bluuebunny/crossref_metadata_2025 huggingface dataset:
Information Extraction from Interlaboratory Comparison in Testing—Temperature Measurement in the Black Test Corner
Authors: Beges Gaber , Jensen Hans Dalsgaard , Drnovsek Janko
Published: April 2008

This paper presents extraction of information from results of an interlaboratory comparison in testing, which was performed in the scope of the 5th Framework Program—INCOLAB (INitiative and CO-ordination to prepare LABoratories in Newly Associated States for full implementation of the (LVD) Low-Voltage Directive) project. The comparison covers all the requirements of classical proficiency testing, but also adds metrological aspects in order to improve the outcome of such tests, which is new in the field of interlaboratory comparisons in testing of electric safety. The objective was to show differences in methods and measurements in the black test corner (BTC, which is one of the tests required by the LVD directive standards), when performing the conformity assessment. A digital convection oven and a cooker were chosen as representative samples for comparison. Different shapes of samples were used to put forward understanding and application of the standard requirements. Additionally, the temperature artifact was used for comparison of the BTCs of different participating laboratories. All participating laboratories in this intercomparison were requested to follow the basic instructions given in the technical protocol, applying their everyday test procedure. Results showed a few problematic areas in safety testing. The entire intercomparison proved that in general, and for LVD in particular, better specification for BTCs as an example for a complex measuring instrument is required. Additional information about test samples was also obtained. The concern arising is that a product can be placed on the EU market with the conformity assessment activity support of testing laboratories with quite different measurement capabilities.
Retinol-binding protein-4 is not strongly associated with insulin sensitivity in normal pregnancies.
Authors: Ueland T , Dalsoren T , Voldner N , Godang K , Henriksen T , Bollerslev J
Published: April 2008

Objective

Recently, experimental and clinical studies suggest that retinol-binding protein-4 (RBP4) may provide a link between obesity and insulin resistance. However, no previous studies have investigated the impact of circulating RBP4 on measures of insulin resistance in normal pregnant women, and the objective of this study is to measure serum RBP4 in early and late pregnancy and relate these to measures of insulin resistance and secretion controlling for changes in fat mass.

Design and methods

Samples were obtained during oral glucose tolerance test (OGTT) from 44 normal pregnancies at weeks 14–16 and 30–32. Measures of fat mass were body mass index (BMI) and leptin while insulin sensitivity and secretion were predicted from OGTT. Leptin and RPB4 were measured by immunoassay.

Results

Insulin sensitivity decreased during the course of pregnancy. Insulin sensitivity and secretion were best explained by BMI and circulating leptin, but not RBP4, both in early and late pregnancy. However, a marked increase in fasting RBP4 from early to late pregnancy was observed, and this change was associated with a decline in insulin sensitivity. A marked increase in RBP4 was found during OGTT at weeks 14–16 with an opposite temporal course at weeks 30–32.

Conclusion

The increased fat mass and insulin resistance during normal pregnancy was best explained by measures of fat mass. However, the increase in RBP4 from early to late pregnancy, associated with a decline in insulin sensitivity, potentially indicates interactions with glucose metabolism.
RANTES/CCL5 gene polymorphisms, serum concentrations, and incident type 2 diabetes: results from the MONICA/KORA Augsburg case–cohort study, 1984–2002
Authors: Herder Christian , Illig Thomas , Baumert Jens , Müller Martina , Klopp Norman , Khuseyinova Natalie , Meisinger Christa , Poschen Ulrike , Martin Stephan , Koenig Wolfgang , Thorand Barbara
Published: April 2008

Objective

Regulated on activation, normal T-cell expressed and secreted (RANTES)/chemokine(C-C motif) ligand (CCL5) is expressed by adipocytes, and serum levels of RANTES are increased in obesity and type 2 diabetes. The aim of this study was to test the hypothesis that RANTES is involved in the pathogenesis of type 2 diabetes by analyzing the triangular association between CCL5 gene polymorphisms, systemic RANTES concentrations, and incident type 2 diabetes in a large prospective study.

Subjects and methods

The study is based on 502 individuals (293 men and 209 women) and 1632 individuals (859 men and 773 women) with and without incident type 2 diabetes from the population-based MONItoring of Trends and Determinants in Cardiovascular Disease (MONICA)/Cooperative Health Research in the Region of Augsburg (KORA) case–cohort study respectively (mean follow-up time±s.d. 10.1±4.9 years). CCL5 genotypes and RANTES serum concentrations were determined and associations between genotypes, haplotypes, serum levels, and incident type 2 diabetes were assessed.

Results

Minor alleles of four single nucleotide polymorphisms were associated with lower RANTES levels (Padditive between 1.2×10−9 and 3.1×10−8), but neither genotypes, haplotypes, nor serum levels were associated with incident type 2 diabetes.

Conclusions

Our data suggest that RANTES/CCL5 gene variants and serum levels are not causally related with type 2 diabetes and that elevated RANTES levels in patients with type 2 diabetes may be a consequence of hyperglycemia. However, our findings cannot preclude a local role in adipose tissue where RANTES expression may contribute to leukocyte infiltration and a proinflammatory state.
Retinol, retinol-binding protein 4, abdominal fat mass, peak bone mineral density, and markers of bone metabolism in men: the Northern Osteoporosis and Obesity (NO2) Study
Authors: Högström Magnus , Nordström Anna , Nordström Peter
Published: April 2008

Context

The association between retinol and bone mineral density (BMD) in males after puberty has not been fully investigated previously.

Objective

To investigate the association between retinol, retinol-binding protein-4 (RBP-4), BMD (g/cm2), abdominal fat mass, and markers of bone metabolism in young men.

Design

Longitudinal study.

Participants

Seventy-eight healthy males with a mean age of 22.6±0.7 years at baseline. A follow-up was conducted in 73 of the participants 2.0±0.4 years later.

Main outcome measures

Associations between serum concentrations of retinol and RBP-4, and BMD of the total body, lumbar spine, and hip, serum concentrations of osteocalcin, and carboxy terminal telopeptide of type 1 collagen (CTX), were investigated.

Results

Both retinol and RBP-4 showed an inverse relationship with that of osteocalcin (r=−0.23 to −0.25, P<0.05). Levels of RBP-4 (r=0.26, P=0.02) and osteocalcin (r=−0.23, P=0.04) were also related to abdominal fat mass, and the relationship between RBP-4, retinol, and osteocalcin disappeared after adjusting for this influence of abdominal fat mass. Neither retinol nor RBP-4 concentrations were associated with BMD at any site, CTX as baseline, or changes in BMD during the 2-year follow-up period. Levels of RBP-4 showed a strong association with levels of retinol (r=0.61, P<0.001).

Conclusion

We found a negative association between the bone formation marker osteocalcin with retinol and RBP-4. The association disappeared when adjusting for the influence of abdominal fat mass. Neither retinol nor RBP-4 were associated with peak BMD in young men.
Somatostatinergic ligands in dopamine-sensitive and -resistant prolactinomas
Authors: Fusco Alessandra , Gunz Ginette , Jaquet Philippe , Dufour Henry , Germanetti Anne Laure , Culler Michael D , Barlier Anne , Saveanu Alexandru
Published: April 2008

Objective

Ten percent of patients with prolactinoma fail to respond with normalization of prolactin (PRL) and tumor shrinkage under dopamine agonist (DA) therapy. The resistance to treatment is linked to a loss of dopamine receptor 2 (D2DR). Prolactinomas express somatostatin (SST) receptor subtypes, SSTR1, 2, and 5. The aim of this study was to determine whether different SST compounds could overcome the resistance to DA in prolactinomas.

Design and methods

The efficacy of SSTR1, SSTR2, and SSTR5 ligands; the universal SST ligand, SOM230; and the chimeric SST-DA compound, BIM-23A760, was compared with cabergoline in suppressing PRL secretion from primary cultures of ten prolactinomas (six DA responders and four DA resistant). Receptor mRNAs were assessed by quantitative PCR.

Results

The mean mRNA levels for D2DR, SSTR1, SSTR2, and SSTR5 were 92.3±47.3, 2.2±1.4, 1.1±0.7, and 1.6±0.6 copy/copy β-glucuronidase (β-Gus) respectively. The SSTR1 agonist, BIM-23926, did not suppress PRL in prolactinomas. In a DA-resistant prolactinoma, it did not inhibit [3H]thymidine incorporation. The SSTR5 compound, BIM-23206, produced a dose-dependent inhibition of PRL release similar to that of cabergoline in three DA-sensitive prolactinomas. BIM-23A760 produced a maximal PRL inhibition superimposable to that obtained with cabergoline with a lower EC50 (0.5±0.1 vs 2.5±1.5 pmol/l). In DA-resistant prolactinomas, BIM-23206 and SOM230 were ineffective. Cabergoline and BIM-23A760 produced a partial inhibition of PRL secretion (19±6 and 21±3% respectively).

Conclusion

Although the SSTRs are expressed in prolactinomas, the somatostatinergic ligands analyzed do not appear to be highly effective in suppressing PRL. D2DR remains the primary target for effective treatment of prolactinomas.
Impact of metformin versus repaglinide on non-glycaemic cardiovascular risk markers related to inflammation and endothelial dysfunction in non-obese patients with type 2 diabetes
Authors: Lund Søren S , Tarnow Lise , Stehouwer Coen D A , Schalkwijk Casper G , Teerlink Tom , Gram Jørgen , Winther Kaj , Frandsen Merete , Smidt Ulla M , Pedersen Oluf , Parving Hans-Henrik , Vaag Allan A
Published: April 2008

Objective

In patients with type 2 diabetes mellitus (T2DM), biomarkers reflecting inflammation and endothelial dysfunction have been linked to cardiovascular disease (CVD biomarkers) and metabolic regulation. In T2DM patients, metformin and insulin secretagogues have demonstrated equal anti-hyperglycaemic potency. Here, we report the effect of metformin versus an insulin secretagogue, repaglinide, on CVD biomarkers in non-obese T2DM patients.

Design and methods

Single-centre, double-masked, double-dummy, crossover study during 2×4 months involving 96 non-obese (body mass index≤27 kg/m2) insulin-naïve T2DM patients. At enrolment, previous oral hypoglycaemic agents were stopped and the patients entered a 1-month run-in on diet-only treatment. Hereafter, patients were randomized to either 2 mg repaglinide thrice daily followed by 1 g metformin twice daily or vice versa each during 4 months with a 1-month washout between interventions.

Results

Levels of tumour necrosis factor-α, plasminogen activator inhibitor-1 antigen, tissue-type plasminogen activator antigen, von Willebrand factor, soluble intercellular adhesion molecule-1 and soluble E-selectin were significantly lower during metformin versus repaglinide treatments. In contrast, Amadori albumin and heart rate were higher during metformin versus repaglinide. Levels of interleukin-6, fibrinogen, soluble vascular cell adhesion molecule-1, asymmetric dimethylarginine and advanced glycation end products as well as glycaemic levels (previously reported) and 24-h blood pressure were similar between treatments. Adjustment for known macrovascular disease did not affect the between-treatment effects.

Conclusions

In non-obese T2DM patients, metformin was more effective in reducing selected biomarkers reflecting inflammation and endothelial dysfunction compared with repaglinide despite similar glycaemic levels between treatments.
Elevated serum parathyroid hormone predicts impaired survival prognosis in a general aged population
Authors: Björkman Mikko P , Sorva Antti J , Tilvis Reijo S
Published: April 2008

Objective

Short-term studies on selected patients have indicated that elevated serum parathyroid hormone (PTH) is an independent risk factor of death. However, long-term data on unselected populations are lacking, thus far. In order to evaluate the predictive value of elevated serum PTH during the last years of life, random persons of age cohorts of 75, 80 and 85 years were followed for 17 years.

Design

A prospective cohort study.

Methods

Subjects (n=567) were investigated for calcaemic status including serum intact PTH, serum total calcium (CaT) and ionized calcium (Ca2+). Thorough clinical examinations included an assessment of co-morbidity. Mortality data were collected from National Census Records.

Results

Up to 93% of the subjects died within the follow-up. In contrast to Ca2+ levels, high serum PTH (≥63 ng/l, IV quartile cut point) was associated with significant over-mortality (HR=1.56, 95% CI: 1.29–1.88) and a 2.3-year reduction of median life expectancy. After controlling for age, gender, co-morbidity and creatinine, the prognostic impact of elevated serum PTH was still significant (HR=1.24, 95% CI: 1.01–1.53). The tendency for over-mortality was consistent in both genders, in all age groups as well as in subjects with varying co-morbidity, renal function, body mass index categories and Ca2+ levels.

Conclusions

Elevated serum PTH level is an independent predictor of impaired long-term survival prognosis in unselected aged population. Serum Ca2+ did not emerge as a significant prognostic indicator. The long-term prognostic impact of vitamin D deficiency, the most common cause of elevated PTH levels in the elderly, remains to be investigated.
Increased Nε-(carboxymethyl)-lysine levels in cerebral blood vessels of diabetic patients and in a (streptozotocin-treated) rat model of diabetes mellitus
Authors: van Deutekom A W , Niessen H W M , Schalkwijk C G , Heine R J , Simsek S
Published: April 2008

Objective

Non-enzymatic glycation of proteins and their end products (advanced glycation end products, AGE) have been implicated in the pathogenesis of diabetic complications. Our aim was to evaluate the association between diabetes mellitus (DM) and the accumulation of one of the most abundant AGEs, Nε-(carboxymethyl)-lysine (CML), in cerebral vessels.

Research design and methods

Brain tissue samples were obtained by autopsy from 20 DM patients and 13 age-matched controls. In addition, we investigated brain tissue samples of seven rats after induction of diabetes with streptozotocin (STZ) and six non-diabetic control rats. We used an immunohistochemical staining method to examine the CML immunoreactivity in the cerebral vessels.

Results

Staining intensity of CML was significantly higher in cerebral vessels of diabetic patients than in non-diabetic subjects (median of the immunohistochemical intensity score/cm2 in the diabetic group of 0.85 (interquartile range (IQR) 0.66–1.52) vs 0.63 in the control group (IQR 0.44–0.70); P=0.002). Furthermore, there was a similar significant difference in CML staining intensity of cerebral vessels between STZ diabetic rats and non-diabetic control rats (median of the immunohistochemical intensity score/cm2 in the diabetic group of 1.08 (IQR 0.73–1.43) vs 0.23 in the control group (IQR 0.12–0.43); P=0.003).

Conclusions

Accumulation of CML-modified proteins is significantly greater in the cerebral vessels of the diabetic patients than their age-matched controls. This association has been confirmed in the insulin-deficient diabetic rat model. It may be possible that the excessive accumulation of AGE-modified proteins in the cerebral vasculature alters the local environment and microcirculation and thereby contributes to the development of cognitive impairments in diabetes. Therefore, additional study on the causal link between AGE accumulation and cognitive dysfunction and the potential benefits of AGE-blocking and/or breaking compounds is indicated.
Relation of 25-hydroxyvitamin D and parathyroid hormone levels with metabolic syndrome among US adults.
Authors: Reis Jared P , von Mühlen Denise , Miller Edgar R
Published: April 2008

Objective

Previous research on the combined association of 25-hydroxyvitamin D (25(OH)D) and parathyroid hormone (PTH) with metabolic syndrome may have been limited by restricted age variability and a lack of representation of the general population. This study examined the combined association of 25(OH)D and PTH with Adult Treatment Panel III-defined MetSyn among a nationally representative sample of US adults.

Design and methods

This population-based cross-sectional study included 834 men and 820 women aged ≥20 years without diagnosed diabetes who completed a physical examination as part of the 2003–2004 US National Health and Nutrition Examination Survey.

Results

After adjusting for age, sex, race/ethnicity, income, lifestyle factors, total calcium, and energy intake, the odds ratio (OR) for MetSyn in the highest quintile of 25(OH)D (median 88.0 nmol/l) compared with the lowest quintile (median 26.8 nmol/l) was 0.27 (0.15, 0.46;Ptrend<0.001). This relation was unchanged after additional adjustment for PTH level (OR, 0.26; 0.15, 0.44;Ptrend<0.001) and did not differ by sex (Pinteraction 0.6) or age (< or ≥50 years;Pinteraction 0.2). In contrast, the multivariable-adjusted odds for MetSyn increased with increasing PTH among older men (Ptrend0.004), but not younger men (Ptrend0.4) or women regardless of age (Ptrend0.4 in younger and older women).

Conclusions

These data suggest an inverse association of 25(OH)D with MetSyn, independent of potential confounding factors, calcium intake, and PTH, and a positive association of PTH with MetSyn among older men.
Heterogeneity in the molecular basis of ACTH resistance syndrome.
Authors: Collares Cristhianna Viesti Advincula , Antunes-Rodrigues Jose , Moreira Ayrton Custodio , Franca Suzana Nesi , Pereira Luiz Alberto , Soares Maria Marta Sarquis , Elias Junior Jorge , Clark Adrian J , de Castro Margaret , Elias Lucila Leico Kagohara
Published: April 2008

Objective

ACTH resistance syndromes are rare, autosomal, and genetically heterogeneous diseases that include familial glucocorticoid deficiency (FGD) and triple A syndrome. FGD has been shown to segregate with mutations in the gene coding for ACTH receptor (MC2R) or melanocortin 2 receptor accessory protein (MRAP), whereas mutations in the triple A syndrome (AAAS, Allgrove syndrome) gene have been found in segregation with triple A syndrome. We describe the clinical findings and molecular analysis ofMC2R,MRAP, andAAASgenes in five Brazilian patients with ACTH resistance syndrome.

Design and methods

Genomic DNA from patients and their unaffected relatives was extracted from peripheral blood leucocytes and amplified by PCR, followed by automated sequencing. Functional analysis was carried out using Y6 cells expressing wild-type and mutant MC2R.

Results

All five patients showed low cortisol and elevated plasma ACTH levels. One patient had achalasia and alacrima, besides the symptoms of adrenal insufficiency. The molecular analysis of FGD patients revealed a novel p.Gly116Val mutation in theMC2Rgene in one patient and p.Met1Ile mutation in theMRAPgene in another patient. Expression of p.Gly116Val MC2R mutant in Y6 cells revealed that this variant failed to stimulate cAMP production. The analysis of theAAASgene in the patient with triple A syndrome showed a novel g.782_783delTG deletion. The molecular analysis of DNA from other two patients showed no mutation inMC2R,MRAP, orAAASgene.

Conclusions

In conclusion, the molecular basis of ACTH resistance syndrome is heterogeneous, segregating with genes coding for proteins involved with ACTH receptor signaling/expression or adrenal gland development and other unknown genes.
High Diversity of Genes for Nonhost Resistance of Barley to Heterologous Rust Fungi
Authors: Jafary Hossein , Albertazzi Giorgia , Marcel Thierry C , Niks Rients E
Published: April 2008

Inheritance studies on the nonhost resistance of plants would normally require interspecific crosses that suffer from sterility and abnormal segregation. Therefore, we developed the barley–Puccinia rust model system to study, using forward genetics, the specificity, number, and diversity of genes involved in nonhost resistance. We developed two mapping populations by crossing the line SusPtrit, with exceptional susceptibility to heterologous rust species, with the immune barley cultivars Vada and Cebada Capa. These two mapping populations along with the Oregon Wolfe Barley population, which showed unexpected segregation for resistance to heterologous rusts, were phenotyped with four heterologous rust fungal species. Positions of QTL conferring nonhost resistance in the three mapping populations were compared using an integrated consensus map. The results confirmed that nonhost resistance in barley to heterologous rust species is controlled by QTL with different and overlapping specificities and by an occasional contribution of an R-gene for hypersensitivity. In each population, different sets of loci were implicated in resistance. Few genes were common between the populations, suggesting a high diversity of genes conferring nonhost resistance to heterologous pathogens. These loci were significantly associated with QTL for partial resistance to the pathogen Puccinia hordei and with defense-related genes.
Quantitative Genetic Analysis of Sleep inDrosophila melanogaster
Authors: Harbison Susan T , Sehgal Amita
Published: April 2008

Although intensively studied, the biological purpose of sleep is not known. To identify candidate genes affecting sleep, we assayed 136 isogenic P-element insertion lines of Drosophila melanogaster. Since sleep has been negatively correlated with energy reserves across taxa, we measured energy stores (whole-body protein, glycogen, and triglycerides) in these lines as well. Twenty-one insertions with known effects on physiology, development, and behavior affect 24-hr sleep time. Thirty-two candidate insertions significantly impact energy stores. Mutational genetic correlations among sleep parameters revealed that the genetic basis of the transition between sleep and waking states in males and females may be different. Furthermore, sleep bout number can be decoupled from waking activity in males, but not in females. Significant genetic correlations are present between sleep phenotypes and glycogen stores in males, while sleep phenotypes are correlated with triglycerides in females. Differences observed in male and female sleep behavior in flies may therefore be related to sex-specific differences in metabolic needs. Sleep thus emerges as a complex trait that exhibits extensive pleiotropy and sex specificity. The large mutational target that we observed implicates genes functioning in a variety of biological processes, suggesting that sleep may serve a number of different functions rather than a single purpose.
The Rate and Spectrum of Microsatellite Mutation in Caenorhabditis elegans and Daphnia pulex
Authors: Seyfert Amanda L , Cristescu Melania E A , Frisse Linda , Schaack Sarah , Thomas W Kelley , Lynch Michael
Published: April 2008

The effective use of microsatellite loci as tools for microevolutionary analysis requires knowledge of the factors influencing the rate and pattern of mutation, much of which is derived from indirect inference from population samples. Interspecific variation in microsatellite stability also provides a glimpse into aspects of phylogenetic constancy of mutational processes. Using long-term series of mutation-accumulation lines, we have obtained direct estimates of the spectrum of microsatellite mutations in two model systems: the nematode Caenorhabditis elegans and the microcrustacean Daphnia pulex. Although the scaling of the mutation rate with the number of tandem repeats is highly consistent across distantly related species, including yeast and human, the per-cell-division mutation rate appears to be elevated in multicellular species. Contrary to the expectations under the stepwise mutation model, most microsatellite mutations in C. elegans and D. pulex involve changes of multiple repeat units, with expansions being much more common than contractions.
Fraction of Informative Recombinations: A Heuristic Approach to Analyze Recombination Rates
Authors: Lefebvre J-F , Labuda D
Published: April 2008

In this article we present a new heuristic approach (informative recombinations, InfRec) to analyze recombination density at the sequence level. InfRec is intuitive and easy and combines previously developed methods that (i) resolve genotypes into haplotypes, (ii) estimate the minimum number of recombinations, and (iii) evaluate the fraction of informative recombinations. We tested this approach in its sliding-window version on 117 genes from the SeattleSNPs program, resequenced in 24 African-Americans (AAs) and 23 European-Americans (EAs). We obtained population recombination rate estimates (ρobs) of 0.85 and 0.37 kb−1 in AAs and EAs, respectively. Coalescence simulations indicated that these values account for both the recombinations and the gene conversions in the history of the sample. The intensity of ρobs varied considerably along the sequence, revealing the presence of recombination hotspots. Overall, we observed ∼80% of recombinations in one-third and ∼50% in only 10% of the sequence. InfRec performance, tested on published simulated and additional experimental data sets, was similar to that of other hotspot detection methods. Fast, intuitive, and visual, InfRec is not constrained by sample size limitations. It facilitates understanding data and provides a simple and flexible tool to analyze recombination intensity along the sequence.
AMutatorTransposon Insertion Is Associated With Ectopic Expression of a Tandemly Repeated MulticopyMybGenepericarp color1of Maize
Authors: Robbins Michael L , Sekhon Rajandeep S , Meeley Robert , Chopra Surinder
Published: April 2008

The molecular basis of tissue-specific pigmentation of maize carrying a tandemly repeated multicopy allele of pericarp color1 (p1) was examined using Mutator (Mu) transposon-mediated mutagenesis. The P1-wr allele conditions a white or colorless pericarp and a red cob glumes phenotype. However, a Mu-insertion allele, designated as P1-wr-mum6, displayed an altered phenotype that was first noted as occasional red stripes on pericarp tissue. This gain-of-pericarp-pigmentation phenotype was heritable, yielding families that displayed variable penetrance and expressivity. In one fully penetrant family, deep red pericarp pigmentation was observed. Several reports on Mu suppressible alleles have shown that Mu transposons can affect gene expression by mechanisms that depend on transposase activity. Conversely, the P1-wr-mum6 phenotype is not affected by transposase activity. The increased pigmentation was associated with elevated mRNA expression of P1-wr-mum6 copy (or copies) that was uninterrupted by the transposons. Genomic bisulfite sequencing analysis showed that the elevated expression was associated with hypomethylation of a floral-specific enhancer that is ∼4.7 kb upstream of the Mu1 insertion site and may be proximal to an adjacent repeated copy. We propose that the Mu1 insertion interferes with the DNA methylation and related chromatin packaging of P1-wr, thereby inducing expression from gene copy (or copies) that is otherwise suppressed.
TheSaccharomyces cerevisiaeActin Cytoskeletal Component Bsp1p Has an Auxiliary Role in Actomyosin Ring Function and in the Maintenance of Bud-Neck Structure
Authors: Wright Daniel J , Munro Ewen , Corbett Mark , Bentley Adam J , Fullwood Nigel J , Murray Stephen , Price Clive
Published: April 2008

Iqg1p is a component of the actomyosin contractile ring that is required for actin recruitment and septum deposition. Cells lacking Iqg1p function have an altered bud-neck structure and fail to form a functional actomyosin contractile ring resulting in a block to cytokinesis and septation. Here it is demonstrated that increased expression of the actin cytoskeleton associated protein Bsp1p bypasses the requirement for contractile ring function. This also correlates with reduced bud-neck width and remedial septum formation. Increased expression of this protein in a temperature-sensitive iqg1-1 background causes remedial septum formation at the bud neck that is reliant upon chitin synthase III activity and restores cell separation. The observed suppression correlates with a restoration of normal bud-neck structure. While Bsp1p is a component of the contractile ring, its recruitment to the bud neck is not required for the observed suppression. Loss of Bsp1p causes a brief delay in the redistribution of the actin cytoskeleton normally observed at the end of actin ring contraction. Compromise of Iqg1p function, in the absence of Bsp1p function, leads to a profound change in the distribution of actin and the pattern of cell growth accompanied by a failure to complete cytokinesis and cell separation.
Genetic Analysis of theCaenorhabditis elegansGLH Family of P-Granule Proteins
Authors: Spike Caroline , Meyer Nicole , Racen Erica , Orsborn April , Kirchner Jay , Kuznicki Kathleen , Yee Christopher , Bennett Karen , Strome Susan
Published: April 2008

The Vasa DEAD-box helicases are widespread markers of germ cells across species, and in some organisms have been shown to be essential for germ-cell formation and development. In contrast to the single Vasa gene in most systems analyzed, Caenorhabditis elegans has four Vasa family members, the germline helicases GLH-1, GLH-2, GLH-3, and GLH-4. Our analysis of deletion alleles of each glh gene demonstrates that GLH-1 is the key member of the family: loss of GLH-1 function causes sterility that is mainly maternal effect, is manifested predominantly at elevated temperature, and is due to reduced germ-cell proliferation and impaired formation of both sperm and oocytes. The other GLHs are not essential. However, GLH-4 serves redundant roles with GLH-1: loss of both genes' function causes glh-1-like sterility at all temperatures. Molecular epistasis analysis demonstrates that GLH-1 and GLH-4 are required for proper association of the PGL family of proteins with P granules, suggesting a pathway of P-granule assembly in which the GLHs are upstream of the PGL proteins and the mRNA cap-binding protein IFE-1. While loss of some P-granule components causes worms to be defective in RNA interference, loss of GLH-1 and GLH-4 does not compromise RNAi. Thus, RNAi likely does not require intact P granules but instead relies on particular P-granule factors. We discuss the evolution of the Vasa/GLH genes and current views of their functions and the assembly and roles of germ granules among species.
Quantitative Trait Loci Mapping in Five New Large Recombinant Inbred Line Populations of Arabidopsis thaliana Genotyped With Consensus Single-Nucleotide Polymorphism Markers
Authors: Simon Matthieu , Loudet Olivier , Durand Stéphanie , Bérard Aurélie , Brunel Dominique , Sennesal François-Xavier , Durand-Tardif Mylène , Pelletier Georges , Camilleri Christine
Published: April 2008

Quantitative approaches conducted in a single mapping population are limited by the extent of genetic variation distinguishing the parental genotypes. To overcome this limitation and allow a more complete dissection of the genetic architecture of complex traits, we built an integrated set of 15 new large Arabidopsis thaliana recombinant inbred line (RIL) populations optimized for quantitative trait loci (QTL) mapping, having Columbia as a common parent crossed to distant accessions. Here we present 5 of these populations that were validated by investigating three traits: flowering time, rosette size, and seed production as an estimate of fitness. The large number of RILs in each population (between 319 and 377 lines) and the high density of evenly spaced genetic markers scored ensure high power and precision in QTL mapping even under a minimal phenotyping framework. Moreover, the use of common markers across the different maps allows a direct comparison of the QTL detected within the different RIL sets. In addition, we show that following a selective phenotyping strategy by performing QTL analyses on genotypically chosen subsets of 164 RILs (core populations) does not impair the power of detection of QTL with phenotypic contributions >7%.
Rapid Evolution of Yeast Centromeres in the Absence of Drive
Authors: Bensasson Douda , Zarowiecki Magdalena , Burt Austin , Koufopanou Vassiliki
Published: April 2008

To find the most rapidly evolving regions in the yeast genome we compared most of chromosome III from three closely related lineages of the wild yeast Saccharomyces paradoxus. Unexpectedly, the centromere appears to be the fastest-evolving part of the chromosome, evolving even faster than DNA sequences unlikely to be under selective constraint (i.e., synonymous sites after correcting for codon usage bias and remnant transposable elements). Centromeres on other chromosomes also show an elevated rate of nucleotide substitution. Rapid centromere evolution has also been reported for some plants and animals and has been attributed to selection for inclusion in the egg or the ovule at female meiosis. But Saccharomyces yeasts have symmetrical meioses with all four products surviving, thus providing no opportunity for meiotic drive. In addition, yeast centromeres show the high levels of polymorphism expected under a neutral model of molecular evolution. We suggest that yeast centromeres suffer an elevated rate of mutation relative to other chromosomal regions and they change through a process of “centromere drift,” not drive.
Adaptive Plasmid Evolution Results in Host-Range Expansion of a Broad-Host-Range Plasmid
Authors: De Gelder Leen , Williams Julia J , Ponciano José M , Sota Masahiro , Top Eva M
Published: April 2008

Little is known about the range of hosts in which broad-host-range (BHR) plasmids can persist in the absence of selection for plasmid-encoded traits, and whether this “long-term host range” can evolve over time. Previously, the BHR multidrug resistance plasmid pB10 was shown to be highly unstable in Stenotrophomonas maltophilia P21 and Pseudomonas putida H2. To investigate whether this plasmid can adapt to such unfavorable hosts, we performed evolution experiments wherein pB10 was maintained in strain P21, strain H2, and alternatingly in P21 and H2. Plasmids that evolved in P21 and in both hosts showed increased stability and decreased cost in ancestral host P21. However, the latter group showed higher variability in stability patterns, suggesting that regular switching between distinct hosts hampered adaptive plasmid evolution. The plasmids evolved in P21 were also equally or more stable in other hosts compared to pB10, which suggested true host-range expansion. The complete genome sequences of four evolved plasmids with improved stability showed only one or two genetic changes. The stability of plasmids evolved in H2 improved only in their coevolved hosts, not in the ancestral host. Thus a BHR plasmid can adapt to an unfavorable host and thereby expand its long-term host range.
Distinct Functions of MLH3 at Recombination Hot Spots in the Mouse
Authors: Svetlanov Anton , Baudat Frederic , Cohen Paula E , de Massy Bernard
Published: April 2008

The four mammalian MutL homologs (MLH1, MLH3, PMS1, and PMS2) participate in a variety of events, including postreplicative DNA repair, prevention of homeologous recombination, and crossover formation during meiosis. In this latter role, MLH1–MLH3 heterodimers predominate and are essential for prophase I progression. Previous studies demonstrated that mice lacking Mlh1 exhibit a 90% reduction in crossing over at the Psmb9 hot spot while noncrossovers, which do not result in exchange of flanking markers but arise from the same double-strand break event, are unaffected. Using a PCR-based strategy that allows for detailed analysis of crossovers and noncrossovers, we show here that Mlh3−/− exhibit a 85–94% reduction in the number of crossovers at the Psmb9 hot spot. Most of the remaining crossovers in Mlh3−/− meiocytes represent simple exchanges similar to those seen in wild-type mice, with a small fraction (6%) representing complex events that can extend far from the initiation zone. Interestingly, we detect an increase of noncrossovers in Mlh3−/− spermatocytes. These results suggest that MLH3 functions predominantly with MLH1 to promote crossovers, while noncrossover events do not require these activities. Furthermore, these results indicate that ∼10% of crossovers in the mouse are independent of MLH3, suggesting the existence of alternative crossover pathways in mammals.
Key Impact of Vgt1 on Flowering Time Adaptation in Maize: Evidence From Association Mapping and Ecogeographical Information
Authors: Ducrocq Sébastien , Madur Delphine , Veyrieras Jean-Baptiste , Camus-Kulandaivelu Létizia , Kloiber-Maitz Monika , Presterl Thomas , Ouzunova Milena , Manicacci Domenica , Charcosset Alain
Published: April 2008

An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation.
Genetic Expectations of Quantitative Trait Loci Main and Interaction Effects Obtained With the Triple Testcross Design and Their Relevance for the Analysis of Heterosis
Authors: Melchinger A E , Utz H F , Schön C C
Published: April 2008

Interpretation of experimental results from quantitative trait loci (QTL) mapping studies on the predominant type of gene action can be severely affected by the choice of statistical model, experimental design, and provision of epistasis. In this study, we derive quantitative genetic expectations of (i) QTL effects obtained from one-dimensional genome scans with the triple testcross (TTC) design and (ii) pairwise interactions between marker loci using two-way analyses of variance (ANOVA) under the F2- and the F∞-metric model. The theoretical results show that genetic expectations of QTL effects estimated with the TTC design are complex, comprising both main and epistatic effects, and that genetic expectations of two-way marker interactions are not straightforward extensions of effects estimated in one-dimensional scans. We also demonstrate that the TTC design can partially overcome the limitations of the design III in separating QTL main effects and their epistatic interactions in the analysis of heterosis and that dominance × additive epistatic interactions of individual QTL with the genetic background can be estimated with a one-dimensional genome scan. Furthermore, we present genetic expectations of variance components for the analysis of TTC progeny tested in a split-plot design, assuming digenic epistasis and arbitrary linkage.
Exploring Population Genetic Models With Recombination Using Efficient Forward-Time Simulations
Authors: Padhukasahasram Badri , Marjoram Paul , Wall Jeffrey D , Bustamante Carlos D , Nordborg Magnus
Published: April 2008

We present an exact forward-in-time algorithm that can efficiently simulate the evolution of a finite population under the Wright–Fisher model. We used simulations based on this algorithm to verify the accuracy of the ancestral recombination graph approximation by comparing it to the exact Wright–Fisher scenario. We find that the recombination graph is generally a very good approximation for models with complete outcrossing, whereas, for models with self-fertilization, the approximation becomes slightly inexact for some combinations of selfing and recombination parameters.
Genetic Variation Affecting Host–Parasite Interactions: Different Genes Affect Different Aspects of Sigma Virus Replication and Transmission in Drosophila melanogaster
Authors: Bangham Jenny , Kim Kang-Wook , Webster Claire L , Jiggins Francis M
Published: April 2008

In natural populations, genetic variation affects resistance to disease. Knowing how much variation exists, and understanding the genetic architecture of this variation, is important for medicine, for agriculture, and for understanding evolutionary processes. To investigate the extent and nature of genetic variation affecting resistance to pathogens, we are studying a tractable model system: Drosophila melanogaster and its natural pathogen the vertically transmitted sigma virus. We show that considerable genetic variation affects transmission of the virus from parent to offspring. However, maternal and paternal transmission of the virus is affected by different genes. Maternal transmission is a simple Mendelian trait: most of the genetic variation is explained by a polymorphism in ref(2)P, a gene already well known to affect resistance to sigma. In contrast, there is considerable genetic variation in paternal transmission that cannot be explained by ref(2)P and is caused by other loci on chromosome 2. Furthermore, we found no genetic correlation between paternal transmission of the virus and resistance to infection by the sigma virus following injection. This suggests that different loci affect viral replication and paternal transmission.
The Role of Regulatory Genes During Maize Domestication: Evidence From Nucleotide Polymorphism and Gene Expression
Authors: Zhao Qiong , Thuillet Anne-Céline , Uhlmann Nathan K , Weber Allison , Rafalski J Antoni , Allen Stephen M , Tingey Scott , Doebley John
Published: April 2008

We investigated DNA sequence variation in 72 candidate genes in maize landraces and the wild ancestor of maize, teosinte. The candidate genes were chosen because they exhibit very low sequence diversity among maize inbreds and have sequence homology to known regulatory genes. We observed signatures of selection in 17 candidate genes, indicating that they were potential targets of artificial selection during domestication. In addition, 21 candidate genes were identified as potential targets of natural selection in teosinte. A comparison of the proportion of selected genes between our regulatory genes and genes unfiltered for their potential function (but also with very low sequence diversity among maize inbreds) provided some weak evidence that regulatory genes are overrepresented among selected genes. We detected no significant association between the positions of genes identified as potential targets of selection during domestication and quantitative trait loci (QTL) responsible for maize domestication traits. However, a subset of these genes, those identified by sequence homology as kinase/phosphatase genes, significantly cluster with the domestication QTL. We also analyzed expression profiles of genes in distinct maize tissues and observed that domestication genes are expressed on average at a significantly higher level than neutral genes in reproductive organs, including kernels.
The Rad52 Homologs Rad22 and Rti1 ofSchizosaccharomyces pombeAre Not Essential for Meiotic Interhomolog Recombination, but Are Required for Meiotic Intrachromosomal Recombination and Mating-Type-Related DNA Repair
Authors: Octobre Guillaume , Lorenz Alexander , Loidl Josef , Kohli Jürg
Published: April 2008

Proteins of the RAD52 epistasis group play an essential role in repair of some types of DNA damage and genetic recombination. In Schizosaccharomyces pombe, Rad22 (a Rad52 ortholog) has been shown to be as necessary for repair and recombination events during vegetative growth as its Saccharomyces cerevisiae counterpart. This finding contrasts with previous reports where, due to suppressor mutations in the fbh1 gene, rad22 mutants did not display a severe defect. We have analyzed the roles of Rad22 and Rti1, another Rad52 homolog, during meiotic recombination and meiosis in general. Both proteins play an important role in spore viability. During meiotic prophase I, they partially colocalize and partially localize to Rad51 foci and linear elements. Genetic analysis showed that meiotic interchromosomal crossover and conversion events were unexpectedly not much affected by deletion of either or both genes. A strong decrease of intrachromosomal recombination assayed by a gene duplication construct was observed. Therefore, we propose that the most important function of Rad22 and Rti1 in S. pombe meiosis is repair of double-strand breaks with involvement of the sister chromatids. In addition, a novel mating-type-related repair function of Rad22 specific to meiosis and spore germination is described.
Schizosaccharomyces pombe Hsp90/Git10 Is Required for Glucose/cAMP Signaling
Authors: Alaamery Manal A , Hoffman Charles S
Published: April 2008

The fission yeast Schizosaccharomyces pombe senses environmental glucose through a cAMP-signaling pathway. Elevated cAMP levels activate protein kinase A (PKA) to inhibit transcription of genes involved in sexual development and gluconeogenesis, including the fbp1+ gene, which encodes fructose-1,6-bisphosphatase. Glucose-mediated activation of PKA requires the function of nine glucose-insensitive transcription (git) genes, encoding adenylate cyclase, the PKA catalytic subunit, and seven “upstream” proteins required for glucose-triggered adenylate cyclase activation. We describe the cloning and characterization of the git10+ gene, which is identical to swo1+ and encodes the S. pombe Hsp90 chaperone protein. Glucose repression of fbp1+ transcription is impaired by both git10− and swo1− mutant alleles of the hsp90+ gene, as well as by chemical inhibition of Hsp90 activity and temperature stress to wild-type cells. Unlike the swo1− mutant alleles, the git10-201 allele supports cell growth at 37°, while severely reducing glucose repression of an fbp1-lacZ reporter, suggesting a separation-of-function defect. Sequence analyses of three swo1− alleles and the one git10− allele indicate that swo1− mutations alter core functional domains of Hsp90, while the git10− mutation affects the Hsp90 central domain involved in client protein binding. These results suggest that Hsp90 plays a specific role in the S. pombe glucose/cAMP pathway.
RNAi ofmet1Reduces DNA Methylation and Induces Genome-Specific Changes in Gene Expression and Centromeric Small RNA Accumulation in Arabidopsis Allopolyploids
Authors: Chen Meng , Ha Misook , Lackey Erika , Wang Jianlin , Chen Z Jeffrey
Published: April 2008

Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of ∼200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcriptionally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.