bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history
Authors: LEGRAS JEAN‐LUC , MERDINOGLU DIDIER , CORNUET JEAN‐MARIE , KARST FRANCIS 
Published: March 2007

AbstractFermented beverages and foods have played a significant role in most societies worldwide for millennia. To better understand how the yeast species Saccharomyces cerevisiae, the main fermenting agent, evolved along this historical and expansion process, we analysed the genetic diversity among 651 strains from 56 different geographical origins, worldwide. Their genotyping at 12 microsatellite loci revealed 575 distinct genotypes organized in subgroups of yeast types, i.e. bread, beer, wine, sake. Some of these groups presented unexpected relatedness: Bread strains displayed a combination of alleles intermediate between beer and wine strains, and strains used for rice wine and sake were most closely related to beer and bread strains. However, up to 28% of genetic diversity between these technological groups was associated with geographical differences which suggests local domestications. Focusing on wine yeasts, a group of Lebanese strains were basal in an FST tree, suggesting a Mesopotamia‐based origin of most wine strains. In Europe, migration of wine strains occurred through the Danube Valley, and around the Mediterranean Sea. An approximate Bayesian computation approach suggested a postglacial divergence (most probable period 10 000–12 000 bp). As our results suggest intimate association between man and wine yeast across centuries, we hypothesize that yeast followed man and vine migrations as a commensal member of grapevine flora.
Phylogeography of the piranha genera Serrasalmus and Pygocentrus: implications for the diversification of the Neotropical ichthyofauna
Authors: HUBERT NICOLAS , DUPONCHELLE FABRICE , NUÑEZ JESUS , GARCIA‐DAVILA CARMEN , PAUGY DIDIER , RENNO JEAN‐FRANÇOIS 
Published: March 2007

AbstractThe phylogenetic relationships within the piranhas were assessed using mitochondrial sequences with the aim of testing several hypotheses proposed to explain the origin of Neotropical diversity (palaeogeography, hydrogeology and museum hypotheses). Sequences of the ribosomal 16S gene (510 bp) and control region (980 bp) were obtained from 15 localities throughout the main South American rivers for 21 of the 28 extant piranha species. The results indicate that the genus Serrasalmus is monophyletic and comprises three major clades. The phylogeographical analyses of these clades allowed the identification of five vicariant events, extensive dispersal and four lineage duplications suggesting the occurrence of sympatric speciation. Biogeographical patterns are consistent with the prediction made by the museum hypothesis that lineages from the Precambrian shields are older than those from the lowlands of the Amazon. The vicariant events inferred here match the distribution of the palaeoarches and several postdispersal speciation events are identified, thereby matching the predictions of the palaeogeography and hydrogeology hypotheses, respectively. Molecular clock calibration of the control region sequences indicates that the main lineages differentiated from their most recent common ancestor at 9 million years ago in the proto Amazon‐Orinoco and the present rate of diversification is the highest reported to date for large carnivorous Characiformes. The present results emphasize that an interaction among geology, sea‐level changes, and hydrography created opportunities for cladogenesis in the piranhas at different temporal and geographical scales.
Range‐wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers
Authors: BUCCI GABRIELE , GONZÁLEZ‐MARTÍNEZ SANTIAGO C. , LE PROVOST GRÉGOIRE , PLOMION CHRISTOPHE , RIBEIRO MARIA MARGARIDA , SEBASTIANI FEDERICO , ALÍA RICARDO , VENDRAMIN GIOVANNI GIUSEPPE 
Published: March 2007

AbstractSome 1339 trees from 48 Pinus pinaster stands were characterized by five chloroplast microsatellites, detecting a total of 103 distinct haplotypes. Frequencies for the 16 most abundant haplotypes (pk > 0.01) were spatially interpolated over a lattice made by 430 grid points. Fitting of spatially interpolated values on raw haplotype frequencies at the same geographical location was tested by regression analysis. A range‐wide ‘diversity map’ based on interpolated haplotype frequencies allowed the identification of one ‘hotspot’ of diversity in central and southeastern Spain, and two areas of low haplotypic diversity located in the western Iberian peninsula and Morocco. Principal component analysis (PCA) carried out on haplotypes frequency surfaces allowed the construction of a colour‐based ‘synthetic’ map of the first three PC components, enabling the detection of the main range‐scale genetic trends and the identification of three main ‘gene pools’ for the species: (i) a ‘southeastern’ gene pool, including southeastern France, Italy, Corsica, Sardinia, Pantelleria and northern Africa; (ii) an ‘Atlantic’ gene pool, including all the western areas of the Iberian peninsula; and (iii) a ‘central’ gene pool, located in southeastern Spain. Multivariate and amova analyses carried out on interpolated grid point frequency values revealed the existence of eight major clusters (‘gene zones’), whose genetic relationships were related with the history of the species. In addition, demographic models showed more ancient expansions in the eastern and southern ranges of maritime pine probably associated to early postglacial recolonization. The delineation of the gene zones provides a baseline for designing conservation areas in this key Mediterranean pine.
Ecology matters: Atlantic–Mediterranean disjunction in the sand‐dune shrub Armeria pungens (Plumbaginaceae)
Authors: PIÑEIRO ROSALÍA , AGUILAR JAVIER FUERTES , MUNT DAVID DRAPER , FELINER GONZALO NIETO 
Published: March 2007

AbstractInferring the evolutionary history of Mediterranean plant lineages from current genetic, distributional and taxonomic patterns is complex because of a number of palaeoclimatic and geological interconnected factors together with landscape heterogeneity and human influence. Therefore, choosing spatially simplified systems as study groups is a suitable approach. An amplified fragment length polymorphism (AFLP) study using two restriction enzyme combinations (EcoRI/MseI and KpnI/MseI) was carried out to estimate the structure of genetic variation throughout the range of Armeria pungens. This species has a West Iberian‐Corso/Sardinian disjunct distribution on coastal sand‐dune ecosystems. Bayesian, amova and genetic distance analyses of the AFLP data revealed the same distinguishable genetic groups, which do not match the main geographical disjunction. Corso‐Sardinian populations were found to be genetically closer to southwest Portuguese than to those from the Gulf of Cadiz (the closest geographically). Eastwards long‐distance dispersal is therefore invoked to explain this geographical disjunction. A GIS analysis based on bioclimatic envelope modelling aiming to characterize the current locations of A. pungens found strong similarities between the Portugal and Corsica‐Sardinia sites and less so between these areas and the Gulf of Cadiz. This coincident pattern between AFLP and climatic data suggests that the geographical disjunction is better explained by climatic factors than by the likeliness of a stochastic dispersal event. Such a combined phylogeographical–GIS modelling approach proves to be enlightening in reconstructing the evolutionary history of plant species.
The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses
Authors: Kilian Joachim , Whitehead Dion , Horak Jakub , Wanke Dierk , Weinl Stefan , Batistic Oliver , D’Angelo Cecilia , Bornberg‐Bauer Erich , Kudla Jörg , Harter Klaus 
Published: March 2007

SummaryThe tolerance responses of plants to many abiotic stresses are conjectured to be controlled by complex gene networks. In the frame of the AtGenExpress project a comprehensive Arabidopsis thaliana genome transcript expression study was performed using the Affymetrix ATH1 microarray in order to understand these regulatory networks in detail. In contrast to earlier studies, we subjected, side‐by‐side and in a high‐resolution kinetic series, Arabidopsis plants, of identical genotype grown under identical conditions, to different environmental stresses comprising heat, cold, drought, salt, high osmolarity, UV‐B light and wounding. Furthermore, the harvesting of tissue and RNA isolation were performed in parallel at the same location using identical experimental protocols. Here we describe the technical performance of the experiments. We also present a general overview of environmental abiotic stress‐induced gene expression patterns and the results of a model bioinformatics analysis of gene expression in response to UV‐B light, drought and cold stress. Our results suggest that the initial transcriptional stress reaction of Arabidopsis might comprise a set of core environmental stress response genes which, by adjustment of the energy balance, could have a crucial function in various stress responses. In addition, there are indications that systemic signals generated by the tissue exposed to stress play a major role in the coordination and execution of stress responses. In summary, the information reported provides a prime reference point and source for the subsequent exploitation of this important resource for research into plant abiotic stress.
An upstream region in the first intron of petunia actin‐depolymerizing factor 1 affects tissue‐specific expression in transgenic Arabidopsis (Arabidopsis thaliana)
Authors: Jeong Young‐Min , Mun Jeong‐Hwan , Kim Hoyeun , Lee So‐Young , Kim Sang‐Gu 
Published: March 2007

SummaryThe first intron of the petunia actin‐depolymerizing factor 1 (PhADF1) gene was previously shown to induce strong and constitutive expression of that gene in vegetative tissues of transgenic Arabidopsis. To examine intron‐mediated enhancement of PhADF1 gene expression in detail, the effects of splicing, deletion and promoter alteration on gene expression were analyzed in this study. Deletion of the 5′ upstream region of the intron significantly reduced the level of enhancement, under the control of both the PhADF1 and the PhADF2 promoters. The ratio of pre‐mRNA and mRNA does not correlate with the level of enhancement. To determine whether there is a promoter–intron interaction, the role of the intron was examined under the control of a heterogeneous promoter. The intron of PhADF1 induced GUS expression in vegetative tissues under the control of the reproductive tissue‐specific Arabidopsis profilin 5 (PRF5) promoter. In transient assays, the presence of the intron increased GUS expression under control of the 35S minimal promoter. Our results suggest that the first intron of the PhADF1 gene alters tissue‐specific expression by a post‐transcriptional mechanism. In addition, we have also shown that intron‐mediated enhancement is a conserved mechanism, which regulates the expression of the petunia and Arabidopsis ADF genes that are expressed in vegetative tissues.
Functional characterization of a glycine‐rich RNA‐binding protein 2 in Arabidopsis thaliana under abiotic stress conditions
Authors: Kim Joo Y. , Park Su J. , Jang Boseung , Jung Che‐Hun , Ahn Sung J. , Goh Chang‐Hyo , Cho Kyoungwon , Han Oksoo , Kang Hunseung 
Published: March 2007

SummaryAlthough glycine‐rich RNA‐binding protein 2 (GRP2) has been implicated in plant responses to environmental stresses, the function and importance of GRP2 in stress responses are largely unknown. Here, we examined the functional roles of GRP2 in Arabidopsis thaliana under high‐salinity, cold or osmotic stress. GRP2 affects seed germination of Arabidopsis plants under salt stress, but does not influence seed germination and seedling growth of Arabidopsis plants under osmotic stress. GRP2 accelerates seed germination and seedling growth in Arabidopsis plants under cold stress, and contributes to enhancement of cold and freezing tolerance in Arabidopsis plants. No differences in germination between the wild‐type and transgenic plants were observed following addition of abscisic acid (ABA) or glucose, implying that GRP2 affects germination through an ABA‐independent pathway. GRP2 complements the cold sensitivity of an Escherichia coli BX04 mutant and exhibits transcription anti‐termination activity, suggesting that it has an RNA chaperone activity during the cold adaptation process. Mitochondrial respiration and catalase and peroxidase activities were affected by expression of mitochondrial‐localized GRP2 in Arabidopsis plants under cold stress. Proteome analysis revealed that expression of several mitochondrial‐encoded genes was modulated by GRP2 under cold stress. These results provide new evidence indicating that GRP2 plays important roles in seed germination, seedling growth and freezing tolerance of Arabidopsis under stress conditions, and that GRP2 exerts its function by modulating the expression and activity of various classes of genes.
Overexpression of BpMADS4 from silver birch (Betula pendula Roth.) induces early‐flowering in apple (Malus × domestica Borkh.)
Authors: Flachowsky H. , Peil A. , Sopanen T. , Elo A. , Hanke V. 
Published: March 2007

AbstractTo shorten the juvenile stage of apple (Malus × domestica Borkh.) the BpMADS4 gene from silver birch (Betula pendula Roth.) was constitutively overexpressed in 25 transgenic apple clones. All clones were characterized by PCR, RT‐PCR and Real Time PCR. Solitary flowers were produced on in vitro shoots of eight transgenic clones and most of them appeared to be morphologically normal. Twenty shoots of each clone were rooted and transferred to a glasshouse. Glasshouse plants of clones T1165, T1187 and T1190 developed flowers. Several plants of T1165 and T1187 started floral initiation within 3–4 months following transfer to the glasshouse. Primary flowers were solitary and in a terminal position on the main shoot. Lateral flower clusters, consisting of three to five individual flowers, were also found. Pollen vitality and tube germination of glasshouse‐grown flowers were investigated, and there were no significant differences compared to pollen of non‐transgenic control plants. Preliminary crosses using flowers of glasshouse plants resulted in small apple fruits. It would seem that this is the first report on in vitro flower induction in transgenic apple.
Genomic regions associated with milling quality and grain shape identified in a set of random introgression lines of rice (Oryza sativa L.)
Authors: Zheng T. Q. , Xu J. L. , Li Z. K. , Zhai H. Q. , Wan J. M. 
Published: March 2007

AbstractRice milling quality is the final part of grain yield making it fit for eating and a complex trait that remains poorly understood genetically. Three components of rice milling quality, i.e. brown rice rate, milled rice rate and head rice rate and related rice grain shape traits were genetically dissected by the QTL mapping approach using a set of 231 random rice introgression lines and 160 SSR markers. A total of 10 genomic regions were found to be associated with rice grain shape and milling quality traits. Of these, one major QTL on chromosome 7 had large effects on rice grain shape and milling quality and was detected consistently in several related populations of rice, which offers an opportunity for marker‐aided improvement of rice milling quality and QTL cloning.
Liver histology in benign biliary stricture: Fibrosis to cirrhosis . . . and reversal?
Authors: Sikora Sadiq S , Srikanth Gadiyaram , Agrawal Vinita , Gupta Ramesh K , Kumar Ashok , Saxena Rajan , Kapoor Vinay K 
Published: March 2007

AbstractBackground:  Secondary biliary cirrhosis is a potential complication of post‐cholecystectomy bile duct stricture (PCBDS). This study addresses the factors that determine the severity of pathological changes on liver biopsy and the correlation with long‐term outcome following repair.Methods:  Liver biopsies obtained at surgery for repair of PCBDS in 71 patients were reviewed and pathological changes were scored from 0 to 3. Patients with fibrosis score 0–2 were categorized as the non‐cirrhotic group and those with score 3 (secondary biliary cirrhosis) were categorized as the cirrhotic group. Clinical and biochemical parameters, stricture type and outcome were analyzed by univariate and multivariate analysis for correlation with degree of fibrosis. Follow‐up liver biopsies (3–60 months) after stricture repair were obtained in five patients.Results:  There were 58 patients in the non‐cirrhotic group and 13 in the cirrhotic group. On univariate analysis, portal hypertension and prolonged injury‐repair duration correlated with secondary biliary cirrhosis. Patients with a fair outcome in the cirrhotic group (4/13) had derangements in liver function tests but had patent biliary enteric anastomosis on evaluation. Of the five patients in whom liver biopsies were obtained at follow up, two had regression, two were static, and one had progression.Conclusion:  All patients with PCBDS had varying degrees of fibrosis. Prolonged injury‐repair interval and portal hypertension were the important parameters correlating with secondary biliary cirrhosis. Early repair of biliary stricture is recommended to prevent liver fibrosis. A successful relief of biliary obstruction may halt and/or reverse pathological changes in the liver.
Applicability of MELD as a short‐term prognostic indicator in patients with chronic liver disease: An Indian experience
Authors: Mishra Peeyush , Desai Nutan , Alexander Jacob , Singh Dharmendra P , Sawant Prabha 
Published: March 2007

AbstractBackground:  The model for end‐stage liver disease (MELD), which employs objective variables, statistical weighting and a continuous scale, has replaced the Child–Turcotte–Pugh (CTP) classification as the scoring system of choice in several liver transplant centers. However, the predictive ability of MELD has never been prospectively evaluated in India. The aim of this study was to examine the MELD score, the CTP score and the recently proposed modified CTP score in Indian patients with liver cirrhosis to determine their correlation and compare their prognostic significance for short‐term survival.Methods:  A total of 76 patients with cirrhosis (mean age 46.97 years) were prospectively evaluated and followed up for 6 months. MELD score, CTP score and modified CTP score were calculated at baseline. The correlation between variables was evaluated by Pearson's correlation test. Receiver‐operating characteristic (ROC) curves were used to determine the cutoff values for each score with the best sensitivity and specificity in discriminating between patients who survived and those who died.Results:  Alcoholic liver disease was the most common (50%) etiology of cirrhosis. MELD score and CTP score showed very good correlation (Pearson correlation r = 0.983). ROC curve showed area under curve (c‐statistics) for MELD score, CTP score and modified CTP score as 0.764, 0.804 and 0.817, respectively.Conclusion:  The MELD score was not found to be superior to CTP score and modified CTP score for short‐term prognostication of patients with cirrhosis in this study.
Predictive value of rapid virological response and early virological response on sustained virological response in HCV patients treated with pegylated interferon α‐2a and ribavirin
Authors: Yu Jian‐Wu , Wang Gui‐Qiang , Sun Li‐Jie , Li Xiao‐Guang , Li Shu‐Chen 
Published: March 2007

AbstractBackground and Aim:  The therapeutic effect of pegylated interferon (peg‐IFN)‐α‐2a combination with ribavirin on patients with chronic hepatitis C virus (HCV) infection is dependent on the rapidity of the virological response. The aim of this study was to investigate the predictive value of rapid virological response (RVR) and early virological response (EVR) on sustained virological response (SVR) in HCV patients treated with peg‐IFN‐α‐2a and ribavirin.Methods:  The HCV genotypes of 105 patients with chronic hepatitis C were detected by enzyme‐immunoassay. Patients received subcutaneous 180 µg peg‐IFN‐α‐2a once weekly plus daily ribavirin. Patients with genotype 1 were treated for 48 weeks and patients with genotype 2 or 3 were treated for 24 weeks. HCV RNA was assessed by qualitative PCR at pretreatment, at weeks 4 and 12 during treatment, and at week 24 of follow‐up. Virological response rates at different weeks were investigated, with RVR defined as serum HCV RNA undetectable after 4 weeks and EVR defined as HCV RNA either undetectable or decrease by ≥2 log10 after 12 weeks. The effects of virological response rates at different weeks on SVR were analyzed.Results:  Of the 105 patients, 44 (41.9%) were genotype 1, 46 (43.8%) were genotype 2, and 15 (14.3%) were genotype 3. RVR rates (19.5%) of patients with genotype 1 were significantly lower than those (60.7%) of genotype 2 or 3 (χ2 = 16.836, P = 0.000); and EVR rates (73.2%) of patients with genotype 1 were significantly lower than those (96.7%) of genotype 2 or 3 (χ2 = 12.220, P = 0.000). The SVR rates (86.7%) of patients who had achieved RVR were significantly higher than those (43.9%) of patients who had not achieved RVR (χ2 = 19.713, P = 0.000). The positive predictive value of RVR in all patients was higher than that of EVR, but there was no significant difference between RVR and EVR. The negative predictive value of RVR in all patients or with genotype 1 was significantly lower than that of EVR. In univariate analysis, HCV RNA level (P = 0.014), genotype (P = 0.001), RVR (P = 0.000) and EVR (P = 0.000) were associated with effect of treatment. However, in stepwise regression analysis, the independent factors associated with effect of antiviral therapy were RVR (OR = 6.501, P = 0.001), EVR (OR = 2.776, P = 0.003) and genotype (OR = 3.061, P = 0.024).Conclusions:  The RVR and EVR rates of patients with genotype 1 were significantly lower than those of patients with genotype 2 or 3. RVR had a similar predictive value as EVR on SVR. Genotype, HCV RNA level, RVR and EVR were associated with SVR. Genotype, RVR and EVR were independent factors for predicting the effect of antiviral therapy.