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Sample records for kak obraz zhizni

  1. Polyarnye siyaniya sistemy avroral'nogo ovala kak kosmoloficheskij obraz drevnej mifologii %t The northern light of the auroral oval system as a cosmological concept of the archaic mythology

    NASA Astrophysics Data System (ADS)

    Alekseeva, L. M.

    Since archaic epochs people attentively observe the sky. They used to associate the sky phenomena with gods, heroes, spirits, etc. People interpreted the regularities in the motion of celestial objects in terms of their mythological model of the Universe. These observations and interpretations were first steps of the archaeoastronomy. Many remarkable features are inherent in the patterns of northern lights of the auroral oval system. Their manifestations are fairly regular. Did the ancients observe and some how classify these northern light phenomena? If yes, with which mythological personages were they associated? When were studies of the polar lights initiated? The present work is an attempt to answer these questions. We shall see that the ancient people assumed the spirit-world to be situated on the North. If so, it should manifest itself in spectacular polar aurorae. The specifically northern mythic cosmology formed the basis for Slavic fairy tales (theme of the Serpent and Serpent Fighter) and folk-beliefs. Other inhabitants of snowy latitudes should also manifest similar views. Studying the mythological reflections of typical auroral phenomena, it is possible to trace up long-standing ideological trends from the late glaciation epoch to the present time. Our results can help geophysicists in studying paleoauroral phenomena.

  2. JPRS Report, Science & Technology, USSR: Computers

    DTIC Science & Technology

    2007-11-02

    information approach in sciences about society has its natural science roots in the corresponding approach to genetics , physiology, and human...introduction. FTD /SNAP /9716 CSO: 1863/164 19 HARDWARE AFFILIATE OF ACADEMY COMPUTER INSTITUTE DEVELOPS PERSONAL COMPUTER Moscow PRAVDA, 24 Dec...processing. FTD /SNAP /9716 CSO: 1863/164 20 HARDWARE BROCHURE: MICROPROCESSORS AND PERSONAL COMPUTERS Moscow NOVOYE V ZHIZNI, NAUKE, TEKHNIKE

  3. Selection and processing of the spatial enhanced multispectral Landsat TM images - comparison between the results from merged and source data. (Polish Title: Selekcja i przetwarzanie wzmocnionych przestrzennie obrazów wielospektralnych Landsat TM - porównanie wyników opartych o dane scalone i dane zródłowe)

    NASA Astrophysics Data System (ADS)

    Pirowski, T.; Szczaciuk, G.

    2013-12-01

    The paper presents results of merging lower-resolution spectral data (Landsat, 30m) with panchromatic images of higher spatial resolution (IRS 5.8m). During the first stage of the research, thirty methods of merging satellite data (including their variants) have been tested. The first assessment was based on statistical measures covering spectral distortion and spatial enhancement of pansharpened images. The second assessment was based on the color composite factors essential for photo interpretation. Comparing both obtained ranks of methods revealed substantial differences in their assessed spectral distortion. On the other hand, there appeared similarities in the obtained values for the spatial enhancement of pansharpened images. The reasons of such discrepancies were defined. The research allowed appointing the HPF (High Pass Filter) and LCM (Local Correlation Modeling) methods as the best according to the tested factors. In the second part of the research, the applicability of the selected methods was tested. Information content of color composites was analyzed as well as tresholding and band ratioing. In the tests there were used images fused through five merging methods: HPF, LCM, IHS (Intensity, Hue, Saturation), PCA (Principal Components Analysis) and WMK (based on band ratioing and having specific photo interpretation features). The findings of the research suggest that none of the merging algorithms provide universal solution. Depending on the data processing technique used, the best results are based on images obtained from various integration methods. It means that the method ranks do not correspond with method applicability. Methods appointed as the best ones obtain poor results in some tests and methods which came low in the rank received high rank in some tests. If this conclusion becomes confirmed, it might be necessary to revise the assessment methods of merged images.

  4. Comparison of point clouds derived from aerial image matching with data from airborne laser scanning. (Polish Title: Porównanie wóaściwości chmury punktów wygenerowanej metodą dopasowania obrazów zdjęć lotniczych z danymi z lotniczego skanowania)

    NASA Astrophysics Data System (ADS)

    Dominik, W.

    2014-12-01

    The aim of this study was to investigate the properties of point clouds derived from aerial image matching and to compare them with point clouds from airborne laser scanning. A set of aerial images acquired in years 2010-2013 over the city of Elblag were used for the analysis. Images were acquired with the use of three digital cameras: DMC II 230, DMC I and DigiCAM60 with a GSD varying from 4.5 cm to 15 cm. Eight sets of images that were used in the study were acquired at different stages of the growing season - from March to December. Two LiDAR point clouds were used for the comparison - one with a density of 1.3 p/m2 and a second with a density of 10 p/m2. Based on the input images point clouds were created with the use of the semi-global matching method. The properties of the obtained point clouds were analyzed in three ways: - by the comparison of the vertical accuracy of point clouds with reference to a terrain profile surveyed on bare ground with GPS-RTK method - by visual assessment of point cloud profiles generated both from SGM and LiDAR point clouds - by visual assessment of a digital surface model generated from a SGM point cloud with reference to a digital surface model generated from a LiDAR point cloud. The conducted studies allowed a number of observations about the quality of SGM point clouds to be formulated with respect to different factors. The main factors having influence on the quality of SGM point clouds are GSD and base/height ratio. The essential problem related to SGM point clouds are areas covered with vegetation where SGM point clouds are visibly worse in terms of both accuracy and the representation of terrain surface. It is difficult to expect that in these areas SGM point clouds could replace LiDAR point clouds. This leads to a general conclusion that SGM point clouds are less reliable, more unpredictable and are dependent on more factors than LiDAR point clouds. Nevertheless, SGM point clouds generated with appropriate parameters can have better accuracy than LiDAR point clouds and present more detailed information about the terrain surface.

  5. Map of land use / land cover changes in Małopolska voivodeship in 1986-2010 created by object based image analysis of. (Polish Title: Mapa zmian pokrycia terenu małwpolski 1986-2011 wykonana w oparciu o klasyfikację obiektową obrazów satelitarnych Landsat oraz RapidEye)

    NASA Astrophysics Data System (ADS)

    Wężyk, P.; Wójtowicz-Nowakowska, A.; Pierzchalski, M.; Mlost, J.; Szafrańska, Beata

    2013-12-01

    Changes in land use / land cover are the result of interaction between natural processes and human activity. Using GIS analysis to estimate the dynamic of these changes we can detect former trends and their simulation in the future. Diagnosed directions of changes can be used e.g. to create local plans of spatial management or region growth policy. Main goal of this study was to diagnose main trends of changes in land use / land cover in Malopolska voivodeship in last 25 years (1986-2010). Results were shown as statistics and map compositions. Project was created based on RapidEye and LANDSAT 5 TM satellite data and aerial imagery from 2009-2010. The best way to process huge amount and various data was to use Object Based Image Analysis (OBIA). As the results of classification we received 10 classes of land use for both terms of analyses (1986-1987 and 2009-2010). Identified classes were: bare soil, grass-covered areas, urban areas, rivers and watercourses, coniferous forest, leaf forest, peatbog, and other areas. Results show, that especially 2 classes arisen much: forest (4.39%) and urban areas (2.40%), mostly at the expanse of agricultural (-3.60%) and grass-covered areas (-1.18%). Based on results we can say, that changes detected in past 25 years in Małopolska region, which we can also notice today, agree with general trends of landscape changes, that we can observe in Poland for the last 3 decades. These general changes are: renewed succession of forest on areas where agricultural production discontinued; also intense development of road infrastructure. Object Based Image Analysis allowed to realize these study for area of more than 15 000 km2for only a few weeks.

  6. Forest Vegetation as a Source of Biogenic and Organic Substances in Natural Inland Waters (Drevesnaya Rastitel’nosti Kak Istochnik Biogenn’ikh i Organicheskikh Veshestv v Prirodn’ikh Vodoemakh),

    DTIC Science & Technology

    1977-03-01

    especially of organic and ammonium nitrogen phosphorus, carbohydrates and aminoacids than coniferous ones (pine). The data obtained can be used when predicting the conditions of new and existing water basins. (Author)

  7. Kak Amerikantsy iskali vetra v pole, a nashli radiatsionnyj poyas i kak Russkie iskali radiatsionnyj poyas, a nashli solnechnyj veter Chast' I %t How Americans looked for "a wind in a field" but found a radiation belt, and how Russians looked for a radiation belt but found a solar wind or physical experiments on the first artificial Earth's satellites and a discovery of radiation belts

    NASA Astrophysics Data System (ADS)

    Zavidonov, I. V.

    The history of the most important scientific discovery of the early space era - the discovery of the inner and outer radiation belts of the Earth in 1958 is reconstructed. The paper uses archival records to bring to light the relative contributions of Soviet and American reseachers to the complex process of discovery. It also shows how misuses of science in mass-media political propaganda led to misrepresentations of the real historical portrayal of early space research.

  8. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis1[OPEN

    PubMed Central

    Lefebvre, Valérie; Ducamp, Aloïse; Trouverie, Jacques; Fortabat, Marie-Noëlle; Guillebaux, Alexia; Baldy, Aurélie; Naquin, Delphine; Lapierre, Catherine; Mouille, Gregory; Horlow, Christine; Durand-Tardif, Mylène

    2015-01-01

    eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants. PMID:25888614

  9. Suppression of Dwarf and irregular xylem Phenotypes Generates Low-Acetylated Biomass Lines in Arabidopsis.

    PubMed

    Bensussan, Matthieu; Lefebvre, Valérie; Ducamp, Aloïse; Trouverie, Jacques; Gineau, Emilie; Fortabat, Marie-Noëlle; Guillebaux, Alexia; Baldy, Aurélie; Naquin, Delphine; Herbette, Stéphane; Lapierre, Catherine; Mouille, Gregory; Horlow, Christine; Durand-Tardif, Mylène

    2015-06-01

    eskimo1-5 (esk1-5) is a dwarf Arabidopsis (Arabidopsis thaliana) mutant that has a constitutive drought syndrome and collapsed xylem vessels, along with low acetylation levels in xylan and mannan. ESK1 has xylan O-acetyltransferase activity in vitro. We used a suppressor strategy on esk1-5 to screen for variants with wild-type growth and low acetylation levels, a favorable combination for ethanol production. We found a recessive mutation in the KAKTUS (KAK) gene that suppressed dwarfism and the collapsed xylem character, the cause of decreased hydraulic conductivity in the esk1-5 mutant. Backcrosses between esk1-5 and two independent knockout kak mutants confirmed suppression of the esk1-5 effect. kak single mutants showed larger stem diameters than the wild type. The KAK promoter fused with a reporter gene showed activity in the vascular cambium, phloem, and primary xylem in the stem and hypocotyl. However, suppression of the collapsed xylem phenotype in esk1 kak double mutants was not associated with the recovery of cell wall O-acetylation or any major cell wall modifications. Therefore, our results indicate that, in addition to its described activity as a repressor of endoreduplication, KAK may play a role in vascular development. Furthermore, orthologous esk1 kak double mutants may hold promise for ethanol production in crop plants.

  10. The Impact of Changes in State Identity on Alliance Cohesion in Northeast Asia

    DTIC Science & Technology

    2009-12-01

    School, Sun Zhe at Tsinghua University, and Zhan Debin at Fudan University, began to publicly express their new perceptions of the capabilities...Rin 4 al Hong Xuezhi 1 henyang MRC Wang Ke General Kim Hak Sam 994 DDM Kim Jong Kak COGS Choe Kwang General Oh Yong Bang 5 S 1995 MDN DFAB Sun...Qixiang AMS PC Zhang Gong Guangzhou MRPC Shi Yuxia DDM Kim Jong Kak 4 1996 ILD Deputy Director Dai Bingguo North Sea FC Wang Jiying

  11. Assessing The Evolutionary Diversity Of Exon Skipping Events In Human, Mouse And Rat

    NASA Astrophysics Data System (ADS)

    Hsu, Fang-Rong; Chen, Chao-Jung; Kuo, Min-Chieh; Chang, Hwan-You; Shia, Wei-Chung

    2008-01-01

    This study is to research on the cross-species comparative analysis of homologous genetic sequence among human, mouse and rat by bioinformatics method, hopefully assessing the evolutionary diversity through exon length, reading frame preservation and KA/KS ratio test of alternative splicing events. Alternative splicing (AS) is an important mechanism in eukaryotic organism. We choose the "exon skipping events" from AS events for research. In the data of "conserved exon skipping events", we get 668 human-mouse conserved events, 179 human-rat conserved events and 266 conserved mouse-rat events. There are some extra data such as "non-conserved exon skipping events" and "species-specific events". We found out that the length of AS exon is shorter in conserved exon skipping event, but the ratio of reading frame preservation is higher. Among them, the minor form is the most special. We even got the same result in non-conserved exon skipping events. We calculated the KA/KS value by KA/KS ratio test and found out that the human-mouse KA/KS ratio is 0.158, the human-rat is 0.182 and the mouse-rat is 0.190. This represents that the human-mouse conserved events have the highest purifying selection pressure. In the end, we adopt KA/KS ratio test to do a further analysis between conserved and non-conserved exon skipping events and evaluate the evolutionary diversity of cross-species comparation.

  12. Atmospheric concentrations of polycyclic aromatic hydrocarbons in the watershed of Lake Victoria, East Africa.

    PubMed

    Arinaitwe, Kenneth; Kiremire, Bernard T; Muir, Derek C G; Fellin, Phil; Li, Henrik; Teixeira, Camilla; Mubiru, Drake N

    2012-11-06

    In the first study of its kind in Africa, PAHs were measured in high volume (24 h) air samples collected from two sampling stations, at Kakira and Entebbe (KAK and EBB, respectively) within the Lake Victoria watershed in Uganda, to assess source contributions and generate a baseline reference data set for future studies in the East African region. Sampling was conducted over two periods [2000-2004 (KAK and EBB1) and 2008-2010 (EBB2)]. The samples were extracted by accelerated solvent extraction and analyzed for 30 PAHs by GC-MS. The mean total PAH concentrations (ng/m(3)) were found to be 74.3 (range; 19.3-311, N = 39) for KAK, 56.8 (range; 13.3-126, N = 22) for EBB1 and 33.1 (range; 4.91-108, N = 56) for EBB2. The 3-ringed PAHs were the most predominant group with mean concentrations of 35.9 ng/m(3)(EBB1), 30.5 ng/m(3)(KAK) and 23.2 ng/m(3)(EBB2). Naphthalene had an exceptionally high mean concentration (21.9 ng/m(3)) for KAK compared to 0.44 and 0.39 ng/m(3) in EBB1 and EBB2 respectively, likely due to intensive agricultural operations nearby KAK. Principal component and diagnostic ratio analyses showed that the measured levels of PAHs were associated with mixed sources, combustion of petroleum, and biomass being the major sources.

  13. The Effect of Autopilot Configuration on Missile Response

    DTIC Science & Technology

    1989-03-01

    1, + M 6) + 6( Mp6 ). (3.8) Combining and rearranging the above equations yields (.l,, + .1,l) (QP, + 31 P6) 414,5 1 .(3.9) In Equation (3.9), the term...KAK2 F, A[, A!p,6- +6 F K, FKd12 = KBR I I P6 (FL, + FL6) FL6 (M/1, + Mp6 ) )- KAKID-F p + M P6) d 2 2 KAK 2 ( 7 in I K I W and 19 K K K (- 1p6 (FL

  14. Land Surface Temperature in Łódź Obtained from Landsat 5TM

    NASA Astrophysics Data System (ADS)

    Jędruszkiewicz, Joanna; Zieliński, Mariusz

    2012-01-01

    The main aim of this paper is to present the spatial differentiation of Land Surface Temperature LST in Łódź based on Landsat 5 Thematic Mapper (L5TM) images. Analysis was performed for all L5TM images from 2011, with clear sky over Łódź. Land surface temperature (LST) play an important role in determination of weather conditions in boundary layer of atmosphere, especially connected with convection. Environmental satellites from Landsat series delivers the high resolution images of Earth's surface and according to the estimations made on the ground of it are precise. LST depends widely on surface emissivity. In this paper the emissivity was estimated from MODIS sensor as well as NDVI index, then both method were compared. The processed images allowed to determine the warmest and the coldest areas in the administrative boundaries of Łódź. The highest LST values has been found in industrial areas and the in the heart of the city. However, there are some places lying in city outskirts, where the LST values are as high, for instance Lodz Airport. On the contrary the lowest LST values occur mostly in terrains covered with vegetation i.e. forests or city parks. Głównym celem tego opracowania było oszacowanie temperatury powierzchni Ziemi w Łodzi, na podstawie obrazów satelitarnych pochodzących z satelity Landsat 5 Thematic Mapper (L5TM). Analizę wykonane dla obrazów wszystkich dostępnych obrazów z 2011 roku, na których zachmurzenie nie wystąpiło nad obszarem Łodzi. Temperatura powierzchni Ziemi odgrywa istotną rolę w kształtowaniu warunków pogodowych w warstwie granicznej, szczególnie związanych z konwekcją. Satelity środowiskowe z serii Landsat dostarczają obrazów w dużej rozdzielczości, dzięki czemu pozwalają na stosunkowo dokładne oszacowanie tego parametru. Wielkość temperatury w dużym stopniu zależy od emisyjności danej powierzchni. W niniejszym opracowaniu porównano temperaturę powierzchniową obliczoną dla emisyjno

  15. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (81st, Baltimore, Maryland, August 5-8, 1998). Advertising.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Advertising section of the Proceedings contains the following 18 papers: "The Birth of Adwatches: Political Advertising Becomes Front-Page News" (Jennifer Greer); "A Cross-Cultural Comparison of the Effects of Source Credibility on Attitudes and Behavioral Intentions" (Kak Yoon, Choong Hyun Kim, and Min-Sun Kim);…

  16. On the reported magnetic precursor of the 1993 guam earthquake

    USGS Publications Warehouse

    Thomas, J.N.; Love, J.J.; Johnston, M.J.S.; Yumoto, K.

    2009-01-01

    Using 1-second magnetometer data recorded 67 km from the epicenter of the 1993 Mw 7.7 Guam earthquake, Hayakawa et al. (1996) and Miyahara et al. (1999) identify anomalous precursory changes in ultra-low frequency magnetic polarization (the ratio of vertical to horizontal field components). In a check of their results, we compare their data (GAM) with 1-second data from the Kakioka observatory (KAK) in Japan and the global magnetic activity index Kp. We also examine log books kept by USGS staff working on the Guam magnetic observatory. We find (1) analysis problems with both Hayakawa et al. and Miyahara et al., (2) significant correlation between the GAM, KAK, and Kp data, and (3) an absence of identifiable localized anomalous signals occurring prior to the earthquake. The changes we do find in polarization are part of normal global magnetic activity; they are unrelated to the earthquake. Copyright 2009 by the American Geophysical Union.

  17. An evaluation of the Kids are Kids disability awareness program: increasing social inclusion among children with physical disabilities.

    PubMed

    Tavares, Wendy

    2011-01-01

    Despite the intent of integration to promote positive social interactions between children with and without disabilities, there is growing concern that many children with special needs who are in inclusive settings feel socially isolated. The evaluation of interventions designed to promote disability awareness is critical if we are to increase opportunities for social success for these children. This research study was designed to determine whether the Kids Are Kids (KAK) program can positively impact the attitudes of children toward their peers with physical disabilities, as well as increase the social inclusion of these children. Results suggest that the KAK program had a positive impact on the attitudes of children toward their peers with disabilities, immediately following the program. Where social skill building was provided to 1 target child, attitude scores for that class remained elevated 1 month after the program. Two of the 3 target children reported increased social inclusion 1 month after the program.

  18. Estimating an Image’s Blur Kernel from Edge Intensity Profiles

    DTIC Science & Technology

    2012-08-01

    B. Singh, A. Hertzmann, S.T. Roweis, and W.T. Freeman “ Removing camera shake from a single photograph ”, SIGGRAPH, 2006. [8] Taeg S. Cho, Sylvain...Estimation for Image Deblurring”, CVGIP: Graphical Models and Image Processing, Vol. 53, No. 4, pp. 364-372, 1991. [14] Azriel Rosenfeld, Avinash Kak, Digital ...of observed distributions”, Journal of Astronomy , Volume 79, number 6, pages 745-754, 1974. [21] L. Yuan, J. Sun, L. Quan,H. Shum, “Progressive

  19. Effect of Fatty Acid Conjugation on Antimicrobial Peptide Activity

    DTIC Science & Technology

    2004-12-01

    killing mechanism of antimicrobial peptides makes them an interesting alternative to traditional antibiotics, as target bacteria may be less able...C14-AKK and C16-AKK to within a 7% error are 220 and 16mM respectively. Since amphipathicity is requisite for antimicrobial action KAK is not...Schnaare, 2000: Antimicrobial evaluation of N-alkyl betaines and N-alkyl-N,N-dimethylamine oxides with variations in chain length. Antimicrobial Agents

  20. Soviet Maintenance Training and the Technological Imperative.

    DTIC Science & Technology

    1980-06-01

    a great deal of pressure on all elements of the military system to raise technical skill levels rapidly. The military commissariats have increased...more attention to the militarv-tecinical training of future soldiers. Military commissariat officials are struggling to ensure 10 that draftees have...V.ooruzhennvkh Sil (ccint. ) Sui’vanov, A. "Sorevnovanive Kak Fakt.or ’V.osp itai a" (- Compt irin as a Factor in Education). No. 7-77. Sushinin, P

  1. Marine Corps Research and Development Objectives Document (RADOD)

    DTIC Science & Technology

    1980-08-08

    DZVELOPMENT AND EDUCATION COMMAND OUANTICO. VIRGINIA 22134S 0 IN REPLY ftEFRA TO D 035/PDD:kak AUG 8 1980 Marine Corps Research and Development...Objectives Document (_ADOD). 1. INTRODUCTION. The Marine Corps Research and Development Objectives Do’ ment (RADOD) was conceived in July 1971. It was...Marine Corps wevelopment and Education Command. 2. PURPOSE. The purpose of RADOD is to provide the research and development community a reference of

  2. Concurrent MR-NIR Imaging for Breast Cancer Diagnosis

    DTIC Science & Technology

    2005-06-01

    significantly different than the true optical coefficients of tissue. As a result, the assumption of strong optical-anatomy correlation may cause ...assumption of strong optical-anatomy correlation may cause undesirable, erroneous bias in optical image reconstruction. Therefore, more flexible prior models...378, 1999. 22 TABLE I FOUR-COMPARTMENT MODEL:ESTIMATED PHARMACOKINETIC PARAMETERS USING EKF ALGORITHM kak ckd 4 k f kout (Sec-1 10-2) (seC- 1 10-2

  3. Mitochondrial genome sequences of Artemia tibetiana and Artemia urmiana: assessing molecular changes for high plateau adaptation.

    PubMed

    Zhang, Hangxiao; Luo, Qibin; Sun, Jing; Liu, Fei; Wu, Gang; Yu, Jun; Wang, Weiwei

    2013-05-01

    Brine shrimps, Artemia (Crustacea, Anostraca), inhabit hypersaline environments and have a broad geographical distribution from sea level to high plateaus. Artemia therefore possess significant genetic diversity, which gives them their outstanding adaptability. To understand this remarkable plasticity, we sequenced the mitochondrial genomes of two Artemia tibetiana isolates from the Tibetan Plateau in China and one Artemia urmiana isolate from Lake Urmia in Iran and compared them with the genome of a low-altitude Artemia, A. franciscana. We compared the ratio of the rate of nonsynonymous (Ka) and synonymous (Ks) substitutions (Ka/Ks ratio) in the mitochondrial protein-coding gene sequences and found that atp8 had the highest Ka/Ks ratios in comparisons of A. franciscana with either A. tibetiana or A. urmiana and that atp6 had the highest Ka/Ks ratio between A. tibetiana and A. urmiana. Atp6 may have experienced strong selective pressure for high-altitude adaptation because although A. tibetiana and A. urmiana are closely related they live at different altitudes. We identified two extended termination-associated sequences and three conserved sequence blocks in the D-loop region of the mitochondrial genomes. We propose that sequence variations in the D-loop region and in the subunits of the respiratory chain complexes independently or collectively contribute to the adaptation of Artemia to different altitudes.

  4. Species-specific duplications of NBS-encoding genes in Chinese chestnut (Castanea mollissima)

    PubMed Central

    Zhong, Yan; Li, Yingjun; Huang, Kaihui; Cheng, Zong-Ming

    2015-01-01

    The disease resistance (R) genes play an important role in protecting plants from infection by diverse pathogens in the environment. The nucleotide-binding site (NBS)-leucine-rich repeat (LRR) class of genes is one of the largest R gene families. Chinese chestnut (Castanea mollissima) is resistant to Chestnut Blight Disease, but relatively little is known about the resistance mechanism. We identified 519 NBS-encoding genes, including 374 NBS-LRR genes and 145 NBS-only genes. The majority of Ka/Ks were less than 1, suggesting the purifying selection operated during the evolutionary history of NBS-encoding genes. A minority (4/34) of Ka/Ks in non-TIR gene families were greater than 1, showing that some genes were under positive selection pressure. Furthermore, Ks peaked at a range of 0.4 to 0.5, indicating that ancient duplications arose during the evolution. The relationship between Ka/Ks and Ks indicated greater selective pressure on the newer and older genes with the critical value of Ks = 0.4–0.5. Notably, species-specific duplications were detected in NBS-encoding genes. In addition, the group of RPW8-NBS-encoding genes clustered together as an independent clade located at a relatively basal position in the phylogenetic tree. Many cis-acting elements related to plant defense responses were detected in promoters of NBS-encoding genes. PMID:26559332

  5. Comparative transcriptome resources of two Dysosma species (Berberidaceae) and molecular evolution of the CYP719A gene in Podophylloideae.

    PubMed

    Mao, Yunrui; Zhang, Yonghua; Xu, Chuan; Qiu, Yingxiong

    2016-01-01

    Dysosma species (Berberidaceae, Podophylloideae) are of great medicinal pharmacogenetic importance and used as model systems to study the drivers and mechanisms of species diversification of temperate plants in East Asia. Recently, we have sequenced the transcriptome of the low-elevation D. versipellis. In this study, we sequenced the transcriptome of the high-elevation D. aurantiocaulis and used comparative genomic approaches to investigate the transcriptome evolution of the two species. We retrieved 53,929 unigenes from D. aurantiocaulis by de novo transcriptome assemblies using the Illumina HiSeq 2000 platform. Comparing the transcriptomes of both species, we identified 4593 orthologs. Estimation of Ka/Ks ratios for 3126 orthologs revealed that none had a Ka/Ks significantly greater than 1, whereas 1273 (Ka/Ks < 0.5, P < 0.05) were inferred to be under purifying selection. A total of 51 primer pairs were successfully designed from 461 EST-SSRs contained in 4593 orthologs. Marker validation assay revealed that 26 (51%) and 41 (80.4%) produced clear fragments with the expected sizes in all Podophylloideae species. Specifically, 19 different sequences of CYP719A were identified from PCR-amplified genomic DNA of all 12 species of Podophylloideae using primers designed from the assembled transcripts. The data further indicated that CYP719A was likely subject to strong selective constraints maintaining only one copy per genome. In Dysosma, there was relaxed purifying selection or more positive selection for high-elevation species. Overall, this study has generated a wealth of molecular resources potentially useful for pharmacogenetic and evolutionary studies in Dysosma and allied taxa.

  6. The relationship between high- and low-latitude Pi2 pulsations simultaneously observed by DE-1, AMPTE/CCE, and ground stations

    NASA Astrophysics Data System (ADS)

    Teramoto, M.; Nose, M.; Takahashi, K.; Sutcliffe, P. R.

    2007-12-01

    Pi2 pulsations (period from 40s to 150s) are observed at substorm onset. Cavity mode resonance is the possible scenario of low-latitude Pi2 pulsations. It is an open question whether the resonance boundary, plasmapause, is good reflector or not. We investigated Pi2 pulsations observed simultaneously by the polar orbiting DE-1 satellite (an apogee: about 3.6 Re altitude and a perigee: about 500km altitude), equatorial orbiting AMPTE/CCE satellite (an apogee: about 8.8 Re altitude and a perigee: about 1100km altitude), and ground stations at 1132-1136 UT on November 14, 1986. DE-1 was located at polar region (Geomagnetic latitude=-83.42 degrees). AMPTE/CCE was located at L=4.57 and 23.6 MLT. AMPTE/CCE might be located outside the plasmasphere. They are observed Pi2 pulsations in the compressional component. The AL index began to decrease at 1114 UT. It showed substorm onset. They had high coherence with that observed at Kakioka (KAK) in the H component, which was located at L=1.25 and 3.21 MLT. The phase difference between KAK and DE-1 and between KAK and AMPTE/CCE were 180 and 90 degrees at 14 mHz. These Pi2 pulsations had high coherence with that observed by Hermanus (HER), which was located at L=1.8 and 12.8 MLT. These observational results may support that the plasmapause is imperfect boundary. Pi2 pulsations at low latitude are excited by the plasmaspheric virtual resonance mode, in which the ambient magnetic fields outside plasmasphere oscillated with the cavity mode resonance. And Pi2 pulsations at the polar cap are also excited by PVR mode. In this presentation, we will show these Pi2 pulsations observed by DE-1, AMPTE/CCE, HER and KAK, in addition to other ground stations (Port Aux Francais, Furstenfeldbruck, and Wingst) and conduct statistical study of Pi2 pulsations, which were simultaneously observed by the DE-1 and AMPTE/CCE satellite.

  7. Process Defects in Composites.

    DTIC Science & Technology

    1995-01-30

    31) are then a(i,L)= dk = n(i) f(i,2A,) = x(k) + ka(k)= ln[n(i,2L)] (33) dk In(X)’ (n(,) Parameter a(i, X), referred to as the Lipschitz -Hoelder... nonuniqueness of intermediate configuration and is given by the well-known isotropic finite elasticity law (Truesdell and Noll, 1965) 2 B , 0 )(2...questioned (Nemat-Nasser, 1982). The difficulty was partly related to the nonuniqueness of the unstressed configuration, its consequences on the anisotropic

  8. 3D modeling of architectural objects from video data obtained with the fixed focal length lens geometry

    NASA Astrophysics Data System (ADS)

    Deliś, Paulina; Kędzierski, Michał; Fryśkowska, Anna; Wilińska, Michalina

    2013-12-01

    The article describes the process of creating 3D models of architectural objects on the basis of video images, which had been acquired by a Sony NEX-VG10E fixed focal length video camera. It was assumed, that based on video and Terrestrial Laser Scanning data it is possible to develop 3D models of architectural objects. The acquisition of video data was preceded by the calibration of video camera. The process of creating 3D models from video data involves the following steps: video frames selection for the orientation process, orientation of video frames using points with known coordinates from Terrestrial Laser Scanning (TLS), generating a TIN model using automatic matching methods. The above objects have been measured with an impulse laser scanner, Leica ScanStation 2. Created 3D models of architectural objects were compared with 3D models of the same objects for which the self-calibration bundle adjustment process was performed. In this order a PhotoModeler Software was used. In order to assess the accuracy of the developed 3D models of architectural objects, points with known coordinates from Terrestrial Laser Scanning were used. To assess the accuracy a shortest distance method was used. Analysis of the accuracy showed that 3D models generated from video images differ by about 0.06 ÷ 0.13 m compared to TLS data. Artykuł zawiera opis procesu opracowania modeli 3D obiektów architektonicznych na podstawie obrazów wideo pozyskanych kamerą wideo Sony NEX-VG10E ze stałoogniskowym obiektywem. Przyjęto założenie, że na podstawie danych wideo i danych z naziemnego skaningu laserowego (NSL) możliwe jest opracowanie modeli 3D obiektów architektonicznych. Pozyskanie danych wideo zostało poprzedzone kalibracją kamery wideo. Model matematyczny kamery był oparty na rzucie perspektywicznym. Proces opracowania modeli 3D na podstawie danych wideo składał się z następujących etapów: wybór klatek wideo do procesu orientacji, orientacja klatek wideo na

  9. The fate of retrotransposed processed genes in Arabidopsis thaliana.

    PubMed

    Abdelkarim, Basma T M; Maranda, Vincent; Drouin, Guy

    2017-04-20

    Processed genes are functional genes that have arisen as a result of the retrotransposition of mRNA molecules. We found 6 genes that generated processed genes in the common ancestor of five Brassicaceae species (Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula). These processed genes have therefore been kept for at least 30millionyears. Analyses of the Ka/Ks ratio of these genes, and of those having given rise to them, show that they evolve relatively slowly and suggest that the processed genes maintained the same function as that of their parental gene. There is a significant negative correlation between the number of ESTs and transcripts produced and the Ka/Ks ratios of the parental genes but not of the processed genes. This suggests that selection has not yet adapted the selective pressure the processed genes experience to their expression level. However, the A. thaliana processed genes tend to be expressed in the same tissues as that of their parental genes. Furthermore, most have a CAATT-box, a TATA-box and are located about 1kb from another protein-coding gene. Altogether, our results suggest that the processed genes found in the A. thaliana genome have been kept to produce more of the same product, and in the same tissues, as that encoded by their parental gene.

  10. Evolutionary dynamics of the gametologous CTNNB1 gene on the Z and W chromosomes of snakes.

    PubMed

    Laopichienpong, Nararat; Muangmai, Narongrit; Chanhome, Lawan; Suntrarachun, Sunutcha; Twilprawat, Panupon; Peyachoknagul, Surin; Srikulnath, Kornsorn

    2016-10-14

    Snakes exhibit genotypic sex determination with female heterogamety (ZZ males and ZW females), and the state of sex chromosome differentiation also varies among lineages. To investigate the evolutionary history of homologous genes located in the non-recombining region of differentiated sex chromosomes in snakes, partial sequences of the gametologous CTNNB1 gene were analyzed for 12 species belonging to henophid (Cylindrophiidae, Xenopeltidae, and Pythonidae) and caenophid snakes (Viperidae, Elapidae, and Colubridae). Nonsynonymous/synonymous substitution ratios (Ka/Ks) in coding sequences were low (Ka/Ks < 1) between CTNNB1Z and CTNNB1W, suggesting that these two genes may have similar functional properties. However, frequencies of intron sequence substitutions and insertion-deletions were higher in CTNNB1Z than CTNNB1W, suggesting that Z-linked sequences evolved faster than W-linked sequences. Molecular phylogeny based on both intron and exon sequences showed the presence of two major clades: (1) Z-linked sequences of Caenophidia, and (2) W-linked sequences of Caenophidia clustered with Z-linked sequences of Henophidia, which suggests that the sequence divergence between CTNNB1Z and CTNNB1W in Caenophidia may have occurred by the cessation of recombination after the split from Henophidia.

  11. Sperm proteome of Mytilus galloprovincialis: Insights into the evolution of fertilization proteins in marine mussels.

    PubMed

    Zhang, Yanjie; Mu, Huawei; Lau, Stanley C K; Zhang, Zhifeng; Qiu, Jian-Wen

    2015-12-01

    Cataloging the sperm proteome of an animal can improve our understanding of its sperm-egg interaction and speciation, but such data are available for only a few free-spawning invertebrates. This study aimed to identify the sperm proteome of Mytilus galloprovincialis, a free-spawning marine mussel. We integrated public transcriptome datasets by de novo assembly, and applied SDS-PAGE coupled LC-MS/MS analysis to profile the sperm proteome, resulting in the identification of 550 proteins. Comparing the homologous sperm protein coding genes between M. galloprovincialis and its closely related species M. edulis revealed that fertilization proteins have the highest mean nonsynonymous substitution rate (Ka/Ks = 0.62) among 11 functional groups, consistent with previous reports of positive selection of several fertilization proteins in Mytilus. Moreover, 78 sperm proteins in different functional groups have Ka/Ks values > 0.5, indicating the presence of many candidate sperm proteins for further analysis of rapid interspecific divergence. The MS data are available in ProteomeXchange with the identifier PXD001665.

  12. Legacy and currently used pesticides in the atmospheric environment of Lake Victoria, East Africa.

    PubMed

    Arinaitwe, Kenneth; Kiremire, Bernard T; Muir, Derek C G; Fellin, Phil; Li, Henrik; Teixeira, Camilla; Mubiru, Drake N

    2016-02-01

    The Lake Victoria watershed has extensive agricultural activity with a long history of pesticide use but there is limited information on historical use or on environmental levels. To address this data gap, high volume air samples were collected from two sites close to the northern shore of Lake Victoria; Kakira (KAK) and Entebbe (EBB). The samples, to be analyzed for pesticides, were collected over various periods between 1999 and 2004 inclusive (KAK 1999-2000, KAK 2003-2004, EBB 2003 and EBB 2004 sample sets) and from 2008 to 2010 inclusive (EBB 2008, EBB 2009 and EBB 2010 sample sets). The latter sample sets (which also included precipitation samples) were also analyzed for currently used pesticides (CUPs) including chlorpyrifos, chlorthalonil, metribuzin, trifluralin, malathion and dacthal. Chlorpyrifos was the predominant CUP in air samples with average concentrations of 93.5, 26.1 and 3.54 ng m(-3) for the EBB 2008, 2009, 2010 sample sets, respectively. Average concentrations of total endosulfan (ΣEndo), total DDT related compounds (ΣDDTs) and hexachlorocyclohexanes (ΣHCHs) ranged from 12.3-282, 22.8-130 and 3.72-81.8 pg m(-3), respectively, for all the sample sets. Atmospheric prevalence of residues of persistent organic pollutants (POPs) increased with fresh emissions of endosulfan, DDT and lindane. Hexachlorobenzene (HCB), pentachlorobenzene (PeCB) and dieldrin were also detected in air samples. Transformation products, pentachloroanisole, 3,4,5-trichloroveratrole and 3,4,5,6-tetrachloroveratrole, were also detected. The five most prevalent compounds in the precipitation samples were in the order chlorpyrifos>chlorothalonil>ΣEndo>ΣDDTs>ΣHCHs with average fluxes of 1123, 396, 130, 41.7 and 41.3 ng m(-2)sample(-1), respectively. PeCB exceeded HCB in precipitation samples. The reverse was true for air samples. Backward air trajectories suggested transboundary and local emission sources of the analytes. The results underscore the need for a concerted

  13. Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

    PubMed Central

    2013-01-01

    Background Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available. Results It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation

  14. A Numerical Technique for the Calculation of Dispersion Relations and Mode Functions for Upper Ocean Internal Waves.

    DTIC Science & Technology

    1980-10-01

    gA) ( S S I STMAXI Cu. EPq )Eao TM 10 XI u KO -10 Ne~~ ESTIMATE OF yh4E EppOp IN K PSIL 35 9A Pem ( K16 FRRvis rS ?!MaTE IN K POASIALF NtDL, / Ka * * 22...FSTmATE. K: IR LOWE R PgTTMbfFo IMF C IMPROE FgTtmar rs RET"lwrng. IN K1. C loss C C CALL GUES9(KA,K9.M11) C C 170) C rNECK FOR EPPOP rOflEg PrTUMNJFO...DSIuAAI TXr(TEPM nr. EPQ MO TO PO Sri * .M,:AQ((K1 - TEwPKl / TENN TEMPPAI) F PC Tr * (;T. K ~Plrp~m’ * ?wwM Kft q FPSK 41 a PI - TFU~l CV1iN TuPkPK KT

  15. Strong purifying selection on the Odysseus gene in two clades of sibling species of the Drosophila montium species subgroup.

    PubMed

    Wen, Shuo-Yang; Shimada, Kimio; Kawai, Kuniko; Toda, Masanori J

    2006-05-01

    The Odysseus (OdsH) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive Darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the Drosophila simulans clade. Has OdsH also experienced similar positive selection between Drosophila sibling species other than those of the simulans clade? We cloned and sequenced OdsH and unc-4 from two clades of the Drosophila montium species subgroup, the Drosophila lini and the Drosophila kikkawai clades. The ratios of Ka/Ks for OdsH were remarkably low between sibling species of these two clades, suggesting that OdsH has been subjected to strong purifying selection in these two clades.

  16. Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

    PubMed Central

    Zhou, Tao; Chen, Chen; Wei, Yue; Chang, Yongxia; Bai, Guoqing; Li, Zhonghu; Kanwal, Nazish; Zhao, Guifang

    2016-01-01

    Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia. PMID:27790228

  17. A tale of two drug targets: the evolutionary history of BACE1 and BACE2

    PubMed Central

    Southan, Christopher; Hancock, John M.

    2013-01-01

    The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35–45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context. PMID:24381583

  18. A tale of two drug targets: the evolutionary history of BACE1 and BACE2.

    PubMed

    Southan, Christopher; Hancock, John M

    2013-01-01

    The beta amyloid (APP) cleaving enzyme (BACE1) has been a drug target for Alzheimer's Disease (AD) since 1999 with lead inhibitors now entering clinical trials. In 2011, the paralog, BACE2, became a new target for type II diabetes (T2DM) having been identified as a TMEM27 secretase regulating pancreatic β cell function. However, the normal roles of both enzymes are unclear. This study outlines their evolutionary history and new opportunities for functional genomics. We identified 30 homologs (UrBACEs) in basal phyla including Placozoans, Cnidarians, Choanoflagellates, Porifera, Echinoderms, Annelids, Mollusks and Ascidians (but not Ecdysozoans). UrBACEs are predominantly single copy, show 35-45% protein sequence identity with mammalian BACE1, are ~100 residues longer than cathepsin paralogs with an aspartyl protease domain flanked by a signal peptide and a C-terminal transmembrane domain. While multiple paralogs in Trichoplax and Monosiga pre-date the nervous system, duplication of the UrBACE in fish gave rise to BACE1 and BACE2 in the vertebrate lineage. The latter evolved more rapidly as the former maintained the emergent neuronal role. In mammals, Ka/Ks for BACE2 is higher than BACE1 but low ratios for both suggest purifying selection. The 5' exons show higher Ka/Ks than the catalytic section. Model organism genomes show the absence of certain BACE human substrates when the UrBACE is present. Experiments could thus reveal undiscovered substrates and roles. The human protease double-target status means that evolutionary trajectories and functional shifts associated with different substrates will have implications for the development of clinical candidates for both AD and T2DM. A rational basis for inhibition specificity ratios and assessing target-related side effects will be facilitated by a more complete picture of BACE1 and BACE2 functions informed by their evolutionary context.

  19. ULF Seismo-electromagnetic Studies in Kanto, Japan: Progress and Challenges

    NASA Astrophysics Data System (ADS)

    Han, P.; Hattori, K.; Zhuang, J.

    2015-12-01

    In order to clarify the ULF seismo-magnetic phenomena, a sensitive geomagnetic network has been installed in Kanto, Japan. In this study, we have analyzed geomagnetic data observed during the past decade in Izu, Boso, and Kakioka (KAK) stations. To verify the relation between ULF geomagnetic anomalies and local seismicity, statistical studies by superposed epoch analysis (SEA) have been carried out. The results have indicated that before a sizeable earthquake there are clearly higher probabilities of ULF anomalies than after the earthquake: for Seikoshi (SKS) station in Izu, about 20~30 days before, one week and few days before, and one day after the event statistical results of daily counts are significant; for Kiyosumi (KYS) station in Boso around two weeks before, few days before, and one day after the event; For KAK station, 30 days before, about 2 weeks before, few days before, and 2 days after the event. To find out the detailed waveform of anomalous magnetic signals, waveform analysis has been performed. The results show that there are mainly two kinds of seismo-magnetic signature. (1) Noise-like signals: Compared with the background, the signals exhibit small increases of amplitudes at a wide frequency range. (2) Transient/quasi-rectangular signals: the signals have transient/quasi-rectangular waveforms with amplitudes of several nT. The noise-like signals usually persist for several days or even a few weeks, and are mainly associated with large earthquakes; the transient/quasi-rectangular signals have durations of few seconds to few ten seconds, and are registered mainly during slow slip events. Finally, we have evaluated the precursory information of ULF geomagnetic signals for local sizeable earthquakes using Molchan's error diagram. The probability gain is around 2-4 against a Poisson model. The above results have indicated that the ULF seismo-magnetic phenomena clearly contain precursory information and have a possibility of improving the forecasting

  20. The roles of gene duplication, gene conversion and positive selection in rodent Esp and Mup pheromone gene families with comparison to the Abp family.

    PubMed

    Karn, Robert C; Laukaitis, Christina M

    2012-01-01

    Three proteinaceous pheromone families, the androgen-binding proteins (ABPs), the exocrine-gland secreting peptides (ESPs) and the major urinary proteins (MUPs) are encoded by large gene families in the genomes of Mus musculus and Rattus norvegicus. We studied the evolutionary histories of the Mup and Esp genes and compared them with what is known about the Abp genes. Apparently gene conversion has played little if any role in the expansion of the mouse Class A and Class B Mup genes and pseudogenes, and the rat Mups. By contrast, we found evidence of extensive gene conversion in many Esp genes although not in all of them. Our studies of selection identified at least two amino acid sites in β-sheets as having evolved under positive selection in the mouse Class A and Class B MUPs and in rat MUPs. We show that selection may have acted on the ESPs by determining K(a)/K(s) for Exon 3 sequences with and without the converted sequence segment. While it appears that purifying selection acted on the ESP signal peptides, the secreted portions of the ESPs probably have undergone much more rapid evolution. When the inner gene converted fragment sequences were removed, eleven Esp paralogs were present in two or more pairs with K(a)/K(s) >1.0 and thus we propose that positive selection is detectable by this means in at least some mouse Esp paralogs. We compare and contrast the evolutionary histories of all three mouse pheromone gene families in light of their proposed functions in mouse communication.

  1. Complete mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus (Crustacea: Decapoda: Caridea): gene rearrangement and phylogeny within Caridea.

    PubMed

    Shen, Xin; Li, Xiao; Sha, Zhongli; Yan, Binlun; Xu, Qihua

    2012-07-01

    The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers (Crustacea: Decapoda: Caridea) is presented here. A comparative analysis based on the currently available mitochondrial genomic data revealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mitochondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mitochondrial genomes of four previously studied carideans (Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra) were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rearrangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving inversion was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mitochondrial genome that has been studied so far; however, the translocation of one transfer RNA gene (trnP or trnT) was reported in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous substitutions rates (Ka/Ks) for the 13 protein coding genes from two Alpheus species (A. japonicus and A. distinguendus) and three Macrobrachium species (M. rosenbergii, M. nipponense, M. lanchesteri) were calculated, the Ka/Ks values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 (between 0.0048 and 0.2057), indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, (Palaemonidae+Alpheidae)+Atyidae, at the family level.

  2. Genetic Basis of Differential Heat Resistance between Two Species of Congeneric Freshwater Snails: Insights from Quantitative Proteomics and Base Substitution Rate Analysis.

    PubMed

    Mu, Huawei; Sun, Jin; Fang, Ling; Luan, Tiangang; Williams, Gray A; Cheung, Siu Gin; Wong, Chris K C; Qiu, Jian-Wen

    2015-10-02

    We compared the heat tolerance, proteomic responses to heat stress, and adaptive sequence divergence in the invasive snail Pomacea canaliculata and its noninvasive congener Pomacea diffusa. The LT50 of P. canaliculata was significantly higher than that of P. diffusa. More than 3350 proteins were identified from the hepatopancreas of the snails exposed to acute and chronic thermal stress using iTRAQ-coupled mass spectrometry. Acute exposure (3 h exposure at 37 °C with 25 °C as control) resulted in similar numbers (27 in P. canaliculata and 23 in P. diffusa) of differentially expressed proteins in the two species. Chronic exposure (3 weeks of exposure at 35 °C with 25 °C as control) caused differential expression of more proteins (58 in P. canaliculata and 118 in P. diffusa), with many of them related to restoration of damaged molecules, ubiquitinating dysfunctional molecules, and utilization of energy reserves in both species; but only in P. diffusa was there a shift from carbohydrate to lipid catabolism. Analysis of orthologous genes encoding the differentially expressed proteins revealed two genes having clear evidence of positive selection (Ka/Ks > 1) and seven candidates for more detailed analysis of positive selection (Ka/Ks between 0.5 and 1). These nine genes are related to energy metabolism, cellular oxidative homeostasis, signaling, and binding processes. Overall, the proteomic and base substitution rate analyses indicate genetic basis of differential resistance to heat stress between the two species, and such differences could affect their further range expansion in a warming climate.

  3. Cracking in Concrete near Joints in Steelconcrete Composite Slab / Zarysowanie Płyty Żelbetowej W Strefie Przywęzłowej Stropu Zespolonego

    NASA Astrophysics Data System (ADS)

    Niedośpiał, Marcin; Knauff, Michał; Barcewicz, Wioleta

    2015-03-01

    In this paper results of the experimental tests of four full-scale composite steel-concrete elements are reported. In the steel-concrete composite elements, a steel beam was connected with a slab cast on profiled sheeting, by shear studs. The end-plates were (the thickness of 8 mm, 10 mm and 12 mm) thinner than in ordinary design. Joints between the column and the beams have been designed as semi-rigid, i.e. the deformations of endplates affect the distribution of forces in the adjacent parts of the slab. The paper presents the theory of cracking in reinforced concrete and steel-concrete composite members (according to the codes), view of crack pattern on the surface of the slabs and a comparison of the tests results and the code calculations. It was observed, that some factors influencing on crack widths are not taken in Eurocode 4 (which is based on Eurocode 2 with taking into account the phenomenon called "tension stiffening"). W artykule przedstawiono wyniki badań czterech elementów zespolonych. Kształtownik stalowy połączony był z betonowym stropem wykonanym na blasze fałdowej. W modelu zastosowano cienkie blachy czołowe (o grubości 8 mm, 10 mm i 12 mm), cieńsze niż zwykle przyjmowane w praktyce projektowej. Połączenie to zaprojektowano jako podatne tzn. takie, w którym odkształcenia blach czołowych mają istotny wpływ na rozkład sił w połączeniu. Przedstawiono normową teorię dotyczącą zarysowania elementów żelbetowych i zespolonych, obraz zarysowania stropu oraz porównano otrzymane wyniki z obliczeniami wykonanymi wg aktualnych norm. Zauważono, iż nie wszystkie czynniki obliczania szerokości rys w konstrukcjach zespolonych są zdefiniowane w normie projektowania konstrukcji zespolonych (która w tej kwestii odwołuje się do normy projektowania konstrukcji żelbetowych z uwzględnieniem zjawiska "tension stiffening").

  4. Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors

    PubMed Central

    Peng, Suna; Tao, Ping; Xu, Feng; Wu, Aiping; Huo, Weige; Wang, Jinxiang

    2016-01-01

    Brassinosteroids (BR) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, the BR receptors in soybean remain largely unknown. Here, in addition to the known receptor gene Glyma06g15270 (GmBRI1a), we identified five putative BR receptor genes in the soybean genome: GmBRI1b, GmBRL1a, GmBRL1b, GmBRL2a, and GmBRL2b. Analysis of their expression patterns by quantitative real-time PCR showed that they are ubiquitously expressed in primary roots, lateral roots, stems, leaves, and hypocotyls. We used rapid amplification of cDNA ends (RACE) to clone GmBRI1b (Glyma04g39160), and found that the predicted amino acid sequence of GmBRI1b showed high similarity to those of AtBRI1 and pea PsBRI1. Structural modeling of the ectodomain also demonstrated similarities between the BR receptors of soybean and Arabidopsis. GFP-fusion experiments verified that GmBRI1b localizes to the cell membrane. We also explored GmBRI1b function in Arabidopsis through complementation experiments. Ectopic over-expression of GmBRI1b in Arabidopsis BR receptor loss-of-function mutant (bri1-5 bak1-1D) restored hypocotyl growth in etiolated seedlings; increased the growth of stems, leaves, and siliques in light; and rescued the developmental defects in leaves of the bri1-6 mutant, and complemented the responses of BR biosynthesis-related genes in the bri1-5 bak1-D mutant grown in light. Bioinformatics analysis demonstrated that the six BR receptor genes in soybean resulted from three gene duplication events during evolution. Phylogenetic analysis classified the BR receptors in dicots and monocots into three subclades. Estimation of the synonymous (Ks) and the nonsynonymous substitution rate (Ka) and selection pressure (Ka/Ks) revealed that the Ka/Ks of BR receptor genes from dicots and monocots were less than 1.0, indicating that BR receptor genes in plants experienced purifying selection during evolution. PMID:27338344

  5. Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes

    PubMed Central

    2011-01-01

    Background Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics. Results We chose human and eleven other high-coverage mammalian genome data–as well as an avian genome as an outgroup–to analyze orthologous protein-coding genes using nonsynonymous (Ka) and synonymous (Ks) substitution rates. After evaluating eight commonly-used methods of Ka and Ks calculation, we observed that these methods yielded a nearly uniform result when estimating Ka, but not Ks (or Ka/Ks). When sorting genes based on Ka, we noticed that fast-evolving and slow-evolving genes often belonged to different functional classes, with respect to species-specificity and lineage-specificity. In particular, we identified two functional classes of genes in the acquired immune system. Fast-evolving genes coded for signal-transducing proteins, such as receptors, ligands, cytokines, and CDs (cluster of differentiation, mostly surface proteins), whereas the slow-evolving genes were for function-modulating proteins, such as kinases and adaptor proteins. In addition, among slow-evolving genes that had functions related to the central nervous system, neurodegenerative disease-related pathways were enriched significantly in most mammalian species. We also confirmed that gene expression was negatively correlated with evolution rate, i.e. slow-evolving genes were expressed at higher levels than fast-evolving genes. Our results indicated that the functional specializations of the three major mammalian clades were: sensory perception and oncogenesis in primates, reproduction and hormone regulation in large mammals, and immunity and angiotensin in rodents. Conclusion Our study suggests that Ka calculation, which is less biased compared to Ks and Ka/Ks, can be used as a

  6. The Research into the Quality of Rock Surfaces Obtained by Abrasive Water Jet Cutting

    NASA Astrophysics Data System (ADS)

    Młynarczuk, Mariusz; Skiba, Marta; Sitek, Libor; Hlaváček, Petr; Kožušníková, Alena

    2014-12-01

    ęcia strumieniem wodnym, czyli dla dużych prędkości cięcia i dla fragmentów powierzchni znacznie oddalonych od brzegu próbki. W badaniach wykazano, że przy optymalnie dobranych parametrach obróbki wpływ wielkości ziarn na jakość powierzchni jest niewielki, a niekiedy nawet pomijalny. W pracy opisano również możliwość zastosowania funkcji madogramu do analizy jakości obrabianej powierzchni. Przy wykorzystaniu tej funkcji można nie tylko potwierdzić rezultaty otrzymane na bazie parametrów zdefiniowanych w ISO, ale otrzymuje się bardziej dogłębny obraz ukształtowania badanej powierzchni.

  7. The Use of 3D Graphic Modelling in Geoarchaeological Investigations (Bykowszczyzna Archaeological Site near Kock, E Poland)

    NASA Astrophysics Data System (ADS)

    Łojek, Jacek

    2012-01-01

    The objective of this paper was to use the ArcView 3.2 application for spatial modelling of the exploration forms (pits) in the Bykowszczyzna 8 archaeological site. The 3D digital documentation at a specific scale makes possible easy archiving, presentation, and simple spatial analyses of the examined objects. The ArcView 3.2 programme and its extensions (Spatial Analyst and 3D Analyst), commonly used as analytical tools in geomorphology, were inventively used for inventory-making in the archaeological site. Traditional field sketches were only a base, which enables entering data into the programme, and don't documentation material in itself as it used to be. The method of data visual ization proposed by the author gives new possibilities for using the GIS platform software. W artykule zaprezentowano projekt wykorzystania aplikacji ArcView 3.2 w modelowaniu obrazu form eksploracyjnych na stanowisku archeologicznym Bykowszczyzna 8. Stanowisko zostało objęte programem ratowniczych badań archeologicznych w związku z budową obwodnicy miasta Kocka na trasie krajowej nr 19 relacji Siemiatycze-Lublin-Nisko. Zasadniczy etap prac archeologicznych na stanowisku Bykowszczyzna 8 obejmował pozyskanie oraz inwentaryzację materiału zabytkowego wypełniającego formy. W wyniku wybrania tego materiału, w obszarze stanowiska pozostają charakterystyczne jamy gospodarcze, które stanowią negatywowy obraz wypełnienia formy. Kształt jam jest dokumentowany w postaci szkiców oraz fotografii. Dokumentacja ta stanowi punkt wyjścia procesu digitalizacji (materiał źródłowy). Treścią artykułu jest sporządzenie cyfrowej dokumentacji zawierającej plany stanowiska w kilku poziomach szczegółowości (dla pasa, pola oraz pojedynczych form) oraz wygenerowanie modeli w standardzie 3D. Dokumentacja taka umożliwia łatwą archiwizację oraz czytelną prezentację wybranych obiektów. Możliwe jest również wykonanie analiz przestrzennych. Funkcje programu ArcView 3.2. oraz

  8. Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

    PubMed Central

    Cao, Yunpeng; Han, Yahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2016-01-01

    Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes. PMID:27933074

  9. Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family.

    PubMed

    Xie, Zhengqing; Si, Weina; Gao, Rongchao; Zhang, Xiaohui; Yang, Sihai

    2015-12-01

    Late blight caused by the oomycete Phytophthora infestans is one of the most severe threats to potato production worldwide. Numerous studies suggest that the most effective protective strategy against the disease would be to provide potato cultivars with durable resistance (R) genes. However, little is known about the origin and evolutional history of these durable R-genes in potato. Addressing this might foster better understanding of the dynamics of these genes in nature and provide clues for identifying potential candidate R-genes. Here, a systematic survey was executed at RB/Rpi-blb1 locus, an exclusive broad-spectrum R-gene locus in potato. As indicated by synteny analysis, RB/Rpi-blb1 homologs were identified in all tested genomes, including potato, tomato, pepper, and Nicotiana, suggesting that the RB/Rpi-blb1 locus has an ancient origin. Two evolutionary patterns, similar to those reported on RGC2 in Lactuca, and Pi2/9 in rice, were detected at this locus. Type I RB/Rpi-blb1 homologs have frequent copy number variations and sequence exchanges, obscured orthologous relationships, considerable nucleotide divergence, and high non-synonymous to synonymous substitutions (Ka/Ks) between or within species, suggesting rapid diversification and balancing selection in response to rapid changes in the oomycete pathogen genomes. These characteristics may serve as signatures for cloning of late blight resistance genes.

  10. Differential evolutionary rates of neuronal transcriptome in Aplysia kurodai and Aplysia californica as a tool for gene mining.

    PubMed

    Choi, Sun-Lim; Lee, Yong-Seok; Rim, Young-Soo; Kim, Tae-Hyung; Moroz, Leonid L; Kandel, Eric R; Bhak, Jong; Kaang, Bong-Kiun

    2010-07-01

    The marine mollusk Aplysia is a fascinating model organism for studying molecular mechanisms underlying learning and memory. However, evolutionary studies about Aplysia have been limited by the lack of its genomic information. Recently, large-scale expressed sequence tag (EST) databases have been acquired by sequencing cDNA libraries from A. californica and A. kurodai. The closeness between the two species allowed us to investigate rapidly evolving genes by comparing their orthologs. Using this method, we found that a subset of signal transduction genes in neurons showed rates of protein evolution higher than those of housekeeping genes. Moreover, we were also able to find several candidate genes that may be involved in learning and memory or synaptic plasticity among genes showing relatively higher K(a)/K(s) ratios. We also investigated the relationship between evolutionary rates and tissue distribution of Aplysia genes. They propose that the estimation of evolutionary rates cannot be a good marker to assess neuronal expression; however, it still can be an efficient way to narrow down the pool of candidate genes involved in neuronal functions for the further studies.

  11. Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri)

    PubMed Central

    Cao, Yunpeng; Han, Yahui; Meng, Dandan; Li, Dahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2016-01-01

    Peroxidases (PRXs) are widely existed in various organisms and could be divided into different types according to their structures and functions. Specifically, the Class III Peroxidase, a plant-specific multi-gene family, involves in many physiological processes, such as the metabolism of auxin, the extension and thickening of cell wall, as well as the formation of lignin. By searching the pear genome database, 94 non-redundant PRXs from Pyrus bretschneideri (PbPRXs) were identified. Subsequently, analysis of phylogenetic relationships, gene structures, conserved motifs, and microsynteny was performed. These PbPRXs were unevenly distributed among 17 chromosomes of pear. In addition, 26 segmental duplication events but only one tandem duplication were occurred in these PbPRXs, implying segmental duplication was the main contributor to the expansion of the PbPRX family. By the Ka/Ks analysis, 26 out of 27 duplicated PbPRXs has experienced purifying selection. Twenty motifs were identified in PbPRXs based on the MEME analysis, 11 of which were enriched in pear. A total of 41 expressed genes were identified from ESTs of pear fruit. According to qRT-PCR, the expression trends of five PbPRXs in subgroup C were consistent with the change of lignin content during pear fruit development. So we inferred that the five PbPRXs were candidate genes involved in the lignin synthesis pathway. These results provided useful information for further researches of PRX genes in pear. PMID:28018406

  12. Evolutionary Pattern of the FAE1 Gene in Brassicaceae and Its Correlation with the Erucic Acid Trait

    PubMed Central

    Li, Mimi; Peng, Bin; Guo, Haisong; Yan, Qinqin; Hang, Yueyu

    2013-01-01

    The fatty acid elongase 1 (FAE1) gene catalyzes the initial condensation step in the elongation pathway of VLCFA (very long chain fatty acid) biosynthesis and is thus a key gene in erucic acid biosynthesis. Based on a worldwide collection of 62 accessions representing 14 tribes, 31 genera, 51 species, 4 subspecies and 7 varieties, we conducted a phylogenetic reconstruction and correlation analysis between genetic variations in the FAE1 gene and the erucic acid trait, attempting to gain insight into the evolutionary patterns and the correlations between genetic variations in FAE1 and trait variations. The five clear, deeply diverged clades detected in the phylogenetic reconstruction are largely congruent with a previous multiple gene-derived phylogeny. The Ka/Ks ratio (<1) and overall low level of nucleotide diversity in the FAE1 gene suggest that purifying selection is the major evolutionary force acting on this gene. Sequence variations in FAE1 show a strong correlation with the content of erucic acid in seeds, suggesting a causal link between the two. Furthermore, we detected 16 mutations that were fixed between the low and high phenotypes of the FAE1 gene, which constitute candidate active sites in this gene for altering the content of erucic acid in seeds. Our findings begin to shed light on the evolutionary pattern of this important gene and represent the first step in elucidating how the sequence variations impact the production of erucic acid in plants. PMID:24358289

  13. Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar.

    PubMed

    Zhang, Jin; Jia, Huixia; Li, Jianbo; Li, Yu; Lu, Mengzhu; Hu, Jianjun

    2016-07-18

    Heat shock transcription factor (Hsf) family is one of the most important regulators in the plant kingdom. Hsf has been demonstrated to be involved in various processes associated with plant growth, development as well as in response to hormone and abiotic stresses. In this study, we carried out a comprehensive analysis of Hsf family in desert poplar, Populus euphratica. Total of 32 genes encoding Hsf were identified and they were classified into three main classes (A, B, and C). Gene structure and conserved motif analyses indicated that the members in each class were relatively conserved. Total of 10 paralogous pairs were identified in PeuHsf family, in which nine pairs were generated by whole genome duplication events. Ka/Ks analysis showed that PeuHsfs underwent purifying selection pressure. In addition, various cis-acting elements involved in hormone and stress responses located in the promoter regions of PeuHsfs. Gene expression analysis indicated that several PeuHsfs were tissue-specific expression. Compared to Arabidopsis, more PeuHsf genes were significantly induced by heat, drought, and salt stresses (21, 19, and 22 PeuHsfs, respectively). Our findings are helpful in understanding the distinguished adaptability of P. euphratica to extreme environment and providing a basis for functional analysis of PeuHsfs in the future.

  14. Local adaptation of Gymnocypris przewalskii (Cyprinidae) on the Tibetan Plateau.

    PubMed

    Zhang, Renyi; Ludwig, Arne; Zhang, Cunfang; Tong, Chao; Li, Guogang; Tang, Yongtao; Peng, Zuogang; Zhao, Kai

    2015-05-06

    Divergent selection among environments affects species distributions and can lead to speciation. In this article, we investigated the transcriptomes of two ecotypes of scaleless carp (Gymnocypris przewalskii przewalskii and G. p. ganzihonensis) from the Tibetan Plateau. We used a transcriptome sequencing approach to screen approximately 250,000 expressed sequence tags (ESTs) from the gill and kidney tissues of twelve individuals from the Ganzi River and Lake Qinghai to understand how this freshwater fish has adapted to an ecological niche shift from saline to freshwater. We identified 9,429 loci in the gill transcriptome and 12,034 loci in the kidney transcriptome with significant differences in their expression, of which 242 protein-coding genes exhibited strong positive selection (Ka/Ks > 1). Many of the genes are involved in ion channel functions (e.g., Ca(2+)-binding proteins), immune responses (e.g., nephrosin) or cellular water absorption functions (e.g., aquaporins). These results have potentially broad importance in understanding shifts from saline to freshwater habitats. Furthermore, this study provides the first transcriptome of G. przewalskii, which will facilitate future ecological genomics studies and aid in the identification of genes underlying adaptation and incipient ecological speciation.

  15. Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

    PubMed Central

    Song, Sheng-Nan; Tang, Pu; Wei, Shu-Jun; Chen, Xue-Xin

    2016-01-01

    The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI-nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)). PMID:26879745

  16. A unified treatment of some iterative algorithms in signal processing and image reconstruction

    NASA Astrophysics Data System (ADS)

    Byrne, Charles

    2004-02-01

    Let T be a (possibly nonlinear) continuous operator on Hilbert space {\\cal H} . If, for some starting vector x, the orbit sequence {Tkx,k = 0,1,...} converges, then the limit z is a fixed point of T; that is, Tz = z. An operator N on a Hilbert space {\\cal H} is nonexpansive (ne) if, for each x and y in {\\cal H} , \\[ \\| Nx-Ny\\| \\leq \\| x-y\\|. \\] Even when N has fixed points the orbit sequence {Nkx} need not converge; consider the example N = -I, where I denotes the identity operator. However, for any \\alpha \\in (0,1) the iterative procedure defined by \\[ x^{k+1}=(1-\\alpha)x^k+\\alpha Nx^k \\] converges (weakly) to a fixed point of N whenever such points exist. This is the Krasnoselskii-Mann (KM) approach to finding fixed points of ne operators. A wide variety of iterative procedures used in signal processing and image reconstruction and elsewhere are special cases of the KM iterative procedure, for particular choices of the ne operator N. These include the Gerchberg-Papoulis method for bandlimited extrapolation, the SART algorithm of Anderson and Kak, the Landweber and projected Landweber algorithms, simultaneous and sequential methods for solving the convex feasibility problem, the ART and Cimmino methods for solving linear systems of equations, the CQ algorithm for solving the split feasibility problem and Dolidze's procedure for the variational inequality problem for monotone operators.

  17. Comparative genome analysis and phylogenetic relationship of order Liliales insight from the complete plastid genome sequences of two Lilies (Lilium longiflorum and Alstroemeria aurea).

    PubMed

    Kim, Jung Sung; Kim, Joo-Hwan

    2013-01-01

    Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Lilium longiflorum (Liliaceae) and 155,510bp in Alstroemeria aurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium.

  18. Characterization of the divergent eosinophil ribonuclease, mEar 6, and its expression in response to Schistosoma mansoni infection in vivo.

    PubMed

    Nitto, T; Dyer, K D; Mejia, R A; Byström, J; Wynn, T A; Rosenberg, H F

    2004-12-01

    The eosinophil-associated ribonucleases (Ears) are rapidly evolving proteins found in multigene clusters that are unique to each rodent species. Of the 15 independent genes in the Mus musculus cluster, only mEars 1 and 2 are expressed at significant levels at homeostasis. Here we characterize the expression of mEar 6 in the liver and spleen in mice in response to infection with the helminthic parasite, Schistosoma mansoni. Interestingly, expression of mEar 6 is not directly related to the elevated levels of serum IL-5 or tissue eosinophilia characteristic of this disease, as no mEar 6 transcripts were detected in the liver or the spleen from uninfected IL-5-transgenic mice. The coding sequence of mEar 6 has diverged under positive selection pressure (K(a)/K(s) > 1.0) and has a unique unpaired cysteine near the carboxy-terminus of the protein. The high catalytic efficiency of recombinant mEar 6 (k(cat)/K(m) = 0.9 x 10(6)/M/s) is similar to that of the cluster's closest human ortholog, eosinophil-derived neurotoxin (EDN/RNase 2). In summary, we have identified mEar 6 as one of only two RNase A superfamily ribonucleases known to be expressed specifically in response to pathophysiologic stress in vivo.

  19. Transcriptome Sequencing and Positive Selected Genes Analysis of Bombyx mandarina

    PubMed Central

    Wu, Yuqian; Long, Renwen; Liu, Chun; Xia, Qingyou

    2015-01-01

    The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG) and posterior silk gland (PSG). Three sericin genes (sericin 1, sericin 2, and sericin 3) were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25) were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs) and 361 insertion-deletions (INDELs) were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research. PMID:25806526

  20. SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes

    PubMed Central

    ÓhÉigeartaigh, Seán S.; Armisén, David; Byrne, Kevin P.

    2014-01-01

    We report the development of SearchDOGS Bacteria, software to automatically detect missing genes in annotated bacterial genomes by combining BLAST searches with comparative genomics. Having successfully applied the approach to yeast genomes, we redeveloped SearchDOGS to function as a standalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST and a synteny-based method; this is followed by a scan of the entire genome of each species for unannotated genes. Results are provided in a HTML interface, providing coordinates, BLAST results, syntenic location, omega values (Ka/Ks, where Ks is the number of synonymous substitutions per synonymous site and Ka is the number of nonsynonymous substitutions per nonsynonymous site) for protein conservation estimates, and other information for each candidate gene. Using SearchDOGS Bacteria, we identified 155 gene candidates in the Shigella boydii sb227 genome, including 56 candidates of length < 60 codons. SearchDOGS Bacteria has two major advantages over currently available annotation software. First, it outperforms current methods in terms of sensitivity and is highly effective at identifying small or highly diverged genes. Second, as a freely downloadable package, it can be used with unpublished or confidential data. PMID:24659774

  1. Structural Stereo Matching Of Laplacian-Of-Gaussian Contour Segments For 3D Perception

    NASA Astrophysics Data System (ADS)

    Boyer, K. L.; Sotak, G. E.

    1989-03-01

    We solve the stereo correspondence problem using Lapla-cian of Gaussian (LoG) zero-crossing contours as a source of primitives for structural stereopsis, as opposed to traditional point-based algorithms. For each image in the stereo pair, we apply the LoG operator, extract and link zero crossing points, filter and segment the contours into meaningful primitives, and compute a parametric structural description over the resulting primitive set. We then apply a variant of the inexact structural matching technique of Boyer and Kak Ill to recover the optimal interprimitive mapping (correspon-dence) function. Since an extended image feature conveys more information than a single point, its spatial and photometric behavior may be exploited to advantage; there are also fewer features to match, resulting in a smaller combinatorial problem. The structural approach allows greater use of spatial relational constraints, which allows us to eliminate (or reduce) the coarse-to-fine tracking of most point-based algorithms. Solving the correspondence problem at this level requires only an approximate probabilistic characterization of the image-to-image structural distortion, and does not require detailed knowledge of the epipolar geometry.

  2. Revealing constitutively expressed resistance genes in Agrostis species using PCR-based motif-directed RNA fingerprinting.

    PubMed

    Budak, Hikmet; Su, Senem; Ergen, Neslihan

    2006-12-01

    Agrostis species are mainly used in athletic fields and golf courses. Their integrity is maintained by fungicides, which makes the development of disease-resistance varieties a high priority. However, there is a lack of knowledge about resistance (R) genes and their use for genetic improvement in Agrostis species. The objective of this study was to identify and clone constitutively expressed cDNAs encoding R gene-like (RGL) sequences from three Agrostis species (colonial bentgrass (A. capillaris L.), creeping bentgrass (A. stolonifera L.) and velvet bentgrass (A. canina L.)) by PCR-based motif-directed RNA fingerprinting towards relatively conserved nucleotide binding site (NBS) domains. Sixty-one constitutively expressed cDNA sequences were identified and characterized. Sequence analysis of ESTs and probable translation products revealed that RGLs are highly conserved among these three Agrostis species. Fifteen of them were shown to share conserved motifs found in other plant disease resistance genes such as MLA13, Xa1, YR6, YR23 and RPP5. The molecular evolutionary forces, analysed using the Ka/Ks ratio, reflected purifying selection both on NBS and leucine-rich repeat (LRR) intervening regions of discovered RGL sequences in these species. This study presents, for the first time, isolation and characterization of constitutively expressed RGL sequences from Agrostis species revealing the presence of TNL (TIR-NBS-LRR) type R genes in monocot plants. The characterized RGLs will further enhance knowledge on the molecular evolution of the R gene family in grasses.

  3. Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling

    PubMed Central

    Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development. PMID:25745864

  4. The phylogenetic and evolutionary history of a novel alpha-globin-type gene in orangutans (Pongo pygmaeus).

    PubMed

    Steiper, Michael E; Wolfe, Nathan D; Karesh, William B; Kilbourn, Annelisa M; Bosi, Edwin J; Ruvolo, Maryellen

    2006-07-01

    The alpha-globin genes are implicated in human resistance to malaria, a disease caused by Plasmodium parasites. This study is the first to analyze DNA sequences from a novel alpha-globin-type gene in orangutans, a species affected by Plasmodium. Phylogenetic methods show that the gene is a duplication of an alpha-globin gene and is located 5' of alpha-2 globin. The alpha-globin-type gene is notable for having four amino acid replacements relative to the orangutan's alpha-1 and alpha-2 globin genes, with no synonymous differences. Pairwise K(a)/K(s) methods and likelihood ratio tests (LRTs) revealed that the evolutionary history of the alpha-globin-type gene has been marked by either neutral or positive evolution, but not purifying selection. A comparative analysis of the amino acid replacements of the alpha-globin-type gene with human hemoglobinopathies and hemoglobin structure showed that two of the four replaced sites are members of the same molecular bond, one that is crucial to the proper functioning of the hemoglobin molecule. This suggested an adaptive evolutionary change. Functionally, this locus may result in a thalassemia-like phenotype in orangutans, possibly as an adaptation to combat Plasmodium.

  5. Diversifying selection drives the evolution of the type III secretion system pilus of Pseudomonas syringae.

    PubMed

    Guttman, David S; Gropp, Susan J; Morgan, Robyn L; Wang, Pauline W

    2006-12-01

    The plant pathogenic bacterium Pseudomonas syringae uses a type III secretion system to inject virulence proteins directly into the cytoplasm of its hosts. The P. syringae type III secretion apparatus is encoded, in part, by the HrpZ operon, which carries the hrpA gene encoding the pilin subunit of the pilus, various components of the structural apparatus, and the HrpZ harpin protein that is believed to produce pores in the host cell membrane. The pilus of the type III system comes into direct contact with the host cell and is, therefore, a likely target of the host's pathogen surveillance systems. We sequenced and analyzed 22 HrpZ operons from P. syringae strains spanning the diversity of the species. Selection analyses, including K(a)/K(s) tests and Tajima's D, revealed strong diversifying selection acting on the hrpA gene. This form of selection enables pathogens to maintain genetic diversity within their populations and is often driven by selection imposed by host defense systems. The HrpZ operon also revealed a single significant recombination event that dramatically changed the evolutionary relationships among P. syringae strains from 2 quite distinct phylogroups. This recombination event appears to have introduced genetic diversity into a clade of strains that may now be undergoing positive selection. The identification of diversifying selection acting on the Hrp pilus across the whole population sample and positive selection within one P. syringae lineage supports a trench warfare coevolutionary model between P. syringae and its plant hosts.

  6. Somatic variation plays a key role in the evolution of the Vf gene family residing in the Vf locus that confers resistance to apple scab disease.

    PubMed

    Xu, Mingliang; Korban, Schuyler S

    2004-07-01

    A cluster of four receptor-like genes has been previously identified in the Vf locus of the crabapple Malus floribunda clone 821 that confers resistance to five races of the fungal pathogen Venturia inaequalis, the casual agent of apple scab disease. Pairwise comparisons of the four Vf paralogs in both promoter and coding regions reveal their timeline evolutionary history. The four Vf paralogs have evolved from four ancient Vf members resulting from two sequential duplication events of a single Vf progenitor initially present in the Malus genome. The coding sequences of the four Vf paralogs are characterized with high numbers of unique polymorphic nucleotides, a number of short duplications/deletions, various deletions of complete LRR copy units, and a casual insert of a transposon-like element. Significant high ratios of nonsynonymous to synonymous substitutions, Ka/Ks, are observed in the putative ligand binding residues in the LRR domains. No sequence exchange between the four Vf paralogs is observed. Compared with promoter regions, only nucleotide substitutions are dramatically elevated in the coding regions. The results presented in this study strongly indicate that the Vf locus is under strong and steady horizontal selective pressures imposed by the fungal pathogen V. inaequalis, and divergent selection on somatic variations plays a key role in shaping the resistance specificity.

  7. Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

    PubMed

    Bhattacharjee, Annapurna; Ghangal, Rajesh; Garg, Rohini; Jain, Mukesh

    2015-01-01

    Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

  8. Sequence and gene expression evolution of paralogous genes in willows

    PubMed Central

    Harikrishnan, Srilakshmy L.; Pucholt, Pascal; Berlin, Sofia

    2015-01-01

    Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows. PMID:26689951

  9. Adaptive introgression of anticoagulant rodent poison resistance by hybridization between Old World mice

    PubMed Central

    Song, Ying; Endepols, Stefan; Klemann, Nicole; Richter, Dania; Matuschka, Franz-Rainer; Shih, Ching-Hua; Nachman, Michael W.; Kohn, Michael H.

    2011-01-01

    Summary It is known that evolution by selection on new or standing single nucleotide polymorphisms (SNPs) in the vitamin K 2,3-epoxide reductase subcomponent 1 (vkorc1) of house mice (Mus musculus domesticus) can cause resistance to anticoagulant rodenticides such as warfarin [1–3]. Here we report an introgression in European M. m. domesticus spanning as much as ~20.3 megabases (Mb) and including vkorc1, the molecular target of anticoagulants [1–4], that stems from hybridization with the Algerian mouse (M. spretus). We show that in the laboratory the homozygous complete vkorc1 allele of M. spretus confers resistance when introgressed into M. m. domesticus. Consistent with selection on the introgression after the introduction of rodenticides in the 1950s we document historically adaptive population genetics of vkorc1 in M. m. domesticus. Furthermore, we detected adaptive protein evolution of vkorc1 in the M. spretus lineage (Ka/Ks=1.54–1.93) resulting in radical amino-acid substitutions that apparently have anticoagulant tolerance of M. spretus as pleiotropic effect. Thus, positive selection produced an adaptive, divergent and pleiotropic vkorc1 allele in the donor species, M. spretus, which crossed a species barrier where it is expressed as adaptive trait in the recipient species, M. m. domesticus. Resistant house mice originated from selection on new or standing vkorc1 polymorphisms and from selection on vkorc1 polymorphisms acquired by adaptive introgressive hybridization. PMID:21782438

  10. Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

    PubMed

    Dubey, Bhawna; Meganathan, P R; Haque, Ikramul

    2012-07-01

    This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

  11. Expansion Mechanisms and Functional Divergence of the Glutathione S-Transferase Family in Sorghum and Other Higher Plants

    PubMed Central

    Chi, Yunhua; Cheng, Yansong; Vanitha, Jeevanandam; Kumar, Nadimuthu; Ramamoorthy, Rengasamy; Ramachandran, Srinivasan; Jiang, Shu-Ye

    2011-01-01

    Glutathione S-transferases (GSTs) exist in various eukaryotes and function in detoxification of xenobiotics and in response to abiotic and biotic stresses. We have carried out a genome-wide survey of this gene family in 10 plant genomes. Our data show that tandem duplication has been regarded as the major expansion mechanism and both monocot and dicot plants may have practiced different expansion and evolutionary history. Non-synonymous substitutions per site (Ka) and synonymous substitutions per site (Ks) analyses showed that N- and C-terminal functional domains of GSTs (GST_N and GST_C) seem to have evolved under a strong purifying selection (Ka/Ks < 1) under different selective pressures. Differential evolutionary rates between GST_N and GST_C and high degree of expression divergence have been regarded as the major drivers for the retention of duplicated genes and the adaptability to various stresses. Expression profiling also indicated that the gene family plays a role not only in stress-related biological processes but also in the sugar-signalling pathway. Our survey provides additional annotation of the plant GST gene family and advance the understanding of plant GSTs in lineage-specific expansion and species diversification. PMID:21169340

  12. Comparative Genome Analysis and Phylogenetic Relationship of Order Liliales Insight from the Complete Plastid Genome Sequences of Two Lilies (Lilium longiflorum and Alstroemeria aurea)

    PubMed Central

    Kim, Jung Sung; Kim, Joo-Hwan

    2013-01-01

    Monocots are one of the most diverse, successful and economically important clades of angiosperms. We attempt to analyse the complete plastid genome sequences of two lilies and their lengths were 152,793bp in Liliumlongiflorum (Liliaceae) and 155,510bp in Alstroemeriaaurea (Alstroemeriaceae). Phylogenetic analyses were performed for 28 taxa including major lineages of monocots using the sequences of 79 plastid genes for clarifying the phylogenetic relationship of the order Liliales. The sister relationship of Liliales and Asparagales-commelinids was improved with high resolution. Comparative analyses of inter-familial and inter-specific sequence variation were also carried out among three families of Liliaceae, Smilacaceae, and Alstroemeriaceae, and between two Lilium species of L. longflorum and L. superbum. Gene content and order were conserved in the order Liliales except infA loss in Smilax and Alstroemeria. IR boundaries were similar in IRa, however, IRb showed different extension patterns as JLB of Smilax and JSB in Alstroemeria. Ka/Ks ratio was high in matK among the pair-wise comparison of three families and the most variable genes were psaJ, ycf1, rpl32, rpl22, matK, and ccsA among the three families and rps15, rpoA, matK, and ndhF between Lilium. PMID:23950788

  13. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  14. Self-incompatibility of Prunus tenella and evidence that reproductively isolated species of Prunus have different SFB alleles coupled with an identical S-RNase allele.

    PubMed

    Surbanovski, Nada; Tobutt, Kenneth R; Konstantinović, Miroslav; Maksimović, Vesna; Sargent, Daniel J; Stevanović, Vladimir; Bosković, Radovan I

    2007-05-01

    Many species of Prunus display an S-RNase-based gametophytic self-incompatibility (SI), controlled by a single highly polymorphic multigene complex termed the S-locus. This comprises tightly linked stylar- and pollen-expressed genes that determine the specificity of the SI response. We investigated SI of Prunus tenella, a wild species found in small, isolated populations on the Balkan peninsula, initially by pollination experiments and identifying stylar-expressed RNase alleles. Nine P. tenella S-RNase alleles (S(1)-S(9)) were cloned; their sequence analysis showed a very high ratio of non-synonymous to synonymous nucleotide substitutions (K(a)/K(s)) and revealed that S-RNase alleles of P. tenella, unlike those of Prunus dulcis, show positive selection in all regions except the conserved regions and that between C2 and RHV. Remarkably, S(8)-RNase, was found to be identical to S(1)-RNase from Prunus avium, a species that does not interbreed with P. tenella and, except for just one amino acid, to S(11) of P. dulcis. However, the corresponding introns and S-RNase-SFB intergenic regions showed considerable differences. Moreover, protein sequences of the pollen-expressed SFB alleles were not identical, harbouring 12 amino-acid replacements between those of P. tenella SFB(8) and P. avium SFB(1). Implications of this finding for hypotheses about the evolution of new S-specificities are discussed.

  15. Molecular evolution, characterization and expression profiling of uterine aldoketoreductase 1B5 gene in endometrium of goat (Capra hircus).

    PubMed

    Kumar, Rohit; Ramteke, P W; Sharma, Sanjeev Kumar; Mitra, Abhijit

    2015-01-01

    Aldoketoreductase 1B5 (AKR1B5), a member of the Aldoketoreductase family, is involved in the production of Prostaglandin F2α (PGF2α) as one of vital prostaglandin F synthase (PGFS). PGs (Prostaglandins) play a crucial role in female reproductive system. In the present study, we cloned and characterized the full-length open reading frame of AKR1B5 gene in Black Bengal (BB) goat. The complete coding sequence of AKR1B5 comprises an entire open reading frame of 951 bp, encoding 316 amino acid (AA) residues. BB AKR1B5 showed >82.9% identity with that of cattle, rabbit, human, and rat at nucleotide and amino acid levels, respectively. Further, a systematic study of AKR1B5 sequence evolution was also conducted using Phylogenetic Analysis by Maximum Likelihood (PAML), entropy plot, and Blossum 62 in a phylogenetic context. Analysis of nonsynonymous to synonymous nucleotide substitution rate ratios (Ka/Ks) revealed that negative selection may have been operating on this gene during evolution in goat, cattle, rabbit, human, and rat, which showed its conservation across species. Further, expression of AKR1B5 was determined by quantitative real-time PCR in goat endometrial tissues at different stages of the estrous cycle and early pregnancy. Our results indicated its high expression at luteolytic phase (stage III; day 16-21) during the estrous cycle. However, during early (day ∼30-40) pregnancy the expression was highest as compared to estrous cycle.

  16. Sequence and gene expression evolution of paralogous genes in willows.

    PubMed

    Harikrishnan, Srilakshmy L; Pucholt, Pascal; Berlin, Sofia

    2015-12-22

    Whole genome duplications (WGD) have had strong impacts on species diversification by triggering evolutionary novelties, however, relatively little is known about the balance between gene loss and forces involved in the retention of duplicated genes originating from a WGD. We analyzed putative Salicoid duplicates in willows, originating from the Salicoid WGD, which took place more than 45 Mya. Contigs were constructed by de novo assembly of RNA-seq data derived from leaves and roots from two genotypes. Among the 48,508 contigs, 3,778 pairs were, based on fourfold synonymous third-codon transversion rates and syntenic positions, predicted to be Salicoid duplicates. Both copies were in most cases expressed in both tissues and 74% were significantly differentially expressed. Mean Ka/Ks was 0.23, suggesting that the Salicoid duplicates are evolving by purifying selection. Gene Ontology enrichment analyses showed that functions related to DNA- and nucleic acid binding were over-represented among the non-differentially expressed Salicoid duplicates, while functions related to biosynthesis and metabolism were over-represented among the differentially expressed Salicoid duplicates. We propose that the differentially expressed Salicoid duplicates are regulatory neo- and/or subfunctionalized, while the non-differentially expressed are dose sensitive, hence, functionally conserved. Multiple evolutionary processes, thus drive the retention of Salicoid duplicates in willows.

  17. Finds in Belize document Late Classic Maya salt making and canoe transport

    PubMed Central

    McKillop, Heather

    2005-01-01

    How did people in preIndustrial ancient civilizations produce and distribute bulk items, such as salt, needed for everyday use by their large urban populations? This report focuses on the ancient Maya who obtained quantities of salt at cities in the interior of the Yucatan peninsula of Mexico, Belize, and Guatemala in an area where salt is scarce. I report the discovery of 41 Late Classic Maya saltworks (anno Domini 600–900) in Punta Ycacos Lagoon on the south coast of Belize, including one with the first-known ancient Maya canoe paddle. The discoveries add important empirical information for evaluating the extent of surplus salt production and river transport during the height of Late Classic civilization in the southern Maya lowlands. The discovery of the saltworks indicates that there was extensive production and distribution of goods and resources outside the cities in the interior of the Yucatan. The discovery of a wooden canoe paddle from one of the Punta Ycacos saltworks, Ka'k' Naab', ties the production of salt to its inland transport by rivers and documents the importance of canoe trade between the coast and the interior during the Late Classic. Archaeological discovery of multiple saltworks on the Belizean coast represents surplus production of salt destined largely for the inland Peten Maya during their Late Classic peak, underscoring the importance of non-state-controlled workshop production in preIndustrial societies. PMID:15809426

  18. An efficient method for correcting the edge artifact due to smoothing.

    PubMed

    Maisog, J M; Chmielowska, J

    1998-01-01

    Spatial smoothing is a common pre-processing step in the analysis of functional brain imaging data. It can increase sensitivity to signals of specific shapes and sizes (Rosenfeld and Kak [1982]: Digital Picture Processing, vol. 2. Orlando, Fla.: Academic; Worsley et al. [1996]: Hum Brain Mapping 4:74-90). Also, some amount of spatial smoothness is required if methods from the theory of Gaussian random fields are to be used (Holmes [1994]: Statistical Issues in Functional Brain Mapping. PhD thesis, University of Glasgow). Smoothing is most often implemented as a convolution of the imaging data with a smoothing kernel, and convolution is most efficiently performed using the Convolution Theorem and the Fast Fourier Transform (Cooley and Tukey [1965]: Math Comput 19:297-301; Priestly [1981]: Spectral Analysis and Time Series. San Diego: Academic; Press et al. [1992]: Numerical Recipes in C: The Art of Scientific Computing, 2nd ed. Cambridge: Cambridge University Press). An undesirable side effect of smoothing is an artifact along the edges of the brain, where brain voxels become smoothed with non-brain voxels. This results in a dark rim which might be mistaken for hypoactivity. In this short methodological paper, we present a method for correcting functional brain images for the edge artifact due to smoothing, while retaining the use of the Convolution Theorem and the Fast Fourier Transform for efficient calculation of convolutions.

  19. Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice

    PubMed Central

    Zhang, Zheng-Feng; Li, Yuan-Yuan; Xiao, Ben-Ze

    2016-01-01

    Drought stress is one of the major adverse environmental factors reducing plant growth. With the aim to elucidate the underlying molecular basis of rice response to drought stress, comparative transcriptome analysis was conducted between drought susceptible rice cultivar Zhenshan97 and tolerant cultivar IRAT109 at the seedling stage. 436 genes showed differential expression and mainly enriched in the Gene Ontology (GO) terms of stress defence. A large number of variations exist between these two genotypes including 2564 high-quality insertion and deletions (INDELs) and 70,264 single nucleotide polymorphism (SNPs). 1041 orthologous gene pairs show the ratio of nonsynonymous nucleotide substitution rate to synonymous nucleotide substitutions rate (Ka/Ks) larger than 1.5, indicating the rapid adaptation to different environments during domestication. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of positive selection genes suggested that photosynthesis represents the most significant category. The collocation of positively selected genes with the QTLs of photosynthesis and the different photosynthesis performance of these two cultivars further illuminate the crucial function of photosynthesis in rice adaptation to drought stress. Our results also provide fruitful functional markers and candidate genes for future genetic research and improvement of drought tolerance in rice. PMID:26777777

  20. Population diversity and adaptive evolution in keratinization genes: impact of environment in shaping skin phenotypes.

    PubMed

    Gautam, Pramod; Chaurasia, Amit; Bhattacharya, Aniket; Grover, Ritika; Mukerji, Mitali; Natarajan, Vivek T

    2015-03-01

    Several studies have demonstrated the role of climatic factors in shaping skin phenotypes, particularly pigmentation. Keratinization is another well-designed feature of human skin, which is involved in modulating transepidermal water loss (TEWL). Although this physiological process is closely linked to climate, presently it is not clear whether genetic diversity is observed in keratinization and whether this process also responds to the environmental pressure. To address this, we adopted a multipronged approach, which involved analysis of 1) copy number variations in diverse Indian and HapMap populations from varied geographical regions; 2) genetic association with geoclimatic parameters in 61 populations of dbCLINE database in a set of 549 genes from four processes namely keratinization, pigmentation, epidermal differentiation, and housekeeping functions; 3) sequence divergence in 4,316 orthologous promoters and corresponding exonic regions of human and chimpanzee with macaque as outgroup, and 4) protein sequence divergence (Ka/Ks) across nine vertebrate classes, which differ in their extent of TEWL. Our analyses demonstrate that keratinization and epidermal differentiation genes are under accelerated evolution in the human lineage, relative to pigmentation and housekeeping genes. We show that this entire pathway may have been driven by environmental selection pressure through concordant functional polymorphisms across several genes involved in skin keratinization. Remarkably, this underappreciated function of skin may be a crucial determinant of adaptation to diverse environmental pressures across world populations.

  1. Genome-wide identification and evolution of the PIN-FORMED (PIN) gene family in Glycine max.

    PubMed

    Liu, Yuan; Wei, Haichao

    2017-03-17

    Soybean is one of the most important crop plants, wild and cultivated soybean varieties have significant differences worth further investigation, such as plant morphology, seed size, seed coat development, these characters may be related to auxin biology. The PIN family is an essential auxin polar transport gene, but little research on soybean PINs (GmPINs) has been done, especially with respect to evolution and the differences between wild and cultivated soybean. In this study, we retrieved 23 GmPINs from the latest updated G. max genome database; six GmPINs protein sequences were changed compared with the previous database. Based on the Plant Genome Duplication Database, 18 GmPINs have been involved in segment duplication. Three pairs of GmPINs arose after the second soybean genome duplication, and six occurred after the first genome duplication. The duplicated GmPINs retained similar expression patterns. All the duplicated GmPINs experienced purifying selection (Ka/Ks<1) to prevent accumulation of non-synonymous mutations and so became more similar. In addition, we also focused on the artificial selection of the soybean PIN genes. Five artificially selected GmPINs were identified by comparing the genome sequence of 17 wild and 14 cultivated soybean varieties. Our research provides useful and comprehensive basic information for understanding GmPINs.

  2. Molecular epidemiology of canine picornavirus in Hong Kong and Dubai and proposal of a novel genus in Picornaviridae.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Choi, Garnet K Y; Huang, Yi; Sivakumar, Saritha; Tsoi, Hoi-Wah; Yip, Cyril C Y; Jose, Shanty V; Bai, Ru; Wong, Emily Y M; Joseph, Marina; Li, Tong; Wernery, Ulrich; Yuen, Kwok-Yung

    2016-07-01

    Previously, we reported the discovery of a novel canine picornavirus (CanPV) in the fecal sample of a dog. In this molecular epidemiology study, CanPV was detected in 15 (1.11%) of 1347 canine fecal samples from Hong Kong and one (0.76%) of 131 canine fecal samples from Dubai, with viral loads 1.06×10(3) to 6.64×10(6) copies/ml. Complete genome sequencing and phylogenetic analysis showed that CanPV was clustered with feline picornavirus (FePV), bat picornavirus (BatPV) 1 to 3, Ia io picornavirus 1 (IaioPV1) and bovine picornavirus (BoPV), and this cluster was most closely related to the genera Enterovirus and Sapelovirus. The Ka/Ks ratios of all the coding regions were <0.1. According to the definition of the Picornavirus Study Group of ICTV, CanPV, FePV, BatPV 1 to 3, IaioPV1 and BoPV should constitute a novel genus in Picornaviridae. BEAST analysis showed that this genus diverged from its most closely related genus, Sapelovirus, about 49 years ago.

  3. Hepatitis E virus quasispecies and the outcome of acute hepatitis E in solid-organ transplant patients.

    PubMed

    Lhomme, Sebastien; Abravanel, Florence; Dubois, Martine; Sandres-Saune, Karine; Rostaing, Lionel; Kamar, Nassim; Izopet, Jacques

    2012-09-01

    Hepatitis E virus (HEV) infections are responsible for chronic hepatitis in immunocompromised patients, and this can evolve to cirrhosis. Like all RNA viruses, HEV exists as a mixture of heterogeneous viruses defining quasispecies. The relationship between the genetic heterogeneity described as a quasispecies, cytokine secretion, and the outcome of acute hepatitis in immunocompromised patients remains to be elucidated. We cloned and sequenced the region encoding the M and P capsid domains of HEV from eight solid-organ transplant (SOT) patients with acute HEV infection who subsequently cleared the virus and from eight SOT patients whose infection became chronic. We analyzed the cytokines and chemokines in the sera of these SOT patients by multianalyte profiling. The nucleotide sequence entropy and genetic distances were greater in patients whose infections became chronic. A lower K(a)/K(s) ratio was associated with the persistence of HEV. The patients who developed chronic infection had lower serum concentrations of interleukin-1 (IL-1) receptor antagonist and soluble IL-2 receptor. Increased concentrations of the chemokines implicated in leukocyte recruitment to the liver were associated with persistent infection. Those patients with chronic HEV infection and progressing liver fibrosis had less quasispecies diversification during the first year than patients without liver fibrosis progression. Great quasispecies heterogeneity, a weak inflammatory response, and high serum concentrations of the chemokines involved in leukocyte recruitment to the liver in the acute phase were associated with persistent HEV infection. Slow quasispecies diversification during the first year was associated with rapidly developing liver fibrosis.

  4. Structural, Evolutionary, and Functional Analysis of the Class III Peroxidase Gene Family in Chinese Pear (Pyrus bretschneideri).

    PubMed

    Cao, Yunpeng; Han, Yahui; Meng, Dandan; Li, Dahui; Jin, Qing; Lin, Yi; Cai, Yongping

    2016-01-01

    Peroxidases (PRXs) are widely existed in various organisms and could be divided into different types according to their structures and functions. Specifically, the Class III Peroxidase, a plant-specific multi-gene family, involves in many physiological processes, such as the metabolism of auxin, the extension and thickening of cell wall, as well as the formation of lignin. By searching the pear genome database, 94 non-redundant PRXs from Pyrus bretschneideri (PbPRXs) were identified. Subsequently, analysis of phylogenetic relationships, gene structures, conserved motifs, and microsynteny was performed. These PbPRXs were unevenly distributed among 17 chromosomes of pear. In addition, 26 segmental duplication events but only one tandem duplication were occurred in these PbPRXs, implying segmental duplication was the main contributor to the expansion of the PbPRX family. By the Ka/Ks analysis, 26 out of 27 duplicated PbPRXs has experienced purifying selection. Twenty motifs were identified in PbPRXs based on the MEME analysis, 11 of which were enriched in pear. A total of 41 expressed genes were identified from ESTs of pear fruit. According to qRT-PCR, the expression trends of five PbPRXs in subgroup C were consistent with the change of lignin content during pear fruit development. So we inferred that the five PbPRXs were candidate genes involved in the lignin synthesis pathway. These results provided useful information for further researches of PRX genes in pear.

  5. Spatiotemporal characteristics of the geomagnetic diurnal variation anomalies prior to the 2011 Tohoku earthquake (Mw 9.0) and the possible coupling of multiple pre-earthquake phenomena

    NASA Astrophysics Data System (ADS)

    Han, Peng; Hattori, Katsumi; Huang, Qinghua; Hirooka, Shinji; Yoshino, Chie

    2016-11-01

    Xu et al. (2013) and Han et al. (2015) have reported unusual behaviors of geomagnetic diurnal variation (GDV) in the vertical component prior to the 2011 off the Pacific coast of Tohoku earthquake (Mw 9.0). To make a better understanding of this phenomenon, temporal-spatial analyses of GDV have been applied in this study. Geomagnetic data of long-term observations at 17 stations in Japan have been analyzed using the same method in Han et al. (2015). Ratios of diurnal variation range between the reference station KAK and the target stations have been computed. After removing seasonal variations, the 15-day backward running mean values of the ratios in the vertical component shows a clear anomaly exceeding the statistical threshold about 2 months before the mega event at both ESA and MIZ stations in the Tohoku Region. Locations of anomalies in spatial distribution show a good correlation with the epicenter of the Mw 9.0 earthquake. These spatiotemporal results are consistent with those obtained from other independent observations such as groundwater level and GPS displacements. The coupling of multiple pre-earthquake phenomena may help to understand the preparation process of a mega earthquake in the subduction zone.

  6. Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

    PubMed Central

    Boo, Ga Hun; Hughey, Jeffery R.; Miller, Kathy Ann; Boo, Sung Min

    2016-01-01

    DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution. PMID:27739454

  7. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response.

    PubMed

    Wang, Qianqian; Liu, Jinyang; Wang, Yu; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

    2015-09-30

    Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses.

  8. Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar

    PubMed Central

    Zhang, Jin; Jia, Huixia; Li, Jianbo; Li, Yu; Lu, Mengzhu; Hu, Jianjun

    2016-01-01

    Heat shock transcription factor (Hsf) family is one of the most important regulators in the plant kingdom. Hsf has been demonstrated to be involved in various processes associated with plant growth, development as well as in response to hormone and abiotic stresses. In this study, we carried out a comprehensive analysis of Hsf family in desert poplar, Populus euphratica. Total of 32 genes encoding Hsf were identified and they were classified into three main classes (A, B, and C). Gene structure and conserved motif analyses indicated that the members in each class were relatively conserved. Total of 10 paralogous pairs were identified in PeuHsf family, in which nine pairs were generated by whole genome duplication events. Ka/Ks analysis showed that PeuHsfs underwent purifying selection pressure. In addition, various cis-acting elements involved in hormone and stress responses located in the promoter regions of PeuHsfs. Gene expression analysis indicated that several PeuHsfs were tissue-specific expression. Compared to Arabidopsis, more PeuHsf genes were significantly induced by heat, drought, and salt stresses (21, 19, and 22 PeuHsfs, respectively). Our findings are helpful in understanding the distinguished adaptability of P. euphratica to extreme environment and providing a basis for functional analysis of PeuHsfs in the future. PMID:27425424

  9. Population-based resequencing analysis of wild and cultivated barley revealed weak domestication signal of selection and bottleneck in the Rrs2 scald resistance gene region.

    PubMed

    Fu, Yong-Bi

    2012-02-01

    Many plant disease resistance (R) genes have been cloned, but the potential of utilizing these plant R-gene genomic resources for genetic inferences of plant domestication history remains unexplored. A population-based resequencing analysis of the genomic region near the Rrs2 scald resistance gene was made in 51 accessions of wild and cultivated barley from 41 countries. Fifteen primer pairs were designed to sample the genomic region with a total length of 10 406 bp. More nucleotide diversity was found in wild (π = 0.01846) than cultivated (π = 0.01507) barley samples. Three distinct groups of 29 haplotypes were detected for all 51 samples, and they were well mixed with wild and cultivated barley samples from different countries and regions. The neutrality tests by Tajima's D were not significant, but a significant (P < 0.05) case by Fu and Li's D* and F* was found in the barley cultivar samples. The estimate of selection intensity by K(a)/K(s) was 0.691 in wild barley and 0.580 in cultivated barley. The estimate of the minimum recombination events was 16 in wild barley and 19 in cultivated barley. A coalescence simulation revealed a bottleneck intensity of 1.5 to 2 since barley domestication. Together, the domestication signal in the genomic region was weak both in human selection and domestication bottleneck.

  10. Criticality features in ULF magnetic fields prior to the 2011 Tohoku earthquake

    PubMed Central

    HAYAKAWA, Masashi; SCHEKOTOV, Alexander; POTIRAKIS, Stelios; EFTAXIAS, Kostas

    2015-01-01

    The criticality of ULF (Ultra-low-frequency) magnetic variations is investigated for the 2011 March 11 Tohoku earthquake (EQ) by natural time analysis. For this attempt, some ULF parameters were considered: (1) Fh (horizontal magnetic field), (2) Fz (vertical magnetic field), and (3) Dh (inverse of horizontal magnetic field). The first two parameters refer to the ULF radiation, while the last parameter refers to another ULF effect of ionospheric signature. Nighttime (L.T. = 3 am ± 2 hours) data at Kakioka (KAK) were used, and the power of each quantity at a particular frequency band of 0.03–0.05 Hz was averaged for nighttime hours. The analysis results indicate that Fh fulfilled all criticality conditions on March 3–5, 2011, and that the additional parameter, Dh reached also a criticality on March 6 or 7. In conclusion, criticality has reached in the pre-EQ fracture region a few days to one week before the main shock of the Tohoku EQ. PMID:25743063

  11. A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication

    PubMed Central

    Zhong, Yan; Cheng, Zong-Ming (Max)

    2016-01-01

    Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs. PMID:27678195

  12. Identification and expression profiling of DNA methyltransferases during development and stress conditions in Solanaceae.

    PubMed

    Kumar, Rahul; Chauhan, Pankaj Kumar; Khurana, Ashima

    2016-09-01

    DNA methyltransferase (DMTase) enzymes contribute to plant development and stress responses by de novo establishment and subsequent maintenance of DNA methylation during replication. However, the molecular mechanism underlying this activity remains obscure, especially in crop species. Using DMTase homolog complement in six Solanaceae species, we demonstrated here that their number remained conserved in Solanum lineage, whereas it was expanded in both pepper and Nicotiana benthamiana. Non-synonymous vs synonymous (Ka/Ks) substitution ratio revealed that most of the Solanaceous DMTase homologs undergo purifying selection. The genomic sequences of tomato DMT homologs in its wild relative, Solanum pennellii, remained highly conserved in their exons and methyltransferase domains. Structure analysis further revealed highly similar folding of DMTase homologs and conservation in the residues participating in protein-protein interaction in Solanum lineage, whereas a considerable diversification was observed of pepper homologs. Transcript profiling of DMTases highlighted both similar and distinct expression patterns of tomato homologs in other species during fruit development and stress responses. Overall, our analysis provides a strong basis for in-depth exploration of both conserved as well as distinct functions of tomato DMTase homologs in other economically important Solanaceae species.

  13. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences.

    PubMed

    Zhang, Chengjun; Wang, Jun; Marowsky, Nicholas C; Long, Manyuan; Wing, Rod A; Fan, Chuanzhu

    2013-01-01

    In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation.

  14. Molecular variation and expansion of a rice black-streaked dwarf virus population based on analysis of segment 1 in Jining, China.

    PubMed

    Zhou, Yu; Meng, Qingchang; Chen, Yanping; Wu, Jirong; Hao, Zhuanfang; Wang, Zhenhua; Zhang, Degui; Li, Mingshun; Yong, Hongjun; Zhang, Shihuang; Li, Xinhai; Weng, Jianfeng

    2016-12-01

    To analyze the variation in rice black-streaked dwarf virus (RBSDV) in an area with high incidence of maize rough dwarf disease (MRDD), the RBSDV S1 segment in a collection of 100 maize isolates (sample population A100) from Jining, Shandong Province, was sequenced. An additional 21 maize and rice isolates (subpopulation B21) that were sampled from nine other geographic locations in China in 2012 and 2013 were used as a control. A total of 914 nucleotide mutations, including 239 singleton variable and 675 parsimony-informative sites were detected among the segment 1 (S1) sequences from A100. A total of 614 nucleotide mutation sites including 164 singleton variable and 450 parsimony-informative sites were detected among the S1 sequences from B21, while 97.55 % of the parsimony-informative sites from B21 were also detected in A100. The nucleotide sequence diversities of A100 (π = 0.0479) and B21 (π = 0.0396) were significantly different (P = 0.0002) but showed similar trends. Phylogenetic analysis showed that the 121 RBSDV isolates could be classified into two groups based on their S1 sequences, independent of subpopulation, with a combination of host species and locations. A100 and B21 were under the same level of negative and purifying selection, with Ka/Ks ratios of 0.0337 and 0.0369, respectively. The combined RBSDV population, including 121 isolates, was expanding, with negative values for Tajima's D, Fu and Li's D, and Fu and Li's F in both A100 and B21, except Tajima's D in A100. Based on S1, the RBSDV population in China has long-term phytogeographic stability, and there do not appear to be any newly-emerging strains.

  15. Interspecific variability of class II hydrophobin GEO1 in the genus Geosmithia.

    PubMed

    Frascella, Arcangela; Bettini, Priscilla P; Kolařík, Miroslav; Comparini, Cecilia; Pazzagli, Luigia; Luti, Simone; Scala, Felice; Scala, Aniello

    2014-11-01

    The genus Geosmithia Pitt (Ascomycota: Hypocreales) comprises cosmopolite fungi living in the galleries built by phloeophagous insects. Following the characterization in Geosmithia species 5 of the class II hydrophobin GEO1 and of the corresponding gene, the presence of the geo1 gene was investigated in 26 strains derived from different host plants and geographic locations and representing the whole phylogenetic diversity of the genus. The geo1 gene was detected in all the species tested where it maintained the general organization shown in Geosmithia species 5, comprising three exons and two introns. Size variations were found in both introns and in the first exon, the latter being due to the presence of an intragenic tandem repeat sequence corresponding to a stretch of glycine residues in the deduced proteins. At the amino acid level the deduced proteins had 44.6 % identity and no major differences in the biochemical parameters (pI, GRAVY index, hydropathy plots) were found. GEO1 release in the fungal culture medium was also assessed by turbidimetric assay and SDS-PAGE, and showed high variability between species. The phylogeny based on the geo1 sequences did not correspond to that generated from a neutral marker (ITS rDNA), suggesting that sequence similarities could be influenced by other factors than phylogenetic relatedness, such as the intimacy of the symbiosis with insect vectors. The hypothesis of a strong selection pressure on the geo1 gene was sustained by the low values (<1) of non synonymous to synonymous nucleotide substitutions ratios (Ka/Ks), which suggest that purifying selection might act on this gene. These results are compatible with either a birth-and-death evolution scenario or horizontal transfer of the gene between Geosmithia species.

  16. A novel dromedary camel enterovirus in the family Picornaviridae from dromedaries in the Middle East.

    PubMed

    Woo, Patrick C Y; Lau, Susanna K P; Li, Tong; Jose, Shanty; Yip, Cyril C Y; Huang, Yi; Wong, Emily Y M; Fan, Rachel Y Y; Cai, Jian-Piao; Wernery, Ulrich; Yuen, Kwok-Yung

    2015-07-01

    The recent emergence of Middle East respiratory syndrome coronavirus from the Middle East and the discovery of the virus from dromedary camels have boosted interest in the search for novel viruses in dromedaries. Whilst picornaviruses are known to infect various animals, their existence in dromedaries was unknown. We describe the discovery of a novel picornavirus, dromedary camel enterovirus (DcEV), from dromedaries in Dubai. Among 215 dromedaries, DcEV was detected in faecal samples of four (1.9 %) dromedaries [one (0.5 %) adult dromedary and three (25 %) dromedary calves] by reverse transcription PCR. Analysis of two DcEV genomes showed that DcEV was clustered with other species of the genus Enterovirus and was most closely related to and possessed highest amino acid identities to the species Enterovirus E and Enterovirus F found in cattle. The G+C content of DcEV was 45 mol%, which differed from that of Enterovirus E and Enterovirus F (49-50 mol%) by 4-5 %. Similar to other members of the genus Enterovirus, the 5' UTR of DcEV possessed a putative type I internal ribosome entry site. The low ratios of the number of nonsynonymous substitutions per non-synonymous site to the number of synonymous substitutions per synonymous site (Ka/Ks) of various coding regions suggested that dromedaries are the natural reservoir in which DcEV has been stably evolving. These results suggest that DcEV is a novel species of the genus Enterovirus in the family Picornaviridae. Western blot analysis using recombinant DcEV VP1 polypeptide showed a high seroprevalence of 52 % among serum samples from 172 dromedaries for IgG, concurring with its much higher infection rates in dromedary calves than in adults. Further studies are important to understand the pathogenicity, epidemiology and genetic evolution of DcEV in this unique group of animals.

  17. The phylogeny and evolutionary history of the Lesion Simulating Disease (LSD) gene family in Viridiplantae.

    PubMed

    Cabreira, Caroline; Cagliari, Alexandro; Bücker-Neto, Lauro; Margis-Pinheiro, Márcia; de Freitas, Loreta B; Bodanese-Zanettini, Maria Helena

    2015-12-01

    The Lesion Simulating Disease (LSD) genes encode a family of zinc finger proteins that play a role in programmed cell death (PCD) and other biological processes, such as plant growth and photosynthesis. In the present study, we report the reconstruction of the evolutionary history of the LSD gene family in Viridiplantae. Phylogenetic analysis revealed that the monocot and eudicot genes were distributed along the phylogeny, indicating that the expansion of the family occurred prior to the diversification between these clades. Sequences encoding proteins that present one, two, or three LSD domains formed separate groups. The secondary structure of these different LSD proteins presented a similar composition, with the β-sheets being their main component. The evolution by gene duplication was identified only to the genes that contain three LSD domains, which generated proteins with equal structure. Moreover, genes encoding proteins with one or two LSD domains evolved as single-copy genes and did not result from loss or gain in LSD domains. These results were corroborated by synteny analysis among regions containing paralogous/orthologous genes in Glycine max and Populus trichocarpa. The Ka/Ks ratio between paralogous/orthologous genes revealed that a subfunctionalization process possibly could be occurring with the LSD genes, explaining the involvement of LSD members in different biological processes, in addition to the negative regulation of PCD. This study presents important novelty in the evolutionary history of the LSD family and provides a basis for future research on individual LSD genes and their involvement in important pathway networks in plants.

  18. Analysis of S-RNase alleles of almond (Prunus dulcis): characterization of new sequences, resolution of synonyms and evidence of intragenic recombination.

    PubMed

    Ortega, Encarnación; Bosković, Radovan I; Sargent, Daniel J; Tobutt, Kenneth R

    2006-11-01

    Cross-compatibility relationships in almond are controlled by a gametophytically expressed incompatibility system partly mediated by stylar RNases, of which 29 have been reported. To resolve possible synonyms and to provide data for phylogenetic analysis, 21 almond S-RNase alleles were cloned and sequenced from SP (signal peptide region) or C1 (first conserved region) to C5, except for the S29 allele, which could be cloned only from SP to C1. Nineteen sequences (S4, S6, S11-S22, S25-S29)) were potentially new whereas S10 and S24 had previously been published but with different labels. The sequences for S16 and S17 were identical to that for S1, published previously; likewise, S15 was identical to S5. In addition, S4 and S20 were identical, as were S13 and S19. A revised version of the standard table of almond incompatibility genotypes is presented. Several alleles had AT or GA tandem repeats in their introns. Sequences of the 23 distinct newly cloned or already published alleles were aligned. Sliding windows analysis of Ka/Ks identified regions where positive selection may operate; in contrast to the Maloideae, most of the region from the beginning of C3 to the beginning of RC4 appeared not to be under positive selection. Phylogenetic analysis indicated four pairs of alleles had "bootstrap" support > 80%: S5/S10, S4/S8, S11/S24, and S3/S6. Various motifs up to 19 residues long occurred in at least two alleles, and their distributions were consistent with intragenic recombination, as were separate phylogenetic analyses of the 5' and 3' sections. Sequence comparison of phylogenetically related alleles indicated the significance of the region between RC4 and C5 in defining specificity.

  19. Patterns of polymorphism and divergence in the VP1 gene of enterovirus 71 circulating in the Asia-Pacific region between 1994 and 2013.

    PubMed

    Wu, Jun-Song; Zhao, Na; Pan, Hao; Wang, Cheng-Min; Wu, Bin; Zhang, Hong-Mei; He, Hong-Xuan; Liu, Dan; Amer, Said; Liu, She-Lan

    2013-11-01

    Enterovirus 71 has been implicated in several outbreaks of hand, foot and mouth disease in the Asia-Pacific region. The present study aimed to achieve comprehensive evolutionary dynamic aspects of EV71 during 1994-2013, based on phylogenetic analyses of the VP1 sequences. The results indicated that 4 genotypes, namely C4, C1, C2 and B4 are the predominant strains, especially in Southeast Asian countries. No common ancestor was shared in different countries. Fourteen sites of substitutions were detected in the VP1 gene sequences; including the most common sites related to neutralization at position V249I [47.1% (189/401)] and A289T [42.6% (171/401)]. However, the sites Q22H and Q22R associated with increased virulence were recognized only in 13.7% (55/401) and 18% (72/401), respectively. None of the above mutations seemed to become fixed because the ratio of Ka/Ks was greater than 1.0. Mutations K43E, A58T, S184T, and T240S could possibly change the spatial structure. Two mutations, G145E and T240S, could obviously affect the hydrophobicity of VP1 and thus alter the EV71 immunoreactivity. In conclusion, the VP1 gene of EV71 strains circulating in the Asia-Pacific region during 1994-2013, showed polymorphisms and divergence with very slow evolution rate, which may be one of the reasons for periodic outbreaks in this area.

  20. Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae).

    PubMed

    Oliveira, Deodoro C S G; Raychoudhury, Rhitoban; Lavrov, Dennis V; Werren, John H

    2008-10-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  1. The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae).

    PubMed

    Zhuang, Yongbin; Tripp, Erin A

    2017-01-27

    The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.

  2. Comparative transcriptome analysis between aquatic and aerial breathing organs of Channa argus to reveal the genetic basis underlying bimodal respiration.

    PubMed

    Jiang, Yanliang; Feng, Shuaisheng; Xu, Jian; Zhang, Songhao; Li, Shangqi; Sun, Xiaoqing; Xu, Peng

    2016-10-01

    Aerial breathing in fish was an important adaption for successful survival in hypoxic water. All aerial breathing fish are bimodal breathers. It is intriguing that they can obtain oxygen from both air and water. However, the genetic basis underlying bimodal breathing has not been extensively studied. In this study, we performed next-generation sequencing on a bimodal breathing fish, the Northern snakehead, Channa argus, and generated a transcriptome profiling of C. argus. A total of 53,591 microsatellites and 26,378 SNPs were identified and classified. A Ka/Ks analysis of the unigenes indicated that 63 genes were under strong positive selection. Furthermore, the transcriptomes from the aquatic breathing organ (gill) and the aerial breathing organ (suprabranchial chamber) were sequenced and compared, and the results showed 1,966 genes up-regulated in the gill and 2,727 genes up-regulated in the suprabranchial chamber. A gene pathway analysis concluded that four functional categories were significant, of which angiogenesis and elastic fibre formation were up-regulated in the suprabranchial chamber, indicating that the aerial breathing organ may be more efficient for gas exchange due to its highly vascularized and elastic structure. In contrast, ion uptake and transport and acid-base balance were up-regulated in the gill, indicating that the aquatic breathing organ functions in ion homeostasis and acid-base balance, in addition to breathing. Understanding the genetic mechanism underlying bimodal breathing will shed light on the initiation and importance of aerial breathing in the evolution of vertebrates.

  3. Characterization of ω-secalin genes from rye, triticale, and a wheat 1BL/1RS translocation line.

    PubMed

    Jiang, Q-T; Wei, Y-M; Andre, L; Lu, Z-X; Pu, Z-E; Peng, Y-Y; Zheng, Y-L

    2010-01-01

    Sixty-two DNA sequences for the coding regions of omega-secalin (ω-secalin) genes have been characterized from rye (Secale cereale L.), hexaploid and octoploid triticale (× Triticosecale Wittmack), and wheat (Triticum aestivum L.) 1BL/1RS translocation line. Only 19 out of the 62 ω-secalin gene sequences were full-length open reading frames (ORFs), which can be expressed into functional proteins. The other 43 DNA sequences were pseudogenes, as their ORFs were interrupted by one or a few stop codons or frameshift mutations. The 19 ω-secalin genes have a typical primary structure, which is different from wheat gliadins. There was no cysteine residue in ω-secalin proteins, and the potential celiac disease (CD) toxic epitope (PQQP) was identified to appear frequently in the repetitive domains. The ω-secalin genes from various cereal species shared high homology in their gene sequences. The ω-secalin gene family has involved fewer variations after the integration of the rye R chromosome or whole genome into the wheat or triticale genome. The higher Ka/Ks ratio (i.e. non-synonymous to synonymous substitutions per site) in ω-secalin pseudogenes than in ω-secalin ORFs indicate that the pseudogenes may be subject to a reduced selection pressure. Based on the conserved sequences of ω-secalin genes, it will be possible to manipulate the expression of this gene family in rye, triticale, or wheat 1BL/1RS translocation lines, to reduce its negative effects on grain quality.

  4. Dimerization and Transactivation Domains as Candidates for Functional Modulation and Diversity of Sox9

    PubMed Central

    Geraldo, Marcos Tadeu; Valente, Guilherme Targino; Nakajima, Rafael Takahiro; Martins, Cesar

    2016-01-01

    Sox9 plays an important role in a large variety of developmental pathways in vertebrates. It is composed of three domains: high-mobility group box (HMG box), dimerization (DIM) and transactivation (TAD). One of the main processes for regulation and variability of the pathways involving Sox9 is the self-gene expression regulation of Sox9. However, the subsequent roles of the Sox9 domains can also generate regulatory modulations. Studies have shown that TADs can bind to different types of proteins and its function seems to be influenced by DIM. Therefore, we hypothesized that both domains are directly associated and can be responsible for the functional variability of Sox9. We applied a method based on a broad phylogenetic context, using sequences of the HMG box domain, to ensure the homology of all the Sox9 copies used herein. The data obtained included 4,921 sequences relative to 657 metazoan species. Based on coevolutionary and selective pressure analyses of the Sox9 sequences, we observed coevolutions involving DIM and TADs. These data, along with the experimental data from literature, indicate a functional relationship between these domains. Moreover, DIM and TADs may be responsible for the functional plasticity of Sox9 because they are more tolerant for molecular changes (higher Ka/Ks ratio than the HMG box domain). This tolerance could allow a differential regulation of target genes or promote novel targets during transcriptional activation. In conclusion, we suggest that DIM and TADs functional association may regulate differentially the target genes or even promote novel targets during transcription activation mediated by Sox9 paralogs, contributing to the subfunctionalization of Sox9a and Sox9b in teleosts. PMID:27196604

  5. The un-uniform observatories location effect in the Dst index

    NASA Astrophysics Data System (ADS)

    Wu, Y.

    2012-12-01

    The Dst index is a major planetary magnetic activity index proposed by Sugiura in 1964, which is designed to depict the temporal development of the magnetic storm and the intensity of the ring current system flowing in the equatorial plane of the magnetosphere at 3 to 8 Earth radii. It is an hourly index derived from the average value of the horizontal component of the geomagnetic field at four low latitudinal observatories (namely, HER, HON, KAK and SJG). For a long time, the Dst index is greatly doubted. Researchers have pointed out that a great proportion of the Dst index is originated from the Substorm Wedge current system, the Cross-tail current and the Partial ring current system [Turner et al., 2000; Liemohn et al., 2001; Ohtani et al., 2001; Rostoker, 2000; Friedrich et al., 1999; Maltsev, 2003; Huang, 2004; Hakkinen et al., 2002]. The ring current system and its disturbed storm-time field (Dst field) take on an enhanced dawn-dusk asymmetry during disturbed time. Therefore, the influence of the non-uniform location of four observatories of the Dst index will enhance. The purpose of this paper is to study the influence of the observatories' location on the Dst index. The hourly data of the horizontal component of the geomagnetic field in the observatories in geomagnetic latitude between 45°S and -45°N is used, to derive the local-time distribution model of the Dst field by the method of Nature Orthogonal Component and Cubic Polynomial Fitting. Results suggest that the maximum difference to the LT-model with four Dst index stations is about 5% lowness on 16UTmp, 3% highness on 05UTmp, and the minimum difference is around 11UTmp (UTmp corresponds to the universal time of the minimum of the Dst index). It proves some certain extent efficiency afforded by adding observatories in the SYM index.

  6. Rapidly Evolving Mitochondrial Genome and Directional Selection in Mitochondrial Genes in the Parasitic Wasp Nasonia (Hymenoptera: Pteromalidae)

    PubMed Central

    Raychoudhury, Rhitoban; Lavrov, Dennis V.; Werren, John H.

    2008-01-01

    We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a “Compensation-Draft Feedback”; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus

  7. Molecular characterization and functional divergence of two Gadd45g homologs in sex determination in half-smooth tongue sole (Cynoglossus semilaevis).

    PubMed

    Liu, Wan-Jun; Zhang, Li-Yan; Shao, Chang-Wei; Wang, Na; Liu, Kun; Wen, Hai-Shen; Zhang, Ning; Dong, Zhong-Dian; Zhang, Jun-Jie; Chen, Song-Lin

    2014-01-01

    The growth arrest and DNA-damage-inducible protein 45 gamma (Gadd45g) is known to play a major role in embryonic development and sex determination. In this study, two Gadd45g genes were isolated from half-smooth tongue sole (Cynoglossus semilaevis). Using chromosomal fluorescence in situ hybridization (FISH), Gadd45g1 and Gadd45g2 were located on the W and Z chromosomes, respectively. The full-length cDNA sequences of Gadd45g1 (1270bp) and Gadd45g2 (1181bp) were predicted to contain a 480-bp coding sequence that could encode a protein of 159 amino acids residues. A phylogenetic tree showed that the predicted Gadd45g1 and Gadd45g2 amino acid sequences clustered closely in one branch. It is proposed that Gadd45g1 and Gadd45g2 are paralogous genes derived from the divergence of the sex chromosome. Ka/Ks ratios indicated that Gadd45g1 and Gadd45g2 may have undergone a high number of mutations and have a divergence time of only about 68,000years, although Gadd45g homologs are highly conserved. The qRT-PCR demonstrated that Gadd45g1 and Gadd45g2 were highly expressed in ovary, and negligibly expressed in testis of male and neo-male. During development of the ovary (from 80 to 150days), the expression levels of both genes reached high levels. Gadd45g1 was also highly expressed at 50days, the stage just before gonad differentiation in C. semilaevis. All these findings imply functional divergence of the two Gadd45g homologs; Gadd45g1 may be necessary for sex differentiation in the early stage of gonad development, and then Gadd45g1 and Gadd45g2 maintain ovary development and the female character of half-smooth tongue sole.

  8. Zeta potential response of human erythrocyte membranes to the modulators of Gardos channel activity under low rate β-radiation.

    PubMed

    Zhirnov, V V; Iakovenko, I N; Voitsitskiy, V M; Khyzhnyak, S V; Zubrikova-Chugainova, O G; Gorobetz, V A

    2015-12-01

    Tsel' raboty. Izuchenie reaktsii dzeta potentsiala (DP) membran éritrotsitov cheloveka pri modifikatsii aktivatorami i blokatorami funktsional'nogo sostoianiia Ca2+-zavisimykh kalievykh kanalov v pole radioizotopnogo izlucheniia 90Sr/90Y maloi moshchnosti.Materialy i metody. Éritrotsity poluchali iz donorskoi krovi. DP vychisliali po poluchennomu znacheniiu élektroforeticheskoi podvizhnosti kletok. V kletochnye suspenzii predvaritel'no vnosili issleduemye veshchestva, a zatem alikvoty rastvora 90Sr(NO3)2, chtoby poluchit' konechnuiu kontsentratsiiu 44,4⋅kBk⋅l-1.Rezul'taty. Radioizotopnoe izluchenie 90Sr/90Y (RI, 15 mkGr/ch) povyshaet absoliutnoe znachenie DP (DPab) membran éritrotsitov i ego deistvie iavliaetsia obratimym. Éto ukazyvaet na to, chto éffekt oposreduetsia neioniziruiushchei komponentoi RI. Dibutiril-tsAMF v diapazone kontsentratsii 1–100 mkM dozonezavisimo povyshaet DPab membran éritrotsitov, no RI ne usilivaet ego éffekt. Anaprilin v kontsentratsiiakh 10 i 100 mkM dozonezavisimo povyshaet DPab. Éffekt maksimal'noi kontsentratsii anaprilina (100 mkM) – snizhaetsia RI. Klotrimazol v diapazone kontsentratsii 0,1–10 mkM povyshaet DPab membran éritrotsitov otnositel'no kontrolia, togda kak ego maksimal'naia kontsentratsiia – snizhet, a minimal'naia – dostoverno ne vliiaet na étot pokazatel'. Deistvie klotrimazola na DP pri kontsentratsiiakh 10–100 mkM otmeniaetsia RI, no ne izmeniaetsia pri 0,1–1 mkM. Nitrendipin vo vsem diapazone kontsentratsii dozonezavisimo povyshaet DPab membran éritrotsitov, a RI usilivaet ego deistvie. Vyvody. 1. Dlia ioniziruiushchei komponenty radionuklidnogo izlucheniia sushchestvuet porog biologicheskogo deistviia na kletki, opredeliaemyi éffektivnost'iu ikh antioksidantnoi sistemy.2. Pri moshchnosti doz nizhe porogovoi deistvie radioizotopnogo izlucheniia oposreduetsia ego neioniziruiushchei komponentoi i iavliaetsia obratimym, a poétomu opredeliaetsia tol'ko v pole izlucheniia.

  9. Molecular Population Genetics of Elicitor-Induced Resistance Genes in European Aspen (Populus tremula L., Salicaceae)

    PubMed Central

    Bernhardsson, Carolina; Ingvarsson, Pär K.

    2011-01-01

    Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated KA/KS ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution. PMID:21949772

  10. Selective Loss of Cysteine Residues and Disulphide Bonds in a Potato Proteinase Inhibitor II Family

    PubMed Central

    Li, Xiu-Qing; Zhang, Tieling; Donnelly, Danielle

    2011-01-01

    Disulphide bonds between cysteine residues in proteins play a key role in protein folding, stability, and function. Loss of a disulphide bond is often associated with functional differentiation of the protein. The evolution of disulphide bonds is still actively debated; analysis of naturally occurring variants can promote understanding of the protein evolutionary process. One of the disulphide bond-containing protein families is the potato proteinase inhibitor II (PI-II, or Pin2, for short) superfamily, which is found in most solanaceous plants and participates in plant development, stress response, and defence. Each PI-II domain contains eight cysteine residues (8C), and two similar PI-II domains form a functional protein that has eight disulphide bonds and two non-identical reaction centres. It is still unclear which patterns and processes affect cysteine residue loss in PI-II. Through cDNA sequencing and data mining, we found six natural variants missing cysteine residues involved in one or two disulphide bonds at the first reaction centre. We named these variants Pi7C and Pi6C for the proteins missing one or two pairs of cysteine residues, respectively. This PI-II-7C/6C family was found exclusively in potato. The missing cysteine residues were in bonding pairs but distant from one another at the nucleotide/protein sequence level. The non-synonymous/synonymous substitution (Ka/Ks) ratio analysis suggested a positive evolutionary gene selection for Pi6C and various Pi7C. The selective deletion of the first reaction centre cysteine residues that are structure-level-paired but sequence-level-distant in PI-II illustrates the flexibility of PI-II domains and suggests the functionality of their transient gene versions during evolution. PMID:21494600

  11. Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats.

    PubMed

    Frankel, Nicolas; Hasson, Esteban; Iusem, Norberto D; Rossi, Maria Susana

    2003-12-01

    The Asr2 gene encodes a putative transcription factor that is up-regulated in leaves and roots of tomato plants exposed to water-deficit stress. This gene was first cloned and characterized in a cultivar of commercial tomato (Lycopersicon esculentum cv. Ailsa Craig). In this work, we report the complete coding sequences of the orthologous Asr2 genes in six wild tomato lineages: L. hirsutum, L. cheesmanii, L. esculentum v. cerasiforme, L. chilense, L. peruvianum v. humifusum and L. peruvianum f. glandulosum. Estimates of the Ka/Ks ratio (omega) in pairwise comparisons within the genus Lycopersicon were equal or greater than 1 (a signature of adaptive evolution) when involving L. chilense and L. peruvianum v. humifusum. Interestingly, these two species are distinct from the others in their adaptation to dry habitats. We also mapped the detected substitutions onto a phylogenetic tree of the genus Lycopersicon. Remarkably, there are two and three amino acid substitutions, which contrast with the absence of synonymous substitutions along the terminal branches leading to L. chilense and L. peruvianum v. humifusum, respectively. Likelihood ratio tests confirmed that omega values in the branches leading to these species are significantly different from the remaining branches of the tree. Moreover, inferred changes in the branches leading to these species that inhabit dry areas are nonconservative and may be associated with dramatic alterations in ASR2 protein conformation. In this work, we demonstrate accelerated rates of amino acid substitutions in the Asr2 gene of tomato lineages living in dry habitats, thus giving support to the hypothesis of adaptive Darwinian evolution.

  12. Whole-genome analysis revealed the positively selected genes during the differentiation of indica and temperate japonica rice.

    PubMed

    Sun, Xinli; Jia, Qi; Guo, Yuchun; Zheng, Xiujuan; Liang, Kangjing

    2015-01-01

    To investigate the selective pressures acting on the protein-coding genes during the differentiation of indica and japonica, all of the possible orthologous genes between the Nipponbare and 93-11 genomes were identified and compared with each other. Among these genes, 8,530 pairs had identical sequences, and 27,384 pairs shared more than 90% sequence identity. Only 2,678 pairs of genes displaying a Ka/Ks ratio significantly greater than one were revealed, and most of these genes contained only nonsynonymous sites. The genes without synonymous site were further analyzed with the SNP data of 1529 O. sativa and O. rufipogon accessions, and 1068 genes were identified to be under positive selection during the differentiation of indica and temperate japonica. The positively selected genes (PSGs) are unevenly distributed on 12 chromosomes, and the proteins encoded by the PSGs are dominant with binding, transferase and hydrolase activities, and especially enriched in the plant responses to stimuli, biological regulations, and transport processes. Meanwhile, the most PSGs of the known function and/or expression were involved in the regulation of biotic/abiotic stresses. The evidence of pervasive positive selection suggested that many factors drove the differentiation of indica and japonica, which has already started in wild rice but is much lower than in cultivated rice. Lower differentiation and less PSGs revealed between the Or-It and Or-IIIt wild rice groups implied that artificial selection provides greater contribution on the differentiation than natural selection. In addition, the phylogenetic tree constructed with positively selected sites showed that the japonica varieties exhibited more diversity than indica on differentiation, and Or-III of O. rufipogon exhibited more than Or-I.

  13. Genome-Wide Identification, Evolution, and Expression Analysis of the ATP-Binding Cassette Transporter Gene Family in Brassica rapa

    PubMed Central

    Yan, Chao; Duan, Weike; Lyu, Shanwu; Li, Ying; Hou, Xilin

    2017-01-01

    ATP-binding cassette (ABC) proteins can act as transporters of different substrates across biological membranes by hydrolyzing ATP. However, little information is available about ABC transporters in Brassica rapa, an important leafy vegetable. In the present study, we carried out genome-wide identification, characterization and molecular evolution analyses of ABC gene family in B. rapa and 9 other plant species. A total of 179 B. rapa ABC genes (BraABCs) were identified. Among them, 173 BraABCs were identified on 10 chromosomes. Based on phylogenetic analysis and domain organization, the BraABC family could be grouped into eight subfamilies. BraABCs in the same subfamily showed similar motif composition and exon-intron organization. Common and unique cis-elements involved in the transcriptional regulation were also identified in the promoter regions of BraABCs. Tissue-expression analysis of BraABCs demonstrated their diverse spatiotemporal expression profiles. Influences of the whole genome triplication (WGT) on the evolution of BraABCs were studied in detail. BraABCs were preferentially retained compared with their neighboring genes during diploidization after WGT. Synteny analysis identified 76 pairs of syntenic BraABC paralogs among the three subgenomes of B. rapa, and 10 paralog pairs underwent positive selection with ω (= Ka/Ks) ratios greater than 1. Analyses of the expression patterns of syntenic BraABC paralogs pairs across five tissues and under stress treatments revealed their functional conservation, sub-functionalization, neo-functionalization and pseudogenization during evolution. Our study presents a comprehensive overview of the ABC gene family in B. rapa and will be helpful for the further functional study of BraABCs in plant growth, development, and stress responses. PMID:28367152

  14. Programmed Genetic Instability: A Tumor-Permissive Mechanism for Maintaining the Evolvability of Higher Species through Methylation-Dependent Mutation of DNA Repair Genes in the Male Germ Line

    PubMed Central

    Zhao, Yongzhong

    2008-01-01

    Tumor suppressor genes are classified by their somatic behavior either as caretakers (CTs) that maintain DNA integrity or as gatekeepers (GKs) that regulate cell survival, but the germ line role of these disease-related gene subgroups may differ. To test this hypothesis, we have used genomic data mining to compare the features of human CTs (n = 38), GKs (n = 36), DNA repair genes (n = 165), apoptosis genes (n = 622), and their orthologs. This analysis reveals that repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms (P < 0.01), whereas CT orthologs are commoner than GK orthologs in unicellular organisms (P < 0.05). Gene targeting data show that CTs are less essential than GKs for survival of multicellular organisms (P < 0.0005) and that CT knockouts often permit offspring viability at the cost of male sterility. Patterns of human familial oncogenic mutations confirm that isolated CT loss is commoner than is isolated GK loss (P < 0.00001). In sexually reproducing species, CTs appear subject to less efficient purifying selection (i.e., higher Ka/Ks) than GKs (P = 0.000003); the faster evolution of CTs seems likely to be mediated by gene methylation and reduced transcription-coupled repair, based on differences in dinucleotide patterns (P = 0.001). These data suggest that germ line CT/repair gene function is relatively dispensable for survival, and imply that milder (e.g., epimutational) male prezygotic repair defects could enhance sperm variation—and hence environmental adaptation and speciation—while sparing fertility. We submit that CTs and repair genes are general targets for epigenetically initiated adaptive evolution, and propose a model in which human cancers arise in part as an evolutionarily programmed side effect of age- and damage-inducible genetic instability affecting both somatic and germ line lineages. PMID:18535014

  15. Progressive and Biased Divergent Evolution Underpins the Origin and Diversification of Peridinin Dinoflagellate Plastids.

    PubMed

    Dorrell, Richard G; Klinger, Christen M; Newby, Robert J; Butterfield, Erin R; Richardson, Elisabeth; Dacks, Joel B; Howe, Christopher J; Nisbet, Ellen R; Bowler, Chris

    2016-11-04

    Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons. Understanding the extent of this divergent evolution has been hampered by the lack of characterized peridinin plastid sequences. We have identified over 300 previously unannotated peridinin plastid mRNAs from published transcriptome projects, vastly increasing the number of sequences available. Using these data, we have produced a well-resolved phylogeny of peridinin plastid lineages, which uncovers several novel relationships within the dinoflagellates. This enables us to define changes to plastid sequences that occurred early in dinoflagellate evolution, and that have contributed to the subsequent diversification of individual dinoflagellate clades. We find that the origin of the peridinin dinoflagellates was specifically accompanied by elevations both in the overall number of substitutions that occurred on plastid sequences, and in the Ka/Ks ratio associated with plastid sequences, consistent with changes in selective pressure. These substitutions, alongside other changes, have accumulated progressively in individual peridinin plastid lineages. Throughout our entire dataset, we identify a persistent bias toward non-synonymous substitutions occurring on sequences encoding photosystem I subunits and stromal regions of peridinin plastid proteins, which may have underpinned the evolution of this unusual organelle.

  16. Vestige: Maximum likelihood phylogenetic footprinting

    PubMed Central

    Wakefield, Matthew J; Maxwell, Peter; Huttley, Gavin A

    2005-01-01

    Background Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA regions that have diverged less than neutral DNA. Vestige is a phylogenetic footprinting package built on the PyEvolve toolkit that uses probabilistic molecular evolutionary modelling to represent aspects of sequence evolution, including the conventional divergence measure employed by other footprinting approaches. In addition to measuring the divergence, Vestige allows the expansion of the definition of a phylogenetic footprint to include variation in the distribution of any molecular evolutionary processes. This is achieved by displaying the distribution of model parameters that represent partitions of molecular evolutionary substitutions. Examination of the spatial incidence of these effects across regions of the genome can identify DNA segments that differ in the nature of the evolutionary process. Results Vestige was applied to a reference dataset of the SCL locus from four species and provided clear identification of the known conserved regions in this dataset. To demonstrate the flexibility to use diverse models of molecular evolution and dissect the nature of the evolutionary process Vestige was used to footprint the Ka/Ks ratio in primate BRCA1 with a codon model of evolution. Two regions of putative adaptive evolution were identified illustrating the ability of Vestige to represent the spatial distribution of distinct molecular evolutionary processes. Conclusion Vestige provides a flexible, open platform for phylogenetic footprinting. Underpinned by the PyEvolve toolkit, Vestige provides a framework for visualising the signatures of evolutionary processes across the genome of numerous organisms simultaneously. By exploiting the maximum-likelihood statistical framework, the complex interplay between mutational processes, DNA repair and

  17. EST-derived SNP discovery and selective pressure analysis in Pacific white shrimp ( Litopenaeus vannamei)

    NASA Astrophysics Data System (ADS)

    Liu, Chengzhang; Wang, Xia; Xiang, Jianhai; Li, Fuhua

    2012-09-01

    Pacific white shrimp has become a major aquaculture and fishery species worldwide. Although a large scale EST resource has been publicly available since 2008, the data have not yet been widely used for SNP discovery or transcriptome-wide assessment of selective pressure. In this study, a set of 155 411 expressed sequence tags (ESTs) from the NCBI database were computationally analyzed and 17 225 single nucleotide polymorphisms (SNPs) were predicted, including 9 546 transitions, 5 124 transversions and 2 481 indels. Among the 7 298 SNP substitutions located in functionally annotated contigs, 58.4% (4 262) are non-synonymous SNPs capable of introducing amino acid mutations. Two hundred and fifty nonsynonymous SNPs in genes associated with economic traits have been identified as candidates for markers in selective breeding. Diversity estimates among the synonymous nucleotides were on average 3.49 times greater than those in non-synonymous, suggesting negative selection. Distribution of non-synonymous to synonymous substitutions (Ka/Ks) ratio ranges from 0 to 4.01, (average 0.42, median 0.26), suggesting that the majority of the affected genes are under purifying selection. Enrichment analysis identified multiple gene ontology categories under positive or negative selection. Categories involved in innate immune response and male gamete generation are rich in positively selected genes, which is similar to reports in Drosophila and primates. This work is the first transcriptome-wide assessment of selective pressure in a Penaeid shrimp species. The functionally annotated SNPs provide a valuable resource of potential molecular markers for selective breeding.

  18. Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?

    PubMed Central

    Soto-Girón, Maria Juliana; Ospina, Oscar E.; Massey, Steven Edward

    2015-01-01

    Helicobacter pylori is a bacterium that lives in the human stomach and is a major risk factor for gastric cancer and ulcers. H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa. We wished to investigate how H.pylori has coevolved with its host during that time, focusing on strains from Japanese and European populations, given that gastric cancer incidence is high in Japanese populations, while low in European. A positive selection analysis of eight H.pylori genomes was conducted, using maximum likelihood based pairwise comparisons in order to maximize the number of strain-specific genes included in the study. Using the genic Ka/Ks ratio, comparisons of four Japanese H.pylori genomes suggests 25–34 genes under positive selection, while four European H.pylori genomes suggests 16–21 genes; few of the genes identified were in common between lineages. Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary ‘arms race’ with the host. Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment. In addition, the larger number of genes inferred as being under positive selection in Japanese strains compared to European implies a stronger overall adaptive pressure, potentially resulting from an elevated immune response which may be linked to increased inflammation, an initial stage in the development of gastric cancer. PMID:25788149

  19. Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus.

    PubMed

    Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

    2014-12-26

    Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.

  20. Evolution of a Bitter Taste Receptor Gene Cluster in a New World Sparrow

    PubMed Central

    Davis, Jamie K.; Lowman, Josh J.; Thomas, Pamela J.; ten Hallers, Boudewijn F. H.; Koriabine, Maxim; Huynh, Lynn Y.; Maney, Donna L.; de Jong, Pieter J.; Martin, Christa L.; Thomas, James W.

    2010-01-01

    Bitter taste perception likely evolved as a protective mechanism against the ingestion of harmful compounds in food. The evolution of the taste receptor type 2 (TAS2R) gene family, which encodes the chemoreceptors that are directly responsible for the detection of bitter compounds, has therefore been of considerable interest. Though TAS2R repertoires have been characterized for a number of species, to date the complement of TAS2Rs from just one bird, the chicken, which had a notably small number of TAS2Rs, has been established. Here, we used targeted mapping and genomic sequencing in the white-throated sparrow (Zonotrichia albicollis) and sample sequencing in other closely related birds to reconstruct the history of a TAS2R gene cluster physically linked to the break points of an evolutionary chromosomal rearrangement. In the white-throated sparrow, this TAS2R cluster encodes up to 18 functional bitter taste receptors and likely underwent a large expansion that predates and/or coincides with the radiation of the Emberizinae subfamily into the New World. In addition to signatures of gene birth-and-death evolution within this cluster, estimates of Ka/Ks for the songbird TAS2Rs were similar to those previously observed in mammals, including humans. Finally, comparison of the complete genomic sequence of the cluster from two common haplotypes in the white-throated sparrow revealed a number of nonsynonymous variants and differences in functional gene content within this species. These results suggest that interspecies and intraspecies genetic variability does exist in avian TAS2Rs and that these differences could contribute to variation in bitter taste perception in birds. PMID:20624740

  1. Overlapping genetic codes for overlapping frameshifted genes in Testudines, and Lepidochelys olivacea as special case.

    PubMed

    Seligmann, Hervé

    2012-12-01

    Mitochondrial genes code for additional proteins after +2 frameshifts by reassigning stops to code for amino acids, which defines overlapping genetic codes for overlapping genes. Turtles recode stops UAR → Trp and AGR → Lys (AGR → Gly in the marine Olive Ridley turtle, Lepidochelys olivacea). In Lepidochelys the +2 frameshifted mitochondrial Cytb gene lacks stops, open reading frames from other genes code for unknown proteins, and for regular mitochondrial proteins after frameshifts according to the overlapping genetic code. Lepidochelys' inversion between proteins coded by regular and overlapping genetic codes substantiates the existence of overlap coding. ND4 differs among Lepidochelys mitochondrial genomes: it is regular in DQ486893; in NC_011516, the open reading frame codes for another protein, the regular ND4 protein is coded by the frameshifted sequence reassigning stops as in other turtles. These systematic patterns are incompatible with Genbank/sequencing errors and DNA decay. Random mixing of synonymous codons, conserving main frame coding properties, shows optimization of natural sequences for overlap coding; Ka/Ks analyses show high positive (directional) selection on overlapping genes. Tests based on circular genetic codes confirm programmed frameshifts in ND3 and ND4l genes, and predicted frameshift sites for overlap coding in Lepidochelys. Chelonian mitochondria adapt for overlapping gene expression: cloverleaf formation by antisense tRNAs with predicted anticodons matching stops coevolves with overlap coding; antisense tRNAs with predicted expanded anticodons (frameshift suppressor tRNAs) associate with frameshift-coding in ND3 and ND4l, a potential regulation of frameshifted overlap coding. Anaeroby perhaps switched between regular and overlap coding genes in Lepidochelys.

  2. MYB Transcription Factors in Chinese Pear (Pyrus bretschneideri Rehd.): Genome-Wide Identification, Classification, and Expression Profiling during Fruit Development.

    PubMed

    Cao, Yunpeng; Han, Yahui; Li, Dahui; Lin, Yi; Cai, Yongping

    2016-01-01

    The MYB family is one of the largest families of transcription factors in plants. Although, some MYBs were reported to play roles in secondary metabolism, no comprehensive study of the MYB family in Chinese pear (Pyrus bretschneideri Rehd.) has been reported. In the present study, we performed genome-wide analysis of MYB genes in Chinese pear, designated as PbMYBs, including analyses of their phylogenic relationships, structures, chromosomal locations, promoter regions, GO annotations, and collinearity. A total of 129 PbMYB genes were identified in the pear genome and were divided into 31 subgroups based on phylogenetic analysis. These PbMYBs were unevenly distributed among 16 chromosomes (total of 17 chromosomes). The occurrence of gene duplication events indicated that whole-genome duplication and segmental duplication likely played key roles in expansion of the PbMYB gene family. Ka/Ks analysis suggested that the duplicated PbMYBs mainly experienced purifying selection with restrictive functional divergence after the duplication events. Interspecies microsynteny analysis revealed maximum orthology between pear and peach, followed by plum and strawberry. Subsequently, the expression patterns of 20 PbMYB genes that may be involved in lignin biosynthesis according to their phylogenetic relationships were examined throughout fruit development. Among the 20 genes examined, PbMYB25 and PbMYB52 exhibited expression patterns consistent with the typical variations in the lignin content previously reported. Moreover, sub-cellular localization analysis revealed that two proteins PbMYB25 and PbMYB52 were localized to the nucleus. All together, PbMYB25 and PbMYB52 were inferred to be candidate genes involved in the regulation of lignin biosynthesis during the development of pear fruit. This study provides useful information for further functional analysis of the MYB gene family in pear.

  3. New insights on the evolution of Leafy cotyledon1 (LEC1) type genes in vascular plants.

    PubMed

    Cagliari, Alexandro; Turchetto-Zolet, Andreia Carina; Korbes, Ana Paula; Maraschin, Felipe Dos Santos; Margis, Rogerio; Margis-Pinheiro, Marcia

    2014-01-01

    NF-Y is a conserved oligomeric transcription factor found in all eukaryotes. In plants, this regulator evolved with a broad diversification of the genes coding for its three subunits (NF-YA, NF-YB and NF-YC). The NF-YB members can be divided into Leafy Cotyledon1 (LEC1) and non-LEC1 types. Here we presented a comparative genomic study using phylogenetic analyses to validate an evolutionary model for the origin of LEC-type genes in plants and their emergence from non-LEC1-type genes. We identified LEC1-type members in all vascular plant genomes, but not in amoebozoa, algae, fungi, metazoa and non-vascular plant representatives, which present exclusively non-LEC1-type genes as constituents of their NF-YB subunits. The non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) between LEC1 and non-LEC1-type genes indicate the presence of positive selection acting on LEC1-type members to the fixation of LEC1-specific amino acid residues. The phylogenetic analyses demonstrated that plant LEC1-type genes are evolutionary divergent from the non-LEC1-type genes of plants, fungi, amoebozoa, algae and animals. Our results point to a scenario in which LEC1-type genes have originated in vascular plants after gene expansion in plants. We suggest that processes of neofunctionalization and/or subfunctionalization were responsible for the emergence of a versatile role for LEC1-type genes in vascular plants, especially in seed plants. LEC1-type genes besides being phylogenetic divergent also present different expression profile when compared with non-LEC1-type genes. Altogether, our data provide new insights about the LEC1 and non-LEC1 evolutionary relationship during the vascular plant evolution.

  4. Head Transcriptomes of Two Closely Related Species of Fruit Flies of the Anastrepha fraterculus Group Reveals Divergent Genes in Species with Extensive Gene Flow

    PubMed Central

    Rezende, Victor Borges; Congrains, Carlos; Lima, André Luís A.; Campanini, Emeline Boni; Nakamura, Aline Minali; de Oliveira, Janaína Lima; Chahad-Ehlers, Samira; Junior, Iderval Sobrinho; Alves de Brito, Reinaldo

    2016-01-01

    Several fruit flies species of the Anastrepha fraterculus group are of great economic importance for the damage they cause to a variety of fleshy fruits. Some species in this group have diverged recently, with evidence of introgression, showing similar morphological attributes that render their identification difficult, reinforcing the relevance of identifying new molecular markers that may differentiate species. We investigated genes expressed in head tissues from two closely related species: A. obliqua and A. fraterculus, aiming to identify fixed single nucleotide polymorphisms (SNPs) and highly differentiated transcripts, which, considering that these species still experience some level of gene flow, could indicate potential candidate genes involved in their differentiation process. We generated multiple libraries from head tissues of these two species, at different reproductive stages, for both sexes. Our analyses indicate that the de novo transcriptome assemblies are fairly complete. We also produced a hybrid assembly to map each species’ reads, and identified 67,470 SNPs in A. fraterculus, 39,252 in A. obliqua, and 6386 that were common to both species. We identified 164 highly differentiated unigenes that had a mean interspecific index (D¯) of at least 0.94. We selected unigenes that had Ka/Ks higher than 0.5, or had at least three or more highly differentiated SNPs as potential candidate genes for species differentiation. Among these candidates, we identified proteases, regulators of redox homeostasis, and an odorant-binding protein (Obp99c), among other genes. The head transcriptomes described here enabled the identification of thousands of genes hitherto unavailable for these species, and generated a set of candidate genes that are potentially important to genetically identify species and understand the speciation process in the presence of gene flow of A. obliqua and A. fraterculus. PMID:27558666

  5. Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus

    PubMed Central

    Yang, Liandong; Wang, Ying; Zhang, Zhaolei; He, Shunping

    2015-01-01

    Elucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes. PMID:25543049

  6. Free Surface of the Liquid-Gas Phase Separation as a Measuring Membrane of a Device for Measuring Small Hydrostatic Pressure Difference Values / Powierzchnia Swobodna Rozdziału Faz Ciecz-Gaz Jako Membrana Pomiarowa Urządzenia Do Pomiaru Małych Wartości Różnicy Ciśnienia Hydrostatycznego

    NASA Astrophysics Data System (ADS)

    Filipek, Wiktor; Broda, Krzysztof; Branny, Marian

    2015-03-01

    wykorzystaniem napisanego w języku Delphi autorskiego programu do obróbki numerycznej zdjęć. Występujące trudności ilustruje rysunek 2 przedstawiający przesunięcie linii odniesienia w trzech kolejno po sobie wykonanych zdjęciach. Następnie omówiono sposób przygotowania stanowiska do pomiarów oraz sposób ich przeprowadzania czego ilustracją są rysunki 3 i 4. Przedstawiono występujące problemy oraz zastosowane sposoby ich rozwiązania. Zarejestrowany przykładowy obraz po przejściu promienia lasera przez badaną strukturę dla wybranych wartości różnicy ciśnień hydrostatycznych uzyskany za pomocą kulek ceramicznych przedstawiono na rysunku 5. Rysunek 6 wyjaśnia metodę obróbki numerycznej zdjęć w oparciu o autorski program i zależności (1),(2),(3). Na rysunkach 7 i 9 zestawiono otrzymane krzywe zmienności intensywności barw uzyskane w trakcie opracowania numerycznego. Zwrócono także uwagę na rozkład zmian intensywności barw dla różnicy między powierzchniami swobodnymi cieczy w cylindrach (Rys. 8-11) dla wybranych serii pomiarowych. W dalszej części artykułu dokonano analizy otrzymanych obrazów zwracając uwagę na włączenie metody transformacji Fouriera lub "Falkowej" (Ziółko, 2000) do numerycznej analizy posiadanych danych (Rys. 12-14). Na rysunku 12 pokazano wybrane trzy zależności opisujące zmienność natężania barwy w funkcji położenia ramki (1), dla których dokonano transformacji Fouriera według zależności (3). Analizy dokonano metodą arytmetyczna Perry'ego (Ziółko, 2000) w okienku o szerokości n = 2300 przyjmując jako położenie startowe wartość x = 1600. Rysunek 13 przedstawia wartości współczynnika Ak a rys.14 przedstawia wartości kąta przesunięcia jk dla pierwszych 58 harmonicznych. Prace nad udoskonaleniem metody trwają. W dalszej części artykułu autorzy podsumowują osiągnięte wyniki zwracając uwagę na uzyskaną precyzję pomiarów oraz korzystne zastosowanie powierzchni swobodnej

  7. Nijmegen breakage syndrome (NBS)

    PubMed Central

    2012-01-01

    both alleles of the NBN gene are known. No specific therapy is available for NBS, however, hematopoietic stem cell transplantation may be one option for some patients. Prognosis is generally poor due to the extremely high rate of malignancies. Zespół Nijmegen (Nijmegen breakage syndrome; NBS) jest rzadkim schorzeniem z wrodzoną niestabilnością chromosomową dziedziczącym się w sposób autosomalny recesywny, charakteryzującym się przede wszystkim wrodzonym małogłowiem, złożonymi niedoborami odporności i predyspozycją do rozwoju nowotworów. Choroba występuje najczęściej w populacjach słowiańskich, w których uwarunkowana jest mutacją założycielską w genie NBN (c.657_661del5). Do najważniejszych objawów zespołu zalicza się: małogłowie obecne od urodzenia i postępujące z wiekiem, charakterystyczne cechy dysmorfii twarzy, opóźnienie wzrastania, niepełnosprawność intelektualną w stopniu lekkim do umiarkowanego oraz hipogonadyzm hipogonadotropowy u dziewcząt. Na obraz choroby składają się także: niedobór odporności komórkowej i humoralnej, który jest przyczyną nawracających infekcji, znaczna predyspozycja do rozwoju nowotworów złośliwych (zwłaszcza układu chłonnego), a także zwiększona wrażliwość na promieniowanie jonizujące. Wyniki badań laboratoryjnych wykazują: (1) spontaniczną łamliwość chromosomów w limfocytach T krwi obwodowej, z preferencją do rearanżacji chromosomów 7 i 14, (2) nadwrażliwość na promieniowanie jonizujące lub radiomimetyki, co można wykazać metodami in vitro, (3) radiooporność syntezy DNA, (4) hipomorficzne mutacje na obu allelach genu NBN, oraz (5) brak w komórkach pełnej cząsteczki białka, nibryny. Małogłowie i niedobór odporności występują także w zespole niedoboru ligazy IV (LIG4) oraz w zespole niedoboru NHEJ1. Rodzice powinni otrzymać poradę genetyczną ze względu na wysokie ryzyko (25%) powtórzenia się choroby u kolejnego potomstwa. Możliwe jest

  8. Characterization of two forms of mouse salivary androgen-binding protein (ABP): implications for evolutionary relationships and ligand-binding function.

    PubMed

    Karn, Robert C; Laukaitis, Christina M

    2003-06-17

    Mouse salivary androgen-binding protein (ABP) is a member of the secretoglobin family produced in the submaxillary glands of house mice (Mus musculus). We report the cDNA sequences and amino acid sequences of the beta and gamma subunits of ABP from a mouse cDNA library, identifying the two subunits by their pIs and molecular weights. An anomalously high molecular weight of the alpha subunit is likely due to glycosylation at a single site. A phylogenetic comparison of the three subunits of ABP with the chains of other mammalian secretoglobins shows that ABP is most closely related to mouse lachrymal protein and to the major cat allergen Fel dI. An evaluation of the most conserved residues in ABP and the other secretoglobins, in light of structural data reported by others [Callebaut, I., Poupon, A., Bally, R., Demaret, J.-P., Housset, D., Delettre, J., Hossenlopp, P., and Mornon, J.-P. (2000) Ann. N.Y. Acad. Sci. 923, 90-112; Pattabiraman, N., Matthews, J., Ward, K., Mantile-Selvaggi, G., Miele, L., and Mukherjee, A. (2000) Ann. N.Y. Acad. Sci. 923, 113-127], allows us to draw conclusions about the critical residues important in ligand binding by the two different ABP dimers and to assess the importance of ligand binding in the function of the molecule. In addition to the cDNAs, which represent those of the musculus subspecies of Mus musculus, we also report the coding regions of the beta and gamma subunit cDNAs from two other mouse inbred strains which represent the other two subspecies: M. musculus domesticus and M. musculus castaneus. The high nonsynonymous/synonymous substitution rate ratios (K(a)/K(s)) for both the beta and gamma subunits suggest that these two proteins are evolving under strong directional selection, as has been reported for the alpha subunit [Hwang, J., Hofstetter, J., Bonhomme, F., and Karn, R. (1997) J. Hered. 88, 93-97; Karn, R., and Clements, M. (1999) Biochem. Genet. 37, 187-199].

  9. Genome-Wide Analysis of the Fasciclin-Like Arabinogalactan Protein Gene Family Reveals Differential Expression Patterns, Localization, and Salt Stress Response in Populus

    PubMed Central

    Zang, Lina; Zheng, Tangchun; Chu, Yanguang; Ding, Changjun; Zhang, Weixi; Huang, Qinjun; Su, Xiaohua

    2015-01-01

    Fasciclin-like arabinogalactan proteins (FLAs) are a subclass of arabinogalactan proteins (AGPs) involved in plant growth, development and response to abiotic stress. Although many studies have been performed to identify molecular functions of individual family members, little information is available on genome-wide identification and characterization of FLAs in the genus Populus. Based on genome-wide analysis, we have identified 35 Populus FLAs which were distributed on 16 chromosomes and phylogenetically clustered into four major groups. Gene structure and motif composition were relatively conserved in each group. All the members contained N-terminal signal peptide, 23 of which included predicted glycosylphosphatidylinositol (GPI) modification sites and were anchored to plasma membranes. Subcellular localization analysis showed that PtrFLA2/20/26 were localized in cell membrane and cytoplasm of protoplasts from Populus stem-differentiating xylem. The Ka/Ks ratios showed that purifying selection has played a leading role in the long-term evolutionary period which greatly maintained the function of this family. The expression profiles showed that 32 PtrFLAs were differentially expressed in four tissues at four seasons based on publicly available microarray data. 18 FLAs were further verified with qRT-PCR in different tissues, which indicated that PtrFLA1/2/3/7/11/12/20/21/22/24/26/30 were significantly expressed in male and female flowers, suggesting close correlations with the reproductive development. In addition, PtrFLA1/9/10/11/17/21/23/24/26/28 were highly expressed in the stems and differentiating xylem, which may be involved in stem development. To determine salt response of FLAs, qRT-PCR was performed to analyze the expression of 18 genes under salinity stress across two time points. Results demonstrated that all the 18 FLAs were expressed in root tissues; especially, PtrFLA2/12/20/21/24/30 were significantly induced at different time points. In summary

  10. Phenylalanine transport in guinea pig jejunum. A general mechanism for organic solute and sodium cotransport.

    PubMed

    Alvarado, F; Lherminier, M

    1982-08-01

    in terms of quantitative differences in the values of certain dissociation constants, all within the framework of the same general mechanism. Thus, apparently pure K-type activation kinetics will be seen when both the absolute value of the constant, K'a, and the ratio between constants, Ka/Ks, are small. The reciprocal situation will be true for systems exhibiting apparently pure V-type activation kinetics.

  11. Evidence of accelerated evolution and ectodermal-specific expression of presumptive BDS toxin cDNAs from Anemonia viridis.

    PubMed

    Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Cuttitta, Angela

    2013-10-30

    Anemonia viridis is a widespread and extensively studied Mediterranean species of sea anemone from which a large number of polypeptide toxins, such as blood depressing substances (BDS) peptides, have been isolated. The first members of this class, BDS-1 and BDS-2, are polypeptides belonging to the β-defensin fold family and were initially described for their antihypertensive and antiviral activities. BDS-1 and BDS-2 are 43 amino acid peptides characterised by three disulfide bonds that act as neurotoxins affecting Kv3.1, Kv3.2 and Kv3.4 channel gating kinetics. In addition, BDS-1 inactivates the Nav1.7 and Nav1.3 channels. The development of a large dataset of A. viridis expressed sequence tags (ESTs) and the identification of 13 putative BDS-like cDNA sequences has attracted interest, especially as scientific and diagnostic tools. A comparison of BDS cDNA sequences showed that the untranslated regions are more conserved than the protein-coding regions. Moreover, the KA/KS ratios calculated for all pairwise comparisons showed values greater than 1, suggesting mechanisms of accelerated evolution. The structures of the BDS homologs were predicted by molecular modelling. All toxins possess similar 3D structures that consist of a triple-stranded antiparallel β-sheet and an additional small antiparallel β-sheet located downstream of the cleavage/maturation site; however, the orientation of the triple-stranded β-sheet appears to differ among the toxins. To characterise the spatial expression profile of the putative BDS cDNA sequences, tissue-specific cDNA libraries, enriched for BDS transcripts, were constructed. In addition, the proper amplification of ectodermal or endodermal markers ensured the tissue specificity of each library. Sequencing randomly selected clones from each library revealed ectodermal-specific expression of ten BDS transcripts, while transcripts of BDS-8, BDS-13, BDS-14 and BDS-15 failed to be retrieved, likely due to under-representation in our

  12. Discovery of a Novel Bottlenose Dolphin Coronavirus Reveals a Distinct Species of Marine Mammal Coronavirus in Gammacoronavirus

    PubMed Central

    Woo, Patrick C. Y.; Lau, Susanna K. P.; Lam, Carol S. F.; Tsang, Alan K. L.; Hui, Suk-Wai; Fan, Rachel Y. Y.; Martelli, Paolo

    2014-01-01

    While gammacoronaviruses mainly comprise infectious bronchitis virus (IBV) and its closely related bird coronaviruses (CoVs), the only mammalian gammacoronavirus was discovered from a white beluga whale (beluga whale CoV [BWCoV] SW1) in 2008. In this study, we discovered a novel gammacoronavirus from fecal samples from three Indo-Pacific bottlenose dolphins (Tursiops aduncus), which we named bottlenose dolphin CoV (BdCoV) HKU22. All the three BdCoV HKU22-positive samples were collected on the same date, suggesting a cluster of infection, with viral loads of 1 × 103 to 1 × 105 copies per ml. Clearance of virus was associated with a specific antibody response against the nucleocapsid of BdCoV HKU22. Complete genome sequencing and comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 have similar genome characteristics and structures. Their genome size is about 32,000 nucleotides, the largest among all CoVs, as a result of multiple unique open reading frames (NS5a, NS5b, NS5c, NS6, NS7, NS8, NS9, and NS10) between their membrane (M) and nucleocapsid (N) protein genes. Although comparative genome analysis showed that BdCoV HKU22 and BWCoV SW1 should belong to the same species, a major difference was observed in the proteins encoded by their spike (S) genes, which showed only 74.3 to 74.7% amino acid identities. The high ratios of the number of synonymous substitutions per synonymous site (Ks) to the number of nonsynonymous substitutions per nonsynonymous site (Ka) in multiple regions of the genome, especially the S gene (Ka/Ks ratio, 2.5), indicated that BdCoV HKU22 may be evolving rapidly, supporting a recent transmission event to the bottlenose dolphins. We propose a distinct species, Cetacean coronavirus, in Gammacoronavirus, to include BdCoV HKU22 and BWCoV SW1, whereas IBV and its closely related bird CoVs represent another species, Avian coronavirus, in Gammacoronavirus. PMID:24227844

  13. Genomic organization, phylogenetic comparison, and expression profiles of the SPL family genes and their regulation in soybean.

    PubMed

    Tripathi, Rajiv K; Goel, Ridhi; Kumari, Sweta; Dahuja, Anil

    2017-03-01

    SQUAMOSA Promoter-Binding Protein-Like (SPL) genes form a major family of plant-specific transcription factors and play an important role in plant growth and development. In this study, we report the identification of 41 SPL genes (GmSPLs) in the soybean genome. Phylogenetic analysis revealed that these genes were divided into five groups (groups 1-5). Further, exon/intron structure and motif composition revealed that the GmSPL genes are conserved within their same group. The N-terminal zinc finger 1 (Zn1) of the SBP domain was a CCCH (Cys3His1) and the C terminus zinc finger 2 (Zn2) was a CCHC (Cys2HisCys) type. The 41 GmSPL genes were distributed unevenly on 17 of the 20 chromosomes, with tandem and segmental duplication events. We found that segmental duplication has made an important contribution to soybean SPL gene family expansion. The Ka/Ks ratios revealed that the duplicated GmSPL genes evolved under the effect of purifying selection. In addition, 17 of the 41 GmSPLs were found as targets of miR156; these might be involved in their posttranscriptional regulation through miR156. Importantly, RLM-RACE analysis confirmed the GmmiR156-mediated cleavage of GmSPL2a transcript in 2-4 mm stage of soybean seed. Alternative splicing events in 9 GmSPLs were detected which produces transcripts and proteins of different lengths that may modulate protein signaling, binding, localization, stability, and other properties. Expression analysis of the soybean SPL genes in various tissues and different developmental stages of seed suggested distinct spatiotemporal patterns. Differences in the expression patterns of miR156-targeted and miR156-non-targeted soybean SPL genes suggest that miR156 plays key functions in soybean development. Our results provide an important foundation for further uncovering the crucial roles of GmSPLs in the development of soybean and other biological processes.

  14. The Complete Chloroplast DNA Sequence of Eleutherococcus senticosus (Araliaceae); Comparative Evolutionary Analyses with Other Three Asterids

    PubMed Central

    Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

    2012-01-01

    This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or

  15. Insights into the Indian Peanut Genotypes for ahFAD2 Gene Polymorphism Regulating Its Oleic and Linoleic Acid Fluxes

    PubMed Central

    Nawade, Bhagwat; Bosamia, Tejas C.; Thankappan, Radhakrishnan; Rathnakumar, Arulthambi L.; Kumar, Abhay; Dobaria, Jentilal R.; Kundu, Rahul; Mishra, Gyan P.

    2016-01-01

    In peanut (Arachis hypogaea L.), the customization of fatty acid profile is an evolving area to fulfill the nutritional needs in the modern market. A total of 174 peanut genotypes, including 167 Indian cultivars, 6 advanced breeding lines and “SunOleic95R”—a double mutant line, were investigated using AS-PCRs, CAPS and gene sequencing for the ahFAD2 allele polymorphism, along with its fatty acid compositions. Of these, 80 genotypes were found having substitution (448G>A) mutation only in ahFAD2A gene, while none recorded 1-bp insertion (441_442insA) mutation in ahFAD2B gene. Moreover, 22 wild peanut accessions found lacking both the mutations. Among botanical types, the ahFAD2A mutation was more frequent in ssp. hypogaea (89%) than in ssp. fastigiata (17%). This single allele mutation, found affecting not only oleic to linoleic acid fluxes, but also the composition of other fatty acids in the genotypes studied. Repeated use of a few selected genotypes in the Indian varietal development programs were also eminently reflected in its ahFAD2 allele polymorphism. Absence of known mutations in the wild-relatives indicated the possible origin of these mutations, after the allotetraploidization of cultivated peanut. The SNP analysis of both ahFAD2A and ahFAD2B genes, revealed haplotype diversity of 1.05% and 0.95%, while Ka/Ks ratio of 0.36 and 0.39, respectively, indicating strong purifying selection pressure on these genes. Cluster analysis, using ahFAD2 gene SNPs, showed presence of both mutant and non-mutant genotypes in the same cluster, which might be due the presence of ahFAD2 gene families. This investigation provided insights into the large number of Indian peanut genotypes, covering various aspects related to O/L flux regulation and ahFAD2 gene polymorphism. PMID:27610115

  16. Polymorphisms and Mutational Covariation Associated with Death in a Prospective Cohort of HIV/AIDS Patients Receiving Long-Term ART in China

    PubMed Central

    Liu, Pengtao; Feng, Yi; Wu, Jianjun; Tian, Suian; Su, Bin; Wang, Zhe; Liao, Lingjie; Xing, Hui; You, Yinghui; Shao, Yiming; Ruan, Yuhua

    2017-01-01

    Background HIV drug resistance is associated with faster clinical progression of AIDS. However, the effect of significant polymorphisms and mutational covariation on mortality among HIV/AIDS patients receiving long-term antiretroviral therapy (ART), have rarely been studied. Methods In this prospective cohort study from December 2003 to December 2014, we present a new computational modelling approach based on bioinformatics-based models and several statistical methods to elucidate the molecular mechanisms involved in the acquisition of polymorphisms and mutations on death in HIV/AIDS patients receiving long-term ART in China. Results This study involved 654 ART-treated patients, who had been followed for 5473.4 person-years, a median of 9.8 years, and 178 died (25.2%, 3.3/100 person-years). The first regimens included AZT/d4T + NVP+ ddI (78.9%) or AZT/d4T + NVP+ 3TC (20.0%). We calculated an individual Ka/Ks value for each specific amino acid mutation. Result showed that 20 polymorphisms (E6D, Q18H, E35D, S37N, T39A, K43E, S68N, L74I, I93L, K103N, V106A, E169D, Y181C, G190A, Q197K, T200V, T200E, T215I, E224D and P225H) were strongly associated with AIDS related deaths. Among them, 7 polymorphisms (L74I, K103N, V106A, Y181C, G190A, T215I and P225H) were known to be drug resistance mutations, 7 polymorphisms (E6D, E35D, S37N, I93L, E169D, T200V and T200E were considered to be potential drug resistance mutations, and 6 polymorphisms (T39A, K43E, S68N, Q197K, T200V and E224D) were newly found to have an association with drug resistance mutations, which formed a complex network of relationships. Conclusions Some polymorphisms and mutational covariation may be the important influencing factors in the failure of treatment. Understanding these mechanisms is essential for the development of new therapies, designing optimal drug combinations, and determining effective clinical management of individual patients. PMID:28099515

  17. An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora

    PubMed Central

    2011-01-01

    Background Coffee is one of the world's most important crops; it is consumed worldwide and plays a significant role in the economy of producing countries. Coffea arabica and C. canephora are responsible for 70 and 30% of commercial production, respectively. C. arabica is an allotetraploid from a recent hybridization of the diploid species, C. canephora and C. eugenioides. C. arabica has lower genetic diversity and results in a higher quality beverage than C. canephora. Research initiatives have been launched to produce genomic and transcriptomic data about Coffea spp. as a strategy to improve breeding efficiency. Results Assembling the expressed sequence tags (ESTs) of C. arabica and C. canephora produced by the Brazilian Coffee Genome Project and the Nestlé-Cornell Consortium revealed 32,007 clusters of C. arabica and 16,665 clusters of C. canephora. We detected different GC3 profiles between these species that are related to their genome structure and mating system. BLAST analysis revealed similarities between coffee and grape (Vitis vinifera) genes. Using KA/KS analysis, we identified coffee genes under purifying and positive selection. Protein domain and gene ontology analyses suggested differences between Coffea spp. data, mainly in relation to complex sugar synthases and nucleotide binding proteins. OrthoMCL was used to identify specific and prevalent coffee protein families when compared to five other plant species. Among the interesting families annotated are new cystatins, glycine-rich proteins and RALF-like peptides. Hierarchical clustering was used to independently group C. arabica and C. canephora expression clusters according to expression data extracted from EST libraries, resulting in the identification of differentially expressed genes. Based on these results, we emphasize gene annotation and discuss plant defenses, abiotic stress and cup quality-related functional categories. Conclusion We present the first comprehensive genome-wide transcript

  18. Molecular Genetic Analysis and Evolution of Segment 7 in Rice Black-Streaked Dwarf Virus in China

    PubMed Central

    Chen, Yanping; Wu, Jirong; Meng, Qingchang; Han, Xiaohua; Hao, Zhuanfang; Li, Mingshun; Yong, Hongjun; Zhang, Degui; Zhang, Shihuang; Li, Xinhai

    2015-01-01

    Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease or rice black-streaked dwarf disease and can lead to severe yield losses in maize and rice. To analyse RBSDV evolution, codon usage bias and genetic structure were investigated in 111 maize and rice RBSDV isolates from eight geographic locations in 2013 and 2014. The linear dsRNA S7 is A+U rich, with overall codon usage biased toward codons ending with A (A3s, S7-1: 32.64%, S7-2: 29.95%) or U (U3s, S7-1: 44.18%, S7-2: 46.06%). Effective number of codons (Nc) values of 45.63 in S7-1 (the first open reading frame of S7) and 39.96 in S7-2 (the second open reading frame of S7) indicate low degrees of RBSDV-S7 codon usage bias, likely driven by mutational bias regardless of year, host, or geographical origin. Twelve optimal codons were detected in S7. The nucleotide diversity (π) of S7 sequences in 2013 isolates (0.0307) was significantly higher than in 2014 isolates (0.0244, P = 0.0226). The nucleotide diversity (π) of S7 sequences in isolates from Jinan (0.0391) was higher than that from the other seven locations (P < 0.01). Only one S7 recombinant was detected in Baoding. RBSDV isolates could be phylogenetically classified into two groups according to S7 sequences, and further classified into two subgroups. S7-1 and S7-2 were under negative and purifying selection, with respective Ka/Ks ratios of 0.0179 and 0.0537. These RBSDV populations were expanding (P < 0.01) as indicated by negative values for Tajima's D, Fu and Li's D, and Fu and Li's F. Genetic differentiation was detected in six RBSDV subpopulations (P < 0.05). Absolute Fst (0.0790) and Nm (65.12) between 2013 and 2014, absolute Fst (0.1720) and Nm (38.49) between maize and rice, and absolute Fst values of 0.0085-0.3069 and Nm values of 0.56-29.61 among these eight geographic locations revealed frequent gene flow between subpopulations. Gene flow between 2013 and 2014 was the most frequent. PMID:26121638

  19. Evidence of Accelerated Evolution and Ectodermal-Specific Expression of Presumptive BDS Toxin cDNAs from Anemonia viridis

    PubMed Central

    Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Cuttitta, Angela

    2013-01-01

    Anemonia viridis is a widespread and extensively studied Mediterranean species of sea anemone from which a large number of polypeptide toxins, such as blood depressing substances (BDS) peptides, have been isolated. The first members of this class, BDS-1 and BDS-2, are polypeptides belonging to the β-defensin fold family and were initially described for their antihypertensive and antiviral activities. BDS-1 and BDS-2 are 43 amino acid peptides characterised by three disulfide bonds that act as neurotoxins affecting Kv3.1, Kv3.2 and Kv3.4 channel gating kinetics. In addition, BDS-1 inactivates the Nav1.7 and Nav1.3 channels. The development of a large dataset of A. viridis expressed sequence tags (ESTs) and the identification of 13 putative BDS-like cDNA sequences has attracted interest, especially as scientific and diagnostic tools. A comparison of BDS cDNA sequences showed that the untranslated regions are more conserved than the protein-coding regions. Moreover, the KA/KS ratios calculated for all pairwise comparisons showed values greater than 1, suggesting mechanisms of accelerated evolution. The structures of the BDS homologs were predicted by molecular modelling. All toxins possess similar 3D structures that consist of a triple-stranded antiparallel β-sheet and an additional small antiparallel β-sheet located downstream of the cleavage/maturation site; however, the orientation of the triple-stranded β-sheet appears to differ among the toxins. To characterise the spatial expression profile of the putative BDS cDNA sequences, tissue-specific cDNA libraries, enriched for BDS transcripts, were constructed. In addition, the proper amplification of ectodermal or endodermal markers ensured the tissue specificity of each library. Sequencing randomly selected clones from each library revealed ectodermal-specific expression of ten BDS transcripts, while transcripts of BDS-8, BDS-13, BDS-14 and BDS-15 failed to be retrieved, likely due to under-representation in our

  20. The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

    PubMed

    Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

    2012-05-01

    This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or

  1. Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination

    PubMed Central

    Lau, Susanna K. P.; Feng, Yun; Chen, Honglin; Luk, Hayes K. H.; Yang, Wei-Hong; Li, Kenneth S. M.; Zhang, Yu-Zhen; Huang, Yi; Song, Zhi-Zhong; Chow, Wang-Ngai; Fan, Rachel Y. Y.; Ahmed, Syed Shakeel; Yeung, Hazel C.; Lam, Carol S. F.; Cai, Jian-Piao; Wong, Samson S. Y.; Chan, Jasper F. W.; Yuen, Kwok-Yung

    2015-01-01

    ABSTRACT Despite the identification of horseshoe bats as the reservoir of severe acute respiratory syndrome (SARS)-related coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nucleotide signature deletion among human strains, remains obscure. Although two SARS-related Rhinolophus sinicus bat CoVs (SARSr-Rs-BatCoVs) previously detected in Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, RsSHC014 and Rs3367, possessed 95% genome identities to human and civet SARSr-CoVs, their ORF8 protein exhibited only 32.2 to 33% amino acid identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nucleotide identities to human/civet SARSr-CoV genomes. Although these two betacoronaviruses displayed lower similarities than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein to civet SARSr-CoVs, their ORF8 proteins demonstrated exceptionally high (80.4 to 81.3%) amino acid identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2 to 37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that the ORF8 protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to that among SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSr-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs in approximately 1990. SARS

  2. The Application of Modern Techniques and Measurement Devices for Identification of Copper Ore Types and Their Properties / Wykorzystanie nowoczesnych technik i urządzeń pomiarowych do identyfikacji typów rud miedzi i ich właściwości

    NASA Astrophysics Data System (ADS)

    Krawczykowska, Aldona; Trybalski, Kazimierz; Krawczykowski, Damian

    2013-06-01

    minerałów miedzionośnych oraz rodzajem ich skupień i wpryśnięć. Niezwykle istotne jest właściwe rozpoznanie rudy pod względem petrograficzno-mineralogicznym. Znajomość właściwości przerabianej rudy pozwala na pełniejsze jej wykorzystanie poprzez właściwe prowadzenie i sterowanie procesami, dobór ich parametrów takich m.in. jak: czas mielenia, parametry klasyfikacji, rodzaj odczynników flotacyjnych, czas flotacji. W artykule przedstawiono wyniki przeprowadzonych analiz mikroskopowych, analizy obrazów zdjęć skaningowych oraz procedury wykorzystania otrzymanych informacji do identyfikacji typów rud (zastosowanie sieci neuronowych do rozpoznawania składów litologicznych). W badaniach wykorzystano rudę miedzi, pochodzącą z jednego z zakładów górniczych KGHM Polska Miedź S.A. Pobrane próbki rudy reprezentowały każdy z trzech typów litologicznych występujących w krajowych złożach: węglanową, łupkową oraz piaskowcową. Przeprowadzono ilościową analizę mineralogiczno-petrograficzną przy pomocy mikroskopu optycznego w świetle odbitym, a wyniki przedstawiono w tabelach 1 i 2. Wyniki te określają ilościowo stopień uwolnienia i zrosty dla jednego rodzaju minerału. Pokazano także przykładowe zdjęcia mikroskopowe zgładów poszczególnych typów litologicznych rud oraz próbek proszkowych tych typów (rys. 1 i 2). W kolejnym etapie badań wykorzystano skaningowy mikroskop elektronowy. Zdjęcia morfologii próbek uzyskane z mikroskopu elektronowego (obrazy SEM) były przedmiotem komputerowej analizy obrazu, umożliwiającej mikrostrukturalną klasyfikację ilościową typów rud. Analizowano wszystkie próbki poszczególnych typów litologicznych rudy miedzi: węglanowej, łupkowej i piaskowcowej oraz mieszanki tych typów w trzech klasach ziarnowych: 0÷45 μm, 45÷71 μm i 71÷100 μm. Celem przekształceń wykorzystanych w procedurze komputerowej analizy obrazu jest otrzymanie poprawnie posegmentowanego obrazu binarnego, kt

  3. Application of Relevance Maps in Multidimensional Classification of Coal Types / Zastosowanie Map Odniesienia W Wielowymiarowej Klasyfikacji Typów Węgla

    NASA Astrophysics Data System (ADS)

    Niedoba, Tomasz

    2015-03-01

    ą na siebie. Przez to nie możemy na podstawie tych rysunków stwierdzić, że analizowane dane pozwalają na prawidłową klasyfikację typów węgla. W celu uzyskania bardziej czytelnych wyników postanowiono przedstawić przy pomocy mapy odniesienia, te same dane w nieco inny sposób. Postanowiono przeanalizować dane reprezentujące różne typy węgla parami. Rysunek 5 przedstawia widok uzyskany dla danych reprezentujących typy węgla 34.2 oraz 35. Widać na nim czytelnie, że obrazy punktów reprezentujących próbki węgla typu 34.2 gromadzą się w skupiskach, które łatwo można odseparować od skupisk obrazów punktów reprezentujących próbki węgla 35. Podobne obserwacje dokonano na podstawie rysunków 6 i 7, gdzie przedstawiono parami, odpowiednio, węgle typu 31 i 34.2 oraz 31 i 35. Przeprowadzona wizualizacja wielowymiarowa przy użyciu map odniesienia pozwala więc stwierdzić, że informacje zawarte w analizowanych siedmiowymiarowych danych są wystarczające do prawidłowej klasyfikacji typów węgla 31, 34.2 oraz 35.