bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of the conserved serine/threonine residues important for gibberellin‐sensitivity of Arabidopsis RGL2 protein
Authors: Hussain Alamgir , Cao Dongni , Cheng Hui , Wen Zilong , Peng Jinrong 
Published: September 2005

SummaryThe DELLA proteins GAI, RGA, RGL1 and RGL2 in Arabidopsis are plant growth repressors, repressing diverse developmental processes. Studies have shown that gibberellin (GA) attenuates the repressive function of DELLA proteins by triggering their degradation via the proteasome pathway. However, it is not known if GA‐induced protein degradation is the only pathway for regulating the bioactivity of DELLA proteins. We show here that tobacco BY2 cells represent a suitable system for studying GA signaling. RGL2 exists in a phosphorylated form in BY2 cells. RGL2 undergoes GA‐induced degradation, and this process is blocked by proteasome inhibitors and serine/threonine phosphatase inhibitors; however, serine/threonine kinase inhibitors had no detectable effect, suggesting that dephosphorylation of serine/threonine is probably a prerequisite for degradation of RGL2 via the proteasome pathway. Site‐directed substitution of all 17 conserved serine and threonine residues showed that six mutants (RGL2S441D, RGL2S542D, RGL2T271E, RGL2T319E, RGL2T411E and RGL2T535E) mimicking the status of constitutive phosphorylation are resistant to GA‐induced degradation. This suggests that these sites are potential phosphorylation sites. A functional assay based on the expression of GA 20‐oxidase revealed that RGL2T271E is probably a null mutant, RGL2S441D, RGL2S542D, RGL2T319E and RGL2T411E only retained about 4–17% of the activity of the wild type RGL2, whereas RGL2T535E retained about 66% of the activity of the wild type RGL2. However, expression of GA 20‐oxidase in BY2 cells expressing these mutant proteins is still responsive to GA, suggesting that the stabilization of RGL2 protein is not the only pathway for regulating its bioactivity.
Pseudomonas syringae pv. tomato type III effectors AvrPto and AvrPtoB promote ethylene‐dependent cell death in tomato
Authors: Cohn Jonathan R. , Martin Gregory B. 
Published: September 2005

SummaryThe type III secretion system (TTSS) of Pseudomonas syringae pv. tomato (Pst) injects into the plant cell effector proteins that play an essential role in the formation of bacterial speck disease. To investigate the molecular roles of TTSS effectors in disease formation, we used a cDNA microarray to analyze the expression of approximately 8600 random tomato genes in response to wild‐type Pst strain DC3000 and a mutant lacking a functional TTSS. Many of the differentially expressed genes identified encode proteins associated with hormone response or hormone biosynthesis pathways. Using isogenic mutant strains of DC3000, we monitored host transcriptional changes in response to the TTSS effector proteins AvrPto and AvrPtoB, both of which are important virulence factors on susceptible tomato lines. We found that AvrPto and AvrPtoB induce a set of host genes involved in ethylene biosynthesis and signaling, and in particular they regulate the expression of two genes, LeACO1 and LeACO2, encoding the ethylene‐forming enzyme ACC oxidase. Analysis of transgenic tomato lines with diminished ACC oxidase activity revealed that ethylene production by the host is required for the full virulence activity of both AvrPto and AvrPtoB. AvrPto and AvrPtoB therefore appear to promote enhanced disease in tomato leaves, in part, by upregulating genes involved in ethylene production.
Predicting longer‐term changes in weed populations under GMHT crop management
Authors: HEARD M S , ROTHERY P , PERRY J N , FIRBANK L G 
Published: September 2005

SummaryThe UK Farm Scale Evaluations (FSE) compared the effects on biodiversity of management of genetically modified herbicide‐tolerant (GMHT) crops and conventional crops over the shorter term. We simulated population changes over seven 4‐year rotations (28 years) for weeds in crop rotations that included cereals and spring‐sown GMHT and conventional oilseed rape and beet, using FSE data and assuming the continuation of the weed management systems practised in the FSE. The weed density dependence that was modelled integrated change caused by population dynamics and farmers’ responses to changes in weed density. Predicted weed seed populations decreased under conventional management and at a greater rate under GMHT. Total seed densities were lower for GMHT cropping by a factor of 0.7–0.8. The predicted distributions of weeds had more fields with lower weed densities under GMHT cropping. Such changes could affect animal populations on farmland, depending on the scale of uptake of GMHT crop cultivars.
Modelling assimilation rates of 14 temperate arable weed species as a function of the environment and leaf traits
Authors: STORKEY J 
Published: September 2005

SummaryInformation on the response of assimilation rate to environmental factors is lacking for many less competitive weed species that need to be considered in the context of increasing farm biodiversity. A pot experiment was sown to parameterize gross assimilation rate at light saturation and initial light use efficiency for 14 common UK annual weeds and winter wheat at four leaf temperatures. Field experiments were also sown to measure inter‐specific differences in specific leaf area (SLA), leaf nitrogen content and assimilation rates in the field at near‐optimum temperatures. A generic relationship describing the response of assimilation rate to temperature and light using SLA and leaf nitrogen content as conversion factors successfully predicted inter‐specific differences in assimilation rates in the field. This relationship could be incorporated into weed–crop competition models to predict the productivity and competitive impact of weed mixtures, including species outside the current data set. Assimilation rates at light saturation in the field were determined largely by SLA. This trait was variable between species and within a species across the growing season and needs to be well described in mechanistic competition models to accurately calculate instantaneous assimilation rates.
‘Universal’ primers for PCR‐sequencing of grass chloroplastic acetyl‐CoA carboxylase domains involved in resistance to herbicides
Authors: DÉLYE C , MICHEL S 
Published: September 2005

SummaryPrimers were designed to amplify two regions involved in sensitivity to herbicides inhibiting the plastidic acetyl‐CoA carboxylase (ACCase) from grasses (Poaceae). The first primer pair amplified a 551‐bp amplicon containing a variable Ile/Leu codon at position 1781 in Alopecurus myosuroides sequence. The second primer pair amplified a 406‐bp amplicon containing four variable codons (Trp/Cys, Ile/Asn, Asp/Gly, Gly/Ala) at positions 2027, 2041, 2078 and 2096, respectively, in A. myosuroides sequence. Both primer pairs amplified the targeted fragments from genes encoding plastidic ACCases, but not from the very similar genes encoding cytosolic ACCases. Clear DNA sequences were obtained from fresh or dried plant material from the field, and from 29 various grass species. Sequences revealed that the gene encoding plastidic ACCase in Poa annua and Festuca rubra contained a Leu1781 codon, in agreement with both species being inherently tolerant to herbicides inhibiting ACCase. Sequencing confirmed the hybrid origin of P. annua. Compared with ACCase enzyme assay, polymerase chain reaction is faster, can be performed from a single plant and suppresses the need for radioactive experiments. It can be completed with basic molecular biology laboratory equipment. It is the tool of choice for diagnosing resistance caused by alteration(s) of the plastidic ACCase.
Using a competition model to quantify the optimal trade‐off between machine vision capability and weed removal effectiveness
Authors: GRUNDY A C , ONYANGO C M , PHELPS K , READER R J , MARCHANT J A , BENJAMIN L R , MEAD A 
Published: September 2005

SummaryThe algorithm of an optical detection system was first investigated for its ability to correctly classify transplanted crops and weeds during the critical early stages of crop establishment and its robustness over a range of different crop species. The trade‐off was then examined between increasing the sensitivity of the detection system vs. the possibility of, in doing so, misclassifying some crop plants as weeds and inadvertently removing them. This was achieved by running a competition model using parameters derived from the image analysis and assessing the outcome of scenarios in terms of yield. The optimum parameter values to maximize the detection of the crop and the optimum parameter values to maximize the detection of the weed appeared relatively insensitive to time of image capture or weed density. They also appeared insensitive for different crop species where the crop had similar growth habit. However, competition scenarios indicated that the detection system parameter settings to achieve optimum yields were sensitive to the competitive ability of the weed species. For Veronica persica, crop yield was more sensitive to accidental crop removal than from competition. In contrast, in the presence of Tripleurospermum inodorum, yield loss was more attributable to weed competition. Importantly, linking the detection system with the competition model illustrated the principle that optimum yield may not necessarily be obtained by maximizing weed removal or minimizing crop removal. This first example of combining a detection system with a competition model presents a new opportunity to quantify the sensitivity of image classification in terms of yield.
Development of arable weed seedbanks during the 6 years after the change from conventional to organic farming
Authors: ALBRECHT H 
Published: September 2005

SummaryAll of the arable land of a farm in southern Germany was investigated during an 8‐year period, starting 2 years before and ending 6 years after the change to organic farming. The first 3 years after the conversion, the total seed number in the soil increased from 4050 to 17 320 m−2. From the fourth to the sixth year, it dropped back to 10 220 m−2. The number of seeds increased particularly at sites with a low crop cover and a high density of weed plants at the soil surface. The increase predominantly occurring on the more fertile soils may have been caused by the rotation commencing with less competitive crops. Crops which increased the seedbank by 30–40% were winter cereals, sunflowers and lupins. Potatoes and sown fallow caused no significant change and grass–clover mixtures even reduced the number of seeds by 39%. Among 44 species occurring frequently enough for statistical analysis, 31 increased and only 3 decreased. The change of management particularly increased summer annual, perennial and dicotyledonous weeds. This can be attributed to both operations which are characteristic of organic farming (e.g. replacing herbicide applications by mechanical weed control) and to general modifications of the management practice which may also occur in non‐organic farming systems (increasing the percentage of broad leaved and spring sown crops in crop rotation). The present study confirms investigations into the aboveground vegetation that indicate that arable organic farming favours plant species diversity and provides evidence that the conversion need not encourage the dominance of a few noxious weeds.
Living donation: focus on public concerns
Authors: Zink Sheldon , Weinreib Robert , Sparling Thalia , Caplan Arthur L 
Published: September 2005

Abstract:  In December 2002, a conference was held in Philadelphia to discuss public concerns about living organ transplantation with the goal of reaching a consensus about new strategies for such transplants. The conference was hosted by the Hospital of the University of Pennsylvania and the Center for Bioethics. A multidisciplinary group of leading experts and stakeholders was called to assess the current status of living donation and suggest productive changes to ensure safer and more ethically sound procedures for both donors and recipients. Prior to the meeting, the research team from the University of Pennsylvania, Center for Bioethics, conducted literature reviews and extensive background research on living organ transplantation. Summary briefs were prepared for all conference participants. Issues were divided into four subcategories; two or three experts led the discussion on each topic. At the conclusion of the conference, the points raised were summarized and discussed, and additional comments were offered before general agreement was reached on each subject. Transcribed minutes and summary statements were reviewed and circulated among participants to allow for additional comments and clarification. All feedback was incorporated into the statement, and a draft of the article was recirculated. Participants who have endorsed the following statements have agreed that these points represent the intent and spirit of the discussion, yet each participant reserves the right to disclaim the document in its entirety. The views represented in the consensus points are held by members of the consensus group and do not necessarily represent the views of the sponsor.A consensus was reached to propose new strategies and make improvements on existing practices and protocols. Specific attention was paid to the widely accepted needs of consistent and responsible communication with the public and press, standardization in donor assessment, a national living donor registry and new research focusing on larger sample numbers and long‐term donor follow‐up. These consensus points support the work carried out by other advisory transplant organizations and should assist in advocating for living organ donors, the live donor transplant process and the concerns of the public.
Older living donors provide excellent quality kidneys: a single center experience (older living donors)
Authors: Johnson Scott R , Khwaja Khalid , Pavlakis Martha , Monaco Anthony P , Hanto Douglas W 
Published: September 2005

Abstract: Background: The role of advanced age live donors remains controversial because of decline in glomerular filtration rate and perceived increased risks of perioperative complications.Methods: A retrospective review of all live donor transplants performed from January 2000 to December 2003.Results: Seventy‐eight live donor transplants were performed during the period of review, 47 (60.3%) female and 31 (39.7%) male. Twenty‐two (28.2%) of the donors were >50 yr old, 15 (68%) female and seven (32%) male. Living related donation was performed in 56 (74.4%) and unrelated in 20 (35.6%). Laparoscopic nephrectomy was performed in 29 (37.2%) and open nephrectomy in 49 (62.8%). More donors >50 underwent laparoscopic nephrectomy, 13 of 22 (59.1%) vs. 16 of 56 (28.6%). Overall patient and graft survival at 1 yr are 97 and 97%. One‐year patient and graft survival is 100% vs. 96% and 100% vs. 96% in the older vs. young donors. Rejection occurred in nine of 78 (11.5%), but was not different between groups. Older donors had a reduced creatinine clearance 107.5 ± 3.4 vs. 124.2 ± 3.1 mL/min (p = 0.002) and a reduced clearance normalized for body surface area 60.6 ± 3.6 mL/(min m2) vs. 70.2 ± 2.6 mL/(min m2) (p = 0.045). Recipient serum creatinine was higher on postoperative day 1 in the older donor group 5.4 mg/dL vs. 4.4 mg/dL (p = 0.009). There was no difference in recipient serum creatinine at postoperative day 7, 30, 90, 180, 365 and 730. Donor serum creatinine was not different between groups on postoperative days 1, 7 and 30 but was higher in group 1 vs. group 2 on postoperative day 365, 1.26 ± 0.26 mg/dL vs. 1.01 ± 0.18 mg/dL (p = 0.020).Conclusions: Despite a reduced initial creatinine clearance, renal function is comparable in recipients of both young and old donor kidneys. Older donors had a slightly reduced serum creatinine 1 yr post‐donation that warrants additional follow‐up to determine if the observations continue. The introduction of laparoscopic nephrectomy may provide additional incentive for older donors to present for live donor nephrectomy.
Is alanine aminotransferase a good marker of histologic hepatic damage in renal transplant patients with hepatitis C virus infection?
Authors: Perez Renata M , Ferreira Adalgisa SP , Medina‐Pestana José O , Lanzoni Valeria P , Silva Antonio Eduardo B , Ferraz Maria Lucia G 
Published: September 2005

Abstract:  Introduction:  Renal transplant (RTx) patients with hepatitis C frequently show normal levels of alanine aminotransferase (ALT) and the significance of ALT in this group has not been established.Aim:  To determine the value of ALT as a marker of histologic hepatic damage in RTx patients with hepatitis C virus (HCV) infection.Materials and methods:  HCV‐RNA‐positive RTx patients with a liver biopsy were analyzed regarding staging and the grading of periportal and lobular necroinflammatory activity. Spearman's correlation coefficient was used to determine the correlation between ALT and histologic variables. Sensitivity, specificity and positive and negative predictive values (PPV and NPV) of ALT in the detection of septal fibrosis and interface hepatitis, and/or confluent necrosis were calculated.Results:  Fifty‐three patients (32 men, 60%), with a mean age of 42 ± 10 yr and time since transplant of 5 ± 4 yr were included. Only 27 (51%) patients showed elevated ALT levels, which were associated with septal fibrosis (p = 0.001), interface hepatitis (p < 0.001) and confluent necrosis (p = 0.05). A correlation was observed between ALT and staging (r = 0.50, p < 0.001), periportal necroinflammatory activity (r = 0.59, p < 0.001) and lobular necroinflammatory activity (r = 0.50, p < 0.001). The sensitivity, specificity, PPV and NPV of ALT were 92, 61, 41 and 96%, respectively, for the detection of septal fibrosis, and 87, 77, 74 and 88% for the detection of interface hepatitis and/or confluent necrosis.Conclusion:  ALT is a good marker of histologic hepatic lesion in HCV‐infected RTx patients and, therefore, liver biopsy can be avoided in patients with persistently normal ALT.
Equal overall rejection rate in pre‐transplant flow‐cytometric cross‐match negative and positive adult recipients in liver transplantation
Authors: Matinlauri Irma H , Höckerstedt Krister A , Isoniemi Helena M 
Published: September 2005

Abstract: T cell IgG flow‐cytometric cross‐matches (FCXM) using 48 stored pre‐transplant patient serum samples and 40 stored serum samples collected 3 wk after liver transplantation and frozen spleen cells of cadaveric donors in 48 consecutive liver transplantations were performed retrospectively. T cell IgG FCXM using pre‐transplant serum samples was compared with 46 complement‐dependent lymphocytotoxic cross‐matches (CDCXM) performed at the time of transplantation. Clinical relevance of these tests was evaluated in relation to acute rejection, 1‐, 3‐ and 5‐yr graft and patient survival. The incidence of positive FCXM was 33% (16 of 48) and 13% (six of 46) by CDCXM. The median time of acute rejection was 29 d after transplantation in FCXM positive group (range 13–101 d) and 22 d in FCXM negative group (range 7–157 d, NS). Rejection rate was similar in 16 pre‐transplant FCXM positive patients (eight of 16, 50%) compared with six pre‐transplant CDCXM positive patients (three of six, 50%; NS). Recipients having graft rejection tended to be more often pre‐transplant FCXM positive (eight of 21, 38%) than CDCXM positive (three of 21, 14%), but the difference was not significant (p > 0.1). No difference was found in the positive predictive value in relation to acute rejection between positive FCXM and CDCXM (69% vs. 50%; NS). Furthermore there was no correlation between post‐transplant positive FCXM and acute rejection. No difference was found between pre‐transplant T cell IgG FCXM positive and negative recipients in relation to graft or patient survival.Our findings are supportive for little risk associated with preformed donor‐specific antibodies in liver transplantation.
Influence of CYP3A5 and MDR1 polymorphisms on tacrolimus concentration in the early stage after renal transplantation
Authors: Zhang Xin , Liu Zhi‐hong , Zheng Jing‐min , Chen Zhao‐hong , Tang Zheng , Chen Jin‐song , Li Lei‐shi 
Published: September 2005

Abstract:  Objective:  Tacrolimus is an immunosuppressive drug with a narrow therapeutic range and wide interindividual variation in its pharmacokinetics. Cytochrome P450 (CYP) 3A and P‐glycoprotein (P‐gp, encoded by MDR1) play an important role in the absorption and metabolism of tacrolimus. The objective of this study was to evaluate whether or not CYP3A5*1/*3 or MDR1 C3435T polymorphisms are associated with the tacrolimus concentration per dose.Methods:  CYP3A5 and MDR1 genotypes were determined by polymerase chain reaction followed by restriction fragment length polymorphism analysis in 118 Chinese renal transplant patients receiving tacrolimus. Whole blood trough tacrolimus concentration was measured by enzyme‐linked immunosorbent assay and dose‐adjusted concentration (ng/mL per mg/kg/d) was calculated at 1 wk, 1 month, and 3 months after transplantation.Results:  The dose‐adjusted concentration of CYP3A5*1/*1 and *1/*3 patients was significantly lower than *3/*3 patients (32.8 ± 17.7 and 41.6 ± 15.8 vs. 102.3 ± 51.2 at 1 wk; 33.1 ± 7.5 and 46.4 ± 12.9 vs. 103 ± 47.5 at 1 month; 35.3 ± 20.9 and 59.0 ± 20.6 vs. 150 ± 85.3 at 3 months after transplantation respectively). At 1 wk, 46% of the CYP3A5*1 allele carriers had a tacrolimus concentration lower than 5 ng/mL and 77% lower than 8 ng/mL, whereas 20% of the *3/*3 patients had a concentration higher than 20 ng/mL. There was a mild difference between *1/*1 homozygotes and *1/*3 heterozygotes at 1 and 3 months after transplantation. No difference was found among the MDR1 genotypes.Conclusion:  CYP3A5*1/*3 polymorphisms are associated with tacrolimus pharmacokinetics and dose requirements in renal transplant recipients. Pharmacogenetic methods could be employed prospectively to help initial dose selection and to individualize immunosuppressive therapy.
Tacrolimus as secondary intervention vs. cyclosporine continuation in patients at risk for chronic renal allograft failure
Authors: Waid Thomas ,   for the CRAF Study Group
Published: September 2005

Abstract:  Background:  Chronic renal allograft failure (CRAF) is the leading cause of graft loss post‐renal transplantation. This study evaluated the efficacy and safety of tacrolimus as secondary intervention in cyclosporine‐treated kidney transplantation patients with impaired allograft function as indicated by elevated serum creatinine (SCr) levels.Methods:  Patients receiving cyclosporine‐based immunosuppression who had an elevated SCr at least 3 months post‐renal transplantation were enrolled. Treatment allocation was 2:1 to switch to tacrolimus or continue cyclosporine. This analysis was performed after 2 yr; patients will be followed for an additional 3 yr.Results:  There were 186 enrolled and evaluable patients. On baseline biopsy, 90% of patients had chronic allograft nephropathy. Baseline median SCr was 2.5 mg/dL in both treatment groups. For patients with graft function at month 24, SCr had decreased to 2.3 mg/dL in the tacrolimus‐treated patients and increased to 2.6 mg/dL in the cyclosporine‐treated patients (p = 0.01). Acute rejection occurred in 4.8% of tacrolimus‐treated patients and 5.0% of cyclosporine‐treated patients during follow‐up. Two‐year allograft survival was comparable between groups (tacrolimus 69%, cyclosporine 67%; p = 0.70). Tacrolimus‐treated patients had significantly lower cholesterol and low‐density lipoprotein levels and also had fewer new‐onset infections. Cardiac conditions developed in significantly fewer tacrolimus‐treated patients (5.6%) than cyclosporine‐treated patients (24.3%; p = 0.004). Glucose levels and the incidences of new‐onset diabetes and new‐onset hyperglycemia did not differ between treatment groups.Conclusions:  Conversion from cyclosporine to tacrolimus results in improved renal function and lipid profiles, and significantly fewer cardiovascular events with no differences in the incidence of acute rejection or new‐onset hyperglycemia.