bluuebunny/crossref_metadata_2025_split huggingface dataset:
The bromodomain‐containing protein Bdf1p acts as a phenotypic and transcriptional multicopy suppressor of YAF9 deletion in yeast
Authors: Bianchi Michele M. , Costanzo Giovanna , Chelstowska Anna , Grabowska Dorota , Mazzoni Cristina , Piccinni Eugenia , Cavalli Antonella , Ciceroni Francesca , Rytka Joanna , Slonimski Piotr P. , Frontali Laura , Negri Rodolfo 
Published: July 2004

SummaryIt was observed previously that the deletion of the open reading frame YNL107w (YAF9) was highly pleiotropic in yeast and caused defective growth phenotypes in the presence of several unrelated inhibitors, including caesium chloride. We have selected multicopy extragenic suppressor genes, revealing that this phenotype can be suppressed by overdosing the transcription factors BDF1 and GAT1 in the yaf9Δ strain. We focused our analysis on suppression by BDF1 and performed a genome‐wide transcript analysis on a yaf9Δ strain, compared with the wild‐type and BDF1‐suppressed strains. YAF9 deletion has a clear effect on transcription and leads to modulation of the level of expression of several genes. Transcription of a considerable portion of the underexpressed genes is restored to wild‐type levels in the BDF1‐suppressed strain. We show by chromatin immunoprecipitation that both Yaf9p and Bdf1p bind to promoters of some of these genes and that the level of H3 and H4 acetylation at one of these promoters is significantly lowered in the yaf9 deleted strain, compared with the wild‐type and the BDF1‐suppressed strains.
Glycosomes: parasites and the divergence of peroxisomal purpose
Authors: Parsons Marilyn 
Published: July 2004

SummaryPeroxisomes are membrane‐bounded organelles that compartmentalize a variety of metabolic functions. Perhaps the most divergent peroxisomes known are the glycosomes of trypanosomes and their relatives. The glycolytic pathway of these organisms resides within the glycosome. The development of robust molecular genetic and proteomic approaches coupled with the completion of the genome sequence of the pathogens Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major provides an opportunity to determine the complement of proteins within the glycosome and the function of compartmentation. Studies now suggest that regulation of glycolysis is a strong driving force for maintenance of the glycosome.
Chemical communication in proteobacteria: biochemical and structural studies of signal synthases and receptors required for intercellular signalling
Authors: Pappas Katherine M. , Weingart Christine L. , Winans Stephen C. 
Published: July 2004

SummaryCell–cell communication via the production and detection of chemical signal molecules has been the focus of a great deal of research over the past decade. One class of chemical signals widely used by proteobacteria consists of N‐acyl‐homoserine lactones, which are synthesized by proteins related to LuxI of Vibrio fischeri and are detected by proteins related to the V. fischeri LuxR protein. A related marine bacterium, Vibrio harveyi, communicates using two chemical signals, one of which, autoinducer‐2 (AI‐2), is a furanone borate diester that is synthesized by the LuxS protein and detected by a periplasmic protein called LuxP. Evidence from a number of laboratories suggests that AI‐2 may be used as a signal by diverse groups of bacteria, and might permit intergeneric signalling. These two families of signalling systems have been studied from the perspectives of physiology, ecology, biochemistry, and more recently, structural biology. Here, we review the biochemistry and structural biology of both acyl‐homoserine‐lactone‐dependent and AI‐2‐dependent signalling systems.
Choosing the best estimate of gestational age from routinely collected population‐based perinatal data
Authors: Blair Eve , Liu Yingxin , Cosgrove Peter 
Published: July 2004

SummaryObtaining gestational data of acceptable validity on whole populations is a considerable challenge, which must be met in order to further epidemiological investigation involving perinatal factors. As the means of estimating gestational duration multiply, routinely available population data pertaining to gestational duration may be conflicting. This exacerbates its reputation for unreliability, which is due primarily to the generally occult nature of conception and secondly to the propensity for data entry errors of the data from which gestational duration is estimated. However, the key to improving reliability may paradoxically lie in the increasing variety of methods for estimating gestational duration, because agreement between independent observations increases the reliability that can be placed on estimates of factors that are inherently difficult to measure.This paper demonstrates that the acceptability of population data for gestational duration can be improved by simple rectification of recurring data entry errors and demanding compatibility of two independent estimates of gestational duration. Compared with the previous algorithm that relied primarily on last menstrual period data, the new algorithm, that considers both antenatal and neonatal indicators of gestational duration, decreased the proportion of births in a geographically defined birth cohort 1986–99 (n = 354 216) without a gestational estimate, from 0.5% to 0.03%, halved the number of births of >400 g estimated to occur before 20 weeks, and almost eliminated gestational estimates of >45 weeks.
Influence of inter‐pregnancy interval on preterm delivery
Authors: Arafa Mostafa A. , Alkhouly Alaa , Youssef Manal E. 
Published: July 2004

SummaryThe influence of pregnancy spacing on preterm delivery (<37 weeks gestation) was examined in a group of mothers attending three Maternal and Child Health centres in three different districts in the city of Alexandria, Egypt between October 2001 and July 2002. All pregnant mothers attending the centres were interviewed or had their medical records reviewed. They were followed up until delivery and were questioned about current and past obstetric history and their medical history; their haemoglobin level was measured. The inter‐pregnancy interval was calculated as the number of months between the delivery date of the women's last previous live infant and the date of the last menstrual period before the current pregnancy. There were 1202 pregnant women eligible for inclusion. The inter‐pregnancy intervals were divided into five categories: <12, 12–36, 37–48, 49–60 and >60 months. We calculated the rates of preterm deliveries for each inter‐pregnancy interval. Unadjusted odds ratios were estimated and stepwise logistic regression analysis was then used to adjust for all confounding factors. The rate of preterm delivery was 9.4%, and the lowest risk occurred in women who had an inter‐pregnancy interval >60 months; 7.3% of those women gave birth to preterm infants. The rate of preterm delivery increased with increasing inter‐pregnancy interval until 49–60 months; however, the association between inter‐pregnancy interval and preterm delivery was not statistically significant whether using the crude or adjusted odds ratios.
Trends in neural tube defects in Western Australia in Indigenous and non‐Indigenous populations
Authors: Bower Carol , Eades Sandra , Payne Jan , D’Antoine Heather , Stanley Fiona 
Published: July 2004

SummaryNeural tube defects (NTD) were 43% more common in Indigenous than in non‐Indigenous infants in Western Australia in the 1980s, and there has been a fall in NTD overall in Western Australia since promotion of folate and voluntary fortification of food has occurred. In order to investigate whether the fall had occurred in both indigenous and non‐Indigenous infants, data on NTD (births and terminations) were obtained from the WA Birth Defects Registry, and on all births from the Maternal and Child Health Research Data Base. Knowledge of folate was asked in a survey of indigenous women interviewed postpartum. Before the promotion of folate (1980–92), there has been a 42% increase in NTD in Indigenous compared with non‐Indigenous infants (prevalence ratio (PR) = 1.42 [95% confidence interval (CI) 1.04, 1.94]); while in the most recent period (1996–2000), the prevalence in Indigenous infants was almost twice that of non‐Indigenous infants (PR 1.98 [CI 1.25, 3.15]). Fifty‐five per cent of Indigenous women knew about folate in pregnancy. Similar to sudden infant death syndrome, this study has highlighted health promotion that has been successful in reducing the risk of a childhood condition overall, but has failed to be effective for Indigenous children.
Association between severe nausea and vomiting in pregnancy and lower rate of preterm births
Authors: Czeizel Andrew E. , Puhó Erzsébet 
Published: July 2004

SummaryNausea and vomiting in pregnancy has been associated with some reduction in miscarriage in other studies. However the relationship between nausea and vomiting during pregnancy and preterm birth/low birthweight in newborns is inconsistent; therefore the objective of the study was to clarify this possible association. The population‐based large control (without any defects) data set of the Hungarian Case‐Control Surveillance System of Congenital Abnormalities was evaluated.Of 38 151 controls, 3869 (10.1%) had medically recorded and treated nausea and vomiting during pregnancy. The proportion of mothers who later delivered girls was higher in this group. Mothers with nausea and vomiting in pregnancy had a somewhat (0.3 week) longer gestational age and a lower proportion of preterm births (6.4% vs. 9.5%). This finding may be connected with the favourable hormonal milieu (larger placenta, higher level of chorionic gonadotrophin and oestrogens) of pregnant women with nausea and vomiting.
Partner violence during pregnancy and risk of adverse pregnancy outcomes
Authors: Coker Ann L. , Sanderson Maureen , Dong Beili 
Published: July 2004

SummaryThe purpose of this cross‐sectional study was to investigate the association between partner physical or emotional abuse during pregnancy and pregnancy outcomes including perinatal death, low birthweight and preterm delivery. Women, aged 18–65, who attended one of two large primary care practices from 1997–98 were recruited for this study. Ever pregnant women were asked the frequency of abuse during each pregnancy and details of the pregnancy outcomes. Information regarding abuse during pregnancy and pregnancy outcomes was available for 755 women surveyed who reported a live birth or late fetal death, 14.7% indicated that an intimate partner was violent or abusive toward them during a pregnancy (274 of 1862 pregnancies). Abuse during pregnancy was significantly associated with an increased risk of perinatal death (adjusted relative risk [aRR] = 2.1, 95% confidence interval [CI] 1.3, 3.4) and, among live births, with preterm low birthweight (aRR = 2.4; 95% CI 1.5, 4.0) and term low birthweight (aRR = 1.9; 95% CI 1.0, 3.4). Greater abuse frequency was associated with increased risk. Abuse during pregnancy was associated with perinatal deaths and preterm low birthweight deliveries.
The Walker Project: a longitudinal study of 48 000 children born 1952–1966 (aged 36–50 years in 2002) and their families
Authors: Libby Gillian , Smith Anne , McEwan Neil F. , Chien Patrick F. W. , Greene Stephen A. , Forsyth J. Stewart , Crombie Iain K. , Macdonald Thomas M. , Morris Andrew D. 
Published: July 2004

SummaryThe Walker cohort is a database of over 48 000 birth records that has recently become available. It contains meticulously recorded details of pregnancy, labour, birth and care before discharge for babies born in hospital in Dundee, Scotland between 1952 and 1966. These babies accounted for 75% of all births in Dundee at this time. Over 34 000 (73%) of these subjects can be identified and this presents the opportunity to link this birth information with a large number of current health‐outcome databases covering both primary and secondary care. Further, it allows linkage of records across siblings and over two and, in future, three generations. The number of birth records available and linkage to current databases make this a unique birth cohort with huge potential for the investigation of the fetal origins of adult disease.
Arabidopsis Yellow Stripe‐Like2 (YSL2): a metal‐regulated gene encoding a plasma membrane transporter of nicotianamine–metal complexes
Authors: DiDonato Raymond J. , Roberts Louis A. , Sanderson Tamara , Eisley Robynn Bosler , Walker Elsbeth L. 
Published: July 2004

SummaryThe Yellow Stripe‐Like (YSL) family of proteins has been identified based on sequence similarity to maize Yellow Stripe1 (YS1), the transporter responsible for the primary uptake of iron from the soil. YS1 transports iron that is complexed by specific plant‐derived Fe(III) chelators called phytosiderophores (PS). Non‐grass species of plants neither make nor use PS, yet YSL family members are found in non‐grass species (monocot, dicot, gymnosperm, and moss species) including Arabidopsis thaliana. YSLs in non‐grasses have been hypothesized to transport metals complexed by nicotianamine (NA), an iron chelator that is structurally similar to PS and which is found in all higher plants. Here we show that Arabidopsis YSL2 (At5g24380) transports iron and copper when these metals are chelated by NA. YSL2 is expressed in many cell types in both roots and shoots, suggesting that diverse cell types obtain metals as metal–NA complexes. YSL2 transcription is regulated by the levels of iron and copper in the growth medium. Based on its expression pattern, a major function of the YSL2 appears to be in the lateral movement of metals in the vasculature.
The chloroplastic protein translocation channel Toc75 and its paralog OEP80 represent two distinct protein families and are targeted to the chloroplastic outer envelope by different mechanisms
Authors: Inoue Kentaro , Potter Daniel 
Published: July 2004

SummaryToc75 is postulated to form the protein translocation channel in the chloroplastic outer envelope membrane. Proteins homologous to Toc75 are present in a wide range of organisms, with the closest homologs occurring in cyanobacteria. Therefore, an endosymbiotic origin of Toc75 has been postulated. Recently, a gene encoding a paralog to Toc75 was identified in Arabidopsis and its product was named atToc75‐V. In the present study, we characterized this new Toc75 paralog, and investigated extensively the relationships among Toc75 homologs from higher plants and bacteria in order to gain insights into the evolutionary origin of the chloroplastic protein translocation channel. First, we found that the native molecular weight of atToc75‐V is 80 kDa and renamed it (AtOEP80) Arabidopsis thalianaouter envelope protein of 80 kDa. Second, we found that AtOEP80 and Toc75 utilize different mechanisms for their targeting to the chloroplastic envelope. Toc75 is directed with a cleavable bipartite transit peptide partly via the general import pathway, whereas AtOEP80 contains the targeting information within its mature sequence, and its targeting is independent of the general pathway. Third, we undertook phylogenetic analyses of Toc75 homologs from various organisms, and found that Toc75 and OEP80 represent two independent gene families that are most likely derived from cyanobacterial sequences. Our results suggest that Toc75 and OEP80 diverged early in the evolution of plastids from their common ancestor with modern cyanobacteria.
Roles of the AtErcc1 protein in recombination
Authors: Dubest Sandra , Gallego Maria E. , White Charles I. 
Published: July 2004

SummaryAtercc1, the recently characterized Arabidopsis homologue of the Ercc1 (Rad10) protein, is a key component of nucleotide excision repair as part of a structure‐specific endonuclease which cleaves 5′ to UV photoproducts in DNA. This endonuclease also acts in removing overhanging non‐homologous DNA ‘tails’ in synapsed recombination intermediates. We have previously demonstrated this recombination function of the Arabidopsis thaliana Xpf homologue, AtRad1p, and show here that recombination between plasmid DNA substrates containing non‐homologous tails is specifically reduced 12‐fold in atercc1 mutant plants compared with the wild type. Furthermore, using chromosomal tandem‐repeat recombination substrates, we show that AtErcc1p is required for bleomycin induction of mitotic recombination in the chromosomal context. This work thus confirms both the specific and general recombination roles of the Atercc1 protein in recombination in Arabidopsis.
Functional identification of rice syn‐copalyl diphosphate synthase and its role in initiating biosynthesis of diterpenoid phytoalexin/allelopathic natural products
Authors: Xu Meimei , Hillwig Matthew L. , Prisic Sladjana , Coates Robert M. , Peters Reuben J. 
Published: July 2004

SummaryRice produces a number of phytoalexins, and at least one allelopathic agent, from syn‐copalyl diphosphate (CPP), representing the only known metabolic fate for this compound. Thus, the class II terpene synthase that converts the universal diterpenoid precursor geranylgeranyl diphosphate to syn‐CPP catalyzes the committed step in biosynthesis of these natural products. Here the extensive sequence information available for rice was coupled to recombinant expression and functional analysis to identify syn‐copalyl diphosphate synthase (OsCPSsyn). In addition, OsCPSsyn mRNA was found to be specifically induced in leaves by conditions that stimulate phytoalexin biosynthesis. Therefore, transcription of OsCPSsyn seems to be an important regulatory point for controlling the production of these defensive compounds. Finally, alignments carried out with OsCPSsyn revealed that class II terpene synthases exhibit a sequence conservation pattern substantially different from that of the prototypical class I enzymes. One particularly notable feature is the specific conservation of the functionally cryptic ‘insertional’ sequence element in class II terpene synthases, indicating that this region is important for the corresponding cyclization reaction.
TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana
Authors: Baudry Antoine , Heim Marc A. , Dubreucq Bertrand , Caboche Michel , Weisshaar Bernd , Lepiniec Loïc 
Published: July 2004

SummaryGenetic analyses have demonstrated that together with TTG1, a WD‐repeat (WDR) protein, TT2 (MYB), and TT8 (bHLH) are necessary for the correct expression of BANYULS (BAN). This gene codes for the core enzyme of proanthocyanidin biosynthesis in Arabidopsis thaliana seed coat. The interplays of TT2, TT8, and their closest MYB/bHLH relatives, with TTG1 and the BAN promoter have been investigated using a combination of genetic and molecular approaches, both in yeast and in planta. The results obtained using glucocorticoid receptor fusion proteins in planta strongly suggest that TT2, TT8, and TTG1 can directly activate BAN expression. Experiments using yeast two‐ and three‐hybrid clearly demonstrated that TT2, TT8, and TTG1 can form a stable ternary complex. Furthermore, although TT2 and TT8 were able to bind to the BAN promoter when simultaneously expressed in yeast, the activity of the complex correlated with the level of TTG1 expression in A. thaliana protoplasts. In addition, transient expression experiments revealed that TTG1 acts mainly through the bHLH partner (i.e. TT8 or related proteins) and that TT2 cannot be replaced by any other related A. thaliana MYB proteins to activate BAN. Finally and consistent with these results, the ectopic expression of TT2 was sufficient to trigger BAN activation in vegetative parts, but only where TTG1 was expressed. Taken together, these results indicate that TT2, TT8, and TTG1 can form a ternary complex directly regulating BAN expression in planta.
Application of a high‐throughput HPLC‐MS/MS assay to Arabidopsis mutant screening; evidence that threonine aldolase plays a role in seed nutritional quality
Authors: Jander Georg , Norris Susan R. , Joshi Vijay , Fraga Michele , Rugg Arthur , Yu Shaoxia , Li Lily , Last Robert L. 
Published: July 2004

SummaryBeyond their essential function as the building blocks of proteins, amino acids contribute to many aspects of plant biochemistry and physiology. Despite this, there are relatively large gaps in our understanding of the biochemical pathways and regulation of amino acid synthesis in plants. A rapid (1.5 min versus 20–90 min for standard methods) HPLC‐MS/MS assay for separating 19 amino acids was developed for quantifying levels of free amino acids in plant tissue. This assay was used to determine the free amino acid content in the seeds of 10,000 randomly mutagenized Arabidopsis lines, and 322 Arabidopsis lines with increased levels of one or more amino acids were identified. The heritability of the mutant phenotype was confirmed for 43 lines with increased seed levels of the aspartate‐derived amino acids Ile, Lys, Thr, or Met. Genetic mapping and DNA sequencing identified a mutation in an Arabidopsis threonine aldolase (AT1G08630, EC 4.1.2.5) as the cause of increased seed Thr levels in one mutant. The assay that was developed for this project has broad applicability to Arabidopsis and other plant species.
Plant growth‐promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1‐independent and jasmonic acid‐dependent signaling pathway
Authors: Ryu Choong‐Min , Murphy John F. , Mysore Kiankumar S. , Kloepper Joseph W. 
Published: July 2004

Summary Arabidopsis thaliana ecotype Columbia plants (Col‐0) treated with plant growth‐promoting rhizobacteria (PGPR) Serattia marcescens strain 90‐166 and Bacillus pumilus strain SE34 had significantly reduced symptom severity by Cucumber mosaic virus (CMV). In some cases, CMV accumulation was also significantly reduced in systemically infected leaves. The signal transduction pathway(s) associated with induced resistance against CMV by strain 90‐166 was determined using mutant strains and transgenic and mutant Arabidopsis lines. NahG plants treated with strains 90‐166 and SE34 had reduced symptom severity indicating that the resistance did not require salicylic acid (SA). Strain 90‐166 naturally produces SA under iron‐limited conditions. Col‐0 and NahG plants treated with the SA‐deficient mutant, 90‐166‐1441, had significantly reduced CMV symptom severity with reduced virus accumulation in Col‐0 plants. Another PGPR mutant, 90‐166‐2882, caused reduced disease severity in Col‐0 and NahG plants. In a time course study, strain 90‐166 reduced virus accumulation at 7 but not at 14 and 21 days post‐inoculation (dpi) on the non‐inoculated leaves of Col‐0 plants. NahG and npr1‐1 plants treated with strain 90‐166 had reduced amounts of virus at 7 and 14 dpi but not at 21 dpi. In contrast, no decrease in CMV accumulation occurred in strain 90‐166‐treated fad3‐2 fad7‐2 fad8 plants. These data indicate that the protection of Arabidopsis against CMV by strain 90‐166 follows a signaling pathway for virus protection that is independent of SA and NPR1, but dependent on jasmonic acid.