bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene silencing in plants using artificial microRNAs and other small RNAs
Authors: Ossowski Stephan , Schwab Rebecca , Weigel Detlef 
Published: February 2008

SummaryComprehensive analysis of gene function requires the detailed examination of mutant alleles. In Arabidopsis thaliana, large collections of sequence‐indexed insertion and chemical mutants provide potential loss‐of‐function alleles for most annotated genes. However, limitations for phenotypic analysis include gametophytic or early sporophytic lethality, and the ability to recombine mutant alleles in closely linked genes, especially those present as tandem duplications. Transgene‐mediated gene silencing can overcome some of these shortcomings through tissue‐specific, inducible and partial gene inactivation, or simultaneous targeting of several, sequence‐related genes. In addition, gene silencing is a convenient approach in species or varieties for which exhaustive mutant collections are not yet available. Typically, gene function is reduced post‐transcriptionally, effected by small RNAs that act in a sequence‐specific manner by base pairing to complementary mRNA molecules. A recently introduced approach is the use of artificial microRNAs (amiRNAs). Here, we review various strategies for small RNA‐based gene silencing, and describe in detail the design and application of amiRNAs in many plant species.
Molecular and cellular approaches for the detection of protein–protein interactions: latest techniques and current limitations
Authors: Lalonde Sylvie , Ehrhardt David W. , Loqué Dominique , Chen Jin , Rhee Seung Y. , Frommer Wolf B. 
Published: February 2008

SummaryHomotypic and heterotypic protein interactions are crucial for all levels of cellular function, including architecture, regulation, metabolism, and signaling. Therefore, protein interaction maps represent essential components of post‐genomic toolkits needed for understanding biological processes at a systems level. Over the past decade, a wide variety of methods have been developed to detect, analyze, and quantify protein interactions, including surface plasmon resonance spectroscopy, NMR, yeast two‐hybrid screens, peptide tagging combined with mass spectrometry and fluorescence‐based technologies. Fluorescence techniques range from co‐localization of tags, which may be limited by the optical resolution of the microscope, to fluorescence resonance energy transfer‐based methods that have molecular resolution and can also report on the dynamics and localization of the interactions within a cell. Proteins interact via highly evolved complementary surfaces with affinities that can vary over many orders of magnitude. Some of the techniques described in this review, such as surface plasmon resonance, provide detailed information on physical properties of these interactions, while others, such as two‐hybrid techniques and mass spectrometry, are amenable to high‐throughput analysis using robotics. In addition to providing an overview of these methods, this review emphasizes techniques that can be applied to determine interactions involving membrane proteins, including the split ubiquitin system and fluorescence‐based technologies for characterizing hits obtained with high‐throughput approaches. Mass spectrometry‐based methods are covered by a review by Miernyk and Thelen (2008; this issue, pp. 597–609). In addition, we discuss the use of interaction data to construct interaction networks and as the basis for the exciting possibility of using to predict interaction surfaces.
Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus
Authors: Sanchez Diego H. , Lippold Felix , Redestig Henning , Hannah Matthew A. , Erban Alexander , Krämer Ute , Kopka Joachim , Udvardi Michael K. 
Published: February 2008

SummaryThe model legume Lotus japonicus was subjected to non‐lethal long‐term salinity and profiled at the ionomic, transcriptomic and metabolomic levels. Two experimental designs with various stress doses were tested: a gradual step acclimatization and an initial acclimatization approach. Ionomic profiling by inductively coupled plasma/atomic emission spectrometry (ICP‐AES) revealed salt stress‐induced reductions in potassium, phosphorus, sulphur, zinc and molybdenum. Microarray profiling using the Lotus Genechip® allowed the identification of 912 probesets that were differentially expressed under the acclimatization regimes. Gas chromatography/mass spectrometry‐based metabolite profiling identified 147 differentially accumulated soluble metabolites, indicating a change in metabolic phenotype upon salt acclimatization. Metabolic changes were characterized by a general increase in the steady‐state levels of many amino acids, sugars and polyols, with a concurrent decrease in most organic acids. Transcript and metabolite changes exhibited a stress dose‐dependent response within the range of NaCl concentrations used, although threshold and plateau behaviours were also observed. The combined observations suggest a successive and increasingly global requirement for the reprogramming of gene expression and metabolic pathways to maintain ionic and osmotic homeostasis. A simple qualitative model is proposed to explain the systems behaviour of plants during salt acclimatization.
FUSCA3 from barley unveils a common transcriptional regulation of seed‐specific genes between cereals and Arabidopsis
Authors: Moreno‐Risueno Miguel Ángel , González Noemi , Díaz Isabel , Parcy François , Carbonero Pilar , Vicente‐Carbajosa Jesús 
Published: February 2008

SummaryAccumulation of storage compounds in the embryo and endosperm of developing seeds is a highly regulated process that allows seedling growth upon germination until photosynthetic capacity is acquired. A critical regulatory element in the promoters of seed storage protein (SSP) genes from dicotyledonous species is the RY box, a target of B3‐type transcription factors. However, the functionality of this motif in the transcriptional regulation of SSP genes from cereals has not been fully established. We report here the identification and molecular characterization of barley FUSCA3, a B3‐type transcription factor as yet uncharacterized in monocotyledonous plants. Our results show that both the barley and Arabidopsis FUS3 genes maintain a conserved functionality for the regulation of SSP genes and anthocyanin biosynthesis in these two distantly related phylogenetic groups. Complementation of the loss‐of‐function mutant fus3 in Arabidopsis by the barley HvFus3 gene resulted in restored transcription from the At2S3 gene promoter and normal accumulation of anthocyanins in the seed. In barley, HvFUS3 participates in transcriptional activation of the endosperm‐specific genes Hor2 and Itr1. HvFUS3, which specifically binds to RY boxes in EMSA experiments, trans‐activates Hor2 and Itr1 promoters containing intact RY boxes in transient expression assays in developing endosperms. Mutations in the RY boxes abolished the HvFUS3‐mediated trans‐activation. HvFus3 transcripts accumulate in the endosperm and in the embryo of developing seeds, peaking at mid maturation phase. Remarkably, HvFUS3 interacts with the Opaque2‐like bZIP factor BLZ2 in yeast, and this interaction is essential for full trans‐activation of the seed‐specific genes in planta.
The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2
Authors: Hanson Johannes , Hanssen Micha , Wiese Anika , Hendriks Margriet M. W. B. , Smeekens Sjef 
Published: February 2008

SummaryTranslation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome‐wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter‐mediated overexpression of bZIP11. This suggests that <20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11‐dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G‐box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.
Quality control for plant metabolomics: reporting MSI‐compliant studies
Authors: Fiehn Oliver , Wohlgemuth Gert , Scholz Martin , Kind Tobias , Lee Do Yup , Lu Yun , Moon Stephanie , Nikolau Basil 
Published: February 2008

SummaryThe Metabolomics Standards Initiative (MSI) has recently released documents describing minimum parameters for reporting metabolomics experiments, in order to validate metabolomic studies and to facilitate data exchange. The reporting parameters encompassed by MSI include the biological study design, sample preparation, data acquisition, data processing, data analysis and interpretation relative to the biological hypotheses being evaluated. Herein we exemplify how such metadata can be reported by using a small case study – the metabolite profiling by GC‐TOF mass spectrometry of Arabidopsis thaliana leaves from a knockout allele of the gene At1g08510 in the Wassilewskija ecotype. Pitfalls in quality control are highlighted that can invalidate results even if MSI reporting standards are fulfilled, including reliable compound identification and integration of unknown metabolites. Standardized data processing methods are proposed for consistent data storage and dissemination via databases.
Evidence of multiple horizontal transfers of the long terminal repeat retrotransposon RIRE1 within the genus Oryza
Authors: Roulin Anne , Piegu Benoît , Wing Rod A. , Panaud Olivier 
Published: February 2008

SummaryHorizontal gene transfer, defined as the transmission of genetic material between reproductively isolated species, has been considered for a long time to be a rare phenomenon. Most well‐documented cases of horizontal gene transfer have been described in prokaryotes or in animals and they often involve transposable elements. The most abundant class of transposable elements in plant genomes are the long terminal repeat (LTR) retrotransposons. Because of their propensity to increase their copy number while active, LTR retrotransposons can have a significant impact on genomics changes during evolution. In a previous study, we showed that in the wild rice species Oryza australiensis, 60% of the genome is composed of only three families of LTR retrotransposons named RIRE1, Wallabi and Kangourou. In the present study, using both in silico and experimental approaches, we show that one of these three families, RIRE1, has been transferred horizontally between O. australiensis and seven other reproductively isolated Oryza species. This constitutes a new case of horizontal transfer in plants.
GASSHO1 and GASSHO2 encoding a putative leucine‐rich repeat transmembrane‐type receptor kinase are essential for the normal development of the epidermal surface in Arabidopsis embryos
Authors: Tsuwamoto Ryo , Fukuoka Hiroyuki , Takahata Yoshihito 
Published: February 2008

SummaryReceptor‐like kinases (RLKs) containing leucine‐rich repeats (LRRs) act as both signal receptor and signal transducer in ligand‐mediated communication between cells. It is believed that many LRR‐RLKs are present in the Arabidopsis genome, but the functions of most are unknown. We recently identified Bnms4D‐82, an expressed sequence tag (EST) in Brassica napus that encodes an LRR‐RLK and is expressed at an early stage of its microspore embryogenesis. To elucidate the function of this gene we used GASSHO1 (GSO1) and GSO2, two Arabidopsis genes with a high degree of homology with Bnms4D‐82. The products of transcripts of GSO1 and GSO2 accumulate in parts of the embryo and in seedlings, but not in true leaves. Plants that lacked both GSO1 and GSO2 exhibited pleiotropy, including abnormal bending of embryos, ectopic adhesion between cotyledons, a highly permeable epidermal structure, and an abnormal pattern of distribution of stomata on cotyledons in embryos and seedlings. However, plants homozygous for either gso1‐1 or gso2‐1 had no visible abnormality. These results suggest that GASSHO genes are essential for the formation of a normal epidermal surface during embryogenesis.
CLINICAL STUDY: Adrenocorticotropic hormone and cortisol plasma levels directly correlate with childhood neglect and depression measures in addicted patients
Authors: Gerra Gilberto , Leonardi Claudio , Cortese Elena , Zaimovic Amir , Dell'Agnello Grazia , Manfredini Matteo , Somaini Lorenzo , Petracca Francesca , Caretti Vincenzo , Baroni Cristina , Donnini Claudio 
Published: February 2008

ABSTRACTHypothalamic–pituitary–adrenal (HPA) axis dysfunction has been reported to be involved in vulnerability to alcohol and drug dependence in humans, possibly underlying both addictive behaviour and depression susceptibility. The aim of the present study was to investigate the possible interactions between childhood adverse experiences, depressive symptoms and HPA axis function in addicted patients, in comparison with healthy control. Eighty‐two abstinent heroin or cocaine dependent patients and 44 normal controls, matched for age and sex, completed the symptoms Check List‐90 (SCL‐90), measuring depressive symptoms, and the Childhood Experience of Care and Abuse Questionnaire. Blood samples were collected to determine adrenocorticotropic hormone (ACTH) and cortisol basal plasma levels at 8:00 and 8:30 a.m. Addicted individuals showed significantly higher neglect and depression scores and ACTH–cortisol plasma levels respect to control subjects. Depression scores at SCL‐90 in addicted patients positively correlated with plasma ACTH and cortisol values. In turn, plasma ACTH levels were directly associated with childhood neglect measures, reaching statistical significance with ‘mother‐neglect’ scores. Plasma cortisol levels were related to ‘father antipathy’ among cocaine addicts. These findings suggest the possibility that childhood experience of neglect and poor parent–child attachment may have a persistent effect on HPA axis function as an adult, partially contributing, together with genetic factors and other environmental conditions, to both depressive traits and substance abuse neurobiological vulnerability.
PRECLINICAL STUDY: Chronic deep brain stimulation in the rat nucleus accumbens and its effect on morphine reinforcement
Authors: Liu Hong‐Yu , Jin Jie , Tang Jing‐Shi , Sun Wei‐Xin , Jia Hong , Yang Xin‐Ping , Cui Jian‐Mei , Wang Chen‐Guang 
Published: February 2008

ABSTRACTIn order to explore a novel method for the treatment of drug abuse, we evaluated the effect of chronic deep brain stimulation (DBS) of the rat nucleus accumbens (NAc) on morphine reinforcement, using a DBS apparatus and an implant method we developed. Thirty‐two adult rats weighing 240–260 g were divided into three groups, which included a DBS group (n = 10, administration of surgery, morphine and DBS), a sham DBS group (n = 12, administration of surgery and morphine) and a control group (n = 10, administration of physiological saline). The DBS electrode was stereotaxically implanted into the core of unilateral NAc and connected to an implantable pulse generator. Then, they were fixed to the rat skull. One week later, the rats in each group were intraperitoneally injected with morphine at an increasing dose (10–60 mg/kg) once daily. The rats in the DBS group were administered a 130‐Hz high‐frequency stimulation (HFS) once daily. A 900‐second conditioned place preference (CPP) paradigm was used for determining the effect of electrical stimulation on morphine reinforcement in rats. The data showed that 7–10 days later, the preference score of the DBS group was significantly lower than that of the sham DBS group. The results suggest that chronic HFS of the rat NAc can block CPP induced by morphine and attenuate morphine reinforcement.
CLINICAL STUDY: P3 components of the event‐related potential and marijuana dependence in Southwest California Indians
Authors: Ehlers Cindy L. , Gilder David A. , Phillips Evelyn 
Published: February 2008

ABSTRACTNative Americans have some of the highest rates of marijuana use and abuse, yet neurobiological measures associated with addiction to marijuana in this population remain unknown. The present investigation evaluated associations between the P350 and P450 components of the event‐related potential (ERP) elicited by affective stimuli, and marijuana dependence in a population of Southwest California (SWC) Indian adults. Three hundred and seventeen participants with a mean age of 30 years who were free of major Axis I and psychiatric diagnoses and antisocial personality disorder were categorized as: (1) no marijuana use disorders or other drug dependence diagnoses; (2) marijuana dependence and no other drug dependence diagnoses; and (3) marijuana dependence and other drug dependence diagnoses. ERPs were collected using a facial discrimination task that generated a late positive component with two peaks at approximately P350 and P450 milliseconds. Multivariate analyses of variance was used to detect associations between the two component peaks and the three participant groups taking into consideration age, gender and the presence of a lifetime diagnosis of alcohol dependence. Increases in the latency of both the P350 and P450 component peaks were found to be associated with the diagnosis of marijuana dependence and marijuana dependence co‐morbid with other drug dependence. Women appeared to be more impacted than men are. A diagnosis of marijuana dependence was not associated with any changes in late component amplitudes. Taken together these studies suggest that marijuana dependence may be associated with delays in the evaluation and identification of emotional stimuli in SWC Indians.
PRECLINICAL STUDY: A microdialysis study of extracellular levels of acamprosate and naltrexone in the rat brain following acute and repeated administration
Authors: Burattini Costanza , Mcgeehan Andrew J. , Griffin William C. , Gass Justin T. , Kinder Jennifer R. , Janak Patricia H. , Olive M. Foster 
Published: February 2008

ABSTRACTAcamprosate and naltrexone are widely used in the treatment of alcoholism. However, numerous studies in rodents have shown differential effects of these compounds on alcohol consumption and/or relapse‐like behavior following acute versus repeated administration. In order to determine if these differential behavioral effects could be attributable to changes in extracellular levels of these compounds, we used in vivo microdialysis to monitor extracellular levels of acamprosate and naltrexone in the rat medial prefrontal cortex following acute and repeated intraperitoneal administration. For acute treatment, animals received a single administration of acamprosate (100 or 300 mg/kg) or naltrexone (1 or 3 mg/kg). For repeated treatment, animals received once daily treatment with saline, acamprosate (300 mg/kg) or naltrexone (3 mg/kg) for 10 days before a subsequent challenge with the compound according to their respective pretreatment group. Dialysate levels of acamprosate and naltrexone were analyzed by liquid chromatography–tandem mass spectrometry and high performance liquid chromatography, respectively. Following acute administration, peak dialysate concentrations of each compound were dose‐dependent, observed within 1 hour of administration, and were found to be in the low micromolar range for acamprosate and in the low to mid‐nanomolar range for naltrexone. Pretreatment with acamprosate, but not naltrexone, for 10 days resulted in higher dialysate concentrations of the compound relative to saline‐pretreated controls. Thus, repeated administration of acamprosate, but not naltrexone, results in augmented extracellular levels of the compound in the brain relative to saline‐pretreated controls, which may explain the need for repeated administration of acamprosate in order to observe effects on alcohol consumption and/or relapse.
Original article: The economic costs of severe anaphylaxis in France: an inquiry carried out by the Allergy Vigilance Network
Authors: Flabbee J. , Petit N. , Jay N. , Guénard L. , Codreanu F. , Mazeyrat R. , Kanny G. , Moneret‐Vautrin D. A. 
Published: February 2008

Background:  The prevalence of severe anaphylaxis, between 1 and 3 per 10 000, has increased sharply over recent years, with a rate of lethality of 1%. The economic burden is unknown.Objective:  The aim of this study was to estimate the economic costs of anaphylaxis, including direct costs of treatment, hospitalization, preventive and long‐care measures, and the indirect cost: absenteeism.Methods:  Analysis of 402 patients of anaphylaxis declared by 384 allergists was reported to the Allergy Vigilance Network. The global cost was estimated from the national data of hospital admissions: ICD‐10 coding available for 2003, 2004 and 2005.Results:  Three work/classroom days were lost per patient. Diagnosis required oral challenge with hospitalization in 18% of cases. The estimated mean total cost was 1895€ for food‐ and drug‐related anaphylaxis (5610€ for the most severe), and 4053€ for Hymenoptera anaphylaxis. National statistics recorded 2575 patients in 2005; 22% more than in 2003. The estimated annual cost was 4 789 500 €. The possible reasons for this being an under‐estimate include: data coming only from hospitalized patients, poor identification by medical teams unfamiliar with ICD‐10 codes, peri‐operative anaphylaxis being insufficiently declared, rush‐immunotherapy and maintenance treatments for Hymenoptera anaphylaxis. Similarly, the extra cost of cow milk substitutes, as well as insurance costs where deaths are followed by litigation were not taken into account.Conclusions:  The mean cost of anaphylaxis was 1895–5610€ in nonfatal patients. The prevalence was under‐estimated because of many biases, leading to under‐estimation of the national cost. Further studies would be necessary to evaluate the value of preventive strategies.