bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphatidylinositol 3‐ and 4‐phosphate modulate actin filament reorganization in guard cells of day flower
Authors: CHOI YUNJUNG , LEE YUREE , JEON BYEONG WOOK , STAIGER CHRISTOPHER J. , LEE YOUNGSOOK 
Published: February 2008

ABSTRACTPhosphatidylinositol 3‐kinases (PtdIns 3‐kinases) that produce phosphatidylinositol (3,4,5) triphosphate (PtdIns(3,4,5)P3) are considered to be important regulators of actin dynamics in animal cells. In plants, neither PtdIns(3,4,5)P3 nor the enzyme that produces this lipid has been reported. However, a PtdIns 3‐kinase that produces phosphatidylinositol 3‐phosphate (PtdIns3P) has been identified, suggesting that PtdIns3P, instead of PtdIns(3,4,5)P3, regulates actin dynamics in plant cells. Phosphatidylinositol 4‐kinase (PtdIns 4‐kinase) is closely associated with the actin cytoskeleton in plant cells, suggesting a role for this lipid kinase and its product phosphatidylinositol 4‐phosphate (PtdIns4P) in actin‐related processes. Here, we investigated whether or not PtdIns3P or PtdIns4P plays a role in actin reorganization induced by a plant hormone abscisic acid (ABA) in guard cells of day flower (Commelina communis). ABA‐induced changes in actin filaments were inhibited by LY294002 (LY) and wortmannin (WM), inhibitors of PtdIns3P and PtdIns4P synthesis. Expression of PtdIns3P‐ and PtdIns4P‐binding domains also inhibited ABA‐induced actin reorganization in a manner similar to LY and WM. These results suggest that PtdIns3P and PtdIns4P regulate actin dynamics in guard cells. Furthermore, we demonstrate that PtdIns3P exerts its effect on actin dynamics, at least in part, via generation of reactive oxygen species (ROS) in response to ABA.
Suppression of clubroot disease under neutral pH caused by inhibition of spore germination of Plasmodiophora brassicae in the rhizosphere
Authors: Niwa R. , Nomura Y. , Osaki M. , Ezawa T. 
Published: February 2008

To elucidate the mechanism of clubroot suppression under neutral soil pH, a highly reproducible germination assay system under soil culture conditions was designed based on the hypothesis that germinated spores of Plasmodiophora brassicae could be identified by the absence of a nucleus (i.e. having released a zoospore to infect a root hair of the host plant). Brassica rapa var. perviridis seedlings were inoculated with a spore suspension of P. brassicae at a rate of 2·0 × 106 spores g−1 soil and grown in a growth chamber for 7 days. The spores were recovered from rhizosphere and non‐rhizosphere soils and stained with both Fluorescent Brightener 28 (cell‐wall‐specific) and SYTO 82 orange fluorescent nucleic‐acid stain (nucleus‐specific stain). Total numbers of spores were counted under UV‐excitation, and spores with a nucleus that fluoresced orange under G‐excitation were counted. The significant increase in the percentage of spores without a nucleus (germinated spores) in the rhizosphere after 7 days’ cultivation and the correlation with root‐hair infections validated the assay system. Applications of calcium‐rich compost or calcium carbonate to neutralize the soil significantly reduced the percentage of germinated spores in the rhizosphere, as well as the number of root‐hair infections. The present study provides direct evidence that the inhibition of spore germination is the primary cause of disease suppression under neutral soil pH.
Proteasome Antibodies in Patients with Cancer or Multiple Sclerosis
Authors: Thuy‐Tien H. , Haugen M. , Aarseth J. , Storstein A. , Vedeler C. A. 
Published: February 2008

AbstractProteasome antibodies were detected by enzyme‐linked immunosorbent assay in two of the 45 (4.4%) patients with lung cancer, 0 of the 39 patients with breast cancer and six of the 51 (11.8%) patients with ovarian cancer. Six of the 47 (12.8%) patients with relapsing remitting multiple sclerosis had proteasome antibodies, as well as two of the 100 (2%) blood donors. Significant higher odds ratios compared to the blood donors were found for the patients with ovarian cancer (OR: 6.4; 95% CI: 1.1–68) and multiple sclerosis (OR: 7.1; 95% CI: 1.2–74). There was no association between proteasome antibodies and metastases or onconeural antibodies. The antibodies showed reactivity to 23, 25 and 27 kD proteins of the 20S proteasome using Western blot. The increased prevalence of proteasome antibodies in patients with ovarian cancer or multiple sclerosis may reflect cellular damage and release of intracellular antigens. Whether the antibodies take part in the clearance of released proteasomes and thus participate in the pathogenesis of cancer or autoimmune disease is not known.
Biochemical approaches for discovering protein–protein interactions
Authors: Miernyk Jan A. , Thelen Jay J. 
Published: February 2008

SummaryProtein–protein interactions or protein complexes are integral in nearly all cellular processes, ranging from metabolism to structure. Elucidating both individual protein associations and complex protein interaction networks, while challenging, is an essential goal of functional genomics. For example, discovering interacting partners for a ‘protein of unknown function’ can provide insight into actual function far beyond what is possible with sequence‐based predictions, and provide a platform for future research. Synthetic genetic approaches such as two‐hybrid screening often reveal a perplexing array of potential interacting partners for any given target protein. It is now known, however, that this type of anonymous screening approach can yield high levels of false‐positive results, and therefore putative interactors must be confirmed by independent methods. In vitro biochemical strategies for identifying interacting proteins are varied and time‐honored, some being as old as the field of protein chemistry itself. Herein we discuss five biochemical approaches for isolating and characterizing protein–protein interactions in vitro: co‐immunoprecipitation, blue native gel electrophoresis, in vitro binding assays, protein cross‐linking, and rate‐zonal centrifugation. A perspective is provided for each method, and where appropriate specific, trial‐tested methods are included.
Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations
Authors: Lisec Jan , Meyer Rhonda C. , Steinfath Matthias , Redestig Henning , Becher Martina , Witucka‐Wall Hanna , Fiehn Oliver , Törjék Ottó , Selbig Joachim , Altmann Thomas , Willmitzer Lothar 
Published: February 2008

SummaryPlant growth and development are tightly linked to primary metabolism and are subject to natural variation. In order to obtain an insight into the genetic factors controlling biomass and primary metabolism and to determine their relationships, two Arabidopsis thaliana populations [429 recombinant inbred lines (RIL) and 97 introgression lines (IL), derived from accessions Col‐0 and C24] were analyzed with respect to biomass and metabolic composition using a mass spectrometry‐based metabolic profiling approach. Six and 157 quantitative trait loci (QTL) were identified for biomass and metabolic content, respectively. Two biomass QTL coincide with significantly more metabolic QTL (mQTL) than statistically expected, supporting the notion that the metabolic profile and biomass accumulation of a plant are linked. On the same basis, three out the six biomass QTL can be simulated purely on the basis of metabolic composition. QTL based on analysis of the introgression lines were in substantial agreement with the RIL‐based results: five of six biomass QTL and 55% of the mQTL found in the RIL population were also found in the IL population at a significance level of P ≤ 0.05, with >80% agreement on the allele effects. Some of the differences could be attributed to epistatic interactions. Depending on the search conditions, metabolic pathway‐derived candidate genes were found for 24–67% of all tested mQTL in the database AraCyc 3.5. This dataset thus provides a comprehensive basis for the detection of functionally relevant variation in known genes with metabolic function and for identification of genes with hitherto unknown roles in the control of metabolism.
A cysteine‐rich receptor‐like kinase NCRK and a pathogen‐induced protein kinase RBK1 are Rop GTPase interactors
Authors: Molendijk Arthur J. , Ruperti Benedetto , Singh Manoj K. , Dovzhenko Alexander , Ditengou Franck A. , Milia Mattia , Westphal Lore , Rosahl Sabine , Soellick Tim‐Robert , Uhrig Joachim , Weingarten Lars , Huber Michael , Palme Klaus 
Published: February 2008

SummaryIn plants, Rop/Rac GTPases have emerged as central regulators of diverse signalling pathways in plant growth and pathogen defence. When active, they interact with a wide range of downstream effectors. Using yeast two‐hybrid screening we have found three previously uncharacterized receptor‐like protein kinases to be Rop GTPase‐interacting molecules: a cysteine‐rich receptor kinase, named NCRK, and two receptor‐like cytosolic kinases from the Arabidopsis RLCK‐VIb family, named RBK1 and RBK2. Uniquely for Rho‐family small GTPases, plant Rop GTPases were found to interact directly with the protein kinase domains. Rop4 bound NCRK preferentially in the GTP‐bound conformation as determined by flow cytometric fluorescence resonance energy transfer measurements in insect cells. The kinase RBK1 did not phosphorylate Rop4 in vitro, suggesting that the protein kinases are targets for Rop signalling. Bimolecular fluorescence complementation assays demonstrated that Rop4 interacted in vivo with NCRK and RBK1 at the plant plasma membrane. In Arabidopsis protoplasts, NCRK was hyperphosphorylated and partially co‐localized with the small GTPase RabF2a in endosomes. Gene expression analysis indicated that the single‐copy NCRK gene was relatively upregulated in vasculature, especially in developing tracheary elements. The seven Arabidopsis RLCK‐VIb genes are ubiquitously expressed in plant development, and highly so in pollen, as in case of RBK2. We show that the developmental context of RBK1 gene expression is predominantly associated with vasculature and is also locally upregulated in leaves exposed to Phytophthora infestans and Botrytis cinerea pathogens. Our data indicate the existence of cross‐talk between Rop GTPases and specific receptor‐like kinases through direct molecular interaction.
Restricting glutathione biosynthesis to the cytosol is sufficient for normal plant development
Authors: Pasternak Maciej , Lim Benson , Wirtz Markus , Hell Rüdiger , Cobbett Christopher S. , Meyer Andreas J. 
Published: February 2008

SummaryGlutathione (GSH) homeostasis in plants is essential for cellular redox control and efficient responses to abiotic and biotic stress. Compartmentation of the GSH biosynthetic pathway is a unique feature of plants. The first enzyme, γ‐glutamate cysteine ligase (GSH1), responsible for synthesis of γ‐glutamylcysteine (γ‐EC), is, in Arabidopsis, exclusively located in the plastids, whereas the second enzyme, glutathione synthetase (GSH2), is located in both plastids and cytosol. In Arabidopsis, gsh2 insertion mutants have a seedling lethal phenotype in contrast to the embryo lethal phenotype of gsh1 null mutants. This difference in phenotype may be due to partial replacement of GSH functions by γ‐EC, which in gsh2 mutants hyperaccumulates to levels 5000‐fold that in the wild type and 200‐fold wild‐type levels of GSH. In situ labelling of thiols with bimane and confocal imaging in combination with HPLC analysis showed high concentrations of γ‐EC in the cytosol. Feedback inhibition of Brassica juncea plastidic GSH1 by γ‐EC in vitro strongly suggests export of γ‐EC as functional explanation for hyperaccumulation. Complementation of gsh2 mutants with the cytosol‐specific GSH2 gave rise to phenotypically wild‐type transgenic plants. These results support the conclusion that cytosolic synthesis of GSH is sufficient for plant growth. The transgenic lines further show that, consistent with the exclusive plastidic localization of GSH1, γ‐EC is exported from the plastids to supply the cytosol with the immediate precursor for GSH biosynthesis, and that there can be efficient re‐import of GSH into the plastids to allow effective control of GSH biosynthesis through feedback inhibition of GSH1.
Evidence for chloroplast control of external Ca2+‐induced cytosolic Ca2+ transients and stomatal closure
Authors: Nomura Hironari , Komori Teiko , Kobori Maki , Nakahira Yoichi , Shiina Takashi 
Published: February 2008

SummaryThe role of guard cell chloroplasts in stomatal function is controversial. It is usually assumed that stomatal closure is preceded by a transient increase in cytosolic free Ca2+ concentration ([Ca2+]cyt) in the guard cells. Here, we provide the evidence that chloroplasts play a critical role in the generation of extracellular Ca2+ ([Ca2+]ext)‐induced [Ca2+]cyt transients and stomatal closure in Arabidopsis. CAS (Ca2+ sensing receptor) is a plant‐specific putative Ca2+‐binding protein that was originally proposed to be a plasma membrane‐localized external Ca2+ sensor. In the present study, we characterized the intracellular localization of CAS in Arabidopsis with a combination of techniques, including (i) in vivo localization of green fluorescent protein (GFP) fused gene expression, (ii) subcellular fractionation and fractional analysis of CAS with Western blots, and (iii) database analysis of thylakoid membrane proteomes. Each technique produced consistent results. CAS was localized mainly to chloroplasts. It is an integral thylakoid membrane protein, and the N‐terminus acidic Ca2+‐binding region is likely exposed to the stromal side of the membrane. The phenotype of T‐DNA insertion CAS knockout mutants and cDNA mutant‐complemented plants revealed that CAS is essential for stomatal closure induced by external Ca2+. In contrast, overexpression of CAS promoted stomatal closure in the absence of externally applied Ca2+. Furthermore, using the transgenic aequorin system, we showed that [Ca2+]ext‐induced [Ca2+]cyt transients were significantly reduced in CAS knockout mutants. Our results suggest that thylakoid membrane‐localized CAS is essential for [Ca2+]ext‐induced [Ca2+]cyt transients and stomatal closure.
Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants
Authors: Cohen Sarit , Houben Andreas , Segal Daniel 
Published: February 2008

SummaryExtrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It was found in various non‐plant organisms from yeast to humans. EccDNA is heterogeneous in size and contains sequences derived primarily from repetitive chromosomal DNA. Here, we report the occurrence of eccDNA in small and large genome plant species, as identified using two‐dimensional gel electrophoresis. We show that eccDNA is readily detected in both Arabidopsis thaliana and Brachycome dichromosomatica, reflecting a normal phenomenon that occurs in wild‐type plants. The size of plant eccDNA ranges from > 2 kb to < 20 kb, which is similar to the sizes found in other organisms. These DNA molecules correspond to 5S ribosomal DNA (rDNA), non‐coding chromosomal high‐copy tandem repeats and telomeric DNA of both species. Circular multimers of the repeating unit of 5S rDNA were identified in both species. In addition, similar multimers were also demonstrated with the B. dichromosomatica repetitive element Bdm29. Such circular multimers of tandem repeats were found in animal models, suggesting a common mechanism for eccDNA formation among eukaryotes. This mechanism may involve looping‐out via intrachromosomal homologous recombination. The implications of these results on genome plasticity and evolutionary processes are discussed.
CLINICAL STUDY: Postmortem diagnosis and toxicological validation of illicit substance use
Authors: Lehrmann Elin , Afanador Zoan R. , Deep‐Soboslay Amy , Gallegos Gloria , Darwin William D. , Lowe Ross H. , Barnes Allan J. , Huestis Marilyn A. , Cadet Jean L. , Herman Mary M. , Hyde Thomas M. , Kleinman Joel E. , Freed William J. 
Published: February 2008

ABSTRACTThe present study examines the diagnostic challenges of identifying ante‐mortem illicit substance use in human postmortem cases. Substance use, assessed by clinical case history reviews, structured next‐of‐kin interviews, by general toxicology of blood, urine and/or brain, and by scalp hair testing, identified 33 cocaine, 29 cannabis, 10 phencyclidine and nine opioid cases. Case history identified 42% cocaine, 76% cannabis, 10% phencyclidine and 33% opioid cases. Next‐of‐kin interviews identified almost twice as many cocaine and cannabis cases as Medical Examiner (ME) case histories, and were crucial in establishing a detailed lifetime substance use history. Toxicology identified 91% cocaine, 68% cannabis, 80% phencyclidine and 100% opioid cases, with hair testing increasing detection for all drug classes. A cocaine or cannabis use history was corroborated by general toxicology with 50% and 32% sensitivity, respectively, and with 82% and 64% sensitivity by hair testing. Hair testing corroborated a positive general toxicology for cocaine and cannabis with 91% and 100% sensitivity, respectively. Case history corroborated hair toxicology with 38% sensitivity for cocaine and 79% sensitivity for cannabis, suggesting that both case history and general toxicology underestimated cocaine use. Identifying ante‐mortem substance use in human postmortem cases are key considerations in case diagnosis and for characterization of disorder‐specific changes in neurobiology. The sensitivity and specificity of substance use assessments increased when ME case history was supplemented with structured next‐of‐kin interviews to establish a detailed lifetime substance use history, while comprehensive toxicology, and hair testing in particular, increased detection of recent illicit substance use.
PRECLINICAL STUDY: Effect of chronic morphine exposure on response properties of rat barrel cortex neurons
Authors: Afarinesh Mohammad Reza , Sheibani Vahid , Arabzadeh Somaye , Shamsizadeh Ali 
Published: February 2008

ABSTRACTChronic exposure to morphine can impair performance in tasks which need sensory processing. Using single unit recordings we investigate the effect of chronic morphine exposure on the firing properties of neurons in layers IV and V of the whisker‐related area of rat primary somatosensory cortex. In urethane‐anesthetized animals, neuronal activity was recorded in response to principal and adjacent whisker deflections either stimulated independently or in a conditioning test paradigm. A condition test ratio (CTR) was calculated for assessing the inhibitory receptive field. In layer IV, chronic morphine treatment did not change the spontaneous discharge activity. On responses to principal and adjacent whisker deflections did not show any significant changes following chronic morphine exposure. The magnitude Off responses to adjacent whisker deflection decreased while its response latency increased. In addition, there was a significant increase in the latency of Off responses to principal whisker deflection. CTR did not change significantly following morphine exposure. Layer V neurons, on the other hand, did not show any significant changes in their spontaneous activity or their evoked responses following morphine exposure. Our results suggest that chronic morphine exposure has a subtle modulatory effect on response properties of neurons in barrel cortex.
GENETIC STUDY: Association between the nociceptin receptor gene (OPRL1) single nucleotide polymorphisms and alcohol dependence
Authors: Huang Jia , Young Brandon , Pletcher Mathew T. , Heilig Markus , Wahlestedt Claes 
Published: February 2008

ABSTRACT OPRL1 encodes the nociceptin receptor, which has been shown to be involved in alcohol dependence in previous studies. In the present study, we investigated the association between genetic polymorphisms of OPRL1 and alcohol dependence in a Scandinavian population. We genotyped 15 single nucleotide polymorphisms (SNPs) spanning the OPRL1 locus and found that SNP rs6010718 was significantly associated with both Type I and Type II alcoholics (P < 0.05). Linkage disequilibrium and haplotype analysis identified two haplotype blocks in this region. Furthermore, two haplotypes composed of five tag SNPs showed significant association with alcohol dependence. These findings suggest that genetic variants of the OPRL1 gene play a role in alcohol dependence in the Scandinavian population, warranting further investigation at the OPRL1 locus.
PRECLINICAL STUDY: Chronic morphine‐induced neuronal morphological changes in the ventral tegmental area in rats are reversed by electroacupuncture treatment
Authors: Chu Ning‐ning , Xia Wei , Yu Peng , Hu Ling , Zhang Rong , Cui Cai‐lian 
Published: February 2008

ABSTRACTThe aim of this study was to observe the effect of electroacupuncture (EA) on chronic morphine‐induced neuronal morphological changes in the ventral tegmental area (VTA) in rats at electron‐microscopic level. Fourteen days of administering escalating doses of morphine induced pathological morphological changes of neurons in the VTA: the rough endoplasmic reticulum swelled, membrane configuration of the nucleus and mitochondria blurred, and structure of myelin sheath changed. Both 2 and 100 Hz EA treatment reversed the morphological alterations induced by chronic morphine administration. The findings provide new evidence that EA may serve as a potential therapy in treating opiate addiction.
Original article: Sinonasal pathology in nonallergic asthma and COPD: ‘united airway disease’ beyond the scope of allergy
Authors: Hens G. , Vanaudenaerde B. M. , Bullens D. M. A. , Piessens M. , Decramer M. , Dupont L. J. , Ceuppens J. L. , Hellings P. W. 
Published: February 2008

Background:  In contrast to the epidemiological and clinical association between allergic rhinitis and asthma, upper airway inflammation is less characterized in patients with nonatopic asthma and virtually unexplored in chronic obstructive pulmonary disease (COPD). Here, sinonasal pathology is studied in patients with allergic asthma, nonallergic asthma and COPD.Methods:  Ninety patients with stable bronchial disease were included in the study, of which 35 were diagnosed with allergic asthma, 24 with nonallergic asthma and 31 with COPD. Concurrently, 61 control subjects without pulmonary disease were included and matched for age and smoking habits respectively with the asthma and the COPD group. Sinonasal symptoms were evaluated on a visual analogue scale and rhinosinusitis‐related impairment of quality of life was assessed with the sino‐nasal outcome test‐22 (SNOT‐22) questionnaire. Nasal mucosal abnormalities were quantified with nasal endoscopy and nasal secretions collected for measuring inflammatory mediators.Results:  Allergic asthmatics, nonallergic asthmatics and COPD patients reported more nasal symptoms than their respective control subjects, had a higher SNOT‐22 score and presented more mucosal abnormalities in the nose. Nasal secretions of both allergic and nonallergic asthmatics contained higher levels of eotaxin, G‐CSF, IFN‐γ and MCP‐1 than controls. Allergic asthmatics had higher nasal IP‐10 levels as well. COPD‐patients had higher nasal levels of eotaxin, G‐CSF and IFN‐γ than controls.Conclusion:  Patients with allergic and nonallergic asthma and COPD show increased nasal symptoms and more nasal inflammation. Hence, our data confirm the ‘united airways’ concept to be beyond the scope of allergic asthma.