bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice
Authors: Movahedi Sara , Van de Peer Yves , Vandepoele Klaas 
Published: May 2011

Abstract
Microarray experiments have yielded massive amounts of expression information measured under various conditions for the model species Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Expression compendia grouping multiple experiments make it possible to define correlated gene expression patterns within one species and to study how expression has evolved between species. We developed a robust framework to measure expression context conservation (ECC) and found, by analyzing 4,630 pairs of orthologous Arabidopsis and rice genes, that 77% showed conserved coexpression. Examples of nonconserved ECC categories suggested a link between regulatory evolution and environmental adaptations and included genes involved in signal transduction, response to different abiotic stresses, and hormone stimuli. To identify genomic features that influence expression evolution, we analyzed the relationship between ECC, tissue specificity, and protein evolution. Tissue-specific genes showed higher expression conservation compared with broadly expressed genes but were fast evolving at the protein level. No significant correlation was found between protein and expression evolution, implying that both modes of gene evolution are not strongly coupled in plants. By integration of cis-regulatory elements, many ECC conserved genes were significantly enriched for shared DNA motifs, hinting at the conservation of ancestral regulatory interactions in both model species. Surprisingly, for several tissue-specific genes, patterns of concerted network evolution were observed, unveiling conserved coexpression in the absence of conservation of tissue specificity. These findings demonstrate that orthologs inferred through sequence similarity in many cases do not share similar biological functions and highlight the importance of incorporating expression information when comparing genes across species.
Regulatory Subunit B′γ of Protein Phosphatase 2A Prevents Unnecessary Defense Reactions under Low Light in Arabidopsis
Authors: Trotta Andrea , Wrzaczek Michael , Scharte Judith , Tikkanen Mikko , Konert Grzegorz , Rahikainen Moona , Holmström Maija , Hiltunen Hanna-Maija , Rips Stephan , Sipari Nina , Mulo Paula , Weis Engelbert , von Schaewen Antje , Aro Eva-Mari , Kangasjärvi Saijaliisa 
Published: May 2011

Abstract
Light is an important environmental factor that modulates acclimation strategies and defense responses in plants. We explored the functional role of the regulatory subunit B′γ (B′γ) of protein phosphatase 2A (PP2A) in light-dependent stress responses of Arabidopsis (Arabidopsis thaliana). The predominant form of PP2A consists of catalytic subunit C, scaffold subunit A, and highly variable regulatory subunit B, which determines the substrate specificity of PP2A holoenzymes. Mutant leaves of knockdown pp2a-b′γ plants show disintegration of chloroplasts and premature yellowing conditionally under moderate light intensity. The cell-death phenotype is accompanied by the accumulation of hydrogen peroxide through a pathway that requires CONSTITUTIVE EXPRESSION OF PR GENES5 (CPR5). Moreover, the pp2a-b′γ cpr5 double mutant additionally displays growth suppression and malformed trichomes. Similar to cpr5, the pp2a-b′γ mutant shows constitutive activation of both salicylic acid- and jasmonic acid-dependent defense pathways. In contrast to cpr5, however, pp2a-b′γ leaves do not contain increased levels of salicylic acid or jasmonic acid. Rather, the constitutive defense response associates with hypomethylation of DNA and increased levels of methionine-salvage pathway components in pp2a-b′γ leaves. We suggest that the specific B′γ subunit of PP2A is functionally connected to CPR5 and operates in the basal repression of defense responses under low irradiance.
Os-GIGANTEA Confers Robust Diurnal Rhythms on the Global Transcriptome of Rice in the Field
Authors: Izawa Takeshi , Mihara Motohiro , Suzuki Yuji , Gupta Meenu , Itoh Hironori , Nagano Atsushi J. , Motoyama Ritsuko , Sawada Yuji , Yano Masahiro , Hirai Masami Yokota , Makino Amane , Nagamura Yoshiaki 
Published: May 2011

Abstract
The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice (Oryza sativa) leaves, using a newly isolated rice circadian clock–related mutant carrying a null mutation in Os-GIGANTEA (Os-GI), we show here that Os-GI controlled 75% (false discovery rate = 0.05) of genes among 27,201 genes tested and was required for strong amplitudes and fine-tuning of the diurnal rhythm phases of global gene expression in the field. However, transcripts involved in primary metabolism were not greatly affected by osgi. Time-course metabolome analyses of leaves revealed no trends of change in primary metabolites in osgi plants, and net photosynthetic rates and grain yields were not affected. By contrast, some transcripts and metabolites in the phenylpropanoid metabolite pathway were consistently affected. Thus, net primary assimilation of rice was still robust in the face of such osgi mutation-related circadian clock defects in the field, unlike the case with defects caused by Arabidopsis thaliana toc1 and ztl mutations in the laboratory.
ArabidopsisNitrate Transporter NRT1.9 Is Important in Phloem Nitrate Transport
Authors: Wang Ya-Yun , Tsay Yi-Fang 
Published: May 2011

AbstractThis study of the Arabidopsis thaliana nitrate transporter NRT1.9 reveals an important function for a NRT1 family member in phloem nitrate transport. Functional analysis in Xenopus laevis oocytes showed that NRT1.9 is a low-affinity nitrate transporter. Green fluorescent protein and β-glucuronidase reporter analyses indicated that NRT1.9 is a plasma membrane transporter expressed in the companion cells of root phloem. In nrt1.9 mutants, nitrate content in root phloem exudates was decreased, and downward nitrate transport was reduced, suggesting that NRT1.9 may facilitate loading of nitrate into the root phloem and enhance downward nitrate transport in roots. Under high nitrate conditions, the nrt1.9 mutant showed enhanced root-to-shoot nitrate transport and plant growth. We conclude that phloem nitrate transport is facilitated by expression of NRT1.9 in root companion cells. In addition, enhanced root-to-shoot xylem transport of nitrate in nrt1.9 mutants points to a negative correlation between xylem and phloem nitrate transport.
TheArabidopsisC2H2 Zinc Finger INDETERMINATE DOMAIN1/ENHYDROUS Promotes the Transition to Germination by Regulating Light and Hormonal Signaling during Seed Maturation
Authors: Feurtado J. Allan , Huang Daiqing , Wicki-Stordeur Leigh , Hemstock Laura E. , Potentier Mireille S. , Tsang Edward W.T. , Cutler Adrian J. 
Published: May 2011

AbstractSeed development ends with a maturation phase that imparts desiccation tolerance, nutrient reserves, and dormancy degree. Here, we report the functional analysis of an Arabidopsis thaliana C2H2 zinc finger protein INDETERMINATE DOMAIN1 (IDD1)/ENHYDROUS (ENY). Ectopic expression of IDD1/ENY (2x35S:ENY) disrupted seed development, delaying endosperm depletion and testa senescence, resulting in an abbreviated maturation program. Consequently, mature 2x35S:ENY seeds had increased endosperm-specific fatty acids, starch retention, and defective mucilage extrusion. Using RAB18 promoter ENY lines (RAB18:ENY) to confine expression to maturation, when native ENY expression increased and peaked, resulted in mature seed with lower abscisic acid (ABA) content and decreased germination sensitivity to applied ABA. Furthermore, results of far-red and red light treatments of 2x35S:ENY and RAB18:ENY germinating seeds, and of artificial microRNA knockdown lines, suggest that ENY acts to promote germination. After using RAB18:ENY seedlings to induce ENY during ABA application, key genes in gibberellin (GA) metabolism and signaling were differentially regulated in a manner suggesting negative feedback regulation. Furthermore, GA treatment resulted in a skotomorphogenic-like phenotype in light-grown 2x35S:ENY and RAB18:ENY seedlings. The physical interaction of ENY with DELLAs and an ENY-triggered accumulation of DELLA transcripts during maturation support the conclusion that ENY mediates GA effects to balance ABA-promoted maturation during late seed development.
DELLAs Regulate Chlorophyll and Carotenoid Biosynthesis to Prevent Photooxidative Damage during Seedling Deetiolation in Arabidopsis
Authors: Cheminant Soizic , Wild Michael , Bouvier Florence , Pelletier Sandra , Renou Jean-Pierre , Erhardt Mathieu , Hayes Scott , Terry Matthew J. , Genschik Pascal , Achard Patrick 
Published: May 2011

Abstract
In plants, light represents an important environmental signal that triggers the production of photosynthetically active chloroplasts. This developmental switch is critical for plant survival because chlorophyll precursors that accumulate in darkness can be extremely destructive when illuminated. Thus, plants have evolved mechanisms to adaptively control plastid development during the transition into light. Here, we report that the gibberellin (GA)-regulated DELLA proteins play a crucial role in the formation of functional chloroplasts during deetiolation. We show that Arabidopsis thaliana DELLAs accumulating in etiolated cotyledons derepress chlorophyll and carotenoid biosynthetic pathways in the dark by repressing the transcriptional activity of the phytochrome-interacting factor proteins. Accordingly, dark-grown GA-deficient ga1-3 mutants (that accumulate DELLAs) display a similar gene expression pattern to wild-type seedlings grown in the light. Consistent with this, ga1-3 seedlings accumulate higher amounts of protochlorophyllide (a phototoxic chlorophyll precursor) in darkness but, surprisingly, are substantially more resistant to photooxidative damage following transfer into light. This is due to the DELLA-dependent upregulation of the photoprotective enzyme protochlorophyllide oxidoreductase (POR) in the dark. Our results emphasize the role of DELLAs in regulating the levels of POR, protochlorophyllide, and carotenoids in the dark and in protecting etiolated seedlings against photooxidative damage during initial light exposure.
Ultrasound‐guided interscalene blocks: understanding where to inject the local anaesthetic
Authors: Spence B. C. , Beach M. L. , Gallagher J. D. , Sites B. D. 
Published: May 2011

SummaryAlthough ultrasound‐guided regional anaesthesia has gained in popularity, few data exist describing the optimal location(s) to inject local anaesthetic. Our objective was to compare, for interscalene blocks, the effectiveness of an injection between the middle scalene muscle and brachial plexus sheath (peri‐plexus) with an injection within the brachial plexus sheath (intra‐plexus). We enrolled 170 patients undergoing shoulder surgery with general anaesthesia and interscalene block in this randomised, controlled trial. Our primary outcome variable was loss of shoulder abduction. Block quality was also measured and defined by an evaluation of onset time, sensory and motor loss and duration. There was no difference between the two groups in block onset times or block quality. After adjusting for sex, age and volume injected, intra‐plexus blocks lasted a mean of 2.6 h (16%) longer (95% CI 0.25–5.01, p = 0.03) than peri‐plexus blocks.
Evidence for a macromolecular complex in poor prognosis CLL that contains CD38, CD49d, CD44 and MMP‐9
Authors: Buggins Andrea G. S. , Levi Ana , Gohil Satyen , Fishlock Keith , Patten Piers E. M. , Calle Yolanda , Yallop Deborah , Devereux Stephen 
Published: May 2011

SummaryProgressive chronic lymphocytic leukaemia is characterized by the accumulation of neoplastic B‐cells in the tissues and correlates with the expression of prognostic biomarkers, such as CD38, CD49d and matrix metalloproteinase‐9 (MMP9), which are involved in migration and tissue invasion. In this study we investigated the physical relationship between these molecules and demonstrated that CD38, CD49d, MMP9 and CD44 were physically associated in a supramolecular cell surface complex. Our findings provide a molecular basis for the correlation between expression of these proteins and prognosis and, as the complex is not present in normal B‐cells, suggest a novel leukaemia‐specific therapeutic target.
Mild haemorheological changes induced by a moderate endurance exercise in patients with sickle cell anaemia
Authors: Balayssac‐Siransy Edwige , Connes Philippe , Tuo Nalourgo , Danho Clotaire , Diaw Mor , Sanogo Ibrahima , Hardy‐Dessources Marie‐Dominique , Samb Abdoulaye , Ballas Samir K , Bogui Pascal 
Published: May 2011

AbstractThe levels and duration of physical activity that can be considered as completely safe in patients with sickle cell anaemia (SCA) is unknown. The present study compared the haemorheological and haematological profile, cell density distribution and basic biochemistry between a group of 17 patients with SCA and 21 healthy subjects before and after a 20 min duration submaximal cycling exercise at the same absolute workload. Blood was sampled at rest and 3 min after the end of exercise for measurement of biological parameters. Exercise did not affect the haematocrit and blood viscosity in the two groups. Plasma viscosity was not different between the two groups at rest and similarly increased with exercise. The proportion of intermediary dense cells (with density between 1·11 and 1·12 g/ml) decreased with exercise in the SCA group resulting in an increase in the proportion of red blood cells with a density >1·12 g/ml. No change was observed in the control group. The present study suggests that mild‐moderate exercise is not very harmful for SCA patients. The haemorheological and haematological changes were very mild, except for the formation of dense cells but no clinically significant signs of medical complication were present in any of the patients.
Outcome of unrelated umbilical cord blood transplantation in 88 patients with primary immunodeficiency in Japan
Authors: Morio Tomohiro , Atsuta Yoshiko , Tomizawa Daisuke , Nagamura‐Inoue Tokiko , Kato Koji , Ariga Tadashi , Kawa Keisei , Koike Kazutoshi , Tauchi Hisamichi , Kajiwara Michiko , Hara Toshiro , Kato Shunichi ,   for the Japanese Cord Blood Bank Network
Published: May 2011

SummaryWe report the results of umbilical cord blood transplantation (UCBT) performed in 88 patients with primary immunodeficiency (PID) between 1998 and 2008 in Japan; severe combined immunodeficiency (SCID, n = 40), Wiskott–Aldrich syndrome (WAS, n = 23), chronic granulomatous disease (n = 7), severe congenital neutropaenia (SCN, n = 5) and other immunodeficiencies (n = 13). Five‐year overall survival (5‐year OS) for all patients was 69% [95% confidence interval (CI), 57–78%], and was 71% and 82% for SCID and WAS, respectively. The main cause of death before day 100 was infection (17/19), while that after day 100 was graft‐versus‐host disease (GVHD) (5/7). Using multivariate analyses, pre‐transplant infection, no conditioning, ≥2 human leucocyte antigen (HLA) mismatches or diagnosis other than SCID, SCN or WAS were all associated with poor prognosis. Reduced‐intensity conditioning was associated with decreased overall mortality compared with myeloablative therapy. The cumulative incidence of grade 2–4 acute GVHD at day 100 was 28% (95% CI, 19–38%), and that of chronic GVHD at day 180 was 13% (95% CI, 7–23%). We conclude that UCBT should be considered for PID patients without an HLA‐matched sibling. The control of pre‐transplant infection and selection of HLA‐matched donors will lead to a better outcome.
EVI1‐mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells
Authors: De Weer An , Van der Meulen Joni , Rondou Pieter , Taghon Tom , Konrad Torsten A. , De Preter Katleen , Mestdagh Pieter , Van Maerken Tom , Van Roy Nadine , Jeison Marta , Yaniv Isaac , Cauwelier Barbara , Noens Lucien , Poirel Hélène‐Antoine , Vandenberghe Peter , Lambert Frédéric , De Paepe Anne , Sánchez Maria García , Odero Maria , Verhasselt Bruno , Philippé Jan , Vandesompele Joke , Wieser Rotraud , Dastugue Nicole , Van Vlierberghe Pieter , Poppe Bruce , Speleman Frank 
Published: May 2011

SummaryChromosomal rearrangements involving the MECOM (MDS1 and EVI1 complex) locus are recurrent genetic events in myeloid leukaemia and are associated with poor prognosis. In this study, we assessed the role of MECOM locus protein EVI1 in the transcriptional regulation of microRNAs (miRNAs) involved in the leukaemic phenotype. For this, we profiled expression of 366 miRNAs in 38 MECOM‐rearranged patient samples, normal bone marrow controls and MECOM (EVI1) knock down/re‐expression models. Cross‐comparison of these miRNA expression profiling data showed that MECOM rearranged leukaemias are characterized by down regulation of MIR449A. Reconstitution of MIR449A expression in MECOM‐rearranged cell line models induced apoptosis resulting in a strong decrease in cell viability. These effects might be mediated in part by MIR449A regulation of NOTCH1 and BCL2, which are shown here to be bona fide MIR449A targets. Finally, we confirmed that MIR449A repression is mediated through direct promoter occupation of the EVI1 transcriptional repressor. In conclusion, this study reveals MIR449A as a crucial direct target of the MECOM locus protein EVI1 involved in the pathogenesis of MECOM‐rearranged leukaemias and unravels NOTCH1 and BCL2 as important novel targets of MIR449A. This EVI1‐MIR449A‐NOTCH1/BCL2 regulatory axis might open new possibilities for the development of therapeutic strategies in this poor prognostic leukaemia subgroup.
Expression of MHC class I dimers and ERAP1 in an ankylosing spondylitis patient cohort
Authors: Campbell Elaine C. , Fettke Franziska , Bhat Smita , Morley Kenneth D. , Powis Simon J. 
Published: May 2011

SummaryThe human leucocyte antigen HLA‐B27 is strongly associated with ankylosing spondylitis, a form of seronegative inflammatory arthritis. In this study aspects related to several hypothesized mechanisms of disease pathogenesis have been investigated. Blood monocyte‐derived dendritic cells (DC) from a small patient cohort of 29 patients with ankylosing spondylitis and one with reactive arthritis, were compared with DC from 34 healthy control subjects, of whom four were found to be HLA‐B27 positive. The ability of HLA‐B27 to form heavy‐chain dimers reactive with monoclonal antibody HC10 was tested, along with the induction of endoplasmic reticulum (ER) stress, assessed by splicing xbp1 mRNA and immunoblotting of Immunoglobulin Binding Protein (BiP). Additionally, the protein expression levels of the ER resident aminopeptidase gene ERAP1 in patients with ankylosing spondylitis was also determined, following its recent identification as a novel disease‐associated gene. No significant difference was noted in the global levels of HC10‐reactive MHC class I dimers formed in either the patient or control DC populations. Stress on the ER, as determined by xbp1 mRNA splicing, was not detected but lower levels of BiP were observed in the DC from patients. Of further potential interest, in this patient cohort the expression of ERAP1 appeared to be higher in a number of patient DC samples when compared with controls, suggesting over‐expression of ERAP1 as a mechanism promoting ankylosing spondylitic pathogenesis.
Arabidopsis mutants of AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility
Authors: Kuromori Takashi , Sugimoto Eriko , Shinozaki Kazuo 
Published: May 2011

SummaryIn plants, water vapour is released into the atmosphere through stomata in a process called transpiration. Abscisic acid (ABA) is a key phytohormone that facilitates stomatal closure through its action on guard cells. Recently, ATP‐binding cassette (ABC) transporter genes, AtABCG25 and AtABCG40, were shown to be involved in ABA transport and responses. However, the functions of many other AtABCG family genes are still unknown. Here, we identified another ABCG gene (AtABCG22) that is required for stomatal regulation in Arabidopsis. The atabcg22 mutant plants had lower leaf temperatures and increased water loss, implying elevated transpiration through an influence on stomatal regulation. We also found that atabcg22 plants were more suspectible to drought stress than wild‐type plants. AtABCG22 was expressed in aerial organs, mainly guard cells, in which the gene expression pattern was consistent with the mutant phenotypes. Using double mutants, we investigated the genetic relationships between the mutations. The atabcg22 mutation further increased the water loss of srk2e/ost1 mutants, which were defective in ABA signalling in guard cells. Also, the atabcg22 mutation enhanced the phenotype of nced3 mutants, which were defective in ABA biosynthesis. Accordingly, the additive roles of AtABCG22 functions in ABA signalling and ABA biosynthesis are discussed.
Meiotic abnormalities underlying pollen sterility in wild potato hybrids and spontaneous populations
Authors: Larrosa F. H. , Maune J. F. , Erazzú L. E. , Camadro E. L. 
Published: May 2011

AbstractWild potato species are widely distributed in the Americas, where they spontaneously grow in very diverse habitats. These species – with low chromosome differentiation – form polyploid series with 2n = 2x, 3x, 4x and 6x (x = 12). They are isolated in nature by external and internal hybridisation barriers that can be incomplete, allowing hybridisation in areas of sympatry. Nevertheless, most accessions in germplasm banks, regardless of genetic background of the sampled spontaneous populations, have been assigned specific categories based on morphological characters. To further investigate the extent of hybridisation in the group and for comparative purposes, pollen viability was estimated in (i) artificial hybrids between a commercial cultivar (Calén INTA) of the common potato (tetraploid Solanum tuberosum ssp. tuberosum) and the tetraploid cytotype of the related wild species S. gourlayi, and (ii) samples of plants (accessions) and inflorescences of natural populations from Argentina, tentatively classified as ‘presumed hybrids’ (S. infundibuliforme–S. gourlayi) and ‘species’ (S. infundibuliforme, S. gourlayi and S. chacoense). Regardless of origin, 98 out of 103 plants analysed had zero to 70% pollen viability (zero to 40% in eight of them). Pollen grains were of variable size and morphology and, in mostly male sterile plants, the only viable pollen grains were 2n and/or 4n. Furthermore, male sterile plants shared various abnormalities in meiosis I and II (unpaired chromosomes, unequal chromosome distribution, precocious/lagging chromosomes, parallel, tripolar, fused and multiple spindles, unequal size nuclei, dyads, triads and pentads in addition to normal tetrads, among others). These results provide novel evidence to support field observations of early potato botanists on the extent of spontaneous hybridisation in wild Argentinian potato populations, which is not reflected in the current taxonomy and has significant consequences for germplasm conservation and breeding.