bluuebunny/crossref_metadata_2025_split huggingface dataset:
TRICHOME BIREFRINGENCEand Its HomologAT5G01360Encode Plant-Specific DUF231 Proteins Required for Cellulose Biosynthesis in Arabidopsis
Authors: Bischoff Volker , Nita Silvia , Neumetzler Lutz , Schindelasch Dana , Urbain Aurélie , Eshed Ravit , Persson Staffan , Delmer Deborah , Scheible Wolf-Rüdiger 
Published: April 2010

AbstractThe Arabidopsis (Arabidopsis thaliana) trichome birefringence (tbr) mutant has severely reduced crystalline cellulose in trichomes, but the molecular nature of TBR was unknown. We determined TBR to belong to the plant-specific DUF231 domain gene family comprising 46 members of unknown function in Arabidopsis. The genes harbor another plant-specific domain, called the TBL domain, which contains a conserved GDSL motif known from some esterases/lipases. TBR and TBR-like3 (TBL3) are transcriptionally coordinated with primary and secondary CELLULOSE SYNTHASE (CESA) genes, respectively. The tbr and tbl3 mutants hold lower levels of crystalline cellulose and have altered pectin composition in trichomes and stems, respectively, tissues generally thought to contain mainly secondary wall crystalline cellulose. In contrast, primary wall cellulose levels remain unchanged in both mutants as measured in etiolated tbr and tbl3 hypocotyls, while the amount of esterified pectins is reduced and pectin methylesterase activity is increased in this tissue. Furthermore, etiolated tbr hypocotyls have reduced length with swollen epidermal cells, a phenotype characteristic for primary cesa mutants or the wild type treated with cellulose synthesis inhibitors. Taken together, we show that two TBL genes contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers.
A Pollen-Specific RALF from Tomato That Regulates Pollen Tube Elongation
Authors: Covey Paul A. , Subbaiah Chalivendra C. , Parsons Ronald L. , Pearce Gregory , Lay Fung T. , Anderson Marilyn A. , Ryan Clarence A. , Bedinger Patricia A. 
Published: April 2010

AbstractRapid Alkalinization Factors (RALFs) are plant peptides that rapidly increase the pH of plant suspension cell culture medium and inhibit root growth. A pollen-specific tomato (Solanum lycopersicum) RALF (SlPRALF) has been identified. The SlPRALF gene encodes a preproprotein that appears to be processed and released from the pollen tube as an active peptide. A synthetic SlPRALF peptide based on the putative active peptide did not affect pollen hydration or viability but inhibited the elongation of normal pollen tubes in an in vitro growth system. Inhibitory effects of SlPRALF were detectable at concentrations as low as 10 nm, and complete inhibition was observed at 1 μ m peptide. At least 10-fold higher levels of alkSlPRALF, which lacks disulfide bonds, were required to see similar effects. A greater effect of peptide was observed in low-pH-buffered medium. Inhibition of pollen tube elongation was reversible if peptide was removed within 15 min of exposure. Addition of 100 nm SlPRALF to actively growing pollen tubes inhibited further elongation until tubes were 40 to 60 μm in length, after which pollen tubes became resistant to the peptide. The onset of resistance correlated with the timing of the exit of the male germ unit from the pollen grain into the tube. Thus, exogenous SlPRALF acts as a negative regulator of pollen tube elongation within a specific developmental window.
Virus-Based MicroRNA Expression for Gene Functional Analysis in Plants
Authors: Tang Yang , Wang Fei , Zhao Jinping , Xie Ke , Hong Yiguo , Liu Yule 
Published: April 2010

AbstractTraditional virus-induced gene silencing (VIGS) is a powerful virus-based short interfering RNA-mediated RNA silencing technique for plant functional genomics. Besides short interfering RNAs, microRNAs (miRNAs) have also been shown to regulate gene expression by RNA silencing in various organisms. However, plant virus-based miRNA silencing has not been reported. In addition, a number of plant miRNAs have been identified or predicted, while their functions are largely unknown. Thus, there is an urgent need for the development of new technologies to study miRNA function. Here, we report that a modified cabbage leaf-curl geminivirus vector can be used to express artificial and endogenous miRNAs in plants. Using this viral miRNA expression system, we demonstrate that VIGS using artificial miRNAs, dubbed as “MIR VIGS,” was effective to silence the expression of endogenous genes, including PDS, Su, CLA1, and SGT1, in Nicotiana benthamiana. Silencing of SGT1 led to the loss of N-mediated resistance to Tobacco mosaic virus. Furthermore, using this viral miRNA expression system, we found that viral ectopic expression of endogenous miR156 and miR165 but not their mutants in N. benthamiana resulted in earlier abnormal developmental phenotypes, and expression of miR165 induced abnormal chlorotic spots on leaves. These results demonstrate that the cabbage leaf-curl geminivirus-based miRNA expression system can be utilized not only to specifically silence genes involved in general metabolism and defense but also to investigate the function of endogenous miRNAs in plants.
Parentage testing of racing camels (Camelus dromedarius) using microsatellite DNA typing
Authors: Spencer P. B. S. , Wilson K. J. , Tinson A. 
Published: April 2010

SummaryThe camel racing industry would have added value in being able to assign parentage with high certainty. This study was aimed at assessing and applying microsatellite multiplexes to construct a parentage testing system for camels. An efficient system of 17 loci from 700 camel samples was used to construct a database of unrelated adults. Based on this, we estimated measures of polymorphism among the markers. In three multiplex reactions, we detected a total of 224 alleles, with 5–23 alleles/locus (mean = 13.18 ± 6.95 SD) and an average heterozygosity (HE) of 0.54 (range 0.032–0.905). The total parentage exclusion probability was 0.99999 for excluding a candidate parent from parentage of an arbitrary offspring, given only the genotype of the offspring, and 0.9999 for excluding a candidate parent from parentage of an arbitrary offspring, given the genotype of the offspring and the other parent. We used 15 juveniles for parentage testing, as well as 17 sires (bull camels) and 21 dams (cows). In the case of parentage assignment, the microsatellite panel assigned all 15 offspring parentage with high confidence. Overall, these findings offer a set of microsatellite markers that are easy, simple and highly informative for parentage testing in camels.
Genetic mapping of quantitative trait loci for milk production in sheep
Authors: Mateescu R. G. , Thonney M. L. 
Published: April 2010

SummaryA backcross pedigree using dairy East Friesian rams and non‐dairy Dorset ewes was established specifically to map quantitative trait loci (QTL) affecting milk production in sheep. Ninety nine microsatellite markers of an initial set of 120 were successfully genotyped and informative on 188 animals of this backcross pedigree. Test‐day milk records on individual ewes were used to estimate several milk yield related traits, including peak milk yield and cumulative milk yield to 50 (MY50), 100 (MY100) and 250 days (MY250). These traits, as well as estimated breeding value of backcross ewes extracted from the genetic evaluation file of the entire flock, were used in interval mapping. Ovine chromosomes 2, 12, 18, 20 and 24 were identified to harbour putative QTL for different measures of milk production. The QTL on Ovis aries chromosomes (OAR) 2 and 20 mapped to locations where similar trait QTL have already been mapped in other studies, whereas QTL on OAR 12, 18 and 24 were unique to our backcross pedigree and have not been reported previously. In addition, all identified QTL regions were syntenic with bovine chromosomal segments revealed to harbour QTL affecting milk production traits, providing supporting evidence for the QTL identified here.
A genome‐wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle
Authors: Huang W. , Kirkpatrick B. W. , Rosa G. J. M. , Khatib H. 
Published: April 2010

SummaryThe decline in the reproductive efficiency of dairy cows, especially those with high producing potential, has become a challenging problem. In this study, a selective DNA pooling approach was applied to a cow population whose oocytes were fertilized and cultured to obtain phenotypic records of fertilization rate and blastocyst rate. Using a stringent 5% genome‐wide significance level, 22 and five single nucleotide polymorphisms (SNPs) were found to be associated with fertilization rate and blastocyst rate, respectively. SNPs that showed significant association in selective DNA pooling were further evaluated by individual genotyping. Interestingly, the majority of the SNP associations were confirmed by individual genotyping, testifying to the effectiveness of selective DNA pooling using a high‐density SNP genotyping array. This study is the first application of the selective DNA pooling approach using the BovineSNP50 array in cattle.
Effect of a major QTL affecting IPN resistance on production traits in Atlantic salmon
Authors: Gheyas A. A. , Haley C. S. , Guy D. R. , Hamilton A. , Tinch A. E. , Mota‐Velasco J. C. , Woolliams J. A. 
Published: April 2010

SummaryThis study investigated the effect of a major QTL for resistance to IPN in salmon on performance and production traits. The traits studied were related to growth, fillet and gutted yields, and fat content. Two different analyses were performed: (1) regression of the phenotypic data of the production traits on the predicted number of resistant IPN‐QTL alleles in individuals and (2) a variance component analysis using the (co)variance matrix calculated at the putative location of the QTL. No significant effect of the QTL was detected on any of the traits investigated by either method. The result has important practical implications in that it encourages the use of MAS to reduce the risks and impact of IPN mortality.
A haplotype ofCYP2C9associated with warfarin sensitivity in mechanical heart valve replacement patients
Authors: Lee Su‐Jun , Jang Yin Jin , Cha Eun‐Young , Kim Ho‐Sook , Lee Sang Seop , Shin Jae‐Gook 
Published: April 2010

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT• CYP2C9single nucleotide polymorphisms (SNPs) are important in safe and effective oral anticoagulation with warfarin use.• AlthoughCYP2C9*2and*3are important genetic factors for the warfarin dose, one of theCYP2C9SNPs, IVS‐65G>C, has been suggested to be associated with warfarin sensitivity. However, as of yet, there has been no explanation about the possible mechanism and linkage analysis.WHAT THIS PAPER ADDS• New information onCYP2C9SNPs and their occurrences in common haplotype structures in healthy unrelated Koreans and in individuals who require low warfarin dose after mechanical heart valve replacements (MHVRs) were studied.• Additional evidence showed that an Asian dominant haplotype consisting of ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G and IVS5‐73A>G could be associated with a low warfarin maintenance dose in mechanical heart valve replacement (MHVR) patients.AIMSThe objectives of this study were to determine the distribution ofCYP2C9variants in Koreans and investigate their association with warfarin dose requirements in patients who received MHVRs.METHODSAll nine exons, intron–exon junction, and promoter region ofCYP2C9were amplified and directly sequenced in 50 healthy normal Koreans. Additional direct DNA sequencing of theCYP2C9gene was conducted in 36 of the 267 MHVR patients who required low maintenance warfarin doses without carryingCYP2C9*3andVKORC1 1173Tmutations. The effects ofCYP2C9genetics on warfarin maintenance dose were assessed in 267 MHVR patients.RESULTSThirty‐nine single nucleotide polymorphisms (SNPs) including seven previously unidentified SNPs were identified in 50 Koreans by direct DNA sequencing. One of theCYP2C9haplotypes exhibited an association with warfarin low dose requirement. The adjusted odds ratio for the haplotype between the low dose group and the normal subjects was 2.5 (95% confidence interval 1.05, 6.16). This haplotype consisting of ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G, and IVS5‐73A>G was found in 15% of 36 MHVR patients who required low warfarin doses, while 4% of 50 normal healthy subjects exhibited this haplotype. One of the SNPs comprising this haplotype, ‐1565C>T, apparently changed a protein binding pattern as observed in electrophoretic mobility shift assay.CONCLUSIONThe haplotype including ‐1565C>T, ‐1188T>C, IVS3+197G>A, IVS3‐334C>T, IVS3‐65G>C, IVS4‐115A>G, and IVS5‐73A>G seems to be associated with low warfarin dose requirement and this haplotype could be considered in the development of a warfarin dose prediction model for Asian populations.
In vitro ovine articular chondrocyte proliferation: experiments and modelling
Authors: Mancuso L. , Liuzzo M. I. , Fadda S. , Pisu M. , Cincotti A. , Arras M. , La Nasa G. , Concas A. , Cao G. 
Published: April 2010

AbstractThis study focuses on analysis of in vitro cultures of chondrocytes from ovine articular cartilage. Isolated cells were seeded in Petri dishes, then expanded to confluence and phenotypically characterized by flow cytometry. The sigmoidal temporal profile of total counts was obtained by classic haemocytometry and corresponding cell size distributions were measured electronically using a Coulter Counter. A mathematical model recently proposed (1) was adopted for quantitative interpretation of these experimental data. The model is based on a 1‐D (that is, mass‐structured), single‐staged population balance approach capable of taking into account contact inhibition at confluence. The model’s parameters were determined by fitting measured total cell counts and size distributions. Model reliability was verified by predicting cell proliferation counts and corresponding size distributions at culture times longer than those used when tuning the model’s parameters. It was found that adoption of cell mass as the intrinsic characteristic of a growing chondrocyte population enables sigmoidal temporal profiles of total counts in the Petri dish, as well as cell size distributions at ‘balanced growth’, to be adequately predicted.
Terrestrial carbon stocks across a gradient of urbanization: a study of the Seattle, WA region
Authors: HUTYRA LUCY R. , YOON BYUNGMAN , ALBERTI MARINA 
Published: April 2010

AbstractMost of our global population and its CO2emissions can be attributed to urban areas. The process of urbanization changes terrestrial carbon stocks and fluxes, which, in turn, impact ecosystem functions and atmospheric CO2concentrations. Using the Seattle, WA, region as a case study, this paper explores the relationships between aboveground carbon stocks and land cover within an urbanizing area. The major objectives were to estimate aboveground live and dead terrestrial carbon stocks across multiple land cover classes and quantify the relationships between urban cover and vegetation across a gradient of urbanization. We established 154 sample plots in the Seattle region to assess carbon stocks as a function of distance from the urban core and land cover [urban (heavy, medium, and low), mixed forest, and conifer forest land covers]. The mean (and 95% CI) aboveground live biomass for the region was 89±22 Mg C ha−1with an additional 11.8±4 Mg C ha−1of coarse woody debris biomass. The average live biomass stored within forested and urban land covers was 140±40 and 18±14 Mg C ha−1, respectively, with a 57% mean vegetated canopy cover regionally. Both the total carbon stocks and mean vegetated canopy cover were surprisingly high, even within the heavily urbanized areas, well exceeding observations within other urbanizing areas and the average US forested carbon stocks. As urban land covers and populations continue to rapidly increase across the globe, these results highlight the importance of considering vegetation in urbanizing areas within the terrestrial carbon cycle.
Does relative time of emergence affect stand composition and yield in a grass–legume mixture? Kura clover (Trifolium ambiguum)–meadow bromegrass (Bromus biebersteinii) and Kura clover–orchardgrass (Dactylis glomerata) mixtures
Authors: Walker J. A. , King J. R. 
Published: April 2010

AbstractEstablishing Kura clover (Trifolium ambiguum) in mixtures with grass species is challenging, because slow growth of clover seedlings results in low competitive ability. This study examined establishment success by altering time of seeding of the grass component to reduce competition with Kura clover seedlings. Two trials, one of Kura clover–meadow bromegrass (Bromus biebersteinii) and the other Kura clover–orchardgrass (Dactylis glomerata) mixtures were planted in Edmonton, Alberta. Grasses were seeded at the same time as the clover, or introduced when the clover reached one true leaf or three true leaves, in the autumn of the planting year or the following spring. Species composition varied significantly between treatments. When sown at the same time, Kura clover contributed 31 and 14% of yield in the establishment year when sown with meadow bromegrass and orchard grass, respectively. Delaying grass sowing until Kura clover had one or three leaves gave a higher percentage of Kura clover compared with planting at the same time. Autumn and spring grass sowing resulted in stands of 78 and 80% clover with meadow bromegrass, and 74 and 67% clover with orchardgrass. Altering the competitive advantage of the grass species to produce a more balanced mixture was successfully achieved by delaying seeding of the grass relative to Kura clover. A long interval before introducing the grass (autumn or following spring), was not successful as established Kura clover seedlings have an increased competitive ability.
Identification and characterization of Alix/AIP1 interacting proteins from the black tiger shrimp,Penaeus monodon
Authors: Sangsuriya P , Rojtinnakorn J , Senapin S , Flegel T W 
Published: April 2010

AbstractApoptosis is proposed to be a major cause of death in shrimp viral infections. From our previous study, an apoptosis‐related gene,Pm‐Alix, was identified from the black tiger shrimp. Its expression was high in defence‐related tissues including haemocytes and the lymphoid organ. To clarify its possible role in shrimp, we usedPm‐Alixas bait in a yeast two‐hybrid analysis to search for Alix interacting proteins in shrimp. Two cDNA sequences discovered had homology to a predicted ubiquitin C of the purple sea urchin,Strongylocentrotus purpuratus,and to a guanylyl cyclase of the red swamp crayfish,Procambarus clarkii.In vitropull‐down assays confirmed positive interaction between Pm‐Alix and both proteins. Tissue distribution analysis revealed thatPm‐Alixand the two binding partners were widely expressed in various tissues but more highly expressed in haemocytes. However, no significant positive or negative correlation was found in the expression of these genes as shrimp approached morbidity and death after challenge with white spot syndrome virus. Thus, the results suggested that Alix and its interacting partners did not play a direct role related to shrimp death.
MtsR is a dual regulator that controls virulence genes and metabolic functions in addition to metal homeostasis in the group A streptococcus
Authors: Toukoki Chadia , Gold Kathryn M. , McIver Kevin S. , Eichenbaum Zehava 
Published: April 2010

SummaryMtsR is a metal‐dependent regulator in the group A streptococcus (GAS) that directly represses the transcription of genes involved in haem and metal uptake. While MtsR has been implicated in GAS virulence, the DNA recognition and full regulatory scope exerted by the protein are unknown. In this study we identified the shr promoter (Pshr) and mapped MtsR binding to a 69 bp segment in Pshr that overlaps the core promoter elements. A global transcriptional analysis demonstrated that MtsR modulates the expression of 64 genes in GAS, 44 of which were upregulated and 20 were downregulated in the mtsR mutant. MtsR controls genes with diverse functions including metal homeostasis, nucleic acid and amino acid metabolism, and protein fate. Importantly, the MtsR regulon includes mga, emm49 and ska, which are central for GAS pathogenesis. MtsR binding to the promoter region of both negatively and positively regulated genes demonstrates that it functions as a dual regulator. MtsR footprints are large (47–130 bp) and vary between target promoters. A 16 bp motif that consists of an interrupted palindrome is implicated in the DNA recognition by the metalloregulator. In conclusion, we report here that MtsR is a global regulator in GAS that shapes the expression of vital virulence factors and genes involved in metabolic functions and metal transport, and we discuss the implications for the GAS disease process.
Farnesol misplaces tip‐localized Rho proteins and inhibits cell wall integrity signalling in Aspergillus fumigatus
Authors: Dichtl Karl , Ebel Frank , Dirr Franziska , Routier Françoise H. , Heesemann Jürgen , Wagener Johannes 
Published: April 2010

SummaryFarnesol is known for inducing apoptosis in some fungi and mammalian cells. To evaluate its potential role as an antifungal agent, we studied its impact on the human pathogen Aspergillus fumigatus. We found that growth of A. fumigatus wild type is inhibited, but two cell wall mutants, Δmnt1 andΔglfA, are much more susceptible to farnesol. This susceptibility is partially rescued by osmotic stabilization, suggesting that farnesol is a cell wall perturbing agent. However, farnesol does not activate but inhibit the cell wall integrity (CWI) pathway. Remarkably, mutants lacking AfMkk2 or AfMpkA, two kinases essential for CWI signalling, are also highly susceptible to farnesol, suggesting that its mode of action goes beyond inhibition of CWI signalling. Farnesyl derivatives are known for interfering with the function of prenylated proteins. We analysed the subcellular localization of two prenylated Rho family GTPases, AfRho1 and AfRho3, which are implicated in controlling CWI and the cytoskeleton. We found that under normal growth conditions AfRho1 and AfRho3 predominantly localize to the hyphal tip. After farnesol treatment this localization is rapidly lost, which is accompanied by swelling of the hyphal tips. Parallel displacement of tropomyosin from the tips suggests a concomitant disorganization of the apical actin cytoskeleton.
Translocation of Borrelia burgdorferi surface lipoprotein OspA through the outer membrane requires an unfolded conformation and can initiate at the C‐terminus
Authors: Schulze Ryan J. , Chen Shiyong , Kumru Ozan S. , Zückert Wolfram R. 
Published: April 2010

Summary Borrelia burgdorferi surface lipoproteins are essential to the pathogenesis of Lyme borreliosis, but the mechanisms responsible for their localization are only beginning to emerge. We have previously demonstrated the critical nature of the amino‐terminal ‘tether’ domain of the mature lipoprotein for sorting a fluorescent reporter to the Borrelia cell surface. Here, we show that individual deletion of four contiguous residues within the tether of major surface lipoprotein OspA results in its inefficient translocation across the Borrelia outer membrane. Intriguingly, C‐terminal epitope tags of these N‐terminal deletion mutants were selectively surface‐exposed. Fold‐destabilizing C‐terminal point mutations and deletions did not block OspA secretion, but rather restored one of the otherwise periplasmic tether mutants to the bacterial surface. Together, these data indicate that disturbance of a confined tether feature leads to premature folding of OspA in the periplasm and thereby prevents secretion through the outer membrane. Furthermore, they suggest that OspA emerges tail‐first on the bacterial surface, yet independent of a specific C‐terminal targeting peptide sequence.