bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics of natural populations: Evolutionary forces that establish and maintain gene arrangements in Drosophila pseudoobscura
Authors: Fuller Zachary L. , Haynes Gwilym D. , Richards Stephen , Schaeffer Stephen W. 
Published: October 2017

AbstractThe evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with >10 inversions with appreciable frequencies and wide geographic distributions. This study analyses the genomic sequences of 54 strains of Drosophila pseudoobscura that carry one of six different chromosomal arrangements to test whether (i) genetic drift, (ii) hitchhiking with an adaptive allele, (iii) direct effects of inversions to create gene disruptions caused by breakpoints, or (iv) indirect effects of inversions in limiting the formation of recombinant gametes are responsible for the establishment of new gene arrangements. We found that the inversion events do not disrupt the structure of protein coding genes at the breakpoints. Population genetic analyses of 2,669 protein coding genes identified 277 outlier loci harbouring elevated frequencies of arrangement‐specific derived alleles. Significant linkage disequilibrium occurs among distant loci interspersed between regions with low levels of association indicating that distant allelic combinations are held together despite shared polymorphism among arrangements. Outlier genes showing evidence of genetic differentiation between arrangements are enriched for sensory perception and detoxification genes. The data presented here support the indirect effect of inversion hypothesis where chromosomal inversions are favoured because they maintain linked associations among multilocus allelic combinations among different arrangements.
Genomic differentiation and patterns of gene flow between two long‐tailed tit species (Aegithalos)
Authors: Zhang Dezhi , Song Gang , Gao Bin , Cheng Yalin , Qu Yanhua , Wu Shaoyuan , Shao Shimiao , Wu Yongjie , Alström Per , Lei Fumin 
Published: October 2017

AbstractPatterns of heterogeneous genomic differentiation have been well documented between closely related species, with some highly differentiated genomic regions (“genomic differentiation islands”) spread throughout the genome. Differential levels of gene flow are proposed to account for this pattern, as genomic differentiation islands are suggested to be resistant to gene flow. Recent studies have also suggested that genomic differentiation islands could be explained by linked selection acting on genomic regions with low recombination rates. Here, we investigate genomic differentiation and gene‐flow patterns for autosomes using RAD‐seq data between two closely related species of long‐tailed tits (Aegithalos bonvaloti and A. fuliginosus) in both allopatric and contact zone populations. The results confirm recent or ongoing gene flow between these two species. However, there is little evidence that the genomic regions that were found to be highly differentiated between the contact zone populations are resistant to gene flow, suggesting that differential levels of gene flow is not the cause of the heterogeneous genomic differentiation. Linked selection may be the cause of genomic differentiation islands between the allopatric populations with no or very limited gene flow, but this could not account for the heterogeneous genomic differentiation between the contact zone populations, which show evidence of recent or ongoing gene flow.
Gene expression changes in male accessory glands during ageing are accompanied by reproductive decline in Drosophila melanogaster
Authors: Koppik Mareike , Fricke Claudia 
Published: October 2017

AbstractSenescence is accompanied by loss of reproductive functions. Here, we studied reproductive ageing in Drosophila melanogaster males and asked whether the expected decline in male reproductive success is due to diminished functionality of the male accessory gland (AG). The male AG produces the majority of seminal fluid proteins (SFPs) transferred to the female at mating. SFPs induce female postmating changes and are key to male reproductive success. We measured age‐dependent gene expression changes for five representative SFP genes in males from four different age groups ranging from 1 to 6 weeks after eclosion. Simultaneously, we also measured male reproductive success in postmating traits mediated by transfer of these five SFPs. We found a decreased in male SFP gene expression with advancing age and an accompanying decline in male postmating success. Hence, male reproductive senescence is associated with a decline in functionality of the male AG. While overall individual SFP genes decreased in expression, our results point towards the idea that the composition of an ejaculate might change with male age as the rate of change was variable for those five genes.
Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm
Authors: Blackburn Gwylim S. , Brunet Bryan M. T. , Muirhead Kevin , Cusson Michel , Béliveau Catherine , Levesque Roger C. , Lumley Lisa M. , Sperling Felix A. H. 
Published: October 2017

AbstractPopulations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1,195 single nucleotide polymorphisms, we documented genomewide, locus‐specific patterns of introgression betweenChoristoneura occidentalis biennisspruce budworms and two ecologically divergent relatives,C. o. occidentalisandChoristoneura fumiferana, that it interacts with at alternate boundaries of its range. We observe contrasting hybrid indexes between the two hybrid zones, no overlap in “gene‐flow outliers” (clines showing relatively extreme extents or rates of locus‐specific introgression) and variable linkage disequilibrium among those outliers. At the same time, correlated genomewide rates of introgression between zones suggest the presence of processes common to both boundaries. These findings highlight the contrasting population genetic dynamics that can occur at separate frontiers of a single population, while also suggesting that shared patterns may frequently accompany cases of divergence‐with‐gene‐flow that involve a lineage in common. Our results point to potentially complex evolutionary outcomes for populations experiencing multiple sources of gene flow.
Novel method for identifying individual cetaceans using facial features and symmetry: A test case using dolphins
Authors: Genov Tilen , Centrih Tina , Wright Andrew J. , Wu Gi‐Mick 
Published: October 2017

AbstractIndividual identification plays a major role in our understanding of the biology, ecology and behavior in cetaceans. Being able to tell individuals apart can provide invaluable insight into basic biological and scientific questions, but is also highly relevant to science‐based conservation. Given the importance of individual identification, it appears vital to improve existing identification methods and find new ones. Here, we present a novel identification method of using facial information, with common bottlenose dolphins (Tursiops truncatus) as a case study. In dolphins, dorsal fins are typically used for identification, but not all individuals or species are sufficiently marked. We show that facial features in bottlenose dolphins are long‐term and consistent across the left and right sides, and may enable calves (which tend to have unmarked fins) to be re‐identified after weaning, thus increasing cross‐generational knowledge. This novel method can complement dorsal fin identification by helping document mark changes over time and reduce false negative or positive errors. It also shows that current identification methods can still be improved. With increasing prevalence of digital photography and computer‐aided matching, it may become more viable to use ‘unconventional’ means of identification. We encourage other researchers to explore their photographic records for similar discoveries.
E‐cadherin gene polymorphisms and susceptibility to urolithiasis in Iraqi children
Authors: Shamran Haidar Ahmed , Ali Shaha Hussein , Ali Mayasa Abdulla , Al‐Mayah Qasim Sharhan , Jasim Elham Ahmed 
Published: October 2017

ABSTRACTAimThis case/control study aimed to assess the impact of two single nucleotide polymorphisms (SNPs) in the promoter region of CDH1 gene (‐160C>A and ‐347G>GA) on urinary stone formation in a sample of Iraqi children.MethodsForty‐seven children with urolithiasis and 50 age‐ and gender‐matched healthy controls were included in the study. DNA was isolated from peripheral blood and direct sequencing was used for genotyping.ResultsThe homozygous genotype of the SNP CHD1 ‐160C>A was more frequent in control than cases (18% vs. 6.38%) with significant difference (OR = 0.229, 95%CI = 0.056–0.943, P = 0.041). Furthermore, cases showed significantly less frequency of the mutant allele (allele A) of this SNP (OR = 0.403, 95%C = 0.210–0.776, P = 0.007).ConclusionThese results strongly indicate a protective role of allele A of the SNP CHD1 ‐160C>A against urinary calculi formation in children.
A retrospective comparison of thoracic epidural infusion and multimodal analgesia protocol for pain management following the minimally invasive repair of pectus excavatum
Authors: Man Janice Y. , Gurnaney Harshad G. , Dubow Scott R. , DiMaggio Theresa J. , Kroeplin Gina R. , Adzick N. Scott , Muhly Wallis T. 
Published: October 2017

SummaryBackgroundPain management following minimally invasive repair of pectus excavatum is variable. We recently adopted a comprehensive multimodal analgesic protocol that standardizes perioperative analgesic management. We hypothesized that patients managed with this protocol would use more opioids postoperatively, have similar pain control, and shorter length of stay compared to patients managed with thoracic epidural infusion.AimsWe retrospectively compared opioid consumption, pain scores, and length of stay between a cohort of patients managed with our multimodal analgesic protocol and a cohort managed with a thoracic epidural infusion.MethodsThis retrospective cohort comparison includes patients, 8 to 21 years of age, managed with either thoracic epidural infusion (n = 21) or multimodal analgesic protocol (n = 29) following minimally invasive repair of pectus excavatum from January 1, 2011 through September 15, 2015. The primary outcome, total daily opioid consumption in morphine equivalents, is presented as an average by postoperative day. Secondary outcomes included median daily pain score and length of stay.ResultsPatients were similar in age, weight, sex, and physical status. Patients managed with thoracic epidural infusion received less opioid (morphine equivalents—mg/kg) intraoperatively compared to multimodal analgesic protocol (difference of mean [95% confidence interval] 0.22 [0.16‐0.28] P ≤ .01) but required more total opioid through postoperative day 3 (difference of mean [95% confidence interval] 1.2 [0.26‐2.14] P = .01). We did not observe a difference in pain scores. Median length of stay was 1 day less in patients managed with multimodal analgesic protocol (difference of median [95% confidence interval] 1 [0.3‐1.7] P = .003).ConclusionImplementation of a standardized comprehensive multimodal analgesic protocol following minimally invasive repair of pectus excavatum resulted in equivalent analgesia with a modest reduction in length of stay when compared to thoracic epidural. We did not observe an opioid sparing effect in our thoracic epidural which may reflect technique variability.
Association Between Genetic Polymorphisms and Pain Sensitivity in Patients with Hip Osteoarthritis
Authors: Olesen Anne E. , Nielsen Lecia M. , Feddersen Søren , Erlenwein Joachim , Petzke Frank , Przemeck Michael , Christrup Lona L. , Drewes Asbjørn M. 
Published: October 2017

AbstractBackgroundFactors such as age, gender, and genetic polymorphisms may explain individual differences in pain phenotype. Genetic associations with pain sensitivity have previously been investigated in osteoarthritis patients, with a focus on the P2X7, TRPV1, and TACR1 genes. However, other genes may play a role as well. Osteoarthritis is a common joint disease, and many patients suffering from this disease are thought to have increased sensitivity to noxious stimuli resulting from sensitization in the nociceptive system. The aim of this study was to investigate if genetic variants of mu, kappa, and delta opioid receptor genes (OPRM1, OPRK1, and OPRD1) and the catechol‐O‐methyltransferase gene (COMT) influenced the pain phenotype in patients with osteoarthritis.MethodsThe frequencies of 17 polymorphisms were examined. Pain sensitivity was assessed preoperatively by (1) hip rotation, (2) contact heat stimulation, (3) conditioned pain modulation effect, and (4) pressure stimulation at the tibia in both the affected and the unaffected leg.ResultsNinety‐two patients (mean age 66 years) with unilateral hip osteoarthritis were included in the study. Carriage of the OPRM1 rs589046T allele was found to be associated with increased pain ratings during hip rotation (P = 0.04) and increased conditioned pain modulation (P = 0.049). Carriage of the OPRD1 rs2234918C allele was found to be associated with an increased pain detection threshold to contact heat stimulation (P = 0.001). No other associations were found (all P > 0.05).ConclusionResults from the present study suggest that, in patients with hip osteoarthritis, genetic variants in OPRM1 and OPRD1 may contribute to the pain phenotype.
The transcriptome, extracellular proteome and active secretome of agroinfiltrated Nicotiana benthamiana uncover a large, diverse protease repertoire
Authors: Grosse‐Holz Friederike , Kelly Steven , Blaskowski Svenja , Kaschani Farnusch , Kaiser Markus , van der Hoorn Renier A.L. 
Published: October 2017

SummaryInfiltration of disarmed Agrobacterium tumefaciens into leaves of Nicotiana benthamiana (agroinfiltration) facilitates quick and safe production of antibodies, vaccines, enzymes and metabolites for industrial use (molecular farming). However, yield and purity of proteins produced by agroinfiltration are hampered by unintended proteolysis, restricting industrial viability of the agroinfiltration platform. Proteolysis may be linked to an immune response to agroinfiltration, but understanding of the response to agroinfiltration is limited. To identify the proteases, we studied the transcriptome, extracellular proteome and active secretome of agroinfiltrated leaves over a time course, with and without the P19 silencing inhibitor. Remarkably, the P19 expression had little effect on the leaf transcriptome and no effect on the extracellular proteome. 25% of the detected transcripts changed in abundance upon agroinfiltration, associated with a gradual up‐regulation of immunity at the expense of photosynthesis. By contrast, 70% of the extracellular proteins increased in abundance, in many cases associated with increased efficiency of extracellular delivery. We detect a dynamic reprogramming of the proteolytic machinery upon agroinfiltration by detecting transcripts encoding for 975 different proteases and protease homologs. The extracellular proteome contains peptides derived from 196 proteases and protease homologs, and activity‐based proteomics displayed 17 active extracellular Ser and Cys proteases in agroinfiltrated leaves. We discuss unique features of the N. benthamiana protease repertoire and highlight abundant extracellular proteases in agroinfiltrated leaves, being targets for reverse genetics. This data set increases our understanding of the plant response to agroinfiltration and indicates ways to improve a key expression platform for both plant science and molecular farming.
Genetic‐based dissection of arsenic accumulation in maize using a genome‐wide association analysis method
Authors: Zhao Zhan , Zhang Huaisheng , Fu Zhongjun , Chen Hao , Lin Yanan , Yan Pengshuai , Li Weihua , Xie Huiling , Guo Zhanyong , Zhang Xuehai , Tang Jihua 
Published: October 2017

SummaryUnderstanding the mechanism of arsenic (As) accumulation in plants is important in reducing As's toxicity to plants and its potential risks to human health. Here, we performed a genome‐wide association study to dissect the genetic basis of the As contents of different maize tissues in Xixian, which was irrigated with As‐rich surface water, and Changge using an association population consisting of 230 representative maize inbred lines. Phenotypic data revealed a wide normal distribution and high repeatability for the As contents in maize tissues. The As concentrations in maize tissues followed the same trend in the two locations: kernels < axes < stems < bracts < leaves. In total, 15, 16 and 15 non‐redundant quantitative trait loci (QTLs) associated with As concentrations were identified (P ≤ 2.04 × 10−6) in five tissues from Xixian, Changge, and the combination of the locations, respectively, explaining 9.70%–24.65% of the phenotypic variation for each QTL, on average. Additionally, four QTLs [involving 15 single nucleotide polymorphisms (SNPs)] were detected in the single and the combined locations, indicating that these loci/SNPs might be stable across different environments. The candidate genes associated with these four loci were predicted. In addition, four non‐redundant QTLs (6 SNPs), including a QTL that was detected in multiple locations according to the genome‐wide association study, were found to co‐localize with four previously reported QTL intervals. These results are valuable to understand the genetic architecture of As mechanism in maize and facilitate the genetic improvement of varieties without As toxicity.
PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine
Authors: Pascual María Belén , Llebrés María‐Teresa , Craven‐Bartle Blanca , Cañas Rafael A. , Cánovas Francisco M. , Ávila Concepción 
Published: October 2017

SummaryThe transcriptional regulation of phenylalanine metabolism is particularly important in conifers, long‐lived species that use large amounts of carbon in wood. Here, we show that the Pinus pinaster transcription factor, PpNAC1, is a main regulator of phenylalanine biosynthesis and utilization. A phylogenetic analysis classified PpNAC1 in the NST proteins group and was selected for functional characterization. PpNAC1 is predominantly expressed in the secondary xylem and compression wood of adult trees. Silencing of PpNAC1 in P. pinaster results in the alteration of stem vascular radial patterning and the down‐regulation of several genes associated with cell wall biogenesis and secondary metabolism. Furthermore, transactivation and EMSA analyses showed that PpNAC1 is able to activate its own expression and PpMyb4 promoter, while PpMyb4 is able to activate PpMyb8, a transcriptional regulator of phenylalanine and lignin biosynthesis in maritime pine. Together, these results suggest that PpNAC1 is a functional ortholog of the ArabidopsisSND1 and NST1 genes and support the idea that key regulators governing secondary cell wall formation could be conserved between gymnosperms and angiosperms. Understanding the molecular switches controlling wood formation is of paramount importance for fundamental tree biology and paves the way for applications in conifer biotechnology.
Evaluation of organic amendments from agro‐industry waste for the control of verticillium wilt of olive
Authors: Varo‐Suárez A. , Raya‐Ortega M.C. , Agustí‐Brisach C. , García‐Ortiz‐Civantos C. , Fernández‐Hernández A. , Mulero‐Aparicio A. , Trapero A. 
Published: October 2017

Biological control of plant diseases using soil amendments such as animal manure and composted materials can minimize organic waste and has been proposed as an effective strategy in crop protection. In this study, 35 organic amendments (OAs) and 16 compost mixtures were evaluated against Verticillium dahliae by assessing both the antagonistic effect on the mycelial growth of two representative isolates of V. dahliae and the effect on the reduction of microsclerotia viability of the pathogen in naturally infested soil. Eleven OAs and five compost mixtures showed a consistent inhibition effect in in vitro sensitivity tests, with solid olive‐oil waste compost one of the most effective. Therefore, a bioassay with olive plants was conducted to evaluate the suppressive effect against V. dahliae of these selected OAs and compost mixtures. Significant reduction in the severity of the symptoms of V. dahliae indicates the potential use of grape marc compost (100% disease severity reduction) and solid olive‐oil waste, combined with other OAs. Microorganism mixtures and dairy waste OAs had a potential suppressive effect when they were combined with compost, showing a 73% and 63% disease severity reduction, respectively. A mixture of agro‐industrial waste with other biological control agents is a promising strategy against verticillium wilt of olive. To the authors' knowledge, this is the first report on the effectiveness of compost extracts (compost teas) on the inhibition of natural microsclerotia of V. dahliae, and also on verticillium wilt suppression in olive with solid olive‐oil waste.
Sensitivity Analysis of Fluid Pre-Swirl and Swirl Brakes Design on the Performance of Labyrinth Seals
Authors: Jin Hanxiang , Untaroiu Alexandrina , Fu Gen , Hayrapetian Vahe , Elebiary Kariem 
Published: October 2017

In non-contact annular labyrinth seals used in turbomachinery, the fluid pre-rotation in the direction of shaft rotation effectively increases the fluid velocity in the circumferential direction and could generate destabilizing fluid forces exerting on the rotor. Swirl brakes are typically employed to reduce the fluid pre-rotation at the inlet of the seal. The inlet flow separates as it follows the swirl brakes, and the ratio between the tangential component of the velocity in the seal and the velocity of the rotor surface varies consequently. Effective swirl brakes can significantly suppress the destabilizing fluid forces as it is effectively reduces the tangential velocity. In literature, it was shown that leakage rate can also be reduced by using swirl brakes with “negative-swirl”.
In this study, a labyrinth seal with inlet swirl brakes is selected as the baseline design and seal performance is evaluated using ANSYS-CFX. The design of experiments (DOE) approach is used to investigate the effects of various design variables on the seal performance. The design space consists of swirl brake’s length, width, curvature at the ends, the tilt angle, as well as the number of swirl brakes in the circumferential direction. Simple random DOE sampling method with Euclidean distances for the design matrix is used to generate the design points. The steady-state CFD simulations are then performed for each design point to analyze the performance of the swirl brakes. The quadratic polynomial fitting is used to evaluate the sensitivity of the average circumferential velocity with respect to the design variables, which gives a qualitative estimation for the performance of the swirl brakes. The results provide a better understanding of which design variables are critical and more effective in reduction of the destabilizing forces acting on the rotor, and thus will support the swirl brake design for annular pressure seals.