bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Mutant of Arabidopsis Lacking the Triose-Phosphate/Phosphate Translocator Reveals Metabolic Regulation of Starch Breakdown in the Light
Authors: Walters Robin G. , Ibrahim Douglas G. , Horton Peter , Kruger Nicholas J. 
Published: June 2004

Abstract
The chloroplast envelope triose-phosphate/phosphate translocator (TPT) is responsible for carbohydrate export during photosynthesis. Using measurements of carbohydrates, partitioning of assimilated 14CO2, photosynthetic gas exchange, and chlorophyll fluorescence, we show that a mutant of Arabidopsis lacking the TPT increases synthesis of starch compared to the wild type, thereby compensating for a deficiency in its ability to export triose-phosphate from the chloroplast. However, during growth under high light, the capacity for starch synthesis becomes limiting so that the chloroplastic phosphate pool is depleted, resulting in a restriction on electron transport, a reduction in the rate of photosynthesis, and slowed plant growth. Under the same conditions but not under low light, we observe release of 14C label from starch, indicating that its synthesis and degradation occur simultaneously in the light. The induction of starch turnover in the mutant specifically under high light conditions leads us to conclude that it is regulated by one or more metabolic signals, which arise as a result of phosphate limitation of photosynthesis.
Analysis of Curated and Predicted Plastid Subproteomes of Arabidopsis. Subcellular Compartmentalization Leads to Distinctive Proteome Properties
Authors: Sun Qi , Emanuelsson Olof , van Wijk Klaas J. 
Published: June 2004

Abstract
Carefully curated proteomes of the inner envelope membrane, the thylakoid membrane, and the thylakoid lumen of chloroplasts from Arabidopsis were assembled based on published, well-documented localizations. These curated proteomes were evaluated for distribution of physical-chemical parameters, with the goal of extracting parameters for improved subcellular prediction and subsequent identification of additional (low abundant) components of each membrane system. The assembly of rigorously curated subcellular proteomes is in itself also important as a parts list for plant and systems biology. Transmembrane and subcellular prediction strategies were evaluated using the curated data sets. The three curated proteomes differ strongly in average isoelectric point and protein size, as well as transmembrane distribution. Removal of the cleavable, N-terminal transit peptide sequences greatly affected isoelectric point and size distribution. Unexpectedly, the Cys content was much lower for the thylakoid proteomes than for the inner envelope. This likely relates to the role of the thylakoid membrane in light-driven electron transport and helps to avoid unwanted oxidation-reduction reactions. A rule of thumb for discriminating between the predicted integral inner envelope membrane and integral thylakoid membrane proteins is suggested. Using a combination of predictors and experimentally derived parameters, four plastid subproteomes were predicted from the fully annotated Arabidopsis genome. These predicted subproteomes were analyzed for their properties and compared to the curated proteomes. The sensitivity and accuracy of the prediction strategies are discussed. Data can be extracted from the new plastid proteome database (http://ppdb.tc.cornell.edu).
TILLING. Traditional Mutagenesis Meets Functional Genomics
Authors: Henikoff Steven , Till Bradley J. , Comai Luca 
Published: June 2004

Abstract
Most of the genes of an organism are known from sequence, but most of the phenotypes are obscure. Thus, reverse genetics has become an important goal for many biologists. However, reverse-genetic methodologies are not similarly applicable to all organisms. In the general strategy for reverse genetics that we call TILLING (for Targeting Induced Local Lesions in Genomes), traditional chemical mutagenesis is followed by high-throughput screening for point mutations. TILLING promises to be generally applicable. Furthermore, because TILLING does not involve transgenic modifications, it is attractive not only for functional genomics but also for agricultural applications. Here, we present an overview of the status of TILLING methodology, including Ecotilling, which entails detection of natural variation. We describe public TILLING efforts in Arabidopsis and other organisms, including maize (Zea mays) and zebrafish. We conclude that TILLING, a technology developed in plants, is rapidly being adopted in other systems.
Purification and Characterization of Enzymes Exhibiting β-d-Xylosidase Activities in Stem Tissues of Arabidopsis
Authors: Minic Zoran , Rihouey Christophe , Do Cao Trung , Lerouge Patrice , Jouanin Lise 
Published: June 2004

Abstract
This work describes the purification and characterization of enzymes that exhibit β-d-xylosidase activity in stem tissues of Arabidopsis. This is the first detailed investigation that concerns the characterization of catalytic properties and sequence identity of enzymes with β-d-xylosidase activities in a dicotyledonous plant. Three different enzymes, ARAf, XYL4, and XYL1 with apparent molecular masses of 75, 67, and 64 kD, respectively, were purified to homogeneity. ARAf was identified as a putative α-l-arabinofuranosidase, and XYL4 and XYL1 as putative β-d-xylosidases using matrix-assisted laser-desorption ionization time of flight. ARAf belongs to family 51 and XYL4 and XYL1 to family 3 of glycoside hydrolases. ARAf and XYL1 have highest specificity for p-nitrophenyl-α-l-arabinofuranoside and XYL4 for p-nitrophenyl-β-d-xylopyranoside and natural substrates such as xylobiose and xylotetraose. XYL4 was shown to release mainly d-Xyl from oat spelt xylan, rye arabinoxylan, wheat arabinoxylan, and oligoarabinoxylans. ARAf and XYL1 can also release d-Xyl from these substrates but less efficiently than XYL4. Moreover, they can also release l-Ara from arabinoxylans and arabinan. Overall, the results indicate that XYL4 possesses enzymatic specificity characteristic for a β-d-xylosidase, while ARAf and XYL1 act as bifunctional α-l-arabinofuranosidase/β-d-xylosidases. Analysis of the activity of these three enzymes in stem tissues at different stages of development has shown that young stems possess the highest activities for all three enzymes in comparison to the activities of the enzymes present in stems at older stages of development. High enzyme activities are most likely related to the necessary modifications of cell wall structure occurring during plant growth.
16,17-Dihydro Gibberellin A5 Competitively Inhibits a Recombinant Arabidopsis GA 3β-Hydroxylase Encoded by the GA4 Gene
Authors: Zhou Rong , Yu Min , Pharis Richard P. 
Published: June 2004

Abstract
Ring D-modified gibberellin (GA) A5 and A20 derivatives are structurally similar to GA20 and GA9 (the precursors to growth-active GA1 and GA4) and, when applied to higher plants, especially grasses, can reduce shoot growth with concomitant reductions in levels of growth-active GAs and increases in levels of their immediate 3-deoxy precursors. The recombinant Arabidopsis GA 3β-hydroxylase (AtGA3ox1) protein was used in vitro to test a number of ring D-modified GA structures as possible inhibitors of AtGA3ox1. This fusion protein was able to 3β-hydroxylate the 3-deoxy GAs, GA9 and GA20, to GA4 and GA1, respectively, and convert the 2,3-didehydro GA, GA5, to its 2,3-epoxide, GA6. Michaelis-Menten constant (K m) values of 1.25 and 10 μ m, respectively, were obtained for the GA9 and GA20 conversions. We utilized the enzyme's ability to convert GA20 to GA1 in order to test the efficacy of GA5, 16,17-dihydro GA5 (dihydro GA5), and a number of other ring D-modified GAs as inhibitors of AtGA3ox activity. For the exo-isomer of dihydro GA5, inhibition increased with the dose of dihydro GA5, with Lineweaver-Burk plots showing that dihydro GA5 changed only the K m of the enzyme reaction, not the V max, giving a dissociation constant of the enzyme-inhibitor complex (K i) of 70 μ m. Other ring D-modified GA derivatives showed similar inhibitory effects on GA1 production, with 16,17-dihydro GA20-13-acetate being the most effective inhibitor. This behavior is consistent with dihydro GA5, at least, functioning as a competitive substrate inhibitor of AtGA3ox1. Finally, the recombinant AtGA3ox1 fusion protein may be a useful screening tool for other effective 3β-hydroxylase inhibitors, including naturally occurring ones.
Beyond Arabidopsis. Translational Biology Meets Evolutionary Developmental Biology
Authors: Irish Vivian F. , Benfey Philip N. 
Published: June 2004

Abstract
Developmental processes shape plant morphologies, which constitute important adaptive traits selected for during evolution. Identifying the genes that act in developmental pathways and determining how they are modified during evolution is the focus of the field of evolutionary developmental biology, or evo-devo. Knowledge of genetic pathways in the plant model Arabidopsis serves as the starting point for investigating how the toolkit of developmental pathways has been used and reused to form different plant body plans. One productive approach is to identify genes in other species that are orthologous to genes known to control developmental pathways in Arabidopsis and then determine what changes have occurred in the protein coding sequence or in the gene's expression to produce an altered morphology. A second approach relies on natural variation among wild populations or crop plants. Natural variation can be exploited to identify quantitative trait loci that underlie important developmental traits and, thus, define those genes that are responsible for adaptive changes. The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development.
Genome-Wide ORFeome Cloning and Analysis of Arabidopsis Transcription Factor Genes
Authors: Gong Wei , Shen Yun-Ping , Ma Li-Geng , Pan Yi , Du Yun-Long , Wang Dong-Hui , Yang Jian-Yu , Hu Li-De , Liu Xin-Fang , Dong Chun-Xia , Ma Li , Chen Yan-Hui , Yang Xiao-Yuan , Gao Ying , Zhu Danmeng , Tan Xiaoli , Mu Jin-Ye , Zhang Da-Bing , Liu Yu-Le , Dinesh-Kumar S.P. , Li Yi , Wang Xi-Ping , Gu Hong-Ya , Qu Li-Jia , Bai Shu-Nong , Lu Ying-Tang , Li Jia-Yang , Zhao Jin-Dong , Zuo Jianru , Huang Hai , Deng Xing Wang , Zhu Yu-Xian 
Published: June 2004

Abstract
Here, we report our effort in generating an ORFeome collection for the Arabidopsis transcription factor (TF) genes. In total, ORFeome clones representing 1,282 Arabidopsis TF genes have been obtained in the Gateway high throughput cloning pENTR vector, including 411 genes whose annotation lack cDNA support. All the ORFeome inserts have also been mobilized into a yeast expression destination vector, with an estimated 85% rate of expressing the respective proteins. Sequence analysis of these clones revealed that 34 of them did not match with either the reported cDNAs or current predicted open-reading-frame sequences. Among those, novel alternative splicing of TF gene transcripts is responsible for the observed differences in at least five genes. However, those alternative splicing events do not appear to be differentially regulated among distinct Arabidopsis tissues examined. Lastly, expression of those TF genes in 17 distinct Arabidopsis organ types and the cultured cells was profiled using a 70-mer oligo microarray.
Positioning Arabidopsis in Plant Biology. A Key Step Toward Unification of Plant Research
Authors: Bevan Michael , Walsh Sean 
Published: June 2004

Abstract
One of the major challenges in biological investigation involves developing a robust predictive framework in which biological outputs can be predicted from input data and knowledge of the state of the system. Currently, genomics-based strategies provide a strong framework for integrating biological knowledge within a species and linking knowledge between diverse organisms, as DNA sequence is a durable, accurate, and complete record of biological information. As such, it provides the best source of information upon which predictive rules can start to be built, tested, and generalized. Generalization is a key component of predictive biology because it defines the extent to which we can accurately predict from one instance to another. In plant science, several important research themes are concerned with generalization, and progress in these areas is reviewed here. The importance of developing a framework for predictive biology that includes a much wider variety of plant species is also emphasized.
Russia's oil potential: prospects and implications
Authors: Bahgat Gawdat 
Published: June 2004

AbstractSince the late 1990s, Russia's oil production has experienced a steady resurgence. As a result, Moscow has regained its status as a major oil producer, exporter and crucial player in global energy markets. This paper argues that this rising Russian role should neither be overestimated nor underestimated. It examines some of the main characteristics of the country's oil industry, notably the investment climate, production‐sharing agreement regime and pipeline capacity.Russia's rising production is likely to enhance global energy security. Moscow and other major oil producers share a similar goal — stability of the oil market and international economy. Today's energy market should not be analysed in zero‐sum terms. Major oil producers coordinate their policy with each other and with major consumers.
Ex vivo analysis of aberrant splicing induced by two donor site mutations in PKLR of a patient with severe pyruvate kinase deficiency
Authors: van Wijk Richard , van Wesel Annet C. W. , Thomas Adri A. M. , Rijksen Gert , van Solinge Wouter W. 
Published: June 2004

SummaryTwo single‐nucleotide substitutions in PKLR constituted the molecular basis underlying pyruvate kinase (PK) deficiency in a patient with severe haemolytic anaemia. One novel mutation, IVS5+1G>A, abolished the intron 5 donor splice site. The other mutation, c.1436G>A, altered the intron 10 donor splice site consensus sequence and, moreover, encoded an R479H substitution. We studied the effects on PKLR pre‐mRNA processing, using ex vivo‐produced nucleated erythroid cells from the patient. Abolition of the intron 5 splice site initiated two events in the majority of transcripts: skipping of exon 5 or, surprisingly, simultaneous skipping of exon 5 and 6 (Δ5,6). Subcellular localization of transcripts suggested that no functional protein was produced by the IVS5+1A allele. The unusual Δ5,6 transcript suggests that efficient inclusion of exon 6 in wild‐type PKLR mRNA depends on the presence of splice‐enhancing elements in exon 5. The c.1436G>A mutation caused skipping of exon 10 but was mainly associated with a severe reduction in transcripts although these were, in general, normally processed. Accordingly, low amounts of PK were detected in nucleated erythroid cells of the patient, thus correlating with the patient's PK‐deficient phenotype. Finally, several low‐abundant transcripts were detected that represent the first examples of ‘leaky‐splicing’ in PKLR.
Restorative proctectomy after emergency laparoscopic colectomy for ulcerative colitis: a case‐matched study
Authors: Maartense S. , Dunker M. S. , Slors J. F. M. , Gouma D. J. , Bemelman W. A. 
Published: June 2004

AbstractObjective  The aim of the study was to evaluate feasibility and safety of restorative proctectomy with ileal pouch anal anastomosis (IPAA) through a Pfannenstiel incision after prior laparoscopic colectomy.Methods  Seventeen patients who underwent restorative proctectomy after laparoscopic emergency colectomy for ulcerative colitis (UC) were prospectively evaluated. Results were compared with results of a group of 21 case matched patients that had restorative proctectomy and IPAA via a midline incision in the same period.Results  Median operation time was longer, although not significantly, in patients who had a restorative proctectomy through a pfannenstiel (186 min) compared to a restorative proctectomy through a midline incision (158 min). Procedure related complications were comparable between the groups, respectively, 1 of 17 patients in the pfannenstiel group and 3 of 21 patients in the median laparotomy group. Median hospital stay in the pfannenstiel group was 10 days and in the midline group 12 days.Conclusions  After laparoscopic assisted emergency colectomy for ulcerative colitis, restorative proctectomy is feasible and can be performed safely through a Pfannenstiel incision.
Reduction in the proportion of patients with colorectal cancer presenting as an emergency following the introduction of fast‐track flexible sigmoidoscopy: a three‐year prospective observational study
Authors: Davies R. J. , Collins C. D. , Vickery C. J. , Eyre‐Brook I. , Welbourn R. 
Published: June 2004

AbstractObjective  We established a fast‐track flexible sigmoidoscopy service to meet the two‐week target for colorectal cancer, and have performed a prospective observational study over three years to assess its impact on the proportion of patients with colorectal cancer presenting as an emergency.Methods  The fast‐track system was established on 1 November 1999 using six screening criteria to select high‐risk patients. Data on all high‐risk patients referred through the fast‐track system and all patients diagnosed with colorectal cancer were recorded prospectively in two time periods: six months before fast‐track (1 November 1998 to 30 April 1999, Period 1) and three years following fast‐track (1 November 1999 to 31 October 2002, Period 2).Results  In Period 2, 2294 fast‐track referrals were received. A total of 635 cases (321 male, 314 female) of colorectal cancer were diagnosed in Period 2 vs. 84 cases (43 male, 41 female) in Period 1. In Period 1, 30 patients with colorectal cancer (35.7% of the total) presented as an emergency vs. 165 patients (25.9%) in Period 2 (P = 0.059, χ2test).Conclusion  Introduction of a fast‐track service to meet the two‐week target has resulted in a trend towards fewer emergency presentations with colorectal cancer.
Topical tacrolimus (FK506) in the treatment of recalcitrant parastomal pyoderma gangrenosum associated with Crohn's disease: report of two cases
Authors: Khurrum Baig M. , Marquez H. , Nogueras J. J. , Weiss E. G. , Wexner S. D. 
Published: June 2004

AbstractIntroduction  Pyoderma gangrenosum is a rare idiopathic skin disorder associated with other diseases, including inflammatory bowel disease. The commonest site is the skin, but sometimes it can occur in the parastomal region. Most of these cases respond to treatment with systemic corticosteroids and cyclosporin or local Kenalog injections.Methods  The following are two cases of parastomal pyoderma in patients not responding to the standard measures. These patients were treated with topical tacrolimus.Results  These patients showed dramatic improvement in one week with complete resolution and re‐epithelialization of skin within two weeks.Conclusion  Pyoderma gangrenosum is a difficult problem to manage and its early resolution is important. In these two reported cases, the improvement was dramatic, therefore topical tacrolimus should be considered early in the management.
One year follow up of a randomized trial comparing Ligasure™ with open haemorrhoidectomy
Authors: Lawes D. A. , Palazzo F. F. , Francis D. L. , Clifton M. A. 
Published: June 2004

AbstractBackground  Ligasure™ haemorrhoidectomy is an effective treatment for prolapsing haemorrhoids, however, concerns exist regarding potential damage to the anal sphincters.Methods  Patients previously included into a randomized trial comparing open and Ligasure™ haemorrhoidectomy were contacted by postal questionnaire to evaluate their overall satisfaction and continence at 12 months post operatively.Results  Thirteen patients who underwent open and 17 who underwent Ligasure™ haemorrhoidectomy were evaluated. Three patients from the open group and 2 from the Ligasure™ group were unhappy with the result (P = 0.37) and minor incontinence was reported in 5 Ligasure™ and 2 open patients (P = 0.42).Conclusion  Patient satisfaction and post operative continence scores at 1 year post operatively are comparable for open and Ligasure™ haemorrhoidectomy.
The circular stapling device as a risk factor for anastomotic leakage
Authors: Folkesson J. , Nilsson J. , Påhlman L. , Glimelius B. , Gunnarsson U. 
Published: June 2004

AbstractAim  To investigate the relation between the type of circular stapler and anastomotic leak in rectal cancer surgery.Background  During the past decades results from rectal cancer surgery have improved considerably regarding risk of local recurrence and survival. Two main paradigm changes are considered to be the cause for this: the introduction of total mesorectal excision (TME) and the increasing use of radiotherapy. However, rectal cancer surgery is associated with an unacceptably high frequency of complications of which anastomotic leak is one of the most severe ones. The hypothesis was raised that the choice of stapler influenced the leakage rates.Methods  A questionnaire was sent to all departments of surgery (n = 66) performing rectal cancer surgery in Sweden to determine the choice of circular stapler when performing anterior resection for rectal cancer. These data were linked to the Swedish Rectal Cancer Registry for the period 1995–99.Results  A total of 3316 patients had an anterior resection. The choice of circular stapling device was determined in 70% of the cases. When stapler A was used, the leakage rate was 11% whereas it was 7% when stapler B was used (P = 0.0039). In the cases where it was impossible to determine which stapler had been used the leakage rate was 8%.Conclusion  Quality control is an important part of medicine and the present study suggests that it also must include surgical instruments. A prospective randomised study is needed to confirm the results.
Real time quantification in plasma of human telomerase reverse transcriptase (hTERT) mRNA in patients with colorectal cancer
Authors: Lledó S. M. , Garcia‐Granero E. , Dasí F. , Ripoli R. , García S. A. , Cervantes A. , Aliño S. F. 
Published: June 2004

AbstractBackground  Increased telomerase activity can be found in almost 90% of colorectal tumours. We aim to describe the preliminary results for quantification in plasma of hTERT mRNA in colorectal cancer patients.Materials and methods  Fifty patients undergoing surgery for colorectal cancer and a control group of 50 healthy volunteers were prospectively studied. Pre‐operative venous blood samples were taken from all cancer patients and volunteers. Plasma hTERT expression was determined from peripheral blood based on real‐time quantitative RT‐PCR (qRT‐PCR) method normalized to the amount of RNA input using 18S rRNA gene expression. Plasma pre‐operative CEA levels were also determined.Results  Median values for normalized hTERT (hTERTN) gene expression were higher in colorectal cancer patients (11.62, range 0.23–47.67) than healthy volunteers (0.29, range 0.00–4.63) (P < 0.001). Individual data showed that 82% of colorectal cancer patients had hTERTN expression values superior to the maximum value observed in the control group. Sensitivity and specificity of the assay for colorectal cancer detection were 98% and 64%, respectively. No significant differences in hTERTN expression between gender or with age (P > 0.05). No significant correlation was found between hTERTN expression and CEA values (Spearman's rank test = 0.136, P = 0.348).Conclusions  These results show that detection of mRNA based on the qRT‐PCR of the telomerase hTERTN gene in plasma clearly differentiates between healthy and colorectal cancer patients and that hTERTN can be detected and quantified in plasma. This opens up a new field as a noninvasive blood test for colorectal cancer diagnosis.