bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terminal protein-primed amplification of heterologous DNA with a minimal replication system based on phage Φ29
Authors: Mencía Mario , Gella Pablo , Camacho Ana , de Vega Miguel , Salas Margarita 
Published: November 2011

The DNA amplification performed by terminal protein-primed replication systems has not yet been developed for its general use to produce high amounts of DNA linked to terminal protein (TP). Here we present a method to amplify in vitro heterologous DNAs using the Φ29 DNA replication machinery and producing DNA with TP covalently attached to the 5′ end. The amplification requires four Φ29 proteins, DNA polymerase, TP, single-stranded DNA binding protein and double-stranded DNA binding protein (p6). The DNA to be amplified is inserted between two sequences that are the Φ29 DNA replication origins, consisting of 191 and 194 bp from the left and right ends of the phage genome, respectively. The replication origins do not need to have TP covalently attached beforehand to be functional in amplification and they can be joined to the DNA to be amplified by cloning or ligation. The facts that two functional origins were required at the ends of a linear template DNA and that the kinetics of DNA synthesis was very similar to that obtained using the TP-containing Φ29 genome as template support the proposal that genuine amplification is taking place. Amplification factors of 30-fold have been obtained. Possible applications of DNAs produced by this method are discussed.
The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis
Authors: Causier Barry , Ashworth Mary , Guo Wenjia , Davies Brendan 
Published: November 2011

AbstractTranscription factors activate or repress target gene expression or switch between activation and repression. In animals and yeast, Groucho/Tup1 corepressor proteins are recruited by diverse transcription factors to induce context-specific transcriptional repression. Two groups of Groucho/Tup1-like corepressors have been described in plants. LEUNIG and LEUNIG_HOMOLOG constitute one group and TOPLESS (TPL) and the four TPL-related (TPR) corepressors form the other. To discover the processes in which TPL and the TPR corepressors operate, high-throughput yeast two-hybrid approaches were used to identify interacting proteins. We found that TPL/TPR corepressors predominantly interact directly with specific transcription factors, many of which were previously implicated in transcriptional repression. The interacting transcription factors reveal that the TPL/TPR family has been coopted multiple times to modulate gene expression in diverse processes, including hormone signaling, stress responses, and the control of flowering time, for which we also show biological validation. The interaction data suggest novel mechanisms for the involvement of TPL/TPR corepressors in auxin and jasmonic acid signaling. A number of short repression domain (RD) sequences have previously been identified in Arabidopsis (Arabidopsis thaliana) transcription factors. All known RD sequences were enriched among the TPL/TPR interactors, and novel TPL-RD interactions were identified. We show that the presence of RD sequences is essential for TPL/TPR recruitment. These data provide a framework for TPL/TPR-dependent transcriptional repression. They allow for predictions about new repressive transcription factors, corepressor interactions, and repression mechanisms and identify a wide range of plant processes that utilize TPL/TPR-mediated gene repression.
Gravistimulation Changes the Accumulation Pattern of the CsPIN1 Auxin Efflux Facilitator in the Endodermis of the Transition Zone in Cucumber Seedlings
Authors: Watanabe Chiaki , Fujii Nobuharu , Yanai Kenichi , Hotta Takuya , Kim Dai-Hee , Kamada Motoshi , Sasagawa-Saito Yuko , Nishimura Takeshi , Koshiba Tomokazu , Miyazawa Yutaka , Kim Kyung-Min , Takahashi Hideyuki 
Published: November 2011

Abstract
Cucumber (Cucumis sativus) seedlings grown in a horizontal position develop a specialized protuberance (or peg) on the lower side of the transition zone between the hypocotyl and the root. This occurs by suppressing peg formation on the upper side via a decrease in auxin resulting from a gravitational response. However, the gravity-stimulated mechanism of inducing asymmetric auxin distribution in the transition zone is poorly understood. The gravity-sensing tissue responsible for regulating auxin distribution in the transition zone is thought to be the endodermal cell. To characterize the gravity-stimulated mechanism, the auxin efflux facilitator PIN-FORMED1 (CsPIN1) in the endodermis was identified and the localization of CsPIN1 proteins during the gravimorphogenesis of cucumber seedlings was examined. Immunohistochemical analysis revealed that the accumulation pattern of CsPIN1 protein in the endodermal cells of the transition zone of cucumber seedlings grown horizontally differed from that of plants grown vertically. Gravistimulation for 30 min prompted changes in the accumulation pattern of CsPIN1 protein in the endodermis as well as the asymmetric distribution of auxin in the transition zone. Furthermore, 2,3,5-triiodobenzoic acid inhibited the differential distribution of auxin as well as changes in the accumulation pattern of CsPIN1 in the endodermis of the transition zone during gravistimulation. These results suggest that the altered pattern of CsPIN1 accumulation in the endodermis in response to gravistimulation influences lateral auxin transport through the endodermis, resulting in asymmetric auxin distribution in the transition zone.
Genetic diversity and population structure of five Ethiopian chicken ecotypes
Authors: Goraga Z. , Weigend S. , Brockmann G. 
Published: November 2011

SummaryThis study aimed to analyse the genetic diversity and population structure of five Ethiopian chicken ecotypes (N = 155), which were compared with six commercial purebreds (N = 180). For the analysis of genetic diversity, 26 AVIANDIV microsatellite markers were used. The number of alleles in Ethiopian ecotypes ranged from 2 to 19 per locus, with a mean of 6.1. The average observed heterozygosity within ecotype varied between 0.53 and 0.57. The overall heterozygote deficiency (FIT) in Ethiopian ecotypes was 0.124 ± 0.037. Over 68% of FIT was because of within‐ecotype deficiency (FIS). In the phylogenetic tree, Ethiopian ecotypes clustered into two groups. The analysis of the relationship between populations using the structure program provided further evidence for the occurrence of at least two subgroups in the Ethiopian ecotypes. Findings of this study may provide the background for future studies to identify the origin of the two gene pools representing the Ethiopian chicken ecotypes and to characterize the gene variants influencing economically important traits.
Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations
Authors: Gärke C. , Ytournel F. , Bed’hom B. , Gut I. , Lathrop M. , Weigend S. , Simianer H. 
Published: November 2011

SummaryMany studies in human genetics compare informativeness of single‐nucleotide polymorphisms (SNPs) and microsatellites (single sequence repeats; SSR) in genome scans, but it is difficult to transfer the results directly to livestock because of different population structures. The aim of this study was to determine the number of SNPs needed to obtain the same differentiation power as with a given standard set of microsatellites. Eight chicken breeds were genotyped for 29 SSRs and 9216 SNPs. After filtering, only 2931 SNPs remained. The differentiation power was evaluated using two methods: partitioning of the Euclidean distance matrix based on a principal component analysis (PCA) and a Bayesian model‐based clustering approach. Generally, with PCA‐based partitioning, 70 SNPs provide a comparable resolution to 29 SSRs. In model‐based clustering, the similarity coefficient showed significantly higher values between repeated runs for SNPs compared to SSRs. For the membership coefficients, reflecting the proportion to which a fraction segment of the genome belongs to the ith cluster, the highest values were obtained for 29 SSRs and 100 SNPs respectively. With a low number of loci (29 SSRs or ≤100 SNPs), neither marker types could detect the admixture in the Gödöllö Nhx population. Using more than 250 SNPs allowed a more detailed insight into the genetic architecture. Thus, the admixed population could be detected. It is concluded that breed differentiation studies will substantially gain power even with moderate numbers of SNPs.
Identification and characterization of C106R, a novel mutation in the DNA‐binding domain of GCMB, in a family with autosomal‐dominant hypoparathyroidism
Authors: Yi Hyon‐Seung , Eom Young Sil , Park Ie Byung , Lee Sangho , Hong Suntaek , Jüppner Harald , Mannstadt Michael , Lee Sihoon 
Published: November 2011

SummaryOverview  Glial cells missing B (GCMB) is a transcription factor that is expressed in the parathyroid hormone (PTH)‐secreting cells of the parathyroid glands. Several mutations in GCMB have been reported to cause hypoparathyroidism (HP). We identified a family with two individuals in two generations (mother and son), who are affected by autosomal‐dominant hypoparathyroidism (AD‐HP). A novel heterozygous mutation in exon 2 of GCMB was identified in both affected individuals that changes cysteine at position 106 of the putative DNA‐binding domain of GCMB to arginine (C106R).Methods  We performed mutational analysis of the genes encoding GCMB, pre‐pro PTH, GATA3 and CaSR using polymerase chain reaction (PCR)‐amplified genomic DNA. The identified GCMB mutant was characterized by functional studies including nuclear localization, electrophoretic mobility shift assays (EMSA) and luciferase reporter assays, and homology modelling was performed to generate a three‐dimensional structural model for the DNA‐binding domain of GCMB to predict the structural consequences of the identified mutation.Results  The C106R mutant of GCMB failed to interact with the DNA consensus recognition motif, as determined by EMSA. Furthermore, in comparison with wild‐type GCMB, the C106R mutant demonstrated reduced transactivation in luciferase reporter assays; however, the mutant GCMB failed to reduce the activity of the wild‐type protein. Consistent with the EMSA findings, homology modelling analysis suggested that replacement of cysteine 106 with arginine would interfere with DNA binding.Conclusions  We have identified a novel GCMB mutation that may explain AD‐HP in our family. However, the exact mechanism by which this heterozygous mutation leads to the disease in the described family remains to be elucidated.
Predicting the onset of Addison’s disease: ACTH, renin, cortisol and 21‐hydroxylase autoantibodies
Authors: Baker Peter R. , Nanduri Priyaanka , Gottlieb Peter A. , Yu Liping , Klingensmith Georgeanna J. , Eisenbarth George S. , Barker Jennifer M. 
Published: November 2011

SummaryContext  Autoantibodies to 21‐hydroxylase (21OH‐AA) precede onset of autoimmune Addison’s disease (AD). Progression to AD can take months to years, and early detection of metabolic decompensation may prevent morbidity and mortality.Objective  To define optimal methods of predicting progression to overt AD (defined by subnormal peak cortisol response to Cosyntropin) in 21OH‐AA+ individuals.Design, Setting and Participants  Individuals were screened for 21OH‐AA at the Barbara Davis Center from 1993 to 2011. Subjects positive for 21OH‐AA (n = 87) were tested, and the majority prospectively followed for the development of Addison’s disease, including seven diagnosed with AD upon 21OH‐AA discovery (discovered), seven who progressed to AD (progressors) and 73 nonprogressors.Main Outcome Measured  Plasma renin activity (PRA), ACTH, baseline cortisol, peak cortisol and 21OH‐AA were measured at various time points relative to diagnosis of AD or last AD‐free follow‐up.Results  Compared with nonprogressors, in the time period 2 months–2 years prior to the onset of AD, progressors were significantly more likely to have elevated ACTH (11–22 pm, P < 1E‐4), with no significant differences in mean PRA (P = 0·07) or baseline cortisol (P = 0·08), and significant but less distinct differences seen with 21OH‐AA levels (P < 1E‐4) and poststimulation cortisol levels (P = 6E‐3).Conclusion  Moderately elevated ACTH is a more useful early indicator of impending AD than 21OH‐AA, PRA or peak cortisol, in the 2 months–2 years preceding the onset of AD.
Intensity of pituitary adenoma on T2‐weighted magnetic resonance imaging predicts the response to octreotide treatment in newly diagnosed acromegaly
Authors: Heck Ansgar , Ringstad Geir , Fougner Stine L. , Casar‐Borota Olivera , Nome Terje , Ramm‐Pettersen Jon , Bollerslev Jens 
Published: November 2011

SummaryBackground  Primary, preoperative medical treatment is an option in selected patients with acromegaly, but a subset of patients respond poorly. Valid prediction of response to somatostatin analogues (SA) might thus alter treatment stratification. The aims of this study were to assess whether T2 signal intensity could determine long‐term response to first‐line SA treatment and to assess clinical and biochemical baseline characteristics, as well as histological subtype in relation to the magnetic resonance imaging (MRI) appearances.Methods  In 45 newly diagnosed patients, T2‐weighted signal intensity of the tumour was classified into hypo‐, iso‐ or hyperintense. Biochemical and clinical baseline variables for the three groups were compared. In 25 patients primarily treated with long‐acting SA for a median of 6 months [interquartile range (IQR):155–180 days], GH and IGF‐1 reduction was assessed, and in 34 cases, immunohistochemical granulation pattern was evaluated.Results  The results showed that 12 (27%) adenomas were hypointense, 15 (33%) isointense and 18 (40%) hyperintense. Median IGF‐1 [ratio IGF‐1/ULN; (upper limit of normal)] was 3·5 (2·3–4·9), 2·9 (2·6–3·8) and 1·9 (1·3–2·6), respectively (P = 0·006 for difference between groups). Median GH values (μg/l) of a 3‐ to 5‐point profile were 17·5 (6·1–35), 9·3 (6·0–32·5) and 4·1 (1·5–8·3), (P = 0·025).Median IGF‐1 reduction (% of baseline) after first‐line SA treatment was 51 (49–70), 36 (19–74) and 13 (5–42) (P = 0·03); median reduction in GH (% of baseline) was 86 (72–94), 78 (62–85) and 46 (1–70) (P = 0·02).T2 hyperintensity was associated with sparse granulation pattern on immunohistochemistry.Conclusion  In patients with acromegaly, T2 signal intensity at diagnosis correlates with histological features and predicts biochemical outcome of first‐line SA treatment.
Forecasting climate change impacts to plant community composition in the Sonoran Desert region
Authors: Munson Seth M. , Webb Robert H. , Belnap Jayne , Andrew Hubbard J. , Swann Don E. , Rutman Sue 
Published: November 2011

AbstractHotter and drier conditions projected for the southwestern United States can have a large impact on the abundance and composition of long‐lived desert plant species. We used long‐term vegetation monitoring results from 39 large plots across four protected sites in the Sonoran Desert region to determine how plant species have responded to past climate variability. This cross‐site analysis identified the plant species and functional types susceptible to climate change, the magnitude of their responses, and potential climate thresholds. In the relatively mesic mesquite savanna communities, perennial grasses declined with a decrease in annual precipitation, cacti increased, and there was a reversal of the Prosopis velutina expansion experienced in the 20th century in response to increasing mean annual temperature (MAT). In the more xeric Arizona Upland communities, the dominant leguminous tree, Cercidium microphyllum, declined on hillslopes, and the shrub Fouquieria splendens decreased, especially on south‐ and west‐facing slopes in response to increasing MAT. In the most xeric shrublands, the codominant species Larrea tridentata and its hemiparasite Krameria grayi decreased with a decrease in cool season precipitation and increased aridity, respectively. This regional‐scale assessment of plant species response to recent climate variability is critical for forecasting future shifts in plant community composition, structure, and productivity.
Effects of food ration on SMR: influence of food consumption on individual variation in metabolic rate in juvenile coho salmon (Onchorhynchus kisutch)
Authors: Van Leeuwen Travis E. , Rosenfeld Jordan S. , Richards Jeffrey G. 
Published: November 2011

Summary1. Consistency of differences in standard metabolic rate (SMR) between individual juvenile salmonids and the apparently limited ability of individuals to regulate their SMR has led many researchers to conclude that differences in individual SMR are fixed (i.e. genetic).2. To test for the effects of food ration on individual performance and metabolism, SMR was estimated by measuring oxygen consumption using flow‐through respirometry on individually separated young of the year coho salmon (Oncorhynchus kisutch) placed on varying food rations over a period of 44 days.3. Results demonstrate that the quantity of food consumed directly affects SMR of juvenile coho salmon, independent of specific dynamic action (SDA, an elevation in metabolic rate from the increased energy demands associated with digestion immediately following a meal) and indicates that higher food consumption is a cause of elevated SMR rather than a consequence of it. Juvenile coho salmon therefore demonstrated an ability to regulate their SMR according to food availability and ultimately food consumption.4. This study indicates that food consumption may play a pivotal role in understanding individual variation in SMR independent of inherent genetic differences. We suggest that studies involving SMR need to be cautious about the effects of intra‐individual differences in food consumption in communal tanks or in different microhabitats in the wild as disproportionate food consumption may contribute more to variation in SMR than intrinsic (genetic) factors.5. In general, our results suggest that evolutionary changes in SMR are likely a response to selection on food consumption and growth, rather than SMR itself.
Full compliance with harvest regulations yields ecological benefits: Northern Gulf of California case study
Authors: Ainsworth Cameron H. , Morzaria‐Luna Hem Nalini , Kaplan Isaac C. , Levin Phillip S. , Fulton Elizabeth A. 
Published: November 2011

Summary1. The Northern Gulf of California is an ecologically important marine area with a high degree of biodiversity, endemism and productivity. Mounting conservation concerns have prompted researchers to propose new management regulations, restricting fishing and protecting sensitive species. Compliance with existing regulations is poor. Rules that are currently in place, if followed, may go a long way towards achieving the ecological goals of management.2. We conduct a review of existing fisheries regulations in this area. Then, using a spatially explicit marine ecosystem model (Atlantis), we estimate the benefits of compliance with existing fisheries regulations.3. Under a full compliance scenario, we find large increases in protected species biomass within 25 years and a slowed rate of ecosystem degradation because of fishing. However, full compliance costs the fishing industry about 30% of its annual revenue.4. We parse out the benefits offered by management instruments (including spatial management protections, seasonal fishery closures, gear restrictions, cessation of illegal fishing and vessel buy‐out programmes) and conclude that a suite of measures is needed to address major conservation objectives.5. Synthesis and applications. This exercise quantifies the benefits of improved fisheries enforcement and provides a benchmark by which the value of future regulatory amendments can be assessed. Where compliance with existing regulations is poor, conservation goals may be better served by strengthening enforcement than by enacting new rules and legislation.
Restoration of the fire–grazing interaction in Artemisia filifolia shrubland
Authors: Winter Stephen L. , Fuhlendorf Samuel D. , Goad Carla L. , Davis Craig A. , Hickman Karen R. , Leslie Jr David M. 
Published: November 2011

Summary1. Patterns of landscape heterogeneity are crucial to the maintenance of biodiversity in shrublands and grasslands, yet management practices in these ecosystems typically seek to homogenize landscapes. Furthermore, there is limited understanding of how the interaction of ecological processes, such as fire and grazing, affects patterns of heterogeneity at different spatial scales.2. We conducted research in Artemisia filifolia (Asteraceae) shrublands located in the southern Great Plains of North America to determine the effect of restoring the fire–grazing interaction on vegetation structure. Data were collected for 3 years in replicated pastures grazed by cattle Bos taurus where the fire–grazing interaction had been restored (fire and grazing = treatment pastures) and in pastures that were grazed but remained unburned (grazing only, no fire = control pastures). The effect of the fire–grazing interaction on heterogeneity (variance) of vegetation structure was assessed at scales from 12·5 m2 to 609 ha.3. Most measurements of vegetation structure within treatment pastures differed from control pastures for 1–3 years after being burned but were thereafter similar to the values found in unburned control pastures.4. Treatment pastures were characterized by a lower amount of total heterogeneity and a lower amount of heterogeneity through time.5. Heterogeneity of vegetation structure tended to decrease as the scale of measurement increased in both treatment and control pastures. There was deviation from this trend, however, in the treatment pastures that exhibited much higher heterogeneity at the patch scale (mean patch size = 202 ha) of measurement, the scale at which patch fires were conducted.6.
Synthesis and applications. Vegetation structure in A. filifolia shrublands of our study was readily altered by the fire–grazing interaction but also demonstrated substantial resilience to these effects. The fire–grazing interaction also changed the total amount of heterogeneity characterizing this system, the scale at which heterogeneity in this system was expressed and the amount of heterogeneity expressed through time. Land managers seeking to impose a shifting mosaic of heterogeneity on this vegetation type can do so by restoring the fire–grazing interaction with potential conservation benefits similar to what has been achieved in other ecosystems where historic cycles of disturbance and rest have been restored.