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Sample records for gene sma region

  1. Acquisition through Horizontal Gene Transfer of Plasmid pSMA198 by Streptococcus macedonicus ACA-DC 198 Points towards the Dairy Origin of the Species

    Papadimitriou, Konstantinos; Anastasiou, Rania; Maistrou, Eleni; Plakas, Thomas; Papandreou, Nikos C.; Hamodrakas, Stavros J.; Ferreira, Stéphanie; Supply, Philip; Renault, Pierre; Pot, Bruno; Tsakalidou, Effie

    2015-01-01

    Background Streptococcus macedonicus is an intriguing streptococcal species whose most frequent source of isolation is fermented foods similarly to Streptococcus thermophilus. However, S. macedonicus is closely related to commensal opportunistic pathogens of the Streptococcus bovis/Streptococcus equinus complex. Methodology/Principal Findings We analyzed the pSMA198 plasmid isolated from the dairy strain Streptococcus macedonicus ACA-DC 198 in order to provide novel clues about the main ecological niche of this bacterium. pSMA198 belongs to the narrow host range pCI305/pWV02 family found primarily in lactococci and to the best of our knowledge it is the first such plasmid to be reported in streptococci. Comparative analysis of the pSMA198 sequence revealed a high degree of similarity with plasmids isolated from Lactococcus lactis strains deriving from milk or its products. Phylogenetic analysis of the pSMA198 Rep showed that the vast majority of closely related proteins derive from lactococcal dairy isolates. Additionally, cloning of the pSMA198 ori in L. lactis revealed a 100% stability of replication over 100 generations. Both pSMA198 and the chromosome of S. macedonicus exhibit a high percentage of potential pseudogenes, indicating that they have co-evolved under the same gene decay processes. We identified chromosomal regions in S. macedonicus that may have originated from pSMA198, also supporting a long co-existence of the two replicons. pSMA198 was also found in divergent biotypes of S. macedonicus and in strains isolated from dispersed geographic locations (e.g. Greece and Switzerland) showing that pSMA198’s acquisition is not a recent event. Conclusions/Significance Here we propose that S. macedonicus acquired plasmid pSMA198 from L. lactis via an ancestral genetic exchange event that took place most probably in milk or dairy products. We provide important evidence that point towards the dairy origin of this species. PMID:25584532

  2. Construction of a yeast artifical chromosome contig spanning the spinal muscular atrophy disease gene region

    Kleyn, P.W.; Wang, C.H.; Vitale, E.; Pan, J.; Ross, B.M.; Grunn, A.; Palmer, D.A.; Warburton, D.; Brzustowicz, L.M.; Gilliam, T.G. (New York State Psychiatric Institute, NY (United States)); Lien, L.L.; Kunkel, L.M. (Howard Hughes Medical Institute, Boston, MA (United States))

    1993-07-15

    The childhood spinal muscular atrophies (SMAs) are the most common, serious neuromuscular disorders of childhood second to Duchenne muscular dystrophy. A single locus for these disorders has been mapped by recombination events to a region of 0.7 centimorgan (range, 0.1-2.1 centimorgans) between loci D5S435 and MAP1B on chromosome 5q11.2-13.3. By using PCR amplification to screen yeast artificial chromosome (YAC) DNA pools and the PCR-vectorette method to amplify YAC ends, a YAC contig was constructed across the disease gene region. Nine walk steps identified 32 YACs, including a minimum of seven overlapping YAC clones (average size, 460 kb) that span the SMA region. The contig is characterized by a collection of 30 YAC-end sequence tag sites together with seven genetic markers. The entire YAC contig spans a minimum of 3.2 Mb; the SMA locus is confined to roughly half of this region. Microsatellite markers generated along the YAC contig segregate with the SMA locus in all families where the flanking markers (D5S435 and MAP1B) recombine. Construction of a YAC contig across the disease gene region is an essential step in isolation of the SMA-encoding gene. 26 refs., 3 figs., 1 tab.

  3. MwoI and SmaI RFLPs polymorphisms of porcine obese gene and their association with carcass and meat characteristics of heavy pigs

    Giorgio Graziosi

    2010-01-01

    Full Text Available The obese gene encodes leptin, a 16-kDa protein involved in the regulation of fat deposition and energy consumption.Backfat is one of the peculiar characteristics of Italian ham, and represents a fundamental quality factor. Therefore, theobese gene can be considered as a candidate marker for determining economically important production traits such asbackfat thickness, feed intake, and growth rate in swine. The aim was to investigate the relationship between obese genepolymorphisms and carcass and meat characteristics of pigs reared for ham production. In the present research, the analysesof three new RFLPs are reported. An MwoI polymorphism occurs at nucleotide 1792, within the intron. Pigs heterozygousat this position have heavier thighs with a thinner layer of fat. Two SmaI polymorphisms occur at nucleotides5018 and 5410 within the 3’ UTR of the obese gene. Animals heterozygous at position 5410 have characteristics suitablefor the production of San Daniele ham: lower backfat thickness and heavier thighs with a thinner fat layer, relative toother genotypes.

  4. How do SMA-linked mutations of SMN1 lead to structural/functional deficiency of the SMA protein?

    Wei Li

    Full Text Available Spinal muscular atrophy (SMA is an autosomal recessive neuromuscular disease with dysfunctional α-motor neurons in the anterior horn of the spinal cord. SMA is caused by loss (∼95% of SMA cases or mutation (∼5% of SMA cases of the survival motor neuron 1 gene SMN1. As the product of SMN1, SMN is a component of the SMN complex, and is also involved in the biosynthesis of the small nuclear ribonucleoproteins (snRNPs, which play critical roles in pre-mRNA splicing in the pathogenesis of SMA. To investigate how SMA-linked mutations of SMN1 lead to structural/functional deficiency of SMN, a set of computational analysis of SMN-related structures were conducted and are described in this article. Of extraordinary interest, the structural analysis highlights three SMN residues (Asp44, Glu134 and Gln136 with SMA-linked missense mutations, which cause disruptions of electrostatic interactions for Asp44, Glu134 and Gln136, and result in three functionally deficient SMA-linked SMN mutants, Asp44Val, Glu134Lys and Gln136Glu. From the computational analysis, it is also possible that SMN's Lys45 and Asp36 act as two electrostatic clips at the SMN-Gemin2 complex structure interface.

  5. Micromechanical analysis of porous SMA

    Sepe, V; Marfia, S; Sacco, E; Auricchio, F

    2015-01-01

    The present paper deals with computational micromechanical analyses of porous shape memory alloy (SMA). Porous SMAs are considered composite materials made of a dense SMA matrix including voids. A three-dimensional constitutive law is presented for the dense SMA able to reproduce the pseudo-elastic as well as the shape memory effects and, moreover, to account for the different elastic properties of the austenite and martensite phases. Furthermore, a numerical procedure is developed and the overall behavior of the porous SMA is recovered studying a representative volume element. Comparisons between the numerical results, recovered using the proposed modeling, and experimental data available in the literature are presented. The case of closed and open porosity is investigated. Parametric studies have been conducted in order to investigate the influence of the porosity, the shape and orientation of the pores on the overall mechanical response and, mainly, on the energy absorption dissipation capability. (paper)

  6. SMA DOE Student Fellowship Initiative

    Steel Manufacturers Association

    2004-12-24

    Steel companies in many areas of the country have found it increasingly difficult to attract talented recent graduates of college and university engineering and applied science programs to the Electric Arc Furnace iron & steel industry. College student involvement in co-operative programs at steel companies can attract needed talent to the industry. Additionally, certain R & D needs identified in the Steel Industry Technology Roadmap are addressed as co-operative program activities. The Steel Manufacturers Association (''SMA'') therefore established a co-operative education program for selected college students who have completed the first or second year of a four or five-year college program, to be recognized as SMA Co-Operative Fellows, in regard to their summer and fall semester projects with SMA's member companies.

  7. Probabilistic fiber tracking of the language and motor white matter pathways of the supplementary motor area (SMA) in patients with brain tumors.

    Jenabi, Mehrnaz; Peck, Kyung K; Young, Robert J; Brennan, Nicole; Holodny, Andrei I

    2014-12-01

    Accurate localization of anatomically and functionally separate SMA tracts is important to improve planning prior to neurosurgery. Using fMRI and probabilistic DTI techniques, we assessed the connectivity between the frontal language area (Broca's area) and the rostral pre-SMA (language SMA) and caudal SMA proper (motor SMA). Twenty brain tumor patients completed motor and language fMRI paradigms and DTI. Peaks of functional activity in the language SMA, motor SMA and Broca's area were used to define seed regions for probabilistic tractography. fMRI and probabilistic tractography identified separate and unique pathways connecting the SMA to Broca's area - the language SMA pathway and the motor SMA pathway. For all subjects, the language SMA pathway had a larger number of voxels (PProbabilistic tractography can identify unique white matter tracts that connect language SMA and motor SMA to Broca's area. The language SMA is more significantly connected to Broca's area than is the motor subdivision of the SMA proper. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  8. Scaling structure loads for SMA

    Lee, Dong Won; Song, Jeong Guk; Jeon, Sang Ho; Lim, Hak Kyu; Lee, Kwang Nam [KEPCO ENC, Yongin (Korea, Republic of)

    2012-10-15

    When the Seismic Margin Analysis(SMA) is conducted, the new structural load generation with Seismic Margin Earthquake(SME) is the time consuming work. For the convenience, EPRI NP 6041 suggests the scaling of the structure load. The report recommend that the fixed base(rock foundation) structure designed using either constant modal damping or modal damping ratios developed for a single material damping. For these cases, the SME loads can easily and accurately be calculated by scaling the spectral accelerations of the individual modes for the new SME response spectra. EPRI NP 6041 provides two simple methodologies for the scaling structure seismic loads which are the dominant frequency scaling methodology and the mode by mode scaling methodology. Scaling of the existing analysis to develop SME loads is much easier and more efficient than performing a new analysis. This paper is intended to compare the calculating results of two different methodologies.

  9. Scaling structure loads for SMA

    Lee, Dong Won; Song, Jeong Guk; Jeon, Sang Ho; Lim, Hak Kyu; Lee, Kwang Nam

    2012-01-01

    When the Seismic Margin Analysis(SMA) is conducted, the new structural load generation with Seismic Margin Earthquake(SME) is the time consuming work. For the convenience, EPRI NP 6041 suggests the scaling of the structure load. The report recommend that the fixed base(rock foundation) structure designed using either constant modal damping or modal damping ratios developed for a single material damping. For these cases, the SME loads can easily and accurately be calculated by scaling the spectral accelerations of the individual modes for the new SME response spectra. EPRI NP 6041 provides two simple methodologies for the scaling structure seismic loads which are the dominant frequency scaling methodology and the mode by mode scaling methodology. Scaling of the existing analysis to develop SME loads is much easier and more efficient than performing a new analysis. This paper is intended to compare the calculating results of two different methodologies

  10. A 44 bp intestine-specific hermaphrodite-specific enhancer from the C. elegans vit-2 vitellogenin gene is directly regulated by ELT-2, MAB-3, FKH-9 and DAF-16 and indirectly regulated by the germline, by daf-2/insulin signaling and by the TGF-β/Sma/Mab pathway.

    Goszczynski, Barbara; Captan, Vasile V; Danielson, Alicia M; Lancaster, Brett R; McGhee, James D

    2016-05-01

    The Caenorhabditis elegans vitellogenin genes are transcribed in the intestine of adult hermaphrodites but not of males. A 44-bp region from the vit-2 gene promoter is able largely to reconstitute this tissue-, stage- and sex-specific-expression. This "enhancer" contains a binding site for the DM-domain factor MAB-3, the male-specific repressor of vitellogenesis, as well as an activator site that we show is the direct target of the intestinal GATA factor ELT-2. We further show that the enhancer is directly activated by the winged-helix/forkhead-factor FKH-9, (whose gene has been shown by others to be a direct target of DAF-16), by an unknown activator binding to the MAB-3 site, and by the full C. elegans TGF-β/Sma/Mab pathway acting within the intestine. The vit-2 gene has been shown by others to be repressed by the daf-2/daf-16 insulin signaling pathway, which so strongly influences aging and longevity in C. elegans. We show that the activity of the 44 bp vit-2 enhancer is abolished by loss of daf-2 but is restored by simultaneous loss of daf-16. DAF-2 acts from outside of the intestine but DAF-16 acts both from outside of the intestine and from within the intestine where it binds directly to the same non-canonical target site that interacts with FKH-9. Activity of the 44 bp vit-2 enhancer is also inhibited by loss of the germline, in a manner that is only weakly influenced by DAF-16 but that is strongly influenced by KRI-1, a key downstream effector in the pathway by which germline loss increases C. elegans lifespan. The complex behavior of this enhancer presumably allows vitellogenin gene transcription to adjust to demands of body size, germline proliferation and nutritional state but we suggest that the apparent involvement of this enhancer in aging and longevity "pathways" could be incidental. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. A Perturbed MicroRNA Expression Pattern Characterizes Embryonic Neural Stem Cells Derived from a Severe Mouse Model of Spinal Muscular Atrophy (SMA

    Andrea Luchetti

    2015-08-01

    Full Text Available Spinal muscular atrophy (SMA is an inherited neuromuscular disorder and the leading genetic cause of death in infants. Despite the disease-causing gene, survival motor neuron (SMN1, encodes a ubiquitous protein, SMN1 deficiency preferentially affects spinal motor neurons (MNs, leaving the basis of this selective cell damage still unexplained. As neural stem cells (NSCs are multipotent self-renewing cells that can differentiate into neurons, they represent an in vitro model for elucidating the pathogenetic mechanism of neurodegenerative diseases such as SMA. Here we characterize for the first time neural stem cells (NSCs derived from embryonic spinal cords of a severe SMNΔ7 SMA mouse model. SMNΔ7 NSCs behave as their wild type (WT counterparts, when we consider neurosphere formation ability and the expression levels of specific regional and self-renewal markers. However, they show a perturbed cell cycle phase distribution and an increased proliferation rate compared to wild type cells. Moreover, SMNΔ7 NSCs are characterized by the differential expression of a limited number of miRNAs, among which miR-335-5p and miR-100-5p, reduced in SMNΔ7 NSCs compared to WT cells. We suggest that such miRNAs may be related to the proliferation differences characterizing SMNΔ7 NSCs, and may be potentially involved in the molecular mechanisms of SMA.

  12. A Perturbed MicroRNA Expression Pattern Characterizes Embryonic Neural Stem Cells Derived from a Severe Mouse Model of Spinal Muscular Atrophy (SMA).

    Luchetti, Andrea; Ciafrè, Silvia Anna; Murdocca, Michela; Malgieri, Arianna; Masotti, Andrea; Sanchez, Massimo; Farace, Maria Giulia; Novelli, Giuseppe; Sangiuolo, Federica

    2015-08-06

    Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder and the leading genetic cause of death in infants. Despite the disease-causing gene, survival motor neuron (SMN1), encodes a ubiquitous protein, SMN1 deficiency preferentially affects spinal motor neurons (MNs), leaving the basis of this selective cell damage still unexplained. As neural stem cells (NSCs) are multipotent self-renewing cells that can differentiate into neurons, they represent an in vitro model for elucidating the pathogenetic mechanism of neurodegenerative diseases such as SMA. Here we characterize for the first time neural stem cells (NSCs) derived from embryonic spinal cords of a severe SMNΔ7 SMA mouse model. SMNΔ7 NSCs behave as their wild type (WT) counterparts, when we consider neurosphere formation ability and the expression levels of specific regional and self-renewal markers. However, they show a perturbed cell cycle phase distribution and an increased proliferation rate compared to wild type cells. Moreover, SMNΔ7 NSCs are characterized by the differential expression of a limited number of miRNAs, among which miR-335-5p and miR-100-5p, reduced in SMNΔ7 NSCs compared to WT cells. We suggest that such miRNAs may be related to the proliferation differences characterizing SMNΔ7 NSCs, and may be potentially involved in the molecular mechanisms of SMA.

  13. Design of shape memory alloy (SMA) actuators

    Rao, Ashwin; Reddy, J N

    2015-01-01

    This short monograph presents an analysis and design methodology for shape memory alloy (SMA) components such as wires, beams, and springs for different applications. The solid-solid, diffusionless phase transformations in thermally responsive SMA allows them to demonstrate unique characteristics like superelasticity and shape memory effects. The combined sensing and actuating capabilities of such materials allows them to provide a system level response by combining multiple functions in a single material system. In SMA, the combined mechanical and thermal loading effects influence the functionality of such materials. The aim of this book is to make the analysis of these materials accessible to designers by developing a "strength of materials" approach to the analysis and design of such SMA components inspired from their various applications with a review of various factors influencing the design process for such materials.

  14. Mechanosensitive promoter region in the human HB-GAM gene

    Liedert, Astrid; Kassem, Moustapha; Claes, Lutz

    2009-01-01

    Mechanical loading is essential for maintaining bone mass in the adult skeleton. However, the underlying process of the transfer of the physical stimulus into a biochemical response, which is termed mechanotransduction is poorly understood. Mechanotransduction results in the modulation of gene...... cells. Analysis of the human HB-GAM gene upstream regulatory region with luciferase reporter gene assays revealed that the upregulation of HB-GAM expression occurred at the transcriptional level and was mainly dependent on the HB-GAM promoter region most upstream containing three potential AP-1 binding...

  15. Nutcracker and SMA syndromes: What is the normal SMA angle in children?

    Arthurs, O.J., E-mail: oja20@owenarthurs.co.uk [Department of Radiology, Box 219, Addenbrooke' s Hospital, Cambridge University Teaching Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ (United Kingdom); Mehta, U. [Department of Radiology, Box 219, Addenbrooke' s Hospital, Cambridge University Teaching Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ (United Kingdom); Set, P.A.K., E-mail: p.set@addenbrookes.nhs.uk [Department of Radiology, Box 219, Addenbrooke' s Hospital, Cambridge University Teaching Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ (United Kingdom)

    2012-08-15

    Objective: The nutcracker and superior mesenteric artery (SMA) syndromes are rare conditions where the left renal vein or duodenum may be compressed by an unusually acute angle between the SMA and aorta, although the normal angle in children is unknown. We measured the SMA angle to define the normal range in children. Methods: We retrospectively measured SMA angles, left renal vein (LRV) distance, and duodenal distance (DD) in 205 consecutive pediatric abdominal CT. Total and visceral intra-abdominal fat at the level of the umbilicus were also assessed. Results: Mean SMA angle was 45.6 {+-} 19.6 Degree-Sign (range 10.6-112.9 Degree-Sign ), mean LRV distance was 8.6 {+-} 3.9 mm (range 2.0-28.6 mm) and mean DD was 11.3 {+-} 4.8 mm (range 3.6-35.3 mm). There was a significant but weak correlation between %visceral fat volume (%VF) and SMA angle (R = 0.30; p < 0.001), LRV distance (R = 0.37, p < 0.001) and DD (R = 0.32; p < 0.001). Conclusion: There is a wide range of SMA angle, LRV and DD in normal children, which correlated weakly with visceral fat volume. Using a definition of SMA angle <25 Degree-Sign would diagnose 9.3% of asymptomatic children with nutcracker syndrome, and using a DD definition of <8 mm would diagnose 20% with SMA compression. Our findings suggest exercising caution when attributing these rare syndromes to an absolute SMA angle.

  16. Nutcracker and SMA syndromes: What is the normal SMA angle in children?

    Arthurs, O.J.; Mehta, U.; Set, P.A.K.

    2012-01-01

    Objective: The nutcracker and superior mesenteric artery (SMA) syndromes are rare conditions where the left renal vein or duodenum may be compressed by an unusually acute angle between the SMA and aorta, although the normal angle in children is unknown. We measured the SMA angle to define the normal range in children. Methods: We retrospectively measured SMA angles, left renal vein (LRV) distance, and duodenal distance (DD) in 205 consecutive pediatric abdominal CT. Total and visceral intra-abdominal fat at the level of the umbilicus were also assessed. Results: Mean SMA angle was 45.6 ± 19.6° (range 10.6–112.9°), mean LRV distance was 8.6 ± 3.9 mm (range 2.0–28.6 mm) and mean DD was 11.3 ± 4.8 mm (range 3.6–35.3 mm). There was a significant but weak correlation between %visceral fat volume (%VF) and SMA angle (R = 0.30; p < 0.001), LRV distance (R = 0.37, p < 0.001) and DD (R = 0.32; p < 0.001). Conclusion: There is a wide range of SMA angle, LRV and DD in normal children, which correlated weakly with visceral fat volume. Using a definition of SMA angle <25° would diagnose 9.3% of asymptomatic children with nutcracker syndrome, and using a DD definition of <8 mm would diagnose 20% with SMA compression. Our findings suggest exercising caution when attributing these rare syndromes to an absolute SMA angle.

  17. Domain general sequence operations contribute to pre-SMA involvement in visuo-spatial processing

    E. Charles eLeek

    2016-01-01

    Full Text Available This study used 3T MRI to elucidate the functional role of supplementary motor area (SMA in relation to visuo-spatial processing. A localizer task contrasting sequential number subtraction and repetitive button pressing was used to functionally delineate non-motor sequence processing in pre-SMA, and activity in SMA-proper associated with motor sequencing. Patterns of BOLD responses in these regions were then contrasted to those from two tasks of visuo-spatial processing. In one task participants performed mental rotation in which recognition memory judgments were made to previously memorized 2D novel patterns across image-plane rotations. The other task involved abstract grid navigation in which observers computed a series of imagined location shifts in response to directional (arrow cues around a mental grid. The results showed overlapping activation in pre-SMA for sequential subtraction and both visuo-spatial tasks. These results suggest that visuo-spatial processing is supported by non-motor sequence operations that involve pre-SMA. More broadly, these data further highlight the functional heterogeneity of pre-SMA, and show that its role extends to processes beyond the planning and online control of movement.

  18. Evaluation of SMN protein, transcript, and copy number in the biomarkers for spinal muscular atrophy (BforSMA clinical study.

    Thomas O Crawford

    Full Text Available The universal presence of a gene (SMN2 nearly identical to the mutated SMN1 gene responsible for Spinal Muscular Atrophy (SMA has proved an enticing incentive to therapeutics development. Early disappointments from putative SMN-enhancing agent clinical trials have increased interest in improving the assessment of SMN expression in blood as an early "biomarker" of treatment effect.A cross-sectional, single visit, multi-center design assessed SMN transcript and protein in 108 SMA and 22 age and gender-matched healthy control subjects, while motor function was assessed by the Modified Hammersmith Functional Motor Scale (MHFMS. Enrollment selectively targeted a broad range of SMA subjects that would permit maximum power to distinguish the relative influence of SMN2 copy number, SMA type, present motor function, and age.SMN2 copy number and levels of full-length SMN2 transcripts correlated with SMA type, and like SMN protein levels, were lower in SMA subjects compared to controls. No measure of SMN expression correlated strongly with MHFMS. A key finding is that SMN2 copy number, levels of transcript and protein showed no correlation with each other.This is a prospective study that uses the most advanced techniques of SMN transcript and protein measurement in a large selectively-recruited cohort of individuals with SMA. There is a relationship between measures of SMN expression in blood and SMA type, but not a strong correlation to motor function as measured by the MHFMS. Low SMN transcript and protein levels in the SMA subjects relative to controls suggest that these measures of SMN in accessible tissues may be amenable to an "early look" for target engagement in clinical trials of putative SMN-enhancing agents. Full length SMN transcript abundance may provide insight into the molecular mechanism of phenotypic variation as a function of SMN2 copy number.Clinicaltrials.gov NCT00756821.

  19. Characteristics Analysis and Testing of SMA Spring Actuator

    Jianzuo Ma

    2013-01-01

    Full Text Available The biasing form two-way shape memory alloy (SMA actuator composed of SMA spring and steel spring is analyzed. Based on the force equilibrium equation, the relationship between load capacity of SMA spring and geometric parameters is established. In order to obtain the characteristics of SMA spring actuator, the output force and output displacement of SMA spring under different temperatures are analyzed by the theoretical model and the experimental method. Based on the shape memory effect of SMA, the relationship of the SMA spring actuator's output displacement with the temperature, the stress and strain, the material parameters, and the size parameters is established. The results indicate that the trend of theoretical results is basically consistent with the experimental data. The output displacement of SMA spring actuator is increased with the increasing temperature.

  20. KESULITAN PEMECAHAN MASALAH FISIKA PADA SISWA SMA

    Rismatul Azizah

    2015-12-01

    Full Text Available Telah dilakukan penelitian untuk mengidentifikasi kesulitan pemecahan masalah fisika pada siswa SMA. Penelitian ini menggunakan metode survey dengan menyebarkan angket. Responden terdiri dari 120 siswa yang berasal dari 3 sekolah yaitu, SMA Negeri 1 Bangil, SMA Negeri 8 Malang, dan SMA YADIKA Bangil. Dilakukan pula wawancara pada beberapa guru dan siswa. Berdasarkan hasil penyebaran angket, diperoleh 26% siswa mengalami kesulitan pada materi Suhu dan Kalor, 25% Optik, 21% Fluida Statik, 17% Elastisitas dan Hukum Hooke, dan 11% Kinematika. Kesulitan tersebut salah satunya disebabkan pembelajaran bagi siswa yang kurang maksimal dalam bentuk hands on activity. Sebanyak 88% siswa mengatakan bahwa pembelajaran fisika yang sering dialami adalah dengan metode ceramah. Siswa mengalami kesulitan belajar fisika dalam menyelesaikan permasalahan pada soal sebesar 32%, kesulitan memahami konsep dan rumus 26%, kesulitan menggunakan persamaan atau rumus dalam soal 18%, kesulitan menganalisis grafik dan gambar 17%, dan kesulitan menyimpulkan materi yang telah dipelajari 7%. Kesulitan tersebut terlihat ketika siswa memecahkan permasalahan pada soal kinematika serta suhu dan kalor. Diperoleh dari hasil angket, bahwa 76% siswa mengalami kesulitan dalam memecahkan permasalahan pada soal dengan alasan lupa atau tidak paham, sebesar 19% siswa kurang memahami solusi pemecahan masalah pada soal, dan hanya sebesar 5% siswa mampu memecahkan permasalahan pada soal.

  1. Submillimeter Array (SMA) Newsletter August 2011

    Blundell, Raymond

    2011-01-01

    Submillimeter Array (SMA) Newsletter August 2011 Blundell, Raymond Submillimeter Array Newsletter | Number 12 | August 2011 CONTENTS 1 From the Director SCIENCE HIGHLIGHTS: 2 Faint Submillimeter Sources behind Massive Lensing Clusters 5 Millimeter Imaging of the β Pictoris Debris Disk: Evidence for a Planetesimal Belt 7 Physical Properties of the Circumnuclear Starburst Ring in the Barred Galaxy NGC1097 TECHNICAL HIGHLIGHTS: 9 ...

  2. Anterior-posterior regionalized gene expression in the Ciona notochord.

    Reeves, Wendy; Thayer, Rachel; Veeman, Michael

    2014-04-01

    In the simple ascidian chordate Ciona, the signaling pathways and gene regulatory networks giving rise to initial notochord induction are largely understood and the mechanisms of notochord morphogenesis are being systematically elucidated. The notochord has generally been thought of as a non-compartmentalized or regionalized organ that is not finely patterned at the level of gene expression. Quantitative imaging methods have recently shown, however, that notochord cell size, shape, and behavior vary consistently along the anterior-posterior (AP) axis. Here we screen candidate genes by whole mount in situ hybridization for potential AP asymmetry. We identify 4 genes that show non-uniform expression in the notochord. Ezrin/radixin/moesin (ERM) is expressed more strongly in the secondary notochord lineage than the primary. CTGF is expressed stochastically in a subset of notochord cells. A novel calmodulin-like gene (BCamL) is expressed more strongly at both the anterior and posterior tips of the notochord. A TGF-β ortholog is expressed in a gradient from posterior to anterior. The asymmetries in ERM, BCamL, and TGF-β expression are evident even before the notochord cells have intercalated into a single-file column. We conclude that the Ciona notochord is not a homogeneous tissue but instead shows distinct patterns of regionalized gene expression. Copyright © 2013 Wiley Periodicals, Inc.

  3. Association between the SMN2 gene copy number and clinical characteristics of patients with spinal muscular atrophy with homozygous deletion of exon 7 of the SMN1 gene

    Žarkov Marija

    2015-01-01

    Full Text Available Background/Aim. Spinal muscular atrophy (SMA is an autosomal recessive disease characterized by degeneration of alpha motor neurons in the spinal cord and the medulla oblongata, causing progressive muscle weakness and atrophy. The aim of this study was to determine association between the SMN2 gene copy number and disease phenotype in Serbian patients with SMA with homozygous deletion of exon 7 of the SMN1 gene. Methods. The patients were identified using regional Serbian hospital databases. Investigated clinical characteristics of the disease were: patients’ gender, age at disease onset, achieved and current developmental milestones, disease duration, current age, and the presence of the spinal deformities and joint contractures. The number of SMN1 and SMN2 gene copies was determined using real-time polymerase chain reaction (PCR. Results. Among 43 identified patients, 37 (86.0% showed homozygous deletion of SMN1 exon 7. One (2.7% of 37 patients had SMA type I with 3 SMN2 copies, 11 (29.7% patients had SMA type II with 3.1 ± 0.7 copies, 17 (45.9% patients had SMA type III with 3.7 ± 0.9 copies, while 8 (21.6% patients had SMA type IV with 4.2 ± 0.9 copies. There was a progressive increase in the SMN2 gene copy number from type II towards type IV (p < 0.05. A higher SMN2 gene copy number was associated with better current motor performance (p < 0.05. Conclusion. In the Serbian patients with SMA, a higher SMN2 gene copy number correlated with less severe disease phenotype. A possible effect of other phenotype modifiers should not be neglected.

  4. Description and physical localization of the bovine survival of motor neuron gene (SMN).

    Pietrowski, D; Goldammer, T; Meinert, S; Schwerin, M; Förster, M

    1998-01-01

    Proximal spinal muscular atrophy (SMA) is an autosomal recessive disease in humans and other mammals, characterized by degeneration of anterior horn cells of the spinal cord. In humans, the survival of motor neuron gene (SMN) has been recognized as the SMA-determining gene and has been mapped to 5q13. In cattle, SMA is a recurrent, inherited disease that plays an important economic role in breeding programs of Brown Swiss stock. Now we have identified the full- length cDNA sequence of the bovine SMN gene. Molecular analysis and characterization of the sequence documents 85% identity to its human counterpart and three evolutionarily conserved domains in different species. Physical mapping data reveals that bovine SMN is localized to chromosome region 20q12-->q13, supporting the conserved synteny of this chromosomal region between humans and cattle.

  5. Analysis of the modifying influence of Plastin 3 (PLS3) on Spinal Muscular Atrophy (SMA) by generation of transgenic mouse models

    Ackermann, Bastian

    2011-01-01

    Spinal muscular atrophy (SMA) is a neurodegenerative disease characterized by the loss of α-motor neurons in the ventral horn of the spinal cord. Depending on the severity, the clinical spectrum of SMA ranges from early infant death to normal adult life with only mild muscle weakness. To date, no cure is available. SMA is caused by the homozygous loss of the survival motor neuron gene 1 (SMN1). Besides SMN1, another nearly identical copy of the gene is present in the human genome, thus called...

  6. Phenotypic and genotypic studies of ALS cases in ALS-SMA families.

    Corcia, Philippe; Vourc'h, Patrick; Blasco, Helene; Couratier, Philippe; Dangoumau, Audrey; Bellance, Remi; Desnuelle, Claude; Viader, Fausto; Pautot, Vivien; Millecamps, Stephanie; Bakkouche, Salah; Salachas, FranÇois; Andres, Christian R; Meininger, Vincent; Camu, William

    2018-03-01

    Amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) are the most frequent motor neuron disorders in adulthood and infancy, respectively. There is a growing literature supporting common pathophysiological patterns between those disorders. One important clinical issue for that is the co-occurrence of both diseases within a family. To collect families in which ALS and SMA patients co-exist and describe the phenotype and the genotype of ALS patients. Nine families with co-occurrence of SMA and ALS have been gathered over the last 15 years. Epidemiological, phenotype and genetic status were collected. Out of the nine families, six corresponded to the criteria of familial ALS (FALS). Clinical data were available for 11 patients out of the 15 ALS cases. Mean age of onset was 58.5 years, site of onset was lower limbs in nine cases (81.8%), median duration was 22 months. Four ALS patients carried a mutation: three mutations in SOD1 gene (G147N in two cases and one with E121G) and one repeat expansion in the C9ORF72 gene. Three patients had abnormal SMN1 copy numbers. While the high proportion of familial history of ALS cases in these ALS-SMA pedigrees could have suggested that these familial clusters of the two most frequent MND rely on a genetic background, we failed to exclude that this occurred by chance.

  7. Candidate proteins, metabolites and transcripts in the Biomarkers for Spinal Muscular Atrophy (BforSMA clinical study.

    Richard S Finkel

    Full Text Available Spinal Muscular Atrophy (SMA is a neurodegenerative motor neuron disorder resulting from a homozygous mutation of the survival of motor neuron 1 (SMN1 gene. The gene product, SMN protein, functions in RNA biosynthesis in all tissues. In humans, a nearly identical gene, SMN2, rescues an otherwise lethal phenotype by producing a small amount of full-length SMN protein. SMN2 copy number inversely correlates with disease severity. Identifying other novel biomarkers could inform clinical trial design and identify novel therapeutic targets.To identify novel candidate biomarkers associated with disease severity in SMA using unbiased proteomic, metabolomic and transcriptomic approaches.A cross-sectional single evaluation was performed in 108 children with genetically confirmed SMA, aged 2-12 years, manifesting a broad range of disease severity and selected to distinguish factors associated with SMA type and present functional ability independent of age. Blood and urine specimens from these and 22 age-matched healthy controls were interrogated using proteomic, metabolomic and transcriptomic discovery platforms. Analyte associations were evaluated against a primary measure of disease severity, the Modified Hammersmith Functional Motor Scale (MHFMS and to a number of secondary clinical measures.A total of 200 candidate biomarkers correlate with MHFMS scores: 97 plasma proteins, 59 plasma metabolites (9 amino acids, 10 free fatty acids, 12 lipids and 28 GC/MS metabolites and 44 urine metabolites. No transcripts correlated with MHFMS.In this cross-sectional study, "BforSMA" (Biomarkers for SMA, candidate protein and metabolite markers were identified. No transcript biomarker candidates were identified. Additional mining of this rich dataset may yield important insights into relevant SMA-related pathophysiology and biological network associations. Additional prospective studies are needed to confirm these findings, demonstrate sensitivity to change with

  8. Genetic recombination is targeted towards gene promoter regions in dogs.

    Auton, Adam; Rui Li, Ying; Kidd, Jeffrey; Oliveira, Kyle; Nadel, Julie; Holloway, J Kim; Hayward, Jessica J; Cohen, Paula E; Greally, John M; Wang, Jun; Bustamante, Carlos D; Boyko, Adam R

    2013-01-01

    The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.

  9. Anhidrotic ectodermal dysplasia gene region cloned in yeast artificial chromosomes

    Kere, J. [Washington Univ. School of Medicine, St. Louis, MO (United States)]|[Univ. of Helsinki (Finland); Grzeschik, K.H. [Univ. of Marburg (Germany); Limon, J. [Medical Academy, Gdansk (Poland); Gremaud, M.; Schlessinger, D. [Washington Univ. School of Medicine, St. Louis, MO (United States); De La Chapelle, A. [Univ. of Helsinki (Finland)

    1993-05-01

    Anhidrotic ectodermal dysplasia (EDA), an X-chromosomal recessive disorder, is expressed in a few females with chromosomal translocations involving bands Xq12-q13. Using available DNA markers from the region and somatic cell hybrids the authors mapped the X-chromosomal breakpoints in two such translocations. The breakpoints were further mapped within a yeast artificial chromosome contig constructed by chromosome walking techniques. Genomic DNA markers that map between the two translocation breakpoints were recovered representing putative portions of the EDA gene. 32 refs., 3 figs., 1 tab.

  10. Parallel Evolution of Genes and Languages in the Caucasus Region

    Balanovsky, Oleg; Dibirova, Khadizhat; Dybo, Anna; Mudrak, Oleg; Frolova, Svetlana; Pocheshkhova, Elvira; Haber, Marc; Platt, Daniel; Schurr, Theodore; Haak, Wolfgang; Kuznetsova, Marina; Radzhabov, Magomed; Balaganskaya, Olga; Romanov, Alexey; Zakharova, Tatiana; Soria Hernanz, David F.; Zalloua, Pierre; Koshel, Sergey; Ruhlen, Merritt; Renfrew, Colin; Wells, R. Spencer; Tyler-Smith, Chris; Balanovska, Elena

    2012-01-01

    We analyzed 40 SNP and 19 STR Y-chromosomal markers in a large sample of 1,525 indigenous individuals from 14 populations in the Caucasus and 254 additional individuals representing potential source populations. We also employed a lexicostatistical approach to reconstruct the history of the languages of the North Caucasian family spoken by the Caucasus populations. We found a different major haplogroup to be prevalent in each of four sets of populations that occupy distinct geographic regions and belong to different linguistic branches. The haplogroup frequencies correlated with geography and, even more strongly, with language. Within haplogroups, a number of haplotype clusters were shown to be specific to individual populations and languages. The data suggested a direct origin of Caucasus male lineages from the Near East, followed by high levels of isolation, differentiation and genetic drift in situ. Comparison of genetic and linguistic reconstructions covering the last few millennia showed striking correspondences between the topology and dates of the respective gene and language trees, and with documented historical events. Overall, in the Caucasus region, unmatched levels of gene-language co-evolution occurred within geographically isolated populations, probably due to its mountainous terrain. PMID:21571925

  11. Anthropogenic antibiotic resistance genes mobilization to the polar regions.

    Hernández, Jorge; González-Acuña, Daniel

    2016-01-01

    Anthropogenic influences in the southern polar region have been rare, but lately microorganisms associated with humans have reached Antarctica, possibly from military bases, fishing boats, scientific expeditions, and/or ship-borne tourism. Studies of seawater in areas of human intervention and proximal to fresh penguin feces revealed the presence of Escherichia coli strains least resistant to antibiotics in penguins, whereas E. coli from seawater elsewhere showed resistance to one or more of the following antibiotics: ampicillin, tetracycline, streptomycin, and trim-sulfa. In seawater samples, bacteria were found carrying extended-spectrum β-lactamase (ESBL)-type CTX-M genes in which multilocus sequencing typing (MLST) showed different sequence types (STs), previously reported in humans. In the Arctic, on the contrary, people have been present for a long time, and the presence of antibiotic resistance genes (ARGs) appears to be much more wide-spread than was previously reported. Studies of E coli from Arctic birds (Bering Strait) revealed reduced susceptibility to antibiotics, but one globally spreading clone of E. coli genotype O25b-ST131, carrying genes of ESBL-type CTX-M, was identified. In the few years between sample collections in the same area, differences in resistance pattern were observed, with E. coli from birds showing resistance to a maximum of five different antibiotics. Presence of resistance-type ESBLs (TEM, SHV, and CTX-M) in E. coli and Klebsiella pneumoniae was also confirmed by specified PCR methods. MLST revealed that those bacteria carried STs that connect them to previously described strains in humans. In conclusion, bacteria previously related to humans could be found in relatively pristine environments, and presently human-associated, antibiotic-resistant bacteria have reached a high global level of distribution that they are now found even in the polar regions.

  12. Deletion analysis of SMN1 and NAIP genes in southern Chinese children with spinal muscular atrophy

    Yu-hua LIANG; Xiao-ling CHEN; Zhong-sheng YU; Chun-yue CHEN; Sheng BI; Lian-gen MAO; Bo-lin ZHOU; Xian-ning ZHANG

    2009-01-01

    Spinal muscular atrophy (SMA) is a disorder characterized by degeneration of lower motor neurons and occasionally bulbar motor neurons leading to progressive limb and trunk paralysis as well as muscular atrophy. Three types of SMA are rec-ognized depending on the age of onset, the maximum muscular activity achieved, and survivorship: SMA1, SMA2, and SMA3. The survival of motor neuron (SMN) gene has been identified as an SMA determining gene, whereas the neuronal apoptosis inhibitory protein (NAIP) gene is considered to be a modifying factor of the severity of SMA. The main objective of this study was to analyze the deletion of SMN1 and NAIP genes in southern Chinese children with SMA. Here, polymerase chain reaction (PCR) combined with restriction fragment length polymorphism (RFLP) was performed to detect the deletion of both exon 7 and exon 8 of SMNI and exon 5 of NAIP in 62 southern Chinese children with strongly suspected clinical symptoms of SMA. All the 32 SMAI patients and 76% (13/17) of SMA2 patients showed homozygous deletions for exon 7 and exon 8, and all the 13 SMA3 patients showed single deletion of SMN1 exon 7 along with 24% (4/17) of SMA2 patients. Eleven out of 32 (34%) SMA1 patients showed NAIP deletion, and none of SMA2 and SMA3 patients was found to have NAIP deletion. The findings of homozygous deletions of exon 7 and/or exon 8 of SMN1 gene confirmed the diagnosis of SMA, and suggested that the deletion of SMN1 exon 7 is a major cause of SMA in southern Chinese children, and that the NA1P gene may be a modifying factor for disease severity of SMA 1. The molecular diagnosis system based on PCR-RFLP analysis can conveniently be applied in the clinical testing, genetic counseling, prenatal diagnosis and preimplantation genetic diagnosis of SMA.

  13. The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

    Baker, Katie; Bayer, Micha; Cook, Nicola; Dreißig, Steven; Dhillon, Taniya; Russell, Joanne; Hedley, Pete E; Morris, Jenny; Ramsay, Luke; Colas, Isabelle; Waugh, Robbie; Steffenson, Brian; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J

    2014-01-01

    The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes. PMID:24947331

  14. Investigation on low velocity impact resistance of SMA composite material

    Hu, Dianyin; Zhang, Long; Wang, Rongqiao; Zhang, Xiaoyong

    2016-04-01

    A method to improve low velocity impact resistance of aeroengine composite casing using shape memory alloy's properties of shape memory(SM) and super-elasticity(SE) is proposed in this study. Firstly, a numerical modeling of SMA reinforced composite laminate under low velocity impact load with impact velocity of 10 m/s is established based on its constitutive model implemented by the VUMAT subroutine of commercial software ABAQUS. Secondly, the responses of SMA composite laminate including stress and deflection distributions were achieved through transient analysis under low velocity impact load. Numerical results show that both peak stress and deflection values of SMA composite laminate are less than that without SMA, which proves that embedding SMA into the composite structure can effectively improve the low velocity impact performance of composite structure. Finally, the influence of SM and SE on low velocity impact resistance is quantitatively investigated. The values of peak stress and deflection of SMA composite based on SM property decrease by 18.28% and 9.43% respectively, compared with those without SMA, instead of 12.87% and 5.19% based on SE. In conclusion, this proposed model described the impact damage of SMA composite structure and turned to be a more beneficial method to enhance the impact resistance by utilizing SM effect.

  15. EVALUASI STRATEGI BERSAING SMA KRISTEN 1 SALATIGA

    Eclesia Tehupeiory

    2015-06-01

    Full Text Available This study aims to evaluate the competitive strategies of SMA Kristen 1 Salatiga. The type of this study was a qualitative evaluation, through data collection by means of interviews, questionnaires, observation and documentation study. Data obtained and analyzed by an evaluation component based on Rumelt (2000 were consistency, consonance, advantage and feasibility. The results showed that: (1 Consistency evaluation of competitive strategy applied by SMA Kristen 1 Salatiga has shown consistency with the goals, values and policies of the school. (2 Consonance evaluation of competitive strategy has demonstrated suitability with the needs of society, while for competition with other schools, the school programs such as Peduli Kasih program, Sekolah Lima Hari, moving class, SMUQI Radio and multimedia extracurricular namely cinematography and photography are not appropriate. (3 Advantage evaluation of competitive strategy in the school programs such as Peduli Kasih, moving class, and Sekolah Lima Hari do not excel the resources, skills and superior positions. Other programs such as multimedia Extracurricular namely photography and cinematography is not superior to the superior position. Meanwhile, special programs such as the education expo, parenting day, career day and the Field Trip program through Live In and outdoor study do not excel in superior skills. (4 Feasibility evaluation shows that multimedia extracurricular programs have not showed the feasibility of the physical resources which involves computer supporting facilities and Wi-Fi. Suggestion to school in order to maintain the consistency that was owned, suitability to the needs of society as well as pay attention to competition with other schools also enhance the achievement of advantage and checking of IT facilities.

  16. Generation of a gene cassette for genetically engineered Salmonella Enteritidis in the specific region of the sipC gene

    M Ghasemi

    2017-05-01

    Full Text Available Introduction: Salmonellosis is an infection caused by eating contaminated food with Salmonella, and it can occur in humans and other animals. Salmonella has acquired the ability to create the infection due to the presence of several virulence genes. One of the virulence genes of salmonella is sipC gene that coding the SipC protein. The aim of this study was creating the gene cassette to genetically engineered Salmonella enteritidis in the specific region of the sipC gene. Methods: In this study, after DNA extraction from Salmonella, the upstream and downstream regions of the sipC gene was amplified based on PCR method. The PCR products were cloned with T/A cloning method and they were inserted into the pGEM vector. In order to generate the final gene cassette, each of the upstream and downstream regions of the sipC gene was subcloned into the pET32 vector, and cloning accuracy was assessed by PCR and enzyme digestion methods. Results: Amplification of the 320 bp upstream and 206 bp downstream of sipC gene was successful by PCR method. T/A cloning of these fragments were caused the formation of two pGEM-up and pGEM-down recombinant vectors. Results that were confirmed the sub-cloning accuracy indicate the formation of the final pET32-up-down gene cassette. Conclusion: The generated gene cassette in this study was considered as a multi-purpose cassette that is able to specific gene manipulation of Salmonella sipC gene by homologous recombination matched. This gene cassette has the necessary potential for sipC gene deletion or insertion of any useful gene instead of sipC gene.

  17. PKCδ as a regulator for TGFβ1-induced α-SMA production in a murine nonalcoholic steatohepatitis model.

    Su Jin Lee

    Full Text Available The precise mechanism of TGFβ1 signaling in the progression of non-alcoholic steatohepatitis (NASH has remained unclear. In particular, a potential regulatory mechanism by which PKCδ affects profibrogenic gene expression had never been explored. In this study, therefore, the role of PKCδ in TGFβ1 mediated α-SMA expression was investigated using NASH model mice. In preparation of the NASH model, male C57BL6/J mice were fed a methionine-choline-deficient (MCD diet for 3 weeks, after which time they were intraperitoneally injected with lipopolysaccharide (LPS. In addition, Tlr4(Lps-d (CH3/HeJ mice were used to demonstrate the TGFβ1 signaling's dependency on TLR4 induction. Liver histology and hepatic hepatitis markers were investigated, and hepatic gene expression levels were determined by real-time PCR. Acute liver injury by LPS injection specifically elevated not only α-SMA expression but also phospho-PKCδ in this model. In contrast, Tlr4(Lps-d (CH3/HeJ and blockade of TGFβ1 receptor by SB431542 resulted in a significant reduction of PKCδ activation and α-SMA expression. Moreover, the TGFβ1-induced α-SMA production was significantly reduced by a specific PKCδ inhibitor. These findings suggested that PKCδ plays a critical role in TGFβ1-induced α-SMA production in a NASH model. Thus, this was the first demonstration of the involvement of PKCδ in the regulation of α-SMA expression in NASH liver tissues, and the impaired induction of PKCδ phosphorylation by LPS in a steatohepatitis condition. Interestingly, treatment by PKCδ inhibitor caused dramatic reduction of myofibroblast activation, indicating that PKCδ represents a promising target for treating NASH.

  18. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes

    Dasgupta Dipayan

    2005-05-01

    Full Text Available Abstract Background Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group. Results In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes. Conclusion The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.

  19. Isolation of Genes from Chromosome Region Ip31 Involved in the Development of Breast Cancer

    Cowell, John

    2000-01-01

    .... Using gene analysis tools, we have been able to demonstrate that few full-length genes are located in this region and that the ESTs from the databases are clustered to a proximal position of the contig...

  20. Genome-wide analysis of regions similar to promoters of histone genes

    Chowdhary, Rajesh

    2010-05-28

    Background: The purpose of this study is to: i) develop a computational model of promoters of human histone-encoding genes (shortly histone genes), an important class of genes that participate in various critical cellular processes, ii) use the model so developed to identify regions across the human genome that have similar structure as promoters of histone genes; such regions could represent potential genomic regulatory regions, e.g. promoters, of genes that may be coregulated with histone genes, and iii/ identify in this way genes that have high likelihood of being coregulated with the histone genes.Results: We successfully developed a histone promoter model using a comprehensive collection of histone genes. Based on leave-one-out cross-validation test, the model produced good prediction accuracy (94.1% sensitivity, 92.6% specificity, and 92.8% positive predictive value). We used this model to predict across the genome a number of genes that shared similar promoter structures with the histone gene promoters. We thus hypothesize that these predicted genes could be coregulated with histone genes. This hypothesis matches well with the available gene expression, gene ontology, and pathways data. Jointly with promoters of the above-mentioned genes, we found a large number of intergenic regions with similar structure as histone promoters.Conclusions: This study represents one of the most comprehensive computational analyses conducted thus far on a genome-wide scale of promoters of human histone genes. Our analysis suggests a number of other human genes that share a high similarity of promoter structure with the histone genes and thus are highly likely to be coregulated, and consequently coexpressed, with the histone genes. We also found that there are a large number of intergenic regions across the genome with their structures similar to promoters of histone genes. These regions may be promoters of yet unidentified genes, or may represent remote control regions that

  1. Sequencing analysis reveals a unique gene organization in the gyrB region of Mycoplasma hominis

    Ladefoged, Søren; Christiansen, Gunna

    1994-01-01

    of which showed similarity to that which encodes the LicA protein of Haemophilus influenzae. The organization of the genes in the region showed no resemblance to that in the corresponding regions of other bacteria sequenced so far. The gyrA gene was mapped 35 kb downstream from the gyrB gene.......The homolog of the gyrB gene, which has been reported to be present in the vicinity of the initiation site of replication in bacteria, was mapped on the Mycoplasma hominis genome, and the region was subsequently sequenced. Five open reading frames were identified flanking the gyrB gene, one...

  2. Sistem Informasi Akademik pada SMA Hang Tuah Belawan

    Tanjung, Dini Syahroni

    2015-01-01

    Informasi yang disampaikan oleh SMA HANG TUAH BELAWAN selama ini disebarkan melalui brosur dan cara yang seperti itu kurang efektif. Oleh karena itu dibuatlah sistem informasi akademik ini agar penyampaian informasinya lebih efektif dan efisien. 092406181

  3. Sistem Informasi Akademik pada SMA Swasta Hang Tuah Belawan

    Syarifuddin, Ruisya

    2015-01-01

    Perancangan Sistem Informasi Akademik pada SMA Swasta Hang Tuah Belawan ini bertujuan untuk mempermudah proses pencarian atau searching data dan informasi untuk seluruh Siswa SMA Swasta Hang Tuah Belawan yang mengalami kesulitan dalam memperoleh data mengenai masalah Akademik tersebut. Faasilitas yang terdapat dalam aplikasi ini berupa penyediaan data dan informasi mengenai beritaberita terbaru, profil agenda kegiatan, dan data-data yang berguna untuk kelangsungan belajar si...

  4. Manajemen kelas dalam pembelajaran matematika di SMA Negeri Yogyakarta

    Nisak Ruwah Ibnatur Husnul; Heri Retnawati

    2017-01-01

    Penelitian ini bertujuan untuk mengetahui manajemen kelas yang berupa perencanaan, pengorganisasian, penggerakan/kepemimpinan dan pengevaluasian dari pembelajaran matematika yang dilakukan oleh guru matematika di SMA Negeri Yogyakarta. Dengan menggunakan penelitian kualitatif jenis studi kasus ini dilakukan di SMA Negeri 5, 8 dan 9 Yogyakarta dengan subjek data adalah kepala sekolah, guru kurikulum, guru matematika dan siswa. Untuk teknik pengumpulan datanya dengan pedoman observasi dan pedom...

  5. Semantic memory retrieval circuit: role of pre-SMA, caudate, and thalamus.

    Hart, John; Maguire, Mandy J; Motes, Michael; Mudar, Raksha Anand; Chiang, Hsueh-Sheng; Womack, Kyle B; Kraut, Michael A

    2013-07-01

    We propose that pre-supplementary motor area (pre-SMA)-thalamic interactions govern processes fundamental to semantic retrieval of an integrated object memory. At the onset of semantic retrieval, pre-SMA initiates electrical interactions between multiple cortical regions associated with semantic memory subsystems encodings as indexed by an increase in theta-band EEG power. This starts between 100-150 ms after stimulus presentation and is sustained throughout the task. We posit that this activity represents initiation of the object memory search, which continues in searching for an object memory. When the correct memory is retrieved, there is a high beta-band EEG power increase, which reflects communication between pre-SMA and thalamus, designates the end of the search process and resultant in object retrieval from multiple semantic memory subsystems. This high beta signal is also detected in cortical regions. This circuit is modulated by the caudate nuclei to facilitate correct and suppress incorrect target memories. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Spliceosome integrity is defective in the motor neuron diseases ALS and SMA

    Tsuiji, Hitomi; Iguchi, Yohei; Furuya, Asako; Kataoka, Ayane; Hatsuta, Hiroyuki; Atsuta, Naoki; Tanaka, Fumiaki; Hashizume, Yoshio; Akatsu, Hiroyasu; Murayama, Shigeo; Sobue, Gen; Yamanaka, Koji

    2013-01-01

    Two motor neuron diseases, amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are caused by distinct genes involved in RNA metabolism, TDP-43 and FUS/TLS, and SMN, respectively. However, whether there is a shared defective mechanism in RNA metabolism common to these two diseases remains unclear. Here, we show that TDP-43 and FUS/TLS localize in nuclear Gems through an association with SMN, and that all three proteins function in spliceosome maintenance. We also show that in ALS, Gems are lost, U snRNA levels are up-regulated and spliceosomal U snRNPs abnormally and extensively accumulate in motor neuron nuclei, but not in the temporal lobe of FTLD with TDP-43 pathology. This aberrant accumulation of U snRNAs in ALS motor neurons is in direct contrast to SMA motor neurons, which show reduced amounts of U snRNAs, while both have defects in the spliceosome. These findings indicate that a profound loss of spliceosome integrity is a critical mechanism common to neurodegeneration in ALS and SMA, and may explain cell-type specific vulnerability of motor neurons. PMID:23255347

  7. EVALUASI DAN STRATEGI PENGEMBANGAN SMA INDONESISCH NERDERLANDSCHE SCHOOL (INS KAYUTANAM

    David David

    2016-06-01

    Full Text Available Penelitian ini bertujuan untuk: (1 mengevaluasi SMA INS Kayutanam dan (2 menyusuan strategi pengembangan SMA INS Kayutanam berdasarkan hasil evaluasi tersebut. Pendekatan yang digunakan dalam penelitian ini adalah kuantitatif dan kualitatif. Sumber data dalam penelitian ini adalah 50 siswa kelas X dan XI, satu kepala sekolah, empat wakil kepala sekolah, 30 guru, dua pembina asrama dan dua orang dari pemerintahan. Hasil penelitian dibagi dalam dua kelompok yaitu hasil evaluasi dan strategi pengembangan. Berdasarkan hasil evaluasi ditemukan bahwa ada beberapa komponen yang perlu perbaikan yaitu kurikulum, kompetensi pendidik dan tenaga kependidikan, fasilitas, peran serta masyarakat, dana dan organisasi. Strategi pengembangan terdiri dari: (1 perumusan kurikulum terintegrasi yang memuat tujuan dan sasaran pendidikan yang diprakarsai oleh Sjafei; (2 perumusan metode mengajar yang sesuai dengan tujuan dan sasaran pendidikan yang diprakasai Sjafei; (3 pengelolaan aset produktif dengan pemanfaatan modal sosial; (4 pemanfaatan basis alumni; (5 membangun kerja sama dengan instansi terkait seperti sekolah lain, pemerintah daerah, dan pihak swasta. Kata kunci: evaluasi, strategi pengembangan   THE EVALUATION AND THE STRATEGY FOR DEVELOPING INDONESISCH NEDERLANDSCHE SCHOOL (INS KAYUTANAM SENIOR HIGH SCHOOL Abstract The study was to: (1 evaluate the development of INS Kayutanam Senior High School; and (2 design the strategy to develop INS Kayutanam Senior High School based on the results of the evaluation. The approach used of in the study was quantitative and qualitative. The data source in the study was 50 students from the X grade and the XI grade, one principal, four vice principals, 30 teachers, two dormitory advisors and two government representatives. The results of the study were divided into two groups namely the evaluation results and the development strategies. Based on the results of the study, the researcher found that there were several

  8. Physical linkage of a human immunoglobulin heavy chain variable region gene segment to diversity and joining region elements

    Schroeder, H.W. Jr.; Walter, M.A.; Hofker, M.H.; Ebens, A.; Van Dijk, K.W.; Liao, L.C.; Cox, D.W.; Milner, E.C.B.; Perlmutter, R.M.

    1988-01-01

    Antibody genes are assembled from a series of germ-line gene segments that are juxtaposed during the maturation of B lymphocytes. Although diversification of the adult antibody repertoire results in large part from the combinatorial joining of these gene segments, a restricted set of antibody heavy chain variable (V H ), diversity (D H ), and joining (J H ) region gene segments appears preferentially in the human fetal repertoire. The authors report here that one of these early-expressed V H elements (termed V H 6) is the most 3' V H gene segment, positioned 77 kilobases on the 5' side of the J H locus and immediately adjacent to a set of previously described D H sequences. In addition to providing a physical map linking human V H , D H , and J H elements, these results support the view that the programmed development of the antibody V H repertoire is determined in part by the chromosomal position of these gene segments

  9. RGmatch: matching genomic regions to proximal genes in omics data integration

    Pedro Furió-Tarí

    2016-11-01

    Full Text Available Abstract Background The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. Results In this work we review the tools that are publicly available for making region-to-gene associations. We also present a novel method, RGmatch, a flexible and easy-to-use Python tool that computes associations either at the gene, transcript, or exon level, applying a set of rules to annotate each region-gene association with the region location within the gene. RGmatch can be applied to any organism as long as genome annotation is available. Furthermore, we qualitatively and quantitatively compare RGmatch to other tools. Conclusions RGmatch simplifies the association of a genomic region with its closest gene. At the same time, it is a powerful tool because the rules used to annotate these associations are very easy to modify according to the researcher’s specific interests. Some important differences between RGmatch and other similar tools already in existence are RGmatch’s flexibility, its wide range of user options, compatibility with any annotatable organism, and its comprehensive and user-friendly output.

  10. The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes.

    Swainsbury, David J K; Scheidelaar, Stefan; Foster, Nicholas; van Grondelle, Rienk; Killian, J Antoinette; Jones, Michael R

    2017-10-01

    Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  11. Regional and temporal differences in gene expression of LH(BETA)T(AG) retinoblastoma tumors.

    Houston, Samuel K; Pina, Yolanda; Clarke, Jennifer; Koru-Sengul, Tulay; Scott, William K; Nathanson, Lubov; Schefler, Amy C; Murray, Timothy G

    2011-07-23

    The purpose of this study was to evaluate by microarray the hypothesis that LH(BETA)T(AG) retinoblastoma tumors exhibit regional and temporal variations in gene expression. LH(BETA)T(AG) mice aged 12, 16, and 20 weeks were euthanatized (n = 9). Specimens were taken from five tumor areas (apex, anterior lateral, center, base, and posterior lateral). Samples were hybridized to gene microarrays. The data were preprocessed and analyzed, and genes with a P 2.5 were considered to be differentially expressed. Differentially expressed genes were analyzed for overlap with known networks by using pathway analysis tools. There were significant temporal (P regional differences in gene expression for LH(BETA)T(AG) retinoblastoma tumors. At P 2.5, there were significant changes in gene expression of 190 genes apically, 84 genes anterolaterally, 126 genes posteriorly, 56 genes centrally, and 134 genes at the base. Differentially expressed genes overlapped with known networks, with significant involvement in regulation of cellular proliferation and growth, response to oxygen levels and hypoxia, regulation of cellular processes, cellular signaling cascades, and angiogenesis. There are significant temporal and regional variations in the LH(BETA)T(AG) retinoblastoma model. Differentially expressed genes overlap with key pathways that may play pivotal roles in murine retinoblastoma development. These findings suggest the mechanisms involved in tumor growth and progression in murine retinoblastoma tumors and identify pathways for analysis at a functional level, to determine significance in human retinoblastoma. Microarray analysis of LH(BETA)T(AG) retinal tumors showed significant regional and temporal variations in gene expression, including dysregulation of genes involved in hypoxic responses and angiogenesis.

  12. Chronic ethanol exposure produces time- and brain region-dependent changes in gene coexpression networks.

    Elizabeth A Osterndorff-Kahanek

    Full Text Available Repeated ethanol exposure and withdrawal in mice increases voluntary drinking and represents an animal model of physical dependence. We examined time- and brain region-dependent changes in gene coexpression networks in amygdala (AMY, nucleus accumbens (NAC, prefrontal cortex (PFC, and liver after four weekly cycles of chronic intermittent ethanol (CIE vapor exposure in C57BL/6J mice. Microarrays were used to compare gene expression profiles at 0-, 8-, and 120-hours following the last ethanol exposure. Each brain region exhibited a large number of differentially expressed genes (2,000-3,000 at the 0- and 8-hour time points, but fewer changes were detected at the 120-hour time point (400-600. Within each region, there was little gene overlap across time (~20%. All brain regions were significantly enriched with differentially expressed immune-related genes at the 8-hour time point. Weighted gene correlation network analysis identified modules that were highly enriched with differentially expressed genes at the 0- and 8-hour time points with virtually no enrichment at 120 hours. Modules enriched for both ethanol-responsive and cell-specific genes were identified in each brain region. These results indicate that chronic alcohol exposure causes global 'rewiring' of coexpression systems involving glial and immune signaling as well as neuronal genes.

  13. Contribution of the pre-SMA to the production of words and non-speech oral motor gestures, as revealed by repetitive transcranial magnetic stimulation (rTMS).

    Tremblay, Pascale; Gracco, Vincent L

    2009-05-01

    An emerging theoretical perspective, largely based on neuroimaging studies, suggests that the pre-SMA is involved in planning cognitive aspects of motor behavior and language, such as linguistic and non-linguistic response selection. Neuroimaging studies, however, cannot indicate whether a brain region is equally important to all tasks in which it is activated. In the present study, we tested the hypothesis that the pre-SMA is an important component of response selection, using an interference technique. High frequency repetitive TMS (10 Hz) was used to interfere with the functioning of the pre-SMA during tasks requiring selection of words and oral gestures under different selection modes (forced, volitional) and attention levels (high attention, low attention). Results show that TMS applied to the pre-SMA interferes selectively with the volitional selection condition, resulting in longer RTs. The low- and high-attention forced selection conditions were unaffected by TMS, demonstrating that the pre-SMA is sensitive to selection mode but not attentional demands. TMS similarly affected the volitional selection of words and oral gestures, reflecting the response-independent nature of the pre-SMA contribution to response selection. The implications of these results are discussed.

  14. The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation

    Zhou Bai-Cheng

    2010-04-01

    Full Text Available Abstract Background Zunongwangia profunda SM-A87, which was isolated from deep-sea sediment, is an aerobic, gram-negative bacterium that represents a new genus of Flavobacteriaceae. This is the first sequenced genome of a deep-sea bacterium from the phylum Bacteroidetes. Results The Z. profunda SM-A87 genome has a single 5 128 187-bp circular chromosome with no extrachromosomal elements and harbors 4 653 predicted protein-coding genes. SM-A87 produces a large amount of capsular polysaccharides and possesses two polysaccharide biosynthesis gene clusters. It has a total of 130 peptidases, 61 of which have signal peptides. In addition to extracellular peptidases, SM-A87 also has various extracellular enzymes for carbohydrate, lipid and DNA degradation. These extracellular enzymes suggest that the bacterium is able to hydrolyze organic materials in the sediment, especially carbohydrates and proteinaceous organic nitrogen. There are two clustered regularly interspaced short palindromic repeats in the genome, but their spacers do not match any sequences in the public sequence databases. SM-A87 is a moderate halophile. Our protein isoelectric point analysis indicates that extracellular proteins have lower predicted isoelectric points than intracellular proteins. SM-A87 accumulates organic osmolytes in the cell, so its extracelluar proteins are more halophilic than its intracellular proteins. Conclusion Here, we present the first complete genome of a deep-sea sedimentary bacterium from the phylum Bacteroidetes. The genome analysis shows that SM-A87 has some common features of deep-sea bacteria, as well as an important capacity to hydrolyze sedimentary organic nitrogen.

  15. DNA methylation of PTEN gene promoter region is not correlated ...

    Tumor suppressor gene PTEN plays an important role in cell cycle. Disorder of PTEN protein can cause cell growth and division in an uncontrolled way, which can lead to the formation of tumors. It has been proven that epigenetic mechanisms, such as promoter hypermethylation, may account for inactivation of PTEN in a ...

  16. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Sahoo, Dipak K; Abeysekara, Nilwala S; Cianzio, Silvia R; Robertson, Alison E; Bhattacharyya, Madan K

    2017-01-01

    Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  17. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes.

    Dipak K Sahoo

    Full Text Available Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs (F7 families were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance.

  18. PENERAPAN TEKNOLOGI WEB SEKOLAH BAGI SMP DAN SMA MUHAMMADIYAH KARTASURA

    Heru Supriyono

    2016-03-01

    Full Text Available Observation and interview with headmasters, teachers and administrative employees results showed that one of main problems faced by SMP Muhammadiyah 1 Kartasura and SMA Muhammadiyah 4 Kartasura is the do not have a representative school website. Based on this observation, after making discussion with headmasters, the community services team proposed an implementation of school website and train one of chosen teacher to manage implemented website. The outcomes of the community service activities are involving a school website for SMP Muhammadiyah 1 Kartasura and SMA Muhammadiyah 4 Kartasura and scientific publication draft. The contribution of each school is including providing information which will be uploaded to the website, providing fee for domain and hosting cost, and providing facilities for administrator training. The duration of this commuity services is three months. The results of the community services is both SMP Muhammadiyah 1 Kartasura dan SMA Muhammadiyah 4 Kartasura are now have representative website for their promotion and administative activities.

  19. Mutations in the S gene region of hepatitis B virus genotype D in ...

    The gene region of the hepatitis B virus (HBV) is responsible for the expression of surface antigens and includes the 'a'-determinant region. Thus, mutation(s) in this region would afford HBV variants a distinct survival advantage, permitting the mutant virus to escape from the immune system. The aim of this study was to ...

  20. Sense of agency is related to gamma band coupling in an inferior parietal-preSMA circuitry

    Anina eRitterband-Rosenbaum

    2014-07-01

    Full Text Available In the present study we tested whether sense of agency (SoA is reflected by changes in coupling between right medio-frontal/supplementary motor area (SMA and inferior parietal cortex (IPC. Twelve healthy adult volunteers participated in the study. They performed a variation of a line-drawing task (Nielsen, 1963;Fourneret and Jeannerod, 1998, in which they moved a cursor on a digital tablet with their right hand without seeing the hand. Visual feedback displayed on a computer monitor was either in correspondence with or deviated from the actual movement. This made participants uncertain as to the agent of the movement and they reported SoA in approximately 50% of trials when the movement was computer-generated. We tested whether IPC-preSMA coupling was associated with SoA, using dynamic causal modelling (DCM for induced responses (Chen et al., 2008;Herz et al., 2012. Nine different DCMs were constructed for the early and late phases of the task, respectively. All models included two regions: a superior medial gyrus (preSMA region and a right supramarginal gyrus (IPC region. Bayesian models selection (Stephan et al., 2009 favoured a model with input to IPC and modulation of the forward connection to SMA in the late task phase, and a model with input to preSMA and modulation of the backward connection was favoured for the early task phase. The analysis shows that IPC source activity in the 50-60Hz range modulated preSMA source activity in the 40-70 Hz range in the presence of SoA compared with no SoA in the late task phase, but the test of the early task phase did not reveal any differences between presence and absence of SoA. We show that SoA is associated with a directionally specific between frequencies coupling from IPC to preSMA in the higher gamma (ɣ band in the late task phase. This suggests that SoA is a retrospective perception, which is highly dependent on interpretation of the outcome of the performed action.

  1. Sense of agency is related to gamma band coupling in an inferior parietal-preSMA circuitry

    Ritterband-Rosenbaum, Anina; Nielsen, Jens B.; Christensen, Mark S.

    2014-01-01

    In the present study we tested whether sense of agency (SoA) is reflected by changes in coupling between right medio-frontal/supplementary motor area (SMA) and inferior parietal cortex (IPC). Twelve healthy adult volunteers participated in the study. They performed a variation of a line-drawing task (Nielsen, 1963; Fourneret and Jeannerod, 1998), in which they moved a cursor on a digital tablet with their right hand without seeing the hand. Visual feedback displayed on a computer monitor was either in correspondence with or deviated from the actual movement. This made participants uncertain as to the agent of the movement and they reported SoA in approximately 50% of trials when the movement was computer-generated. We tested whether IPC-preSMA coupling was associated with SoA, using dynamic causal modeling (DCM) for induced responses (Chen et al., 2008; Herz et al., 2012). Nine different DCMs were constructed for the early and late phases of the task, respectively. All models included two regions: a superior medial gyrus (preSMA) region and a right supramarginal gyrus (IPC) region. Bayesian models selection (Stephan et al., 2009) favored a model with input to IPC and modulation of the forward connection to SMA in the late task phase, and a model with input to preSMA and modulation of the backward connection was favored for the early task phase. The analysis shows that IPC source activity in the 50–60 Hz range modulated preSMA source activity in the 40–70 Hz range in the presence of SoA compared with no SoA in the late task phase, but the test of the early task phase did not reveal any differences between presence and absence of SoA. We show that SoA is associated with a directionally specific between frequencies coupling from IPC to preSMA in the higher gamma (ɣ) band in the late task phase. This suggests that SoA is a retrospective perception, which is highly dependent on interpretation of the outcome of the performed action. PMID:25076883

  2. Adaptive and energy efficient SMA-based handling systems

    Motzki, P.; Kunze, J.; Holz, B.; York, A.; Seelecke, S.

    2015-04-01

    Shape Memory Alloys (SMA's) are known as actuators with very high energy density. This fact allows for the construction of very light weight and energy-efficient systems. In the field of material handling and automated assembly process, the avoidance of big moments of inertia in robots and kinematic units is essential. High inertial forces require bigger and stronger robot actuators and thus higher energy consumption and costs. For material handling in assembly processes, many different individual grippers for various work piece geometries are used. If one robot has to handle different work pieces, the gripper has to be exchanged and the assembly process is interrupted, which results in higher costs. In this paper, the advantages of using high energy density Shape Memory Alloy actuators in applications of material-handling and gripping-technology are explored. In particular, light-weight SMA actuated prototypes of an adaptive end-effector and a vacuum-gripper are constructed via rapid-prototyping and evaluated. The adaptive end-effector can change its configuration according to the work piece geometry and allows the handling of multiple different shaped objects without exchanging gripper tooling. SMA wires are used to move four independent arms, each arm adds one degree of freedom to the kinematic unit. At the tips of these end-effector arms, SMA-activated suction cups can be installed. The suction cup prototypes are developed separately. The flexible membranes of these suction cups are pulled up by SMA wires and thus a vacuum is created between the membrane and the work piece surface. The self-sensing ability of the SMA wires are used in both prototypes for monitoring their actuation.

  3. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

    Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A.

    2005-01-01

    Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes

  4. Sequences of the joining region genes for immunoglobulin heavy chains and their role in generation of antibody diversity.

    Gough, N M; Bernard, O

    1981-01-01

    To assess the contribution to immunoglobulin heavy chain diversity made by recombination between variable region (VH) genes and joining region (JH) genes, we have determined the sequence of about 2000 nucleotides spanning the rearranged JH gene cluster associated with the VH gene expressed in plasmacytoma HPC76. The active VH76 gene has recombined with the second germ-line JH gene. The region we have studied contains two other JH genes, designated JH3 and JH4. No other JH gene was found withi...

  5. Regional differences in gene expression and promoter usage in aged human brains

    Pardo, Luba M.; Rizzu, Patrizia; Francescatto, Margherita; Vitezic, Morana; Leday, Gwenaë l G.R.; Sanchez, Javier Simon; Khamis, Abdullah M.; Takahashi, Hazuki; van de Berg, Wilma D.J.; Medvedeva, Yulia A.; van de Wiel, Mark A.; Daub, Carsten O.; Carninci, Piero; Heutink, Peter

    2013-01-01

    To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites

  6. Regional differences in gene expression and promoter usage in aged human brains

    Pardo, Luba M.

    2013-02-19

    To characterize the promoterome of caudate and putamen regions (striatum), frontal and temporal cortices, and hippocampi from aged human brains, we used high-throughput cap analysis of gene expression to profile the transcription start sites and to quantify the differences in gene expression across the 5 brain regions. We also analyzed the extent to which methylation influenced the observed expression profiles. We sequenced more than 71 million cap analysis of gene expression tags corresponding to 70,202 promoter regions and 16,888 genes. More than 7000 transcripts were differentially expressed, mainly because of differential alternative promoter usage. Unexpectedly, 7% of differentially expressed genes were neurodevelopmental transcription factors. Functional pathway analysis on the differentially expressed genes revealed an overrepresentation of several signaling pathways (e.g., fibroblast growth factor and wnt signaling) in hippocampus and striatum. We also found that although 73% of methylation signals mapped within genes, the influence of methylation on the expression profile was small. Our study underscores alternative promoter usage as an important mechanism for determining the regional differences in gene expression at old age.

  7. Gene expression meta-analysis identifies chromosomal regions involved in ovarian cancer survival

    Thomassen, Mads; Jochumsen, Kirsten M; Mogensen, Ole

    2009-01-01

    the relation of gene expression and chromosomal position to identify chromosomal regions of importance for early recurrence of ovarian cancer. By use of *Gene Set Enrichment Analysis*, we have ranked chromosomal regions according to their association to survival. Over-representation analysis including 1...... using death (P = 0.015) and recurrence (P = 0.002) as outcome. The combined mutation score is strongly associated to upregulation of several growth factor pathways....

  8. Pemanfaatan Informasi Olahraga di Media Massa Cetak oleh Guru Pendidikan Jasmani dan Kesehatan dalam Pembelajaran Pendidikan Jasmani dan Kesehatan di SMA 5, SMA 6, SMA 11 Semarang

    Muhaimin Muhaimin

    2011-01-01

    Full Text Available Utilization of information in mass media print by master of physical education and health in physical education and health in SMA 5, SMA 6, SMA 11 Semarang. The presence of print media is now a community needs. That's because, the print media presents a variety of information including information of actual politics, culture, economy, crime, entertainment, and sports. Basically, sports information in the print media have educational value and can add insight to a reading of new knowledge. The study produced these findings: (1 third physical education and health teacher at school who becomes the object research have made use of sports information in the print media to support the success of teaching and learning process, (2 the type of information they use to support the success of learning teaching is a form of news, articles about health, (3 form of utilization is appropriate to set clipping and through direct delivery of the material in the field while providing practice in the field. This method is considered more effective because all students can immediately practice, (4 sports information in the print media meets the needs of teachers and physical health education in supporting the learning process.

  9. Genetic organization of the unc-22 IV gene and the adjacent region in Caenorhabditis elegans.

    Rogalski, T M; Baillie, D L

    1985-01-01

    The genetic organization of the region immediately adjacent to the unc-22 IV gene in Caenorhabditis elegans has been studied. We have identified twenty essential genes in this interval of approximately 1.5-map units on Linkage Group IV. The mutations that define these genes were positioned by recombination mapping and complementation with several deficiencies. With few exceptions, the positions obtained by these two methods agreed. Eight of the twenty essential genes identified are represented by more than one allele. Three possible internal deletions of the unc-22 gene have been located by intra-genic mapping. In addition, the right end point of a deficiency or an inversion affecting the adjacent genes let-56 and unc-22 has been positioned inside the unc-22 gene.

  10. Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

    Ersland, Kari M; Christoforou, Andrea; Stansberg, Christine

    2012-01-01

    the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n...

  11. Fabricating Composite-Material Structures Containing SMA Ribbons

    Turner, Travis L.; Cano, Roberto J.; Lach, Cynthia L.

    2003-01-01

    An improved method of designing and fabricating laminated composite-material (matrix/fiber) structures containing embedded shape-memory-alloy (SMA) actuators has been devised. Structures made by this method have repeatable, predictable properties, and fabrication processes can readily be automated. Such structures, denoted as shape-memory-alloy hybrid composite (SMAHC) structures, have been investigated for their potential to satisfy requirements to control the shapes or thermoelastic responses of themselves or of other structures into which they might be incorporated, or to control noise and vibrations. Much of the prior work on SMAHC structures has involved the use SMA wires embedded within matrices or within sleeves through parent structures. The disadvantages of using SMA wires as the embedded actuators include (1) complexity of fabrication procedures because of the relatively large numbers of actuators usually needed; (2) sensitivity to actuator/ matrix interface flaws because voids can be of significant size, relative to wires; (3) relatively high rates of breakage of actuators during curing of matrix materials because of sensitivity to stress concentrations at mechanical restraints; and (4) difficulty of achieving desirable overall volume fractions of SMA wires when trying to optimize the integration of the wires by placing them in selected layers only.

  12. Identification of a locus control region for quadruplicated green-sensitive opsin genes in zebrafish

    Tsujimura, Taro; Chinen, Akito; Kawamura, Shoji

    2007-01-01

    Duplication of opsin genes has a crucial role in the evolution of visual system. Zebrafish have four green-sensitive (RH2) opsin genes (RH2–1, RH2–2, RH2–3, and RH2–4) arrayed in tandem. They are expressed in the short member of the double cones (SDC) but differ in expression areas in the retina and absorption spectra of their encoding photopigments. The shortest and the second shortest wavelength subtypes, RH2–1 and RH2–2, are expressed in the central-to-dorsal retina. The longer wavelength subtype, RH2–3, is expressed circumscribing the RH2–1/RH2–2 area, and the longest subtype, RH2–4, is expressed further circumscribing the RH2–3 area and mainly occupying the ventral retina. The present report shows that a 0.5-kb region located 15 kb upstream of the RH2 gene array is an essential regulator for their expression. When the 0.5-kb region was deleted from a P1-artificial chromosome (PAC) clone encompassing the four RH2 genes and when one of these genes was replaced with a reporter GFP gene, the GFP expression in SDCs was abolished in the zebrafish to which a series of the modified PAC clones were introduced. Transgenic studies also showed that the 0.5-kb region conferred the SDC-specific expression for promoters of a non-SDC (UV opsin) and a nonretinal (keratin 8) gene. Changing the location of the 0.5-kb region in the PAC clone conferred the highest expression for its proximal gene. The 0.5-kb region was thus designated as RH2-LCR analogous to the locus control region of the L-M opsin genes of primates. PMID:17646658

  13. The clinical impact of hypoxia-regulated gene expression in loco-regional gastroesophageal cancer

    Winther, M.; Alsner, J.; Tramm, T.

    2015-01-01

    Purpose/Objective: In a former study (1), the hypoxia gene expression classifier, developed in head and neck squamous cell carcinomas, was applied in 89 patients with loco-regional gastroesophageal cancer (GC). Analysis of the 15 genes was indicative of hypoxia being more profound in esophagus...... and display greater heterogeneity compared to AC. However, previous indications that the hypoxia classifier might hold prognostic significance in ESCC patients could not be confirmed. Ongoing work includes in vitro studies of esophageal cancer cell lines in order to identify alternative hypoxia induced genes...... and to further explore the prognostic value of hypoxia in patients with loco-regional gastroesophageal cancer. (Figure Presented)....

  14. Cloning and characterization of the 5'-flanking region of the Ehox gene

    Lee, Woon Kyu; Kim, Yong-Man; Malik, Nasir; Ma Chang; Westphal, Heiner

    2006-01-01

    The paired-like homeobox-containing gene Ehox plays a role in embryonic stem cell differentiation and is highly expressed in the developing placenta and thymus. To understand the mechanisms of regulation of Ehox gene expression, the 5'-flanking region of the Ehox gene was isolated from a mouse BAC library. 5'-RACE analysis revealed a single transcriptional start site 130 nucleotides upstream of the translation initiation codon. Transient transfection with a luciferase reporter gene under the control of serially deleted 5'-flanking sequences revealed that the nt -84 to -68 region contained a positive cis-acting element for efficient expression of the Ehox gene. Mutational analysis of this region and oligonucleotide competition in the electrophoretic mobility shift assay revealed the presence of a CCAAT box, which is a target for transcription nuclear factor Y (NFY). NFY is essential for positive gene regulation. No tissue-specific enhancer was identified in the 1.9-kb 5'-flanking region of the Ehox gene. Ehox is expressed during the early stages of embryo development, specifically in Brain at 9.5 dpc, as well as during the late stages of embryo development. These results suggest that NFY is an essential regulatory factor for Ehox transcriptional activity, which is important for the post-implantation stage of the developing embryo

  15. Growth and gene expression are predominantly controlled by distinct regions of the human IL-4 receptor.

    Ryan, J J; McReynolds, L J; Keegan, A; Wang, L H; Garfein, E; Rothman, P; Nelms, K; Paul, W E

    1996-02-01

    IL-4 causes hematopoietic cells to proliferate and express a series of genes, including CD23. We examined whether IL-4-mediated growth, as measured by 4PS phosphorylation, and gene induction were similarly controlled. Studies of M12.4.1 cells expressing human IL-4R truncation mutants indicated that the region between amino acids 557-657 is necessary for full gene expression, which correlated with Stat6 DNA binding activity. This region was not required for 4PS phosphorylation. Tyrosine-to-phenylalanine mutations in the interval between amino acids 557-657 revealed that as long as one tyrosine remained unmutated, CD23 was fully induced. When all three tyrosines were mutated, the receptor was unable to induce CD23. The results indicate that growth regulation and gene expression are principally controlled by distinct regions of IL-4R.

  16. Dynamics study of free volume properties of SMA/SMMA blends by PAL method

    Jiang, Z.Y.; Jiang, X.Q.; Huang, Y.J.; Lin, J.; Li, S.M.; Li, S.Z.; Hsia, Y.F.

    2006-01-01

    Miscibility of poly(styrene-co-maleic anhydride) (containing 7 wt% maleic anhydride)/poly(styrene-co-methyl methacrylate) (containing 40 wt% styrene) blends were previously studied. It was obtained that SMA70 (containing 70 wt% of SMA in SMA/SMMA blends) is miscible in molecular level but SMA20 is not. In this paper, the two blends selected were used to investigate the temperature dependence of free volume parameters. It showed there are different deviations of free volume parameters in SMA20 and SMA70, and it was interesting that temperature dependence of ortho-positronium lifetime τ 3 of the SMA20 mixture exhibits two breaks in the range temperature from 90 deg. C to 120 deg. C, which revealed that the mixture has two glass transition ranges. Also, ortho-positronium lifetime τ 3 of the SMA20 mixture is nearly constant in the temperature range from 130 deg. C to 160 deg. C. These indicated that SMA20 blend is phase-separated in room temperature and become miscible above 130 deg. C, which may be due to steric hindrance effect of phenyl rings of SMMA and SMA. From the deviation of o-Ps lifetimes of SMA70, the single glass transition temperature of SMA70 blend was shown. Combining the previous study, it was further concluded that PAL method seems to be a powerful method to detect in situ phase behavior of immiscible polymer blends and glass transition of miscible polymer blends

  17. Molecular methods for bacterial genotyping and analyzed gene regions

    İbrahim Halil Yıldırım1, Seval Cing Yıldırım2, Nadir Koçak3

    2011-06-01

    Full Text Available Bacterial strain typing is an important process for diagnosis, treatment and epidemiological investigations. Current bacterial strain typing methods may be classified into two main categories: phenotyping and genotyping. Phenotypic characters are the reflection of genetic contents. Genotyping, which refers discrimination of bacterial strains based on their genetic content, has recently become widely used for bacterial strain typing. The methods already used in genotypingof bacteria are quite different from each other. In this review we tried to summarize the basic principles of DNA-based methods used in genotyping of bacteria and describe some important DNA regions that are used in genotyping of bacteria. J Microbiol Infect Dis 2011;1(1:42-46.

  18. Mapping the transcription termination region of the mouse immunoglobulin kappa gene

    Xu, M.; Garrard, W.T.

    1986-01-01

    To define the transcription termination region of the mouse immunoglobulin kappa gene, they have subcloned single copy DNA sequences corresponding to both the template and the non-template strands of this locus. In vitro nuclear transcription with isolated MPC-11 nuclei was performed and the resulting 32 P-labeled RNA was hybridized to slot-blotted, single-stranded M13 probes covering regions within and flanking the kappa gene. The hybridization pattern for the template-strand reveals that transcription terminates within the region between 1.1 to 2.3 kb downstream from the poly(A) site. Ten different short sequences (8-13 bp) reside within 460 bp of this region that exhibit homology with sequences found in the termination regions of mouse β-globin and chicken ovalbumin genes. Transcription of the non-template strand occurs on either side of this termination region. They note that no transcription is detectable on the non-template strand downstream of the enhancer, indicating that if RNA polymerase II enters at this site, it does not initiate transcription during transit to the promoter region. They conclude that transcription of the kappa gene passes the poly(A) addition site and terminates within 2.3 Kb downstream

  19. Gene study within the 5' flanking regions of growth hormone gene of ...

    user

    2011-01-17

    Jan 17, 2011 ... Expression of more than one gene for GH has been reported, indicating ..... hormone levels of palsmáticos IGF-1 and carcass traits in beef cattle. Dissertation ... Structure-function relation of somatotropin with reference to ...

  20. Identification of a set of genes showing regionally enriched expression in the mouse brain

    Marra Marco A

    2008-07-01

    Full Text Available Abstract Background The Pleiades Promoter Project aims to improve gene therapy by designing human mini-promoters ( Results We have utilized LongSAGE to identify regionally enriched transcripts in the adult mouse brain. As supplemental strategies, we also performed a meta-analysis of published literature and inspected the Allen Brain Atlas in situ hybridization data. From a set of approximately 30,000 mouse genes, 237 were identified as showing specific or enriched expression in 30 target regions of the mouse brain. GO term over-representation among these genes revealed co-involvement in various aspects of central nervous system development and physiology. Conclusion Using a multi-faceted expression validation approach, we have identified mouse genes whose human orthologs are good candidates for design of mini-promoters. These mouse genes represent molecular markers in several discrete brain regions/cell-types, which could potentially provide a mechanistic explanation of unique functions performed by each region. This set of markers may also serve as a resource for further studies of gene regulatory elements influencing brain expression.

  1. Scarless and sequential gene modification in Pseudomonas using PCR product flanked by short homology regions

    Liang Rubing

    2010-08-01

    Full Text Available Abstract Background The lambda Red recombination system has been used to inactivate chromosomal genes in various bacteria and fungi. The procedure consists of electroporating a polymerase chain reaction (PCR fragment containing antibiotic cassette flanked by homology regions to the target locus into a strain that can express the lambda Red proteins (Gam, Bet, Exo. Results Here a scarless gene modification strategy based on the Red recombination system has been developed to modify Pseudomonas genome DNA via sequential deletion of multiple targets. This process was mediated by plasmid pRKaraRed encoding the Red proteins regulated by PBAD promoter, which was functional in P. aeruginosa as well as in other bacteria. First the target gene was substituted for the sacB-bla cassette flanked by short homology regions (50 bp, and then this marker gene cassette could be replaced by the PCR fragment flanking itself, generating target-deleted genome without any remnants and no change happened to the surrounding region. Twenty genes involved in the synthesis and regulation pathways of the phenazine derivate, pyocyanin, were modified, including one single-point mutation and deletion of two large operons. The recombination efficiencies ranged from 88% to 98%. Multiple-gene modification was also achieved, generating a triple-gene deletion strain PCA (PAO1, ΔphzHΔphzMΔphzS, which could produce another phenazine derivate, phenazine-1-carboxylic acid (PCA, efficiently and exclusively. Conclusions This lambda Red-based technique can be used to generate scarless and sequential gene modification mutants of P. aeruginosa efficiently, using one-step PCR product flanked by short homology regions. Single-point mutation, scarless deletion of genes can be achieved easily in less than three days. This method may give a new way to construct genetically modified P. aeruginosa strains more efficiently and advance the regulatory network study of this organism.

  2. Fatigue crack behavior on a Cu-Zn-Al SMA

    V. Di Cocco

    2014-10-01

    Full Text Available In recent years, mechanical property of many SMA has improved in order to introduce these alloys in specific field of industry. Main examples of these alloys are the NiTi, Cu-Zn-Al and Cu-Al-Ni which are used in many fields of engineering such as aerospace or mechanical systems. Cu-Zn-Al alloys are characterized by good shape memory properties due to a bcc disordered structure stable at high temperature called β-phase, which is able to change by means of a reversible transition to a B2 structure after appropriate cooling, and reversible transition from B2 secondary to DO3 order, under other types of cooling. In β-Cu-Zn-Al shape memory alloys, the martensitic transformation is not in equilibrium at room temperature. It is therefore often necessary to obtain the martensitic structure, using a thermal treatment at high temperature followed by quenching. The martensitic phases can be either thermally-induced spontaneous transformation, or stressinduced, or cooling, or stressing the β- phase. Direct quenching from high temperatures to the martensite phase is the most effective because of the non-diffusive character of the transformation. The martensite inherits the atomic order from the β-phase. Precipitation of many kinds of intermetallic phases is the main problem of treatment on cu-based shape memory alloy. For instance, a precipitation of α-phase occurs in many low aluminum copper based SMA alloy and presence of α-phase implies a strong degradation of shape recovery. However, Cu-Zn-Al SMA alloys characterized by aluminum contents less than 5% cover a good cold machining and cost is lower than traditional NiTi SMA alloys. In order to improve the SMA performance, it is always necessary to identify the microstructural changing in mechanical and thermal conditions, using X-Ray analyses. In this work a Cu-Zn-Al SMA alloy obtained in laboratory has been microstructurally and metallographically characterized by means of X-Ray diffraction and Light

  3. Kinetics and regional specificity of irinotecan-induced gene expression in the gastrointestinal tract

    Bowen, Joanne M.; Tsykin, Anna; Stringer, Andrea M.; Logan, Richard M.; Gibson, Rachel J.; Keefe, Dorothy M.K.

    2010-01-01

    Gastrointestinal toxicity remains a significant and dose-limiting complication of cancer treatment. While the pathophysiology is becoming clearer, considerable gaps in the knowledge remain surrounding the timing and site-specific gene changes which occur in response to insult. As such, this study aimed to assess gene expression profiles in a number of regions along the gastrointestinal tract following treatment with the chemotherapy agent, irinotecan, and correlate them with markers of cell death and tissue damage. Data analysis of microarray results found that genes involved in apoptosis, mitogen activated kinase (MAPK) signalling and inflammation were upregulated within 6 h, while genes involved in cell proliferation, wound healing and blood vessel formation were upregulated at later time points up to 72 h. Cell death was significantly increased at 6 and 24 h, and the stomach showed the lowest severity of overt tissue damage. Real time PCR of MAPK signalling pathway genes found that the jejunum and colon had significantly increased expression in a number of genes at 72 h, where as the stomach was unchanged. These results indicate that overall severity of tissue damage may be determined by precisely timed target gene responses specific to each region. Therapeutic targeting of key gene responses at the appropriate time point may prove to be effective for prevention of chemotherapy-induced gastrointestinal damage.

  4. Comparative Transcriptome Analysis Reveals That Lactose Acts as an Inducer and Provides Proper Carbon Sources for Enhancing Exopolysaccharide Yield in the Deep-Sea Bacterium Zunongwangia profunda SM-A87

    Qin, Qi-Long; Li, Yi; Sun, Mei-Ling; Rong, Jin-Cheng; Liu, Sheng-Bo; Chen, Xiu-Lan; Su, Hai-Nan; Zhou, Bai-Cheng; Xie, Bin-Bin; Zhang, Yu-Zhong; Zhang, Xi-Ying

    2015-01-01

    Many marine bacteria secrete exopolysaccharides (EPSs) that have important ecological and physiological functions. Numerous nutritional and environmental factors influence bacterial EPS production. However, the regulatory mechanisms of EPS production are poorly understood. The deep-sea Bacteroidetes bacterium Zunongwangia profunda SM-A87 can produce high quantities of EPS, and its EPS production is enhanced significantly by lactose. Here, we studied the reasons behind the significant advantage that lactose has over other carbon sources in EPS production in SM-A87. RNA-seq technologies were used to study lactose-regulated genes in SM-A87. The expression level of genes within the EPS gene cluster was up-regulated when lactose was added. Supplement of lactose also influenced the expression of genes located outside the EPS gene cluster that are also involved in EPS biosynthesis. The major glycosyl components of SM-A87 EPS are mannose, glucose and galactose. Genomic metabolic pathway analyses showed that the EPS precursor GDP-mannose can be synthesized from glucose, while the precursor UDP-glucose must be synthesized from galactose. Lactose can provide glucose and galactose simultaneously and prevent glucose inhibition. Lactose can also greatly stimulate the growth of SM-A87. Taken together, lactose acts not only as an inducer but also as a carbohydrate source for EPS production. This research broadens our knowledge of the regulation of EPS production in marine bacteria. PMID:25679965

  5. Identification of Differentially Expressed Genes through Integrated Study of Alzheimer's Disease Affected Brain Regions.

    Nisha Puthiyedth

    Full Text Available Alzheimer's disease (AD is the most common form of dementia in older adults that damages the brain and results in impaired memory, thinking and behaviour. The identification of differentially expressed genes and related pathways among affected brain regions can provide more information on the mechanisms of AD. In the past decade, several studies have reported many genes that are associated with AD. This wealth of information has become difficult to follow and interpret as most of the results are conflicting. In that case, it is worth doing an integrated study of multiple datasets that helps to increase the total number of samples and the statistical power in detecting biomarkers. In this study, we present an integrated analysis of five different brain region datasets and introduce new genes that warrant further investigation.The aim of our study is to apply a novel combinatorial optimisation based meta-analysis approach to identify differentially expressed genes that are associated to AD across brain regions. In this study, microarray gene expression data from 161 samples (74 non-demented controls, 87 AD from the Entorhinal Cortex (EC, Hippocampus (HIP, Middle temporal gyrus (MTG, Posterior cingulate cortex (PC, Superior frontal gyrus (SFG and visual cortex (VCX brain regions were integrated and analysed using our method. The results are then compared to two popular meta-analysis methods, RankProd and GeneMeta, and to what can be obtained by analysing the individual datasets.We find genes related with AD that are consistent with existing studies, and new candidate genes not previously related with AD. Our study confirms the up-regualtion of INFAR2 and PTMA along with the down regulation of GPHN, RAB2A, PSMD14 and FGF. Novel genes PSMB2, WNK1, RPL15, SEMA4C, RWDD2A and LARGE are found to be differentially expressed across all brain regions. Further investigation on these genes may provide new insights into the development of AD. In addition, we

  6. PreSMA stimulation changes task-free functional connectivity in the fronto-basal-ganglia that correlates with response inhibition efficiency.

    Xu, Benjamin; Sandrini, Marco; Wang, Wen-Tung; Smith, Jason F; Sarlls, Joelle E; Awosika, Oluwole; Butman, John A; Horwitz, Barry; Cohen, Leonardo G

    2016-09-01

    Previous work using transcranial magnetic stimulation (TMS) demonstrated that the right presupplementary motor area (preSMA), a node in the fronto-basal-ganglia network, is critical for response inhibition. However, TMS influences interconnected regions, raising the possibility of a link between the preSMA activity and the functional connectivity within the network. To understand this relationship, we applied single-pulse TMS to the right preSMA during functional magnetic resonance imaging when the subjects were at rest to examine changes in neural activity and functional connectivity within the network in relation to the efficiency of response inhibition evaluated with a stop-signal task. The results showed that preSMA-TMS increased activation in the right inferior-frontal cortex (rIFC) and basal ganglia and modulated their task-free functional connectivity. Both the TMS-induced changes in the basal-ganglia activation and the functional connectivity between rIFC and left striatum, and of the overall network correlated with the efficiency of response inhibition and with the white-matter microstructure along the preSMA-rIFC pathway. These results suggest that the task-free functional and structural connectivity between the rIFCop and basal ganglia are critical to the efficiency of response inhibition. Hum Brain Mapp 37:3236-3249, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. Characterization of a gene from the EDM1-PSACH region of human chromosome 19p

    Lennon, G.G.; Giorgi, D.; Martin, J.R. [Lawrence Livermore National Lab., CA (United States)] [and others

    1994-09-01

    Genetic linkage mapping has indicated that both multiple epiphyseal dysplasia (EDM1), a dominantly inherited chondrodysplasia, and pseudoachondroplasia (PSACH), a skeletal disorder associated with dwarfism, map to a 2-3 Mb region of human chromosome 19p. We have isolated a partial cDNA from this region using hybrid selection, and report on progress towards the characterization of the genomic structure and transcription of the corresponding gene. Sequence analysis of the cDNA to date indicates that this gene is likely to be expressed within extracellular matrix tissues. Defects in this gene or neighboring gene family members may therefore lead to EDM1, PSACH, or other connective tissue and skeletal disorders.

  8. Fast rate of evolution in alternatively spliced coding regions of mammalian genes

    Nurtdinov Ramil N

    2006-04-01

    Full Text Available Abstract Background At least half of mammalian genes are alternatively spliced. Alternative isoforms are often genome-specific and it has been suggested that alternative splicing is one of the major mechanisms for generating protein diversity in the course of evolution. Another way of looking at alternative splicing is to consider sequence evolution of constitutive and alternative regions of protein-coding genes. Indeed, it turns out that constitutive and alternative regions evolve in different ways. Results A set of 3029 orthologous pairs of human and mouse alternatively spliced genes was considered. The rate of nonsynonymous substitutions (dN, the rate of synonymous substitutions (dS, and their ratio (ω = dN/dS appear to be significantly higher in alternatively spliced coding regions compared to constitutive regions. When N-terminal, internal and C-terminal alternatives are analysed separately, C-terminal alternatives appear to make the main contribution to the observed difference. The effects become even more pronounced in a subset of fast evolving genes. Conclusion These results provide evidence of weaker purifying selection and/or stronger positive selection in alternative regions and thus one more confirmation of accelerated evolution in alternative regions. This study corroborates the theory that alternative splicing serves as a testing ground for molecular evolution.

  9. Buckling analysis of SMA bonded sandwich structure – using FEM

    Katariya, Pankaj V.; Das, Arijit; Panda, Subrata K.

    2018-03-01

    Thermal buckling strength of smart sandwich composite structure (bonded with shape memory alloy; SMA) examined numerically via a higher-order finite element model in association with marching technique. The excess geometrical distortion of the structure under the elevated environment modeled through Green’s strain function whereas the material nonlinearity counted with the help of marching method. The system responses are computed numerically by solving the generalized eigenvalue equations via a customized MATLAB code. The comprehensive behaviour of the current finite element solutions (minimum buckling load parameter) is established by solving the adequate number of numerical examples including the given input parameter. The current numerical model is extended further to check the influence of various structural parameter of the sandwich panel on the buckling temperature including the SMA effect and reported in details.

  10. The Norrie disease gene maps to a 150 kb region on chromosome Xp11.3.

    Sims, K B; Lebo, R V; Benson, G; Shalish, C; Schuback, D; Chen, Z Y; Bruns, G; Craig, I W; Golbus, M S; Breakefield, X O

    1992-05-01

    Norrie disease is a human X-linked recessive disorder of unknown etiology characterized by congenital blindness, sensory neural deafness and mental retardation. This disease gene was previously linked to the DXS7 (L1.28) locus and the MAO genes in band Xp11.3. We report here fine physical mapping of the obligate region containing the Norrie disease gene (NDP) defined by a recombination and by the smallest submicroscopic chromosomal deletion associated with Norrie disease identified to date. Analysis, using in addition two overlapping YAC clones from this region, allowed orientation of the MAOA and MAOB genes in a 5'-3'-3'-5' configuration. A recombination event between a (GT)n polymorphism in intron 2 of the MAOB gene and the NDP locus, in a family previously reported to have a recombination between DXS7 and NDP, delineates a flanking marker telomeric to this disease gene. An anonymous DNA probe, dc12, present in one of the YACs and in a patient with a submicroscopic deletion which includes MAOA and MAOB but not L1.28, serves as a flanking marker centromeric to the disease gene. An Alu-PCR fragment from the right arm of the MAO YAC (YMAO.AluR) is not deleted in this patient and also delineates the centromeric extent of the obligate disease region. The apparent order of these loci is telomere ... DXS7-MAOA-MAOB-NDP-dc12-YMAO.AluR ... centromere. Together these data define the obligate region containing the NDP gene to a chromosomal segment less than 150 kb.

  11. 5' Region of the human interleukin 4 gene: structure and potential regulatory elements

    Eder, A; Krafft-Czepa, H; Krammer, P H

    1988-01-25

    The lymphokine Interleukin 4 (IL-4) is secreted by antigen or mitogen activated T lymphocytes. IL-4 stimulates activation and differentiation of B lymphocytes and growth of T lymphocytes and mast cells. The authors isolated the human IL-4 gene from a lambda EMBL3 genomic library. As a probe they used a synthetic oligonucleotide spanning position 40 to 79 of the published IL-4 cDNA sequence. The 5' promoter region contains several sequence elements which may have a cis-acting regulatory function for IL-4 gene expression. These elements include a TATA-box, three CCAAT-elements (two are on the non-coding strand) and an octamer motif. A comparison of the 5' flanking region of the human murine IL-4 gene (4) shows that the region between position -306 and +44 is highly conserved (83% homology).

  12. Organization and annotation of the Xcat critical region: elimination of seven positional candidate genes.

    Huang, Kristen M; Geunes-Boyer, Scarlett; Wu, Sufen; Dutra, Amalia; Favor, Jack; Stambolian, Dwight

    2004-05-01

    Xcat mice display X-linked congenital cataracts and are a mouse model for the human X-linked cataract disease Nance Horan syndrome (NHS). The genetic defect in Xcat mice and NHS patients is not known. We isolated and sequenced a BAC contig representing a portion of the Xcat critical region. We combined our sequencing data with the most recent mouse sequence assemblies from both Celera and public databases. The sequence of the 2.2-Mb Xcat critical region was then analyzed for potential Xcat candidate genes. The coding regions of the seven known genes within this area (Rai2, Rbbp7, Ctps2, Calb3, Grpr, Reps2, and Syap1) were sequenced in Xcat mice and no mutations were detected. The expression of Rai2 was quantitatively identical in wild-type and Xcat mutant eyes. These results indicate that the Xcat mutation is within a novel, undiscovered gene.

  13. Gene mutation in ATM/PI3K region of nasopharyngeal carcinoma cell lines

    Wang Hongmei; Wu Xinyao; Xia Yunfei

    2002-01-01

    Objective: To define the correlation between nasopharyngeal carcinoma (NPC) cell radiosensitivity and gene mutation in the ATM/PI3K coding region. Methods: The gene mutation in the ATM/PI3K region of nasopharyngeal carcinoma cell lines which vary in radiosensitivity, was monitored by reverse transcription-polymerase chain reaction (RT-PCR) and fluorescence-marked ddNTP cycle sequencing technique. Results: No gene mutation was detected in the ATM/PI3K region of either CNE1 or CNE2. Conclusion: Disparity in intrinsic radiosensitivity between different NPC cell lines depends on some other factors and mechanism without being related to ATM/PI3K mutations

  14. Kondisi Stres Akademik Siswa SMA Negeri di Kota Padang

    Taufik Taufik; Ifdil Ifdil

    2014-01-01

    This research conduct base from increasing the National Examination standards from recent years, and overload student’s learning activity in Senior High School (SMA). These conditions as triggers stress students, from a long time, its influence on their learning. Based that, the research is to identify level of student academic stress, and differences base gender, and school location. This research use Cluster Random Sampling. Samples are grouped into 3 (three), that’s school is located in do...

  15. Optimization of SMA layers in composite structures to enhance damping

    Haghdoust, P.; Cinquemani, S.; Lecis, N.; Bassani, P.

    2016-04-01

    The performance of lightweight structures can be severely affected by vibration. New design concepts leading to lightweight, slender structural components can increase the vulnerability of the components to failure due to excessive vibration. The intelligent approach to address the problem would be the use of materials which are more capable in dissipating the energy due to their high value of loss factor. Among the different materials available to achieve damping, much attention has been attached to the use of shape memory alloys (SMAs) because of their unique microstructure, leading to good damping capacity. This work describes the design and optimization of a hybrid layered composite structure for the passive suppression of flexural vibrations in slender and light structures. Embedding the SMA layers in composite structure allows to combine different properties: the lightness of the base composite (e.g. fiber glass), the mechanical strength of the insert of metallic material and the relevant damping properties of SMA, in the martensitic phase. In particular, we put our attention on embedding the CuZnAl in the form of thin sheet in a layered composite made by glass fiber reinforced epoxy. By appropriately positioning of the SMA sheets so that they are subjected to the maximum curvature, the damping of the hybrid system can be considerably enhanced. Accordingly analytical method for evaluating the energy dissipation of the thin sheets with different shapes and patterns is developed and is followed by a shape optimization based on genetic algorithm. Eventually different configurations of the hybrid beam structure with different patterns of SMA layer are proposed and compared in the term of damping capacity.

  16. Development of a Simple Structured Artificial Muscle Using SMA Wire

    Ibuki, Ryuta; Maruyama, Shigenao; Komiya, Atsuki

    2006-01-01

    Artificial heart muscle using SMA wire is developed to assist weaken heartbeat. Simple structure design was adopted for large output force, large displacement and rapid cyclic motion of the actuator. The actuator was designed and fabricated from the viewpoint of heat transfer. Moving performance of the actuator was experimentally measured under 10N of loading condition. Under the maximum efficiency condition, the actuator shows cyclic motion with 1mm of displacement and time period of about 2 seconds in one cycle

  17. PENGEMBANGAN PERANGKAT PEMBELAJARAN KOMPETENSI SULIT MATEMATIKA SMA DI RIAU

    Ummi Aisyah

    2014-05-01

    Full Text Available Tujuan penelitian ini adalah untuk menghasilkan perangkat pembelajaran kompetensi sulit matematika SMA di Provinsi Riau yang berkualitas baik/layak yaitu valid, praktis, dan efektif. Penelitian ini merupakan penelitian pengembangan yang mengembangkan perangkat pembelajaran kompetensi sulit matematika SMA dengan menggunakan model pengembangan 4-D yang dikembangkan oleh Thiagarajan, Semmel & Semmel yang telah dimodifikasi sehingga hanya memuat tahap pen-definisian, perancangan, dan pengembangan. Penelitian ini menghasilkan perangkat pembelajaran kompetensi sulit matematika SMA yang meliputi silabus, rencana pelaksanaan pembelajaran (RPP, lembar kegiatan siswa (LKS, dan instrumen tes. Hasil validasi menunjukkan bahwa silabus, RPP, LKS yang dikembangkan memiliki kategori sangat valid untuk masing-masing silabus, RPP, LKS, dan test instrument. Hasil uji coba lapangan menunjukkan bahwa perangkat yang dikembangkan praktis dan efektif. Kepraktisan mencapai hasil sangat baik ditinjau dari penilaian guru dan siswa. Keefektifan ditinjau dari ketuntasan belajar siswa dan hasil observasi keterlaksanaan pembelajaran. Secara klasikal ketuntasan belajar mencapai 84,38%. Secara keseluruhan, hasil penelitian menunjukkan bahwa perangkat pembelajaran yang dikembangkan adalah layak untuk digunakan. Kata Kunci: pengembangan, perangkat pembelajaran, kompetensi sulit matematika

  18. Low power consumption mini rotary actuator with SMA wires

    Manfredi, Luigi; Huan, Yu; Cuschieri, Alfred

    2017-11-01

    Shape memory alloys (SMAs) are smart materials widely used as actuators for their high power to weight ratio despite their well-known low energy efficiency and limited mechanical bandwidth. For robotic applications, SMAs exhibit limitations due to high power consumption and limited stroke, varying from 4% to 7% of the total length. Hysteresis, during the contraction and extension cycle, requires a complex control algorithm. On the positive side, the small size and low weight are eminently suited for the design of mini actuators for robotic platforms. This paper describes the design and construction of a light weight and low power consuming mini rotary actuator with on-board contact-less position and force sensors. The design is specifically intended to reduce (i) energy consumption, (ii) dimensions of the sensory system, and (iii) provide a simple control without any need for SMA characterisation. The torque produced is controlled by on-board force sensors. Experiments were performed to investigate the energy consumption and performance (step and sinusoidal angle profiles with a frequency varying from 0.5 to 10 Hz and maximal amplitude of {15}\\circ ). We describe a transient capacitor effect related to the SMA wires during the sinusoidal profile when the active SMA wire is powered and the antagonist one switched-off, resulting in a transient current time varying from 300 to 400 ms.

  19. Passive base isolation with superelastic nitinol SMA helical springs

    Huang, Bin; Zhang, Haiyang; Wang, Han; Song, Gangbing

    2014-01-01

    Seismic isolation of structures such as multi-story buildings, nuclear reactors, bridges, and liquid storage tanks should be designed to preserve structural integrity. By implementing seismic isolation technology, the deformation of superstructures can be dramatically reduced, consequently helping to protect their safety as well. In this paper, an innovative type of passive base isolation system, which is mainly composed of superelastic nitinol SMA helical springs, is developed. In order to verify the effectiveness of the proposed system, a two-story experimental steel frame model is constructed, and two superelastic SMA helical springs are thermo-mechanically built in the laboratory. To describe the nonlinear mechanical properties of the superelastic SMA helical springs under reciprocating load, a phenomenological model is presented in terms of a series of tensile tests. Afterwards, a numerical model of the two-story frame with the suggested isolation system is set up to simulate the response of the isolated frame subjected to an earthquake. Both the experimental and the numerical simulation results indicate that the proposed base isolation system can remarkably suppress structural vibrations and has improved isolation effects when compared with a steel spring isolation system. Due to the capabilities of energy dissipation as well as fully re-centering, it is very applicable to utilize the suggested isolation system in base isolated structures to resist earthquakes. (paper)

  20. SMA bellows as reversible thermal sensors/actuators

    Damanpack, A R; Bodaghi, M; Liao, W H

    2015-01-01

    In this paper, the feasibility of reversible bellows made of shape memory alloys (SMAs) in sensory and actuated applications to transfer pressure and/or temperature into a linear motion is investigated. An analytical three-dimensional model is developed to simulate key features of SMAs including martensitic transformation, reorientation of martensite variants, the shape memory effect, and pseudo-elasticity. Axisymmetric two-dimensional theory of thermo-inelasticity based on the non-linear Green–Lagrange strain tensor is employed to derive the equilibrium equations. A finite element method along with an iterative incremental elastic-predictor–inelastic-corrector procedure is developed to solve the governing equations with both material and geometrical non-linearities. The feasibility of reversible SMA bellows in transferring pressure and/or temperature into a linear motion is numerically demonstrated. In this respect, the effects of geometric parameters, magnitude of thermo-mechanical loadings and end conditions on the performances of SMA bellows are evaluated and discussed in depth. This study provides pertinent results toward an efficient and reliable design of reversible thermally-driven SMA bellows. (paper)

  1. Pengembangan Program Macromedia Flash 8 untuk Pembelajaran Fisika di SMA

    Wiji Susilowati

    2007-12-01

    Full Text Available Tujuan penelitian adalah membuat dan mengevaluasi media pembelajaran fisika SMA menggunakan program Macromedia Flash 8. Subjek coba pada penelitian ini berjumlah 40 orang yang terdiri dari 10 siswa untuk uji coba instrumen penelitian, 10 siswa untuk ujicoba kelompok kecdl, dan 20 siswa untuk uji coba lapangan. Pengumpulan data dilakukan dengan mengguna­kan kuesioner dan tes fisika (pre-test dan post-test. Evaluasi terhadap program ditinjau dari aspek pembelajaran dan aspek media. Kritik dan saran digunakan untuk memperbaiki program. Hasil penelitian menunjukkan bahwa program Macromedia Flash 8 untuk pembelajaran fisika di SMA: (1 dirancang sesuai dengan prinsip-prinsip desain pembelajaran, (2 terbukti mampu menaikkan skor rerata tes fisika siswa sebesar 55,42%, (3 memiliki efisiensi waktu yang tinggi, (4 ditinjau dari aspek media Hinilai cukup bagus/menarik (dinilai/dikategorikan sedang oleh siswa, (5 ditinjau dari aspek pembelajaran secara keseluruhan program ini dinilai tinggi/jelas dimengerti oleh siswa, (6 ditinjau dari aspek media dinilai menarik (bagus/kategori tinggi oleh guru fisika, dan (7 ditinjau dari aspek pembelajaran juga dinilai menarik (bagus/kategori tinggi oleh guru fisika. Kata kunci: media pembelajaran fisika diSMA.

  2. KEEFEKTIFAN TEKNIK RELAKSASI UNTUK MENURUNKAN STRES AKADEMIK SISWA SMA

    Suyono Suyono

    2016-08-01

    Full Text Available Abstract: This study aims at examining the effectiveness of relaxation techniques to release students’stress and tension regarding academic within Senior High School Assádah in Gresik City. This study employed quasi-experiment design using one group pretest-posttest model. The data of this study were obtained through academic stress inventory to attain a depiction of stress level encountered by the subject. The subjects of this study were seven students of Tenth Graders in SMA Assaadah Bungah Gresik who experienced low to average stress regarding exam preparation. The data were, then, analyzed by using Wilcoxon Statistic Analysis. The result of the study indicated that relaxation technique could lower and release the level of students stress in exam preparation. Key Words: relaxation technique, student academic stress   Abstrak: Penelitian ini bertujuan untuk  menguji keefektifan teknik relaksasi untuk menurunkan stres akademik siswa SMA Ass’adah di Kota Gresik dengan menggunakan rancangan kuasi eksperimen dengan model “one group pretest posttest design. Pengumpulan data dengan menggunakan inventori stres akademik tujuannya untuk memperoleh gambaran tingkat stres akademik pada subjek penelitian. Subjek penelitian adalah siswa yang mengalami stres akademik sedang dan rendah  dalam menghadapi ujian berjumlah 7 orang siswa pada kelas X SMA Assaadah Bungah Gresik. Teknik analisis data dengan menggunakanan analisis statistic Wilcoxon. Hasil penelitian menunjukkan adanya penurunan tingkat stres akademik menjelang ujian sesudah subjek mendapatkan layanan dengan teknik  relaksasi. Kata kunci: Teknik relaksasi, stres akademik siswa

  3. Human heavy-chain variable region gene family nonrandomly rearranged in familial chronic lymphocytic leukemia

    Shen, A.; Humphries, C.; Tucker, P.; Blattner, F.

    1987-01-01

    The authors have identified a family of human immunoglobulin heavy-chain variable-region (V/sub H/) genes, one member of which is rearranged in two affected members of a family in which the father and four of five siblings developed chronic lymphocytic leukemia. Cloning and sequencing of the rearranged V/sub H/ genes from leukemic lymphocytes of three affected siblings showed that two siblings had rearranged V/sub H/ genes (V/sub H/TS1 and V/sub H/WS1) that were 90% homologous. The corresponding germ-line gene, V/sub H/251, was found to part of a small (four gene) V/sub H/ gene family, which they term V/sub H/V. The DNA sequence homology to V/sub H/WS1 (95%) and V/sub H/TS1 (88%) and identical restriction sites on the 5' side of V/sub H/ confirm that rearrangement of V/sub H/251 followed by somatic mutation produced the identical V/sub H/ gene rearrangements in the two siblings. V/sub H/TS1 is not a functional V/sub H/ gene; a functional V/sub H/ rearrangement was found on the other chromosome of this patient. The other two siblings had different V/sub H/ gene rearrangements. All used different diversity genes. Mechanisms proposed for nonrandom selection of a single V/sub H/ gene include developmental regulation of this V/sub H/ gene rearrangement or selection of a subpopulation of B cells in which this V/sub H/ has been rearranged

  4. Analysis of gene expression profile microarray data in complex regional pain syndrome.

    Tan, Wulin; Song, Yiyan; Mo, Chengqiang; Jiang, Shuangjian; Wang, Zhongxing

    2017-09-01

    The aim of the present study was to predict key genes and proteins associated with complex regional pain syndrome (CRPS) using bioinformatics analysis. The gene expression profiling microarray data, GSE47603, which included peripheral blood samples from 4 patients with CRPS and 5 healthy controls, was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in CRPS patients compared with healthy controls were identified using the GEO2R online tool. Functional enrichment analysis was then performed using The Database for Annotation Visualization and Integrated Discovery online tool. Protein‑protein interaction (PPI) network analysis was subsequently performed using Search Tool for the Retrieval of Interaction Genes database and analyzed with Cytoscape software. A total of 257 DEGs were identified, including 243 upregulated genes and 14 downregulated ones. Genes in the human leukocyte antigen (HLA) family were most significantly differentially expressed. Enrichment analysis demonstrated that signaling pathways, including immune response, cell motion, adhesion and angiogenesis were associated with CRPS. PPI network analysis revealed that key genes, including early region 1A binding protein p300 (EP300), CREB‑binding protein (CREBBP), signal transducer and activator of transcription (STAT)3, STAT5A and integrin α M were associated with CRPS. The results suggest that the immune response may therefore serve an important role in CRPS development. In addition, genes in the HLA family, such as HLA‑DQB1 and HLA‑DRB1, may present potential biomarkers for the diagnosis of CRPS. Furthermore, EP300, its paralog CREBBP, and the STAT family genes, STAT3 and STAT5 may be important in the development of CRPS.

  5. Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

    Walker Angela M

    2009-04-01

    Full Text Available Abstract Background The Pregnancy-associated glycoproteins (PAGs belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprised of at least 22 transcribed genes, as well as some variants. Phylogenetic analyses have shown that the PAG family segregates into 'ancient' and 'modern' groupings. Along with sequence differences between family members, there are clear distinctions in their spatio-temporal distribution and in their relative level of expression. In this report, 1 we performed an in silico analysis of the bovine genome to further characterize the PAG gene family, 2 we scrutinized proximal promoter sequences of the PAG genes to evaluate the evolution pressures operating on them and to identify putative regulatory regions, 3 we determined relative transcript abundance of selected PAGs during pregnancy and, 4 we performed preliminary characterization of the putative regulatory elements for one of the candidate PAGs, bovine (bo PAG-2. Results From our analysis of the bovine genome, we identified 18 distinct PAG genes and 14 pseudogenes. We observed that the first 500 base pairs upstream of the translational start site contained multiple regions that are conserved among all boPAGs. However, a preponderance of conserved regions, that harbor recognition sites for putative transcriptional factors (TFs, were found to be unique to the modern boPAG grouping, but not the ancient boPAGs. We gathered evidence by means of Q-PCR and screening of EST databases to show that boPAG-2 is the most abundant of all boPAG transcripts. Finally, we provided preliminary evidence for the role of ETS- and DDVL-related TFs in the regulation of the boPAG-2 gene. Conclusion PAGs represent a relatively large gene family in the bovine genome. The proximal promoter regions of these genes display differences in putative TF binding sites, likely contributing to observed

  6. A Region-Based GeneSIS Segmentation Algorithm for the Classification of Remotely Sensed Images

    Stelios K. Mylonas

    2015-03-01

    Full Text Available This paper proposes an object-based segmentation/classification scheme for remotely sensed images, based on a novel variant of the recently proposed Genetic Sequential Image Segmentation (GeneSIS algorithm. GeneSIS segments the image in an iterative manner, whereby at each iteration a single object is extracted via a genetic-based object extraction algorithm. Contrary to the previous pixel-based GeneSIS where the candidate objects to be extracted were evaluated through the fuzzy content of their included pixels, in the newly developed region-based GeneSIS algorithm, a watershed-driven fine segmentation map is initially obtained from the original image, which serves as the basis for the forthcoming GeneSIS segmentation. Furthermore, in order to enhance the spatial search capabilities, we introduce a more descriptive encoding scheme in the object extraction algorithm, where the structural search modules are represented by polygonal shapes. Our objectives in the new framework are posed as follows: enhance the flexibility of the algorithm in extracting more flexible object shapes, assure high level classification accuracies, and reduce the execution time of the segmentation, while at the same time preserving all the inherent attributes of the GeneSIS approach. Finally, exploiting the inherent attribute of GeneSIS to produce multiple segmentations, we also propose two segmentation fusion schemes that operate on the ensemble of segmentations generated by GeneSIS. Our approaches are tested on an urban and two agricultural images. The results show that region-based GeneSIS has considerably lower computational demands compared to the pixel-based one. Furthermore, the suggested methods achieve higher classification accuracies and good segmentation maps compared to a series of existing algorithms.

  7. Characterization of class II alpha genes and DLA-D region allelic associations in the dog.

    Sarmiento, U M; Storb, R F

    1988-10-01

    Human major histocompatibility complex (HLA) cDNA probes were used to analyze the restriction fragment length polymorphism (RFLP) of the alpha genes of the DLA-D region in dogs. Genomic DNA from peripheral blood leucocytes of 23 unrelated DLA-D homozygous dogs representing nine DLA-D types (defined by mixed leucocyte reaction) was digested with restriction enzymes (BamHI, EcoRI, Hind III, Pvu II, Taq I, Rsa I, Msp I, Pst I and Bgl II), separated by agarose gel electrophoresis and transferred onto Biotrace membrane. The Southern blots were successively hybridized with radiolabelled HLA cDNA probes corresponding to DQ, DP, DZ and DR alpha genes. Clear evidence was obtained for the canine homologues of DQ and DR alpha genes with simple bi- or tri-allelic polymorphism respectively. Evidence for a single, nonpolymorphic DP alpha gene was also obtained. However, the presence of a DZ alpha gene could not be clearly demonstrated in canine genomic DNA. This report extends our previous RFLP analysis documenting polymorphism of DLA class II beta genes in the same panel of homozygous typing cell dogs, and provides the basis for DLA-D genotyping at a population level. This study also characterizes the RFLP-defined preferential allelic associations across the DLA-D region in nine different homozygous typing cell specificities.

  8. Identification of 2 novel genes developmentally regulated in the mouse aorta-gonad-mesonephros region

    C. Orelio; E.A. Dzierzak (Elaine)

    2003-01-01

    textabstractThe first adult-repopulating hematopoietic stem cells (HSCs) emerge in the mouse aorta-gonad-mesonephros (AGM) region at embryonic day 10.5 prior to their appearance in the yolk sac and fetal liver. Although several genes are implicated in the regulation of HSCs, there

  9. BIALLELIC POLYMORPHISM IN THE INTRON REGION OF B-TUBULIN GENE OF CRYPTOSPORIDIUM PARASITES

    Nucleotide sequencing of polymerase chain reaction-amplified intron region of the Cryptosporidium parvum B-tubulin gene in 26 human and 15 animal isolates revealed distinct genetic polymorphism between the human and bovine genotypes. The separation of 2 genotypes of C. parvum is...

  10. A study of the frequency of methylation of gene promoter regions in ...

    2013-04-02

    Apr 2, 2013 ... colorectal cancer in the Taiwanese population. CHANG-CHIEH WU1 ... hypermethylation of promoter-region CpG islands is an important ... mismatch repair gene MLH1 plays an important role in dele- ..... Asia Pac. J. Clin.

  11. upstream region of the myostatin gene in four chicken breeds and its

    user

    2012-05-17

    May 17, 2012 ... processing site and a carboxy-terminal region containing nine cysteines ... cultivated meat breed (minitype) and the Youxi chicken is a local breed raised for ..... Allele R was the additive gene on growth traits. Bian chickens ...

  12. Gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions.

    Sivrikoz, Emre; Timirci-Kahraman, Özlem; Ergen, Arzu; Zeybek, Ümit; Aksoy, Murat; Yanar, Fatih; İsbir, Turgay; Kurtoğlu, Mehmet

    2015-01-01

    The purpose of this study was to investigate the gene expression levels of elastin and fibulin-5 according to differences between carotid plaque regions and to correlate it with clinical features of plaque destabilization. The study included 44 endarterectomy specimens available from operated symptomatic carotid artery stenoses. The specimens were separated according to anatomic location: internal carotid artery (ICA), external carotid artery (ECA) and common carotid artery (CCA), and then stored in liquid nitrogen. The amounts of cDNA for elastin and fibulin-5 were determined by Quantitative real-time PCR (Q-RT-PCR). Target gene copy numbers were normalized using hypoxanthine-guanine phosphoribosyltransferase (HPRT1) gene. The delta-delta CT method was applied for relative quantification. Q-RT-PCR data showed that relative fibulin-5 gene expression was increased in ICA plaque regions when compared to CCA regions but not reaching significance (p=0.061). At the same time, no differences were observed in elastin mRNA level between different anatomic plaque regions (p>0.05). Moreover, elastin and fibulin-5 mRNA expression and clinical parameters were compared in ICA plaques versus CCA and ECA regions, respectively. Up-regulation of elastin and fibulin-5 mRNA levels in ICA were strongly correlated with family history of cardiovascular disease when compared to CCA (p<0.05). Up-regulation of fibulin-5 in ICA was significantly associated with diabetes, and elevated triglycerides and very low density lipoprotein (VLDL) when compared to ECA (p<0.05). The clinical significance is the differences between the proximal and distal regions of the lesion, associated with the ICA, CCA and ECA respectively, with increased fibulin-5 in the ICA region. Copyright © 2015 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  13. Frequent gene conversion events between the X and Y homologous chromosomal regions in primates

    Hirai Hirohisa

    2010-07-01

    Full Text Available Abstract Background Mammalian sex-chromosomes originated from a pair of autosomes. A step-wise cessation of recombination is necessary for the proper maintenance of sex-determination and, consequently, generates a four strata structure on the X chromosome. Each stratum shows a specific per-site nucleotide sequence difference (p-distance between the X and Y chromosomes, depending on the time of recombination arrest. Stratum 4 covers the distal half of the human X chromosome short arm and the p-distance of the stratum is ~10%, on average. However, a 100-kb region, which includes KALX and VCX, in the middle of stratum 4 shows a significantly lower p-distance (1-5%, suggesting frequent sequence exchanges or gene conversions between the X and Y chromosomes in humans. To examine the evolutionary mechanism for this low p-distance region, sequences of a corresponding region including KALX/Y from seven species of non-human primates were analyzed. Results Phylogenetic analysis of this low p-distance region in humans and non-human primate species revealed that gene conversion like events have taken place at least ten times after the divergence of New World monkeys and Catarrhini (i.e., Old World monkeys and hominoids. A KALY-converted KALX allele in white-handed gibbons also suggests a possible recent gene conversion between the X and Y chromosomes. In these primate sequences, the proximal boundary of this low p-distance region is located in a LINE element shared between the X and Y chromosomes, suggesting the involvement of this element in frequent gene conversions. Together with a palindrome on the Y chromosome, a segmental palindrome structure on the X chromosome at the distal boundary near VCX, in humans and chimpanzees, may mediate frequent sequence exchanges between X and Y chromosomes. Conclusion Gene conversion events between the X and Y homologous regions have been suggested, mainly in humans. Here, we found frequent gene conversions in the

  14. The cld mutation: narrowing the critical chromosomal region and selecting candidate genes.

    Péterfy, Miklós; Mao, Hui Z; Doolittle, Mark H

    2006-10-01

    Combined lipase deficiency (cld) is a recessive, lethal mutation specific to the tw73 haplotype on mouse Chromosome 17. While the cld mutation results in lipase proteins that are inactive, aggregated, and retained in the endoplasmic reticulum (ER), it maps separately from the lipase structural genes. We have narrowed the gene critical region by about 50% using the tw18 haplotype for deletion mapping and a recombinant chromosome used originally to map cld with respect to the phenotypic marker tf. The region now extends from 22 to 25.6 Mbp on the wild-type chromosome, currently containing 149 genes and 50 expressed sequence tags (ESTs). To identify the affected gene, we have selected candidates based on their known role in associated biological processes, cellular components, and molecular functions that best fit with the predicted function of the cld gene. A secondary approach was based on differences in mRNA levels between mutant (cld/cld) and unaffected (+/cld) cells. Using both approaches, we have identified seven functional candidates with an ER localization and/or an involvement in protein maturation and folding that could explain the lipase deficiency, and six expression candidates that exhibit large differences in mRNA levels between mutant and unaffected cells. Significantly, two genes were found to be candidates with regard to both function and expression, thus emerging as the strongest candidates for cld. We discuss the implications of our mapping results and our selection of candidates with respect to other genes, deletions, and mutations occurring in the cld critical region.

  15. Aberrant DNA methylation in 5'regions of DNA methyltransferase genes in aborted bovine clones

    2008-01-01

    High rate of abortion and developmental abnormalities is thought to be closely associated with inefficient epigenetic reprogramming of the transplanted nuclei during bovine cloning.It is known that one of the important mechanisms for epigenetic reprogramming is DNA methylation.DNA methylation is established and maintained by DNA methyltransferases(DNMTs),therefore,it is postulated that the inefficient epigenetic reprogramming of transplanted nuclei may be due to abnormal expression of DNMTs.Since DNA methylation can strongly inhibit gene expression,aberrant DNA methylation of DNMT genes may disturb gene expression.But presently,it is not clear whether the methylation abnormality of DNMT genes is related to developmental failure of somatic cell nuclear transfer embryos.In our study,we analyzed methylation patterns of the 5' regions of four DNMT genes including Dnmt3a,Dnmt3b,Dnmtl and Dnmt2 in four aborted bovine clones.Using bisulfite sequencing method,we found that 3 out of 4 aborted bovine clones(AF1,AF2 and AF3)showed either hypermethylation or hypomethylation in the 5' regions of Dnmt3a and Dnmt3b.indicating that Dnmt3a and Dnmt3b genes are not properly reprogrammed.However,the individual AF4 exhibited similar methylation level and pattern to age-matched in vitro fertilized (IVF)fetuses.Besides,we found that tle 5'regions of Dnmtl and Dnmt2 were nearly completely unmethylated in all normal adults.IVF fetuses,sperm and aborted clones.Together,our results suggest that the aberrant methylation of Dnmt3a and Dnmt3b 5' regions is probably associated with the high abortion of bovine clones.

  16. Genic regions of a large salamander genome contain long introns and novel genes

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  17. Pseudotyped Lentiviral Vectors for Retrograde Gene Delivery into Target Brain Regions

    Kenta Kobayashi

    2017-08-01

    Full Text Available Gene transfer through retrograde axonal transport of viral vectors offers a substantial advantage for analyzing roles of specific neuronal pathways or cell types forming complex neural networks. This genetic approach may also be useful in gene therapy trials by enabling delivery of transgenes into a target brain region distant from the injection site of the vectors. Pseudotyping of a lentiviral vector based on human immunodeficiency virus type 1 (HIV-1 with various fusion envelope glycoproteins composed of different combinations of rabies virus glycoprotein (RV-G and vesicular stomatitis virus glycoprotein (VSV-G enhances the efficiency of retrograde gene transfer in both rodent and nonhuman primate brains. The most recently developed lentiviral vector is a pseudotype with fusion glycoprotein type E (FuG-E, which demonstrates highly efficient retrograde gene transfer in the brain. The FuG-E–pseudotyped vector permits powerful experimental strategies for more precisely investigating the mechanisms underlying various brain functions. It also contributes to the development of new gene therapy approaches for neurodegenerative disorders, such as Parkinson’s disease, by delivering genes required for survival and protection into specific neuronal populations. In this review article, we report the properties of the FuG-E–pseudotyped vector, and we describe the application of the vector to neural circuit analysis and the potential use of the FuG-E vector in gene therapy for Parkinson’s disease.

  18. MICB gene diversity and balancing selection on its promoter region in Yao population in southern China.

    Chen, Xiang; Liu, Xuexiang; Wei, Xiaomou; Meng, Yuming; Liu, Limin; Qin, Shini; Liu, Yanyu; Dai, Shengming

    2016-12-01

    To comprehensively examine the MICB gene polymorphism and identify its differences in Chinese Yao population from other ethnic groups, we investigated the polymorphism in the 5'-upstream regulation region (5'-URR), coding region (exons 2-4), and the 3'-untranslated region (3'-UTR) of MICB gene by using PCR-SBT method in 125 healthy unrelated Yao individuals in Guangxi Zhuang Autonomous Region. Higher polymorphism was observed in the 5'-URR, nine single nucleotide polymorphisms (SNPs) and a two base pairs deletion at position -139/-138 were found in our study. Only five different variation sites, however, were detected in exons 2-4 and three were observed in the 3'-UTR. The minor allele frequencies of all variants were greater than 5%, except for rs3828916, rs3131639, rs45627734, rs113620316, rs779737471, and the variation at position +11803 in the 3'-UTR. The first nine SNPs of 5'-URR and rs1065075, rs1051788 of the coding region showed significant linkage disequilibrium with each other. Ten different MICB extended haplotypes (EH) encompassing the 5'-URR, exons 2-4, and 3'-UTR were found in this population, and the most frequent was EH1 (23.2%). We provided several evidences for balancing selection effect on the 5'-URR of MICB gene in Yao population. Copyright © 2016 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

  19. Cloning and characterization of stress responsive Glp genes and their promotor regions from rice (abstract)

    Naqvi, S.M.S.; Mahmood, T.

    2005-01-01

    Plants respond to a number of environmental stimuli by modulating expression of genes. One such family of genes is now known as germin/germin-like protein genes (Glps). In order to detect any Glp gene response in rice, a pair of degenerate primers was designed based on consensus region from Glp sequences in Genbank. Using these primers a DNA fragment of about 550 bp was obtained by PCR amplification from genomic template. This 550 bp DNA was used as probe in Northern analysis. These studies provided evidence pointing to differential response of Glp expression to salt stress. RNA obtained from the roots was used for synthesis of cDNA. This cDNA was amplifiable with sense primer (RGLP1) from above mentioned pair and oligo-(dt) yielding a fragment of approx. 800 bp. Restriction analysis revealed that the PCR product was heterogeneous. After establishing that 800 bp fragment was the desired product, it was cloned in pCRII-TOPO. Five clones were picked up and analyzed by restriction analysis and sequencing. Two different Glp cDNAs were represented by these partial clones. Remaining sequence of the 5' end for clone 4 and 16 was obtained by Rapid Amplification of cDNA ends (RACE). The resultant sequences have been submitted to Genbank as Oryza sativa Rice Germin-like Protein 1 and 2 (osRGLP1 and 2). When full length genes corresponding to these sequences were amplified from genomic templates, resulting fragments were nearly 150 by larger than cDNAs. Cloning of structural genes for osRGLP1 revealed presence of a 162 bp intron in the coding region near 3' end. Preliminary evidence shows that expression of both osRGLP1 and 2 is severely reduced during salt stress. Another approach to establish both osRGLP1 and 2 genes involvement in stress tolerance is to study the ability of their promotor regions to drive expression of some reporter gene during stress. Promotor regions of about 1100 bp has been amplified and cloned and has been confirmed by restriction analysis and nested

  20. Characterisation of five candidate genes within the ETEC F4ab/ac candidate region in pigs

    Jacobsen, Mette Juul; Cirera Salicio, Susanna; Joller, David

    2011-01-01

    by haplotype sharing to a 2.5 Mb region on pig chromosome 13, a region containing 18 annotated genes. FINDINGS: The coding regions of five candidate genes for susceptibility to ETEC F4ab/ac infection (TFRC, ACK1, MUC20, MUC4 and KIAA0226), all located in the 2.5 Mb region, were investigated for the presence...... polymorphism in exon 22 of KIAA0226. Transcriptional profiles of the five genes were investigated in a porcine tissue panel including various intestinal tissues. All five genes were expressed in intestinal tissues at different levels but none of the genes were found differentially expressed between ETEC F4ab/ac...... of the amino acids composition. However, we cannot exclude that the five tested genes are bona fide candidate genes for susceptibility to ETEC F4ab/ac infection since the identified polymorphism might affect the translational apparatus, alternative splice forms may exist and post translational mechanisms might...

  1. Confinement of NORMAL- AND HIGH-STRENGTH CONCRETE by Shape Memory Alloy (SMA) Spirals

    Gholampour, A.; Ozbakkaloglu, T.

    2018-01-01

    This paper presents the results of an experimental study on the axial compressive behaviour of normal- and high-strength concrete (NSC and HSC) confined by shape memory alloy (SMA) spirals. A spiral pitch space of 36 and 20 mm was used for SMA confinement of NSC and HSC columns, respectively. The confining pressure was applied on the concrete cylinders by SMA spirals that were prestrained at 0, 5.5, and 9.5%. The compression test results on the SMA-confined specimens indicate that the prestrain level of SMA significantly affects the axial compressive behaviour of both NSC and HSC. An increase in the level of prestrain leads to an increase in the peak axial stress and corresponding strain of SMA-confined concrete.

  2. PENGARUH MODEL EXPERIENTIAL LEARNING TERHADAP KEMAMPUAN BERPIKIR SISWA SMA

    Mar’atus Sholihah

    2016-11-01

    Full Text Available The purpose of this study was to determine the effect of Experiential Learning models developed by Kolb's theory of the critical thinking skills of high school students. This study uses a quasi experiment conducted in SMA Assa'adah Gresik. The population of students of class X IS second semester of academic year 2015/2016. Samples are 2 classes that are homogeneous. Methods of data collection using test questions and the ability to think critically using observation sheet. Data were analyzed by comparing the average acquisition value of critical thinking skills with experimental class control class. Average value of the critical thinking skills using model Experiential Learning higher at 80.9 while the control class is 71.2. Based on the average it can be concluded that the learning model of Experiential Learning can improve students' critical thinking skills. This study is expected to provide information on the application and benefits of the model Experiential Learning in teaching geography and make it more meaningful for students. Tujuan dari penelitian ini adalah mengetahui pengaruh model Experiential Learning yang dikembangkan oleh teori Kolb terhadap kemampuan berpikir kritis siswa SMA. Penelitian ini menggunakan metode quasi experimen yang dilakukan di SMA Assa’adah Gresik. Populasi siswa kelas X IS semester genap tahun pelajaran 2015/2016. Sampel yang digunakan sebanyak 2 kelas yang bersifat homogen. Metode pengumpulan data menggunakan soal tes kemampuan berpikir kritis serta menggunakan lembar observasi. Data yang diperoleh kemudian dianalisis dengan membandingkan rata-rata perolehan nilai kemampuan berpikir kritis kelas kontrol dengan kelas eksperimen. Nilai rata rata kemampuan berpikir kritis yang menggunakan model pembelajaran Experiential Learning lebih tinggi, yaitu sebesar 80,9, sedangkan kelas kontrol sebesar 71,2. Berdasarkan nilai rata-rata tersebut dapat disimpulkan bahwa model pembelajaran Experiential Learning dapat

  3. PENGARUH PENDEKATAN KONTEKSTUAL TERHADAP HASIL BELAJAR BIOLOGI SISWA SMA

    Irwandi -

    2013-05-01

    Full Text Available Abstract: Contextual Teaching and Learning and Biology Learning Achievement among Senior High School Students. This quasi experimental study was designed to explain the effects of inquiry learning of Contextual Teaching and Learning (CTL, learning community of CTL, and entry behavior on Biology learning achievement of senior high school students of Bengkulu. The subjects were randomly selected from year-10 classes of eight schools and assigned to eight experimental classes. The study shows that: (1 the inquiry learning of CTL has no effect on the students’ cognitive learning achievement; (2 the learning community, particularly the extended one, of CTL  contributes to the students’ cognitive learning achievement; and (3 the students’ entry behavior did not affect their cognitive learning achievement when the students learned through inquiry process of CTL. Abstrak: Pengaruh Pendekatan Kontekstual terhadap Hasil Belajar Biologi Siswa SMA. Penelitian ini bertujuan untuk mengetahui: 1 pengaruh pendekatan kontekstual melalui strategi inkuiri terhadap hasil belajar kognitif siswa; 2 pengaruh pendekatan kontekstual melalui masyarakat belajar terhadap hasil belajar kognitif siswa; dan 3 pengaruh kemampuan awal siswa terhadap hasil belajar kognitifnya, pada pembela­jaran kontekstual melalui strategi inkuiri tingkat 1 dan 2. Penelitian dilakukan terhadap siswa-siswa pada pembelajaran biologi di 8 buah kelas X, masing-masing dari salah satu SMAN Bengkulu yang dipilih secara random. Penelitian ini menggunakan rancangan kuasi eksperimen Pretest-posttest Nonequivalent Control Group Design dengan rancangan penelitian faktorial 2 x 2 x 2. Hasil penelitian menunjukkan bahwa 1 pendekatan kontekstual melalui strategi inkuiri, tidak berpengaruh terhadap hasil belajar kognitif siswa di SMA 2 pendekatan kontekstual melalui masyarakat belajar berpengaruh terhadap hasil belajar kognitif siswa di SMA di mana hasil belajar kognitif melalui masyarakat belajar

  4. Evidence for widespread degradation of gene control regions in hominid genomes.

    Peter D Keightley

    2005-02-01

    Full Text Available Although sequences containing regulatory elements located close to protein-coding genes are often only weakly conserved during evolution, comparisons of rodent genomes have implied that these sequences are subject to some selective constraints. Evolutionary conservation is particularly apparent upstream of coding sequences and in first introns, regions that are enriched for regulatory elements. By comparing the human and chimpanzee genomes, we show here that there is almost no evidence for conservation in these regions in hominids. Furthermore, we show that gene expression is diverging more rapidly in hominids than in murids per unit of neutral sequence divergence. By combining data on polymorphism levels in human noncoding DNA and the corresponding human-chimpanzee divergence, we show that the proportion of adaptive substitutions in these regions in hominids is very low. It therefore seems likely that the lack of conservation and increased rate of gene expression divergence are caused by a reduction in the effectiveness of natural selection against deleterious mutations because of the low effective population sizes of hominids. This has resulted in the accumulation of a large number of deleterious mutations in sequences containing gene control elements and hence a widespread degradation of the genome during the evolution of humans and chimpanzees.

  5. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

    Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

    2016-06-01

    Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Evaluasi Kenyamanan Termal Ruang Sekolah SMA Negeri di Kota Padang

    Lusi Susanti; Nike Aulia

    2016-01-01

    This research aims to determine thermal conditions and sensation of thermal comfort in classrooms of high schools in Padang. This study was conducted in 11 State Senior High School (SMA) represented 11 districts in Padang. About 10% of total student body in each schools were participated in this study to vote thermal comfort questioners. To determine thermal comfort level in this study, PMV (Predicted mean Vote) and PPD (Predicted Percentage of dissatisfied) method were used according to stan...

  7. KONTRIBUSI KONSELOR DALAM MEMBENTUK KARAKTER PESERTA DIDIK SMA

    Agung Slamet Kusmanto

    2015-11-01

    Full Text Available Pengembangan model Pendidikan Holistik Berbasis Karakter, yang memfokuskan pada pembentukan seluruh aspek dimensi manusia, sehingga dapat menjadi manusia yang berkarakter. Kurikulum Holistik Berbasis Karakter ini disusun berdasarkan Kurikulum Berbasis Kompetensi (KBK dan diterapkan dengan menggunakan pendekatan Student Active Learning, Integrated Learning, Developmentally Appropriate Practices, Contextual Learning, Collaborative Learning, dan Multiple Intelligences yang semuanya dapat menciptakan suasana belajar yang efektif dan menyenangkan, serta dapat mengembangkan seluruh aspek dimensi manusia secara holistik. Maka diperlukan peran yang sangat besar dari guru pembimbing (konselor SMA dalam mengembangkan potensi peserta didiknya dalam mengembangkan potensinya dan membentuk karakter individu itu sendiri dan memberikan warna positif dalam suasana pembelajaran.

  8. Design and control of a linearity-enhanced SMA actuator

    Son, Hyung-Min; Tak, Chul-Gon; Lee, Yun-Jung; Kang, Seok-Won; Nam, Tae-Hyun; Kim, Jae-Il

    2010-01-01

    For the accurate and dexterous operation of mechanical systems, continuous-type actuation, rather than on/off-type actuation, is an indispensable function. However, conventional Ti-Ni alloys present difficulties for continuous positioning control, due to their hysteretic and abruptly changing relationship between strain and temperature. Therefore, this paper proposes a new linearity-enhanced SMA actuator using a temperature-gradient annealed alloy and an inverse hysteresis controller. In comparative experiments, the proposed controller and alloy exhibit superior performance for continuous actuation.

  9. MODEL PENGEMBANGAN PERANGKAT PEMBELAJARAN SEJARAH BERORIENTASI METAKOGNITIF JENJANG SMA

    Cahyo Budi Utomo

    2015-01-01

    Full Text Available The importance of metacognitive based history learning in the high school level as requested in the “curriculum 2013” is the main background of this research. The research is focused to find the model of development of metacognitive based learning through research and development (R&D type research. The results showed an essential component in achieving successful management of metacognitive based history learning in high school education which the curriculum as a core competency analysis and basic competencies, lesson plan development, and the development of assessment tools. Development model of metacognitive based learning at high school education have main characteristic of the inclusion of explicit metacognitive learning goals and assignments and devices equipped with a rubric and assessment questionnaire. Metacognitive based history learning instructional tools that are developed in senior high school level has been carried out as optimally as possible by involving history teachers in the process of development and testing through focus group discussions and questionnaire.Keywords: Model, Instructional tool, Metacognitive, senior high school levelPentingnya orientasi metakognitif dalam perangkat pembelajaran sejarah jenjang SMA sebagaimana yang dikehendaki dalam implementasi kurikulum 2013 merupakan latar belakang utama penelitian ini. Penelitian difokuskan untuk menemukan model pengembangan perangkat pembelajaran berorientasi metakognitif melalui penelitian berjenis riset dan pengembangan (R&D. Metode penelitian R&D dilaksanakan melalui tiga tahap utama yaitu: tahap studi pendahuluan, tahap pengembangan, dan tahap uji publik. Hasil penelitian menunjukkan komponen esensial dalam mewujudkan keberhasilan penge-lolaan pembelajaran sejarah berorientasi metakognitif pada jenjang pendidikan SMA adalah kurikulum sebagai bahan analisis kompetensi inti dan kompetensi dasar, pengembangan RPP, dan pengembangan perangkat assesmen. Model

  10. MODEL EVALUASI INTERNAL KOMPETENSI GURU BAHASA INGGRIS (MODEL_EIKGBI) SMA

    Sahraini Sahraini; Suwarsih Madya

    2015-01-01

    Studi ini bertujuan untuk: (1) mengembangkan model evaluasi kompetensi guru bahasa Inggris SMA yang dapat digunakan untuk mengidentifikasi kelebihan dan kekurangan guru dalam proses pemelajaran dan (2) mengetahui efektivitas implementasi evaluasi internal kompetensi guru bahasa Inggris SMA. Studi ini menggunakan metode penelitian dan pengembangan yang dikembangkan oleh Borg & Gall (1983, p.775). Subjek penelitian berjumlah 17 guru yang berasal dari 7 SMA di Sulawesi Selatan. Konstruk instrume...

  11. PENGEMBANGAN MODEL PEMBELAJARAN KIMIA UNTUK MENINGKATKAN KETERAMPILAN PROSES DAN KETERAMPILAN BERPIKIR SISWA SMA

    Siti Darsati

    2015-01-01

    Full Text Available Tujuan penyusunan model pembelajaran kimia ini untuk meningkatkan keterampilan proses dan keterampilan berpikir siswa SMA. Model Pembelajaran Laju Reaksi untuk SMA mengandung 17 konsep, meliputi konsep abstrak, konsep yang berdasarkan prinsip dan konsep yang menyatakan simbol. Keterampilan Berpikir Kritis dan Keterampilan Proses Sains yang dikembangkan lebih banyak pada keterampilan menyimpulkan. Model ini telah di implementasikan pada 2 SMA di Kodya/Kabupaten Bandung. Kata kunci: Model pembelajaran, keterampilan proses, keterampilan berpikir

  12. Administrative Record Index for SMA 4 - Former Chemical Plant and SMA 5 - Former Pig Iron Foundry

    The Administrative Record Index lists the documents, data and other technical information that the EPA - Region 4 considered in preparing the Statement of Basis for the Former Chemical Plant and the Former Pig Iron Foundry at ERP Compliant Coke.

  13. Segmental Duplication, Microinversion, and Gene Loss Associated with a Complex Inversion Breakpoint Region in Drosophila

    Calvete, Oriol; González, Josefa; Betrán, Esther; Ruiz, Alfredo

    2012-01-01

    Chromosomal inversions are usually portrayed as simple two-breakpoint rearrangements changing gene order but not gene number or structure. However, increasing evidence suggests that inversion breakpoints may often have a complex structure and entail gene duplications with potential functional consequences. Here, we used a combination of different techniques to investigate the breakpoint structure and the functional consequences of a complex rearrangement fixed in Drosophila buzzatii and comprising two tandemly arranged inversions sharing the middle breakpoint: 2m and 2n. By comparing the sequence in the breakpoint regions between D. buzzatii (inverted chromosome) and D. mojavensis (noninverted chromosome), we corroborate the breakpoint reuse at the molecular level and infer that inversion 2m was associated with a duplication of a ∼13 kb segment and likely generated by staggered breaks plus repair by nonhomologous end joining. The duplicated segment contained the gene CG4673, involved in nuclear transport, and its two nested genes CG5071 and CG5079. Interestingly, we found that other than the inversion and the associated duplication, both breakpoints suffered additional rearrangements, that is, the proximal breakpoint experienced a microinversion event associated at both ends with a 121-bp long duplication that contains a promoter. As a consequence of all these different rearrangements, CG5079 has been lost from the genome, CG5071 is now a single copy nonnested gene, and CG4673 has a transcript ∼9 kb shorter and seems to have acquired a more complex gene regulation. Our results illustrate the complex effects of chromosomal rearrangements and highlight the need of complementing genomic approaches with detailed sequence-level and functional analyses of breakpoint regions if we are to fully understand genome structure, function, and evolutionary dynamics. PMID:22328714

  14. Association analysis of PRNP gene region with chronic wasting disease in Rocky Mountain elk

    Spraker Terry R

    2010-11-01

    Full Text Available Abstract Background Chronic wasting disease (CWD is a transmissible spongiform encephalopathy (TSE of cervids including white-tailed (Odocoileus virginianus and mule deer (Odocoileus hemionus, Rocky Mountain elk (Cervus elaphus nelsoni, and moose (Alces alces. A leucine variant at position 132 (132L in prion protein of Rocky Mountain elk confers a long incubation time with CWD, but not complete resistance. However, variants in regulatory regions outside the open reading frame of PRNP have been associated with varying degrees of susceptibility to prion disease in other species, and some variants have been observed in similar regions of Rocky Mountain elk PRNP. Thus, additional genetic variants might provide increased protection, either alone or in combination with 132L. Findings This study provided genomic sequence of all exons for PRNP of Rocky Mountain elk. Many functional sites in and around the PRNP gene region were sequenced, and this report approximately doubled (to 75 the number of known variants in this region. A haplotype-tagging approach was used to reduce the number of genetic variants required to survey this variation in the PRNP gene region of 559 Rocky Mountain elk. Eight haplotypes were observed with frequencies over 1.0%, and one haplotype was present at 71.2% frequency, reflecting limited genetic diversity in the PRNP gene region. Conclusions The presence of 132L cut odds of CWD by more than half (Odds Ratio = 0.43; P = 0.0031, which was similar to a previous report. However after accounting for 132L, no association with CWD was found for any additional variants in the PRNP region (P > 0.05.

  15. The primary structures of two yeast enolase genes. Homology between the 5' noncoding flanking regions of yeast enolase and glyceraldehyde-3-phosphate dehydrogenase genes.

    Holland, M J; Holland, J P; Thill, G P; Jackson, K A

    1981-02-10

    Segments of yeast genomic DNA containing two enolase structural genes have been isolated by subculture cloning procedures using a cDNA hybridization probe synthesized from purified yeast enolase mRNA. Based on restriction endonuclease and transcriptional maps of these two segments of yeast DNA, each hybrid plasmid contains a region of extensive nucleotide sequence homology which forms hybrids with the cDNA probe. The DNA sequences which flank this homologous region in the two hybrid plasmids are nonhomologous indicating that these sequences are nontandemly repeated in the yeast genome. The complete nucleotide sequence of the coding as well as the flanking noncoding regions of these genes has been determined. The amino acid sequence predicted from one reading frame of both structural genes is extremely similar to that determined for yeast enolase (Chin, C. C. Q., Brewer, J. M., Eckard, E., and Wold, F. (1981) J. Biol. Chem. 256, 1370-1376), confirming that these isolated structural genes encode yeast enolase. The nucleotide sequences of the coding regions of the genes are approximately 95% homologous, and neither gene contains an intervening sequence. Codon utilization in the enolase genes follows the same biased pattern previously described for two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes (Holland, J. P., and Holland, M. J. (1980) J. Biol. Chem. 255, 2596-2605). DNA blotting analysis confirmed that the isolated segments of yeast DNA are colinear with yeast genomic DNA and that there are two nontandemly repeated enolase genes per haploid yeast genome. The noncoding portions of the two enolase genes adjacent to the initiation and termination codons are approximately 70% homologous and contain sequences thought to be involved in the synthesis and processing messenger RNA. Finally there are regions of extensive homology between the two enolase structural genes and two yeast glyceraldehyde-3-phosphate dehydrogenase structural genes within the 5

  16. Regional mapping of the phenylalanine hydroxylase gene and the phenylketonuria locus in the human genome

    Lidsky, A.S.; Law, M.L.; Morse, H.G.; Kao, F.T.; Rabin, M.; Ruddle, F.H.; Woo, S.L.C.

    1985-09-01

    Phenylketonuria (PKU) is an autosomal recessive disorder of amino acid metabolism caused by a deficiency of the hepatic enzyme phenylalanine hydroxylase. To define the regional map position of the disease locus and the PAH gene on human chromosome 12, DNA was isolated from human-hamster somatic cell hybrids with various deletions of human chromosome 12 and was analyzed by Southern blot analysis using the human cDNA PAH clone as a hybridization probe. From these results, together with detailed biochemical and cytogenetic characterization of the hybrid cells, the region on chromosome 12 containing the human PAH gene has been defined as 12q14.3..-->..qter. The PAH map position on chromosome 12 was further localized by in situ hybridization of /sup 125/I-labeled human PAH cDNA to chromosomes prepared from a human lymphoblastoid cell line. Results of these experiments demonstrated that the region on chromosome 12 containing the PAH gene and the PKU locus in man is 12q22..-->..12q24.1. These results not only provide a regionalized map position for a major human disease locus but also can serve as a reference point for linkage analysis with other DNA markers on human chromosome 12.

  17. Regional mapping of the phenylalanine hydroxylase gene and the phenylketonuria locus in the human genome

    Lidsky, A.S.; Law, M.L.; Morse, H.G.; Kao, F.T.; Rabin, M.; Ruddle, F.H.; Woo, S.L.C.

    1985-01-01

    Phenylketonuria (PKU) is an autosomal recessive disorder of amino acid metabolism caused by a deficiency of the hepatic enzyme phenylalanine hydroxylase. To define the regional map position of the disease locus and the PAH gene on human chromosome 12, DNA was isolated from human-hamster somatic cell hybrids with various deletions of human chromosome 12 and was analyzed by Southern blot analysis using the human cDNA PAH clone as a hybridization probe. From these results, together with detailed biochemical and cytogenetic characterization of the hybrid cells, the region on chromosome 12 containing the human PAH gene has been defined as 12q14.3→qter. The PAH map position on chromosome 12 was further localized by in situ hybridization of 125 I-labeled human PAH cDNA to chromosomes prepared from a human lymphoblastoid cell line. Results of these experiments demonstrated that the region on chromosome 12 containing the PAH gene and the PKU locus in man is 12q22→12q24.1. These results not only provide a regionalized map position for a major human disease locus but also can serve as a reference point for linkage analysis with other DNA markers on human chromosome 12

  18. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean

    Puji eLestari

    2013-06-01

    Full Text Available Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both chromosomes. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22 are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.

  19. Tensile and fatigue behavior of polymer composites reinforced with superelastic SMA strands

    Daghash, Sherif M.; Ozbulut, Osman E.

    2018-06-01

    This study explores the use of superelastic shape memory alloy (SMA) strands, which consist of seven individual small-diameter wires, in an epoxy matrix and characterizes the tensile and fatigue responses of the developed SMA/epoxy composites. Using a vacuum assisted hand lay-up technique, twelve SMA fiber reinforced polymer (FRP) specimens were fabricated. The developed SMA-FRP composites had a fiber volume ratio of 50%. Tensile response of SMA-FRP specimens were characterized under both monotonic loading and increasing amplitude loading and unloading cycles. The degradation in superelastic properties of the developed SMA-FRP composites during fatigue loading at different strain amplitudes was investigated. The effect of loading rate on the fatigue response of SMA-FRP composites was also explored. In addition, fractured specimens were examined using the scanning electron microscopy (SEM) technique to study the failure mechanisms of the tested specimens. A good interfacial bonding between the SMA strands and epoxy matrix was observed. The developed SMA-FRP composites exhibited good superelastic behavior at different strain amplitudes up to at least 800 cycle after which significant degradation occurred.

  20. Genetic and expression studies of SMN2 gene in Russian patients with spinal muscular atrophy type II and III

    Schiöth Helgi B

    2011-07-01

    Full Text Available Abstract Background Spinal muscular atrophy (SMA type I, II and III is an autosomal recessive neuromuscular disorder caused by mutations in the survival motor neuron gene (SMN1. SMN2 is a centromeric copy gene that has been characterized as a major modifier of SMA severity. SMA type I patients have one or two SMN2 copies while most SMA type II patients carry three SMN2 copies and SMA III patients have three or four SMN2 copies. The SMN1 gene produces a full-length transcript (FL-SMN while SMN2 is only able to produce a small portion of the FL-SMN because of a splice mutation which results in the production of abnormal SMNΔ7 mRNA. Methods In this study we performed quantification of the SMN2 gene copy number in Russian patients affected by SMA type II and III (42 and 19 patients, respectively by means of real-time PCR. Moreover, we present two families consisting of asymptomatic carriers of a homozygous absence of the SMN1 gene. We also developed a novel RT-qPCR-based assay to determine the FL-SMN/SMNΔ7 mRNA ratio as SMA biomarker. Results Comparison of the SMN2 copy number and clinical features revealed a significant correlation between mild clinical phenotype (SMA type III and presence of four copies of the SMN2 gene. In both asymptomatic cases we found an increased number of SMN2 copies in the healthy carriers and a biallelic SMN1 absence. Furthermore, the novel assay revealed a difference between SMA patients and healthy controls. Conclusions We suggest that the SMN2 gene copy quantification in SMA patients could be used as a prognostic tool for discrimination between the SMA type II and SMA type III diagnoses, whereas the FL-SMN/SMNΔ7 mRNA ratio could be a useful biomarker for detecting changes during SMA pharmacotherapy.

  1. Brain region-specific altered expression and association of mitochondria-related genes in autism.

    Anitha, Ayyappan; Nakamura, Kazuhiko; Thanseem, Ismail; Yamada, Kazuo; Iwayama, Yoshimi; Toyota, Tomoko; Matsuzaki, Hideo; Miyachi, Taishi; Yamada, Satoru; Tsujii, Masatsugu; Tsuchiya, Kenji J; Matsumoto, Kaori; Iwata, Yasuhide; Suzuki, Katsuaki; Ichikawa, Hironobu; Sugiyama, Toshiro; Yoshikawa, Takeo; Mori, Norio

    2012-11-01

    Mitochondrial dysfunction (MtD) has been observed in approximately five percent of children with autism spectrum disorders (ASD). MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA). Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG), motor cortex (MC) and thalamus (THL)) from autism patients (n=8) and controls (n=10) were obtained from the Autism Tissue Program (Princeton, NJ, USA). Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct) method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2), neurofilament, light polypeptide (NEFL) and solute carrier family 25, member 27 (SLC25A27) showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066) and SLC25A27 (P = 0.046; Z-score 1.990) showed genetic association with autism in Caucasian and Japanese samples, respectively. The expression of DNAJC19, DNM1L, LRPPRC

  2. Brain region-specific altered expression and association of mitochondria-related genes in autism

    Anitha Ayyappan

    2012-11-01

    Full Text Available Abstract Background Mitochondrial dysfunction (MtD has been observed in approximately five percent of children with autism spectrum disorders (ASD. MtD could impair highly energy-dependent processes such as neurodevelopment, thereby contributing to autism. Most of the previous studies of MtD in autism have been restricted to the biomarkers of energy metabolism, while most of the genetic studies have been based on mutations in the mitochondrial DNA (mtDNA. Despite the mtDNA, most of the proteins essential for mitochondrial replication and function are encoded by the genomic DNA; so far, there have been very few studies of those genes. Therefore, we carried out a detailed study involving gene expression and genetic association studies of genes related to diverse mitochondrial functions. Methods For gene expression analysis, postmortem brain tissues (anterior cingulate gyrus (ACG, motor cortex (MC and thalamus (THL from autism patients (n=8 and controls (n=10 were obtained from the Autism Tissue Program (Princeton, NJ, USA. Quantitative real-time PCR arrays were used to quantify the expression of 84 genes related to diverse functions of mitochondria, including biogenesis, transport, translocation and apoptosis. We used the delta delta Ct (∆∆Ct method for quantification of gene expression. DNA samples from 841 Caucasian and 188 Japanese families were used in the association study of genes selected from the gene expression analysis. FBAT was used to examine genetic association with autism. Results Several genes showed brain region-specific expression alterations in autism patients compared to controls. Metaxin 2 (MTX2, neurofilament, light polypeptide (NEFL and solute carrier family 25, member 27 (SLC25A27 showed consistently reduced expression in the ACG, MC and THL of autism patients. NEFL (P = 0.038; Z-score 2.066 and SLC25A27 (P = 0.046; Z-score 1.990 showed genetic association with autism in Caucasian and Japanese samples, respectively. The

  3. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

    Kohane Isaac

    2005-11-01

    Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

  4. Gene copy number reduction in the azoospermia factor c (AZFc) region and its effect on total motile sperm count

    Noordam, Michiel J.; Westerveld, G. Henrike; Hovingh, Suzanne E.; van Daalen, Saskia K. M.; Korver, Cindy M.; van der Veen, Fulco; van Pelt, Ans M. M.; Repping, Sjoerd

    2011-01-01

    The azoospermia factor c (AZFc) region harbors multi-copy genes that are expressed in the testis. Deletions of the AZFc region lead to reduced copy numbers of these genes. Four (partial) AZFc deletions have been described of which the b2/b4 and gr/gr deletions affect semen quality. In most studies,

  5. PENGEMBANGAN MODUL LATIHAN FORGIVENESS UNTUK SISWA SMA DI KOTA MALANG

    Ari Dwi Yudhianto

    2016-12-01

    Full Text Available This research aims to develop a training modules forgiveness based on the appraisement of experts (reviewers and high school student's response to the training modules forgiveness that have been developed. This study adapting the model development of Borg and Gall (1983, while the structure of the writing module refers to the guide preparation of module which prepared by the Director General module PMPTK (2008. The results of this study are drafting a training module forgiveness for senior high school students in Malang. Based appraisement materials experts, media specialists, and linguists classified as good, according to school counselors classified very good and yield response of students classified as good. So, that these modules worthy be used in the awarding of guidance services in schools. Penelitian ini bertujuan untuk mengembangkan modul latihan forgiveness  berdasarkan penilaian para ahli (reviewer dan respon siswa SMA terhadap Modul latihan forgiveness yang telah dikembangkan. Penelitian ini mengadaptasi model pengembangan Borg and gall (1983, sedangkan struktur penulisan modul mengacu pada panduan penyusunan modul yang disusun oleh dirjen PMPTK (2008. Hasil penelitian ini adalah tersusunnya modul latihan forgiveness untuk siswa SMA di Kota Malang yang berdasarkan penilaian ahli materi, ahli media, dan ahli bahasa tergolong baik, menurut konselor sekolah tergolong sangat baik dan hasil respon siswa tergolong baik. sehingga modul ini layak digunakan dalam pemberian layanan bimbingan di sekolah.

  6. Design optimization and uncertainty analysis of SMA morphing structures

    Oehler, S D; Hartl, D J; Lopez, R; Malak, R J; Lagoudas, D C

    2012-01-01

    The continuing implementation of shape memory alloys (SMAs) as lightweight solid-state actuators in morphing structures has now motivated research into finding optimized designs for use in aerospace control systems. This work proposes methods that use iterative analysis techniques to determine optimized designs for morphing aerostructures and consider the impact of uncertainty in model variables on the solution. A combination of commercially available and custom coded tools is utilized. ModelCenter, a suite of optimization algorithms and simulation process management tools, is coupled with the Abaqus finite element analysis suite and a custom SMA constitutive model to assess morphing structure designs in an automated fashion. The chosen case study involves determining the optimized configuration of a morphing aerostructure assembly that includes SMA flexures. This is accomplished by altering design inputs representing the placement of active components to minimize a specified cost function. An uncertainty analysis is also conducted using design of experiment methods to determine the sensitivity of the solution to a set of uncertainty variables. This second study demonstrates the effective use of Monte Carlo techniques to simulate the variance of model variables representing the inherent uncertainty in component fabrication processes. This paper outlines the modeling tools used to execute each case study, details the procedures for constructing the optimization problem and uncertainty analysis, and highlights the results from both studies. (paper)

  7. REKAYASA PERANGKAT LUNAK MEDIA INFORMASI SMA QURANIAH PALEMBANG

    Herlinda Kusmiati

    2017-08-01

    Full Text Available Seiring dengan semakin berkembangnya teknologi informasi dan meningkatnya penggunaan internet sebagai media informasi dikalangan masyarakat Indonesia. Hal ini mendorong SMA Quraniah Palembang untuk membenahi media informasi yang ada saat ini untuk meningkatkan jumlah siswa.  Media informasi yang dibuat berbasis website menggantikan Media  informasi saat ini yang masih menggunakan media brosur dan banner, dimana informasi yang diberikan masih sebatas informasi mengenai visi misi, profile, dan syarat pendaftaran siswa baru yang tidak dapat diakses dengan mudah oleh masyarakat. Dengan media informasi berbasis website dapat memberikan kemudahan kepada masyarakat dalam mendapatkan informasi mengenai profil sekolah, persyaratan pendafataran siswa baru. Selain itu, media informasi ini menyediakan informasi mengenai kegiatan-kegiatan yang ada di sekolah, ektrakulikuler siswa, serta fasilitas yang ada di sekolah. Media informasi ini dikelola oleh admin tata usaha, sehingga kesalahan-kesalahan dalam penyampaian informasi akan lebih mudah diperbaiki. Informasi-informasi mengenai SMA Quraniah Palembang dapat diakses kapanpun dan dimanapu, tidak terbatas pada salah satu wilayah saja. Media informasi ini dibuat dengan menggunakan Php & Mysql dan Waterfall sebagai metode pengembangan sistem.

  8. KESANTUNAN TUTURAN DIREKTIF DALAM INTERAKSI PEMBELAJARAN DI SMA

    Mardiyah Putri Astuti

    2017-03-01

    Full Text Available Politeness speech in learning interactions in the classroom tend to be effected through a directive speech. Assessment of form directive speech made by using a guide to the theory and analysis based on speech act theory directive Bach and Harnish. This study aims to determine the form of politeness directive in an interaction study in SMA 1 Batu. Forms directive speech in learning interactions are marked with (1 directive requests, (2 directive question, (3 directive command, (4 The prohibition directive, (5 directive licensing, and (6 the directive advice. The results of the analysis of the forms of speech directive shows that teachers do politeness predominantly through commands, prohibitions, permissions, and advice, while the shape of the directive utterances made by teachers and students to consider cultural aspects. Kesantunan tuturan dalam interaksi pembelajaran di dalam kelas cenderung dilakukan melalui bentuk tuturan direktif. Pengkajian terhadap bentuk tuturan direktif dilakukan dengan mengggunakan teori dan panduan analisis berdasarkan teori tindak tutur direktif Bach dan Harnish. Penelitian ini bertujuan untuk mengetahui bentuk kesantunan direktif dalam interaksi pembelajaran di SMA 1 Batu. Bentuk tuturan direktif dalam interaksi pembelajaran ditandai dengan (1 direktif permintaan, (2 direktif pertanyaan, (3 direktif perintah, (4 direktif larangan, (5 direktif pemberian izin, dan (6 direktif nasihat. Hasil analisis mengenai bentuk tuturan direktif menunjukkan bahwa guru melakukan kesantunan secara dominan melalui perintah, larangan, izin, dan nasihat, sedangkan bentuk tuturan direktif dilakukan oleh guru dan siswa dengan mempertimbangkan aspek budaya.

  9. A Novel SMA-based Concept for Airfoil Structural Morphing

    Barbarino, S.; Pecora, R.; Lecce, L.; Concilio, A.; Ameduri, S.; Calvi, E.

    2009-08-01

    The adaptive structures concept is of great interest in the aerospace field because of the several benefits which can be accomplished in the fields including noise reduction, load alleviation, weight reduction, etc., at a level in which they can be considered as compulsory in the design of future aircraft. Improvements in terms of the aerodynamic efficiency, aeroelastic behavior, stability, and manoeuvrability performance have already been proved through many international studies in the past. In the family of the Smart Materials, Shape Memory Alloys (SMA) seem to be a suitable solution for many static applications. Their high structural integrability in conjunction with actuation capabilities and a favorable performance per weight ratio, allows the development of original architectures. In this study, a morphing wing trailing edge concept is presented; morphing ability was introduced with the aim of replacing a conventional flap device. A compliant rib structure was designed, based on SMA actuators exhibiting structural potential (bearing external aerodynamic loads). Numerical results, achieved through a FE approach, are presented in terms of trailing edge induced displacement and morphed shape.

  10. Shape Memory Alloy (SMA)-Based Launch Lock

    Badescu, Mircea; Bao, Xiaoqi; Bar-Cohen, Yoseph

    2014-01-01

    Most NASA missions require the use of a launch lock for securing moving components during the launch or securing the payload before release. A launch lock is a device used to prevent unwanted motion and secure the controlled components. The current launch locks are based on pyrotechnic, electro mechanically or NiTi driven pin pullers and they are mostly one time use mechanisms that are usually bulky and involve a relatively high mass. Generally, the use of piezoelectric actuation provides high precession nanometer accuracy but it relies on friction to generate displacement. During launch, the generated vibrations can release the normal force between the actuator components allowing shaft's free motion which could result in damage to the actuated structures or instruments. This problem is common to other linear actuators that consist of a ball screw mechanism. The authors are exploring the development of a novel launch lock mechanism that is activated by a shape memory alloy (SMA) material ring, a rigid element and an SMA ring holding flexure. The proposed design and analytical model will be described and discussed in this paper.

  11. Porcine MYF6 gene: sequence, homology analysis, and variation in the promoter region.

    Wyszyńska-Koko, J; Kurył, J

    2004-01-01

    MYF6 gene codes for the bHLH transcription factor belonging to MyoD family. Its expression accompanies the processes of differentiation and maturation of myotubes during embriogenesis and continues on a relatively high level after birth, affecting the muscle phenotype. The porcine MYF6 gene was amplified and sequenced and compared with MYF6 gene sequences of other species. The amino acid sequence was deduced and an interspecies homology analysis was performed. Myf-6 protein shows a high conservation among species of 99 and 97% identity when comparing pig with cow and human, respectively, and of 93% when comparing pig with mouse and rat. The single nucleotide polymorphism (SNP) was revealed within the promoter region, which appeared to be T --> C transition recognized by a MspI restriction enzyme.

  12. Comparison of regional gene expression differences in the brains of the domestic dog and human

    Kennerly Erin

    2004-11-01

    Full Text Available Abstract Comparison of the expression profiles of 2,721 genes in the cerebellum, cortex and pituitary gland of three American Staffordshire terriers, one beagle and one fox hound revealed regional expression differences in the brain but failed to reveal marked differences among breeds, or even individual dogs. Approximately 85 per cent (42 of 49 orthologue comparisons of the regional differences in the dog are similar to those that differentiate the analogous human brain regions. A smaller percentage of human differences were replicated in the dog, particularly in the cortex, which may generally be evolving more rapidly than other brain regions in mammals. This study lays the foundation for detailed analysis of the population structure of transcriptional variation as it relates to cognitive and neurological phenotypes in the domestic dog.

  13. Regional heterogeneity and gene flow maintain variance in a quantitative trait within populations of lodgepole pine

    Yeaman, Sam; Jarvis, Andy

    2006-01-01

    Genetic variation is of fundamental importance to biological evolution, yet we still know very little about how it is maintained in nature. Because many species inhabit heterogeneous environments and have pronounced local adaptations, gene flow between differently adapted populations may be a persistent source of genetic variation within populations. If this migration–selection balance is biologically important then there should be strong correlations between genetic variance within populations and the amount of heterogeneity in the environment surrounding them. Here, we use data from a long-term study of 142 populations of lodgepole pine (Pinus contorta) to compare levels of genetic variation in growth response with measures of climatic heterogeneity in the surrounding region. We find that regional heterogeneity explains at least 20% of the variation in genetic variance, suggesting that gene flow and heterogeneous selection may play an important role in maintaining the high levels of genetic variation found within natural populations. PMID:16769628

  14. Nuclear scaffold attachment sites within ENCODE regions associate with actively transcribed genes.

    Mignon A Keaton

    2011-03-01

    Full Text Available The human genome must be packaged and organized in a functional manner for the regulation of DNA replication and transcription. The nuclear scaffold/matrix, consisting of structural and functional nuclear proteins, remains after extraction of nuclei and anchors loops of DNA. In the search for cis-elements functioning as chromatin domain boundaries, we identified 453 nuclear scaffold attachment sites purified by lithium-3,5-iodosalicylate extraction of HeLa nuclei across 30 Mb of the human genome studied by the ENCODE pilot project. The scaffold attachment sites mapped predominately near expressed genes and localized near transcription start sites and the ends of genes but not to boundary elements. In addition, these regions were enriched for RNA polymerase II and transcription factor binding sites and were located in early replicating regions of the genome. We believe these sites correspond to genome-interactions mediated by transcription factors and transcriptional machinery immobilized on a nuclear substructure.

  15. Localisation of the gene for achondroplasia to the telomeric region of chromosome 4p

    Stoilov, I.; Velinov, M.; Kilpatrick, M.W. [and others

    1994-09-01

    Achondroplasia (ACH), the most common type of genetic dwarfism, is characterized by a variety of skeletal anomalies including disproportionate short stature and rhizomelic shortening of the extremities. The disorder is inherited as an autosomal dominant trait, with a prevalence of 1-15 per 100,000 live births. The etiology of ACH remains unknown, although evidence points to a defect in the maturation of the chondrocytes in the growth plate of the cartilage. To determine the location of the gene responsible for ACH, a panel of 14 families with a total of 43 meioses was genotyped for 40 polymorphic markers for loci randomly distributed throughout the genome. The first significant positive Lod score was obtained for the locus D4S127 (Zmax=3.65 at {theta}=0.03). A series of 20 markers for chromosome 4p16.3 loci were then used to determine the most likely position of the ACH gene. Two additional loci, D4S412 and IDUA, showed strong linkage to the disease (Zmax=3.34 at {theta}=0.03 and Zmax=3.35 at {theta}=0.0, respectively). Multipoint analysis and direct counting of recombinants places the ACH gene in a 2.5 cM region between the marker D4S43 and the chromosome 4p telomere. No evidence was found for genetic heterogeneity. The ACH region contains a number of genes, including that for the fibroblast growth factor receptor FGFR3, which are being evaluated as candidates for the ACH gene. This identification of tightly linked polymorphic markers, as well as being the first step in the characterization of the ACH gene, offers the possibility of DNA based prenatal diagnosis of this disorder.

  16. Selection of reference genes in different myocardial regions of an in vivo ischemia/reperfusion rat model for normalization of antioxidant gene expression

    Vesentini Nicoletta

    2012-02-01

    Full Text Available Abstract Background Changes in cardiac gene expression due to myocardial injury are usually assessed in whole heart tissue. However, as the heart is a heterogeneous system, spatial and temporal heterogeneity is expected in gene expression. Results In an ischemia/reperfusion (I/R rat model we evaluated gene expression of mitochondrial and cytoplasmatic superoxide dismutase (MnSod, Cu-ZnSod and thioredoxin reductase (trxr1 upon short (4 h and long (72 h reperfusion times in the right ventricle (RV, and in the ischemic/reperfused (IRR and the remote region (RR of the left ventricle. Gene expression was assessed by Real-time reverse-transcription quantitative PCR (RT-qPCR. In order to select most stable reference genes suitable for normalization purposes, in each myocardial region we tested nine putative reference genes by geNorm analysis. The genes investigated were: Actin beta (actb, Glyceraldehyde-3-P-dehydrogenase (gapdh, Ribosomal protein L13A (rpl13a, Tyrosine 3-monooxygenase (ywhaz, Beta-glucuronidase (gusb, Hypoxanthine guanine Phosphoribosyltransferase 1 (hprt, TATA binding box protein (tbp, Hydroxymethylbilane synthase (hmbs, Polyadenylate-binding protein 1 (papbn1. According to our findings, most stable reference genes in the RV and RR were hmbs/hprt and hmbs/tbp/hprt respectively. In the IRR, six reference genes were recommended for normalization purposes; however, in view of experimental feasibility limitations, target gene expression could be normalized against the three most stable reference genes (ywhaz/pabp/hmbs without loss of sensitivity. In all cases MnSod and Cu-ZnSod expression decreased upon long reperfusion, the former in all myocardial regions and the latter in IRR alone. trxr1 expression did not vary. Conclusions This study provides a validation of reference genes in the RV and in the anterior and posterior wall of the LV of cardiac ischemia/reperfusion model and shows that gene expression should be assessed separately in

  17. Interactions of early adversity with stress-related gene polymorphisms impact regional brain structure in females.

    Gupta, Arpana; Labus, Jennifer; Kilpatrick, Lisa A; Bonyadi, Mariam; Ashe-McNalley, Cody; Heendeniya, Nuwanthi; Bradesi, Sylvie; Chang, Lin; Mayer, Emeran A

    2016-04-01

    Early adverse life events (EALs) have been associated with regional thinning of the subgenual cingulate cortex (sgACC), a brain region implicated in the development of disorders of mood and affect, and often comorbid functional pain disorders, such as irritable bowel syndrome (IBS). Regional neuroinflammation related to chronic stress system activation has been suggested as a possible mechanism underlying these neuroplastic changes. However, the interaction of genetic and environmental factors in these changes is poorly understood. The current study aimed to evaluate the interactions of EALs and candidate gene polymorphisms in influencing thickness of the sgACC. 210 female subjects (137 healthy controls; 73 IBS) were genotyped for stress and inflammation-related gene polymorphisms. Genetic variation with EALs, and diagnosis on sgACC thickness was examined, while controlling for race, age, and total brain volume. Compared to HCs, IBS had significantly reduced sgACC thickness (p = 0.03). Regardless of disease group (IBS vs. HC), thinning of the left sgACC was associated with a significant gene-gene environment interaction between the IL-1β genotype, the NR3C1 haplotype, and a history of EALs (p = 0.05). Reduced sgACC thickness in women with the minor IL-1β allele, was associated with EAL total scores regardless of NR3C1 haplotype status (p = 0.02). In subjects homozygous for the major IL-1β allele, reduced sgACC with increasing levels of EALs was seen only with the less common NR3C1 haplotype (p = 0.02). These findings support an interaction between polymorphisms related to stress and inflammation and early adverse life events in modulating a key region of the emotion arousal circuit.

  18. DNA Methylation of Regulatory Regions of Imprinted Genes at Birth and Its Relation to Infant Temperament

    Bernard F. Fuemmeler

    2016-01-01

    Full Text Available BACKGROUND DNA methylation of the differentially methylated regions (DMRs of imprinted genes is relevant to neurodevelopment. METHODS DNA methylation status of the DMRs of nine imprinted genes in umbilical cord blood leukocytes was analyzed in relation to infant behaviors and temperament (n = 158. RESULTS MEG3 DMR levels were positively associated with internalizing ( β = 0.15, P = 0.044 and surgency ( β = 0.19, P = 0.018 behaviors, after adjusting for birth weight, gender, gestational age at birth, maternal age at delivery, race/ethnicity, education level, smoking status, parity, and a history of anxiety or depression. Higher methylation levels at the intergenic MEG3-IG methylation regions were associated with surgency ( β = 0.28, P = 0.0003 and PEG3 was positively related to externalizing ( β = 0.20, P = 0.01 and negative affectivity ( β = 0.18, P = 0.02. CONCLUSION While the small sample size limits inference, these pilot data support gene-specific associations between epigenetic differences in regulatory regions of imprinted domains at birth and later infant temperament.

  19. Cloning and functional analysis of 5'-upstream region of the Pokemon gene.

    Yang, Yutao; Zhou, Xiaowei; Zhu, Xudong; Zhang, Chuanfu; Yang, Zhixin; Xu, Long; Huang, Peitang

    2008-04-01

    Pokemon, the POK erythroid myeloid ontogenic factor, not only regulates the expression of many genes, but also plays an important role in cell tumorigenesis. To investigate the molecular mechanism regulating expression of the Pokemon gene in humans, its 5'-upstream region was cloned and analyzed. Transient analysis revealed that the Pokemon promoter is constitutive. Deletion analysis and a DNA decoy assay indicated that the NEG-U and NEG-D elements were involved in negative regulation of the Pokemon promoter, whereas the POS-D element was mainly responsible for its strong activity. Electrophoretic mobility shift assays suggested that the NEG-U, NEG-D and POS-D elements were specifically bound by the nuclear extract from A549 cells in vitro. Mutation analysis demonstrated that cooperation of the NEG-U and NEG-D elements led to negative regulation of the Pokemon promoter. Moreover, the NEG-U and NEG-D elements needed to be an appropriate distance apart in the Pokemon promoter in order to cooperate. Taken together, our results elucidate the mechanism underlying the regulation of Pokemon gene transcription, and also define a novel regulatory sequence that may be used to decrease expression of the Pokemon gene in cancer gene therapy.

  20. Relationship of interleukin-1B gene promoter region polymorphism with Helicobacter pylori infection and gastritis.

    Ramis, Ivy Bastos; Vianna, Júlia Silveira; Halicki, Priscila Cristina Bartolomeu; Lara, Caroline; Tadiotto, Thássia Fernanda; da Silva Maciel, João Batista; Gonçalves, Carla Vitola; von Groll, Andrea; Dellagostin, Odir Antônio; da Silva, Pedro Eduardo Almeida

    2015-09-29

    Helicobacter pylori infection is associated with gastritis, peptic ulcer disease and gastric carcinoma. The severity of damage is determined by the interplay between environmental/behavioral factors, bacterial pathogenicity genes and host genetic polymorphisms that can influence the secretion levels of inflammatory cytokines. Accordingly, this study aimed to identify polymorphisms in the IL-1B and IL-1RN genes and their associations with H. pylori infection, cagA gene of H. pylori, and gastroduodenal diseases. Gastric biopsy samples from 151 patients infected with H. pylori and 76 uninfected individuals were analyzed. H. pylori infection was diagnosed by histology and PCR. Polymorphisms at positions -511, -31 and +3954 of the IL-1B gene were detected by PCR-RFLP, and an analysis of the VNTR polymorphism of the IL-1RN gene was performed by PCR. It was observed that the presence of the T/T genotype at position -511 and the C/C genotype at position -31 were associated with H. pylori infection and with an increased risk of gastritis in H. pylori-positive patients. Additionally, strains from patients H. pylori-positive carrying the cagA gene was significantly related with the T/T genotype at position -511 of IL-1B.  No association of polymorphisms at position +3954 of IL-1B and in the IL-1RN with H. pylori infection and with risk of severe gastric diseases was found. We demonstrated that polymorphisms in the promoter region of the IL-1B gene (at positions -511 and -31) are associated with an enhanced risk of H. pylori infection as well as gastritis in H. pylori-positive patients.

  1. Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions

    Brenner Sydney

    2008-06-01

    Full Text Available Abstract Background One of the many gene families that expanded in early vertebrate evolution is the neuropeptide (NPY receptor family of G-protein coupled receptors. Earlier work by our lab suggested that several of the NPY receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. In this study we have investigated, in five vertebrate genomes, 45 gene families with members close to the NPY receptor genes in the compact genomes of the teleost fishes Tetraodon nigroviridis and Takifugu rubripes. These correspond to Homo sapiens chromosomes 4, 5, 8 and 10. Results Chromosome regions with conserved synteny were identified and confirmed by phylogenetic analyses in H. sapiens, M. musculus, D. rerio, T. rubripes and T. nigroviridis. 26 gene families, including the NPY receptor genes, (plus 3 described recently by other labs showed a tree topology consistent with duplications in early vertebrate evolution and in the actinopterygian lineage, thereby supporting expansion through block duplications. Eight gene families had complications that precluded analysis (such as short sequence length or variable number of repeated domains and another eight families did not support block duplications (because the paralogs in these families seem to have originated in another time window than the proposed genome duplication events. RT-PCR carried out with several tissues in T. rubripes revealed that all five NPY receptors were expressed in the brain and subtypes Y2, Y4 and Y8 were also expressed in peripheral organs. Conclusion We conclude that the phylogenetic analyses and chromosomal locations of these gene families support duplications of large blocks of genes or even entire chromosomes. Thus, these results are consistent with two early vertebrate

  2. Early life adversity and serotonin transporter gene variation interact to affect DNA methylation of the corticotropin-releasing factor gene promoter region in the adult rat brain

    Doelen, R.H.A. van der; Arnoldussen, I.A.C.; Ghareh, H.; Och, L. van; Homberg, J.R.; Kozicz, L.T.

    2015-01-01

    The interaction between childhood maltreatment and the serotonin transporter (5-HTT) gene linked polymorphic region has been associated with increased risk to develop major depression. This Gene x Environment interaction has furthermore been linked with increased levels of anxiety and glucocorticoid

  3. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

    Khan, Aziz; Mathelier, Anthony

    2017-05-31

    A common task for scientists relies on comparing lists of genes or genomic regions derived from high-throughput sequencing experiments. While several tools exist to intersect and visualize sets of genes, similar tools dedicated to the visualization of genomic region sets are currently limited. To address this gap, we have developed the Intervene tool, which provides an easy and automated interface for the effective intersection and visualization of genomic region or list sets, thus facilitating their analysis and interpretation. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. Intervene, and its interactive web ShinyApp companion, generate publication-quality figures for the interpretation of genomic region and list sets. Intervene and its web application companion provide an easy command line and an interactive web interface to compute intersections of multiple genomic and list sets. They have the capacity to plot intersections using easy-to-interpret visual approaches. Intervene is developed and designed to meet the needs of both computer scientists and biologists. The source code is freely available at https://bitbucket.org/CBGR/intervene , with the web application available at https://asntech.shinyapps.io/intervene .

  4. Transcriptional organization of the DNA region controlling expression of the K99 gene cluster.

    Roosendaal, B; Damoiseaux, J; Jordi, W; de Graaf, F K

    1989-01-01

    The transcriptional organization of the K99 gene cluster was investigated in two ways. First, the DNA region, containing the transcriptional signals was analyzed using a transcription vector system with Escherichia coli galactokinase (GalK) as assayable marker and second, an in vitro transcription system was employed. A detailed analysis of the transcription signals revealed that a strong promoter PA and a moderate promoter PB are located upstream of fanA and fanB, respectively. No promoter activity was detected in the intercistronic region between fanB and fanC. Factor-dependent terminators of transcription were detected and are probably located in the intercistronic region between fanA and fanB (T1), and between fanB and fanC (T2). A third terminator (T3) was observed between fanC and fanD and has an efficiency of 90%. Analysis of the regulatory region in an in vitro transcription system confirmed the location of the respective transcription signals. A model for the transcriptional organization of the K99 cluster is presented. Indications were obtained that the trans-acting regulatory polypeptides FanA and FanB both function as anti-terminators. A model for the regulation of expression of the K99 gene cluster is postulated.

  5. Characterization and expression of the maize β-carbonic anhydrase gene repeat regions.

    Tems, Ursula; Burnell, James N

    2010-12-01

    In maize, carbonic anhydrase (CA; EC 4.2.1.1) catalyzes the first reaction of the C(4) photosynthetic pathway; it catalyzes the hydration of CO(2) to bicarbonate and provides an inorganic carbon source for the primary carboxylation reaction catalyzed by phosphoenolpyruvate (PEP) carboxylase. The β-CA isozymes from maize, as well as other agronomically important NADP-malic enzyme (NADP-ME) type C(4) crops, have remained relatively uncharacterized but differ significantly from the β-CAs of other C(4) monocot species primarily due to transcript length and the presence of repeat sequences. This research confirmed earlier findings of repeat sequences in maize CA transcripts, and demonstrated that the gene encoding these transcripts is also composed of repeat sequences. One of the maize CA genes was sequenced and found to encode two domains, with distinct groups of exons corresponding to the repeat regions of the transcript. We have also shown that expression of a single repeat region of the CA transcript produced active enzyme that associated as a dimer and was composed primarily of α-helices, consistent with that observed for other plant CAs. As the presence of repeat regions in the CA gene is unique to NADP-ME type C(4) monocot species, the implications of these findings in the context of the evolution of the location and function of this C(4) pathway enzyme are strongly suggestive of CA gene duplication resulting in an evolutionary advantage and a higher photosynthetic efficiency. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  6. DNA rearrangement in human follicular lymphoma can involve the 5' or the 3' region of the bcl-2 gene

    Tsujimoto, Y.; Bashir, M.M.; Givol, I.; Cossman, J.; Jaffe, E.; Croce, C.M.

    1987-01-01

    In most human lymphomas, the chromosome translocation t(14;18) occurs within two breakpoint clustering regions on chromosome 18, the major one at the 3' untranslated region of the bcl-2 gene and the minor one at 3' of the gene. Analysis of a panel of follicular lymphoma DNAs using probes for the first exon of the bcl-2 gene indicates that DNA rearrangements may also occur 5' to the involved bcl-2 gene. In this case the IgH locus and the bcl-2 gene are found in an order suggesting that an inversion also occurred during the translocation process. The coding region of the bcl-2 gene, however, are left intact in all cases of follicular lymphoma studied to date

  7. Analysis of tissue-specific region in sericin 1 gene promoter of Bombyx mori

    Yan, Liu [College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027 (China); Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Lian, Yu [College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027 (China); Zhejiang Province Key Laboratory of Preventive Veterinary Medicine, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310029 (China); Xiuyang, Guo [Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Tingqing, Guo [Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Shengpeng, Wang [Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Changde, Lu [Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China)

    2006-03-31

    The gene encoding sericin 1 (Ser1) of silkworm (Bombyx mori) is specifically expressed in the middle silk gland cells. To identify element involved in this transcription-dependent spatial restriction, truncation of the 5' terminal from the sericin 1 (Ser1) promoter is studied in vivo. A 209 bp DNA sequence upstream of the transcriptional start site (-586 to -378) is found to be responsible for promoting tissue-specific transcription. Analysis of this 209 bp region by overlapping deletion studies showed that a 25 bp region (-500 to -476) suppresses the ectopic expression of the Ser1 promoter. An unknown factor abundant in fat body nuclear extracts is shown to bind to this 25 bp fragment. These results suggest that this 25 bp region and the unknown factor are necessary for determining the tissue-specificity of the Ser1 promoter.

  8. Absence of mutation at the 5'-upstream promoter region of the TPM4 gene from cardiac mutant axolotl (Ambystoma mexicanum).

    Denz, Christopher R; Zhang, Chi; Jia, Pingping; Du, Jianfeng; Huang, Xupei; Dube, Syamalima; Thomas, Anish; Poiesz, Bernard J; Dube, Dipak K

    2011-09-01

    Tropomyosins are a family of actin-binding proteins that show cell-specific diversity by a combination of multiple genes and alternative RNA splicing. Of the 4 different tropomyosin genes, TPM4 plays a pivotal role in myofibrillogenesis as well as cardiac contractility in amphibians. In this study, we amplified and sequenced the upstream regulatory region of the TPM4 gene from both normal and mutant axolotl hearts. To identify the cis-elements that are essential for the expression of the TPM4, we created various deletion mutants of the TPM4 promoter DNA, inserted the deleted segments into PGL3 vector, and performed promoter-reporter assay using luciferase as the reporter gene. Comparison of sequences of the promoter region of the TPM4 gene from normal and mutant axolotl revealed no mutations in the promoter sequence of the mutant TPM4 gene. CArG box elements that are generally involved in controlling the expression of several other muscle-specific gene promoters were not found in the upstream regulatory region of the TPM4 gene. In deletion experiments, loss of activity of the reporter gene was noted upon deletion which was then restored upon further deletion suggesting the presence of both positive and negative cis-elements in the upstream regulatory region of the TPM4 gene. We believe that this is the first axolotl promoter that has ever been cloned and studied with clear evidence that it functions in mammalian cell lines. Although striated muscle-specific cis-acting elements are absent from the promoter region of TPM4 gene, our results suggest the presence of positive and negative cis-elements in the promoter region, which in conjunction with positive and negative trans-elements may be involved in regulating the expression of TPM4 gene in a tissue-specific manner.

  9. Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig.

    Fan, B; Glenn, K L; Geiger, B; Mileham, A; Rothschild, M F

    2008-08-01

    Previous studies have uncovered several significant quantitative trait loci (QTL) relevant to meat colour traits mapped at the end of SSC17 in the pig. Furthermore, results released from the porcine genome sequencing project have identified genes underlying the entire QTL regions and can further contribute to mining the region for likely causative genes. Ten protein coding genes or novel transcripts located within the QTL regions were screened for single nucleotide polymorphisms (SNPs). Linkage mapping and association studies were carried out in the ISU Berkshire x Yorkshire (B x Y) pig resource family. The total length of the new SSC17 linkage map was 126.6 cM and additional markers including endothelin 3 (EDN3) and phosphatase and actin regulator 3 (PHACTR3) genes were assigned at positions 119.4 cM and 122.9 cM, respectively. A new QTL peak was noted at approximately 120 cM, close to the EDN3 gene, and for some colour traits QTL exceeded the 5% chromosome-wise significance threshold. The association analyses in the B x Y family showed that the EDN3 BslI and PHACTR3 PstI polymorphisms were strongly associated with the subjective colour score and objective colour reflectance measures in the loin, as well as average drip loss percentage and pH value. The RNPC1 DpnII and CTCFL HpyCH4III polymorphisms were associated with some meat colour traits. No significant association between CBLN4, TFAP2C, and four novel transcripts and meat colour traits were detected. The association analyses conducted in one commercial pig line found that both EDN3 BslI and PHACTR3 PstI polymorphisms were associated with meat colour reflectance traits such as centre loin hue angle and Minolta Lightness score. The present findings suggested that the EDN3 and PHACTR3 genes might have potential effects on meat colour in pigs, and molecular mechanisms of their functions are worth exploring.

  10. Artificial heart for humanoid robot using coiled SMA actuators

    Potnuru, Akshay; Tadesse, Yonas

    2015-03-01

    Previously, we have presented the design and characterization of artificial heart using cylindrical shape memory alloy (SMA) actuators for humanoids [1]. The robotic heart was primarily designed to pump a blood-like fluid to parts of the robot such as the face to simulate blushing or anger by the use of elastomeric substrates for the transport of fluids. It can also be used for other applications. In this paper, we present an improved design by using high strain coiled SMAs and a novel pumping mechanism that uses sequential actuation to create peristalsis-like motions, and hence pump the fluid. Various placements of actuators will be investigated with respect to the silicone elastomeric body. This new approach provides a better performance in terms of the fluid volume pumped.

  11. Kelompok Sebaya dan Perilaku Makan Menyimpang Remaja SMA di Jakarta

    Rizky Ibrahim Isra

    2017-02-01

    Full Text Available                                                                          AbstrakTulisan ini membahas hubungan tekanan kelompok sebaya (peer group terhadap gejala perilaku makan menyimpang pada remaja SMA di Jakarta. Banyak studi lain yang mengkaji hal serupa, namun kajian yang membahas permasalahan perilaku makan menyimpang secara sosiologis masih sangat minim. Ketika studi lain hanya memfokuskan pada jenis kelamin perempuan saja, dalam tulisan ini jenis kelamin (laki-laki dan perempuan digunakan sebagai variabel kontrol. Studi sebelumnya yang hanya berfokus pada perempuan memiliki kelemahan karena kelompok sebaya tidak hanya memengaruhi perilaku remaja perempuan, tetapi juga memengaruhi laki-laki. Oleh karena itu, penulis berargumen bahwa kelompok sebaya dapat memengaruhi munculnya gejala perilaku makan menyimpang pada remaja SMA di Jakarta, baik pada laki-laki maupun perempuan. Tulisan ini merupakan hasil studi yang menggunakan metode kuantitatif dengan teknik pengambilan sampel secara acak bertingkat (stratified random sampling sebanyak 235 siswa salah satu SMA negeri di Jakarta. Tulisan ini mengungkapkan bahwa terdapat hubungan antara tekanan kelompok sebaya terhadap gejala perilaku makan menyimpang pada remaja SMA di Jakarta, di mana laki-laki lebih terpengaruh oleh pesan (message dari kelompok sebayanya, sedangkan perempuan lebih kuat terpengaruh oleh interaksi dan likeability.                                                                      AbstractThis article discusses the correlation between peer group pressure and eating disorder behavior symptoms in Jakarta Senior High School students. Many of studies talk about it, but the discussion about eating disorder behavior on sociology was rarely found. In this article, gender was used as a control variable while many of studies only focused on the

  12. [Gene geography of Chile: regional distribution of American, European and African genetic contributions].

    Fuentes, Macarena; Pulgar, Iván; Gallo, Carla; Bortolini, María-Cátira; Canizales-Quinteros, Samuel; Bedoya, Gabriel; González-José, Rolando; Ruiz-Linares, Andrés; Rothhammer, Francisco

    2014-03-01

    The geographical distribution of genes plays a key role in genetic epidemiology. The Chilean population has three major stem groups (Native American, European and African). To estimate the regional rate of American, European and African admixture of the Chilean population. Forty single nucleotide polymorphisms (SNP´s) which exhibit substantially different frequencies between Amerindian populations (ancestry-informative markers or AIM´s), were genotyped in a sample of 923 Chilean participants to estimate individual genetic ancestry. The American, European and African individual average admixture estimates for the 15 Chilean Regions were relatively homogeneous and not statistically different. However, higher American components were found in northern and southern Chile and higher European components were found in central Chile. A negative correlation between African admixture and latitude was observed. On the average, American and European genetic contributions were similar and significantly higher than the African contribution. Weighted mean American, European and African genetic contributions of 44.34% ± 3 9%, 51.85% ± 5.44% and 3.81% ± 0.45%, were estimated. Fifty two percent of subjects harbor African genes. Individuals with Aymara and Mapuche surnames have an American admixture of 58.64% and 68.33%, respectively. Half of the Chilean population harbors African genes. Participants with Aymara and Mapuche surnames had a higher American genetic contribution than the general Chilean population. These results confirm the usefulness of surnames as a first approximation to determine genetic ancestry.

  13. Identifying Regulatory Patterns at the 3'end Regions of Over-expressed and Under-expressed Genes

    Othoum, Ghofran K

    2013-05-01

    Promoters, neighboring regulatory regions and those extending further upstream of the 5’end of genes, are considered one of the main components affecting the expression status of genes in a specific phenotype. More recently research by Chen et al. (2006, 2012) and Mapendano et al. (2010) demonstrated that the 3’end regulatory regions of genes also influence gene expression. However, the association between the regulatory regions surrounding 3’end of genes and their over- or under-expression status in a particular phenotype has not been systematically studied. The aim of this study is to ascertain if regulatory regions surrounding the 3’end of genes contain sufficient regulatory information to correlate genes with their expression status in a particular phenotype. Over- and under-expressed ovarian cancer (OC) genes were used as a model. Exploratory analysis of the 3’end regions were performed by transforming the annotated regions using principal component analysis (PCA), followed by clustering the transformed data thereby achieving a clear separation of genes with different expression status. Additionally, several classification algorithms such as Naïve Bayes, Random Forest and Support Vector Machine (SVM) were tested with different parameter settings to analyze the discriminatory capacity of the 3’end regions of genes related to their gene expression status. The best performance was achieved using the SVM classification model with 10-fold cross-validation that yielded an accuracy of 98.4%, sensitivity of 99.5% and specificity of 92.5%. For gene expression status for newly available instances, based on information derived from the 3’end regions, an SVM predictive model was developed with 10-fold cross-validation that yielded an accuracy of 67.0%, sensitivity of 73.2% and specificity of 61.0%. Moreover, building an SVM with polynomial kernel model to PCA transformed data yielded an accuracy of 83.1%, sensitivity of 92.5% and specificity of 74.8% using

  14. Identifying Regulatory Patterns at the 3'end Regions of Over-expressed and Under-expressed Genes

    Othoum, Ghofran K

    2013-01-01

    Promoters, neighboring regulatory regions and those extending further upstream of the 5’end of genes, are considered one of the main components affecting the expression status of genes in a specific phenotype. More recently research by Chen et al. (2006, 2012) and Mapendano et al. (2010) demonstrated that the 3’end regulatory regions of genes also influence gene expression. However, the association between the regulatory regions surrounding 3’end of genes and their over- or under-expression status in a particular phenotype has not been systematically studied. The aim of this study is to ascertain if regulatory regions surrounding the 3’end of genes contain sufficient regulatory information to correlate genes with their expression status in a particular phenotype. Over- and under-expressed ovarian cancer (OC) genes were used as a model. Exploratory analysis of the 3’end regions were performed by transforming the annotated regions using principal component analysis (PCA), followed by clustering the transformed data thereby achieving a clear separation of genes with different expression status. Additionally, several classification algorithms such as Naïve Bayes, Random Forest and Support Vector Machine (SVM) were tested with different parameter settings to analyze the discriminatory capacity of the 3’end regions of genes related to their gene expression status. The best performance was achieved using the SVM classification model with 10-fold cross-validation that yielded an accuracy of 98.4%, sensitivity of 99.5% and specificity of 92.5%. For gene expression status for newly available instances, based on information derived from the 3’end regions, an SVM predictive model was developed with 10-fold cross-validation that yielded an accuracy of 67.0%, sensitivity of 73.2% and specificity of 61.0%. Moreover, building an SVM with polynomial kernel model to PCA transformed data yielded an accuracy of 83.1%, sensitivity of 92.5% and specificity of 74.8% using

  15. CHARACTER EDUCATION IN ISLAMIC BOARDING SCHOOL- BASED SMA AMANAH

    Nana Herdiana Abdurrahman

    2016-06-01

    Full Text Available This paper aims to describe findings of the study in pesantren-based SMA Amanah covering: 1 the principal policy in developing character education, 2 the methods used in developing character education, 3 students’ characteristics as the result of the character education process, 4 the problems encountered in the implementation of character education and the efforts made in addressing the implementation of character education at the school. This study applied qualitative method using descriptive technique. The data were collected through observation, interviews, and documentation. The findings of study showed that: 1 the principal’s policy in developing character education was carried out by implementing government policies in line with the school’s vision, mission, and programs; 2 the methods used in the process of character education were through role-modelling, assignments and nurturing, habituation, training programs, and  students’ participation in various types of activities, as well as the application of rewards and punishments; 3 the student's characteristics resulted from the character  education process were piousness and devotion as well as being able to apply their knowledge and piety in everyday life; 4 problems encountered in the implementation of character education  were different values and norms students brought from home; imbalance of facilities compared to the number of students; as well as teachers’ readiness to actually implement the new program, which  was character education. Meanwhile the efforts made to overcome those problems were namely developing personal, family, neighborhood or community characters, and making commitment of all related parties/stakeholdres of SMA Amanah.

  16. KONSUMSI SUPLEMEN ATLET REMAJA DI SMA RAGUNAN JAKARTA

    Muhammad Q Aliyyan Wijaya

    2015-05-01

    Full Text Available ABSTRACTThe objective of this study was to investigate consumption of supplement among Ragunan High School Jakarta athletes. The cross sectional study was done with total subjects were 79 students of Ragunan high school who were willing to join the study and they were at school when the study was conducted. There was 92.4% athletes consumed supplement in last one year. All athletes from light and heavy sport category were found consumed supplement. The most popular supplement were vitamin, mineral, and phytonutrition in tablet form. There was 89.0% athletes consumed supplement everyday. Moreover, the main reason for supplementation was to meet a nutrition requirement. The source of information about food supplement was mostly from coach advisor. More than half of athletes got supplement for free from any sources. There was a significant correlation between category of sport and number of supplement used (p<0.05.Keywords: adolescent, athlete, high school, supplementABSTRAKTujuan penelitian adalah menggambarkan konsumsi suplemen pada atlet remaja di SMA Ragunan Jakarta. Desain penelitian ini menggunakan cross sectional dengan total subjek sebanyak 79 siswa SMA Ragunan yang bersedia mengikuti penelitian dan berada di sekolah saat penelitian dilakukan. Sebanyak 92,4% atlet mengaku mengonsumsi suplemen dalam satu tahun terakhir. Atlet dari kategori olahraga ringan dan berat sekali semuanya mengonsumsi suplemen. Suplemen vitamin, mineral, dan fitonutrisi dalam bentuk tablet merupakan jenis dan bentuk suplemen yang paling banyak dikonsumsi. Sebanyak 89,0% dari atlet mengonsumsi suplemen setiap hari. Alasan utama atlet mengonsumsi suplemen adalah untuk memenuhi kebutuhan gizi. Pelatih merupakan sumber infomasi tentang suplemen yang paling banyak dipilih oleh atlet. Lebih dari 50,0% atlet mendapatkan suplemen dengan cara diberi. Kategori olahraga dan jumlah suplemen yang dikonsumsi menunjukkan hubungan positif signifikan (p<0,05.Kata kunci: atlet, remaja

  17. [Characteristics of phenylalanine hydroxylase gene mutations among patients with phenylketonuria from Linyi region of Shandong Province].

    Li, Huafeng; Li, Yongli; Zhang, Li

    2017-06-10

    To explore the characteristics of (PAH) gene mutations among patients with phenylketonuria (PKU) from Linyi area of Shandong Province. For 51 children affected with PKU and their parents, the 13 exons and their flanking intronic sequences of the PAH gene were directly sequenced with Sanger method. PAH gene mutations were detected in all of the 102 alleles of the patients, which included 31 types of mutations. Common mutations included R243Q (17/102, 16.67%), IVS4-1G to A (9/102, 8.82%), R241C (8/102, 7.84%), R111X (8/102, 7.84%), and V399V (8/102, 7.84%). In addition, two novel mutations, D101N, 345-347del, have been detected. The 31 types of mutations included missense, nonsense, deletion, and splicing mutations, which were mainly located in exons 7 (29, 28.43%), 11 (18, 17.65%), 3 (16, 15.69%) and 12 (13, 12.75%). Mutations of the PAH gene in Linyi region mainly distributed in exons 7, 11, and 3, and the most common mutation were R243Q. Two novel mutations, D101N and 345-347del, have been detected.

  18. Hairpin formation within the enhancer region of the human enkephalin gene

    McMurray, C.T.; Douglass, J.O.; Wilson, W.D.

    1991-01-01

    The 3',5'-cyclic adenosine monophosphate (cAMP)-inducible enhancer of the human enkephaline gene is located within an imperfect palindrom of 23 base pairs. The authors have found that a 23-base-pair oligonucleotide duplex containing the enhancer undergoes a reversible conformational transition from the duplex to two individual hairpin structures each formed from one strand of the duplex. Each individual hairpin forms with mismatched base pairs, one containing two GT pairs and the other containing two AC pairs. The conformational transition is stabilized by proton transfer to the hairpin containing AC mismatched pairs. The unique physical and thermodynamic properties of the enkephalin enhancer DNA suggest a model in which DNA secondary structure within the enhancer region plays and active role incAMP-inducible activation of the human enkephalin gene via formation of cruciform structures

  19. Hairpin formation within the enhancer region of the human enkephalin gene

    McMurray, C.T.; Douglass, J.O. (Oregon Health Sciences Univ., Portland (United States)); Wilson, W.D. (Georgia State Univ., Atlanta (United States))

    1991-01-15

    The 3{prime},5{prime}-cyclic adenosine monophosphate (cAMP)-inducible enhancer of the human enkephaline gene is located within an imperfect palindrom of 23 base pairs. The authors have found that a 23-base-pair oligonucleotide duplex containing the enhancer undergoes a reversible conformational transition from the duplex to two individual hairpin structures each formed from one strand of the duplex. Each individual hairpin forms with mismatched base pairs, one containing two GT pairs and the other containing two AC pairs. The conformational transition is stabilized by proton transfer to the hairpin containing AC mismatched pairs. The unique physical and thermodynamic properties of the enkephalin enhancer DNA suggest a model in which DNA secondary structure within the enhancer region plays and active role incAMP-inducible activation of the human enkephalin gene via formation of cruciform structures.

  20. Cis-acting elements in the promoter region of the human aldolase C gene.

    Buono, P; de Conciliis, L; Olivetta, E; Izzo, P; Salvatore, F

    1993-08-16

    We investigated the cis-acting sequences involved in the expression of the human aldolase C gene by transient transfections into human neuroblastoma cells (SKNBE). We demonstrate that 420 bp of the 5'-flanking DNA direct at high efficiency the transcription of the CAT reporter gene. A deletion between -420 bp and -164 bp causes a 60% decrease of CAT activity. Gel shift and DNase I footprinting analyses revealed four protected elements: A, B, C and D. Competition analyses indicate that Sp1 or factors sharing a similar sequence specificity bind to elements A and B, but not to elements C and D. Sequence analysis shows a half palindromic ERE motif (GGTCA), in elements B and D. Region D binds a transactivating factor which appears also essential to stabilize the initiation complex.

  1. Novel candidate genes and regions for childhood apraxia of speech identified by array comparative genomic hybridization.

    Laffin, Jennifer J S; Raca, Gordana; Jackson, Craig A; Strand, Edythe A; Jakielski, Kathy J; Shriberg, Lawrence D

    2012-11-01

    The goal of this study was to identify new candidate genes and genomic copy-number variations associated with a rare, severe, and persistent speech disorder termed childhood apraxia of speech. Childhood apraxia of speech is the speech disorder segregating with a mutation in FOXP2 in a multigenerational London pedigree widely studied for its role in the development of speech-language in humans. A total of 24 participants who were suspected to have childhood apraxia of speech were assessed using a comprehensive protocol that samples speech in challenging contexts. All participants met clinical-research criteria for childhood apraxia of speech. Array comparative genomic hybridization analyses were completed using a customized 385K Nimblegen array (Roche Nimblegen, Madison, WI) with increased coverage of genes and regions previously associated with childhood apraxia of speech. A total of 16 copy-number variations with potential consequences for speech-language development were detected in 12 or half of the 24 participants. The copy-number variations occurred on 10 chromosomes, 3 of which had two to four candidate regions. Several participants were identified with copy-number variations in two to three regions. In addition, one participant had a heterozygous FOXP2 mutation and a copy-number variation on chromosome 2, and one participant had a 16p11.2 microdeletion and copy-number variations on chromosomes 13 and 14. Findings support the likelihood of heterogeneous genomic pathways associated with childhood apraxia of speech.

  2. Identification and characterization of a novel serine-threonine kinase gene from the Xp22 region.

    Montini, E; Andolfi, G; Caruso, A; Buchner, G; Walpole, S M; Mariani, M; Consalez, G; Trump, D; Ballabio, A; Franco, B

    1998-08-01

    Eukaryotic protein kinases are part of a large and expanding family of proteins. Through our transcriptional mapping effort in the Xp22 region, we have isolated and sequenced the full-length transcript of STK9, a novel cDNA highly homologous to serine-threonine kinases. A number of human genetic disorders have been mapped to the region where STK9 has been localized including Nance-Horan (NH) syndrome, oral-facial-digital syndrome type 1 (OFD1), and a novel locus for nonsyndromic sensorineural deafness (DFN6). To evaluate the possible involvement of STK9 in any of the above-mentioned disorders, a 2416-bp full-length cDNA was assembled. The entire genomic structure of the gene, which is composed of 20 coding exons, was determined. Northern analysis revealed a transcript larger than 9.5 kb in several tissues including brain, lung, and kidney. The mouse homologue (Stk9) was identified and mapped in the mouse in the region syntenic to human Xp. This location is compatible with the location of the Xcat mutant, which shows congenital cataracts very similar to those observed in NH patients. Sequence homologies, expression pattern, and mapping information in both human and mouse make STK9 a candidate gene for the above-mentioned disorders. Copyright 1998 Academic Press.

  3. Region-specific expression of mitochondrial complex I genes during murine brain development.

    Stefanie Wirtz

    Full Text Available Mutations in the nuclear encoded subunits of mitochondrial complex I (NADH:ubiquinone oxidoreductase may cause circumscribed cerebral lesions ranging from degeneration of the striatal and brainstem gray matter (Leigh syndrome to leukodystrophy. We hypothesized that such pattern of regional pathology might be due to local differences in the dependence on complex I function. Using in situ hybridization we investigated the relative expression of 33 nuclear encoded complex I subunits in different brain regions of the mouse at E11.5, E17.5, P1, P11, P28 and adult (12 weeks. With respect to timing and relative intensity of complex I gene expression we found a highly variant pattern in different regions during development. High average expression levels were detected in periods of intense neurogenesis. In cerebellar Purkinje and in hippocampal CA1/CA3 pyramidal neurons we found a second even higher peak during the period of synaptogenesis and maturation. The extraordinary dependence of these structures on complex I gene expression during synaptogenesis is in accord with our recent findings that gamma oscillations--known to be associated with higher cognitive functions of the mammalian brain--strongly depend on the complex I activity. However, with the exception of the mesencephalon, we detected only average complex I expression levels in the striatum and basal ganglia, which does not explain the exquisite vulnerability of these structures in mitochondrial disorders.

  4. Cloning and characterization of the promoter regions from the parent and paralogous creatine transporter genes.

    Ndika, Joseph D T; Lusink, Vera; Beaubrun, Claudine; Kanhai, Warsha; Martinez-Munoz, Cristina; Jakobs, Cornelis; Salomons, Gajja S

    2014-01-10

    Interconversion between phosphocreatine and creatine, catalyzed by creatine kinase is crucial in the supply of ATP to tissues with high energy demand. Creatine's importance has been established by its use as an ergogenic aid in sport, as well as the development of intellectual disability in patients with congenital creatine deficiency. Creatine biosynthesis is complemented by dietary creatine uptake. Intracellular transport of creatine is carried out by a creatine transporter protein (CT1/CRT/CRTR) encoded by the SLC6A8 gene. Most tissues express this gene, with highest levels detected in skeletal muscle and kidney. There are lower levels of the gene detected in colon, brain, heart, testis and prostate. The mechanism(s) by which this regulation occurs is still poorly understood. A duplicated unprocessed pseudogene of SLC6A8-SLC6A10P has been mapped to chromosome 16p11.2 (contains the entire SLC6A8 gene, plus 2293 bp of 5'flanking sequence and its entire 3'UTR). Expression of SLC6A10P has so far only been shown in human testis and brain. It is still unclear as to what is the function of SLC6A10P. In a patient with autism, a chromosomal breakpoint that intersects the 5'flanking region of SLC6A10P was identified; suggesting that SLC6A10P is a non-coding RNA involved in autism. Our aim was to investigate the presence of cis-acting factor(s) that regulate expression of the creatine transporter, as well as to determine if these factors are functionally conserved upstream of the creatine transporter pseudogene. Via gene-specific PCR, cloning and functional luciferase assays we identified a 1104 bp sequence proximal to the mRNA start site of the SLC6A8 gene with promoter activity in five cell types. The corresponding 5'flanking sequence (1050 bp) on the pseudogene also had promoter activity in all 5 cell lines. Surprisingly the pseudogene promoter was stronger than that of its parent gene in 4 of the cell lines tested. To the best of our knowledge, this is the first

  5. Mutational analysis of the promoter and the coding region of the 5-HT1A gene

    Erdmann, J.; Noethen, M.M.; Shimron-Abarbanell, D. [Univ. of Bonn (Germany)] [and others

    1994-09-01

    Disturbances of serotonergic pathways have been implicated in many neuropsychiatric disorders. Serotonin (5HT) receptors can be subdivided into at least three major families (5HT1, 5HT2, and 5HT3). Five human 5HT1 receptor subtypes have been cloned, namely 1A, 1D{alpha}, 1D{beta}, 1E, and 1F. Of these, the 5HT1A receptor is the best characterized subtype. In the present study we sought to identify genetic variation in the 5HT1A receptor gene which through alteration of protein function or level of expression might contribute to the genetics of neuropsychiatric diseases. The coding region and the 5{prime} promoter region of the 5HT1A gene from 159 unrelated subjects (45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 controls) were analyzed using SSCA. SSCA revealed the presence of two mutations both located in the coding region of the 5HT1A receptor gene. The first mutation is a rare silent C{r_arrow}T substitution at nucleotide position 549. The second mutation is characterized by a base pair substitution (A{r_arrow}G) at the first position of codon 28 and results in an amino acid exchange (Ile{r_arrow}Val). Since Val28 was found only in a single schizophrenic patient and in none of the other patients or controls, we decided to extend our samples and to use a restriction assay for screening a further 74 schizophrenic, 95 bipolar affective, and 49 patients with Tourette`s syndrome, as well as 185 controls, for the presence of the mutation. In total, the mutation was found in 2 schizophrenic patients, in 3 bipolars, in 1 Tourette patient, and in 5 controls. To our knowledge the Ile-28-Val substitution reported here is the first natural occuring molecular variant which has been identified for a serotonin receptor so far.

  6. Evolution of the DAZ gene and the AZFc region on primate Y chromosomes

    Yu Jane-Fang

    2008-03-01

    Full Text Available Abstract Background The Azoospermia Factor c (AZFc region of the human Y chromosome is a unique product of segmental duplication. It consists almost entirely of very long amplicons, represented by different colors, and is frequently deleted in subfertile men. Most of the AZFc amplicons have high sequence similarity with autosomal segments, indicating recent duplication and transposition to the Y chromosome. The Deleted in Azoospermia (DAZ gene within the red-amplicon arose from an ancestral autosomal DAZ-like (DAZL gene. It varies significantly between different men regarding to its copy number and the numbers of RNA recognition motif and DAZ repeat it encodes. We used Southern analyses to study the evolution of DAZ and AZFc amplicons on the Y chromosomes of primates. Results The Old World monkey rhesus macaque has only one DAZ gene. In contrast, the great apes have multiple copies of DAZ, ranging from 2 copies in bonobos and gorillas to at least 6 copies in orangutans, and these DAZ genes have polymorphic structures similar to those of their human counterparts. Sequences homologous to the various AZFc amplicons are present on the Y chromosomes of some but not all primates, indicating that they arrived on the Y chromosome at different times during primate evolution. Conclusion The duplication and transposition of AZFc amplicons to the human Y chromosome occurred in three waves, i.e., after the branching of the New World monkey, the gorilla, and the chimpanzee/bonobo lineages, respectively. The red-amplicon, one of the first to arrive on the Y chromosome, amplified by inverted duplication followed by direct duplication after the separation of the Old World monkey and the great ape lineages. Subsequent duplication/deletion in the various lineages gave rise to a spectrum of DAZ gene structure and copy number found in today's great apes.

  7. Use of Gene Expression Programming in regionalization of flow duration curve

    Hashmi, Muhammad Z.; Shamseldin, Asaad Y.

    2014-06-01

    In this paper, a recently introduced artificial intelligence technique known as Gene Expression Programming (GEP) has been employed to perform symbolic regression for developing a parametric scheme of flow duration curve (FDC) regionalization, to relate selected FDC characteristics to catchment characteristics. Stream flow records of selected catchments located in the Auckland Region of New Zealand were used. FDCs of the selected catchments were normalised by dividing the ordinates by their median value. Input for the symbolic regression analysis using GEP was (a) selected characteristics of normalised FDCs; and (b) 26 catchment characteristics related to climate, morphology, soil properties and land cover properties obtained using the observed data and GIS analysis. Our study showed that application of this artificial intelligence technique expedites the selection of a set of the most relevant independent variables out of a large set, because these are automatically selected through the GEP process. Values of the FDC characteristics obtained from the developed relationships have high correlations with the observed values.

  8. Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

    Michael H. Kohn

    2008-01-01

    Full Text Available While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d5’ were found to increase as a function of synonymous (dS, and to a lesser extend, amino-acid (dA site divergence between duplicates. The rate d5’/dS was found to rapidly decay from values > 1 in young duplicate pairs (dS 0.8. Such rapid rates of 5 prime evolution exceeding 1 (~neutral predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization or division of labor among duplicate genes (subfunctionalization. In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

  9. Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes

    White Bradley N

    2010-07-01

    Full Text Available Abstract Background Phylogenetic studies of wild Canis species have relied heavily on the mitochondrial DNA control region (mtDNA CR to infer species relationships and evolutionary lineages. Previous analyses of the CR provided evidence for a North American evolved eastern wolf (C. lycaon, that is more closely related to red wolves (C. rufus and coyotes (C. latrans than grey wolves (C. lupus. Eastern wolf origins, however, continue to be questioned. Therefore, we analyzed mtDNA from 89 wolves and coyotes across North America and Eurasia at 347 base pairs (bp of the CR and 1067 bp that included the ATPase6 and ATPase8 genes. Phylogenies and divergence estimates were used to clarify the evolutionary history of eastern wolves, and regional comparisons of nonsynonomous to synonomous substitutions (dN/dS at the ATPase6 and ATPase8 genes were used to elucidate the potential role of selection in shaping mtDNA geographic distribution. Results We found high concordance across analyses between the mtDNA regions studied. Both had a high percentage of variable sites (CR = 14.6%; ATP = 9.7% and both phylogenies clustered eastern wolf haplotypes monophyletically within a North American evolved lineage apart from coyotes. Divergence estimates suggest the putative red wolf sequence is more closely related to coyotes (DxyCR = 0.01982 ± 0.00494 SD; DxyATP = 0.00332 ± 0.00097 SD than the eastern wolf sequences (DxyCR = 0.03047 ± 0.00664 SD; DxyATP = 0.00931 ± 0.00205 SD. Neutrality tests on both genes were indicative of the population expansion of coyotes across eastern North America, and dN/dS ratios suggest a possible role for purifying selection in the evolution of North American lineages. dN/dS ratios were higher in European evolved lineages from northern climates compared to North American evolved lineages from temperate regions, but these differences were not statistically significant. Conclusions These results demonstrate high concordance between coding

  10. Monotonic and cyclic bond behavior of confined concrete using NiTiNb SMA wires

    Choi, Eunsoo; Chung, Young-Soo; Kim, Yeon-Wook; Kim, Joo-Woo

    2011-01-01

    This study conducts bond tests of reinforced concrete confined by shape memory alloy (SMA) wires which provide active and passive confinement of concrete. This study uses NiTiNb SMA which usually shows wide temperature hysteresis; this is a good advantage for the application of shape memory effects. The aims of this study are to investigate the behavior of SMA wire under residual stress and the performance of SMA wire jackets in improving bond behavior through monotonic-loading tests. This study also conducts cyclic bond tests and analyzes cyclic bond behavior. The use of SMA wire jackets transfers the bond failure from splitting to pull-out mode and satisfactorily increases bond strength and ductile behavior. The active confinement provided by the SMA plays a major role in providing external pressure on the concrete because the developed passive confinement is much smaller than the active confinement. For cyclic behavior, slip and circumferential strain are recovered more with larger bond stress. This recovery of slip and circumferential strain are mainly due to the external pressure of the SMA wires since cracked concrete cannot provide any elastic recovery

  11. Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions.

    Pezer, Željka; Chung, Amanda G; Karn, Robert C; Laukaitis, Christina M

    2017-06-01

    The Androgen-binding protein ( Abp ) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus ( Mmd ) and Mus musculus musculus ( Mmm ), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd , primarily representing the presence/absence of the final duplications described for the mouse genome. Clustering of Mmd individuals based on this variation did not reflect their geographical origin, suggesting no population divergence in the Abp gene cluster. However, copy number variation patterns differ substantially between Mmd and other mouse taxa. Large blocks of Abp genes are absent in Mmm , Mus musculus castaneus and an outgroup, Mus spretus , although with differences in variation and breakpoint locations. Our analysis calls into question the reliance on a reference genome for interpreting the detailed organization of genes in taxa more distant from the Mmd reference genome. The polymorphic nature of the gene family expansion in all four taxa suggests that the number of Abp genes, especially in the central gene region, is not critical to the survival and reproduction of the mouse. However, Abp haplotypes of variable length may serve as a source of raw genetic material for new signals influencing reproductive communication and thus speciation of mice. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. [Variation of CAG repeats in coding region of ATXN2 gene in different ethnic groups].

    Chen, Xiao-Chen; Sun, Hao; Mi, Dong-Qing; Huang, Xiao-Qin; Lin, Ke-Qin; Yi, Wen; Yu, Liang; Shi, Lei; Shi, Li; Yang, Zhao-Qing; Chu, Jia-You

    2011-04-01

    Toinvestigate CAG repeats variation of ATXN2 gene coding region in six ethnic groups that live in comparatively different environments, to evaluate whether these variations are under positive selection, and to find factors driving selection effects, 291 unrelated healthy individuals were collected from six ethnic groups and their STR geneotyping was performed. The frequencies of alleles and genotypes were counted and thereby Slatkin's linearized Fst values were calculated. The UPGMA tree against this gene was constructed. The MDS analysis among these groups was carried out as well. The results from the linearized Fst values indicated that there were significant evolutionary differences of the STR in ATXN2 gene between Hui and Yi groups, but not among the other 4 groups. Further analysis was performed by combining our data with published data obtained from other groups. These results indicated that there were significant differences between Japanese and other groups including Hui, Hani, Yunnan Mongolian, and Inner Mongolian. Both Hui and Mongolian from Inner Mongolia were significantly different from Han. In conclusion, the six ethnic groups had their own distribution characterizations of allelic frequencies of ATXN2 STR, and the potential cause of frequency changes in rare alleles could be the consequence of positive selection.

  13. Low levels of Survival Motor Neuron protein are sufficient for normal muscle function in the SMNΔ7 mouse model of SMA.

    Iyer, Chitra C; McGovern, Vicki L; Murray, Jason D; Gombash, Sara E; Zaworski, Phillip G; Foust, Kevin D; Janssen, Paul M L; Burghes, Arthur H M

    2015-11-01

    Spinal Muscular Atrophy (SMA) is an autosomal recessive disorder characterized by loss of lower motor neurons. SMA is caused by deletion or mutation of the Survival Motor Neuron 1 (SMN1) gene and retention of the SMN2 gene. The loss of SMN1 results in reduced levels of the SMN protein. SMN levels appear to be particularly important in motor neurons; however SMN levels above that produced by two copies of SMN2 have been suggested to be important in muscle. Studying the spatial requirement of SMN is important in both understanding how SMN deficiency causes SMA and in the development of effective therapies. Using Myf5-Cre, a muscle-specific Cre driver, and the Cre-loxP recombination system, we deleted mouse Smn in the muscle of mice with SMN2 and SMNΔ7 transgenes in the background, thus providing low level of SMN in the muscle. As a reciprocal experiment, we restored normal levels of SMN in the muscle with low SMN levels in all other tissues. We observed that decreasing SMN in the muscle has no phenotypic effect. This was corroborated by muscle physiology studies with twitch force, tetanic and eccentric contraction all being normal. In addition, electrocardiogram and muscle fiber size distribution were also normal. Replacement of Smn in muscle did not rescue SMA mice. Thus the muscle does not appear to require high levels of SMN above what is produced by two copies of SMN2 (and SMNΔ7). © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. National education ideology as the orientation of the school culture development policy at SMA N 1 and SMA N 3 Yogyakarta

    Lusila Andriani Purwastuti

    2017-09-01

    Full Text Available This study aimed at describing the national education ideology as the orientation of the school culture development policy at SMA N 1 and SMAN 3 Yogyakarta. This research employed the qualitative approach through ethnography method. The subjects of the research were the school community. The object was the implementation of Pancasila on the development of the school culture. The data were collected through interviews, observations, and documentation. The data were analyzed using ethnography analysis as suggested by Spradley and they were validated by data triangulation and member checks. The results show that the national education ideology as the orientation of the school culture development is understood: (1 as an open ideology; (2 implemented on the basis value; instrumental values; the value of practices in the school culture; (3 The school culture in SMA N 1 and SMA N 3 is the implementation and contextualization of the values of Pancasila, along with the uniqueness of SMA N 1 with its “Teladan” icon which represents the religious morality and intellectual, as well as at SMA N 3 with its “Padmanaba” icon representing noble behavior. (4  Both schools have developed the school culture, namely: religious morality, social-culture, intellectual, and environment/management/leadership.

  15. Percutaneous Thrombin Injection to Complete SMA Pseudoaneurysm Exclusion After Failing of Endograft Placement

    Szopinski, Piotr; Ciostek, Piotr; Pleban, Eliza; Iwanowski, Jaroslaw; Krol, Malgorzata Serafin-; Marianowska, Agnieszka; Noszczyk, Wojciech

    2005-01-01

    Visceral aneurysms are potentially life-threatening vascular lesions. Superior mesenteric artery (SMA) pseudoaneurysms are a rare but well-recognized complication of chronic pancreatitis. Open surgical repair of such an aneurysm, especially in patients after previous surgical treatment, might be dangerous and risky. Stent graft implantation makes SMA pseudoaneurysm exclusion possible and therefore avoids a major abdominal operation. Percutaneous direct thrombin injection is also one of the methods of treating aneurysms in this area. We report a first case of percutaneous ultrasound-guided thrombin injection to complete SMA pseudoaneurysm exclusion after an unsuccessful endograft placement. Six-month follow-up did not demonstrate any signs of aneurysm recurrence

  16. Influenza NA and PB1 Gene Segments Interact during the Formation of Viral Progeny: Localization of the Binding Region within the PB1 Gene

    Brad Gilbertson

    2016-08-01

    Full Text Available The influenza A virus genome comprises eight negative-sense viral RNAs (vRNAs that form individual ribonucleoprotein (RNP complexes. In order to incorporate a complete set of each of these vRNAs, the virus uses a selective packaging mechanism that facilitates co-packaging of specific gene segments but whose molecular basis is still not fully understood. Recently, we used a competitive transfection model where plasmids encoding the A/Puerto Rico/8/34 (PR8 and A/Udorn/307/72 (Udorn PB1 gene segments were competed to show that the Udorn PB1 gene segment is preferentially co-packaged into progeny virions with the Udorn NA gene segment. Here we created chimeric PB1 genes combining both Udorn and PR8 PB1 sequences to further define the location within the Udorn PB1 gene that drives co-segregation of these genes and show that nucleotides 1776–2070 of the PB1 gene are crucial for preferential selection. In vitro assays examining specific interactions between Udorn NA vRNA and purified vRNAs transcribed from chimeric PB1 genes also supported the importance of this region in the PB1-NA interaction. Hence, this work identifies an association between viral genes that are co-selected during packaging. It also reveals a region potentially important in the RNP-RNP interactions within the supramolecular complex that is predicted to form prior to budding to allow one of each segment to be packaged in the viral progeny. Our study lays the foundation to understand the co-selection of specific genes, which may be critical to the emergence of new viruses with pandemic potential.

  17. Transcription mapping and expression patterns of genes in the major immediate-early region of Kaposi's sarcoma-associated herpesvirus.

    Saveliev, Alexei; Zhu, Fan; Yuan, Yan

    2002-08-01

    Viral immediate-early (IE) genes are the first class of viral genes expressed during primary infection or reactivation from latency. They usually encode regulatory proteins that play crucial roles in viral life cycle. In a previous study, four regions in the KSHV genome were found to be actively transcribed in the immediate-early stage of viral reactivation in primary effusion lymphoma cells. Three immediate-early transcripts were characterized in these regions, as follows: mRNAs for ORF50 (KIE-1), ORF-45 (KIE-2), and ORF K4.2 (KIE-3) (F. X. Zhu, T. Cusano, and Y. Yuan, 1999, J. Virol. 73, 5556-5567). In the present study, we further analyzed the expression of genes in these IE regions in BC-1 and BCBL-1 cells. One of the immediate-early regions (KIE-1) that encompasses ORF50 and other genes was intensively studied to establish a detailed transcription map and expression patterns of genes in this region. This study led to identification of several novel IE transcripts in this region. They include a 2.6-kb mRNA which encodes ORF48/ORF29b, a family of transcripts that are complementary to ORF50 mRNA and a novel K8 IE mRNA of 1.5 kb. Together with the IE mRNA for ORF50 which was identified previously, four immediate-early genes have been mapped to KIE-1 region. Therefore, we would designate KIE-1 the major immediate-early region of KSHV. In addition, we showed that transcription of K8 gene is controlled by two promoters, yielding two transcripts, an immediate-early mRNA of 1.5 kb and a delayed-early mRNA of 1.3 kb.

  18. Exon organization of the mouse entactin gene corresponds to the structural domains of the polypeptide and has regional homology to the low-density lipoprotein receptor gene

    Durkin, M E; Wewer, U M; Chung, A E

    1995-01-01

    of the mouse entactin gene closely corresponds to the organization of the polypeptide into distinct structural and functional domains. The two amino-terminal globular domains are encoded by three exons each. Single exons encode the two protease-sensitive, O-glycosylated linking regions. The six EGF......Entactin is a widespread basement membrane protein of 150 kDa that binds to type IV collagen and laminin. The complete exon-intron structure of the mouse entactin gene has been determined from lambda genomic DNA clones. The gene spans at least 65 kb and contains 20 exons. The exon organization...

  19. Kondisi Stres Akademik Siswa SMA Negeri di Kota Padang

    Taufik Taufik

    2014-01-01

    Full Text Available This research conduct base from increasing the National Examination standards from recent years, and overload student’s learning activity in Senior High School (SMA. These conditions as triggers stress students, from a long time, its influence on their learning. Based that, the research is to identify level of student academic stress, and differences base gender, and school location. This research use Cluster Random Sampling. Samples are grouped into 3 (three, that’s school is located in downtown, midtown and the Suburbs. Research findings show that there are 15% of student’s stress academic at low levels of, 71,8% experiencing stress academic at medium level, and 13.2% of students experiencing stress academic at high level. There was no significant difference between the academic stress Student SMAN in Padang by location and gender. These research findings can then be an important basic need for guidance and counseling services in order to decrease the level of stress of academic students in Padang city, so that they can learn by making every effort that is optimal.

  20. Mesoscale simulation of elastocaloric cooling in SMA films

    Wendler, Frank; Ossmer, Hinnerk; Chluba, Christoph; Quandt, Eckhard; Kohl, Manfred

    2017-01-01

    A model for the evolution of the mechanical and thermal properties of shape memory alloy (SMA) films during elastocaloric cycling is developed and compared with experiments. The focus is on Ti-Ni-Cu-Co films of 20 μm thickness showing ultra-low fatigue properties. The films undergo a highly localized pseudoelastic transformation under tensile load cycling featuring strain and temperature band patterns that depend on the loading conditions. The corresponding temperature change is of special interest for film-based elastocaloric cooling applications. Starting from a thermodynamics-based Gibbs free energy model comprising mechanical and chemical contributions, we include a martensite-austenite interface free energy term, for which formulations from a phase-field model are adapted. A 3D continuum mechanics description is modified to treat plane stress conditions appropriate for polycrystalline thin films. The nucleation mechanism of strain bands under dynamic loading is described by introducing a spatial random distribution of the transformation stress barriers reflecting the degree of material inhomogeneity. Heat transfer due to conduction and convection is taken into account. The simulations predict the correlated mechanical and thermal local response of the films including band formation and evolution, tilt angle as well as strain-rate dependence. Macroscopic stress-strain characteristics and thermal evolution curves well represent the experimental results.

  1. Identification of T1D susceptibility genes within the MHC region by combining protein interaction networks and SNP genotyping data

    Brorsson, C.; Hansen, Niclas Tue; Hansen, Kasper Lage

    2009-01-01

    genes. We have developed a novel method that combines single nucleotide polymorphism (SNP) genotyping data with protein-protein interaction (ppi) networks to identify disease-associated network modules enriched for proteins encoded from the MHC region. Approximately 2500 SNPs located in the 4 Mb MHC......To develop novel methods for identifying new genes that contribute to the risk of developing type 1 diabetes within the Major Histocompatibility Complex (MHC) region on chromosome 6, independently of the known linkage disequilibrium (LD) between human leucocyte antigen (HLA)-DRB1, -DQA1, -DQB1...... region were analysed in 1000 affected offspring trios generated by the Type 1 Diabetes Genetics Consortium (T1DGC). The most associated SNP in each gene was chosen and genes were mapped to ppi networks for identification of interaction partners. The association testing and resulting interacting protein...

  2. Identification of distal regulatory regions in the human alpha IIb gene locus necessary for consistent, high-level megakaryocyte expression.

    Thornton, Michael A; Zhang, Chunyan; Kowalska, Maria A; Poncz, Mortimer

    2002-11-15

    The alphaIIb/beta3-integrin receptor is present at high levels only in megakaryocytes and platelets. Its presence on platelets is critical for hemostasis. The tissue-specific nature of this receptor's expression is secondary to the restricted expression of alphaIIb, and studies of the alphaIIb proximal promoter have served as a model of a megakaryocyte-specific promoter. We have examined the alphaIIb gene locus for distal regulatory elements. Sequence comparison between the human (h) and murine (m) alphaIIb loci revealed high levels of conservation at intergenic regions both 5' and 3' to the alphaIIb gene. Additionally, deoxyribonuclease (DNase) I sensitivity mapping defined tissue-specific hypersensitive (HS) sites that coincide, in part, with these conserved regions. Transgenic mice containing various lengths of the h(alpha)IIb gene locus, which included or excluded the various conserved/HS regions, demonstrated that the proximal promoter was sufficient for tissue specificity, but that a region 2.5 to 7.1 kb upstream of the h(alpha)IIb gene was necessary for consistent expression. Another region 2.2 to 7.4 kb downstream of the gene enhanced expression 1000-fold and led to levels of h(alpha)IIb mRNA that were about 30% of the native m(alpha)IIb mRNA level. These constructs also resulted in detectable h(alpha)IIb/m(beta)3 on the platelet surface. This work not only confirms the importance of the proximal promoter of the alphaIIb gene for tissue specificity, but also characterizes the distal organization of the alphaIIb gene locus and provides an initial localization of 2 important regulatory regions needed for the expression of the alphaIIb gene at high levels during megakaryopoiesis.

  3. PERANGKAT PENGEMBANGAN DIRI UNTUK MENINGKATKAN KOMPETENSI GURU DAN PENGEMBANGAN KEPRIBADIAN SISWA SMA

    Wenny Hulukati

    2014-06-01

    Abstrak: Perangkat Pengembangan Diri untuk Meningkatkan Kompetensi Guru dan Pengembangan Kepribadian Siswa SMA. Penelitian ini bertujuan mengembangkan perangkat pengembangan diri untuk meningkatkan kompetensi guru dan pengembangan kepribadian siswa SMA. Kegiatan penelitian ini diawali dengan studi pendahuluan yang berkaitan dengan kompentensi guru pembimbing dalam melaksanakan pelayanan bimbingan dan konseling dan kecenderungan kepribadian siswa SMA. Langkah berikutnya adalah mendesain dan mengembangkan draf, dan diakhiri dengan kegiatan uji keefektifan produk. Dari kegiatan penelitian pengembangan ini telah dihasilkan produk pengembangan yang valid dan handal yang meliputi panduan guru, panduan siswa, dan panduan penilaian. Berdasarkan hasil uji keefektifan terhadap produk pengembangan diperoleh informasi bahwa perangkat panduan pengembangan diri efektif diguna­kan untuk meningkatkan kompetensi guru pembimbing dalam melaksanakan pelayanan bimbingan dan konseling dan pengembangan kepribadian siswa SMA.

  4. Persepsi Siswa Terhadap Pembelajaran Guru Pendidikan Jasmani Di SMA Muhammadiyah Kediri

    Hendra Mashuri

    2017-05-01

    Full Text Available Tujuan yang ingin dicapai dalam penelitian ini adalah untuk memperoleh informasi tentang persepsi siswa terhadap pembelajaran guru pendidikan jasmani di SMA Muhammadiyah Kediri. Rumusan masalah dalam penelitian ini adalah bagaimana persepsi siswa terhadap pembelajaran guru pendidikan jasmani di SMA Muhammadiyah Kediri? Jenis penelitian ini adalah penelitian survei. Populasi yang digunakan adalah seluruh siswa SMA Muhammadiyah Kediri, sampel yang diambil berjumlah 60 siswa yang terdiri dari 20 siswa dari masing-masing kelas. Instrumen yang digunakan adalah angket dan dokumentasi. Teknik analisis data menggunakan persentase. Hasil penelitian menunjukkan bahwa persepsi siswa terhadap proses pembelajaran SMA Muhammadiyah Kediri mendapatkan skor 3115 atau rata-rata jawaban siswa 51,917 dengan persentase sebesar 74% dan masuk dalam kategori “Baik”. Dengan demikian dapat dikatakan bahwa persepsi siswa terhadap pembelajaran guru pendidikan jasmani adalah baik.

  5. Klasifikasi Kecamatan Berdasarkan Nilai Akhir SMA/MA di Kabupaten Aceh Selatan Menggunakan Analisis Diskriminan

    Fitriana A.R.

    2015-11-01

    Full Text Available Analisis diskriminan merupakan bagian dari analisis peubah ganda. Analisis diskriminan digunakan untuk memodelkan variabel tak bebas yang bersifat kualitatif dengan variabel bebas yang bersifat kuantitatif. Pada penelitian ini, analisis diskriminan lebih dari dua kelompok diterapkan pada data nilai akhir SMA/MA di Kabupaten Aceh Selatan yang bertujuan untuk mendapatkan model untuk pengklasifikasian kecamatan. Pengklasifikasian ini bertujuan untuk melihat perbedaan kualitas siswa SMA/MA yang berada di masing-masing kecamatan Kabupaten Aceh Selatan berdasarkan data nilai akhir. Variabel tak bebas yang digunakan berupa klasifikasi kecamatan berdasarkan rata-rata jumlah nilai akhir SMA/MA yang berada di masing-masing kecamatan yang dibentuk dengan K-Means Cluster. Sedangkan variabel bebas yang digunakan adalah data rata-rata nilai akhir SMA/MA untuk setiap mata pelajaran yang diujiankan pada masing-masing jurusan setiap kecamatan. Model yang didapatkan adalah dua model diskriminan untuk jurusan IPA dan IPS.

  6. Specific methanogenic activity (SMA of industrial sludge from the aerobic and anaerobic biological treatment

    Danieli Schneiders

    2013-08-01

    Full Text Available In this study, specific methanogenic activity (SMA tests were performed on textile sludge and food industry sludge. The textile sludge from an activated sludge was collected at the entrance of the secondary biologic clarifier and the food sludge was collected in a UASB reactor. Once collected, the sludges were characterized and tested for SMA. It was found that the microrganisms present in the food sludge had SMA of 0.17 gCOD-CH4 gSSV.d-1 and 337.05 mL of methane production, while the microrganisms of the textile sludge presented 0.10 gCOD-CH4 gSSV.d-1 of SMA and 3.04 mL of methane production. Therefore, the food sludge was more suitable to be used as a starting inoculum in UASB.

  7. PENGEMBANGAN KINERJA GURU MELALUI PENELITIAN TINDAKAN KELAS PADA SMA NEGERI DI KOTA PALOPO

    Hilal Muhammad

    2015-12-01

    Tujuan penelitian ini adalah untuk mengungkap: (1 pelaksanaan pengembangan kinerja guru melalui PTK pada SMA Negeri di Kota Palopo; dan (2 hambatan da-lam pelaksanaan pengembangan kinerja guru melalui PTK pada SMA Negeri di Kota Palopo. Jenis penelitian adalah penelitian lapangan yang kajiannya bersifat kualitatif-verifikatif. Pendekatan yang digunakan adalah pendekatan fenomeno-logi. Metode pengumpulan data yang digunakan dalam penelitian ini adalah wawancara, observasi, dan dokumentasi. Hasil penelitian ini menunjukkan dua hal. Pertama, pengembangan kinerja guru melalui PTK pada SMA Negeri di Kota Palopo belum berjalan optimal dan baru sebatas memenuhi kebutuhan persyarat-an kenaikan pangkat. Potensi guru belum dimanfaatkan melalui pemberdayaan, khususnya penelitian tindakan kelas. Kedua, hambatan dalam pelaksanaan pe-ngembangan kinerja guru melalui PTK pada SMA Negeri di Kota Palopo adalah keterbatasan waktu, dana, sumber referensi kurang, lingkungan tidak kondusif, dan motivasi kurang. Selain itu, sebagian guru juga masih mengalami kesulitan dalam melakukan dan menyusun laporan hasil PTK.

  8. Optimal design of damping layers in SMA/GFRP laminated hybrid composites

    Haghdoust, P.; Cinquemani, S.; Lo Conte, A.; Lecis, N.

    2017-10-01

    This work describes the optimization of the shape profiles for shape memory alloys (SMA) sheets in hybrid layered composite structures, i.e. slender beams or thinner plates, designed for the passive attenuation of flexural vibrations. The paper starts with the description of the material and architecture of the investigated hybrid layered composite. An analytical method, for evaluating the energy dissipation inside a vibrating cantilever beam is developed. The analytical solution is then followed by a shape profile optimization of the inserts, using a genetic algorithm to minimize the SMA material layer usage, while maintaining target level of structural damping. Delamination problem at SMA/glass fiber reinforced polymer interface is discussed. At the end, the proposed methodology has been applied to study the hybridization of a wind turbine layered structure blade with SMA material, in order to increase its passive damping.

  9. Faktor Penghambat Operasionalisasi Kunjungan Rumah di SMA Negeri se-Kota Semarang

    Juwita Nasruddin

    2015-09-01

    Full Text Available Penelitian dilaksanakan berdasarkan fenomena di lapangan pada saat penulis melaksanakan Praktik Pengalaman Lapangan (PPL di SMP Negeri 8 Semarang dan observasi awal di SMA Negeri 8 Semarang. Tujuan dari penelitian ini untuk mengetahui apa faktor penghambat operasionalisasi Home Visit di SMA Negeri se-kota Semarang tahun ajaran 2014/2015. Jenis penelitian yang digunakan oleh penulis dalam penelitian ini yaitu jenis penelitian survei. Untuk populasi pada penelitian ini adalah semua guru BK di SMA se-kota Semarang yaitu sejumlah 59 guru BK. Sampel yang digunakan adalah sejumlah populasi yang ada. Sedangkan instrumen yang digunakan dalam penelitian ini merupakan angket. Analisis data yang digunakan dalam penelitian ini adalah deskriptif persentase. Hasil yang ditemukan bahwa faktor penghambat operasionalisasi Home Visit di SMA Negeri se-kota Semarang mengalami hambatan cukup tinggi dengan presentase sebesar 65,03%. Simpulan yang didapatkan adalah Faktor Penghambat Operasionalisasi Kunjungan Rumah (Home visit di SMA Negeri se-kota Semarang adalah kurangnya pemahaman dari guru BK berkaitan dengan Home Visit. Adapun saran yang diberikan kepada guru BK SMA Negeri se-kota Semarang adalah untuk mempelajari hakikat Home Visit dan melaksanakan prosedur operasionalisasi Home Visit dengan baik dan benar dari perencanaan, pelaksanaan, evaluasi, analisis evaluasi, tindak lanjut hingga laporan. The research was conducted based on the phenomenon on the ground when implementing writer Practice Field Experience (PPL in SMPN 8 Semarang and preliminary observations in SMAN 8 Semarang. The purpose of this study to determine what factors inhibiting the operation of the Home Visit at all SMA Negeri in Semarang throughout the academic year 2014/2015. The type research used by the writer in this study is a survey research. The population in this study were all counselors at SMA in Semarang city. There were 59 counselors. The sample used were as many as the population

  10. Numerical and Experimental Investigation on Aerodynamic Characteristics of SMA Actuated Smart Wing Model

    Iyyappan Balaguru; Sathiavelu Sendhilkumar

    2013-01-01

    Due to the advancements in smart actuators, morphing (changing) of aircraft wings has been investigated by increasing number of researchers in recent years. In this research article, the concept of morphing is introduced to the conventional aircraft wing model with the utilization of Shape memory alloys (SMAs). An actuating mechanism is developed and built inside the aircraft wing model along with the SMA actuators which is used to morph its shape. The aircraft wing model with the SMA actuati...

  11. Investigations on Vibration Characteristics of Sma Embedded Horizontal Axis Wind Turbine Blade

    Jagadeesh, V.; Yuvaraja, M.; Chandhru, A.; Viswanathan, P.; Senthil kumar, M.

    2018-02-01

    Vibration induced in wind turbine blade is a solemn problem as it reduces the life of the blade and also it can create critical vibration onto the tower, which may cause serious damage to the tower. The aim of this paper is to investigate the vibration characteristics of the prototype horizontal axis wind turbine blade. Shape memory alloys (SMA), with its variable physical properties, provides an alternative actuating mechanism. Heating an SMA causes a change in the elastic modulus of the material and hence SMAs are used as a damping material. A prototype blade with S1223 profile has been manufactured and the natural frequency is found. The natural frequency is found by incorporating the single SMA wire of 0.5mm diameter over the surface of the blade for a length of 240 mm. Similarly, number of SMA wires over the blade is increased up to 3 and the natural frequency is found. Frequency responses showed that the embedment of SMA over the blade’s surface will increase the natural frequency and reduce the amplitude of vibration. This is because of super elastic nature of SMA. In this paper, when SMA wire of 0.5 mm diameter and of length of 720 mm is embedded on the blade, an increase in the natural frequency by 6.3% and reducing the amplitude by 64.8%. Results of the experimental modal and harmonic indicates the effectiveness of SMA as a passive vibration absorber and that it has potential as a modest and high-performance method for controlling vibration of the blade.

  12. Peningkatan Mutu Pendidikan SMA Muhammadiyah 2 Sidoarjo sebagai Sekolah Berkategori The Outstanding School of Muhammadiyah

    Hidayatulloh Hidayatulloh

    2016-01-01

    This article examines about improving the education quality of SMA Muhammadiyah 2 Sidoarjo as the Outstanding School of Muhammadiyah. This article reveals that the quality improvement of SMA Muhammadiyah 2 Sidoarjo was conducted through: the arrangement of school program and self evaluation, the reinforcement of vision, mission and education objective, the reinforcement of leadership and teamwork, the improvement of teachers and educators competence, the improvement learners quality input, th...

  13. Perancangan Sistem Informasi SMA Negeri 1 Babalan Dengan Menggunakan Pemrograman PHP Dan MySQL

    Yulita, Devi

    2014-01-01

    Tulisan ini bertujuan untuk membangun suatu sistem informasi pada SMA Negeri 1 Babalan. Sistem ini dikembangkan dengan menggunakan perangkat lunak PHP, MySQL, Apache, dan Mozilla Firefox juga software pembantu lainnya seperti Adobe Dreamweaver CS5. Tujuan dari sistem informasi ini adalah untuk menyajikan informasi profil sekolah, visi, misi dan tujuan, daftar siswa, daftar guru. Merancang sebuah website untuk membantu siswa dalam memperoleh informasi SMA Negeri 1 Babalan dan website ini dapat...

  14. Enriched expression of the ciliopathy gene Ick in cell proliferating regions of adult mice.

    Tsutsumi, Ryotaro; Chaya, Taro; Furukawa, Takahisa

    2018-04-07

    Cilia are essential for sensory and motile functions across species. In humans, ciliary dysfunction causes "ciliopathies", which show severe developmental abnormalities in various tissues. Several missense mutations in intestinal cell kinase (ICK) gene lead to endocrine-cerebro-osteodysplasia syndrome or short rib-polydactyly syndrome, lethal recessive developmental ciliopathies. We and others previously reported that Ick-deficient mice exhibit neonatal lethality with developmental defects. Mechanistically, Ick regulates intraflagellar transport and cilia length at ciliary tips. Although Ick plays important roles during mammalian development, roles of Ick at the adult stage are poorly understood. In the current study, we investigated the Ick gene expression in adult mouse tissues. RT-PCR analysis showed that Ick is ubiquitously expressed, with enrichment in the retina, brain, lung, intestine, and reproductive system. In the adult brain, we found that Ick expression is enriched in the walls of the lateral ventricle, in the rostral migratory stream of the olfactory bulb, and in the subgranular zone of the hippocampal dentate gyrus by in situ hybridization analysis. We also observed that Ick staining pattern is similar to pachytene spermatocyte to spermatid markers in the mature testis and to an intestinal stem cell marker in the adult small intestine. These results suggest that Ick is expressed in proliferating regions in the adult mouse brain, testis, and intestine. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. RhoA, Rac1 and Cdc42 differentially regulate aSMA and collagen I expression in mesenchymal stem cells.

    Ge, Jianfeng; Burnier, Laurent; Adamopoulou, Maria; Kwa, Mei Qi; Schaks, Matthias; Rottner, Klemens; Brakebusch, Cord

    2018-04-26

    Mesenchymal stem cells (MSC) are suggested to be important progenitors of myofibroblasts in fibrosis. To understand the role of Rho GTPase signaling in TGFβ-induced myofibroblast differentiation of MSC, we generated a novel MSC line and descendants of it lacking functional Rho GTPases and Rho GTPase signaling components. Unexpectedly, our data revealed that Rho GTPase signaling is required for TGFβ-induced expression of αSMA, but not of collagen I α1 (col1a1). While loss of RhoA and Cdc42 reduced αSMA expression, ablation of the Rac1 gene had the opposite effect. Although actin polymerization and MRTFa were crucial for TGFβ-induced αSMA expression, neither Arp2/3 dependent actin polymerization nor cofilin dependent severing and depolymerization of F-actin were required. Instead, F-actin levels were dependent on cell contraction and TGFβ-induced actin polymerisation correlated with increased cell contraction mediated by RhoA and Cdc42. Finally, we observed impaired collagen I secretion in MSC lacking RhoA or Cdc42. These data give novel molecular insights into the role of Rho GTPases in TGFβ signaling and have implications for our understanding of MSC function in fibrosis. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Human terminal deoxyribonucleotidyltransferase: molecular cloning and structural analysis of the gene and 5' flanking region

    Riley, L.K.; Morrow, J.K.; Danton, M.J.; Coleman, M.S.

    1988-01-01

    Human terminal deoxyribonucleotidyltransferase cDNA contains an open reading frame of 1530 base pairs (bp) corresponding to a protein containing 510 amino acids. The encoded protein is a template-independent DNA polymerase found only in a restricted population of normal and malignant prelymphocytes. To begin to investigate the genetic elements responsible for the tissue-specific expression of terminal deoxyribonucleotidyltransferase, genomic clones, containing the entire human gene were isolated and characterized. Initially, cDNA clones were isolated from a library generated from the human lymphoblastoid cell line, MOLT-4R. A cDNA clone containing the entire coding region of the protein was used to isolate a series of overlapping clones from two human genomic libraries. The gene comprises 11 exons and 10 introns and spans 49.4 kilobases. The 5' flanking region (709 bp) including exon 1 was sequenced. Several putative transcription initiation sites were mapped. Within 500 nucleotides of the translation start site, a series of promoter elements was detected. TATA and CAAT sequences, respectively, were found to start at nucleotides -185 and -204, -328 and -370, and -465 and -505. Start sites were found for a cyclic AMP-dependent promoter analog at nucleotide -121, an eight-base sequence corresponding to the IgG promoter enhancer (cd) at nucleotide -455, and an analog of the IgG promoter (pd) at nucleotide -159. These findings suggest that transcripts coding for terminal deoxyribonucleotidyltransferase may be variable in length and that transcription may be influenced by a variety of genetic elements

  17. Gene Map of the HLA Region, Graves' Disease and Hashimoto Thyroiditis, and Hematopoietic Stem Cell Transplantation.

    Sasazuki, Takehiko; Inoko, Hidetoshi; Morishima, Satoko; Morishima, Yasuo

    2016-01-01

    The human leukocyte antigen (HLA) genomic region spanning about 4 Mb is the most gene dense and the polymorphic stretches in the human genome. A total of the 269 loci were identified, including 145 protein coding genes mostly important for immunity and 50 noncoding RNAs (ncRNAs). Biological function of these ncRNAs remains unknown, becoming hot spot in the studies of HLA-associated diseases. The genomic diversity analysis in the HLA region facilitated by next-generation sequencing will pave the way to molecular understanding of linkage disequilibrium structure, population diversity, histocompatibility in transplantation, and associations with autoimmune diseases. The 4-digit DNA genotyping of HLA for six HLA loci, HLA-A through DP, in the patients with Graves' disease (GD) and Hashimoto thyroiditis (HT) identified six susceptible and three resistant HLA alleles. Their epistatic interactions in controlling the development of these diseases are shown. Four susceptible and one resistant HLA alleles are shared by GD and HT. Two HLA alleles associated with GD or HT control the titers of autoantibodies to thyroid antigens. All these observations led us to propose a new model for the development of GD and HT. Hematopoietic stem cell transplantation from unrelated donor (UR-HSCT) provides a natural experiment to elucidate the role of allogenic HLA molecules in immune response. Large cohort studies using HLA allele and clinical outcome data have elucidated that (1) HLA locus, allele, and haplotype mismatches between donor and patient, (2) specific amino acid substitution at specific positions of HLA molecules, and (3) ethnic background are all responsible for the immunological events related to UR-HSCT including acute graft-versus-host disease (GVHD), chronic GVHD, graft-versus-leukemia (GvL) effect, and graft failure. © 2016 Elsevier Inc. All rights reserved.

  18. Numerical tool for SMA material simulation: application to composite structure design

    Chemisky, Yves; Tahiri, Vanessa; Duval, Arnaud; Piotrowski, Boris; Ben Zineb, Tarak; Patoor, Etienne

    2009-01-01

    Composite materials based on shape memory alloys (SMA) have received growing attention over these last few years. In this paper, two particular morphologies of composites are studied. The first one is an SMA/elastomer composite in which a snake-like wire NiTi SMA is embedded into an elastomer ribbon. The second one is a commercial Ni 47 Ti 44 Nb 9 which presents elastic–plastic inclusions in an NiTi SMA matrix. In both cases, the design of such composites required the development of an SMA design tool, based on a macroscopic 3D constitutive law for NiTi alloys. Two different strategies are then applied to compute these composite behaviors. For the SMA/elastomer composite, the macroscopic behavior law is implemented in commercial FEM software, and for the Ni 47 Ti 44 Nb 9 a scale transition approach based on the Mori–Tanaka scheme is developed. In both cases, simulations are compared to experimental data

  19. Experimental characterization of self-sensing SMA actuators under controlled convective cooling

    Lewis, N; York, A; Seelecke, S

    2013-01-01

    Shape memory alloy (SMA) wires are attractive for actuation systems due to their high energy density, light weight and silent operation. In addition, they feature self-sensing capabilities by relating electrical resistance measurements to strain changes. In real world applications SMAs typically operate in non-ambient air and it is imperative to understand an actuator’s behavior under varying convective cooling conditions, especially for smaller diameter wires, where convective effects are amplified. This paper shows that the multi-functionality of SMA actuators can be further extended by related heating power to convective air speed. It investigates the relationship between the normalized excess power needed and corresponding airspeed under controlled, laminar airflow patterns in a small-scale wind tunnel. For each experiment, airflow through the wind tunnel, strain in the SMA wire, and power supplied to the SMA wire were controlled, while the stress and resistance of the wire were measured. The ability to understand and predict an SMA wire’s behavior under various external airflows will aid in the design and understanding of future SMA actuated structures, such as micro-air vehicles, and shows that SMAs can function as self-sensing actuators and airspeed sensors. (paper)

  20. Energy-dissipating and self-repairing SMA-ECC composite material system

    Li, Xiaopeng; Li, Mo; Song, Gangbing

    2015-01-01

    Structural component ductility and energy dissipation capacity are crucial factors for achieving reinforced concrete structures more resistant to dynamic loading such as earthquakes. Furthermore, limiting post-event residual damage and deformation allows for immediate re-operation or minimal repairs. These desirable characteristics for structural ‘resilience’, however, present significant challenges due to the brittle nature of concrete, its deformation incompatibility with ductile steel, and the plastic yielding of steel reinforcement. Here, we developed a new composite material system that integrates the unique ductile feature of engineered cementitious composites (ECC) with superelastic shape memory alloy (SMA). In contrast to steel reinforced concrete (RC) and SMA reinforced concrete (SMA-RC), the SMA-ECC beams studied in this research exhibited extraordinary energy dissipation capacity, minimal residual deformation, and full self-recovery of damage under cyclic flexural loading. We found that the tensile strain capacity of ECC, tailored up to 5.5% in this study, allows it to work compatibly with superelastic SMA. Furthermore, the distributed microcracking damage mechanism in ECC is critical for sufficient and reliable recovery of damage upon unloading. This research demonstrates the potential of SMA-ECC for improving resilience of concrete structures under extreme hazard events. (paper)

  1. Feasibility study of an active soft catheter actuated by SMA wires

    Konh, Bardia; Karimi, Saeed; Miller, Scott

    2018-03-01

    This study aims to assess the feasibility of using a combination of thin elastomer tubes and SMA wires to develop an active catheter. Cardiac catheters have been widely used in investigational and interventional procedures such as angiography, angioplasty, electro- physiology, and endocardial ablation. The commercial models manually steer inside the patient's body via internally installed pull wires. Active catheters, on the other hand, have the potential to revolutionize surgical procedures because of their computer-controlled and enhanced motion. Shape memory alloys have been used for almost a decade as a trustworthy actuator for biomedical applications. In this work, SMA wires were attached to a small pressurized elastomer tube to realize deflection. The tube was pressurized to maintain a constant stress on the SMA wires. The tip motion via actuation of SMA wires was then measured and reported. The results of this study showed that by adopting an appropriate training process for the SMA wires prior to performing the experiments and adopting an appropriate internal pressure for the elastomer tube, less external loads on SMA wires would be needed for a consistent actuation.

  2. SMA Foils for MEMS: From Material Properties to the Engineering of Microdevices

    Kohl, Manfred; Ossmer, Hinnerk; Gueltig, Marcel; Megnin, Christof

    2018-03-01

    In the early nineties, microelectromechanical systems (MEMS) technology has been still in its infancy. As silicon (Si) is not a transducer material, it was clear at the very beginning that mechanically active materials had to be introduced to MEMS in order to enable functional microdevices with actuation capability beyond electrostatics. At that time, shape memory alloys (SMAs) have been available in bulk form, mainly as SMA wires and SMA plates. On the macro scale, these materials show highest work densities compared to other actuation principles in the order of 107 J/m3, which stimulated research on the integration of SMA to MEMS. Subsequently, two approaches for producing planar materials have been initiated (1) magnetron sputtering of SMA thin films and (2) the integration of rolled SMA foils, which both turned out to be very successful creating a paradigm change in microactuation technology. The following review covers important milestones of the research and development of SMA foil-based microactuators including materials characterization, design engineering, technology, and demonstrator development as well as first commercial products.

  3. Behavior of NiTiNb SMA wires under recovery stress or prestressing.

    Choi, Eunsoo; Nam, Tae-Hyun; Chung, Young-Soo; Kim, Yeon-Wook; Lee, Seung-Yong

    2012-01-05

    The recovery stress of martensitic shape-memory alloy [SMA] wires can be used to confine concrete, and the confining effectiveness of the SMA wires was previously proved through experimental tests. However, the behavior of SMA wires under recovery stress has not been seriously investigated. Thus, this study conducted a series of tests of NiTiNb martensitic SMA wires under recovery stress with varying degrees of prestrain on the wires and compared the behavior under recovery stress with that under prestressing of the wires. The remaining stress was reduced by the procedure of additional strain loading and unloading. More additional strains reduced more remaining stresses. When the SMA wires were heated up to the transformation temperature under prestress, the stress on the wires increased due to the state transformation. Furthermore, the stress decreased with a decreasing temperature of the wires down to room temperature. The stress of the NiTiNb wires was higher than the prestress, and the developed stress seemed to depend on the composition of the SMAs. When an additional strain was subsequently loaded and unloaded on the prestressed SMA wires, the remaining stress decreased. Finally, the remaining stress becomes zero when loading and unloading a specific large strain.

  4. SMA Foils for MEMS: From Material Properties to the Engineering of Microdevices

    Kohl, Manfred; Ossmer, Hinnerk; Gueltig, Marcel; Megnin, Christof

    2017-12-01

    In the early nineties, microelectromechanical systems (MEMS) technology has been still in its infancy. As silicon (Si) is not a transducer material, it was clear at the very beginning that mechanically active materials had to be introduced to MEMS in order to enable functional microdevices with actuation capability beyond electrostatics. At that time, shape memory alloys (SMAs) have been available in bulk form, mainly as SMA wires and SMA plates. On the macro scale, these materials show highest work densities compared to other actuation principles in the order of 107 J/m3, which stimulated research on the integration of SMA to MEMS. Subsequently, two approaches for producing planar materials have been initiated (1) magnetron sputtering of SMA thin films and (2) the integration of rolled SMA foils, which both turned out to be very successful creating a paradigm change in microactuation technology. The following review covers important milestones of the research and development of SMA foil-based microactuators including materials characterization, design engineering, technology, and demonstrator development as well as first commercial products.

  5. MicroRNA genes and their target 3'-untranslated regions are infrequently somatically mutated in ovarian cancers.

    Georgina L Ryland

    Full Text Available MicroRNAs are key regulators of gene expression and have been shown to have altered expression in a variety of cancer types, including epithelial ovarian cancer. MiRNA function is most often achieved through binding to the 3'-untranslated region of the target protein coding gene. Mutation screening using massively-parallel sequencing of 712 miRNA genes in 86 ovarian cancer cases identified only 5 mutated miRNA genes, each in a different case. One mutation was located in the mature miRNA, and three mutations were predicted to alter the secondary structure of the miRNA transcript. Screening of the 3'-untranslated region of 18 candidate cancer genes identified one mutation in each of AKT2, EGFR, ERRB2 and CTNNB1. The functional effect of these mutations is unclear, as expression data available for AKT2 and EGFR showed no increase in gene transcript. Mutations in miRNA genes and 3'-untranslated regions are thus uncommon in ovarian cancer.

  6. A distinct regulatory region of the Bmp5 locus activates gene expression following adult bone fracture or soft tissue injury.

    Guenther, Catherine A; Wang, Zhen; Li, Emma; Tran, Misha C; Logan, Catriona Y; Nusse, Roel; Pantalena-Filho, Luiz; Yang, George P; Kingsley, David M

    2015-08-01

    Bone morphogenetic proteins (BMPs) are key signaling molecules required for normal development of bones and other tissues. Previous studies have shown that null mutations in the mouse Bmp5 gene alter the size, shape and number of multiple bone and cartilage structures during development. Bmp5 mutations also delay healing of rib fractures in adult mutants, suggesting that the same signals used to pattern embryonic bone and cartilage are also reused during skeletal regeneration and repair. Despite intense interest in BMPs as agents for stimulating bone formation in clinical applications, little is known about the regulatory elements that control developmental or injury-induced BMP expression. To compare the DNA sequences that activate gene expression during embryonic bone formation and following acute injuries in adult animals, we assayed regions surrounding the Bmp5 gene for their ability to stimulate lacZ reporter gene expression in transgenic mice. Multiple genomic fragments, distributed across the Bmp5 locus, collectively coordinate expression in discrete anatomic domains during normal development, including in embryonic ribs. In contrast, a distinct regulatory region activated expression following rib fracture in adult animals. The same injury control region triggered gene expression in mesenchymal cells following tibia fracture, in migrating keratinocytes following dorsal skin wounding, and in regenerating epithelial cells following lung injury. The Bmp5 gene thus contains an "injury response" control region that is distinct from embryonic enhancers, and that is activated by multiple types of injury in adult animals. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Chronic intermittent hypoxia exerts CNS region-specific effects on rat microglial inflammatory and TLR4 gene expression.

    Stephanie M C Smith

    Full Text Available Intermittent hypoxia (IH during sleep is a hallmark of sleep apnea, causing significant neuronal apoptosis, and cognitive and behavioral deficits in CNS regions underlying memory processing and executive functions. IH-induced neuroinflammation is thought to contribute to cognitive deficits after IH. In the present studies, we tested the hypothesis that IH would differentially induce inflammatory factor gene expression in microglia in a CNS region-dependent manner, and that the effects of IH would differ temporally. To test this hypothesis, adult rats were exposed to intermittent hypoxia (2 min intervals of 10.5% O2 for 8 hours/day during their respective sleep cycles for 1, 3 or 14 days. Cortex, medulla and spinal cord tissues were dissected, microglia were immunomagnetically isolated and mRNA levels of the inflammatory genes iNOS, COX-2, TNFα, IL-1β and IL-6 and the innate immune receptor TLR4 were compared to levels in normoxia. Inflammatory gene expression was also assessed in tissue homogenates (containing all CNS cells. We found that microglia from different CNS regions responded to IH differently. Cortical microglia had longer lasting inflammatory gene expression whereas spinal microglial gene expression was rapid and transient. We also observed that inflammatory gene expression in microglia frequently differed from that in tissue homogenates from the same region, indicating that cells other than microglia also contribute to IH-induced neuroinflammation. Lastly, microglial TLR4 mRNA levels were strongly upregulated by IH in a region- and time-dependent manner, and the increase in TLR4 expression appeared to coincide with timing of peak inflammatory gene expression, suggesting that TLR4 may play a role in IH-induced neuroinflammation. Together, these data indicate that microglial-specific neuroinflammation may play distinct roles in the effects of intermittent hypoxia in different CNS regions.

  8. Dynamic expression of desmin, α-SMA and TGF-β1 during hepatic fibrogenesis induced by selective bile duct ligation in young rats

    Gonçalves, J.O.; Tannuri, A.C.A.; Coelho, M.C.M.; Bendit, I.; Tannuri, U.

    2014-01-01

    We previously described a selective bile duct ligation model to elucidate the process of hepatic fibrogenesis in children with biliary atresia or intrahepatic biliary stenosis. Using this model, we identified changes in the expression of alpha smooth muscle actin (α-SMA) both in the obstructed parenchyma and in the hepatic parenchyma adjacent to the obstruction. However, the expression profiles of desmin and TGF-β1, molecules known to be involved in hepatic fibrogenesis, were unchanged when analyzed by semiquantitative polymerase chain reaction (RT-PCR). Thus, the molecular mechanisms involved in the modulation of liver fibrosis in this experimental model are not fully understood. This study aimed to evaluate the molecular changes in an experimental model of selective bile duct ligation and to compare the gene expression changes observed in RT-PCR and in real-time quantitative PCR (qRT‐PCR). Twenty-eight Wistar rats of both sexes and weaning age (21-23 days old) were used. The rats were separated into groups that were assessed 7 or 60 days after selective biliary duct ligation. The expression of desmin, α-SMA and TGF-β1 was examined in tissue from hepatic parenchyma with biliary obstruction (BO) and in hepatic parenchyma without biliary obstruction (WBO), using RT-PCR and qRT‐PCR. The results obtained in this study using these two methods were significantly different. The BO parenchyma had a more severe fibrogenic reaction, with increased α-SMA and TGF-β1 expression after 7 days. The WBO parenchyma presented a later, fibrotic response, with increased desmin expression 7 days after surgery and increased α-SMA 60 days after surgery. The qRT‐PCR technique was more sensitive to expression changes than the semiquantitative method

  9. Dynamic expression of desmin, α-SMA and TGF-β1 during hepatic fibrogenesis induced by selective bile duct ligation in young rats

    Gonçalves, J.O.; Tannuri, A.C.A.; Coelho, M.C.M.; Bendit, I.; Tannuri, U. [Laboratório de Pesquisa em Cirurgia Pediátrica (LIM-30), Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP (Brazil)

    2014-08-15

    We previously described a selective bile duct ligation model to elucidate the process of hepatic fibrogenesis in children with biliary atresia or intrahepatic biliary stenosis. Using this model, we identified changes in the expression of alpha smooth muscle actin (α-SMA) both in the obstructed parenchyma and in the hepatic parenchyma adjacent to the obstruction. However, the expression profiles of desmin and TGF-β1, molecules known to be involved in hepatic fibrogenesis, were unchanged when analyzed by semiquantitative polymerase chain reaction (RT-PCR). Thus, the molecular mechanisms involved in the modulation of liver fibrosis in this experimental model are not fully understood. This study aimed to evaluate the molecular changes in an experimental model of selective bile duct ligation and to compare the gene expression changes observed in RT-PCR and in real-time quantitative PCR (qRT‐PCR). Twenty-eight Wistar rats of both sexes and weaning age (21-23 days old) were used. The rats were separated into groups that were assessed 7 or 60 days after selective biliary duct ligation. The expression of desmin, α-SMA and TGF-β1 was examined in tissue from hepatic parenchyma with biliary obstruction (BO) and in hepatic parenchyma without biliary obstruction (WBO), using RT-PCR and qRT‐PCR. The results obtained in this study using these two methods were significantly different. The BO parenchyma had a more severe fibrogenic reaction, with increased α-SMA and TGF-β1 expression after 7 days. The WBO parenchyma presented a later, fibrotic response, with increased desmin expression 7 days after surgery and increased α-SMA 60 days after surgery. The qRT‐PCR technique was more sensitive to expression changes than the semiquantitative method.

  10. Study on the binding sites of radiosensitivity associated transcription factor in the promoter region of Ier5 gene

    Cui Wei; Yin Lingling; Dong Lingyue

    2012-01-01

    Objective: To clarify the mechanism of immediate early response gene 5 (Ier5) transcription induced by radiation. Methods: Deletant construction, site-specific mutagenesis,electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) were used to forecast the promoter region, binding sites and transcription factors of Ier5 gene in HeLa cells. Results: The promoter region of Ier5 gene might be in the region of Ier5 -8 deletant (-408 - -238 bp). The Ier5 gene had two transcription factors of GCF and NFI, and GCF had two binding sites located in the region of -388 - -382 bp and -274 - -270 bp of Ier5 promoter. The binding site of NFI was located in -362 - -357 bp of Ier5 promoter. GCF could inhibit the expression of Ier5 gene and this inhibition was diminished when the radiation dose increased. In contrast, NFI increased the expression of Ier5. Conclusions: The most possible region of Ier5 promoter is from -408 to -238 bp which has two binding sites for the radiosensitivity transcription factors of GCF and NFI that could negatively and positively regulate the expression of Ier5 respectively. (authors)

  11. Profil Antisipasi Siswa SMA Dalam Memecahkan Masalah Integral

    Erfan Yudianto

    2015-06-01

    Full Text Available Penelitian ini dilatarbelakangi oleh sulitnya siswa dalam menyelesaikan masalah integral khusunya luas daerah. Banyak siswa hanya menyelesaikan masalah integral hanya berdasarkan rumus yang sudah disediakan. Siswa jarang mengaitkan konsep-konsep yang saling terkait, dalam hal ini konsep integral subpokokbahasan luas daerah.Tujuan penelitian ini untuk mendeskripsikan Profil antisipasi siswa SMA dalam memecahkan masalah integral. Hasil penelitian ini dapat dimanfaatkan oleh guru untuk membantu siswa mengaitkan konsep-konsep yang belum terkait.  Penelitian ini menggunakan metode tes dan wawancara. Tes berupa  tes kemampuan matematika yang diberikan kepada siswa, sehingga diperoleh siswa berkemampuan tinggi dan wawancara diberikan kepada siswa yang bersangkutan untuk menggali dan melihat jaringan konsep yang dimiliki siswa dalam menyelesaikan masalah integral. Subjek dalam penelitian ini termasuk dalam antisipasi terinternasilsasi dikarenakan siswa secara spontan menerapkan rumus integral tanpa menganalisis soal yang diberikan.This research is motivated by the difficulty of students in solving integral problems especially the area. Many students just completed the integral problems just based on a formula that has been provided. Students rarely associate the concepts are interrelated, in this case the integral concept of the area. The purpose of this study was to describe the profile anticipation of high school students in problem solving integrals. The results could be used by teachers to help students link the concepts are not related. This study uses tests and interviews. The tests such as math skills test given to students, in order to obtain a high ability students and interviews given to the student to explore and see the network concept of the students in problem solving integrals. Subjects in this study are included in anticipation terinternasilsasi because students spontaneously apply the integral formula without analyzing the questions

  12. [Identification of Clonorchis sinensis metacercariae based on PCR targeting ribosomal DNA ITS regions and COX1 gene].

    Yang, Qing-Li; Shen, Ji-Qing; Jiang, Zhi-Hua; Yang, Yi-Chao; Li, Hong-Mei; Chen, Ying-Dan; Zhou, Xiao-Nong

    2014-06-01

    To identify Clonorchis sinensis metacercariae using PCR targeting ribosomal DNA ITS region and COX1 gene. Pseudorasbora parva were collected from Hengxian County of Guangxi at the end of May 2013. Single metacercaria of C. sinensis and other trematodes were separated from muscle tissue of P. parva by digestion method. Primers targeting ribosomal DNA ITS region and COX1 gene of C. sinensis were designed for PCR and the universal primers were used as control. The sensitivity and specificity of the PCR detection were analyzed. C. sinensis metacercariae at different stages were identified by PCR. DNA from single C. sinensis metacercaria was detected by PCR targeting ribosomal DNA ITS region and COX1 gene. The specific amplicans have sizes of 437/549, 156/249 and 195/166 bp, respectively. The ratio of the two positive numbers in PCR with universal primers and specific primers targeting C. sinensis ribosomal DNA ITS1 and ITS2 regions was 0.905 and 0.952, respectively. The target gene fragments were amplified by PCR using COX1 gene-specific primers. The PCR with specific primers did not show any non-specific amplification. However, the PCR with universal primers targeting ribosomal DNA ITS regions performed serious non-specific amplification. C. sinensis metacercariae at different stages are identified by morphological observation and PCR method. Species-specific primers targeting ribosomal DNA ITS region show higher sensitivity and specificity than the universal primers. PCR targeting COX1 gene shows similar sensitivity and specificity to PCR with specific primers targeting ribosomal DNA ITS regions.

  13. Enrichment of short interspersed transposable elements to embryonic stem cell-specific hypomethylated gene regions.

    Muramoto, Hiroki; Yagi, Shintaro; Hirabayashi, Keiji; Sato, Shinya; Ohgane, Jun; Tanaka, Satoshi; Shiota, Kunio

    2010-08-01

    Embryonic stem cells (ESCs) have a distinctive epigenome, which includes their genome-wide DNA methylation modification status, as represented by the ESC-specific hypomethylation of tissue-dependent and differentially methylated regions (T-DMRs) of Pou5f1 and Nanog. Here, we conducted a genome-wide investigation of sequence characteristics associated with T-DMRs that were differentially methylated between ESCs and somatic cells, by focusing on transposable elements including short interspersed elements (SINEs), long interspersed elements (LINEs) and long terminal repeats (LTRs). We found that hypomethylated T-DMRs were predominantly present in SINE-rich/LINE-poor genomic loci. The enrichment for SINEs spread over 300 kb in cis and there existed SINE-rich genomic domains spreading continuously over 1 Mb, which contained multiple hypomethylated T-DMRs. The characterization of sequence information showed that the enriched SINEs were relatively CpG rich and belonged to specific subfamilies. A subset of the enriched SINEs were hypomethylated T-DMRs in ESCs at Dppa3 gene locus, although SINEs are overall methylated in both ESCs and the liver. In conclusion, we propose that SINE enrichment is the genomic property of regions harboring hypomethylated T-DMRs in ESCs, which is a novel aspect of the ESC-specific epigenomic information.

  14. Cloning and analysis of the promoter region of the human fibronectin gene

    Dean, D.C.; Bowlus, C.L.; Bourgeois, S.

    1987-01-01

    Human fibronectin (FN) genomic clones were isolated by screening a human genomic library with a 75-base oligonucleotide. The sequence of the oligonucleotide corresponds to a region near the 5' end of the human FN cDNA clone pFH6 that contains the amino-terminal coding sequences but does not extend to the 5' end of the mRNA. The 5' end of the FN gene is found on a 3.7-kilobase-pair EcoRI fragment that contains about 2.7 kilobase pairs of flanking sequence. The first exon is 414 base pairs long, with a 5' untranslated region of 267 base pairs. As deduced on the basis of the position of the initiation codon, FN is synthesized with a 31-residue amino acid extension on the amion terminus that is not present in the mature polypeptide. This amino-terminal extension appears to contain both a signal peptide and a propeptide. The first 200 base pairs of 5'-flanking sequence is very G+C rich. Upstream of this the sequence becomes relatively A+T rich. The sequence ATATAA is found at -25 and the sequence CAAT is present at -150. The sequence GGGGCGGGGC at -102 exhibits homology to the binding site for the transcription factor SP1, and the sequence TGACGTCA at -173 exhibits homology to 5'-flanking sequences important for induction by cAMP

  15. Plasticity Region Genes jhp0940, jhp0945, jhp0947, and jhp0949 of Helicobacter pylori in Isolates from Mexican Children.

    Romo-González, Carolina; Consuelo-Sánchez, Alejandra; Camorlinga-Ponce, Margarita; Velázquez-Guadarrama, Norma; García-Zúñiga, Magdalena; Burgueño-Ferreira, Juan; Coria-Jiménez, Rafael

    2015-06-01

    The genes jhp0940, jhp0945, jhp0947, and jhp0949 belong to the plasticity region of the Helicobacter pylori genome. Due to their prevalence in isolates from patients with gastritis, duodenal ulcer, and gastric cancer, they have been proposed as markers of gastroduodenal diseases. These genes are associated with pro-inflammatory cytokine induction through the NF-κB activation pathway. Nevertheless, the status of these genes is unknown in H. pylori isolates from children. The aim of the present work was to determine the frequency of the jhp0940-jhp0945-jhp0947-jhp0949 genes in H. pylori isolates from children. We identified the jhp0940, jhp0945, jhp0947, and jhp0949 genes and the relationship of each with the virulence factors cagA, cagPAI, and dupA by PCR in 49 isolates of H. pylori from children. The results were corroborated using dot blots. In addition, we compared the prevalence of these genes with the prevalence in adults. The prevalence of jhp0940 (53.1%), jhp0945 (44.9%), jhp0947 (77.6%), and jhp0949 (83.7%) was determined in the isolates from children, as was the prevalence of the virulence genes cagA (63.3%), cagPAI (71.4%), and dupA (37.5%). No association was found between the four genes of the plasticity region and the virulence genes. The presence of the intact locus integrated by jhp0940-jhp0945-jhp0947-jhp0949 was very common among the isolates from children. The genes jhp0940, jhp0947, and jhp0949 were present in more than 50% of the H. pylori isolates, and the joint presence of jhp0940-jhp0945-jhp0947-jhp0949 was very frequent. The frequency of these genes in isolates from children could contribute to the virulence of H. pylori and the evolution of the infection. © 2015 John Wiley & Sons Ltd.

  16. Association of MICA gene polymorphisms with liver fibrosis in schistosomiasis patients in the Dongting Lake region

    Gong, Zheng; Luo, Qi-Zhi; Lin, Lin [Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan Province (China); Su, Yu-Ping; Peng, Hai-Bo [Central Blood Bank in Yueyang, Yueyang, Hunan Province (China); Du, Kun; Yu, Ping [Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan Province (China); Wang, Shi-Ping [Key Laboratory of Schistosomiasis in Hunan, Department of Parasitology, College of Basic Medical Sciences, Central South University, Changsha, Hunan Province (China)

    2012-03-02

    Major histocompatibility complex class I chain-related A (MICA) is a highly polymorphic gene located within the MHC class I region of the human genome. Expressed as a cell surface glycoprotein, MICA modulates immune surveillance by binding to its cognate receptor on natural killer cells, NKG2D, and its genetic polymorphisms have been recently associated with susceptibility to some infectious diseases. We determined whether MICA polymorphisms were associated with the high rate of Schistosoma parasitic worm infection or severity of disease outcome in the Dongting Lake region of Hunan Province, China. Polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (SBT) were applied for high-resolution allele typing of schistosomiasis cases (N = 103, age range = 36.2-80.5 years, 64 males and 39 females) and healthy controls (N = 141, age range = 28.6-73.3 years, 73 males and 68 females). Fourteen MICA alleles and five short-tandem repeat (STR) alleles were identified among the two populations. Three (MICA*012:01/02, MICA*017 and MICA*027) showed a higher frequency in healthy controls than in schistosomiasis patients, but the difference was not significantly correlated with susceptibility to S. japonicum infection (Pc > 0.05). In contrast, higher MICA*A5 allele frequency was significantly correlated with advanced liver fibrosis (Pc < 0.05). Furthermore, the distribution profile of MICA alleles in this Hunan Han population was significantly different from those published for Korean, Thai, American-Caucasian, and Afro-American populations (P < 0.01), but similar to other Han populations within China (P > 0.05). This study provides the initial evidence that MICA genetic polymorphisms may underlie the severity of liver fibrosis occurring in schistosomiasis patients from the Dongting Lake region.

  17. Epigenetic changes within the promoter region of the HLA-G gene in ovarian tumors

    Matyunina Lilya V

    2008-05-01

    Full Text Available Abstract Background Previous findings have suggested that epigenetic-mediated HLA-G expression in tumor cells may be associated with resistance to host immunosurveillance. To explore the potential role of DNA methylation on HLA-G expression in ovarian cancer, we correlated differences in HLA-G expression with methylation changes within the HLA-G regulatory region in an ovarian cancer cell line treated with 5-aza-deoxycytidine (5-aza-dC and in malignant and benign ovarian tumor samples and ovarian surface epithelial cells (OSE isolated from patients with normal ovaries. Results A region containing an intact hypoxia response element (HRE remained completely methylated in the cell line after treatment with 5-aza-dC and was completely methylated in all of the ovarian tumor (malignant and benign samples examined, but only variably methylated in normal OSE samples. HLA-G expression was significantly increased in the 5-aza-dC treated cell line but no significant difference was detected between the tumor and OSE samples examined. Conclusion Since HRE is the binding site of a known repressor of HLA-G expression (HIF-1, we hypothesize that methylation of the region surrounding the HRE may help maintain the potential for expression of HLA-G in ovarian tumors. The fact that no correlation exists between methylation and HLA-G gene expression between ovarian tumor samples and OSE, suggests that changes in methylation may be necessary but not sufficient for HLA-G expression in ovarian cancer.

  18. Association of MICA gene polymorphisms with liver fibrosis in schistosomiasis patients in the Dongting Lake region

    Gong, Zheng; Luo, Qi-Zhi; Lin, Lin; Su, Yu-Ping; Peng, Hai-Bo; Du, Kun; Yu, Ping; Wang, Shi-Ping

    2012-01-01

    Major histocompatibility complex class I chain-related A (MICA) is a highly polymorphic gene located within the MHC class I region of the human genome. Expressed as a cell surface glycoprotein, MICA modulates immune surveillance by binding to its cognate receptor on natural killer cells, NKG2D, and its genetic polymorphisms have been recently associated with susceptibility to some infectious diseases. We determined whether MICA polymorphisms were associated with the high rate of Schistosoma parasitic worm infection or severity of disease outcome in the Dongting Lake region of Hunan Province, China. Polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (SBT) were applied for high-resolution allele typing of schistosomiasis cases (N = 103, age range = 36.2-80.5 years, 64 males and 39 females) and healthy controls (N = 141, age range = 28.6-73.3 years, 73 males and 68 females). Fourteen MICA alleles and five short-tandem repeat (STR) alleles were identified among the two populations. Three (MICA*012:01/02, MICA*017 and MICA*027) showed a higher frequency in healthy controls than in schistosomiasis patients, but the difference was not significantly correlated with susceptibility to S. japonicum infection (Pc > 0.05). In contrast, higher MICA*A5 allele frequency was significantly correlated with advanced liver fibrosis (Pc < 0.05). Furthermore, the distribution profile of MICA alleles in this Hunan Han population was significantly different from those published for Korean, Thai, American-Caucasian, and Afro-American populations (P < 0.01), but similar to other Han populations within China (P > 0.05). This study provides the initial evidence that MICA genetic polymorphisms may underlie the severity of liver fibrosis occurring in schistosomiasis patients from the Dongting Lake region

  19. Preclinical evaluation of gene delivery methods for the treatment of loco-regional disease in breast cancer.

    Rajendran, Simon

    2011-04-01

    Preclinical results with various gene therapy strategies indicate significant potential for new cancer treatments. However, many therapeutics fail at clinical trial, often due to differences in tissue physiology between animal models and humans, and tumor phenotype variation. Clinical data relevant to treatment strategies may be generated prior to clinical trial through experimentation using intact patient tissue ex vivo. We developed a novel tumor slice model culture system that is universally applicable to gene delivery methods, using a realtime luminescence detection method to assess gene delivery. Methods investigated include viruses (adenovirus [Ad] and adeno-associated virus), lipofection, ultrasound (US), electroporation and naked DNA. Viability and tumor populations within the slices were well maintained for seven days, and gene delivery was qualitatively and quantitatively examinable for all vectors. Ad was the most efficient gene delivery vector with transduction efficiency >50%. US proved the optimal non-viral gene delivery method in human tumor slices. The nature of the ex vivo culture system permitted examination of specific elements. Parameters shown to diminish Ad gene delivery included blood, regions of low viability and secondary disease. US gene delivery was significantly reduced by blood and skin, while tissue hyperthermia improved gene delivery. US achieved improved efficacy for secondary disease. The ex vivo model was also suitable for examination of tissue-specific effects on vector expression, with Ad expression mediated by the CXCR4 promoter shown to provide a tumor selective advantage over the ubiquitously active cytomegalovirus promoter. In conclusion, this is the first study incorporating patient tissue models in comparing gene delivery from various vectors, providing knowledge on cell-type specificity and examining the crucial biological factors determining successful gene delivery. The results highlight the importance of in

  20. Preclinical evaluation of gene delivery methods for the treatment of loco-regional disease in breast cancer.

    Rajendran, Simon

    2012-01-31

    Preclinical results with various gene therapy strategies indicate significant potential for new cancer treatments. However, many therapeutics fail at clinical trial, often due to differences in tissue physiology between animal models and humans, and tumor phenotype variation. Clinical data relevant to treatment strategies may be generated prior to clinical trial through experimentation using intact patient tissue ex vivo. We developed a novel tumor slice model culture system that is universally applicable to gene delivery methods, using a realtime luminescence detection method to assess gene delivery. Methods investigated include viruses (adenovirus [Ad] and adeno-associated virus), lipofection, ultrasound (US), electroporation and naked DNA. Viability and tumor populations within the slices were well maintained for seven days, and gene delivery was qualitatively and quantitatively examinable for all vectors. Ad was the most efficient gene delivery vector with transduction efficiency >50%. US proved the optimal non-viral gene delivery method in human tumor slices. The nature of the ex vivo culture system permitted examination of specific elements. Parameters shown to diminish Ad gene delivery included blood, regions of low viability and secondary disease. US gene delivery was significantly reduced by blood and skin, while tissue hyperthermia improved gene delivery. US achieved improved efficacy for secondary disease. The ex vivo model was also suitable for examination of tissue-specific effects on vector expression, with Ad expression mediated by the CXCR4 promoter shown to provide a tumor selective advantage over the ubiquitously active cytomegalovirus promoter. In conclusion, this is the first study incorporating patient tissue models in comparing gene delivery from various vectors, providing knowledge on cell-type specificity and examining the crucial biological factors determining successful gene delivery. The results highlight the importance of in

  1. Miskonsepsi Buku Ajar Fisika SMA Kelas X Pada Pokok Bahasan Dinamika Gerak

    Fachmi Nurdiansyah

    2018-03-01

    Full Text Available Penelitian ini bertujuan untuk memaparkan bentuk-bentuk miskonsepsi pada pokok bahasan dinamika gerak dalam buku ajar fisika SMA kelas X. Adapun buku ajar yang digunakan dalam penelitian ini, yaitu: (1 Fisika untuk SMA/MA Kelas X Semester I karangan RA dan SI yang diterbitkan tahun 2012 oleh penerbit IP, (2 Fisika untuk SMA/MA Kelas X Semester I karangan TPM yang diterbitkan tahun 2013 oleh penerbit VP, dan (3 Fisika Peminatan untuk SMA/MA Kelas X karangan SN dan SZ yang diterbitkan tahun 2013 oleh penerbit YW. Penelitian ini merupakan penelitian kualitatif deskriptif. Objek dalam penelitian ini adalah data berupa aspek penjelasan konsep, penulisan rumus, penulisan simbol, penulisan satuan, dan penyajian gambar pada pokok bahasan dinamika gerak dalam buku ajar fisika SMA. Penelitian dilakukan dengan cara menganalisis data dalam buku ajar fisika SMA yang dibandingkan dengan buku teks fisika universitas. Berdasarkan analisis data yang telah dilakukan, dapat disimpulkan bahwa miskonsepsi pada pokok bahasan dinamika gerak terdapat dalam buku ajar fisika SMA. Buku ajar IP mengalami miskonsepsi pada aspek penjelasan konsep dengan persentase 10%, penulisan rumus dengan persentase 57,14%, penulisan simbol dengan persentase 46,15%, dan penyajian gambar dengan persentase 20%. Buku ajar VP mengalami miskonsepsi pada aspek penjelasan konsep dengan persentase 10%, penulisan rumus dengan persentase 85,71%, penulisan simbol dengan persentase 79,62%, dan penyajian gambar dengan persentase 80%. Buku ajar YW mengalami miskonsepsi pada aspek penjelasan konsep dengan persentase 10%, penulisan rumus dengan persentase 85,71%, penulisan simbol dengan persentase 69,23, dan penyajian gambar dengan persentase 20%. Pada aspek penulisan satuan, tidak terdapat miskonsepsi dalam buku ajar IP, VP, dan YW.

  2. An evolutionary conserved region (ECR in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex

    Haddley Kate

    2011-05-01

    Full Text Available Abstract Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs, in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1 supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a a strong enhancer that functions in neurons and b a transcription factor that may modulate the function of that enhancer.

  3. New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro.

    Klaassen, Kristel; Stankovic, Biljana; Kotur, Nikola; Djordjevic, Maja; Zukic, Branka; Nikcevic, Gordana; Ugrin, Milena; Spasovski, Vesna; Srzentic, Sanja; Pavlovic, Sonja; Stojiljkovic, Maja

    2017-02-01

    Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.

  4. Functional Versatility of AGY Serine Codons in Immunoglobulin Variable Region Genes

    Thiago Detanico

    2016-11-01

    Full Text Available In systemic autoimmunity, autoantibodies directed against nuclear antigens (Ag often arise by somatic hypermutation (SHM that converts AGT and AGC (AGY Ser codons into Arg codons. This can occur by three different single-base changes. Curiously, AGY Ser codons are far more abundant in complementarity-determining regions (CDRs of IgV-region genes than expected for random codon use or from species-specific codon frequency data. CDR AGY codons are also more abundant than TCN Ser codons. We show that these trends hold even in cartilaginous fishes. Because AGC is a preferred target for SHM by activation-induced cytidine deaminase (AID, we asked whether the AGY abundance was solely due to a selection pressure to conserve high mutability in CDRs regardless of codon context but found that this was not the case. Instead, AGY triplets were selectively enriched in the Ser codon reading frame. Motivated by reports implicating a functional role for poly/autoreactive specificities in anti-viral antibodies, we also analyzed mutations at AGY in antibodies directed against a number of different viruses, and found that mutations producing Arg codons in anti-viral antibodies were indeed frequent. Unexpectedly, however, we also found that AGY codons mutated often to encode nearly all of the amino acids that are reported to provide the most frequent contacts with antigen (Ag. In many cases, mutations producing codons for these alternative amino acids in anti-viral antibodies were more frequent than those producing Arg codons. Mutations producing each of these key amino acids required only single-base changes in AGY. AGY is the only codon group in which 2/3rds of random mutations generate codons for these key residues. Finally, by directly analyzing x-ray structures of immune complexes from the RCSB protein database, we found that Ag-contact residues generated via somatic hypermutation occurred more often at AGY than at any other codon group. Thus, preservation of

  5. An integrated tool to study MHC region: accurate SNV detection and HLA genes typing in human MHC region using targeted high-throughput sequencing.

    Hongzhi Cao

    Full Text Available The major histocompatibility complex (MHC is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants in the MHC region, and diagnostic HLA typing, still lacks a coherent, standardized, cost effective and high coverage protocol of clinical quality and reliability. In this paper, we presented such a method for the accurate detection of minor variants and HLA types in the human MHC region, using high-throughput, high-coverage sequencing of target regions. A probe set was designed to template upon the 8 annotated human MHC haplotypes, and to encompass the 5 megabases (Mb of the extended MHC region. We deployed our probes upon three, genetically diverse human samples for probe set evaluation, and sequencing data show that ∼97% of the MHC region, and over 99% of the genes in MHC region, are covered with sufficient depth and good evenness. 98% of genotypes called by this capture sequencing prove consistent with established HapMap genotypes. We have concurrently developed a one-step pipeline for calling any HLA type referenced in the IMGT/HLA database from this target capture sequencing data, which shows over 96% typing accuracy when deployed at 4 digital resolution. This cost-effective and highly accurate approach for variant detection and HLA typing in the MHC region may lend further insight into immune-mediated diseases studies, and may find clinical utility in transplantation medicine research. This one-step pipeline is released for general evaluation and use by the scientific community.

  6. Dysregulation of RNA Mediated Gene Expression in Motor Neuron Diseases.

    Gonçalves, Inês do Carmo G; Rehorst, Wiebke A; Kye, Min Jeong

    2016-01-01

    Recent findings indicate an important role for RNA-mediated gene expression in motor neuron diseases, including ALS (amyotrophic lateral sclerosis) and SMA (spinal muscular atrophy). ALS, also known as Lou Gehrig's disease, is an adult-onset progressive neurodegenerative disorder, whereby SMA or "children's Lou Gehrig's disease" is considered a pediatric neurodevelopmental disorder. Despite the difference in genetic causes, both ALS and SMA share common phenotypes; dysfunction/loss of motor neurons that eventually leads to muscle weakness and atrophy. With advanced techniques in molecular genetics and cell biology, current data suggest that these two distinct motor neuron diseases share more than phenotypes; ALS and SMA have similar cellular pathological mechanisms including mitochondrial dysfunction, oxidative stress and dysregulation in RNA-mediated gene expression. Here, we will discuss the current findings on these two diseases with specific focus on RNA-mediated gene regulation including miRNA expression, pre-mRNA processing and RNA binding proteins.

  7. Identification and characterization of a silencer regulatory element in the 3'-flanking region of the murine CD46 gene.

    Nomura, M; Tsujimura, A; Begum, N A; Matsumoto, M; Wabiko, H; Toyoshima, K; Seya, T

    2000-01-01

    The murine membrane cofactor protein (CD46) gene is expressed exclusively in testis, in contrast to human CD46, which is expressed ubiquitously. To elucidate the mechanism of differential CD46 gene expression among species, we cloned entire murine CD46 genomic DNA and possible regulatory regions were placed in the flanking region of the luciferase reporter gene. The reporter gene assay revealed a silencing activity not in the promoter, but in the 3'-flanking region of the gene and the silencer-like element was identified within a 0.2-kb region between 0.6 and 0.8 kb downstream of the stop codon. This silencer-like element was highly similar to that of the pig MHC class-I gene. The introduction of a mutation into this putative silencer element of murine CD46 resulted in an abrogation of the silencing effect. Electrophoretic mobility-shift assay indicated the presence of the binding molecule(s) for this silencer sequence in murine cell lines and tissues. A size difference of the protein-silencer-element complex was observed depending upon the solubilizers used for preparation of the nuclear extracts. A mutated silencer sequence failed to interact with the binding molecules. The level of the binding factor was lower in the testicular germ cells compared with other organs. Thus the silencer element and its binding factor may play a role in transcriptional regulation of murine CD46 gene expression. These results imply that the effects of the CD46 silencer element encompass the innate immune and reproductive systems, and in mice may determine the testicular germ-cell-dominant expression of CD46. PMID:11023821

  8. Putative carotenoid genes expressed under the regulation of Shine-Dalgarno regions in Escherichia coli for efficient lycopene production.

    Jin, Weiyue; Xu, Xian; Jiang, Ling; Zhang, Zhidong; Li, Shuang; Huang, He

    2015-11-01

    Putative genes crtE, crtB, and crtI from Deinococcus wulumiqiensis R12, a novel species, were identified by genome mining and were co-expressed using the optimized Shine-Dalgarno (SD) regions to improve lycopene yield. A lycopene biosynthesis pathway was constructed by co-expressing these three genes in Escherichia coli. After optimizing the upstream SD regions and the culture medium, the recombinant strain EDW11 produced 88 mg lycopene g(-1) dry cell wt (780 mg lycopene l(-1)) after 40 h fermentation without IPTG induction, while the strain EDW without optimized SD regions only produced 49 mg lycopene g(-1) dry cell wt (417 mg lycopene l(-1)). Based on the optimization of the upstream SD regions and culture medium, the yield of the strain EDW11 reached a high level during microbial lycopene production until now.

  9. Origin of the CMS gene locus in rapeseed cybrid mitochondria: active and inactive recombination produces the complex CMS gene region in the mitochondrial genomes of Brassicaceae.

    Oshima, Masao; Kikuchi, Rie; Imamura, Jun; Handa, Hirokazu

    2010-01-01

    CMS (cytoplasmic male sterile) rapeseed is produced by asymmetrical somatic cell fusion between the Brassica napus cv. Westar and the Raphanus sativus Kosena CMS line (Kosena radish). The CMS rapeseed contains a CMS gene, orf125, which is derived from Kosena radish. Our sequence analyses revealed that the orf125 region in CMS rapeseed originated from recombination between the orf125/orfB region and the nad1C/ccmFN1 region by way of a 63 bp repeat. A precise sequence comparison among the related sequences in CMS rapeseed, Kosena radish and normal rapeseed showed that the orf125 region in CMS rapeseed consisted of the Kosena orf125/orfB region and the rapeseed nad1C/ccmFN1 region, even though Kosena radish had both the orf125/orfB region and the nad1C/ccmFN1 region in its mitochondrial genome. We also identified three tandem repeat sequences in the regions surrounding orf125, including a 63 bp repeat, which were involved in several recombination events. Interestingly, differences in the recombination activity for each repeat sequence were observed, even though these sequences were located adjacent to each other in the mitochondrial genome. We report results indicating that recombination events within the mitochondrial genomes are regulated at the level of specific repeat sequences depending on the cellular environment.

  10. A BMP responsive transcriptional region in the chicken type X collagen gene.

    Volk, S W; Luvalle, P; Leask, T; Leboy, P S

    1998-10-01

    Bone morphogenetic proteins (BMPs) were originally identified by their ability to induce ectopic bone formation and have been shown to promote both chondrogenesis and chondrocyte hypertrophy. BMPs have recently been found to activate a membrane serine/threonine kinase signaling mechanism in a variety of cell types, but the downstream effectors of BMP signaling in chondrocyte differentiation remain unidentified. We have previously reported that BMP-2 markedly stimulates type X collagen expression in prehypertrophic chick sternal chondrocytes, and that type X collagen mRNA levels in chondrocytes cultured under serum-free (SF) conditions are elevated 3- to 5-fold within 24 h. To better define the molecular mechanisms of induction of chondrocyte hypertrophy by BMPs, we examined the effect of BMPs on type X collagen production by 15-day chick embryo sternal chondrocytes cultured under SF conditions in the presence or absence of 30 ng/ml BMP-2, BMP-4, or BMP-7. Two populations of chondrocytes were used: one representing resting cartilage isolated from the caudal third of the sterna and the second representing prehypertrophic cartilage from the cephalic third of the sterna. BMP-2, BMP-4, and BMP-7 all effectively promoted chondrocyte maturation of cephalic sternal chondrocytes as measured by high levels of alkaline phosphatase, diminished levels of type II collagen, and induction of the hypertrophic chondrocyte-specific marker, type X collagen. To test whether BMP control of type X collagen expression occurs at the transcriptional level, we utilized plasmid constructs containing the chicken collagen X promoter and 5' flanking regions fused to a reporter gene. Constructs were transiently transfected into sternal chondrocytes cultured under SF conditions in the presence or absence of 30 ng/ml BMP-2, BMP-4, or BMP-7. A 533 bp region located 2.4-2.9 kb upstream from the type X collagen transcriptional start site was both necessary and sufficient for strong BMP responsiveness

  11. Genome-wide analysis of regions similar to promoters of histone genes

    Chowdhary, Rajesh; Bajic, Vladimir B.; Dong, Difeng; Wong, Limsoon; Liu, Jun S

    2010-01-01

    of histone and histone-coregulated gene transcription initiation. While these hypotheses still remain to be verified, we believe that these form a useful resource for researchers to further explore regulation of human histone genes and human genome

  12. Biolistic transformation of Schistosoma mansoni: Studies with modified reporter-gene constructs containing regulatory regions of protease genes

    Dvořák, Jan; Beckmann, S.; Lim, K.-C.; Engel, J. C.; Grevelding, C. G.; McKerrow, J. H.; Caffrey, C. R.

    2010-01-01

    Roč. 170, č. 1 (2010), s. 37-40 ISSN 0166-6851 Institutional research plan: CEZ:AV0Z60220518 Keywords : Schistosoma * Protease * Transgene * Gene promoter * Biolistics * Electroporation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.875, year: 2010

  13. Isolation of probes specific to human chromosomal region 6p21 from immunoselected irradiation-fusion gene transfer hybrids

    Ragoussis, J.; Jones, T.A.; Sheer, D.; Shrimpton, A.E.; Goodfellow, P.N.; Trowsdale, J.; Ziegler, A.

    1991-01-01

    A hybrid cell line (R21/B1) containing a truncated human chromosome 6 (6pter-6q21) and a human Y chromosome on a hamster background was irradiated and fused to A23 (TK-) or W3GH (HPRT-) hamster cells. Clones containing expressed HLA class I genes (4/40) were selected using monoclonal antibodies. These clones were recloned and analyzed with a panel of probes from the HLA region. One hybrid (4G6) contained the entire HLA complex. Two other hybrids (4J4 and 4H2) contained only the HLA class I region, while the fourth hybrid (5P9) contained HLA class I and III genes in addition to other genes located in the 6p21 chromosomal region. In situ hybridization showed that the hybrid cells contained more than one fragment of human DNA. Alu and LINE PCR products were derived from these cells and compared to each other as well as to products from two somatic cell hybrids having the 6p21 region in common. The PCR fragments were then screened on conventional Southern blots of the somatic cell hybrids to select a panel of novel probes encompassing the 6p21 region. In addition, the origin of the human DNA fragments in hybrid 4J4 was determined by regional mapping of PCR products

  14. Protective effects of long-term lithium administration in a slowly progressive SMA mouse model.

    Biagioni, Francesca; Ferrucci, Michela; Ryskalin, Larisa; Fulceri, Federica; Lazzeri, Gloria; Calierno, Maria Teresa; Busceti, Carla L; Ruffoli, Riccardo; Fornai, Francesco

    2017-12-01

    In the present study we evaluated the long-term effects of lithium administration to a knock-out double transgenic mouse model (Smn-/-; SMN1A2G+/-; SMN2+/+) of Spinal Muscle Atrophy type III (SMA-III). This model is characterized by very low levels of the survival motor neuron protein, slow disease progression and motor neuron loss, which enables to detect disease-modifying effects at delayed time intervals. Lithium administration attenuates the decrease in motor activity and provides full protection from motor neuron loss occurring in SMA-III mice, throughout the disease course. In addition, lithium prevents motor neuron enlargement and motor neuron heterotopy and suppresses the occurrence of radial-like glial fibrillary acidic protein immunostaining in the ventral white matter of SMA-III mice. In SMA-III mice long-term lithium administration determines a dramatic increase of survival motor neuron protein levels in the spinal cord. These data demonstrate that long-term lithium administration during a long-lasting motor neuron disorder attenuates behavioural deficit and neuropathology. Since low level of survival motor neuron protein is bound to disease severity in SMA, the robust increase in protein level produced by lithium provides solid evidence which calls for further investigations considering lithium in the long-term treatment of spinal muscle atrophy.

  15. PEMBELAJARAN THINK-PAIR-SHARE, KETERAMPILAN METAKOGNITIF, DAN HASIL BELAJAR KOGNITIF SISWA SMA

    Sri Amnah S.

    2012-05-01

    Full Text Available Abstract: Think-Pair-Share Learning, Meta-cognitive Skills and Cognitive Learning Outcomes. The study investigates the effects of meta-cognitive skills based Think-Pair-Share cooperative learning on meta-cognitive skills and cognitive learning outcomes of 11th grade students of Senior High Schools in Pekanbaru. The sample consists of 11th grade students of SMA 9 as an experiment group and 11th grade students SMA 10 as a control group. Based on analyzing the data using ANCOVA, the results show that there is a signifi­cant difference in meta-cognitive skills and cognitive learning outcomes of the students in the experimental and the control groups, and there is no significant difference between students who have high and low academic levels in their meta-cognitive skills and cognitive learning outcomes. Abstrak: Pembelajaran Think-Pair-Share, Keterampilan Metakognitif, dan Hasil Belajar Kognitif Siswa SMA. Penelitian ini bertujuan mengukur pengaruh pembela­jaran koperatif Think-Pair-Share terha­dap keterampilan metakognitif dan hasil belajar kognitif siswa SMA. Sampel dipilih secara acak dari popu­lasi 13 SMA di Pekanbaru. Dengan menggunakan ANAKOVA, hasilnya menunjukkan bahwa terdapat per­bedaan yang nyata keterampilan metakognitif dan hasil belajar kognitif siswa di kelompok eksperimental dan kelompok control, dan tidak ada perbedaan yang nyata antara siswa berkemampuan akademik tinggi dan akademik rendah pada keterampilan metakognitif dan hasil belajar kognitifnya.

  16. An improved tuned mass damper (SMA-TMD) assisted by a shape memory alloy spring

    Mishra, Sudib K; Gur, Sourav; Chakraborty, Subrata

    2013-01-01

    The tuned mass damper (TMD) is a well acclaimed passive control device for vibration control of structures. However, the requirement of a higher mass ratio restricts its applicability for seismic vibration control of civil engineering structures. Improving the performance of TMDs has been attempted by supplementing them with nonlinear restoring devices. In this regard, the ability of shape memory alloy (SMA) in dissipating energy through a hysteretic phase transformation of its microstructure triggered by cyclic loading is notable. An improved version of TMD assisted by a nonlinear shape memory alloy (SMA) spring, referred as SMA-TMD, is studied here for seismic vibration mitigation. Extensive numerical simulations are conducted based on nonlinear random vibration analysis via stochastic linearization of the nonlinear force–deformation hysteresis of the SMA. A design optimization based on minimizing the root mean square displacement of the main structure is also carried out to postulate the optimal design parameters for the proposed system. The viability of the optimal design is verified with respect to its performance under recorded earthquake motions. Significant improvements of the control efficiency and a reduction of the TMD displacement at a much reduced mass ratio are shown to be achieved in the proposed SMA-TMD over those in the linear TMD. (paper)

  17. EFEKTIVITAS FOCUS GROUP DISCUSSION UNTUK MENGURANGI STRES PADA SISWA SMA YANG AKAN MENGHADAPI UJIAN AKHIR NASIONAL

    Dina Aprilia

    2016-10-01

    Full Text Available This research is aimed to find the effectivity of Focus Group Discussion (FGD to decrease the feeling stress for senior high school students (SMA who will face the national final examination (UAN. Stress on SMA students is a circumstance which gets negative assessment. It intimidates and pushes the students, in this case is UAN would appear a reaction such as emotional disorder, cognition, physiology and behavior disorder of SMA students. This research concerned 21 SMA students in grade XII, who had high stress level in facing UAN. The subjects were divided into two groups. First group was the experiment group (include 11 students and it was the group who got the FGD treatment. The second group was control group (include 10 students and this group didn’t get the FGD treatment. Collecting data was done by using Stress Scale in facing UAN. It was given (a before FGD (pre-test and (b after FGD (post-test. The hypothesis is examined by using difference examination (t-test by comparing mean pre-test and post-test. The result showed that there was a significant influence to decrease the stress in SMA students who were in experiment group (t = 6,540, p < 0,01 after they got FGD treatment. Experiment group had decreased the stress score to face UAN (Mean=7,476.

  18. Hypothyroidism coordinately and transiently affects myelin protein gene expression in most rat brain regions during postnatal development.

    Ibarrola, N; Rodríguez-Peña, A

    1997-03-28

    To assess the role of thyroid hormone on myelin gene expression, we have studied the effect of hypothyroidism on the mRNA steady state levels for the major myelin protein genes: myelin basic protein (MBP), proteolipid protein (PLP), myelin-associated glycoprotein (MAG) and 2':3'-cyclic nucleotide 3'-phosphodiesterase (CNP) in different rat brain regions, during the first postnatal month. We found that hypothyroidism reduces the levels of every myelin protein transcript, with striking differences between the different brain regions. Thus, in the more caudal regions, the effect of hypothyroidism was extremely modest, being only evident at the earlier stages of myelination. In contrast, in the striatum and the cerebral cortex the important decrease in the myelin protein transcripts is maintained beyond the first postnatal month. Therefore, thyroid hormone modulates in a synchronous fashion the expression of the myelin genes and the length of its effect depends on the brain region. On the other hand, hyperthyroidism leads to an increase of the major myelin protein transcripts above control values. Finally, lack of thyroid hormone does not change the expression of the oligodendrocyte progenitor-specific gene, the platelet derived growth factor receptor alpha.

  19. Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.

    Rahmatalla, Siham A; Arends, Danny; Reissmann, Monika; Said Ahmed, Ammar; Wimmers, Klaus; Reyer, Henry; Brockmann, Gudrun A

    2017-10-23

    Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (F IS ) did not differ from zero. F st coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei's genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high F st values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system. The information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high F st values in Taggar goat and allowed to identify candidate genes which can be used in the

  20. Identification of Region-Specific Myocardial Gene Expression Patterns in a Chronic Swine Model of Repaired Tetralogy of Fallot.

    Sabine Charron

    Full Text Available Surgical repair of Tetralogy of Fallot (TOF is highly successful but may be complicated in adulthood by arrhythmias, sudden death, and right ventricular or biventricular dysfunction. To better understand the molecular and cellular mechanisms of these delayed cardiac events, a chronic animal model of postoperative TOF was studied using microarrays to perform cardiac transcriptomic studies. The experimental study included 12 piglets (7 rTOF and 5 controls that underwent surgery at age 2 months and were further studied after 23 (+/- 1 weeks of postoperative recovery. Two distinct regions (endocardium and epicardium from both ventricles were analyzed. Expression levels from each localization were compared in order to decipher mechanisms and signaling pathways leading to ventricular dysfunction and arrhythmias in surgically repaired TOF. Several genes were confirmed to participate in ventricular remodeling and cardiac failure and some new candidate genes were described. In particular, these data pointed out FRZB as a heart failure marker. Moreover, calcium handling and contractile function genes (SLN, ACTC1, PLCD4, PLCZ, potential arrhythmia-related genes (MYO5B, KCNA5, and cytoskeleton and cellular organization-related genes (XIRP2, COL8A1, KCNA6 were among the most deregulated genes in rTOF ventricles. To our knowledge, this is the first comprehensive report on global gene expression profiling in the heart of a long-term swine model of repaired TOF.

  1. Note: A component-level frequency tunable isolator for vibration-sensitive chips using SMA beams

    Zhang, Xiaoyong, E-mail: zhangxy@buaa.edu.cn, E-mail: yanxiaojun@buaa.edu.cn; Yan, Xiaojun, E-mail: zhangxy@buaa.edu.cn, E-mail: yanxiaojun@buaa.edu.cn [School of Energy and Power Engineering, Beihang University, Beijing 100191 (China); Collaborative Innovation Center of Advanced Aero-Engine, Beijing 100191 (China); National Key Laboratory of Science and Technology on Aero-Engine Aero-Thermodynamics, Beijing 100191 (China); Beijing Key Laboratory of Aero-Engine Structure and Strength, Beijing 100191 (China); Ding, Xin; Wu, Di; Qi, Junlei; Wang, Ruixin; Lu, Siwei [School of Energy and Power Engineering, Beihang University, Beijing 100191 (China)

    2016-06-15

    This note presents a component-level frequency tunable isolator for vibration-sensitive chips. The isolator employed 8 U-shaped shape memory alloy (SMA) beams to support an isolation island (used for mounting chips). Due to the temperature-induced Young’s modulus variation of SMA, the system stiffness of the isolator can be controlled through heating the SMA beams. In such a way, the natural frequency of the isolator can be tuned. A prototype was fabricated to evaluate the concept. The test results show that the natural frequency of the isolator can be tuned in the range of 64 Hz–97 Hz by applying different heating strategies. Moreover, resonant vibration can be suppressed significantly (the transmissibility decreases about 65% near the resonant frequency) using a real-time tuning method.

  2. Pemodelan Enterprise Architecture Sistem Informasi Akademik SMA PL Don Bosko Semarang Dengan Framework Zachman

    Maria Alfonsa Chintia Dea Prananingrum

    2017-05-01

    Full Text Available Abstrak SMA PL Don Bosko Semarang belum dapat memanfaatkan teknologi komputer secara optimal karena masih menggunakan cara manual dalam pengelolaan berbagai macam data akademik sehingga memberikan masalah seperti lambatnya dalam pembuatan laporan yang menyulitkan kepala sekolah dalam pengambilan keputusan. Oleh sebab itu, SMA PL Don Bosko Semarang membutuhkan Sistem Informasi Akademik untuk memberikan kemudahan dalam mengelola berbagai macam data akademik secara terintegrasi serta memberikan layanan yang lebih baik kepada siswanya. Sebuah model architecture enterprise Sistem Informasi Akademik dibutuhkan agar meminimalisir kegagalan ketika menerapkan sistem tersebut sekaligus dapat berjalan sesuai kebutuhan di SMA PL Don Bosko Semarang. Metode analisis dalam penelitian ini menggunakan Framework Zachman yang memberikan pondasi dalam membantu menyediakan struktur dasar organisasi sehingga dapat mendukung perancangan dan pengembangan sistem informasi suatu organisasi. Hasil dari penelitian ini berupa blueprint (cetak biru pemodelan Sistem Informasi Akademik. Kata kunci— sistem informasi akademik, architecture enterprise, framework zachman, bluprint

  3. PENGEMBANGAN MEDIA PEMBELAJARAN PENDIDIKAN JASMANI OLAHRAGA DAN KESEHATAN BERBASIS KOMPUTER UNTUK SMA

    Suci Cahyati

    2014-04-01

    Full Text Available Penelitian ini bertujuan untuk menghasilkan produk berupa CD pembelajaran pendidikan jasmani olahraga dan kesehatan berbasis komputer untuk SMA yang valid dan efektif. Penelitian ini menggunakan metode Research and Development (R&D. Media yang dikembangkan memuat materi tentang HIV/AIDS. Pengembangan media pembelajaran ini menggunakan software Adobe Flash Cs3 Professional. Media yang telah dikembangkan melalui dua tahap penelitiannya itu validasi ahli dan uji coba lapangan. Berdasarkan validasi ahli dan uji coba lapangan hasil penelitian menunjukkan produk termasuk kriteria “Sangat baik” dengan rerata skor 4,25. Hasil tes siswa mengalami peningkatan dari rerata skor pretest 5,53 dan rerata skor posttest 7,56. Berdasarkan hasil tes tersebut dapat disimpulkan bahwa media pembelajaran pendidikan jasmani olahraga dan kesehatan efektif digunakan dalam pembelajaran di SMA. Kata kunci: Pengembangan media, penjasorkes, SMA

  4. Development of SMA Actuated Morphing Airfoil for Wind Turbine Load Alleviation

    Karakalas, A.; Machairas, T.; Solomou, A.; Riziotis, V.; Saravanos, D.

    Wind turbine rotor upscaling has entered a range of rotor diameters where the blade structure cannot sustain the increased aerodynamic loads without novel load alleviation concepts. Research on load alleviation using morphing blade sections is presented. Antagonistic shape memory alloy (SMA) actuators are implemented to deflect the section trailing edge (TE) to target shapes and target time-series relating TE movement with changes in lift coefficient. Challenges encountered by the complex thermomechanical response of morphing section and the enhancement of SMA transient response to achieve frequencies meaningful for aerodynamic load alleviation are addressed. Using a recently developed finite element for SMA actuators [1], actuator configurations are considered for fast cooling and heating cycles. Numerical results quantify the attained ranges of TE angle movement, the moving time period and the developed stresses. Estimations of the attained variations of lift coefficient vs. time are also presented to assess the performance of the morphing section.

  5. Note: A component-level frequency tunable isolator for vibration-sensitive chips using SMA beams

    Zhang, Xiaoyong; Yan, Xiaojun; Ding, Xin; Wu, Di; Qi, Junlei; Wang, Ruixin; Lu, Siwei

    2016-01-01

    This note presents a component-level frequency tunable isolator for vibration-sensitive chips. The isolator employed 8 U-shaped shape memory alloy (SMA) beams to support an isolation island (used for mounting chips). Due to the temperature-induced Young’s modulus variation of SMA, the system stiffness of the isolator can be controlled through heating the SMA beams. In such a way, the natural frequency of the isolator can be tuned. A prototype was fabricated to evaluate the concept. The test results show that the natural frequency of the isolator can be tuned in the range of 64 Hz–97 Hz by applying different heating strategies. Moreover, resonant vibration can be suppressed significantly (the transmissibility decreases about 65% near the resonant frequency) using a real-time tuning method.

  6. PENGGUNAAN STRATEGI PEMBELAJARAN INKUIRI UNTUK MENINGKATKAN METAKOGNISI SISWA SMA

    Maulida Fitriana

    2016-05-01

    Full Text Available Penelitian ini bertujuan untuk mengetahui (1 peningkatkan metakognisi siswa melalui strategi pembelajaran inkuiri materi kelarutan dan hasil kali kelarutan di suatu SMA di Donorojo, (2 perbedaan antara penggunaan strategi pembelajaran inkuiri dan pembelajaran langsung terhadap peningkatan metakognisi siswa. Metode eksperimen dengan desain pretest-posttest group design digunakan dalam penelitian ini. Objek penelitian ini adalah siswa kelas XI IPA. Teknik pengambilan sampel adalah cluster random sampling karena populasi berdistribusi normal dan homogen. Hasil penelitian menunjukkan bahwa rata-rata nilai posttes kelas eksperimen 75,15 dan kelas kontrol 72,42. Berdasarkan hasil analisis N-gain pada kelas eksperimen menunjukkan peningkatan metakognisi sebesar 0,68 antara sebelum dan sesudah penggunaan strategi pembelajaran inkuiri. Sedangkan hasil analisis N-gain pada kelas kontrol menunjukkan peningkatan metakognisi sebesar 0,62 antara sebelum dan sesudah penggunaan strategi pembelajaran langsung. Pada uji hipotesis diperoleh t hitung sebesar 1,65 kurang dari t 1,66 yang berarti rata-rata hasil belajar kognitif kelas eksperimen tidak berbeda dari kelas kontrol. Kesimpulan dari penelitian ini adalah (1 strategi pembelajaran inkuiri dapat meningkatkan metakognisi siswa, (2 tidak ada perbedaan yang signifikan antara penggunaan strategi pembelajaran inkuiri dan pembelajaran langsung terhadap peningkatan metakognisi siswa.The objective of this study is to find out (1 the improvement of the students’ metacognition by using the inquiry learning method on the water-soluble substance and the result of its product in a high school in Donorojo, (2 the significant difference between the use of inquiry learning method and the direct instruction method to the improvement of students' metacognition. This study is an experimental research and the design was pretest-posttest group design. Object of this study is eleventh grade students of science program. The

  7. Evidence for gene-specific rather than transcription rate-dependent histone H3 exchange in yeast coding regions.

    Gat-Viks, Irit; Vingron, Martin

    2009-02-01

    In eukaryotic organisms, histones are dynamically exchanged independently of DNA replication. Recent reports show that different coding regions differ in their amount of replication-independent histone H3 exchange. The current paradigm is that this histone exchange variability among coding regions is a consequence of transcription rate. Here we put forward the idea that this variability might be also modulated in a gene-specific manner independently of transcription rate. To that end, we study transcription rate-independent replication-independent coding region histone H3 exchange. We term such events relative exchange. Our genome-wide analysis shows conclusively that in yeast, relative exchange is a novel consistent feature of coding regions. Outside of replication, each coding region has a characteristic pattern of histone H3 exchange that is either higher or lower than what was expected by its RNAPII transcription rate alone. Histone H3 exchange in coding regions might be a way to add or remove certain histone modifications that are important for transcription elongation. Therefore, our results that gene-specific coding region histone H3 exchange is decoupled from transcription rate might hint at a new epigenetic mechanism of transcription regulation.

  8. Constitutive modeling of SMA SMP multifunctional high performance smart adaptive shape memory composite

    Jarali, Chetan S; Raja, S; Upadhya, A R

    2010-01-01

    Materials design involving the thermomechanical constitutive modeling of shape memory alloy (SMA) and shape memory polymer (SMP) composites is a key topic in the development of smart adaptive shape memory composites (SASMC). In this work, a constitutive model for SASMC is developed. First, a one-dimensional SMA model, which can simulate the pseudoelastic (PE) and shape memory effects (SME) is presented. Subsequently, a one-dimensional SMP model able to reproduce the SME is addressed. Both SMA and SMP models are based on a single internal state variable, namely the martensite fraction and the frozen fraction, which can be expressed as a function of temperature. A consistent form of the analytical solution for the SMP model is obtained using the fourth-order Runge–Kutta method. Finally, the SASMC constitutive model is proposed, following two analytical homogenization approaches. One approach is based on an equivalent inclusion method and the other approach is the rule of mixtures. The SMA and SMP constitutive models are validated independently with experimental results. However, the validation of the composite model is performed using the two homogenization approaches and a close agreement in results is observed. Results regarding the isothermal and thermomechanical stress–strain responses are analyzed as a function of SMA volume fraction. Further, it is concluded that the proposed composite model is able to reproduce consistently the overall composite response by taking into consideration not only the phase transformations, variable modulus and transformation stresses in SMA but also the variable modulus, the evolution of stored strain and thermal strain in the SMP

  9. Immunoglobulin Heavy Chain Variable Region and Major Histocompatibility Region Genes Are Linked to Induced Graves' Disease in Females From Two Very Large Families of Recombinant Inbred Mice

    Aliesky, Holly; Banuelos, Bianca; Magana, Jessica; Williams, Robert W.; Rapoport, Basil

    2014-01-01

    Graves' hyperthyroidism is caused by antibodies to the TSH receptor (TSHR) that mimic thyroid stimulation by TSH. Stimulating TSHR antibodies and hyperthyroidism can be induced by immunizing mice with adenovirus expressing the human TSHR A-subunit. Prior analysis of induced Graves' disease in small families of recombinant inbred (RI) female mice demonstrated strong genetic control but did not resolve trait loci for TSHR antibodies or elevated serum T4. We investigated the genetic basis for induced Graves' disease in female mice of two large RI families and combined data with earlier findings to provide phenotypes for 178 genotypes. TSHR antibodies measured by inhibition of TSH binding to its receptor were highly significantly linked in the BXD set to the major histocompatibility region (chromosome 17), consistent with observations in 3 other RI families. In the LXS family, we detected linkage between T4 levels after TSHR-adenovirus immunization and the Ig heavy chain variable region (Igvh, chromosome 12). This observation is a key finding because components of the antigen binding region of Igs determine antibody specificity and have been previously linked to induced thyroid-stimulating antibodies. Data from the LXS family provide the first evidence in mice of a direct link between induced hyperthyroidism and Igvh genes. A role for major histocompatibility genes has now been established for genetic susceptibility to Graves' disease in both humans and mice. Future studies using arrays incorporating variation in the complex human Ig gene locus will be necessary to determine whether Igvh genes are also linked to Graves' disease in humans. PMID:25051451

  10. Functional Analysis of Promoter Region from Eel Cytochrome P450 1A1 Gene in Transgenic Medaka.

    Ogino; Itakura; Kato; Aoki; Sato

    1999-07-01

    : Transcription of the CYP1A1 genes in mammals and fish is stimulated by polyaromatic hydrocarbons. DNA sequencing analysis revealed that CYP1A1 gene in eel (Anguilla japonica) contains two kinds of putative cis-acting regulatory elements, XRE (xenobiotic-responsive element) and ERE (estrogen-responsive element). XRE is known as the enhancer that is responsible for the inducibility of the genes of CYP1A1 and some other drug-metabolizing enzymes. In the eel CYP1A1 gene, XRE motifs are distributed as follows: five times in the region from -2136 to -1125 bp, XRE(-6) to (-2); once in the proximal basal promoter region, XRE(-1); and once in the first intron, XRE(+1). The region between XRE(-2) and XRE(-1) contains three ERE motifs. To investigate the function of the cis-acting regulatory elements in the eel CYP1A1 gene, recombinant plasmids prepared with its 5' upstream sequence and the structural gene for luciferase were microinjected into fertilized eggs of medaka at the one-cell stage. Hatched fry were treated with 3-methylcholanthrene, and the transcription efficiency was assayed using competitive polymerase chain reaction analysis. Deletion of the region containing the five XREs, XRE(-6) to XRE(-2), and the point mutation of XRE(-1) reduced the inducible expressions by 75% and 56%, respectively, showing apparent dependency of the drug induction on the XREs. Constitutive expression, however, was not significantly affected by deletion or disruption of the XREs. When the region between XRE(-2) and XRE(-1) containing no XREs but three ERE motifs was internally deleted, the inducible expression and the constitutive expression were reduced by 88% and 75%, respectively. Replacement of this region with a partial fragment of eel CYP1A1 complementary DNA, with slight alteration of the distance between the five XREs and XRE(-1), reduced the inducible expression and the constitutive expression by 91% and 60%, respectively. These results strongly suggest that not only XRE but

  11. Group-SMA Algorithm Based Joint Estimation of Train Parameter and State

    Wei Zheng

    2015-03-01

    Full Text Available The braking rate and train arresting operation is important in the train braking performance. It is difficult to obtain the states of the train on time because of the measurement noise and a long calculation time. A type of Group Stochastic M-algorithm (GSMA based on Rao-Blackwellization Particle Filter (RBPF algorithm and Stochastic M-algorithm (SMA is proposed in this paper. Compared with RBPF, GSMA based estimation precisions for the train braking rate and the control accelerations were improved by 78% and 62%, respectively. The calculation time of the GSMA was decreased by 70% compared with SMA.

  12. MENINGKATKAN KEMAMPUAN BERPIKIR KREATIF MATEMATIS SISWA SMA MELALUI PEMBELAJARAN OPEN ENDED PADA MATERI SPLDV

    Firdaus Firdaus

    2016-02-01

    Penelitian ini bertujuan untuk mendeskripsikan kemampuan berpikir kreatif matematis siswa SMA melalui pembelajaran open ended problem materi SPLDV. Jenis penelitian ini, yaitu deskriptif kualitatif. Subjeknya adalah siswa kelas X.2 SMA Negeri 1 Woja Dompu. Tahap pembelajaran dalam penelitian ini adalah (1 Orientasi, (2 pembekalan materi, (3 penyajian dan pengerjaan soal open ended, (4 presentasi, (5 kesimpulan. Kemampuan berpikir kreatif matematis siswa meliputi: (a fluency, kemampuan siswa lancar dalam memberikan jawaban benar, (b flexibility, kemampuan siswa dalam menggunakan berbagai cara penyelesaian masalah, (c novelty, kemampuan siswa dalam memberikan jawaban yang baru dan berbeda dengan siswa lain. Penelitian ini hasilnya, bahwa siswa mempunyai kemampuan berpikir kreatif matematis.

  13. Immediate-early gene region of human cytomegalovirus trans-activates the promoter of human immunodeficiency virus

    Davis, M.G.; Kenney, S.C.; Kamine, J.; Pagano, J.S.; Huang, E.S.

    1987-01-01

    Almost all homosexual patients with acquired immunodeficiency syndrome are also actively infected with human cytomegalovirus (HCMV). The authors have hypothesized that an interaction between HCMV and human immunodeficiency virus (HIV), the agent that causes acquired immunodeficiency syndrome, may exist at a molecular level and contribute to the manifestations of HIV infection. In this report, they demonstrate that the immediate-early gene region of HCMV, in particular immediate-early region 2, trans-activates the expression of the bacterial gene chloramphenicol acetyltransferase that is fused to the HIV long terminal repeat and carried by plasmid pHIV-CAT. The HCMV immediate-early trans-activator increases the level of mRNA from the plamid pHIV-CAT. The sequences of HIV that are responsive to trans-activation by the HDMV immediate-early region are distinct from HIV sequences that are required for response to the HIV tat. The stimulation of HIV gene expression by HDMV gene functions could enhance the consequences of HIV infection in persons with previous or concurrent HCMV infection

  14. The in vitro transcription of a rainbow trout (Salmo gairdnerii) protamine gene. II. Controlled mutation of the cap site region.

    Jankowski, J M; Dixon, G H

    1985-02-01

    A series of plasmids containing new fusion genes in which the trout protamine gene is placed under the control of the complete herpes virus (HSV-1) tk promoter Pvu II-Bgl II fragment (pM8), or a shortened thymidine kinase (tk) promoter in which the region between the TATA box and the cap site is altered by using the Pvu II-Mlu I fragment (pM7), have been constructed. An additional recombinant plasmid was constructed in which the Bgl II-Ava II fragment of the protamine gene containing the entire protamine promoter but missing the protamine coding region was cloned into pBR322 between the Xho II 1666 and Hind III sites (pP5). For in vitro transcription, a HeLa cell lysate system was prepared and the RNA transcription products, after glyoxalation, were electrophoretically analyzed on 5% polyacrylamide gels. In constructing pM8 the DNA sequence between the tk promoter and the cap site was present while in pM7 it was deleted. Similar multiple transcripts were seen in both cases, indicating that the region between the promoter and the cap site has no effect upon transcription in vitro. The multiple transcripts appear to be due to the presence of a cryptic promoter in the complementary strand of the protamine gene. The activity of this cryptic promoter has been confirmed by comparison of the transcription of plasmid pP5, in which the protamine mRNA coding region has been deleted, with a previously described plasmid, pJBRP (Jankowski JM and Dixon GH (1984) Can. J. Biochem. Cell. Biol. 62, 291-300), containing the intact protamine gene.

  15. Role of the tau gene region chromosome inversion in progressive supranuclear palsy, corticobasal degeneration, and related disorders.

    Webb, Amy; Miller, Bruce; Bonasera, Stephen; Boxer, Adam; Karydas, Anna; Wilhelmsen, Kirk C

    2008-11-01

    An inverted region on chromosome 17 has been previously linked to many Pick complex diseases. Due to the inversion, an exact causal locus has been difficult to identify, but the microtubule-associated protein tau gene is a likely candidate gene for its involvement in these diseases with tau inclusion. To search for variants that confer susceptibility to 4 tauopathies and clinically related disorders. Genomewide association study. University research laboratory. A total of 231 samples were genotyped from an unrelated white population of patients with progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), frontotemporal dementia, and frontotemporal dementia with amyotrophy. Unaffected individuals from the same population were used as controls. The results from an inverted region of chromosome 17 that contains the MAPT gene. Genotypes of cases and controls were compared using a Fisher exact test on a marker-by-marker basis. Haplotypes were determined by visually inspecting genotypes. Comparing any particular disease and controls, the association was constant across the inverted chromosome segment. Significant associations were seen for PSP and PSP combined with CBD. Of the 2 haplotypes seen in the region, H1 was overrepresented in PSP and CBD cases compared with controls. As expected, the markers are highly correlated and the association is seen across the entire region, which makes it difficult to narrow down a disease-causing variant or even a possible candidate gene. However, considering the pathologic abnormalities of these diseases and the involvement of tau mutations seen in familial forms, the MAPT gene represents the most likely cause driving the association.

  16. The Hsp60C gene in the 25F cytogenetic region in Drosophila ...

    Unknown

    Earlier studies have shown that of the four genes (Hsp60A, Hsp60B, Hsp60C, Hsp60D genes) predicted to encode the conserved Hsp60 family chaperones in Drosophila melanogaster, the ..... C. Genomic organization and the predicted.

  17. Isolation and characterization of the genomic region from Drosophila kuntzei containing the Adh and Adhr genes

    Oppentocht, JE; van Delden, W; van de Zande, L

    The nucleotide sequences of the Adh and Adhr genes of Drosophila kuntzei were derived from combined overlapping sequences of clones isolated from a genomic library and from cloned PCR and inverse-PCR fragments. Only a proximal promoter was detected upstream of the Adh gene, indicating that D.

  18. Genome walk of an unknown upstream region of myostatin gene in Spanish goats

    Myostatin (MSTN) gene product also known as growth differentiation factor (GDF8) is a member of the TGF-ß family of secreted proteins. It is shown to be a negative regulator of muscle mass development. Mutations in the MSTN gene have been reported in mice, cattle and humans that lead to muscular hyp...

  19. Identifying polymorphisms in the Rattus norvegicus D3 dopamine receptor gene and regulatory region

    Smits, B.M.; D'Souza, U.M.; Berezikov, E.; Cuppen, E.; Sluyter, F.

    2004-01-01

    The D(3) dopamine receptor has been implicated in several neuropsychiatric disorders, including schizophrenia, Parkinson's disease and addiction. Sequence variation in the D(3) gene can lead to subtle alteration in receptor structure or gene expression and thus to a different phenotype. In this

  20. Dominant control region of the human β- like globin gene cluster

    Blom van Assendelft, Margaretha van

    1989-01-01

    The structure and regulation of the human β -like globin gene cluster has been studied extensively. Genetic disorders connected with this gene cluster are responsible for human diseases associated with high levels of morbidity and mortality, such as β-thalassaemia and sickle cell anaemia. The work

  1. Altered phenotypic expression of immunoglobulin heavy-chain variable-region (VH) genes in Alicia rabbits probably reflects a small deletion in the VH genes closest to the joining region.

    Allegrucci, M; Newman, B A; Young-Cooper, G O; Alexander, C B; Meier, D; Kelus, A S; Mage, R G

    1990-07-01

    Rabbits of the Alicia strain have a mutation (ali) that segregates with the immunoglobulin heavy-chain (lgh) locus and has a cis effect upon the expression of heavy-chain variable-region (VH) genes encoding the a2 allotype. In heterozygous a1/ali or a3/ali rabbits, serum immunoglobulins are almost entirely the products of the normal a1 or a3 allele and only traces of a2 immunoglobulin are detectable. Adult homozygous ali/ali rabbits likewise have normal immunoglobulin levels resulting from increased production of a-negative immunoglobulins and some residual ability to produce the a2 allotype. By contrast, the majority of the immunoglobulins of wild-type a2 rabbits are a2-positive and only a small percentage are a-negative. Genomic DNAs from homozygous mutant and wild-type animals were indistinguishable by Southern analyses using a variety of restriction enzyme digests and lgh probes. However, when digests with infrequently cutting enzymes were analyzed by transverse alternating-field electrophoresis, the ali DNA fragments were 10-15 kilobases smaller than the wild type. These fragments hybridized to probes both for VH and for a region of DNA a few kilobases downstream of the VH genes nearest the joining region. We suggest that this relatively small deletion affects a segment containing 3' VH genes with important regulatory functions, the loss of which leads to the ali phenotype. These results, and the fact that the 3' VH genes rearrange early in B-cell development, indicate that the 3' end of the VH locus probably plays a key role in regulation of VH gene expression.

  2. Crack-closing of cement mortar beams using NiTi cold-drawn SMA short fibers

    Choi, Eunsoo; Kim, Dong Joo; Chung, Young-Soo; Kim, Hee Sun; Jung, Chungsung

    2015-01-01

    In this study, crack-closing tests of mortar beams reinforced by shape memory alloy (SMA) short fibers were performed. For this purpose, NiTi SMA fibers with a diameter of 0.965 mm and a length of 30 mm were made from SMA wires of 1.0 mm diameter by cold drawing. Four types of SMA fibers were prepared, namely, straight and dog-bone-shaped fiber and the two types of fibers with paper wrapping in the middle of the fibers. The paper provides an unbonded length of 15 mm. For bending tests, six types of mortar beams with the dimensions of 40 mm × 40 mm × 160 mm (B×H×L) were prepared. The SMA fibers were placed at the bottom center of the beams along with an artificial crack of 10 mm depth and 1 mm thickness. This study investigated the influence of SMA fibers on the flexural strength of the beams from the measured force- deflection curves. After cracking, the beams were heated at the bottom by fire to activate the SMA fibers. Then, the beams recovered the deflection, and the cracks were closed. This study evaluated crack-closing capacity using the degree of crack recovery and deflection-recovery factor. The first factor is estimated from the crack-width before and after crack-closing, and the second one is obtained from the downward deflection due to loading and the upward deflection due to the closing force of the SMA fibers.

  3. A Third Approach to Gene Prediction Suggests Thousands of Additional Human Transcribed Regions

    Glusman, Gustavo; Qin, Shizhen; El-Gewely, M. Raafat; Siegel, Andrew F; Roach, Jared C; Hood, Leroy; Smit, Arian F. A

    2006-01-01

    The identification and characterization of the complete ensemble of genes is a main goal of deciphering the digital information stored in the human genome. Many algorithms for computational gene prediction have been described, ultimately derived from two basic concepts: (1) modeling gene structure and (2) recognizing sequence similarity. Successful hybrid methods combining these two concepts have also been developed. We present a third orthogonal approach to gene prediction, based on detecting the genomic signatures of transcription, accumulated over evolutionary time. We discuss four algorithms based on this third concept: Greens and CHOWDER, which quantify mutational strand biases caused by transcription-coupled DNA repair, and ROAST and PASTA, which are based on strand-specific selection against polyadenylation signals. We combined these algorithms into an integrated method called FEAST, which we used to predict the location and orientation of thousands of putative transcription units not overlapping known genes. Many of the newly predicted transcriptional units do not appear to code for proteins. The new algorithms are particularly apt at detecting genes with long introns and lacking sequence conservation. They therefore complement existing gene prediction methods and will help identify functional transcripts within many apparent “genomic deserts.” PMID:16543943

  4. Gibberellin-regulated gene in the basal region of rice leaf sheath encodes basic helix-loop-helix transcription factor.

    Komatsu, Setsuko; Takasaki, Hironori

    2009-07-01

    Genes regulated by gibberellin (GA) during leaf sheath elongation in rice seedlings were identified using the transcriptome approach. mRNA from the basal regions of leaf sheaths treated with GA3 was analyzed by high-coverage gene expression profiling. 33,004 peaks were detected, and 30 transcripts showed significant changes in the presence of GA3. Among these, basic helix-loop-helix transcription factor (AK073385) was significantly upregulated. Quantitative PCR analysis confirmed that expression of AK073385 was controlled by GA3 in a time- and dose-dependent manner. Basic helix-loop-helix transcription factor (AK073385) is therefore involved in the regulation of gene expression by GA3.

  5. Evolution of Regions Containing Antibiotic Resistance Genes in FII-2-FIB-1 ColV-Colla Virulence Plasmids.

    Moran, Robert A; Hall, Ruth M

    2018-05-01

    Three ColV virulence plasmids carrying antibiotic resistance genes were assembled from draft genome sequences of commensal ST95, ST131, and ST2705 Escherichia coli isolates from healthy Australians. Plasmids pCERC4, pCERC5, and pCERC9 include almost identical backbones containing FII-2 and FIB-1 replicons and the conserved ColV virulence region with an additional ColIa determinant. Only pCERC5 includes a complete, uninterrupted F-like transfer region and was able to conjugate. pCERC5 and pCERC9 contain Tn1721, carrying the tet(A) tetracycline resistance determinant in the same location, with Tn2 (bla TEM ; ampicillin resistance) interrupting the Tn1721 in pCERC5. pCERC4 has a Tn1721/Tn21 hybrid transposon carrying dfrA5 (trimethoprim resistance) and sul1 (sulfamethoxazole resistance) in a class 1 integron. Four FII-2:FIB-1 ColV-ColIa plasmids in the GenBank nucleotide database have a related transposon in the same position, but an IS26 has reshaped the resistance gene region, deleting 2,069 bp of the integron 3'-CS, including sul1, and serving as a target for IS26 translocatable units containing bla TEM , sul2 and strAB (streptomycin resistance), or aphA1 (kanamycin/neomycin resistance). Another ColV-ColIa plasmid containing a related resistance gene region has lost the FII replicon and acquired a unique transfer region via recombination within the resistance region and at oriT. Eighteen further complete ColV plasmid sequences in GenBank contained FIB-1, but the FII replicons were of three types, FII-24, FII-18, and a variant of FII-36.

  6. Allelic variation of the inducible costimulator (ICOS) gene: detection of polymorphisms, analysis of the promoter region, and extended haplotype estimation

    Andersen, A.D.H.; Lange, Marianne; Lillevang, S.T.

    2003-01-01

    The human chromosome region 2q33 including the three costimulatory molecules CD28, CTLA-4 and ICOS, has been subject to much attention due to its linkage to a number of autoimmune diseases. The search for the causal relationship of this linkage has revealed several polymorphisms, but no variations...... in the amino acid sequences except for one polymorphism in, the leader sequence of CTLA-4. In the present study, we examined the ICOS gene of an unrelated group of healthy donors from the Danish population. We were able to report 16 intronic SNP, one intronic G-insert and two repeat regions in intron 4......, consistent with the [T](n) and the [GT](n) regions reported in a Japanese study. Putative haplotypes for the established SNP and repeat polymorphisms have been estimated by computational analysis. Sequencing of similar to3500 by of the upstream region of ICOS revealed an additional eight SNP of which two...

  7. Metal muscles and nerves—a self-sensing SMA-actuated hand concept

    Simone, F.; Rizzello, G.; Seelecke, S.

    2017-09-01

    Bio-inspired hand-like grippers actuated by Shape Memory Alloy (SMA) wires represent an emerging new technology with potential applications in many different fields, ranging from industrial assembly processes to biomedical systems. The inherently high energy density makes SMAs a natural choice for compact, lightweight, and silent actuator systems capable of producing a high amount of work, such as hand prostheses or robotic systems in industrial human/machine environments. In this work, a concept for a compact and versatile gripping system is developed, in which SMA wires are implemented as antagonistic muscles actuating an artificial hand with three fingers. In order to combine high gripping force with sufficient actuation speed, the muscle implementation pursues a multi-wire concept with several 0.1 mm diameter NiTi wires connected in parallel, in order to increase the surface-to-volume ratio for accelerated cooling. The paper starts with an illustration of the design concept of an individual 3-phalanx-finger, along with kinematic considerations for optimal placement of SMA wires. Three identical fingers are subsequently fabricated via 3D printing and assembled into a hand-like gripper. The maximum displacement of each finger phalanx is measured, and an average phalanxes dynamic responsiveness is evaluated. SMA self-sensing is documented by experiments relating the wires change in resistance to the finger motion. Several finger force measurements are also performed. The versatility of the gripper is finally documented by displaying a variety of achievable grasping configurations.

  8. PENGARUH MODEL PEMBELAJARAN KONSTRUKTIVIS 5E TERHADAP HASIL BELAJAR DI SMA LAKSAMANA MARTADINATA

    Nazila Ramadhani

    2012-06-01

    sehingga thitung > ttabel. Ini berarti Ha diterima, sehingga dapat disimpulkan ada pengaruh yang signifikan penerapan model pembelajaran konstruktivis 5E terhadap hasil belajar siswa pada materi pokok Medan Magnet di kelas XII semester ganjil SMA Laksamana Martadinata T.P 2011/2012.

  9. PELAKSANAAN PROGRAM BOARDING SCHOOL DALAM PEMBINAAN MORAL SISWA DI SMA TARUNA INDONESIA PALEMBANG

    Hendriyenti H

    2014-12-01

    Full Text Available AbstractIndonesia nowadays faces some moral issues in teenagers scope or adult scope such as the use of drugs, violence, rascality, abortion, persecution, gambling, prostitution, and so on. Those problems are very danger for the country. Therefore, moral education is very important in this situation. The study was done at SMA Taruna Indonesia Palembang by the tittle: “the Implementation of boarding School Program for Students Moral education at SMA Taruna Indonesia Palembang”.Based on the result of the stuy, it was found that the implementation of boarding school program to educate students’moral at SMA Taruna Indonesia Palembang was applied throug dicipline implementation program and religion education program. Those two programs were applied by preventive and currative treatment. Moreover, there were some factors which support students’ moral education at SMA Taruna Indonesia Palembang such as students motivation, advisors dedication, 24 hours education and guidance, good coordination between advisors, teachers, securities, and other staff, and far location of boarding school from city center. As long as the teenager is an unstable period, there weremany difficulties in educate them. Finally,it is hoped that school stakeholders could improve the school management so that those difficulties could be solved and moral education could be applied.  Keywords: boarding school, morality building

  10. iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.

    Panero, Riccardo; Rinaldi, Antonio; Memoli, Domenico; Nassa, Giovanni; Ravo, Maria; Rizzo, Francesca; Tarallo, Roberta; Milanesi, Luciano; Weisz, Alessandro; Giurato, Giorgio

    2017-03-15

    The interest in investigating the biological roles of small non-coding RNAs (sncRNAs) is increasing, due to the pleiotropic effects of these molecules exert in many biological contexts. While several methods and tools are available to study microRNAs (miRNAs), only few focus on novel classes of sncRNAs, in particular PIWI-interacting RNAs (piRNAs). To overcome these limitations, we implemented iSmaRT ( i ntegrative Sm all R NA T ool-kit), an automated pipeline to analyze smallRNA-Seq data. iSmaRT is a collection of bioinformatics tools and own algorithms, interconnected through a Graphical User Interface (GUI). In addition to performing comprehensive analyses on miRNAs, it implements specific computational modules to analyze piRNAs, predicting novel ones and identifying their RNA targets. A smallRNA-Seq dataset generated from brain samples of Huntington's Disease patients was used here to illustrate iSmaRT performances, demonstrating how the pipeline can provide, in a rapid and user friendly way, a comprehensive analysis of different classes of sncRNAs. iSmaRT is freely available on the web at ftp://labmedmolge-1.unisa.it (User: iSmart - Password: password). aweisz@unisa.it or ggiurato@unisa.it. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  11. Recovery and residual stress of SMA wires and applications for concrete structures

    Choi, Eunsoo; Cho, Sung-Chul; Park, Taehyo; Hu, Jong Wan; Chung, Young-Soo

    2010-01-01

    In general, NiTi shape memory alloys are used for applications in civil structures. NiTi SMAs show good superelasticity and shape memory effect properties. However, for application of the shape memory effect, it is desirable for SMAs to show a wide temperature hysteresis, especially for civil structures which are exposed to severe environmental conditions. NiTiNb SMAs, in general, show a wider temperature hysteresis than NiTi SMAs and are more applicable for civil structures. This study examines the temperature hysteresis of NiTiNb and NiTi SMAs, and their recovery and residual stress are investigated. In addition, the tensile behaviors of SMA wires under residual stress are evaluated. This study explains the possible applications for concrete structures with the shape memory effect and illustrates two experimental results of concrete cylinders and reinforced concrete columns. For both tests, SMA wires of NiTiNb and NiTi are used to confine concrete using residual stress. The SMA wire jackets on the concrete cylinders increase the peak strength and the ductility compared to the plain concrete cylinders. In addition, the SMA wire jackets on reinforced concrete columns increase the ductility greatly without flexural strength degradation

  12. KREATIVITAS GURU BIOLOGI DALAM MEMETAKAN KOMODITAS HAYATI UNGGULAN LOKAL KE DALAM PEMBELAJARAN BIOLOGI SMA

    Asep Agus Sulaeman

    2015-03-01

    Full Text Available Tujuan penelitian ini adalah untuk mengetahui kreativitas guru Biologi SMA dalam memetakan topik-topik dari berbagai aspek komoditas hayati unggulan lokal melalui penggunaan metode mind map dan mengetahui kemampuan guru dalam memetakan topik-topik komoditas hayati unggulan lokal ke dalam pembelajaran Biologi di SMA. Analisis data kreativitas guru Biologi SMA dilakukan secara deskriptif kuantitatif terhadap mind map dengan menggunakan kriteria sesuai instrumen yang dikembangkan. Adapun analisis data tentang jumlah topik-topik Biologi dan jenis kegiatan pembelajaran berbasis komoditas hayati unggulan lokal dilakukan secara deskriptif kuantatif dan kualitatif. Hasil kajian ini menunjukkan nilai aspek-aspek kreativitas guru Biologi yang tinggi, yaitu kemampuan berpikir asli (91,67, peka terhadap masalah (91,67, kemampuan berpikir lancar (90, kemampuan berpikir luwes (88,33, dan kemampuan berpikir terperinci (86,67. Berdasarkan hasil pemetaan yang dilakukan guru, dapat diidentifikasi 15 topik Biologi SMA yang berkaitan dengan komoditas hayati unggulan lokal di Kabupaten Majalengka. Adapun kegiatan pembelajaran berbasis komoditas hayati unggulan yang diusulkan oleh guru tersebar di masing-masing tingkatan kelas dan semesternya dengan jumlah yang berbeda-beda.

  13. Superelastic SMA U-shaped dampers with self-centering functions

    Wang, Bin; Zhu, Songye

    2018-05-01

    As high-performance metallic materials, shape memory alloys (SMAs) have been investigated increasingly by the earthquake engineering community in recent years, because of their remarkable self-centering (SC) and energy-dissipating capabilities. This paper systematically presents an experimental study on a novel superelastic SMA U-shaped damper (SMA-UD) with SC function under cyclic loading. The mechanical properties, including strength, SC ability, and energy-dissipating capability with varying loading amplitudes and strain rates are evaluated. Test results show that excellent and stable flag-shaped hysteresis loops are exhibited in multiple loading cycles. Strain rate has a negligible effect on the cyclic behavior of the SMA-UD within the dynamic frequency range of typical interest in earthquake engineering. Furthermore, a numerical investigation is performed to understand the mechanical behavior of the SMA-UD. The numerical model is calibrated against the experimental results with reasonable accuracy. Then, the stress–strain states with different phase transformations are also discussed.

  14. Stress Relaxation Effects in TiNi SMA During Superelastic Deformation: Experiment and Constitutive Model

    Pieczyska, Elżbieta A.; Kowalewski, Zbigniew L.; Dunić, Vladimir Lj.

    2017-12-01

    This paper presents an investigation of thermomechanical effects related to the phenomena of stress relaxation occurring in TiNi SMA subjected to modified program of displacement-controlled tension. The deformation data were taken from testing machine, whereas the temperature changes accompanying the exothermic/endothermic martensite forward/reverse transformation were measured by infrared camera. At the advanced stages of the transformations, the strain was kept constant for a few minutes and the SMA load and temperature were recorded continuously. As a consequence, the stress and temperature changed significantly during the loading stops. A large stress drop, caused by the transformation, was observed during the relaxation stage in both courses of the SMA loading and unloading. Moreover, the non-uniform temperature distribution, reflecting macroscopically inhomogeneous transformation, lapsed while the strain was kept constant, yet restarted at the end of the relaxation stop and developed at the reloading stage. Along with the experimental results, the mechanical and thermal responses induced by the transformation were obtained by 3D coupled thermomechanical numerical analysis, realized in partitioned approach. Latent heat production was correlated with an amount of the martensitic volume fraction. The stress and temperature drops recorded during the experiment were satisfactorily reproduced by the model proposed for the SMA thermomechanical coupling.

  15. PENGEMBANGAN BUKU PEDOMAN GURU PADA PEMBELAJARAN FISIKA SMA MENGGUNAKAN MODEL PROBLEM SOLVING LEVEL INKUIRI

    Susi Fatikhah Setiyawati; Heru Kuswanto

    2015-01-01

    Penelitian ini bertujuan: (1) menghasilkan buku pedoman guru untuk pembelajaran fisika SMA menggunakan model problem solving sesuai level inkuiri yang layak digunakan; (2) mendeskripsikan keberhasilan pembelajaran fisika menggunakan model problem solving (MPS) sesuai dengan level inkuiri sesuai dengan buku pedoman terhadap peningkatan aktivitas peserta didik dan kemampuan berpikir kritis peserta didik. Penelitian ini merupakan penelitian pengembangan, sesuai langkah yang dikembangkan oleh Bor...

  16. Genome-wide Anaplasma phagocytophilum AnkA-DNA interactions are enriched in intergenic regions and gene promoters and correlate with infection-induced differential gene expression.

    J Stephen Dumler

    2016-09-01

    Full Text Available Anaplasma phagocytophilum, an obligate intracellular prokaryote, infects neutrophils and alters cardinal functions via reprogrammed transcription. Large contiguous regions of neutrophil chromosomes are differentially expressed during infection. Secreted A. phagocytophilum effector AnkA transits into the neutrophil or granulocyte nucleus to complex with DNA in heterochromatin across all chromosomes. AnkA binds to gene promoters to dampen cis-transcription and also has features of matrix attachment region (MAR-binding proteins that regulate three-dimensional chromatin architecture and coordinate transcriptional programs encoded in topologically-associated chromatin domains. We hypothesize that identification of additional AnkA binding sites will better delineate how A. phagocytophilum infection results in reprogramming of the neutrophil genome. Using AnkA-binding ChIP-seq, we showed that AnkA binds broadly throughout all chromosomes in a reproducible pattern, especially at: i intergenic regions predicted to be matrix attachment regions (MARs; ii within predicted lamina-associated domains; and iii at promoters ≤3,000 bp upstream of transcriptional start sites. These findings provide genome-wide support for AnkA as a regulator of cis-gene transcription. Moreover, the dominant mark of AnkA in distal intergenic regions known to be AT-enriched, coupled with frequent enrichment in the nuclear lamina, provides strong support for its role as a MAR-binding protein and genome re-organizer. AnkA must be considered a prime candidate to promote neutrophil reprogramming and subsequent functional changes that belie improved microbial fitness and pathogenicity.

  17. SNPs in the 5'-regulatory region of the tyrosinase gene do not affect plumage color in ducks (Anas platyrhynchos).

    Zhang, N N; Hu, J W; Liu, H H; Xu, H Y; He, H; Li, L

    2015-12-29

    Tyrosinase, encoded by the TYR gene, is the rate-limiting enzyme in the production of melanin pigment. In this study, plumage color separation was observed in Cherry Valley duck line D and F1 and F2 hybrid generations of Liancheng white ducks. Gene sequencing and bioinformatic analysis were applied to the 5'-regulatory region of TYR, to explore the connection between TYR sequence variation and duck plumage color. Four SNPs were found in the 5'-regulatory region. The SNPs were in tight linkage and formed three haplotypes. However, the genotype distribution in groups with different plumage color was not significantly different, and there were no changes in the transcription factor binding sites between the different genotypes. In conclusion, these SNP variations may not cause the differences in feather color observed in this test group.

  18. [Using exon combined target region capture sequencing chip to detect the disease-causing genes of retinitis pigmentosa].

    Rong, Weining; Chen, Xuejuan; Li, Huiping; Liu, Yani; Sheng, Xunlun

    2014-06-01

    To detect the disease-causing genes of 10 retinitis pigmentosa pedigrees by using exon combined target region capture sequencing chip. Pedigree investigation study. From October 2010 to December 2013, 10 RP pedigrees were recruited for this study in Ningxia Eye Hospital. All the patients and family members received complete ophthalmic examinations. DNA was abstracted from patients, family members and controls. Using exon combined target region capture sequencing chip to screen the candidate disease-causing mutations. Polymerase chain reaction (PCR) and direct sequencing were used to confirm the disease-causing mutations. Seventy patients and 23 normal family members were recruited from 10 pedigrees. Among 10 RP pedigrees, 1 was autosomal dominant pedigrees and 9 were autosomal recessive pedigrees. 7 mutations related to 5 genes of 5 pedigrees were detected. A frameshift mutation on BBS7 gene was detected in No.2 pedigree, the patients of this pedigree combined with central obesity, polydactyly and mental handicap. No.2 pedigree was diagnosed as Bardet-Biedl syndrome finally. A missense mutation was detected in No.7 and No.10 pedigrees respectively. Because the patients suffered deafness meanwhile, the final diagnosis was Usher syndrome. A missense mutation on C3 gene related to age-related macular degeneration was also detected in No. 7 pedigrees. A nonsense mutation and a missense mutation on CRB1 gene were detected in No. 1 pedigree and a splicesite mutation on PROM1 gene was detected in No. 5 pedigree. Retinitis pigmentosa is a kind of genetic eye disease with diversity clinical phenotypes. Rapid and effective genetic diagnosis technology combined with clinical characteristics analysis is helpful to improve the level of clinical diagnosis of RP.

  19. A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family

    Hansen, Martin A; Nielsen, John E; Retelska, Dorota

    2008-01-01

    , sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA...... cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together......Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search...

  20. Genomic organization and identification of promoter regions for the BDNF gene in the pond turtle Trachemys scripta elegans.

    Ambigapathy, Ganesh; Zheng, Zhaoqing; Keifer, Joyce

    2014-08-01

    Brain-derived neurotrophic factor (BDNF) is an important regulator of neuronal development and synaptic function. The BDNF gene undergoes significant activity-dependent regulation during learning. Here, we identified the BDNF promoter regions, transcription start sites, and potential regulatory sequences for BDNF exons I-III that may contribute to activity-dependent gene and protein expression in the pond turtle Trachemys scripta elegans (tBDNF). By using transfection of BDNF promoter/luciferase plasmid constructs into human neuroblastoma SHSY5Y cells and mouse embryonic fibroblast NIH3T3 cells, we identified the basal regulatory activity of promoter sequences located upstream of each tBDNF exon, designated as pBDNFI-III. Further, through chromatin immunoprecipitation (ChIP) assays, we detected CREB binding directly to exon I and exon III promoters, while BHLHB2, but not CREB, binds within the exon II promoter. Elucidation of the promoter regions and regulatory protein binding sites in the tBDNF gene is essential for understanding the regulatory mechanisms that control tBDNF gene expression.

  1. Two distinct genomic regions, harbouring the period and fruitless genes, affect male courtship song in Drosophila montana.

    Lagisz, M; Wen, S-Y; Routtu, J; Klappert, K; Mazzi, D; Morales-Hojas, R; Schäfer, M A; Vieira, J; Hoikkala, A; Ritchie, M G; Butlin, R K

    2012-06-01

    Acoustic signals often have a significant role in pair formation and in species recognition. Determining the genetic basis of signal divergence will help to understand signal evolution by sexual selection and its role in the speciation process. An earlier study investigated quantitative trait locus for male courtship song carrier frequency (FRE) in Drosophila montana using microsatellite markers. We refined this study by adding to the linkage map markers for 10 candidate genes known to affect song production in Drosophila melanogaster. We also extended the analyses to additional song characters (pulse train length (PTL), pulse number (PN), interpulse interval, pulse length (PL) and cycle number (CN)). Our results indicate that loci in two different regions of the genome control distinct features of the courtship song. Pulse train traits (PTL and PN) mapped to the X chromosome, showing significant linkage with the period gene. In contrast, characters related to song pulse properties (PL, CN and carrier FRE) mapped to the region of chromosome 2 near the candidate gene fruitless, identifying these genes as suitable loci for further investigations. In previous studies, the pulse train traits have been found to vary substantially between Drosophila species, and so are potential species recognition signals, while the pulse traits may be more important in intra-specific mate choice.

  2. Full-scale flight tests of aircraft morphing structures using SMA actuators

    Mabe, James H.; Calkins, Frederick T.; Ruggeri, Robert T.

    2007-04-01

    In August of 2005 The Boeing Company conducted a full-scale flight test utilizing Shape Memory Alloy (SMA) actuators to morph an engine's fan exhaust to correlate exhaust geometry with jet noise reduction. The test was conducted on a 777-300ER with GE-115B engines. The presence of chevrons, serrated aerodynamic surfaces mounted at the trailing edge of the thrust reverser, have been shown to greatly reduce jet noise by encouraging advantageous mixing of the free, and fan streams. The morphing, or Variable Geometry Chevrons (VGC), utilized compact, light weight, and robust SMA actuators to morph the chevron shape to optimize the noise reduction or meet acoustic test objectives. The VGC system was designed for two modes of operation. The entirely autonomous operation utilized changes in the ambient temperature from take-off to cruise to activate the chevron shape change. It required no internal heaters, wiring, control system, or sensing. By design this provided one tip immersion at the warmer take-off temperatures to reduce community noise and another during the cooler cruise state for more efficient engine operation, i.e. reduced specific fuel consumption. For the flight tests a powered mode was added where internal heaters were used to individually control the VGC temperatures. This enabled us to vary the immersions and test a variety of chevron configurations. The flight test demonstrated the value of SMA actuators to solve a real world aerospace problem, validated that the technology could be safely integrated into the airplane's structure and flight system, and represented a large step forward in the realization of SMA actuators for production applications. In this paper the authors describe the development of the actuator system, the steps required to integrate the morphing structure into the thrust reverser, and the analysis and testing that was required to gain approval for flight. Issues related to material strength, thermal environment, vibration

  3. ANALISIS KESULITAN KOGNITIF DAN MASALAH AFEKTIF SISWA SMA DALAM BELAJAR MATEMATIKA MENGHADAPI UJIAN NASIONAL

    Azis Azis

    2015-11-01

    Full Text Available Penelitian untuk mendeskripsikan tingkat dan letak kesulitan belajar matematika siswa pada aspek kognitif dan kategorisasi masalah belajar matematika siswa pada aspek afektif dalam menghadapi Ujian Nasional tahun pelajaran 2013/2014 SMA di Kota Baubau. Penelitian ini menggunakan penelitian dengan metode survei. Pengumpulan data yang digunakan adalah teknik pengukuran (tes diagnostik, kuisioner, dan wawancara. Hasil penelitian menunjukkan bahwa tingkat kesulitan belajar matematika yang dialami oleh siswa untuk menyelesaikan soal-soal Ujian Nasional berada pada kategori sedang; letak kesulitan belajar matematika siswa pada aspek kognitif dalam menyelesaikan soal-soal Ujian Nasional dilihat dari segi pengetahuan faktual dengan persentase interval kesulitan sebesar, segi pengetahuan konseptual dengan persentase interval kesulitan sebesar, dan segi pengetahuan prosedural dengan persentase interval kesulitan sebesar; dan kategorisasi masalah belajar matematika siswa pada kategori aspek afektif dalam menghadapi Ujian Nasional tahun pelajaran 2013/2014 SMA di Kota Baubau secara umum berada pada kategori rendah. Kata kunci: kesulitan belajar matematika, kognitif, afektif, ujian nasional SMA   AN ANALYSIS OF DIFFICULTY ON COGNITIVE AND PROBLEM ON AFFECTIVE OF SMA STUDENTS IN MATHEMATICS LEARNING FACING NATIONAL EXAMINATION Abstract This study aims to describe the degree of student’s learning difficulty of mathematics on cognitive and categorization of student’s learning problem on affective aspect in accomplishing mathematic items in facing national final exam of SMA Baubau municipality in 2013/2014 academic year. The research type uses survey method. The technique of data collecting made use of diagnostic test that is National final exam items in 2012/2013 academic year which was modified by the researcher, questionnaires, and interviews. The research result indicates that the degree of students’ learning difficulty of mathematics to accomplish

  4. Methylation of Promoter Regions of Genes of the Human Intrauterine Renin Angiotensin System and Their Expression

    Shane D. Sykes

    2015-01-01

    Full Text Available The intrauterine renin angiotensin system (RAS is implicated in placentation and labour onset. Here we investigate whether promoter methylation of RAS genes changes with gestation or labour and if it affects gene expression. Early gestation amnion and placenta were studied, as were term amnion, decidua, and placenta collected before labour (at elective caesarean section or after spontaneous labour and delivery. The expression and degree of methylation of the prorenin receptor (ATP6AP2, angiotensin converting enzyme (ACE, angiotensin II type 1 receptor (AGTR1, and two proteases that can activate prorenin (kallikrein, KLK1, and cathepsin D, CTSD were measured by qPCR and a DNA methylation array. There was no effect of gestation or labour on the methylation of RAS genes and CTSD. Amnion and decidua displayed strong correlations between the percent hypermethylation of RAS genes and CTSD, suggestive of global methylation. There were no correlations between the degree of methylation and mRNA abundance of any genes studied. KLK1 was the most methylated gene and the proportion of hypermethylated KLK1 alleles was lower in placenta than decidua. The presence of intermediate methylated alleles of KLK1 in early gestation placenta and in amnion after labour suggests that KLK1 methylation is uniquely dynamic in these tissues.

  5. Mutation of the RDR1 gene caused genome-wide changes in gene expression, regional variation in small RNA clusters and localized alteration in DNA methylation in rice.

    Wang, Ningning; Zhang, Di; Wang, Zhenhui; Xun, Hongwei; Ma, Jian; Wang, Hui; Huang, Wei; Liu, Ying; Lin, Xiuyun; Li, Ning; Ou, Xiufang; Zhang, Chunyu; Wang, Ming-Bo; Liu, Bao

    2014-06-30

    Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA biogenesis. It has been established that RDR2 is involved in the 24 nt siRNA-dependent RNA-directed DNA methylation (RdDM) pathway. Recent studies have suggested that RDR1 is involved in a second RdDM pathway that relies mostly on 21 nt smRNAs and functions to silence a subset of genomic loci that are usually refractory to the normal RdDM pathway in Arabidopsis. Whether and to what extent the homologs of RDR1 may have similar functions in other plants remained unknown. We characterized a loss-of-function mutant (Osrdr1) of the OsRDR1 gene in rice (Oryza sativa L.) derived from a retrotransposon Tos17 insertion. Microarray analysis identified 1,175 differentially expressed genes (5.2% of all expressed genes in the shoot-tip tissue of rice) between Osrdr1 and WT, of which 896 and 279 genes were up- and down-regulated, respectively, in Osrdr1. smRNA sequencing revealed regional alterations in smRNA clusters across the rice genome. Some of the regions with altered smRNA clusters were associated with changes in DNA methylation. In addition, altered expression of several miRNAs was detected in Osrdr1, and at least some of which were associated with altered expression of predicted miRNA target genes. Despite these changes, no phenotypic difference was identified in Osrdr1 relative to WT under normal condition; however, ephemeral phenotypic fluctuations occurred under some abiotic stress conditions. Our results showed that OsRDR1 plays a role in regulating a substantial number of endogenous genes with diverse functions in rice through smRNA-mediated pathways involving DNA methylation, and which participates in abiotic stress response.

  6. Analysis of upstream promoter region and corresponding 5’ UTR of glucokinase (GCK gene in horse breeds

    L. Minieri

    2010-04-01

    Full Text Available A region of glucokinase (GCK gene was sequenced in 14 horses of 14 different breeds. The resulting GCK nucleotide sequence (GenBank number EF136885 showed 77% homology with human GCK gene portion containing the upstream promoter region and the corresponding 5’ UTR of the exon 1. Conserved regulatory sequences near the putative transcriptional start site were identified. The obtained sequences were aligned to detect polymorphism. A new C>T transition within the 5’ UTR of exon 1 was found. Allele frequencies of this polymorphism were studied by PCR-RFLP in 193 horses of 14 breeds (Bardigiano, 21; Esperia Pony, 5; Haflinger, 10; Italian Heavy Draught Horse, 28; Italian Saddle, 25; Italian Trotter, 16; Lipizzan, 12; Maremmano, 15; Murgese, 14; Norico, 10; Salernitano, 12; Thoroughbred, 10; Tolfetano, 7 and Ventasso Horse, 8. The polymorphism was found in all breeds and differences in allelic frequencies among the breeds were observed. The new SNP identified within a regulative region of GCK gene, which plays an important role in insulin secretion and feeding behaviour, could be used for association studies with performance traits of the horses.

  7. Design and fabrication of a three-finger prosthetic hand using SMA muscle wires

    Simone, Filomena; York, Alexander; Seelecke, Stefan

    2015-03-01

    Bio-inspired hand-like gripper systems based on shape memory alloy (SMA) wire actuation have the potential to enable a number of useful applications in, e.g., the biomedical field or industrial assembly systems. The inherent high energy density makes SMA solutions a natural choice for systems with lightweight, low noise and high force requirements, such as hand prostheses or robotic systems in a human/machine environment. The focus of this research is the development, design and realization of a SMA-actuated prosthetic hand prototype with three fingers. The use of thin wires (100 μm diameter) allows for high cooling rates and therefore fast movement of each finger. Grouping several small wires mechanically in parallel allows for high force actuation. To save space and to allow for a direct transmission of the motion to each finger, the SMA wires are attached directly within each finger, across each phalanx. In this way, the contraction of the wires will allow the movement of the fingers without the use of any additional gears. Within each finger, two different bundles of wires are mounted: protagonist ones that create bending movement and the antagonist ones that enable stretching of each phalanx. The resistance change in the SMA wires is measured during actuation, which allows for monitoring of the wire stroke and potentially the gripping force without the use of additional sensors. The hand is built with modern 3D-printing technologies and its performance while grasping objects of different size and shape is experimentally investigated illustrating the usefulness of the actuator concept.

  8. Seismic fragility analysis of lap-spliced reinforced concrete columns retrofitted by SMA wire jackets

    Choi, Eunsoo; Park, Sun-Hee; Chung, Young-Soo; Kim, Hee Sun

    2013-01-01

    The aim of this study is to provide seismic fragility curves of reinforced concrete columns retrofitted by shape memory alloy wire jackets and thus assess the seismic performance of the columns against earthquakes, comparing them with reinforced concrete columns with lap-spliced and continuous reinforcement. For that purpose, this study first developed analytical models of the experimental results of the three types of columns, (1) lap-spliced reinforcement, (2) continuous reinforcement and (3) lap-spliced reinforcement and retrofitted by SMA wire jackets, using the OpenSEES program, which is oriented to nonlinear dynamic analysis. Then, a suite of ten recorded ground motions was used to conduct dynamic analyses of the analytical models with scaling of the peak ground acceleration from 0.1g to 1.0g in steps of 0.1g. From the static experimental tests, the column retrofitted with SMA wire jackets had a larger displacement ductility by a factor of 2.3 times that of the lap-spliced column, which was 6% larger compared with the ductility of the continuous reinforcement column. From the fragility analyses, the SMA wire jacketed column had median values of 0.162g and 0.567g for yield and collapse, respectively. For the yield damage state, the SMA wire jacketed column had a median value similar to the continuous reinforcement column. However, for the complete damage state, the SMA wire jacketed column showed a 1.33 times larger median value than the continuously reinforcement column. (paper)

  9. Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture.

    Tomova, Alexandra; Ivanova, Larisa; Buschmann, Alejandro H; Rioseco, Maria Luisa; Kalsi, Rajinder K; Godfrey, Henry P; Cabello, Felipe C

    2015-10-01

    Antimicrobials are heavily used in Chilean salmon aquaculture. We previously found significant differences in antimicrobial-resistant bacteria between sediments from an aquaculture and a non-aquaculture site. We now show that levels of antimicrobial resistance genes (ARG) are significantly higher in antimicrobial-selected marine bacteria than in unselected bacteria from these sites. While ARG in tetracycline- and florfenicol-selected bacteria from aquaculture and non-aquaculture sites were equally frequent, there were significantly more plasmid-mediated quinolone resistance genes per bacterium and significantly higher numbers of qnrB genes in quinolone-selected bacteria from the aquaculture site. Quinolone-resistant urinary Escherichia coli from patients in the Chilean aquacultural region were significantly enriched for qnrB (including a novel qnrB gene), qnrS, qnrA and aac(6')-1b, compared with isolates from New York City. Sequences of qnrA1, qnrB1 and qnrS1 in quinolone-resistant Chilean E. coli and Chilean marine bacteria were identical, suggesting horizontal gene transfer between antimicrobial-resistant marine bacteria and human pathogens. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  10. Common and rare variants in the exons and regulatory regions of osteoporosis-related genes improve osteoporotic fracture risk prediction.

    Lee, Seung Hun; Kang, Moo Il; Ahn, Seong Hee; Lim, Kyeong-Hye; Lee, Gun Eui; Shin, Eun-Soon; Lee, Jong-Eun; Kim, Beom-Jun; Cho, Eun-Hee; Kim, Sang-Wook; Kim, Tae-Ho; Kim, Hyun-Ju; Yoon, Kun-Ho; Lee, Won Chul; Kim, Ghi Su; Koh, Jung-Min; Kim, Shin-Yoon

    2014-11-01

    Osteoporotic fracture risk is highly heritable, but genome-wide association studies have explained only a small proportion of the heritability to date. Genetic data may improve prediction of fracture risk in osteopenic subjects and assist early intervention and management. To detect common and rare variants in coding and regulatory regions related to osteoporosis-related traits, and to investigate whether genetic profiling improves the prediction of fracture risk. This cross-sectional study was conducted in three clinical units in Korea. Postmenopausal women with extreme phenotypes (n = 982) were used for the discovery set, and 3895 participants were used for the replication set. We performed targeted resequencing of 198 genes. Genetic risk scores from common variants (GRS-C) and from common and rare variants (GRS-T) were calculated. Nineteen common variants in 17 genes (of the discovered 34 functional variants in 26 genes) and 31 rare variants in five genes (of the discovered 87 functional variants in 15 genes) were associated with one or more osteoporosis-related traits. Accuracy of fracture risk classification was improved in the osteopenic patients by adding GRS-C to fracture risk assessment models (6.8%; P risk in an osteopenic individual.

  11. Synaptic genes are extensively downregulated across multiple brain regions in normal human aging and Alzheimer’s disease

    Berchtold, Nicole C.; Coleman, Paul D.; Cribbs, David H.; Rogers, Joseph; Gillen, Daniel L.; Cotman, Carl W.

    2014-01-01

    Synapses are essential for transmitting, processing, and storing information, all of which decline in aging and Alzheimer’s disease (AD). Because synapse loss only partially accounts for the cognitive declines seen in aging and AD, we hypothesized that existing synapses might undergo molecular changes that reduce their functional capacity. Microarrays were used to evaluate expression profiles of 340 synaptic genes in aging (20–99 years) and AD across 4 brain regions from 81 cases. The analysis revealed an unexpectedly large number of significant expression changes in synapse-related genes in aging, with many undergoing progressive downregulation across aging and AD. Functional classification of the genes showing altered expression revealed that multiple aspects of synaptic function are affected, notably synaptic vesicle trafficking and release, neurotransmitter receptors and receptor trafficking, postsynaptic density scaffolding, cell adhesion regulating synaptic stability, and neuromodulatory systems. The widespread declines in synaptic gene expression in normal aging suggests that function of existing synapses might be impaired, and that a common set of synaptic genes are vulnerable to change in aging and AD. PMID:23273601

  12. TPH2 gene polymorphisms in the regulatory region are associated with paranoid schizophrenia in Northern Han Chinese.

    Xu, X M; Ding, M; Pang, H; Wang, B J

    2014-03-12

    In the last years, serotonin (5-HT) has been related with the pathophysiology of several psychiatric disorders, including schizophrenia. Thus, genes related to the serotonergic (5-HTergic) system are good candidate genes for schizophrenia. The rate-limiting enzyme of 5-HT synthesis is tryptophan hydroxylase 2 (TPH2). Single nucleotide polymorphisms (SNPs) in the regulatory regions of TPH2 gene may affect gene expression and biosynthesis of 5-HT triggering to various neuropsychiatric disorders related to 5-HT dysfunction. The present study explored the association of SNPs within the TPH2 gene with paranoid schizophrenia in Han Chinese. A total of 164 patients with schizophrenia and 244 healthy controls were genotyped for six TPH2 SNPs (rs4570625, rs11178997, rs11178998, rs41317118, rs17110747, and rs41317114). Significant group differences were observed in the allele and genotype frequencies of rs4570625 and in the frequencies of GTA and TTA haplotypes corresponding to rs4570625-rs11178997-rs11178998. Our findings suggest that common genetic variations of TPH2 are likely to contribute to genetic susceptibility to paranoid schizophrenia in Han Chinese. Further studies in larger samples are needed to replicate this association.

  13. Acute and repeated ECS treatment increases CRF, POMC and PENK gene expression in selected regions of the rat hypothalamus.

    Garcia-Garcia, L; Llewellyn-Jones, V; Fernandez Fernandez, I; Fuentes, J A; Manzanares, J

    1998-01-05

    The purpose of this study was to investigate the effects of acute and repeated electroconvulsive shock (ECS) on corticotropin releasing factor (CRF), proopiomelanocortin (POMC) and proenkephalin (PENK) gene expression in selected regions of the brain and pituitary of the rat. Acute ECS increased CRF gene expression in the paraventricular nucleus (PVN) by 20%, an effect that was further enhanced to 38% when rats received repeated ECS treatment. Acute and repeated ECS increased POMC gene expression in the arcuate nucleus (ARC) by 49-59% but failed to alter these mRNA levels in the anterior lobe (AL) of the pituitary gland. PENK gene expression was increased by 35% in the nucleus accumbens (NA) and by 180% the ventromedial nucleus (VMN) after acute or repeated ECS treatment but no significant changes were found in the PVN or striatum (ST). Taken together, these results indicate a differential CRF and opioid gene expression regulation after acute or repeated ECS treatment that may be relevant to their therapeutic or side effects in depression.

  14. Mutations inside rifampicin-resistance determining region of rpoB gene associated with rifampicin-resistance in Mycobacterium tuberculosis.

    Zaw, Myo T; Emran, Nor A; Lin, Zaw

    2018-04-26

    Rifampicin (RIF) plays a pivotal role in the treatment of tuberculosis due to its bactericidal effects. Because the action of RIF is on rpoB gene encoding RNA polymerase β subunit, 95% of RIF resistant mutations are present in rpoB gene. The majority of the mutations in rpoB gene are found within an 81bp RIF-resistance determining region (RRDR). Literatures on RIF resistant mutations published between 2010 and 2016 were thoroughly reviewed. The most commonly mutated codons in RRDR of rpoB gene are 531, 526 and 516. The possibilities of absence of mutation in RRDR of rpoB gene in MDR-TB isolates in few studies was due to existence of other rare rpoB mutations outside RRDR or different mechanism of rifampicin resistance. Molecular methods which can identify extensive mutations associated with multiple anti-tuberculous drugs are in urgent need so that the research on drug resistant mutations should be extended. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  15. Single nucleotide polymorphisms (SNPs in coding regions of canine dopamine- and serotonin-related genes

    Lingaas Frode

    2008-01-01

    Full Text Available Abstract Background Polymorphism in genes of regulating enzymes, transporters and receptors of the neurotransmitters of the central nervous system have been associated with altered behaviour, and single nucleotide polymorphisms (SNPs represent the most frequent type of genetic variation. The serotonin and dopamine signalling systems have a central influence on different behavioural phenotypes, both of invertebrates and vertebrates, and this study was undertaken in order to explore genetic variation that may be associated with variation in behaviour. Results Single nucleotide polymorphisms in canine genes related to behaviour were identified by individually sequencing eight dogs (Canis familiaris of different breeds. Eighteen genes from the dopamine and the serotonin systems were screened, revealing 34 SNPs distributed in 14 of the 18 selected genes. A total of 24,895 bp coding sequence was sequenced yielding an average frequency of one SNP per 732 bp (1/732. A total of 11 non-synonymous SNPs (nsSNPs, which may be involved in alteration of protein function, were detected. Of these 11 nsSNPs, six resulted in a substitution of amino acid residue with concomitant change in structural parameters. Conclusion We have identified a number of coding SNPs in behaviour-related genes, several of which change the amino acids of the proteins. Some of the canine SNPs exist in codons that are evolutionary conserved between five compared species, and predictions indicate that they may have a functional effect on the protein. The reported coding SNP frequency of the studied genes falls within the range of SNP frequencies reported earlier in the dog and other mammalian species. Novel SNPs are presented and the results show a significant genetic variation in expressed sequences in this group of genes. The results can contribute to an improved understanding of the genetics of behaviour.

  16. Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes.

    Marone, Daniela; Russo, Maria A; Laidò, Giovanni; De Vita, Pasquale; Papa, Roberto; Blanco, Antonio; Gadaleta, Agata; Rubiales, Diego; Mastrangelo, Anna M

    2013-08-19

    Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2-6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore

  17. Identification of an ICP27-responsive element in the coding region of a herpes simplex virus type 1 late gene.

    Sedlackova, Lenka; Perkins, Keith D; Meyer, Julia; Strain, Anna K; Goldman, Oksana; Rice, Stephen A

    2010-03-01

    During productive herpes simplex virus type 1 (HSV-1) infection, a subset of viral delayed-early (DE) and late (L) genes require the immediate-early (IE) protein ICP27 for their expression. However, the cis-acting regulatory sequences in DE and L genes that mediate their specific induction by ICP27 are unknown. One viral L gene that is highly dependent on ICP27 is that encoding glycoprotein C (gC). We previously demonstrated that this gene is posttranscriptionally transactivated by ICP27 in a plasmid cotransfection assay. Based on our past results, we hypothesized that the gC gene possesses a cis-acting inhibitory sequence and that ICP27 overcomes the effects of this sequence to enable efficient gC expression. To test this model, we systematically deleted sequences from the body of the gC gene and tested the resulting constructs for expression. In so doing, we identified a 258-bp "silencing element" (SE) in the 5' portion of the gC coding region. When present, the SE inhibits gC mRNA accumulation from a transiently transfected gC gene, unless ICP27 is present. Moreover, the SE can be transferred to another HSV-1 gene, where it inhibits mRNA accumulation in the absence of ICP27 and confers high-level expression in the presence of ICP27. Thus, for the first time, an ICP27-responsive sequence has been identified in a physiologically relevant ICP27 target gene. To see if the SE functions during viral infection, we engineered HSV-1 recombinants that lack the SE, either in a wild-type (WT) or ICP27-null genetic background. In an ICP27-null background, deletion of the SE led to ICP27-independent expression of the gC gene, demonstrating that the SE functions during viral infection. Surprisingly, the ICP27-independent gC expression seen with the mutant occurred even in the absence of viral DNA synthesis, indicating that the SE helps to regulate the tight DNA replication-dependent expression of gC.

  18. Association of polymorphisms of interleukin-18 gene promoter region with polycystic ovary syndrome in chinese population

    Li Mei-zhi

    2010-10-01

    Full Text Available Abstract Background Recent research shows that polycystic ovary syndrome (PCOS may have an association with low-grade chronic inflammation, and that PCOS may induce an increase in serum interleukin-18 (IL-18 levels. Methods To investigate the polymorphisms of the IL-18 gene promoters with PCOS, two single nucleotide polymorphisms (SNPs in the promoter of the IL-18 gene (at positions -607C/A and -137G/C in 118 Chinese women with PCOS and 79 controls were evaluated using polymerase chain reaction (PCR. Results No significant differences were found in the genotype distribution, allele frequency and haplotype frequency between the PCOS and control groups. Further analysis demonstrated a relationship between IL-18 gene promoter polymorphisms and PCOS insulin resistance (IR. Regarding the -137 allele frequency, G and C allele frequencies were 93.5% and 6.5%, respectively, in the PCOS with IR patients; G and C allele frequencies were 85.4% and 14.6%, respectively, in PCOS patients without IR (chi2 = 3.601, P = 0.048. Conclusions The presence of a polymorphism in the IL-18 gene was found to have no correlation with the occurrence of PCOS. Carriage of the C allele at position -137 in the promoter of the IL-18 gene may play a protective role from the development of PCOS IR.

  19. Determination of transcriptional units and gene products from the ftsA region of Escherichia coli.

    Lutkenhaus, J F; Wu, H C

    1980-01-01

    Lambda transducing phage gamma 16-2 carries the genes envA, ftsZ, ftsA, ddl, and murC and directs the synthesis of six unique proteins in ultraviolet-irradiated cells. Various derivatives of gamma 16-2 carrying smaller segments of the bacterial deoxyribonucleic acid have also been analyzed for their capacity to direct protein synthesis in ultraviolet-irradiated cells. These results, in combination with genetic results, have allowed the gene product of each of these genes to be assigned. In addition, an unidentified gene was located counterclockwise to murC between murC and murF. Analysis of the direction of transcription indicates that murC, ddl, ftsA, and ftsZ are transcribed clockwise on the Escherichia coli genetic map, and envA is transcribed counterclockwise. In addition, it is shown that each of the genes envA, ftsZ, and ftsA can be expressed independently. Images PMID:6447690

  20. Characterization of the immuno dominant regions within gp41 of env gene of HIV in Pakistan

    Nisar, L.; Qadir, M.I.; Nisa, T.; Malik, S.A.; Tabassum, N.

    2011-01-01

    Objective of the present study was to characterize the immuno dominant sequences of gp41 in HIV strain in Pakistani population so that vaccine may be prepared based upon these regions. A total of 25 specimens were collected from HIV patients of different areas of Pakistan. The viral RNA was isolated using QIAamp MinElute Spin Kit manufactured by Quiagen, California, USA. RT-PCR was done for amplification of the required region and confirmed by gel electrophoresis. The nucleotides of the required regions were sequenced using Big Dye terminator. Less than 20% of the specimens had mutations in immuno dominant regions, so it may be concluded that immuno dominant regions of gp41 in HIV strain in Pakistani population are conservatives and vaccine based upon these regions may prove active immunization against the disease. (author)

  1. Characterization of the immuno dominant regions within gp41 of env gene of HIV in Pakistan

    Nisar, L; Qadir, M I; Nisa, T; Malik, S A; Tabassum, N

    2011-08-15

    Objective of the present study was to characterize the immuno dominant sequences of gp41 in HIV strain in Pakistani population so that vaccine may be prepared based upon these regions. A total of 25 specimens were collected from HIV patients of different areas of Pakistan. The viral RNA was isolated using QIAamp MinElute Spin Kit manufactured by Quiagen, California, USA. RT-PCR was done for amplification of the required region and confirmed by gel electrophoresis. The nucleotides of the required regions were sequenced using Big Dye terminator. Less than 20% of the specimens had mutations in immuno dominant regions, so it may be concluded that immuno dominant regions of gp41 in HIV strain in Pakistani population are conservatives and vaccine based upon these regions may prove active immunization against the disease. (author)

  2. Mutation analysis of the human CYP3A4 gene 5' regulatory region: population screening using non-radioactive SSCP.

    Hamzeiy, Hossein; Vahdati-Mashhadian, Nasser; Edwards, Helen J; Goldfarb, Peter S

    2002-03-20

    Human CYP3A4 is the major cytochrome P450 isoenzyme in adult human liver and is known to metabolise many xenobiotic and endogenous compounds. There is substantial inter-individual variation in the hepatic levels of CYP3A4. Although, polymorphic mutations have been reported in the 5' regulatory region of the CYP3A4 gene, those that have been investigated so far do not appear to have any effect on gene expression. To determine whether other mutations exist in this region of the gene, we have performed a new population screen on a panel of 101 human DNA samples. A 1140 bp section of the 5' proximal regulatory region of the CYP3A4 gene, containing numerous regulatory motifs, was amplified from genomic DNA as three overlapping segments. The 300 bp distal enhancer region at -7.9kb containing additional regulatory motifs was also amplified. Mutation analysis of the resulting PCR products was carried out using non-radioactive single strand conformation polymorphism (SSCP) and confirmatory sequencing of both DNA strands in those samples showing extra SSCP bands. In addition to detection of the previously reported CYP3A4*1B allele in nine subjects, three novel alleles were found: CYP3A4*1E (having a T-->A transversion at -369 in one subject), CYP3A4*1F (having a C-->G tranversion at -747 in 17 subjects) and CYP3A4*15B containing a nine-nucleotide insertion between -845 and -844 linked to an A-->G transition at -392 and a G-->A transition in exon 6 (position 485 in the cDNA) in one subject. All the novel alleles were heterozygous. No mutations were found in the upstream distal enhancer region. Our results clearly indicate that this rapid and simple SSCP approach can reveal mutant alleles in drug metabolising enzyme genes. Detection and determination of the frequency of novel alleles in CYP3A4 will assist investigation of the relationship between genotype, xenobiotic metabolism and toxicity in the CYP3A family of isoenzymes.

  3. Differential Expression of FosB Proteins and Potential Target Genes in Select Brain Regions of Addiction and Depression Patients.

    Paula A Gajewski

    Full Text Available Chronic exposure to stress or drugs of abuse has been linked to altered gene expression throughout the body, and changes in gene expression in discrete brain regions are thought to underlie many psychiatric diseases, including major depressive disorder and drug addiction. Preclinical models of these disorders have provided evidence for mechanisms of this altered gene expression, including transcription factors, but evidence supporting a role for these factors in human patients has been slow to emerge. The transcription factor ΔFosB is induced in the prefrontal cortex (PFC and hippocampus (HPC of rodents in response to stress or cocaine, and its expression in these regions is thought to regulate their "top down" control of reward circuitry, including the nucleus accumbens (NAc. Here, we use biochemistry to examine the expression of the FosB family of transcription factors and their potential gene targets in PFC and HPC postmortem samples from depressed patients and cocaine addicts. We demonstrate that ΔFosB and other FosB isoforms are downregulated in the HPC but not the PFC in the brains of both depressed and addicted individuals. Further, we show that potential ΔFosB transcriptional targets, including GluA2, are also downregulated in the HPC but not PFC of cocaine addicts. Thus, we provide the first evidence of FosB gene expression in human HPC and PFC in these psychiatric disorders, and in light of recent findings demonstrating the critical role of HPC ΔFosB in rodent models of learning and memory, these data suggest that reduced ΔFosB in HPC could potentially underlie cognitive deficits accompanying chronic cocaine abuse or depression.

  4. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  5. Polymorphism of the promoter region and exon 1 of the CTLA4 gene in endemic pemphigus foliaceus (fogo selvagem

    D.P. Pavoni

    2006-09-01

    Full Text Available Endemic pemphigus foliaceus (EPF is an autoimmune bullous skin disease characterized by acantholysis and antibodies against a desmosomal protein, desmoglein 1. Genetic and environmental factors contribute to development of this multifactorial disease. HLA class II and some cytokine gene polymorphisms are the only genetic markers thus far known to be associated with susceptibility to or protection from EPF. The cytotoxic T-lymphocyte antigen-4 gene (CTLA4 encodes a key immunoreceptor molecule that regulates and inhibits T-cell proliferation. It participates in the regulatory process controlling autoreactivity and therefore has been considered a strong candidate gene in autoimmune diseases. In the search for genes that might influence EPF pathogenesis, we analyzed variants of the CTLA4 gene in a sample of 118 patients and 291 controls from a Brazilian population. This is the first study investigating the possible role of polymorphisms of the 2q33 chromosomal region in differential susceptibility to pemphigus foliaceus. Promoter region and exon 1 single nucleotide polymorphisms -318 (C,T and 49 (A,G were genotyped using sequence-specific oligonucleotide probes after amplification by the polymerase chain reaction. The allelic and genotypic frequencies did not differ significantly between the patient and the control groups (-318T: 9.8 and 10.9%, 49G: 33.0 and 35.2% were the allelic frequencies in patients and controls, respectively. In addition, no significant difference was found when the patient and control population samples were stratified by the presence of HLA-DRB1 alleles. We conclude that the CTLA4 -318 (C,T and 49 (A,G polymorphisms do not play a major role in EPF development.

  6. Orthologous microRNA genes are located in cancer-associated genomic regions in human and mouse.

    Igor V Makunin

    Full Text Available BACKGROUND: MicroRNAs (miRNAs are short non-coding RNAs that regulate differentiation and development in many organisms and play an important role in cancer. METHODOLOGY/PRINCIPAL FINDINGS: Using a public database of mapped retroviral insertion sites from various mouse models of cancer we demonstrate that MLV-derived retroviral inserts are enriched in close proximity to mouse miRNA loci. Clustered inserts from cancer-associated regions (Common Integration Sites, CIS have a higher association with miRNAs than non-clustered inserts. Ten CIS-associated miRNA loci containing 22 miRNAs are located within 10 kb of known CIS insertions. Only one CIS-associated miRNA locus overlaps a RefSeq protein-coding gene and six loci are located more than 10 kb from any RefSeq gene. CIS-associated miRNAs on average are more conserved in vertebrates than miRNAs associated with non-CIS inserts and their human homologs are also located in regions perturbed in cancer. In addition we show that miRNA genes are enriched around promoter and/or terminator regions of RefSeq genes in both mouse and human. CONCLUSIONS/SIGNIFICANCE: We provide a list of ten miRNA loci potentially involved in the development of blood cancer or brain tumors. There is independent experimental support from other studies for the involvement of miRNAs from at least three CIS-associated miRNA loci in cancer development.

  7. Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

    Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S. [Univ. of Bonn (Germany)] [and others

    1995-10-09

    In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains a functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.

  8. Identification, characterization and functional analysis of regulatory region of nanos gene from half-smooth tongue sole (Cynoglossus semilaevis).

    Huang, Jinqiang; Li, Yongjuan; Shao, Changwei; Wang, Na; Chen, Songlin

    2017-06-20

    The nanos gene encodes an RNA-binding zinc finger protein, which is required in the development and maintenance of germ cells. However, there is very limited information about nanos in flatfish, which impedes its application in fish breeding. In this study, we report the molecular cloning, characterization and functional analysis of the 3'-untranslated region of the nanos gene (Csnanos) from half-smooth tongue sole (Cynoglossus semilaevis), which is an economically important flatfish in China. The 1233-bp cDNA sequence, 1709-bp genomic sequence and flanking sequences (2.8-kb 5'- and 1.6-kb 3'-flanking regions) of Csnanos were cloned and characterized. Sequence analysis revealed that CsNanos shares low homology with Nanos in other species, but the zinc finger domain of CsNanos is highly similar. Phylogenetic analysis indicated that CsNanos belongs to the Nanos2 subfamily. Csnanos expression was widely detected in various tissues, but the expression level was higher in testis and ovary. During early development and sex differentiation, Csnanos expression exhibited a clear sexually dimorphic pattern, suggesting its different roles in the migration and differentiation of primordial germ cells (PGCs). Higher expression levels of Csnanos mRNA in normal females and males than in neomales indicated that the nanos gene may play key roles in maintaining the differentiation of gonad. Moreover, medaka PGCs were successfully labeled by the microinjection of synthesized mRNA consisting of green fluorescence protein and the 3'-untranslated region of Csnanos. These findings provide new insights into nanos gene expression and function, and lay the foundation for further study of PGC development and applications in tongue sole breeding. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. CAGE-defined promoter regions of the genes implicated in Rett Syndrome

    Vitezic, Morana; Bertin, Nicolas; Andersson, Robin

    2014-01-01

    BACKGROUND: Mutations in three functionally diverse genes cause Rett Syndrome. Although the functions of Forkhead box G1 (FOXG1), Methyl CpG binding protein 2 (MECP2) and Cyclin-dependent kinase-like 5 (CDKL5) have been studied individually, not much is known about their relation to each other...... reveal the predominantly used transcription start sites (TSSs) for each gene including novel transcription start sites for FOXG1. We show that FOXG1 expression is poorly correlated with the expression of MECP2 and CDKL5. We identify promoter shapes for each TSS, the predicted location of enhancers...

  10. Exclusion of candidate genes from the chromosome 1q juvenile glaucoma region and mapping of the peripheral cannabis receptor gene (CNR2) to chromosome 1

    Sunden, S.L.F.; Nichols, B.E.; Alward, W.L.M. [Univ. of Iowa, Iowa City, IA (United States)] [and others

    1994-09-01

    Juvenile onset primary open angle glaucoma has been mapped by linkage to 1q21-q31. Several candidate genes were evaluated in the same family used to identify the primary linkage. Atrionatriuretic peptide receptor A (NPR1) and laminin C1 (LAMC1) have been previously mapped to this region and could putatively play a role in the pathogenesis of glaucoma. A third gene, the peripheral cannabis receptor (CNR2) was not initially mapped in humans but was a candidate because of the relief that cannabis affords some patients with primary open angle glaucoma. Microsatellites associated with NPR1 and LAMC1 revealed multiple recombinations in affected members of this pedigree. CNR2 was shown to be on chromosome 1 by PCR amplification of a 150 bp fragment of the 3{prime} untranslated region in monochromosomal somatic cell hybrids (NIGMS panel No. 2). These primers also revealed a two allele single strand conformation polymorphism which showed multiple recombinants with juvenile onset primary open angle glaucoma in large pedigrees, segregating this disorder. The marker was then mapped to 1p34-p36 by linkage, with the most likely location between liver alkaline phosphatase (ALPL) and alpha-L-1 fucosidase (FUCA1).

  11. An experimental and analytical study on the feasibility of SMA spring driven actuation of an iris mechanism

    Rajan, Aravindh; Abouseada, Mostafa; Manghaipathy, Pavithra; Ozalp, Nesrin; Majid, Feras Abdul; Salem, Ayman; Srinivasa, Arun

    2016-01-01

    Highlights: • An iris mechanism proposed in response to fluctuations in solar energy. • Iris motion controlled with the use of Nickel–Titanium Shape Memory Alloy springs. • Variation of the force exerted by SMA spring w.r.t. temperature tested experimentally. • An analytical expression that relates the aperture area and crank rotation is given. • SMA springs showed promising actuation mechanism as a replacement to motor. - Abstract: Variation in incoming solar energy adversely affects the temperature inside a solar reactor and lowers its efficiency. Therefore, it is important to develop a mechanism that can maintain semi-constant temperatures inside the reactor from sunrise to sunset. In this paper, we present an iris mechanism that reduces or enlarges its circular opening with the use of Nickel–Titanium Shape Memory Alloy (SMA) springs. SMA springs possess memory of their shapes at certain temperatures. Hence, by controlling the temperature of the spring, it is possible to exert different forces that may then be transferred to the variable aperture mechanism. In this study, variation of the force exerted by an SMA spring with respect to temperature was experimentally tested and the viability of an SMA spring’s use in actuating an iris mechanism aperture was examined. In order to simulate conditions under fluctuating solar radiation, a 7 kW solar simulator was used in experiments at varying power levels. It was observed that SMA springs are promising as a replacement of the actuation mechanism driven by a motor.

  12. Fabrication and characterization of a dual-joint smart inhaler nozzle actuated by embedded SMA wires

    Furst, Stephen J; Seelecke, Stefan

    2014-01-01

    Shape memory alloy (SMA) wires offer a novel solution for many embedded actuator and sensor applications. Small SMA wires in particular can be heated with a relatively low electric current, cool rapidly, and serve as a sensor thanks to a measurable resistance change. However, the challenges of fabrication with SMA actuator wires as well as their hysteretic nature have prevented them from finding mainstream application. This work focuses on the process used to control the fabrication of an SMA-actuated adaptive nozzle for the previously presented Smart Inhaler application. The elements of nozzle design that facilitate fabrication are summarized and an assembly setup and procedure is presented for controlling the stress and strain in the SMA wires while they are attached to the nozzle structure via temperature-resistant adhesives. Finally, the performance of the nozzle is characterized by measuring the changes in nozzle deflection and SMA wire strain and resistance in response to a controlled Joule heating power input. Results show controlling pre-stress in the wires during assembly can lead to reproducible behavior, an input heating power serves to control nozzle deflection, and a measured resistance can provide a useful sensor of SMA wire strain and nozzle joint deflection. (paper)

  13. Characterization of Antimicrobial Resistance Patterns and Detection of Virulence Genes in Campylobacter Isolates in Italy

    Di Giannatale, Elisabetta; Di Serafino, Gabriella; Zilli, Katiuscia; Alessiani, Alessandra; Sacchini, Lorena; Garofolo, Giuliano; Aprea, Giuseppe; Marotta, Francesca

    2014-01-01

    Campylobacter has developed resistance to several antimicrobial agents over the years, including macrolides, quinolones and fluoroquinolones, becoming a significant public health hazard. A total of 145 strains derived from raw milk, chicken faeces, chicken carcasses, cattle faeces and human faeces collected from various Italian regions, were screened for antimicrobial susceptibility, molecular characterization (SmaI pulsed-field gel electrophoresis) and detection of virulence genes (sequencing and DNA microarray analysis). The prevalence of C. jejuni and C. coli was 62.75% and 37.24% respectively. Antimicrobial susceptibility revealed a high level of resistance for ciprofloxacin (62.76%), tetracycline (55.86%) and nalidixic acid (55.17%). Genotyping of Campylobacter isolates using PFGE revealed a total of 86 unique SmaI patterns. Virulence gene profiles were determined using a new microbial diagnostic microarray composed of 70-mer oligonucleotide probes targeting genes implicated in Campylobacter pathogenicity. Correspondence between PFGE and microarray clusters was observed. Comparisons of PFGE and virulence profiles reflected the high genetic diversity of the strains examined, leading us to speculate different degrees of pathogenicity inside Campylobacter populations. PMID:24556669

  14. Gene

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  15. Regulatory regions in the rat lactase-phlorizin hydrolase gene that control cell-specific expression

    Verhave, Menno; Krasinski, Stephen D.; Christian, Sara I.; van Schaik, Sandrijn; van den Brink, Gijs R.; Doting, Edwina M. H.; Maas, Saskia M.; Wolthers, Katja C.; Grand, Richard J.; Montgomery, Robert K.

    2004-01-01

    OBJECTIVES: Lactase-phlorizin hydrolase (LPH) is an enterocyte-specific gene whose expression has been well-characterized, not only developmentally but also along the crypt-villus axis and along the length of the small bowel. Previous studies from the authors' laboratory have demonstrated that 2 kb

  16. A novel polymorphism in the coding region of the vasopressin type 2 receptor gene

    J.L. Rocha

    1997-04-01

    Full Text Available Nephrogenic diabetes insipidus (NDI is a rare disease characterized by renal inability to respond properly to arginine vasopressin due to mutations in the vasopressin type 2 receptor (V2(R gene in affected kindreds. In most kindreds thus far reported, the mode of inheritance follows an X chromosome-linked recessive pattern although autosomal-dominant and autosomal-recessive modes of inheritance have also been described. Studies demonstrating mutations in the V2(R gene in affected kindreds that modify the receptor structure, resulting in a dys- or nonfunctional receptor have been described, but phenotypically indistinguishable NDI patients with a structurally normal V2(R gene have also been reported. In the present study, we analyzed exon 3 of the V2(R gene in 20 unrelated individuals by direct sequencing. A C®T alteration in the third position of codon 331 (AGC®AGT, which did not alter the encoded amino acid, was found in nine individuals, including two unrelated patients with NDI. Taken together, these observations emphasize the molecular heterogeneity of a phenotypically homogeneous syndrome

  17. Synteny in toxigenic Fusarium species: the fumonisin gene cluster and the mating type region as examples

    Waalwijk, C.; Lee, van der T.A.J.; Vries, de P.M.; Hesselink, T.; Arts, J.; Kema, G.H.J.

    2004-01-01

    A comparative genomic approach was used to study the mating type locus and the gene cluster involved in toxin production ( fumonisin) in Fusarium proliferatum, a pathogen with a wide host range and a complex toxin profile. A BAC library, generated from F. proliferatum isolate ITEM 2287, was used to

  18. Haplotypes in the promoter region of the CIDEC gene associated with growth traits in Nanyang cattle

    Cell death-inducing DFFA-like effector c (CIDEC, also known as Fsp27) has emerged as an important regulator of metabolism associated with lipodystrophy, diabetes, and hepatic steatosis. It is required for unilocular lipid droplet formation and optimal energy storage. The mechanism between this gene ...

  19. Genetic interactions between Shox2 and Hox genes during the regional growth and development of the mouse limb.

    Neufeld, Stanley J; Wang, Fan; Cobb, John

    2014-11-01

    The growth and development of the vertebrate limb relies on homeobox genes of the Hox and Shox families, with their independent mutation often giving dose-dependent effects. Here we investigate whether Shox2 and Hox genes function together during mouse limb development by modulating their relative dosage and examining the limb for nonadditive effects on growth. Using double mRNA fluorescence in situ hybridization (FISH) in single embryos, we first show that Shox2 and Hox genes have associated spatial expression dynamics, with Shox2 expression restricted to the proximal limb along with Hoxd9 and Hoxa11 expression, juxtaposing the distal expression of Hoxa13 and Hoxd13. By generating mice with all possible dosage combinations of mutant Shox2 alleles and HoxA/D cluster deletions, we then show that their coordinated proximal limb expression is critical to generate normally proportioned limb segments. These epistatic interactions tune limb length, where Shox2 underexpression enhances, and Shox2 overexpression suppresses, Hox-mutant phenotypes. Disruption of either Shox2 or Hox genes leads to a similar reduction in Runx2 expression in the developing humerus, suggesting their concerted action drives cartilage maturation during normal development. While we furthermore provide evidence that Hox gene function influences Shox2 expression, this regulation is limited in extent and is unlikely on its own to be a major explanation for their genetic interaction. Given the similar effect of human SHOX mutations on regional limb growth, Shox and Hox genes may generally function as genetic interaction partners during the growth and development of the proximal vertebrate limb. Copyright © 2014 by the Genetics Society of America.

  20. No evidence for promoter region methylation of the succinate dehydrogenase and fumarate hydratase tumour suppressor genes in breast cancer

    Dobrovic Alexander

    2009-09-01

    Full Text Available Abstract Background Succinate dehydrogenase (SDH and fumarate hydratase (FH are tricarboxylic acid (TCA cycle enzymes that are also known to act as tumour suppressor genes. Increased succinate or fumarate levels as a consequence of SDH and FH deficiency inhibit hypoxia inducible factor-1α (HIF-1α prolyl hydroxylases leading to sustained HIF-1α expression in tumours. Since HIF-1α is frequently expressed in breast carcinomas, DNA methylation at the promoter regions of the SDHA, SDHB, SDHC and SDHD and FH genes was evaluated as a possible mechanism in silencing of SDH and FH expression in breast carcinomas. Findings No DNA methylation was identified in the promoter regions of the SDHA, SDHB, SDHC, SDHD and FH genes in 72 breast carcinomas and 10 breast cancer cell lines using methylation-sensitive high resolution melting which detects both homogeneous and heterogeneous methylation. Conclusion These results show that inactivation via DNA methylation of the promoter CpG islands of SDH and FH is unlikely to play a major role in sporadic breast carcinomas.

  1. Inflammatory peeling skin syndrome caused by homozygous genomic deletion in the PSORS1 region encompassing the CDSN gene.

    Ishida-Yamamoto, Akemi; Furio, Laetitia; Igawa, Satomi; Honma, Masaru; Tron, Elodie; Malan, Valerie; Murakami, Masamoto; Hovnanian, Alain

    2014-01-01

    Peeling skin syndrome (PSS) type B is a rare recessive genodermatosis characterized by lifelong widespread, reddish peeling of the skin with pruritus. The disease is caused by small-scale mutations in the Corneodesmosin gene (CDSN) leading to premature termination codons. We report for the first time a Japanese case resulting from complete deletion of CDSN. Corneodesmosin was undetectable in the epidermis, and CDSN was unamplifiable by PCR. QMPSF analysis demonstrated deletion of CDSN exons inherited from each parent. Deletion mapping using microsatellite haplotyping, CGH array and PCR analysis established that the genomic deletion spanned 49-72 kb between HCG22 and TCF19, removing CDSN as well as five other genes within the psoriasis susceptibility region 1 (PSORS1) on 6p21.33. This observation widens the spectrum of molecular defects underlying PSS type B and shows that loss of these five genes from the PSORS1 region does not result in an additional cutaneous phenotype. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  2. Genetic variants in promoters and coding regions of the muscle glycogen synthase and the insulin-responsive GLUT4 genes in NIDDM

    Bjørbaek, C; Echwald, Søren Morgenthaler; Hubricht, P

    1994-01-01

    To examine the hypothesis that variants in the regulatory or coding regions of the glycogen synthase (GS) and insulin-responsive glucose transporter (GLUT4) genes contribute to insulin-resistant glucose processing of muscle from non-insulin-dependent diabetes mellitus (NIDDM) patients, promoter...... volunteers. By applying inverse polymerase chain reaction and direct DNA sequencing, 532 base pairs (bp) of the GS promoter were identified and the transcriptional start site determined by primer extension. SSCP scanning of the promoter region detected five single nucleotide substitutions, positioned at 42......'-untranslated region, and the coding region of the GLUT4 gene showed four polymorphisms, all single nucleotide substitutions, positioned at -581, 1, 30, and 582. None of the three changes in the regulatory region of the gene had any major influence on expression of the GLUT4 gene in muscle. The variant at 582...

  3. RNA polymerase II interacts with the promoter region of the noninduced hsp70 gene in Drosophila melanogaster cells

    Gilmour, D.S.; Lis, J.T.

    1986-01-01

    By using a protein-DNA cross-linking method, we examined the in vivo distribution of RNA polymerase II on the hsp70 heat shock gene in Drosophila melanogaster Schneider line 2 cells. In heat shock-induced cells, a high level of RNA polymerase II was detected on the entire gene, while in noninduced cells, the RNA polymerase II was confined to the 5' end of the hsp70 gene, predominantly between nucleotides -12 and +65 relative to the start of transcription. This association of RNA polymerase II was apparent whether the cross-linking was performed by a 10-min UV irradiation of chilled cells with mercury vapor lamps or by a 40-microsecond irradiation of cells with a high-energy xenon flash lamp. We hypothesize that RNA polymerase II has access to, and a high affinity for, the promoter region of this gene before induction, and this poised RNA polymerase II may be critical in the mechanism of transcription activation

  4. Sex- and brain region-specific patterns of gene expression associated with socially-mediated puberty in a eusocial mammal.

    Mariela Faykoo-Martinez

    Full Text Available The social environment can alter pubertal timing through neuroendocrine mechanisms that are not fully understood; it is thought that stress hormones (e.g., glucocorticoids or corticotropin-releasing hormone influence the hypothalamic-pituitary-gonadal axis to inhibit puberty. Here, we use the eusocial naked mole-rat, a unique species in which social interactions in a colony (i.e. dominance of a breeding female suppress puberty in subordinate animals. Removing subordinate naked mole-rats from this social context initiates puberty, allowing for experimental control of pubertal timing. The present study quantified gene expression for reproduction- and stress-relevant genes acting upstream of gonadotropin-releasing hormone in brain regions with reproductive and social functions in pre-pubertal, post-pubertal, and opposite sex-paired animals (which are in various stages of pubertal transition. Results indicate sex differences in patterns of neural gene expression. Known functions of genes in brain suggest stress as a key contributing factor in regulating male pubertal delay. Network analysis implicates neurokinin B (Tac3 in the arcuate nucleus of the hypothalamus as a key node in this pathway. Results also suggest an unappreciated role for the nucleus accumbens in regulating puberty.

  5. VEGF selectively induces Down syndrome critical region 1 gene expression in endothelial cells: a mechanism for feedback regulation of angiogenesis?

    Yao, Y.-G; Duh, Elia J.

    2004-01-01

    The Down syndrome critical region 1 (DSCR1) gene (also known as MCIP1, Adapt78) encodes a regulatory protein that binds to calcineurin catalytic A subunit and acts as a regulator of the calcineurin-mediated signaling pathway. We show in this study that DSCR1 is greatly induced in endothelial cells in response to VEGF, TNF-α, and A23187 treatment, and that this up-regulation is inhibited by inhibitors of the calcineurin-NFAT (nuclear factor of activated T cells) signaling pathway as well as by PKC inhibition and a Ca 2+ chelator. We hypothesized that the up-regulation of DSCR1 gene expression in endothelial cells could act as an endogenous feedback inhibitor for angiogenesis by regulating the calcineurin-NFAT signaling pathway. Our transient transfection analyses confirm that the overexpression of DSCR1 abrogates the up-regulation of reporter gene expression driven by both the cyclooxygenase 2 and DSCR1 promoters in response to stimulators. Our results indicate that DSCR1 up-regulation may represent a potential molecular mechanism underlying the regulation of angiogenic genes activated by the calcineurin-NFAT signaling pathway in endothelial cells

  6. Genetic Diversity of Toxoplasma gondii Strains from Different Hosts and Geographical Regions by Sequence Analysis of GRA20 Gene.

    Ning, Hong-Rui; Huang, Si-Yang; Wang, Jin-Lei; Xu, Qian-Ming; Zhu, Xing-Quan

    2015-06-01

    Toxoplasma gondii is a eukaryotic parasite of the phylum Apicomplexa, which infects all warm-blood animals, including humans. In the present study, we examined sequence variation in dense granule 20 (GRA20) genes among T. gondii isolates collected from different hosts and geographical regions worldwide. The complete GRA20 genes were amplified from 16 T. gondii isolates using PCR, sequence were analyzed, and phylogenetic reconstruction was analyzed by maximum parsimony (MP) and maximum likelihood (ML) methods. The results showed that the complete GRA20 gene sequence was 1,586 bp in length among all the isolates used in this study, and the sequence variations in nucleotides were 0-7.9% among all strains. However, removing the type III strains (CTG, VEG), the sequence variations became very low, only 0-0.7%. These results indicated that the GRA20 sequence in type III was more divergence. Phylogenetic analysis of GRA20 sequences using MP and ML methods can differentiate 2 major clonal lineage types (type I and type III) into their respective clusters, indicating the GRA20 gene may represent a novel genetic marker for intraspecific phylogenetic analyses of T. gondii.

  7. Absence of linkage of apparently single gene mediated ADHD with the human syntenic region of the mouse mutant coloboma

    Hess, E.J.; Rogan, P.K.; Domoto, M. [Pennsylvania State Univ. College of Medicine, Hershey, PA (United States)] [and others

    1995-12-18

    Attention deficit disorder (ADHD) is a complex biobehavioral phenotype which affects up to 8% of the general population and often impairs social, academic, and job performance. Its origins are heterogeneous, but a significant genetic component is suggested by family and twin studies. The murine strain, coloboma, displays a spontaneously hyperactive phenotype that is responsive to dextroamphetamine and has been proposed as a genetic model for ADHD. Coloboma is a semi-dominant mutation that is caused by a hemizygous deletion of the SNAP-25 and other genes on mouse chromosome 2q. To test the possibility that the human homolog of the mouse coloboma gene(s) could be responsible for ADHD, we have carried out linkage studies with polymorphic markers in the region syntenic to coloboma (20p11-p12). Five families in which the pattern of inheritance of ADHD appears to be autosomal dominant were studied. Segregation analysis of the traits studied suggested that the best fitting model was a sex-influenced, single gene, Mendelian pattern. Several genetic models were evaluated based on estimates of penetrance, phenocopy rate, and allele frequency derived from our patient population and those of other investigators. No significant linkage was detected between the disease locus and markers spanning this chromosome 20 interval. 39 refs., 2 figs., 1 tab.

  8. Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

    Zhang, Yan-Cong; Lin, Kui

    2015-01-01

    Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

  9. Deletion of Xpter encompassing the SHOX gene and PAR1 region in familial patients with Leri-Weill Dyschondrosteosis syndrome.

    Mutesa, L; Vanbellinghen, J F; Hellin, A C; Segers, K; Jamar, M; Pierquin, G; Bours, V

    2009-01-01

    Heterozygote deletions or mutations of pseudoautosomal 1 region (PAR1) encompassing the short stature homeobox-containing (SHOX) gene cause Leri-Weill Dyschondrosteosis (LWD), which is a dominantly inherited osteochondroplasia characterized by short stature with mesomelic shortening of the upper and lower limbs and Madelung deformity of the wrists. SHOX is expressed by both sex chromosomes in males and females and plays an important role in bone growth and development. Clinically, the LWD expression is variable and more severe in females than males due to sex differences in oestrogen levels. Here, we report two familial cases of LWD with a large Xp terminal deletion (approximately 943 kb) of distal PAR1 encompassing the SHOX gene. In addition, the proband had mental retardation which appeared to be from recessive inheritance in the family.

  10. Localization of the MEN1 gene to a small region within chromosome 11q13 by deletion mapping in tumors

    Bystroem, C.; Larsson, C.; Blomberg, C.; Nordenskjoeld, M.; Sandelin, K.; Falkmer, U.; Werner, S.; Skogseid, B.; Oeberg, K.

    1990-01-01

    The gene for multiple endocrine neoplasia type 1 (MEN1), and inherited predisposition to neuroendocrine neoplasm of the parathyroid glands, the pancreatic islet parenchyma, and the anterior pituitary gland, was recently mapped to chromosome 11q13 based on genetic linkage in families. The authors now show that the pathogenesis of MEN1-associated parathyroid lesions involves unmasking of a recessive mutation at the disease locus and that sporadic primary hyperparathyroidism shares the same mechanisms. By examination of allele losses in MEN1-associated lesions, they could define deletions of chromosome 11 and map the MEN1 locus to a small region within chromosome band 11q13, telomeric to the PYGM locus. In contrast, a low incidence of deletions involving the MEN1 gene was found in sporadic pituitary adenomas

  11. Finding Combination of Features from Promoter Regions for Ovarian Cancer-related Gene Group Classification

    Olayan, Rawan S.

    2012-12-01

    In classification problems, it is always important to use the suitable combination of features that will be employed by classifiers. Generating the right combination of features usually results in good classifiers. In the situation when the problem is not well understood, data items are usually described by many features in the hope that some of these may be the relevant or most relevant ones. In this study, we focus on one such problem related to genes implicated in ovarian cancer (OC). We try to recognize two important OC-related gene groups: oncogenes, which support the development and progression of OC, and oncosuppressors, which oppose such tendencies. For this, we use the properties of promoters of these genes. We identified potential “regulatory features” that characterize OC-related oncogenes and oncosuppressors promoters. In our study, we used 211 oncogenes and 39 oncosuppressors. For these, we identified 538 characteristic sequence motifs from their promoters. Promoters are annotated by these motifs and derived feature vectors used to develop classification models. We made a comparison of a number of classification models in their ability to distinguish oncogenes from oncosuppressors. Based on 10-fold cross-validation, the resultant model was able to separate the two classes with sensitivity of 96% and specificity of 100% with the complete set of features. Moreover, we developed another recognition model where we attempted to distinguish oncogenes and oncosuppressors as one group from other OC-related genes. That model achieved accuracy of 82%. We believe that the results of this study will help in discovering other OC-related oncogenes and oncosuppressors not identified as yet.

  12. Finding Combination of Features from Promoter Regions for Ovarian Cancer-related Gene Group Classification

    Olayan, Rawan S.

    2012-01-01

    In classification problems, it is always important to use the suitable combination of features that will be employed by classifiers. Generating the right combination of features usually results in good classifiers. In the situation when the problem is not well understood, data items are usually described by many features in the hope that some of these may be the relevant or most relevant ones. In this study, we focus on one such problem related to genes implicated in ovarian cancer (OC). We try to recognize two important OC-related gene groups: oncogenes, which support the development and progression of OC, and oncosuppressors, which oppose such tendencies. For this, we use the properties of promoters of these genes. We identified potential “regulatory features” that characterize OC-related oncogenes and oncosuppressors promoters. In our study, we used 211 oncogenes and 39 oncosuppressors. For these, we identified 538 characteristic sequence motifs from their promoters. Promoters are annotated by these motifs and derived feature vectors used to develop classification models. We made a comparison of a number of classification models in their ability to distinguish oncogenes from oncosuppressors. Based on 10-fold cross-validation, the resultant model was able to separate the two classes with sensitivity of 96% and specificity of 100% with the complete set of features. Moreover, we developed another recognition model where we attempted to distinguish oncogenes and oncosuppressors as one group from other OC-related genes. That model achieved accuracy of 82%. We believe that the results of this study will help in discovering other OC-related oncogenes and oncosuppressors not identified as yet.

  13. Unique Trichomonas vaginalis gene sequences identified in multinational regions of Northwest China.

    Liu, Jun; Feng, Meng; Wang, Xiaolan; Fu, Yongfeng; Ma, Cailing; Cheng, Xunjia

    2017-07-24

    Trichomonas vaginalis (T. vaginalis) is a flagellated protozoan parasite that infects humans worldwide. This study determined the sequence of the 18S ribosomal RNA gene of T. vaginalis infecting both females and males in Xinjiang, China. Samples from 73 females and 28 males were collected and confirmed for infection with T. vaginalis, a total of 110 sequences were identified when the T. vaginalis 18S ribosomal RNA gene was sequenced. These sequences were used to prepare a phylogenetic network. The rooted network comprised three large clades and several independent branches. Most of the Xinjiang sequences were in one group. Preliminary results suggest that Xinjiang T. vaginalis isolates might be genetically unique, as indicated by the sequence of their 18S ribosomal RNA gene. Low migration rate of local people in this province may contribute to a genetic conservativeness of T. vaginalis. The unique genetic feature of our isolates may suggest a different clinical presentation of trichomoniasis, including metronidazole susceptibility, T. vaginalis virus or Mycoplasma co-infection characteristics. The transmission and evolution of Xinjiang T. vaginalis is of interest and should be studied further. More attention should be given to T. vaginalis infection in both females and males in Xinjiang.

  14. Novel procedure for genotyping of the human serotonin transporter gene-linked polymorphic region (5-HTTLPR)--a region with a high level of allele diversity

    Rasmussen, Henrik B; Werge, Thomas M

    2007-01-01

    determination. After having developed a 5-HTTLPR genotyping assay, we examined all samples of DNA in two separate rounds of analyses and found complete agreement between the results from these two rounds. CONCLUSION: On the basis of simultaneous analysis of tandem repeat size variation and variation of single......BACKGROUND: The serotonin transporter, the target of a group of antidepressant drugs, is involved in the regulation of the availability and reuptake of serotonin. A variable number of tandem repeats in the promoter region of the serotonin transporter gene, designated 5-HTTLPR, affects...... for detailed genotyping of 5-HTTLPR based upon simultaneous analysis of tandem repeat size variation and single nucleotide variations. METHODS: We elaborated a list of all known 5-HTTLPR alleles to provide an overview of the allele repertoire at this polymorphic locus. Fragments of 5-HTTLPR were PCR...

  15. PENGARUH LINGKUNGAN KELUARGA, LINGKUNGAN SEKOLAH, DISIPLIN BELAJAR DAN MOTIVASI BELAJAR TERHADAP PRESTASI BELAJAR EKONOMI SISWA SMA KELAS XI IPS SMA PGRI 1 TAMAN PEMALANG

    Iyut Sustiasih Sudikno

    2014-02-01

    Full Text Available Penelitian ini bertujuan untuk mengetahui pengaruh lingkungan keluarga, lingkungan sekolah dan disiplin belajar terhadap prestasi belajar melalui motivasi belajar siswa kelas XI IPS SMA PGRI 1 Taman Pemalang. Subyek penelitian ini adalah siswa kelas XI IPS SMA PGRI 1 Taman Pemalang. Latar belakang penelitian ini adalah prestasi belajar siswa kelas XI IPS yang kurang optimal. Penelitian ini merupakan penelitian kuantitatif. Variabel bebas yang dikaji dalam penelitian ini adalah Lingkungan Keluarga (X1, Lingkungan Sekolah (X2, Disiplin Belajar (X3. Variabel terikat adalah Prestasi Belajar (Y2 dan Variabel intervening adalah Motivasi Belajar (Y1. Metode pengumpulan data yang digunakan adalah dokumentasi dan angket. Metode analisis data yaitu analisis deskriptif persentase dan analisis uji jalur (path analysis. Hasil analisis regresi linier berganda diperoleh persamaan regresi Y1 = 10,011 + 0,233X1 + 0,391X 2+ 0,522X3 +e1, dan Y2 = 71,062 + 0,227X1 + 0,704Y1 + 0,349X3 + e2. Hasil analisi jalur menunjukkan bahwa pengaruh secara tidak langsung (LK-PB sebesar 22,7%, (LS-PB sebesar 10,5%, (DB-PB sebesar 34,9%, (MB-PB sebesar 70,4% dan pengaruh secara tidak langsung (LK-MB-PB sebesar 16,4%, (LS-MB-PB sebesar 27,5%, (DP-MB-PB sebesar 36,7%. This research aims to determine the effect of on family environment, school environment, learning discipline on students’ achievements through student motivation SMA PGRI 1 Taman Pemalang. The subjects were students of class XI IPS Students of SMA PGRI 1 Taman Pemalang. The background of this research is the student’ achievements XI IPS Stuents of SMA PGRI 1 Taman Pemalang. This research is a quantitative study. The independent variables were examined in this study is family environment (X1, school environment (X2, learning discipline (X3. The dependent variable is the students, achievements (Y2 and the intervening variable is learning motivation (Y1. Data collection methods used are documentation and

  16. Genetic polymorphisms within tumor necrosis factor gene promoter region: a role for susceptibility to ventilator-associated pneumonia.

    Kotsaki, Antigoni; Raftogiannis, Maria; Routsi, Christina; Baziaka, Fotini; Kotanidou, Anastasia; Antonopoulou, Anastasia; Orfanos, Stylianos E; Katsenos, Chrisostomos; Koutoukas, Pantelis; Plachouras, Diamantis; Mandragos, Konstantinos; Giamarellos-Bourboulis, Evangelos J

    2012-08-01

    Debatable findings exist among various studies regarding the impact of single nucleotide polymorphisms (SNPs) within the promoter region of the tumor necrosis factor (TNF) gene for susceptibility to infections. Their impact was investigated in a cohort of mechanically ventilated patients who developed ventilator-associated pneumonia (VAP). Two-hundred and thirteen mechanically ventilated patients who developed VAP were enrolled. Genomic DNA was extracted and SNPs at the -376, -308 and -238 position of the promoter region of the TNF gene were assessed by restriction fragment length polymorphisms. Monocytes were isolated from 47 patients when they developed sepsis and stimulated by bacterial endotoxin for the production of TNFα and of interleukin-6 (IL-6). Patients were divided into two groups; 166 patients bearing only wild-type alleles of all three studied polymorphisms; and 47 patients carrying at least one A allele of the three studied SNPs. Time between start of mechanical ventilation and advent of VAP was significantly shorter in the second group than in the first group (log-rank: 4.416, p: 0.041). When VAP supervened, disease severity did not differ between groups. Stimulation of TNFα and of IL-6 was much greater by monocytes for patients carrying A alleles. Carriage of at least one A allele of the three studied SNPs at the promoter region of the TNF-gene is associated with shorter time to development of VAP but it is not associated with disease severity. Findings may be related with a role of the studied SNPs in the production of pro-inflammatory cytokines. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. PELATIHAN PENULISAN KARYA ILMIAH BIDANG SOSIAL ( HUKUM DI SMA NEGERI 3 DENPASAR

    I KETUT SUDIARTA

    2012-09-01

    Full Text Available ABSRACT Training of Constructing Scientific Report on Social Major (Law has done on SMA Negeri 3 Denpasar, by the Guiding Team of the Lecturers of Law Faculty of Udayana University through a practice of constructing a report in a class through a workshop. Aproximately, 40% are for meanwhile, 60% are by practice of composing and providing some reference which is related to the constructing of a social-scientific report, and there all are done well so far. This fact was indicated by the responds which were given by the students of SMA Negeri 3 Denpasar, especially for those who join the KIR group.This activity has been done once a week.

  18. A 3D Printed Implantable Device for Voiding the Bladder Using Shape Memory Alloy (SMA) Actuators.

    Hassani, Faezeh Arab; Peh, Wendy Yen Xian; Gammad, Gil Gerald Lasam; Mogan, Roshini Priya; Ng, Tze Kiat; Kuo, Tricia Li Chuen; Ng, Lay Guat; Luu, Percy; Yen, Shih-Cheng; Lee, Chengkuo

    2017-11-01

    Underactive bladder or detrusor underactivity (DU) is defined as a reduction of contraction strength or duration of the bladder wall. Despite the serious healthcare implications of DU, there are limited solutions for affected individuals. A flexible 3D printed implantable device driven by shape memory alloys (SMA) actuators is presented here for the first time to physically contract the bladder to restore voluntary control of the bladder for individuals suffering from DU. This approach is used initially in benchtop experiments with a rubber balloon acting as a model for the rat bladder to verify its potential for voiding, and that the operating temperatures are safe for the eventual implantation of the device in a rat. The device is then implanted and tested on an anesthetized rat, and a voiding volume of more than 8% is successfully achieved for the SMA-based device without any surgical intervention or drug injection to relax the external sphincter.

  19. RTC simulations on large branched sewer systems with SmaRTControl.

    de Korte, Kees; van Beest, Dick; van der Plaat, Marcel; de Graaf, Erno; Schaart, Niels

    2009-01-01

    In The Netherlands many large branched sewer systems exist. RTC can improve the performance of these systems. The objective of the universal algorithm of SmaRTControl is to improve the performance of the sewer system and the WWTP. The effect of RTC under rain weather flow conditions is simulated using a hydrological model with 19 drainage districts. The system related inefficiency coefficient (SIC) is introduced for assessment of the performance of sewer systems. The performance can be improved by RTC in combination with increased pumping capacities in the drainage districts, but without increasing the flow to the WWTP. Under dry weather flow conditions the flow to the WWTP can be equalized by storage of wastewater in the sewer system. It is concluded that SmaRTControl can improve the performance, that simulations are necessary and that SIC is an excellent parameter for assessment of the performance.

  20. Dynamical analysis and development of a biologically inspired SMA caterpillar robot.

    Daily-Diamond, Christopher A; Novelia, Alyssa; O'Reilly, Oliver M

    2017-09-26

    With the goal of robustly designing and fabricating a soft robot based on a caterpillar featuring shape memory alloy (SMA) actuators, analytical and numerical models for a soft robot were created based on the forward crawling motion of the Manduca sexta caterpillar. The analytical model features a rod theory and the mechanics of undulation were analyzed using a motion pattern based on the 'Witch of Agnesi' curve. Complementing these models, experiments on a SMA actuator sample were performed in order to determine its flexural rigidity and curvature as a function of the actuation voltage. A series of these actuators can be modeled as a system of rigid bodies connected by torsional springs. As these bodies are actuated according to the motion pattern based on the individual caterpillar segments, ground contact forces are calculated and analyzed to determine the requirements of successful forward locomotion. The energetics of the analytical and numerical models are then compared and discussed.

  1. Assessing upper limb function in nonambulant SMA patients: development of a new module.

    Mazzone, Elena; Bianco, Flaviana; Martinelli, Diego; Glanzman, Allan M; Messina, Sonia; De Sanctis, Roberto; Main, Marion; Eagle, Michelle; Florence, Julaine; Krosschell, Kristin; Vasco, Gessica; Pelliccioni, Marco; Lombardo, Marilena; Pane, Marika; Finkel, Richard; Muntoni, Francesco; Bertini, Enrico; Mercuri, Eugenio

    2011-06-01

    We report the development of a module specifically designed for assessing upper limb function in nonambulant SMA patients, including young children and those with severe contractures. The application of the module to a preschool cohort of 40 children (age 30-48 months) showed that all the items could be completed by 30 months. The module was also used in 45 nonambulant SMA patients (age 30 months to 27 years). Their scores were more variable than in the preschool cohort, ranging from 0 to 18. The magnitude of scores was not related to age (r=-0.19). The upper limb scores had a good correlation with the Hammersmith Functional Motor Scale, r=0.75, but the upper limb function did not always strictly follow the overall gross motor function. These findings suggest that even some of the very weak nonambulant children possess upper limb skills that can be measured. Copyright © 2011 Elsevier B.V. All rights reserved.

  2. BF integrase genes of HIV-1 circulating in São Paulo, Brazil, with a recurrent recombination region.

    Atila Iamarino

    Full Text Available Although some studies have shown diversity in HIV integrase (IN genes, none has focused particularly on the gene evolving in epidemics in the context of recombination. The IN gene in 157 HIV-1 integrase inhibitor-naïve patients from the São Paulo State, Brazil, were sequenced tallying 128 of subtype B (23 of which were found in non-B genomes, 17 of subtype F (8 of which were found in recombinant genomes, 11 integrases were BF recombinants, and 1 from subtype C. Crucially, we found that 4 BF recombinant viruses shared a recurrent recombination breakpoint region between positions 4900 and 4924 (relative to the HXB2 that includes 2 gRNA loops, where the RT may stutter. Since these recombinants had independent phylogenetic origin, we argue that these results suggest a possible recombination hotspot not observed so far in BF CRF in particular, or in any other HIV-1 CRF in general. Additionally, 40% of the drug-naïve and 45% of the drug-treated patients had at least 1 raltegravir (RAL or elvitegravir (EVG resistance-associated amino acid change, but no major resistance mutations were found, in line with other studies. Importantly, V151I was the most common minor resistance mutation among B, F, and BF IN genes. Most codon sites of the IN genes had higher rates of synonymous substitutions (dS indicative of a strong negative selection. Nevertheless, several codon sites mainly in the subtype B were found under positive selection. Consequently, we observed a higher genetic diversity in the B portions of the mosaics, possibly due to the more recent introduction of subtype F on top of an ongoing subtype B epidemics and a fast spread of subtype F alleles among the B population.

  3. [Phylogenetic analysis of CO I gene of Oncomelania snails from project of afforestation for schistosomiasis control in marshland endemic regions].

    Xu, Yu-Mei; Zhang, Shi-Qing; Zhu, Chuan-Gang

    2012-04-01

    To investigate the genetic difference of cytochrome oxidase I (CO I ) of Oncomelania snails from the project of afforestation for schistosomiasis control in marshland regions, so as to explore the effects of different ecological environments. The snails were collected from 3 different areas, Anqing, Tongling, Wuwei, i.e. the upstream, midstream and downstream regions along the Yangtz River in Anhui Province. Genomic DNA was extracted from the snails, and CO I gene fragments were amplified by PCR, then purified and sequenced. The sequences were edited by using Blast. The CO I genes of O. h. minima and Biomphalaria glabrata were used as the reference of exogenous gene. The genetic distances of the various regions were calculated by the Kimura method and phylogenetic trees were constructed with UPGMA and the NJ method of MEGA (3.1) software. The amplified CO I gene of the snail was a fragment about 700 bp including 2 primers in length. There were little genetic diversity among the different areas, the identities were higher than or equal to 98%. The genetic distances indicated that the distance between the projects of afforestation and woodland in Anqing was 0.003, while Tongling was 0.019, Wuwei was 0.007. The distances among the three projects of afforestation were 0.003-0.012. The two phylogenetic trees were constructed by the methods of UPGMA and NJ respectively, which took on very similar topo-structure in which isolates of Biomphalaria glabrata located in one clade and all the others in the other one. In the other one clade, O. H. minima located in one clade. There was little genetic diversity among Anqing, Tongling, Wuwei clusters. The afforestations of Anqing and Wuwei clustered into one group, while the woodlands of Anqing and Wuwei appeared as another group. There is a little genetic diversity of the snail cytochrome oxidase I (CO I ) in different ecological environments among the upstream, midstream and downstream regions along the Yangtz River in Anhui

  4. Experiment feedbacks in micromechanics modeling of thermomechanical behaviour of SMA polycrystals

    Šittner, Petr; Novák, Václav

    2004-01-01

    Roč. 51, - (2004), s. 321-326 ISSN 1359-6462 R&D Projects: GA AV ČR IAA1048107; GA ČR GA202/04/2016 Institutional research plan: CEZ:AV0Z1010914 Keywords : shape memory alloys (SMA) * martensitic phase transformation * micromechanical modeling * neutron diffraction Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.112, year: 2004

  5. Hubungan Penggunaan Media Sosial Dengan Kemampuan Interaksi Sosial Remaja di SMA Negeri 1 Kota Medan

    Nugraheni, Auliya Tunnisaa

    2016-01-01

    Social media today is considered as an important daily need. The intensity of using it by adolescents is influenced by their need for information, either academic or non-academic information. The inclination of using it as a communication facility can directly effects one of the social interactions aspect among individual. The objective of this research was to find out the correlation of using social media with the capacity of social interaction in adolescents at SMA Negeri 1, Medan, using co...

  6. Hubungan Facebook Addiction Disorder (Fad) dengan Perilaku Asertif Remaja di SMA Kristen 1 Tomohon

    Polii, Gloria Gratia; Bidjuni, Hendro; Wowiling, Ferdinand

    2014-01-01

    : Facebook addiction berarti menghabiskan jumlah waktu yang berlebihan di facebook. Facebook merupakan situs jejaring sosial yang mudah digunakan, dan yang paling penting adalah mempunyai efek mencandu. Secara psikologis, dampak negatif kecanduan facebook dapat dibagi atas: Pribadi yang anti sosial dan Dualisme kepribadian. Tujuan penelitian ini untuk mengetahui hubungan Facebook Addiction Disorder (FAD) dengan Perilaku Asertif Remaja di SMA Kristen 1 Tomohon. Desain penelitian ini dilaksanak...

  7. Sistem Informasi Data Kepegawaian Dan Kesiswaan SMA Negeri 1 P. Brandan

    Ramadhani, Tiara

    2015-01-01

    Tulisan ini bertujuan untuk membangun suatu sistem informasi pada SMA Negeri 1 Babalan P.Brandan. Sistem informasi ini dikembangkan dengan menggunakan perangkat lunak PHP, MySQL, Apache, dan Mozilla Firefox juga software pembantu lainnya seperti Adobe Dreamweaver CS5. Tujuan dari sistem informasi ini adalah untuk menyajikan informasi data kepegawaian, guru, serta kesiswaan kepada user/pengguna dengan baik dan dapat meng-update isi dari informasi yang terdapat pada web tersebut dengan mudah pa...

  8. Hubungan Bermain Video Game Terhadap Kejadian Insomnia Pada Kalangan Remaja Di Sma Negeri 12 Medan

    Pangaribuan, Hotman Parasian

    2015-01-01

    The number of adolescent who played video game was increased now days. This can cause many problems in social relationship, behavioral, and their sleep pattern like insomnia. This cross sectional study aimed to evaluate the relationship between playing video game with insomnia among the adolescent. Our total sample was 100 students in SMA Negeri 12 Medan. The sample was chosen by consequtive sampling. The data was taken by interview using questionnaire. From our result, the major...

  9. Pembanguna Sistem Informasi Manajemen Keluhan Siswa Berbasi Web pada SMA PGRI 6 Malang Menggunakan Metode Waterfall

    Wiwin Kuswinardi, Marissa Renny Leon/

    2014-01-01

    Leon, Marissa Renny. 2014. Development of web based Management Information System of Student Complaints In SMA PGRI 6 Malang Using Waterfall Method. 109Thesis, information systems Study Program, Faculty of Information Technology, kanjuruhan Universitas of Malang. Supervisor: Wiwin Kuswinardi,Kom., M.KomDelivering complaint of students is still less effective Students write complaints on paper, but there are some constraints faced by the homeroom teacher, if the paper of ...

  10. Identificación de variantes de riesgo en regiones reguladoras de genes asociados a esquizofrenia

    González Peñas, Javier

    2016-01-01

    La esquizofrenia es una enfermedad de elevada prevalencia en la población (0,5%), altamente incapacitante y de una naturaleza multicausal, aunque se trata de uno de los trastornos complejos más genéticos que existen (con una heredabilidad del 65–80%). Recientes trabajos sugieren un papel muy relevante de variación genética en las regiones no codificantes en la etiología de la enfermedad. El presente proyecto de tesis se ha centrado en el estudio de la variación genética en regiones reguladora...

  11. Acetylcholinesterase (AChE) gene modification in transgenic animals: functional consequences of selected exon and regulatory region deletion.

    Camp, Shelley; Zhang, Limin; Marquez, Michael; de la Torre, Brian; Long, Jeffery M; Bucht, Goran; Taylor, Palmer

    2005-12-15

    AChE is an alternatively spliced gene. Exons 2, 3 and 4 are invariantly spliced, and this sequence is responsible for catalytic function. The 3' alternatively spliced exons, 5 and 6, are responsible for AChE disposition in tissue [J. Massoulie, The origin of the molecular diversity and functional anchoring of cholinesterases. Neurosignals 11 (3) (2002) 130-143; Y. Li, S. Camp, P. Taylor, Tissue-specific expression and alternative mRNA processing of the mammalian acetylcholinesterase gene. J. Biol. Chem. 268 (8) (1993) 5790-5797]. The splice to exon 5 produces the GPI anchored form of AChE found in the hematopoietic system, whereas the splice to exon 6 produces a sequence that binds to the structural subunits PRiMA and ColQ, producing AChE expression in brain and muscle. A third alternative RNA species is present that is not spliced at the 3' end; the intron 3' of exon 4 is used as coding sequence and produces the read-through, unanchored form of AChE. In order to further understand the role of alternative splicing in the expression of the AChE gene, we have used homologous recombination in stem cells to produce gene specific deletions in mice. Alternatively and together exon 5 and exon 6 were deleted. A cassette containing the neomycin gene flanked by loxP sites was used to replace the exon(s) of interest. Tissue analysis of mice with exon 5 deleted and the neomycin cassette retained showed very low levels of AChE expression, far less than would have been anticipated. Only the read-through species of the enzyme was produced; clearly the inclusion of the selection cassette disrupted splicing of exon 4 to exon 6. The selection cassette was then deleted in exon 5, exon 6 and exons 5 + 6 deleted mice by breeding to Ella-cre transgenic mice. AChE expression in serum, brain and muscle has been analyzed. Another AChE gene targeted mouse strain involving a region in the first intron, found to be critical for AChE expression in muscle cells [S. Camp, L. Zhang, M. Marquez, B

  12. Force-Deformation Response of a SMA-Based Actuator Considering the Electric Current Intensity as Step-Input

    Ion-Cornel Mituletu

    2015-06-01

    Full Text Available The goal of the paper is to accomplish the response regarding the force-displacement characteristic evolution, of a Shape Memory Alloy (SMA actuator element. This reveals the first research stage in controlling the SMA behavior, providing important information about the heating-cooling time intervals. Step excitation of the SMA is performed by few values of electric current intensity, which produces the heating of SMA element up to 90-95 oC. To meet the testing requirements, an adequate test stand has been set up, consisting of sensors for force, displacement and temperature. The analog values provided by sensors were acquired and afterwards analyzed. The values of temperature, displacement and force were achieved, and their characteristic evolution has been performed. Thus, the time intervals are resulted and some other important aspects have been observed, regarding the delay between parameters and the temperature overshoot

  13. Design and demonstration of a fish robot actuated by a SMA-driven actuation system

    Le, Chan H.; Nguyen, Quang S.; Park, Hoon C.

    2010-04-01

    This paper presents a concept of a fish robot actuated by an SMA-based actuator. The bending-type actuator system is composed of a 0.1mm diameter SMA wire and a 0.5mm thick glass/epoxy strip. The SMA wire is installed to the bent composite strip. The actuator can produce about 200gf of blocking force and 3.5mm displacement at the center of the glass/epoxy strip. The bending motion of the actuator is converted into the tail-beat motion of a fish robot through a linkage system. The fish robot is evaluated by measuring the tail-beat angle, swimming speed and thrust produced by the fish robot. The tail-beat angle is about 20° and the maximum swimming speed is about 1.6cm/s. The measured thrust is about 0.4gf when the fish robot is operated at 0.9Hz.

  14. Kajian Fisis Energi Terbarukan Panel Surya Melalui Eksperimen Sederhana untuk Siswa SMA

    Sunaryo Sunaryo

    2015-12-01

    Full Text Available Abstract Has conducted research on the effects of light intensity on the output voltage, current, and power. Research conducted generate data in the form of quantitative and graphs that show a link between the intensity of light, the output voltage, current, and power. The data obtained were used as sources of learning in senior high school (SMA. The implication is capable of enhancing creativity, motivation and learning outcomes of Physics subject of high school students in future studies. Keywords: light intensity, current, voltage, solar panel Abstrak Telah dilakukan penelitian tentang pengaruh intensitas cahaya terhadap tegangan output, arus, dan daya listrik. Penelitian yang dilakukan menghasilkan data dalam bentuk kuantitatif dan grafik yang menunjukkan adanya kaitan antara intensitas cahaya, tegangan output, arus, dan daya listrik. Data yang diperoleh dijadikan sebagai sumber informasi dalam pembelajaran di Sekolah Menengah Atas (SMA. Implikasinya adalah mampu meningkatkan kreativitas, motivasi, dan hasil belajar Fisika siswa SMA pada penelitian selanjutnya. Kata-kata kunci: intensitas cahaya, arus, tegangan, panel surya

  15. Experimental multiphysical characterization of an SMA driven, camber morphing owl wing section

    Stroud, Hannah R.; Leal, Pedro B. C.; Hartl, Darren J.

    2018-03-01

    In the context of aerospace engineering, morphing structures are useful in their ability to change the outer mold line (OML) while improving or maintaining certain aerodynamic performance metrics. Skin-based morphing is of particular interest in that it minimizes installation volume. Shape memory alloys (SMAs) have a high force to volume ratio that makes them a suitable choice for skin-based morphing. Because the thermomechanical properties of SMAs are coupled, strain can be generated via a temperature variation; this phenomenon is used as the actuation method. Therefore, it is necessary to determine the interaction of the system not only with aerodynamic loads, but with thermal loads as well. This paper describes the wind tunnel testing and in situ thermomechanical analysis of an SMA actuated, avian inspired morphing wing. The morphing wing is embedded with two SMA composite actuators and consists of a foam core enveloped in a fiberglass-epoxy composite. As the SMA wire is heated, the actuator contracts, morphing the wing from the original owl OML to a highly cambered, high lift OML. Configuration characteristics are analyzed in situ using simultaneous three dimensional digital image correlation (DIC) and infrared thermography, thereby coupling strain and thermal measurements. This method of testing allows for the nonintrusive, multiphysical data acquisition of each actuator separately and the system as a whole.

  16. Minimizing the Moisture Damage and Drain down of Iraqi SMA Mixtures Using Waste Additives

    Ali Al-Hadidy

    2013-04-01

    Full Text Available This research deals with the viability of using polyester fiber (PF, crumb rubber tire (CRT and cellulose fiber (CF as stabilizing waste additives in producing Iraqi SMA mixtures that sustain drain down phenomenon and moisture damage sensitivity. Different ratios of these additives (0.1, 0.2, and 0.3% by weight of aggregate and filler were mixed with 40/50 paving asphalt by means of dry process. Unmodified and modified SMA mixtures were subjected to drain down, Marshall, static indirect tensile strength, tensile stiffness modulus, static compressive strength, tensile strength ratio and index of retained strength tests. A set of regression equations between these tests were established. In addition, an optimization table based on these tests, which can be used to select the type or amount of additive for any field applications has been determined and reported. The results indicated that the inclusion of these additives in SMA mixtures can satisfy the performance requirement of high temperature and much rain zone.

  17. TGF-beta Sma/Mab signaling mutations uncouple reproductive aging from somatic aging.

    Shijing Luo

    2009-12-01

    Full Text Available Female reproductive cessation is one of the earliest age-related declines humans experience, occurring in mid-adulthood. Similarly, Caenorhabditis elegans' reproductive span is short relative to its total life span, with reproduction ceasing about a third into its 15-20 day adulthood. All of the known mutations and treatments that extend C. elegans' reproductive period also regulate longevity, suggesting that reproductive span is normally linked to life span. C. elegans has two canonical TGF-beta signaling pathways. We recently found that the TGF-beta Dauer pathway regulates longevity through the Insulin/IGF-1 Signaling (IIS pathway; here we show that this pathway has a moderate effect on reproductive span. By contrast, TGF-beta Sma/Mab signaling mutants exhibit a substantially extended reproductive period, more than doubling reproductive span in some cases. Sma/Mab mutations extend reproductive span disproportionately to life span and act independently of known regulators of somatic aging, such as Insulin/IGF-1 Signaling and Dietary Restriction. This is the first discovery of a pathway that regulates reproductive span independently of longevity and the first identification of the TGF-beta Sma/Mab pathway as a regulator of reproductive aging. Our results suggest that longevity and reproductive span regulation can be uncoupled, although they appear to normally be linked through regulatory pathways.

  18. SMA-Based System for Environmental Sensors Released from an Unmanned Aerial Vehicle

    Lorenzo Pellone

    2017-01-01

    Full Text Available In the work at hand, a shape memory alloy (SMA-based system is presented. The system, conceived for releasing environmental sensors from ground or small unmanned aerial vehicles, UAV (often named UAS, unmanned aerial system, is made of a door, integrated into the bottom of the fuselage, a device distributor, operated by a couple of antagonistic SMA springs, and a kinematic chain, to synchronize the deployment operation with the system movement. On the basis of the specifications (weight, available space, energy supply, sensors size, etc., the system design was addressed. After having identified the main system characteristics, a representative mock-up was manufactured, featuring the bottom part of the reference fuselage. Functionality tests were performed to prove the system capability to release the sensors; a detailed characterization was finally carried out, mainly finalized at correlating the kinematic chain displacement with the SMA spring temperature and the supplied electrical power. A comparison between theoretical predictions and experimental outcomes showed good agreement.

  19. A fuzzy PID-controlled SMA actuator for a two-DOF joint

    Shi Zhenyun

    2014-04-01

    Full Text Available Shape memory alloy (SMA actuator is a potential advanced component for servo-systems of aerospace vehicles and aircraft. This paper presents a joint with two degrees of freedom (DOF and a mobility range close to ±60° when driven by SMA triple wires. The fuzzy proportional-integral-derivative (PID-controlled actuator drive was designed using antagonistic SMA triple wires, and the resistance feedback signal made a closed loop. Experiments showed that, with the driving responding frequency increasing, the overstress became harder to be avoided at the position under the maximum friction force. Furthermore, the hysteresis gap between the heating and cooling paths of the strain-to-resistance curve expanded under this condition. A fuzzy logic control was considered as a solution, and the curves of the wires were then modeled by fitting polynomials so that the measured resistance was used directly to determine the control signal. Accurate control was demonstrated through the step response, and the experimental results showed that under the fuzzy PID-control program, the mean absolute error (MAE of the rotation angle was about 3.147°. In addition, the investigation of the external interference to the system proved the controllable maximum output.

  20. Evaluation of Fatigue Life of CRM-Reinforced SMA and Its Relationship to Dynamic Stiffness

    Nuha Salim Mashaan

    2014-01-01

    Full Text Available Fatigue cracking is an essential problem of asphalt concrete that contributes to pavement damage. Although stone matrix asphalt (SMA has significantly provided resistance to rutting failure, its resistance to fatigue failure is yet to be fully addressed. The aim of this study is to evaluate the effect of crumb rubber modifier (CRM on stiffness and fatigue properties of SMA mixtures at optimum binder content, using four different modification levels, namely, 6%, 8%, 10%, and 12% CRM by weight of the bitumen. The testing undertaken on the asphalt mix comprises the dynamic stiffness (indirect tensile test, dynamic creep (repeated load creep, and fatigue test (indirect tensile fatigue test at temperature of 25°C. The indirect tensile fatigue test was conducted at three different stress levels (200, 300, and 400 kPa. Experimental results indicate that CRM-reinforced SMA mixtures exhibit significantly higher fatigue life compared to the mixtures without CRM. Further, higher correlation coefficient was obtained between the fatigue life and resilient modulus as compared to permanent strain; thus resilient modulus might be a more reliable indicator in evaluating the fatigue life of asphalt mixture.

  1. Evaluation of fatigue life of CRM-reinforced SMA and its relationship to dynamic stiffness.

    Mashaan, Nuha Salim; Karim, Mohamed Rehan; Abdel Aziz, Mahrez; Ibrahim, Mohd Rasdan; Katman, Herda Yati; Koting, Suhana

    2014-01-01

    Fatigue cracking is an essential problem of asphalt concrete that contributes to pavement damage. Although stone matrix asphalt (SMA) has significantly provided resistance to rutting failure, its resistance to fatigue failure is yet to be fully addressed. The aim of this study is to evaluate the effect of crumb rubber modifier (CRM) on stiffness and fatigue properties of SMA mixtures at optimum binder content, using four different modification levels, namely, 6%, 8%, 10%, and 12% CRM by weight of the bitumen. The testing undertaken on the asphalt mix comprises the dynamic stiffness (indirect tensile test), dynamic creep (repeated load creep), and fatigue test (indirect tensile fatigue test) at temperature of 25°C. The indirect tensile fatigue test was conducted at three different stress levels (200, 300, and 400 kPa). Experimental results indicate that CRM-reinforced SMA mixtures exhibit significantly higher fatigue life compared to the mixtures without CRM. Further, higher correlation coefficient was obtained between the fatigue life and resilient modulus as compared to permanent strain; thus resilient modulus might be a more reliable indicator in evaluating the fatigue life of asphalt mixture.

  2. PENGARUH KOMPETENSI SUMBER DAYA MANUSIA TERHADAP KINERJA PEGAWAI DAN GURU PADA SMA SARIBUANA MAKASSAR

    Novita _

    2017-08-01

    Full Text Available NOVITA. 2017.Essay . The Influence of Human Resource Competency on Employee and Teacher Performance at SMA SARIBUANA Makassar South Sulawesi Province.Guided by Indrayani Nur, S. Pd SE., M.Si. An employee is an individual who works for an employer, by contract or agreement whether in writing or in writing, to carry out a job or occupation in a particular activity by obtaining compensation paid under a specified period. This study aims to analyze the influence of human resource competencies on the performance of employees and teachers in SMA SARIBUANA Makassar. Analyzer used is multiple linear regression. Respondents of this research are employees and teachers of SMA Saribuana Makassar. The results of the analysis show that knowledge, mastery of science of technology and motivation affect the improvement of employee and teacher performance From the ANOVA or F test, the significant number (Sig (0,000 is below 0.05 and the Fcount is 19.614 where the Fcount is greater than the Ftable of 3.35. Thus, Fcount > Ftable then this result indicates that the independent variable (knowledge, mastery of technology science, motivation influence together to the dependent variable (employee and teacher performance.

  3. Free vibration response of a multilayer smart hybrid composite plate with embedded SMA wires

    K. Malekzadeh

    Full Text Available In this paper, free vibration response of a hybrid composite plate was studied. Effects of some geometrical, physical and material parameters on response of the composite plates embedded with shape memory alloy (SMA wires were investigated, which have not been reported in the literature thus far. Some of these parameters included important factors affecting free vibration response of the smart hybrid composite plates. The SMA wires were embedded within the layers of the composite laminate. First-order shear deformation theory (FSDT was utilized to obtain the governing equations of hybrid composite plates. Transverse shear and rotary inertia effects of the plate were taken into consideration. For simply-supported boundary conditions, systematic closed form solutions were obtained by Navier's technique. It was established that dynamic behavior of the smart hybrid composite plate depended on various parameters such as volume fraction, temperature dependent recovery stress and tensile pre-strain of SMA wires and aspect ratio of the laminated hybrid plate.

  4. Analysis of SMA Hybrid Composite Structures in MSC.Nastran and ABAQUS

    Turner, Travis L.; Patel, Hemant D.

    2005-01-01

    A thermoelastic constitutive model for shape memory alloy (SMA) actuators and SMA hybrid composite (SMAHC) structures was recently implemented in the commercial finite element codes MSC.Nastran and ABAQUS. The model may be easily implemented in any code that has the capability for analysis of laminated composite structures with temperature dependent material properties. The model is also relatively easy to use and requires input of only fundamental engineering properties. A brief description of the model is presented, followed by discussion of implementation and usage in the commercial codes. Results are presented from static and dynamic analysis of SMAHC beams of two types; a beam clamped at each end and a cantilever beam. Nonlinear static (post-buckling) and random response analyses are demonstrated for the first specimen. Static deflection (shape) control is demonstrated for the cantilever beam. Approaches for modeling SMAHC material systems with embedded SMA in ribbon and small round wire product forms are demonstrated and compared. The results from the commercial codes are compared to those from a research code as validation of the commercial implementations; excellent correlation is achieved in all cases.

  5. Peningkatan Mutu Pendidikan SMA Muhammadiyah 2 Sidoarjo sebagai Sekolah Berkategori The Outstanding School of Muhammadiyah

    Hidayatulloh Hidayatulloh

    2016-09-01

    Full Text Available This article examines about improving the education quality of SMA Muhammadiyah 2 Sidoarjo as the Outstanding School of Muhammadiyah. This article reveals that the quality improvement of SMA Muhammadiyah 2 Sidoarjo was conducted through: the arrangement of school program and self evaluation, the reinforcement of vision, mission and education objective, the reinforcement of leadership and teamwork, the improvement of teachers and educators competence, the improvement learners quality input, the development of curriculum and learning, the development of school culture, the development of facilities and infrastructure, the development of community service, the cooperation of education and student exchange, the mobilization of education funding resources, the develop-ment of SIM, monitoring and evaluation, and education quality system. The management quality of SMA Muhammadiyah 2 Sidoarjo was run through input-process-output formula. The process of quality containes the process of quality planning, main process, supporting process, dan quality improvement process. Factors supporting the quality improvement are: Muhammadiyah’s popular name, the doctrine of education quality improvement, the leadership of TORSIE paradigm, the school academicians’ spirit of gaining achievement, the synergy of school academicians, the appropriate facilities, and the supports of all stakeholders.

  6. Implementasi Sistem Informasi Akademik Menggunakan Aplikasi Jibas pada SMA Negeri 9 Padang

    Ricky Akbar

    2015-10-01

    Full Text Available SMA Negeri 9 Padang is one of the institutions engaged in the field of education, which requires the design of software to manage and run all school activities, one of which is the Academic Information System (SIA. SIA currently in SMA 9 Padang yet well integrated, so it still has many shortcomings in meeting the needs of the school or institution, in particular to deal with academic problems. Therefore, it needs to be implemented Academic Information System that can overcome the various shortcomings earlier. Implementation of this application starts with a preliminary study. Activities, the introduction of the school as a whole with interviews and observations, identify business processes academically at school is running and then make the proposed system as terkomputerisasinya, which is described by using the tools of Business Process Model Notation (BPMN, as well as the depiction of a working model of the system to be applied using use case diagram. The next stage is to study the literature of various books and journals to find the theoretical basis and related research. Then selecting software for SIA School, after the configuration and customization of the software modules, and the latter carry out the implementation and testing. These results indicate that the software SIA Schools that have been selected and applied that JIBAS applications, which can solve the problems on SMA Negeri 9 Padang

  7. Hubungan antara Aktivitas Fisik Terhadap Memori Kerja Murid SMA Don Bosco III Bekasi

    Michelle Clarissa Junaidi

    2017-03-01

    Full Text Available Latar belakang. Memori kerja merupakan bagian dari memori jangka pendek yang berperan penting dalam membantu proses pembelajaran dan dipengaruhi oleh aktivitas fisik, memori kerja yang rendah akan menimbulkan kesulitan untuk menerima informasi baru serta penurunan prestasi belajar. Tujuan. Mengetahui pengaruh aktivitas fisik terhadap kapasitas memori kerja murid SMA Don Bosco III. Metode. Penelitian metode analitik dengan pendekatan potong lintang pada 113 murid SMA Don Bosco III, Bekasi, pada 18 – 20 Juli 2016. Penelitian dilakukan dengan menggunakan kuesioner demografi, kuesioner skrining gangguan mental dan penyakit kronis, Physical Acitivity Questionnaire of Adolescent (PAQ-A dan Operation Span (O-SPAN. Analisis data dengan univariat dan bivariat menggunakan uji korelasi Spearman. Hasil. Terdapat 113 murid SMA Don Bosco III dengan kisaran usia 14 – 17 tahun, usia terbanyak 15 tahun (47.8%, laki-laki 61,1%, murid kelas X 44.2%. Mayoritas responden memiliki aktivitas fisik “kurang baik” dan rerata memori kerja 6,16. Analisis Spearman menunjukkan terdapat hubungan bermakna (p<0,05 antara aktivitas fisik terhadap memori kerja dengan korelasi positif lemah (r=0,384. Kesimpulan. Terdapat korelasi positif antara aktivitas fisik dan memori kerja, aktivitas fisik yang semakin tinggi cenderung akan meningkatkan memori kerja.

  8. Simulación basada en SMA de sistemas originalmente representados con EDO

    Ekaitz Zulueta Guerrero

    2011-10-01

    Full Text Available Resumen: En el presente trabajo se expone una metodología para modelar mediante un Sistema Multi-Agente (SMA sistemas biológicos y fisiológicos dinámicos con variables cuantificadas discretas, como el crecimiento y decrecimiento de poblaciones o el modelado epidemiológico de enfermedades. Se muestra un procedimiento para transformar un sistema de Ecuaciones Diferenciales Ordinarias (EDO (que modela un entorno de forma correcta en un SMA equivalente mediante un esquema basado en el método de Monte Carlo. Se utiliza un caso práctico fundamentado en un modelo matemático de Leucemia Mieloide Crónica (LMC para comparar la metodología basada en agentes con el modelado tradicional basado en un sistema de EDO. Se realiza una simulación con cada modelo (SMA y EDO y se compara los resultados obtenidos con ambas metodologías. Palabras clave: Ecuaciones diferenciales, modelo basado en agentes, Monte Carlo

  9. Mechanical behavior and fatigue performance of SMA short fiber reinforced MMC

    Al-Matar, Basem Jawad

    The mechanical behavior and performance of Shape Memory Alloy (SMA) short fiber NiTi reinforced Al was experimentally investigated for monotonic and fatigue test Al 6061 NiTi-SiC T6 was superior to unreinforced materials as well as to the reinforced Al T4. Taya three-dimensional model was performed on the monotonic tensile test at room temperature. It showed good agreement with experimental results. In order to utilize the compressive criterion for SMA, the NiTi reinforced Al composite was cooled at -10°C and prestrained at 1.2%. Beyond this limit composite suffered from damage. The net enhancement of SMA effect was around 10 MPa on composite yield stress. Results showed that the elastic constant for the composite did not change with loading and unloading suggesting that the inelastic behavior is plasticity. Further investigation on the inelastic behavior model as damage and/or plasticity by evaluating Poisson's ratio during loading was carried out by Adaptive Image Correlation Technique for Full-Field Strain Measurement. Poisson's ratio increased from around 0.33 to 0.5 demonstrating that it is plasticity that is responsible for the inelastic behavior. Scanning electron microscopy was also used and confirmed model results. The overall damage-behavior was quantified in terms of the post fatigue failure strength for low-cycle fatigue tests. Power law model was best to fit experimental findings.

  10. PROFIL KESULITAN BELAJAR FISIKA POKOK BAHASAN KELISTRIKAN SISWA SMA DI KOTA SEMARANG

    Ani Rusilowati

    2012-01-01

    Full Text Available Tujuan penelitian ini adalah menentukan profil kesulitan belajar Fisika, khususnya pokok bahasan Kelistrikan yang dialami oleh siswa SMA di kota Semarang. Sampel penelitian adalah siswa SMA kelas X di kota Semarang, diambil secara cluster, dari SMA negeri dan swasta peringkat I, II, dan III, sebanyak 214 siswa. Kesulitan belajar didiagnosis dengan lima pendekatan, yaitu tujuan pembelajaran, pengetahuan prasyarat, profil materi, miskonsepsi, dan pengetahuan terstruktur. Kesulitan belajar Kelistrikan antara lain disebabkan oleh rendahnya penguasaan konsep, lemahnya kemampuan matematis, dan kekurangmampuan mengkonversi satuan. Penyebab kesulitan belajar dalam pengetahuan terstruktur adalah rendahnya kemampuan: verbal, menggunakan skema, membuat strategi pemecahan masalah, dan membuat algoritma. Hasil penelitian menunjukkan bahwa kesulitan belajar Kelistrikan rata-rata terjadi pada sub pokok bahasan: Kuat Arus Listrik, Hukum Ohm, Hambatan Penghantar, Hukum Kirchof II, Energi & Daya Listrik, dan Transformator. Sebagian siswa masih mengalami miskonsepsi terhadap konsep Hukum Ohm dan Hambatan Penghantar. Bagi siswa  sekolah peringkat III mengalami kesulitan belajar di semua aspek dan materi Kelistrikan Kata kunci : profil, kesulitan belajar, kelistrikan

  11. Association of a Human FABP1 Gene Promoter Region Polymorphism with Altered Serum Triglyceride Levels.

    Xian-E Peng

    Full Text Available Liver fatty acid-binding protein (L-FABP, also known as fatty acid-binding protein 1 (FABP1, is a key regulator of hepatic lipid metabolism. Elevated FABP1 levels are associated with an increased risk of cardiovascular disease (CVD and metabolic syndromes. In this study, we examine the association of FABP1 gene promoter variants with serum FABP1 and lipid levels in a Chinese population. Four promoter single-nucleotide polymorphisms (SNPs of FABP1 gene were genotyped in a cross-sectional survey of healthy volunteers (n = 1,182 from Fuzhou city of China. Results showed that only the rs2919872 G>A variant was significantly associated with serum TG concentration(P = 0.032.Compared with the rs2919872 G allele, rs2919872 A allele contributed significantly to reduced serum TG concentration, and this allele dramatically decreased the FABP1 promoter activity(P < 0.05. The rs2919872 A allele carriers had considerably lower serum FABP1 levels than G allele carriers (P < 0.01. In the multivariable linear regression analysis, the rs2919872 A allele was negatively associated with serum FABP1 levels (β = -0.320, P = 0.003, while serum TG levels were positively associated with serum FABP1 levels (β = 0.487, P = 0.014. Our data suggest that compared with the rs2919872 G allele, the rs2919872 A allele reduces the transcriptional activity of FABP1 promoter, and thereby may link FABP1 gene variation to TG level in humans.

  12. A Gene Catalogue of the Euchromatic Male-Specific Region of the Horse Y Chromosome: Comparison with Human and Other Mammals

    Paria, Nandina; Raudsepp, Terje; Pearks Wilkerson, Alison J.; O'Brien, Patricia C. M.; Ferguson-Smith, Malcom A.; Love, Charles C.; Arnold, Carolyn; Rakestraw, Peter; Murphy, William J.; Chowdhary, Bhanu P.

    2011-01-01

    Studies of the Y chromosome in primates, rodents and carnivores provide compelling evidence that the male specific region of Y (MSY) contains functional genes, many of which have specialized roles in spermatogenesis and male-fertility. Little similarity, however, has been found between the gene content and sequence of MSY in different species. This hinders the discovery of species-specific male fertility genes and limits our understanding about MSY evolution in mammals. Here, a detailed MSY g...

  13. Polymorphisms in genes of interleukin 12 and its receptors and their association with protection against severe malarial anaemia in children in western Kenya

    Slutsker Laurence

    2010-03-01

    Full Text Available Abstract Background Malarial anaemia is characterized by destruction of malaria infected red blood cells and suppression of erythropoiesis. Interleukin 12 (IL12 significantly boosts erythropoietic responses in murine models of malarial anaemia and decreased IL12 levels are associated with severe malarial anaemia (SMA in children. Based on the biological relevance of IL12 in malaria anaemia, the relationship between genetic polymorphisms of IL12 and its receptors and SMA was examined. Methods Fifty-five tagging single nucleotide polymorphisms covering genes encoding two IL12 subunits, IL12A and IL12B, and its receptors, IL12RB1 and IL12RB2, were examined in a cohort of 913 children residing in Asembo Bay region of western Kenya. Results An increasing copy number of minor variant (C in IL12A (rs2243140 was significantly associated with a decreased risk of SMA (P = 0.006; risk ratio, 0.52 for carrying one copy of allele C and 0.28 for two copies. Individuals possessing two copies of a rare variant (C in IL12RB1 (rs429774 also appeared to be strongly protective against SMA (P = 0.00005; risk ratio, 0.18. In addition, children homozygous for another rare allele (T in IL12A (rs22431348 were associated with reduced risk of severe anaemia (SA (P = 0.004; risk ratio, 0.69 and of severe anaemia with any parasitaemia (SAP (P = 0.004; risk ratio, 0.66. In contrast, AG genotype for another variant in IL12RB1 (rs383483 was associated with susceptibility to high-density parasitaemia (HDP (P = 0.003; risk ratio, 1.21. Conclusions This study has shown strong associations between polymorphisms in the genes of IL12A and IL12RB1 and protection from SMA in Kenyan children, suggesting that human genetic variants of IL12 related genes may significantly contribute to the development of anaemia in malaria patients.

  14. SMA spring-based artificial muscle actuated by hot and cool water using faucet-like valve

    Park, Cheol Hoon; Son, Young Su

    2017-04-01

    An artificial muscle for a human arm-like manipulator with high strain and high power density are under development, and an SMA(Shape memory alloy) spring is a good actuator for this application. In this study, an artificial muscle composed of a silicon tube and a bundle of SMA(Shape memory alloy) springs is evaluated. A bundle of SMA springs consists of five SMA springs which are fabricated by using SMA wires with a diameter of 0.5 mm, and hot and cool water actuates it by heating and cooling SMA springs. A faucet-like valve was also developed to mix hot water and cool water and control the water temperature. The mass of silicon tube and a bundle of SMA springs is only 3.3 g and 2.25 g, respectively, and the total mass of artificial muscle is 5.55 g. It showed good actuating performance for a load with a mass of 2.3 kg and the power density was more than 800 W/kg for continuous valve switching with a cycle of 0.6 s. The faucet-like valve can switch a water output from hot water to cold water within 0.3s, and the artificial muscle is actuated well in response to the valve position and speed. It is also presented that the temperature of the mixed water can be controlled depending on the valve position, and the displacement of the artificial muscle can be controlled well by the mixed water. Based on these results, SMA spring-based artificial muscle actuated by hot and cool water could be applicable to the human arm-like robot manipulators.

  15. Studi Kasus Tentang Siswi yang Memiliki Konsep Diri Negatif pada Kelas X SMA Mujahidin Pontianak Tahun 2017

    Ningsih, Dwi Purwanti

    2017-01-01

    This research entitled case study about student who have negative self concept in class X SMA Mujahidin Pontianak. Common problem in this research is how effort to help student having negatif self concept in class X SMA Mujahidin Pontianak? As for the sub-problems: 1) How are the characteristics of student who have negative self concept?, 2) What psychological factors that cause student to have negative self concept?, 3) What physiological factors that cause student to have a negative self co...

  16. Cloning of the pig aminopeptidase N gene. Identification of possible regulatory elements and the exon distribution in relation to the membrane-spanning region

    Sjöström, H; Norén, O; Olsen, Jørgen

    1989-01-01

    . By sequence comparisons we have found three domains showing similarity to promoter regions of the genes encoding human alpha 1-antitrypsin and human intestinal alkaline phosphatase. The gene sequence includes the first three exons and two introns. It shows that a single exon encodes the cytoplasmic tail...

  17. Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis

    Jozef Madzo

    2014-01-01

    Full Text Available Hematopoietic stem cell differentiation involves the silencing of self-renewal genes and induction of a specific transcriptional program. Identification of multiple covalent cytosine modifications raises the question of how these derivatized bases influence stem cell commitment. Using a replicative primary human hematopoietic stem/progenitor cell differentiation system, we demonstrate dynamic changes of 5-hydroxymethylcytosine (5-hmC during stem cell commitment and differentiation to the erythroid lineage. Genomic loci that maintain or gain 5-hmC density throughout erythroid differentiation contain binding sites for erythroid transcription factors and several factors not previously recognized as erythroid-specific factors. The functional importance of 5-hmC was demonstrated by impaired erythroid differentiation, with augmentation of myeloid potential, and disrupted 5-hmC patterning in leukemia patient-derived CD34+ stem/early progenitor cells with TET methylcytosine dioxygenase 2 (TET2 mutations. Thus, chemical conjugation and affinity purification of 5-hmC-enriched sequences followed by sequencing serve as resources for deciphering functional implications for gene expression during stem cell commitment and differentiation along a particular lineage.

  18. Association of the Resistin Gene Promoter Region Polymorphism with Kawasaki Disease in Chinese Children

    Ruixi Liu

    2012-01-01

    Full Text Available Objectives. The −420C>G polymorphism located in the resistin gene (RETN promoter has recently been suggested to play a potential role in proinflammatory conditions and cardiovascular disease. This study investigated the association of the RETN promoter polymorphism with Kawasaki disease (KD and its clinical parameters in Chinese children. Methods. We compared patients with complete KD to incomplete KD children. Genotyping of the RETN promoter polymorphism was performed using MassARRAY system, and serum resistin levels were estimated using the sandwich enzyme immunoassay method. Results. There was no significant difference in RETN (−420C>G genotypes between KD and control groups. However, the frequency of the G allele was higher in iKD patients than in cKD children due to a significantly increased frequency of the GG genotypes. Serum levels of resistin were significantly higher in KD patients than in controls regardless of the presence of coronary artery lesions (CALs. Conclusion. The present findings suggest that while resistin may play a role in the pathogenesis of KD, there is no apparent association between CAL and the RETN (−420C>G gene polymorphism in KD children. However, the diagnosis of iKD is challenging but can be supported by the presence of the G allele and the GG genotypes.

  19. Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome

    Takase, I.; Ishino, F.; Wachi, M.; Kamata, H.; Doi, M.; Asoh, S.; Matsuzawa, H.; Ohta, T.; Matsuhashi, M.

    1987-01-01

    The coding of two rare lipoproteins by two genes, rlpA and rlpB, located in the leuS-dacA region (15 min) on the Escherichia coli chromosome was demonstrated by expression of subcloned genes in a maxicell system. The formation of these two proteins was inhibited by globomycin, which is an inhibitor of the signal peptidase for the known lipoproteins of E. coli. In each case, this inhibition was accompanied by formation of a new protein, which showed a slightly lower mobility on sodium dodecyl sulfate-polyacrylamide gel electrophoresis and which we suppose to be a prolipoprotein with an N-terminal signal peptide sequence similar to those of the bacterial major lipoproteins and lysis proteins of some bacteriocins. The incorporation of 3 H-labeled palmitate and glycerol into the two lipoproteins was also observed. Sequencing of DNA showed that the two lipoprotein genes contained sequences that could code for signal peptide sequences of 17 amino acids (rlpA lipoprotein) and 18 amino acids (rlpB lipoprotein). The deduced sequences of the mature peptides consisted of 345 amino acids (M/sub r/ 35,615, rlpA lipoprotein) and 175 amino acids (M/sub r/ 19,445, rlpB lipoprotein), with an N-terminal cysteine to which thioglyceride and N-fatty acyl residues may be attached. These two lioproteins may be important in duplication of the cells

  20. Superior mesenteric artery (SMA) resection during pancreatectomy for malignant disease of the pancreas: a systematic review.

    Jegatheeswaran, Santhalingam; Baltatzis, Minas; Jamdar, Saurabh; Siriwardena, Ajith K

    2017-06-01

    Resection of the superior mesenteric artery (SMA) during pancreatectomy is performed infrequently and is undertaken with the aim of removing non-metastatic locally advanced pancreatic tumours. SMA resection reports also encompass resection of other visceral vessels. The consequences of resection of these different arteries are not necessarily equivalent. This is a focused systematic review of the outcome of SMA resection during pancreatectomy for cancer. A computerized search of the English language literature was undertaken for the period 1st January 2000 through 30th April 2016. The keywords "Pancreatic surgery" and "Vascular resections" were used. Thirteen studies reported 70 patients undergoing pancreatectomy with SMA resection from 10,726 undergoing pancreatectomy. Individual patient-level outcome data were available for 25. Median (range) accrual period was 132 (48-372) months. Reported peri-operative morbidity ranged from 39% to 91%. There were 5 peri-operative deaths in the 25 patients with individual-outcome data. Median survival was 11 months (95% Confidence interval 9.5-12.5 months; standard error 0.8 months). SMA resection during pancreatectomy is undertaken infrequently incurring high peri-operative morbidity and mortality. Median survival is 11 (95% CI 9.5-12.5) months. In contemporary practice there is no evidence to support SMA resection during pancreatectomy. Copyright © 2017 International Hepato-Pancreato-Biliary Association Inc. All rights reserved.

  1. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    2011-01-01

    Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and

  2. Porcine SOX9 Gene Expression Is Influenced by an 18 bp Indel in the 5'-Untranslated Region.

    Bertram Brenig

    Full Text Available Sex determining region Y-box 9 (SOX9 is an important regulator of sex and skeletal development and is expressed in a variety of embryonal and adult tissues. Loss or gain of function resulting from mutations within the coding region or chromosomal aberrations of the SOX9 locus lead to a plethora of detrimental phenotypes in humans and animals. One of these phenotypes is the so-called male-to-female or female-to-male sex-reversal which has been observed in several mammals including pig, dog, cat, goat, horse, and deer. In 38,XX sex-reversal French Large White pigs, a genome-wide association study suggested SOX9 as the causal gene, although no functional mutations were identified in affected animals. However, besides others an 18 bp indel had been detected in the 5'-untranslated region of the SOX9 gene by comparing affected animals and controls. We have identified the same indel (Δ18 between position +247 bp and +266 bp downstream the transcription start site of the porcine SOX9 gene in four other pig breeds; i.e., German Large White, Laiwu Black, Bamei, and Erhualian. These animals have been genotyped in an attempt to identify candidate genes for porcine inguinal and/or scrotal hernia. Because the 18 bp segment in the wild type 5'-UTR harbours a highly conserved cAMP-response element (CRE half-site, we analysed its role in SOX9 expression in vitro. Competition and immunodepletion electromobility shift assays demonstrate that the CRE half-site is specifically recognized by CREB. Both binding of CREB to the wild type as well as the absence of the CRE half-site in Δ18 reduced expression efficiency in HEK293T, PK-15, and ATDC5 cells significantly. Transfection experiments of wild type and Δ18 SOX9 promoter luciferase constructs show a significant reduction of RNA and protein levels depending on the presence or absence of the 18 bp segment. Hence, the data presented here demonstrate that the 18 bp indel in the porcine SOX9 5'-UTR is of functional

  3. Quantitative variation in obesity-related traits and insulin precursors linked to the OB gene region on human chromosome 7

    Duggirala, R.; Stern, M.P.; Reinhart, L.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

    1996-09-01

    Despite the evidence that human obesity has strong genetic determinants, efforts at identifying specific genes that influence human obesity have largely been unsuccessful. Using the sibship data obtained from 32 low-income Mexican American pedigrees ascertained on a type II diabetic proband and a multipoint variance-components method, we tested for linkage between various obesity-related traits plus associated metabolic traits and 15 markers on human chromosome 7. We found evidence for linkage between markers in the OB gene region and various traits, as follows: D7S514 and extremity skinfolds (LOD = 3.1), human carboxypeptidase A1 (HCPA1) and 32,33-split proinsulin level (LOD = 4.2), and HCPA1 and proinsulin level (LOD = 3.2). A putative susceptibility locus linked to the marker D7S514 explained 56% of the total phenotypic variation in extremity skinfolds. Variation at the HCPA1 locus explained 64% of phenotypic variation in proinsulin level and {approximately}73% of phenotypic variation in split proinsulin concentration, respectively. Weaker evidence for linkage to several other obesity-related traits (e.g., waist circumference, body-mass index, fat mass by bioimpedance, etc.) was observed for a genetic location, which is {approximately}15 cM telomeric to OB. In conclusion, our study reveals that the OB region plays a significant role in determining the phenotypic variation of both insulin precursors and obesity-related traits, at least in Mexican Americans. 66 refs., 3 figs., 4 tabs.

  4. Transcriptional response of Hoxb genes to retinoid signalling is regionally restricted along the neural tube rostrocaudal axis.

    Carucci, Nicoletta; Cacci, Emanuele; Nisi, Paola S; Licursi, Valerio; Paul, Yu-Lee; Biagioni, Stefano; Negri, Rodolfo; Rugg-Gunn, Peter J; Lupo, Giuseppe

    2017-04-01

    During vertebrate neural development, positional information is largely specified by extracellular morphogens. Their distribution, however, is very dynamic due to the multiple roles played by the same signals in the developing and adult neural tissue. This suggests that neural progenitors are able to modify their competence to respond to morphogen signalling and autonomously maintain positional identities after their initial specification. In this work, we take advantage of in vitro culture systems of mouse neural stem/progenitor cells (NSPCs) to show that NSPCs isolated from rostral or caudal regions of the mouse neural tube are differentially responsive to retinoic acid (RA), a pivotal morphogen for the specification of posterior neural fates. Hoxb genes are among the best known RA direct targets in the neural tissue, yet we found that RA could promote their transcription only in caudal but not in rostral NSPCs. Correlating with these effects, key RA-responsive regulatory regions in the Hoxb cluster displayed opposite enrichment of activating or repressing histone marks in rostral and caudal NSPCs. Finally, RA was able to strengthen Hoxb chromatin activation in caudal NSPCs, but was ineffective on the repressed Hoxb chromatin of rostral NSPCs. These results suggest that the response of NSPCs to morphogen signalling across the rostrocaudal axis of the neural tube may be gated by the epigenetic configuration of target patterning genes, allowing long-term maintenance of intrinsic positional values in spite of continuously changing extrinsic signals.

  5. Nuclear proteins interacting with the promoter region of the human granulocyte/macrophage colony-stimulating factor gene

    Shannon, M.F.; Gamble, J.R.; Vadas, M.A.

    1988-01-01

    The gene for human granulocyte/macrophage colony-stimulating factor (GM-CSF) is expressed in a tissue-specific as well as an activation-dependent manner. The interaction of nuclear proteins with the promoter region of the GM-CSF gene that is likely to be responsible for this pattern of GM-CSF expression was investigated. The authors show that nuclear proteins interact with DNA fragments from the GM-CSF promoter in a cell-specific manner. A region spanning two cytokine-specific sequences, cytokine 1 (CK-1, 5', GAGATTCCAC 3') and cytokine 2 (CK-2, 5' TCAGGTA 3') bound two nuclear proteins from GM-CSF-expressing cells in gel retardation assays. NF-GMb was inducible with phorbol 12-myristate 13-acetate and accompanied induction of GM-CSF message. NF-GMb was absent in cell lines not producing GM-CSF, some of which had other distinct binding proteins. NF-GMa and NF-GMb eluted from a heparin-Sepharose column at 0.3 and 0.6 M KCl, respectively. They hypothesize that the sequences CK-1 and CK-2 bind specific proteins and regulate GM-CSF transcription

  6. Molecular analysis of two genes between let-653 and let-56 in the unc-22(IV) region of Caenorhabditis elegans.

    Marra, M A; Prasad, S S; Baillie, D L

    1993-01-01

    A previous study of genomic organization described the identification of nine potential coding regions in 150 kb of genomic DNA from the unc-22(IV) region of Caenorhabditis elegans. In this study, we focus on the genomic organization of a small interval of 0.1 map unit bordered on the right by unc-22 and on the left by the left-hand breakpoints of the deficiencies sDf9, sDf19 and sDf65. This small interval at present contains a single mutagenically defined locus, the essential gene let-56. The cosmid C11F2 has previously been used to rescue let-56. Therefore, at least some of C11F2 must reside in the interval. In this paper, we report the characterization of two coding elements that reside on C11F2. Analysis of nucleotide sequence data obtained from cDNAs and cosmid subclones revealed that one of the coding elements closely resembles aromatic amino acid decarboxylases from several species. The other of these coding elements was found to closely resemble a human growth factor activatable Na+/H+ antiporter. Paris of oligonucleotide primers, predicted from both coding elements, have been used in PCR experiments to position these coding elements between the left breakpoint of sDf19 and the left breakpoint of sDf65, between the essential genes let-653 and let-56.

  7. Studi Kasus Pengembangan Program Bimbingan dan Konseling di SMA Negeri Kota Surakarta

    Anna Annisa

    2015-12-01

    Full Text Available Penelitian berdasarkan fenomena program bimbingan dan konseling di sekolah belum berjalan dengan baik terutama pada bagian perencanaan dan pelaksanaan program BK. Tujuan penelitian ini untuk mengetahui pengembangan program di SMA Negeri 7 Surakarta dan SMA N 8 Surakarta mulai dari (1 pelaksanaan asesmen kebutuhan melalui pengumpulan data, (2 interpretasi data asesmen kebutuhan, (3 penetapan prioritas kebutuhan, (4 penetapan tujuan program, (5 penetapan prosedur program, dan (6 perencanaan bagi perbaikan peningkatan penyempurnaan program. Jenis penelitian ini adalah deskriptif kualitatif dengan pendekatan studi kasus. Penelitian ini melibatkan guru BK di SMA Negeri Kota Surakarta. Metode pengumpulan data yang digunakan adalah menggunakan wawancara, observasi dan dokumentasi. Teknik analisis data menggunakan pengumpulan data, reduksi data, penyajian data dan penarikan kesimpulan. Simpulan dari penelitian ini adalah pada SMA N 7 Surakarta pengembangan program fokus pada penggunaan instrumen dalam asesmen, sasaran asesmen, kesesuaian asesmen dengan kebutuhan siswa, layann klasikal dan layanan kelompok. Sedangkan SMA N 8 Surakarta  difokuskan pada penentuan prioritas kebutuhan dan analisis data kebutuhan siswa. This research of program guidance and counselling in schools has not fully well especially at the planning and execution of counseling and guidance program. The purpose to know the development program at senior high school 7 Surakarta and senior high school 8 Surakarta ranging from (1 the implementation of needs assessment through data collection, data interpretation (2 the assessment of needs, (3 the determination of priority needs, (4 The goal setting program, (5 the determination of the procedures of the program, and (6 The planning for improvements to increase refinement program. Type of this research is descriptive qualitative approach to case studies. This research involves guidance and counseling teachers in senior high school of

  8. Faktor Penghambat Proses Layanan Konseling Individual di SMA se-Kota Cilacap

    Fenti Nurindahsari

    2015-12-01

    Full Text Available Berdasarkan penuturan guru BK di salah satu SMA di kota Cilacap yang pernah menjadi tempat observasi oleh peneliti, ditemukan fenomena terkait dengan layanan konseling individual di sekolah tersebut yang tidak sesuai dengan teori-teori mengenai konseling individual yang ada dalam bimbingan konseling. Contoh yang tidak sesuai dengan teori  ketika proses konseling berakhir guru BK di sekolah tersebut tidak ada upaya tindak lanjut. Tujuan penelitian ini untuk mengetahui faktor penghambat proses layanan konseling individual di SMA sekota Cilacap. Jenis penelitian deskriptif kuantitatif. Populasi dalam penelitian ini adalah konselor yang ada di SMA sekota Cilacap. Teknik sampel untuk konselor yang dipilih praktikan adalah sampling jenuh. Instrumen yang digunakan adalah angket. Validitas menggunakan rumus Product Moment. Uji reliabitilitas menggunakan rumus Alpha. Metode analisis data menggunakan deskriptif persentase. Hasil penelitian menunjukan faktor internal penghambat berasal dari konselor dalam kriteria tinggi (71,74% faktor eksternal penghambat termasuk kriteria tinggi yaitu norma (71,59%, sarpras (71,38% dan lingkungan fisik (72,39%. Dapat disimpulkan hambatan yang ada dalam proses layanan konseling individual di SMA sekota Cilacap berasal dari faktor internal dan eksternal yang memiliki kriteria yang sama yaitu dalam kategori tinggi. Based the narrative counseling teacher in one high school in Cilacap town that  once a place observation, discovered the phenomenon associated with individual counseling services in the school is not in accordance with the theories about the existing individual counseling in counseling. Examples that don’t fit with theory when the counseling process ends counseling teacher the school is’n follow-up effort. The purpose of this study to determine inhibiting factors individual counseling service process In senior high school Cilacap derby. Pupolasi in research is senior high school counselors. Technical

  9. MEDIA FOTO UNTUK MENINGKATKAN KETERAMPILAN MENULIS DESKRIPSI SISWA SMA NEGERI 2 KEBUMEN

    Rina Tri Indrianingrum

    2015-05-01

    Full Text Available Penelitian ini bertujuan untuk menjelaskan meningkatnya keterampilan menulis deskripsi berbahasa Jawa siswa kelas X SMA N 2 Kebumen dengan menggunakan pendekatan proses dan media foto. Penelitian ini merupakan penelitian tindakan kelas atau classroom action research. Desain yang digunakan dalam penelitian ini adalah desain penelitian tindakan Kemmis dan Taggart. Penelitian ini dilaksanakan dua siklus. Subjek penelitian ini adalah siswa kelas X2 SMA Negeri 2 Kebumen tahun pelajaran 2011/2012 yang berjumlah 32 siswa. Pengumpulan data dilakukan dengan menggunakan observasi, catatan lapangan dan tes. Validitas yang digunakan adalah validitas demo-krasi, validitas proses dan validitas dialogis. Teknik yang digunakan untuk menganalisis data dalam penelitian tindakan ini adalah deskriptif. Hasil penelitian menunjukkan (1 siswa dapat menemukan ide lebih cepat, (2 siswa dapat membuat kerangka karangan, (3 siswa dapat mengembangkan kerang-ka karangan, (4 siswa dapat berpikir sistematis, (5 siswa semakin antusiasnya dalam mengikuti pembelajaran menulis karangan, (6 siswa paham melakukan proses mengarang. _________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ PHOTOGRAPH MEDIA TO IMPROVE THE DESCRIPTION WRITING SKILL OF THE STUDENTS AT SMA NEGERI 2 KEBUMEN   Abstract This research is aimed to describe and to explain the improvement in the description writing skill of the tenth grade students at SMA N 2 Kebumen by using  approach process and photography media. This research is classroom action research or classroom action research. The design used in this research was action research design by Kemmis and Taggart. The subject of the research was X2 class students at SMA Negeri 2 Kebumen in the academic year of 2011/2012, consisted of 32

  10. Development of transformation bands in TiNi SMA for various stress and strain rates studied by a fast and sensitive infrared camera

    Pieczyska, E A; Kulasinski, K; Tobushi, H

    2013-01-01

    TiNi shape memory alloy (SMA) was subjected to tension at various strain rates for stress- and strain-controlled tests. The nucleation, development and saturation of the stress-induced martensitic transformation were investigated, based on the specimen temperature changes, measured by a fast and sensitive infrared camera. It was found that the initial, macroscopically homogeneous phase transformation occurs at the same stress level for all strain rates applied, regardless of the loading manner, while the stress of the localized transformation increases with the strain rate. At higher strain rate, a more dynamic course of the transformation process was observed, revealed in the creation of numerous fine transformation bands. An inflection point was noticed on the stress–strain curve, dividing the transformation range into two stages: the first heterogeneous, where transformation bands nucleate and evolve throughout the sample; the second, where the bands overlap, related to significant temperature increase and an upswing region of the curve. In the final part of the SMA loading a decrease of the average sample temperature revealed the saturation stage of the transformation. It was also observed that nucleation of the localized martensitic forward transformation takes place in the weakest area of the sample in both approaches, whereas the reverse transformation always initiates in its central part. (paper)

  11. HFE gene C282Y, H63D and S65C mutations frequency in the Transylvania region, Romania.

    Trifa, Adrian P; Popp, Radu A; Militaru, Mariela S; Farcaş, Marius F; Crişan, Tania O; Gana, Ionuţ; Cucuianu, Andrei; Pop, Ioan V

    2012-06-01

    HFE-associated haemochromatosis is one of the most frequent autosomal recessive disorders in the Caucasian population. Although most of the cases are homozygous individuals for the C282Y mutation, another two mutations, H63D and S65C, have been reported to be associated with milder forms of the disease. This study was a first attempt to evaluate the distribution of these HFE gene mutations in the Transylvania region. Two-hundred and twenty-five healthy, unrelated volunteers originating from the Transylvania region, Romania, were screened for the HFE gene C282Y, H63D and S65C mutations, using molecular genetics assays (Polymerase Chain Reaction-Restriction Fragments Length Polymorphism). For the C282Y mutation, 7 heterozygotes (3.1%) were found, but no homozygous individual. In the case of the H63D mutation, 40 heterozygotes (17.8%) and 4 homozygotes (1.75%) for the mutant allele were evidenced. We found a compound heterozygous genotype (C282Y/H63D) in one individual (0.45%). Thus, the allele frequencies of the C282Y and H63D were 1.75% and 10.9%, respectively. Three individuals (1.3%) were found to harbour the S65C mutation in a heterozygous state, but none in a homozygous state: the allele frequency of the mutant allele was 0.75%. The distribution of the HFE gene C282Y, H63D and S65C mutations found in our group matches the tendencies observed in other European countries: a decreasing gradient from Northern to Southern Europe for the C282Y mutation; high frequency for the H63D mutation, and low frequency for the S65C mutation in most of the countries.

  12. Effects of different endocrine disruptor (EDC) mixtures on gene expression in neonatal rat brain regions

    Lichtensteiger, Walter; Bassetti-Gaille, Catherine; Faass, Oliver

    2013-01-01

    Sexual brain differentiation is a potential EDC target. It depends on a combination of estrogen receptor- and androgen receptor-mediated effects in males and on estrogens in females. It is not known how these processes are affected by real-world mixtures of EDCs. We investigated the effect of three...... EDC mixtures on gene expression in developing brain. Amix (8 anti-androgenic chemicals), Emix (4 estrogenic chemicals) and Tmix (Amix + Emix + paracetamol recently identified as anti-androgenic) were administered by oral gavage to rat dams from gestational day 7 until weaning, at doses corresponding...... to 450×, 200× and 100× high end human intakes (S. Christiansen et al., 2012. International Journal of Andrology 35, 303). At postnatal day 6, during the last part of sexual brain differentiation, exon microarray analyses were performed in medial preoptic area (MPO) in the highest dose group, and real...

  13. FHL1 reduces dystrophy in transgenic mice overexpressing FSHD muscular dystrophy region gene 1 (FRG1.

    Sandra J Feeney

    Full Text Available Facioscapulohumeral muscular dystrophy (FSHD is an autosomal-dominant disease with no effective treatment. The genetic cause of FSHD is complex and the primary pathogenic insult underlying the muscle disease is unknown. Several disease candidate genes have been proposed including DUX4 and FRG1. Expression analysis studies of FSHD report the deregulation of genes which mediate myoblast differentiation and fusion. Transgenic mice overexpressing FRG1 recapitulate the FSHD muscular dystrophy phenotype. Our current study selectively examines how increased expression of FRG1 may contribute to myoblast differentiation defects. We generated stable C2C12 cell lines overexpressing FRG1, which exhibited a myoblast fusion defect upon differentiation. To determine if myoblast fusion defects contribute to the FRG1 mouse dystrophic phenotype, this strain was crossed with skeletal muscle specific FHL1-transgenic mice. We previously reported that FHL1 promotes myoblast fusion in vitro and FHL1-transgenic mice develop skeletal muscle hypertrophy. In the current study, FRG1 mice overexpressing FHL1 showed an improvement in the dystrophic phenotype, including a reduced spinal kyphosis, increased muscle mass and myofiber size, and decreased muscle fibrosis. FHL1 expression in FRG1 mice, did not alter satellite cell number or activation, but enhanced myoblast fusion. Primary myoblasts isolated from FRG1 mice showed a myoblast fusion defect that was rescued by FHL1 expression. Therefore, increased FRG1 expression may contribute to a muscular dystrophy phenotype resembling FSHD by impairing myoblast fusion, a defect that can be rescued by enhanced myoblast fusion via expression of FHL1.

  14. S&MA Internship to Support Orion and the European Service Module

    Hutcheson, Connor

    2016-01-01

    As a University Space Research Association (USRA) intern for NASA Johnson Space Center (JSC) during the summer 2016 work term, I worked on three main projects for the Space Exploration Division (NC) of the Safety and Mission Assurance (S&MA) Directorate. I worked on all three projects concurrently. One of the projects involved facilitating the status and closure of technical actions that were created during European Service Module (ESM) safety reviews by the MPCV Safety & Engineering Review Panel (MSERP). The two main duties included accurately collecting and summarizing qualitative data, and communicating that information to the European Space Agency (ESA) and Airbus (ESA's prime contractor) in a clear, succinct and precise manner. This project also required that I create a report on the challenges and opportunities of international S&MA. With its heavy emphasis on soft skills, this project taught me how to communicate better, by showing me how to present and share information in an easy-to-read and understandable format, and by showing me how to cooperate with and culturally respect international partners on a technical project. The second project involved working with the Orion Thermal Protection System (TPS) Process Failure Modes and Effects Analysis (PFMEA) Working Group to create the first full version of the Orion TPS PFMEA. The Orion TPS PFMEA Working Group met twice a week to analyze the Avcoat block installation process for failure modes, the failure modes effects, and how such failure modes could be controlled. I was in charge of implementing changes that were discussed in meeting, but were not implemented real time. Another major task included creating a significant portion of the content alongside another team member outside the two weekly meetings. This project caused me to become knowledgeable about TPS, heatshields, space-rated manufacturing, and non-destructive evaluation (NDE). The project also helped me to become better at working with a small

  15. Proteasome, transporter associated with antigen processing, and class I genes in the nurse shark Ginglymostoma cirratum: evidence for a stable class I region and MHC haplotype lineages.

    Ohta, Yuko; McKinney, E Churchill; Criscitiello, Michael F; Flajnik, Martin F

    2002-01-15

    Cartilaginous fish (e.g., sharks) are derived from the oldest vertebrate ancestor having an adaptive immune system, and thus are key models for examining MHC evolution. Previously, family studies in two shark species showed that classical class I (UAA) and class II genes are genetically linked. In this study, we show that proteasome genes LMP2 and LMP7, shark-specific LMP7-like, and the TAP1/2 genes are linked to class I/II. Functional LMP7 and LMP7-like genes, as well as multiple LMP2 genes or gene fragments, are found only in some sharks, suggesting that different sets of peptides might be generated depending upon inherited MHC haplotypes. Cosmid clones bearing the MHC-linked classical class I genes were isolated and shown to contain proteasome gene fragments. A non-MHC-linked LMP7 gene also was identified on another cosmid, but only two exons of this gene were detected, closely linked to a class I pseudogene (UAA-NC2); this region probably resulted from a recent duplication and translocation from the functional MHC. Tight linkage of proteasome and class I genes, in comparison with gene organizations of other vertebrates, suggests a primordial MHC organization. Another nonclassical class I gene (UAA-NC1) was detected that is linked neither to MHC nor to UAA-NC2; its high level of sequence similarity to UAA suggests that UAA-NC1 also was recently derived from UAA and translocated from MHC. These data further support the principle of a primordial class I region with few class I genes. Finally, multiple paternities in one family were demonstrated, with potential segregation distortions.

  16. CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23

    Michels, Evi; Speleman, Frank; Hoebeeck, Jasmien; De Preter, Katleen; Schramm, Alexander; Brichard, Bénédicte; De Paepe, Anne; Eggert, Angelika; Laureys, Geneviève; Vandesompele, Jo

    2008-01-01

    Recurrent loss of part of the long arm of chromosome 11 is a well established hallmark of a subtype of aggressive neuroblastomas. Despite intensive mapping efforts to localize the culprit 11q tumour suppressor gene, this search has been unsuccessful thus far as no sufficiently small critical region could be delineated for selection of candidate genes. To refine the critical region of 11q loss, the chromosome 11 status of 100 primary neuroblastoma tumours and 29 cell lines was analyzed using a BAC array containing a chromosome 11 tiling path. For the genes mapping within our refined region of loss, meta-analysis on published neuroblastoma mRNA gene expression datasets was performed for candidate gene selection. The DNA methylation status of the resulting candidate gene was determined using re-expression experiments by treatment of neuroblastoma cells with the demethylating agent 5-aza-2'-deoxycytidine and bisulphite sequencing. Two small critical regions of loss within 11q23 at chromosomal band 11q23.1-q23.2 (1.79 Mb) and 11q23.2-q23.3 (3.72 Mb) were identified. In a first step towards further selection of candidate neuroblastoma tumour suppressor genes, we performed a meta-analysis on published expression profiles of 692 neuroblastoma tumours. Integration of the resulting candidate gene list with expression data of neuroblastoma progenitor cells pinpointed CADM1 as a compelling candidate gene. Meta-analysis indicated that CADM1 expression has prognostic significance and differential expression for the gene was noted in unfavourable neuroblastoma versus normal neuroblasts. Methylation analysis provided no evidence for a two-hit mechanism in 11q deleted cell lines. Our study puts CADM1 forward as a strong candidate neuroblastoma suppressor gene. Further functional studies are warranted to elucidate the role of CADM1 in neuroblastoma development and to investigate the possibility of CADM1 haploinsufficiency in neuroblastoma

  17. DNMT 1 maintains hypermethylation of CAG promoter specific region and prevents expression of exogenous gene in fat-1 transgenic sheep.

    Yang, Chunrong; Shang, Xueying; Cheng, Lei; Yang, Lei; Liu, Xuefei; Bai, Chunling; Wei, Zhuying; Hua, Jinlian; Li, Guangpeng

    2017-01-01

    Methylation is an important issue in gene expression regulation and also in the fields of genetics and reproduction. In this study, we created fat-1 transgenic sheep, investigated the fine-mapping and the modulatory mechanisms of promoter methylation. Sheep fetal fibroblasts were transfected by pCAG-fat1-IRES-EGFP. Monoclonal cell line was screened as nuclear donor and carried out nuclear transfer (441 transgenic cloned embryos, 52 synchronism recipient sheep). Six offsprings were obtained. Expressions of exogenous genes fat-1 and EGFP were detectable in 10 examined tissues and upregulated omega-3 fatty acid content. Interestingly, more or less EGFP negative cells were detectable in the positive transgenic fetal skin cells. EGFP negative and positive cells were sorted by flow cytometry, and their methylation status in the whole promoter region (1701 nt) were investigated by bisulphate sequencing. The fine-mapping of methylation in CAG promoter were proposed. The results suggested that exogenous gene expression was determined by the methylation status from 721-1346 nt and modulated by methylation levels at 101, 108 and 115 nt sites in CAG promoter. To clarify the regulatory mechanism of methylation, examination of four DNA methyltransferases (DNMTs) demonstrated that hypermethylation of CAG promoter is mainly maintained by DNMT 1 in EGFP negative cells. Furthermore, investigation of the cell surface antigen CD34, CD45 and CD166 indicated that EGFP positive and negative cells belong to different types. The present study systematically clarified methylation status of CAG promoter in transgenic sheep and regulatory mechanism, which will provide research strategies for gene expression regulation in transgenic animals.

  18. Nucleotide sequence of soybean chloroplast DNA regions which contain the psb A and trn H genes and cover the ends of the large single copy region and one end of the inverted repeats.

    Spielmann, A; Stutz, E

    1983-10-25

    The soybean chloroplast psb A gene (photosystem II thylakoid membrane protein of Mr 32 000, lysine-free) and the trn H gene (tRNAHisGUG), which both map in the large single copy region adjacent to one of the inverted repeat structures (IR1), have been sequenced including flanking regions. The psb A gene shows in its structural part 92% sequence homology with the corresponding genes of spinach and N. debneyi and contains also an open reading frame for 353 aminoacids. The aminoacid sequence of a potential primary translation product (calculated Mr, 38 904, no lysine) diverges from that of spinach and N. debneyi in only two positions in the C-terminal part. The trn H gene has the same polarity as the psb A gene and the coding region is located at the very end of the large single copy region. The deduced sequence of the soybean chloroplast tRNAHisGUG is identical with that of Zea mays chloroplasts. Both ends of the large single copy region were sequenced including a small segment of the adjacent IR1 and IR2.

  19. Natural selection in a population of Drosophila melanogaster explained by changes in gene expression caused by sequence variation in core promoter regions.

    Sato, Mitsuhiko P; Makino, Takashi; Kawata, Masakado

    2016-02-09

    Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations could promote adaptive phenotypic evolution. Recently, whole-genome sequence analyses have identified regulatory regions subject to natural selection. However, these studies could not identify the relationship between sequence variation in the detected regions and change in gene expression levels. We analyzed sequence variations in core promoter regions, which are critical regions for gene regulation in higher eukaryotes, in a natural population of Drosophila melanogaster, and identified core promoter sequence variations associated with differences in gene expression levels subjected to natural selection. Among the core promoter regions whose sequence variation could change transcription factor binding sites and explain differences in expression levels, three core promoter regions were detected as candidates associated with purifying selection or selective sweep and seven as candidates associated with balancing selection, excluding the possibility of linkage between these regions and core promoter regions. CHKov1, which confers resistance to the sigma virus and related insecticides, was identified as core promoter regions that has been subject to selective sweep, although it could not be denied that selection for variation in core promoter regions was due to linked single nucleotide polymorphisms in the regulatory region outside core promoter regions. Nucleotide changes in core promoter regions of CHKov1 caused the loss of two basal transcription factor binding sites and acquisition of one transcription factor binding site, resulting in decreased gene expression levels. Of nine core promoter regions regions associated with balancing selection, brat, and CG9044 are associated with neuromuscular junction development, and Nmda1 are associated with learning

  20. Association between VNTR polymorphism in promoter region of prodynorphin (PDYN) gene and heroin dependence.

    Saify, Khyber; Saadat, Iraj; Saadat, Mostafa

    2014-11-30

    Within the core promoter region of prodynorphin (PDYN), a 68-bp sequence was found to occur as a polymorphism element, either singular or as tandemly repeated two, three or four times. We report the sequence of a novel allele (5-repeats). Our study revealed the existence of an ancestral nucleotide (A) at 29th position of the VNTR in human. In total, 442 heroin addicts and 799 controls were included in this study. The present findings revealed a male-limited association between VNTR polymorphism and heroin dependence risk. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. [Association of single nucleotide polymorphisms of susceptibility genes of type 2 diabetes mellitus with liability to gout among ethnic Han Chinese males from coastal region of Shandong].

    Han, Lin; Xin, Ruosai; Sun, Jian; Hou, Feng; Li, Changgui; Hu, Xinlin; Liu, Zhen; Wang, Yao; Li, Xinde; Ren, Wei; Wang, Xuefeng; Jia, Zhaotong

    2015-10-01

    OBJECTIVE To assess the association of single nucleotide polymorphisms (SNPs) of susceptibility genes of type 2 diabetes mellitus (T2DM) with liability to gout among ethnic Han Chinese males from coastal region of Shandong province. METHODS Seven SNPs within the susceptibility genes of T2DM, including rs10773971(G/C) and rs4766398(G/C) of WNT5B gene, rs10225163(G/C) of JAZF1 gene, rs2069590(T/A) of BDKRB2 gene, rs5745709(G/A) of HGF gene, rs1991914(C/A) of OTOP1 gene and rs2236479(G/A) of COL18A1 gene, were typed with a custom-made Illumina GoldenGate Genotyping assay in 480 male patients with gout and 480 male controls. Potential association was assessed with the chi-square test. RESULTS No significant difference was detected for the 7 selected SNPs in terms of genotypic and allelic frequencies (P > 0.05). When age and body mass index (BMI) were adjusted, the 7 genetic variants still showed no significant association with gout. CONCLUSION The genotypes of the 7 selected SNPs are not associated with gout in ethnic Han Chinese male patients from the coastal region of Shandong province. However, the results need to be replicated in larger sets of patients collected from other regions and populations.

  2. A novel gene therapy-based approach that selectively targets hypoxic regions within solid tumors

    Dougherty, S.T.; Dougherty, G.J.; Davis, P.D.

    2003-01-01

    There is compelling evidence that malignant cells present within the hypoxic regions that are commonly found within solid tumors contribute significantly to local recurrence following radiation therapy. We describe now a novel strategy designed to target such cells that exploits the differential production within hypoxic regions of the pro-angiogenic cytokine vascular endothelial cell growth factor (VEGF). Specifically, we have generated cDNA constructs that encode two distinct chimeric cell surface proteins that incorporate, respectively, the extracellular domains of the VEGF receptors Flk-1 or Flt-1, fused in frame to the membrane spanning and cytoplasmic domains of the pro-apoptotic protein Fas. Both chimeric proteins (Flk/Fas and Flt/Fas) appear stable and can be readily detected on the surface of transfected cells by Western blot and/or FACS analysis. Importantly, tumor cells expressing the chimeric proteins were rapidly killed in a dose-dependent fashion upon the addition of exogenous recombinant VEGF. Adenoviral vectors encoding Flk/Fas have been generated and shown to induce tumor cells to undergo apoptosis upon transfer to hypoxic conditions in vitro. This activity is dependent upon the endogenous production of VEGF. Studies are currently underway to test the ability of adenoviral Flk/Fas (Ad.Flk/Fas) to reduce tumor recurrence in vivo when used as an adjuvant therapy in conjunction with clinically relevant doses of ionizing radiation

  3. Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5

    Hunt, Lilian E; Noyvert, Boris; Bhaw-Rosun, Leena

    2015-01-01

    BACKGROUND: Association studies have identified a number of loci that contribute to an increased body mass index (BMI), the strongest of which is in the first intron of the FTO gene on human chromosome 16q12.2. However, this region is both non-coding and under strong linkage disequilibrium, making...... it recalcitrant to functional interpretation. Furthermore, the FTO gene is located within a complex cis-regulatory landscape defined by a topologically associated domain that includes the IRXB gene cluster, a trio of developmental regulators. Consequently, at least three genes in this interval have been...... implicated in the aetiology of obesity. METHODS: Here, we sequence a 2 Mb region encompassing the FTO, RPGRIP1L and IRXB cluster genes in 284 individuals from a well-characterised study group of Danish men containing extremely overweight young adults and controls. We further replicate our findings both...

  4. Nucleotide sequence of the promoter region of the gene encoding chicken Calbindin D28K

    Ferrari, S; Drusiani, E; Battini, R; Fregni, M

    1988-01-11

    Calbindin D28K (formerly Vitamin D-Dependent Calcium Binding Protein) is a protein induced by 1,25-dihydroxycholecalciferol in several chicken tissues. A chicken genomic DNA library was screened with a synthetic oligonucleotide representing the sequence of Calbindin D18K cDNA from nt 146 to nt 176. The positive clone CBAl extends the 5'-end of the first exon by 451 bp. The sequence of a BamHI-SacII restriction fragment with coordinates -451 + 50 is shown. The BamHI-SacII fragment was subcloned 5' to the CAT gene of pUCCAT. The result is shown of a CAT assay on mouse fibroblasts 3T6 transiently transfected with pUCCAT, pUCCAT containing the BamHI-SacII fragment in the correct or opposite orientation or the SV40 promoter. /sup 14/C-chloramphenicol and its acetyl derivatives generated by purified CAT are also shown. The expression of CAT appears to be constitutive since the enzyme activity is not influenced by the presence (+) or absence (-) of 1,25-dihydroxycholecalciferol in the culture medium.

  5. Ellagic Acid-Changed Epigenome of Ribosomal Genes and Condensed RPA194-Positive Regions of Nucleoli in Tumour Cells.

    Legartová, S; Sbardella, G; Kozubek, S; Bártová, E

    2015-01-01

    We studied the effect of ellagic acid (EA) on the morphology of nucleoli and on the pattern of major proteins of the nucleolus. After EA treatment of HeLa cells, we observed condensation of nucleoli as documented by the pattern of argyrophilic nucleolar organizer regions (AgNORs). EA also induced condensation of RPA194-positive nucleolar regions, but no morphological changes were observed in nucleolar compartments positive for UBF1/2 proteins or fibrillarin. Studied morphological changes induced by EA were compared with the morphology of control, non-treated cells and with pronounced condensation of all nucleolar domains caused by actinomycin D (ACT-D) treatment. Similarly as ACT-D, but in a lesser extent, EA induced an increased number of 53BP1-positive DNA lesions. However, the main marker of DNA lesions, γH2AX, was not accumulated in body-like nuclear structures. An increased level of γH2AX was found by immunofluorescence and Western blots only after EA treatment. Intriguingly, the levels of fibrillarin, UBF1/2 and γH2AX were increased at the promoters of ribosomal genes, while 53BP1 and CARM1 levels were decreased by EA treatment at these genomic regions. In the entire genome, EA reduced H3R17 dimethylation. Taken together, ellagic acid is capable of significantly changing the nucleolar morphology and protein levels inside the nucleolus.

  6. Copy Number Variations in Candidate Genes and Intergenic Regions Affect Body Mass Index and Abdominal Obesity in Mexican Children

    Burguete-García, Ana Isabel; Bonnefond, Amélie; Peralta-Romero, Jesús; Froguel, Philippe

    2017-01-01

    Introduction. Increase in body weight is a gradual process that usually begins in childhood and in adolescence as a result of multiple interactions among environmental and genetic factors. This study aimed to analyze the relationship between copy number variants (CNVs) in five genes and four intergenic regions with obesity in Mexican children. Methods. We studied 1423 children aged 6–12 years. Anthropometric measurements and blood levels of biochemical parameters were obtained. Identification of CNVs was performed by real-time PCR. The effect of CNVs on obesity or body composition was assessed using regression models adjusted for age, gender, and family history of obesity. Results. Gains in copy numbers of LEPR and NEGR1 were associated with decreased body mass index (BMI), waist circumference (WC), and risk of abdominal obesity, whereas gain in ARHGEF4 and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d and losses in INS were associated with increased BMI and WC. Conclusion. Our results indicate a possible contribution of CNVs in LEPR, NEGR1, ARHGEF4, and CPXCR1 and the intergenic regions 12q15c, 15q21.1a, and 22q11.21d to the development of obesity, particularly abdominal obesity in Mexican children. PMID:28428959

  7. 3D printed hyperelastic "bone" scaffolds and regional gene therapy: A novel approach to bone healing.

    Alluri, Ram; Jakus, Adam; Bougioukli, Sofia; Pannell, William; Sugiyama, Osamu; Tang, Amy; Shah, Ramille; Lieberman, Jay R

    2018-04-01

    The purpose of this study was to evaluate the viability of human adipose-derived stem cells (ADSCs) transduced with a lentiviral (LV) vector to overexpress bone morphogenetic protein-2 (BMP-2) loaded onto a novel 3D printed scaffold. Human ADSCs were transduced with a LV vector carrying the cDNA for BMP-2. The transduced cells were loaded onto a 3D printed Hyperelastic "Bone" (HB) scaffold. In vitro BMP-2 production was assessed using enzyme-linked immunosorbent assay analysis. The ability of ADSCs loaded on the HB scaffold to induce in vivo bone formation in a hind limb muscle pouch model was assessed in the following groups: ADSCs transduced with LV-BMP-2, LV-green fluorescent protein, ADSCs alone, and empty HB scaffolds. Bone formation was assessed using radiographs, histology and histomorphometry. Transduced ADSCs BMP-2 production on the HB scaffold at 24 hours was similar on 3D printed HB scaffolds versus control wells with transduced cells alone, and continued to increase after 1 and 2 weeks of culture. Bone formation was noted in LV-BMP-2 animals on plain radiographs at 2 and 4 weeks after implantation; no bone formation was noted in the other groups. Histology demonstrated that the LV-BMP-2 group was the only group that formed woven bone and the mean bone area/tissue area was significantly greater when compared with the other groups. 3D printed HB scaffolds are effective carriers for transduced ADSCs to promote bone repair. The combination of gene therapy and tissue engineered scaffolds is a promising multidisciplinary approach to bone repair with significant clinical potential. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 106A: 1104-1110, 2018. © 2018 Wiley Periodicals, Inc.

  8. Variants in adjacent oxytocin/vasopressin gene region and associations with ASD diagnosis and other autism related endophenotypes

    Sunday M. Francis

    2016-05-01

    Full Text Available Background: There has been increasing interest in oxytocin (peptide: OT, gene: OXT as a treatment pathway for neurodevelopmental disorders such as Autism Spectrum Disorder (ASD. Neurodevelopmental disorders affect functional, social, and intellectual abilities. With advances in molecular biology, research has connected multiple gene regions to the clinical presentation of ASD. Studies have also shown that the neuropeptide hormones OT and arginine vasopressin (AVP influence mammalian social and territorial behaviors and may have treatment potential for neurodevelopmental disorders. Published data examining molecular and phenotypic variation in ASD, such as cognitive abilities, are limited. Since most studies have focused on the receptors in the OT-AVP system, we investigated genetic variation within peptide genes for association with phenotypic ASD features that help identify subgroups within the spectrum.Methods: In this study, TDT analysis was carried out utilizing FBAT in 207 probands (156 trios and a European Ancestry (EA subsample (108 trios. The evolutionarily related and adjacent genes of OXT and AVP were studied for associations between the tagged single nucleotide polymorphisms and ASD diagnosis, social abilities, restrictive and repetitive behaviors, and IQ for cognitive abilities. Additionally, relationships with whole blood serotonin (WB5HT were explored because of the developmental relationships connecting plasma levels of OT and WB5HT within ASD.Results: Results indicate significant association between OXT rs6084258 (p=0.001 and ASD. Associations with several intermediate phenotypes were also noted: OXT rs6133010 was associated with IQ (full scale IQ, p=0.008; nonverbal IQ, p=0.010, verbal IQ, p=0.006; and OXT rs4813625 and OXT rs877172 were associated with WB5HT levels (EA, p=0.027 and p=0.033, respectively. Additionally, we measured plasma OT (pOT levels in a subsample (N=54. Results show the three polymorphisms, OXT rs6084258

  9. Variants in Adjacent Oxytocin/Vasopressin Gene Region and Associations with ASD Diagnosis and Other Autism Related Endophenotypes.

    Francis, Sunday M; Kistner-Griffin, Emily; Yan, Zhongyu; Guter, Stephen; Cook, Edwin H; Jacob, Suma

    2016-01-01

    There has been increasing interest in oxytocin (peptide: OT, gene: OXT) as a treatment pathway for neurodevelopmental disorders such as Autism Spectrum Disorder (ASD). Neurodevelopmental disorders affect functional, social, and intellectual abilities. With advances in molecular biology, research has connected multiple gene regions to the clinical presentation of ASD. Studies have also shown that the neuropeptide hormones OT and arginine vasopressin (AVP) influence mammalian social and territorial behaviors and may have treatment potential for neurodevelopmental disorders. Published data examining molecular and phenotypic variation in ASD, such as cognitive abilities, are limited. Since most studies have focused on the receptors in the OT-AVP system, we investigated genetic variation within peptide genes for association with phenotypic ASD features that help identify subgroups within the spectrum. In this study, TDT analysis was carried out utilizing FBAT in 207 probands (156 trios) and a European Ancestry (EA) subsample (108 trios).The evolutionarily related and adjacent genes of OXT and AVP were studied for associations between the tagged single nucleotide polymorphisms and ASD diagnosis, social abilities, restrictive and repetitive behaviors, and IQ for cognitive abilities. Additionally, relationships with whole blood serotonin (WB5HT) were explored because of the developmental relationships connecting plasma levels of OT and WB5HT within ASD. RESULTS indicate significant association between OXT rs6084258 (p = 0.001) and ASD. Associations with several endophenotypes were also noted: OXT rs6133010 was associated with IQ (full scale IQ, p = 0.008; nonverbal IQ, p = 0.010, verbal IQ, p = 0.006); and OXT rs4813625 and OXT rs877172 were associated with WB5HT levels (EA, p = 0.027 and p = 0.033, respectively). Additionally, we measured plasma OT (pOT) levels in a subsample (N = 54). RESULTS show the three polymorphisms, OXT rs6084258, OXT rs11697250, and OXT rs877172

  10. A novel TaqI polymorphism in the coding region of the ovine TNXB gene in the MHC class III region: morphostructural and physiological influences.

    Ajayi, Oyeyemi O; Adefenwa, Mufliat A; Agaviezor, Brilliant O; Ikeobi, Christian O N; Wheto, Matthew; Okpeku, Moses; Amusan, Samuel A; Yakubu, Abdulmojeed; De Donato, Marcos; Peters, Sunday O; Imumorin, Ikhide G

    2014-02-01

    The tenascin-XB (TNXB) gene has antiadhesive effects, functions in matrix maturation in connective tissues, and localizes to the major histocompatibility complex class III region. We hypothesized that it may influence adaptive physiological response through an effect on blood vessel function. We identified a novel g.1324 A→G polymorphism at a TaqI recognition site in a 454 bp fragment of ovine TNXB and genotyped it in 150 Nigerian sheep using PCR-RFLP. The missense mutation changes glutamic acid (GAA) to glycine (GGA). Among SNP genotypes, significant differences (P bone length. Interaction effects of breed, SNP genotype, and geographic location had a significant effect (P < 0.05) on chest girth. The SNP genotype was significantly (P < 0.05) associated with physiological traits of pulse rate and skin temperature. The observed effect of this novel polymorphism may be mediated through its role in connective tissue biology, requiring further association and functional studies.

  11. Modifier genes: Moving from pathogenesis to therapy.

    McCabe, Edward R B

    2017-09-01

    This commentary will focus on how we can use our knowledge about the complexity of human disease and its pathogenesis to identify novel approaches to therapy. We know that even for single gene Mendelian disorders, patients with identical mutations often have different presentations and outcomes. This lack of genotype-phenotype correlation led us and others to examine the roles of modifier genes in the context of biological networks. These investigations have utilized vertebrate and invertebrate model organisms. Since one of the goals of research on modifier genes and networks is to identify novel therapeutic targets, the challenges to patient access and compliance because of the high costs of medications for rare genetic diseases must be recognized. A recent article explored protective modifiers, including plastin 3 (PLS3) and coronin 1C (CORO1C), in spinal muscular atrophy (SMA). SMA is an autosomal recessive deficit of survival motor neuron protein (SMN) caused by mutations in SMN1. However, the severity of SMA is determined primarily by the number of SMN2 copies, and this results in significant phenotypic variability. PLS3 was upregulated in siblings who were asymptomatic compared with those who had SMA2 or SMA3, but identical homozygous SMN1 deletions and equal numbers of SMN2 copies. CORO1C was identified by interrogation of the PLS3 interactome. Overexpression of these proteins rescued endocytosis in SMA models. In addition, antisense RNA for upregulation of SMN2 protein expression is being developed as another way of modifying the SMA phenotype. These investigations suggest the practical application of protective modifiers to rescue SMA phenotypes. Other examples of the potential therapeutic value of novel protective modifiers will be discussed, including in Duchenne muscular dystrophy and glycerol kinase deficiency. This work shows that while we live in an exciting era of genomic sequencing, a functional understanding of biology, the impact of its

  12. Cure SMA

    ... 2, 2017 New Clinical Trial Data Published in New England Journal of Medicine Two new papers of clinical trial data for spinal muscular atrophy were published today in the November issue of the New England Journal of... READ MORE October 25, 2017 Fall 2017 ...

  13. High-Throughput Screening for Spermatogenesis Candidate Genes in the AZFc Region of the Y Chromosome by Multiplex Real Time PCR Followed by High Resolution Melting Analysis

    Alechine, Evguenia; Corach, Daniel

    2014-01-01

    Microdeletions in the AZF region of the Y chromosome are among the most frequent genetic causes of male infertility, although the specific role of the genes located in this region is not fully understood. AZFa and AZFb deletions impair spermatogenesis since no spermatozoa are found in the testis. Deletions of the AZFc region, despite being the most frequent in azoospermic patients, do not correlate with spermatogenic failure. Therefore, the aim of this work was to develop a screening method t...

  14. High-throughput screening for spermatogenesis candidate genes in the AZFc region of the Y chromosome by multiplex real time PCR followed by high resolution melting analysis

    Alechine, Evguenia; Corach, Daniel

    2017-01-01

    Microdeletions in the AZF region of the Y chromosome are among the most frequent genetic causes of male infertility, although the specific role of the genes located in this region is not fully understood. AZFa and AZFb deletions impair spermatogenesis since no spermatozoa are found in the testis. Deletions of the AZFc region, despite being the most frequent in azoospermic patients, do not correlate with spermatogenic failure. Therefore, the aim of this work was to develop a screening method t...

  15. FOXC2 mRNA Expression and a 5' untranslated region polymorphism of the gene are associated with insulin resistance

    Ridderstråle, Martin; Carlsson, Emma; Klannemark, Mia

    2002-01-01

    with subcutaneous fat from obese subjects (12 +/- 4-fold; P = 0.0001), and there was a correlation between whole-body insulin sensitivity and FOXC2 mRNA levels in visceral fat (fS-insulin R = -0.64, P = 0.01, and homeostasis model assessment of insulin resistance [HOMA-IR] R = -0.68, P = 0.007) and skeletal muscle...... (fS-insulin R = -0.57, P = 0.03, and HOMA-IR R = -0.55, P = 0.04). Mutation screening of the FOXC2 gene identified a common polymorphism in the 5' untranslated region (C-512T). The T allele was associated with enhanced insulin sensitivity (HOMA-IR P = 0.007) and lower plasma triglyceride levels...

  16. Analysis of polymorphisms in the promoter region and protein levels of interleukin-6 gene among gout patients.

    Tsai, P-C; Chen, C-J; Lai, H-M; Chang, S-J

    2008-01-01

    To explore the associations between the polymorphisms and protein levels of interleukin-6 (IL-6) gene and gout disease. A total of 120 male gout patients and 184 healthy controls were enrolled. Each patient was matched with 1-2 gout-free controls by age within three years. Four polymorphisms in the promoter of IL-6 gene, including -597G/A, -572C/G, -373A(m)T(n), and -174G/C, and the IL-6 levels were analyzed. The clinical characteristics and biochemical markers in plasma were measured, including age of gout onset, duration of gout history, tophus number, gout attack frequency, uric acid, total cholesterol, triglycerides and creatinine. The mean IL-6 level for gout patients was 9.80 (+/-11.76 pg/ml) which showed no significant difference from the controls (7.06+/-7.58 pg/ml, p=0.230). When the IL-6 levels were dichotomized according to the median value (5 pg/ml), there were significantly higher proportions of the gout patients (59.66%) than controls (44%) with high IL-6 levels (OR=1.88, 95% CI=1.17-3.02, p=0.008). Unique genotype was found at polymorphisms -174G/C and -597G/A. Neither the polymorphisms -572C/G nor -373A(m)T(n) in the genotype or allele distributions showed a significant association related to clinical characteristics, biochemical markers, IL-6 levels or gout disease (all p>0.05). Those with gout disease have greater proportions of high IL-6 levels in plasma than controls, and there is no significant association between the four polymorphisms in the promoter region of IL-6 gene and gout disease.

  17. Taq I polymorphism in the 5' region of the von Willebrand Factor (vWF) gene

    Lavergne, J M; Bahnak, B R; Assouline, Z; Pietu, G; Kerbiriou-Nabias, D; Meulien, P; Pavirani, A; Meyer, D

    1988-03-25

    pvWFIPC8 is a 2.28 Kb partial cDNA clone for human von Willebrand factor (vWF) isolated from a human lung cDNA library and inserted into the EcoRI site of pUC9. The sequence includes the last 1330 nucleotides that encode for vWF propeptide and 950 nucleotides that encode for mature vWF. Taq I (TCGA) identifies plural invariant bands and two variant bands with alleles at 2.3 (Al) and 1.0 (A2). The frequency was determined in 33 unrelated European and North American caucasians. The extreme 3' region of pvWFIPC8 corresponds to the 5' boundary of an area that could possibly hybridize with similar sequences on human chromosome 22. The 5' 1.74 Kb portion of pvWFIPC8 generated by Bam HI digestion that corresponds to sequences only on chromosome 12 also demonstrates the polymorphism. Co-dominant segregation was demonstrated in 6 families of 48 individuals.

  18. In silico comparison of genomic regions containing genes coding for enzymes and transcription factors for the phenylpropanoid pathway in Phaseolus vulgaris L. and Glycine max L. Merr

    Yarmilla eReinprecht

    2013-09-01

    Full Text Available Legumes contain a variety of phytochemicals derived from the phenylpropanoid pathway that have important effects on human health as well as seed coat color, plant disease resistance and nodulation. However, the information about the genes involved in this important pathway is fragmentary in common bean (Phaseolus vulgaris L.. The objectives of this research were to isolate genes that function in and control the phenylpropanoid pathway in common bean, determine their genomic locations in silico in common bean and soybean, and analyze sequences of the 4CL gene family in two common bean genotypes. Sequences of phenylpropanoid pathway genes available for common bean or other plant species were aligned, and the conserved regions were used to design sequence-specific primers. The PCR products were cloned and sequenced and the gene sequences along with common bean gene-based (g markers were BLASTed against the Glycine max v.1.0 genome and the P. vulgaris v.1.0 (Andean early release genome. In addition, gene sequences were BLASTed against the OAC Rex (Mesoamerican genome sequence assembly. In total, fragments of 46 structural and regulatory phenylpropanoid pathway genes were characterized in this way and placed in silico on common bean and soybean sequence maps. The maps contain over 250 common bean g and SSR (simple sequence repeat markers and identify the positions of more than 60 additional phenylpropanoid pathway gene sequences, plus the putative locations of seed coat color genes. The majority of cloned phenylpropanoid pathway gene sequences were mapped to one location in the common bean genome but had two positions in soybean. The comparison of the genomic maps confirmed previous studies, which show that common bean and soybean share genomic regions, including those containing phenylpropanoid pathway gene sequences, with conserved synteny. Indels identified in the comparison of Andean and Mesoamerican common bean sequences might be used to develop

  19. Expression profile analysis of aorta-gonad-mesonephros region-derived stromal cells reveals genes that regulate hematopoiesis

    Nagao, Kenji; Ohta, Takayuki; Hinohara, Atsushi; Tahara, Tomoyuki; Hagiwara, Tetsuya; Maeda, Yoshitake; Yoneya, Takashi; Sohma, Yoshiaki; Heike, Toshio; Nakahata, Tatsutoshi; Inagaki, Yoshimasa; Nishikawa, Mitsuo

    2008-01-01

    The aorta-gonad-mesonephros (AGM) region is involved in the generation and maintenance of the first definitive hematopoietic stem cells (HSCs). A mouse AGM-derived cell line, AGM-S3, was shown to support the development of HSCs. To elucidate the molecular mechanisms regulating early hematopoiesis, we obtained subclones from AGM-S3, one of which was hematopoiesis supportive (S3-A9) and the other one of which was non-supportive (S3-A7), and we analyzed their gene expression profiles by gene chip analysis. In the present study, we found that Glypican-1 (GPC1) was highly expressed in the supportive subclone AGM-S3-A9. Over-expression of GPC1 in non-supportive cells led to the proliferation of progenitor cells in human cord blood when cocultured with the transfected-stromal cells. Thus, GPC1 may have an important role in the establishment of a microenvironment that supports early events in hematopoiesis

  20. Association study between a polymorphism at the 3'-untranslated region of CLOCK gene and attention deficit hyperactivity disorder

    Xu Xiaohui

    2010-08-01

    Full Text Available Abstract Background The circadian locomotor output cycles kaput (CLOCK gene encodes protein regulation circadian rhythm and also plays some roles in neural transmitter systems including the dopamine system. Several lines of evidence implicate a relationship between attention-deficit hyperactivity disorder (ADHD, circadian rythmicity and sleeping disturbances. A recent study has reported that a polymorphism (rs1801260 at the 3'-untranslated region of the CLOCK gene is associated with adult ADHD. Methods To investigate the association between the polymorphism (rs1801260 in ADHD, two samples of ADHD probands from the United Kingdom (n = 180 and Taiwan (n = 212 were genotyped and analysed using within-family transmission disequilibrium test (TDT. Bonferroni correction procedures were used to just for multiple comparisons. Results We found evidence of increased transmission of the T allele of the rs1801260 polymorphism in Taiwanese samples (P = 0.010. There was also evidence of preferential transmission of the T allele of the rs1801260 polymorphism in combined samples from the Taiwan and UK (P = 0.008. Conclusion This study provides evidence for the possible involvement of CLOCK in susceptibility to ADHD.

  1. The 3'-untranslated region of the HLA-G gene in relation to pre-eclampsia: revisited

    Larsen, M H; Hylenius, S; Andersen, Anne-Marie Nybo

    2010-01-01

    Abnormal human leukocyte antigen G (HLA-G) expression may be involved in pre-eclampsia. A 14 bp insertion/deletion polymorphism exists in exon 8 of the HLA-G gene. Fetal +14/+14 bp HLA-G genotype may predispose to pre-eclampsia in the mother. Other polymorphisms, besides the 14 bp polymorphism (rs......66554220), in the 3'-untranslated region (3'-UTR) (exon 8) of the HLA-G gene might be associated with severe pre-eclampsia, especially in primiparas. By haplotype-specific polymerase chain reaction amplification and DNA sequence analysis in the offspring from 50 pre-eclamptic cases and 85 controls (35.......008, P(C) = 0.04) were significantly associated with severe pre-eclampsia in primiparas. In conclusion, this study indicates that the +14 bp HLA-G allele defines a nearly unique exon 8 haplotype, and fetuses homozygous for this haplotype [SNP 2995(C)/SNP 3127(G)/SNP 3172(A)/SNP 3181(G)/+14 bp...

  2. [Structure of the gene pool of ethnic groups from the Altai-Sayan region from data on mitochondrial polymorphism].

    Derenko, M V; Denisova, G A; Maliarchuk, B A; Dambueva, I K; Luzina, F A; Lotosh, E A; Dorzhu, Ch M; Karamchakova, O N; Solovenchuk, L L; Zakharov, I A

    2001-10-01

    Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the four Turkic-speaking ethnic groups of Altai-Sayan highlands, Southern Altaians (Altai-Kizhi), Khakassians, Shorians, and Sojots, were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E, G, A, B, and F) and Caucasoid (H, U, T, J, and K) mtDNA lineages. All the populations studied had a strongly pronounced Mongoloid component, the frequency of which was 88.2% in Sojots, 75.9% in Khakassians, 67.4% in Altaians, and 64.3% in Shorians. Maximum frequency of the Caucasoid component (35.7%) was observed in Shorians. Phylogenetic and statistical analyses of the mtDNA group frequency distribution patterns in the gene pools of the ethnic populations of Altai-Sayan highlands and the adjacent territories showed that the populations of the region fell into three groups. The first group included Khakassians, Tuvinians and Altaians, the second group consisted of Sojots, Buryats, and Mongols, while the third group was composed of Uigurs, Kazakhs, and Kyrgyzes. The isolated position of Shorians among the populations examined can be explained by their different anthropological composition and their presumptive relatedness to Finno-Ugric populations of Siberia.

  3. Association analysis between genetic variants in interleukin genes among different populations with hyperuricemia in Xinjiang Autonomous Region

    Zhang, Bei; Sun, Yuping; Li, Yuanyuan; Yu, Jiahui; Wang, Tingting; Xia, He; Li, Changgui; Liu, Shiguo; Yao, Hua

    2015-01-01

    To investigate whether functional variants of five interleukin genes (IL-1β, IL-10, IL-8, IL-18 and IL-18RAP) are associated with susceptibility to hyperuricemia among different nationalities (including Uygur, Kazak and Han populations) in the Xinjiang Autonomous Region of China. A total of 884 hyperuricemia patients and 1316 matched controls were recruited from the First Affiliated Hospital of Xinjiang Medical University in Urumqi. After genotyping of rs4073 in IL-8, rs16944 in IL-1, rs187238 in IL-18, rs1800871 in IL-10 and rs13015714 in IL-18RAP by TaqMan allele discrimination assays, an association analysis was performed using the χ2 test as well as a genotype-phenotype analysis. For the Uygur population, IL-8 rs4073, IL-18 rs187238 and IL-18RAP rs130154 polymorphisms were all associated with hyperuricemia (P<0.001 by genotype and P=0.008, OR 0.802 by allele for IL-8; P=0.01 by genotype and P=0.006, OR 1.332 by allele for IL-18 rs187238; P=0.007 by genotype and P=0.005, OR 1.27 by allele for IL-18RAP rs130154). For the Kazak population, only IL-18 rs187238 showed statistical significance with hyperuricemia (P=0.002 by genotype and P=0.007, OR 1.823 by allele). However, no differences were found between the five SNPs and hyperuricemia among the Han population. This study demonstrated genetic polymorphisms of different interleukin genes related to hyperuricemia vary in different nationalities in the Xinjiang Autonomous Region because of different geographical environments. IL-8, IL-1RL1 and IL-18 might be involved in the development of hyperuricemia in the Uygur population, whereas only IL-18 might be involved in the Kazak population. PMID:26722554

  4. Profil Problem Emosi/ Perilaku Pada Remaja Pelajar SMP-SMA Di Kota Semarang

    Annastasia Ediati

    2015-10-01

    Full Text Available The aims of this study is to identify the profile of emotional/behavioral problems on adolescents students of junior and senior high school (SMP-SMA in Semarang, Central Java. The subjects comprised 568 students (grade VII and X; males and females, aged between 13-17 years. Data were collected using the Indonesian translation of the Youth Self Report (YSR. The results of data analysis showed that adolescents in the junior high school/SMP reported emotional/behavioral problems more frequently than the adolescents in the senior high school/SMA (t (566 = 2.08, p = .038, especially in terms of social relations (t (566 = 2.92, p = .004, thought problems (t (566 = 2.47, p = .014, somatic complaints (t(566 = 2.98, p = .002, rule-breaking behavior (t (566 = 6.63, p < .001, and externalizing problems (t(566 = 3,37; p = .001. Gender differences was found in the adolescents’ emotional/behavioral problems. In group of junior high school students (SMP, girls reported more emotional problems than boys (t(335 = -3.55; p < .001, particularly in anxiety/depression (t(335 = -6.51; p < .001; withdrawal (t(335 = -4.26; p < .001, somatic complaints (t(335 = -2.86; p = .004; social problems (t(335 = -3.30; p = .001, attention problems (t(335 = -2.39; p = .017; and internalizing problem (t(335 = -5.76; p < .001. In group of senior high school students (SMA, boys reported more externalizing problems (t(229 = 2.10; p = .037 and rule-breaking behavior (t(229 = 4.44; p < .001 than girls. In contrasts, girls reported more somatic complaints than boys (t(229 = -3.09; p = .001. Adolescents’ emotional/behavioral problems should gained more attention. Preventive as well as curative intervention is needed, particularly intervention that sensitive to gender and age, which also involve significant figures for adolescents (parents, school teachers, and peers.

  5. Experimental study on tunnel lining joints temporarily strengthened by SMA bolts

    Wu, Bo; Ou, Yunlong

    2014-01-01

    Shield tunnels have been widely used in city metros all over the world. During the long-term period of the metro operation, the joints of shield tunnel’s neighboring segments may degrade due to some environmental factors, leading to the increasing of the joint opening and some resulting adverse consequences. In this paper, a temporary strengthening method by using shape memory alloy (SMA) bolts is proposed and experimentally studied for the joints of neighboring segments, and a revised electric heating method which suits with the strengthening method is presented and experimentally validated for the SMA bolts. The purpose of the proposed temporary strengthening method is to create favorable conditions for the following permanent strengthening. Test results show that: (a) for the joints of shield tunnel’s neighboring segments, the strengthening method can effectively reduce the joint opening, joint deflection, concrete strain in joint’s compression zone, and strain of joint’s steel bolts; (b) the revised electric heating method can be used to heat the SMA rod to a temperature higher than the SMA’s austenite finish temperature quickly, and the average heating rate related to Type 2 inner resistance element is larger than that related to Type 1 inner resistance element; and (c) the reduction percentages of the joint opening increment, joint deflection, concrete strain in joint’s compression zone, and strain of joint’s steel bolts for Specimen I are all larger than those for Specimen II, implying that the less the joint opening is, the more significant the strengthening effect is. (paper)

  6. KEMAMPUAN PROFESIONAL GURU BIOLOGI DALAM MEMAHAMI DAN MERANCANG MODEL PEMBELAJARAN KONSERVASI BIODIVERSITAS DI SMA

    Suroso Mukti Leksono

    2013-11-01

    Full Text Available Abstrak: Tujuan penelitian ini adalah untuk mengetahui penguasaan konsep konservasi biodiversitas guru biologi dan cara mengajarkannya. Penelitian ini menggunakan metode deskriptif dengan menggunakan angket pada 31 guru SMA/MA di Kota/Kab Serang. Hasil penelitian menunjukkan bahwa 52% guru telah memahami konsep biodiversitas, namun hanya 3% yang memahami konsep konservasi. Model yang digunakan guru dalam mengajarkan konservasi biodiversitas, 58% menggunakan observasi, 45% diskusi, 23% ceramah dan 16% tanya jawab. Untuk tingkat kesukaran, 87% guru beranggapan mudah memahami materi konservasi biodiversitas dan 81% beranggapan mudah mengajarkannya dibandingkan dengan materi IPA lainnya. Guru-guru selama ini hanya 6% saja yang memperoleh pengetahuan tentang konservasi biodiversitas pada saat pelatihan. Oleh sebab itu diperlukan pelatihan-pelatihan melalui Continuing Professional Development (CPD. Kata Kunci: guru profesional, konservasi biodiversitas, continuing professional development (CPD BIOLOGY TEACHERS’ PROFESSIONAL ABILITY IN UNDERSTANDING AND DESIGNING INSTRUCTION ON BIODIVERSITY CONSERVATION IN SMA Abstract: The purpose of this study was to gain the knowledge about biology teachers’ concept mastery on biodiversity conservation as well as how to teach it. This study used descriptive methods with the questionnaires to 31 respondents of SMA/MA in Kota/KabSerang. The research result showed that 52% respondents had mastered the biodiversity concept. However, only 3% of respondents had fully mastered biodiversity conservation. In addition, for the teaching methods 58% respondents used observation, 45% respondents used discussion, 23% respondents used lecturing and 16% respondents used an interactive method. Moreover, for the difficulty level, 87% of respondents argued that it was easy to master the biodiversity conservation materials and 81% said that it was easier to teach the concept than other concepts. Only 6% of the teachers had gained

  7. Pola Pembinaan Kompetensi Kepribadian dan Kompetensi Sosial Guru di SMA Muhammadiyah 1 Ponorogo

    Bambang Wahrudin

    2017-11-01

    Full Text Available This research is motivated by the importance of personal competence and social competence teacher as the spirit of education. The focus of reasearch is know the program fostering personal competence and social competence teacherin SMA Muhammadiyah 1 Ponorogo . Deep observation and interview used in this research by qualitative aproach. The result shows that personality competence development programs conducted in six (6 forms include: 1 Dhuhr and Asr prayers in congregation, 2 Baitul Arqom for teachers and employees, 3 Course / tahsin read the Koran for teachers and employees, 4 Pray tahajud ahad congregation every morning, and 5 Training Motivation and 6 Counseling, whereas social competence training program conducted by three (3 forms, namely: 1 Piket Sympathetic, 2 MGMPs and 3 Sinergy Building. These patern have made theacher have stong  professionaly and  authority Abstrak Penelitian ini dilatarbelakangi oleh pentingnya kompetensi kepribadian dan kompetensi sosial bagi guru sebagai ruh pendidikan. Penelitian ini bertujuan untuk mengetahui program pembinaan kompetensi kepribadian dan kompetensi sosial guru di SMA Muhammadiyah 1 Ponorogo. Reset mendalam dilakukan secara kualitatif. Hasil penelitian menunjukkaan bahwa Program pembinaan kompetensi kepribadian dan kompetensi sosial sumber daya manusia di SMA Muhammadiyah 1 Ponorogo menggunakan 6 (enam bentuk meliputi: 1. sholat Dhuhur dan Ashar berjamaah, 2. baitul Arqom untuk guru dan karyawan, 3. kursus/tahsin baca al-Qur’an untuk guru dan karyawan, 4. sholat tahajud berjamaah setiap ahad dini hari, dan 5. training motivasi dan 6. konseling, sedangkan program pembinaan kompetensi sosial dilakukan dengan 3 (tiga bentuk, yaitu: 1. paket Simpatik, 2.  MGMP dan 3. sinergy Building. Pola ini telah berhasil menghantarkan guru sebagai guru yang profesional yang kuat dan berwibawa.

  8. Advanced methods for the analysis, design, and optimization of SMA-based aerostructures

    Hartl, D J; Lagoudas, D C; Calkins, F T

    2011-01-01

    Engineers continue to apply shape memory alloys to aerospace actuation applications due to their high energy density, robust solid-state actuation, and silent and shock-free operation. Past design and development of such actuators relied on experimental trial and error and empirically derived graphical methods. Over the last two decades, however, it has been repeatedly demonstrated that existing SMA constitutive models can capture stabilized SMA transformation behaviors with sufficient accuracy. This work builds upon past successes and suggests a general framework by which predictive tools can be used to assess the responses of many possible design configurations in an automated fashion. By applying methods of design optimization, it is shown that the integrated implementation of appropriate analysis tools can guide engineers and designers to the best design configurations. A general design optimization framework is proposed for the consideration of any SMA component or assembly of such components that applies when the set of design variables includes many members. This is accomplished by relying on commercially available software and utilizing tools already well established in the design optimization community. Such tools are combined with finite element analysis (FEA) packages that consider a multitude of structural effects. The foundation of this work is a three-dimensional thermomechanical constitutive model for SMAs applicable for arbitrarily shaped bodies. A reduced-order implementation also allows computationally efficient analysis of structural components such as wires, rods, beams and shells. The use of multiple optimization schemes, the consideration of assembled components, and the accuracy of the implemented constitutive model in full and reduced-order forms are all demonstrated

  9. Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains.

    Monerawela, Chandre; James, Tharappel C; Wolfe, Kenneth H; Bond, Ursula

    2015-03-01

    Lager yeasts, Saccharomyces pastorianus, are interspecies hybrids between S. cerevisiae and S. eubayanus and are classified into Group I and Group II clades. The genome of the Group II strain, Weihenstephan 34/70, contains eight so-called 'lager-specific' genes that are located in subtelomeric regions. We evaluated the origins of these genes through bioinformatic and PCR analyses of Saccharomyces genomes. We determined that four are of cerevisiae origin while four originate from S. eubayanus. The Group I yeasts contain all four S. eubayanus genes but individual strains contain only a subset of the cerevisiae genes. We identified S. cerevisiae strains that contain all four cerevisiae 'lager-specific' genes, and distinct patterns of loss of these genes in other strains. Analysis of the subtelomeric regions uncovered patterns of loss in different S. cerevisiae strains. We identify two classes of S. cerevisiae strains: ale yeasts (Foster O) and stout yeasts with patterns of 'lager-specific' genes and subtelomeric regions identical to Group I and II S. pastorianus yeasts, respectively. These findings lead us to propose that Group I and II S. pastorianus strains originate from separate hybridization events involving different S. cerevisiae lineages. Using the combined bioinformatic and PCR data, we describe a potential classification map for industrial yeasts. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  10. Structure and expression of MHC class Ib genes of the central M region in rat and mouse: M4, M5, and M6.

    Lambracht-Washington, Doris; Moore, Yuki F; Wonigeit, Kurt; Lindahl, Kirsten Fischer

    2008-04-01

    The M region at the telomeric end of the murine major histocompatibility complex (MHC) contains class I genes that are highly conserved in rat and mouse. We have sequenced a cosmid clone of the LEW rat strain (RT1 haplotype) containing three class I genes, RT1.M6-1, RT1.M4, and RT1.M5. The sequences of allelic genes of the BN strain (RT1n haplotype) were obtained either from cDNAs or genomic clones. For the coding parts of the genes few differences were found between the two RT1 haplotypes. In LEW, however, only RT1.M5 and RT1.M6 have open reading frames; whereas in BN all three genes were intact. In line with the findings in BN, transcription was found for all three rat genes in several tissues from strain Sprague Dawley. Protein expression in transfectants could be demonstrated for RT1.M6-1 using the monoclonal antibody OX18. By sequencing of transcripts obtained by RT-PCR, a second, transcribed M6 gene, RT1.M6-2, was discovered, which maps next to RT1.M6-1 outside of the region covered by the cosmid. In addition, alternatively spliced forms for RT1.M5 and RT1.M6 were detected. Of the orthologous mouse genes, H2-M4, H2-M5, and H2-M6, only H2-M5 has an open reading frame. Other important differences between the corresponding parts of the M region of the two species are insertion of long LINE repeats, duplication of RT1.M6, and the inversion of RT1.M5 in the rat. This demonstrates substantial evolutionary dynamics in this region despite conservation of the class I gene sequences themselves.

  11. Analisis Dampak Negatif Facebook pada Remaja Kelas X IPS SMA Kemala Bhayangkari Kubu Raya

    Malindo, Hari

    2017-01-01

    The negative impact of the use of facebook is a result caused the use of facebook excessively that can give rise to abuse and diversion to brpengaruh directly to the consumer, and often waste time just to tamper with his facebook account, if not used wisely facebook will have a negative impact to pengggunanya it sendiri..Oleh because the researchers wanted to know more profound analysis of the negative impact on teenagers facebook IPS class X SMA Kemala Bhayangkari Kubu Raya.A common problem ...

  12. MODEL EVALUASI INTERNAL KOMPETENSI GURU BAHASA INGGRIS (MODEL_EIKGBI SMA

    Sahraini Sahraini

    2015-10-01

    Full Text Available Studi ini bertujuan untuk: (1 mengembangkan model evaluasi kompetensi guru bahasa Inggris SMA yang dapat digunakan untuk mengidentifikasi kelebihan dan kekurangan guru dalam proses pemelajaran dan (2 mengetahui efektivitas implementasi evaluasi internal kompetensi guru bahasa Inggris SMA. Studi ini menggunakan metode penelitian dan pengembangan yang dikembangkan oleh Borg & Gall (1983, p.775. Subjek penelitian berjumlah 17 guru yang berasal dari 7 SMA di Sulawesi Selatan. Konstruk instrumen terdiri atas instrumen untuk mengevaluasi kompetensi guru bahasa Inggris dalam merencanakan pemelajaran, instrumen untuk mengevaluasi kompetensi guru dalam melaksanaan proses pemelajaran, dan instrumen untuk mengevaluai kompetensi guru dalam mengevaluasi hasil proses pemelajaran. Hasil penelitian menunjukkan bahwa instrumen yang dikembangkan dapat digunakan untuk mengevaluasi kompetensi guru bahasa Inggris. Untuk mengetahui sejauh mana tingkat efektivitas Model Evaluasi Internal Kompetensi Guru Bahasa Inggris SMA, model ini kemudian dievaluasi oleh teman sejawat guru bahasa Inggris dan guru bahasa Inggris itu sendiri. Mereka menyimpulkan bahwa komponen dari model tersebut adalah komprehensip, praktis, ekonomis, dan telah didukung oleh instrumen yang valid dan reliabel. Kata kunci: evaluasi internal, model evaluasi, kompetensi guru   INTERNAL EVALUATION MODEL OF ENGLISH TEACHERS’ COMPETENCY (IEMET FOR SENIOR HIGH SCHOOL Abstract High School that can be used to identify the teacher’s strengths and weaknesses in learning and teaching processes and (2 find out the implementation effectiveness of the Internal Evaluation Model of English Teachers’ Competency for Senior High School. This study used research & development methods by following the pattern of phases developed by Borg & Gall (1983, p.775.  The subjects of this study were seventeen English teachers from seven Senior High Schools in South Sulawesi. The constructs of instruments consist of the

  13. Hubungan Merokok Dengan Kejadian Insomnia Pada Remaja Di SMA Negeri 1 Remboken Kabupaten Minahasa

    Kairupan, Juwinda Meini Ayu; Rottie, Julia; Malara, Reginus

    2016-01-01

    : Insomnia is difficulty initiating and maintaining sleep so can not meet the need for adequate sleep , both quantity and quality. Smoking is one of the causes of insomnia. Smoking is an act of burning a tabacco which inhaled the smoke from the burning process in a form of cigarette or a pipe. The purpose of this study was to analyze the relationship of smoking with the incidence of insomnia in adolescents at SMA N 1 Remboken Minahasa District. The research method is used observational analy...

  14. PENGARUH PROJECT BASED LEARNING TERHADAP KETERAMPILAN PROSES SAINS SISWA KELAS X SMA NEGERI SIDOARJO

    Nuril Maghfiroh

    2016-08-01

    Tujuan penelitian ini adalah untuk mengetahui pengaruh pembelajaran Project Based Learning terhadap keterampilan proses sains siswa kelas X SMA Negeri 4 Sidoarjo. Penelitian ini menggunakan metode Quasi Eksperimen dengan rancangan pretest postest non-equivalent control group design. Penentuan sampel mempertimbangkan kemampuan kognitif yang setara antara dua kelas yang menjadi kelompok kontrol dan kelompok eksperimen. Keterampilan proses sains diukur melalui tes tulis yang kemudian dianalisis dengan rubrik penilaian yang sudah disesuaikan untuk setiap aspek keterampilan proses sains. Hasil penelitian menunjukkan bahwa ada pengaruh pembelajaran Project Based Learning terhadap keterampilan proses sains siswa.

  15. Analisis Kemampuan Berpikir Matematis Siswa SMA kota Sorong terhadap Butir Soal dengan Graded Response Model

    Muhammad Syahrul Kahar

    2017-06-01

    Full Text Available This research aims to know the level of mathematical thinking ability of students by using scored model Graded Response Model (GRM. The subject here is the students of Class XI IPA 1 SMA Negeri 3 Sorong the 2016/2017 academic year, which amounted to 38 students with 22 students are male and 16 female students. This research is a descriptive research experiment. The results of this study indicate that the scored model GRM is effective in analyzing the ability of mathematical thinking of students. The effectiveness is shown an increase in student learning outcomes grade XI IPA 1 SMA Negeri 3 Kota Sorong, where the average grade results visible increase of 56.7 until 78, and the value of the completeness students improved significantly, and student learning outcomes were shown in graded contents relevance criteria students with score 4 there are 18 students (47.37%, while the relevance of the contents with a score of 1 there are 4 students (10.53%. From the criteria of completeness students who achieve complete answers by a score of 4, there are 1 students (2.64%, and the answers are far from finished with a score of 1 there were 7 students (19.52%. Then to organizing criteria, students are working on a very systematic, there are 8 students (21.05%, and organizing with not systematically there are 10 students (26.32%. Penelitian ini bertujuan untuk mengetahui tingkat kemampuan berpikir matematis siswa dengan menggunakan model penyekoran Graded Response Model (GRM. Subjek penelitian disini adalah siswa kelas XI IPA 1 SMA Negeri 3 Kota Sorong tahun ajaran 2016/2017, yang berjumlah 38 siswa dengan 22 siswa laki-laki dan 16 siswa perempuan. Penelitian ini adalah penelitian eksperimen yang bersifat Deskriptif. Hasil penelitian ini menunjukkan bahwa model penyekoran GRM ini efektif dalam menganalisis kemampuan berpikir matematis siswa. Keefektifan tersebut terlihat adanya peningkatan hasil belajar siswa kelas XI IPA 1 SMA Negeri 3 Kota Sorong, dimana

  16. Analisis pengelolaan peralatan praktikum fisika kelas XI SMA Muhammadiyah 1 Yogyakarta menggunakan model countenance stake

    Hanin Fathan Nurfina Istiqomah

    2016-11-01

    Full Text Available Penelitian ini bertujuan untuk mengetahui ketersediaan dan pengelolaan peralatan praktikum serta mengetahui hasil dari pengelolaan dan penggunaan peralatan praktikum fisika kelas XI di laboratorium fisika SMA Muhammadiyah 1 Yogyakarta. Penelitian ini merupakan penelitian evalusi model countenance stake. Subjek penelitian meliputi penanggungjawab laboratorium fisika, guru, laboran, dan siswa kelas XI MIA SMA Muhammadiyah 1 Yogyakarta. Penelitian dilakukan pada akhir pelaksanaan praktikum pada semester genap tahun pelajaran 2015-2016. Data dikumpulkan dengan wawancara terstruktur, pengamatan (observasi, angket, dokumentasi. Hasil penelitian menunjukkan bahwa ketersediaan peralatan praktikum (masukan [antecedents] yang terdiri dari sarana, prasarana dan alat praktikum tersedia sangat baik dengan persentase sebesar 78,16%. Pengelolaan laboratorium fisika (proses [transaction] yang terdiri dari persiapan pelaksanaan praktikum; kesiapan siswa, guru, laboran; dan pelaksanaan praktikum mendapatkan hasil sangat baik dengan persentase sebesar 81,78%. Hasil yang diperoleh (outcomes dari ketersediaan dan pengelolaan peralatan praktikum di laboratorium fisika termasuk kategori baik (B+ dengan pencapaian Kriteria Ketuntasan Minimal (KKM 100% dari total 233 siswa kelas XI MIA (Matematika dan Ilmu Alam dan beberapa siswa berhasil meraih juara 1 Olimpiade Fisika. This research is aimed to know the availability, management of the laboratory equipment’s and also the result of maintaining and using physics laboratory equipment’s in 11th class of MIA SMA 1 Muhammadiyah Yogyakarta. And this evaluation research used “countenance stake” approach, hence, such as the objects of it is the physics laboratory care taker, teachers, laboratory assistant, and the students. This research was conducted in the last meeting of practicum on last semester 2015-2016 periods. The data was assembled by interview, observation, questionnaire and documentation. The result of this

  17. Self-repairing performance of concrete beams strengthened using superelastic SMA wires in combination with adhesives released from hollow fibers

    Kuang Yachuan; Ou Jinping

    2008-01-01

    By taking advantage of the superelastic effect of shape memory alloy (SMA) and the cohering characteristic of repairing adhesive, a smart self-repairing concrete beam with damage self-repairing performance has been developed. In order to verify the potential self-repairing capacity of smart concrete beams reinforced with SMA wires and brittle fibers containing adhesives, static loading tests were conducted. Experimental results show that the superelastic SMA wires added self-restoration capacity to concrete beams, the deflection of the beams reversed and the crack closed almost completely after unloading. After the release of adhesive from the broken-open fibers into the cracks from the first loading, stress was redistributed to the uncracked section where a new crack was formed, while the sealed crack remained closed during reloading for the smart concrete beams reinforced with SMA wires and brittle fibers containing adhesives. While the original cracks experienced reopening, the load was carried directly by the wires during reloading for concrete beams reinforced with SMA wires

  18. Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene.

    Choudhury, Baharul I; Khan, Mohammed L; Dayanandan, Selvadurai

    2014-12-29

    Indigenous rice varieties in the Eastern Himalayan region of Northeast India are traditionally classified into sali, boro and jum ecotypes based on geographical locality and the season of cultivation. In this study, we used DNA sequence data from the Waxy (Wx) gene to infer the genetic relatedness among indigenous rice varieties in Northeast India and to assess the genetic distinctiveness of ecotypes. The results of all three analyses (Bayesian, Maximum Parsimony and Neighbor Joining) were congruent and revealed two genetically distinct clusters of rice varieties in the region. The large group comprised several varieties of sali and boro ecotypes, and all agronomically improved varieties. The small group consisted of only traditionally cultivated indigenous rice varieties, which included one boro, few sali and all jum varieties. The fixation index analysis revealed a very low level of differentiation between sali and boro (F(ST) = 0.005), moderate differentiation between sali and jum (F(ST) = 0.108) and high differentiation between jum and boro (F(ST) = 0.230) ecotypes. The genetic relatedness analyses revealed that sali, boro and jum ecotypes are genetically heterogeneous, and the current classification based on cultivation type is not congruent with the genetic background of rice varieties. Indigenous rice varieties chosen from genetically distinct clusters could be used in breeding programs to improve genetic gain through heterosis, while maintaining high genetic diversity.

  19. Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions.

    Xia, Zhi; Wang, Yin-Zheng; Smith, James F

    2009-02-01

    Accurate classification systems based on evolution are imperative for biological investigations. The recent explosion of molecular phylogenetics has resulted in a much improved classification of angiosperms. More than five phylogenetic lineages have been recognized from Scrophulariaceae sensu lato since the family was determined to be polyphyletic; however, questions remain about the genera that have not been assigned to one of the segregate families of Scrophulariaceae s.l. Rehmannia Liboschitz and Triaenophora Solereder are such genera with uncertain familial placement. There also is debate whether Triaenophora should be segregated from Rehmannia. To evaluate the phylogenetic relations between Rehmannia and Triaenophora, to find their closest relatives, and to verify their familial placement, we conducted phylogenetic analyses of the sequences of one nuclear DNA (ITS) region and four chloroplast DNA gene regions (trnL-F, rps16, rbcL, and rps2) individually and combined. The analyses showed that Rehmannia and Triaenophora are each strongly supported as monophyletic and together are sister to Orobanchaceae. This relation was corroborated by phytochemical and morphological data. Based on these data, we suggest that Rehmannia and Triaenophora represent the second nonparasitic branch sister to the remainder of Orobanchaceae (including Lindenbergia).

  20. Construction of a restriction map and gene map of the lettuce chloroplast small single-copy region using Southern cross-hybridization.

    Mitchelson, K R

    1996-01-01

    The small single-copy region (SSCR) of the chloroplast genome of many higher plants typically contain ndh genes encoding proteins that share homology with subunits of the respiratory-chain reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase complex of mitochondria. A map of the lettuce chloroplast SSCR has been determined by Southern cross-hybridization, taking advantage of the high degree of homology between a tobacco small single-copy fragment and a corresponding lettuce chloroplast fragment. The gene order of the SSCR of lettuce and tobacco chloroplasts is similar. The cross-hybridization method can rapidly create a primary gene map of unknown chloroplast fragments, thus providing detailed information of the localization and arrangement of genes and conserved open reading frame regions.

  1. Localization of the endpoints of deletions in the 5' region of the Duchenne gene using a sequence isolated by chromosome jumping

    Kenwrick, S.J.; Smith, T.J.; England, S.; Collins, F.; Davies, K.E.

    1988-02-25

    The authors have used chromosome jumping technology to move from within a large intron sequence in the Duchenne muscular dystrophy (DMD) gene to a region adjacent to exons of the gene. The single copy jump clone, HH1, was used to characterize deletions in patients previously shown to be deleted for DNA markers in the 5' end of the gene. 12 out of 15 such patients have breakpoints which lie between HH1 and the genomic locus J-47. Thus the vast majority of the deletions in these patients have proximal breakpoints in a similar region distal to the 5'end of the gene. HH1 was mapped with respect to the X;1 translocation in a DMD female and was shown to lie at least 80 kb from the starting point of the chromosome jump, HIP25.

  2. Localization of the endpoints of deletions in the 5' region of the Duchenne gene using a sequence isolated by chromosome jumping

    Kenwrick, S J; Smith, T J; England, S; Collins, F; Davies, K E

    1988-02-25

    The authors have used chromosome jumping technology to move from within a large intron sequence in the Duchenne muscular dystrophy (DMD) gene to a region adjacent to exons of the gene. The single copy jump clone, HH1, was used to characterize deletions in patients previously shown to be deleted for DNA markers in the 5' end of the gene. 12 out of 15 such patients have breakpoints which lie between HH1 and the genomic locus J-47. Thus the vast majority of the deletions in these patients have proximal breakpoints in a similar region distal to the 5'end of the gene. HH1 was mapped with respect to the X;1 translocation in a DMD female and was shown to lie at least 80 kb from the starting point of the chromosome jump, HIP25.

  3. The distribution of cagA and dupA genes in Helicobacter pylori strains in Kurdistan region, northern Iraq.

    Salih, Azad M; Goreal, Amer; Hussein, Nawfal R; Abdullah, Shahla M; Hawrami, Khidir; Assafi, Mahde

    2013-01-01

    Helicobacter pylori is a Gram negative bacteria that causes peptic ulceration and gastric adenocarcinoma. H pylori virulence factors, such as cagA and dupA, are important to study in populations as they contribute to disease risk. This study aimed to look at the distribution of the cagA and dupA genes in H pylori strains isolated from patients suffering from gastroduodenal diseases in Kurdistan region, Iraq. A cross-sectional study conducted between June 2011 and January 2012. Biopsies were collected from the Endoscopy Department in Duhok and Sulaimania hospitals, Kurdistan region, northern Iraq. Upper gastrointestinal (GI) endoscopy examination was performed and 4 gastric biopsies (2 from the antrum and 2 from the corpus) were obtained from 204 patients. H pylori positivity was examined by CLO test; then the association between disease status and virulence factors was assessed by polymerase chain reaction. 154 (75%) of our samples were found to be H pylori + by CLO test. Endoscopic diagnoses for those who were positive were as follows: peptic ulcer disease (PUD) including duodenal ulcer, 45; gastric ulcer, 23; and no ulcer (NPUD), 86. The overall prevalence rates of cagA and dupA were 72.7% and 18.8%, respectively. While a significant association between cagA and PUD was observed (P. ≤.017; OR=0.4; CI=0.18–0.85), no relationship between dupA and PUD could be seen. These data suggested that the presence of cagA may be a predictor of clinical outcome in Kurdistan region, northern Iraq.

  4. Biomechanics of smart wings in a bat robot: morphing wings using SMA actuators

    Colorado, J; Barrientos, A; Rossi, C; Breuer, K S

    2012-01-01

    This paper presents the design of a bat-like micro aerial vehicle with actuated morphing wings. NiTi shape memory alloys (SMAs) acting as artificial biceps and triceps muscles are used for mimicking the morphing wing mechanism of the bat flight apparatus. Our objective is twofold. Firstly, we have implemented a control architecture that allows an accurate and fast SMA actuation. This control makes use of the electrical resistance measurements of SMAs to adjust morphing wing motions. Secondly, the feasibility of using SMA actuation technology is evaluated for the application at hand. To this purpose, experiments are conducted to analyze the control performance in terms of nominal and overloaded operation modes of the SMAs. This analysis includes: (i) inertial forces regarding the stretchable wing membrane and aerodynamic loads, and (ii) uncertainties due to impact of airflow conditions over the resistance–motion relationship of SMAs. With the proposed control, morphing actuation speed can be increased up to 2.5 Hz, being sufficient to generate lift forces at a cruising speed of 5 m s −1 . (paper)

  5. Fabrication of wrist-like SMA-based actuator by double smart soft composite casting

    Rodrigue, Hugo; Wei, Wang; Bhandari, Binayak; Ahn, Sung-Hoon

    2015-12-01

    A new manufacturing method for smart soft composite (SSC) actuators that consists of double casting a SSC actuator to produce an actuator with non-linear shape memory alloy (SMA) wire positioning is proposed. This method is used to manufacture a tube-shaped SSC actuator in which the SMA wires follow the curvature of the tube and is capable of pure-twisting deformations while sustaining a cantilever load. The concept is tested by measuring the maximum twisting angle and a simple control method is proposed to control the twisting angle of the actuator. Then, a soft robotic wrist with a length of 18 cm is built, its load-carrying capability is tested by measuring the cantilever force required for deforming the actuator, and its load-carrying capability during actuation is tested by loading one end with different objects and actuating the actuator. This wrist actuator shows good repeatability, is capable of twisting deformations up to 25° while holding objects weighing 100 g, and can sustain loads above 2 N without undergoing buckling.

  6. Fabrication of wrist-like SMA-based actuator by double smart soft composite casting

    Rodrigue, Hugo; Wei, Wang; Bhandari, Binayak; Ahn, Sung-Hoon

    2015-01-01

    A new manufacturing method for smart soft composite (SSC) actuators that consists of double casting a SSC actuator to produce an actuator with non-linear shape memory alloy (SMA) wire positioning is proposed. This method is used to manufacture a tube-shaped SSC actuator in which the SMA wires follow the curvature of the tube and is capable of pure-twisting deformations while sustaining a cantilever load. The concept is tested by measuring the maximum twisting angle and a simple control method is proposed to control the twisting angle of the actuator. Then, a soft robotic wrist with a length of 18 cm is built, its load-carrying capability is tested by measuring the cantilever force required for deforming the actuator, and its load-carrying capability during actuation is tested by loading one end with different objects and actuating the actuator. This wrist actuator shows good repeatability, is capable of twisting deformations up to 25° while holding objects weighing 100 g, and can sustain loads above 2 N without undergoing buckling. (paper)

  7. PENGEMBANGAN MODEL PANDUAN PEMBELAJARAN KETERAMPILAN PROSES SAINS BIOLOGI SMA/MA

    triana asih

    2015-10-01

    Full Text Available Abstract: Science learning in senior high school was designed with the goal of achieving the competencies of graduates that includes aspects of attitudes, skills, and knowledge competency. Skill aspect refers to the Scientific Approach. Skills such as observing the process are observing, trying, processing, serving, and reasoning. All of these skills, leading to the aspects that exist within SPS. Learning needs analysis conducted by researchers at the SMA/ MA class XI IPA that is in the Purbolinggo district of East Lampung SPS shows a lack of provision in the learning process. Supposedly, learning based  on SPS is further enhanced, the researchers created a learning guide model based on SPS. The objectives of the reasearch: 1 produce a learning guide model based on SPS class XI, 2 improve outcomes (process and output (learning cutcomes biology learning class XI. Type of the research is Research and Development (R&D. The research was conducted in SMA N 1 Purbolinggo in class XI Science. Procedures R&D is adapted from Borg and Gall consisting of five steps: 1 literature review and the results of relevant research, 2 Design and carry out preliminary study, 3 the development/conceptualization models, 4 test the model through experimentation, 5 revision of the model. conclusion; 1 learning guide SPS models has been validated by the user and learning experts, instrument validation, model validation, and it is suitable.

  8. PENGARUH SUPERVISI AKADEMIK, KOMPETENSI GURU DAN KEDISIPLINAN TERHADAP KINERJA GURU SMA NEGERI 3 SLAWI KABUPATEN TEGAL

    Sussono Hadi

    2009-09-01

    Full Text Available This research is aimed at finding out the impact of academic supervision, teacher’s competence, and discipline towards the performance of teachers of SMA Negeri 3 Slawi, Tegal. This research used survey method. The data was collected using questionnaire and observation. There were 52 teachers as respondents. The data analysis used was percentage, multiple linear regression, F test and t test. The finding was : 1 academic supervision, teacher’s competence and discipline of SMA 3 Slawi teachers were very good, 2 academic supervision, teacher’s competence, and discipline together had impact towards teachers’ performance, 3 academic supervision, teacher’s competence, and discipline separately had impact on teachers’ performance, and 4 discipline had the strongest impact towards teachers’ performance. With this result it is suggested that the Diknas (the regential ministry of education intensify the academic supervision, continually developing teacher’s competence, and enforcing discipline on teachers and schools. Key words: academic supervision, competence, discipline, teacher’s performance

  9. A phenomenological SMA model for combined axial–torsional proportional/non-proportional loading conditions

    Bodaghi, M.; Damanpack, A.R.; Aghdam, M.M.; Shakeri, M.

    2013-01-01

    In this paper, a simple and robust phenomenological model for shape memory alloys (SMAs) is proposed to simulate main features of SMAs under uniaxial as well as biaxial combined axial–torsional proportional/non-proportional loadings. The constitutive model for polycrystalline SMAs is developed within the framework of continuum thermodynamics of irreversible processes. The model nominates the volume fractions of self-accommodated and oriented martensite as scalar internal variables and the preferred direction of oriented martensitic variants as directional internal variable. An algorithm is introduced to develop explicit relationships for the thermo-mechanical behavior of SMAs under uniaxial and biaxial combined axial–torsional proportional/non-proportional loading conditions and also thermal loading. It is shown that the model is able to simulate main aspects of SMAs including self-accommodation, martensitic transformation, orientation and reorientation of martensite, shape memory effect, ferro-elasticity and pseudo-elasticity. A description of the time-discrete counterpart of the proposed SMA model is presented. Experimental results of uniaxial tension and biaxial combined tension–torsion non-proportional tests are simulated and a good qualitative correlation between numerical and experimental responses is achieved. Due to simplicity and accuracy, the model is expected to be used in the future studies dealing with the analysis of SMA devices in which two stress components including one normal and one shear stress are dominant

  10. SMA foil-based elastocaloric cooling: from material behavior to device engineering

    Bruederlin, F.; Ossmer, H.; Wendler, F.; Miyazaki, S.; Kohl, M.

    2017-10-01

    The elastocaloric effect associated with the stress-induced first order phase transformation in pseudoelastic shape memory alloy (SMA) films and foils is of special interest for cooling applications on a miniature scale enabling fast heat transfer and high cycling frequencies as well as tunable transformation temperatures. The focus is on TiNi-based materials having the potential to meet the various challenges associated with elastocaloric cooling including large adiabatic temperature change and ultra-low fatigue. The evolution of strain and temperature bands during tensile load cycling is investigated with respect to strain and strain-rate by in situ digital image correlation and infrared thermography with a spatial resolution in the order of 25 µm. Major design issues and challenges in fabrication of SMA film-based elastocaloric cooling devices are discussed including the efficiency of heat transfer as well as force recovery to enhance the coefficient of performance (COP) on the system level. Advanced demonstrators show a temperature span of 13 °C after 30 s, while the COP of the overall device reaches almost 10% of Carnot efficiency.

  11. Biomechanics of smart wings in a bat robot: morphing wings using SMA actuators.

    Colorado, J; Barrientos, A; Rossi, C; Bahlman, J W; Breuer, K S

    2012-09-01

    This paper presents the design of a bat-like micro aerial vehicle with actuated morphing wings. NiTi shape memory alloys (SMAs) acting as artificial biceps and triceps muscles are used for mimicking the morphing wing mechanism of the bat flight apparatus. Our objective is twofold. Firstly, we have implemented a control architecture that allows an accurate and fast SMA actuation. This control makes use of the electrical resistance measurements of SMAs to adjust morphing wing motions. Secondly, the feasibility of using SMA actuation technology is evaluated for the application at hand. To this purpose, experiments are conducted to analyze the control performance in terms of nominal and overloaded operation modes of the SMAs. This analysis includes: (i) inertial forces regarding the stretchable wing membrane and aerodynamic loads, and (ii) uncertainties due to impact of airflow conditions over the resistance-motion relationship of SMAs. With the proposed control, morphing actuation speed can be increased up to 2.5 Hz, being sufficient to generate lift forces at a cruising speed of 5 m s(-1).

  12. Design, fabrication, and testing of a SMA hybrid composite jet engine chevron

    Turner, Travis L.; Cabell, Randolph H.; Cano, Roberto J.; Fleming, Gary A.

    2006-01-01

    Control of jet noise continues to be an important research topic. Exhaust nozzle chevrons have been shown to reduce jet noise, but parametric effects are not well understood. Additionally, thrust loss due to chevrons at cruise suggests significant benefit from deployable chevrons. The focus of this study is development of an active chevron concept for the primary purpose of parametric studies for jet noise reduction in the laboratory and technology development to leverage for full scale systems. The active chevron concept employed in this work consists of a laminated composite structure with embedded shape memory alloy (SMA) actuators, termed a SMA hybrid composite (SMAHC). The actuators are embedded on one side of the middle surface such that thermal excitation generates a moment and deflects the structure. A brief description of the chevron design is given followed by details of the fabrication approach. Results from bench top tests are presented and correlated with numerical predictions from a model for such structures that was recently implemented in MSC.Nastran and ABAQUS. Excellent performance and agreement with predictions is demonstrated. Results from tests in a representative flow environment are also presented. Excellent performance is again achieved for both open- and closed-loop tests, the latter demonstrating control to a specified immersion into the flow. The actuation authority and immersion performance is shown to be relatively insensitive to nozzle pressure ratio (NPR). Very repeatable immersion control with modest power requirements is demonstrated.

  13. Recent developments on SMA actuators: predicting the actuation fatigue life for variable loading schemes

    Wheeler, Robert W.; Lagoudas, Dimitris C.

    2017-04-01

    Shape memory alloys (SMAs), due to their ability to repeatably recover substantial deformations under applied mechanical loading, have the potential to impact the aerospace, automotive, biomedical, and energy industries as weight and volume saving replacements for conventional actuators. While numerous applications of SMA actuators have been flight tested and can be found in industrial applications, these actuators are generally limited to non-critical components, are not widely implemented and frequently one-off designs, and are generally overdesigned due to a lack of understanding of the effect of the loading path on the fatigue life and the lack of an accurate method for predicting actuator lifetimes. In recent years, multiple research efforts have increased our understanding of the actuation fatigue process of SMAs. These advances can be utilized to predict the fatigue lives and failure loads in SMA actuators. Additionally, these prediction methods can be implemented in order to intelligently design actuators in accordance with their fatigue and failure limits. In the following paper, both simple and complex thermomechanical loading paths have been considered. Experimental data was utilized from two material systems: equiatomic Nickel-Titanium and Nickelrich Nickel-Titanium.

  14. Zebrafish homologs of genes within 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes

    Alicia Blaker-Lee

    2012-11-01

    Deletion or duplication of one copy of the human 16p11.2 interval is tightly associated with impaired brain function, including autism spectrum disorders (ASDs, intellectual disability disorder (IDD and other phenotypes, indicating the importance of gene dosage in this copy number variant region (CNV. The core of this CNV includes 25 genes; however, the number of genes that contribute to these phenotypes is not known. Furthermore, genes whose functional levels change with deletion or duplication (termed ‘dosage sensors’, which can associate the CNV with pathologies, have not been identified in this region. Using the zebrafish as a tool, a set of 16p11.2 homologs was identified, primarily on chromosomes 3 and 12. Use of 11 phenotypic assays, spanning the first 5 days of development, demonstrated that this set of genes is highly active, such that 21 out of the 22 homologs tested showed loss-of-function phenotypes. Most genes in this region were required for nervous system development – impacting brain morphology, eye development, axonal density or organization, and motor response. In general, human genes were able to substitute for the fish homolog, demonstrating orthology and suggesting conserved molecular pathways. In a screen for 16p11.2 genes whose function is sensitive to hemizygosity, the aldolase a (aldoaa and kinesin family member 22 (kif22 genes were identified as giving clear phenotypes when RNA levels were reduced by ∼50%, suggesting that these genes are deletion dosage sensors. This study leads to two major findings. The first is that the 16p11.2 region comprises a highly active set of genes, which could present a large genetic target and might explain why multiple brain function, and other, phenotypes are associated with this interval. The second major finding is that there are (at least two genes with deletion dosage sensor properties among the 16p11.2 set, and these could link this CNV to brain disorders such as ASD and IDD.

  15. FRECUENCIAS NATURALES EN VIGAS ACTIVAMENTE TORSIONADAS USANDO ALAMBRES DE ALEACIÓN CON MEMORIA DE FORMA (SMA | NATURAL FREQUENCIES IN ACTVELY TWISTED BEAMS USING SHAPE MEMORY ALLOY (SMA WIRES

    Gaetano Starlacci

    2016-08-01

    Full Text Available Changes in the geometry and stiffness of structural members can be obtained using Shape Memory Alloys (SMA wires, previously stretched, and externally attached to the member in a helical pattern. The wire was modeled assuming transformation from a pure martensitic phase to a pure austenitic phase. Natural frequency values before and after the SMA wire activation attached to the beam were calculated using the finite element method and these values were compared with those obtained from a model developed for pre-twisted stress-free cantilever members. The results obtained showed the active torsion influence over the structural element in the values of natural frequencies calculated.

  16. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    Lo Fang-Yi

    2012-06-01

    Full Text Available Abstract Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR, chromogenic in situ hybridization (CISH, reverse transcriptase-qPCR (RT-qPCR, and immunohistochemistry (IHC in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1 functioning in Rho activity control, FRAT2 (10q24.1 involved in Wnt signaling, PAFAH1B1 (17p13.3 functioning in motility control, and ZNF322A (6p22.1 involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (PP=0.06. In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of

  17. The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

    Lo, Fang-Yi; Nandi, Suvobroto; Salgia, Ravi; Wang, Yi-Ching; Chang, Jer-Wei; Chang, I-Shou; Chen, Yann-Jang; Hsu, Han-Shui; Huang, Shiu-Feng Kathy; Tsai, Fang-Yu; Jiang, Shih Sheng; Kanteti, Rajani

    2012-01-01

    Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68

  18. Mapping of the gene encoding the. beta. -amyloid precursor protein and its relationship to the Down syndrome region of chromosome 21

    Patterson, D.; Gardiner, K.; Kao, F.T.; Tanzi, R.; Watkins, P.; Gusella, J.F. (Eleanor Roosevelt Institute for Cancer Research, Denver, CO (USA))

    1988-11-01

    The gene encoding the {beta}-amyloid precursor protein has been assigned to human chromosome 21, as has a gene responsible for at least some cases of familial Alzheimer disease. Linkage studies strongly suggest that the {beta}-amyloid precursor protein and the product corresponding to familial Alzheimer disease are from two genes, or at least that several million base pairs of DNA separate the markers. The precise location of the {beta}-amyloid precursor protein gene on chromosome 21 has not yet been determined. Here the authors show, by using a somatic-cell/hybrid-cell mapping panel, in situ hybridization, and transverse-alternating-field electrophoresis, that the {beta}-amyloid precursor protein gene is located on chromosome 21 very near the 21q21/21q/22 border and probably within the region of chromosome 21 that, when trisomic, results in Down syndrome.

  19. MODEL PERMAINAN AKTIVITAS LUAR KELAS UNTUK MENGEMBANGKAN RANAH KOGNITIF, AFEKTIF, DAN PSIKOMOTORIK SISWA SMA

    Hendra Setyawan

    2015-10-01

    Full Text Available Penelitian ini bertujuan menghasilkan model-model permainan Aktivitas Luar kelas (ALK yang layak digunakan sebagai materi pembelajaran penjas, serta efektif untuk mengembangkan ranah kognitif, afektif, dan psikomotorik siswa SMA. Penelitian ini dilakukan dengan langkah-langkah sebagai berikut: (1 pengumpulan informasi di lapangan, (2 menganalisis informasi yang telah dikumpulkan, (3 mengembangkan produk awal, (4 validasi ahli dan revisi, (5 uji coba skala kecil dan  revisi, (6 uji coba skala besar dan revisi, dan (7 pembuatan produk final. Uji coba skala kecil dilakukan terhadap siswa kelas X-D dan XI-IPA 4 dari SMA N I Prambanan berjumlah 66 orang. Uji coba skala besar dilakukan terhadap siswa kelas X-G, X-H, XI-IPS 3, dan XI-BHS dari SMA N I Prambanan berjumlah 132 orang. Instrumen pengumpulan data yang digunakan yaitu; (1 pedoman wawancara, (2 skala nilai, (3 pedoman observasi permainan, (4 pedoman observasi keefektifan permainan, (5 pedoman observasi terhadap guru pelaku uji coba, dan (6 rubrik penilaian siswa. Teknik analisis data dengan analisis deskriptif kuantitatif dan kualitatif. Hasil penelitian berupa tujuh model permainan yang layak dan efektif digunakan dalam pembelajaran penjas, hal ini dibuktikan dengan perolehan persentase sebesar 100% dari data hasil kuesioner skala nilai, observasi model permainan, observasi keefektifan permainan, dan observasi guru pelaku uji coba. Model permainan juga efektif untuk mengembangkan ranah kognitif, afektif, dan psikomotorik, yang dibuktikan dengan terjadinya peningkatan persentase nilai rata-rata siswa sebesar 21%. Kata kunci: model, permainan, aktivitas luar kelas, kognitif, afektif, psikomotorik THE OUTDOOR ACTIVITY GAME MODEL TO DEVELOP THE ASPECT OF COGNITIVE, AFFECTIVE, AND PSYCHOMOTOR OF THE SENIOR HIGH SCHOOL STUDENTS Abstract This study aims at producing outdoor activity game models which are proper to be used for physicall education learning and developing cognitive, affective, and

  20. Pengembangan Instrumen Ranah Kognitif pada Pokok Bahasan Fluida Statis SMA/MA

    Mukarramah Mustari

    2016-04-01

    Full Text Available This study aims to: 1 Develop Instrument Domains Cognitive at Static Fluid material in SMA / MA, 2 determine the validity of the instrument of cognitive tests on the static fluid material, 3 determine the reliability of cognitive principal static fluid discussion, 4 determine the level of difficulty of the cognitive tests on the static fluid material, 5 determine distinguishing cognitive test on static fluid material. The result products include cognitive aspects such instruments multiple choice tests and essay tests. Instrument developed on cognitive aspects in the form of multiple choice tests and a description to the extent of competence Bloom C1 to C6 on the material of Static Fluid. The Design of this study is used the development procedure Reasearch and Depelopment (R & D from Borg and Gall adopted by Sugiono ie; up to the stage seven form consisting of: the potential and problems, data collection, product design, design validation, design revisions, product trials, product revision. The data collecting is obtained from the results of expert validation instrument, the response of teachers, and product trials, and then analyzed by quantitative descriptive. The results of the analysis of the development of the instrument can be concluded that the cognitive instruments on the material of static fluid SMA / MA is excellent to be used by teachers in the assessment of competence of learners. Penelitian Pengembangan Instrumen Ranah Kognitif pada Pokok Bahasan Fluida Statis SMA/MA Ini dilakukan bertujuan;1 mengembangkan Instrumen Ranah Kognitif pada Pokok Bahasan Fluida Statis SMA/MA, 2 mengetahui validitas instrumen tes kognitif pokok bahasan fluida statis, 3 mengetahui reliabilitas kognitif pokok bahasan fluida statis, 4 mengetahui tingkat kesukaran tes kognitif pokok bahasan fluida statis, 5 mengetahui daya pembeda tes kognitif pada pokok bahasan fluida statis. Produk yang dihasilkan meliputi instrumen aspek kognitif berupa