and if the embolism formation/removal affects vessel functional status after sample excision. Our data show that embolism removal in excised stems was driven by water droplet growth and was qualitatively identical to refilling in intact plants. When stem segments were rehydrated with H2O after excision, vessel refilling occurred rapidly (<1 h). The refilling process was substantially slower when polyethylene glycol was added to the H2O source, thereby providing new support for an osmotically driven refilling mechanism. In contrast, segments not supplied with H2O showed no refilling and increased embolism formation. Dynamic changes in liquid/wall contact angles indicated that the processes of embolism removal (i.e. vessel refilling) by water influx and embolism formation by water efflux were directly linked to the activity of vessel-associated living tissue. Overall, our results emphasize that root pressure is not required as a driving force for vessel refilling, and care should be taken when performing hydraulics measurements on excised plant organs containing living vessel-associated tissue, because the vessel behavior may not be static.
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors

MOTIVATION Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware. RESULTS A fast implementation of the Smith-Waterman sequence-alignment algorithm using Single-Instruction, Multiple-Data (SIMD) technology is presented. This implementation is based on the MultiMedia eXtensions (MMX) and Streaming SIMD Extensions (SSE) technology that is embedded in Intel's latest microprocessors. Similar technology exists also in other modern microprocessors. Six-fold speed-up relative to the fastest previously known Smith-Waterman implementation on the same hardware was achieved by an optimized 8-way parallel processing approach. A speed of more than 150 million cell updates per second was obtained on a single Intel Pentium III 500 MHz microprocessor. This is probably the fastest implementation of this algorithm on a single general-purpose microprocessor described to date.
AcePrimer: automation of PCR primer design based on gene structure

AcePrimer is an internet-accessed application based on CGI/Perl programming that designs PCR primers to search for deletion alleles in Caenorhabditis elegans gene knockout experiments and uses electronic PCR to search the entire genomic DNA sequence for potential false priming or multiple PCR amplification targets. Features such as the ability to target specific exons with the 'poison primer' approach and evaluation of primers with electronic PCR provide a flexible, web-based approach to design effective primers whilst minimizing the need for empirical optimization of PCR experiments.
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

MOTIVATION Large-scale sequence data require methods for the automated annotation of protein domains. Many of the predictive methods are based either on a Position Specific Scoring Matrix (PSSM) of fixed length or on a window-less Hidden Markov Model (HMM). The performance of the two approaches is tested for Coiled-Coil Domains (CCDs). The prediction of CCDs is used frequently, and its optimization seems worthwhile. RESULTS We have conceived MARCOIL, an HMM for the recognition of proteins with a CCD on a genomic scale. A cross-validated study suggests that MARCOIL improves predictions compared to the traditional PSSM algorithm, especially for some protein families and for short CCDs. The study was designed to reveal differences inherent in the two methods. Potential confounding factors such as differences in the dimension of parameter space and in the parameter values were avoided by using the same amino acid propensities and by keeping the transition probabilities of the HMM constant during cross-validation. AVAILABILTY The prediction program and the databases are available at http://www.wehi. edu.au/bioweb/Mauro/Marcoil
Lack of FTSH4 Protease Affects Protein Carbonylation, Mitochondrial Morphology, and Phospholipid Content in Mitochondria of Arabidopsis: New Insights into a Complex Interplay1

Plants devoid of FTSH4, one of the ATP-dependent metalloproteases in mitochondria, reveal an increased number of abnormal mitochondria, decreased respiratory complexes, and lower amounts of cardiolipins, which is suggested to cause the observed accumulation of oxidative damage. FTSH4 is one of the inner membrane-embedded ATP-dependent metalloproteases in mitochondria of Arabidopsis (Arabidopsis thaliana). In mutants impaired to express FTSH4, carbonylated proteins accumulated and leaf morphology was altered when grown under a short-day photoperiod, at 22°C, and a long-day photoperiod, at 30°C. To provide better insight into the function of FTSH4, we compared the mitochondrial proteomes and oxyproteomes of two ftsh4 mutants and wild-type plants grown under conditions inducing the phenotypic alterations. Numerous proteins from various submitochondrial compartments were observed to be carbonylated in the ftsh4 mutants, indicating a widespread oxidative stress. One of the reasons for the accumulation of carbonylated proteins in ftsh4 was the limited ATP-dependent proteolytic capacity of ftsh4 mitochondria, arising from insufficient ATP amount, probably as a result of an impaired oxidative phosphorylation (OXPHOS), especially complex V. In ftsh4, we further observed giant, spherical mitochondria coexisting among normal ones. Both effects, the increased number of abnormal mitochondria and the decreased stability/activity of the OXPHOS complexes, were probably caused by the lower amount of the mitochondrial membrane phospholipid cardiolipin. We postulate that the reduced cardiolipin content in ftsh4 mitochondria leads to perturbations within the OXPHOS complexes, generating more reactive oxygen species and less ATP, and to the deregulation of mitochondrial dynamics, causing in consequence the accumulation of oxidative damage.
Propriétés psychométriques de la version française des échelles de la demande psychologique, de la latitude décisionnelle et du soutien social du « Job Content Questionnaire » de Karasek : résultats de l'enquête nationale SUMER

Psychosocial factors at work have been found to be associated with having potential risk for adverse health effects. The main instrument used to measure these factors and their impact is the Job Content Questionnaire (JCQ) by Karasek. The objective of this study was to evaluate the psychometric properties of the French version of the JCQ, and in particular to assess its internal coherence and consistency, as well as the factorial and convergent validity of psychological demands, decisional latitude and social support at work based upon the SUMER survey, which was the first French national survey of its kind to include the JCQ. The study was based on a sample of 24, 486 workers who answered the JCQ in 2003 (96.5% response rate). Internal consistency was satisfactory, as Cronbach's alpha coefficients were observed as being higher than 0.65. Confirmatory factor analysis showed that the best model was composed of 5 latent variables: demands and pressures, the two dimensions of latitude (utilization of skills and autonomous decision-making), and the two dimensions of support (from supervisors and from colleagues). Convergent validity tests confirmed the expected association with key variables, which were: age, work status, sector of activity, occupation, job satisfaction, perception of job stress, and intent to change job. This study demonstrated satisfactory psychometric properties of Karasek's JCQ scales for the French working population.
The Microtubule-Associated Protein MAP18 Affects ROP2 GTPase Activity during Root Hair Growth1[OPEN]

MAP18 physically interacts with ROP2 and competes with AtRhoGDI1/SCN1 for binding to ROP2 during root hair growth in Arabidopsis. Establishment and maintenance of the polar site are important for root hair tip growth. We previously reported that Arabidopsis (Arabidopsis thaliana) MICROTUBULE-ASSOCIATED PROTEIN18 (MAP18) functions in controlling the direction of pollen tube growth and root hair elongation. Additionally, the Rop GTPase ROP2 was reported as a positive regulator of both root hair initiation and tip growth in Arabidopsis. Both loss of function of ROP2 and knockdown of MAP18 lead to a decrease in root hair length, whereas overexpression of either MAP18 or ROP2 causes multiple tips or a branching hair phenotype. However, it is unclear whether MAP18 and ROP2 coordinately regulate root hair growth. In this study, we demonstrate that MAP18 and ROP2 interact genetically and functionally. MAP18 interacts physically with ROP2 in vitro and in vivo and preferentially binds to the inactive form of the ROP2 protein. MAP18 promotes ROP2 activity during root hair tip growth. Further investigation revealed that MAP18 competes with RhoGTPase GDP DISSOCIATION INHIBITOR1/SUPERCENTIPEDE1 for binding to ROP2, in turn affecting the localization of active ROP2 in the plasma membrane of the root hair tip. These results reveal a novel function of MAP18 in the regulation of ROP2 activation during root hair growth.
The Binding Specificity of the PHD-Finger Domain of VIN3 Moderates Vernalization Response1[OPEN]

Vernalization-induced VIN3 enhances the PRC2 activity through its histone binding motif, PHD-finger domain, to mediate proper vernalization response in Arabidopsis. Vernalization is a response to winter cold to initiate flowering in spring. VERNALIZATION INSENSITIVE3 (VIN3) is induced by winter cold and is essential to vernalization response in Arabidopsis (Arabidopsis thaliana). VIN3 encodes a PHD-finger domain that binds to modified histones in vitro. An alteration in the binding specificity of the PHD-finger domain of VIN3 results in a hypervernalization response. The hypervernalization response is achieved by increased enrichments of VIN3 and trimethylation of Histone H3 Lys 27 at the FLC locus without invoking the increased enrichment of Polycomb Repressive Complex 2. Our result shows that the binding specificity of the PHD-finger domain of VIN3 plays a role in mediating a proper vernalization response in Arabidopsis.
A One-Day Field Test Battery for the Assessment of Aerobic Capacity, Anaerobic Capacity, Speed, and Agility of Soccer Players

THE PURPOSE OF THIS ARTICLE IS TO PROVIDE THE STRENGTH AND CONDITIONING PROFESSIONAL WITH INFORMATION TO EFFECTIVELY IMPLEMENT A BATTERY OF VALID AND RELIABLE SOCCER-SPECIFIC FIELD TESTS FOR AEROBIC CAPACITY, ANAEROBIC CAPACITY, SPEED, AND AGILITY. INITIALLY, THIS ARTICLE WILL DEAL WITH THE RATIONALE FOR FITNESS TESTING, SPECIFICALLY FIELD TESTING. VARIOUS FIELD TESTS, WHICH ASSESS THE DIFFERENT COMPONENTS OF FITNESS, WILL BE DESCRIBED, COMPARED, AND CONTRASTED. WHAT DATA ARE GENERATED FROM THESE TESTS AND HOW TO ANALYZE THESE DATA WILL BE DISCUSSED. A RATIONALE FOR THE CHOICE OF RECOMMENDED TESTS WILL BE REASONED. AND FINALLY, A TIMELINE FOR IMPLEMENTATION WILL BE OUTLINED.
Rice Sucrose Partitioning Mediated by a Putative Pectin Methyltransferase and Homogalacturonan Methylesterification1

OsQUA2 is necessary for high-HG methylesterification in the rice culm sieve element cell wall to facilitate source-to-sink sucrose allocation by ensuring the normal long-distance inter-SE movement of sucrose. Homogalacturonan (HG) is the main component of pectins. HG methylesterification has recently emerged as a key determinant controlling cell attachment, organ formation, and phyllotaxy. However, whether and how HG methylesterification affects intercellular metabolite transport has rarely been reported. Here, we identified and characterized knockout mutants of the rice (Oryza sativa) OsQUA2 gene encoding a putative pectin methyltransferase. Osqua2 mutants exhibit a remarkable decrease in the degree of methylesterification of HG in the culm-sieve element cell wall and a markedly reduced grain yield. The culm of Osqua2 mutant plants contains excessive sucrose (Suc), and a 13CO2 feeding experiment showed that the Suc overaccumulation in the culm was caused by blocked Suc translocation. These and other findings demonstrate that OsQUA2 is essential for maintaining a high degree of methylesterification of HG in the rice culm-sieve element cell wall, which may be critical for efficient Suc partitioning and grain filling. In addition, our results suggest that the apoplastic pathway is involved in long-distance Suc transport in rice. The identification and characterization of the OsQUA2 gene and its functionality revealed a previously unknown contribution of HG methylesterification and provided insight into how modification of the cell wall regulates intercellular transport in plants.
Awake1, an ABC-Type Transporter, Reveals an Essential Role for Suberin in the Control of Seed Dormancy[OPEN]

A mutant screen reveals a role for seed coat suberin in temperature-responsive seed dormancy through the exclusion of molecular oxygen from the seed. The mother plant plays an important dynamic role in the control of dormancy of her progeny seed in response to environmental signals. In order to further understand the mechanisms by which this dormancy control takes place in Arabidopsis (Arabidopsis thaliana), we conducted a forward genetic screen to isolate mutants that fail to enter dormancy in response to variation in temperature during seed set. We show that, for the first of these mutants, designated awake1, the maternal allele is required for entry into strongly dormant states and that awake1 mutants show seed phenotypes shown previously to be associated with the loss of suberin in the seed. We identify awake1 as an allele of ABCG20, an ATP-binding cassette transporter-encoding gene required for the transport of fatty acids during suberin deposition, and show that further suberin-deficient mutants have seed dormancy defects. Seed coat suberin composition is affected by temperature during seed maturation, but this response appears to be independent of ABCG20. We conclude that seed coat suberin is essential for seed dormancy imposition by low temperature and that the exclusion of oxygen and water from the seed by the suberin and tannin layers is important for dormancy imposition.
Two h-Type Thioredoxins Interact with the E2 Ubiquitin Conjugase PHO2 to Fine-Tune Phosphate Homeostasis in Rice1

Oryza sativa PHO2 interacts with two h-type thioredoxins, which links phosphate homeostasis with redox balance in rice. Phosphate overaccumulator2 (PHO2) encodes a ubiquitin-conjugating E2 enzyme that is a major negative regulator of the inorganic phosphate (Pi)-starvation response-signaling pathway. A yeast two-hybrid (Y2H) screen in rice (Oryza sativa; Os) using OsPHO2 as bait revealed an interaction between OsPHO2 and two h-type thioredoxins, OsTrxh1 and OsTrxh4. These interactions were confirmed in vivo using bimolecular fluorescence complementation (BiFC) of OsPHO2 and OsTrxh1/h4 in rice protoplasts and by in vitro pull-down assays with 6His-tagged OsTrxh1/h4 and GST-tagged OsPHO2. Y2H assays revealed that amino acid Cys-445 of OsPHO2 and an N-terminal Cys in the “WCGPC” motif of Trxhs were required for the interaction. Split-ubiquitin Y2H analyses and BiFC assays in rice protoplasts confirmed the interaction of OsPHO2 with PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 (OsPHF1), and PHOSPHATE1;2 (OsPHO1;2) in the endoplasmic reticulum and Golgi membrane system, where OsPHO2 mediates the degradation of OsPHF1 in both tobacco (Nicotiana benthamiana) leaves and rice seedlings. Characterization of rice pho2 complemented lines, transformed with an endogenous genomic OsPHO2 or OsPHO2C445S (a constitutively reduced form) fragment, indicated that OsPHO2C445S restored Pi concentration in rice to statistically significant lower levels compared to native OsPHO2. Moreover, the suppression of OsTrxh1 (knockdown and knockout) resulted in slightly higher Pi concentration than that of wild-type Nipponbare in leaves. These results demonstrate that OsPHO2 is under redox control by thioredoxins, which fine-tune its activity and link Pi homeostasis with redox balance in rice.
Automatic updating of the EMBL database via EMBNet

The paper describes a procedure for updating the EMBL (European Molecular Biology Laboratory, Heidelberg) database of nucleic acid sequences and its indexes used by the University of Wisconsin Genetics Computer Group (GCG) software package, using updated entries for this database distributed via EMBNet. At present the procedure is being run on a MRC Clinical Research Centre's (CRC) SUN 4/280 server using SUNOS version 4.0. 1 operating system.
Mitochondrial ABC Transporter ATM3 Is Essential for Cytosolic Iron-Sulfur Cluster Assembly1

Mitochondrial transporter ATM3-dependent cytosolic Fe-S cluster assembly is important for the development of lateral roots, root apical meristem, and shoot apical meristem in rice. The mitochondrial ATP-binding cassette transporter ATM3 has been studied in Arabidopsis. Its function, however, is poorly understood in other model plant species. This study reports that the ATM3 is required for cytosolic iron-sulfur cluster assembly and is essential for meristem maintenance in rice (Oryza sativa). The loss of function of OsATM3 is lethal in rice at the four-leaf stage. In the osatm3 T-DNA insertion mutant, the fourth leaf fails to develop and the lateral roots are short. Cytosolic iron-sulfur protein activities were significantly reduced in both osatm3 and RNA interference transgenic lines. The expression profiles of many iron metabolism genes were altered in the osatm3 and RNA interference lines. Glutathione metabolism was impaired and reactive oxygen species, particularly superoxide, accumulated in osatm3. Promoter-β-glucuronidase staining of the transgenic line indicated that OsATM3 is highly expressed in lateral root primordia, root tip meristem zones, and shoot apical meristem regions. The average cell size was significantly greater in osatm3 than in the wild type. Massive cell death occurred in the osatm3 root tip meristem zone. Quantitative RT-PCR revealed transcriptional reprogramming of the genes in the osatm3 and RNAi lines involved in DNA repair and cell cycle arrest. Our results suggest that the mitochondrial ATM3 is essential for iron homeostasis in rice.
Gain-of-Function Mutants of the Cytokinin Receptors AHK2 and AHK3 Regulate Plant Organ Size, Flowering Time and Plant Longevity1

Gain-of-function variants of two Arabidopsis cytokinin receptors show the impact of cytokinin on regulating shoot organ size, flowering time, plant longevity, and seed yield. The phytohormone cytokinin is a regulator of numerous processes in plants. In Arabidopsis (Arabidopsis thaliana), the cytokinin signal is perceived by three membrane-located receptors named ARABIDOPSIS HISTIDINE KINASE2 (AHK2), AHK3, and AHK4/CRE1. How the signal is transmitted across the membrane is an entirely unknown process. The three receptors have been shown to operate mostly in a redundant fashion, and very few specific roles have been attributed to single receptors. Using a forward genetic approach, we isolated constitutively active gain-of-function variants of the AHK2 and AHK3 genes, named repressor of cytokinin deficiency2 (rock2) and rock3, respectively. It is hypothesized that the structural changes caused by these mutations in the sensory and adjacent transmembrane domains emulate the structural changes caused by cytokinin binding, resulting in domain motion propagating the signal across the membrane. Detailed analysis of lines carrying rock2 and rock3 alleles revealed how plants respond to locally enhanced cytokinin signaling. Early flowering time, a prolonged reproductive growth phase, and, thereby, increased seed yield suggest that cytokinin regulates various aspects of reproductive growth. In particular, it counteracts the global proliferative arrest, a correlative inhibition of maternal growth by seeds, an as yet unknown activity of the hormone.
Poplar MYB115 and MYB134 Transcription Factors Regulate Proanthocyanidin Synthesis and Structure1[OPEN]

Two MYB transcription factors form the core of a gene regulatory network that controls the accumulation and hydroxylation pattern of proanthocyanidins in poplar. The accumulation of proanthocyanidins is regulated by a complex of transcription factors composed of R2R3 MYB, basic helix-loop-helix, and WD40 proteins that activate the promoters of biosynthetic genes. In poplar (genus Populus), MYB134 is known to regulate proanthocyanidin biosynthesis by activating key flavonoid genes. Here, we characterize a second MYB regulator of proanthocyanidins, MYB115. Transgenic poplar overexpressing MYB115 showed a high-proanthocyanidin phenotype and reduced salicinoid accumulation, similar to the effects of MYB134 overexpression. Transcriptomic analysis of MYB115- and MYB134-overexpressing poplar plants identified a set of common up-regulated genes encoding proanthocyanidin biosynthetic enzymes and several novel uncharacterized MYB transcriptional repressors. Transient expression experiments demonstrated the capacity of both MYB134 and MYB115 to activate flavonoid promoters, but only in the presence of a basic helix-loop-helix cofactor. Yeast two-hybrid experiments confirmed the direct interaction of these transcription factors. The unexpected identification of dihydromyricetin in leaf extracts of both MYB115- and MYB134-overexpressing poplar led to the discovery of enhanced flavonoid B-ring hydroxylation and an increased proportion of prodelphinidins in proanthocyanidin of the transgenics. The dramatic hydroxylation phenotype of MYB115 overexpressors is likely due to the up-regulation of both flavonoid 3′,5′-hydroxylases and cytochrome b5. Overall, this work provides new insight into the complexity of the gene regulatory network for proanthocyanidin synthesis in poplar.
Immunological Changes After Both Exercise and Activity in Chronic Fatigue Syndrome: A Pilot Study

AbstractBackground: The chronic fatigue syndrome (CFS) is characterized by post-exertional malaise and fatigue. We designed this pilot study to explore whether the illness was associated with alterations in immunological markers following exercise.Methods: We measured immunological markers before and up to three days after either a sub-maximal or maximal bicycle exercise test. We studied nine patients with CFS and nine age-and sex-matched healthy but sedentary controls. We also studied the same patients with CFS at home after a night's sleep and then after traveling to the study center.Results: There were no significant differences in any of the cell markers after a sub-maximal exercise test compared to a maximal test. However, we found elevated concentrations of plasma transforming growth factor beta (TGF-s), even before exercise, in subjects with CFS (median (IQR) of 904 (182-1072) pg/ml) versus controls (median (IQR) of 50 (45-68) pg/ml) (P < .001). Traveling from home to the hospital significantly ele.