The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Science.gov (United States)

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Sudden shrinkage of free rectus abdominis musculocutaneous flap 15 years after maxilla reconstruction

Directory of Open Access Journals (Sweden)

Yasushi Mochizuki

2018-03-01

Full Text Available A 60-year-old male displayed sudden shrinkage of a left free rectus abdominis musculocutaneous flap, which had been grafted to his left maxilla 15 years previously. No post-reconstructive irradiation had been performed, and no late occlusion of the vascular anastomosis, local infection, recurrence of the maxillary cancer, or body weight loss was observed. However, the shrinkage amounted to approximately 50%. This is considerably more than previously reported cases of shrinkage of various free flaps, which ranged between 10% and 25%. The resultant depression was successfully augmented with a right free deep inferior epigastric artery perforator flap. The residual fat volume of the previously grafted shrunken flap was revealed to be compatible with that of the newly harvested contralateral perforator flap. Thus, the volume of the previously grafted flap may reflect the status of the intact contralateral donor site, although the mechanism of sudden flap shrinkage is unclear.

Volumetric polymerization shrinkage of contemporary composite resins

Directory of Open Access Journals (Sweden)

Halim Nagem Filho

2007-10-01

Full Text Available The polymerization shrinkage of composite resins may affect negatively the clinical outcome of the restoration. Extensive research has been carried out to develop new formulations of composite resins in order to provide good handling characteristics and some dimensional stability during polymerization. The purpose of this study was to analyze, in vitro, the magnitude of the volumetric polymerization shrinkage of 7 contemporary composite resins (Definite, Suprafill, SureFil, Filtek Z250, Fill Magic, Alert, and Solitaire to determine whether there are differences among these materials. The tests were conducted with precision of 0.1 mg. The volumetric shrinkage was measured by hydrostatic weighing before and after polymerization and calculated by known mathematical equations. One-way ANOVA (a or = 0.05 was used to determine statistically significant differences in volumetric shrinkage among the tested composite resins. Suprafill (1.87±0.01 and Definite (1.89±0.01 shrank significantly less than the other composite resins. SureFil (2.01±0.06, Filtek Z250 (1.99±0.03, and Fill Magic (2.02±0.02 presented intermediate levels of polymerization shrinkage. Alert and Solitaire presented the highest degree of polymerization shrinkage. Knowing the polymerization shrinkage rates of the commercially available composite resins, the dentist would be able to choose between using composite resins with lower polymerization shrinkage rates or adopting technical or operational procedures to minimize the adverse effects deriving from resin contraction during light-activation.

Silorane- and high filled-based"low-shrinkage" resin composites: shrinkage, flexural strength and modulus

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Cesar Augusto Galvão Arrais

2013-04-01

Full Text Available This study compared the volumetric shrinkage (VS, flexural strength (FS and flexural modulus (FM properties of the low-shrinkage resin composite Aelite LS (Bisco to those of Filtek LS (3M ESPE and two regular dimethacrylate-based resin composites, the microfilled Heliomolar (Ivoclar Vivadent and the microhybrid Aelite Universal (Bisco. The composites (n = 5 were placed on the Teflon pedestal of a video-imaging device, and VS was recorded every minute for 5 min after 40 s of light exposure. For the FS and FM tests, resin discs (0.6 mm in thickness and 6.0 mm in diameter were obtained (n = 12 and submitted to a piston-ring biaxial test in a universal testing machine. VS, FS, and FM data were submitted to two-way repeated measures and one-way ANOVA, respectively, followed by Tukey's post-hoc test (a = 5%. Filtek LS showed lower VS than did Aelite LS, which in turn showed lower shrinkage than did the other composites. Aelite Universal and Filtek LS exhibited higher FS than did Heliomolar and Aelite LS, both of which exhibited the highest FM. No significant difference in FM was noted between Filtek LS and Aelite Universal, while Heliomolar exhibited the lowest values. Aelite LS was not as effective as Filtek LS regarding shrinkage, although both low-shrinkage composites showed lower VS than did the other composites. Only Filtek LS exhibited FS and FM comparable to those of the regular microhybrid dimethacrylate-based resin composite.

GENERALIZED DOUBLE PARETO SHRINKAGE.

Science.gov (United States)

Armagan, Artin; Dunson, David B; Lee, Jaeyong

2013-01-01

We propose a generalized double Pareto prior for Bayesian shrinkage estimation and inferences in linear models. The prior can be obtained via a scale mixture of Laplace or normal distributions, forming a bridge between the Laplace and Normal-Jeffreys' priors. While it has a spike at zero like the Laplace density, it also has a Student's t -like tail behavior. Bayesian computation is straightforward via a simple Gibbs sampling algorithm. We investigate the properties of the maximum a posteriori estimator, as sparse estimation plays an important role in many problems, reveal connections with some well-established regularization procedures, and show some asymptotic results. The performance of the prior is tested through simulations and an application.

Genes but not genomes reveal bacterial domestication of Lactococcus lactis.

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Delphine Passerini

Full Text Available BACKGROUND: The population structure and diversity of Lactococcus lactis subsp. lactis, a major industrial bacterium involved in milk fermentation, was determined at both gene and genome level. Seventy-six lactococcal isolates of various origins were studied by different genotyping methods and thirty-six strains displaying unique macrorestriction fingerprints were analyzed by a new multilocus sequence typing (MLST scheme. This gene-based analysis was compared to genomic characteristics determined by pulsed-field gel electrophoresis (PFGE. METHODOLOGY/PRINCIPAL FINDINGS: The MLST analysis revealed that L. lactis subsp. lactis is essentially clonal with infrequent intra- and intergenic recombination; also, despite its taxonomical classification as a subspecies, it displays a genetic diversity as substantial as that within several other bacterial species. Genome-based analysis revealed a genome size variability of 20%, a value typical of bacteria inhabiting different ecological niches, and that suggests a large pan-genome for this subspecies. However, the genomic characteristics (macrorestriction pattern, genome or chromosome size, plasmid content did not correlate to the MLST-based phylogeny, with strains from the same sequence type (ST differing by up to 230 kb in genome size. CONCLUSION/SIGNIFICANCE: The gene-based phylogeny was not fully consistent with the traditional classification into dairy and non-dairy strains but supported a new classification based on ecological separation between "environmental" strains, the main contributors to the genetic diversity within the subspecies, and "domesticated" strains, subject to recent genetic bottlenecks. Comparison between gene- and genome-based analyses revealed little relationship between core and dispensable genome phylogenies, indicating that clonal diversification and phenotypic variability of the "domesticated" strains essentially arose through substantial genomic flux within the dispensable

Distinct spontaneous shrinkage of a sporadic vestibular schwannoma

DEFF Research Database (Denmark)

Huang, Xiaowen; Cayé-Thomasen, Per; Stangerup, Sven-Eric

2013-01-01

on "shrinkage" or "negative growth" or "regression" or "involution" of the tumor were selected, and the contents on the rate, extent and mechanism of spontaneous tumor shrinkage were extracted and reviewed. The reported rate of spontaneous shrinkage of vestibular schwannoma is 5-10% of patients managed......We present a case with outspoken spontaneous vestibular schwannoma shrinkage and review the related literature. The patient was initially diagnosed with a left-sided, intrameatal vestibular schwannoma, which subsequently grew into the cerebello-pontine angle (CPA), followed by total shrinkage...... of the CPA component without any intervention over a 12-year observation period. The literature on spontaneous tumor shrinkage was retrieved by searching the subject terms "vestibular schwannoma, conservative management" in PubMed/MEDLINE database, without a time limit. Of the published data, the articles...

Water storage change estimation from in situ shrinkage measurements of clay soils

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B. te Brake

2013-05-01

Full Text Available The objective of this study is to assess the applicability of clay soil elevation change measurements to estimate soil water storage changes, using a simplified approach. We measured moisture contents in aggregates by EC-5 sensors, and in multiple aggregate and inter-aggregate spaces (bulk soil by CS616 sensors. In a long dry period, the assumption of constant isotropic shrinkage proved invalid and a soil moisture dependant geometry factor was applied. The relative overestimation made by assuming constant isotropic shrinkage in the linear (basic shrinkage phase was 26.4% (17.5 mm for the actively shrinking layer between 0 and 60 cm. Aggregate-scale water storage and volume change revealed a linear relation for layers ≥ 30 cm depth. The range of basic shrinkage in the bulk soil was limited by delayed drying of deep soil layers, and maximum water loss in the structural shrinkage phase was 40% of total water loss in the 0–60 cm layer, and over 60% in deeper layers. In the dry period, fitted slopes of the ΔV–ΔW relationship ranged from 0.41 to 0.56 (EC-5 and 0.42 to 0.55 (CS616. Under a dynamic drying and wetting regime, slopes ranged from 0.21 to 0.38 (EC-5 and 0.22 to 0.36 (CS616. Alternating shrinkage and incomplete swelling resulted in limited volume change relative to water storage change. The slope of the ΔV–ΔW relationship depended on the drying regime, measurement scale and combined effect of different soil layers. Therefore, solely relying on surface level elevation changes to infer soil water storage changes will lead to large underestimations. Recent and future developments might provide a basis for application of shrinkage relations to field situations, but in situ observations will be required to do so.

Dynamics of tissue shrinkage during ablative temperature exposures

International Nuclear Information System (INIS)

Rossmann, Christian; Haemmerich, Dieter; Garrett-Mayer, Elizabeth; Rattay, Frank

2014-01-01

There is a lack of studies that examine the dynamics of heat-induced shrinkage of organ tissues. Clinical procedures such as radiofrequency ablation, microwave ablation or high-intensity focused ultrasound, use heat to treat diseases such as cancer and cardiac arrhythmia. When heat is applied to tissues, shrinkage occurs due to protein denaturation, dehydration and contraction of collagen at temperatures greater 50 °C. This is particularly relevant for image-guided procedures such as tumor ablation, where pre- and post-treatment images are compared and any changes in dimensions must be considered to avoid misinterpretations of the treatment outcome. We present data from ex vivo, isothermal shrinkage tests in porcine liver tissue, where axial changes in tissue length were recorded during 15 min of heating to temperatures between 60 and 95 °C. A mathematical model was developed to accurately describe the time and temperature-dependent shrinkage behavior. The shrinkage dynamics had the same characteristics independent of temperature; the estimated relative shrinkage, adjusted for time since death, after 15 min heating to temperatures of 60, 65, 75, 85 and 95 °C, was 12.3, 13.8, 16.6, 19.2 and 21.7%, respectively. Our results demonstrate the shrinkage dynamics of organ tissues, and suggest the importance of considering tissue shrinkage for thermal ablative treatments. (paper)

The shrinkage of hardening cement paste and mortar

NARCIS (Netherlands)

Haas, de G.D.; Kreijger, P.C.; Niël, E.M.M.G.; Slagter, J.C.; Stein, H.N.; Theissing, E.M.; Wallendael, van M.

1975-01-01

This paper is an abstract from the report of the commission B10: "The influence of the shrinkage of cement on the shrink-age of concrete", of the Netherlands Committee for Concrete Research. Measurements of pulse velocity, volume shrinkage and heat of hydration on hardening portland cement support

Durability and Shrinkage Characteristics of Self-Compacting Concretes Containing Recycled Coarse and/or Fine Aggregates

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Mehmet Gesoglu

2015-01-01

Full Text Available This paper addresses durability and shrinkage performance of the self-compacting concretes (SCCs in which natural coarse aggregate (NCA and/or natural fine aggregate (NFA were replaced by recycled coarse aggregate (RCA and/or recycled fine aggregate (RFA, respectively. A total of 16 SCCs were produced and classified into four series, each of which included four mixes designed with two water to binder (w/b ratios of 0.3 and 0.43 and two silica fume replacement levels of 0 and 10%. Durability properties of SCCs were tested for rapid chloride penetration, water sorptivity, gas permeability, and water permeability at 56 days. Also, drying shrinkage accompanied by the water loss and restrained shrinkage of SCCs were monitored over 56 days of drying period. Test results revealed that incorporating recycled coarse and/or fine aggregates aggravated the durability properties of SCCs tested in this study. The drying shrinkage and restrained shrinkage cracking of recycled aggregate (RA concretes had significantly poorer performance than natural aggregate (NA concretes. The time of cracking greatly prolonged as the RAs were used along with the increase in water/binder ratio.

Thermal Shrinkage for Shoulder Instability

OpenAIRE

Toth, Alison P.; Warren, Russell F.; Petrigliano, Frank A.; Doward, David A.; Cordasco, Frank A.; Altchek, David W.; O’Brien, Stephen J.

2010-01-01

Thermal capsular shrinkage was popular for the treatment of shoulder instability, despite a paucity of outcomes data in the literature defining the indications for this procedure or supporting its long-term efficacy. The purpose of this study was to perform a clinical evaluation of radiofrequency thermal capsular shrinkage for the treatment of shoulder instability, with a minimum 2-year follow-up. From 1999 to 2001, 101 consecutive patients with mild to moderate shoulder instability underwent...

Shrinkage Degree in $L_{2}$ -Rescale Boosting for Regression.

Science.gov (United States)

Xu, Lin; Lin, Shaobo; Wang, Yao; Xu, Zongben

2017-08-01

L 2 -rescale boosting ( L 2 -RBoosting) is a variant of L 2 -Boosting, which can essentially improve the generalization performance of L 2 -Boosting. The key feature of L 2 -RBoosting lies in introducing a shrinkage degree to rescale the ensemble estimate in each iteration. Thus, the shrinkage degree determines the performance of L 2 -RBoosting. The aim of this paper is to develop a concrete analysis concerning how to determine the shrinkage degree in L 2 -RBoosting. We propose two feasible ways to select the shrinkage degree. The first one is to parameterize the shrinkage degree and the other one is to develop a data-driven approach. After rigorously analyzing the importance of the shrinkage degree in L 2 -RBoosting, we compare the pros and cons of the proposed methods. We find that although these approaches can reach the same learning rates, the structure of the final estimator of the parameterized approach is better, which sometimes yields a better generalization capability when the number of sample is finite. With this, we recommend to parameterize the shrinkage degree of L 2 -RBoosting. We also present an adaptive parameter-selection strategy for shrinkage degree and verify its feasibility through both theoretical analysis and numerical verification. The obtained results enhance the understanding of L 2 -RBoosting and give guidance on how to use it for regression tasks.

The influence of shrinkage reducing admixtures on plastic shrinkage

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Mora, J.

2003-12-01

Full Text Available Shrinkage reducing admixtures (SRAs are viable alternatives for reducing plastic shrinkage cracking in concrete. The objective of the present paper is to study early age plastic shrinkage in restrained concrete elements, where three different SRAs have been used. The influence of the admixture is analyzed through the following measurements: capillary pressure, evaporation, temperature evolution, crack evolution and settlement. The tests for studying the cracking and deformation were made on two different configurations (i.e., restrained prisms with reduced cross-section and restrained panel, in a wind tunnel, with controlled wind temperature and velocity. The conclusions obtained indicate the viability of the use of this type of admixture and the usefulness of the test methods.

Los aditivos reductores de retracción (SRAs se plantean, hoy en día, como una alternativa viable para reducir la fisuración por retracción plástica. El objetivo del presente artículo es conocer mejor y predecir el comportamiento a primeras edades de la retracción plástica en elementos estructurales coaccionados, a los que se les ha añadido diversos aditivos reductores de retracción (tres tipos diferentes. Esta influencia se analiza a través de las siguientes propiedades: presión capilar, evaporación, evolución de temperaturas, evolución de fisuración, y deformaciones verticales de asentamiento. Los ensayos para estudiar la fisuración y las deformaciones se han realizado sobre diferentes configuraciones (prisma restringido con estrangulamiento y panel restringido, en un túnel de viento, con temperaturas y velocidades de viento controladas. Las conclusiones obtenidas señalan la viabilidad del empleo de este tipo de aditivos y la bondad de los métodos experimentales utilizados.

Assessment of concrete creep and shrinkage

International Nuclear Information System (INIS)

Trivedi, Neha; Singh, R.K.

2012-01-01

B-3 model prediction of concrete creep and shrinkage strains on cylindrical specimen and BARC Containment test model (BARCOM) are presented. Experimental shrinkage strain is shown to be in agreement with B-3 model predictions for cylindrical specimen and BARCOM. Creep strain in cylindrical specimen is found to be in agreement with B-3 model. In BARCOM for wall cast in different pores, creep strain is in agreement with B-3 model in hoop direction however in longitudinal direction, observed creep strain in higher than B-3 model. For dome structure cast in a single pour, experimental creep strain shows confirmity with B-3 model both in hoop and longitudinal directions. The study on concrete aging and average longitudinal shrinkage strain is carried out. (author)

Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

DEFF Research Database (Denmark)

Kaas, Christian Schrøder; Kristensen, Claus; Betenbaugh, Michael J.

2015-01-01

Background: The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins.  Results: Here we present the genomic sequence...... of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC -> AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing...... in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find similar to 2...

PLASTIC SHRINKAGE CONTROLLING EFFECT BY POLYPROPYLENE SHORT FIBER WITH HYDROPHILY

Science.gov (United States)

Hosoda, Akira; Sadatsuki, Yoshitomo; Oshima, Akihiro; Ishii, Akina; Tsubaki, Tatsuya

The aim of this research is to clarify the mechanism of controlling plastic shrinkage crack by adding small amout of synthetic short fiber, and to propose optimum polypropylene short fiber to control plastic shrinkage crack. In this research, the effect of the hydrophily of polypropylene fiber was investigated in the amount of plastic shrinkage of mortar, total area of plastic shrinkage crack, and bond properties between fiber and mortar. The plastic shrinkage test of morar was conducted under high temperature, low relative humidity, and constant wind velocity. When polypropylene fiber had hydrophily, the amount of plastic shrinkage of mortar was restrained, which was because cement paste in morar was captured by hydrophilic fiber and then bleeding of mortar was restrained. With hydrophily, plastic shrinkage of mortar was restrained and bridging effect was improved due to better bond, which led to remarkable reduction of plastic shrinkage crack. Based on experimental results, the way of developing optimum polypropylene short fiber for actual construction was proposed. The fiber should have large hydrophily and small diameter, and should be used in as small amount as possible in order not to disturb workability of concrete.

Photo-crosslinkable cyanoacrylate bioadhesive: shrinkage kinetics, dynamic mechanical properties, and biocompatibility of adhesives containing TMPTMA and POSS nanostructures as crosslinking agents.

Science.gov (United States)

Ghasaban, S; Atai, M; Imani, M; Zandi, M; Shokrgozar, M-A

2011-11-01

The study investigates the photo-polymerization shrinkage behavior, dynamic mechanical properties, and biocompatibility of cyanoacrylate bioadhesives containing POSS nanostructures and TMPTMA as crosslinking agents. Adhesives containing 2-octyl cyanoacrylate (2-OCA) and different percentages of POSS nanostructures and TMPTMA as crosslinking agents were prepared. The 1-phenyl-1, 2-propanedione (PPD) was incorporated as photo-initiator into the adhesive in 1.5, 3, and 4 wt %. The shrinkage strain of the specimens was measured using bonded-disk technique. Shrinkage strain, shrinkage strain rate, maximum and time at maximum shrinkage strain rate were measured and compared. Mechanical properties of the adhesives were also studied using dynamic mechanical thermal analysis (DMTA). Biocompatibility of the adhesives was examined by MTT method. The results showed that shrinkage strain increased with increasing the initiator concentration up to 3 wt % in POSS-containing and 1.5 wt % in TMPTMA-containing specimens and plateaued out at higher concentrations. By increasing the crosslinking agent, shrinkage strain, and shrinkage strain rate increased and the time at maximum shrinkage strain rate decreased. The study indicates that the incorporation of crosslinking agents into the cyanoacrylate adhesives resulted in improved mechanical properties. Preliminary MTT studies also revealed better biocompatibility profile for the adhesives containing crosslinking agents comparing to the neat specimens. Copyright © 2011 Wiley Periodicals, Inc.

Drying Shrinkage Microcracking in Cement-based Materials

NARCIS (Netherlands)

Bisschop, J.; Van Mier, J.G.M.

2002-01-01

In this paper the nature of drying shrinkage microcracking in a variety of model cementbased materials, as well as in more practical types of concrete is described. The model mixtures were studied to elucidate the mechanisms of drying shrinkage microcracking and the factors that influence these

Evaluation of shrinkage polymerization and temperature of different acrylic resins used to splinting transfer copings in indirect impression technique

Science.gov (United States)

Franco, Ana Paula G. O.; Karam, Leandro Z.; Galvão, José R.; Kalinowski, Hypolito J.

2015-09-01

The aim of the present study was evaluate the shrinkage polymerization and temperature of different acrylic resins used to splinting transfer copings in indirect impression technique. Two implants were placed in an artificial bone, with the two transfer copings joined with dental floss and acrylic resins; two dental resins are used. Measurements of deformation and temperature were performed with Fiber Braggs grating sensor for 17 minutes. The results revealed that one type of resin shows greater values of polymerization shrinkage than the other. Pattern resins did not present lower values of shrinkage, as usually reported by the manufacturer.

Ultrasonic assessment of shrinkage type discontinuities

International Nuclear Information System (INIS)

Hubber, John

2010-01-01

This investigation into ultrasonic internal discontinuities is intended to demonstrate typical examples of internal 'shrinkage' type discontinuities and its connection with the casting suitability, integrity and reliability in service. This type of discontinuity can be misinterpreted by ultrasonic technicians and can lead to the rejection of castings unnecessarily, due to the mis-characterization of fine shrinkage - discrete porosity. The samples for this investigation were taken from thirty ton heavy section ductile iron mill flange castings, manufactured by Graham Campbell Ferrum International. The sampled area was of discontinuities that were recorded for sizing on an area due to loss of back wall echo, but had acceptable reflectivity. A comparative sample was taken adjacent to the area of discrete porosity. The discontinuities found by this investigation are of a 'spongy' type, gaseous in appearance and are surrounded by acoustically sound material. All discontinuities discussed in this paper are centrally located in the through thickness of the casting. The porous nature of this type of discontinuity consisting of approximately 80-90% metal has its own residual strength, as indicated by the proof stress results which reveal a residual strength of up to 50-60% of that of the unaffected area of the casting. The affected areas are elliptical in shape and vary in density and through thickness throughout.

Computation of shrinkage stresses in prestressed concrete containments

International Nuclear Information System (INIS)

Wu, R.F.; Ouyang, H.

1989-01-01

According to a survey, surface cracking on PCRVs and PCCs under the investigations is confined to drying shrinkage and thermal strain effects and no instances of structurally significant cracking was been found. In this paper, the authors use FEM to compute humidity distribution in drying concrete and shrinkage stresses by internal restraint. Since PCC is built segment by segment in several years, a computational model taking into account construction sequence is presented and shrinkage stresses by external restraints are calculated with the model

Dry shrinkage characteristics of buffer materials

Energy Technology Data Exchange (ETDEWEB)

Suzuki, H. [ITC, Tokai, Ibaraki (Japan); Fujita, A.

1999-03-01

Generation of cracks due to drying of compressed bentonite was observed by changing the initial water content to obtain shrinkage constants such as shrinkage limit and shrinking rate. As a result, generation of practically no cracks was observed when the initial water content of samples was below 13%. The volume change due to drying increased with the water content in the sample, and the shrinkage constants were found to depend on the initial water content. Further, the one-dimensional compression strength after drying was compared with that before drying in order to clarify the effect of cracks generated by drying on the mechanical strength. As a result, the dry sample with cracks proved to have large one-dimensional compression strength or E{sub 50} compared to wet samples, so that the mechanical strength was kept even after drying. (H. Baba)

Integrated genomics of Mucorales reveals novel therapeutic targets

Science.gov (United States)

Mucormycosis is a life-threatening infection caused by Mucorales fungi. We sequenced 30 fungal genomes and performed transcriptomics with three representative Rhizopus and Mucor strains with human airway epithelial cells during fungal invasion to reveal key host and fungal determinants contributing ...

Drying shrinkage problems in high PI subgrade soils.

Science.gov (United States)

2014-01-01

The main objective of this study was to investigate the longitudinal cracking in pavements due to drying : shrinkage of high PI subgrade soils. The study involved laboartory soil testing and modeling. The : shrinkage cracks usually occur within the v...

Camelid genomes reveal evolution and adaptation to desert environments.

Science.gov (United States)

Wu, Huiguang; Guang, Xuanmin; Al-Fageeh, Mohamed B; Cao, Junwei; Pan, Shengkai; Zhou, Huanmin; Zhang, Li; Abutarboush, Mohammed H; Xing, Yanping; Xie, Zhiyuan; Alshanqeeti, Ali S; Zhang, Yanru; Yao, Qiulin; Al-Shomrani, Badr M; Zhang, Dong; Li, Jiang; Manee, Manee M; Yang, Zili; Yang, Linfeng; Liu, Yiyi; Zhang, Jilin; Altammami, Musaad A; Wang, Shenyuan; Yu, Lili; Zhang, Wenbin; Liu, Sanyang; Ba, La; Liu, Chunxia; Yang, Xukui; Meng, Fanhua; Wang, Shaowei; Li, Lu; Li, Erli; Li, Xueqiong; Wu, Kaifeng; Zhang, Shu; Wang, Junyi; Yin, Ye; Yang, Huanming; Al-Swailem, Abdulaziz M; Wang, Jun

2014-10-21

Bactrian camel (Camelus bactrianus), dromedary (Camelus dromedarius) and alpaca (Vicugna pacos) are economically important livestock. Although the Bactrian camel and dromedary are large, typically arid-desert-adapted mammals, alpacas are adapted to plateaus. Here we present high-quality genome sequences of these three species. Our analysis reveals the demographic history of these species since the Tortonian Stage of the Miocene and uncovers a striking correlation between large fluctuations in population size and geological time boundaries. Comparative genomic analysis reveals complex features related to desert adaptations, including fat and water metabolism, stress responses to heat, aridity, intense ultraviolet radiation and choking dust. Transcriptomic analysis of Bactrian camels further reveals unique osmoregulation, osmoprotection and compensatory mechanisms for water reservation underpinned by high blood glucose levels. We hypothesize that these physiological mechanisms represent kidney evolutionary adaptations to the desert environment. This study advances our understanding of camelid evolution and the adaptation of camels to arid-desert environments.

Variation of Shrinkage Strain within the Depth of Concrete Beams

Directory of Open Access Journals (Sweden)

Jong-Hyun Jeong

2015-11-01

Full Text Available The variation of shrinkage strain within beam depth was examined through four series of time-dependent laboratory experiments on unreinforced concrete beam specimens. Two types of beam specimens, horizontally cast and vertically cast, were tested; shrinkage variation was observed in the horizontally cast specimens. This indicated that the shrinkage variation within the beam depth was due to water bleeding and tamping during the placement of the fresh concrete. Shrinkage strains were measured within the beam depth by two types of strain gages, surface-attached and embedded. The shrinkage strain distribution within the beam depth showed a consistent tendency for the two types of gages. The test beams were cut into four sections after completion of the test, and the cutting planes were divided into four equal sub-areas to measure the aggregate concentration for each sub-area of the cutting plane. The aggregate concentration increased towards the bottom of the beam. The shrinkage strain distribution was estimated by Hobbs’ equation, which accounts for the change of aggregate volume concentration.

Volume change of limestone and its effects on drying shrinkage of concrete

OpenAIRE

YAGI, Shogo; AQUINO, Carlos; INOUE, Masumi; OKAMOTO, Takahisa

2010-01-01

Recently, the cracks of concrete by drying shrinkage become one of the problems in the construction industry in Japan. The drying shrinkage decreases when the concrete is produced with limestone aggregate. However, it is not clear why the drying shrinkage is decreased. The purpose of this study is to clarify the relation between the drying shrinkage of concrete and the limestone aggregate. In this study, the experiments about the strength, elasticity and drying shrinkage of concrete and the p...

Creep and shrinkage of concrete according to Eurocode 2

Directory of Open Access Journals (Sweden)

Milićević Ivan M.

2017-01-01

Full Text Available This paper presents the procedure for calculation of creep coefficient and shrinkage strain according to Eurocode 2 (SRPS EN 1992-1-1:2004. The calculated values of final creep coefficient and shrinkage strain, for the usual design conditions, are given in Annexes. The influence of key parameters on final creep coefficient and shrinkage strain is analyzed and the comparison between their final values calculated according to Eurocode 2 and BAB 87 is presented.

Reduction of the Early Autogenous Shrinkage of High Strength Concrete

Directory of Open Access Journals (Sweden)

Drago Saje

2015-01-01

Full Text Available The results of a laboratory investigation on the early autogenous shrinkage of high strength concrete, and the possibilities of its reduction, are presented. Such concrete demonstrates significant autogenous shrinkage, which should, however, be limited in the early stages of its development in order to prevent the occurrence of cracks and/or drop in the load-carrying capacity of concrete structures. The following possibilities for reducing autogenous shrinkage were investigated: the use of low-heat cement, a shrinkage-reducing admixture, steel fibres, premoistened polypropylene fibres, and presoaked lightweight aggregate. In the case of the use of presoaked natural lightweight aggregate, with a fraction from 2 to 4 mm, the early autogenous shrinkage of one-day-old high strength concrete decreased by about 90%, with no change to the concrete's compressive strength in comparison with that of the reference concrete.

Evaluation of polymerization shrinkage, polymerization shrinkage stress, wear resistance, and compressive strength of a silorane-based composite: A finite element analysis study

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Suresh Mitthra

2017-01-01

Full Text Available Background: Understanding the mechanical properties is important in predicting the clinical behavior of composites. Finite element analysis (FEA evaluates properties of materials replicating clinical scenario. Aim: This study evaluated polymerization shrinkage and stress, wear resistance (WR, and compressive strength (CS of silorane in comparison with two methacrylate resins. Settings and Design: This study design was a numerical study using FEA. Materials and Methods: Three-dimensional (3D models of maxillary premolar with Class I cavities (2 mm depth, 4 mm length, and 2.5 mm width created and restored with silorane, nanohybrid, and microhybrid; Groups I, II, and III, respectively. Loads of 200–600 N were applied. Polymerization shrinkage was first determined by displacement produced in the X, Y, and Z planes. Maximum stress distribution due to shrinkage was calculated using AN SYS software. 3D cube models of composite resins were simulated with varying filler particle size. Similar loads were applied. WR and compressive stress were calculated: K W L/H and load/cross-sectional area, respectively. Statistical analysis done using one-way ANOVA, Kruskal–Wallis, and Tukey's honestly significant difference test (P < 0.05. Results: Polymerization shrinkage (0.99% and shrinkage stress (233.21 Mpa of silorane were less compared to microhybrid (2.14% and 472.43 Mpa and nanohybrid (2.32% and 464.88 Mpa. Silorane (7.92×/1011 μm/mm3 and nanohybrid (7.79×/1011 showed superior WR than microhybrid (1.113×/1017. There was no significant difference in compressive stress among the groups. Conclusion: Silorane exhibited less polymerization shrinkage and shrinkage stress compared to methacrylates. Silorane and nanohybrid showed greater WR compared to microhybrid. CS of all groups was similar.

Influence of length-to-diameter ratio on shrinkage of basalt fiber concrete

Science.gov (United States)

Ruijie, MA; Yang, Jiansen; Liu, Yuan; Zheng, Xiaojun

2017-09-01

In order to study the shrinkage performance of basalt concrete, using the shrinkage rate as index, the work not only studied the influence of different length-to-diameter ratio (LDR) on plastic shrinkage and drying shrinkage of basalt fiber concrete, but also analyzed the action mechanism. The results show that when the fiber content is 0.1%, the LDR of 800 and 1200 take better effects on reducing plastic shrinkage, however the fiber content is 0.3%, that of LDR 600 is better. To improve drying shrinkage, the fiber of LDR 800 takes best effect. In the concrete structure, the adding basalt fibers form a uniform and chaotic supporting system, optimize the pore and the void structure of concrete, make the material further compacted, reduce the water loss, so as to decrease the shrinkage of concrete effectively.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

Science.gov (United States)

Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

Volumetric polymerization shrinkage of contemporary composite resins

OpenAIRE

Nagem Filho, Halim; Nagem, Haline Drumond; Francisconi, Paulo Afonso Silveira; Franco, Eduardo Batista; Mondelli, Rafael Francisco Lia; Coutinho, Kennedy Queiroz

2007-01-01

The polymerization shrinkage of composite resins may affect negatively the clinical outcome of the restoration. Extensive research has been carried out to develop new formulations of composite resins in order to provide good handling characteristics and some dimensional stability during polymerization. The purpose of this study was to analyze, in vitro, the magnitude of the volumetric polymerization shrinkage of 7 contemporary composite resins (Definite, Suprafill, SureFil, Filtek Z250, Fill ...

Direct voxel-based comparisons between grey matter shrinkage and glucose hypometabolism in chronic alcoholism.

Science.gov (United States)

Ritz, Ludivine; Segobin, Shailendra; Lannuzel, Coralie; Boudehent, Céline; Vabret, François; Eustache, Francis; Beaunieux, Hélène; Pitel, Anne L

2016-09-01

Alcoholism is associated with widespread brain structural abnormalities affecting mainly the frontocerebellar and the Papez's circuits. Brain glucose metabolism has received limited attention, and few studies used regions of interest approach and showed reduced global brain metabolism predominantly in the frontal and parietal lobes. Even though these studies have examined the relationship between grey matter shrinkage and hypometabolism, none has performed a direct voxel-by-voxel comparison between the degrees of structural and metabolic abnormalities. Seventeen alcoholic patients and 16 control subjects underwent both structural magnetic resonance imaging and (18)F-2-fluoro-deoxy-glucose-positron emission tomography examinations. Structural abnormalities and hypometabolism were examined in alcoholic patients compared with control subjects using two-sample t-tests. Then, these two patterns of brain damage were directly compared with a paired t-test. Compared to controls, alcoholic patients had grey matter shrinkage and hypometabolism in the fronto-cerebellar circuit and several nodes of Papez's circuit. The direct comparison revealed greater shrinkage than hypometabolism in the cerebellum, cingulate cortex, thalamus and hippocampus and parahippocampal gyrus. Conversely, hypometabolism was more severe than shrinkage in the dorsolateral, premotor and parietal cortices. The distinct profiles of abnormalities found within the Papez's circuit, the fronto-cerebellar circuit and the parietal gyrus in chronic alcoholism suggest the involvement of different pathological mechanisms. © The Author(s) 2015.

Shrinkage Module of Soil Samples with Different Cement Content

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Mohannad Sabry

2017-12-01

Full Text Available The differences in soil's body mass during shrinkage over time have changes in soil physical properties which provide an important reason to check the design of underground foundations in expansive soils. In this paper, a state-of-art of the soil heat stress-strain relationship prediction methods is checked using soil engineering laboratory experiments and Matlab R2013b numerical modelling. The shrinkage of soils with different cement content of (0%, 2%, 4%, 6% and 8% with the same water content of 20 percent in room temperature for 24 hours, are critically reviewed in terms of their predictive shrinkage along with their strengths and flexural behaviour. The review highlights the prediction methods present to determine the effect of heat stress on the shrinkage of soil samples with different cement content after classifying the soils into clay, silt and sand depending on their particle size using sieve and hydrometer experiments. The results of the soil engineering laboratory experiments showed that as the cement content increases, the shrinkage of soil decreases as a result of increased elasticity in soil. The numerical analysis using finite element method in Matlab R2013b shows that as the cement content increases the displacement in the soil sample decreases and that the soil sample with 8% cement content has more resistance to shrinkage and less displacement than the soil with 6% cement, which has less resistance to heat stresses and more displacement.

Creep and shrinkage analysis for concrete spent fuel dry storage module

Energy Technology Data Exchange (ETDEWEB)

Zhang, D. [Atomic Energy of Canada Limited, Chalk River, Ontario (Canada)], E-mail: zhangd@aecl.ca

2009-07-01

CANDU reactors are designed in Canada and are built and operated worldwide to produce electricity economically with no emission of green house gases. This paper presents creep and shrinkage analysis for a concrete spent fuel dry storage module of a CANDU nuclear power plant. Creep and shrinkage analysis was performed using a method outlined in American Concrete Institute (ACI) code, and then the creep and shrinkage strains were analyzed in a finite element model to obtain the structural behavior of the concrete module. This demonstrated that the creep and shrinkage analysis for concrete spent fuel dry storage is reasonable. AECL's spent fuel dry storage module is adequate to resist the time-dependent effects due to creep and shrinkage of concrete. (author)

Creep and shrinkage analysis for concrete spent fuel dry storage module

International Nuclear Information System (INIS)

Zhang, D.

2009-01-01

CANDU reactors are designed in Canada and are built and operated worldwide to produce electricity economically with no emission of green house gases. This paper presents creep and shrinkage analysis for a concrete spent fuel dry storage module of a CANDU nuclear power plant. Creep and shrinkage analysis was performed using a method outlined in American Concrete Institute (ACI) code, and then the creep and shrinkage strains were analyzed in a finite element model to obtain the structural behavior of the concrete module. This demonstrated that the creep and shrinkage analysis for concrete spent fuel dry storage is reasonable. AECL's spent fuel dry storage module is adequate to resist the time-dependent effects due to creep and shrinkage of concrete. (author)

Measuring method for heat-shrinkage of fuel pellet

International Nuclear Information System (INIS)

Komono, Akira; Ishizaki, Jin; Inaki, Kiyohiro.

1997-01-01

The present invention concerns a method of determining an amount of heat-shrinkage of UR 2 pellets containing gadolinium oxide (Gd 2 O 2 ) based on the difference of the density thereof before and after heating. In a heat shrinkage test of UO 2 pellets containing from 1.0 to 15.0% by weight of gadolinium oxide, the amount of heat-shrinkage is measured under the condition of heat-retaining temperature: from 1700 to 1750degC, temperature elevation time and lowering time: from 90 to 120mins, heat-retaining time: 24hours, inert gas atmosphere, gas pressure: 0.35kg/cm 2 and gas dew point: from -55 to 40degC without changing O/M. This invention has a feature in the use of the inert gas and the elevation of the dew point of the gas. Then, oxygen dissociation phenomenon from crystal lattices of the fuel pellets is suppressed, and normal densification value is shown. Then, fuel pellets of good quality with less fluctuation of the heat-shrinkage can be obtained. (N.H.)

Linear Shrinkage Behaviour of Compacted Loam Masonry Blocks

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NAWAB ALI LAKHO

2017-04-01

Full Text Available Walls of wet loam, used in earthen houses, generally experience more shrinkage which results in cracks and less compressive strength. This paper presents a technique of producing loam masonry blocks that are compacted in drained state during casting process in order to minimize shrinkage. For this purpose, loam masonry blocks were cast and compacted at a pressure of 6 MPa and then dried in shade by covering them in plastic sheet. The results show that linear shrinkage of 2% occurred which is smaller when compared to un-compacted wet loam walls. This implies that the loam masonry blocks compacted in drained state is expected to perform better than un-compacted wet loam walls.

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

DEFF Research Database (Denmark)

Schubert, Mikkel; Jáónsson, Hákon; Chang, Dan

2014-01-01

genetics alone. We therefore sequenced two complete horse genomes, predating domestication by thousands of years, to characterize the genetic footprint of domestication. These ancient genomes reveal predomestic population structure and a significant fraction of genetic variation shared with the domestic...... breeds but absent from Przewalski’s horses. We find positive selection on genes involved in various aspects of locomotion, physiology, and cognition. Finally, we show that modern horse genomes contain an excess of deleterious mutations, likely representing the genetic cost of domestication....

Shrinkage measurement for holographic recording materials

Science.gov (United States)

Fernández, R.; Gallego, S.; Márquez, A.; Francés, J.; Navarro Fuster, V.; Neipp, C.; Ortuño, M.; Beléndez, A.; Pascual, I.

2017-05-01

There is an increasing demand for new holographic recording materials. One of them are photopolymers, which are becoming a classic media in this field. Their versatility is well known and new possibilities are being created by including new components, such as nanoparticles or dispersed liquid crystal molecules in classical formulations, making them interesting for additional applications in which the thin film preparation and the structural modification have a fundamental importance. Prior to obtaining a wide commercialization of displays based on photopolymers, one of the key aspects is to achieve a complete characterization of them. In this sense, one of the main parameters to estimate and control is the shrinkage of these materials. The volume variations change the angular response of the hologram in two aspects, the angular selectivity and the maximum diffraction efficiency. One criteria for the recording material to be used in a holographic data storage application is the shrinkage, maximum of 0.5%. Along this work, we compare two different methods to measure the holographic recording material shrinkage. The first one is measuring the angle of propagation for both diffracted orders +/-1 when slanted gratings are recorded, so that an accurate value of the grating vector can be calculated. The second one is based on interference measurements at zero spatial frequency limit. We calculate the shrinkage for three different photopolymers: a polyvinyl alcohol acrylamide (PVA/AA) based photopolymer, one of the greenest photopolymers whose patent belongs to the Alicante University called Biophotopol and on the last place a holographic-dispersed liquid crystal photopolymer (H-PDLC).

Comprehensive Genomic Profiling of Esthesioneuroblastoma Reveals Additional Treatment Options.

Science.gov (United States)

Gay, Laurie M; Kim, Sungeun; Fedorchak, Kyle; Kundranda, Madappa; Odia, Yazmin; Nangia, Chaitali; Battiste, James; Colon-Otero, Gerardo; Powell, Steven; Russell, Jeffery; Elvin, Julia A; Vergilio, Jo-Anne; Suh, James; Ali, Siraj M; Stephens, Philip J; Miller, Vincent A; Ross, Jeffrey S

2017-07-01

Esthesioneuroblastoma (ENB), also known as olfactory neuroblastoma, is a rare malignant neoplasm of the olfactory mucosa. Despite surgical resection combined with radiotherapy and adjuvant chemotherapy, ENB often relapses with rapid progression. Current multimodality, nontargeted therapy for relapsed ENB is of limited clinical benefit. We queried whether comprehensive genomic profiling (CGP) of relapsed or refractory ENB can uncover genomic alterations (GA) that could identify potential targeted therapies for these patients. CGP was performed on formalin-fixed, paraffin-embedded sections from 41 consecutive clinical cases of ENBs using a hybrid-capture, adaptor ligation based next-generation sequencing assay to a mean coverage depth of 593X. The results were analyzed for base substitutions, insertions and deletions, select rearrangements, and copy number changes (amplifications and homozygous deletions). Clinically relevant GA (CRGA) were defined as GA linked to drugs on the market or under evaluation in clinical trials. A total of 28 ENBs harbored GA, with a mean of 1.5 GA per sample. Approximately half of the ENBs (21, 51%) featured at least one CRGA, with an average of 1 CRGA per sample. The most commonly altered gene was TP53 (17%), with GA in PIK3CA , NF1 , CDKN2A , and CDKN2C occurring in 7% of samples. We report comprehensive genomic profiles for 41 ENB tumors. CGP revealed potential new therapeutic targets, including targetable GA in the mTOR, CDK and growth factor signaling pathways, highlighting the clinical value of genomic profiling in ENB. Comprehensive genomic profiling of 41 relapsed or refractory ENBs reveals recurrent alterations or classes of mutation, including amplification of tyrosine kinases encoded on chromosome 5q and mutations affecting genes in the mTOR/PI3K pathway. Approximately half of the ENBs (21, 51%) featured at least one clinically relevant genomic alteration (CRGA), with an average of 1 CRGA per sample. The most commonly altered

Effect of shrinkage porosity on mechanical properties of ferritic ductile iron

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Wang Zehua

2013-05-01

Full Text Available Casting defects could largely affect the mechanical properties of casting products. A number of test pieces made of ductile iron (EN-GJS-400-18-LT with different levels of shrinkage porosity were prepared and then tensile and fatigue tests were performed to investigate the impact of shrinkage porosity on their mechanical properties. The results showed that the tensile strength decreases linearly with increasing of the shrinkage porosity. The tensile elongation decreases sharply with the increase of the shrinkage porosity mainly due to the non-uniform plastic deformation. The fatigue life also dramatically declines with increasing of the porosity and follows a power law relationship with the area percentage of porosity. The existence of the shrinkage porosity made the fatigue fracture complex. The shrinkage pores, especially those close to the surface usually became the crack initiation sites. For test pieces with less porosity, the fatigue fracture was clearly composed of crack initiation, propagation, and overloading. While for samples with high level of porosity, multiple crack initiation sites were observed.

Effect of temperature and humidity on post-gel shrinkage, cusp deformation, bond strength and shrinkage stress - Construction of a chamber to simulate the oral environment.

Science.gov (United States)

Bicalho, Aline Aredes; de Souza, Silas Júnior Boaventura; de Rosatto, Camila Maria Peres; Tantbirojn, Daranee; Versluis, Antheunis; Soares, Carlos José

2015-12-01

Evaluate the effect of environment on post-gel shrinkage (Shr), cuspal strains (CS), microtensile bond strength (μTBS), elastic modulus (E) and shrinkage stress in molars with large class II restorations. Sixty human molars received standardized Class II mesio-oclusal-distal cavity preparations. Restorations were made with two composites (CHA, Charisma Diamond, Heraus Kulzer and IPS Empress Direct, Ivoclar-Vivadent) using three environment conditions (22°C/50% humidity, 37°C/50% humidity and 37°C/90% humidity) simulated in custom developed chamber. Shr was measured using the strain gauge technique (n=10). CS was measured using strain gauges. Half of the teeth (n=5) were used to assess the elastic modulus (E) and Knoop hardness (KHN) at different depths using microhardness indentation. The other half (n=5) was used to measure the μTBS. The composites and environment conditions were simulated in a two-dimensional finite element analysis of a tooth restoration. Polymerization shrinkage was modeled using Shr data. The Shr, CS, μTBS, KHN and E data were statistically analyzed using two-way ANOVA and Tukey test (significance level: 0.05). Both composites had similar Shr, CS, μTBS and shrinkage stress. CHA had higher elastic modulus than IPS. Increasing temperature and humidity significantly increased Shr, CS and shrinkage stress. μTBS were similar for groups with lower humidity, irrespective of temperature, and higher with higher humidity. E and KHN were constant through the depth for CHA. E and KHN values were affected by environment only for IPS, mainly deeper in the cavity. Shrinkage stress at dentin/composite interface had high inverse correlation with μTBS. Shrinkage stress in enamel had high correlation with CS. Increasing temperature and humidity caused higher post-gel shrinkage and cusp deformation with higher shrinkage stresses in the tooth structure and tooth/restoration interface for both composites tested. The chamber developed for simulating the

Creep and Shrinkage of High Strength Concretes: an Experimental Analysis

Directory of Open Access Journals (Sweden)

Berenice Martins Toralles carbonari

2002-01-01

Full Text Available The creep and shrinkage behaviour of high strength silica fume concretes is significantly different from that of conventional concretes. In order to represent the proper time-dependent response of the material in structural analysis and design, these aspects should be adequately quantified. This paper discusses an experimental setup that is able to determine the creep and shrinkage of concrete from the time of placing. It also compares different gages that can be used for measuring the strains. The method is applied to five different concretes in the laboratory under controlled environmental conditions. The phenomena that are quantified can be classified as basic shrinkage, drying shrinkage, basic creep and drying creep. The relative importance of these mechanisms in high strength concrete will also be presented.

Comparison of shrinkage related properties of various patch repair materials

Science.gov (United States)

Kristiawan, S. A.; Fitrianto, R. S.

2017-02-01

A patch repair material has been developed in the form of unsaturated polyester resin (UPR)-mortar. The performance and durability of this material are governed by its compatibility with the concrete being repaired. One of the compatibility issue that should be tackled is the dimensional compatibility as a result of differential shrinkage between the repair material and the concrete substrate. This research aims to evaluate such shrinkage related properties of UPR-mortar and to compare with those of other patch repair materials. The investigation includes the following aspects: free shrinkage, resistance to delamination and cracking. The results indicate that UPR-mortar poses a lower free shrinkage, lower risk of both delamination and cracking tendency in comparison to other repair materials.

Geosynthetic clay liners shrinkage under simulated daily thermal cycles.

Science.gov (United States)

Sarabadani, Hamid; Rayhani, Mohammad T

2014-06-01

Geosynthetic clay liners are used as part of composite liner systems in municipal solid waste landfills and other applications to restrict the escape of contaminants into the surrounding environment. This is attainable provided that the geosynthetic clay liner panels continuously cover the subsoil. Previous case histories, however, have shown that some geosynthetic clay liner panels are prone to significant shrinkage and separation when an overlying geomembrane is exposed to solar radiation. Experimental models were initiated to evaluate the potential shrinkage of different geosynthetic clay liner products placed over sand and clay subsoils, subjected to simulated daily thermal cycles (60°C for 8 hours and 22°C for 16 hours) modelling field conditions in which the liner is exposed to solar radiation. The variation of geosynthetic clay liner shrinkage was evaluated at specified times by a photogrammetry technique. The manufacturing techniques, the initial moisture content, and the aspect ratio (ratio of length to width) of the geosynthetic clay liner were found to considerably affect the shrinkage of geosynthetic clay liners. The particle size distribution of the subsoil and the associated suction at the geosynthetic clay liner-subsoil interface was also found to have significant effects on the shrinkage of the geosynthetic clay liner. © The Author(s) 2014.

Restrained Shrinkage Cracking of Fiber-Reinforced High-Strength Concrete

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Ashkan Saradar

2018-02-01

Full Text Available Concrete shrinkage and volume reduction happens due to the loss of moisture, which eventually results in cracks and more concrete deformation. In this study, the effect of polypropylene (PP, steel, glass, basalt, and polyolefin fibers on compressive and flexural strength, drying shrinkage, and cracking potential, using the ring test at early ages of high-strength concrete mixtures, was investigated. The restrained shrinkage test was performed on concrete ring specimens according to the ASTM C1581 standard. The crack width and age of restrained shrinkage cracking were the main parameters studied in this research. The results indicated that the addition of fiber increases the compressive strength by 16%, 20%, and 3% at the age of 3, 7, and 28 days, respectively, and increases the flexural toughness index up to 7.7 times. Steel and glass fibers had a better performance in flexural strength, but relatively poor action in the velocity reduction and cracking time of the restrained shrinkage. Additionally, cracks in all concrete ring specimens except for the polypropylene-containing mixture, was developed to a full depth crack. The mixture with polypropylene fiber indicated a reduction in crack width up to 62% and an increasing age cracking up to 84%.

Effectiveness of Fiber Reinforcement on the Mechanical Properties and Shrinkage Cracking of Recycled Fine Aggregate Concrete

Science.gov (United States)

Nam, Jeongsoo; Kim, Gyuyong; Yoo, Jaechul; Choe, Gyeongcheol; Kim, Hongseop; Choi, Hyeonggil; Kim, Youngduck

2016-01-01

This paper presents an experimental study conducted to investigate the effect of fiber reinforcement on the mechanical properties and shrinkage cracking of recycled fine aggregate concrete (RFAC) with two types of fiber—polyvinyl alcohol (PVA) and nylon. A small fiber volume fraction, such as 0.05% or 0.1%, in RFAC with polyvinyl alcohol or nylon fibers was used for optimum efficiency in minimum quantity. Additionally, to make a comparative evaluation of the mechanical properties and shrinkage cracking, we examined natural fine aggregate concrete as well. The test results revealed that the addition of fibers and fine aggregates plays an important role in improving the mechanical performance of the investigated concrete specimens as well as controlling their cracking behavior. The mechanical properties such as compressive strength, splitting tensile strength, and flexural strength of fiber-reinforced RFAC were slightly better than those of non-fiber-reinforced RFAC. The shrinkage cracking behavior was examined using plat-ring-type and slab-type tests. The fiber-reinforced RFAC showed a greater reduction in the surface cracks than non-fiber-reinforced concrete. The addition of fibers at a small volume fraction in RFAC is more effective for drying shrinkage cracks than for improving mechanical performance. PMID:28773256

Effectiveness of Fiber Reinforcement on the Mechanical Properties and Shrinkage Cracking of Recycled Fine Aggregate Concrete.

Science.gov (United States)

Nam, Jeongsoo; Kim, Gyuyong; Yoo, Jaechul; Choe, Gyeongcheol; Kim, Hongseop; Choi, Hyeonggil; Kim, Youngduck

2016-02-26

This paper presents an experimental study conducted to investigate the effect of fiber reinforcement on the mechanical properties and shrinkage cracking of recycled fine aggregate concrete (RFAC) with two types of fiber-polyvinyl alcohol (PVA) and nylon. A small fiber volume fraction, such as 0.05% or 0.1%, in RFAC with polyvinyl alcohol or nylon fibers was used for optimum efficiency in minimum quantity. Additionally, to make a comparative evaluation of the mechanical properties and shrinkage cracking, we examined natural fine aggregate concrete as well. The test results revealed that the addition of fibers and fine aggregates plays an important role in improving the mechanical performance of the investigated concrete specimens as well as controlling their cracking behavior. The mechanical properties such as compressive strength, splitting tensile strength, and flexural strength of fiber-reinforced RFAC were slightly better than those of non-fiber-reinforced RFAC. The shrinkage cracking behavior was examined using plat-ring-type and slab-type tests. The fiber-reinforced RFAC showed a greater reduction in the surface cracks than non-fiber-reinforced concrete. The addition of fibers at a small volume fraction in RFAC is more effective for drying shrinkage cracks than for improving mechanical performance.

Shrinkage deformation of cement foam concrete

Science.gov (United States)

Kudyakov, A. I.; Steshenko, A. B.

2015-01-01

The article presents the results of research of dispersion-reinforced cement foam concrete with chrysotile asbestos fibers. The goal was to study the patterns of influence of chrysotile asbestos fibers on drying shrinkage deformation of cement foam concrete of natural hardening. The chrysotile asbestos fiber contains cylindrical fiber shaped particles with a diameter of 0.55 micron to 8 microns, which are composed of nanostructures of the same form with diameters up to 55 nm and length up to 22 microns. Taking into account the wall thickness, effective reinforcement can be achieved only by microtube foam materials, the so- called carbon nanotubes, the dimensions of which are of power less that the wall pore diameter. The presence of not reinforced foam concrete pores with perforated walls causes a decrease in its strength, decreases the mechanical properties of the investigated material and increases its shrinkage. The microstructure investigation results have shown that introduction of chrysotile asbestos fibers in an amount of 2 % by weight of cement provides the finely porous foam concrete structure with more uniform size closed pores, which are uniformly distributed over the volume. This reduces the shrinkage deformation of foam concrete by 50%.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Science.gov (United States)

Thybert, David; Roller, Maša; Navarro, Fábio C.P.; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C.; Laukaitis, Christina M.; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A.; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J.; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M.; Odom, Duncan T.; Flicek, Paul

2018-01-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. PMID:29563166

Estimation of the profile of cross-machine shrinkage of paper

International Nuclear Information System (INIS)

I'Anson, S J; Sampson, W W; Constantino, R P A; Hoole, S M

2008-01-01

In common with many other materials, paper tends to shrink as it dries. Although every attempt is made to restrain paper, some shrinkage occurs on all paper machines in the direction perpendicular to that of manufacture and this shrinkage is always much higher at the edges of the machine than in the centre. Measurement of the profile of this cross-machine shrinkage is possible using the fast Fourier transform to locate and measure periodic elements imprinted by the filtration fabrics used during the formation of the paper web. This paper describes a new method which allows the geometrical relationships within the fabric to be used along with dimensional changes to estimate shrinkage. The method has the advantages over previous methods of more tolerant sampling protocols, operator independent analysis and improved accuracy

Shrinkage calibration method for μPIM manufactured parts

DEFF Research Database (Denmark)

Quagliotti, Danilo; Tosello, Guido; Salaga, J.

2016-01-01

Five green and five sintered parts of a micro mechanical component, produced by micro powder injection moulding, were measured using an optical coordinate measuring machine. The aim was to establish a method for quality assurance of the final produced parts. Initially, the so called “green” parts...... were compared with the sintered parts (final products) calculating the percentage of shrinkage after sintering. Successively, the expanded uncertainty of the measured dimensions were evaluated for each single part as well as for the overall parts. Finally, the estimated uncertainty for the shrinkage...... was evaluated propagating the expanded uncertainty previously stated and considering green and sintered parts correlated. Results showed that the proposed method can be effective instating tolerances if it is assumed that the variability on the dimensions induced by the shrinkage equals the propagated expanded...

Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

Directory of Open Access Journals (Sweden)

Beverly E. Flood

2016-05-01

Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

Development and Performance Assessment of the High-Performance Shrinkage Reducing Agent for Concrete

Directory of Open Access Journals (Sweden)

Hyung Sub Han

2016-01-01

Full Text Available To develop a high-performance shrinkage reducing agent, this study investigated several shrinkage reducing materials and supplements for those materials. Fluidity and air content were satisfactory for the various shrinkage reducing materials. The decrease in viscosity was the lowest for glycol-based materials. The decrease in drying shrinkage was most prominent for mixtures containing glycol-based materials. In particular, mixtures containing G2 achieved a 40% decrease in the amount of drying shrinkage. Most shrinkage reducing materials had weaker level of compressive strength than that of the plain mixture. When 3% triethanolamine was used for early strength improvement, the strength was enhanced by 158% compared to that of the plain mixture on day 1; enhancement values were 135% on day 7 and 113% on day 28. To assess the performance of the developed high-performance shrinkage reducing agent and to determine the optimal amount, 2.0% shrinkage reducing agent was set as 40% of the value of the plain mixture. While the effect was more prominent at higher amounts, to prevent deterioration of the compressive strength and the other physical properties, the recommended amount is less than 2.0%.

Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities

DEFF Research Database (Denmark)

Aylward, Frank O.; McDonald, Bradon R.; Adams, Sandra M.

2013-01-01

to the genus Sphingobium. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer...... and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible...... a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling....

Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments

Science.gov (United States)

Trojan, Daniela; Roux, Simon; Herbold, Craig; Rattei, Thomas; Woebken, Dagmar

2018-01-01

Summary Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed a large‐scale comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8 and 23 (n = 24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. Our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low‐ and high‐affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients. Among many genomes, the capacity to use a diverse collection of carbohydrates, as well as inorganic and organic nitrogen sources (such as via extracellular peptidases), was detected – both advantageous traits in environments with fluctuating nutrient environments. We also identified multiple soil acidobacteria with the potential to scavenge atmospheric concentrations of H2, now encompassing mesophilic soil strains within the subdivision 1 and 3, in addition to a previously identified thermophilic strain in subdivision 4. This large‐scale acidobacteria genome analysis reveal traits that provide genomic, physiological and metabolic versatility, presumably allowing flexibility and versatility in the challenging and fluctuating soil environment. PMID:29327410

Polymerization shrinkage stress of composite resins and resin cements - What do we need to know?

Science.gov (United States)

Soares, Carlos José; Faria-E-Silva, André Luis; Rodrigues, Monise de Paula; Vilela, Andomar Bruno Fernandes; Pfeifer, Carmem Silvia; Tantbirojn, Daranee; Versluis, Antheunis

2017-08-28

Polymerization shrinkage stress of resin-based materials have been related to several unwanted clinical consequences, such as enamel crack propagation, cusp deflection, marginal and internal gaps, and decreased bond strength. Despite the absence of strong evidence relating polymerization shrinkage to secondary caries or fracture of posterior teeth, shrinkage stress has been associated with post-operative sensitivity and marginal stain. The latter is often erroneously used as a criterion for replacement of composite restorations. Therefore, an indirect correlation can emerge between shrinkage stress and the longevity of composite restorations or resin-bonded ceramic restorations. The relationship between shrinkage and stress can be best studied in laboratory experiments and a combination of various methodologies. The objective of this review article is to discuss the concept and consequences of polymerization shrinkage and shrinkage stress of composite resins and resin cements. Literature relating to polymerization shrinkage and shrinkage stress generation, research methodologies, and contributing factors are selected and reviewed. Clinical techniques that could reduce shrinkage stress and new developments on low-shrink dental materials are also discussed.

Characterisation of tissue shrinkage during microwave thermal ablation.

Science.gov (United States)

Farina, Laura; Weiss, Noam; Nissenbaum, Yitzhak; Cavagnaro, Marta; Lopresto, Vanni; Pinto, Rosanna; Tosoratti, Nevio; Amabile, Claudio; Cassarino, Simone; Goldberg, S Nahum

2014-11-01

The aim of this study was to characterise changes in tissue volume during image-guided microwave ablation in order to arrive at a more precise determination of the true ablation zone. The effect of power (20-80 W) and time (1-10 min) on microwave-induced tissue contraction was experimentally evaluated in various-sized cubes of ex vivo liver (10-40 mm ± 2 mm) and muscle (20 and 40 mm ± 2 mm) embedded in agar phantoms (N = 119). Post-ablation linear and volumetric dimensions of the tissue cubes were measured and compared with pre-ablation dimensions. Subsequently, the process of tissue contraction was investigated dynamically during the ablation procedure through real-time X-ray CT scanning. Overall, substantial shrinkage of 52-74% of initial tissue volume was noted. The shrinkage was non-uniform over time and space, with observed asymmetry favouring the radial (23-43 % range) over the longitudinal (21-29%) direction. Algorithmic relationships for the shrinkage as a function of time were demonstrated. Furthermore, the smallest cubes showed more substantial and faster contraction (28-40% after 1 min), with more considerable volumetric shrinkage (>10%) in muscle than in liver tissue. Additionally, CT imaging demonstrated initial expansion of the tissue volume, lasting in some cases up to 3 min during the microwave ablation procedure, prior to the contraction phenomenon. In addition to an asymmetric substantial shrinkage of the ablated tissue volume, an initial expansion phenomenon occurs during MW ablation. Thus, complex modifications of the tissue close to a radiating antenna will likely need to be taken into account for future methods of real-time ablation monitoring.

Time-Dependent Behavior of Shrinkage Strain for Early Age Concrete Affected by Temperature Variation

OpenAIRE

Qin, Yu; Yi, Zhijian; Wang, Weina; Wang, Di

2017-01-01

Shrinkage has been proven to be an important property of early age concrete. The shrinkage strain leads to inherent engineering problems, such as cracking and loss of prestress. Atmospheric temperature is an important factor in shrinkage strain. However, current research does not provide much attention to the effect of atmospheric temperature on shrinkage of early age concrete. In this paper, a laboratory study was undertaken to present the time-dependent shrinkage of early age concrete under...

Effect of the key mixture parameters on shrinkage of reactive powder concrete.

Science.gov (United States)

Ahmad, Shamsad; Zubair, Ahmed; Maslehuddin, Mohammed

2014-01-01

Reactive powder concrete (RPC) mixtures are reported to have excellent mechanical and durability characteristics. However, such concrete mixtures having high amount of cementitious materials may have high early shrinkage causing cracking of concrete. In the present work, an attempt has been made to study the simultaneous effects of three key mixture parameters on shrinkage of the RPC mixtures. Considering three different levels of the three key mixture factors, a total of 27 mixtures of RPC were prepared according to 3(3) factorial experiment design. The specimens belonging to all 27 mixtures were monitored for shrinkage at different ages over a total period of 90 days. The test results were plotted to observe the variation of shrinkage with time and to see the effects of the key mixture factors. The experimental data pertaining to 90-day shrinkage were used to conduct analysis of variance to identify significance of each factor and to obtain an empirical equation correlating the shrinkage of RPC with the three key mixture factors. The rate of development of shrinkage at early ages was higher. The water to binder ratio was found to be the most prominent factor followed by cement content with the least effect of silica fume content.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Science.gov (United States)

Thybert, David; Roller, Maša; Navarro, Fábio C P; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C; Laukaitis, Christina M; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M; Odom, Duncan T; Flicek, Paul

2018-04-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli , which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. © 2018 Thybert et al.; Published by Cold Spring Harbor Laboratory Press.

Prevention of shrinkage cracking in tight concrete structures

International Nuclear Information System (INIS)

Alvaredo, A.M.; Wittmann, F.H.

1995-01-01

It is shown that crack formation and propagation in concrete members subjected to restrained shrinkage can be realistically predicted by means of a comprehensive approach including a diffusion analysis and fracture mechanics considerations. The conditions for stable crack propagation regarding dimensions of the concrete member, degree of restraint to the imposed deformation and material properties are discussed. Guidelines on the prevention of shrinkage cracking of concrete structures are given. (author). 10 refs., 5 figs

Evaluation of shrinkage and cracking in concrete of ring test by acoustic emission method

Science.gov (United States)

Watanabe, Takeshi; Hashimoto, Chikanori

2015-03-01

Drying shrinkage of concrete is one of the typical problems related to reduce durability and defilation of concrete structures. Lime stone, expansive additive and low-heat Portland cement are used to reduce drying shrinkage in Japan. Drying shrinkage is commonly evaluated by methods of measurement for length change of mortar and concrete. In these methods, there is detected strain due to drying shrinkage of free body, although visible cracking does not occur. In this study, the ring test was employed to detect strain and age cracking of concrete. The acoustic emission (AE) method was adopted to detect micro cracking due to shrinkage. It was recognized that in concrete using lime stone, expansive additive and low-heat Portland cement are effective to decrease drying shrinkage and visible cracking. Micro cracking due to shrinkage of this concrete was detected and evaluated by the AE method.

Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.

Science.gov (United States)

Kang, Yu; Gu, Chaohao; Yuan, Lina; Wang, Yue; Zhu, Yanmin; Li, Xinna; Luo, Qibin; Xiao, Jingfa; Jiang, Daquan; Qian, Minping; Ahmed Khan, Aftab; Chen, Fei; Zhang, Zhang; Yu, Jun

2014-11-25

The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis. Prokaryotic genomes are frequently interrupted by horizontal gene transfer (HGT) and rearrangement. To know whether there is a set of genes not only conserved in position

Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.

Science.gov (United States)

Cohrs, Randall J; Lee, Katherine S; Beach, Addilynn; Sanford, Bridget; Baird, Nicholas L; Como, Christina; Graybill, Chiharu; Jones, Dallas; Tekeste, Eden; Ballard, Mitchell; Chen, Xiaomi; Yalacki, David; Frietze, Seth; Jones, Kenneth; Lenac Rovis, Tihana; Jonjić, Stipan; Haas, Jürgen; Gilden, Don

2017-10-15

The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture. Copyright © 2017 American Society for Microbiology.

Shrinkage Behaviour of Fibre Reinforced Concrete with Recycled Tyre Polymer Fibres

Directory of Open Access Journals (Sweden)

Marijana Serdar

2015-01-01

Full Text Available Different types of fibres are often used in concrete to prevent microcracking due to shrinkage, and polypropylene fibres are among the most often used ones. If not prevented, microcracks can lead to the development of larger cracks as drying shrinkage occurs, enabling penetration of aggressive substances from the environment and reducing durability of concrete structures. The hypothesis of the present research is that polypropylene fibres, used in concrete for controlling formation of microcracks due to shrinkage, can be replaced with recycled polymer fibres obtained from end-of-life tyres. To test the hypothesis, concrete mixtures containing polypropylene fibres and recycled tyre polymer fibres were prepared and tested. Experimental programme focused on autogenous, free, and restrained shrinkage. It was shown that PP fibres can be substituted with higher amount of recycled tyre polymer fibres obtaining concrete with similar shrinkage behaviour. The results indicate promising possibilities of using recycled tyre polymer fibres in concrete products. At the same time, such applications would contribute to solving the problem of waste tyre disposal.

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Energy Technology Data Exchange (ETDEWEB)

Ma, Li Jun; van der Does, H. C.; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Jose; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Wolochuk, Charles; Xie, Xiaohui; Xu, Jin Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald; Goff, Steven; Hammond-Kossack, Kim; Hilburn, Karen; Hua-Van, Aurelie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. C.; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, Barbara G.; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

2010-03-18

Fusarium species are among the most important phytopathogenic and toxigenic fungi, having significant impact on crop production and animal health. Distinctively, members of the F. oxysporum species complex exhibit wide host range but discontinuously distributed host specificity, reflecting remarkable genetic adaptability. To understand the molecular underpinnings of diverse phenotypic traits and their evolution in Fusarium, we compared the genomes of three economically important and phylogenetically related, yet phenotypically diverse plant-pathogenic species, F. graminearum, F. verticillioides and F. oxysporum f. sp. lycopersici. Our analysis revealed greatly expanded lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes, accounting for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity. Experimentally, we demonstrate for the first time the transfer of two LS chromosomes between strains of F. oxysporum, resulting in the conversion of a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in the F. oxysporum species complex, putting the evolution of fungal pathogenicity into a new perspective.

Hydration of mineral shrinkage-compensating admixture for concrete : an experimental and numerical study

NARCIS (Netherlands)

Chen, Wei; Brouwers, H.J.H.

2012-01-01

The use of shrinkage-compensating admixture in concrete has been proven to be an effective way to mitigate the shrinkage of concrete. The hydration of a shrinkage-compensating admixture in cement paste and concrete is investigated in this paper with numerical simulation and experimental study. An

Differential metabolism of Mycoplasma species as revealed by their genomes

Directory of Open Access Journals (Sweden)

Fabricio B.M. Arraes

2007-01-01

Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

Strength and Drying Shrinkage of Alkali-Activated Slag Paste and Mortar

Directory of Open Access Journals (Sweden)

Mao-chieh Chi

2012-01-01

Full Text Available The aim of this study is to investigate the strengths and drying shrinkage of alkali-activated slag paste and mortar. Compressive strength, tensile strength, and drying shrinkage of alkali-activated slag paste and mortar were measured with various liquid/slag ratios, sand/slag ratios, curing ages, and curing temperatures. Experimental results show that the higher compressive strength and tensile strength have been observed in the higher curing temperature. At the age of 56 days, AAS mortars show higher compressive strength than Portland cement mortars and AAS mortars with liquid/slag ratio of 0.54 have the highest tensile strength in all AAS mortars. In addition, AAS pastes of the drying shrinkage are higher than AAS mortars. Meanwhile, higher drying shrinkage was observed in AAS mortars than that observed comparable Portland cement mortars.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

Science.gov (United States)

Schwager, Evelyn E; Sharma, Prashant P; Clarke, Thomas; Leite, Daniel J; Wierschin, Torsten; Pechmann, Matthias; Akiyama-Oda, Yasuko; Esposito, Lauren; Bechsgaard, Jesper; Bilde, Trine; Buffry, Alexandra D; Chao, Hsu; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dugan, Shannon; Eibner, Cornelius; Extavour, Cassandra G; Funch, Peter; Garb, Jessica; Gonzalez, Luis B; Gonzalez, Vanessa L; Griffiths-Jones, Sam; Han, Yi; Hayashi, Cheryl; Hilbrant, Maarten; Hughes, Daniel S T; Janssen, Ralf; Lee, Sandra L; Maeso, Ignacio; Murali, Shwetha C; Muzny, Donna M; Nunes da Fonseca, Rodrigo; Paese, Christian L B; Qu, Jiaxin; Ronshaugen, Matthew; Schomburg, Christoph; Schönauer, Anna; Stollewerk, Angelika; Torres-Oliva, Montserrat; Turetzek, Natascha; Vanthournout, Bram; Werren, John H; Wolff, Carsten; Worley, Kim C; Bucher, Gregor; Gibbs, Richard A; Coddington, Jonathan; Oda, Hiroki; Stanke, Mario; Ayoub, Nadia A; Prpic, Nikola-Michael; Flot, Jean-François; Posnien, Nico; Richards, Stephen; McGregor, Alistair P

2017-07-31

The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Polymerization shrinkage stress of composite resins and resin cements – What do we need to know?

Directory of Open Access Journals (Sweden)

Carlos José SOARES

2017-08-01

Full Text Available Abstract Polymerization shrinkage stress of resin-based materials have been related to several unwanted clinical consequences, such as enamel crack propagation, cusp deflection, marginal and internal gaps, and decreased bond strength. Despite the absence of strong evidence relating polymerization shrinkage to secondary caries or fracture of posterior teeth, shrinkage stress has been associated with post-operative sensitivity and marginal stain. The latter is often erroneously used as a criterion for replacement of composite restorations. Therefore, an indirect correlation can emerge between shrinkage stress and the longevity of composite restorations or resin-bonded ceramic restorations. The relationship between shrinkage and stress can be best studied in laboratory experiments and a combination of various methodologies. The objective of this review article is to discuss the concept and consequences of polymerization shrinkage and shrinkage stress of composite resins and resin cements. Literature relating to polymerization shrinkage and shrinkage stress generation, research methodologies, and contributing factors are selected and reviewed. Clinical techniques that could reduce shrinkage stress and new developments on low-shrink dental materials are also discussed.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

Science.gov (United States)

Macas, Jiří; Novák, Petr; Pellicer, Jaume; Čížková, Jana; Koblížková, Andrea; Neumann, Pavel; Fuková, Iva; Doležel, Jaroslav; Kelly, Laura J; Leitch, Ilia J

2015-01-01

The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57%) of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%). Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

In Depth Characterization of Repetitive DNA in 23 Plant Genomes Reveals Sources of Genome Size Variation in the Legume Tribe Fabeae.

Directory of Open Access Journals (Sweden)

Jiří Macas

Full Text Available The differential accumulation and elimination of repetitive DNA are key drivers of genome size variation in flowering plants, yet there have been few studies which have analysed how different types of repeats in related species contribute to genome size evolution within a phylogenetic context. This question is addressed here by conducting large-scale comparative analysis of repeats in 23 species from four genera of the monophyletic legume tribe Fabeae, representing a 7.6-fold variation in genome size. Phylogenetic analysis and genome size reconstruction revealed that this diversity arose from genome size expansions and contractions in different lineages during the evolution of Fabeae. Employing a combination of low-pass genome sequencing with novel bioinformatic approaches resulted in identification and quantification of repeats making up 55-83% of the investigated genomes. In turn, this enabled an analysis of how each major repeat type contributed to the genome size variation encountered. Differential accumulation of repetitive DNA was found to account for 85% of the genome size differences between the species, and most (57% of this variation was found to be driven by a single lineage of Ty3/gypsy LTR-retrotransposons, the Ogre elements. Although the amounts of several other lineages of LTR-retrotransposons and the total amount of satellite DNA were also positively correlated with genome size, their contributions to genome size variation were much smaller (up to 6%. Repeat analysis within a phylogenetic framework also revealed profound differences in the extent of sequence conservation between different repeat types across Fabeae. In addition to these findings, the study has provided a proof of concept for the approach combining recent developments in sequencing and bioinformatics to perform comparative analyses of repetitive DNAs in a large number of non-model species without the need to assemble their genomes.

Modeling for prediction of restrained shrinkage effect in concrete repair

International Nuclear Information System (INIS)

Yuan Yingshu; Li Guo; Cai Yue

2003-01-01

A general model of autogenous shrinkage caused by chemical reaction (chemical shrinkage) is developed by means of Arrhenius' law and a degree of chemical reaction. Models of tensile creep and relaxation modulus are built based on a viscoelastic, three-element model. Tests of free shrinkage and tensile creep were carried out to determine some coefficients in the models. Two-dimensional FEM analysis based on the models and other constitutions can predict the development of tensile strength and cracking. Three groups of patch-repaired beams were designed for analysis and testing. The prediction from the analysis shows agreement with the test results. The cracking mechanism after repair is discussed

Design changes of device to investigation of alloys linear contraction and shrinkage stresses

Directory of Open Access Journals (Sweden)

J. Mutwil

2009-07-01

Full Text Available Some design changes in device elaborated by author to examination of linear contraction and shrinkage stresses progress of metals and alloys during– and after solidification have been described. The introduced changes have been focused on design of closing of shrinkage test rod mould. The introduced changes have been allowed to simplify a mounting procedure of thermocouples measuring a temperature of the shrinkage rod casting (in 6 points. Exemplary investigation results of linear contraction and shrinkage stresses development in Al-Si13.5% alloy have been presented.

Drying Shrinkage of Mortar Incorporating High Volume Oil Palm Biomass Waste

Science.gov (United States)

Shukor Lim, Nor Hasanah Abdul; Samadi, Mostafa; Rahman Mohd. Sam, Abdul; Khalid, Nur Hafizah Abd; Nabilah Sarbini, Noor; Farhayu Ariffin, Nur; Warid Hussin, Mohd; Ismail, Mohammed A.

2018-03-01

This paper studies the drying shrinkage of mortar incorporating oil palm biomass waste including Palm Oil Fuel Ash, Oil Palm Kernel Shell and Oil Palm Fibre. Nano size of palm oil fuel ash was used up to 80 % as cement replacement by weight. The ash has been treated to improve the physical and chemical properties of mortar. The mass ratio of sand to blended ashes was 3:1. The test was carried out using 25 × 25 × 160 mm prism for drying shrinkage tests and 70 × 70 ×70 mm for compressive strength test. The results show that the shrinkage value of biomass mortar is reduced by 31% compared with OPC mortar thus, showing better performance in restraining deformation of the mortar while the compressive strength increased by 24% compared with OPC mortar at later age. The study gives a better understanding of how the biomass waste affect on mortar compressive strength and drying shrinkage behaviour. Overall, the oil palm biomass waste can be used to produce a better performance mortar at later age in terms of compressive strength and drying shrinkage.

Plastic shrinkage of mortars with shrinkage reducing admixture and lightweight aggregates studied by neutron tomography

International Nuclear Information System (INIS)

Wyrzykowski, Mateusz; Trtik, Pavel; Münch, Beat; Weiss, Jason; Vontobel, Peter; Lura, Pietro

2015-01-01

Water transport in fresh, highly permeable concrete and rapid water evaporation from the concrete surface during the first few hours after placement are the key parameters influencing plastic shrinkage cracking. In this work, neutron tomography was used to determine both the water loss from the concrete surface due to evaporation and the redistribution of fluid that occurs in fresh mortars exposed to external drying. In addition to the reference mortar with a water to cement ratio (w/c) of 0.30, a mortar with the addition of pre-wetted lightweight aggregates (LWA) and a mortar with a shrinkage reducing admixture (SRA) were tested. The addition of SRA reduced the evaporation rate from the mortar at the initial stages of drying and reduced the total water loss. The pre-wetted LWA released a large part of the absorbed water as a consequence of capillary pressure developing in the fresh mortar due to evaporation

Plastic shrinkage of mortars with shrinkage reducing admixture and lightweight aggregates studied by neutron tomography

Energy Technology Data Exchange (ETDEWEB)

Wyrzykowski, Mateusz, E-mail: mateusz.wyrzykowski@empa.ch [Empa, Swiss Federal Laboratories for Materials Science and Technology, Concrete and Construction Chemistry Laboratory, Dübendorf (Switzerland); Lodz University of Technology, Department of Building Physics and Building Materials, Lodz (Poland); Trtik, Pavel [Paul Scherrer Institute, Laboratory for Neutron Scattering and Imaging, Villigen (Switzerland); Empa, Swiss Federal Laboratories for Materials Science and Technology, Concrete and Construction Chemistry Laboratory, Dübendorf (Switzerland); Münch, Beat [Empa, Swiss Federal Laboratories for Materials Science and Technology, Concrete and Construction Chemistry Laboratory, Dübendorf (Switzerland); Weiss, Jason [Purdue University, School of Civil Engineering, West Lafayette (United States); Vontobel, Peter [Paul Scherrer Institute, Laboratory for Neutron Scattering and Imaging, Villigen (Switzerland); Lura, Pietro [Empa, Swiss Federal Laboratories for Materials Science and Technology, Concrete and Construction Chemistry Laboratory, Dübendorf (Switzerland); ETH Zurich, Institute for Building Materials (IfB), Zurich (Switzerland)

2015-07-15

Water transport in fresh, highly permeable concrete and rapid water evaporation from the concrete surface during the first few hours after placement are the key parameters influencing plastic shrinkage cracking. In this work, neutron tomography was used to determine both the water loss from the concrete surface due to evaporation and the redistribution of fluid that occurs in fresh mortars exposed to external drying. In addition to the reference mortar with a water to cement ratio (w/c) of 0.30, a mortar with the addition of pre-wetted lightweight aggregates (LWA) and a mortar with a shrinkage reducing admixture (SRA) were tested. The addition of SRA reduced the evaporation rate from the mortar at the initial stages of drying and reduced the total water loss. The pre-wetted LWA released a large part of the absorbed water as a consequence of capillary pressure developing in the fresh mortar due to evaporation.

Influence of shrinkage porosity on fatigue performance of iron castings and life estimation method

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Wei Liu

2016-01-01

Full Text Available Shrinkage porosity exists more or less in heavy castings, and it plays an important role in the fatigue behavior of cast materials. In this study, fatigue tests were carried out on the QT400-18 cast iron specimens containing random degrees of shrinkage porosity defect. Experimental results showed that the order of magnitude of life scattered from 103 to 106 cycles when the shrinkage percentage ranged from 0.67% to 5.91%. SEM analyses were carried out on the shrinkage porosity region. The inter-granular discontinuous, micro cracks and inclusions interfered with the fatigue sliding or hindering process. The slip in shrinkage porosity region was not as orderly as the ordinary continuous medium. The shrinkage porosity area on fracture surface (SPAFS and alternating stress intensity factor (ASIF were applied to evaluate the tendency of residual life distribution; their relationship was fitted by negative exponent functions. Based on the intermediate variable of ASIF, a fatigue life prediction model of nodular cast iron containing shrinkage porosity defects was established. The modeling prediction was in agreement with the experimental results.

Influence of fly ash fineness on water requirement and shrinkage of blended cement mortars

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Vanissorn Vimonsatit

2015-12-01

Full Text Available In this paper, the influence of fly ash fineness on water requirement and shrinkage of blended cement mortar was studied. The results indicate that the water requirement and shrinkage characteristic of the blended cement mortar are dependent on fly ash fineness and replacement level. The use of coarse fly ash slightly reduces the water requirement but greatly reduced the drying and the autogenous shrinkage of the blended cement mortars and the reduction is more with an increase in the fly ash replacement level. The finer fly ashes further reduce the water requirement, but increase the drying and the autogenous shrinkages as compared with coarser fly ash. The incorporation of superplasticizer drastically reduces the water requirement, but the effect on the drying and autogenous shrinkages of the normal Portland cement mortar is small. However, for the fly ash mortar, the use of superplasticizer results in a decrease in drying shrinkage and in a substantial increase in the autogenous shrinkage particularly for the fine fly ash at a high replacement level.

Prediction of shrinkage cracking age of concrete with and without expansive additive

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Dung Tien Nguyen

2010-10-01

Full Text Available The aim of this research is to propose a model for predicting cracking age of concrete due to restrained shrinkage. Thisstudy focuses on analyzing shrinkage and expansion mechanisms in the expansive concrete to formulate a model that can beemployed to predict whether shrinkage cracking occurs or not. In case of conventional (non-expansive concrete, this modelcan be applied by neglecting the early expansion due to expansive additive. Parameters considered in this model are restrainedexpansion, free shrinkage, cracking strain that can be experimentally measured by experiment and tensile creep which isderived by back calculation. The model was verified by test results of expansive concrete mixtures as well as normal concretemixtures both with and without fly ash.

Can superabsorbent polymers mitigate shrinkage in cementitious materials blended with supplementary cementitious materials?

DEFF Research Database (Denmark)

Snoeck, Didier; Jensen, Ole Mejlhede; De Belie, Nele

2016-01-01

A promising way to mitigate autogenous shrinkage in cementitious materials with a low water-to-binder ratio is internal curing by the use of superabsorbent polymers. Superabsorbent polymers are able to absorb multiple times their weight in water and can be applied as an internal water reservoir...... to induce internal curing and mitigation of self-desiccation. Their purposefulness has been demonstrated in Portland cement pastes with and without silica fume. Nowadays, fly ash and blast-furnace slag containing binders are also frequently used in the construction industry. The results on autogenous...... shrinkage in materials blended with fly ash or blast-furnace slag remain scarce, especially after one week of age. This paper focuses on the autogenous shrinkage by performing manual and automated shrinkage measurements up to one month of age. Without superabsorbent polymers, autogenous shrinkage...

Effects of Shrinkage Reducing Agent and Expansive Additive on Mortar Properties

OpenAIRE

Treesuwan, Sarapon; Maleesee, Komsan

2017-01-01

This research is to study the effect of mortar mixed with shrinkage reducing agent (polyoxyalkylene alkyl ether type), expansive additive (CaO type), and fly ash (hereinafter “SRA,” “EX,” and “FA,” resp.). Moreover, steam curing was studied to improve the properties of mortar. The plastic shrinkage test was conducted by using the strain gauge embedded at 0.5 cm from the surface according to the ASTM C1579-06 standard within early age followed by the total shrinkage test and compressive streng...

Modeling Restrained Shrinkage Induced Cracking in Concrete Rings Using the Thick Level Set Approach

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Rebecca Nakhoul

2018-03-01

Full Text Available Modeling restrained shrinkage-induced damage and cracking in concrete is addressed herein. The novel Thick Level Set (TLS damage growth and crack propagation model is used and adapted by introducing shrinkage contribution into the formulation. The TLS capacity to predict damage evolution, crack initiation and growth triggered by restrained shrinkage in absence of external loads is evaluated. A study dealing with shrinkage-induced cracking in elliptical concrete rings is presented herein. Key results such as the effect of rings oblateness on stress distribution and critical shrinkage strain needed to initiate damage are highlighted. In addition, crack positions are compared to those observed in experiments and are found satisfactory.

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction

Energy Technology Data Exchange (ETDEWEB)

Kyrpides, Nikos; Anderson, Iain; Rodriguez, Jason; Susanti, Dwi; Porat, Iris; Reich, Claudia; Ulrich, Luke E.; Elkins, James G.; Mavromatis, Kostas; Lykidis, Athanasios; Kim, Edwin; Thompson, Linda S.; Nolan, Matt; Land, Miriam; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Detter, Chris; Zhulin, Igor B.; Olsen, Gary J.; Whitman, William; Mukhopadhyay, Biswarup; Bristow, James; Kyrpides, Nikos

2008-01-01

We report the complete genome of Thermofilum pendens, a deep-branching, hyperthermophilic member of the order Thermoproteales within the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known to utilize peptides as an energy source, but the genome reveals substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may gain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogenlyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time this enzyme has been found outside of Methanosarcinales, and a presenilin-related protein. Predicted highly expressed proteins do not include housekeeping genes, and instead include ABC transporters for carbohydrates and peptides, and CRISPR-associated proteins.

Neolithic and Medieval virus genomes reveal complex evolution of Hepatitis B.

Science.gov (United States)

Krause-Kyora, Ben; Susat, Julian; Key, Felix M; Kühnert, Denise; Bosse, Esther; Immel, Alexander; Rinne, Christoph; Kornell, Sabin-Christin; Yepes, Diego; Franzenburg, Sören; Heyne, Henrike O; Meier, Thomas; Lösch, Sandra; Meller, Harald; Friederich, Susanne; Nicklisch, Nicole; Alt, Kurt W; Schreiber, Stefan; Tholey, Andreas; Herbig, Alexander; Nebel, Almut; Krause, Johannes

2018-05-10

The hepatitis B virus (HBV) is one of the most widespread human pathogens known today, yet its origin and evolutionary history are still unclear and controversial. Here, we report the analysis of three ancient HBV genomes recovered from human skeletons found at three different archaeological sites in Germany. We reconstructed two Neolithic and one medieval HBV genomes by de novo assembly from shotgun DNA sequencing data. Additionally, we observed HBV-specific peptides using paleo-proteomics. Our results show that HBV circulates in the European population for at least 7000 years. The Neolithic HBV genomes show a high genomic similarity to each other. In a phylogenetic network, they do not group with any human-associated HBV genome and are most closely related to those infecting African non-human primates. These ancient virus forms appear to represent distinct lineages that have no close relatives today and possibly went extinct. Our results reveal the great potential of ancient DNA from human skeletons in order to study the long-time evolution of blood borne viruses. © 2018, Krause-Kyora et al.

Self-compacting fine-grained concretes with compensated shrinkage

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Alimov Lev

2017-01-01

Full Text Available This paper substantiates the efficiency of application of fine-grained concrete for erection of cast-in-place concrete and reinforced concrete structures of different purpose. On the basis of analysis of experimental research results it was established that the introduction of microfillers with expansion effect to composite binder allows not only improving the rheological properties of fine-grained concrete, but also decreasing of value of shrinkage strain and improving of concrete crack resistance and durability. The analysis of the results of industrial use of fine-grained concretes with compensated shrinkage is given.

Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

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Pierre Lefeuvre

Full Text Available Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.

Topology optimization of reinforced concrete structures considering control of shrinkage and strength failure

DEFF Research Database (Denmark)

Luo, Yangjun; Wang, Michael Yu; Zhou, Mingdong

2015-01-01

To take into account the shrinkage effect in the early stage of Reinforced Concrete (RC) design, an effective continuum topology optimization method is presented in this paper. Based on the power-law interpolation, shrinkage of concrete is numerically simulated by introducing an additional design......-dependent force. Under multi-axial stress conditions, the concrete failure surface is well fitted by two Drucker-Prager yield functions. The optimization problem aims at minimizing the cost function under yield strength constraints on concrete elements and a structural shrinkage volume constraint. In conjunction...... to ensure the structural safety under the combined action of external loads and shrinkage....

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

DEFF Research Database (Denmark)

Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.

2014-01-01

,000-year-old individual (MA-1), from Mal'ta in south-central Siberia, to an average depth of 1×. To our knowledge this is the oldest anatomically modern human genome reported to date. The MA-1 mitochondrial genome belongs to haplogroup U, which has also been found at high frequency among Upper Palaeolithic......The origins of the First Americans remain contentious. Although Native Americans seem to be genetically most closely related to east Asians, there is no consensus with regard to which specific Old World populations they are closest to. Here we sequence the draft genome of an approximately 24...... that the region was continuously occupied by humans throughout the Last Glacial Maximum. Our findings reveal that western Eurasian genetic signatures in modern-day Native Americans derive not only from post-Columbian admixture, as commonly thought, but also from a mixed ancestry of the First Americans....

Adaptations to a Subterranean Environment and Longevity Revealed by the Analysis of Mole Rat Genomes

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Xiaodong Fang

2014-09-01

Full Text Available Subterranean mammals spend their lives in dark, unventilated environments that are rich in carbon dioxide and ammonia and low in oxygen. Many of these animals are also long-lived and exhibit reduced aging-associated diseases, such as neurodegenerative disorders and cancer. We sequenced the genome of the Damaraland mole rat (DMR, Fukomys damarensis and improved the genome assembly of the naked mole rat (NMR, Heterocephalus glaber. Comparative genome analyses, along with the transcriptomes of related subterranean rodents, revealed candidate molecular adaptations for subterranean life and longevity, including a divergent insulin peptide, expression of oxygen-carrying globins in the brain, prevention of high CO2-induced pain perception, and enhanced ammonia detoxification. Juxtaposition of the genomes of DMR and other more conventional animals with the genome of NMR revealed several truly exceptional NMR features: unusual thermogenesis, an aberrant melatonin system, pain insensitivity, and unique processing of 28S rRNA. Together, these genomes and transcriptomes extend our understanding of subterranean adaptations, stress resistance, and longevity.

Investigations of linear contraction and shrinkage stresses development in hypereutectic al-si binary alloys

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J. Mutwil

2009-07-01

Full Text Available Shrinkage phenomena during solidification and cooling of hypereutectic aluminium-silicon alloys (AlSi18, AlSi21 have been examined. A vertical shrinkage rod casting with circular cross-section (constant or fixed: tapered has been used as a test sample. Two type of experiments have been conducted: 1 on development of the test sample linear dimension changes (linear expansion/contraction, 2 on development of shrinkage stresses in the test sample. By the linear contraction experiments the linear dimension changes of the test sample and the metal test mould as well a temperature in six points of the test sample have been registered. By shrinkage stresses examination a shrinkage tension force and linear dimension changes of the test sample as well a temperature in three points of the test sample have been registered. Registered time dependences of the test bar and the test mould linear dimension changes have shown, that so-called pre-shrinkage extension has been mainly by mould thermal extension caused. The investigation results have shown that both: the linear contraction as well as the shrinkage stresses development are evident dependent on metal temperature in a warmest region the sample (thermal centre.

Effects of drying conditions, admixtures and specimen size on shrinkage strains

International Nuclear Information System (INIS)

Al-Saleh, Saleh A.; Al-Zaid, Rajeh Z.

2006-01-01

The paper presents the results of an experimental investigation on the effects of drying conditions, specimen size and presence of plasticizing admixture on the development of shrinkage strains. The measurements are taken in a harsh (50 deg. C and 5% R.H.) and a moderate environment (28 deg. C and 50% R.H.). The results include strain development at various levels of cross sections of concrete prisms. The drying conditions are found to be the dominant parameter affecting the shrinkage strain development particularly in specimens of smaller sizes. The effect of plasticizing admixture on shrinkage strains is negligible

Porcine intestinal mast cells. Evaluation of different fixatives for histochemical staining techniques considering tissue shrinkage

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J. Rieger

2013-07-01

Full Text Available Staining of mast cells (MCs, including porcine ones, is critically dependent upon the fixation and staining technique. In the pig, mucosal and submucosal MCs do not stain or stain only faintly after formalin fixation. Some fixation methods are particularly recommended for MC staining, for example the fixation with Carnoy or lead salts. Zinc salt fixation (ZSF has been reported to work excellently for the preservation of fixation-sensitive antigens. The aim of this study was to establish a reliable histological method for counting of MCs in the porcine intestinum. For this purpose, different tissue fixation and staining methods that also allow potential subsequent immunohistochemical investigations were evaluated in the porcine mucosa, as well as submucosa of small and large intestine. Tissues were fixed in Carnoy, lead acetate, lead nitrate, Zamboni and ZSF and stained subsequently with either polychromatic methylene blue, alcian blue or toluidine blue. For the first time our study reveals that ZSF, a heavy metal fixative, preserves metachromatic staining of porcine MCs. Zamboni fixation was not suitable for histochemical visualization of MCs in the pig intestine. All other tested fixatives were suitable. Alcian blue and toluidine blue co-stained intestinal goblet cells which made a prima facie identification of MCs difficult. The polychromatic methylene blue proved to be the optimal staining. In order to compare MC counting results of the different fixation methods, tissue shrinkage was taken into account. As even the same fixation caused shrinkage-differences between tissue from small and large intestine, different factors for each single fixation and intestinal localization had to be calculated. Tissue shrinkage varied between 19% and 57%, the highest tissue shrinkage was found after fixation with ZSF in the large intestine, the lowest one in the small intestine after lead acetate fixation. Our study emphasizes that MC counting results from

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

DEFF Research Database (Denmark)

Machado, Henrique; Gram, Lone

2017-01-01

was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

Shrinkage stress in concrete under dry-wet cycles: an example with concrete column

Science.gov (United States)

Gao, Yuan; Zhang, Jun; Luosun, Yiming

2014-02-01

This paper focuses on the simulation of shrinkage stress in concrete structures under dry-wet environments. In the modeling, an integrative model for autogenous and drying shrinkage predictions of concrete under dry-wet cycles is introduced first. Second, a model taking both cement hydration and moisture diffusion into account synchronously is used to calculate the distribution of interior humidity in concrete. Using the above two models, the distributions of shrinkage strain and stress in concrete columns made by normal and high strength concrete respectively under dry-wet cycles are calculated. The model results show that shrinkage gradient along the radial direction of the column from the center to outer surface increases with age as the outer circumference suffers to dry. The maximum and minimum shrinkage occur at the outer surface and the center of the column, respectively, under drying condition. As wetting starts, the shrinkage strain decreases with increase of interior humidity. The closer to the wetting face, the higher the humidity and the lower the shrinkage strain, as well as the lower the shrinkage stress. As results of the dry-wet cycles acting on the outer circumference of the column, cyclic stress status is developed within the area close to the outer surface of the column. The depth of the influencing zone of dry-wet cyclic action is influenced by concrete strength and dry-wet regime. For low strength concrete, relatively deeper influencing zone is expected compared with that of high strength concrete. The models are verified by concrete-steel composite ring tests and a good agreement between model and test results is found.

The effect of fibers on the loss of water by evaporation and shrinkage of concrete

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N. M. P. Pillar

Full Text Available Shrinkage is one of the least desirable attributes in concrete. Large areas of exposed concrete surfaces , such as in shotcrete tunnel linings, where it is practically impossible to make a moist cure, are highly susceptible to plastic shrinkage at early ages. The autogenous and drying shrinkage can lead to states of greater than threshold strength, causing fracture, mechanical damage and lack of durability of concrete structures. The addition of fibers can greatly reduce plastic shrinkage, but has limited effect in mitigating autogenous and drying shrinkage. To evaluate the performance of polypropylene and steel fibers to understand their effect on shrinkage of concrete, a study was carried out to relate the loss of water from the paste and the shrinkage during the first 28 days of age, and compare it with a control mix without fiber. The loss of water was obtained by the weight loss of the specimens at different ages, since the only component that could contribute for the loss of weight was the water lost by the paste of the concrete. And the paste itself is the only source of shrinkage. Uniaxial compressive tests from very early ages enabled the determination of time when plastic shrinkage ended. It was observed that the control concrete mix lost three times more water and developed plastic and drying shrinkage 60 % higher than the fiber reinforced concrete mixes. It was possible to demonstrate that the reduced loss of water caused by the incorporation of fibers is related to the mitigation of plastic shrinkage. It was observed that the fibers are effective to restrain the movement of water through the cement paste in the plastic state, however such effect is limited after concrete starts the hardening state.

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

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Zhiliang Yu

2017-07-01

Full Text Available Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.

Digital image analysis of radial shrinkage of fresh spruce (Picea abies L.) wood.

Science.gov (United States)

Hansmann, Christian; Konnerth, Johannes; Rosner, Sabine

2011-03-21

Contact-free digital image analysis was performed of the radial shrinkage of fresh, fully saturated small spruce wood beams. An experimental test set-up was developed to ensure constant distance from the charge-coupled device camera to the sample surface as well as constant climate and light conditions during the whole experiment. Dimensional changes were observed immediately after the drying process began. An unexpected distinct effect could be observed which could not be explained by drying surface layers only. After a fast initial radial shrinkage a slowing down of the dimensional changes occurred at high mean moisture contents. A complete interruption of any dimensional changes followed. Finally, a recovery from shrinkage was even observed. It is assumed that strong negative pressure occurred in the fully saturated capillaries owing to dehydration which led to additional dimensional changes. As a consequence, the break of the water column and aeration in these capillaries finally resulted in a recovery period in the shrinkage rate due to the pressure release. After this effect, the dehydration was characterized by a phase of fast and almost linear shrinkage due to drying surface layers. Finally, the shrinkage slowed down to zero when reaching equilibrium moisture content.

Astrocytic mechanisms explaining neural-activity-induced shrinkage of extraneuronal space

DEFF Research Database (Denmark)

Østby, Ivar; Øyehaug, Leiv; Einevoll, Gaute T

2009-01-01

Neuronal stimulation causes approximately 30% shrinkage of the extracellular space (ECS) between neurons and surrounding astrocytes in grey and white matter under experimental conditions. Despite its possible implications for a proper understanding of basic aspects of potassium clearance and astr......Neuronal stimulation causes approximately 30% shrinkage of the extracellular space (ECS) between neurons and surrounding astrocytes in grey and white matter under experimental conditions. Despite its possible implications for a proper understanding of basic aspects of potassium clearance...... concentrations observed in connection with neuronal stimulation, the actions of the Na(+)/K(+)/Cl(-) (NKCC1) and the Na(+)/HCO(3) (-) (NBC) cotransporters appear to be critical determinants for achieving observed quantitative levels of ECS shrinkage. Considering the current state of knowledge, the model...

Moisture migration and shrinkage of hardened cement paste at elevated temperatures

International Nuclear Information System (INIS)

Numao, Tatsuya; Mihashi, Hirozo.

1991-01-01

The drying shrinkage of concrete is caused by the loss of water in the concrete. The moisture diffusion behavior influences the mechanical properties of concrete. When concrete is exposed to high temperature, the rate of moisture migration becomes fast, and moisture gradient is formed. This gradient causes cracks on the concrete surface. Accordingly, it is important to study on the relation between the drying shrinkage and the water diffusion in concrete when its mechanical properties at elevated temperature are discussed. In this paper, the results of the experiment which was carried out by using thin-walled cylinder specimens kept at different temperature and stress are reported. The specimens, the drying shrinkage of concrete and acoustic emission (AE), the thermal expansion of hardened cement paste, the influence that temperature change exerted to the drying shrinkage, and the influence that compressive stress and temperature exerted to water migration are described. The thin-walled cylinder specimens were useful for these experimental studies. (K.I.)

Shrinkage reduction of dental composites by addition of expandable zirconia filler

DEFF Research Database (Denmark)

Skovgaard, M.; Almdal, Kristoffer; Sørensen, Bent F.

2011-01-01

. The shrinkage of the composite was calculated from density measurements using Archimedes method. The rate of the phase transformation in resin was measured by determining the volume fraction of monoclinic zirconia (vm). The composite had a vm of 0.5 after 8 h of water storage. The overall shrinkage...

Aerosol particle shrinkage event phenomenology in a South European suburban area during 2009-2015

Science.gov (United States)

Alonso-Blanco, E.; Gómez-Moreno, F. J.; Núñez, L.; Pujadas, M.; Cusack, M.; Artíñano, B.

2017-07-01

A high number of aerosol particle shrinkage cases (70) have been identified and analyzed from an extensive and representative database of aerosol size distributions obtained between 2009 and 2015 at an urban background site in Madrid (Spain). A descriptive classification based on the process from which the shrinkage began is proposed according which shrinkage events were divided into three groups: (1) NPF + shrinkage (NPF + S) events, (2) aerosol particle growth process + shrinkage (G + S) events, and (3) pure shrinkage (S) events. The largest number of shrinkages corresponded to the S-type followed by NPF + S, while the G + S events were the least frequent group recorded. Duration of shrinkages varied widely from 0.75 to 8.5 h and SR from -1.0 to -11.1 nm h-1. These processes typically occurred in the afternoon, around 18:00 UTC, caused by two situations: i) a wind speed increase usually associated with a change in the wind direction (over 60% of the observations) and ii) the reduction of photochemical activity at the end of the day. All shrinkages were detected during the warm period, mainly between May and August, when local meteorological conditions (high solar irradiance and temperature and low relative humidity), atmospheric processes (high photochemical activity) and availability of aerosol-forming precursors were favorable for their development. As a consequence of these processes, the particles concentration corresponding to the Aitken mode decreased into the nucleation mode. The accumulation mode did not undergo significant changes during these processes. In some cases, a dilution of the particulate content in the ambient air was observed. This work, goes further than others works dealing with aerosol particles shrinkages, as it incorporates as a main novelty a classification methodology for studying these processes. Moreover, compared to other studies, it is supported by a high and representative number of observations. Thus, this study contributes to

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

Science.gov (United States)

Stata, Matt; Wang, Wei; White, Merlin M.; Moncalvo, Jean-Marc

2018-01-01

ABSTRACT Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. PMID:29764946

Shrinkage Characteristics of Experimental Polymer Containing Composites under Controlled Light Curing Modes

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Alain Pefferkorn

2012-01-01

Full Text Available The adsorption of polymethylmethacrylate polymer of different molecular weight at the aerosil/ethyleneglycol- or 1,3 butanediol-dimethacrylate interfaces was determined to provide microstructured networks. Their structural characteristics were determined to be controlled by the amount of polymer initially supplied to the system. The sediment (the settled phase characteristics, determined as a function of the polymer concentration and the rate of the polymerization shrinkage determined for composite resins, obtained by extrusion of the sediment after centrifugation, were found to be correlated. The specific role of the adsorbed polymer was found to be differently perturbed with the supplementary supply of dimethacrylate based monomer additives. Particularly, the bisphenol A dimethacrylate that generated crystals within the sediment was found to impede the shrinkage along the crystal lateral faces and strongly limit the shrinkage along its basal faces. Addition of ethyleneglycol- or polyethylene-glycoldimethacrylate monomers was determined to modify the sedimentation characteristics of the aerosil suspension and the shrinkage properties of the composites. Finally, the effects of stepwise light curing methods with prolonged lighting-off periods were investigated and found to modify the development and the final values of the composite shrinkage.

Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes

Science.gov (United States)

In this study, we identified and compared nucleotide-binding site (NBS) domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China). Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approxima...

A numerical analysis method on thermal and shrinkage stress of concrete

International Nuclear Information System (INIS)

Takiguchi, Katsuki; Hotta, Hisato

1991-01-01

Thermal stress often causes cracks in large scale concrete such as that for dam construction. The drying shrinkage of concrete causes cracks in concrete structures. These thermal stress and drying shrinkage stress may be the main reasons cracks occur in concrete, however there is few research which dealt with both stresses together. The problems on the thermal stress and the drying shrinkage are not independent, and should be dealt with together, because both temperature and water content of concrete affect hydration reaction, and the degree of hydration determines all the characteristics of concrete at early age. In this study, the degree of hydration is formulated experimentally, and a numerical stress analysis method taking the hydration reaction in consideration is presented. The formulation of the rate of hydration reaction, the method of analyzing thermal and drying shrinkage stresses, the analytical results for a concrete column and the influence that continuous load exerted to the tensile strength of concrete are reported. The relatively high stress nearly equal to the tensile strength of concrete arises near the surface. (K.I.)

Calcium silicate structure and carbonation shrinkage of a tobermorite-based material

International Nuclear Information System (INIS)

Matsushita, Fumiaki; Aono, Yoshimichi; Shibata, Sumio

2004-01-01

Carbonated autoclaved aerated concretes (AACs) show no shrinkage at a degree of carbonation approximately less than 20%. The 29 Si MAS NMR spectrum showed that at a degree of carbonation less than 25%, the typical double-chain silicate anion structure of tobermorite-11A was well maintained and interlayer Ca ions were exchanged with protons. This corresponded to the absence of carbonation shrinkage at a degree of carbonation less than 20%. When the degree of carbonation increased from 25% to 50% up to 60%, the double-chain silicate anion structure of tobermorite-11A was decomposed and Ca ions in the Ca-O layers were dissolved, showing a possible mechanism of carbonation shrinkage

Astrocytic mechanisms explaining neural-activity-induced shrinkage of extraneuronal space.

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Ivar Østby

2009-01-01

Full Text Available Neuronal stimulation causes approximately 30% shrinkage of the extracellular space (ECS between neurons and surrounding astrocytes in grey and white matter under experimental conditions. Despite its possible implications for a proper understanding of basic aspects of potassium clearance and astrocyte function, the phenomenon remains unexplained. Here we present a dynamic model that accounts for current experimental data related to the shrinkage phenomenon in wild-type as well as in gene knockout individuals. We find that neuronal release of potassium and uptake of sodium during stimulation, astrocyte uptake of potassium, sodium, and chloride in passive channels, action of the Na/K/ATPase pump, and osmotically driven transport of water through the astrocyte membrane together seem sufficient for generating ECS shrinkage as such. However, when taking into account ECS and astrocyte ion concentrations observed in connection with neuronal stimulation, the actions of the Na(+/K(+/Cl(- (NKCC1 and the Na(+/HCO(3 (- (NBC cotransporters appear to be critical determinants for achieving observed quantitative levels of ECS shrinkage. Considering the current state of knowledge, the model framework appears sufficiently detailed and constrained to guide future key experiments and pave the way for more comprehensive astroglia-neuron interaction models for normal as well as pathophysiological situations.

Comparative genomics analyses revealed two virulent Listeria monocytogenes strains isolated from ready-to-eat food.

Science.gov (United States)

Lim, Shu Yong; Yap, Kien-Pong; Thong, Kwai Lin

2016-01-01

Listeria monocytogenes is an important foodborne pathogen that causes considerable morbidity in humans with high mortality rates. In this study, we have sequenced the genomes and performed comparative genomics analyses on two strains, LM115 and LM41, isolated from ready-to-eat food in Malaysia. The genome size of LM115 and LM41 was 2,959,041 and 2,963,111 bp, respectively. These two strains shared approximately 90% homologous genes. Comparative genomics and phylogenomic analyses revealed that LM115 and LM41 were more closely related to the reference strains F2365 and EGD-e, respectively. Our virulence profiling indicated a total of 31 virulence genes shared by both analysed strains. These shared genes included those that encode for internalins and L. monocytogenes pathogenicity island 1 (LIPI-1). Both the Malaysian L. monocytogenes strains also harboured several genes associated with stress tolerance to counter the adverse conditions. Seven antibiotic and efflux pump related genes which may confer resistance against lincomycin, erythromycin, fosfomycin, quinolone, tetracycline, and penicillin, and macrolides were identified in the genomes of both strains. Whole genome sequencing and comparative genomics analyses revealed two virulent L. monocytogenes strains isolated from ready-to-eat foods in Malaysia. The identification of strains with pathogenic, persistent, and antibiotic resistant potentials from minimally processed food warrant close attention from both healthcare and food industry.

Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers.

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Yuichi Shiraishi

Full Text Available Recent studies applying high-throughput sequencing technologies have identified several recurrently mutated genes and pathways in multiple cancer genomes. However, transcriptional consequences from these genomic alterations in cancer genome remain unclear. In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis B virus (HBV-related hepatocellular carcinomas (HCCs and their matched controls. Comparison of whole genome sequence (WGS and RNA-Seq revealed much evidence that various types of genomic mutations triggered diverse transcriptional changes. Not only splice-site mutations, but also silent mutations in coding regions, deep intronic mutations and structural changes caused splicing aberrations. HBV integrations generated diverse patterns of virus-human fusion transcripts depending on affected gene, such as TERT, CDK15, FN1 and MLL4. Structural variations could drive over-expression of genes such as WNT ligands, with/without creating gene fusions. Furthermore, by taking account of genomic mutations causing transcriptional aberrations, we could improve the sensitivity of deleterious mutation detection in known cancer driver genes (TP53, AXIN1, ARID2, RPS6KA3, and identified recurrent disruptions in putative cancer driver genes such as HNF4A, CPS1, TSC1 and THRAP3 in HCCs. These findings indicate genomic alterations in cancer genome have diverse transcriptomic effects, and integrated analysis of WGS and RNA-Seq can facilitate the interpretation of a large number of genomic alterations detected in cancer genome.

Shrinkage modeling of concrete reinforced by palm fibres in hot dry environments

Science.gov (United States)

Akchiche, Hamida; Kriker, Abdelouahed

2017-02-01

The cement materials, such as concrete and conventional mortar present very little resistance to traction and cracking, these hydraulic materials which induces large withdrawals on materials and cracks in structures. The hot dry environments such as: the Saharan regions of Algeria, Indeed, concrete structures in these regions are very fragile, and present high shrinkage. Strengthening of these materials by fibers can provide technical solutions for improving the mechanical performance. The aim of this study is firstly, to reduce the shrinkage of conventional concrete with its reinforcement with date palm fibers. In fact, Algeria has an extraordinary resources in natural fibers (from Palm, Abaca, Hemp) but without valorization in practical areas, especially in building materials. Secondly, to model the shrinkage behavior of concrete was reinforced by date palm fibers. In the literature, several models for still fiber concrete were founded but few are offers for natural fiber concretes. To do so, a still fiber concretes model of YOUNG - CHERN was used. According to the results, a reduction of shrinkage with reinforcement by date palm fibers was showed. A good ability of molding of shrinkage of date palm reinforced concrete with YOUNG - CHERN Modified model was obtained. In fact, a good correlation between experimental data and the model data was recorded.

Genome sequencing and comparative genomics reveal a repertoire of putative pathogenicity genes in chilli anthracnose fungus Colletotrichum truncatum.

Science.gov (United States)

Rao, Soumya; Nandineni, Madhusudan R

2017-01-01

Colletotrichum truncatum, a major fungal phytopathogen, causes the anthracnose disease on an economically important spice crop chilli (Capsicum annuum), resulting in huge economic losses in tropical and sub-tropical countries. It follows a subcuticular intramural infection strategy on chilli with a short, asymptomatic, endophytic phase, which contrasts with the intracellular hemibiotrophic lifestyle adopted by most of the Colletotrichum species. However, little is known about the molecular determinants and the mechanism of pathogenicity in this fungus. A high quality whole genome sequence and gene annotation based on transcriptome data of an Indian isolate of C. truncatum from chilli has been obtained. Analysis of the genome sequence revealed a rich repertoire of pathogenicity genes in C. truncatum encoding secreted proteins, effectors, plant cell wall degrading enzymes, secondary metabolism associated proteins, with potential roles in the host-specific infection strategy, placing it next only to the Fusarium species. The size of genome assembly, number of predicted genes and some of the functional categories were similar to other sequenced Colletotrichum species. The comparative genomic analyses with other species and related fungi identified some unique genes and certain highly expanded gene families of CAZymes, proteases and secondary metabolism associated genes in the genome of C. truncatum. The draft genome assembly and functional annotation of potential pathogenicity genes of C. truncatum provide an important genomic resource for understanding the biology and lifestyle of this important phytopathogen and will pave the way for designing efficient disease control regimens.

A break-even analysis of RFID technology for inventory sensitive to shrinkage

NARCIS (Netherlands)

Kok, de A.G.; Donselaar, van K.H.; Woensel, van T.

2008-01-01

By embedding RFID tags onto their products, both manufacturers and retailers try to control for shrinkage (e.g. due to theft). Current inventory control systems do not take into account the disappearing inventory due to this shrinkage. As a response, corrective actions are made by performing costly

Study of SEM preparation artefacts with correlative microscopy: Cell shrinkage of adherent cells by HMDS-drying.

Science.gov (United States)

Katsen-Globa, Alisa; Puetz, Norbert; Gepp, Michael M; Neubauer, Julia C; Zimmermann, Heiko

2016-11-01

One of the often reported artefacts during cell preparation to scanning electron microscopy (SEM) is the shrinkage of cellular objects, that mostly occurs at a certain time-dependent stage of cell drying. Various methods of drying for SEM, such as critical point drying, freeze-drying, as well as hexamethyldisilazane (HMDS)-drying, were usually used. The latter becomes popular since it is a low cost and fast method. However, the correlation of drying duration and real shrinkage of objects was not investigated yet. In this paper, cell shrinkage at each stage of preparation for SEM was studied. We introduce a shrinkage coefficient using correlative light microscopy (LM) and SEM of the same human mesenchymal stem cells (hMSCs). The influence of HMDS-drying duration on the cell shrinkage is shown: the longer drying duration, the more shrinkage is observed. Furthermore, it was demonstrated that cell shrinkage is inversely proportional to cultivation time: the longer cultivation time, the more cell spreading area and the less cell shrinkage. Our results can be applicable for an exact SEM quantification of cell size and determination of cell spreading area in engineering of artificial cellular environments using biomaterials. SCANNING 38:625-633, 2016. © 2016 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

Shrinkage Analysis on Thick Plate Part using Response Surface Methodology (RSM

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Isafiq M.

2016-01-01

Full Text Available The work reported herein is about an analysis on the quality (shrinkage on a thick plate part using Response Surface Methodology (RSM. Previous researches showed that the most influential factor affecting the shrinkage on moulded parts are mould and melt temperature. Autodesk Moldflow Insight software was used for the analysis, while specifications of Nessei NEX 1000 injection moulding machine and P20 mould material were incorporated in this study on top of Acrylonitrile Butadiene Styrene (ABS as a moulded thermoplastic material. Mould temperature, melt temperature, packing pressure and packing time were selected as variable parameters. The results show that the shrinkage have improved 42.48% and 14.41% in parallel and normal directions respectively after the optimisation process.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

OpenAIRE

Henrique Machado; Henrique Machado; Lone Gram

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

PREDIKSI SHRINKAGE UNTUK MENGHINDARI CACAT PRODUK PADA PLASTIC INJECTION

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Agus Dwi Anggono

2015-05-01

Full Text Available Plastic injection merupakan proses manufactur untuk membuat produk dengan bahan dasar plastic atau dalam kesempatan ini polypropylene. Pada proses tersebut seringkali terjadi cacat produk seperti pengerutan, retak, dimensi tidak sesuai dan kerusakan saat produk keluar dari mould, sehingga banyak material yang terbuang percuma. Meskipun cacat produk tersebut dipengaruhi banyak factor, tetapi yang paling utama adalah masalah shrinkage, atau penyusutan material setelah terjadi pendinginan. Sangat penting untuk melakukan prediksi lebih awal terjadinya penyusutan setelah pendinginan untuk menghindari cacat produk. Dalam penelitian ini akan dilakukan prediksi shrinkage yang akan digunakan untuk material polypropylene dengan cara perhitungan standar. Pembuatan modeling dalam bentuk 3D (tiga dimensi injection molding baik cavity maupun corenya dengan menggunakan CATIA, kemudian dilakukan analisis dengan software MoldFlow untuk pembuatan mesh dan memberikan batasan panas pada komponen sehingga dapat diketahui mode penyusutannya. Analisis ini akan memberikan gambaran tentang distribusi panas pada mould dan memberikan tentang gambaran aliran fluida. Pada analisis tersebut dapat dilihat gejala terjadinya cacat produk, jika hal itu terjadi maka perlu dilakukan perubahan shrinkage, sampai diperoleh hasil analisis yang baik.

Effect of steel fibers on plastic shrinkage cracking of normal and high strength concretes

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Özgür Eren

2010-06-01

Full Text Available Naturally concrete shrinks when it is subjected to a drying environment. If this shrinkage is restrained, tensile stresses develop and concrete may crack. Plastic shrinkage cracks are especially harmful on slabs. One of the methods to reduce the adverse effects of shrinkage cracking of concrete is by reinforcing concrete with short randomly distributed fibers. The main objective of this study was to investigate the effect of fiber volume and aspect ratio of hooked steel fibers on plastic shrinkage cracking behavior together with some other properties of concrete. In this research two different compressive strength levels namely 56 and 73 MPa were studied. Concretes were produced by adding steel fibers of 3 different volumes of 3 different aspect ratios. From this research study, it is observed that steel fibers can significantly reduce plastic shrinkage cracking behavior of concretes. On the other hand, it was observed that these steel fibers can adversely affect some other properties of concrete during fresh and hardened states.

Drying Shrinkage Behaviour of Fibre Reinforced Concrete Incorporating Polyvinyl Alcohol Fibres and Fly Ash

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Amin Noushini

2014-01-01

Full Text Available The current study assesses the drying shrinkage behaviour of polyvinyl alcohol fibre reinforced concrete (PVA-FRC containing short-length (6 mm and long-length (12 mm uncoated monofilament PVA fibres at 0.125%, 0.25%, 0.375%, and 0.5% volumetric fractions. Fly ash is also used as a partial replacement of Portland cement in all mixes. PVA-FRC mixes have been compared to length change of control concrete (devoid of fibres at 3 storage intervals: early-age (0–7 days, short-term (0–28 days, and long-term (28–112 days intervals. The shrinkage results of FRC and control concrete up to 112 days indicated that all PVA-FRC mixes exhibited higher drying shrinkage than control. The shrinkage exhibited by PVA-FRC mixes ranged from 449 to 480 microstrain, where this value was only 427 microstrain in the case of control. In addition, the longer fibres exhibited higher mass loss, thus potentially contributing to higher shrinkage.

The Shrinkage Cracking Behavior in Reinforced Reactive Powder Concrete Walls

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Samir A. Al-Mashhadi

2017-07-01

Full Text Available In this study, the reduced scale wall models were used (they are believed to resemble as much as possible the field conditions to study the shrinkage behavior of reactive powder concrete (RPC base restrained walls. Six base restrained RPC walls were casted in different length/height ratios of two ratios of steel fiber by volume in Summer. These walls were restrained by reinforced concrete bases to provide the continuous base restraint to the walls. The mechanical properties of reactive powder concrete investigated were; compressive strength between (75.3 – 140.1 MPa, splitting tensile strength between (5.7 – 13.9 MPa, flexural tensile strength (7.7 – 24.5 MPa, and static modulus of elasticity (32.7 – 47.1GPa. Based on the observations of this work, it was found that the cracks did not develop in the reduced scale of the reactive powder concrete (RPC walls restrained from movement at their bases for different L/H ratios (2, 5, and 10 and for two ratio of steel fiber (1% & 2% during 90 days period of drying conditions. Moreover, the shrinkage values increase toward the edges. Based on the results of this work, the increase in the maximum shrinkage values of walls with 1% steel fiber were (29%, 28%, 28% of the maximum shrinkage values of walls with 2% steel fiber of length/height ratios of (2, 5, and 10 respectively. The experimental observation in beam specimens showed that the free shrinkage, tensile strain capacity and elastic tensile strain capacity (at date of cracking of beams with 1% steel fiber were higher than the beams with 2% steel fiber by about (24%, (45% and (42% respectively

The influence of superabsorbent polymers on the autogenous shrinkage properties of cement pastes with supplementary cementitious materials

DEFF Research Database (Denmark)

Snoeck, D.; Jensen, Ole Mejlhede; De Belie, N.

2015-01-01

Fly ash and blast-furnace slag containing binders are frequently used in the construction industry and it is important to know the extent of autogenous shrinkage and its (ideal) mitigation by superabsorbent polymers in these systems as a function of their age. In this paper, the autogenous...... shrinkage was determined by manual and automated shrinkage measurements. Autogenous shrinkage was reduced in cement pastes with the supplementary cementitious materials versus Portland cement pastes. At later ages, the rate of autogenous shrinkage is higher due to the pozzolanic activity. Internal curing...

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats.

Science.gov (United States)

Martino, Maria Elena; Bayjanov, Jumamurat R; Caffrey, Brian E; Wels, Michiel; Joncour, Pauline; Hughes, Sandrine; Gillet, Benjamin; Kleerebezem, Michiel; van Hijum, Sacha A F T; Leulier, François

2016-12-01

The ability of bacteria to adapt to diverse environmental conditions is well-known. The process of bacterial adaptation to a niche has been linked to large changes in the genome content, showing that many bacterial genomes reflect the constraints imposed by their habitat. However, some highly versatile bacteria are found in diverse habitats that almost share nothing in common. Lactobacillus plantarum is a lactic acid bacterium that is found in a large variety of habitat. With the aim of unravelling the link between evolution and ecological versatility of L. plantarum, we analysed the genomes of 54 L. plantarum strains isolated from different environments. Comparative genome analysis identified a high level of genomic diversity and plasticity among the strains analysed. Phylogenomic and functional divergence studies coupled with gene-trait matching analyses revealed a mixed distribution of the strains, which was uncoupled from their environmental origin. Our findings revealed the absence of specific genomic signatures marking adaptations of L. plantarum towards the diverse habitats it is associated with. This suggests fundamentally similar trends of genome evolution in L. plantarum, which occur in a manner that is apparently uncoupled from ecological constraint and reflects the nomadic lifestyle of this species. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Shrinkage-reducing admixtures and early-age desiccation in cement pastes and mortars

DEFF Research Database (Denmark)

Bentz, D. P.; Geiker, Mette Rica; Hansen, Kurt Kielsgaard

2001-01-01

Fundamental studies of the early-age desiccation of cement-based materials with and without a shrinkage-reducing admixture (SRA) have been performed. Studies have been conducted under both sealed and drying conditions. Physical measurements include mass loss, surface tension, X-ray absorption to ...... to low w/c ratio concretes undergoing self-desiccation, in addition to their normal usage to reduce drying shrinkage.......Fundamental studies of the early-age desiccation of cement-based materials with and without a shrinkage-reducing admixture (SRA) have been performed. Studies have been conducted under both sealed and drying conditions. Physical measurements include mass loss, surface tension, X-ray absorption...

Effects of Shrinkage Reducing Agent and Expansive Admixture on the Volume Deformation of Ultrahigh Performance Concrete

OpenAIRE

Anshuang, Su; Ling, Qin; Shoujie, Zhang; Jiayang, Zhang; Zhaoyu, Li

2017-01-01

This paper investigated the influences of shrinkage reducing agent and expansive admixture on autogenous and drying shrinkage of ultrahigh performance concrete (UHPC) containing antifoaming admixture. The shrinkage reducing agent was used at dosage of 0.5%, 1%, and 2% and the expansive admixture was used at dosage of 2% to 4% by mass of cementitious material. The results show that the air content of UHPC increases with the higher addition of shrinkage reducing agent and expansive admixtures. ...

The effect of mucosal cuff shrinkage around dental implants during healing abutment replacement.

Science.gov (United States)

Nissan, J; Zenziper, E; Rosner, O; Kolerman, R; Chaushu, L; Chaushu, G

2015-10-01

Soft tissue shrinkage during the course of restoring dental implants may result in biological and prosthodontic difficulties. This study was conducted to measure the continuous shrinkage of the mucosal cuff around dental implants following the removal of the healing abutment up to 60 s. Individuals treated with implant-supported fixed partial dentures were included. Implant data--location, type, length, diameter and healing abutments' dimensions--were recorded. Mucosal cuff shrinkage, following removal of the healing abutments, was measured in bucco-lingual direction at four time points--immediately after 20, 40 and 60 s. anova was used to for statistical analysis. Eighty-seven patients (49 women and 38 men) with a total of 311 implants were evaluated (120 maxilla; 191 mandible; 291 posterior segments; 20 anterior segments). Two-hundred and five (66%) implants displayed thick and 106 (34%) thin gingival biotype. Time was the sole statistically significant parameter affecting mucosal cuff shrinkage around dental implants (P < 0.001). From time 0 to 20, 40 and 60 s, the mean diameter changed from 4.1 to 4.07, 3.4 and 2.81 mm, respectively. The shrinkage was 1%, 17% and 31%, respectively. The gingival biotype had no statistically significant influence on mucosal cuff shrinkage (P = 0.672). Time required replacing a healing abutment with a prosthetic element should be minimised (up to 20/40 s), to avoid pain, discomfort and misfit. © 2015 John Wiley & Sons Ltd.

A generalized DEMATEL theory with a shrinkage coefficient for an indirect relation matrix

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Liu Hsiang-Chuan

2017-01-01

Full Text Available In this paper, a novel decision-making trial and evaluation laboratory (DEMATEL theory with a shrinkage coefficient of indirect relation matrix is proposed, and a useful validity index, called Liu’s validity index, is also proposed for evaluating the performance of any DEMATEL model. If the shrinkage coefficient of an indirect relation matrix is equal to 1, then this new theory is identical to the traditional theory; in other words, it is a generalization of the traditional theory. Furthermore, the indirect relation is always considerably greater than the direct one in traditional DEMATEL theory, which is unreasonable and unfair because it overemphasizes the influence of the indirect relation. We prove in this paper that if the shrinkage coefficient is equal to 0.5, then the indirect relation is less than its direct relation. Because the shrinkage coefficient belongs to [0.5, 1], according to Liu’s validity index, we can find a more appropriate shrinkage coefficient to obtain a more efficient DEMATEL method. Some crucial properties of this new theory are discussed, and a simple example is provided to illustrate the advantages of the proposed theory.

DH and ESPI laser interferometry applied to the restoration shrinkage assessment

International Nuclear Information System (INIS)

Campos, L.M.P.; Parra, D.F.; Vasconcelos, M.R.; Vaz, M.; Monteiro, J.

2014-01-01

In dental restoration postoperative marginal leakage is commonly associated to polymerization shrinkage effects. In consequence the longevity and quality of restorative treatment depends on the shrinkage mechanisms of the composite filling during the polymerization. In this work the development of new techniques for evaluation of those effects under light-induced polymerization of dental nano composite fillings is reported. The composite resins activated by visible light, initiate the polymerization process by absorbing light in wavelengths at about 470 nm. The techniques employed in the contraction assessment were digital holography (DH) and Electronic Speckle Pattern Interferometry (ESPI) based on laser interferometry. A satisfactory resolution was achieved in the non-contact displacement field measurements on small objects concerning the experimental dental samples. According to a specific clinical protocol, natural teeth were used (human mandibular premolars). A class I cavity was drilled and restored with nano composite material, according to Black principles. The polymerization was monitored by DH and ESPI in real time during the cure reaction of the restoration. The total displacement reported for the material in relation of the tooth wall was 3.7 μm (natural tooth). The technique showed the entire tooth surface (wall) deforming during polymerization shrinkage. - Highlights: • Both of holographic techniques were able to measure the polymerization shrinkage. • The entire tooth surface was deformed during the polymerization shrinkage. • The group with greater percentage of filler showed the lowest value of deformation. • The values of displacement ranged from 0.9 to 3.4 μm

Effectiveness of shrinkage-reducing admixtures on Portland pozzolan cement concrete

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Videla, C.

2005-06-01

Full Text Available Drying shrinkage causes tensile stress in restrained concrete members. Since all structural elements are subject to some degree of restraint, drying shrinkage is regarded to be one of the main causes of concrete cracking. The purpose of the present study was to evaluate the effectiveness of SRA in reducing drying shrinkage strain in Portland pozzolan cement concrete. The major variables examined included slump, admixture type and dose, and specimen size. The measured results indicate that any of the admixtures used in the study significantly reduced shrinkage. Concrete manufactured with shrinkage reducing admixtures shrank an average of 43% less than concrete without admixtures. As a rule, the higher the dose of admixture, the higher was its shrinkage reduction performance. The experimental results were compared to the shrinkage strain estimated with the ACI 209, CEB MC 90, B3, GL 2000, Sakata 1993 and Sakata 2001 models. Although none of these models was observed to accurately describe the behaviour of Portland pozzolan cement concrete with shrinkage reducing admixtures, the Sakata 2001 model, with a weighted coefficient of variation of under 30%, may be regarded to be roughly adequate.

La retracción por secado es un fenómeno intrínseco del hormigón que produce tensiones de tracción en elementos restringidos de hormigón. Puesto que todos los elementos presentan algún grado de retracción, se considera a la retracción por secado como una de las principales causas de agrietamiento en proyectos de construcción en hormigón. Por lo tanto, el objetivo de esta investigación fue evaluar la efectividad de los aditivos reductores de retracción (SRA en hormigones fabricados con cemento Portland puzolánico. Las variables principales estudiadas incluyen el asentamiento de cono de Abrams, marca y dosis de aditivo reductor de retracción, y tamaño de espécimen de hormigón. Los resultados obtenidos permiten concluir que el uso de

Void shrinkage in stainless steel during high energy electron irradiation

International Nuclear Information System (INIS)

Singh, B.N.; Foreman, A.J.E.

1976-03-01

During irradiation of thin foils of an austenitic stainless steel in a high voltage electron microscope, steadily growing voids have been observed to suddenly shrink and disappear at the irradiation temperature of 650 0 Cthe phenomenon has been observed in specimens both with and withoutimplanted helium. Possible mechanisms for void shrinkage during irradiation are considered. It is suggested that the dislocation-pipe-diffusion of vacancies from or of self-interstitial atoms to the voids can explain the shrinkage behaviour of voids observed during our experiments. (author)

Strength, shrinkage, erodibility and capillary flow characteristics of cement-treated recycled pavement materials

Directory of Open Access Journals (Sweden)

William Fedrigo

2017-09-01

Full Text Available Full-depth recycling with portland cement (FDR-PC has been widely used for pavement rehabilitation; however, doubts remain regarding factors affecting some properties of the recycled material. Aiming on quantifying the effects of those factors on the strength, drying shrinkage, erodibility, capillary rise and absorption of cement-treated mixtures (CTM of reclaimed asphalt pavement (RAP and graded crushed stone, tests were conducted considering different RAP contents, cement contents, compaction efforts and curing times. Cement addition increased the mixtures strength and reduced their erodibility and capillary flow characteristics, but increased shrinkage. Low cement contents resulted in acceptable strength for CTM, but in high capillary rise and absorption, not being suitable if the layer is exposed to long periods of water soaking. Higher compaction effort led to similar effects as cement addition, counterbalancing low cement contents usage and reducing costs and shrinkage cracking risk. Strength and shrinkage showed higher growth rates at early stages, and then precautions should be taken in order to avoid moisture loss. Increasing RAP content decreased strength; though, RAP effect on the other properties was statistically non-significant, indicating a similar behaviour as CTM without RAP. Considering the studied properties, the mixture with most satisfactory behaviour for field applications was identified. The results highlighted strength is not the only property to be considered when designing FDR-PC mixtures; although presenting acceptable strength, some mixtures may fail due to shrinkage cracking or erosion, when exposed to water content variations. Keywords: Full-depth recycling with cement, Strength, Drying shrinkage, Erodibility, Capillary rise, Absorption

Diversity shrinkage: Cross-validating pareto-optimal weights to enhance diversity via hiring practices.

Science.gov (United States)

Song, Q Chelsea; Wee, Serena; Newman, Daniel A

2017-12-01

To reduce adverse impact potential and improve diversity outcomes from personnel selection, one promising technique is De Corte, Lievens, and Sackett's (2007) Pareto-optimal weighting strategy. De Corte et al.'s strategy has been demonstrated on (a) a composite of cognitive and noncognitive (e.g., personality) tests (De Corte, Lievens, & Sackett, 2008) and (b) a composite of specific cognitive ability subtests (Wee, Newman, & Joseph, 2014). Both studies illustrated how Pareto-weighting (in contrast to unit weighting) could lead to substantial improvement in diversity outcomes (i.e., diversity improvement), sometimes more than doubling the number of job offers for minority applicants. The current work addresses a key limitation of the technique-the possibility of shrinkage, especially diversity shrinkage, in the Pareto-optimal solutions. Using Monte Carlo simulations, sample size and predictor combinations were varied and cross-validated Pareto-optimal solutions were obtained. Although diversity shrinkage was sizable for a composite of cognitive and noncognitive predictors when sample size was at or below 500, diversity shrinkage was typically negligible for a composite of specific cognitive subtest predictors when sample size was at least 100. Diversity shrinkage was larger when the Pareto-optimal solution suggested substantial diversity improvement. When sample size was at least 100, cross-validated Pareto-optimal weights typically outperformed unit weights-suggesting that diversity improvement is often possible, despite diversity shrinkage. Implications for Pareto-optimal weighting, adverse impact, sample size of validation studies, and optimizing the diversity-job performance tradeoff are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

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David B. Neale

2017-09-01

Full Text Available A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb. Franco (Coastal Douglas-fir is reported, thus providing a reference sequence for a third genus of the family Pinaceae. The contiguity and quality of the genome assembly far exceeds that of other conifer reference genome sequences (contig N50 = 44,136 bp and scaffold N50 = 340,704 bp. Incremental improvements in sequencing and assembly technologies are in part responsible for the higher quality reference genome, but it may also be due to a slightly lower exact repeat content in Douglas-fir vs. pine and spruce. Comparative genome annotation with angiosperm species reveals gene-family expansion and contraction in Douglas-fir and other conifers which may account for some of the major morphological and physiological differences between the two major plant groups. Notable differences in the size of the NDH-complex gene family and genes underlying the functional basis of shade tolerance/intolerance were observed. This reference genome sequence not only provides an important resource for Douglas-fir breeders and geneticists but also sheds additional light on the evolutionary processes that have led to the divergence of modern angiosperms from the more ancient gymnosperms.

Experimental Analysis on Shrinkage and Swelling in Ordinary Concrete

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Barbara Kucharczyková

2017-01-01

Full Text Available The paper deals with the experimental determination of shrinkage development during concrete ageing. Three concrete mixtures were made. They differed in the amount of cement in the fresh mixture, 300, 350, and 400 kg/m3. In order to determine the influence of plasticiser on the progress of volume changes, another three concrete mixtures were prepared with plasticiser in the amount of 0.25% by cement mass. Measurements were performed with the goal of observing the influence of cement and plasticiser content on the overall development of volume changes in the concrete. Changes in length and mass losses of the concrete during ageing were measured simultaneously. The continuous measurement of concrete mass losses caused by drying of the specimen’s surface proved useful during the interpretation of results obtained from the concrete shrinkage measurement. During the first 24 hours of ageing, all the concrete mixtures exhibited swelling. Its magnitude and progress were influenced by cement, water, and plasticiser content. However, a loss of mass caused by water evaporation from the surface of the specimens was also recorded in this stage. The measured progress of shrinkage corresponded well to the progress of mass loss.

Shrinkage Approach for Gene Expression Data Analysis

Czech Academy of Sciences Publication Activity Database

Haman, Jiří; Valenta, Zdeněk; Kalina, Jan

2013-01-01

Roč. 1, č. 1 (2013), s. 65-65 ISSN 1805-8698. [EFMI 2013 Special Topic Conference. 17.04.2013-19.04.2013, Prague] Institutional support: RVO:67985807 Keywords : shrinkage estimation * covariance matrix * high dimensional data * gene expression Subject RIV: IN - Informatics, Computer Science

Comparative genomics reveals insights into avian genome evolution and adaptation

DEFF Research Database (Denmark)

Zhang, Guojie; Li, Cai; Li, Qiye

2014-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, ...

Shrinkage and durability study of bridge deck concrete.

Science.gov (United States)

2010-12-01

The Mississippi Department of Transportation is incorporating changes to material : specifications and construction procedures for bridge decks in an effort to reduce shrinkage : cracking. These changes are currently being implemented into a limited ...

Genomic view of bipolar disorder revealed by whole genome sequencing in a genetic isolate.

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Benjamin Georgi

2014-03-01

Full Text Available Bipolar disorder is a common, heritable mental illness characterized by recurrent episodes of mania and depression. Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder, causative genetic risk factors remain elusive. We conducted a comprehensive genomic analysis of bipolar disorder in a large Old Order Amish pedigree. Microsatellite genotypes and high-density SNP-array genotypes of 388 family members were combined with whole genome sequence data for 50 of these subjects, comprising 18 parent-child trios. This study design permitted evaluation of candidate variants within the context of haplotype structure by resolving the phase in sequenced parent-child trios and by imputation of variants into multiple unsequenced siblings. Non-parametric and parametric linkage analysis of the entire pedigree as well as on smaller clusters of families identified several nominally significant linkage peaks, each of which included dozens of predicted deleterious variants. Close inspection of exonic and regulatory variants in genes under the linkage peaks using family-based association tests revealed additional credible candidate genes for functional studies and further replication in population-based cohorts. However, despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders.

Genomic View of Bipolar Disorder Revealed by Whole Genome Sequencing in a Genetic Isolate

Science.gov (United States)

Georgi, Benjamin; Craig, David; Kember, Rachel L.; Liu, Wencheng; Lindquist, Ingrid; Nasser, Sara; Brown, Christopher; Egeland, Janice A.; Paul, Steven M.; Bućan, Maja

2014-01-01

Bipolar disorder is a common, heritable mental illness characterized by recurrent episodes of mania and depression. Despite considerable effort to elucidate the genetic underpinnings of bipolar disorder, causative genetic risk factors remain elusive. We conducted a comprehensive genomic analysis of bipolar disorder in a large Old Order Amish pedigree. Microsatellite genotypes and high-density SNP-array genotypes of 388 family members were combined with whole genome sequence data for 50 of these subjects, comprising 18 parent-child trios. This study design permitted evaluation of candidate variants within the context of haplotype structure by resolving the phase in sequenced parent-child trios and by imputation of variants into multiple unsequenced siblings. Non-parametric and parametric linkage analysis of the entire pedigree as well as on smaller clusters of families identified several nominally significant linkage peaks, each of which included dozens of predicted deleterious variants. Close inspection of exonic and regulatory variants in genes under the linkage peaks using family-based association tests revealed additional credible candidate genes for functional studies and further replication in population-based cohorts. However, despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders. PMID:24625924

Hydration of Portoguese cements, measurement and modelling of chemical shrinkage

DEFF Research Database (Denmark)

Maia, Lino; Geiker, Mette Rica; Figueiras, Joaquim A.

2008-01-01

form of the dispersion model. The development of hydration varied between the investigated cements; based on the measured data the degree of hydration after 24 h hydration at 20 C varied between 40 and 50%. This should be taken into account when comparing properties of concrete made from the different......Development of cement hydration was studied by measuring the chemical shrinkage of pastes. Five types of Portuguese Portland cement were used in cement pastes with . Chemical shrinkage was measured by gravimetry and dilatometry. In gravimeters results were recorded automatically during at least...

Clay Mineralogy of Brazilian Oxisols with Shrinkage Properties

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Samara Alves Testoni

2017-08-01

Full Text Available ABSTRACT Shrinkage capacity (caráter retrátil in Portuguese is a new diagnostic characteristic recently introduced in the Brazilian System of Soil Classification (SiBCS to indicate shrink and swell properties observed in subtropical soils from highland plateaus in southern Brazil, specifically in Oxisols with brown colors. In soils located in road cuts exposed to drying for some weeks, strong shrinkage of soil volume is observed in these soils, resulting in the formation of pronounced vertical cracks and large and very large prismatic structures, which crumble in blocks when handled. We hypothesize that such properties are related to their clay mineralogy, although there are no conclusive studies about this, the motive for the present study. Samples of the A and B horizons from six Oxisols with expansive capacity from the states of Santa Catarina and Rio Grande do Sul were analyzed. One Rhodic Hapludox, from the state of Paraná, without expansive capacity, was used for comparison. All the soils are very clayey, originated from basalt, and have similar iron oxide content. For identification of clay mineralogy, X-ray diffraction techniques were employed, together with the use of NEWMOD® software to investigate and describe the interstratified minerals. The results showed that most expansive soils have a similar mineralogical composition, with kaolinite, interstratified kaolinite-smectite (K-S, and hydroxy-Al interlayered smectites (HIS, unlike the non-expansive Rhodic Hapludox, which exhibited kaolinite with significant amounts of gibbsite and low amount of interstratified K-S. According to the mineralogical assemblage identified in the expansive soils, we can affirm that the mechanism of smectite expansion and contraction is related to the shrinkage capacity of the soil, considering that the level of hydroxy-Al intercalation is low. In addition, these mechanisms also are related to the presence of quasicrystals and domains that control the

Characteristics of low polymerization shrinkage flowable resin composites in newly-developed cavity base materials for bulk filling technique.

Science.gov (United States)

Nitta, Keiko; Nomoto, Rie; Tsubota, Yuji; Tsuchikawa, Masuji; Hayakawa, Tohru

2017-11-29

The purpose of this study was to evaluate polymerization shrinkage and other physical properties of newly-developed cavity base materials for bulk filling technique, with the brand name BULK BASE (BBS). Polymerization shrinkage was measured according to ISO/FDIS 17304. BBS showed the significantly lowest polymerization shrinkage and significantly higher depth of cure than conventional flowable resin composites (p<0.05). The Knoop hardness, flexural strength and elastic modulus of that were significantly lower than conventional flowable resin composites (p<0.05). BBS had the significantly greatest filler content (p<0.05). SEM images of the surface showed failure of fillers. The lowest polymerization shrinkage was due to the incorporation of a new type of low shrinkage monomer, which has urethane moieties. There were no clear correlations between inorganic filler contents and polymerization shrinkage, flexural strength and elastic modulus. In conclusion, the low polymerization shrinkage of BBS will be useful for cavity treatment in dental clinics.

Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae.

Science.gov (United States)

Gubala, Aneta J; Proll, David F; Barnard, Ross T; Cowled, Chris J; Crameri, Sandra G; Hyatt, Alex D; Boyle, David B

2008-06-20

Viruses belonging to the family Rhabdoviridae infect a variety of different hosts, including insects, vertebrates and plants. Currently, there are approximately 200 ICTV-recognised rhabdoviruses isolated around the world. However, the majority remain poorly characterised and only a fraction have been definitively assigned to genera. The genomic and transcriptional complexity displayed by several of the characterised rhabdoviruses indicates large diversity and complexity within this family. To enable an improved taxonomic understanding of this family, it is necessary to gain further information about the poorly characterised members of this family. Here we present the complete genome sequence and predicted transcription strategy of Wongabel virus (WONV), a previously uncharacterised rhabdovirus isolated from biting midges (Culicoides austropalpalis) collected in northern Queensland, Australia. The 13,196 nucleotide genome of WONV encodes five typical rhabdovirus genes N, P, M, G and L. In addition, the WONV genome contains three genes located between the P and M genes (U1, U2, U3) and two open reading frames overlapping with the N and G genes (U4, U5). These five additional genes and their putative protein products appear to be novel, and their functions are unknown. Predictive analysis of the U5 gene product revealed characteristics typical of viroporins, and indicated structural similarities with the alpha-1 protein (putative viroporin) of viruses in the genus Ephemerovirus. Phylogenetic analyses of the N and G proteins of WONV indicated closest similarity with the avian-associated Flanders virus; however, the genomes of these two viruses are significantly diverged. WONV displays a novel and unique genome structure that has not previously been described for any animal rhabdovirus.

Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

LENUS (Irish Health Repository)

Potnis, Neha

2011-03-11

Abstract Background Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10. Results We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity. Conclusions Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster

The Methanosarcina barkeri genome: comparative analysis withMethanosarcina acetivorans and Methanosarcina mazei reveals extensiverearrangement within methanosarcinal genomes

Energy Technology Data Exchange (ETDEWEB)

Maeder, Dennis L.; Anderson, Iain; Brettin, Thomas S.; Bruce,David C.; Gilna, Paul; Han, Cliff S.; Lapidus, Alla; Metcalf, William W.; Saunders, Elizabeth; Tapia, Roxanne; Sowers, Kevin R.

2006-05-19

We report here a comparative analysis of the genome sequence of Methanosarcina barkeri with those of Methanosarcina acetivorans and Methanosarcina mazei. All three genomes share a conserved double origin of replication and many gene clusters. M. barkeri is distinguished by having an organization that is well conserved with respect to the other Methanosarcinae in the region proximal to the origin of replication with interspecies gene similarities as high as 95%. However it is disordered and marked by increased transposase frequency and decreased gene synteny and gene density in the proximal semi-genome. Of the 3680 open reading frames in M. barkeri, 678 had paralogs with better than 80% similarity to both M. acetivorans and M. mazei while 128 nonhypothetical orfs were unique (non-paralogous) amongst these species including a complete formate dehydrogenase operon, two genes required for N-acetylmuramic acid synthesis, a 14 gene gas vesicle cluster and a bacterial P450-specific ferredoxin reductase cluster not previously observed or characterized in this genus. A cryptic 36 kbp plasmid sequence was detected in M. barkeri that contains an orc1 gene flanked by a presumptive origin of replication consisting of 38 tandem repeats of a 143 nt motif. Three-way comparison of these genomes reveals differing mechanisms for the accrual of changes. Elongation of the large M. acetivorans is the result of multiple gene-scale insertions and duplications uniformly distributed in that genome, while M. barkeri is characterized by localized inversions associated with the loss of gene content. In contrast, the relatively short M. mazei most closely approximates the ancestral organizational state.

A case study of shrinkage-in place leaching of low grade uranium ore deposit

International Nuclear Information System (INIS)

Ding Dexin; Zhou Guohe

1998-09-01

A case study of shrinkage-in place leaching of low grade uranium ore deposit is dealt with. A test block was selected, and the shrinkage mining method was employed to construct the in place heap for leaching. Blast parameters and operations were carefully tried in order to make sure that the fragment size composition was adequate for leaching. A leaching system was planned and the corresponding leaching parameters were tried, too. The results show that the shrinkage method and the parameters for blasting and leaching are all adequate for the in-situ leaching of the blasted ore. This shrinkage-in place leaching system combines the mining and metallurgy processes into one and produces a lot of profits and could be applicable to many low grade uranium ore deposits which are so hard and compact that they have to be fragmented before being leached

Fabrication and characterization of self-folding thermoplastic sheets using unbalanced thermal shrinkage.

Science.gov (United States)

Danielson, Christian; Mehrnezhad, Ali; YekrangSafakar, Ashkan; Park, Kidong

2017-06-14

Self-folding or micro-origami technologies are actively investigated as a novel manufacturing process to fabricate three-dimensional macro/micro-structures. In this paper, we present a simple process to produce a self-folding structure with a biaxially oriented polystyrene sheet (BOPS) or Shrinky Dinks. A BOPS sheet is known to shrink to one-third of its original size in plane, when it is heated above 160 °C. A grid pattern is engraved on one side of the BOPS film with a laser engraver to decrease the thermal shrinkage of the engraved side. The thermal shrinkage of the non-engraved side remains the same and this unbalanced thermal shrinkage causes folding of the structure as the structure shrinks at high temperature. We investigated the self-folding mechanism and characterized how the grid geometry, the grid size, and the power of the laser engraver affect the bending curvature. The developed fabrication process to locally modulate thermomechanical properties of the material by engraving the grid pattern and the demonstrated design methodology to harness the unbalanced thermal shrinkage can be applied to develop complicated self-folding macro/micro structures.

Predicting shrinkage and warpage in injection molding: Towards automatized mold design

Science.gov (United States)

Zwicke, Florian; Behr, Marek; Elgeti, Stefanie

2017-10-01

It is an inevitable part of any plastics molding process that the material undergoes some shrinkage during solidification. Mainly due to unavoidable inhomogeneities in the cooling process, the overall shrinkage cannot be assumed as homogeneous in all volumetric directions. The direct consequence is warpage. The accurate prediction of such shrinkage and warpage effects has been the subject of a considerable amount of research, but it is important to note that this behavior depends greatly on the type of material that is used as well as the process details. Without limiting ourselves to any specific properties of certain materials or process designs, we aim to develop a method for the automatized design of a mold cavity that will produce correctly shaped moldings after solidification. Essentially, this can be stated as a shape optimization problem, where the cavity shape is optimized to fulfill some objective function that measures defects in the molding shape. In order to be able to develop and evaluate such a method, we first require simulation methods for the diffierent steps involved in the injection molding process that can represent the phenomena responsible for shrinkage and warpage ina sufficiently accurate manner. As a starting point, we consider the solidification of purely amorphous materials. In this case, the material slowly transitions from fluid-like to solid-like behavior as it cools down. This behavior is modeled using adjusted viscoelastic material models. Once the material has passed a certain temperature threshold during cooling, any viscous effects are neglected and the behavior is assumed to be fully elastic. Non-linear elastic laws are used to predict shrinkage and warpage that occur after this point. We will present the current state of these simulation methods and show some first approaches towards optimizing the mold cavity shape based on these methods.

Quantitative analyses of shrinkage characteristics of neem ...

African Journals Online (AJOL)

Quantitative analyses of shrinkage characteristics of neem (Azadirachta indica A. Juss.) wood were carried out. Forty five wood specimens were prepared from the three ecological zones of north eastern Nigeria, viz: sahel savanna, sudan savanna and guinea savanna for the research. The results indicated that the wood ...

Study of Drying Shrinkage Cracking by Lattice Gas Automaton and Environmental Scanning Electron Microscope

NARCIS (Netherlands)

Van Mier, J.G.M.; Jankovic, D.

2005-01-01

Numerical modeling of moisture flow, drying shrinkage and crack phenomena in cement microstructure, by coupling a Lattice Gas Automaton and a Lattice Fracture Model, highlighted the importance of a shrinkage coefficient (?sh) as the most significant parameter for achieving realistic numerical

Effects of Shrinkage Reducing Agent and Expansive Additive on Mortar Properties

Directory of Open Access Journals (Sweden)

Sarapon Treesuwan

2017-01-01

Full Text Available This research is to study the effect of mortar mixed with shrinkage reducing agent (polyoxyalkylene alkyl ether type, expansive additive (CaO type, and fly ash (hereinafter “SRA,” “EX,” and “FA,” resp.. Moreover, steam curing was studied to improve the properties of mortar. The plastic shrinkage test was conducted by using the strain gauge embedded at 0.5 cm from the surface according to the ASTM C1579-06 standard within early age followed by the total shrinkage test and compressive strength test. The test results showed that mixing both the EX and SRA increases the plastic enlargement of the mortar during the early age more than using either the EX or SRA solely. The steam curing helps to reduce the plastic shrinkage when the mortar is added with the FA and SRA while adding the EX increases the enlargement compared to the normal curing. When the EX, SRA, and FA are all added to the mortar mixing, great attention should be paid due to the increase of greater enlargement. For the compressive strength view, the steam curing increases the compressive strength in all types of mixture. The steam curing significantly helps increasing the compressive strength of mortar with combination of EX, SRA, and FA. Nevertheless, the XRD and SEM tests explain such enlargement accordingly.

Pattern of Tumor Shrinkage during Neoadjuvant Chemotherapy Is Associated with Prognosis in Low-Grade Luminal Early Breast Cancer.

Science.gov (United States)

Fukada, Ippei; Araki, Kazuhiro; Kobayashi, Kokoro; Shibayama, Tomoko; Takahashi, Shunji; Gomi, Naoya; Kokubu, Yumi; Oikado, Katsunori; Horii, Rie; Akiyama, Futoshi; Iwase, Takuji; Ohno, Shinji; Hatake, Kiyohiko; Sata, Naohiro; Ito, Yoshinori

2018-01-01

Purpose To evaluate the association between tumor shrinkage patterns shown with magnetic resonance (MR) imaging during neoadjuvant chemotherapy (NAC) and prognosis in patients with low-grade luminal breast cancer. Materials and Methods This retrospective study was approved by the institutional review board and informed consent was obtained from all subjects. The low-grade luminal breast cancer was defined as hormone receptor-positive and human epidermal growth factor receptor 2-negative with nuclear grades 1 or 2. The patterns of tumor shrinkage as revealed at MR imaging were categorized into two types: concentric shrinkage (CS) and non-CS. Among 854 patients who had received NAC in a single institution from January 2000 to December 2009, 183 patients with low-grade luminal breast cancer were retrospectively evaluated for the development set. Another data set from 292 patients who had received NAC in the same institution between January 2010 and December 2012 was used for the validation set. Among these 292 patients, 121 patients with low-grade luminal breast cancer were retrospectively evaluated. Results In the development set, the median observation period was 67.9 months. Recurrence was observed in 31 patients, and 16 deaths were related to breast cancer. There were statistically significant differences in both the disease-free survival (DFS) and overall survival (OS) rates between patterns of tumor shrinkage (P breast cancer. DFS rate was significantly longer in patients with the CS pattern (72.8 months; 95% confidence interval [CI]: 69.9, 75.6 months) than in those with the non-CS pattern (56.0 months; 95% CI: 49.1, 62.9 months; P ≤ .001). The CS pattern was associated with an excellent prognosis (median OS, 80.6 months; 95% CI: 79.3, 81.8 months vs 65.0 months; 95% CI: 60.1, 69.8 months; P = .004). Multivariate analysis demonstrated that the CS pattern had the only significant independent association with DFS (P = .007) and OS (P = .037) rates. Conclusion

Sparse contrast-source inversion using linear-shrinkage-enhanced inexact Newton method

KAUST Repository

Desmal, Abdulla

2014-07-01

A contrast-source inversion scheme is proposed for microwave imaging of domains with sparse content. The scheme uses inexact Newton and linear shrinkage methods to account for the nonlinearity and ill-posedness of the electromagnetic inverse scattering problem, respectively. Thresholded shrinkage iterations are accelerated using a preconditioning technique. Additionally, during Newton iterations, the weight of the penalty term is reduced consistently with the quadratic convergence of the Newton method to increase accuracy and efficiency. Numerical results demonstrate the applicability of the proposed method.

Sparse contrast-source inversion using linear-shrinkage-enhanced inexact Newton method

KAUST Repository

Desmal, Abdulla; Bagci, Hakan

2014-01-01

A contrast-source inversion scheme is proposed for microwave imaging of domains with sparse content. The scheme uses inexact Newton and linear shrinkage methods to account for the nonlinearity and ill-posedness of the electromagnetic inverse scattering problem, respectively. Thresholded shrinkage iterations are accelerated using a preconditioning technique. Additionally, during Newton iterations, the weight of the penalty term is reduced consistently with the quadratic convergence of the Newton method to increase accuracy and efficiency. Numerical results demonstrate the applicability of the proposed method.

The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

Energy Technology Data Exchange (ETDEWEB)

Rensing, Stefan A.; Lang, Daniel; Zimmer, Andreas D.; Terry, Astrid; Salamov, Asaf; Shapiro, Harris; Nishiyama, Tomaoki; Perroud, Pierre-Francois; Lindquist, Erika A.; Kamisugi, Yasuko; Tanahashi, Takako; Sakakibara, Keiko; Fujita, Tomomichi; Oishi, Kazuko; Shin, Tadasu; Kuroki, Yoko; Toyoda, Atsushi; Suzuki, Yutaka; Hashimoto, Shin-ichi; Yamaguchi, Kazuo; Sugano, Sumio; Kohara, Yuji; Fujiyama, Asao; Anterola, Aldwin; Aoki, Setsuyuki; Ashton, Neil; Barbazuk, W. Brad; Barker, Elizabeth; Bennetzen, Jeffrey L.; Blankenship, Robert; Cho, Sung Hyun; Dutcher, Susan K.; Estelle, Mark; Fawcett, Jeffrey A.; Gundlach, Heidrum; Hanada, Kousuke; Melkozernov, Alexander; Murata, Takashi; Nelson, David R.; Pils, Birgit; Prigge, Michael; Reiss, Bernd; Renner, Tanya; Rombauts, Stephane; Rushton, Paul J.; Sanderfoot, Anton; Schween, Gabriele; Shiu, Shin-Han; Stueber, Kurt; Theodoulou, Frederica L.; Tu, Hank; Van de Peer, Yves; Verrier, Paul J.; Waters, Elizabeth; Wood, Andrew; Yang, Lixing; Cove, David; Cuming, Andrew C.; Hasebe, Mitsayasu; Lucas, Susan; Mishler, Brent D.; Reski, Ralf; Grigoriev, Igor V.; Quatrano, Rakph S.; Boore, Jeffrey L.

2007-09-18

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

Autogenous and drying shrinkage of sodium carbonate activated slag altered by limestone powder incorporation

NARCIS (Netherlands)

Yuan, B.; Yu, Q.L.; Dainese, E.; Brouwers, H.J.H.

2017-01-01

This paper aims to study the shrinkage mechanism of sodium carbonate activated slag containing limestone powder (LP). The workability, pore structure, reaction kinetics and strength development were characterized. The results show that the autogenous shrinkage increases when the dosage of LP is low

Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments.

Directory of Open Access Journals (Sweden)

Paul J Wichgers Schreur

2016-08-01

Full Text Available The bunyavirus genome comprises a small (S, medium (M, and large (L RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging. Accumulating evidence suggests that genomes of viruses with eight or more genome segments are incorporated into virions by highly selective processes. Remarkably, little is known about the genome packaging process of the tri-segmented bunyaviruses. Here, we evaluated, by single-molecule RNA fluorescence in situ hybridization (FISH, the intracellular spatio-temporal distribution and replication kinetics of the Rift Valley fever virus (RVFV genome and determined the segment composition of mature virions. The results reveal that the RVFV genome segments start to replicate near the site of infection before spreading and replicating throughout the cytoplasm followed by translocation to the virion assembly site at the Golgi network. Despite the average intracellular S, M and L genome segments approached a 1:1:1 ratio, major differences in genome segment ratios were observed among cells. We also observed a significant amount of cells lacking evidence of M-segment replication. Analysis of two-segmented replicons and four-segmented viruses subsequently confirmed the previous notion that Golgi recruitment is mediated by the Gn glycoprotein. The absence of colocalization of the different segments in the cytoplasm and the successful rescue of a tri-segmented variant with a codon shuffled M-segment suggested that inter-segment interactions are unlikely to drive the copackaging of the different segments into a single virion. The latter was confirmed by direct visualization of RNPs inside mature virions which showed that the majority of virions lack one or more genome segments. Altogether, this study suggests that RVFV genome packaging is a non-selective process.

Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

Directory of Open Access Journals (Sweden)

Siragusa Gregory R

2011-06-01

Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs

Energy Technology Data Exchange (ETDEWEB)

Curtis, Bruce A.; Tanifuji, Goro; Burki, Fabien; Gruber, Ansgar; Irimia, Manuuel; Maruyama, Shinichiro; Arias, Maria C.; Ball, Steven G.; Gile, Gillian H.; Hirakawa, Yoshihisa; Hopkins, Julia F.; Kuo, Alan; Rensing, Stefan A.; Schmutz, Jeremy; Symeonidi, Aikaterini; Elias, Marek; Eveleigh, Robert J. M.; Herman, Emily K.; Klute, Mary J.; Nakayama, Takuro; Obornik, Miroslav; Reyes-Prieto, Adrian; Armbrust, E. Virginia; Aves, Stephen J.; Beiko, Robert G.; Coutinho, Pedro; Dacks, Joel B.; Durnford, Dion G.; Fast, Naomi M.; Green, Beverley R.; Grisdale, Cameron J.; Hempel, Franziska; Henrissat, Bernard; Hoppner, Marc P.; Ishida, Ken-Ichiro; Kim, Eunsoo; Koreny, Ludek; Kroth, Peter G.; Liu, Yuan; Malik, Shehre-Banoo; Maier, Uwe G.; McRose, Darcy; Mock, Thomas; Neilson, Jonathan A. D.; Onodera, Naoko T.; Poole, Anthony M.; Pritham, Ellen J.; Richards, Thomas A.; Rocap, Gabrielle; Roy, Scott W.; Sarai, Chihiro; Schaack, Sarah; Shirato, Shu; Slamovits, Claudio H.; Spencer, Davie F.; Suzuki, Shigekatsu; Worden, Alexandra Z.; Zauner, Stefan; Barry, Kerrie; Bell, Callum; Bharti, Arvind K.; Crow, John A.; Grimwood, Jane; Kramer, Robin; Lindquist, Erika; Lucas, Susan; Salamov, Asaf; McFadden, Geoffrey I.; Lane, Christopher E.; Keeling, Patrick J.; Gray, Michael W.; Grigoriev, Igor V.; Archibald, John M.

2012-08-10

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

Draft whole genome sequence of groundnut stem rot fungus Athelia rolfsii revealing genetic architect of its pathogenicity and virulence.

Science.gov (United States)

Iquebal, M A; Tomar, Rukam S; Parakhia, M V; Singla, Deepak; Jaiswal, Sarika; Rathod, V M; Padhiyar, S M; Kumar, Neeraj; Rai, Anil; Kumar, Dinesh

2017-07-13

Groundnut (Arachis hypogaea L.) is an important oil seed crop having major biotic constraint in production due to stem rot disease caused by fungus, Athelia rolfsii causing 25-80% loss in productivity. As chemical and biological combating strategies of this fungus are not very effective, thus genome sequencing can reveal virulence and pathogenicity related genes for better understanding of the host-parasite interaction. We report draft assembly of Athelia rolfsii genome of ~73 Mb having 8919 contigs. Annotation analysis revealed 16830 genes which are involved in fungicide resistance, virulence and pathogenicity along with putative effector and lethal genes. Secretome analysis revealed CAZY genes representing 1085 enzymatic genes, glycoside hydrolases, carbohydrate esterases, carbohydrate-binding modules, auxillary activities, glycosyl transferases and polysaccharide lyases. Repeat analysis revealed 11171 SSRs, LTR, GYPSY and COPIA elements. Comparative analysis with other existing ascomycotina genome predicted conserved domain family of WD40, CYP450, Pkinase and ABC transporter revealing insight of evolution of pathogenicity and virulence. This study would help in understanding pathogenicity and virulence at molecular level and development of new combating strategies. Such approach is imperative in endeavour of genome based solution in stem rot disease management leading to better productivity of groundnut crop in tropical region of world.

Modified creep and shrinkage prediction model B3 for serviceability limit state analysis of composite slabs

Science.gov (United States)

Gholamhoseini, Alireza

2016-03-01

Relatively little research has been reported on the time-dependent in-service behavior of composite concrete slabs with profiled steel decking as permanent formwork and little guidance is available for calculating long-term deflections. The drying shrinkage profile through the thickness of a composite slab is greatly affected by the impermeable steel deck at the slab soffit, and this has only recently been quantified. This paper presents the results of long-term laboratory tests on composite slabs subjected to both drying shrinkage and sustained loads. Based on laboratory measurements, a design model for the shrinkage strain profile through the thickness of a slab is proposed. The design model is based on some modifications to an existing creep and shrinkage prediction model B3. In addition, an analytical model is developed to calculate the time-dependent deflection of composite slabs taking into account the time-dependent effects of creep and shrinkage. The calculated deflections are shown to be in good agreement with the experimental measurements.

Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice

OpenAIRE

Wei Tong; Qiang He; Yong-Jin Park

2017-01-01

Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucle...

Polymerization stresses in low-shrinkage dental resin composites measured by crack analysis.

Science.gov (United States)

Yamamoto, Takatsugu; Kubota, Yu; Momoi, Yasuko; Ferracane, Jack L

2012-09-01

The objective of this study was to compare several dental restoratives currently advertised as low-shrinkage composites (Clearfil Majesty Posterior, Kalore, Reflexions XLS Dentin and Venus Diamond) with a microfill composite (Heliomolar) in terms of polymerization stress, polymerization shrinkage and elastic modulus. Cracks were made at several distances from the edge of a precision cavity in a soda-lime glass disk. The composites were placed into the cavity and lengths of the cracks were measured before and after light curing. Polymerization stresses generated in the glass at 2 and 10 min after the irradiation were calculated from the crack lengths and K(c) of the glass. Polymerization shrinkage and elastic modulus of the composites also were measured at 2 and 10 min after irradiation using a video-imaging device and a nanoindenter, respectively. The data were statistically analyzed by ANOVAs and Tukey's test (pelastic moduli of Clearfil Majesty Posterior and Reflexions XLS Dentin were greatest at 2 and 10 min, respectively. Among the four low-shrinkage composites, two demonstrated significantly reduced polymerization stress compared to Heliomolar, which has previously been shown in in vitro tests to generate low curing stress. Copyright © 2012 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Mathematical model for creep and thermal shrinkage of concrete at high temperature

International Nuclear Information System (INIS)

Bazant, Z.P.

1983-01-01

Based on the existing limited test data, it is possible to set up an approximate constitutive model for creep and shrinkage at temperatures above 100 0 C, up to about 400 0 C. The model presented here describes the effect of various constant temperatures on the creep rate and the rate of aging, similar effects of the specific water content, the creep increase caused by simultaneous changes in moisture content, the thermal volume changes as well as the volume changes caused by changes in moisture content (drying shrinkage or thermal shrinkage), and the effect of pore pressure produced by heating. Generalizations to time-variable stresses and multiaxial stresses are also given. The model should allow more realistic analysis of reactor vessels and containments for accident situations, of concrete structures subjected to fire, of vessels for coal gasification or liquefaction, etc. (orig.)

Shrinkage Approach for Gene Expression Data Analysis

Czech Academy of Sciences Publication Activity Database

Haman, Jiří; Valenta, Zdeněk

2013-01-01

Roč. 9, č. 3 (2013), s. 2-8 ISSN 1801-5603 Grant - others:UK(CZ) SVV-2013-266517 Institutional support: RVO:67985807 Keywords : microarray technology * high dimensional data * mean squared error * James-Stein shrinkage estimator * mutual information Subject RIV: IN - Informatics, Computer Science http://www.ejbi.org/img/ejbi/2013/3/Haman_en.pdf

Further Evaluation of Covariate Analysis using Empirical Bayes Estimates in Population Pharmacokinetics: the Perception of Shrinkage and Likelihood Ratio Test.

Science.gov (United States)

Xu, Xu Steven; Yuan, Min; Yang, Haitao; Feng, Yan; Xu, Jinfeng; Pinheiro, Jose

2017-01-01

Covariate analysis based on population pharmacokinetics (PPK) is used to identify clinically relevant factors. The likelihood ratio test (LRT) based on nonlinear mixed effect model fits is currently recommended for covariate identification, whereas individual empirical Bayesian estimates (EBEs) are considered unreliable due to the presence of shrinkage. The objectives of this research were to investigate the type I error for LRT and EBE approaches, to confirm the similarity of power between the LRT and EBE approaches from a previous report and to explore the influence of shrinkage on LRT and EBE inferences. Using an oral one-compartment PK model with a single covariate impacting on clearance, we conducted a wide range of simulations according to a two-way factorial design. The results revealed that the EBE-based regression not only provided almost identical power for detecting a covariate effect, but also controlled the false positive rate better than the LRT approach. Shrinkage of EBEs is likely not the root cause for decrease in power or inflated false positive rate although the size of the covariate effect tends to be underestimated at high shrinkage. In summary, contrary to the current recommendations, EBEs may be a better choice for statistical tests in PPK covariate analysis compared to LRT. We proposed a three-step covariate modeling approach for population PK analysis to utilize the advantages of EBEs while overcoming their shortcomings, which allows not only markedly reducing the run time for population PK analysis, but also providing more accurate covariate tests.

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

Science.gov (United States)

Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

2014-01-01

Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

Science.gov (United States)

Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

2014-01-01

The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

Four-Phase Dendritic Model for the Prediction of Macrosegregation, Shrinkage Cavity, and Porosity in a 55-Ton Ingot

Science.gov (United States)

Ge, Honghao; Ren, Fengli; Li, Jun; Han, Xiujun; Xia, Mingxu; Li, Jianguo

2017-03-01

A four-phase dendritic model was developed to predict the macrosegregation, shrinkage cavity, and porosity during solidification. In this four-phase dendritic model, some important factors, including dendritic structure for equiaxed crystals, melt convection, crystals sedimentation, nucleation, growth, and shrinkage of solidified phases, were taken into consideration. Furthermore, in this four-phase dendritic model, a modified shrinkage criterion was established to predict shrinkage porosity (microporosity) of a 55-ton industrial Fe-3.3 wt pct C ingot. The predicted macrosegregation pattern and shrinkage cavity shape are in a good agreement with experimental results. The shrinkage cavity has a significant effect on the formation of positive segregation in hot top region, which generally forms during the last stage of ingot casting. The dendritic equiaxed grains also play an important role on the formation of A-segregation. A three-dimensional laminar structure of A-segregation in industrial ingot was, for the first time, predicted by using a 3D case simulation.

Effects of Prepolymerized Particle Size and Polymerization Kinetics on Volumetric Shrinkage of Dental Modeling Resins

Directory of Open Access Journals (Sweden)

Tae-Yub Kwon

2014-01-01

Full Text Available Dental modeling resins have been developed for use in areas where highly precise resin structures are needed. The manufacturers claim that these polymethyl methacrylate/methyl methacrylate (PMMA/MMA resins show little or no shrinkage after polymerization. This study examined the polymerization shrinkage of five dental modeling resins as well as one temporary PMMA/MMA resin (control. The morphology and the particle size of the prepolymerized PMMA powders were investigated by scanning electron microscopy and laser diffraction particle size analysis, respectively. Linear polymerization shrinkage strains of the resins were monitored for 20 minutes using a custom-made linometer, and the final values (at 20 minutes were converted into volumetric shrinkages. The final volumetric shrinkage values for the modeling resins were statistically similar (P>0.05 or significantly larger (P<0.05 than that of the control resin and were related to the polymerization kinetics (P<0.05 rather than the PMMA bead size (P=0.335. Therefore, the optimal control of the polymerization kinetics seems to be more important for producing high-precision resin structures rather than the use of dental modeling resins.

The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants

Science.gov (United States)

The American cranberry (Vaccinium macrocarpon Ait.) mitochondrial genome was assembled and reconstructed from whole genome 454 Roche GS-FLX and Illumina shotgun sequences. Compared with other Asterids, the reconstruction of the genome revealed an average size mitochondrion (459,678 nt) with comparat...

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

NARCIS (Netherlands)

Olsen, Jeanine; Rouzé, Pierre; Verhelst, Bram; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; De Paoli, Emanuele; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna; Lauritano, Chiara; Lohaus, Rolf; Töpel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Boström, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J; Pearson, Gareth A; Procaccini, Gabriele; Duarte, Carlos M; Schmutz, Jeremy; Reusch, Thorsten B H; Van de Peer, Yves

2016-01-01

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes.

Science.gov (United States)

Chen, Poyin; den Bakker, Henk C; Korlach, Jonas; Kong, Nguyet; Storey, Dylan B; Paxinos, Ellen E; Ashby, Meredith; Clark, Tyson; Luong, Khai; Wiedmann, Martin; Weimer, Bart C

2017-02-01

which manifests as gastroenteritis, meningoencephalitis, and abortion. Among Salmonella, Escherichia coli, Campylobacter, and Listeria-causing the most prevalent foodborne illnesses-infection by L. monocytogenes carries the highest mortality rate. The ability of L. monocytogenes to regulate its response to various harsh environments enables its persistence and transmission. Small-scale comparisons of L. monocytogenes focusing solely on genome contents reveal a highly syntenic genome yet fail to address the observed diversity in phenotypic regulation. This study provides a large-scale comparison of 302 L. monocytogenes isolates, revealing the importance of the epigenome and restriction-modification systems as major determinants of L. monocytogenes phylogenetic grouping and subsequent phenotypic expression. Further examination of virulence genes of select outbreak strains reveals an unprecedented diversity in methylation statuses despite high degrees of genome conservation. Copyright © 2017 American Society for Microbiology.

Combined Use of Shrinkage Reducing Admixture and CaO in Cement Based Materials

Science.gov (United States)

Tittarelli, Francesca; Giosuè, Chiara; Monosi, Saveria

2017-10-01

The combined addition of a Shrinkage-Reducing Admixture (SRA) with a CaO-based expansive agent (CaO) has been found to have a synergistic effect to improve the dimensional stability of cement based materials. In this work, aimed to further investigate the effect, mortar and self-compacting concrete specimens were prepared either without admixtures, as reference, or with SRA alone and/or CaO. Their performance was compared in terms of compressive strength and free shrinkage measurements. Results showed that the synergistic effect in reducing shrinkage is confirmed in the specimens manufactured with SRA and CaO. In order to clarify this phenomenon, the effect of SRA on the hydration of CaO as well as cement was evaluated through different techniques. The obtained results show that SRA induces a finer microstructure of the CaO hydration products and a retarding effect on the microstructure development of cement based materials. A more deformable mortar or concrete, due to the delay in microstructure development by SRA, coupled with a finer microstructure of CaO hydration products could allow higher early expansion, which might contribute in contrasting better the successive drying shrinkage.

A korarchaeal genome reveals insights into the evolution of the Archaea

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain J; Elkins, James G.; Podar, Mircea; Graham, David E.; Makarova, Kira S.; Wolf, Yuri; Randau, Lennart; Hedlund, Brian P.; Brochier-Armanet, Celine; Kunin, Victor; Anderson, Iain; Lapidus, Alla; Goltsman, Eugene; Barry, Kerrie; Koonin, Eugene V.; Hugenholtz, Phil; Kyrpides, Nikos; Wanner, Gerhard; Richardson, Paul; Keller, Martin; Stetter, Karl O.

2008-06-05

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name,"Candidatus Korarchaeum cryptofilum," which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent. Of the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

A Korarchael Genome Reveals Insights into the Evolution of the Archaea

Energy Technology Data Exchange (ETDEWEB)

Lapidus, Alla; Elkins, James G.; Podar, Mircea; Graham, David E.; Makarova, Kira S.; Wolf, Yuri; Randau, Lennart; Hedlund, Brian P.; Brochier-Armanet, Celine; Kunin, Victor; Anderson, Iain; Lapidus, Alla; Goltsman, Eugene; Barry, Kerrie; Koonin, Eugene V.; Hugenholtz, Phil; Kyrpides, Nikos; Wanner, Gerhard; Richardson, Paul; Keller, Martin; Stetter, Karl O.

2008-01-07

The candidate division Korarchaeota comprises a group of uncultivated microorganisms that, by their small subunit rRNA phylogeny, may have diverged early from the major archaeal phyla Crenarchaeota and Euryarchaeota. Here, we report the initial characterization of a member of the Korarchaeota with the proposed name, ?Candidatus Korarchaeum cryptofilum,? which exhibits an ultrathin filamentous morphology. To investigate possible ancestral relationships between deep-branching Korarchaeota and other phyla, we used whole-genome shotgun sequencing to construct a complete composite korarchaeal genome from enriched cells. The genome was assembled into a single contig 1.59 Mb in length with a G + C content of 49percent. Of the 1,617 predicted protein-coding genes, 1,382 (85percent) could be assigned to a revised set of archaeal Clusters of Orthologous Groups (COGs). The predicted gene functions suggest that the organism relies on a simple mode of peptide fermentation for carbon and energy and lacks the ability to synthesize de novo purines, CoA, and several other cofactors. Phylogenetic analyses based on conserved single genes and concatenated protein sequences positioned the korarchaeote as a deep archaeal lineage with an apparent affinity to the Crenarchaeota. However, the predicted gene content revealed that several conserved cellular systems, such as cell division, DNA replication, and tRNA maturation, resemble the counterparts in the Euryarchaeota. In light of the known composition of archaeal genomes, the Korarchaeota might have retained a set of cellular features that represents the ancestral archaeal form.

Experimental evaluation and simulation of volumetric shrinkage and warpage on polymeric composite reinforced with short natural fibers

Science.gov (United States)

Santos, Jonnathan D.; Fajardo, Jorge I.; Cuji, Alvaro R.; García, Jaime A.; Garzón, Luis E.; López, Luis M.

2015-09-01

A polymeric natural fiber-reinforced composite is developed by extrusion and injection molding process. The shrinkage and warpage of high-density polyethylene reinforced with short natural fibers of Guadua angustifolia Kunth are analyzed by experimental measurements and computer simulations. Autodesk Moldflow® and Solid Works® are employed to simulate both volumetric shrinkage and warpage of injected parts at different configurations: 0 wt.%, 20 wt.%, 30 wt.% and 40 wt.% reinforcing on shrinkage and warpage behavior of polymer composite. Become evident the restrictive effect of reinforcing on the volumetric shrinkage and warpage of injected parts. The results indicate that volumetric shrinkage of natural composite is reduced up to 58% with fiber increasing, whereas the warpage shows a reduction form 79% to 86% with major fiber content. These results suggest that it is a highly beneficial use of natural fibers to improve the assembly properties of polymeric natural fiber-reinforced composites.

Reoxygenation of hypoxic cells by tumor shrinkage during irradiation. A computer simulation

International Nuclear Information System (INIS)

Kocher, M.; Treuer, H.

1995-01-01

A 3-dimensional computer simulation was developed in order to estimate the impact of tumor shrinkage on reoxygenation of chronic hypoxic tumor cells during a full course of fractionated irradiation. The growth of a small tumor situated in a vascularized stroma with 350 capillary cross-sections/mm 3 which were displaced by the growing tumor was simulated. Tumors contained 10 4 cells when irradiation started, intrinsic radiosensitivity was set to either low (α=0.3 Gy -1 , β=0.03 Gy -2 ) or high (α=0.4 Gy -1 , β=0.04 Gy -2 ) values. Oxygen enhancement ratio was 3.0, potential tumor doubling time T pot =1, 2 or 5 days. A simulated fractionated radiotherapy was carried out with daily fractions of 2.0 Gy, total dose 50 to 70 Gy. The presence or absence of factors preventing tumor cord shrinkage was also included. During the growth phase, all tumors developed a necrotic core with a hypoxic cell fraction of 25% under these conditions. During irradiation, the slower growing tumors (T pot =2 to 5 days) showed complete reoxygenation of the hypoxic cells after 30 to 40 Gy independent from radiosensitivity, undisturbed tumor shrinkage provided. If shrinkage was prevented, the hypoxic fraction rose to 100% after 30 to 50 Gy. Local tumor control, defined as the destruction of all clonogenic and hypoxic tumor cells increased by 20 to 100% due to reoxygenation and 50 Gy were enough in order to sterilize the tumors in these cases. In the fast growing tumors (T pot =1 day), reoxygenation was only observed in the case of high radiosensitivity and undisturbed tumor shrinkage. In these tumors reoxygenation increased the control rates by up to 60%. (orig./MG) [de

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

Energy Technology Data Exchange (ETDEWEB)

Merchant, Sabeeha S

2007-04-09

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

Reduction of cracking and shrinkage in compressed clay beams during dying

International Nuclear Information System (INIS)

Lakho, N.A.; Zardari, M.A.; Memon, N.A.

2016-01-01

Uncontrolled evaporation of moisture from compressed clay beams can cause surface cracks, resulting in reduction of strength. This paper presents various treatments applied to clay beams during the process of casting, compacting and drying in order to curtail the possibility of cracking and to decrease percentage of drying shrinkage. Following treatments were applied to the beams during casting and drying: (i) a steel plate and double layer of plastic sheet was provided between the beam and the plank, (ii) the beam was enveloped with a propylene fabric sheet during casting and (iii) beams were covered with plastic sheet during drying. Using these treatments, the clay beams were cast and compacted at various intensities of compaction. The results show that the drying shrinkage was reduced to minimum and the cracks were curtailed. The rate of drying shrinkage was decreased depending upon the level of compaction. Thus at the higher degree of compaction, more density of clay beams was achieved, which resulted in higher degree of compressive strength in baked and unbaked state. (author)

Development of high shrinkage polyethylene terephthalate (PET) shape memory polymer tendons for concrete crack closure

Science.gov (United States)

Teall, Oliver; Pilegis, Martins; Sweeney, John; Gough, Tim; Thompson, Glen; Jefferson, Anthony; Lark, Robert; Gardner, Diane

2017-04-01

The shrinkage force exerted by restrained shape memory polymers (SMPs) can potentially be used to close cracks in structural concrete. This paper describes the physical processing and experimental work undertaken to develop high shrinkage die-drawn polyethylene terephthalate (PET) SMP tendons for use within a crack closure system. The extrusion and die-drawing procedure used to manufacture a series of PET tendon samples is described. The results from a set of restrained shrinkage tests, undertaken at differing activation temperatures, are also presented along with the mechanical properties of the most promising samples. The stress developed within the tendons is found to be related to the activation temperature, the cross-sectional area and to the draw rate used during manufacture. Comparisons with commercially-available PET strip samples used in previous research are made, demonstrating an increase in restrained shrinkage stress by a factor of two for manufactured PET filament samples.

Numerical Simulation on Open Wellbore Shrinkage and Casing Equivalent Stress in Bedded Salt Rock Stratum

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Jianjun Liu

2013-01-01

Full Text Available Most salt rock has interbed of mudstone in China. Owing to the enormous difference of mechanical properties between the mudstone interbed and salt rock, the stress-strain and creep behaviors of salt rock are significantly influenced by neighboring mudstone interbed. In order to identify the rules of wellbore shrinkage and casings equivalent stress in bedded salt rock stratum, three-dimensional finite difference models were established. The effects of thickness and elasticity modulus of mudstone interbed on the open wellbore shrinkage and equivalent stress of casing after cementing operation were studied, respectively. The results indicate that the shrinkage of open wellbore and equivalent stress of casings decreases with the increase of mudstone interbed thickness. The increasing of elasticity modulus will reduce the shrinkage of open wellbore and casing equivalent stress. Research results can provide the scientific basis for the design of mud density and casing strength.

A thermal active restrained shrinkage ring test to study the early age concrete behaviour of massive structures

International Nuclear Information System (INIS)

Briffaut, M.; Benboudjema, F.; Torrenti, J.M.; Nahas, G.

2011-01-01

In massive concrete structures, cracking may occur during hardening, especially if autogenous and thermal strains are restrained. The concrete permeability due to this cracking may rise significantly and thus increase leakage (in tank, nuclear containment...) and reduce the durability. The restrained shrinkage ring test is used to study the early age concrete behaviour (delayed strains evolution and cracking). This test shows, at 20 o C and without drying, for a concrete mix which is representative of a French nuclear power plant containment vessel (w/c ratio equal to 0.57), that the amplitude of autogenous shrinkage (about 40 μm/m for the studied concrete mix) is not high enough to cause cracking. Indeed, in this configuration, thermal shrinkage is not significant, whereas this is a major concern for massive structures. Therefore, an active test has been developed to study cracking due to restrained thermal shrinkage. This test is an evolution of the classical restrained shrinkage ring test. It allows to take into account both autogenous and thermal shrinkages. Its principle is to create the thermal strain effects by increasing the temperature of the brass ring (by a fluid circulation) in order to expand it. With this test, the early age cracking due to restrained shrinkage, the influence of reinforcement and construction joints have been experimentally studied. It shows that, as expected, reinforcement leads to an increase of the number of cracks but a decrease of crack widths. Moreover, cracking occurs preferentially at the construction joint.

Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria

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Keeling Patrick J

2007-09-01

Full Text Available Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes. Results From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression. Conclusion The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements

Analysis of Shrinkage on Thick Plate Part using Genetic Algorithm

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Najihah S.N.

2016-01-01

Full Text Available Injection moulding is the most widely used processes in manufacturing plastic products. Since the quality of injection improves plastic parts are mostly influenced by process conditions, the method to determine the optimum process conditions becomes the key to improving the part quality. This paper presents a systematic methodology to analyse the shrinkage of the thick plate part during the injection moulding process. Genetic Algorithm (GA method was proposed to optimise the process parameters that would result in optimal solutions of optimisation goals. Using the GA, the shrinkage of the thick plate part was improved by 39.1% in parallel direction and 17.21% in the normal direction of melt flow.

Whole Genome Analyses of a Well-Differentiated Liposarcoma Reveals Novel SYT1 and DDR2 Rearrangements

Science.gov (United States)

Egan, Jan B.; Barrett, Michael T.; Champion, Mia D.; Middha, Sumit; Lenkiewicz, Elizabeth; Evers, Lisa; Francis, Princy; Schmidt, Jessica; Shi, Chang-Xin; Van Wier, Scott; Badar, Sandra; Ahmann, Gregory; Kortuem, K. Martin; Boczek, Nicole J.; Fonseca, Rafael; Craig, David W.; Carpten, John D.; Borad, Mitesh J.; Stewart, A. Keith

2014-01-01

Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR) where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2. PMID:24505276

Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements.

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Jan B Egan

Full Text Available Liposarcoma is the most common soft tissue sarcoma, but little is known about the genomic basis of this disease. Given the low cell content of this tumor type, we utilized flow cytometry to isolate the diploid normal and aneuploid tumor populations from a well-differentiated liposarcoma prior to array comparative genomic hybridization and whole genome sequencing. This work revealed massive highly focal amplifications throughout the aneuploid tumor genome including MDM2, a gene that has previously been found to be amplified in well-differentiated liposarcoma. Structural analysis revealed massive rearrangement of chromosome 12 and 11 gene fusions, some of which may be part of double minute chromosomes commonly present in well-differentiated liposarcoma. We identified a hotspot of genomic instability localized to a region of chromosome 12 that includes a highly conserved, putative L1 retrotransposon element, LOC100507498 which resides within a gene cluster (NAV3, SYT1, PAWR where 6 of the 11 fusion events occurred. Interestingly, a potential gene fusion was also identified in amplified DDR2, which is a potential therapeutic target of kinase inhibitors such as dastinib, that are not routinely used in the treatment of patients with liposarcoma. Furthermore, 7 somatic, damaging single nucleotide variants have also been identified, including D125N in the PTPRQ protein. In conclusion, this work is the first to report the entire genome of a well-differentiated liposarcoma with novel chromosomal rearrangements associated with amplification of therapeutically targetable genes such as MDM2 and DDR2.

Comparative genome and transcriptome analysis reveals distinctive surface characteristics and unique physiological potentials of Pseudomonas aeruginosa ATCC 27853

KAUST Repository

Cao, Huiluo

2017-06-12

Pseudomonas aeruginosa ATCC 27853 was isolated from a hospital blood specimen in 1971 and has been widely used as a model strain to survey antibiotics susceptibilities, biofilm development, and metabolic activities of Pseudomonas spp.. Although four draft genomes of P. aeruginosa ATCC 27853 have been sequenced, the complete genome of this strain is still lacking, hindering a comprehensive understanding of its physiology and functional genome.Here we sequenced and assembled the complete genome of P. aeruginosa ATCC 27853 using the Pacific Biosciences SMRT (PacBio) technology and Illumina sequencing platform. We found that accessory genes of ATCC 27853 including prophages and genomic islands (GIs) mainly contribute to the difference between P. aeruginosa ATCC 27853 and other P. aeruginosa strains. Seven prophages were identified within the genome of P. aeruginosa ATCC 27853. Of the predicted 25 GIs, three contain genes that encode monoxoygenases, dioxygenases and hydrolases that could be involved in the metabolism of aromatic compounds. Surveying virulence-related genes revealed that a series of genes that encode the B-band O-antigen of LPS are lacking in ATCC 27853. Distinctive SNPs in genes of cellular adhesion proteins such as type IV pili and flagella biosynthesis were also observed in this strain. Colony morphology analysis confirmed an enhanced biofilm formation capability of ATCC 27853 on solid agar surface compared to Pseudomonas aeruginosa PAO1. We then performed transcriptome analysis of ATCC 27853 and PAO1 using RNA-seq and compared the expression of orthologous genes to understand the functional genome and the genomic details underlying the distinctive colony morphogenesis. These analyses revealed an increased expression of genes involved in cellular adhesion and biofilm maturation such as type IV pili, exopolysaccharide and electron transport chain components in ATCC 27853 compared with PAO1. In addition, distinctive expression profiles of the

Ultra low-K shrinkage behavior when under electron beam in a scanning electron microscope

Energy Technology Data Exchange (ETDEWEB)

Lorut, F.; Imbert, G. [ST Microelectronics, 850 rue Jean Monnet, 38926 Crolles Cedex (France); Roggero, A. [Centre National d' Etudes Spatiales, 18 Avenue Edouard Belin, 31400 Toulouse (France)

2013-08-28

In this paper, we investigate the tendency of porous low-K dielectrics (also named Ultra Low-K, ULK) behavior to shrink when exposed to the electron beam of a scanning electron microscope. Various experimental electron beam conditions have been used for irradiating ULK thin films, and the resulting shrinkage has been measured through use of an atomic force microscope tool. We report the shrinkage to be a fast, cumulative, and dose dependent effect. Correlation of the shrinkage with incident electron beam energy loss has also been evidenced. The chemical modification of the ULK films within the interaction volume has been demonstrated, with a densification of the layer and a loss of carbon and hydrogen elements being observed.

Experimental drying shrinkage of hardened cement pastes as a function of relative humidity

DEFF Research Database (Denmark)

Hansen, Kurt Kielsgaard; Baroghel, V.B.

1996-01-01

The results of an experimental study concerning drying shrinkage measured as a function of relative humidity on thin specimens of mature hardened cement pastes are presented. The results obtained at two laboratories are compared.......The results of an experimental study concerning drying shrinkage measured as a function of relative humidity on thin specimens of mature hardened cement pastes are presented. The results obtained at two laboratories are compared....

Influence of Aggregate Wettability with Different Lithology Aggregates on Concrete Drying Shrinkage

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Yuanchen Guo

2015-01-01

Full Text Available The correlation of the wettability of different lithology aggregates and the drying shrinkage of concrete materials is studied, and some influential factors such as wettability and wetting angle are analyzed. A mercury porosimeter is used to measure the porosities of different lithology aggregates accurately, and the pore size ranges that significantly affect the drying shrinkage of different lithology aggregate concretes are confirmed. The pore distribution curve of the different coarse aggregates is also measured through a statistical method, and the contact angle of different coarse aggregates and concrete is calculated according to the linear fitting relationship. Research shows that concrete strength is determined by aggregate strength. Aggregate wettability is not directly correlated with concrete strength, but wettability significantly affects concrete drying shrinkage. In all types’ pores, the greatest impacts on wettability are capillary pores and gel pores, especially for the pores of the size locating 2.5–50 nm and 50–100 nm two ranges.

Temperature dependence of autogenous shrinkage of silica fume cement pastes with a very low water–binder ratio

Energy Technology Data Exchange (ETDEWEB)

Maruyama, I., E-mail: ippei@dali.nuac.nagoya-u.ac.jp [Graduate School of Environmental Studies, Nagoya University, ES Building, No. 539, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Teramoto, A. [Graduate School of Environmental Studies, Nagoya University, Faculty of Engineering, ES Building, No. 546, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)

2013-08-15

Ultra-high-strength concrete with a large unit cement content undergoes considerable temperature increase inside members due to hydration heat, leading to a higher risk of internal cracking. Hence, the temperature dependence of autogenous shrinkage of cement pastes made with silica fume premixed cement with a water–binder ratio of 0.15 was studied extensively. Development of autogenous shrinkage showed different behaviors before and after the inflection point, and dependence on the temperature after mixing and subsequent temperature histories. The difference in autogenous shrinkage behavior poses problems for winter construction because autogenous shrinkage may increase with decrease in temperature after mixing before the inflection point and with increase in temperature inside concrete members with large cross sections.

Temperature dependence of autogenous shrinkage of silica fume cement pastes with a very low water–binder ratio

International Nuclear Information System (INIS)

Maruyama, I.; Teramoto, A.

2013-01-01

Ultra-high-strength concrete with a large unit cement content undergoes considerable temperature increase inside members due to hydration heat, leading to a higher risk of internal cracking. Hence, the temperature dependence of autogenous shrinkage of cement pastes made with silica fume premixed cement with a water–binder ratio of 0.15 was studied extensively. Development of autogenous shrinkage showed different behaviors before and after the inflection point, and dependence on the temperature after mixing and subsequent temperature histories. The difference in autogenous shrinkage behavior poses problems for winter construction because autogenous shrinkage may increase with decrease in temperature after mixing before the inflection point and with increase in temperature inside concrete members with large cross sections

Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing.

Science.gov (United States)

Jo, Yeong Deuk; Choi, Yoomi; Kim, Dong-Hwan; Kim, Byung-Dong; Kang, Byoung-Cheorl

2014-07-04

Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. Although large portion of sequence context was

Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing.

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Zhen-Hui Wang

Full Text Available BACKGROUND: Hybridization between genetically diverged organisms is known as an important avenue that drives plant genome evolution. The possible outcomes of hybridization would be the occurrences of genetic instabilities in the resultant hybrids. It remained under-investigated however whether pollination by alien pollens of a closely related but sexually "incompatible" species could evoke genomic changes and to what extent it may result in phenotypic novelties in the derived progenies. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have re-sequenced the genomes of Oryza sativa ssp. japonica cv. Matsumae and one of its derived introgressant RZ35 that was obtained from an introgressive hybridization between Matsumae and Zizanialatifolia Griseb. in general, 131 millions 90 base pair (bp paired-end reads were generated which covered 13.2 and 21.9 folds of the Matsumae and RZ35 genomes, respectively. Relative to Matsumae, a total of 41,724 homozygous single nucleotide polymorphisms (SNPs and 17,839 homozygous insertions/deletions (indels were identified in RZ35, of which 3,797 SNPs were nonsynonymous mutations. Furthermore, rampant mobilization of transposable elements (TEs was found in the RZ35 genome. The results of pathogen inoculation revealed that RZ35 exhibited enhanced resistance to blast relative to Matsumae. Notably, one nonsynonymous mutation was found in the known blast resistance gene Pid3/Pi25 and real-time quantitative (q RT-PCR analysis revealed constitutive up-regulation of its expression, suggesting both altered function and expression of Pid3/Pi25 may be responsible for the enhanced resistance to rice blast by RZ35. CONCLUSIONS/SIGNIFICANCE: Our results demonstrate that introgressive hybridization by Zizania has provoked genomewide, extensive genomic changes in the rice genome, and some of which have resulted in important phenotypic novelties. These findings suggest that introgressive hybridization by alien pollens of even a

Genome Sequencing Reveals the Potential of Achromobacter sp. HZ01 for Bioremediation

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Yue-Hui Hong

2017-08-01

Full Text Available Petroleum pollution is a severe environmental issue. Comprehensively revealing the genetic backgrounds of hydrocarbon-degrading microorganisms contributes to developing effective methods for bioremediation of crude oil-polluted environments. Marine bacterium Achromobacter sp. HZ01 is capable of degrading hydrocarbons and producing biosurfactants. In this study, the draft genome (5.5 Mbp of strain HZ01 has been obtained by Illumina sequencing, containing 5,162 predicted genes. Genome annotation shows that “amino acid metabolism” is the most abundant metabolic pathway. Strain HZ01 is not capable of using some common carbohydrates as the sole carbon sources, which is due to that it contains few genes associated with carbohydrate transport and lacks some important enzymes related to glycometabolism. It contains abundant proteins directly related to petroleum hydrocarbon degradation. AlkB hydroxylase and its homologs were not identified. It harbors a complete enzyme system of terminal oxidation pathway for n-alkane degradation, which may be initiated by cytochrome P450. The enzymes involved in the catechol pathway are relatively complete for the degradation of aromatic compounds. This bacterium lacks several essential enzymes for methane oxidation, and Baeyer-Villiger monooxygenase involved in the subterminal oxidation pathway and cycloalkane degradation was not identified. These results suggest that strain HZ01 degrades n-alkanes via the terminal oxidation pathway, degrades aromatic compounds primarily via the catechol pathway and cannot perform methane oxidation or cycloalkane degradation. Additionally, strain HZ01 possesses abundant genes related to the metabolism of secondary metabolites, including some genes involved in biosurfactant (such as glycolipids and lipopeptides synthesis. The genome analysis also reveals its genetic basis for nitrogen metabolism, antibiotic resistance, regulatory responses to environmental changes, cell motility

Genome and metagenome enabled analyses reveal new insight into the global biogeography and potential urea utilization in marine Thaumarchaeota.

Science.gov (United States)

Ahlgren, N.; Parada, A. E.; Fuhrman, J. A.

2016-02-01

Marine Thaumarchaea are an abundant, important group of marine microbial communities as they fix carbon, oxidize ammonium, and thus contribute to key N and C cycles in the oceans. From an enrichment culture, we have sequenced the complete genome of a new Thaumarchaeota strain, SPOT01. Analysis of this genome and other Thaumarchaeal genomes contributes new insight into its role in N cycling and clarifies the broader biogeography of marine Thaumarchaeal genera. Phylogenomics of Thaumarchaeota genomes reveal coherent separation into clusters roughly equivalent to the genus level, and SPOT01 represents a new genus of marine Thaumarchaea. Competitive fragment recruitment of globally distributed metagenomes from TARA, Ocean Sampling Day, and those generated from a station off California shows that the SPOT01 genus is often the most abundant genus, especially where total Thaumarchaea are most abundant in the overall community. The SPOT01 genome contains urease genes allowing it to use an alternative form of N. Genomic and metagenomic analysis also reveal that among planktonic genomes and populations, the urease genes in general are more frequently found in members of the SPOT01 genus and another genus dominant in deep waters, thus we predict these two genera contribute most significantly to urea utilization among marine Thaumarchaea. Recruitment also revealed broader biogeographic and ecological patterns of the putative genera. The SPOT01 genus was most abundant at colder temperatures (45 degrees). The genus containing Nitrosopumilus maritimus had the highest temperature range, and the genus containing Candidatus Nitrosopelagicus brevis was typically most abundant at intermediate temperatures and intermediate latitudes ( 35-45 degrees). Together these genome and metagenome enabled analyses provide significant new insight into the ecology and biogeochemical contributions of marine archaea.

The Influence of Water Sorption of Dental Light-Cured Composites on Shrinkage Stress

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Kinga Bociong

2017-09-01

Full Text Available The contraction stress generated during the photopolymerization of resin dental composites is the major disadvantage. The water sorption in the oral environment should counteract the contraction stress. The purpose was to evaluate the influence of the water sorption of composite materials on polymerization shrinkage stress generated at the restoration-tooth interface. The following materials were tested: Filtek Ultimate, Gradia Direct LoFlo, Heliomolar Flow, Tetric EvoCeram, Tetric EvoCeram Bulk Fill, Tetric EvoFlow, Tetric EvoFlow Bulk Fill, X-tra Base, Venus BulkFil, and Ceram.X One. The shrinkage stress was measured immediately after curing and after: 0.5 h, 24 h, 72 h, 96 h, 168 h, 240 h, 336 h, 504 h, 672 h, and 1344 h by means of photoelastic study. Moreover, water sorption and solubility were evaluated. Material samples were weighted on scale in time intervals to measure the water absorbency and the dynamic of this process. The tested materials during polymerization generated shrinkage stresses ranging from 6.3 MPa to 12.5 MPa. Upon water conditioning (56 days, the decrease in shrinkage strain (not less than 48% was observed. The decrease in value stress in time is material-dependent.

Regional Brain Shrinkage over Two Years: Individual Differences and Effects of Pro-Inflammatory Genetic Polymorphisms

Science.gov (United States)

Persson, N.; Ghisletta, P.; Dahle, C.L.; Bender, A.R.; Yang, Y.; Yuan, P.; Daugherty, A.M.; Raz, N.

2014-01-01

We examined regional changes in brain volume in healthy adults (N = 167, age 19-79 years at baseline; N = 90 at follow-up) over approximately two years. With latent change score models, we evaluated mean change and individual differences in rates of change in 10 anatomically-defined and manually-traced regions of interest (ROIs): lateral prefrontal cortex (LPFC), orbital frontal cortex (OF), prefrontal white matter (PFw), hippocampus (HC), parahippocampal gyrus (PhG), caudate nucleus (Cd), putamen (Pt), insula (In), cerebellar hemispheres (CbH), and primary visual cortex (VC). Significant mean shrinkage was observed in the HC, CbH, In, OF, and the PhG, and individual differences in change were noted in all regions, except the OF. Pro-inflammatory genetic variants mediated shrinkage in PhG and CbH. Carriers of two T alleles of interleukin-1β (IL-1βC-511T, rs16944) and a T allele of methylenetetrahydrofolate reductase (MTHFRC677T, rs1801133) polymorphisms showed increased PhG shrinkage. No effects of a pro-inflammatory polymorphism for C-reactive protein (CRP-286C>A>T, rs3091244) or apolipoprotein (APOE) ε4 allele were noted. These results replicate the pattern of brain shrinkage observed in previous studies, with a notable exception of the LPFC thus casting doubt on the unique importance of prefrontal cortex in aging. Larger baseline volumes of CbH and In were associated with increased shrinkage, in conflict with the brain reserve hypothesis. Contrary to previous reports, we observed no significant linear effects of age and hypertension on regional brain shrinkage. Our findings warrant further investigation of the effects of neuroinflammation on structural brain change throughout the lifespan. PMID:25264227

Effects of molecular structure of the resins on the volumetric shrinkage and the mechanical strength of dental restorative composites.

Science.gov (United States)

Kim, L U; Kim, J W; Kim, C K

2006-09-01

To prepare a dental composite that has a low amount of curing shrinkage and excellent mechanical strength, various 2,2-bis[4-(2-hydroxy-3-methacryloyloxy propoxy) phenyl] propane (Bis-GMA) derivatives were synthesized via molecular structure design, and afterward, properties of their mixtures were explored. Bis-GMA derivatives, which were obtained by substituting methyl groups for hydrogen on the phenyl ring in the Bis-GMA, exhibited lower curing shrinkage than Bis-GMA, whereas their viscosities were higher than that of Bis-GMA. Other Bis-GMA derivatives, which contained a glycidyl methacrylate as a molecular end group exhibited reduced curing shrinkage and viscosity. Methoxy substitution for hydroxyl groups on the Bis-GMA derivatives was performed for the further reduction of the viscosity and curing shrinkage. Various resin mixtures, which had the same viscosity as the commercial one, were prepared, and their curing shrinkage was examined. A resin mixture containing 2,2-bis[3,5-dimethyl, 4-(2-methoxy-3-methacryloyloxy propoxy) phenyl] propane] (TMBis-M-GMA) as a base resin and 4-tert-butylphenoxy-2-methyoxypropyl methacrylate (t-BP-M-GMA) as a diluent exhibited the lowest curing shrinkage among them. The composite prepared from this resin mixture also exhibited the lowest curing shrinkage along with enhanced mechanical properties.

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome

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Ferrari Francesco

2009-06-01

Full Text Available Abstract Background Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS, a Chinese Spring terminal deletion line (CS_5AL-10 and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions. Results The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed in Creso (which lacks the D genome or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region. Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10. Conclusion Bread and durum wheat genotypes were characterized by a different physiological reaction to water

A Mesoscopic Simulation for the Early-Age Shrinkage Cracking Process of High Performance Concrete in Bridge Engineering

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Guodong Li

2017-01-01

Full Text Available On a mesoscopic level, high performance concrete (HPC was assumed to be a heterogeneous composite material consisting of aggregates, mortar, and pores. The concrete mesoscopic structure model had been established based on CT image reconstruction. By combining this model with continuum mechanics, damage mechanics, and fracture mechanics, a relatively complete system for concrete mesoscopic mechanics analysis was established to simulate the process of early-age shrinkage cracking in HPC. This process was based on the dispersion crack model. The results indicated that the interface between the aggregate and mortar was the crack point caused by shrinkage cracks in HPC. The locations of early-age shrinkage cracks in HPC were associated with the spacing and the size of the aggregate particle. However, the shrinkage deformation size of the mortar was related to the scope of concrete cracking and was independent of the crack position. Whereas lower water to cement ratios can improve the early strength of concrete, this ratio cannot control early-age shrinkage cracks in HPC.

Conjugation of diisocyanate side chains to dimethacrylate reduces polymerization shrinkage and increases the hardness of composite resins.

Science.gov (United States)

Jan, Yih-Dean; Lee, Bor-Shiunn; Lin, Chun-Pin; Tseng, Wan-Yu

2014-04-01

Polymerization shrinkage is one of the main causes of dental restoration failure. This study tried to conjugate two diisocyanate side chains to dimethacrylate resins in order to reduce polymerization shrinkage and increase the hardness of composite resins. Diisocyanate, 2-hydroxyethyl methacrylate, and bisphenol A dimethacrylate were reacted in different ratios to form urethane-modified new resin matrices, and then mixed with 50 wt.% silica fillers. The viscosities of matrices, polymerization shrinkage, surface hardness, and degrees of conversion of experimental composite resins were then evaluated and compared with a non-modified control group. The viscosities of resin matrices increased with increasing diisocyanate side chain density. Polymerization shrinkage and degree of conversion, however, decreased with increasing diisocyanate side chain density. The surface hardness of all diisocyanate-modified groups was equal to or significantly higher than that of the control group. Conjugation of diisocyanate side chains to dimethacrylate represents an effective means of reducing polymerization shrinkage and increasing the surface hardness of dental composite resins. Copyright © 2012. Published by Elsevier B.V.

SHRINKAGE REDUCTION AND CRACK PREVENTION OF ALKALI-ACTIVATED PHOSPHOROUS SLAG CEMENT

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Yanan Wang

2016-05-01

Full Text Available The effects of fly ash, calcium oxide and polypropylene fiber on the physical and mechanical properties, shrinkage and cracking behaviors of alkali-activated phosphorous slag cement (AA-PS-C were studied. The results show that replacing 10-15% phosphorous slag by fly ash and adding calcium oxide as an expansive agent reduce the shrinkage of AA-PS-C. Fly ash will increase the flexural strength, although the compressive strength will be slightly decreased, while the calcium oxide expansive agent coated with aluminum stearate will slightly shorten the setting time and reduce the strength. Adding polypropylene fiber can greatly increase the crack-resistance of AA-PS-C.

Nannochloropsis genomes reveal evolution of microalgal oleaginous traits.

Directory of Open Access Journals (Sweden)

Dongmei Wang

2014-01-01

Full Text Available Oleaginous microalgae are promising feedstock for biofuels, yet the genetic diversity, origin and evolution of oleaginous traits remain largely unknown. Here we present a detailed phylogenomic analysis of five oleaginous Nannochloropsis species (a total of six strains and one time-series transcriptome dataset for triacylglycerol (TAG synthesis on one representative strain. Despite small genome sizes, high coding potential and relative paucity of mobile elements, the genomes feature small cores of ca. 2,700 protein-coding genes and a large pan-genome of >38,000 genes. The six genomes share key oleaginous traits, such as the enrichment of selected lipid biosynthesis genes and certain glycoside hydrolase genes that potentially shift carbon flux from chrysolaminaran to TAG synthesis. The eleven type II diacylglycerol acyltransferase genes (DGAT-2 in every strain, each expressed during TAG synthesis, likely originated from three ancient genomes, including the secondary endosymbiosis host and the engulfed green and red algae. Horizontal gene transfers were inferred in most lipid synthesis nodes with expanded gene doses and many glycoside hydrolase genes. Thus multiple genome pooling and horizontal genetic exchange, together with selective inheritance of lipid synthesis genes and species-specific gene loss, have led to the enormous genetic apparatus for oleaginousness and the wide genomic divergence among present-day Nannochloropsis. These findings have important implications in the screening and genetic engineering of microalgae for biofuels.

Evaluation of the polymerization shrinkage of experimental flowable composite resins through optical coherence tomography

Science.gov (United States)

Carneiro, Vanda S. M.; Mota, Cláudia C. B. O.; Souza, Alex F.; Cajazeira, Marlus R. R.; Gerbi, Marleny E. M. M.; Gomes, Anderson S. L.

2018-02-01

This study evaluated the polymerization shrinkage of two experimental flowable composite resins (CR) with different proportions of Urethane dimethacrylate (UDMA)/triethylene glycol dimethacrylate (TEGDMA) monomers in the organic matrix (50:50 and 60:40, respectively). A commercially available flowable CR, Tetric N-Flow (Ivoclair Vivadent, Liechtenstein, Germany), was employed as the control group. The resins were inserted in a cylindrical teflon mold (7 mm diameter, 0.6 mm height) and scanned with OCT before photoactivation, immediately after and 15 minutes after light-curing (Radii-Cal, SDI, Australia, 1,200 mW/cm2 ) exposure. A Callisto SD-OCT system (Thorlabs Inc, USA), operating at 930 nm central wavelength was employed for imaging acquisition. Cross-sectional OCT images were captured with 8 mm transverse scanning (2000x512 matrix), and processed by the ImageJ software, for comparison between the scanning times and between groups. Pearson correlation showed significant shrinkage for all groups in each time analyzed. Kruskal-Wallis test showed greater polymerization shrinkage for the 50:50 UDMA/TEGDMA group (p=0.001), followed by the control group (p=0.018). TEGDMA concentration was proportionally related to the polymerization shrinkage of the flowable composite resins.

Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

Directory of Open Access Journals (Sweden)

Lu Xin-Yan

2009-11-01

Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

Investigation on Failures of Composite Beam and Substrate Concrete due to Drying Shrinkage Property of Repair Materials

Science.gov (United States)

Pattnaik, Rashmi Ranjan

2017-06-01

A Finite Element Analysis (FEA) and an experimental study was conducted on composite beam of repair material and substrate concrete to investigate the failures of the composite beam due to drying shrinkage property of the repair materials. In FEA, the stress distribution in the composite beam due to two concentrate load and shrinkage of repair materials were investigated in addition to the deflected shape of the composite beam. The stress distributions and load deflection shapes of the finite element model were investigated to aid in analysis of the experimental findings. In the experimental findings, the mechanical properties such as compressive strength, split tensile strength, flexural strength, and load-deflection curves were studied in addition to slant shear bond strength, drying shrinkage and failure patterns of the composite beam specimens. Flexure test was conducted to simulate tensile stress at the interface between the repair material and substrate concrete. The results of FEA were used to analyze the experimental results. It was observed that the repair materials with low drying shrinkage are showing compatible failure in the flexure test of the composite beam and deform adequately in the load deflection curves. Also, the flexural strength of the composite beam with low drying shrinkage repair materials showed higher flexural strength as compared to the composite beams with higher drying shrinkage value of the repair materials even though the strength of those materials were more.

Exploiting tumor shrinkage through temporal optimization of radiotherapy

International Nuclear Information System (INIS)

Unkelbach, Jan; Craft, David; Hong, Theodore; Papp, Dávid; Wolfgang, John; Bortfeld, Thomas; Ramakrishnan, Jagdish; Salari, Ehsan

2014-01-01

In multi-stage radiotherapy, a patient is treated in several stages separated by weeks or months. This regimen has been motivated mostly by radiobiological considerations, but also provides an approach to reduce normal tissue dose by exploiting tumor shrinkage. The paper considers the optimal design of multi-stage treatments, motivated by the clinical management of large liver tumors for which normal liver dose constraints prohibit the administration of an ablative radiation dose in a single treatment. We introduce a dynamic tumor model that incorporates three factors: radiation induced cell kill, tumor shrinkage, and tumor cell repopulation. The design of multi-stage radiotherapy is formulated as a mathematical optimization problem in which the total dose to the normal tissue is minimized, subject to delivering the prescribed dose to the tumor. Based on the model, we gain insight into the optimal administration of radiation over time, i.e. the optimal treatment gaps and dose levels. We analyze treatments consisting of two stages in detail. The analysis confirms the intuition that the second stage should be delivered just before the tumor size reaches a minimum and repopulation overcompensates shrinking. Furthermore, it was found that, for a large range of model parameters, approximately one-third of the dose should be delivered in the first stage. The projected benefit of multi-stage treatments in terms of normal tissue sparing depends on model assumptions. However, the model predicts large dose reductions by more than a factor of 2 for plausible model parameters. The analysis of the tumor model suggests that substantial reduction in normal tissue dose can be achieved by exploiting tumor shrinkage via an optimal design of multi-stage treatments. This suggests taking a fresh look at multi-stage radiotherapy for selected disease sites where substantial tumor regression translates into reduced target volumes. (paper)

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

Science.gov (United States)

Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

Directory of Open Access Journals (Sweden)

Fagen Li

Full Text Available Dense genetic maps, along with quantitative trait loci (QTLs detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR, expressed sequence tag (EST derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS, and diversity arrays technology (DArT markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age and wood density (56 months were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Illumina based whole mitochondrial genome of Junonia iphita reveals minor intraspecific variation

Directory of Open Access Journals (Sweden)

Catherine Vanlalruati

2015-12-01

Full Text Available In the present study, the near complete mitochondrial genome (mitogenome of Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae was determined to be 14,892 bp. The gene order and orientation are identical to those in other butterfly species. The phylogenetic tree constructed from the whole mitogenomes using the 13 protein coding genes (PCGs defines the genetic relatedness of the two J. iphita species collected from two different regions. All the Junonia species clustered together, and were further subdivided into clade one consisting of J. almana and J. orithya and clade two comprising of the two J. iphita which were collected from Indo and Indochinese subregions separated by river barrier. Comparison between the two J. iphita sequences revealed minor variations and Single Nucleotide Polymorphisms were identified at 51 sites amounting to 0.4% of the entire mitochondrial genome.

The evolution of shrinkage strain of pet-mortar composite eco ...

African Journals Online (AJOL)

... resulting from the cement hydration and are governed by various physical and ... of PET volumetric additive amounts for cement substituting and for the behavior ... Keywords: Composite Eco-materials; Cement substitution; Shrinkage strain; ...

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.

Science.gov (United States)

Wragg, David; Mason, Andrew S; Yu, Le; Kuo, Richard; Lawal, Raman A; Desta, Takele Taye; Mwacharo, Joram M; Cho, Chang-Yeon; Kemp, Steve; Burt, David W; Hanotte, Olivier

2015-10-14

EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.

Directory of Open Access Journals (Sweden)

Kui Lin

2014-01-01

Full Text Available Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

Analysis of the shrinkage at the thick plate part using response surface methodology

Science.gov (United States)

Hatta, N. M.; Azlan, M. Z.; Shayfull, Z.; Roselina, S.; Nasir, S. M.

2017-09-01

Injection moulding is well known for its manufacturing process especially in producing plastic products. To measure the final product quality, there are lots of precautions to be taken into such as parameters setting at the initial stage of the process. Sometimes, if these parameters were set up wrongly, defects may be occurred and one of the well-known defects in the injection moulding process is a shrinkage. To overcome this problem, a maximisation at the precaution stage by making an optimal adjustment on the parameter setting need to be done and this paper focuses on analysing the shrinkage by optimising the parameter at thick plate part with the help of Response Surface Methodology (RSM) and ANOVA analysis. From the previous study, the outstanding parameter gained from the optimisation method in minimising the shrinkage at the moulded part was packing pressure. Therefore, with the reference from the previous literature, packing pressure was selected as the parameter setting for this study with other three parameters which are melt temperature, cooling time and mould temperature. The analysis of the process was obtained from the simulation by Autodesk Moldflow Insight (AMI) software and the material used for moulded part was Acrylonitrile Butadiene Styrene (ABS). The analysis and result were obtained and it found that the shrinkage can be minimised and the significant parameters were found as packing pressure, mould temperature and melt temperature.

Genome-wide comparative analysis reveals similar types of NBS genes in hybrid Citrus sinensis genome and original Citrus clementine genome and provides new insights into non-TIR NBS genes.

Directory of Open Access Journals (Sweden)

Yunsheng Wang

Full Text Available In this study, we identified and compared nucleotide-binding site (NBS domain-containing genes from three Citrus genomes (C. clementina, C. sinensis from USA and C. sinensis from China. Phylogenetic analysis of all Citrus NBS genes across these three genomes revealed that there are three approximately evenly numbered groups: one group contains the Toll-Interleukin receptor (TIR domain and two different Non-TIR groups in which most of proteins contain the Coiled Coil (CC domain. Motif analysis confirmed that the two groups of CC-containing NBS genes are from different evolutionary origins. We partitioned NBS genes into clades using NBS domain sequence distances and found most clades include NBS genes from all three Citrus genomes. This suggests that three Citrus genomes have similar numbers and types of NBS genes. We also mapped the re-sequenced reads of three pomelo and three mandarin genomes onto the C. sinensis genome. We found that most NBS genes of the hybrid C. sinensis genome have corresponding homologous genes in both pomelo and mandarin genomes. The homologous NBS genes in pomelo and mandarin suggest that the parental species of C. sinensis may contain similar types of NBS genes. This explains why the hybrid C. sinensis and original C. clementina have similar types of NBS genes in this study. Furthermore, we found that sequence variation amongst Citrus NBS genes were shaped by multiple independent and shared accelerated mutation accumulation events among different groups of NBS genes and in different Citrus genomes. Our comparative analyses yield valuable insight into the structure, organization and evolution of NBS genes in Citrus genomes. Furthermore, our comprehensive analysis showed that the non-TIR NBS genes can be divided into two groups that come from different evolutionary origins. This provides new insights into non-TIR genes, which have not received much attention.

Effect of processing conditions on shrinkage in injection moulding

NARCIS (Netherlands)

Jansen, K.M.B.; van Dijk, D.J.; Husselman, M.H.

1998-01-01

A systematic study on the effect of processing conditions on mold shrinkage was undertaken for seven common thermoplastic polymers. It turned out that the holding pressure was always the key parameter. The effect of the melt temperature is slightly less important. Injection velocity and mold

Shrinkage of Newly Formed Particles in an Urban Environment

Czech Academy of Sciences Publication Activity Database

Škrabalová, Lenka; Zíková, Naděžda; Ždímal, Vladimír

2015-01-01

Roč. 15, č. 4 (2015), s. 1313-1324 ISSN 1680-8584 R&D Projects: GA ČR GAP209/11/1342 Institutional support: RVO:67985858 Keywords : aerosol dynamics * ultrafine particles * particle shrinkage Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.393, year: 2015

Diverse circovirus-like genome architectures revealed by environmental metagenomics.

Science.gov (United States)

Rosario, Karyna; Duffy, Siobain; Breitbart, Mya

2009-10-01

Single-stranded DNA (ssDNA) viruses with circular genomes are the smallest viruses known to infect eukaryotes. The present study identified 10 novel genomes similar to ssDNA circoviruses through data-mining of public viral metagenomes. The metagenomic libraries included samples from reclaimed water and three different marine environments (Chesapeake Bay, British Columbia coastal waters and Sargasso Sea). All the genomes have similarities to the replication (Rep) protein of circoviruses; however, only half have genomic features consistent with known circoviruses. Some of the genomes exhibit a mixture of genomic features associated with different families of ssDNA viruses (i.e. circoviruses, geminiviruses and parvoviruses). Unique genome architectures and phylogenetic analysis of the Rep protein suggest that these viruses belong to novel genera and/or families. Investigating the complex community of ssDNA viruses in the environment can lead to the discovery of divergent species and help elucidate evolutionary links between ssDNA viruses.

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

Science.gov (United States)

Mao, Peng; Brown, Alexander J; Malc, Ewa P; Mieczkowski, Piotr A; Smerdon, Michael J; Roberts, Steven A; Wyrick, John J

2017-10-01

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers. © 2017 Mao et al.; Published by Cold Spring Harbor Laboratory Press.

Shrinkage-based diagonal Hotelling’s tests for high-dimensional small sample size data

KAUST Repository

Dong, Kai

2015-09-16

DNA sequencing techniques bring novel tools and also statistical challenges to genetic research. In addition to detecting differentially expressed genes, testing the significance of gene sets or pathway analysis has been recognized as an equally important problem. Owing to the “large pp small nn” paradigm, the traditional Hotelling’s T2T2 test suffers from the singularity problem and therefore is not valid in this setting. In this paper, we propose a shrinkage-based diagonal Hotelling’s test for both one-sample and two-sample cases. We also suggest several different ways to derive the approximate null distribution under different scenarios of pp and nn for our proposed shrinkage-based test. Simulation studies show that the proposed method performs comparably to existing competitors when nn is moderate or large, but it is better when nn is small. In addition, we analyze four gene expression data sets and they demonstrate the advantage of our proposed shrinkage-based diagonal Hotelling’s test.

Shrinkage-based diagonal Hotelling’s tests for high-dimensional small sample size data

KAUST Repository

Dong, Kai; Pang, Herbert; Tong, Tiejun; Genton, Marc G.

2015-01-01

DNA sequencing techniques bring novel tools and also statistical challenges to genetic research. In addition to detecting differentially expressed genes, testing the significance of gene sets or pathway analysis has been recognized as an equally important problem. Owing to the “large pp small nn” paradigm, the traditional Hotelling’s T2T2 test suffers from the singularity problem and therefore is not valid in this setting. In this paper, we propose a shrinkage-based diagonal Hotelling’s test for both one-sample and two-sample cases. We also suggest several different ways to derive the approximate null distribution under different scenarios of pp and nn for our proposed shrinkage-based test. Simulation studies show that the proposed method performs comparably to existing competitors when nn is moderate or large, but it is better when nn is small. In addition, we analyze four gene expression data sets and they demonstrate the advantage of our proposed shrinkage-based diagonal Hotelling’s test.

Marginal adaptation of a low-shrinkage silorane-based composite: A SEM-analysis

DEFF Research Database (Denmark)

Schmidt, Malene; Bindslev, Preben Hørsted; Poulsen, Sven

2012-01-01

shrinkage, has been marketed. Objective. To investigate whether reduced polymerization shrinkage improves the marginal adaptation of composite restorations. Material and methods. A total of 156 scanning electron microscopy (SEM) pictures (78 baseline, 78 follow-up) of the occlusal part of Class II......-casts of the restorations were used for SEM pictures at x 16 magnification. Pictures from baseline and follow-up (398 days, SD 29 days) were randomized and the examiner was blinded to the material and the age of the restoration. Stereologic measurements were used to calculate the length and the width of the marginal...

Experimental investigation on shrinkage and surface replication of injection moulded ceramic parts

DEFF Research Database (Denmark)

Islam, Aminul; Giannekas, Nikolaos; Marhöfer, David Maximilian

2014-01-01

Ceramic moulded parts are increasingly being used in advanced components and devices due to their unprecedented material and performance attributes. The surface finish, replication quality and material shrinkage are of immense importance for moulded ceramic parts intended for precision applications....... The current paper presents a thorough investigation on the process of ceramic moulding where it systematically characterizes the surface replication and shrinkage behaviours of precision moulded ceramic components. The test parts are moulded from Catamold TZP-A which is Y2O3-stabilised ZrO2 having widespread...... distribution for the moulded ceramic parts is presented....

Accurate characterisation of post moulding shrinkage of polymer parts

DEFF Research Database (Denmark)

Neves, L. C.; De Chiffre, L.; González-Madruga, D.

2015-01-01

The work deals with experimental determination of the shrinkage of polymer parts after injection moulding. A fixture for length measurements on 8 parts at the same time was designed and manufactured in Invar, mounted with 8 electronic gauges, and provided with 3 temperature sensors. The fixture w...

Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

KAUST Repository

Black, PA

2015-10-24

Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions Our study demonstrated true levels of genetic diversity

Shrinkages in heavy-sized cast components of nodular cast iron – NDT and fatigue

Directory of Open Access Journals (Sweden)

Bleicher Christoph

2014-06-01

Full Text Available Material defects like shrinkages, dross, pores and chunky graphite are likely to occur in thick-walled castings and are a challenge for the foundries and their customers. These defects are mostly detected with handheld ultrasonic testing (UT or X-ray analysis. Within a research project done at the Fraunhofer Institute for Structural Durability and System Reliability LBF, the fatigue of Dross, shrinkages and chunky graphite in thick-walled cast material GGG-40 was estimated based on X-ray and fatigue tests on bending specimens. High fatigue reductions were received for the different material imperfections. Based on these impressions a further research project was executed at the Fraunhofer LBF to get an estimation of the informational value of UT in relation to fatigue of shrinkages in thick-walled castings of the material EN-GJS-400-18U-LT, EN-GJS-450-18 and EN-GJS-700-2. With the help of X-ray analysis and the UT technique Sampling Phased Array (SPA information about geometry and density were derived for a numerical analysis of shrinkages in thick-walled castings concerning fatigue. The following text summarizes the fatigue results achieved in the two research projects with the help of the X-ray and UT analysis.

OPTIMAL SHRINKAGE ESTIMATION OF MEAN PARAMETERS IN FAMILY OF DISTRIBUTIONS WITH QUADRATIC VARIANCE.

Science.gov (United States)

Xie, Xianchao; Kou, S C; Brown, Lawrence

2016-03-01

This paper discusses the simultaneous inference of mean parameters in a family of distributions with quadratic variance function. We first introduce a class of semi-parametric/parametric shrinkage estimators and establish their asymptotic optimality properties. Two specific cases, the location-scale family and the natural exponential family with quadratic variance function, are then studied in detail. We conduct a comprehensive simulation study to compare the performance of the proposed methods with existing shrinkage estimators. We also apply the method to real data and obtain encouraging results.

Effect of vacuum arc melting/casting parameters on shrinkage cavity/piping of austenitic stainless steel ingot

International Nuclear Information System (INIS)

Kamran, J.; Feroz, M.; Sarwar, M.

2009-01-01

Shrinkage cavity/piping at the end of the solidified ingot of steels is one of the most common casting problem in 316L austenitic stainless steel ingot, when consumable electrode is melted and cast in a water-cooled copper mould by vacuum arc re-melting furnace. In present study an effort has been made to reduce the size of shrinkage cavity/ piping by establishing the optimum value of hot topping process parameters at the end of the melting process. It is concluded that the shrinkage cavity/piping at the top of the solidified ingot can be reduced to minimum by adjusting the process parameters particularly the melting current density. (author)

Self-Shrinkage Behaviors of Waste Paper Fiber Reinforced Cement Paste considering Its Self-Curing Effect at Early-Ages

Directory of Open Access Journals (Sweden)

Zhengwu Jiang

2016-01-01

Full Text Available The aim of this paper was to study how the early-age self-shrinkage behavior of cement paste is affected by the addition of the waste paper fibers under sealed conditions. Although the primary focus was to determine whether the waste paper fibers are suitable to mitigate self-shrinkage as an internal curing agent under different adding ways, evaluating their strength, pore structure, and hydration properties provided further insight into the self-cured behavior of cement paste. Under the wet mixing condition, the waste paper fibers could mitigate the self-shrinkage of cement paste and, at additions of 0.2% by mass of cement, the waste paper fibers were found to show significant self-shrinkage cracking control while providing some internal curing. In addition, the self-curing efficiency results were analyzed based on the strength and the self-shrinkage behaviors of cement paste. Results indicated that, under a low water cement ratio, an optimal dosage and adding ways of the waste paper fibers could enhance the self-curing efficiency of cement paste.

Draft genome sequence of Streptomyces coelicoflavus ZG0656 reveals the putative biosynthetic gene cluster of acarviostatin family α-amylase inhibitors.

Science.gov (United States)

Guo, X; Geng, P; Bai, F; Bai, G; Sun, T; Li, X; Shi, L; Zhong, Q

2012-08-01

The aims of this study are to obtain the draft genome sequence of Streptomyces coelicoflavus ZG0656, which produces novel acarviostatin family α-amylase inhibitors, and then to reveal the putative acarviostatin-related gene cluster and the biosynthetic pathway. The draft genome sequence of S. coelicoflavus ZG0656 was generated using a shotgun approach employing a combination of 454 and Solexa sequencing technologies. Genome analysis revealed a putative gene cluster for acarviostatin biosynthesis, termed sct-cluster. The cluster contains 13 acarviostatin synthetic genes, six transporter genes, four starch degrading or transglycosylation enzyme genes and two regulator genes. On the basis of bioinformatic analysis, we proposed a putative biosynthetic pathway of acarviostatins. The intracellular steps produce a structural core, acarviostatin I00-7-P, and the extracellular assemblies lead to diverse acarviostatin end products. The draft genome sequence of S. coelicoflavus ZG0656 revealed the putative biosynthetic gene cluster of acarviostatins and a putative pathway of acarviostatin production. To our knowledge, S. coelicoflavus ZG0656 is the first strain in this species for which a genome sequence has been reported. The analysis of sct-cluster provided important insights into the biosynthesis of acarviostatins. This work will be a platform for producing novel variants and yield improvement. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

The Shrinkage Model And Expert System Of Plastic Lens Formation

Science.gov (United States)

Chang, Rong-Seng

1988-06-01

Shrinkage causes both the appearance & dimension defects of the injected plastic lens. We have built up a model of state equations with the help of finite element analysis program to estimate the volume change (shrinkage and swelling) under the combinations of injection variables such as pressure and temperature etc., then the personal computer expert system has been build up to make that knowledge conveniently available to the user in the model design, process planning, process operation and some other work. The domain knowledge is represented by a R-graph (Relationship-graph) model which states the relationships of variables & equations. This model could be compare with other models in the expert system. If the user has better model to solve the shrinkage problem, the program will evaluate it automatically and a learning file will be trigger by the expert system to teach the user to update their knowledge base and modify the old model by this better model. The Rubin's model and Gilmore's model have been input to the expert system. The conflict has been solved both from the user and the deeper knowledge base. A cube prism and the convex lens examples have been shown in this paper. This program is written by MULISP language in IBM PC-AT. The natural language provides English Explaination of know why and know how and the automatic English translation for the equation rules and the production rules.

Influence of gelatinous fibers on the shrinkage of silver maple

Science.gov (United States)

Donals G. Arganbright; Dwight W. Bensend; Floyd G. Manwiller

1970-01-01

The degree of lean was found to have a significant influence on the logitudinal and transverse shrinkage of three soft maple trees. This may be accounted for by differences in the cell wall layer thickness and fibril angle.

Genome editing reveals a role for OCT4 in human embryogenesis.

Science.gov (United States)

Fogarty, Norah M E; McCarthy, Afshan; Snijders, Kirsten E; Powell, Benjamin E; Kubikova, Nada; Blakeley, Paul; Lea, Rebecca; Elder, Kay; Wamaitha, Sissy E; Kim, Daesik; Maciulyte, Valdone; Kleinjung, Jens; Kim, Jin-Soo; Wells, Dagan; Vallier, Ludovic; Bertero, Alessandro; Turner, James M A; Niakan, Kathy K

2017-10-05

Despite their fundamental biological and clinical importance, the molecular mechanisms that regulate the first cell fate decisions in the human embryo are not well understood. Here we use CRISPR-Cas9-mediated genome editing to investigate the function of the pluripotency transcription factor OCT4 during human embryogenesis. We identified an efficient OCT4-targeting guide RNA using an inducible human embryonic stem cell-based system and microinjection of mouse zygotes. Using these refined methods, we efficiently and specifically targeted the gene encoding OCT4 (POU5F1) in diploid human zygotes and found that blastocyst development was compromised. Transcriptomics analysis revealed that, in POU5F1-null cells, gene expression was downregulated not only for extra-embryonic trophectoderm genes, such as CDX2, but also for regulators of the pluripotent epiblast, including NANOG. By contrast, Pou5f1-null mouse embryos maintained the expression of orthologous genes, and blastocyst development was established, but maintenance was compromised. We conclude that CRISPR-Cas9-mediated genome editing is a powerful method for investigating gene function in the context of human development.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

Science.gov (United States)

Krishnan S, Gopala; Waters, Daniel L E; Henry, Robert J

2014-01-01

Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts). Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome.

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Gopala Krishnan S

Full Text Available BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice. Oryza meridionalis is a related annual species in Australia. RESULTS: We have examined the sequence of the genomes of AA genome wild rices from Australia that are close relatives of cultivated rice through whole genome re-sequencing. Assembly of the resequencing data to the O. sativa ssp. japonica cv. Nipponbare shows that Australian wild rices possess 2.5 times more single nucleotide polymorphisms than in the Asian wild rice and cultivated O. sativa ssp. indica. Analysis of the genome of domesticated rice reveals regions of low diversity that show very little variation (polymorphism deserts. Both the perennial and annual wild rice from Australia show a high degree of conservation of sequence with that found in cultivated rice in the same 4.58 Mbp region on chromosome 5, which suggests that some of the 'polymorphism deserts' in this and other parts of the rice genome may have originated prior to domestication due to natural selection. CONCLUSIONS: Analysis of genes in the 'polymorphism deserts' indicates that this selection may have been due to biotic or abiotic stress in the environment of early rice relatives. Despite having closely related sequences in these genome regions, the Australian wild populations represent an invaluable source of diversity supporting rice food security.

Urban shrinkage in Germany and the USA: a comparison of transformation patterns and local strategies.

Science.gov (United States)

Wiechmann, Thorsten; Pallagst, Karina M

2012-01-01

Many American and European cities have to deal with demographic and economic trajectories leading to urban shrinkage. According to official data, 13% of urban regions in the US and 54% of those in the EU have lost population in recent years. However, the extent and spatial distribution of declining populations differ significantly between Europe and the US. In Germany, the situation is driven by falling birth rates and the effects of German reunification. In the US, shrinkage is basically related to long-term industrial transformation. But the challenges of shrinking cities seldom appeared on the agendas of politicians and urban planners until recently. This article provides a critical overview of the development paths and local strategies of four shrinking cities: Schwedt and Dresden in eastern Germany; Youngstown and Pittsburgh in the US. A typology of urban growth and shrinkage, from economic and demographic perspectives, enables four types of city to be differentiated and the differences between the US and eastern Germany to be discussed. The article suggests that a new transatlantic debate on policy and planning strategies for restructuring shrinking cities is needed to overcome the dominant growth orientation that in most cases intensifies the negative consequences of shrinkage.

The mitochondrial genomes of Amphiascoides atopus and Schizopera knabeni (Harpacticoida: Miraciidae) reveal similarities between the copepod orders Harpacticoida and Poecilostomatoida.

Science.gov (United States)

Easton, Erin E; Darrow, Emily M; Spears, Trisha; Thistle, David

2014-03-15

Members of subclass Copepoda are abundant, diverse, and-as a result of their variety of ecological roles in marine and freshwater environments-important, but their phylogenetic interrelationships are unclear. Recent studies of arthropods have used gene arrangements in the mitochondrial (mt) genome to infer phylogenies, but for copepods, only seven complete mt genomes have been published. These data revealed several within-order and few among-order similarities. To increase the data available for comparisons, we sequenced the complete mt genome (13,831base pairs) of Amphiascoides atopus and 10,649base pairs of the mt genome of Schizopera knabeni (both in the family Miraciidae of the order Harpacticoida). Comparison of our data to those for Tigriopus japonicus (family Harpacticidae, order Harpacticoida) revealed similarities in gene arrangement among these three species that were consistent with those found within and among families of other copepod orders. Comparison of the mt genomes of our species with those known from other copepod orders revealed the arrangement of mt genes of our Harpacticoida species to be more similar to that of Sinergasilus polycolpus (order Poecilostomatoida) than to that of T. japonicus. The similarities between S. polycolpus and our species are the first to be noted across the boundaries of copepod orders and support the possibility that mt-gene arrangement might be used to infer copepod phylogenies. We also found that our two species had extremely truncated transfer RNAs and that gene overlaps occurred much more frequently than has been reported for other copepod mt genomes. Published by Elsevier B.V.

Evaluation of shrinkage temperature of bovine pericardium tissue for bioprosthetic heart valve application by differential scanning calorimetry and freeze-drying microscopy

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Virgilio Tattini Jr

2007-03-01

Full Text Available Bovine pericardium bioprosthesis has become a commonly accepted device for heart valve replacement. Present practice relies on the measurement of shrinkage temperature, observed as a dramatic shortening of tissue length. Several reports in the last decade have utilized differential scanning calorimetry (DSC as an alternative method to determine the shrinkage temperature, which is accompanied by the absorption of heat, giving rise to an endothermic peak over the shrinkage temperature range of biological tissues. Usually, freeze-drying microscope is used to determine collapse temperature during the lyophilization of solutions. On this experiment we used this technique to study the shrinkage event. The aim of this work was to compare the results of shrinkage temperature obtained by DSC with the results obtained by freeze-drying microscopy. The results showed that both techniques provided excellent sensitivity and reproducibility, and gave information on the thermal shrinkage transition via the thermodynamical parameters inherent of each method.

Whole genome PCR scanning reveals the syntenic genome structure of toxigenic Vibrio cholerae strains in the O1/O139 population.

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Bo Pang

Full Text Available Vibrio cholerae is commonly found in estuarine water systems. Toxigenic O1 and O139 V. cholerae strains have caused cholera epidemics and pandemics, whereas the nontoxigenic strains within these serogroups only occasionally lead to disease. To understand the differences in the genome and clonality between the toxigenic and nontoxigenic strains of V. cholerae serogroups O1 and O139, we employed a whole genome PCR scanning (WGPScanning method, an rrn operon-mediated fragment rearrangement analysis and comparative genomic hybridization (CGH to analyze the genome structure of different strains. WGPScanning in conjunction with CGH revealed that the genomic contents of the toxigenic strains were conservative, except for a few indels located mainly in mobile elements. Minor nucleotide variation in orthologous genes appeared to be the major difference between the toxigenic strains. rrn operon-mediated rearrangements were infrequent in El Tor toxigenic strains tested using I-CeuI digested pulsed-field gel electrophoresis (PFGE analysis and PCR analysis based on flanking sequence of rrn operons. Using these methods, we found that the genomic structures of toxigenic El Tor and O139 strains were syntenic. The nontoxigenic strains exhibited more extensive sequence variations, but toxin coregulated pilus positive (TCP+ strains had a similar structure. TCP+ nontoxigenic strains could be subdivided into multiple lineages according to the TCP type, suggesting the existence of complex intermediates in the evolution of toxigenic strains. The data indicate that toxigenic O1 El Tor and O139 strains were derived from a single lineage of intermediates from complex clones in the environment. The nontoxigenic strains with non-El Tor type TCP may yet evolve into new epidemic clones after attaining toxigenic attributes.

Drying shrinkage problems in high-plastic clay soils in Oklahoma.

Science.gov (United States)

2013-08-01

Longitudinal cracking in pavements due to drying shrinkage of high-plastic subgrade soils has been a major : problem in Oklahoma. Annual maintenance to seal and repair these distress problems costs significant amount of : money to the state. The long...

Effects of moisture migration on shrinkage, pore pressure and other concrete properties

International Nuclear Information System (INIS)

Chapman, D.A.; England, G.L.

1977-01-01

This work investigates the uniaxial migration of moisture in long, upright, limestone concrete cylinders, sealed at the base and sides, and open at the top. The design represents a section through a concrete pressure vessel wall. The cylinders are subjected to a sustained temperature difference between their ends, with maximum temperatures between 105 0 C and 200 0 C. Readings of pore pressure, water content and temperature are taken at various positions along the axis of the cylinders. In one cylinder transverse and longitudinal shrinkage readings are also recorded. The results for the cylinders show that moisture migration is away from the hot face of the specimens, causing reduction in both pore pressure and water content values in this region. The moisture migration creates a drying front which moves slowly up the specimens. Evaporation drying takes place from the unsealed end of the specimen. A drying front moves into the concrete and considerable weight loss is recorded as moisture escapes to the atmosphere. The rate of movement of the drying front is slower than that of the hot front and is proportional to the temperature difference between the top of the specimen and the surrounding atmosphere. In the shrinkage specimen, values of transverse and longitudinal shrinkage reflect the water content results. The specimen indicates that shrinkage occurs in a concrete pressure vessel, in the regions where moisture is lost. The restraint of the mass of concrete surrounding these regions sets up a three dimensional state of internal tensile stress. The areas into which the moisture migrates tend to swell, creating an internal stress situation, which is this

Genomic Analysis of Hepatitis B Virus Reveals Antigen State and Genotype as Sources of Evolutionary Rate Variation

Science.gov (United States)

Harrison, Abby; Lemey, Philippe; Hurles, Matthew; Moyes, Chris; Horn, Susanne; Pryor, Jan; Malani, Joji; Supuri, Mathias; Masta, Andrew; Teriboriki, Burentau; Toatu, Tebuka; Penny, David; Rambaut, Andrew; Shapiro, Beth

2011-01-01

Hepatitis B virus (HBV) genomes are small, semi-double-stranded DNA circular genomes that contain alternating overlapping reading frames and replicate through an RNA intermediary phase. This complex biology has presented a challenge to estimating an evolutionary rate for HBV, leading to difficulties resolving the evolutionary and epidemiological history of the virus. Here, we re-examine rates of HBV evolution using a novel data set of 112 within-host, transmission history (pedigree) and among-host genomes isolated over 20 years from the indigenous peoples of the South Pacific, combined with 313 previously published HBV genomes. We employ Bayesian phylogenetic approaches to examine several potential causes and consequences of evolutionary rate variation in HBV. Our results reveal rate variation both between genotypes and across the genome, as well as strikingly slower rates when genomes are sampled in the Hepatitis B e antigen positive state, compared to the e antigen negative state. This Hepatitis B e antigen rate variation was found to be largely attributable to changes during the course of infection in the preCore and Core genes and their regulatory elements. PMID:21765983

Drying and radial shrinkage characteristics and changes in color ...

African Journals Online (AJOL)

Drying and radial shrinkage characteristics and changes in color and shape of carrots tissues during air drying were studied. Slices dimensions were obtained by computer vision and the color was quantified by chroma, hue, whitening index and total carotenoids contents. The drying time became shorter of 1 h when ...

Numerical simulation of early-age shrinkage effects on RC member deflections and cracking development

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P. Bernardi

2016-07-01

Full Text Available Shrinkage effects on short-term behavior of reinforced concrete elements are often neglected both in design code provisions and in numerical simulations. However, it is known that their influence on serviceability performance can be significant, especially in case of lightly-reinforced beams. As a matter of fact, the restraint provided by the reinforcement on concrete determines a reduction of the cracking load of the structural element, as well as an increase of its deflection. This paper deals with the modeling of early-age shrinkage effects in the field of smeared crack approaches. To this aim, an existing non-linear constitutive relation for cracked reinforced concrete elements is extended herein to include early-age concrete shrinkage. Careful verifications of the model are carried out by comparing numerical results with significant experimental data reported in technical literature, providing a good agreement both in terms of global and local behavior.

Polymerization Behavior and Mechanical Properties of High-Viscosity Bulk Fill and Low Shrinkage Resin Composites.

Science.gov (United States)

Shibasaki, S; Takamizawa, T; Nojiri, K; Imai, A; Tsujimoto, A; Endo, H; Suzuki, S; Suda, S; Barkmeier, W W; Latta, M A; Miyazaki, M

The present study determined the mechanical properties and volumetric polymerization shrinkage of different categories of resin composite. Three high viscosity bulk fill resin composites were tested: Tetric EvoCeram Bulk Fill (TB, Ivoclar Vivadent), Filtek Bulk Fill posterior restorative (FB, 3M ESPE), and Sonic Fill (SF, Kerr Corp). Two low-shrinkage resin composites, Kalore (KL, GC Corp) and Filtek LS Posterior (LS, 3M ESPE), were used. Three conventional resin composites, Herculite Ultra (HU, Kerr Corp), Estelite ∑ Quick (EQ, Tokuyama Dental), and Filtek Supreme Ultra (SU, 3M ESPE), were used as comparison materials. Following ISO Specification 4049, six specimens for each resin composite were used to determine flexural strength, elastic modulus, and resilience. Volumetric polymerization shrinkage was determined using a water-filled dilatometer. Data were evaluated using analysis of variance followed by Tukey's honestly significant difference test (α=0.05). The flexural strength of the resin composites ranged from 115.4 to 148.1 MPa, the elastic modulus ranged from 5.6 to 13.4 GPa, and the resilience ranged from 0.70 to 1.0 MJ/m 3 . There were significant differences in flexural properties between the materials but no clear outliers. Volumetric changes as a function of time over a duration of 180 seconds depended on the type of resin composite. However, for all the resin composites, apart from LS, volumetric shrinkage began soon after the start of light irradiation, and a rapid decrease in volume during light irradiation followed by a slower decrease was observed. The low shrinkage resin composites KL and LS showed significantly lower volumetric shrinkage than the other tested materials at the measuring point of 180 seconds. In contrast, the three bulk fill resin composites showed higher volumetric change than the other resin composites. The findings from this study provide clinicians with valuable information regarding the mechanical properties and

Comparative Genomic Analysis of Clinical and Environmental Vibrio Vulnificus Isolates Revealed Biotype 3 Evolutionary Relationships

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Yael eKotton

2015-01-01

Full Text Available In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59% and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 kbp to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C and environmental (E, all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins were present in all human pathogenic strains (both biotype 3 and non-biotype 3 and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and

Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

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James J Collins

Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus) and the Scaled Quail (Callipepla squamata) Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size.

Science.gov (United States)

Oldeschulte, David L; Halley, Yvette A; Wilson, Miranda L; Bhattarai, Eric K; Brashear, Wesley; Hill, Joshua; Metz, Richard P; Johnson, Charles D; Rollins, Dale; Peterson, Markus J; Bickhart, Derek M; Decker, Jared E; Sewell, John F; Seabury, Christopher M

2017-09-07

Northern bobwhite ( Colinus virginianus ; hereafter bobwhite) and scaled quail ( Callipepla squamata ) populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0) and second- (v2.0) generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb) was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb), which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%), genome-wide repetitive content (10.40%; 10.43%), and MAKER-predicted protein coding genes (17,131; 17,165) were similar for the scaled quail (v1.0) and bobwhite (v2.0) assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8%) and the bobwhite (v2.0; 82.5%), as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0), and 711 in the bobwhite genome (v2.0), including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0) and bobwhite (v2.0) genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15-20 KYA. Copyright © 2017 Oldeschulte et al.

Annotated Draft Genome Assemblies for the Northern Bobwhite (Colinus virginianus and the Scaled Quail (Callipepla squamata Reveal Disparate Estimates of Modern Genome Diversity and Historic Effective Population Size

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David L. Oldeschulte

2017-09-01

Full Text Available Northern bobwhite (Colinus virginianus; hereafter bobwhite and scaled quail (Callipepla squamata populations have suffered precipitous declines across most of their US ranges. Illumina-based first- (v1.0 and second- (v2.0 generation draft genome assemblies for the scaled quail and the bobwhite produced N50 scaffold sizes of 1.035 and 2.042 Mb, thereby producing a 45-fold improvement in contiguity over the existing bobwhite assembly, and ≥90% of the assembled genomes were captured within 1313 and 8990 scaffolds, respectively. The scaled quail assembly (v1.0 = 1.045 Gb was ∼20% smaller than the bobwhite (v2.0 = 1.254 Gb, which was supported by kmer-based estimates of genome size. Nevertheless, estimates of GC content (41.72%; 42.66%, genome-wide repetitive content (10.40%; 10.43%, and MAKER-predicted protein coding genes (17,131; 17,165 were similar for the scaled quail (v1.0 and bobwhite (v2.0 assemblies, respectively. BUSCO analyses utilizing 3023 single-copy orthologs revealed a high level of assembly completeness for the scaled quail (v1.0; 84.8% and the bobwhite (v2.0; 82.5%, as verified by comparison with well-established avian genomes. We also detected 273 putative segmental duplications in the scaled quail genome (v1.0, and 711 in the bobwhite genome (v2.0, including some that were shared among both species. Autosomal variant prediction revealed ∼2.48 and 4.17 heterozygous variants per kilobase within the scaled quail (v1.0 and bobwhite (v2.0 genomes, respectively, and estimates of historic effective population size were uniformly higher for the bobwhite across all time points in a coalescent model. However, large-scale declines were predicted for both species beginning ∼15–20 KYA.

Genomic analysis of primordial dwarfism reveals novel disease genes.

Science.gov (United States)

Shaheen, Ranad; Faqeih, Eissa; Ansari, Shinu; Abdel-Salam, Ghada; Al-Hassnan, Zuhair N; Al-Shidi, Tarfa; Alomar, Rana; Sogaty, Sameera; Alkuraya, Fowzan S

2014-02-01

Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in defining clinical subgroups. In this study, we present the results of clinical and genomic characterization of 16 new patients in whom a broad definition of PD was used (e.g., 3M syndrome was included). We report a novel PD syndrome with distinct facies in two unrelated patients, each with a different homozygous truncating mutation in CRIPT. Our analysis also reveals, in addition to mutations in known PD disease genes, the first instance of biallelic truncating BRCA2 mutation causing PD with normal bone marrow analysis. In addition, we have identified a novel locus for Seckel syndrome based on a consanguineous multiplex family and identified a homozygous truncating mutation in DNA2 as the likely cause. An additional novel PD disease candidate gene XRCC4 was identified by autozygome/exome analysis, and the knockout mouse phenotype is highly compatible with PD. Thus, we add a number of novel genes to the growing list of PD-linked genes, including one which we show to be linked to a novel PD syndrome with a distinct facial appearance. PD is extremely heterogeneous genetically and clinically, and genomic tools are often required to reach a molecular diagnosis.

Self-healing of drying shrinkage cracks in cement-based materials incorporating reactive MgO

Science.gov (United States)

Qureshi, T. S.; Al-Tabbaa, A.

2016-08-01

Excessive drying shrinkage is one of the major issues of concern for longevity and reduced strength performance of concrete structures. It can cause the formation of cracks in the concrete. This research aims to improve the autogenous self-healing capacity of traditional Portland cement (PC) systems, adding expansive minerals such as reactive magnesium oxide (MgO) in terms of drying shrinkage crack healing. Two different reactive grades (high ‘N50’and moderately high ‘92-200’) of MgO were added with PC. Cracks were induced in the samples with restraining end prisms through natural drying shrinkage over 28 days after casting. Samples were then cured under water for 28 and 56 days, and self-healing capacity was investigated in terms of mechanical strength recovery, crack sealing efficiency and improvement in durability. Finally, microstructures of the healing materials were investigated using FT-IR, XRD, and SEM-EDX. Overall N50 mixes show higher expansion and drying shrinkage compared to 92-200 mixes. Autogenous self-healing performance of the MgO containing samples were much higher compared to control (only PC) mixes. Cracks up to 500 μm were sealed in most MgO containing samples after 28 days. In the microstructural investigations, highly expansive Mg-rich hydro-carbonate bridges were found along with traditional calcium-based, self-healing compounds (calcite, portlandite, calcium silicate hydrates and ettringite).

Drying and Radial Shrinkage Characteristics and Changes in Color ...

African Journals Online (AJOL)

nahimana

2011-08-12

Aug 12, 2011 ... A pre-test experiment was carried out following the. Thompson ... energy saving potential and the ability to control drying temperature and air humidity. ..... structural collapse by shrinkage, case hardening, etc. From the slopes of .... Thus, the Nahimana et al. model is proposed as a new model predicting with ...

Sparsity-based shrinkage approach for practicability improvement of H-LBP-based edge extraction

Energy Technology Data Exchange (ETDEWEB)

Zhao, Chenyi [School of Physics, Northeast Normal University, Changchun 130024 (China); Qiao, Shuang, E-mail: qiaos810@nenu.edu.cn [School of Physics, Northeast Normal University, Changchun 130024 (China); Sun, Jianing, E-mail: sunjn118@nenu.edu.cn [School of Mathematics and Statistics, Northeast Normal University, Changchun 130024 (China); Zhao, Ruikun; Wu, Wei [Jilin Cancer Hospital, Changchun 130021 (China)

2016-07-21

The local binary pattern with H function (H-LBP) technique enables fast and efficient edge extraction in digital radiography. In this paper, we reformulate the model of H-LBP and propose a novel sparsity-based shrinkage approach, in which the threshold can be adapted to the data sparsity. Using this model, we upgrade fast H-LBP framework and apply it to real digital radiography. The experiments show that the method improved using the new shrinkage approach can avoid elaborately artificial modulation of parameters and possess greater robustness in edge extraction compared with the other current methods without increasing processing time. - Highlights: • An novel sparsity-based shrinkage approach for edge extraction on digital radiography is proposed. • The threshold of SS-LBP can be adaptive to the data sparsity. • SS-LBP is the development of AH-LBP and H-LBP. • Without boosting processing time and losing processing efficiency, SS-LBP can avoid elaborately artificial modulation of parameters provides. • SS-LBP has more robust performance in edge extraction compared with the existing methods.

Large-proportional shrunken bio-replication of shark skin based on UV-curing shrinkage

International Nuclear Information System (INIS)

Chen, Huawei; Che, Da; Zhang, Xin; Yue, Yue; Zhang, Deyuan

2015-01-01

The shark skin effect has attracted worldwide attention because of its superior drag reduction. As the product of natural selection, the maximum drag reduction of shark skin is found in its normal living environment. Large-proportional shrinkage of shark skin morphology is greatly anticipated for its adaptation to faster fluid flow. One novel approach, large-proportional shrunken bio-replication, is proposed as a method to adjust the optimal drag reduction region of shark skin based on the shrinkage of UV-cured material. The shark skin is taken as a replica template to allow large-proportional shrinking in the drag reduction morphology by taking advantage of the shrinkage of UV-curable material. The accuracy of the large-proportional shrunken bio-replication approach is verified by a comparison between original and shrunken bio-replicated shark skin, which shows that the shrinking ratio can reach 23% and the bio-replication accuracy is higher than 95%. In addition, the translation of the optimum drag reduction peak of natural surface function to various applications and environments is proved by drag reduction experiments. (technical note)

Shrinkage Porosity Criterion and Its Application to A 5.5 Ton Steel Ingot

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Zhang C.

2016-06-01

Full Text Available In order to predict the distribution of shrinkage porosity in steel ingot efficiently and accurately, a criterion R√L and a method to obtain its threshold value were proposed. The criterion R√L was derived based on the solidification characteristics of steel ingot and pressure gradient in the mushy zone, in which the physical properties, the thermal parameters, the structure of the mushy zone and the secondary dendrite arm spacing were all taken into consideration. The threshold value of the criterion R√L was obtained with combination of numerical simulation of ingot solidification and total solidification shrinkage rate. Prediction of the shrinkage porosity in a 5.5 ton ingot of 2Cr13 steel with criterion R√L>0.21 m · °C1/2 · s−3/2 agreed well with the results of experimental sectioning. Based on this criterion, optimization of the ingot was carried out by decreasing the height-to-diameter ratio and increasing the taper, which successfully eliminated the centreline porosity and further proved the applicability of this criterion.

The correlation between aldehyde dehydrogenase-1A1 level and tumor shrinkage after preoperative chemoradiation in locally advanced rectal cancer

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Rhandyka Rafli

2015-12-01

Full Text Available This study was performed to determine the correlation between aldehyde dehydrogenase-1A1 (ALDH1A1 level and tumor shrinkage after chemoradiation in locally advanced rectal cancer. This is a retrospective study of 14 locally advanced rectal cancer patients with long course neoadjuvant chemoradiation. ALDH1A1 level was measured using ELISA from paraffin embedded tissue. Tumor shrinkage was measured from computed tomography (CT scan or magnetic resonance imaging (MRI based on Response Evaluation Criteria in Solid Tumor v1.1 (RECIST v1.1. The mean of ALDH1A1 level was 9.014 ± 3.3 pg/mL and the mean of tumor shrinkage was 7.89 ± 35.7%. Partial response proportion was 28.6%, stable disease proportion was 50% and progressive disease proportion was 21.4%. There was a significant strong negative correlation (r = –0.890, plt; 0.001 between ALDH1A1 and tumor shrinkage. In conclusion, tumor shrinkage in locally advanced rectal cancer after preoperative chemoradiation was influenced by ALDH1A1 level. Higher level of ALDH1A1 suggests decreased tumor shrinkage after preoperative chemoradiation.

The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.

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Garret Suen

Full Text Available Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs, carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.

Supervised machine learning reveals introgressed loci in the genomes of Drosophila simulans and D. sechellia.

Science.gov (United States)

Schrider, Daniel R; Ayroles, Julien; Matute, Daniel R; Kern, Andrew D

2018-04-01

Hybridization and gene flow between species appears to be common. Even though it is clear that hybridization is widespread across all surveyed taxonomic groups, the magnitude and consequences of introgression are still largely unknown. Thus it is crucial to develop the statistical machinery required to uncover which genomic regions have recently acquired haplotypes via introgression from a sister population. We developed a novel machine learning framework, called FILET (Finding Introgressed Loci via Extra-Trees) capable of revealing genomic introgression with far greater power than competing methods. FILET works by combining information from a number of population genetic summary statistics, including several new statistics that we introduce, that capture patterns of variation across two populations. We show that FILET is able to identify loci that have experienced gene flow between related species with high accuracy, and in most situations can correctly infer which population was the donor and which was the recipient. Here we describe a data set of outbred diploid Drosophila sechellia genomes, and combine them with data from D. simulans to examine recent introgression between these species using FILET. Although we find that these populations may have split more recently than previously appreciated, FILET confirms that there has indeed been appreciable recent introgression (some of which might have been adaptive) between these species, and reveals that this gene flow is primarily in the direction of D. simulans to D. sechellia.

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth

Science.gov (United States)

Palkopoulou, Eleftheria; Mallick, Swapan; Skoglund, Pontus; Enk, Jacob; Rohland, Nadin; Li, Heng; Omrak, Ayça; Vartanyan, Sergey; Poinar, Hendrik; Götherström, Anders; Reich, David; Dalén, Love

2015-01-01

Summary The processes leading up to species extinctions are typically characterized by prolonged declines in population size and geographic distribution, followed by a phase in which populations are very small and may be subject to intrinsic threats, including loss of genetic diversity and inbreeding [1]. However, whether such genetic factors have had an impact on species prior to their extinction is unclear [2, 3]; examining this would require a detailed reconstruction of a species’ demographic history as well as changes in genome-wide diversity leading up to its extinction. Here, we present high-quality complete genome sequences from two woolly mammoths (Mammuthus primigenius). The first mammoth was sequenced at 17.1-fold coverage, and dates to ~4,300 years before present, constituting one of the last surviving individuals on Wrangel Island. The second mammoth, sequenced at 11.2-fold coverage, was obtained from a ~44,800 year old specimen from the Late Pleistocene population in northeastern Siberia. The demographic trajectories inferred from the two genomes are qualitatively similar and reveal a population bottleneck during the Middle or Early Pleistocene, and a more recent severe decline in the ancestors of the Wrangel mammoth at the end of the last glaciation. A comparison of the two genomes shows that the Wrangel mammoth has a 20% reduction in heterozygosity as well as a 28-fold increase in the fraction of the genome that is comprised of runs of homozygosity. We conclude that the population on Wrangel Island, which was the last surviving woolly mammoth population, was subject to reduced genetic diversity shortly before it became extinct. PMID:25913407

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

Science.gov (United States)

Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

The evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders. We present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis. Phylogenetic analyses on the mt genome sequences and the distinct gene orders provide further

Comparative genomic hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans

OpenAIRE

Jayapal, Karthik P; Lian, Wei; Glod, Frank; Sherman, David H; Hu, Wei-Shou

2007-01-01

Abstract Background The genomes of Streptomyces coelicolor and Streptomyces lividans bear a considerable degree of synteny. While S. coelicolor is the model streptomycete for studying antibiotic synthesis and differentiation, S. lividans is almost exclusively considered as the preferred host, among actinomycetes, for cloning and expression of exogenous DNA. We used whole genome microarrays as a comparative genomics tool for identifying the subtle differences between these two chromosomes. Res...

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

Science.gov (United States)

2014-01-01

Abstract The version of this article published in BMC Genomics 2013, 14: 274, contains 9 unpublished genomes (Botryobasidium botryosum, Gymnopus luxurians, Hypholoma sublateritium, Jaapia argillacea, Hebeloma cylindrosporum, Conidiobolus coronatus, Laccaria amethystina, Paxillus involutus, and P. rubicundulus) downloaded from JGI website. In this correction, we removed these genomes after discussion with editors and data producers whom we should have contacted before downloading these genomes. Removing these data did not alter the principle results and conclusions of our original work. The relevant Figures 1, 2, 3, 4 and 6; and Table 1 have been revised. Additional files 1, 3, 4, and 5 were also revised. We would like to apologize for any confusion or inconvenience this may have caused. Background Fungi produce a variety of carbohydrate activity enzymes (CAZymes) for the degradation of plant polysaccharide materials to facilitate infection and/or gain nutrition. Identifying and comparing CAZymes from fungi with different nutritional modes or infection mechanisms may provide information for better understanding of their life styles and infection models. To date, over hundreds of fungal genomes are publicly available. However, a systematic comparative analysis of fungal CAZymes across the entire fungal kingdom has not been reported. Results In this study, we systemically identified glycoside hydrolases (GHs), polysaccharide lyases (PLs), carbohydrate esterases (CEs), and glycosyltransferases (GTs) as well as carbohydrate-binding modules (CBMs) in the predicted proteomes of 94 representative fungi from Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. Comparative analysis of these CAZymes that play major roles in plant polysaccharide degradation revealed that fungi exhibit tremendous diversity in the number and variety of CAZymes. Among them, some families of GHs and CEs are the most prevalent CAZymes that are distributed in all of the fungi analyzed

Non-uniform shrinkage of multiple-walled carbon nanotubes under in situ electron beam irradiation

Energy Technology Data Exchange (ETDEWEB)

Li, Lunxiong [South China Normal University, Brain Science Institute, Guangzhou (China); Xiamen University, China-Australia Joint Laboratory for Functional Nanomaterials and Physics Department, Xiamen (China); Su, Jiangbin [Xiamen University, China-Australia Joint Laboratory for Functional Nanomaterials and Physics Department, Xiamen (China); Chang Zhou University, School of Mathematics and Physics, Changzhou (China); Zhu, Xianfang [Xiamen University, China-Australia Joint Laboratory for Functional Nanomaterials and Physics Department, Xiamen (China)

2016-10-15

Instability of multiple-walled carbon nanotubes (MWCNTs) was investigated by in situ transmission electron microscopy at room temperature. Specially, the non-uniform shrinkage of tubes was found: The pristine MWCNT shrank preferentially in its axial direction from the most curved free cap end of the tube, but the shrinkage of the tube diameter was offset by the axial shrinkage: For the complex MWCNT, the two inner MWCNTs also preferentially axially shrank from their most curved cap ends and separated from each other. However, for the effect of the radial pressure from the out walls which enveloped the two inner tubes and the tube amorphization, the two inner tubes were extruded to come close to each other and finally touched again. The new ''evaporation'' and ''diffusion'' mechanisms of carbon atoms as driven by the nano-curvature of CNT and the electron beam-induced athermal activation were suggested to explain the above phenomena. (orig.)

Genomic and transcriptomic analyses reveal differential regulation of diverse terpenoid and polyketides secondary metabolites in Hericium erinaceus.

Science.gov (United States)

Chen, Juan; Zeng, Xu; Yang, Yan Long; Xing, Yong Mei; Zhang, Qi; Li, Jia Mei; Ma, Ke; Liu, Hong Wei; Guo, Shun Xing

2017-08-31

The lion's mane mushroom Hericium erinaceus is a famous traditional medicinal fungus credited with anti-dementia activity and a producer of cyathane diterpenoid natural products (erinacines) useful against nervous system diseases. To date, few studies have explored the biosynthesis of these compounds, although their chemical synthesis is known. Here, we report the first genome and tanscriptome sequence of the medicinal fungus H. erinaceus. The size of the genome is 39.35 Mb, containing 9895 gene models. The genome of H. erinaceus reveals diverse enzymes and a large family of cytochrome P450 (CYP) proteins involved in the biosynthesis of terpenoid backbones, diterpenoids, sesquiterpenes and polyketides. Three gene clusters related to terpene biosynthesis and one gene cluster for polyketides biosynthesis (PKS) were predicted. Genes involved in terpenoid biosynthesis were generally upregulated in mycelia, while the PKS gene was upregulated in the fruiting body. Comparative genome analysis of 42 fungal species of Basidiomycota revealed that most edible and medicinal mushroom show many more gene clusters involved in terpenoid and polyketide biosynthesis compared to the pathogenic fungi. None of the gene clusters for terpenoid or polyketide biosynthesis were predicted in the poisonous mushroom Amanita muscaria. Our findings may facilitate future discovery and biosynthesis of bioactive secondary metabolites from H. erinaceus and provide fundamental information for exploring the secondary metabolites in other Basidiomycetes.

Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds.

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Yao Xu

Full Text Available Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus and Qinchuan (Bos taurus are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 to 12 fold on average of 97.86% and 98.98% coverage of genomes, respectively. Comparison with the Bos_taurus_UMD_3.1 reference assembly yielded 9,010,096 SNPs for Nanyang, and 6,965,062 for Qinchuan cattle, 51% and 29% of which were novel SNPs, respectively. A total of 154,934 and 115,032 small indels (1 to 3 bp were found in the Nanyang and Qinchuan genomes, respectively. The SNP and indel distribution revealed that Nanyang showed a genetically high diversity as compared to Qinchuan cattle. Furthermore, a total of 2,907 putative cases of copy number variation (CNV were identified by aligning Nanyang to Qinchuan genome, 783 of which (27% encompassed the coding regions of 495 functional genes. The gene ontology (GO analysis revealed that many CNV genes were enriched in the immune system and environment adaptability. Among several CNV genes related to lipid transport and fat metabolism, Lepin receptor gene (LEPR overlapping with CNV_1815 showed remarkably higher copy number in Qinchuan than Nanyang (log2 (ratio = -2.34988; P value = 1.53E-102. Further qPCR and association analysis investigated that the copy number of the LEPR gene presented positive correlations with transcriptional expression and phenotypic traits, suggesting the LEPR CNV may contribute to the higher fat deposition in muscles of Qinchuan cattle. Our findings provide evidence that the distinct phenotypes of Nanyang and Qinchuan breeds may be due to the different genetic variations including SNPs

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Czech Academy of Sciences Publication Activity Database

Bowler, Ch.; Allen, A. E.; Badger, J. H.; Grimwood, J.; Jabbari, K.; Kuo, A.; Maheswari, U.; Martens, C.; Maumus, F.; Otillar, R. P.; Rayko, E.; Salamov, A.; Vandepoele, K.; Beszteri, B.; Gruber, A.; Heijde, M.; Katinka, M.; Mock, T.; Valentin, K.; Verret, F.; Berges, J. A.; Brownlee, C.; Cadoret, J.-P.; Chiovitti, A.; Choi, Ch. J.; Coesel, S.; De Martino, A.; Detter, J. Ch.; Durkin, C.; Falciatore, A.; Fournet, J.; Haruta, M.; Huysman, M. J. J.; Jenkins, B. D.; Jiroutová, Kateřina; Jorgensen, R. E.; Joubert, Y.; Kaplan, A.; Kröger, N.; Kroth, P. G.; La Roche, J.; Lindquist, E.; Lommer, M.; Martin–Jézéquel, V.; Lopez, P. J.; Lucas, S.; Mangogna, M.; McGinnis, K.; Medlin, L. K.; Montsant, A.; Oudot–Le Secq, M.-P.; Napoli, C.; Oborník, Miroslav; Schnitzler Parker, M.; Petit, J.-L.; Porcel, B. M.; Poulsen, N.; Robison, M.; Rychlewski, L.; Rynearson, T. A.; Schmutz, J.; Shapiro, H.; Siaut, M.; Stanley, M.; Sussman, M. R.; Taylor, A. R.; Vardi, A.; von Dassow, P.; Vyverman, W.; Willis, A.; Wyrwicz, L. S.; Rokhsar, D. S.; Weissenbach, J.; Armbrust, E. V.; Green, B. R.; Van de Peer, Y.; Grigoriev, I. V.

2008-01-01

Roč. 456, 13-11-2008 (2008), s. 239-244 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z60220518 Keywords : Phaeodactylum * genome * evolution * diatom Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

Early age volume changes in concrete due to chemical shrinkage of cement paste

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Ebensperger, L.

1991-12-01

Full Text Available Unrestrained early age volume changes due to chemical shrinkage in cement pastes, mortars and concretes have been determined. The measurements were performed on sealed and unsealed samples which were stored under water. The chemical shrinkage of unsealed specimens represents the amount of absorbed water due to the chemical reaction of the cement It depends only on the cement content of the sample and does not lead to changes of the external dimensions. However the chemical shrinkage of sealed specimens is connected with a real volume change due to self-desiccation and the effect of internal pressures. The shrinkage depends in this case on the restraining effect of coarse aggregates as well as the cement content. The chemical shrinkage measured on sealed concretes was much higher than the one expected to ocurr on concretes, because normally an equalization of pressure takes place to some extent in the interior of the concrete. The use of expansive additives showed that they may compensate the chemical shrinkage, but its dosage is very sensitive and should be defined exactly for each case particularly.

Se han determinado los cambios volumétricos que ocurren en pastas de cemento, morteros y hormigones a edad temprana debido al efecto de la retracción química. Las mediciones se realizaron en probetas selladas y no selladas sumergidas bajo agua. La retracción química en probetas no selladas representa la cantidad de agua absorbida debido a la reacción química del cemento. Depende solamente del contenido de cemento de la probeta y no produce ningún cambio en las dimensiones de la probeta. Por el contrario, la retracción química en probetas selladas está relacionada con un cambio volumétrico real debido al efecto de la autodesecación y presiones internas. La retracción en este caso depende tanto de la restricción que imponen los áridos, como del contenido de cemento. La retracción química medida en hormigones sellados

Comprehensive genomic characterization of campylobacter genus reveals some underlying mechanisms for its genomic diversification.

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Yizhuang Zhou

Full Text Available Campylobacter species.are phenotypically diverse in many aspects including host habitats and pathogenicities, which demands comprehensive characterization of the entire Campylobacter genus to study their underlying genetic diversification. Up to now, 34 Campylobacter strains have been sequenced and published in public databases, providing good opportunity to systemically analyze their genomic diversities. In this study, we first conducted genomic characterization, which includes genome-wide alignments, pan-genome analysis, and phylogenetic identification, to depict the genetic diversity of Campylobacter genus. Afterward, we improved the tetranucleotide usage pattern-based naïve Bayesian classifier to identify the abnormal composition fragments (ACFs, fragments with significantly different tetranucleotide frequency profiles from its genomic tetranucleotide frequency profiles including horizontal gene transfers (HGTs to explore the mechanisms for the genetic diversity of this organism. Finally, we analyzed the HGTs transferred via bacteriophage transductions. To our knowledge, this study is the first to use single nucleotide polymorphism information to construct liable microevolution phylogeny of 21 Campylobacter jejuni strains. Combined with the phylogeny of all the collected Campylobacter species based on genome-wide core gene information, comprehensive phylogenetic inference of all 34 Campylobacter organisms was determined. It was found that C. jejuni harbors a high fraction of ACFs possibly through intraspecies recombination, whereas other Campylobacter members possess numerous ACFs possibly via intragenus recombination. Furthermore, some Campylobacter strains have undergone significant ancient viral integration during their evolution process. The improved method is a powerful tool for bacterial genomic analysis. Moreover, the findings would provide useful information for future research on Campylobacter genus.

First time observation of local current shrinkage during the MARFE behavior on the J-TEXT tokamak

Science.gov (United States)

Shi, Peng; Zhuang, G.; Gentle, K.; Hu, Qiming; Chen, Jie; Li, Qiang; Liu, Yang; Gao, Li; Zhang, Xiaolong; Liu, Hai; Chen, Zhipeng; Zhu, Lizhi; Li, Fuming; Zhou, Yinan; Zeng, Zhong; Liu, Linzi; He, Jiyang

2017-11-01

Multifaceted asymmetric radiation as well as strong poloidal asymmetry of the electron density from the edge, dubbed as ‘MARFE’, has been observed in high electron density Ohmically heated plasmas on J-TEXT tokamak. Equilibrium reconstruction based on the measured data from the 17-channel FIR polarimeter-interferometer indicates that an asymmetric plasma current density distribution forms at the edge region and the plasma current shrinkage locates at the MARFE affected region. Furthermore, associated with the localized plasma current shrinkage, a locked mode MHD activity is excited, which then terminate the discharge with a major disruption. Localized plasma current shrinkage at the MARFE region is considered to be the direct cause for the density limit disruptions, and the proposed interpretation is consistent with the experimental observations.

Shrinkage Simulation of Holographic Grating Using Diffusion Model in PQ-PMMA Photopolymer

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Wei Zepeng

2015-01-01

Full Text Available An extended model based on nonlocal polymerization-driven diffusion model is derived by introducing shrinkage process for describing photopolymerized dynamics in PQ-PMMA photopolymer. The kinetic parameters, polymerization rate and diffusion rate are experimentally determined to provide quantitative simulation. The numerical results show that the fringes at edge of grating are firstly shifted and consequently, it leads to a contrast reduction of holograms. Finally, theoretical results are experimentally checked by temporal evolution of diffraction efficiency, and the shrinkage coefficient 0.5% is approximately achieved under incident intensity 25.3mw/cm2. This work can enhance the applicability of diffusion model and contribute to the reasonable description of the grating formation in the photopolymer.

Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis.

Science.gov (United States)

Tsementzi, Despina; Castro Gordillo, Juan; Mahagna, Mustafa; Gottlieb, Yuval; Konstantinidis, Konstantinos T

2018-05-01

Understanding the symbiotic interaction between Coxiella-like endosymbionts (CLE) and their tick hosts is challenging due to lack of isolates and difficulties in tick functional assays. Here we sequenced the metagenome of a CLE population from wild Rhipicephalus sanguineus ticks (CRs) and compared it to the previously published genome of its close relative, CLE of R. turanicus (CRt). The tick hosts are closely related sympatric species, and their two endosymbiont genomes are highly similar with only minor differences in gene content. Both genomes encode numerous pseudogenes, consistent with an ongoing genome reduction process. In silico flux balance metabolic analysis (FBA) revealed the excess production of L-proline for both genomes, indicating a possible proline transport from Coxiella to the tick. Additionally, both CR genomes encode multiple copies of the proline/betaine transporter, proP gene. Modelling additional Coxiellaceae members including other tick CLE, did not identify proline as an excreted metabolite. Although both CRs and CRt genomes encode intact B vitamin synthesis pathway genes, which are presumed to underlay the mechanism of CLE-tick symbiosis, the FBA analysis indicated no changes for their products. Therefore, this study provides new testable hypotheses for the symbiosis mechanism and a better understanding of CLE genome evolution and diversity. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Novel phage group infecting Lactobacillus delbrueckii subsp. lactis, as revealed by genomic and proteomic analysis of bacteriophage Ldl1.

Science.gov (United States)

Casey, Eoghan; Mahony, Jennifer; Neve, Horst; Noben, Jean-Paul; Dal Bello, Fabio; van Sinderen, Douwe

2015-02-01

Ldl1 is a virulent phage infecting the dairy starter Lactobacillus delbrueckii subsp. lactis LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting Lactobacillus delbrueckii. In vitro propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 +/- 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of Lactobacillus plantarum phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized L. delbrueckii phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.

In-depth comparative analysis of malaria parasite genomes reveals protein-coding genes linked to human disease in Plasmodium falciparum genome.

Science.gov (United States)

Liu, Xuewu; Wang, Yuanyuan; Liang, Jiao; Wang, Luojun; Qin, Na; Zhao, Ya; Zhao, Gang

2018-05-02

Plasmodium falciparum is the most virulent malaria parasite capable of parasitizing human erythrocytes. The identification of genes related to this capability can enhance our understanding of the molecular mechanisms underlying human malaria and lead to the development of new therapeutic strategies for malaria control. With the availability of several malaria parasite genome sequences, performing computational analysis is now a practical strategy to identify genes contributing to this disease. Here, we developed and used a virtual genome method to assign 33,314 genes from three human malaria parasites, namely, P. falciparum, P. knowlesi and P. vivax, and three rodent malaria parasites, namely, P. berghei, P. chabaudi and P. yoelii, to 4605 clusters. Each cluster consisted of genes whose protein sequences were significantly similar and was considered as a virtual gene. Comparing the enriched values of all clusters in human malaria parasites with those in rodent malaria parasites revealed 115 P. falciparum genes putatively responsible for parasitizing human erythrocytes. These genes are mainly located in the chromosome internal regions and participate in many biological processes, including membrane protein trafficking and thiamine biosynthesis. Meanwhile, 289 P. berghei genes were included in the rodent parasite-enriched clusters. Most are located in subtelomeric regions and encode erythrocyte surface proteins. Comparing cluster values in P. falciparum with those in P. vivax and P. knowlesi revealed 493 candidate genes linked to virulence. Some of them encode proteins present on the erythrocyte surface and participate in cytoadhesion, virulence factor trafficking, or erythrocyte invasion, but many genes with unknown function were also identified. Cerebral malaria is characterized by accumulation of infected erythrocytes at trophozoite stage in brain microvascular. To discover cerebral malaria-related genes, fast Fourier transformation (FFT) was introduced to extract

Within-Host Variations of Human Papillomavirus Reveal APOBEC-Signature Mutagenesis in the Viral Genome.

Science.gov (United States)

Hirose, Yusuke; Onuki, Mamiko; Tenjimbayashi, Yuri; Mori, Seiichiro; Ishii, Yoshiyuki; Takeuchi, Takamasa; Tasaka, Nobutaka; Satoh, Toyomi; Morisada, Tohru; Iwata, Takashi; Miyamoto, Shingo; Matsumoto, Koji; Sekizawa, Akihiko; Kukimoto, Iwao

2018-03-28

Persistent infection with oncogenic human papillomaviruses (HPVs) causes cervical cancer, accompanied with the accumulation of somatic mutations into the host genome. There are concomitant genetic changes in the HPV genome during viral infection; however, their relevance to cervical carcinogenesis is poorly understood. Here we explored within-host genetic diversity of HPV by performing deep sequencing analyses of viral whole-genome sequences in clinical specimens. The whole genomes of HPV types 16, 52 and 58 were amplified by type-specific PCR from total cellular DNA of cervical exfoliated cells collected from patients with cervical intraepithelial neoplasia (CIN) and invasive cervical cancer (ICC), and were deep-sequenced. After constructing a reference vial genome sequence for each specimen, nucleotide positions showing changes with > 0.5% frequencies compared to the reference sequence were determined for individual samples. In total, 1,052 positions of nucleotide variations were detected in HPV genomes from 151 samples (CIN1, n = 56; CIN2/3, n = 68; ICC, n = 27), with varying numbers per sample. Overall, C-to-T and C-to-A substitutions were the dominant changes observed across all histological grades. While C-to-T transitions were predominantly detected in CIN1, their prevalence was decreased in CIN2/3 and fell below that of C-to-A transversions in ICC. Analysis of the tri-nucleotides context encompassing substituted bases revealed that Tp C pN, a preferred target sequence for cellular APOBEC cytosine deaminases, was a primary site for C-to-T substitutions in the HPV genome. These results strongly imply that the APOBEC proteins are drivers of HPV genome mutation, particularly in CIN1 lesions. IMPORTANCE HPVs exhibit surprisingly high levels of genetic diversity, including a large repertoire of minor genomic variants in each viral genotype. Here, by conducting deep sequencing analyses, we show for the first time a comprehensive snapshot of the "within

Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

Science.gov (United States)

Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

2012-01-15

Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

Thoracoscopic CO laser coagulation shrinkage of blebs in treatment of spontaneous pneumothorax

Science.gov (United States)

Sensaki, Koji; Arai, Tsunenori; Kikuchi, Keiichi; Takagi, Keigo; Tanaka, Susumu; Kikuchi, Makoto

1992-06-01

Spontaneous pneumothorax is a common disease in young people. Operative intervention has been done in most of the recurrent cases. Recently thoracoscopic treatment has been tested as a less invasive treatment modarity. We adopted carbon monoxide (CO) laser for thoracoscopic treatment of recurrent spontaneous pneumothorax. CO laser (wavelength; 5.4 micrometers ) could be delivered by chalcogenide glass (As - S) covered with a teflon sheath and ZnSe fiber tip. The sterilized flexible bronchoscope was inserted through the thoracoscopic outer sheath under local anesthesia. Shrinkage of blebs was obtained by non-contact method of CO laser irradiation. Laser power at the tip was 2.5 - 5 W and irradiation duration was 0.5 s each. Excellent shrinkage of bleb and bulla could be obtained by CO laser without perforation complication. Advantages of CO laser as a thoracoscopic treatment were: (1) capability of fiber delivery (flexible thoracoscopy was easy to operate and clear to visualize the blebs which were frequently found at the apical portion of the lung, and (2) shallow extinction length (good shrinkage of blebs, low risk of perforation, and thin layer of carbonization). In conclusion, our new technique of thoracoscopic CO laser irradiation was found to be a safe and effective treatment of spontaneous pneumothorax.

Remote sensing appraisal of Lake Chad shrinkage connotes severe impacts on green economics and socio-economics of the catchment area.

Science.gov (United States)

Onamuti, Olapeju Y; Okogbue, Emmanuel C; Orimoloye, Israel R

2017-11-01

Lake Chad commonly serves as a major hub of fertile economic activities for the border communities and contributes immensely to the national growth of all the countries that form its boundaries. However, incessant and multi-decadal drying via climate change pose greater threats to this transnational water resource, and adverse effects on ecological sustainability and socio-economic status of the catchment area. Therefore, this study assessed the extent of shrinkage of Lake Chad using remote sensing. Landsat imageries of the lake and its surroundings between 1987 and 2005 were retrieved from Global Land Cover Facility website and analysed using Integrated Land and Water Information System version 3.3 (ILWIS 3.3). Supervised classification of area around the lake was performed into various land use/land cover classes, and the shrunk part of its environs was assessed based on the land cover changes. The shrinkage trend within the study period was also analysed. The lake water size reduced from 1339.018 to 130.686 km 2 (4.08-3.39%) in 1987-2005. The supervised classification of the Landsat imageries revealed an increase in portion of the lake covered by bare ground and sandy soil within the reference years (13 490.8-17 503.10 km 2 ) with 4.98% total range of increase. The lake portion intersected with vegetated ground and soil also reduced within the period (11 046.44-10 078.82 km 2 ) with 5.40% (967.62 km 2 ) total decrease. The shrunk part of the lake covered singly with vegetation increased by 2.74% from 1987 to 2005. The shrunk part of the lake reduced to sand and turbid water showed 5.62% total decrease from 1987 to 2005 and a total decrease of 1805.942 km 2 in area. The study disclosed an appalling rate of shrinkage and damaging influences on the hydrologic potential, eco-sustainability and socio-economics of the drainage area as revealed using ILWIS 3.3.

Effect of LED and Argon Laser on Degree of Conversion and Temperature Rise of Hybrid and Low Shrinkage Composite Resins.

Science.gov (United States)

Pahlevan, Ayob; Tabatabaei, Masumeh Hasani; Arami, Sakineh; Valizadeh, Sara

2016-01-01

Different light curing units are used for polymerization of composite resins. The aim of this study was to evaluate the degree of conversion (DC) and temperature rise in hybrid and low shrinkage composite resins cured by LED and Argon Laser curing lights. DC was measured using FTIR spectroscopy. For measuring temperature rise, composite resin samples were placed in Teflon molds and cured from the top. The thermocouple under samples recorded the temperature rise. After initial radiation and specimens reaching the ambient temperature, reirradiation was done and temperature was recorded again. Both temperature rise and DC data submitted to one-way ANOVA and Tukey-HSD tests (5% significance). The obtained results revealed that DC was not significantly different between the understudy composite resins or curing units. Low shrinkage composite resin showed a significantly higher temperature rise than hybrid composite resin. Argon laser caused the lowest temperature rise among the curing units. Energy density of light curing units was correlated with the DC. Type of composite resin and light curing unit had a significant effect on temperature rise due to polymerization and curing unit, respectively.

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations.

Science.gov (United States)

Zheng, Jinshui; Zhao, Xin; Lin, Xiaoxi B; Gänzle, Michael

2015-12-11

Lactobacillus reuteri is a dominant member of intestinal microbiota of vertebrates, and occurs in food fermentations. The stable presence of L. reuteri in sourdough provides the opportunity to study the adaptation of vertebrate symbionts to an extra-intestinal habitat. This study evaluated this adaptation by comparative genomics of 16 strains of L. reuteri. A core genome phylogenetic tree grouped L. reuteri into 5 clusters corresponding to the host-adapted lineages. The topology of a gene content tree, which includes accessory genes, differed from the core genome phylogenetic tree, suggesting that the differentiation of L. reuteri is shaped by gene loss or acquisition. About 10% of the core genome (124 core genes) were under positive selection. In lineage III sourdough isolates, 177 genes were under positive selection, mainly related to energy conversion and carbohydrate metabolism. The analysis of the competitiveness of L. reuteri in sourdough revealed that the competitivess of sourdough isolates was equal or higher when compared to rodent isolates. This study provides new insights into the adaptation of L. reuteri to food and intestinal habitats, suggesting that these two habitats exert different selective pressure related to growth rate and energy (carbohydrate) metabolism.

Polyploid genome of Camelina sativa revealed by isolation of fatty acid synthesis genes

Directory of Open Access Journals (Sweden)

Shewmaker Christine K

2010-10-01

Full Text Available Abstract Background Camelina sativa, an oilseed crop in the Brassicaceae family, has inspired renewed interest due to its potential for biofuels applications. Little is understood of the nature of the C. sativa genome, however. A study was undertaken to characterize two genes in the fatty acid biosynthesis pathway, fatty acid desaturase (FAD 2 and fatty acid elongase (FAE 1, which revealed unexpected complexity in the C. sativa genome. Results In C. sativa, Southern analysis indicates the presence of three copies of both FAD2 and FAE1 as well as LFY, a known single copy gene in other species. All three copies of both CsFAD2 and CsFAE1 are expressed in developing seeds, and sequence alignments show that previously described conserved sites are present, suggesting that all three copies of both genes could be functional. The regions downstream of CsFAD2 and upstream of CsFAE1 demonstrate co-linearity with the Arabidopsis genome. In addition, three expressed haplotypes were observed for six predicted single-copy genes in 454 sequencing analysis and results from flow cytometry indicate that the DNA content of C. sativa is approximately three-fold that of diploid Camelina relatives. Phylogenetic analyses further support a history of duplication and indicate that C. sativa and C. microcarpa might share a parental genome. Conclusions There is compelling evidence for triplication of the C. sativa genome, including a larger chromosome number and three-fold larger measured genome size than other Camelina relatives, three isolated copies of FAD2, FAE1, and the KCS17-FAE1 intergenic region, and three expressed haplotypes observed for six predicted single-copy genes. Based on these results, we propose that C. sativa be considered an allohexaploid. The characterization of fatty acid synthesis pathway genes will allow for the future manipulation of oil composition of this emerging biofuel crop; however, targeted manipulations of oil composition and general

Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes

Directory of Open Access Journals (Sweden)

Deng Xuemei

2007-11-01

Full Text Available Abstract Background Bird genomes have very different compositional structure compared with other warm-blooded animals. The variation in the base skew rules in the vertebrate genomes remains puzzling, but it must relate somehow to large-scale genome evolution. Current research is inclined to relate base skew with mutations and their fixation. Here we wish to explore base skew correlations in bird genomes, to develop methods for displaying and quantifying such correlations at different scales, and to discuss possible explanations for the peculiarities of the bird genomes in skew correlation. Results We have developed a method called Base Skew Double Triangle (BSDT for exhibiting the genome-scale change of AT/CG skew as a two-dimensional square picture, showing base skews at many scales simultaneously in a single image. By this method we found that most chicken chromosomes have high AT/CG skew correlation (symmetry in 2D picture, except for some microchromosomes. No other organisms studied (18 species show such high skew correlations. This visualized high correlation was validated by three kinds of quantitative calculations with overlapping and non-overlapping windows, all indicating that chicken and birds in general have a special genome structure. Similar features were also found in some of the mammal genomes, but clearly much weaker than in chickens. We presume that the skew correlation feature evolved near the time that birds separated from other vertebrate lineages. When we eliminated the repeat sequences from the genomes, the AT and CG skews correlation increased for some mammal genomes, but were still clearly lower than in chickens. Conclusion Our results suggest that BSDT is an expressive visualization method for AT and CG skew and enabled the discovery of the very high skew correlation in bird genomes; this peculiarity is worth further study. Computational analysis indicated that this correlation might be a compositional characteristic

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Science.gov (United States)

Jun, Se-Ran; Wassenaar, Trudy M; Nookaew, Intawat; Hauser, Loren; Wanchai, Visanu; Land, Miriam; Timm, Collin M; Lu, Tse-Yuan S; Schadt, Christopher W; Doktycz, Mitchel J; Pelletier, Dale A; Ussery, David W

2016-01-01

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. Copyright © 2015 Jun et al.

Creep and shrinkage of Mo(Ni)

International Nuclear Information System (INIS)

Kaysser, W.A.; Hofmann-Amtenbrink, M.; Petzow, G.

1984-01-01

To avoid some of the errors inherent in a quantitative interpretation of shrinkage of powder compacts as Mo-Ni, other experiments were looked for, where the influence of Ni on the material transport properties of Mo could be measured semi-quantitatively during heating up to temperature and subsequent isothermal annealing. The bending of thin Mo foils under small loads was found to be an experimental arrangement, where variations in stress, in Ni-concentration and in intrinsic material properties could be realized. The results of these creep experiments will be compared in a qualitative sense with sintering experiments in Mo-Ni done under similar conditions as the creep experiments

Supplementary Material for: Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

KAUST Repository

Black, PA; Vos, M. de; Louw, GE; Merwe, RG van der; Dippenaar, A.; Streicher, EM; Abdallah, AM; Sampson, SL; Victor, TC; Dolby, T.; Simpson, JA; Helden, PD van; Warren, RM; Pain, Arnab

2015-01-01

Abstract Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug

Comparative genomic analysis of Brucella abortus vaccine strain 104M reveals a set of candidate genes associated with its virulence attenuation.

Science.gov (United States)

Yu, Dong; Hui, Yiming; Zai, Xiaodong; Xu, Junjie; Liang, Long; Wang, Bingxiang; Yue, Junjie; Li, Shanhu

2015-01-01

The Brucella abortus strain 104M, a spontaneously attenuated strain, has been used as a vaccine strain in humans against brucellosis for 6 decades in China. Despite many studies, the molecular mechanisms that cause the attenuation are still unclear. Here, we determined the whole-genome sequence of 104M and conducted a comprehensive comparative analysis against the whole genome sequences of the virulent strain, A13334, and other reference strains. This analysis revealed a highly similar genome structure between 104M and A13334. The further comparative genomic analysis between 104M and A13334 revealed a set of genes missing in 104M. Some of these genes were identified to be directly or indirectly associated with virulence. Similarly, a set of mutations in the virulence-related genes was also identified, which may be related to virulence alteration. This study provides a set of candidate genes associated with virulence attenuation in B.abortus vaccine strain 104M.

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses.

Science.gov (United States)

Li, Ci-Xiu; Shi, Mang; Tian, Jun-Hua; Lin, Xian-Dan; Kang, Yan-Jun; Chen, Liang-Jun; Qin, Xin-Cheng; Xu, Jianguo; Holmes, Edward C; Zhang, Yong-Zhen

2015-01-29

Although arthropods are important viral vectors, the biodiversity of arthropod viruses, as well as the role that arthropods have played in viral origins and evolution, is unclear. Through RNA sequencing of 70 arthropod species we discovered 112 novel viruses that appear to be ancestral to much of the documented genetic diversity of negative-sense RNA viruses, a number of which are also present as endogenous genomic copies. With this greatly enriched diversity we revealed that arthropods contain viruses that fall basal to major virus groups, including the vertebrate-specific arenaviruses, filoviruses, hantaviruses, influenza viruses, lyssaviruses, and paramyxoviruses. We similarly documented a remarkable diversity of genome structures in arthropod viruses, including a putative circular form, that sheds new light on the evolution of genome organization. Hence, arthropods are a major reservoir of viral genetic diversity and have likely been central to viral evolution.

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles.

Science.gov (United States)

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-Yu; Zhang, Xiao-Mei; Song, Da-Feng; Zhang, Chen

2016-08-01

In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate.

Comparative genomic analysis of Lactobacillus plantarum ZJ316 reveals its genetic adaptation and potential probiotic profiles* #

Science.gov (United States)

Li, Ping; Li, Xuan; Gu, Qing; Lou, Xiu-yu; Zhang, Xiao-mei; Song, Da-feng; Zhang, Chen

2016-01-01

Objective: In previous studies, Lactobacillus plantarum ZJ316 showed probiotic properties, such as antimicrobial activity against various pathogens and the capacity to significantly improve pig growth and pork quality. The purpose of this study was to reveal the genes potentially related to its genetic adaptation and probiotic profiles based on comparative genomic analysis. Methods: The genome sequence of L. plantarum ZJ316 was compared with those of eight L. plantarum strains deposited in GenBank. BLASTN, Mauve, and MUMmer programs were used for genome alignment and comparison. CRISPRFinder was applied for searching the clustered regularly interspaced short palindromic repeats (CRISPRs). Results: We identified genes that encode proteins related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, bile salt resistance, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Conclusions: Comparative characterization of the L. plantarum ZJ316 genome provided the genetic basis for further elucidating the functional mechanisms of its probiotic properties. ZJ316 could be considered a potential probiotic candidate. PMID:27487802

Reducing Shrinkage in Canned and Frozen Mushrooms

OpenAIRE

Gormley, T. R. (Thomas Ronan); Walshe, P.E.

1982-01-01

The process involving a preliminary soaking of the mushrooms in water for 20 min followed by a chill storage period followed by a further water soak for 2 hr, and known as the 3S process, gave a considerable reduction in total shrinkage in both brown and white strain canned mushrooms compared with the control samples. Water uptake by the mushrooms in the 3S process was greatest when the soaking water temperature was between 20 and 30°C and had a pH of 8. Citric acid in the blanch water enhanc...

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

Science.gov (United States)

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

Energy Technology Data Exchange (ETDEWEB)

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

2014-05-12

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

Energy Technology Data Exchange (ETDEWEB)

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

2014-06-18

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

Infectious diseases of marine molluscs and host responses as revealed by genomic tools

Science.gov (United States)

Ford, Susan E.

2016-01-01

More and more infectious diseases affect marine molluscs. Some diseases have impacted commercial species including MSX and Dermo of the eastern oyster, QPX of hard clams, withering syndrome of abalone and ostreid herpesvirus 1 (OsHV-1) infections of many molluscs. Although the exact transmission mechanisms are not well understood, human activities and associated environmental changes often correlate with increased disease prevalence. For instance, hatcheries and large-scale aquaculture create high host densities, which, along with increasing ocean temperature, might have contributed to OsHV-1 epizootics in scallops and oysters. A key to understanding linkages between the environment and disease is to understand how the environment affects the host immune system. Although we might be tempted to downplay the role of immunity in invertebrates, recent advances in genomics have provided insights into host and parasite genomes and revealed surprisingly sophisticated innate immune systems in molluscs. All major innate immune pathways are found in molluscs with many immune receptors, regulators and effectors expanded. The expanded gene families provide great diversity and complexity in innate immune response, which may be key to mollusc's defence against diverse pathogens in the absence of adaptive immunity. Further advances in host and parasite genomics should improve our understanding of genetic variation in parasite virulence and host disease resistance. PMID:26880838

Fast generation of computer-generated holograms using wavelet shrinkage.

Science.gov (United States)

Shimobaba, Tomoyoshi; Ito, Tomoyoshi

2017-01-09

Computer-generated holograms (CGHs) are generated by superimposing complex amplitudes emitted from a number of object points. However, this superposition process remains very time-consuming even when using the latest computers. We propose a fast calculation algorithm for CGHs that uses a wavelet shrinkage method, eliminating small wavelet coefficient values to express approximated complex amplitudes using only a few representative wavelet coefficients.

Modelling of shrinkage cavity defects during the wheel and belt casting process

International Nuclear Information System (INIS)

Dablement, S; Mortensen, D; Fjaer, H; Lee, M; Grandfield, J; Savage, G; Nguyen, V

2012-01-01

Properzi continuous casting is a wheel and belt casting process used for producing aluminium wire rod which is essential to the making of electrical cables and over head lines. One of the main concerns of Properzi process users is to ensure good quality of the final product and to avoid cast defects especially the presence of shrinkage cavity. Numerical models developed with the Alsim software, which allows an automatic calculation of gap dependent heat transfer coefficients at the metal-mould interface due to thermal deformation, are used in order to get a better understanding on the shrinkage cavity formation. Models show the effect of process parameters on the cavity defect development and provide initial guidance for users in order to avoid this kind of casting defect.

Use of rice husk ash for mitigating the autogenous shrinkage of cement pastes at low water cement ratio

NARCIS (Netherlands)

Huang, H.; Ye, G.; Fehling, Ekkehard; Middendorf, Bernhard; Thiemicke, Jenny

2016-01-01

It is well recognized that the high risk of early age micro-crack of HPC/UHPC is attributed to the large magnitude of early age autogenous shrinkage caused by self-desiccation in binder hydration. Over the years, several methods have been proposed to mitigate autogenous shrinkage based on internal

Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

Science.gov (United States)

2012-01-01

Background Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event. Results We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp. Conclusions The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future. PMID:22424280

Comparative Analysis of 35 Basidiomycete Genomes Reveals Diversity and Uniqueness of the Phylum

Energy Technology Data Exchange (ETDEWEB)

Riley, Robert; Salamov, Asaf; Otillar, Robert; Fagnan, Kirsten; Boussau, Bastien; Brown, Daren; Henrissat, Bernard; Levasseur, Anthony; Held, Benjamin; Nagy, Laszlo; Floudas, Dimitris; Morin, Emmanuelle; Manning, Gerard; Baker, Scott; Martin, Francis; Blanchette, Robert; Hibbett, David; Grigoriev, Igor V.

2013-03-11

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprobes including wood decaying fungi. To better understand the diversity of this phylum we compared the genomes of 35 basidiomycete fungi including 6 newly sequenced genomes. The genomes of basidiomycetes span extremes of genome size, gene number, and repeat content. A phylogenetic tree of Basidiomycota was generated using the Phyldog software, which uses all available protein sequence data to simultaneously infer gene and species trees. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) comprising proteins found in only one organism. Phylogenetic patterns of plant biomass-degrading genes suggest a continuum rather than a sharp dichotomy between the white rot and brown rot modes of wood decay among the members of Agaricomycotina subphylum. There is a correlation of the profile of certain gene families to nutritional mode in Agaricomycotina. Based on phylogenetically-informed PCA analysis of such profiles, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has liginolytic class II fungal peroxidases. Furthermore, we find that both fungi exhibit wood decay with white rot-like characteristics in growth assays. Analysis of the rate of discovery of proteins with no or few homologs suggests the high value of continued sequencing of basidiomycete fungi.

Evaluation of linear polymerization shrinkage, flexural strength and modulus of elasticity of dental composites

Directory of Open Access Journals (Sweden)

Gabriela Queiroz de Melo Monteiro

2010-03-01

Full Text Available Linear polymerization shrinkage (LPS, flexural strength (FS and modulus of elasticity (ME of 7 dental composites (Filtek Z350™, Filtek Z250™/3M ESPE; Grandio™, Polofil Supra™/VOCO; TPH Spectrum™, TPH3™, Esthet-X™/Denstply were measured. For the measurement of LPS, composites were applied to a cylindrical metallic mold and polymerized (n = 8. The gap formed at the resin/mold interface was observed using scanning electron microscopy (1500×. For FS and ME, specimens were prepared according to the ISO 4049 specifications (n = 10. Statistical analysis of the data was performed with one-way ANOVA and the Tukey test. TPH Spectrum presented significantly higher LPS values (29.45 µm. Grandio had significantly higher mean values for FS (141.07 MPa and ME (13.91 GPa. The relationship between modulus of elasticity and polymerization shrinkage is the main challenge for maintenance of the adhesive interface, thus composites presenting high shrinkage values, associated with a high modulus of elasticity tend to disrupt the adhesive interface under polymerization.

Genome sequencing and analysis reveals possible determinants of Staphylococcus aureus nasal carriage

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Cole Alexander M

2008-09-01

Full Text Available Abstract Background Nasal carriage of Staphylococcus aureus is a major risk factor in clinical and community settings due to the range of etiologies caused by the organism. We have identified unique immunological and ultrastructural properties associated with nasal carriage isolates denoting a role for bacterial factors in nasal carriage. However, despite extensive molecular level characterizations by several groups suggesting factors necessary for colonization on nasal epithelium, genetic determinants of nasal carriage are unknown. Herein, we have set a genomic foundation for unraveling the bacterial determinants of nasal carriage in S. aureus. Results MLST analysis revealed no lineage specific differences between carrier and non-carrier strains suggesting a role for mobile genetic elements. We completely sequenced a model carrier isolate (D30 and a model non-carrier strain (930918-3 to identify differential gene content. Comparison revealed the presence of 84 genes unique to the carrier strain and strongly suggests a role for Type VII secretion systems in nasal carriage. These genes, along with a putative pathogenicity island (SaPIBov present uniquely in the carrier strains are likely important in affecting carriage. Further, PCR-based genotyping of other clinical isolates for a specific subset of these 84 genes raise the possibility of nasal carriage being caused by multiple gene sets. Conclusion Our data suggest that carriage is likely a heterogeneic phenotypic trait and implies a role for nucleotide level polymorphism in carriage. Complete genome level analyses of multiple carriage strains of S. aureus will be important in clarifying molecular determinants of S. aureus nasal carriage.

In-Situ Observation of Sintering Shrinkage of UO2 Compacts Derived from Different Powder Routes

International Nuclear Information System (INIS)

Rhee, Young Woo; Oh, Jang Soo; Kim, Dong Joo; Kim, Keon Sik; Kim, Jong Hun; Yang, Jae Ho; Koo, Yang Hyun

2015-01-01

In-situ observations on the shrinkage of green pellets with precisely controlled dimensions were carefully conducted by using TOM during H2 atmosphere sintering. The shrinkage retardation in IDR-UO 2 might be attributed to the larger primary particle size of IDRUO 2 than those of ADU- and AUC- UO 2 powders. It would be important to understand the different sintering characteristics of UO 2 powders according to the powder routes, when it comes to designing a new sintering process or choosing a sintering additive for new fuel pellet like PCI (Pellet Cladding Interaction) remedy pellet. In this paper, we have investigated the initial and intermediate sintering shrinkage of UO 2 from different powder routes by in-situ observation of green samples during H2 atmosphere sintering. Effect of powder characteristics of three different UO 2 powders on the initial and intermediate sintering were closely reviewed including crystal structure, powder size, specific surface area, primary crystal size, and O/U ratio

Statistical mechanics provides novel insights into microtubule stability and mechanism of shrinkage.

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Ishutesh Jain

2015-02-01

Full Text Available Microtubules are nano-machines that grow and shrink stochastically, making use of the coupling between chemical kinetics and mechanics of its constituent protofilaments (PFs. We investigate the stability and shrinkage of microtubules taking into account inter-protofilament interactions and bending interactions of intrinsically curved PFs. Computing the free energy as a function of PF tip position, we show that the competition between curvature energy, inter-PF interaction energy and entropy leads to a rich landscape with a series of minima that repeat over a length-scale determined by the intrinsic curvature. Computing Langevin dynamics of the tip through the landscape and accounting for depolymerization, we calculate the average unzippering and shrinkage velocities of GDP protofilaments and compare them with the experimentally known results. Our analysis predicts that the strength of the inter-PF interaction (E(s(m has to be comparable to the strength of the curvature energy (E(b(m such that E(s(m - E(b(m ≈ 1kBT, and questions the prevalent notion that unzippering results from the domination of bending energy of curved GDP PFs. Our work demonstrates how the shape of the free energy landscape is crucial in explaining the mechanism of MT shrinkage where the unzippered PFs will fluctuate in a set of partially peeled off states and subunit dissociation will reduce the length.

clınıcal EVALUATION OF FREE GINGIVAL GRAFT SHRINKAGE IN HORIZONTAL AND VERTICAL DIMENSIONS

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Emine ÇİFCİBAŞI

2015-10-01

Full Text Available Purpose: To assess the shrinkage of Free Gingival Graft (FGG in horizontal and vertical dimensions and calculate the changes in the surface area of the transplanted tissue in a 3 months period. Materials and Methods: A total of 30 FGG were placed aiming to increase attached gingiva around recession sites. Vertical recessions, horizontal recessions, surface area, plaque index, gingival index, periodontal probing depth and clinical attachment level were assesed at baseline, 1 and 3 months postoperatively. Results: Graft shrinkage between baseline and 1 month was more evident than 1 to 3 months in either dimensions. Both horizontal and vertical dimensions were significantly decreased (p0.05. . Conclusion: The shrinkage of vertical and horizontal dimensions of the grafts were almost equal unlike the literature. In addition, the different dimensional changes observed in individual level deserve further research.

Shifts in the evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication.

Science.gov (United States)

Zhao, Meixia; Du, Jianchang; Lin, Feng; Tong, Chaobo; Yu, Jingyin; Huang, Shunmou; Wang, Xiaowu; Liu, Shengyi; Ma, Jianxin

2013-10-01

Recent sequencing of the Brassica rapa and Brassica oleracea genomes revealed extremely contrasting genomic features such as the abundance and distribution of transposable elements between the two genomes. However, whether and how these structural differentiations may have influenced the evolutionary rates of the two genomes since their split from a common ancestor are unknown. Here, we investigated and compared the rates of nucleotide substitution between two long terminal repeats (LTRs) of individual orthologous LTR-retrotransposons, the rates of synonymous and non-synonymous substitution among triplicated genes retained in both genomes from a shared whole genome triplication event, and the rates of genetic recombination estimated/deduced by the comparison of physical and genetic distances along chromosomes and ratios of solo LTRs to intact elements. Overall, LTR sequences and genic sequences showed more rapid nucleotide substitution in B. rapa than in B. oleracea. Synonymous substitution of triplicated genes retained from a shared whole genome triplication was detected at higher rates in B. rapa than in B. oleracea. Interestingly, non-synonymous substitution was observed at lower rates in the former than in the latter, indicating shifted densities of purifying selection between the two genomes. In addition to evolutionary asymmetry, orthologous genes differentially regulated and/or disrupted by transposable elements between the two genomes were also characterized. Our analyses suggest that local genomic and epigenomic features, such as recombination rates and chromatin dynamics reshaped by independent proliferation of transposable elements and elimination between the two genomes, are perhaps partially the causes and partially the outcomes of the observed inter-specific asymmetric evolution. © 2013 Purdue University The Plant Journal © 2013 John Wiley & Sons Ltd.

Integrative Genomics Reveals Mechanisms of Copy Number Alterations Responsible for Transcriptional Deregulation in Colorectal Cancer

Science.gov (United States)

Camps, Jordi; Nguyen, Quang Tri; Padilla-Nash, Hesed M.; Knutsen, Turid; McNeil, Nicole E.; Wangsa, Danny; Hummon, Amanda B.; Grade, Marian; Ried, Thomas; Difilippantonio, Michael J.

2016-01-01

To evaluate the mechanisms and consequences of chromosomal aberrations in colorectal cancer (CRC), we used a combination of spectral karyotyping, array comparative genomic hybridization (aCGH), and array-based global gene expression profiling on 31 primary carcinomas and 15 established cell lines. Importantly, aCGH showed that the genomic profiles of primary tumors are recapitulated in the cell lines. We revealed a preponderance of chromosome breakpoints at sites of copy number variants (CNVs) in the CRC cell lines, a novel mechanism of DNA breakage in cancer. The integration of gene expression and aCGH led to the identification of 157 genes localized within high-level copy number changes whose transcriptional deregulation was significantly affected across all of the samples, thereby suggesting that these genes play a functional role in CRC. Genomic amplification at 8q24 was the most recurrent event and led to the overexpression of MYC and FAM84B. Copy number dependent gene expression resulted in deregulation of known cancer genes such as APC, FGFR2, and ERBB2. The identification of only 36 genes whose localization near a breakpoint could account for their observed deregulated expression demonstrates that the major mechanism for transcriptional deregulation in CRC is genomic copy number changes resulting from chromosomal aberrations. PMID:19691111

A semi-automated 2D/3D marker-based registration algorithm modelling prostate shrinkage during radiotherapy for prostate cancer

International Nuclear Information System (INIS)

Budiharto, Tom; Slagmolen, Pieter; Hermans, Jeroen; Maes, Frederik; Verstraete, Jan; Heuvel, Frank Van den; Depuydt, Tom; Oyen, Raymond; Haustermans, Karin

2009-01-01

Background and purpose: Currently, most available patient alignment tools based on implanted markers use manual marker matching and rigid registration transformations to measure the needed translational shifts. To quantify the particular effect of prostate gland shrinkage, implanted gold markers were tracked during a course of radiotherapy including an isotropic scaling factor to model prostate shrinkage. Materials and methods: Eight patients with prostate cancer had gold markers implanted transrectally and seven were treated with (neo) adjuvant androgen deprivation therapy. After patient alignment to skin tattoos, orthogonal electronic portal images (EPIs) were taken. A semi-automated 2D/3D marker-based registration was performed to calculate the necessary couch shifts. The registration consists of a rigid transformation combined with an isotropic scaling to model prostate shrinkage. Results: The inclusion of an isotropic shrinkage model in the registration algorithm cancelled the corresponding increase in registration error. The mean scaling factor was 0.89 ± 0.09. For all but two patients, a decrease of the isotropic scaling factor during treatment was observed. However, there was almost no difference in the translation offset between the manual matching of the EPIs to the digitally reconstructed radiographs and the semi-automated 2D/3D registration. A decrease in the intermarker distance was found correlating with prostate shrinkage rather than with random marker migration. Conclusions: Inclusion of shrinkage in the registration process reduces registration errors during a course of radiotherapy. Nevertheless, this did not lead to a clinically significant change in the proposed table translations when compared to translations obtained with manual marker matching without a scaling correction

Assembly of the Lactuca sativa, L. cv. Tizian draft genome sequence reveals differences within major resistance complex 1 as compared to the cv. Salinas reference genome.

Science.gov (United States)

Verwaaijen, Bart; Wibberg, Daniel; Nelkner, Johanna; Gordin, Miriam; Rupp, Oliver; Winkler, Anika; Bremges, Andreas; Blom, Jochen; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

2018-02-10

Lettuce (Lactuca sativa, L.) is an important annual plant of the family Asteraceae (Compositae). The commercial lettuce cultivar Tizian has been used in various scientific studies investigating the interaction of the plant with phytopathogens or biological control agents. Here, we present the de novo draft genome sequencing and gene prediction for this specific cultivar derived from transcriptome sequence data. The assembled scaffolds amount to a size of 2.22 Gb. Based on RNAseq data, 31,112 transcript isoforms were identified. Functional predictions for these transcripts were determined within the GenDBE annotation platform. Comparison with the cv. Salinas reference genome revealed a high degree of sequence similarity on genome and transcriptome levels, with an average amino acid identity of 99%. Furthermore, it was observed that two large regions are either missing or are highly divergent within the cv. Tizian genome compared to cv. Salinas. One of these regions covers the major resistance complex 1 region of cv. Salinas. The cv. Tizian draft genome sequence provides a valuable resource for future functional and transcriptome analyses focused on this lettuce cultivar. Copyright © 2017 Elsevier B.V. All rights reserved.

Denoising of Mechanical Vibration Signals Using Quantum-Inspired Adaptive Wavelet Shrinkage

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Yan-long Chen

2014-01-01

Full Text Available The potential application of a quantum-inspired adaptive wavelet shrinkage (QAWS technique to mechanical vibration signals with a focus on noise reduction is studied in this paper. This quantum-inspired shrinkage algorithm combines three elements: an adaptive non-Gaussian statistical model of dual-tree complex wavelet transform (DTCWT coefficients proposed to improve practicability of prior information, the quantum superposition introduced to describe the interscale dependencies of DTCWT coefficients, and the quantum-inspired probability of noise defined to shrink wavelet coefficients in a Bayesian framework. By combining all these elements, this signal processing scheme incorporating the DTCWT with quantum theory can both reduce noise and preserve signal details. A practical vibration signal measured from a power-shift steering transmission is utilized to evaluate the denoising ability of QAWS. Application results demonstrate the effectiveness of the proposed method. Moreover, it achieves better performance than hard and soft thresholding.

Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

KAUST Repository

Liu, Huanle; Stephens, Timothy G.; Gonzá lez-Pech, Raú l; Beltran, Victor H.; Lapeyre, Bruno; Bongaerts, Pim; Cooke, Ira; Bourne, David G.; Forê t, Sylvain; Miller, David John; van Oppen, Madeleine J. H.; Voolstra, Christian R.; Ragan, Mark A.; Chan, Cheong Xin

2017-01-01

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world's coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

Symbiodinium genomes reveal adaptive evolution of functions related to symbiosis

KAUST Repository

Liu, Huanle

2017-10-06

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world\\'s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp), previously sequenced as strain CCMP2468, to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identified extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding Symbiodinium biology and the coral-algal symbiosis.

Draft genome of an Aerophobetes bacterium reveals a facultative lifestyle in deep-sea anaerobic sediments

KAUST Repository

Wang, Yong

2016-07-01

Aerophobetes (or CD12) is a recently defined bacterial phylum, of which the metabolic processes and ecological importance remain unclear. In the present study, we obtained the draft genome of an Aerophobetes bacterium TCS1 from saline sediment near the Thuwal cold seep in the Red Sea using a genome binning method. Analysis of 16S rRNA genes of TCS1 and close relatives revealed wide distribution of Aerophobetes in deep-sea sediments. Phylogenetic relationships showed affinity between Aerophobetes TCS1 and some thermophilic bacterial phyla. The genome of TCS1 (at least 1.27 Mbp) contains a full set of genes encoding core metabolic pathways, including glycolysis and pyruvate fermentation to produce acetyl-CoA and acetate. The identification of cross-membrane sugar transporter genes further indicates its potential ability to consume carbohydrates preserved in the sediment under the microbial mat. Aerophobetes bacterium TCS1 therefore probably carried out saccharolytic and fermentative metabolism. The genes responsible for autotrophic synthesis of acetyl-CoA via the Wood–Ljungdahl pathway were also found in the genome. Phylogenetic study of the essential genes for the Wood–Ljungdahl pathway implied relative independence of Aerophobetes bacterium from the known acetogens and methanogens. Compared with genomes of acetogenic bacteria, Aerophobetes bacterium TCS1 genome lacks the genes involved in nitrogen metabolism, sulfur metabolism, signal transduction and cell motility. The metabolic activities of TCS1 might depend on geochemical conditions such as supplies of CO2, hydrogen and sugars, and therefore the TCS1 might be a facultative bacterium in anaerobic saline sediments near cold seeps. © 2016, Science China Press and Springer-Verlag Berlin Heidelberg.

A moment projection method for population balance dynamics with a shrinkage term

Energy Technology Data Exchange (ETDEWEB)

Wu, Shaohua [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Yapp, Edward K.Y.; Akroyd, Jethro; Mosbach, Sebastian [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); Xu, Rong [School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore); Yang, Wenming [Department of Mechanical Engineering, National University of Singapore, Engineering Block EA, Engineering Drive 1, 117576 (Singapore); Kraft, Markus, E-mail: mk306@cam.ac.uk [Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA (United Kingdom); School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 (Singapore)

2017-02-01

A new method of moments for solving the population balance equation is developed and presented. The moment projection method (MPM) is numerically simple and easy to implement and attempts to address the challenge of particle shrinkage due to processes such as oxidation, evaporation or dissolution. It directly solves the moment transport equation for the moments and tracks the number of the smallest particles using the algorithm by Blumstein and Wheeler (1973) . The performance of the new method is measured against the method of moments (MOM) and the hybrid method of moments (HMOM). The results suggest that MPM performs much better than MOM and HMOM where shrinkage is dominant. The new method predicts mean quantities which are almost as accurate as a high-precision stochastic method calculated using the established direct simulation algorithm (DSA).

Autogenous shrinkage in high-performance cement paste: An evaluation of basic mechanisms

DEFF Research Database (Denmark)

Lura, Pietro; Jensen, Ole Mejlhede; van Breugel, Klaas

2003-01-01

In this paper, various mechanisms Suggested to cause autogenous shrinkage are presented. The mechanisms are evaluated from the point of view of their soundness and applicability to quantitative modeling of autogenous shrinkage. The capillary tension approach is advantageous, because it has a sound...... mechanical and thermodynamical basis. Furthermore, this mechanism is easily applicable in a numerical model when dealing with a continuously changing microstructure. In order to test the numerical model, autogenous deformation and internal relative humidity (RH) of a Portland cement paste were measured...... on the capillary tension approach. Because a part of the RH drop in the cement paste is due to dissolved salts in the pore solution, a method is suggested to separate this effect from self-desiccation and to calculate the actual stress in the pore fluid associated with menisci formation....

Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium.

Science.gov (United States)

Iskandar, Christelle F; Borges, Frédéric; Taminiau, Bernard; Daube, Georges; Zagorec, Monique; Remenant, Benoît; Leisner, Jørgen J; Hansen, Martin A; Sørensen, Søren J; Mangavel, Cécile; Cailliez-Grimal, Catherine; Revol-Junelles, Anne-Marie

2017-01-01

Lactic acid bacteria (LAB) differ in their ability to colonize food and animal-associated habitats: while some species are specialized and colonize a limited number of habitats, other are generalist and are able to colonize multiple animal-linked habitats. In the current study, Carnobacterium was used as a model genus to elucidate the genetic basis of these colonization differences. Analyses of 16S rRNA gene meta-barcoding data showed that C. maltaromaticum followed by C. divergens are the most prevalent species in foods derived from animals (meat, fish, dairy products), and in the gut. According to phylogenetic analyses, these two animal-adapted species belong to one of two deeply branched lineages. The second lineage contains species isolated from habitats where contact with animal is rare. Genome analyses revealed that members of the animal-adapted lineage harbor a larger secretome than members of the other lineage. The predicted cell-surface proteome is highly diversified in C. maltaromaticum and C. divergens with genes involved in adaptation to the animal milieu such as those encoding biopolymer hydrolytic enzymes, a heme uptake system, and biopolymer-binding adhesins. These species also exhibit genes for gut adaptation and respiration. In contrast, Carnobacterium species belonging to the second lineage encode a poorly diversified cell-surface proteome, lack genes for gut adaptation and are unable to respire. These results shed light on the important genomics traits required for adaptation to animal-linked habitats in generalist Carnobacterium .

Virus Genomes Reveal the Factors that Spread and Sustained the West African Ebola Epidemic

Science.gov (United States)

2016-08-09

Ladner, J. T. et al. Evolution and Spread of Ebola Virus in Liberia , 2014--2015. Cell Host Microbe 18, 659–669 (2015). 15. Lemey, P. et al. Unifying...Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic. Gytis Dudas1,2, Luiz Max Carvalho1, Trevor Bedford2...Charlesville, Liberia ., 19University of Sierra Leone, Freetown, Sierra Leone , 20Center for Systems Biology, Department of Organismic and Evolutionary

Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis

OpenAIRE

Zheng, Wenning; Tan, Mui Fern; Old, Lesley A.; Paterson, Ian C.; Jakubovics, Nicholas S.; Choo, Siew Woh

2017-01-01

Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virule...

A modelling study of drying shrinkage damage in concrete repair systems

NARCIS (Netherlands)

Lukovic, M.; Savija, B.; Schlangen, E.; Ye, G.; van Breugel, K.

2014-01-01

Differential shrinkage between repair material and concrete substrate is considered to be the main cause of premature failure of repair systems (Martinola, Sadouki et al. 2001, Beushausen and Alexander 2007). Magnitude of induced stresses depends on many factors, for example the amount of restraint,

Porous stainless steel hollow fibers with shrinkage-controlled small radial dimensions

NARCIS (Netherlands)

Luiten-Olieman, Maria W.J.; Raaijmakers, Michiel; Raaijmakers, Michiel J.T.; Winnubst, Aloysius J.A.; Wessling, Matthias; Nijmeijer, Arian; Benes, Nieck Edwin

2011-01-01

A method is presented for the preparation of thin (∼250 μm) porous stainless steel hollow fiber membranes based on dry–wet spinning of a particle-loaded polymer solution followed by heat treatment. Extraordinarily small radial dimensions were achieved by controlled shrinkage during thermal

Whole genome analysis of linezolid resistance in Streptococcus pneumoniae reveals resistance and compensatory mutations

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Légaré Danielle

2011-10-01

Full Text Available Abstract Background Several mutations were present in the genome of Streptococcus pneumoniae linezolid-resistant strains but the role of several of these mutations had not been experimentally tested. To analyze the role of these mutations, we reconstituted resistance by serial whole genome transformation of a novel resistant isolate into two strains with sensitive background. We sequenced the parent mutant and two independent transformants exhibiting similar minimum inhibitory concentration to linezolid. Results Comparative genomic analyses revealed that transformants acquired G2576T transversions in every gene copy of 23S rRNA and that the number of altered copies correlated with the level of linezolid resistance and cross-resistance to florfenicol and chloramphenicol. One of the transformants also acquired a mutation present in the parent mutant leading to the overexpression of an ABC transporter (spr1021. The acquisition of these mutations conferred a fitness cost however, which was further enhanced by the acquisition of a mutation in a RNA methyltransferase implicated in resistance. Interestingly, the fitness of the transformants could be restored in part by the acquisition of altered copies of the L3 and L16 ribosomal proteins and by mutations leading to the overexpression of the spr1887 ABC transporter that were present in the original linezolid-resistant mutant. Conclusions Our results demonstrate the usefulness of whole genome approaches at detecting major determinants of resistance as well as compensatory mutations that alleviate the fitness cost associated with resistance.

A comparative study of bulk-fill composites: degree of conversion, post-gel shrinkage and cytotoxicity

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Flávia Gonçalves

2018-03-01

Full Text Available Abstract: Bulk-fill composites are claimed to be restorative materials used in deep preparations and effectively photoactivated in layers up to 4 mm. The aim of the present study was to evaluate the degree of conversion, post-gel volumetric shrinkage, and cytotoxicity of six bulk-fill and two conventional composites. Degree of conversion was determined by FTIR spectroscopy; post-gel volumetric shrinkage was determined using the strain gauge method; and cytotoxicity in human fibroblasts was evaluated indirectly by the MTT assay. Data were subjected to one-way ANOVA/Tukey's test (α = 0.05. All materials, including bulk-fill and conventional composites, were classified as non-toxic, with cell viability higher than 70%. Bulk-fill composites exhibited volumetric shrinkage similar to or lower (1.4 to 0.4% than that of conventional composites (1.7–2.1%. However, only four of the bulk-fill composites were able to sustain a homogeneous conversion at the 4-mm depth. Despite their non-toxicity and shrinkage similar to that of conventional materials, not all commercial bulk-fill materials were able to maintain a conversion as high as 80% of the superficial layer, at the 4-mm depth, indicating some failure in the bulk-fill design of some commercial brands. Therefore, the use of bulk-fill materials in dental practice is advantageous, but special attention should be given to the selection and correct use of the materials.

Shrinkage covariance matrix approach based on robust trimmed mean in gene sets detection

Science.gov (United States)

Karjanto, Suryaefiza; Ramli, Norazan Mohamed; Ghani, Nor Azura Md; Aripin, Rasimah; Yusop, Noorezatty Mohd

2015-02-01

Microarray involves of placing an orderly arrangement of thousands of gene sequences in a grid on a suitable surface. The technology has made a novelty discovery since its development and obtained an increasing attention among researchers. The widespread of microarray technology is largely due to its ability to perform simultaneous analysis of thousands of genes in a massively parallel manner in one experiment. Hence, it provides valuable knowledge on gene interaction and function. The microarray data set typically consists of tens of thousands of genes (variables) from just dozens of samples due to various constraints. Therefore, the sample covariance matrix in Hotelling's T2 statistic is not positive definite and become singular, thus it cannot be inverted. In this research, the Hotelling's T2 statistic is combined with a shrinkage approach as an alternative estimation to estimate the covariance matrix to detect significant gene sets. The use of shrinkage covariance matrix overcomes the singularity problem by converting an unbiased to an improved biased estimator of covariance matrix. Robust trimmed mean is integrated into the shrinkage matrix to reduce the influence of outliers and consequently increases its efficiency. The performance of the proposed method is measured using several simulation designs. The results are expected to outperform existing techniques in many tested conditions.

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Directory of Open Access Journals (Sweden)

Ahn Jong Hwa

2011-01-01

Full Text Available Abstract Background Among the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato. Results For sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation. Conclusions Compared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops

Directory of Open Access Journals (Sweden)

Hongwei Wang

2017-06-01

Full Text Available Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.

Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

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Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

2017-11-23

Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Science.gov (United States)

Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

2015-01-01

To provide context for the diversifications of archosaurs, the group that includes crocodilians, dinosaurs and birds, we generated draft genomes of three crocodilians, Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the relatively rapid evolution of bird genomes represents an autapomorphy within that clade. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs. PMID:25504731

The genome of Tetranychus urticae reveals herbivorous pest adaptations

NARCIS (Netherlands)

Grbić, M.; Van Leeuwen, T.; Clark, R.M.; Rombauts, S.; Grbić, V.; Osborne, E.J.; Dermauw, W.; Phuong, C.T.N.; Ortego, F.; Hernández-Crespo, P.; Diaz, I.; Martinez, M.; Navajas, M.; Sucena, E.; Magalhães, S.; Nagy, L.; Pace, R.M.; Djuranović, S.; Smagghe, G.; Iga, M.; Christiaens, O.; Veenstra, J.A.; Ewer, J.; Villalobos, R.M.; Hutter, J.L.; Hudson, S.D.; Velez, M.; Yi, S.V.; Zeng, J.; Pires-dasilva, A.; Roch, F.; Cazaux, M.; Navarro, M.; Zhurov, V.; Acevedo, G.; Bjelica, A.; Fawcett, J.A.; Bonnet, E.; Martens, C.; Baele, G.; Wissler, L.; Sanchez-Rodriguez, A.; Tirry, L.; Blais, C.; Demeestere, K.; Henz, S.R.; Gregory, T.R.; Mathieu, J.; Verdon, L.; Farinelli, L.; Schmutz, J.; Lindquist, E.; Feyereisen, R.; Van de Peer, Y.

2011-01-01

The spider mite Tetranychus urticae is a cosmopolitan agricultural pest with an extensive host plant range and an extreme record of pesticide resistance. Here we present the completely sequenced and annotated spider mite genome, representing the first complete chelicerate genome. At 90 megabases T.

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.

Science.gov (United States)

Zeng, Xingquan; Long, Hai; Wang, Zhuo; Zhao, Shancen; Tang, Yawei; Huang, Zhiyong; Wang, Yulin; Xu, Qijun; Mao, Likai; Deng, Guangbing; Yao, Xiaoming; Li, Xiangfeng; Bai, Lijun; Yuan, Hongjun; Pan, Zhifen; Liu, Renjian; Chen, Xin; WangMu, QiMei; Chen, Ming; Yu, Lili; Liang, Junjun; DunZhu, DaWa; Zheng, Yuan; Yu, Shuiyang; LuoBu, ZhaXi; Guang, Xuanmin; Li, Jiang; Deng, Cao; Hu, Wushu; Chen, Chunhai; TaBa, XiongNu; Gao, Liyun; Lv, Xiaodan; Abu, Yuval Ben; Fang, Xiaodong; Nevo, Eviatar; Yu, Maoqun; Wang, Jun; Tashi, Nyima

2015-01-27

The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

Mechanical properties and polymerization shrinkage of composite resins light-cured using two different lasers.

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Kim, Tae-Wan; Lee, Jang-Hoon; Jeong, Seung-Hwa; Ko, Ching-Chang; Kim, Hyung-Il; Kwon, Yong Hoon

2015-04-01

The purpose of the present study was to investigate the usefulness of 457 and 473 nm lasers for the curing of composite resins during the restoration of damaged tooth cavity. Monochromaticity and coherence are attractive features of laser compared with most other light sources. Better polymerization of composite resins can be expected. Eight composite resins were light cured using these two lasers and a light-emitting diode (LED) light-curing unit (LCU). To evaluate the degrees of polymerization achieved, polymerization shrinkage and flexural and compressive properties were measured and compared. Polymerization shrinkage values by 457 and 473 nm laser, and LED ranged from 10.9 to 26.8, from 13.2 to 26.1, and from 11.5 to 26.3 μm, respectively. The values by 457 nm laser was significantly different from those by 473 and LED LCU (p0.05). For the tested LCUs, no specific LCU could consistently achieve highest strength and modulus from the specimens tested. Two lasers (457 and 473 nm) can polymerize composite resins to the level that LED LCU can achieve despite inconsistent trends of polymerization shrinkage and flexural and compressive properties of the tested specimens.

Analysis of an RNA-seq Strand-Specific Library from an East Timorese Cucumber Sample Reveals a Complete Cucurbit aphid-borne yellows virus Genome.

Science.gov (United States)

Maina, Solomon; Edwards, Owain R; de Almeida, Luis; Ximenes, Abel; Jones, Roger A C

2017-05-11

Analysis of an RNA-seq library from cucumber leaf RNA extracted from a fast technology for analysis of nucleic acids (FTA) card revealed the first complete genome of Cucurbit aphid-borne yellows virus (CABYV) from East Timor. We compare it with 35 complete CABYV genomes from other world regions. It most resembled the genome of the South Korean isolate HD118. Copyright © 2017 Maina et al.

Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome

DEFF Research Database (Denmark)

Lewis, Nathan E; Liu, Xin; Li, Yuxiang

2013-01-01

stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages...

Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing.

Directory of Open Access Journals (Sweden)

Lance D Eckerle

2010-05-01

Full Text Available Most RNA viruses lack the mechanisms to recognize and correct mutations that arise during genome replication, resulting in quasispecies diversity that is required for pathogenesis and adaptation. However, it is not known how viruses encoding large viral RNA genomes such as the Coronaviridae (26 to 32 kb balance the requirements for genome stability and quasispecies diversity. Further, the limits of replication infidelity during replication of large RNA genomes and how decreased fidelity impacts virus fitness over time are not known. Our previous work demonstrated that genetic inactivation of the coronavirus exoribonuclease (ExoN in nonstructural protein 14 (nsp14 of murine hepatitis virus results in a 15-fold decrease in replication fidelity. However, it is not known whether nsp14-ExoN is required for replication fidelity of all coronaviruses, nor the impact of decreased fidelity on genome diversity and fitness during replication and passage. We report here the engineering and recovery of nsp14-ExoN mutant viruses of severe acute respiratory syndrome coronavirus (SARS-CoV that have stable growth defects and demonstrate a 21-fold increase in mutation frequency during replication in culture. Analysis of complete genome sequences from SARS-ExoN mutant viral clones revealed unique mutation sets in every genome examined from the same round of replication and a total of 100 unique mutations across the genome. Using novel bioinformatic tools and deep sequencing across the full-length genome following 10 population passages in vitro, we demonstrate retention of ExoN mutations and continued increased diversity and mutational load compared to wild-type SARS-CoV. The results define a novel genetic and bioinformatics model for introduction and identification of multi-allelic mutations in replication competent viruses that will be powerful tools for testing the effects of decreased fidelity and increased quasispecies diversity on viral replication

Cell shrinkage as a signal to apoptosis in NIH 3T3 fibroblasts

DEFF Research Database (Denmark)

Friis, Martin B; Friborg, Christel R; Schneider, Linda

2005-01-01

Cell shrinkage is a hallmark of the apoptotic mode of programmed cell death, but it is as yet unclear whether a reduction in cell volume is a primary activation signal of apoptosis. Here we studied the effect of an acute elevation of osmolarity (NaCl or sucrose additions, final osmolarity 687...... accelerated in fibroblasts overexpressing Rac. Conversely, the activation of the extracellular signal-regulated kinase (Erk1/2) was initially significantly decreased. Subsequent to activation of p38, p53 was activated through serine-15 phosphorylation, and active p53 was translocated from the cytosol......: cellular shrinkage activates Rac, with activation of p38, followed by phosphorylation and nuclear translocation of p53, resulting in permeability increases and caspase-3 activation....

Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales

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Jordan T Bird

2016-08-01

Full Text Available The recently proposed candidatus order Altiarchaeales remains an uncultured archaeal lineage composed of genetically diverse, globally widespread organisms frequently observed in anoxic subsurface environments. In spite of 15 years of studies on the psychrophilic biofilm-producing Candidatus (Ca. Altiarchaeum hamiconexum and its close relatives, very little is known about the phylogenetic and functional diversity of the widespread free-living marine members of this taxon. From methanogenic sediments in the White Oak River Estuary, NC, we sequenced a single cell amplified genome (SAG, WOR_SCG_SM1, and used it to identify and refine two high-quality genomes from metagenomes, WOR_79 and WOR_86-2, from the same site in a different year. These three genomic reconstructions form a monophyletic group which also includes three previously published genomes from metagenomes from terrestrial springs and a SAG from Sakinaw Lake in a group previously designated as pMC2A384. A synapomorphic mutation in the Altiarchaeales tRNA synthetase β subunit, pheT, causes the protein to be encoded as two subunits at distant loci. Consistent with the terrestrial spring clades, our estuarine genomes contain a near-complete autotrophic metabolism, H2 or CO as potential electron donors, a reductive acetyl-CoA pathway for carbon fixation, and methylotroph-like NADP(H-dependent dehydrogenase. Phylogenies based on 16S rRNA genes and concatenated conserved proteins identify two distinct sub-clades of Altiarchaeales, Alti-1 populated by organisms from actively flowing springs, and Alti-2 which is more widespread, diverse, and not associated with visible mats. The core Alti-1 genome supports Alti-1 as adapted for the stream environment, with lipopolysaccharide production capacity, extracellular hami structures. The core Alti-2 genome members of this clade are free-living, with distinct mechanisms for energy maintenance, motility, osmoregulation, and sulfur redox reactions. These

Deep sequencing of foot-and-mouth disease virus reveals RNA sequences involved in genome packaging.

Science.gov (United States)

Logan, Grace; Newman, Joseph; Wright, Caroline F; Lasecka-Dykes, Lidia; Haydon, Daniel T; Cottam, Eleanor M; Tuthill, Tobias J

2017-10-18

Non-enveloped viruses protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. Packaging and capsid assembly in RNA viruses can involve interactions between capsid proteins and secondary structures in the viral genome as exemplified by the RNA bacteriophage MS2 and as proposed for other RNA viruses of plants, animals and human. In the picornavirus family of non-enveloped RNA viruses, the requirements for genome packaging remain poorly understood. Here we show a novel and simple approach to identify predicted RNA secondary structures involved in genome packaging in the picornavirus foot-and-mouth disease virus (FMDV). By interrogating deep sequencing data generated from both packaged and unpackaged populations of RNA we have determined multiple regions of the genome with constrained variation in the packaged population. Predicted secondary structures of these regions revealed stem loops with conservation of structure and a common motif at the loop. Disruption of these features resulted in attenuation of virus growth in cell culture due to a reduction in assembly of mature virions. This study provides evidence for the involvement of predicted RNA structures in picornavirus packaging and offers a readily transferable methodology for identifying packaging requirements in many other viruses. Importance In order to transmit their genetic material to a new host, non-enveloped viruses must protect their genomes by packaging them into an outer shell or capsid of virus-encoded proteins. For many non-enveloped RNA viruses the requirements for this critical part of the viral life cycle remain poorly understood. We have identified RNA sequences involved in genome packaging of the picornavirus foot-and-mouth disease virus. This virus causes an economically devastating disease of livestock affecting both the developed and developing world. The experimental methods developed to carry out this work are novel, simple and transferable to the

The Capsaspora genome reveals a complex unicellular prehistory of animals.

Science.gov (United States)

Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

2013-01-01

To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

Science.gov (United States)

Studt, Lena; Niehaus, Eva-Maria; Espino, Jose J.; Huß, Kathleen; Michielse, Caroline B.; Albermann, Sabine; Wagner, Dominik; Bergner, Sonja V.; Connolly, Lanelle R.; Fischer, Andreas; Reuter, Gunter; Kleigrewe, Karin; Bald, Till; Wingfield, Brenda D.; Ophir, Ron; Freeman, Stanley; Hippler, Michael; Smith, Kristina M.; Brown, Daren W.; Proctor, Robert H.; Münsterkötter, Martin; Freitag, Michael; Humpf, Hans-Ulrich; Güldener, Ulrich; Tudzynski, Bettina

2013-01-01

The fungus Fusarium fujikuroi causes “bakanae” disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we present a high-quality genome sequence of F. fujikuroi that was assembled into 12 scaffolds corresponding to the 12 chromosomes described for the fungus. We used the genome sequence along with ChIP-seq, transcriptome, proteome, and HPLC-FTMS-based metabolome analyses to identify the potential secondary metabolite biosynthetic gene clusters and to examine their regulation in response to nitrogen availability and plant signals. The results indicate that expression of most but not all gene clusters correlate with proteome and ChIP-seq data. Comparison of the F. fujikuroi genome to those of six other fusaria revealed that only a small number of gene clusters are conserved among these species, thus providing new insights into the divergence of secondary metabolism in the genus Fusarium. Noteworthy, GA biosynthetic genes are present in some related species, but GA biosynthesis is limited to F. fujikuroi, suggesting that this provides a selective advantage during infection of the preferred host plant rice. Among the genome sequences analyzed, one cluster that includes a polyketide synthase gene (PKS19) and another that includes a non-ribosomal peptide synthetase gene (NRPS31) are unique to F. fujikuroi. The metabolites derived from these clusters were identified by HPLC-FTMS-based analyses of engineered F. fujikuroi strains overexpressing cluster genes. In planta expression studies suggest a specific role for the PKS19-derived product during rice infection. Thus, our results indicate that combined comparative genomics and genome-wide experimental analyses identified novel genes and secondary metabolites that contribute to the evolutionary success of F

Shrinkage and porosity evolution during air-drying of non-cellular food systems: Experimental data versus mathematical modelling.

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Nguyen, Thanh Khuong; Khalloufi, Seddik; Mondor, Martin; Ratti, Cristina

2018-01-01

In the present work, the impact of glass transition on shrinkage of non-cellular food systems (NCFS) during air-drying will be assessed from experimental data and the interpretation of a 'shrinkage' function involved in a mathematical model. Two NCFS made from a mixture of water/maltodextrin/agar (w/w/w: 1/0.15/0.015) were created out of maltodextrins with dextrose equivalent 19 (MD19) or 36 (MD36). The NCFS made with MD19 had 30°C higher Tg than those with MD36. This information indicated that, during drying, the NCFS with MD19 would pass from rubbery to glassy state sooner than NCFS MD36, for which glass transition only happens close to the end of drying. For the two NCFS, porosity and volume reduction as a function of moisture content were captured with high accuracy when represented by the mathematical models previously developed. No significant differences in porosity and in maximum shrinkage between both samples during drying were observed. As well, no change in the slope of the shrinkage curve as a function of moisture content was perceived. These results indicate that glass transition alone is not a determinant factor in changes of porosity or volume during air-drying. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements.

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Meghana Deepak Shirke

Full Text Available Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck, finger millet (leaf and neck, foxtail millet (leaf and buffel grass (leaf. Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors.

The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex

Energy Technology Data Exchange (ETDEWEB)

Blanc, Guillaume; Duncan, Garry A.; Agarakova, Irina; Borodovsky, Mark; Gurnon, James; Kuo, Alan; Lindquist, Erika; Lucas, Susan; Pangailinan, Jasmyn; Polle, Juergen; Salamov, Asaf; Terry, Astrid; Yamada, Takashi; Dunigan, David D.; Grigoriev, Igor V.; Claverie, Jean-Michel; Etten, James L. Van

2010-05-06

Chlorella variabilis NC64A, a unicellular photosynthetic green alga (Trebouxiophyceae), is an intracellular photobiont of Paramecium bursaria and a model system for studying virus/algal interactions. We sequenced its 46-Mb nuclear genome, revealing an expansion of protein families that could have participated in adaptation to symbiosis. NC64A exhibits variations in GC content across its genome that correlate with global expression level, average intron size, and codon usage bias. Although Chlorella species have been assumed to be asexual and nonmotile, the NC64A genome encodes all the known meiosis-specific proteins and a subset of proteins found in flagella. We hypothesize that Chlorella might have retained a flagella-derived structure that could be involved in sexual reproduction. Furthermore, a survey of phytohormone pathways in chlorophyte algae identified algal orthologs of Arabidopsis thaliana genes involved in hormone biosynthesis and signaling, suggesting that these functions were established prior to the evolution of land plants. We show that the ability of Chlorella to produce chitinous cell walls likely resulted from the capture of metabolic genes by horizontal gene transfer from algal viruses, prokaryotes, or fungi. Analysis of the NC64A genome substantially advances our understanding of the green lineage evolution, including the genomic interplay with viruses and symbiosis between eukaryotes.

In-Situ Observation of Sintering Shrinkage of UO{sub 2} Compacts Derived from Different Powder Routes

Energy Technology Data Exchange (ETDEWEB)

Rhee, Young Woo; Oh, Jang Soo; Kim, Dong Joo; Kim, Keon Sik; Kim, Jong Hun; Yang, Jae Ho; Koo, Yang Hyun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2015-10-15

In-situ observations on the shrinkage of green pellets with precisely controlled dimensions were carefully conducted by using TOM during H2 atmosphere sintering. The shrinkage retardation in IDR-UO{sub 2} might be attributed to the larger primary particle size of IDRUO{sub 2} than those of ADU- and AUC- UO{sub 2} powders. It would be important to understand the different sintering characteristics of UO{sub 2} powders according to the powder routes, when it comes to designing a new sintering process or choosing a sintering additive for new fuel pellet like PCI (Pellet Cladding Interaction) remedy pellet. In this paper, we have investigated the initial and intermediate sintering shrinkage of UO{sub 2} from different powder routes by in-situ observation of green samples during H2 atmosphere sintering. Effect of powder characteristics of three different UO{sub 2} powders on the initial and intermediate sintering were closely reviewed including crystal structure, powder size, specific surface area, primary crystal size, and O/U ratio.

Distinct Biological Potential of Streptococcus gordonii and Streptococcus sanguinis Revealed by Comparative Genome Analysis.

Science.gov (United States)

Zheng, Wenning; Tan, Mui Fern; Old, Lesley A; Paterson, Ian C; Jakubovics, Nicholas S; Choo, Siew Woh

2017-06-07

Streptococcus gordonii and Streptococcus sanguinis are pioneer colonizers of dental plaque and important agents of bacterial infective endocarditis (IE). To gain a greater understanding of these two closely related species, we performed comparative analyses on 14 new S. gordonii and 5 S. sanguinis strains using various bioinformatics approaches. We revealed S. gordonii and S. sanguinis harbor open pan-genomes and share generally high sequence homology and number of core genes including virulence genes. However, we observed subtle differences in genomic islands and prophages between the species. Comparative pathogenomics analysis identified S. sanguinis strains have genes encoding IgA proteases, mitogenic factor deoxyribonucleases, nickel/cobalt uptake and cobalamin biosynthesis. On the contrary, genomic islands of S. gordonii strains contain additional copies of comCDE quorum-sensing system components involved in genetic competence. Two distinct polysaccharide locus architectures were identified, one of which was exclusively present in S. gordonii strains. The first evidence of genes encoding the CylA and CylB system by the α-haemolytic S. gordonii is presented. This study provides new insights into the genetic distinctions between S. gordonii and S. sanguinis, which yields understanding of tooth surfaces colonization and contributions to dental plaque formation, as well as their potential roles in the pathogenesis of IE.

Genome scan for nonadditive heterotic trait loci reveals mainly underdominant effects in Saccharomyces cerevisiae.

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Laiba, Efrat; Glikaite, Ilana; Levy, Yael; Pasternak, Zohar; Fridman, Eyal

2016-04-01

The overdominant model of heterosis explains the superior phenotype of hybrids by synergistic allelic interaction within heterozygous loci. To map such genetic variation in yeast, we used a population doubling time dataset of Saccharomyces cerevisiae 16 × 16 diallel and searched for major contributing heterotic trait loci (HTL). Heterosis was observed for the majority of hybrids, as they surpassed their best parent growth rate. However, most of the local heterozygous loci identified by genome scan were surprisingly underdominant, i.e., reduced growth. We speculated that in these loci adverse effects on growth resulted from incompatible allelic interactions. To test this assumption, we eliminated these allelic interactions by creating hybrids with local hemizygosity for the underdominant HTLs, as well as for control random loci. Growth of hybrids was indeed elevated for most hemizygous to HTL genes but not for control genes, hence validating the results of our genome scan. Assessing the consequences of local heterozygosity by reciprocal hemizygosity and allele replacement assays revealed the influence of genetic background on the underdominant effects of HTLs. Overall, this genome-wide study on a multi-parental hybrid population provides a strong argument against single gene overdominance as a major contributor to heterosis, and favors the dominance complementation model.

Genomic regulation of natural variation in cortical and noncortical brain volume

Directory of Open Access Journals (Sweden)

Laughlin Rick E

2006-02-01

Full Text Available Abstract Background The relative growth of the neocortex parallels the emergence of complex cognitive functions across species. To determine the regions of the mammalian genome responsible for natural variations in cortical volume, we conducted a complex trait analysis using 34 strains of recombinant inbred (Rl strains of mice (BXD, as well as their two parental strains (C57BL/6J and DBA/2J. We measured both neocortical volume and total brain volume in 155 coronally sectioned mouse brains that were Nissl stained and embedded in celloidin. After correction for shrinkage, the measured cortical and noncortical brain volumes were entered into a multiple regression analysis, which removed the effects of body size and age from the measurements. Marker regression and interval mapping were computed using WebQTL. Results An ANOVA revealed that more than half of the variance of these regressed phenotypes is genetically determined. We then identified the regions of the genome regulating this heritability. We located genomic regions in which a linkage disequilibrium was present using WebQTL as both a mapping engine and genomic database. For neocortex, we found a genome-wide significant quantitative trait locus (QTL on chromosome 11 (marker D11Mit19, as well as a suggestive QTL on chromosome 16 (marker D16Mit100. In contrast, for noncortex the effect of chromosome 11 was markedly reduced, and a significant QTL appeared on chromosome 19 (D19Mit22. Conclusion This classic pattern of double dissociation argues strongly for different genetic factors regulating relative cortical size, as opposed to brain volume more generally. It is likely, however, that the effects of proximal chromosome 11 extend beyond the neocortex strictly defined. An analysis of single nucleotide polymorphisms in these regions indicated that ciliary neurotrophic factor (Cntf is quite possibly the gene underlying the noncortical QTL. Evidence for a candidate gene modulating neocortical

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

Science.gov (United States)

Leisner, Courtney P; Hamilton, John P; Crisovan, Emily; Manrique-Carpintero, Norma C; Marand, Alexandre P; Newton, Linsey; Pham, Gina M; Jiang, Jiming; Douches, David S; Jansky, Shelley H; Buell, C Robin

2018-05-01

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Science.gov (United States)

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

Design and evaluation of high-volume fly ash (HVFA) concrete mixes, report D : creep, shrinkage, and abrasion resistance of HVFA concrete.

Science.gov (United States)

2012-10-01

The main objective of this study was to determine the effect on shrinkage, creep, : and abrasion resistance of high-volume fly ash (HVFA) concrete. The HVFA concrete : test program consisted of comparing the shrinkage, creep, and abrasion performance...

Sparse electromagnetic imaging using nonlinear iterative shrinkage thresholding

KAUST Repository

Desmal, Abdulla; Bagci, Hakan

2015-01-01

A sparse nonlinear electromagnetic imaging scheme is proposed for reconstructing dielectric contrast of investigation domains from measured fields. The proposed approach constructs the optimization problem by introducing the sparsity constraint to the data misfit between the scattered fields expressed as a nonlinear function of the contrast and the measured fields and solves it using the nonlinear iterative shrinkage thresholding algorithm. The thresholding is applied to the result of every nonlinear Landweber iteration to enforce the sparsity constraint. Numerical results demonstrate the accuracy and efficiency of the proposed method in reconstructing sparse dielectric profiles.

Sparse electromagnetic imaging using nonlinear iterative shrinkage thresholding

KAUST Repository

Desmal, Abdulla

2015-04-13

A sparse nonlinear electromagnetic imaging scheme is proposed for reconstructing dielectric contrast of investigation domains from measured fields. The proposed approach constructs the optimization problem by introducing the sparsity constraint to the data misfit between the scattered fields expressed as a nonlinear function of the contrast and the measured fields and solves it using the nonlinear iterative shrinkage thresholding algorithm. The thresholding is applied to the result of every nonlinear Landweber iteration to enforce the sparsity constraint. Numerical results demonstrate the accuracy and efficiency of the proposed method in reconstructing sparse dielectric profiles.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

KAUST Repository

Olsen, Jeanine L.

2016-01-27

Seagrasses colonized the sea1 on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet2. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes3, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae4 and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming5, 6, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants7.

C-O-H-S magmatic fluid system in shrinkage bubbles of melt inclusions

Science.gov (United States)

Robidoux, P.; Frezzotti, M. L.; Hauri, E. H.; Aiuppa, A.

2016-12-01

Magmatic volatiles include multiple phases in the C-O-H-S system of shrinkage bubbles for which a conceptual model is still unclear during melt inclusion formation [1,2,3,4]. The present study aims to qualitatively explore the evolution of the volatile migration, during and after the formation of the shrinkage bubble in melt inclusions trapped by olivines from Holocene to present at San Cristóbal volcano (Nicaragua), Central American Volcanic Arc (CAVA). Combined scanning electron microscope (SEM) and Raman spectroscopy observations allow to define the mineral-fluid phases inside typical shrinkage bubbles at ambient temperature. The existence of residual liquid water is demonstrated in the shrinkage bubbles of naturally quenched melt inclusion and this water could represents the principal agent for chemical reactions with other dissolved ionic species (SO42-, CO32-, etc.) and major elements (Mg, Fe, Cu, etc.) [4,5]. With the objective of following the cooling story of the bubble-inclusion system, the new methodological approach here estimate the interval of equilibrium temperatures for each SEM-Raman identified mineral phase (carbonates, hydrous carbonates, sulfurs, sulfates, etc.). Finally, two distinct mechanisms are proposed to describe the evolution of this heterogeneous fluid system in bubble samples at San Cristóbal which imply a close re-examination for similar volcanoes in subduction zone settings: (1) bubbles are already contracted and filled by volatiles by diffusion processes from the glass and leading to a C-O-H-S fluid-glass reaction enriched in Mg-Fe-Cu elements (2) bubbles are formed by oversaturation of the volatiles from the magma which is producing an immiscible metal-rich fluid. [1]Moore et al. (2015). Am. Mineral. 100, 806-823 [2]Wallace et al. (2015). Am. Mineral. 100, 787-794 [3]Lowenstern (2015). Am. Mineral. 100, 672-673 [4]Esposito, et al. (2016). Am. Mineral. 101, 1691-1708 [5]Kamenetsky et al. (2001). Earth Planet. Sci. Lett. 184, 685-702

Investigation of Shrinkage Defect in Castings by Quantitative Ishikawa Diagram

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Chokkalingam B.

2017-03-01

Full Text Available Metal casting process involves processes such as pattern making, moulding and melting etc. Casting defects occur due to combination of various processes even though efforts are taken to control them. The first step in the defect analysis is to identify the major casting defect among the many casting defects. Then the analysis is to be made to find the root cause of the particular defect. Moreover, it is especially difficult to identify the root causes of the defect. Therefore, a systematic method is required to identify the root cause of the defect among possible causes, consequently specific remedial measures have to be implemented to control them. This paper presents a systematic procedure to identify the root cause of shrinkage defect in an automobile body casting (SG 500/7 and control it by the application of Pareto chart and Ishikawa diagram. with quantitative Weightage. It was found that the root causes were larger volume section in the cope, insufficient feeding of riser and insufficient poured metal in the riser. The necessary remedial measures were taken and castings were reproduced. The shrinkage defect in the castings was completely eliminated.

Recycling of rubble from building demolition for low-shrinkage concretes.

Science.gov (United States)

Corinaldesi, Valeria; Moriconi, Giacomo

2010-04-01

In this project concrete mixtures were prepared that were characterized by low ductility due to desiccation by using debris from building demolition, which after a suitable treatment was used as aggregate for partial replacement of natural aggregates. The recycled aggregate used came from a recycling plant, in which rubble from building demolition was selected, crushed, cleaned, sieved, and graded. Such aggregates are known to be more porous as indicated by the Saturated Surface Dry (SSD) moisture content. The recycled concrete used as aggregates were added to the concrete mixture in order to study their influence on the fresh and hardened concrete properties. They were added either after water pre-soaking or in dry condition, in order to evaluate the influence of moisture in aggregates on the performance of concrete containing recycled aggregate. In particular, the effect of internal curing, due to the use of such aggregates, was studied. Concrete behavior due to desiccation under dehydration was studied by means of both drying shrinkage test and German angle test, through which shrinkage under the restrained condition of early age concrete can be evaluated. Copyright 2009 Elsevier Ltd. All rights reserved.

Specimen Shrinkage and Its Influence on Margin Assessment in Breast Cancer

Directory of Open Access Journals (Sweden)

Badrul H. Yeap

2007-07-01

Conclusion: Breast specimens undergo shrinkage after histological fixation, losing more than a third of their original closest free margin, whilst the tumour itself does not shrink substantially. This phenomenon has vital implications in the accuracy of margin analysis and consequent decisions on further management, including re-operation and the institution of adjuvant radiotherapy.

Supplementary Material for: Whole genome sequencing reveals genomic heterogeneity and antibiotic purification in Mycobacterium tuberculosis isolates

KAUST Repository

Black, PA

2015-01-01

Abstract Background Whole genome sequencing has revolutionised the interrogation of mycobacterial genomes. Recent studies have reported conflicting findings on the genomic stability of Mycobacterium tuberculosis during the evolution of drug resistance. In an age where whole genome sequencing is increasingly relied upon for defining the structure of bacterial genomes, it is important to investigate the reliability of next generation sequencing to identify clonal variants present in a minor percentage of the population. This study aimed to define a reliable cut-off for identification of low frequency sequence variants and to subsequently investigate genetic heterogeneity and the evolution of drug resistance in M. tuberculosis. Methods Genomic DNA was isolated from single colonies from 14 rifampicin mono-resistant M. tuberculosis isolates, as well as the primary cultures and follow up MDR cultures from two of these patients. The whole genomes of the M. tuberculosis isolates were sequenced using either the Illumina MiSeq or Illumina HiSeq platforms. Sequences were analysed with an in-house pipeline. Results Using next-generation sequencing in combination with Sanger sequencing and statistical analysis we defined a read frequency cut-off of 30 % to identify low frequency M. tuberculosis variants with high confidence. Using this cut-off we demonstrated a high rate of genetic diversity between single colonies isolated from one population, showing that by using the current sequencing technology, single colonies are not a true reflection of the genetic diversity within a whole population and vice versa. We further showed that numerous heterogeneous variants emerge and then disappear during the evolution of isoniazid resistance within individual patients. Our findings allowed us to formulate a model for the selective bottleneck which occurs during the course of infection, acting as a genomic purification event. Conclusions Our study demonstrated true levels of genetic

Genome-Wide RNAi Ionomics Screen Reveals New Genes and Regulation of Human Trace Element Metabolism

OpenAIRE

Malinouski, Mikalai; Hasan, Nesrin M.; Zhang, Yan; Seravalli, Javier; Lin, Jie; Avanesov, Andrei; Lutsenko, Svetlana; Gladyshev, Vadim N.

2017-01-01

Trace elements are essential for human metabolism and dysregulation of their homeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundam...

TH-E-BRF-01: Exploiting Tumor Shrinkage in Split-Course Radiotherapy

International Nuclear Information System (INIS)

Unkelbach, J; Craft, D; Hong, T; Papp, D; Wolfgang, J; Bortfeld, T; Ramakrishnan, J; Salari, E

2014-01-01

Purpose: In split-course radiotherapy, a patient is treated in several stages separated by weeks or months. This regimen has been motivated by radiobiological considerations. However, using modern image-guidance, it also provides an approach to reduce normal tissue dose by exploiting tumor shrinkage. In this work, we consider the optimal design of split-course treatments, motivated by the clinical management of large liver tumors for which normal liver dose constraints prohibit the administration of an ablative radiation dose in a single treatment. Methods: We introduce a dynamic tumor model that incorporates three factors: radiation induced cell kill, tumor shrinkage, and tumor cell repopulation. The design of splitcourse radiotherapy is formulated as a mathematical optimization problem in which the total dose to the liver is minimized, subject to delivering the prescribed dose to the tumor. Based on the model, we gain insight into the optimal administration of radiation over time, i.e. the optimal treatment gaps and dose levels. Results: We analyze treatments consisting of two stages in detail. The analysis confirms the intuition that the second stage should be delivered just before the tumor size reaches a minimum and repopulation overcompensates shrinking. Furthermore, it was found that, for a large range of model parameters, approximately one third of the dose should be delivered in the first stage. The projected benefit of split-course treatments in terms of liver sparing depends on model assumptions. However, the model predicts large liver dose reductions by more than a factor of two for plausible model parameters. Conclusion: The analysis of the tumor model suggests that substantial reduction in normal tissue dose can be achieved by exploiting tumor shrinkage via an optimal design of multi-stage treatments. This suggests taking a fresh look at split-course radiotherapy for selected disease sites where substantial tumor regression translates into reduced

TH-E-BRF-01: Exploiting Tumor Shrinkage in Split-Course Radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Unkelbach, J; Craft, D; Hong, T; Papp, D; Wolfgang, J; Bortfeld, T [Massachusetts General Hospital, Boston, MA (United States); Ramakrishnan, J [University of Wisconsin, Madison, Wisconsin (United States); Salari, E [Wichita State University, Wichita, KS (United States)

2014-06-15

Purpose: In split-course radiotherapy, a patient is treated in several stages separated by weeks or months. This regimen has been motivated by radiobiological considerations. However, using modern image-guidance, it also provides an approach to reduce normal tissue dose by exploiting tumor shrinkage. In this work, we consider the optimal design of split-course treatments, motivated by the clinical management of large liver tumors for which normal liver dose constraints prohibit the administration of an ablative radiation dose in a single treatment. Methods: We introduce a dynamic tumor model that incorporates three factors: radiation induced cell kill, tumor shrinkage, and tumor cell repopulation. The design of splitcourse radiotherapy is formulated as a mathematical optimization problem in which the total dose to the liver is minimized, subject to delivering the prescribed dose to the tumor. Based on the model, we gain insight into the optimal administration of radiation over time, i.e. the optimal treatment gaps and dose levels. Results: We analyze treatments consisting of two stages in detail. The analysis confirms the intuition that the second stage should be delivered just before the tumor size reaches a minimum and repopulation overcompensates shrinking. Furthermore, it was found that, for a large range of model parameters, approximately one third of the dose should be delivered in the first stage. The projected benefit of split-course treatments in terms of liver sparing depends on model assumptions. However, the model predicts large liver dose reductions by more than a factor of two for plausible model parameters. Conclusion: The analysis of the tumor model suggests that substantial reduction in normal tissue dose can be achieved by exploiting tumor shrinkage via an optimal design of multi-stage treatments. This suggests taking a fresh look at split-course radiotherapy for selected disease sites where substantial tumor regression translates into reduced

Shrinkage stress compensation in composite-restored teeth: relaxation or hygroscopic expansion?

Science.gov (United States)

Meriwether, Laurel A; Blen, Bernard J; Benson, Jarred H; Hatch, Robert H; Tantbirojn, Daranee; Versluis, Antheunis

2013-05-01

Polymerization of composite restorations causes shrinkage, which deforms and thus stresses restored teeth. This shrinkage deformation, however, has been shown to decrease over time. The objective was to investigate whether this reduction was caused by hygroscopic expansion or stress relaxation of the composite/tooth complex. Extracted molars were mounted in rigid stainless steel rings with four spherical reference areas. Twelve molars were prepared with large mesioocclusodistal slots, etched, bonded, and restored with a composite material (Filtek Supreme, 3M ESPE) in two horizontal layers. Ten intact molars were the controls. The teeth were stored either in deionized water or silicone oil. They were scanned after preparation (baseline), restoration (0-week), and after 1, 2, and 4 weeks storage. Scanned tooth surfaces were aligned with the baseline using the unchanged reference areas. Cuspal flexure was calculated from lingual and buccal surface deformation. To verify that the restorations had remained bonded, dye penetration at the interfaces was assessed using basic fuchsin dye. Statistical assessment was done by ANOVA followed by Student-Newman-Keuls post hoc test (p=0.05). Substantial cuspal contraction was found for restored teeth after the composite was cured (13-14 μm cuspal flexure). After 4 weeks cuspal contraction decreased significantly for restored teeth stored in water (7.3 ± 3.2) but not for those stored in silicone oil (11.4 ± 5.0). Dye penetration of the occlusal interface was minimal in both groups (106 ± 87 and 21 ± 28 μm in water and silicone oil, respectively). The results suggest that hygroscopic expansion was the main mechanism for shrinkage stress compensation. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Influence of nano-material on the expansive and shrinkage soil behavior

International Nuclear Information System (INIS)

Taha, Mohd Raihan; Taha, Omer Muhie Eldeen

2012-01-01

This paper presents an experimental study performed on four types of soils mixed with three types of nano-material of different percentages. The expansion and shrinkage tests were conducted to investigate the effect of three type of nano-materials (nano-clay, nano-alumina, and nano-copper) additive on repressing strains in compacted residual soil mixed with different ratios of bentonite (S1 = 0 % bentonite, S2 = 5 % bentonite, S3 = 10 % bentonite, and S4 = 20 % bentonite). The soil specimens were compacted under the condition of maximum dry unit weight and optimum water content (w opt ) using standard compaction test. The physical and mechanical results of the treated samples were determined. The untreated soil values were used as control points for comparison purposes. It was found that with the addition of optimum percentage of nano-material, both the swell strain and shrinkage strain reduced. The results show that nano-material decreases the development of desiccation cracks on the surface of compacted samples without decrease in the hydraulic conductivity.

High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

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Kevin A Wilkinson

2008-04-01

Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further

Signatures of selection in tilapia revealed by whole genome resequencing.

Science.gov (United States)

Xia, Jun Hong; Bai, Zhiyi; Meng, Zining; Zhang, Yong; Wang, Le; Liu, Feng; Jing, Wu; Wan, Zi Yi; Li, Jiale; Lin, Haoran; Yue, Gen Hua

2015-09-16

Natural selection and selective breeding for genetic improvement have left detectable signatures within the genome of a species. Identification of selection signatures is important in evolutionary biology and for detecting genes that facilitate to accelerate genetic improvement. However, selection signatures, including artificial selection and natural selection, have only been identified at the whole genome level in several genetically improved fish species. Tilapia is one of the most important genetically improved fish species in the world. Using next-generation sequencing, we sequenced the genomes of 47 tilapia individuals. We identified a total of 1.43 million high-quality SNPs and found that the LD block sizes ranged from 10-100 kb in tilapia. We detected over a hundred putative selective sweep regions in each line of tilapia. Most selection signatures were located in non-coding regions of the tilapia genome. The Wnt signaling, gonadotropin-releasing hormone receptor and integrin signaling pathways were under positive selection in all improved tilapia lines. Our study provides a genome-wide map of genetic variation and selection footprints in tilapia, which could be important for genetic studies and accelerating genetic improvement of tilapia.

Shrinkage-thresholding enhanced born iterative method for solving 2D inverse electromagnetic scattering problem

KAUST Repository

Desmal, Abdulla; Bagci, Hakan

2014-01-01

A numerical framework that incorporates recently developed iterative shrinkage thresholding (IST) algorithms within the Born iterative method (BIM) is proposed for solving the two-dimensional inverse electromagnetic scattering problem. IST

Comparative Genomics Analysis of Streptococcus Isolates from the Human Small Intestine Reveals their Adaptation to a Highly Dynamic Ecosystem

Science.gov (United States)

Van den Bogert, Bartholomeus; Boekhorst, Jos; Herrmann, Ruth; Smid, Eddy J.; Zoetendal, Erwin G.; Kleerebezem, Michiel

2013-01-01

The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine. PMID:24386196

Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

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Eunyoung Seo

2016-08-01

Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

Science.gov (United States)

Alex, Anoop; Antunes, Agostinho

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

Science.gov (United States)

Romanchuk, Artur; Chang, Jeff H.; Mukhtar, M. Shahid; Cherkis, Karen; Roach, Jeff; Grant, Sarah R.; Jones, Corbin D.; Dangl, Jeffery L.

2011-01-01

Closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. In many Gram- negative bacteria, including the phytopathogen Pseudomonas syringae, type III effectors (TTEs) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. To capture the dynamic nature of virulence gene repertoires across P. syringae, we screened 11 diverse strains for novel TTE families and coupled this nearly saturating screen with the sequencing and assembly of 14 phylogenetically diverse isolates from a broad collection of diseased host plants. TTE repertoires vary dramatically in size and content across all P. syringae clades; surprisingly few TTEs are conserved and present in all strains. Those that are likely provide basal requirements for pathogenicity. We demonstrate that functional divergence within one conserved locus, hopM1, leads to dramatic differences in pathogenicity, and we demonstrate that phylogenetics-informed mutagenesis can be used to identify functionally critical residues of TTEs. The dynamism of the TTE repertoire is mirrored by diversity in pathways affecting the synthesis of secreted phytotoxins, highlighting the likely role of both types of virulence factors in determination of host range. We used these 14 draft genome sequences, plus five additional genome sequences previously reported, to identify the core genome for P. syringae and we compared this core to that of two closely related non-pathogenic pseudomonad species. These data revealed the recent acquisition of a 1 Mb megaplasmid by a sub-clade of cucumber pathogens. This megaplasmid encodes a type IV secretion system and a diverse set of unknown proteins, which dramatically increases both the genomic content of these strains and the pan-genome of the species. PMID:21799664

Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle.

Science.gov (United States)

Załuga, Joanna; Stragier, Pieter; Baeyen, Steve; Haegeman, Annelies; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

2014-05-22

The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health. To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes. The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and

Genomic and epigenomic analysis of high-risk prostate cancer reveals changes in hydroxymethylation and TET1.

Science.gov (United States)

Spans, Lien; Van den Broeck, Thomas; Smeets, Elien; Prekovic, Stefan; Thienpont, Bernard; Lambrechts, Diether; Karnes, R Jeffrey; Erho, Nicholas; Alshalalfa, Mohammed; Davicioni, Elai; Helsen, Christine; Gevaert, Thomas; Tosco, Lorenzo; Haustermans, Karin; Lerut, Evelyne; Joniau, Steven; Claessens, Frank

2016-04-26

The clinical heterogeneity of prostate cancer (PCa) makes it difficult to identify those patients that could benefit from more aggressive treatments. As a contribution to a better understanding of the genomic changes in the primary tumor that are associated with the development of high-risk disease, we performed exome sequencing and copy number determination of a clinically homogeneous cohort of 47 high-risk PCas. We confirmed recurrent mutations in SPOP, PTEN and TP53 among the 850 point mutations we detected. In seven cases, we discovered genomic aberrations in the TET1 (Ten-Eleven Translocation 1) gene which encodes a DNA hydroxymethylase than can modify methylated cytosines in genomic DNA and thus is linked with gene expression changes. TET1 protein levels were reduced in tumor versus non-tumor prostate tissue in 39 of 40 cases. The clinical relevance of changes in TET1 levels was demonstrated in an independent PCa cohort, in which low TET1 mRNA levels were significantly associated with worse metastases-free survival. We also demonstrate a strong reduction in hydroxymethylated DNA in tumor tissue in 27 of 41 cases. Furthermore, we report the first exploratory (h)MeDIP-Seq analyses of eight high-risk PCa samples. This reveals a large heterogeneity in hydroxymethylation changes in tumor versus non-tumor genomes which can be linked with cell polarity.

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Directory of Open Access Journals (Sweden)

Verena J Schuenemann

2018-05-01

Full Text Available Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Science.gov (United States)

Schuenemann, Verena J; Avanzi, Charlotte; Krause-Kyora, Ben; Seitz, Alexander; Herbig, Alexander; Inskip, Sarah; Bonazzi, Marion; Reiter, Ella; Urban, Christian; Dangvard Pedersen, Dorthe; Taylor, G Michael; Singh, Pushpendra; Stewart, Graham R; Velemínský, Petr; Likovsky, Jakub; Marcsik, Antónia; Molnár, Erika; Pálfi, György; Mariotti, Valentina; Riga, Alessandro; Belcastro, M Giovanna; Boldsen, Jesper L; Nebel, Almut; Mays, Simon; Donoghue, Helen D; Zakrzewski, Sonia; Benjak, Andrej; Nieselt, Kay; Cole, Stewart T; Krause, Johannes

2018-05-01

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

Directory of Open Access Journals (Sweden)

Shuiquan eTang

2016-02-01

, a complete heme biosynthesis pathway is present in the five Dehalobacter genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring Firmicutes and Chloroflexi reveals profound evolutionary differences despite very similar niche-specific metabolism and function.

Low baseline and subsequent higher aortic abdominal aneurysm FDG uptake are associated with poor sac shrinkage post endovascular repair

Energy Technology Data Exchange (ETDEWEB)

Marie, Pierre-Yves [CHRU-Nancy, Universite de Lorraine, Nuclear Medecine and Nancyclotep Platform, Nancy (France); INSERM, University of Lorraine, UMR 1116, Nancy (France); CHRU-Nancy, Hopitaux de BRABOIS, Service de Medecine Nucleaire, Vandoeuvre (France); Plissonnier, Didier; Rouer, Martin [CHU-Rouen, Department of Vascular Surgery, Rouen (France); Bravetti, Stephanie [CHRU-Nancy, Universite de Lorraine, Department of Radiology, Nancy (France); Coscas, Raphael [Hopital Ambroise Pare, APHP, Chirurgie Vasculaire, Boulogne-Billancourt (France); Haulon, Stephan [CHU-Lille, Department of Vascular Surgery, Lille (France); Mandry, Damien [CHRU-Nancy, Universite de Lorraine, Department of Radiology, Nancy (France); INSERM, University of Lorraine, UMR 947, Nancy (France); Alsac, Jean-Marc [grid.414093.b, APHP, HEGP, Department of Vascular Surgery, Paris (France); Malikov, Serguei; Settembre, Nicla [CHRU-Nancy, Universite de Lorraine, Vascular Surgery, Nancy (France); Goueffic, Yann [CHU-Nantes, Department of Vascular Surgery, Nantes (France); Morel, Olivier [CHU-Besancon, Department of Nuclear Medecine, Besancon (France); Roch, Veronique [CHRU-Nancy, Universite de Lorraine, Nuclear Medecine and Nancyclotep Platform, Nancy (France); Micard, Emilien [INSERM, University of Lorraine, UMR 947, Nancy (France); INSERM, CHRU-Nancy, Universite de Lorraine, CIC-1433, FCRIN INI-CRCT, Nancy (France); Lamiral, Zohra [INSERM, CHRU-Nancy, Universite de Lorraine, CIC-1433, FCRIN INI-CRCT, Nancy (France); Michel, Jean-Baptiste [INSERM, Bichat, UMR 698, Paris (France); Rossignol, Patrick [INSERM, University of Lorraine, UMR 1116, Nancy (France); INSERM, CHRU-Nancy, Universite de Lorraine, CIC-1433, FCRIN INI-CRCT, Nancy (France)

2018-04-15

The growth phases of medically treated abdominal aortic aneurysms (AAA) are frequently associated with an {sup 18}F-fluorodesoxyglucose positron emission tomography (FDG-PET) pattern involving low baseline and subsequent higher FDG uptake. However, the FDG-PET patterns associated with the endovascular aneurysm repair (EVAR) of larger AAA are presently unknown. This study aimed to investigate the relationship between serial AAA FDG uptake measurements, obtained before EVAR and 1 and 6 months post-intervention and subsequent sac shrinkage at 6 months, a well-recognized indicator of successful repair. Thirty-three AAA patients referred for EVAR (maximal diameter: 55.4 ± 6.0 mm, total volume: 205.7 ± 63.0 mL) underwent FDG-PET/computed tomography (CT) before EVAR and at 1 and 6 months thereafter, with the monitoring of AAA volume and of a maximal standardized FDG uptake [SUVmax] averaged between the axial slices encompassing the AAA. Sac shrinkage was highly variable and could be stratified into three terciles: a first tercile in which shrinkage was absent or very limited (0-29 mL) and a third tercile with pronounced shrinkage (56-165 mL). SUVmax values were relatively low at baseline in the 1st tercile (SUVmax: 1.69 ± 0.33), but markedly increased at 6 months (2.42 ± 0.69, p = 0.02 vs. baseline). These SUV max values were by contrast much higher at baseline in the 3rd tercile (SUVmax: 2.53 ± 0.83 p = 0.009 vs. 1st tercile) and stable at 6 months (2.49 ± 0.80), while intermediate results were documented in the 2nd tercile. Lastly, the amount of sac shrinkage, expressed in absolute values or in percentages of baseline AAA volumes, was positively correlated with baseline SUVmax (p = 0.001 for both). A low pre-EVAR FDG uptake and increased AAA FDG uptake at 6 months are associated with reduced sac shrinkage. This sequential FDG-PET pattern is similar to that already shown to accompany growth phases of medically treated AAA. (orig.)

Low baseline and subsequent higher aortic abdominal aneurysm FDG uptake are associated with poor sac shrinkage post endovascular repair

International Nuclear Information System (INIS)

Marie, Pierre-Yves; Plissonnier, Didier; Rouer, Martin; Bravetti, Stephanie; Coscas, Raphael; Haulon, Stephan; Mandry, Damien; Alsac, Jean-Marc; Malikov, Serguei; Settembre, Nicla; Goueffic, Yann; Morel, Olivier; Roch, Veronique; Micard, Emilien; Lamiral, Zohra; Michel, Jean-Baptiste; Rossignol, Patrick

2018-01-01

The growth phases of medically treated abdominal aortic aneurysms (AAA) are frequently associated with an 18 F-fluorodesoxyglucose positron emission tomography (FDG-PET) pattern involving low baseline and subsequent higher FDG uptake. However, the FDG-PET patterns associated with the endovascular aneurysm repair (EVAR) of larger AAA are presently unknown. This study aimed to investigate the relationship between serial AAA FDG uptake measurements, obtained before EVAR and 1 and 6 months post-intervention and subsequent sac shrinkage at 6 months, a well-recognized indicator of successful repair. Thirty-three AAA patients referred for EVAR (maximal diameter: 55.4 ± 6.0 mm, total volume: 205.7 ± 63.0 mL) underwent FDG-PET/computed tomography (CT) before EVAR and at 1 and 6 months thereafter, with the monitoring of AAA volume and of a maximal standardized FDG uptake [SUVmax] averaged between the axial slices encompassing the AAA. Sac shrinkage was highly variable and could be stratified into three terciles: a first tercile in which shrinkage was absent or very limited (0-29 mL) and a third tercile with pronounced shrinkage (56-165 mL). SUVmax values were relatively low at baseline in the 1st tercile (SUVmax: 1.69 ± 0.33), but markedly increased at 6 months (2.42 ± 0.69, p = 0.02 vs. baseline). These SUV max values were by contrast much higher at baseline in the 3rd tercile (SUVmax: 2.53 ± 0.83 p = 0.009 vs. 1st tercile) and stable at 6 months (2.49 ± 0.80), while intermediate results were documented in the 2nd tercile. Lastly, the amount of sac shrinkage, expressed in absolute values or in percentages of baseline AAA volumes, was positively correlated with baseline SUVmax (p = 0.001 for both). A low pre-EVAR FDG uptake and increased AAA FDG uptake at 6 months are associated with reduced sac shrinkage. This sequential FDG-PET pattern is similar to that already shown to accompany growth phases of medically treated AAA. (orig.)

Comparative Analyses of Nonpathogenic, Opportunistic, and Totally Pathogenic Mycobacteria Reveal Genomic and Biochemical Variabilities and Highlight the Survival Attributes of Mycobacterium tuberculosis

Science.gov (United States)

Singh, Yadvir; Kohli, Sakshi; Ahmad, Javeed; Ehtesham, Nasreen Z.; Tyagi, Anil K.

2014-01-01

ABSTRACT Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition. Our comparative genome size analysis of 44 mycobacterial genomes revealed that the nonpathogenic (NP) genomes were bigger than those of opportunistic (OP) or totally pathogenic (TP) mycobacteria, with the TP genomes being smaller yet variable in size—their genomic plasticity reflected their ability to evolve and survive under various environmental conditions. From the 44 mycobacterial species, 13 species, representing TP, OP, and NP, were selected for genomic-relatedness analyses. Analysis of homologous protein-coding genes shared between Mycobacterium indicus pranii (NP), Mycobacterium intracellulare ATCC 13950 (OP), and Mycobacterium tuberculosis H37Rv (TP) revealed that 4,995 (i.e., ~95%) M. indicaus pranii proteins have homology with M. intracellulare, whereas the homologies among M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively. Comparative metabolic pathway analyses of TP/OP/NP mycobacteria showed enzymatic plasticity between M. indicus pranii (NP) and M. intracellulare ATCC 13950 (OP), Mycobacterium avium 104 (OP), and M. tuberculosis H37Rv (TP). Mycobacterium tuberculosis seems to have acquired novel alternate pathways with possible roles in metabolism, host-pathogen interactions, virulence, and intracellular survival, and by implication some of these could be potential drug targets. PMID:25370496

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages.

Science.gov (United States)

Marandino, Ana; Tomás, Gonzalo; Panzera, Yanina; Greif, Gonzalo; Parodi-Talice, Adriana; Hernández, Martín; Techera, Claudia; Hernández, Diego; Pérez, Ruben

2017-10-01

Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.

Science.gov (United States)

Brown, Christopher T; Sharon, Itai; Thomas, Brian C; Castelle, Cindy J; Morowitz, Michael J; Banfield, Jillian F

2013-12-17

The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored. To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences

The genome of the Erwinia amylovora phage PhiEaH1 reveals greater diversity and broadens the applicability of phages for the treatment of fire blight.

Science.gov (United States)

Meczker, Katalin; Dömötör, Dóra; Vass, János; Rákhely, Gábor; Schneider, György; Kovács, Tamás

2014-01-01

The enterobacterium Erwinia amylovora is the causal agent of fire blight. This study presents the analysis of the complete genome of phage PhiEaH1, isolated from the soil surrounding an E. amylovora-infected apple tree in Hungary. Its genome is 218 kb in size, containing 244 ORFs. PhiEaH1 is the second E. amylovora infecting phage from the Siphoviridae family whose complete genome sequence was determined. Beside PhiEaH2, PhiEaH1 is the other active component of Erwiphage, the first bacteriophage-based pesticide on the market against E. amylovora. Comparative genome analysis in this study has revealed that PhiEaH1 not only differs from the 10 formerly sequenced E. amylovora bacteriophages belonging to other phage families, but also from PhiEaH2. Sequencing of more Siphoviridae phage genomes might reveal further diversity, providing opportunities for the development of even more effective biological control agents, phage cocktails against Erwinia fire blight disease of commercial fruit crops.

Measurement with corrugated tubes of early-age autogenous shrinkage of cement-based material

DEFF Research Database (Denmark)

Tian, Qian; Jensen, Ole Mejlhede

2009-01-01

The use of a special corrugated mould enables transformation of volume strain into horizontal, linear strain measurement in the fluid stage. This allows continuous measurement of the autogenous shrinkage of cement-based materials since casting, and also effectively eliminates unwanted influence...

ISTA-Net: Iterative Shrinkage-Thresholding Algorithm Inspired Deep Network for Image Compressive Sensing

KAUST Repository

Zhang, Jian; Ghanem, Bernard

2017-01-01

and the performance/speed of network-based ones. We propose a novel structured deep network, dubbed ISTA-Net, which is inspired by the Iterative Shrinkage-Thresholding Algorithm (ISTA) for optimizing a general $l_1$ norm CS reconstruction model. ISTA-Net essentially

Imaging mass spectrometry and genome mining reveal highly antifungal virulence factor of mushroom soft rot pathogen.

Science.gov (United States)

Graupner, Katharina; Scherlach, Kirstin; Bretschneider, Tom; Lackner, Gerald; Roth, Martin; Gross, Harald; Hertweck, Christian

2012-12-21

Caught in the act: imaging mass spectrometry of a button mushroom infected with the soft rot pathogen Janthinobacterium agaricidamnosum in conjunction with genome mining revealed jagaricin as a highly antifungal virulence factor that is not produced under standard cultivation conditions. The structure of jagaricin was rigorously elucidated by a combination of physicochemical analyses, chemical derivatization, and bioinformatics. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Report D : self-consolidating concrete (SCC) for infrastructure elements - creep, shrinkage and abrasion resistance.

Science.gov (United States)

2012-08-01

Concrete specimens were fabricated for shrinkage, creep, and abrasion resistance : testing. Variations of self-consolidating concrete (SCC) and conventional concrete were : all tested. The results were compared to previous similar testing programs an...

Genome-size Variation in Switchgrass (Panicum virgatum: Flow Cytometry and Cytology Reveal Rampant Aneuploidy

Directory of Open Access Journals (Sweden)

Denise E. Costich

2010-11-01

Full Text Available Switchgrass ( L., a native perennial dominant of the prairies of North America, has been targeted as a model herbaceous species for biofeedstock development. A flow-cytometric survey of a core set of 11 primarily upland polyploid switchgrass accessions indicated that there was considerable variation in genome size within each accession, particularly at the octoploid (2 = 8 = 72 chromosome ploidy level. Highly variable chromosome counts in mitotic cell preparations indicated that aneuploidy was more common in octoploids (86.3% than tetraploids (23.2%. Furthermore, the incidence of hyper- versus hypoaneuploidy is equivalent in tetraploids. This is clearly not the case in octoploids, where close to 90% of the aneuploid counts are lower than the euploid number. Cytogenetic investigation using fluorescent in situ hybridization (FISH revealed an unexpected degree of variation in chromosome structure underlying the apparent genomic instability of this species. These results indicate that rapid advances in the breeding of polyploid biofuel feedstocks, based on the molecular-genetic dissection of biomass characteristics and yield, will be predicated on the continual improvement of our understanding of the cytogenetics of these species.

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

Science.gov (United States)

Bos, Kirsten I.; Harkins, Kelly M.; Herbig, Alexander; Coscolla, Mireia; Weber, Nico; Comas, Iñaki; Forrest, Stephen A.; Bryant, Josephine M.; Harris, Simon R.; Schuenemann, Verena J.; Campbell, Tessa J.; Majander, Kerrtu; Wilbur, Alicia K.; Guichon, Ricardo A.; Wolfe Steadman, Dawnie L.; Cook, Della Collins; Niemann, Stefan; Behr, Marcel A.; Zumarraga, Martin; Bastida, Ricardo; Huson, Daniel; Nieselt, Kay; Young, Douglas; Parkhill, Julian; Buikstra, Jane E.; Gagneux, Sebastien; Stone, Anne C.; Krause, Johannes

2015-01-01

Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean. PMID:25141181

Gain and loss of phototrophic genes revealed by comparison of two Citromicrobium bacterial genomes.

Directory of Open Access Journals (Sweden)

Qiang Zheng

Full Text Available Proteobacteria are thought to have diverged from a phototrophic ancestor, according to the scattered distribution of phototrophy throughout the proteobacterial clade, and so the occurrence of numerous closely related phototrophic and chemotrophic microorganisms may be the result of the loss of genes for phototrophy. A widespread form of bacterial phototrophy is based on the photochemical reaction center, encoded by puf and puh operons that typically are in a 'photosynthesis gene cluster' (abbreviated as the PGC with pigment biosynthesis genes. Comparison of two closely related Citromicrobial genomes (98.1% sequence identity of complete 16S rRNA genes, Citromicrobium sp. JL354, which contains two copies of reaction center genes, and Citromicrobium strain JLT1363, which is chemotrophic, revealed evidence for the loss of phototrophic genes. However, evidence of horizontal gene transfer was found in these two bacterial genomes. An incomplete PGC (pufLMC-puhCBA in strain JL354 was located within an integrating conjugative element, which indicates a potential mechanism for the horizontal transfer of genes for phototrophy.

The effect of mold surface topography on plastic parat in-process shrinkage in injection molding

DEFF Research Database (Denmark)

Arlø, Uffe Rolf; Hansen, Hans Nørgaard; Kjær, Erik Michael

2003-01-01

An experimental study of the effect of mold surface roughness on in-process in-flow linear part shrinkage in injection molding has been carried out. The investigation is based on an experimental two-cavity tool, where the cavities have different surface topographies, but are otherwise identical....... The study has been carried out for typical commercial polystyrene and polypropylene grades. The relationship between mold surface topography and linear shrinkage has been investigated with an experimental two-cavity mold producing simple rectangular parts with the nominal dimensions 1 x 25 x 50 mm (see...... figure 1). The cavities have different surface topographies on one side, but are otherwise identical (see discussion of other contribution factors)....

Early age shrinkage pattern of concrete on replacement of fine aggregate with industrial by-product

Directory of Open Access Journals (Sweden)

R.K. Mishra

2016-10-01

Full Text Available This is an experimental work carried out to investigate early age shrinkage pattern of concrete, prepared, on 50% replacement of industrial by-product (like pond ash and granulated blast furnace slag as fine aggregate using OPC, PPC and PSC as a binder. This is to observe the effect of pond ash and slag as they are having some cementitious properties and effect of cement type is also discussed. All the mixes were prepared keeping in view of pumpable concrete without any super plasticizers. Higher shrinkage value indicates the presence of more bleed water or internal moisture. It is concluded that slag is the best option for fine aggregate replacement for concrete making and durable structure.

Polymerization shrinkage of different types of composite resins and microleakage with and without liner in class II cavities.

Science.gov (United States)

Karaman, E; Ozgunaltay, G

2014-01-01

To determine the volumetric polymerization shrinkage of four different types of composite resin and to evaluate microleakage of these materials in class II (MOD) cavities with and without a resin-modified glass ionomer cement (RMGIC) liner, in vitro. One hundred twenty-eight extracted human upper premolar teeth were used. After the teeth were divided into eight groups (n=16), standardized MOD cavities were prepared. Then the teeth were restored with different resin composites (Filtek Supreme XT, Filtek P 60, Filtek Silorane, Filtek Z 250) with and without a RMGIC liner (Vitrebond). The restorations were finished and polished after 24 hours. Following thermocycling, the teeth were immersed in 0.5% basic fuchsin for 24 hours, then midsagitally sectioned in a mesiodistal plane and examined for microleakage using a stereomicroscope. The volumetric polymerization shrinkage of materials was measured using a video imaging device (Acuvol, Bisco, Inc). Data were statistically analyzed with Kruskal-Wallis and Mann-Whitney U-tests. All teeth showed microleakage, but placement of RMGIC liner reduced microleakage. No statistically significant differences were found in microleakage between the teeth restored without RMGIC liner (p>0.05). Filtek Silorane showed significantly less volumetric polymerization shrinkage than the methacrylate-based composite resins (pcomposite resin restorations resulted in reduced microleakage. The volumetric polymerization shrinkage was least with the silorane-based composite.

A parts list for fungal cellulosomes revealed by comparative genomics

Energy Technology Data Exchange (ETDEWEB)

Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K.; Solomon, Kevin V.; de Groot, Randall; Kuo, Alan; Mondo, Stephen J.; Salamov, Asaf A.; LaButti, Kurt; Zhao, Zhiying; Chiniquy, Jennifer; Barry, Kerrie; Brewer, Heather M.; Purvine, Samuel O.; Wright, Aaron T.; Hainaut, Matthieu; Boxma, Brigitte; van Alen, Theo; Hackstein, Johannes H. P.; Henrissat, Bernard; Baker, Scott E.; Grigoriev, Igor V.; O' Malley, Michelle A.

2017-05-26

Cellulosomes are large, multi-protein complexes that tether plant biomass degrading enzymes together for improved hydrolysis1. These complexes were first described in anaerobic bacteria where species specific dockerin domains mediate assembly of enzymes onto complementary cohesin motifs interspersed within non-catalytic protein scaffolds1. The versatile protein assembly mechanism conferred by the bacterial cohesin-dockerin interaction is now a standard design principle for synthetic protein-scale pathways2,3. For decades, analogous structures have been reported in the early branching anaerobic fungi, which are known to assemble by sequence divergent non-catalytic dockerin domains (NCDD)4. However, the enzyme components, modular assembly mechanism, and functional role of fungal cellulosomes remain unknown5,6. Here, we describe the comprehensive set of proteins critical to fungal cellulosome assembly, including novel, conserved scaffolding proteins unique to the Neocallimastigomycota. High quality genomes of the anaerobic fungi Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis were assembled with long-read, single molecule technology to overcome their repeat-richness and extremely low GC content. Genomic analysis coupled with proteomic validation revealed an average 320 NCDD-containing proteins per fungal strain that were overwhelmingly carbohydrate active enzymes (CAZymes), with 95 large fungal scaffoldins identified across 4 genera that contain a conserved amino acid sequence repeat that binds to NCDDs. Fungal dockerin and scaffoldin domains have no similarity to their bacterial counterparts, yet several catalytic domains originated via horizontal gene transfer with gut bacteria. Though many catalytic domains are shared with bacteria, the biocatalytic activity of anaerobic fungi is expanded by the inclusion of GH3, GH6, and GH45 enzymes in the enzyme complexes. Collectively, these findings suggest that the fungal cellulosome is an evolutionarily

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

KAUST Repository

Jones, Eppie R.

2015-11-16

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Upper Palaeolithic genomes reveal deep roots of modern Eurasians

KAUST Repository

Jones, Eppie R.; Gonzalez-Fortes, Gloria; Connell, Sarah; Siska, Veronika; Eriksson, Anders; Martiniano, Rui; McLaughlin, Russell L.; Gallego Llorente, Marcos; Cassidy, Lara M.; Gamba, Cristina; Meshveliani, Tengiz; Bar-Yosef, Ofer; Mü ller, Werner; Belfer-Cohen, Anna; Matskevich, Zinovi; Jakeli, Nino; Higham, Thomas F. G.; Currat, Mathias; Lordkipanidze, David; Hofreiter, Michael; Manica, Andrea; Pinhasi, Ron; Bradley, Daniel G.

2015-01-01

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Restrained shrinkage experiments on coated particle fuel compacts in the temperature range 600-1200 deg C

International Nuclear Information System (INIS)

Blackstone, R.; Veringa, H.J.; Loelgen, R.

1976-05-01

Information on irradiation induced creep in reactor graphite and in fuel compact material is an essential ingredient in the design of any reactor core layout, because the creep plasticity of these materials diminishes the stresses which are built up in the fuel element during reactor operation. The restrained shrinkage method in which the shrinkage of a dumbbell shaped creep specimen is restrained by a graphite material which shows less irradiation shrinkage, offers a good possibility of performing a large series of tensile creep experiments in a limited irradiation volume. The irradiations, evaluations and the results of a series of restrained shrinkage experiments in which six different materials were tested, of which five were dummy coated particle compacts and one pure matrix material are described and discussed. These materials were irradiated in the High Flux Reactor of the Euratom Joint Research Centre in Petten/Netherlands. The irradiations were performed in three successive capsules at irradiation temperatures of 600 deg C, 900 deg C, 1050 deg C and 1200 deg C up to a neutron fluence of maximum 3x10 21 n.cm 2 (DNE). The post-irradiation examinations yielded plastic strains up to 2,3%, and values for the radiation creep coefficient were calculated, ranging from 4 to 8.10 -12 at 600 deg C and 8 to 30.10 -12 at 1200 deg C always given per dyn.cm -2 tensile stresses and per 10 20 n.cm -2 fluence units. Generally it was found that the creep behavior of these materials and the temperature dependence of the creep process could be compared with those for normal reactor graphites

Assessment and prediction of drying shrinkage cracking in bonded mortar overlays

Energy Technology Data Exchange (ETDEWEB)

Beushausen, Hans, E-mail: hans.beushausen@uct.ac.za; Chilwesa, Masuzyo

2013-11-15

Restrained drying shrinkage cracking was investigated on composite beams consisting of substrate concrete and bonded mortar overlays, and compared to the performance of the same mortars when subjected to the ring test. Stress development and cracking in the composite specimens were analytically modeled and predicted based on the measurement of relevant time-dependent material properties such as drying shrinkage, elastic modulus, tensile relaxation and tensile strength. Overlay cracking in the composite beams could be very well predicted with the analytical model. The ring test provided a useful qualitative comparison of the cracking performance of the mortars. The duration of curing was found to only have a minor influence on crack development. This was ascribed to the fact that prolonged curing has a beneficial effect on tensile strength at the onset of stress development, but is in the same time not beneficial to the values of tensile relaxation and elastic modulus. -- Highlights: •Parameter study on material characteristics influencing overlay cracking. •Analytical model gives good quantitative indication of overlay cracking. •Ring test presents good qualitative indication of overlay cracking. •Curing duration has little effect on overlay cracking.

Assessment and prediction of drying shrinkage cracking in bonded mortar overlays

International Nuclear Information System (INIS)

Beushausen, Hans; Chilwesa, Masuzyo

2013-01-01

Restrained drying shrinkage cracking was investigated on composite beams consisting of substrate concrete and bonded mortar overlays, and compared to the performance of the same mortars when subjected to the ring test. Stress development and cracking in the composite specimens were analytically modeled and predicted based on the measurement of relevant time-dependent material properties such as drying shrinkage, elastic modulus, tensile relaxation and tensile strength. Overlay cracking in the composite beams could be very well predicted with the analytical model. The ring test provided a useful qualitative comparison of the cracking performance of the mortars. The duration of curing was found to only have a minor influence on crack development. This was ascribed to the fact that prolonged curing has a beneficial effect on tensile strength at the onset of stress development, but is in the same time not beneficial to the values of tensile relaxation and elastic modulus. -- Highlights: •Parameter study on material characteristics influencing overlay cracking. •Analytical model gives good quantitative indication of overlay cracking. •Ring test presents good qualitative indication of overlay cracking. •Curing duration has little effect on overlay cracking

Predicting the drying shrinkage behavior of high strength portland cement mortar under the combined influence of fine aggregate and steel micro fiber

International Nuclear Information System (INIS)

Li, Zhengqi

2017-01-01

The workability, 28-day compressive strength and free drying shrinkage of a very high strength (121-142 MPa) steel micro fiber reinforced portland cement mortar were studied under a combined influence of fine aggregate content and fiber content. The test results showed that an increase in the fine aggregate content resulted in decreases in the workability, 28-day compressive strength and drying shrinkage of mortar at a fixed fiber content. An increase in the fiber content resulted in decreases in the workability and drying shrinkage of mortar, but an increase in the 28-day compressive strength of mortar at a fixed fine aggregate content. The modified Gardner model most accurately predicted the drying shrinkage development of the high strength mortars, followed by the Ross model and the ACI 209R-92 model. The Gardner model gave the least accurate prediction for it was developed based on a database of normal strength concrete. [es

Predicting the drying shrinkage behavior of high strength portland cement mortar under the combined influence of fine aggregate and steel micro fiber

Directory of Open Access Journals (Sweden)

Zhengqi Li

2017-03-01

Full Text Available The workability, 28-day compressive strength and free drying shrinkage of a very high strength (121-142 MPa steel micro fiber reinforced portland cement mortar were studied under a combined influence of fine aggregate content and fiber content. The test results showed that an increase in the fine aggregate content resulted in decreases in the workability, 28-day compressive strength and drying shrinkage of mortar at a fixed fiber content. An increase in the fiber content resulted in decreases in the workability and drying shrinkage of mortar, but an increase in the 28-day compressive strength of mortar at a fixed fine aggregate content. The modified Gardner model most accurately predicted the drying shrinkage development of the high strength mortars, followed by the Ross model and the ACI 209R-92 model. The Gardner model gave the least accurate prediction for it was developed based on a database of normal strength concrete.

Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Science.gov (United States)

Li, Cai; Zhang, Yong; Li, Jianwen; Kong, Lesheng; Hu, Haofu; Pan, Hailin; Xu, Luohao; Deng, Yuan; Li, Qiye; Jin, Lijun; Yu, Hao; Chen, Yan; Liu, Binghang; Yang, Linfeng; Liu, Shiping; Zhang, Yan; Lang, Yongshan; Xia, Jinquan; He, Weiming; Shi, Qiong; Subramanian, Sankar; Millar, Craig D; Meader, Stephen; Rands, Chris M; Fujita, Matthew K; Greenwold, Matthew J; Castoe, Todd A; Pollock, David D; Gu, Wanjun; Nam, Kiwoong; Ellegren, Hans; Ho, Simon Yw; Burt, David W; Ponting, Chris P; Jarvis, Erich D; Gilbert, M Thomas P; Yang, Huanming; Wang, Jian; Lambert, David M; Wang, Jun; Zhang, Guojie

2014-01-01

Penguins are flightless aquatic birds widely distributed in the Southern Hemisphere. The distinctive morphological and physiological features of penguins allow them to live an aquatic life, and some of them have successfully adapted to the hostile environments in Antarctica. To study the phylogenetic and population history of penguins and the molecular basis of their adaptations to Antarctica, we sequenced the genomes of the two Antarctic dwelling penguin species, the Adélie penguin [Pygoscelis adeliae] and emperor penguin [Aptenodytes forsteri]. Phylogenetic dating suggests that early penguins arose ~60 million years ago, coinciding with a period of global warming. Analysis of effective population sizes reveals that the two penguin species experienced population expansions from ~1 million years ago to ~100 thousand years ago, but responded differently to the climatic cooling of the last glacial period. Comparative genomic analyses with other available avian genomes identified molecular changes in genes related to epidermal structure, phototransduction, lipid metabolism, and forelimb morphology. Our sequencing and initial analyses of the first two penguin genomes provide insights into the timing of penguin origin, fluctuations in effective population sizes of the two penguin species over the past 10 million years, and the potential associations between these biological patterns and global climate change. The molecular changes compared with other avian genomes reflect both shared and diverse adaptations of the two penguin species to the Antarctic environment.

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

Science.gov (United States)

Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

2015-10-01

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Genomic Insights and Its Comparative Analysis with Yersinia enterocolitica Reveals the Potential Virulence Determinants and Further Pathogenicity for Foodborne Outbreaks.

Science.gov (United States)

Gnanasekaran, Gopalsamy; Na, Eun Jung; Chung, Han Young; Kim, Suyeon; Kim, You-Tae; Kwak, Woori; Kim, Heebal; Ryu, Sangryeol; Choi, Sang Ho; Lee, Ju-Hoon

2017-02-28

Yersinia enterocolitica is a well-known foodborne pathogen causing gastrointestinal infections worldwide. The strain Y. enterocolitica FORC_002 was isolated from the gill of flatfish (plaice) and its genome was sequenced. The genomic DNA consists of 4,837,317 bp with a GC content of 47.1%, and is predicted to contain 4,221 open reading frames, 81 tRNA genes, and 26 rRNA genes. Interestingly, genomic analysis revealed pathogenesis and host immune evasion-associated genes encoding guanylate cyclase (Yst), invasin (Ail and Inv), outer membrane protein (Yops), autotransporter adhesin A (YadA), RTX-like toxins, and a type III secretion system. In particular, guanylate cyclase is a heat-stable enterotoxin causing Yersinia -associated diarrhea, and RTX-like toxins are responsible for attachment to integrin on the target cell for cytotoxic action. This genome can be used to identify virulence factors that can be applied for the development of novel biomarkers for the rapid detection of this pathogen in foods.

Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.

Science.gov (United States)

Yang, J; Liu, G; Zhao, N; Chen, S; Liu, D; Ma, W; Hu, Z; Zhang, M

2016-05-01

The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

The Process of Shrinkage as a Challenge to Urban Governance

Directory of Open Access Journals (Sweden)

Stryjakiewicz Tadeusz

2016-06-01

Full Text Available For many decades most researchers, planners and local authorities have been focusing almost exclusively on urban growth and its socio-economic and spatial consequences. However, in the current debate concerning the future of cities and regions in Europe the process of their shrinkage starts to attract more attention. In the conditions of a declining population, urban governance is an important challenge for local authorities, being usually much more difficult than during the periods of population growth.

Influence of inert fillers on shrinkage cracking of meta-kaolin geo-polymers

International Nuclear Information System (INIS)

Kuenzel, C.; Boccaccini, A.R.

2012-01-01

Geo-polymers contain a network of tetrahedral coordinated aluminate and silicate, and are potential materials to immobilize/encapsulate nuclear wastes. They can exhibit shrinkage cracking when water is removed by drying, and in order to use geo-polymers for waste encapsulation this effect needs to be investigated and controlled. In this study, six different fillers were mixed with meta-kaolin and sodium silicate solution at high pH to form geo-polymers, and the influence of filler addition on mechanical properties has been determined. The fillers used were Fe 2 O 3 , Al 2 O 3 , CaCO 3 , sand, glass and rubber and these do not react during geo-polymerisation reactions. Geo-polymers were prepared containing 30 weight percent of filler. The mechanical properties of the geo-polymers were influenced by the type of filler, with low density fillers increasing mortar viscosity. Geo-polymer samples containing fine filler particles exhibited shrinkage cracking on drying. This was not observed when coarser particles were added and these samples also had significantly improved mechanical properties. (authors)

Autogenous shrinkage in high-performance cement paste: An evaluation of basic mechanisms

International Nuclear Information System (INIS)

Lura, Pietro; Jensen, Ole Mejlhede; Breugel, Klaas van

2003-01-01

In this paper, various mechanisms suggested to cause autogenous shrinkage are presented. The mechanisms are evaluated from the point of view of their soundness and applicability to quantitative modeling of autogenous shrinkage. The capillary tension approach is advantageous, because it has a sound mechanical and thermodynamical basis. Furthermore, this mechanism is easily applicable in a numerical model when dealing with a continuously changing microstructure. In order to test the numerical model, autogenous deformation and internal relative humidity (RH) of a Portland cement paste were measured during the first week of hardening. The isothermal heat evolution was also recorded to monitor the progress of hydration and the elastic modulus in compression was measured. RH change, degree of hydration and elastic modulus were used as input data for the calculation of autogenous deformation based on the capillary tension approach. Because a part of the RH drop in the cement paste is due to dissolved salts in the pore solution, a method is suggested to separate this effect from self-desiccation and to calculate the actual stress in the pore fluid associated with menisci formation

Creep and drying shrinkage of high performance concrete for the skyway structures of the new San Francisco-Oakland Bay Bridge and cement paste

Science.gov (United States)

2011-03-01

The objective of this study was to determine the influence of admixtures on long term drying shrinkage and creep of high : strength concrete (HSC). Creep and shrinkage of the mix utilized in segments of the Skyway Structure of the San : Francisco-Oak...

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

Directory of Open Access Journals (Sweden)

McGuire Patrick E

2010-12-01

Full Text Available Abstract Background A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. Results Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. Conclusions In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large

Hydro-mechanical coupling in non-saturated medium with phase change. Application to desiccation shrinkage

International Nuclear Information System (INIS)

Lassabatere, Thierry

1994-01-01

The target of this research is to set up a unified and coherent working frame based upon the rigorous principles of thermodynamics and making it possible to model a large class of physical phenomena acting in unsaturated porous media, as well as the related interactions with the mechanical state of the structures. This class corresponds to reactive phenomena among which one finds the phase change (desiccation) for which the whole of its subsequent actions (creep but essentially shrinkage) is modelled and which will be treated as a specific application example. The first chapter recalls the bases of the adopted description of the porous medium as well as the global thermodynamical frame which underlays the whole modelling. Chapter II deals with the mainly new formulation and the identification of a non linear elastic constitutive law of the medium involved. Various reflexion elements related to the microscopic behaviours of the components and to experiments have orientated the model towards some more limitative hypotheses making it possible to have a complete and explicit determination of a law for the macroscopic behaviour. Chapter IV and V are examples of application: chapter IV studies the problem of shrinkage and creep in a coupled linear elastic behaviour. Chapter V is limited to the case of shrinkage treated by a numerical application of the whole non-linear elastic model. The results obtained are in good agreement with the corresponding experiments. (author) [fr

Influence of vertical holes on creep and shrinkage of railway prestressed concrete sleepers

Science.gov (United States)

Li, Dan; Ngamkhanong, Chayut; Kaewunruen, Sakdirat

2017-09-01

Railway prestressed concrete sleepers (or railroad ties) must successfully perform two critical duties: first, to carry wheel loads from the rails to the ground; and second, to secure rail gauge for dynamic safe movements of trains. The second duty is often fouled by inappropriate design of the time-dependent behaviors due to their creep, shrinkage and elastic shortening responses of the materials. In addition, the concrete sleepers are often modified on construction sites to fit in other systems such as cables, signalling gears, drainage pipes, etc. Accordingly, this study is the world first to investigate creep and shrinkage effects on the railway prestressed concrete sleepers with vertical holes. This paper will highlight constitutive models of concrete materials within the railway sleepers under different environmental conditions over time. It will present a comparative investigation using a variety of methods to evaluate shortening effects in railway prestressed concrete sleepers. The outcome of this study will improve material design, which is very critical to the durability of railway track components.

Fissure formation in coke. 2: Effect of heating rate, shrinkage and coke strength

Energy Technology Data Exchange (ETDEWEB)

D.R. Jenkins; M.R. Mahoney [CSIRO, North Ryde, NSW (Australia). Mathematical and Information Sciences

2010-07-15

We investigate the effects of the heating rate, coke shrinkage and coke breakage strength upon the fissure pattern developed in a coke oven charge during carbonisation. This is done principally using a mechanistic model of the formation of fissures, which considers them to be an array of equally spaced fissures, whose depth follows a 'period doubling' pattern based upon the time history of the fissures. The model results are compared with pilot scale coke oven experiments. The results show that the effect of heating rate on the fissure pattern is different to the effect of coke shrinkage, while the effect of coke breakage strength on the pattern is less pronounced. The results can be seen in both the shape and size of resulting coke lumps after stabilisation. The approach gives the opportunity to consider means of controlling the carbonisation process in order to tune the size of the coke lumps produced. 7 refs., 18 figs., 4 tabs.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice.

Science.gov (United States)

Brozynska, Marta; Copetti, Dario; Furtado, Agnelo; Wing, Rod A; Crayn, Darren; Fox, Glen; Ishikawa, Ryuji; Henry, Robert J

2017-06-01

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Minimal volume regulation after shrinkage of red blood cells from five species of reptiles

DEFF Research Database (Denmark)

Kristensen, Karina; Berenbrink, Michael; Koldkjær, Pia

2008-01-01

Red blood cells (RBCs) from most vertebrates restore volume upon hypertonic shrinkage and the mechanisms underlying this regulatory volume increase (RVI) have been studied extensively in these cells. Despite the phylogenetically interesting position of reptiles, very little is known about their red...... cell function. The present study demonstrates that oxygenated RBCs in all major groups of reptiles exhibit no or a very reduced RVI upon ~ 25% calculated hyperosmotic shrinkage. Thus, RBCs from the snakes Crotalus durissus and Python regius, the turtle Trachemys scripta and the alligator Alligator...... was not characterized. It seems, therefore, that the RVI response based on NHE activation was lost among the early sauropsids that gave rise to modern reptiles and birds, while it was retained in mammals. An RVI response has then reappeared in birds, but based on activation of the NKCC. Alternatively, the absence...

Ant-infecting Ophiocordyceps genomes reveal a high diversity of potential behavioral manipulation genes and a possible major role for enterotoxins

NARCIS (Netherlands)

De Bekker, Charissa; Ohm, Robin A.; Evans, Harry C.; Brachmann, Andreas; Hughes, David P

2017-01-01

Much can be gained from revealing the mechanisms fungal entomopathogens employ. Especially intriguing are fungal parasites that manipulate insect behavior because, presumably, they secrete a wealth of bioactive compounds. To gain more insight into their strategies, we compared the genomes of five

Effect of Addition of A Marble Dust on Drying Shrinkage Cracks of Cement Mortar Reinforced with Various Fibers

Directory of Open Access Journals (Sweden)

Basim Thabit Al-Khafaji

2017-05-01

Full Text Available This investigation is conducted to study the effect of addition of marble powder (marble dust and different fibers on drying shrinkage cracks and some properties of fibers reinforcment cement mortar. Steel molds having a trapezoidal section, and the end restrained at square shape with( 2.7 meter at length are used to study restrained drying shrinkage of cement mortar. Specimens of ( compressive .flextural. splitting strength were cast. The admixture (marble dust was used to replacie weight of cement with three levels of (4%, 8% and 16% and the fiber hemp and sisal fiber were added for all mixes with proportion by volum of cement . All specimens were cured for (14 days. Average of three results was taken for any test of compressive, tensil and flextural strength. The experimental results showed that the adding of this admixture(marble dust cause adelay in a formation of cracks predicted from a drying shrinkage ,decreases of its width , and hence increases of (compressive, splitting tensil and flextural strength at levels of (4%, and 8%. Thus there is a the positive effect when fiberes added for all mixes of cement mortar with addition of (marble dust. All The admixtures (marble dust and fibers have the obvious visible effect in the delay of the information of shrinkage cracks and the decrease of its width as Compared to the cement mortar mixes when marble dust added a alone.

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1

KAUST Repository

Guan, Yue

2017-05-11

Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea. Functional annotation of the MSBL1 single cell amplified genomes (SAGs) also revealed a complete corrinoid-dependent methyl-transfer pathway suggesting that members of MSBL1 may possibly be capable of synthesizing Pyl and metabolizing methylated amines. This article is protected by copyright. All rights reserved.

Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1

KAUST Repository

Guan, Yue; Haroon, Mohamed; Alam, Intikhab; Ferry, James G.; Stingl, Ulrich

2017-01-01

Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea. Functional annotation of the MSBL1 single cell amplified genomes (SAGs) also revealed a complete corrinoid-dependent methyl-transfer pathway suggesting that members of MSBL1 may possibly be capable of synthesizing Pyl and metabolizing methylated amines. This article is protected by copyright. All rights reserved.

Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements.

Science.gov (United States)

Laurie, John D; Ali, Shawkat; Linning, Rob; Mannhaupt, Gertrud; Wong, Philip; Güldener, Ulrich; Münsterkötter, Martin; Moore, Richard; Kahmann, Regine; Bakkeren, Guus; Schirawski, Jan

2012-05-01

Ustilago hordei is a biotrophic parasite of barley (Hordeum vulgare). After seedling infection, the fungus persists in the plant until head emergence when fungal spores develop and are released from sori formed at kernel positions. The 26.1-Mb U. hordei genome contains 7113 protein encoding genes with high synteny to the smaller genomes of the related, maize-infecting smut fungi Ustilago maydis and Sporisorium reilianum but has a larger repeat content that affected genome evolution at important loci, including mating-type and effector loci. The U. hordei genome encodes components involved in RNA interference and heterochromatin formation, normally involved in genome defense, that are lacking in the U. maydis genome due to clean excision events. These excision events were possibly a result of former presence of repetitive DNA and of an efficient homologous recombination system in U. maydis. We found evidence of repeat-induced point mutations in the genome of U. hordei, indicating that smut fungi use different strategies to counteract the deleterious effects of repetitive DNA. The complement of U. hordei effector genes is comparable to the other two smuts but reveals differences in family expansion and clustering. The availability of the genome sequence will facilitate the identification of genes responsible for virulence and evolution of smut fungi on their respective hosts.

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

KAUST Repository

Diez Benavente, Ernest

2017-09-18

The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.

Analysis of nuclear and organellar genomes of Plasmodium knowlesi in humans reveals ancient population structure and recent recombination among host-specific subpopulations

KAUST Repository

Diez Benavente, Ernest; Florez de Sessions, Paola; Moon, Robert W.; Holder, Anthony A.; Blackman, Michael J.; Roper, Cally; Drakeley, Christopher J.; Pain, Arnab; Sutherland, Colin J.; Hibberd, Martin L.; Campino, Susana; Clark, Taane G.

2017-01-01

The macaque parasite Plasmodium knowlesi is a significant concern in Malaysia where cases of human infection are increasing. Parasites infecting humans originate from genetically distinct subpopulations associated with the long-tailed (Macaca fascicularis (Mf)) or pig-tailed macaques (Macaca nemestrina (Mn)). We used a new high-quality reference genome to re-evaluate previously described subpopulations among human and macaque isolates from Malaysian-Borneo and Peninsular-Malaysia. Nuclear genomes were dimorphic, as expected, but new evidence of chromosomal-segment exchanges between subpopulations was found. A large segment on chromosome 8 originating from the Mn subpopulation and containing genes encoding proteins expressed in mosquito-borne parasite stages, was found in Mf genotypes. By contrast, non-recombining organelle genomes partitioned into 3 deeply branched lineages, unlinked with nuclear genomic dimorphism. Subpopulations which diverged in isolation have re-connected, possibly due to deforestation and disruption of wild macaque habitats. The resulting genomic mosaics reveal traits selected by host-vector-parasite interactions in a setting of ecological transition.

Ultra high performance concrete made with rice husk ash for reduced autogenous shrinkage

NARCIS (Netherlands)

Van Breugel, K.; Van Tuan, N.

2014-01-01

Ultra High Strength Concrete (UHPC) is generally made with low w/c mixtures and by adding silica fume. Low w/c mixtures, however, exhibit high autogenous shrinkage, while a high amount of silica fume increases the price of these mixtures. For designing ultra high strength mixtures with low

Autogenous shrinkage of Ducorit S5R ASTM C 1698-09 test method

DEFF Research Database (Denmark)

Damkilde, Lars

The report deals with experimental measurement of autogenous shrinkage of Ducorit S5R according to the test method ASTM C 1698-09. This test method measures the bulk strain of a sealed cementitious specimen, at constant temperature and not subjected to external forces, from the time of final...

Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites

Directory of Open Access Journals (Sweden)

Sibley L David

2005-12-01

Full Text Available Abstract Background The phylum Apicomplexa is an early-branching eukaryotic lineage that contains a number of important human and animal pathogens. Their complex life cycles and unique cytoskeletal features distinguish them from other model eukaryotes. Apicomplexans rely on actin-based motility for cell invasion, yet the regulation of this system remains largely unknown. Consequently, we focused our efforts on identifying actin-related proteins in the recently completed genomes of Toxoplasma gondii, Plasmodium spp., Cryptosporidium spp., and Theileria spp. Results Comparative genomic and phylogenetic studies of apicomplexan genomes reveals that most contain only a single conventional actin and yet they each have 8–10 additional actin-related proteins. Among these are a highly conserved Arp1 protein (likely part of a conserved dynactin complex, and Arp4 and Arp6 homologues (subunits of the chromatin-remodeling machinery. In contrast, apicomplexans lack canonical Arp2 or Arp3 proteins, suggesting they lost the Arp2/3 actin polymerization complex on their evolutionary path towards intracellular parasitism. Seven of these actin-like proteins (ALPs are novel to apicomplexans. They show no phylogenetic associations to the known Arp groups and likely serve functions specific to this important group of intracellular parasites. Conclusion The large diversity of actin-like proteins in apicomplexans suggests that the actin protein family has diverged to fulfill various roles in the unique biology of intracellular parasites. Conserved Arps likely participate in vesicular transport and gene expression, while apicomplexan-specific ALPs may control unique biological traits such as actin-based gliding motility.

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

Science.gov (United States)

Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

2015-05-19

Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest.

Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

Czech Academy of Sciences Publication Activity Database

Vu, G.T.H.; Schmutzer, T.; Bull, F.; Cao, H.X.; Fuchs, J.; Tran, T.D.; Jovtchev, G.; Pistrick, K.; Stein, N.; Pečinka, A.; Neumann, Pavel; Novák, Petr; Macas, Jiří; Dear, P.H.; Blattner, F.R.; Scholz, U.; Schubert, I.

2015-01-01

Roč. 8, č. 3 (2015) ISSN 1940-3372 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Genlisea * genome * repetitive sequences Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.509, year: 2015

Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

Directory of Open Access Journals (Sweden)

O'Brien Kimberly

2008-06-01

Full Text Available Abstract Background The Solanaceae family contains a number of important crop species including potato (Solanum tuberosum which is grown for its underground storage organ known as a tuber. Albeit the 4th most important food crop in the world, other than a collection of ~220,000 Expressed Sequence Tags, limited genomic sequence information is currently available for potato and advances in potato yield and nutrition content would be greatly assisted through access to a complete genome sequence. While morphologically diverse, Solanaceae species such as potato, tomato, pepper, and eggplant share not only genes but also gene order thereby permitting highly informative comparative genomic analyses. Results In this study, we report on analysis 89.9 Mb of potato genomic sequence representing 10.2% of the genome generated through end sequencing of a potato bacterial artificial chromosome (BAC clone library (87 Mb and sequencing of 22 potato BAC clones (2.9 Mb. The GC content of potato is very similar to Solanum lycopersicon (tomato and other dicotyledonous species yet distinct from the monocotyledonous grass species, Oryza sativa. Parallel analyses of repetitive sequences in potato and tomato revealed substantial differences in their abundance, 34.2% in potato versus 46.3% in tomato, which is consistent with the increased genome size per haploid genome of these two Solanum species. Specific classes and types of repetitive sequences were also differentially represented between these two species including a telomeric-related repetitive sequence, ribosomal DNA, and a number of unclassified repetitive sequences. Comparative analyses between tomato and potato at the gene level revealed a high level of conservation of gene content, genic feature, and gene order although discordances in synteny were observed. Conclusion Genomic level analyses of potato and tomato confirm that gene sequence and gene order are conserved between these solanaceous species and that

Chimpanzee genomic diversity reveals ancient admixture with bonobos

DEFF Research Database (Denmark)

de Manuel, Marc; Kuhlwilm, Martin; Frandsen, Peter

2016-01-01

Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor...

Significance of Shrinkage Induced Clamping Pressure in Fiber-Matrix Bonding in Cementitious Composite Materials

DEFF Research Database (Denmark)

Stang, Henrik

1996-01-01

used in high performance cementitious composite materials.Assuming a Coulomb type of friction on the fiber/matrix interface andusing typical values for the frictional coefficient it is shownthat the shrinkage induced clamping pressure could be one of the mostimportant factors determining the frictional...

The origin of early age expansions induced in cementitious materials containing shrinkage reducing admixtures

International Nuclear Information System (INIS)

Sant, Gaurav; Lothenbach, Barbara; Juilland, Patrick; Le Saout, Gwenn; Weiss, Jason; Scrivener, Karen

2011-01-01

Studies on the early-age shrinkage behavior of cement pastes, mortars, and concretes containing shrinkage reducing admixtures (SRAs) have indicated these mixtures frequently exhibit an expansion shortly after setting. While the magnitude of the expansion has been noted to be a function of the chemistry of the cement and the admixture dosage; the cause of the expansion is not clearly understood. This investigation uses measurements of autogenous deformation, X-ray diffraction, pore solution analysis, thermogravimetry, and scanning electron microscopy to study the early-age properties and describe the mechanism of the expansion in OPC pastes made with and without SRA. The composition of the pore solution indicates that the presence of the SRA increases the portlandite oversaturation level in solution which can result in higher crystallization stresses which could lead to an expansion. This observation is supported by deformation calculations for the systems examined.

Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function

Science.gov (United States)

Fuchsberger, Christian; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Chouraki, Vincent; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank B.; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H.-Erich; Kolcic, Ivana; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Endlich, Karlhans; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Giulianini, Franco; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Metzger, Marie; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid; Kardia, Sharon L. R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline C. M.; Hayward, Caroline; Ridker, Paul; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Goessling, Wolfram; Chasman, Daniel I.; Kao, W. H. Linda; Fox, Caroline S.

2012-01-01

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD. PMID:22479191

Genome-wide association and functional follow-up reveals new loci for kidney function.

Science.gov (United States)

Pattaro, Cristian; Köttgen, Anna; Teumer, Alexander; Garnaas, Maija; Böger, Carsten A; Fuchsberger, Christian; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; O'Seaghdha, Conall M; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D; Gierman, Hinco J; Feitosa, Mary; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Chouraki, Vincent; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank B; Demirkan, Ayse; Oostra, Ben A; de Andrade, Mariza; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H-Erich; Kolcic, Ivana; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Endlich, Karlhans; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Giulianini, Franco; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Metzger, Marie; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S; van Duijn, Cornelia M; Borecki, Ingrid; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline C M; Hayward, Caroline; Ridker, Paul; Parsa, Afshin; Bochud, Murielle; Heid, Iris M; Goessling, Wolfram; Chasman, Daniel I; Kao, W H Linda; Fox, Caroline S

2012-01-01

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.

Genome-wide association and functional follow-up reveals new loci for kidney function.

Directory of Open Access Journals (Sweden)

Cristian Pattaro

Full Text Available Chronic kidney disease (CKD is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR, the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche

Energy Technology Data Exchange (ETDEWEB)

Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R.; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G.; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L.; Bailey, Andrew M.; Billette, Christophe; Coutinho, Pedro M.; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hilden, Kristiina; Kues, Ursula; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lucas, Susan M.; Murat, Claude; Riley, Robert W.; Salamov, Asaf A.; Schmutz, Jeremy; Subramanian, Venkataramanan; Wosten, Han A. B.; Xu, Jianping; Eastwood, Daniel C.; Foster, Gary D.; Sonnenberg, Anton S. M.; Cullen, Dan; de Vries, Ronald P.; Lundell, Taina; Hibbett, David S.; Henrissat, Bernard; Burton, Kerry S.; Kerrigan, Richard W.; Challen, Michael P.; Grigoriev, Igor V.; Martin, Francis

2012-04-27

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the button mushroom forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche.

Science.gov (United States)

Morin, Emmanuelle; Kohler, Annegret; Baker, Adam R; Foulongne-Oriol, Marie; Lombard, Vincent; Nagy, Laszlo G; Ohm, Robin A; Patyshakuliyeva, Aleksandrina; Brun, Annick; Aerts, Andrea L; Bailey, Andrew M; Billette, Christophe; Coutinho, Pedro M; Deakin, Greg; Doddapaneni, Harshavardhan; Floudas, Dimitrios; Grimwood, Jane; Hildén, Kristiina; Kües, Ursula; Labutti, Kurt M; Lapidus, Alla; Lindquist, Erika A; Lucas, Susan M; Murat, Claude; Riley, Robert W; Salamov, Asaf A; Schmutz, Jeremy; Subramanian, Venkataramanan; Wösten, Han A B; Xu, Jianping; Eastwood, Daniel C; Foster, Gary D; Sonnenberg, Anton S M; Cullen, Dan; de Vries, Ronald P; Lundell, Taina; Hibbett, David S; Henrissat, Bernard; Burton, Kerry S; Kerrigan, Richard W; Challen, Michael P; Grigoriev, Igor V; Martin, Francis

2012-10-23

Agaricus bisporus is the model fungus for the adaptation, persistence, and growth in the humic-rich leaf-litter environment. Aside from its ecological role, A. bisporus has been an important component of the human diet for over 200 y and worldwide cultivation of the "button mushroom" forms a multibillion dollar industry. We present two A. bisporus genomes, their gene repertoires and transcript profiles on compost and during mushroom formation. The genomes encode a full repertoire of polysaccharide-degrading enzymes similar to that of wood-decayers. Comparative transcriptomics of mycelium grown on defined medium, casing-soil, and compost revealed genes encoding enzymes involved in xylan, cellulose, pectin, and protein degradation are more highly expressed in compost. The striking expansion of heme-thiolate peroxidases and β-etherases is distinctive from Agaricomycotina wood-decayers and suggests a broad attack on decaying lignin and related metabolites found in humic acid-rich environment. Similarly, up-regulation of these genes together with a lignolytic manganese peroxidase, multiple copper radical oxidases, and cytochrome P450s is consistent with challenges posed by complex humic-rich substrates. The gene repertoire and expression of hydrolytic enzymes in A. bisporus is substantially different from the taxonomically related ectomycorrhizal symbiont Laccaria bicolor. A common promoter motif was also identified in genes very highly expressed in humic-rich substrates. These observations reveal genetic and enzymatic mechanisms governing adaptation to the humic-rich ecological niche formed during plant degradation, further defining the critical role such fungi contribute to soil structure and carbon sequestration in terrestrial ecosystems. Genome sequence will expedite mushroom breeding for improved agronomic characteristics.

Phylogeny of Banana Streak Virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.).

Science.gov (United States)

Gayral, Philippe; Iskra-Caruana, Marie-Line

2009-07-01

Banana streak virus (BSV) is a plant dsDNA pararetrovirus (family Caulimoviridae, genus badnavirus). Although integration is not an essential step in the BSV replication cycle, the nuclear genome of banana (Musa sp.) contains BSV endogenous pararetrovirus sequences (BSV EPRVs). Some BSV EPRVs are infectious by reconstituting a functional viral genome. Recent studies revealed a large molecular diversity of episomal BSV viruses (i.e., nonintegrated) while others focused on BSV EPRV sequences only. In this study, the evolutionary history of badnavirus integration in banana was inferred from phylogenetic relationships between BSV and BSV EPRVs. The relative evolution rates and selective pressures (d(N)/d(S) ratio) were also compared between endogenous and episomal viral sequences. At least 27 recent independent integration events occurred after the divergence of three banana species, indicating that viral integration is a recent and frequent phenomenon. Relaxation of selective pressure on badnaviral sequences that experienced neutral evolution after integration in the plant genome was recorded. Additionally, a significant decrease (35%) in the EPRV evolution rate was observed compared to BSV, reflecting the difference in the evolution rate between episomal dsDNA viruses and plant genome. The comparison of our results with the evolution rate of the Musa genome and other reverse-transcribing viruses suggests that EPRVs play an active role in episomal BSV diversity and evolution.

Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

NARCIS (Netherlands)

Wichgers Schreur, Paul J.; Kortekaas, Jeroen

2016-01-01

The bunyavirus genome comprises a small (S), medium (M), and large (L) RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging.