bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of promoter strength, supercoiling and secondary structure on mutation rates in Escherichia coli
Authors: Schmidt Karen H. , Reimers Jacqueline M. , Wright Barbara E. 
Published: April 2006

SummaryFour mutations resulting in opal stop codons were individually engineered into a plasmid‐borne chloramphenicol‐resistance (cat) gene driven by the lac promoter. These four mutations were located at different sites in secondary structures. The mutations were analysed with the computer program mfg, which predicted their relative reversion frequencies. Reversion frequencies determined experimentally correlated with the mutability of the bases as predicted by mfg. To examine the effect of increased transcription on reversion frequencies, the lac promoter was replaced with the stronger tac promoter, which resulted in 12‐ to 30‐fold increases in reversion rates. The effect of increased and decreased supercoiling was also investigated. The cat mutants had higher reversion rates in a topA mutant strain with increased negative supercoiling compared with wild‐type levels, and the cat reversion rates were lower in a topA gyrB mutant strain with decreased negative supercoiling, as predicted.
Using a standard framework for the phenotypic analysis of Medicago truncatula: an effective method for characterizing the plant material used for functional genomics approaches
Authors: MOREAU DELPHINE , SALON CHRISTOPHE , MUNIER‐JOLAIN NATHALIE 
Published: April 2006

ABSTRACTA crucial step for identifying genes of interest in legume crops is to determine gene function in Medicago truncatula. To facilitate functional genomics in this species, an ecophysiological framework of analysis was developed. Our primary aim was to establish a standard terminology for identifying each organ on the plant. A standard system for the characterization of the vegetative and the reproductive developmental stages was then proposed. Using these tools, the time course of vegetative development of nitrogen‐fixing A17 plants was analysed in experiments conducted under different environmental conditions. To take into account the influence of temperature on plant development timing, an original approach was used by modelling vegetative development as a function of thermal time. Interestingly, the use of thermal time highlighted genotypic constants in plant development. Thereafter, to illustrate how this methodology can be used in explaining phenotypic alterations, the phenotype of two allelic mutants was analysed. Because the tools proposed in this paper allow the following: (1) standardization of how the plant material should be characterized to be used for functional genomics; (2) prediction of plant vegetative development; and (3) a more accurate phenotyping, the use of these tools by the M. truncatula community should provide a relevant framework for facilitating the production of reproducible functional genomics data.
Transitions in the functioning of the shoot apical meristem in birch (Betula pendula) involve ethylene
Authors: Ruonala Raili , Rinne Päivi L.H. , Baghour Mourad , Moritz Thomas , Tuominen Hannele , Kangasjärvi Jaakko 
Published: April 2006

SummaryIn many trees, a short photoperiod (SD) triggers substantial physiological adjustments necessary for over‐wintering. We have used transgenic ethylene‐insensitive birches (Betula pendula), which express the Arabidopsis ethylene receptor gene ETR1 carrying the dominant mutation etr1‐1, to investigate the role of ethylene in SD‐induced responses in the shoot apical meristem (SAM). Under SD, the ethylene‐insensitive trees ceased elongation growth comparably to the wild‐type. In contrast, the formation of terminal buds, which in trees is typically induced by SD, was abolished. However, although delayed, endo‐dormancy did eventually develop in the ethylene‐insensitive trees. This, together with the rapid resumption of growth in the ethylene‐insensitive trees after transfer from non‐permissive to permissive conditions suggests that ethylene facilitates the SD‐induced terminal bud formation, as well as growth arrest. In addition, apical buds of the ethylene‐insensitive birch did not accumulate abscisic acid (ABA) under SD, suggesting interaction between ethylene and ABA signalling in the bud. Alterations in SAM functioning were further exemplified by reduced apical dominance and early flowering in ethylene‐insensitive birches. Gene expression analysis of shoot apices revealed that the ethylene‐insensitive birch lacked the marked increase in expression of a beta‐xylosidase gene typical to the SD‐exposed wild‐type. The ethylene‐dependent beta‐xylosidase gene expression is hypothesized to relate to modification of cell walls in terminal buds during SD‐induced growth cessation. Our results suggest that ethylene is involved in terminal bud formation and in the timely suppression of SAM activity, not only in the shoot apex, but also in axillary and reproductive meristems.
AhSSK1, a novel SKP1‐like protein that interacts with the S‐locus F‐box protein SLF
Authors: Huang Jian , Zhao Lan , Yang Qiuying , Xue Yongbiao 
Published: April 2006

SummaryThe S‐locus F‐box (SLF/SFB) protein, recently identified as the pollen determinant of S‐RNase‐based self‐incompatibility (SI) in Solanaceae, Scrophulariaceae and Rosaceae, has been proposed to serve as the subunit of an SCF (SKP1–CUL1–F‐box) ubiquitin ligase and to target its pistil counterpart S‐RNase during the SI response. However, the underlying mechanism is still in dispute, and the putative SLF‐binding SKP1‐equivalent protein remains unknown. Here, we report the identification of AhSSK1, Antirrhinum hispanicumSLF‐interacting SKP1‐like1, using a yeast two‐hybrid screen against a pollen cDNA library. GST pull‐down assays confirmed the SSK1–SLF interaction, and showed that AhSSK1 could connect AhSLF to a CUL1‐like protein. AhSSK1, despite having a similar secondary structure to other SKP1‐like proteins, appeared quite distinctive in sequence and unique in a phylogenetic analysis, in which no SSK1 ortholog could be predicted in the sequenced genomes of Arabidopsis and rice. Thus, our results suggest that the pollen‐specific SSK1 could be recruited exclusively as the adaptor of putative SCFSLF in those plants with S‐RNase‐based SI, providing an important clue to dissecting the function of the pollen determinant.
Contribution of polymeric immunoglobulin receptor to regulation of intestinal inflammation in dextran sulfate sodium‐induced colitis
Authors: Murthy Ashlesh K , Dubose Candice N , Banas Jeffrey A , Coalson Jacqueline J , Arulanandam Bernard P 
Published: April 2006

AbstractBackground:  Inflammatory bowel disease (IBD) affects approximately 4 million people worldwide and can be caused by dysregulated mucosal immune responses to the intestinal commensal microflora. Immunoglobulin A (IgA) is considered to be the principal antibody in intestinal secretions and functions to prevent commensals and pathogenic organisms from gaining access to epithelial cell surfaces. Immunoglobulin A deficiency in humans has been associated with celiac disease and ulcerative colitis. However, the precise role of IgA in the pathogenesis of these disorders is yet to be fully understood.Methods:  Mice with a targeted disruption in IgA production (IgA–/– mice) and polymeric immunoglobulin receptor (pIgR–/– mice) were analyzed for the contribution of secretory immunity in the pathogenesis of dextran sulfate sodium (2.5%)‐induced colitis.Results:  It was found that dextran sulfate sodium‐treated pIgR–/– mice displayed greater loss of bodyweight and had severe clinical illness compared to similarly treated IgA–/– mice and wild‐type animals. Additionally, colonic tissues from the pIgR–/– mice exhibited progressively and significantly greater degrees of mucosal edema, ulceration, crypt abscesses and macrophage infiltration when compared to similarly treated IgA–/– mice and wild‐type animals.Conclusions:  The results indicate that secretory immunoglobulins contribute to protection of the colonic mucosa against dextran sulfate sodium‐induced epithelial injury, although the isotype of the secretory immunoglobulin (IgA or IgM) may not be a decisive factor in such protection. Collectively, the pIgR and/or the secretory component are important for the maintenance of epithelial integrity and mucosal homeostasis in the colonic epithelium.
Transabdominal gastroesophageal devascularization without transection for bleeding varices: Results and indicators of prognosis
Authors: Goyal Neerav , Singhal Dinesh , Gupta Subash , Soin Arvinder S , Nundy Samiran 
Published: April 2006

AbstractBackground:  Esophagogastric devascularization is an operation that can be performed for endoscopically uncontrolled variceal bleeding in hospitals having only basic surgical instruments and is therefore an appropriate procedure for small hospitals in developing countries. The aim of this study was to analyze one hospital’s experience of this operation in consecutive patients with variceal bleeding.Methods:  Between 1996 and 2003, 45 patients (30 male, 15 female) who had a mean age of 40 years (range 7–78 years) underwent devascularization procedures. Of the 45, 23 had cirrhosis and 22 had non‐cirrhotic portal hypertension (11 extrahepatic portal venous obstruction, 11 non‐cirrhotic portal fibrosis), and 18 patients had emergency procedures and 27 were elective. Mortality, morbidity, rebleeding rates and the prognostic factors for death were assessed.Results:  Elective and emergency mortality was one (3.7%) and 11 (61%) patients, respectively. There was no rebleeding in hospital. At follow up (mean 48 months, range 3–92 months) overall survival in patients with cirrhosis was 7 out of 20 and in patients with non‐cirrhotic portal hypertension was 19 of 21. Five (17%) had recurrent variceal hemorrhage, of whom three, all cirrhotic patients, died. Preoperative prognostic indicators for death were emergency surgery, a Child–Pugh score ≥10, preoperative blood transfusion ≥20 units and renal failure.Conclusions:  Gastroesophageal devascularization effectively controls variceal bleeding especially in non‐cirrhotic patients with portal hypertension. In the elective situation it carries a low mortality and rebleed rate. In emergencies the prognosis is poor with advanced cirrhosis, following large quantities of blood transfusion and deranged renal function. It is suggested that this operation be offered especially to non‐cirrhotic patients in hospitals in developing countries where facilities for more sophisticated procedures are not available.
Specific COX‐2 inhibitor, meloxicam, suppresses proliferation and induces apoptosis in human HepG2 hepatocellular carcinoma cells
Authors: Li Jie , Chen Xiaoping , Dong Xuesong , Xu Zongzhen , Jiang Hongchi , Sun Xueying 
Published: April 2006

AbstractBackground and Aims:  Cyclooxygenase‐2 (COX‐2) is associated with carcinogenesis. The aim of this study was to investigate the expression of COX‐2 in four hepatocellular carcinoma (HCC) cell lines, and evaluate the effect of a selective COX‐2 inhibitor, meloxicam, in HepG2, a high COX‐2 expressing cell line.Methods:  Expression of COX‐2 was detected using RT‐PCR, Western blotting and immunohistochemical analysis. Cell proliferation was measured using MTT assay. Cell cycle distribution was determined by flow cytometry. Apoptosis was detected with TUNEL method. Expression of proliferating cell nuclear antigen (PCNA), cell cycle regulatory proteins including cyclins A, B1, D1 and E, and apoptosis‐related proteins including Fas, Fas ligand and Bcl‐2 were examined using Western blotting.Results:  Cyclooxygenase‐2 was intensely expressed in HepG2, HLE and BEL7402 cells, but weakly expressed in SMMC‐7402 cells. Meloxicam suppressed proliferation of HepG2 cells in a dose‐ and time‐dependent manner, resulting in cell cycle arrest in S phase and cell accumulation in G0/G1 phase. Expression of PCNA, cyclin A but not cyclin B1, cyclin D1 or cyclin E was down‐regulated by meloxicam. Meloxicam also induced apoptosis of HepG2 cells, with increased expression of Fas ligand, but the expression of Fas and Bcl‐2 was not affected by meloxicam treatment.Conclusions:  The present study demonstrates that the specific COX‐2 inhibitor meloxicam suppresses proliferation and induces apoptosis in HCC cells that express COX‐2, suggesting that COX‐2 inhibition may offer a novel chemopreventive and therapeutic approach for HCC.
Evaluation of epitope tags for protein detection after in vivo CNS gene transfer
Authors: Shevtsova Z. , Malik J. M. I. , Michel U. , Schöll U. , Bähr M. , Kügler S. 
Published: April 2006

AbstractFunctional characterization of disease‐related proteins, their splice variants and dominant negative mutants in the context of complex CNS tissues such as brain and retina is frequently assessed by in vivo gene transfer. For correct interpretation of results it is imperative that the protein under investigation is unambiguously detected in the transduced cell types and can be distinguished from any endogenously expressed physiological variants. Therefore the first systematic evaluation of epitope tags used to trace ectopically expressed proteins in the central nervous system is presented here. Substantial differences in the performances of various epitope tag–antibody combinations with respect to sensitivity, specificity and influence of the epitope tag on the fusion protein are elucidated. Epitope tags already established for protein detection in vitro and to some extent in vivo (c‐Myc, HA and FLAG tags) were immunohistochemically detected with high sensitivity. However, detection of these tags revealed problems with background staining and we also document structural and functional influence of the tags on the fusion protein. In order to prevent such unwanted side‐effects, epitope tags which have not yet been used for in vivo applications (IRS, EE and AU1 tags) were characterized in brain, retina and cultured neurons. While use of the IRS and EE tags was hindered by low sensitivity or specificity, optimal results were obtained with the AU1 epitope, which may develop into a standard tool for detection of ectopic protein expression in the central nervous system.
Persistent changes in action potential broadening and the slow afterhyperpolarization in rat CA1 pyramidal cells after febrile seizures
Authors: Kamal Amer , Notenboom Robbert G. E. , De Graan Pierre N. E. , Ramakers Geert M. J. 
Published: April 2006

AbstractFebrile (fever‐induced) seizures (FS) are the most common form of seizures during childhood and have been associated with an increased risk of epilepsy later in life. The relationship of FS to subsequent epilepsy is, however, still controversial. Insights from animal models do indicate that especially complex FS are harmful to the developing brain and contribute to a hyperexcitable state that may persist for life. Here, we determined long‐lasting changes in neuronal excitability of rat hippocampal CA1 pyramidal cells after prolonged (complex) FS induced by hyperthermia on postnatal day 10. We show that hyperthermia‐induced seizures at postnatal day 10 induce a long‐lasting increase in the hyperpolarization‐activated current Ih. Furthermore, we show that a reduction in the amount of spike broadening and in the amplitude of the slow afterhyperpolarization following FS are also likely to contribute to the hyperexcitability of the hippocampus long term.
The uncelebrated parent: stories of mothers with learning difficulties caught in the child protection net
Authors: Booth Tim , Booth Wendy 
Published: April 2006

SummaryThis paper presents the stories of three mothers with learning difficulties whose children have been involved in care proceedings. Drawing on the example of the legendary interviewer, Studs Terkel, the authors let the mothers describe their experiences of the child protection system in their own words. From out of their intensely personal accounts comes a political narrative about the role of the state in the policing of marginalized and vulnerable families.
Toward a More Reliable Federal Survey for Tracking Health Insurance Coverage and Access
Authors: Kenney Genevieve , Holahan John , Nichols Len 
Published: April 2006

Objective. Examination of the extent to which federal surveys provide the data needed to estimate the coverage/cost impacts of policy alternatives to address the problem of uninsurance.Data Sources/Study Setting. Assessment of the major federal household surveys that regularly provide information on health insurance and access to care based on an examination of each survey instrument and related survey documentation and the methodological literature.Study Design. Identification of the data needed to address key policy questions on insurance coverage, assessment of how well existing surveys meet this need, definition of the critical elements of an ideal survey, and examination of the potential for building on existing surveys.Data Collection/Extraction Methods. Collection and critical assessment of pertinent survey documentation and methodological studies.Principal Findings. While all the federal surveys examined provide valuable information, the information available to guide key policy decisions still has major gaps. Issues include measurement of insurance coverage and critical content gaps, inadequate sample sizes to support precise state and substate estimates, considerable delays between data collection and availability, and concerns about response rates and item nonresponse. Our assessment is that the Current Population Survey (CPS) and the National Health Interview Survey could be most readily modified to address these issues.Conclusions. The vast resources devoted to health care and the magnitude of the uninsurance problem make it critical that we have a reliable source for tracking health care and coverage at the national and state levels and for major local areas. It is plausible that this could be more cost effectively done by building on existing surveys than by designing and fielding a new one, but further research is needed to make a definitive judgment. At a minimum, the health insurance information collected on the CPS should be revised to address existing measurement problems.
Provider Characteristics Related to Antidepressant Use in Older People
Authors: Fillenbaum Gerda G. , Hybels Celia F. , Pieper Carl F. , Konrad Thomas R. , Burchett Bruce M. , Blazer Dan G. 
Published: April 2006

OBJECTIVES: To determine whether the characteristics of the usual medical care providers of older antidepressant users changed between 1986 and 1997 with the introduction of selective serotonin reuptake inhibitors.DESIGN: Longitudinal study.SETTING: Five‐county Piedmont area of North Carolina.PARTICIPANTS: Stratified random sample of African‐American (n=2,261) and white (n=1,875) community residents aged 65 to 105.MEASUREMENTS: Sample members provided information on prescription medications, demographic and health status, and usual medical care provider (matched to North Carolina Health Professions Data Systems files to ascertain provider characteristics) in 1986/87, 1989/90, 1992/93, and 1996/97. Most (77.5%) named a provider (name unmatchable for 4.1%). Sample member characteristics were aggregated into probability (propensity) scores summarizing predisposing (demographic), enabling (medical care access), and need (health status) categories. Along with wave of study and whether a provider was named, these were entered as control variables in generalized estimating equation models that examined the association between provider race (white vs nonwhite), sex, age, location of practice, and primary versus specialist care and antidepressant use.RESULTS: The characteristics of the usual medical care providers remained stable over the decade, although prevalence of antidepressant use increased. Two provider characteristics—race and area of practice (but not the interaction between them)—were significantly associated with patients' use of antidepressants. Patients of white physicians and of physicians with urban practices were more likely to use antidepressants.CONCLUSION: Although use of antidepressants has increased over time, there has been little change in the characteristics of users' usual medical care providers.
Long‐Term Risks of Death and Institutionalization of Elderly People in Relation to Deficit Accumulation at Age 70
Authors: Rockwood Kenneth , Mitnitski Arnold , Song Xiaowei , Steen Bertil , Skoog Ingmar 
Published: April 2006

OBJECTIVES:To measure relative fitness and frailty in older people without specific frailty instruments and to relate that measurement to long‐term health outcomes.DESIGN:Retrospective cohort studies.SETTING:Two population‐based studies of people aged approximately 70 at baseline and followed up to 10 years (in the Canadian Study of Health and Aging (CSHA)) or 26 years in the Gothenburg H‐70 cohort study.PARTICIPANTS:Nine hundred sixty‐two men and 1,178 women.MEASUREMENTS:Deficit accumulation (the exposure) was counted using self‐reported (CSHA) or clinically designated (H‐70) symptoms, signs, diseases, and disabilities. Relative fitness and frailty were measured in relation to the degree of deficit accumulation evaluated in four quartiles, representing those most fit to those most frail. The items that made up the frailty index were selected randomly without replacement in 1,000 iterations. The outcomes were risks of death or residential long‐term care.RESULTS:Worse frailty, however measured, was associated with worse survival; the Kaplan‐Meier curves of random iterations of the frailty definition showed virtually no interquartile overlap for mortality. For any given level of frailty, men died younger than women. Worse frailty was also associated with a higher risk of institutionalization.CONCLUSION:Frailty appears to be a robust concept that is readily operationalized, with the risk of adverse outcomes being largely established by age 70.