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Sample records for red-clay sequence insights

  1. Can the magnetic susceptibility record of Chinese Red Clay sequence be used for palaeomonsoon reconstructions?

    Science.gov (United States)

    Zhao, Guoyong; Han, Yan; Liu, Xiuming; Chang, Liao; Lü, Bin; Chen, Qu; Guo, Xuelian; Yan, Junhui; Yan, Jun

    2016-03-01

    Red Clay underlying the loess-palaeosol sequences on the Chinese Loess Plateau is an eolian deposit. There is a controversy over whether magnetic susceptibility (χ) variations in Red Clay sequence can be used as an indicator of summer palaeomonsoon intensity. This study investigates the magnetic mineralogy, magnetic concentration and magnetic grain size distribution of Jiaxian Red Clay with multimagnetic methods. Our results indicate that the magnetic properties of Jiaxian Red Clay are similar to those of the Quaternary loess-palaeosol sequences, and ultrafine ferrimagnetic grains produced during pedogenesis are responsible for an increase in susceptibility, therefore the χ enhancement mechanism of Red Clay is similar to that of the overlying loess-palaeosol sequences. This paper explores χ variations in the Red Clay sequence through spatial and temporal analysis. The susceptibility variation of six sites along a NNE to SSW transect correlate to palaeoclimatic cycles, so χ can be used to trace the summer palaeomonsoon intensity from a spatial perspective. However, a simple loess-derived calibration function cannot be used to quantitative reconstruct the palaeomonsoon intensity variations thought time. An adjusted calibration function for palaeosols from Red Clay sequence needs to be developed, so that χ can be used to quantitative reconstruct palaeomonsoon intensity. Further study is necessary to develop such a transfer function.

  2. Magnetic properties of Jiaxian red clay sequences from northern Chinese Loess Plateau and its paleoclimatic significance

    Institute of Scientific and Technical Information of China (English)

    QIANG; Xiaoke; AN; Zhisheng; LI; Huamei; CHANG; Hong

    2005-01-01

    Detailed rock magnetism investigation of the Jiaxian red clay sequences indicated that there are common magnetic mineralogy properties in red clay and loess-paleosol sequences from the Chinese Loess Plateau as well as the marked properties of themselves, magnetic minerals mainly with magnetite, maghemite, hematite, and possibly limonite/goethite contributing to the magnetic behavior. Meanwhile, it is found that the strong paleosol in red clay sequences has a lower coercivity and higher content of ultra-fine ferrimagnetic grains than that of the weak paleosol, which is similar to loess and paleosol in upper Wucheng Loess sequences, and indicates that humid conditions and relatively strong pedogenesis play a significant role in the increase of ultra-fine magnetic minerals and transformation of the magnetic minerals. This suggests that, like Quaternary loess-paleosols, the change of characteristics of paleoclimatic conditions of the late Tertiary red clay deposits is fluctuant. In addition, the results of magnetic hysteresis properties show that the applied saturated field for samples from the Jiaxian red clay sequences is higher than that of the samples from eastern and southern Chinese Loess Plateau. It is obviously shown that there exist more hard magnetic minerals and relatively weak biochemical processes in the Jiaxian red clay sequences on northern Chinese Loess Plateau. We conclude that the paleoclimatic environment is different between northern and eastern/southern Chinese Loess Plateau, and it should be more arid in northern Chinese Loess Plateau.

  3. Cyclostratigraphy for Chinese red clay sequences: Implications to changing previous age models and paleoclimate interpretations

    Science.gov (United States)

    Anwar, T.; Kravchinsky, V. A.; Zhang, R.

    2015-12-01

    The Chinese Loess Plateau contains red clay sequence which has continuous alternation of sedimentary cycles with recurrent paleoclimatic fluctuations. Absence of abundant fossils and inability of radiometric dating method made magnetostratigraphy a leading method to build age model for the red clay. Here magnetostratigraphic age model in red clay sequence is tested using cyclostratigraphy as orbital parameters of Earth are known. Milankovitch periodicities recorded in magnetic susceptibility and grain size in the Shilou red clay section are investigated and previously found age of 11 Ma for this section is re-evaluated. Magnetostratigraphy dating based on only visual correlation could potentially lead to erroneous age model. In this study the correlation is executed through the iteration procedure until it is supported by cyclostratigraphy; i.e. Milankovitch cycles are resolved in the best possible manner. Our new approach provides an age of 5.2 Ma for the Shilou profile. Wavelet analysis reveals that a 400 kyr eccentricity cycle is well preserved and the existence of a 100 kyr eccentricity in the red clay sequence on the eastern Chinese Loess Plateau suggests that eccentricity plays a vital role in Pliocene climate evolution. Paleomonsoon evolution is reconstructed and divided into three intervals (5.2-4.5 Ma, 4.5-3.6 Ma and 3.6-2.58 Ma). The earliest stage indicates that summer and winter monsoon cycles may rapidly alter, whereas the middle stage reflects an intensification of winter monsoon and aridification in Asia, and the youngest stage is characterized by relatively intensified summer monsoon. This study demonstrates that cyclostratigraphy can greatly assist magnetostratigraphy in dating the red clay sequences, and implies that many published age models for the red clay sequences should likely be re-assessed where possible. An evaluation of the monsoon system and climate change in eastern Asia might prominently benefit from this approach.

  4. Unmixing hysteresis loops of the late Miocene-early Pleistocene loess-red clay sequence.

    Science.gov (United States)

    Zhang, Rui; Necula, Cristian; Heslop, David; Nie, Junsheng

    2016-07-08

    Magnetic paleoclimatic records often represent mixed environmental signals. Unmixing these signals may improve our understanding of the paleoenvironmental information contained within these records, but such a task is challenging. Here we report an example of numerical unmixing of magnetic hysteresis data obtained from Chinese loess and red clay sequences. We find that the mixed magnetic assemblages of the loess and red clay sediments both contain a component characterized by a narrow hysteresis loop, the abundance of which is positively correlated with magnetic susceptibility. This component has grain sizes close to the superparamagnetic/stable single domain boundary and is attributed to pedogenic activity. Furthermore, a wasp-waisted component is found in both the loess and red clay, however, the wasp-waisted form is more constricted in the red clay. We attribute this component to a mixture of detrital ferrimagnetic grains with pedogenic hematite. The abundance of this component decreases from the base to the top of the red clay, a pattern we attribute to decreased hematite production over the Chinese Loess Plateau (CLP) due to long-term climate cooling. This work demonstrates the potential of hysteresis loop unmixing to recover quantitative paleoclimatic information carried by both low and high coercivity magnetic minerals.

  5. Unmixing hysteresis loops of the late Miocene-early Pleistocene loess-red clay sequence

    Science.gov (United States)

    Zhang, R.; Necula, C.; Heslop, D.; Nie, J.

    2016-12-01

    Magnetic paleoclimatic records often represent mixed environmental signals. Unmixing these signals may improve our understanding of the paleoenvironmental information contained within these records, but such a task is challenging. Here we report an example of numerical unmixing of magnetic hysteresis data obtained from Chinese loess and red clay sequences. We find that the mixed magnetic assemblages of the loess and red clay sediments both contain a component characterized by a narrow hysteresis loop, the abundance of which is positively correlated with magnetic susceptibility. This component has grain sizes close to the superparamagnetic/stable single domain boundary and is attributed to pedogenic activity. Furthermore, a wasp-waisted component is found in both the loess and red clay, however, the wasp-waisted form is more constricted in the red clay. We attribute this component to a mixture of detrital ferrimagnetic grains with pedogenic hematite. The abundance of this component decreases from the base to the top of the red clay, a pattern we attribute to decreased hematite production over the Chinese Loess Plateau (CLP) due to long-term climate cooling. This work demonstrates the potential of hysteresis loop unmixing to recover quantitative paleoclimatic information carried by both low and high coercivity magnetic minerals.

  6. Magnetostratigraphy and palaeoclimate of Red Clay sequences from Chinese Loess Plateau

    Institute of Scientific and Technical Information of China (English)

    孙东怀; 刘东生; 陈明扬; 安芷生; John Shaw

    1997-01-01

    Two Red Clay profiles near Xi’ an and Xifeng were investigated in an attempt to determine magne-tostratigraphic and palaeoclimatic records. The results show that aeolian dust accumulation and the related East Asia palaeomonsoon system had begun by 6.5 Ma, and it is deduced that the Tibetan Plateau had reached a significant elevation at that time. The late Tertiary palaeoclimatic history of the Red Clay as reflected by magnetic susceptibility is reconstructed during the period of 6.5-2.5 Ma. Stepwise increase in susceptibility of aeolian dust accumulation appears to have a close correlation to the uplift processes of the Tibetan Plateau. The remarkable increase of aeolian dust accumulation at 3.2 Ma appears to be due to the influence of global ice volume on the East Asia monsoon. Palaeomonsoon variation during the late Tertiary as recorded in the Red Clay sequences from the Chinese Loess Plateau can be regarded as the product of a number of interacting factors, such as uplift of the Tibetan Plateau, sola

  7. Seven million year iron geochemistry record from a thick eolian red clay-loess sequence in Chinese Loess Plateau and the implications for paleomonsoon evolution

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Recently, the Tertiary red clay sequence underlying Pleistoceneloess has attracted much attention. The remarkable progress is the recognition that the Tertiary red clay sequence is also wind-blown in origin, thus providing a good opportunity to reconstruct long-term monsoon changes. In contrast to the loess deposits, the magnetic susceptibility and the pedogenic characteristics are almost independent of each other in the red clay, thus challenging the validity of the readily measurable magnetic susceptibility in describing the monsoon history recorded by the red clay. With the objective to address the long-term East Asia summer monsoon evolution, the free to total Fe2O3 ratios were calculated in a continuous eolian red clay-loess sequence at Lingtai, the Chinese Loess Plateau, which has a thickness of 305 m and a basal age of 7.0 Ma. The seven million year Fe2O3 ratio record from the red clay-loess sequence indicates that (ⅰ) variations of the free to total Fe2O3 ratios of the loess can correlate generally with the alternations of the loess and paleosol horizons; (ⅱ) the East Asia summer monsoon was stronger as a whole in Neogene than that in Quaternary; (ⅲ) the strongest East Asia summer monsoon may occur between 4.0 and 4.8 Ma. The relatively small ice volume and high global temperature may be responsible for the strong summer monsoon during the early Pliocene.

  8. A comparison of heavy mineral assemblage between the loess and the Red Clay sequences on the Chinese Loess Plateau

    Science.gov (United States)

    Peng, Wenbin; Wang, Zhao; Song, Yougui; Pfaff, Katharina; Luo, Zeng; Nie, Junsheng; Chen, Wenhan

    2016-06-01

    QEMSCAN-based (Quantitative Evaluation of Minerals by Scanning Electron Microscopy) heavy mineral analysis has recently been demonstrated an efficient way to allow a rapid extraction of provenance information from sediments. However, one key issue to correctly obtain a provenance signal using this technique is to clearly separate effects of diagenetic alteration on heavy minerals in sediments, especially in fine-grained loess. Here we compare heavy mineral assemblages of bottom Quaternary loess (L33) and upper Pliocene Red Clay of three sites on the Chinese Loess Plateau (CLP). Two sites (Chaona and Luochuan) with similar modern climate conditions show similar heavy mineral assemblages but contain much less of the unstable heavy mineral amphibole than the drier Xifeng site. This result provides strong evidence supporting that climate-caused diagenesis is an important factor controlling heavy mineral assemblages of fine-grained loess. However, heavy mineral assemblages are similar for loess and paleosol layers deposited after 0.5 Ma on the Chinese Loess Plateau regardless of climate differences, suggesting that time is also a factor controlling heavy mineral assemblages of loess and Red Clay. Our high resolution sampling of the upper Miocene-Pliocene Chaona Red Clay sequence reveals similar heavy mineral compositions with a minor amphibole content, different from the drier Xifeng site results of the same age. This result indicates that the monsoonal climate pattern might have been maintained since the late Miocene. Furthermore, it indicates that the heavy mineral method is promising in tracing provenance for sites northwest of the Xifeng site on the Loess Plateau.

  9. A comparison of zircon U-Pb age results of the Red Clay sequence on the central Chinese Loess Plateau

    Science.gov (United States)

    Gong, Hujun; Nie, Junsheng; Wang, Zhao; Peng, Wenbin; Zhang, Rui; Zhang, Yunxiang

    2016-08-01

    Single grain zircon U-Pb geochronology has demonstrated great potentials in extracting tectonic and atmospheric circulation signal carried by aeolian, fluvial, and fluviolacustrine sediments. A routine in this sort of studies is analyzing 100-150 grains and then compares zircon U-Pb age spectra between the measured sample and the potential sources. Here we compared the zircon U-Pb age results of the late Miocene-Pliocene Red Clay sequence of two neighboring sites from the Chinese Loess Plateau where similar provenance signal is expected. Although the results from the 5.5 Ma sediment support this prediction, the results from the 3 Ma sediment at these two sites differ from each other significantly. These results emphasize the importance of increasing analysis number per sample and combining the zircon U-Pb geochronology with other provenance tools in order to get reliable provenance information.

  10. Pollen record from red clay sequence in the central Loess Plateau between 8.10 and 2.60 Ma

    Institute of Scientific and Technical Information of China (English)

    MA Yuzhen; WU Fuli; FANG Xiaomin; LI Jijun; AN Zhisheng; WANG Wei

    2005-01-01

    The Late Miocene and Pliocene are the key periods for understanding the origin and development of the present Asian monsoon circulations and ecologic environments. Here we present a pollen record from Chaona Red Clay section located in the central Loess Plateau in attempt to establish the histories of vegetation and associated climate changes between 8.10 and 2.60 Ma. Our results show that Gramineae-dominated woodland-grasslands developed in this region with Cedrus- and Pinus-characterized montane coniferous forests distributing in higher elevations from 8.10 to 6.73 Ma, probably suggesting a semi-humid climate in a warm-temperate zone. A subsequent expansion of Ulmus- dominated deciduous forests and a synchronous increase of Gramineae-dominated grassland reflect a warmer and more humid climate between 6.73 and 5.67 Ma. The vegetation changed to an Artemisia- and Gramineae-characterized steppe in lower elevations and to a coniferous forest in higher elevations from 5.67 to 3.71 Ma, implying probably a warm and semiarid climate in lowland and hill, and a colder and moister climate in mountain. During this period, a considerable warmer and more humid climate occurred between 4.61 and 4.07 Ma as indicated by pollen assemblages. The period between 3.71 and 2.58 Ma was characterized by the disappearance of Cedrus and Tsuga and also by an abrupt expansion of Cupressaceae, reflecting a drastic enhancement of monsoon-related climatic seasonality.

  11. Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay.

    Science.gov (United States)

    Jung, Jaejoon; Jang, In-Ae; Ahn, Sungeun; Shin, Bora; Kim, Jisun; Park, Chulwoo; Jee, Seung Cheol; Sung, Jung-Suk; Park, Woojun

    2015-11-01

    Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.

  12. Effect of red clay on diesel bioremediation and soil bacterial community.

    Science.gov (United States)

    Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun

    2014-08-01

    Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.

  13. Magnetic properties of the Tertiary red clay from Gansu Province, China and its paleoclimatic significance

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The study on magnetic properties of the red clay indicates that the red clay and loess- paleosol sequence have a common magnetic mineralogy, with magnetite, maghemite, hematite (and possibly goethite) contributing to the magnetic behavior. The red clay magnetic susceptibility is also found to have a positive relation with extrafine superparamagnetic grains. This suggests that, like the Quaternary loess-paleosols, an ultrafine ferrimagnetic component produced during pe-dogenesis in the red clay under humid conditions also plays an important role in susceptibility enhancement in the soil units. This is supported by the correlation between Rb/Sr ratio and magnetic susceptibility. This signifies that, like the above loess-paleosol sequence, the magnetic susceptibility of the red clay can be used as a general proxy paleoclimatic indicator, although whether its susceptibility in the red clay is comparable to pedogenesis intensity and requires further investigation. Magnetic susceptibility variation in the red clay thus also provides an eo-lian/pedogenic record of paleoclimatic evolution. Study of the background susceptibility indicates that, on average, the absolute scale of the paleoclimatic shift from red clay development to Quaternary loess deposition is similar to the climatic shift from stage 5 (S1) to stage 2-4 (L1). This may suggest that during the Quaternary there is an evident strengthening of the absolute wind intensity to bring more (about double) coarser and less weathered (non-SP fraction) eolian magnetic input from the source regions to the Loess Plateau than during the Pliocene. The presence of eolian red clay since 7.5 Ma BP in central-northern China implies an important envi-ronmental change from the underlying Cretaceous red sandstone. The red clay development was closely related to global drying and climate cooling since the Cretaceous and closely associated with the abrupt uplift of the Qinghai-Xizang Plateau at about that time. This uplift of the

  14. Magnetic fabric from red clay sediments in the Chinese Loess Plateau.

    Science.gov (United States)

    Gong, Hujun; Zhang, Rui; Yue, Leping; Zhang, Yunxiang; Li, Jianxing

    2015-04-27

    Well-distributed eolian red clay in a wide area of northern China is believed to imply the onset of an ancient East Asian monsoon system since Late Miocene. Two continuous red clay sequences spanning the time interval 7-2.6 Ma and 11-2.6 Ma in the Chinese Loess Plateau was investigated to determine the magnetic orientation and grain alignment in the primary fabric of eolian sediments. The north-westerly orientation of the AMS of the eolian red clay sequences parallels the material transportation direction, which differs from the model that suggests that airborne dust from overlying loess-paleosol sequences were transported by the East Asian winter monsoon and fixed by the East Asian summer monsoon. Our results further reveal that present-day climate and air circulation patterns differ from those of the pre-Quaternary, and may provide evidence of a prevailing wind during deposition of the red clay.

  15. The evol ution of coupling of Asian winter monsoon and high latitude climate of Northern Hemisphere——Grain evidence from 8.1 Ma loess-red clay sequence on the Chinese central Loess Plateau

    Institute of Scientific and Technical Information of China (English)

    吕连清; 方小敏; JosephA.Mason; 李吉均; 安芷生

    2001-01-01

    The evolution and driving mechanism of the Asian winter monsoon system are of great importance to understanding the present-day climate. Through high-resolution particle size analysis of the oldest loess-red clay sequence known so far (with a basal age of about 8 Ma) and comparison of the results with oxygen isotope curves from North Atlantic marine sediments, 4 stages of the evolution of the Asian winter monsoon were clearly demonstrated. During the first stage, between about 8.1 and 4.3 Ma, there was no relation between Asian winter monsoon and Northern Hemisphere ice volume and high latitude climate inferred from marine sediments. A weak relation developed during the second stage, about 4.3 to 3.5 Ma. During the third stage (3.5 to 2.6 Ma) an Asian winter monsoon system similar to the present formed, initiating a stronger relation between the winter monsoon and Northern Hemisphere ice volume and high latitude climate. In the final stage (2.6 to 0 Ma) the present Asian winter monsoon system was fortifi

  16. Red Clay Sediment in the Central Chinese Loess Plateau and Its Implication for the Uplift of the Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    SONG Yougui; LI Jijun; FANG Xiaomin; XIA Fei; DONG Hongmei

    2005-01-01

    The widely distributed red clay sediment underlying the Chinese Loess Plateau truly records the Neogene environmental evolution, and its genesis and development are intrinsically related to the uplift processes of the Tibetan Plateau and the evolution of East Asia monsoon system. In this paper, a detailed magnetostratigraphy of a loess-red clay section (107°13′E, 35°02′N) from the central Loess Plateau is reported. The loess-red clay sequence is composed of 175 m Quaternary loess-paleosol sequence and 128 m Neogene red clay sediments. Based on the correlation with the standard geomagnetic polarity time scale, the paleomagnetic results indicate that the age of Chaona red clay sequence extends to 8.1Ma, which is the older red clay deposition in the central Chinese Loess Plateau. The commencement of red clay at ~8.1 Ma may imply that the Ordos planation surface was broken by the movement of the Haiyuan-Liupanshan Faults, which was related to the uplift of the Tibetan Plateau induced by the collision of India Plate and Eurasian Plate. And the western part adjacent to the Tibetan Plateau was uplifted to form the embryo of the Liupan Shan (Mts.) and the eastern part was down-faulted to receive red clay deposition. We link this faulting to an initial uplift of the Tibetan Plateau. The undulating nature of the broken Ordos planation surface may explain the chronological differences and depth discrepancies among various cross-sections of red clay.

  17. A review of recent advances in red-clay environmental magnetism and paleoclimate history on the Chinese Loess Plateau

    Directory of Open Access Journals (Sweden)

    Junsheng eNie

    2016-03-01

    Full Text Available The red-clay sequence on the Chinese Loess Plateau (CLP was deposited during the late Miocene-Pliocene and is encoded with important information of past climate changes. However, it has received much less study in comparison to the overlying Pleistocene loess-paleosol sequence. In this paper, we review recent progress in characterizing the environmental magnetic parameter-based paleoclimate history recorded by the red-clay sequence. Several key conclusions are as follows. 1 the red clay and the loess-paleosol sequences have similar magnetic enhancement mechanisms but magnetic minerals in the red clay sequence have experienced a higher degree of oxidation than in the loess-paleosol sequence. 2 The CLP experienced a cooling and wetting trend from 4.5 to 2.7 Ma, caused by ice sheet expansion and East Asian summer monsoon intensification, respectively. 3 The above conclusions benefit from backfield remanence curve unmixing and comparison of magnetic grain size/concentration records, which are particularly useful in separating the temperature from the precipitation signal. A clear need in future studies is to explore the concentration and the grain size variations of hematite and goethite in the red-clay sequence and their formation mechanisms. The payback would be a clear understanding of climate history during the late Miocene-Pliocene, a possible analog for future warmer climate.

  18. Terrestrial mollusk evidence for the origin and sedimentary environment of the Late Tertiary Red Clay Formation in the Loess Plateau, China

    Institute of Scientific and Technical Information of China (English)

    PEI Yunpeng; WU Naiqin; LI Fengjiang

    2004-01-01

    The origin and sedimentary environment of the Late Tertiary (Neogene) Red Clay Formation in northern China had long been controversial. A new mollusk record from the Xifeng red clay (red-earth) sequence in the central Loess Plateau provides the biological evidence for addressing questions of its origin and environmental implication. The study of composition and preservation condition of seventy mollusk fossil assemblages reveals the initial ecological condition of the red clay formation, avoiding the effect of post-deposited alteration. The result shows that all of identifiable mollusk species are composed of terrestrial taxa, most of them are the common species found in the overlying Quaternary loess-paleosol sequence. Most of fossil individuals preserved in the red clay strata are in living conditions based on the investigation of fieldwork, indicating the original population. Thus, the mollusk fossil assemblages can be used as an indicator of primary environment of the red clay formation. The mollusk record from the Xifeng red clay sequence supports the view that the red clay is an aeolian origin, similar to the overlying Quaternary loess deposits. Our data also reveal the history of environmental changes at Xifeng from 6.2-2.4 Ma, which is coupled in phase with the formation and development of the Arctic ice sheets and the process of the Tibetan Plateau uplift. Both may be the major cause and forcing mechanisms of the late Tertiary environmental changes in the Loess Plateau.

  19. 3Ma以来黄土高原朝那黄土-红粘土序列赤铁矿记录及其古气候意义%HEMATITE RECORD OF 3Ma LOESS-RED CLAY SEQUENCES IN THE CENTRAL CHINESE LOESS PLATEAU 3Ma AND ITS PALEOCLIMATIC SIGNIFICANCE

    Institute of Scientific and Technical Information of China (English)

    李香钰; 方小敏; 杨一博; 昝金波

    2012-01-01

    Many significant warm and cool climate events occurred during the Cenozoic, and one of the most intriguing climate events of the Neogene was the Middle Miocene Climate Optimum ( MMCO) , which occurred at about 15 Ma and represents a geologically recent warming event unrelated to human activity that may mirror future climate change in terms of the average global surface temperature increase. Zhuanglang( ZL) County ( 35°13'N, 106°05'E) ,on the western CLP,is 50km northeast of Qin'an section and is widely covered with red clay sediments, in order to get a continuous high-resolution record,the ZL drilling core was obtained. From the study of the magnetostratigraphic we can know that the Late Cenozoic eolian red clay sequences of ZL covering an age range from 25. 6Ma to 4. 8Ma also include the warm climate change period of the Middle Miocene Climate Optimum, which is rich archive of paleoclimatic changes. We choose red clay experimental samples of susceptibility with a spacing of 20cm, then according to the susceptibility variations choose typical samples to do other rock magnetic experiment. The MMCO representative samples were collected from 300 - 420m, covering an age range of 17.5 ~ 13. 5Ma. To make a comparison of the characteristic of rock magnetism about the MMCO representative samples, we also collected representative samples from the Preceding-MMCO ( samples collected from 420 ~ 450m, covering an age range of 18. 0 ~ 17. 5Ma) and Post-MMCO( samples collected from 250 ~ 300m, covering an age range of 13. 5 -12. Oma) . In this study, a multi-parameter rock magnetic investigation such as the magnetic susceptibility ( x) temperature-dependent magnetic susceptibility curve(x-T curves) ,x-T curves of the representative samples heated to different temperatures, IRM acquisition and reverse field demagnetization of IRM2.7T ( IRM acquires at an applied field of 2. 7T)and magnetic hysteresis loops were carried on samples collected from the Zhuanglang red clay drilling

  20. Origin of Quaternary Red Clay of Southern Anhui Province

    Institute of Scientific and Technical Information of China (English)

    HUXUEFENG; YUANGUODONG; 等

    1998-01-01

    The particle-size distribution,heavy mineral constituents and rare earth elements(REE) characteristics of the Quaternary red clay of southern Anhui Province were studied to explore the origin of the clay.The results showed that the clay had some properties of areolian deposits,which could be compared with,those of the loess in North China ;and its chondrite-normalized curves of REE were similar to those of the Xiashu loess implying tha they shared the same orighin.It was concluded in combination with the results rported by other researchers that the Quaternary red clay of southern Anhui Province originated from aolian deposts, and this could reveal the cycles of warm and cold climates in the area during the Quaternary period.

  1. Efficient uranium immobilization on red clay with phosphates.

    Science.gov (United States)

    Grabias, Ewelina; Gładysz-Płaska, Agnieszka; Książek, Anna; Majdan, Marek

    2014-01-01

    Uranium is a very toxic and radioactive element. Removal of uranium from wastewaters requires remediation technologies. Actual methods are costly and ineffective when uranium concentration is very low. Little is known about the enhancement of sorption of uranyl ions by phosphate ions on aluminosilicates. Here, we studied sorption of uranyl acetate on red clay in the presence of phosphates. The concentration of U(VI) ranged 0.0001-0.001 mol/L, whereas the concentration of PO4(3-) was constant at 0.0001 mol/L. We designed a new method for the analysis of ternary surface complexes. We observed for the first time a remarkable improvement of U(VI) sorption on red clay under the influence of phosphates. We also found that at least two different ternary surface complexes U(VI)-phosphate-clay are formed in the sorbent phase. The complexation of UO2(2+) cations by phosphate ligands in the sorbent phase was confirmed by the X-ray photoelectron spectra of U 4f electrons.

  2. Uncertainty Concerning the Efficiency and Effectiveness of Red Clay's Data Management and Processing Services

    Science.gov (United States)

    Ammann, Charles

    2010-01-01

    For twenty-nine years, Red Clay Consolidated School District has managed data processing in a unique manner. Red Clay participates in the Data Service Center consortium to provide data management and processing services. This consortium is more independent than a department in the district but not as autonomous as an outsourced arrangement. While…

  3. Material Composition and Engineering Characteristics of Red Clay in Guigang,Guangxi

    Institute of Scientific and Technical Information of China (English)

    Xiao Minggui; Wang Jieguang; Chen Xuejun

    2005-01-01

    There is fine and uniform clay with aluminous and ferrous cementation in the red clay found in Guigang, Guangxi. It has the characteristics of shrinkage outwardly, rigid upper but soft lower and well-grown fissure. In addition there are engineering characteristics such as high water content, low compactness and low compressibility, high strength and high contractility but slight expansibility. This paper discusses the red clay's engineering characteristics and its change regulation with depth by analyzing changes in the red clay's grain size composition, mineralogical constitution, and chemical composition.

  4. U-Pb ages of detrital zircon and provenances of Red Clay in the Chinese Loess Plateau

    Science.gov (United States)

    Gong, Hujun; Xie, Wenbin; Zhang, Rui; Zhang, Yunxiang

    2017-05-01

    The Chinese Loess Plateau (CLP), which is located in the central part of China, mainly contains two sequences: the Quaternary loess-paleosol sequence and the late Miocene-Pliocene Red Clay sequence. U-Pb ages of detrital zircon from the Quaternary loess-paleosol sequences indicate that the current spatial pattern of central Asian aridification was largely established during the early Quaternary. U-Pb ages of detrital zircon from the underlying Red Clay sequences demonstrate that the northern source regions were important contributors for the dust since the late Miocene, except for the periods of ∼8 Ma and ∼5.5 to ∼4 Ma. These two periods correspond to increased and decreased dust deposition in the North Pacific, respectively, ascribed to the late Miocene aridification of the Qaidam Basin (in the west of the CLP) and the early Pliocene aridification of the Tarim Basin (in the west of the CLP). We attribute the increase of the Qaidam Basin-derived North Pacific dust fluxes to the uplift of the NE Tibetan Plateau. Such uplift also controlled the climatic and environmental changes in central Asian during the late Miocene. This study highlights the dynamical process of the central Asian aridification during the late Miocene-Pliocene.

  5. On the decay of strength in Guilin red clay with cracks

    National Research Council Canada - National Science Library

    Yi Li; Keneng Zhang; Baochen Liu; Zongyuan Pan

    2015-01-01

      In order to research the effect of cracks in red clay on shear strength through dry-wet cycle test, the experimenters used imaging software and a mathematical model to determine fractal dimension...

  6. Nondestructive Measurement of Water Content and Moisture Migration of Unsaturated Red Clays in South China

    Directory of Open Access Journals (Sweden)

    Junhui Zhang

    2015-01-01

    Full Text Available To reveal the moisture migration mechanism of the unsaturated red clays, which are sensitive to water content change and widely distributed in South China, and then rationally use them as a filling material for highway embankments, a method to measure the water content of red clay cylinders using X-ray computed tomography (CT was proposed and verified. Then, studies on the moisture migrations in the red clays under the rainfall and ground water level were performed at different degrees of compaction. The results show that the relationship between dry density, water content, and CT value determined from X-ray CT tests can be used to nondestructively measure the water content of red clay cylinders at different migration time, which avoids the error reduced by the sample-to-sample variation. The rainfall, ground water level, and degree of compaction are factors that can significantly affect the moisture migration distance and migration rate. Some techniques, such as lowering groundwater table and increasing degree of compaction of the red clays, can be used to prevent or delay the moisture migration in highway embankments filled with red clays.

  7. High Concentration of Red Clay as an Alternative for Antibiotics in Aquaculture.

    Science.gov (United States)

    Jung, Jaejoon; Jee, Seung Cheol; Sung, Jung-Suk; Park, Woojun

    2016-01-01

    The use of antibiotics in aquaculture raises environmental and food safety concerns because chronic exposure of an aquatic ecosystem to antibiotics can result in the spread of antibiotic resistance, bioaccumulation of antibiotics in the organisms, and transfer of antibiotics to humans. In an attempt to overcome these problems, high-concentration red clay was applied as an alternative antibiotic against the following common fish pathogens: Aeromonas salmonicida, Vibrio alginolyticus, and Streptococcus equinus. The growth of A. salmonicida and V. alginolyticus was retarded by red clay, whereas that of S. equinus was promoted. Phase contrast and scanning electron microscopy analyses confirmed the attachment of red clay on cell surfaces, resulting in rapid gravitational removal and cell surface damage in both A. salmonicida and V. alginolyticus, but not in S. equinus. Different cell wall properties of grampositive species may explain the unharmed cell surface of S. equinus. Significant levels of oxidative stress were generated in only the former two species, whereas significant changes in membrane permeability were found only in S. equinus, probably because of its physiological adaptation. The bacterial communities in water samples from Oncorhynchus mykiss aquacultures supplemented with red clay showed similar structure and diversity as those from oxytetracycline-treated water. Taken together, the antibiotic effects of high concentrations of red clay in aquaculture can be attributed to gravitational removal, cell surface damage, and oxidative stress production, and suggest that red clay may be used as an alternative for antibiotics in aquaculture.

  8. Geosorption of As(III) from aqueous solution by red clays: kinetic studies.

    Science.gov (United States)

    Rivera-Hernández, José R; Green-Ruiz, Carlos

    2014-05-01

    The geosorption of As(III) on red clays from aqueous solution under different environmental conditions (i.e. initial concentration, pH and temperature) was studied. This process reached its equilibrium quickly (red clays at 0.1 mg As(III) L(-1) was 10, while for 10 mg As(III) L(-1) was 4. There wasn't a significant effect of temperature on the As(III) adsorption. The kinetic pseudo-second order and the isothermal Langmuir were the models that best described the experimental data, suggesting an adsorption process in multistep. Likewise, there are not interactions between neighbor active sites on the red clay surface.

  9. A“Yellow Cap” on Quaternary Red Clay in Jiujiang,Jiangxi Province

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A thin layer of yellow-brown-colored earth was generally found on Quaternary red clay in Jiujing,Jiangxi Province,A typical profile was established.Both particle size distribution and REE(rare earth elements)characteristics of the yellow-brown-colored earth of the profile fully suggested its aeolian origin and close similarity of Nanjing Xiashu Loess.The study also implied aeolian origin of the underlying Quaternary red clay,Compared with the red clay,the yellow-brown-colored earth was less weathered because of its lower content of free iron and higher mole ratios of SiO2/Al2O3 and SiO2(Fe2O3+Al2O3) as well as its less developed chemical microtextures of quartz grains.In order to study the ages of the two deposits comparatively,the thermoluminescent dating method was used.As a result,the bottom of the yellow-brown-colored earth was dated to 60±5 ka B.P.and the upper part of the red clay 388±54 ka B.P.It was suggested that the yellow-brown-colored earth earth was formed in the Late Pleistocene and was probably the aeolian deposit of the Last Glacial,which corresponded with the Malan Loess in the Loess Plateau of the northwestern part of China,while the underlying red clay was formed in the Middle Pleistocene.A“yellow cap” on Quaternary red clay in Jiujiang implied a great climatic and environmental variation in the beginning of the Late Pleistocene in the southern part of China,especially in the middle and lower reaches of the Yangtze River,The event not only halted the rubification,once dominating the region but also produced a widespread covering of aeolian deposit,as only occurred in the cold and dry environment.

  10. Grain-size evidence for multiple origins of the reticulate red clay in southern China

    Institute of Scientific and Technical Information of China (English)

    HU Xuefeng; ZHU Yu; SHEN Mingneng

    2005-01-01

    Grain-size distributions of the reticulate red clay in Xuancheng, Anhui Province, and Jiujiang, Taihe and Ganzhou, Jiangxi Province, are analyzed. The results are as follows: (1) Generally fine and uniform, grain-size characteristics of the reticulate red clay in Xuancheng and Jiujiang are much similar, with no >2 mm gravels, 0.30% and 1.14% of >63 μm fraction on average, respectively, and 34.65% and 37.20% of 10―50 μm fraction, which is apparently accumulated. The patterns of the grain-size distribution curves of the uppermost yellow-brown earth of the profiles in the two areas much resemble those of the loess in northern China and the Xiashu loess in southeastern China, while the patterns of the other layers also apparently show some attributes inherited from the above. The grain-size distribution patterns of the quartz separated from the whole profiles in the areas are almost identical, which could also be compared with those of the loess and the Xiashu loess. All the features above reveal aeolian characteristics of the reticulated red clay in these two areas. (2) The reticulate red clay in Taihe and Ganzhou is much coarser than that in Xuancheng and Jiujiang, with high content of >63 μm fraction and relatively low content of 10―50 μm fraction. The variations in grain-size distributions of the profiles are also observed. The grain-size distribution patterns of both the original samples and the quartz of the red clay could hardly be compared with those of the loess and the Xiashu loess. All the features above reveal their alluvial or diluvial origins. (3) The multiple origins of the reticulate red clay in the areas reflect the diversity and complexity of the Quaternary environment in southern China. The existence of the reticulate red clay with aeolian characteristics brings forth objective evidence for the occurrence of large-scale dust deposition in southern China during the Quaternary glacial periods. Further investigation and study on the regional

  11. Astrobiological implications of dim light phototrophy in deep-sea red clays

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A; Tanya S.; LokaBharathi, P.A; Dhakephalkar, P.K.; Mallik, S.; Kshirsagar, P.R.; Khadge, N; Nath, B.N; Bhattacharya, S.; Dagar, A; Kaur, P.; Ray, D.; Shukla, A.D.; Fernandes, C.E.G.; Fernandes, S.O.; Thomas, T.R.A.; Mamatha, S.S.; Mourya, B.S.; Meena, R.M.

    and white LED light illumination, with average irradiance 30.66 W m-2, were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°±2°C and 25°±2°C, representing ambient...

  12. Do multiple cycles of aeolian deposit-pedogenesis exist in the reticulate red clay sections in southern China?

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The Xiangyang reticulate red clay section was newly sampled in high-resolution. The viewpoints different from the previous studies[1-7] are put forward after studying Munsell color values, weathering degrees, magnetic parameters and stable carbon isotopic compositions of the section. They are as follows: (1) The curves of hue, DCB extracted iron (Fed), DCB extracted iron/total iron ratio (Fed/Fet), weathering index (BA) of the section show that the redness is not significantly correlated with the weathering degree of the layers though the uppermost yellow-brown-colored layer is relatively weakly weathered. The variation in hues of the section is possibly attributed to the change of hematite and goethite contents. It is insufficient to determine the existence of the multiple deposit-pedogenesis cycles in the section, like the loess-paleosol sequence in Chinese Loess Plateau, only by the color variation. (2) Magnetic susceptibility (?) values in the non-reticulate and weakly reticulate layers are high; but are quite low in the reticulate red clay layer. The former are more than ten times higher than the latter because of the leaching and collapse of superparamagnetic (SP) and stable single domain (SSD) magnetic particles during the plinthitic processes. Hence, ? values in the section are not controlled by weathering and pedogenic processes, and no longer have clear paleoclimatic implication. It is not correct to prove the existence of the multiple deposit-pedogenesis cycles in the section using ? curves. (3) The organic ??13C curve of the section illustrates the reduction of forests and increasing of C4 plants in the study area since the late stage of the Quaternary period. It could not prove the existence of the multiple deposit-pedogenesis cycles in the section either. (4) As a matter of fact, it is difficult to prove the existence of the multiple deposit-pedogenesis cycles in the Xiangyang section like the loess-paleosol sequence in Chinese Loess Plateau using the

  13. Production of building elements based on alkali-activated red clay brick waste

    Directory of Open Access Journals (Sweden)

    Rafael Andres Robayo-Salazar

    2016-09-01

    Full Text Available This paper analyzes the feasibility of reusing a red clay brick waste (RCBW in order to produce building elements such as blocks, pavers and tiles, by using the technique of alkaline activation. The production of these building elements was based on the design of a hybrid mortar with 48.61 MPa of compressive strength, at 28 curing days at room temperature (25 °C. The hybrid mortar was synthesized by adding 10% by weight of Portland cement (OPC to the RCBW, Red Clay Brick Waste. As alkaline activators were used commercial industrial grade sodium hydroxide (NaOH and sodium silicate (Na2SiO3. Building elements were physically and mechanically characterized, according to Colombian Technical Standards (NTC. This technology process is presented as an alternative for the reuse of RCBW and its contribution to the environmental sustainability.

  14. 红粘土的强度机理%Shear strength proprieties of red clay

    Institute of Scientific and Technical Information of China (English)

    傅鑫晖; 颜荣涛; 于海浩; 吴二林; 韦昌富; 张芹

    2014-01-01

    从红粘土的水敏性、密实程度与胶结作用这三方面对其抗剪强度的影响进行了试验,研究发现:随着干密度的增大,红粘土的抗剪强度与粘聚力也有了较大的提高,而内摩擦角在干密度较大情况下随含水率变化较为明显。为了探究胶结作用对红粘土抗剪强度的影响,用丙三醇溶液替代水溶液配制土样进行试验,发现胶结物质减少的红粘土试样,其抗剪强度也有了明显的降低,进一步从胶结作用对红粘土的影响方面分析了红粘土的强度变化规律。%Compared with common clay,the strength behavior of red clay which contains cementing material is more complicated.Research on the water-sensitive properties,degree of compaction and adhesion action of the red clay shows that the shear strength and cohesion of samples appear double stress peak value with the solution concentration increased.The shear strength and cohesion increase with the increase of dry densities.When the dry density of specimen is larger,the change of internal friction angle is more obvious.To investigate the effect of cementing on the strength of the red clay,the shearing tests were performed on the specimen saturated with the glycerol solution instead of water.Test result shows that the strength of the red clay decreases rapidly with the decrease of the cementing material.The variation laws of strength of red clays is also analyzed from the ce-menting effect.

  15. Performance Evaluation and Field Application of Red Clay Green Roof Vegetation Blocks for Ecological Restoration Projects

    Directory of Open Access Journals (Sweden)

    Hwang-Hee Kim

    2017-02-01

    Full Text Available In this study, for restoration of ecological systems in buildings, porous vegetation red clay green roof blocks were designed for performance evaluation. Blast furnace slag (BFS; fine aggregates (agg., coarse aggregates, polyvinyl alcohol (PVA fiber (hydrophilic fiber, and red clay (ecofriendly additive material were applied to the construction of the porous vegetation red clay green roof blocks. A decrease in cement use is one way of reducing carbon emissions. To increase the water retentivity and the efficiency of roof vegetation blocks, blast furnace slag aggregates with excellent water absorptivity and polyvinyl alcohol fiber with a water absorption rate above 20% were added. In particular, the addition of polyvinyl alcohol fiber prevents performance reduction of the green roof vegetation blocks during freezing and melting in winter. Compressive strength, void ratio, and unit-mass tests were conducted to evaluate the performance of the roof vegetation blocks. After their application to roof vegetation, the effect of water purification was evaluated. According to the experimental results, the mix that satisfies the target performance of green roof vegetation blocks (compression strength above 8 MPa, void ratio above 20%, unit mass 2.0 kg/cm3 or below is: cement = 128.95 kg/m3, BFS = 96.75 kg/m3, red clay = 96.75 kg/m3, water = 81.50 kg/m3, BFS agg. = 1450 kg/m3, PVA fiber = 1.26 kg/m3. The green roof vegetation blocks were designed using the mix that satisfied the target performance. To find the amount of attainable water due to rainfall, a rainfall meter was installed after application of the roof vegetation to measure daily rainfall and calculate the amount of attainable water. The results show that, for 1 mm of rainfall, it is possible to attain about 0.53 L of water per 1 m2. In addition, the water quality of effluents after application of roof vegetation was analyzed, and the results satisfied Class 4 of the River-life Environmental

  16. Aqueous dispersion of red clay-based ceramic powder with the addition of starch

    Directory of Open Access Journals (Sweden)

    Maria Victoria Alcantar Umaran

    2013-04-01

    Full Text Available The optimum dispersion and rheological properties of red clay-based ceramic suspension loaded with unary and binary starch were investigated in aqueous medium. The aqueous ceramic suspension was prepared consisting of red clay, quartz, feldspar, and distilled water. Using a polyelectrolyte dispersant (Darvan 821A, the ternary ceramic powder was initially optimized to give the smallest average particle size at 0.8 wt. (% dispersant dosage as supported by sedimentation test. This resulted into an optimum high solid loading of 55 wt. (%. The addition of either unary or binary starches to the optimized ceramic slurry increased the viscosity but maintained an acceptable fluidity. The mechanism of such viscosity increase was found to be due to an adsorption of starch granules onto ceramic surfaces causing tolerable agglomeration. Correspondingly, the rheological evaluations showed that the flow behaviors of all starch-loaded ceramic slurries can be described using Herschel-Bulkley model. The parameters from this model indicated that all ceramic slurries loaded with starch are shear thinning that is required for direct casting process.

  17. Environmental rock-magnetism of Cenozoic red clay in the South Pacific Gyre

    Science.gov (United States)

    Shimono, Takaya; Yamazaki, Toshitsugu

    2016-04-01

    Nonfossiliferous red clay can be used for elucidating long-range environmental changes, although such studies were limited so far because of the difficulty in precise age estimation and extremely low sedimentation rates. We conducted an environmental rock-magnetic study of Cenozoic red clay at the Integrated Ocean Drilling Program Site U1365 in the South Pacific Gyre. Magnetostratigraphy could be established only above ˜6 m below the seafloor (mbsf) (˜5 Ma). Below ˜6 mbsf, the ages of the cores were transferred from the published ages of nearby Deep Sea Drilling Project Site 596, which is based mainly on a constant Cobalt flux model, by intercore correlation using magnetic susceptibility and rare earth element content variation patterns. Rock-magnetic analyses including first-order reversal curve diagrams, the ratio of anhysteretic remanent magnetization susceptibility to saturation isothermal remanent magnetization (SIRM), and IRM component analyses revealed that magnetic minerals consist mainly of biogenic magnetite and terrigenous maghemite, and that the proportion of the terrigenous component increased since ˜23 Ma. We consider that the increase reflects a growth of eolian dust flux associated with a northward shift of Australia and the site to an arid region of the middle latitudes. The increase of the terrigenous component accelerated after ˜5 Ma, which may be associated with a further growth of the Antarctic glaciation at that time. This is coeval with the onset of the preservation of magnetostratigraphy, suggesting that the primary remanent magnetization is carried by the terrigenous component.

  18. Electrostatic painting residues as an alternative raw material for red clay industry.

    Science.gov (United States)

    Basegio, Tania; Machado, Andréa; Bernardes, Andréa Moura; Bergmann, Carlos Pérez

    2006-12-01

    In this study, the viability of using electrostatic painting residues--paint sludge--as a raw material to the red clay industry was investigated. Red clay-based ceramic masses containing electrostatic paint residues were formulated during the study. The clays were obtained from the Rio do Rastro deposit, in Gravataí, and were of the standard formulation used in industry. Different ceramic mass formulations with additions of 0.5, 1.0, 2.5 and 5.0 wt.% electrostatic painting residue in addition to a formulation with no residue addition (standard formulation), were evaluated. The samples were uniaxially pressed in a double-effect press and were fired in an electric oven at 900, 950 and 1000 degrees C. The firing at constant temperature lasted 8 h, and heating rate was 150 K h(-1). After processing the samples were characterized in terms of their physical and mechanical properties. Environmental compatibility was also considered by the evaluation of gaseous emissions and leaching and solubilization tests according to the Brazilian standards NBR 10.005 and NBR 10.006, respectively. The results showed that it was possible to produce ceramic materials containing electrostatic painting residues within their formulations.

  19. AGE OF RED CLAY AT CHAONA SECTION NEAR EASTERN LIUPAN MOUNTAIN AND ITS TECTONIC SIGNIFICANCE%六盘山东麓朝那剖面红粘土-年代及其构造意义

    Institute of Scientific and Technical Information of China (English)

    宋友桂; 方小敏; 李吉均; 安芷生; 杨东; 吕连清

    2000-01-01

    The red clay underlying the Chinese Loess Plateau was thought to be an eoliandeposition continuous to loess and thus was linked to the history of monsoon anddrying Asia in relation to the Tibet uplift. The lower boundary of red bed has beenregarded as a signal to indicate the Tibetan uplift or the initiation of the polar icesheet. Thus, the age and origin of red clay hold the key to unravel uplift of LiupanMountain and disintegration of Ordos plantation surface. Here we report a 303mcomplete loess-red clay sequence, which contains 175m of Quaternary loess-paleosolsand 128m of red clay, from Chaona at the eastern foot of Liupan Mountain borderedby Liupan Mountain thrust connected physically to north boundary thrusts of the TibetPlateau. Detailed paleomagnefism shows that the age of Chaona red clay reaches~8.1Ma B.P., at least 0.5 Ma older than previously reported oldest ages of the red claysections in the Loess Plateau. It provides so far an oldest constraint to the Ordosplanafion surface below red clay. Morphostrafigraphy shows that the tectonism was relatively stable between the lateCretaceous and the red clay, which led the relief in the region be greatly reduced toform a gently undulate but roughly horizontal planation surface. During the formationof the planation surface, even if dusts could have, it would be hard for them to bepreserved. Thus, the start of red clay at~8.1Ma B.P. may imply that the planationsurface was broken by the Haiyuan-Liupan Mountain faults at that time with one partto be uplifted to form Liupan Mountain and the other to be down-faulted to begin toreceive dust deposition. We link this faulting to an initial uplift of the Tibet Plateaualong its northern boundary faults synchroneous with the rise of the Himalaya-SouthTibet, which may result in the large environmental change and the inception of eolianred clay.%黄土高原地区黄土之下的红粘土的年代和形成可为六盘山隆起、鄂尔多斯夷平面解 体以及青藏高

  20. The influence of water and salt content on the thermal conductivity coefficient of red clay brick

    Science.gov (United States)

    Bednarska, Dalia; Koniorczyk, Marcin

    2017-07-01

    This paper presents the results of experiments aimed at the determination of hygro-thermal properties of red clay brick containing water or salt. The main objective of the research is the determination of the relation between the apparent thermal conductivity of brick and its water or Na2SO4 in water solution content. The research is conducted using stationary technique for the dry specimens, as well as the ones containing 25%, 50%, 75% and 100% water or sodium sulphate solution. The experimental results confirm the negative influence of water or sodium sulphate solution on thermal properties of material. However we observe that the presence of Na2SO4 in pores slightly weakens this negative impact.

  1. Astrobiological implications of dim light phototrophy in deep-sea red clays.

    Science.gov (United States)

    Das, Anindita; Singh, Tanya; LokaBharathi, P A; Dhakephalkar, Prashant K; Mallik, Sweta; Kshirsagar, Pranav R; Khadge, N H; Nath, B Nagender; Bhattacharya, Satadru; Dagar, Aditya Kumar; Kaur, Prabhjot; Ray, Dwijesh; Shukla, Anil D; Fernandes, Christabelle E G; Fernandes, Sheryl O; Thomas, Tresa Remya A; S S, Mamatha; Mourya, Babu Shashikant; Meena, Ram Murti

    2017-02-01

    Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66Wm(-2), were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2°C and 25°± 2°C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably

  2. Astrobiological implications of dim light phototrophy in deep-sea red clays

    Science.gov (United States)

    Das, Anindita; Singh, Tanya; LokaBharathi, P. A.; Dhakephalkar, Prashant K.; Mallik, Sweta; Kshirsagar, Pranav R.; Khadge, N. H.; Nath, B. Nagender; Bhattacharya, Satadru; Dagar, Aditya Kumar; Kaur, Prabhjot; Ray, Dwijesh; Shukla, Anil D.; Fernandes, Christabelle E. G.; Fernandes, Sheryl O.; Thomas, Tresa Remya A.; Mamatha, s. S.; Mourya, Babu Shashikant; Meena, Ram Murti

    2017-02-01

    Red clays of Central Indian Basin (CIB) under influence of trace of Rodriguez Triple Junction exhibited chemoautotrophy, low temperature hydrothermal alterations and photoautotrophic potential. Seamount flank TVBC-08, hosting such signatures revealed dominance of aerobic anoxygenic phototroph Erythrobacter, with 93% of total 454 pyrosequencing tags. Subsequently, enrichments for both aerobic (Erythrobacter) and anaerobic anoxygenic phototrophs (green and purple sulphur bacteria) under red and white LED light illumination, with average irradiance 30.66 W m-2, were attempted for three red-clay sediment cores. Successful enrichments were obtained after incubation for c.a. 120 days at 4°± 2 °C and 25°± 2 °C, representing ambient psychrophilic and low temperature hydrothermal alteration conditions respectively. During hydrothermal cooling, a microbial succession from anaerobic chemolithotrophy to oxygenic photoautotrophy through anaerobic/aerobic anoxygenic phototrophic microbes is indicated. Spectral absorbance patterns of the methanol extracted cell pellets showed peaks corresponding to metal sulphide precipitations, the Soret band of chlorosome absorbance by photosystem II and absence of peaks at Qy transition band. Dendritic nano-structures of metal sulphides are common in these sediments and are comparable with other sulphidic paleo-marine Martian analogues. Significant blue and redshifts have been observed for the experimental samples relative to the un-inoculated medium. These observations indicate the propensity of metal-sulphide deposits contributing to chemiluminiscence supporting the growth of phototrophs at least partially, in the otherwise dark abyss. The effects of other geothermal heat and light sources are also under further consideration. The potential of phototrophic microbial cells to exhibit Doppler shift in absorbance patterns is significant towards understanding planetary microbial habitability. Planetary desiccation could considerably

  3. Development and validation of an analytical method for the extraction and quantification of soluble sulfates in red clay

    Directory of Open Access Journals (Sweden)

    V. I. Cáceres

    2015-09-01

    Full Text Available AbstractIn this work a fast and environmentally friendly method for the extraction and quantification of soluble sulphates in red clay using microwave assisted extraction (MAE and determination by turbidimetry was developed and validated. The favorable conditions for the extraction of soluble sulphates in red clay by MAE were: 1 g of sample, with particle size of 63μm, dissolved in 50 mL of distilled water, it was extracted using a microwave oven with 70% of power during 5 min, later the sample was centrifuged during 5 min and then filtered. The soluble sulphates in red clays were quantified at 420 nm. The procedure proposed showed linear behaviour in the tested rank (5-7000 mg SO42-/kg of clay with R2 0.9993. The limits of detection and quantification were 4.30 and 14.33 mg/kg, respectively, with a variation coefficient of 1.41%. The method proposed in this work allows to determine soluble sulphates in red clay with a recovery of 94%.

  4. Dynamic compaction treatment technology research of red clay soil embankment in southern mountains

    Institute of Scientific and Technical Information of China (English)

    刘建华; 袁剑波; 熊虎; 陈伟

    2008-01-01

    High liquid limit soil generally adopted in expressway embankment construction of southern mountains, which often expresses some characteristics including high moisture content, high porosity ratio, low permeability, high compressibility, certain disintegration, and so on. Spring soil phenomenon and inhomogeneous compaction have effects on the quality of embankment construction, just because the water in soil is difficult to evaporate. Based on the study of reinforcement mechanism for high liquid limit soil, in situ tests for dynamic compaction treatment in Yizhang-Fengtouling expressway embankment were developed. The reliable and economical dynamic compaction treatment methods and the construction technology for large range high liquid limit soil embankment in southern mountains expressway were discussed. In the process, convenient measurement methods were adopted to evaluate the treatment effects. The test results show that the dynamic compaction method has good treatment effects on the local red clay embankment. The embankment compaction degree is improved with compactness coming to 90% around tamping pits and compactness over 95% in tamping pits interior after tamping. The bearing capacity, the physical mechanic-property and the shear strength for soil are obviously improved, which are enhanced with cohesive strength increasing over 10 kPa and compression modulus increasing over 3 MPa.

  5. Utilization of hard rock dust with red clay to produce roof tiles

    Directory of Open Access Journals (Sweden)

    Mst. Shanjida Sultana

    2015-03-01

    Full Text Available Utilization of rock dust to produce roof tiles and its effects on properties of tiles, mixed with red clay collected from Naogaon district of Bangladesh were investigated. After proper characterization of the raw materials, tiles were prepared with different percentages of rock dust (10-50% mixed with clay sintered from 850-1100 °C temperature. Rock dust has been found good for using as fluxing material after XRF study. The samples were tested for different properties such as water absorption, porosity, mechanical strength, linear shrinkage, and bulk density. The strength values have exceeded the minimum standard requirement for roof tiles with low water absorption in most samples. The results obtained made it possible to conclude about the possibility of producing roof tiles incorporating up to 40% of rock dust having better properties (lower water absorption 6.5%, strength value 31.97 MPa fired at 900 °C. Therefore these dust acts as a fluxing agent and reducing the sinteringtemperature of the clay material.

  6. Influence of insecticides flubendiamide and spinosad on biological activities in tropical black and red clay soils.

    Science.gov (United States)

    Mohiddin, G Jaffer; Srinivasulu, M; Subramanyam, K; Madakka, M; Meghana, D; Rangaswamy, V

    2015-02-01

    A laboratory experiment has been conducted to investigate the ecological toxicity of flubendiamide and spinosad at their recommended field rates and higher rates (1.0, 2.5, 5.0, 7.5, 10.0 kg ha(-1)) on cellulase, invertase and amylase in black and red clay soils after 10, 20, 30 and 40-day exposure under controlled conditions in groundnut (Arachis hypogaea L.) soils of Anantapur District, Andhra Pradesh, India. Flubendiamide and spinosad were stimulatory to the activities of cellulase, invertase and amylase at lower concentrations at 10-day interval. The striking stimulation in soil enzyme activities noticed at 2.5 kg ha(-1), persists for 20 days in both soils. Overall, the higher concentrations (5.0-10.0 kg ha(-1)) of flubendiamide, and spinosad were toxic or innocuous to cellulase, invertase and amylase activities, respectively. The results of the present study thus, clearly, indicate that application of the insecticides in cultivation of groundnut, at field application rates improved the activities of cellulase, invertase and amylase in soils.

  7. Leaching of Nutrient Elements in a Red Soil Derived from Quaternary Red Clay

    Institute of Scientific and Technical Information of China (English)

    SHENRENFANG; ZHAOQIGUO

    1998-01-01

    A red soil derived from Quaternary red clay was employed to study nutrient leaching with woil columns repacked in laboratory,The objective was to identify the effects of fertilization practices on leaching patterns and magnitudes of Ca2+,Mg2+,K+,NH4+,and NO3-,The treatments were CK (as a control),CaCO3, CaSO4,MgCO3,Ca(H2PO4)2,urea,KCl,and multiple (a mixture of the above-mentioned fertilizers),The fertilizers were added to the bare surface of the soil columns,and then the columns were leached with 120 mL deionized water daily through peristaltic pumps over a period of 92 days.Leaching processes of NH4+,and NO3- wer e only measured in CK,ured,and multiple treatments which were directly related to N leaching, Results showed that sole application of CaSO4,and Ca(H2PO4)2 scarcely hd any effect on the leching losses of Ca2+,Mg2+,and K+; the application of MgCO3 sthimulated the leaching of Mg2+;the application of CaCO3 promoted the leaching of Ca2+,Mg2+ and K+; urea treatment also promoted the leaching of K+ and NH4+,and NO3- leaching mainly occurred at late stage of leaching process in particular;under KCl treatment,leaching of Ca2+,Mg2+,and K+ was promoted to a large extent;under multiple treatment, leaching of Ca2+,Mg2+,K+,NH4+,and NO3- was all increased and NO3- was mainly leached at the end of leaching process and still had a trend of increase.

  8. Dynamic Strength and Accumulated Plastic Strain Development Laws and Models of the Remolded Red Clay under Long-Term Cyclic Loads: Laboratory Test Results

    Directory of Open Access Journals (Sweden)

    Li Jian

    2015-09-01

    Full Text Available The dynamic strength and accumulated plastic strain are two important parameters for evaluating the dynamic response of soil. As a special clay, the remolded red clay is often used as the high speed railway subgrade filling, but studies on its dynamic characteristics are few. For a thorough analysis of the suitability of the remolded red clay as the subgrade filling, a series of long-term cyclic load triaxial test under different load histories are carried out. Considering the influence of compactness, confining pressure, consolidation ratio, vibration frequency and dynamic load to the remolded red clay dynamic property, the tests obtain the development curves of the dynamic strength and accumulated plastic strain under different test conditions. Then, through curve fitting method, two different hyperbolic models respectively for the dynamic strength and accumulated plastic strain are built, which can match the test datum well. By applying the dynamic strength model, the critical dynamic strength of the remolded red clay are gained. Meanwhile, for providing basic datum and reference for relevant projects, all key parameters for the dynamic strength and accumulated plastic strain of the remolded red clay are given in the paper.

  9. Influence of the insecticides acetamiprid and carbofuran on arylamidase and myrosinase activities in the tropical black and red clay soils.

    Science.gov (United States)

    Mohiddin, G Jaffer; Srinivasulu, M; Maddela, N R; Manjunatha, B; Rangaswamy, V; Koch Kaiser, Alma Rosel; Maisincho Asqui, Jessica Cristina; Darwin Rueda, O

    2015-06-01

    The objective of this study was to determine the effects of two insecticides, namely, acetamiprid and carbofuran on the enzymatic activities of arylamidase (as glucose formed from sinigrin) and myrosinase (as β-naphthylamine formed from L-leucine β-naphthylamide) in the black and red clay soils collected from a fallow groundnut (Arachis hypogaea L.) fields in the Anantapur District, Andhra Pradesh, India. The study was realized within the framework of the laboratory experiments in which the acetamiprid and carbofuran were applied to the soils at different doses (1.0, 2.5, 5.0, 7.5, 10.0 kg ha(-1)). Initially, the physicochechemical properties of the soil samples were analyzed. After 10 days of pesticide application, the soil samples were analyzed for the enzyme activities. Acetamiprid and carbofuran stimulated the arylamidase and myrosinase activities at lower concentrations after 10 days incubation. Striking stimulation in soil enzyme activities was noticed at 2.5 kg ha(-1), persists for 20 days in both the soils. Overall, higher concentrations (5.0-10.0 kg ha(-1)) of acetamiprid and carbofuran were toxic or innocuous to the arylamidase and myrosinase activities. Nevertheless, the outcomes of the present study clearly indicate that the use of these insecticides (at field application rates) in the groundnut fields (black and red clay soils) stimulated the enzyme (arylamidase and myrosinase) activities.

  10. Stable isotope geochemistry of calcrete nodules and septarian concretions in a Quaternary 'red clay' paleovertisol from Hungary.

    Science.gov (United States)

    Bajnóczi, Bernadett; Horváth, Zoltán; Demény, Attila; Mindszenty, Andrea

    2006-12-01

    Calcrete nodules and concretions in unusually large amounts are embedded in the Quaternary clay-rich (Vertisol-type) 'red clay' soil-sedimentary complex at the pediment of the Mátra Mountains (Hungary). Stable isotope signatures were studied in nodules and septarian concretions, uncommon due to their several millimeter sized calcite crystals filling voids and fractures, to reveal their origin. The isotope composition of calcrete covers a wide range: delta18O=-5.9 to-10.4 per thousand and delta13C=-8.9 to-12.3 per thousand (vs. V-PDB). Isotope compositions support pedogenic (sensu stricto) and/or shallow groundwater origin for the calcrete nodules and concretions, the role of 'evolved' (isotopically modified) groundwaters in the formation of secondary carbonate was possibly subordinate. Late-stage, large, Mn-rich euhedral calcite crystals in concretions have the lowest delta13C values, which are interpreted as a result of larger contribution of isotopically light organic carbon due to decomposition of organic matter under reducing conditions. Precipitation of late calcite crystals in concretions occurred in early diagenetic environment after shallow burial of the 'red clay' paleovertisol.

  11. Insights from 20 years of bacterial genome sequencing

    DEFF Research Database (Denmark)

    Land, Miriam; Hauser, Loren; Jun, Se-Ran

    2015-01-01

    the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...... (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident...

  12. A Report on the Impact of Special Education on Minority Students in the Brandywine, Christina, Colonial, and Red Clay Consolidated School Districts in Delaware, 1987.

    Science.gov (United States)

    Matthews, Cherritta L.

    The study evaluated special education services to minority students in four Delaware school districts (Brandywine, Christina, Colonial, and Red Clay). The study identified three major concerns: (1) reduction of the high percentage of minorities in special education, (2) employment of minority professionals in special education, (3) and services to…

  13. An Analysis of Programs and Implementation of Professional Learning Communities in the Red Clay Consolidated School District with Recommendations for Future Implementation

    Science.gov (United States)

    Goodwin, Kenneth L., Jr.

    2012-01-01

    During the 2010-2011 school year, schools throughout the Red Clay Consolidated School District were expected to implement Professional Learning Communities (PLCs); however, little to no guidance was provided to school-level administrators and teacher teams. Not surprisingly, many schools implemented team meetings that were not aligned with…

  14. Marsupial Genome Sequences: Providing Insight into Evolution and Disease

    Directory of Open Access Journals (Sweden)

    Janine E. Deakin

    2012-01-01

    Full Text Available Marsupials (metatherians, with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil, with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. The emergence of a transmissible cancer, which is obliterating the Tasmanian devil population, has increased the importance of obtaining and analysing marsupial genome sequence for understanding such diseases as well as for conservation efforts. In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences.

  15. Insights from twenty years of bacterial genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jun, Se Ran [ORNL; Nookaew, Intawat [ORNL; Leuze, Michael Rex [ORNL; Ahn, Tae-Hyuk [ORNL; Karpinets, Tatiana V [ORNL; Lund, Ole [Technical University of Denmark; Kora, Guruprasad H [ORNL; Wassenaar, Trudy [Molecular Microbiology & Genomics Consultants, Zotzenheim, Germany; Poudel, Suresh [ORNL; Ussery, David W [ORNL

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome

  16. Mechanical and tribological behavior of red clay ceramic tiles coated with fly ash powders by thermal spraying technique.

    Science.gov (United States)

    Peña-Rodríguez, G.; Dulce-Moreno, H.; Daza-Ramírez, J.; Orozco-Hernández, S.; Vargas-Galvis, F.

    2017-01-01

    The mechanical and tribological performance of red clay ceramic tiles uncoated and coated by oxy-fuel thermal spraying process from fly ash powders was evaluated. The ceramic tile substrates were manufactured by uniaxial pressing at 26.17 bar pressure, and sintered at 1100 °C. The coating thickness was determined based on the number of projection-cycles oxyacetylene flame over substrate. Coal fly ash coatings were deposited, with average thickness of 56.18±12.18 μm, 180.42±20.32 μm, and 258.26±25.88μm. The mechanical resistance to bending and wear by abrasion deep, were studied using ISO 10545-4 standards and ISO 10545-6 respectively; adhesion was measured using Elcometer equipment Type III according to ASTM D-4541-02 and the average roughness (Ra) was found according to ASTM standard D7127-13, using the profilometer Mitutoyo SJ 201. The surface morphology presented the heterogeneous molten or semi molten splats with average size of 35.262±3.48 micrometers with good adhesion, justifying increased mechanical resistance to bending by 5%, as well as wear by abrasion deep. These results contribute to the development of ceramic products with added value, to be used in various technological applications.

  17. Some Fertility Characteristics and Fertilizer Requirements of a Newly Reclaimed Upland Red Soil Derived from Quaternary Red Clay

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A series of field experiments from 1990 to 1994 in Yingtan, Jiangxi Province, were conducted on an upland red soil derived from Quaternary red clay which had been reclaimed three years before the experiments, in order to study the fertility characteristics and fertilizer requirements of the newly reclaimed soil. The field experiments included that on nutrient characteristics and fertilizer effect, that on K-supplying potential and K-Mg relationship, that on fertilization rates of K and N, etc. The newly reclaimed upland soil was low in both N and P, and its responses to nitrogen and phosphate application were very significant. The K-supplying potential was also low, so the soil was highly responsive to K fertilizer. The effect of Ca and Mg fertilizers was not so great for the reason that certain amounts of Ca and Mg were incorporated into the soil through application of calcium magnesium phosphate during land leveling before the experiments. Among the four micronutrients, B, Mo, Zn and Cu, B had the greatest effect on the soil. The fertilizer requirements of the soil were in an order of P and N > K > lime and B > Mg > Mo, Zn and Cu. Eight crops tested had different fertilizer-requiring characteristics. Rapeseed was very sensitive to P and B fertilizers. Barely was especially sensitive to P and lime and it also responded to B, Mo, Zn and Cu. And sweet potato was especially sensitive to K.

  18. Magnetic properties of the Tertiary red clay from Gansu Province, China and its paleoclimatic significance

    Institute of Scientific and Technical Information of China (English)

    LIU; Xiuming

    2001-01-01

    [1]Liu, T. S., Loess and the Environment, Beijing: China Ocean Press, 1985, 1-251.[2]Chen, L. X., Zhu, Q. G., Luo, H. B. et al., East Asian Monsoon, Beijing: China Meteorology Press, 1991, 28-61.[3]An, Z. S., Liu, T. S., Lu, Y. C. et al., The long-term palaeomonsoon variation recorded by the loess-palaeosol sequence in central China, Quaternary International, 1990, (7/8): 91-95.[4]Guo, Z. T., Liu, T. S., Fedoroff, N. et al., Shift of the monsoon intensity on the Loess Plateau at ca. 0.85 MaBP, Chinese Science Bulletin, 1993, 38(2): 586-591.[5]Chen, J., An, Z. S., Wang, Y. J. et al., Distributions of Rb and Sr in the Luochuan loess-paleosol sequence of China during the last 800 ka: Implications for paleomonsoon variations, Science in China, Ser. D, 1999, 42(3): 225-232.[6]Chen, J., Wang, Y. J., Ji, J. F. et al., Rb/Sr variations and its climatic stratigraphical significance of a loess-paleosol profile from Luochuan, Shaanxi Province, Quaternary Sciences (in Chinese), 1999, 19(4): 350-356.[7]Guo, Z. T.,Liu, T. S., Fedoroff, N. et al., Climate extremes in loess of China coupled with the strength of deep-water for-mation in the North Atlantic, Global and Planetary Change, 1998, 18: 113-128.[8]Guo, Z. T., Liu, T. S., An, Z. S., Paleosols of the last 0.15 Ma in the Weinan loess section and their paleoclimate signifi-cance, Quaternary Sciences (in Chinese), 1994, 14(3): 256-269.[9]Guo, Z, T,, Fedoroff, N., Liu, T. S., Micromorphology of the loess-paleosol sequence of the last 130 ka in China and pa-leoclimatic event, Science in China (in Chinese), Ser. D, 1996, 26(3): 392-398.[10]Guo, Z., Liu, T., Guiot, J., et al., High frequency pulses of East Asian monsoon climate in the last two glaciations: Link with the North Atlantic, Climate Dynamics, 1996, 12: 701-709.[11]Guo, Z. T., Peng, S. Z., Wei, L. Y. et al., Weathering signals of Millennial-Scale oscillations of the East Asian Summer monsoon over the last 220 ka, Chinese Science

  19. Characterization of non-calcareous 'thin' red clay from south-eastern Brazil: applicability in wall tile manufacture

    Energy Technology Data Exchange (ETDEWEB)

    Sousa, S.J.G.; Holanda, J.N.F., E-mail: sidnei_rjsousa@yahoo.com.br, E-mail: holanda@uenf.br [Grupo de Materiais Ceramicos - LAMAV-CCT, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ (Brazil)

    2012-04-15

    In this work the use of 'thin' red clay from south-eastern Brazil (Campos dos Goytacazes, RJ) as raw material for the manufacture of wall tile was investigated. A wide range of characterization techniques was employed, including X-ray diffraction (XRD), X-ray fluorescence (XRF), scanning electron microscopy (SEM), grain-size analysis, and thermogravimetric analysis. The wall tile body was prepared by the dry process. The tile pieces were uniaxially pressed and fired between 1080 - 1180 deg C using a fast-firing cycle. The following technological properties were determined: linear shrinkage, water absorption, apparent density, and flexural strength. The development of the microstructure was followed by SEM and XRD analyses. It was found that the 'thin' red clay is kaolinitic type containing a substantial amount of quartz. The results also showed that the 'thin' red clay could be used in the manufacture of wall tiles, as they present properties compatible with those specified for class BIII of ISO 13006 standard. (author)

  20. Changes in grain-size and sedimentation rate of the Neogene Red Clay deposits along the Chinese Loess Plateau and implications for the palaeowind system

    Institute of Scientific and Technical Information of China (English)

    WEN Lingjuan; LU Huayu; QIANG Xiaoke

    2005-01-01

    The wind system responsible for transporting dust onto the Chinese Loess Plateau during the late Miocene and Pliocene is still unknown and recent investigations highlight many controversies. This report aims to investigate spatiotemporal changes in grain-size and sedimentation rate of the Neogene Red Clay deposits in north China and to explore palaeoclimatic changes during the late Miocene and Pliocene, in particular the palaeowind system that transported dust. Samples were collected from eight Red Clay sections on the Loess Plateau. Measurement and analysis show that there is a clear southward decrease in the mean grain-size index and in the coarse particle fraction (>20 μm). At Jiaxian site on the northern Loess Plateau, the average mean grain-size is around 20 μm, while at Lantian site in the south, the mean is around 9 μm. The coarse particle fraction >20 μm makes up 24.4% and 5.6%, at the two sites respectively. This distinct diversity of grain-size in the aeolian Red Clay deposit between the north and south indicate that the palaeodust was transported mainly by northerly low-level winds. The grain-size variations in the Red Clay deposits can also be divided into three stages (the lower, the middle and the upper interval): grain-size of the lower stage is significantly coarser than that of the middle stage, but finer than that of the upper stage. As a consequence, the intensity of palaeowind and desiccation of the dust source region during the late Miocene and Pliocene can be divided into three stages: 6.2-5.4 Ma, 5.4-3.5 Ma and 3.5-2.6 Ma. Strength of the palaeowind during the middle stage (5.4-3.5 Ma) is weaker than that of the previous and subsequent stages and the intensity of palaeowind during the latest stage (3.5-2.6 Ma) is stronger than that of the early time (6.2-5.4 Ma). Variations in the sedimentation rate of the Red Clay deposit can also be divided into three stages: the earlier, the middle and the later interval. The sedimentation rate of the

  1. Evolutionary insights from suffix array-based genome sequence analysis

    Indian Academy of Sciences (India)

    Anindya Poddar; Nagasuma Chandra; Madhavi Ganapathiraju; K Sekar; Judith Klein-Seetharaman; Raj Reddy; N Balakrishnan

    2007-08-01

    Gene and protein sequence analyses, central components of studies in modern biology are easily amenable to string matching and pattern recognition algorithms. The growing need of analysing whole genome sequences more efficiently and thoroughly, has led to the emergence of new computational methods. Suffix trees and suffix arrays are data structures, well known in many other areas and are highly suited for sequence analysis too. Here we report an improvement to the design of construction of suffix arrays. Enhancement in versatility and scalability, enabled by this approach, is demonstrated through the use of real-life examples. The scalability of the algorithm to whole genomes renders it suitable to address many biologically interesting problems. One example is the evolutionary insight gained by analysing unigrams, bi-grams and higher n-grams, indicating that the genetic code has a direct influence on the overall composition of the genome. Further, different proteomes have been analysed for the coverage of the possible peptide space, which indicate that as much as a quarter of the total space at the tetra-peptide level is left un-sampled in prokaryotic organisms, although almost all tri-peptides can be seen in one protein or another in a proteome. Besides, distinct patterns begin to emerge for the counts of particular tetra and higher peptides, indicative of a ‘meaning’ for tetra and higher n-grams. The toolkit has also been used to demonstrate the usefulness of identifying repeats in whole proteomes efficiently. As an example, 16 members of one COG, coded by the genome of Mycobacterium tuberculosis H37Rv have been found to contain a repeating sequence of 300 amino acids.

  2. Assessment of stream quality using biological indices at selected sites in the Red Clay and White Clay Creek basins, Chester County, Pennsylvania, 1981-97

    Science.gov (United States)

    Reif, Andrew G.

    2002-01-01

    In 1970, the Chester County Water Resources Authority (Pennsylvania) and the U.S. Geological Survey (USGS) established a longterm water-quality network with the goal of assessing the quality of streams in the county and understanding stream changes in response to urbanization using benthic-macroinvertebrate data (Lium, 1977). This database represents one of the longest continuous water-quality data sets in the country. Benthic macroinvertebrates are aquatic insects, such as mayflies, caddisflies, riffle beetles, and midges, and other invertebrates that live on the stream bottom. Benthic macroinvertebrates are useful in evaluating stream quality because their habitat preference and low motility cause them to be affected directly by substances that enter the aquatic system. By evaluating the diversity and community structure of benthic-macroinvertebrate populations, a determination of stream quality can be made. Between 1981 and 1997, the water-quality network consisted of 43 sites in 5 major basins in Chester County—Delaware, Schuylkill, Brandywine, Big Elk and Octoraro, and Red and White Clay. Benthicmacroinvertebrate, water-chemistry, and habitat data were collected each year in October or November during base-flow conditions (Reif, 1999; 2000). Using these data, Reif (2002) evaluates the overall water-quality condition of Chester County streams. This Fact Sheet summarizes the key findings from Reif (2002) for streams in the Red Clay and White Clay Creek Basins. These streams include East Branch Red Clay Creek (site 26), West Branch Red Clay Creek (site 27), East Branch White Clay Creek (site 28), the Middle Branch White Clay Creek (site 29), and West Branch White Clay Creek (site 30) (fig. 1). This summary includes an analysis of stream conditions on the basis of benthic-macroinvertebrate samples and an analysis of trends in stream conditions for the 17-year study period.

  3. Tracing multiple resedimentation on an isolated karstified plateau: The bauxite-bearing Miocene red clay of the Southern Bakony Mountains, Hungary

    Science.gov (United States)

    Kelemen, Péter; Dunkl, István; Csillag, Gábor; Mindszenty, Andrea; von Eynatten, Hilmar; Józsa, Sándor

    2017-08-01

    The Vöröstó (= Red Lake) Formation, located in the Southern Bakony Mountains and the Balaton Highlands (Hungary), is a red, clayey continental assemblage containing hard, up to fist-sized bauxite pebbles, occurring in a large apparent stratigraphic gap between underlying karstified Triassic carbonates and mid' Miocene to Quaternary cover. The origin and the exact stratigraphic position of the assemblage have been controversial for a long time. In this study, petrographic observations on the bauxite pebbles revealed common features with Cretaceous bauxite deposits known in the region, whereas heavy mineral composition of the red clay matrix is similar to those known from the Eocene bauxite horizon of the region. Single grain zircon U-Pb ages obtained from the bauxite pebbles and their red clayey matrix show similar late Archean to Jurassic age components. Additionally, Cenozoic U-Pb ages are well represented in the mostly euhedral zircon crystals separated from the red clays, whereas this volcanogenic contribution completely missing from the bauxite pebbles. SEM morphology and related EDX chemical analysis of clay minerals indicate polygenetic, detrital origin for the red clays. The main source material of the bauxite bearing Vöröstó Formation is most probably local Cretaceous and Eocene bauxite deposits exposed during the middle-late Miocene. These tropical weathering products were partly decomposed and degraded, but dilution by siliciclastic contribution is negligible. We suggest a transport mechanism dominated by local redeposition of mostly pelitic and allitic material through seasonal muddy debris flows within a karstic landscape.

  4. Simulation of streamflow and water quality in the Red Clay Creek subbasin of the Christina River Basin, Pennsylvania and Delaware, 1994-98

    Science.gov (United States)

    Senior, Lisa A.; Koerkle, Edward H.

    2003-01-01

    (mi2) in Pennsylvania and Delaware and includes the major subbasins of Red Clay Creek, White Clay Creek, Brandywine Creek, and Christina River. The Red Clay Creek is the smallest of the subbasins and drains an area of 54 mi2. Streams in the Christina River Basin are used for recreation, drinking-water supply, and to support aquatic life. Water quality in some parts of the Christina River Basin is impaired and does not support designated uses of the stream. A multi-agency, waterquality management strategy included a modeling component to evaluate the effects of point and nonpointsource contributions of nutrients and suspended sediment on stream water quality. To assist in nonpointsource evaluation, four independent models, one for each of the four main subbasins of the Christina River Basin, were developed and calibrated using the model code Hydrological Simulation Program?Fortran (HSPF). Water-quality data for model calibration were collected in each of the four main subbasins and in smaller subbasins predominantly covered by one land use following a nonpoint-source monitoring plan. Under this plan, stormflow and base-flow samples were collected during 1998 at 1 site in the Red Clay Creek subbasin and at 10 sites elsewhere in the Christina River Basin. The HSPF model for the Red Clay Creek subbasin simulates streamflow, suspended sediment, and the nutrients, nitrogen and phosphorus. In addition, the model simulates water temperature, dissolved oxygen, biochemical oxygen demand, and plankton as secondary objectives needed to support the sediment and nutrient simulations. For the model, the basin was subdivided into nine reaches draining areas that ranged from 1.7 to 10 mi2. One of the reaches contains a regulated reservoir. Ten different pervious land uses and two impervious land uses were selected for simulation. Land-use areas were determined from 1995 land-use data. The predominant land uses in the Red Clay Creek subbasin are agricultural, forested, residential

  5. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation r...

  6. Development of new ceramic materials from the waste of serpentinite and red clay; Desenvolvimento de novos materiais ceramicos a partir de residuo de serpentinito e argila vermelha

    Energy Technology Data Exchange (ETDEWEB)

    Presotto, P., E-mail: petula.presotto@gmail.com [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Mymrine, V. [Universidade Tecnologica Federal do Parana (UFTPR), Curitiba, PR (Brazil)

    2012-07-01

    The objective of this work is to develop new ceramic materials using serpentine and glass waste and clay red. The raw materials were characterized through morphological, granulometric, mineralogical and chemical analysis. Six formulations have been developed based on the serpentine and red clay, which three of the six compositions have been adjusted with the addition of residual glass. The ceramic bodies were formed by uniaxial pressing and subjected to burn in an electric oven at temperatures of 1100 ° C, 1200 ° C, 1250 ° C and 1300 ° C. The ceramic samples obtained this way were characterized according to their physical properties (specific mass and linear retraction) and the mechanical (three points bending strength). The final properties varied according to the proportions of raw materials and firing temperature. In general, the different formulations fit the standards for traditional ceramics such as tiles and ceramic blocks. (author)

  7. Expression profiling and comparative sequence derived insights into lipid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Callow, Matthew J.; Rubin, Edward M.

    2001-12-19

    Expression profiling and genomic DNA sequence comparisons are increasingly being applied to the identification and analysis of the genes involved in lipid metabolism. Not only has genome-wide expression profiling aided in the identification of novel genes involved in important processes in lipid metabolism such as sterol efflux, but the utilization of information from these studies has added to our understanding of the regulation of pathways participating in the process. Coupled with these gene expression studies, cross species comparison, searching for sequences conserved through evolution, has proven to be a powerful tool to identify important non-coding regulatory sequences as well as the discovery of novel genes relevant to lipid biology. An example of the value of this approach was the recent chance discovery of a new apolipoprotein gene (apo AV) that has dramatic effects upon triglyceride metabolism in mice and humans.

  8. Developing an inverted Barrovian sequence; insights from monazite petrochronology

    Science.gov (United States)

    Mottram, Catherine M.; Warren, Clare J.; Regis, Daniele; Roberts, Nick M. W.; Harris, Nigel B. W.; Argles, Tom W.; Parrish, Randall R.

    2014-10-01

    In the Himalayan region of Sikkim, the well-developed inverted metamorphic sequence of the Main Central Thrust (MCT) zone is folded, thus exposing several transects through the structure that reached similar metamorphic grades at different times. In-situ LA-ICP-MS U-Th-Pb monazite ages, linked to pressure-temperature conditions via trace-element reaction fingerprints, allow key aspects of the evolution of the thrust zone to be understood for the first time. The ages show that peak metamorphic conditions were reached earliest in the structurally highest part of the inverted metamorphic sequence, in the Greater Himalayan Sequence (GHS) in the hanging wall of the MCT. Monazite in this unit grew over a prolonged period between ∼37 and 16 Ma in the southerly leading-edge of the thrust zone and between ∼37 and 14.5 Ma in the northern rear-edge of the thrust zone, at peak metamorphic conditions of ∼790 °C and 10 kbar. Monazite ages in Lesser Himalayan Sequence (LHS) footwall rocks show that identical metamorphic conditions were reached ∼4-6 Ma apart along the ∼60 km separating samples along the MCT transport direction. Upper LHS footwall rocks reached peak metamorphic conditions of ∼655 °C and 9 kbar between ∼21 and 16 Ma in the more southerly-exposed transect and ∼14.5-12 Ma in the northern transect. Similarly, lower LHS footwall rocks reached peak metamorphic conditions of ∼580 °C and 8.5 kbar at ∼16 Ma in the south, and 9-10 Ma in the north. In the southern transect, the timing of partial melting in the GHS hanging wall (∼23-19.5 Ma) overlaps with the timing of prograde metamorphism (∼21 Ma) in the LHS footwall, confirming that the hanging wall may have provided the heat necessary for the metamorphism of the footwall. Overall, the data provide robust evidence for progressively downwards-penetrating deformation and accretion of original LHS footwall material to the GHS hanging wall over a period of ∼5 Ma. These processes appear to have

  9. Structural insight into the sequence dependence of nucleosome positioning.

    Science.gov (United States)

    Wu, Bin; Mohideen, Kareem; Vasudevan, Dileep; Davey, Curt A

    2010-03-14

    Nucleosome positioning displays sequence dependency and contributes to genomic regulation in a site-specific manner. We solved the structures of nucleosome core particle composed of strong positioning TTTAA elements flanking the nucleosome center. The positioning strength of the super flexible TA dinucleotide is consistent with its observed central location within minor groove inward regions, where it can contribute maximally to energetically challenging minor groove bending, kinking and compression. The marked preference for TTTAA and positioning power of the site 1.5 double helix turns from the nucleosome center relates to a unique histone protein motif at this location, which enforces a sustained, extremely narrow minor groove via a hydrophobic "sugar clamp." Our analysis sheds light on the basis of nucleosome positioning and indicates that the histone octamer has evolved not to fully minimize sequence discrimination in DNA binding.

  10. Early insights into the genome sequence of Uromyces fabae

    Directory of Open Access Journals (Sweden)

    Tobias eLink

    2014-10-01

    Full Text Available Uromyces fabae is a major pathogen of broad bean, Vicia faba. U. fabae has served as a model among rust fungi to elucidate the development of infection structures, expression and secretion of cell wall degrading enzymes and gene expression. Using U. fabae, enormous progress was made regarding nutrient uptake and metabolism and in the search for secreted proteins and effectors. Here, we present results from a genome survey of U. fabae. Paired end Illumina sequencing provided 53 Gb of data. An assembly gave 59,735 scaffolds with a total length of 216 Mb. K-mer analysis estimated the genome size to be 329 Mb. Of a representative set of 23,153 predicted proteins we could annotate 10,209, and predict 599 secreted proteins. Clustering of the protein set indicates families of highly likely effectors. We also found new homologs of RTP1p, a prototype rust effector. The U. fabae genome will be an important resource for comparative analyses with U. appendiculatus and P. pachyrhizi and provide information regarding the phylogenetic relationship of the genus Uromyces with respect to other rust fungi already sequenced, namely Puccinia graminis f. sp. tritici, P. striiformis f. sp. tritici, Melampsora lini, and Melampsora larici-populina.

  11. DISSECTING THE QUASAR MAIN SEQUENCE: INSIGHT FROM HOST GALAXY PROPERTIES

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jiayi [Tsinghua Center for Astrophysics, Department of Physics, Tsinghua University, Beijing 100084 (China); Shen, Yue [Carnegie Observatories, 813 Santa Barbara Street, Pasadena, CA 91101 (United States)

    2015-05-01

    The diverse properties of broad-line quasars appear to follow a well-defined main sequence along which the optical Fe ii strength increases. It has been suggested that this sequence is mainly driven by the Eddington ratio (L/L{sub Edd}) of the black hole (BH) accretion. Shen and Ho demonstrated with quasar clustering analysis that the average BH mass decreases with increasing Fe ii strength when quasar luminosity is fixed, consistent with this suggestion. Here we perform an independent test by measuring the stellar velocity dispersion σ{sub *} (hence, the BH mass via the M–σ{sub *} relation) from decomposed host spectra in low-redshift Sloan Digital Sky Survey quasars. We found that at fixed quasar luminosity, σ{sub *} systematically decreases with increasing Fe ii strength, confirming that the Eddington ratio increases with Fe ii strength. We also found that at fixed luminosity and Fe ii strength, there is little dependence of σ{sub *} on the broad Hβ FWHM. These new results reinforce the framework that the Eddington ratio and orientation govern most of the diversity seen in broad-line quasar properties.

  12. Dissecting the Quasar Main Sequence: Insight from Host Galaxy Properties

    Science.gov (United States)

    Sun, Jiayi; Shen, Yue

    2015-05-01

    The diverse properties of broad-line quasars appear to follow a well-defined main sequence along which the optical Fe ii strength increases. It has been suggested that this sequence is mainly driven by the Eddington ratio (L/LEdd) of the black hole (BH) accretion. Shen & Ho demonstrated with quasar clustering analysis that the average BH mass decreases with increasing Fe ii strength when quasar luminosity is fixed, consistent with this suggestion. Here we perform an independent test by measuring the stellar velocity dispersion σ* (hence, the BH mass via the M-σ* relation) from decomposed host spectra in low-redshift Sloan Digital Sky Survey quasars. We found that at fixed quasar luminosity, σ* systematically decreases with increasing Fe ii strength, confirming that the Eddington ratio increases with Fe ii strength. We also found that at fixed luminosity and Fe ii strength, there is little dependence of σ* on the broad Hβ FWHM. These new results reinforce the framework that the Eddington ratio and orientation govern most of the diversity seen in broad-line quasar properties.

  13. Dissecting the quasar main sequence: insight from host galaxy properties

    CERN Document Server

    Sun, Jiayi

    2015-01-01

    The diverse properties of broad-line quasars appear to follow a well-defined main sequence along which the optical FeII strength increases. It has been suggested that this sequence is mainly driven by the Eddington ratio (L/L_Edd) of the black hole (BH) accretion. Shen & Ho demonstrated with quasar clustering analysis that the average BH mass decreases with increasing FeII strength when quasar luminosity is fixed, consistent with this suggestion. Here we perform an independent test by measuring the stellar velocity dispersion sigma* (hence the BH mass via the M-sigma* relation) from decomposed host spectra in low-redshift Sloan Digital Sky Survey quasars. We found that at fixed quasar luminosity, sigma* systematically decreases with increasing FeII strength, confirming that Eddington ratio increases with FeII strength. We also found that at fixed luminosity and FeII strength, there is little dependence of sigma* on the broad Hbeta FWHM. These new results reinforce the framework put forward by Shen & H...

  14. Sequencing and Analysis of a Genomic Fragment Provide an Insight into the Dunaliella viridis Genomic Sequence

    Institute of Scientific and Technical Information of China (English)

    Xiao-Ming SUN; Yuan-Ping TANG; Xiang-Zong MENG; Wen-Wen ZHANG; Shan LI; Zhi-Rui DENG; Zheng-Kai XU; Ren-Tao SONG

    2006-01-01

    Dunaliella is a genus of wall-less unicellular eukaryotic green alga. Its exceptional resistances to salt and various other stresses have made it an ideal model for stress tolerance study. However, very little is known about its genome and genomic sequences. In this study, we sequenced and analyzed a 29,268 bp genomic fragment from Dunaliella viridis. The fragment showed low sequence homology to the GenBank database. At the nucleotide level, only a segment with significant sequence homology to 18S rRNA was found. The fragment contained six putative genes, but only one gene showed significant homology at the protein level to GenBank database. The average GC content of this sequence was 51.1%, which was much lower than that of close related green algae Chlamydomonas (65.7%). Significant segmental duplications were found within this fragment. The duplicated sequences accounted for about 35.7% of the entire region. Large amounts of simple sequence repeats (microsatellites) were found, with strong bias towards (AC)n type (76%). Analysis of other Dunaliella genomic sequences in the GenBank database (total 25,749 bp) was in agreement with these findings. These sequence features made it difficult to sequence Dunaliella genomic sequences. Further investigation should be made to reveal the biological significance of these unique sequence features.

  15. Geohydrology and simulation of ground-water flow in the Red Clay Creek Basin, Chester County, Pennsylvania, and New Castle County, Delaware

    Science.gov (United States)

    Vogel, K.L.; Reif, A.G.

    1993-01-01

    The 54-square-mile Red Clay Creek Basin, located in the lower Delaware River Basin, is underlain primarily by metamorphic rocks that range from Precambrian to Lower Paleozoic in age. Ground water flows through secondary openings in fractured crystalline rock and through primary openings below the water table in the overlying saprolite. Secondary porosity and permeability vary with hydrogeologic unit, topographic setting, and depth. Thirty-nine percent of the water-bearing zones are encountered within 100 feet of the land surface, and 79 percent are within 200 feet. The fractured crystalline rock and overlying saprolite act as a single aquifer under unconfined conditions. The water table is a subdued replica of the land surface. Local ground-water flow systems predominate in the basin, and natural ground-water discharge is to streams, comprising 62 to 71 percent of streamflow. Water budgets for 1988-90 for the 45-square-mile effective drainage area above the Woodale, Del., streamflow-measurement station show that annual precipitation ranged from 43.59 to 59.14 inches and averaged 49.81 inches, annual streamflow ranged from 15.35 to 26.33 inches and averaged 20.24 inches, and annual evapotranspiration ranged from 27.87 to 30.43 inches and averaged 28.98 inches. The crystalline rocks of the Red Clay Creek Basin were simulated two-dimensionally as a single aquifer under unconfined conditions. The model was calibrated for short-term steady-state conditions on November 2, 1990. Recharge was 8.32 inches per year. Values of aquifer hydraulic conductivity in hillside topographic settings ranged from 0.07 to 2.60 feet per day. Values of streambed hydraulic conductivity ranged from 0.08 to 26.0 feet per day. Prior to simulations where ground-water development was increased, the calibrated steady-state model was modified to approximate long-term average conditions in the basin. Base flow of 11.98 inches per year and a ground-water evapotranspiration rate of 2.17 inches per

  16. 红粘土边坡降雨冲刷试验研究%Rainfall Erosion Test on Red Clay Slope

    Institute of Scientific and Technical Information of China (English)

    陈开圣

    2015-01-01

    红粘土边坡冲刷破坏的研究对工程设计和水土保持有着重要意义。以红粘土边坡为研究对象,进行了室内边坡冲刷模型试验,对边坡的冲刷破坏过程进行了全程观测,同时对降雨过程中边坡土体的含水率湿润锋面、孔隙水压力、坡体位移及滑动面破坏特征进行了监测,研究结果表明:从坡顶到坡脚水流侵蚀能力呈递增趋势,坡脚处的侵蚀破坏最为严重。整个降雨过程中未见明显的滑动面,验证了降雨条件下红粘土边坡的破坏和其它土类不同。%Research on rainfall erosion of red clay slope is of great significance to engineering de-sign and soil conservation.In this paper red clay slope was taken as research object,model test of rainfall erosion was done in laboratory,whole erosion process of the slope was observed,and the moisture in soil mass was monitored during the test.From the test result it was found the infiltration area at toe of the slope was larger than other positions,degree of erosion there also was the most serious.The paper analyzed water content,the moist frontal edge,power water pressure,slope displacement and sliding surface during the rainfall.The result was shown that the erosion capacity of water flow was increasing from top to toe of the slope,the degree of erosion at toe of the slope was the most serious.The clear sliding surface has not been taken place during the rainfall,which is not different from its clay slope.

  17. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

    Science.gov (United States)

    2010-01-01

    Background In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past. Results Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae) and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position. Conclusions Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a fully resolved plastid tree of

  18. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences

    Directory of Open Access Journals (Sweden)

    Heubl Günther

    2010-11-01

    Full Text Available Abstract Background In the large angiosperm order Lamiales, a diverse array of highly specialized life strategies such as carnivory, parasitism, epiphytism, and desiccation tolerance occur, and some lineages possess drastically accelerated DNA substitutional rates or miniaturized genomes. However, understanding the evolution of these phenomena in the order, and clarifying borders of and relationships among lamialean families, has been hindered by largely unresolved trees in the past. Results Our analysis of the rapidly evolving trnK/matK, trnL-F and rps16 chloroplast regions enabled us to infer more precise phylogenetic hypotheses for the Lamiales. Relationships among the nine first-branching families in the Lamiales tree are now resolved with very strong support. Subsequent to Plocospermataceae, a clade consisting of Carlemanniaceae plus Oleaceae branches, followed by Tetrachondraceae and a newly inferred clade composed of Gesneriaceae plus Calceolariaceae, which is also supported by morphological characters. Plantaginaceae (incl. Gratioleae and Scrophulariaceae are well separated in the backbone grade; Lamiaceae and Verbenaceae appear in distant clades, while the recently described Linderniaceae are confirmed to be monophyletic and in an isolated position. Conclusions Confidence about deep nodes of the Lamiales tree is an important step towards understanding the evolutionary diversification of a major clade of flowering plants. The degree of resolution obtained here now provides a first opportunity to discuss the evolution of morphological and biochemical traits in Lamiales. The multiple independent evolution of the carnivorous syndrome, once in Lentibulariaceae and a second time in Byblidaceae, is strongly supported by all analyses and topological tests. The evolution of selected morphological characters such as flower symmetry is discussed. The addition of further sequence data from introns and spacers holds promise to eventually obtain a

  19. Insights into a dinoflagellate genome through expressed sequence tag analysis

    Directory of Open Access Journals (Sweden)

    Bonaldo Maria F

    2005-05-01

    Full Text Available Abstract Background Dinoflagellates are important marine primary producers and grazers and cause toxic "red tides". These taxa are characterized by many unique features such as immense genomes, the absence of nucleosomes, and photosynthetic organelles (plastids that have been gained and lost multiple times. We generated EST sequences from non-normalized and normalized cDNA libraries from a culture of the toxic species Alexandrium tamarense to elucidate dinoflagellate evolution. Previous analyses of these data have clarified plastid origin and here we study the gene content, annotate the ESTs, and analyze the genes that are putatively involved in DNA packaging. Results Approximately 20% of the 6,723 unique (11,171 total 3'-reads ESTs data could be annotated using Blast searches against GenBank. Several putative dinoflagellate-specific mRNAs were identified, including one novel plastid protein. Dinoflagellate genes, similar to other eukaryotes, have a high GC-content that is reflected in the amino acid codon usage. Highly represented transcripts include histone-like (HLP and luciferin binding proteins and several genes occur in families that encode nearly identical proteins. We also identified rare transcripts encoding a predicted protein highly similar to histone H2A.X. We speculate this histone may be retained for its role in DNA double-strand break repair. Conclusion This is the most extensive collection to date of ESTs from a toxic dinoflagellate. These data will be instrumental to future research to understand the unique and complex cell biology of these organisms and for potentially identifying the genes involved in toxin production.

  20. Application of SPSS Software in Statistic Analysis of Property Index in Red Clay%SPSS软件在红粘土性质指标统计分析中的应用

    Institute of Scientific and Technical Information of China (English)

    易庆波; 廖义玲; 康长平; 黄颖光; 杨昌金

    2011-01-01

    By applying the SPSS software, combining the test data of red clay in Guiyang.the physical and mechanical properties and index characteristics are statistics analyzed descriptively, and the confidence interval of average value of each index is statistic analyzed exploratorily. The property index of red clay is classified by using hierarchical clustering method, and the relationship of each kind of index is seeked. At last, applying the drawing function of SPSS software, the location plan on the plasticity chart of red clay in Guiyang is drawn, and the feature is searched. The statistic analysis results are conform to the actual results, and it offers the reference for engineering practice in the area, and it also finds new method for the statistic analysis of the physical and mechanical property index in red clay.%应用SPSS软件,结合贵阳市红粘土的测试数据,描述性统计分析其物理力学性质指标特征,探索性统计各个指标的平均值置信区间.用系统聚类法对红粘土的性质指标进行分类,并探求每类内各指标的相关关系.最后应用SPSS软件的制图功能,绘制贵阳市红粘土在塑性图上的位置图,并寻找其特点.统计分析结果符合实际,为该地区的工程实践提供参考,也为统计分析红粘土的物理力学性质指标找到了新的方法.

  1. Paleoenvironments indicated by the fossil mammalian assemblages from red clay-loess sequence in the Chinese Loess Plateau since 8.0 Ma B.P.

    Institute of Scientific and Technical Information of China (English)

    XUE; Xiangxu; ZHANG; Yunxiang; YUE; Leping

    2006-01-01

    Information from eleven profiles of eolian earthy red silty clay and loess of the middle of the Late Miocene to Holocene age have been studied and correlated. A complete summary profile with projected isotopic ages and fossil-bearing beds has been assembled. The profile is subdivided into 12 stratigraphic units proceeding from the lower (older) to the upper (younger) one. The character of mammalian assemblages contained in each unit was analyzed and the corresponding paleo-climatic environments were deduced. The environmental character of each period and the change from the middle of the Late Miocene at about 8.0 Ma B.P. up to the Holocene progressed from the hot semiarid and semi-moist, warmer-moist, warm-moister of the Late Miocene. To slightly less warm moist, cool-dry, slight-warmer-moister of the Pliocene; later the cool to cold dry periods alternated frequently with the mild semiarid and semi-moist periods of the Quaternary. Vegetation progressed from the grasslands with sparse woods, wooded shrub-grasslands and subtropical forest-grasslands of the Late Miocene age to sparse grasslands and dry grasslands of the Pliocene; and to sparse grasslands, dry grasslands and tundras of the Quaternary. The climate changes in the Neogene were of low-amplitute in a generally warm-humid background. Those of the Quaternary were of higher amplitude with a longer phase. Cool or cold dry and slightly warm semiarid and semi-moist climates alternated on a generally cool-dry background. The tendency since the start of the Quaternary was the change to more northern and western shift in the Loess Plateau, with progressively cooler and dryer conditions. The dramatic uplift of the Qinghai-Xizang (Tibet) Plateau and the forming and expansion of the Arctic ice sheet might be the main reasons of the more pronounced changes in the Quaternary.

  2. 宣城第四纪红色粘土剖面的发育特征%CHARACTERISTICS OF DEVELOPMENT OF QUATERNARY RED CLAY IN XUANCHENG, ANHUI PROVINCE

    Institute of Scientific and Technical Information of China (English)

    刘良梧; 龚子同

    2000-01-01

    A section of Quaternary red clay, located in Xuancheng, Anhui province, isrecognized a typical and good one for the study of red paleosols in the southem partof China. It was divided in earlier studies into 14 layers (7 formations) except a gravelformation in the bottom. Each formation consists of a "red layer" ("red paleosol") andtmderlying "brown-yellow layer"("deposit"). To elucidate its characteristics of developm-ent, main chemical and physical properties for 14 layers of the section were analyzed. The results indicated that the silica content in each "red layer" was not always lessthan that in the underlying "brown-yellow layer", and the contents of aluminum andclay in each of the "red paleosols" were not more than those in the corresponding"sedimentary layer", respectively. In the same way, other research data also hadanalogous phenomena. Based on the indexes of weathering and soil formation, includingsilica-aluminum milo, indexes of weathering and leaching, cation exchange capacity,base saturation, as well as the clay content, we conclude that there were no regularcycles between soil formation of "red layer" and deposition of "brown-yellow layer" inthe section. In fact, each layer of the "red paleosols" didn′t develop from the underlying"brown-yellow sedimentary layer". Each of the 14 layers within the profile only tocertain extent showed its difference of deposition and soil formation. Moreover,pedogenesis was sometimes weaker, sometimes stronger than the sedimentation. On thebasis of these characteristics, the authors think that these are buried red paleosols,which consist of uniform red soil, iron-manganese illuvial, plinthiilc horizons, andoverlain by a yelloW-brown horizon derived from the Xiashu Loess.%宣城第四纪红色粘土14层土体硅铝率、风化淋溶系数,以及阳离子交换量、盐基饱和 度和粘粒含量等风化、成土作用指标表明,该剖面各层次之间仅显示出一定程度沉积作用和成土作用的差

  3. Sequencing of Bacterial Genomes: Principles and Insights into Pathogenesis and Development of Antibiotics

    Directory of Open Access Journals (Sweden)

    Eric S. Donkor

    2013-10-01

    Full Text Available The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics.

  4. Ground-water quality and its relation to hydrogeology, land use, and surface-water quality in the Red Clay Creek basin, Piedmont Physiographic Province, Pennsylvania and Delaware

    Science.gov (United States)

    Senior, Lisa A.

    1996-01-01

    The Red Clay Creek Basin in the Piedmont Physiographic Province of Pennsylvania and Delaware is a 54-square-mile area underlain by a structurally complex assemblage of fractured metamorphosed sedimentary and igneous rocks that form a water-table aquifer. Ground-water-flow systems generally are local, and ground water discharges to streams. Both ground water and surface water in the basin are used for drinking-water supply. Ground-water quality and the relation between ground-water quality and hydrogeologic and land-use factors were assessed in 1993 in bedrock aquifers of the basin. A total of 82 wells were sampled from July to November 1993 using a stratified random sampling scheme that included 8 hydrogeologic and 4 land-use categories to distribute the samples evenly over the area of the basin. The eight hydrogeologic units were determined by formation or lithology. The land-use categories were (1) forested, open, and undeveloped; (2) agricultural; (3) residential; and (4) industrial and commercial. Well-water samples were analyzed for major and minor ions, nutrients, volatile organic compounds (VOC's), pesticides, polychlorinated biphenyl compounds (PCB's), and radon-222. Concentrations of some constituents exceeded maximum contaminant levels (MCL) or secondary maximum contaminant levels (SMCL) established by the U.S. Environmental Protection Agency for drinking water. Concentrations of nitrate were greater than the MCL of 10 mg/L (milligrams per liter) as nitrogen (N) in water from 11 (13 percent) of 82 wells sampled; the maximum concentration was 38 mg/L as N. Water from only 1 of 82 wells sampled contained VOC's or pesticides that exceeded a MCL; water from that well contained 3 mg/L chlordane and 1 mg/L of PCB's. Constituents or properties of well-water samples that exceeded SMCL's included iron, manganese, dissolved solids, pH, and corrosivity. Water from 70 (85 percent) of the 82 wells sampled contained radon-222 activities greater than the proposed MCL of

  5. Ground-water quality and its relation to hydrogeology, land use, and surface-water quality in the Red Clay Creek basin, Piedmont Physiographic Province, Pennsylvania and Delaware

    Science.gov (United States)

    Senior, Lisa A.

    1996-01-01

    The Red Clay Creek Basin in the Piedmont Physiographic Province of Pennsylvania and Delaware is a 54-square-mile area underlain by a structurally complex assemblage of fractured metamorphosed sedimentary and igneous rocks that form a water-table aquifer. Ground-water-flow systems generally are local, and ground water discharges to streams. Both ground water and surface water in the basin are used for drinking-water supply. Ground-water quality and the relation between ground-water quality and hydrogeologic and land-use factors were assessed in 1993 in bedrock aquifers of the basin. A total of 82 wells were sampled from July to November 1993 using a stratified random sampling scheme that included 8 hydrogeologic and 4 land-use categories to distribute the samples evenly over the area of the basin. The eight hydrogeologic units were determined by formation or lithology. The land-use categories were (1) forested, open, and undeveloped; (2) agricultural; (3) residential; and (4) industrial and commercial. Well-water samples were analyzed for major and minor ions, nutrients, volatile organic compounds (VOC's), pesticides, polychlorinated biphenyl compounds (PCB's), and radon-222. Concentrations of some constituents exceeded maximum contaminant levels (MCL) or secondary maximum contaminant levels (SMCL) established by the U.S. Environmental Protection Agency for drinking water. Concentrations of nitrate were greater than the MCL of 10 mg/L (milligrams per liter) as nitrogen (N) in water from 11 (13 percent) of 82 wells sampled; the maximum concentration was 38 mg/L as N. Water from only 1 of 82 wells sampled contained VOC's or pesticides that exceeded a MCL; water from that well contained 3 mg/L chlordane and 1 mg/L of PCB's. Constituents or properties of well-water samples that exceeded SMCL's included iron, manganese, dissolved solids, pH, and corrosivity. Water from 70 (85 percent) of the 82 wells sampled contained radon-222 activities greater than the proposed MCL of

  6. 基于 ABAQUS 的红黏土地基排水固结沉降分析%Analysis on Drainage Consolidation Settlement of Red Clay Foundation by Using ABAQUS

    Institute of Scientific and Technical Information of China (English)

    赵蕾; 陈筠; 邬忠虎; 刘磊磊

    2015-01-01

    针对红黏土地区地基排水固结过程的复杂性,对红黏土地基排水固结沉降进行数值分析。采用大型通用有限元分析软件 ABAQUS /Standard 中的固结计算模块 Soils 和自带的修正剑桥模型,以某铝厂的改造工程项目为算例,对红黏土地基中的沉降随时间的变化规律、孔隙水压力消散规律、孔隙比随深度的非线性分布以及土体的有效应力增长进行了研究。研究表明:计算结果与土力学规律吻合,能准确反映红黏土地基固结沉降的实际情况,可为红黏土地基上的建(构)物改造工程地基处理和工程设计提供参考。%Due to the complexity of drainage consolidation of red clay foundation,we simulated and analyzed the consolidation settlement by using the consolidation calculation module Soils and modified Cambridge model of ABAQUS /Standard.The reconstruction project of an aluminum factory was taken as an example.The variation of red clay foundation’s settlement with time,the dissipation of pore water pressure,the non-linear distribution of void ratio with depth,and the effective stress growth of soil were researched.Results suggest that the calculated re-sults are in good agreement with the law of soil mechanics,and the actual situation of the red clay foundation con-solidation settlement could be reflected accurately.This research provides references for the foundation treatment and engineering design of buildings on red clay ground.

  7. Correction: Synergism between genome sequencing, tandem mass spectrometry and bio-inspired synthesis reveals insights into nocardioazine B biogenesis.

    Science.gov (United States)

    Alqahtani, Norah; Porwal, Suheel K; James, Elle D; Bis, Dana M; Karty, Jonathan A; Lane, Amy L; Viswanathan, Rajesh

    2015-09-21

    Correction for 'Synergism between genome sequencing, tandem mass spectrometry and bio-inspired synthesis reveals insights into nocardioazine B biogenesis' by Norah Alqahtani et al., Org. Biomol. Chem., 2015, 13, 7177-7192.

  8. Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome

    Directory of Open Access Journals (Sweden)

    Amiruddin Nadzirah

    2012-01-01

    . tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence.

  9. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  10. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments.

    Science.gov (United States)

    Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

    2016-10-01

    Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8-9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (1500 m) versus low-altitude region (600 mm), and arid zone (400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change.

  11. Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses.

    Science.gov (United States)

    Demirkan, Ayşe; Henneman, Peter; Verhoeven, Aswin; Dharuri, Harish; Amin, Najaf; van Klinken, Jan Bert; Karssen, Lennart C; de Vries, Boukje; Meissner, Axel; Göraler, Sibel; van den Maagdenberg, Arn M J M; Deelder, André M; C 't Hoen, Peter A; van Duijn, Cornelia M; van Dijk, Ko Willems

    2015-01-01

    Metabolite quantitative traits carry great promise for epidemiological studies, and their genetic background has been addressed using Genome-Wide Association Studies (GWAS). Thus far, the role of less common variants has not been exhaustively studied. Here, we set out a GWAS for metabolite quantitative traits in serum, followed by exome sequence analysis to zoom in on putative causal variants in the associated genes. 1H Nuclear Magnetic Resonance (1H-NMR) spectroscopy experiments yielded successful quantification of 42 unique metabolites in 2,482 individuals from The Erasmus Rucphen Family (ERF) study. Heritability of metabolites were estimated by SOLAR. GWAS was performed by linear mixed models, using HapMap imputations. Based on physical vicinity and pathway analyses, candidate genes were screened for coding region variation using exome sequence data. Heritability estimates for metabolites ranged between 10% and 52%. GWAS replicated three known loci in the metabolome wide significance: CPS1 with glycine (P-value  = 1.27×10-32), PRODH with proline (P-value  = 1.11×10-19), SLC16A9 with carnitine level (P-value  = 4.81×10-14) and uncovered a novel association between DMGDH and dimethyl-glycine (P-value  = 1.65×10-19) level. In addition, we found three novel, suggestively significant loci: TNP1 with pyruvate (P-value  = 1.26×10-8), KCNJ16 with 3-hydroxybutyrate (P-value  = 1.65×10-8) and 2p12 locus with valine (P-value  = 3.49×10-8). Exome sequence analysis identified potentially causal coding and regulatory variants located in the genes CPS1, KCNJ2 and PRODH, and revealed allelic heterogeneity for CPS1 and PRODH. Combined GWAS and exome analyses of metabolites detected by high-resolution 1H-NMR is a robust approach to uncover metabolite quantitative trait loci (mQTL), and the likely causative variants in these loci. It is anticipated that insight in the genetics of intermediate phenotypes will provide additional insight into the

  12. Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses.

    Directory of Open Access Journals (Sweden)

    Ayşe Demirkan

    2015-01-01

    Full Text Available Metabolite quantitative traits carry great promise for epidemiological studies, and their genetic background has been addressed using Genome-Wide Association Studies (GWAS. Thus far, the role of less common variants has not been exhaustively studied. Here, we set out a GWAS for metabolite quantitative traits in serum, followed by exome sequence analysis to zoom in on putative causal variants in the associated genes. 1H Nuclear Magnetic Resonance (1H-NMR spectroscopy experiments yielded successful quantification of 42 unique metabolites in 2,482 individuals from The Erasmus Rucphen Family (ERF study. Heritability of metabolites were estimated by SOLAR. GWAS was performed by linear mixed models, using HapMap imputations. Based on physical vicinity and pathway analyses, candidate genes were screened for coding region variation using exome sequence data. Heritability estimates for metabolites ranged between 10% and 52%. GWAS replicated three known loci in the metabolome wide significance: CPS1 with glycine (P-value  = 1.27×10-32, PRODH with proline (P-value  = 1.11×10-19, SLC16A9 with carnitine level (P-value  = 4.81×10-14 and uncovered a novel association between DMGDH and dimethyl-glycine (P-value  = 1.65×10-19 level. In addition, we found three novel, suggestively significant loci: TNP1 with pyruvate (P-value  = 1.26×10-8, KCNJ16 with 3-hydroxybutyrate (P-value  = 1.65×10-8 and 2p12 locus with valine (P-value  = 3.49×10-8. Exome sequence analysis identified potentially causal coding and regulatory variants located in the genes CPS1, KCNJ2 and PRODH, and revealed allelic heterogeneity for CPS1 and PRODH. Combined GWAS and exome analyses of metabolites detected by high-resolution 1H-NMR is a robust approach to uncover metabolite quantitative trait loci (mQTL, and the likely causative variants in these loci. It is anticipated that insight in the genetics of intermediate phenotypes will provide additional insight

  13. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta.

    Science.gov (United States)

    Kanost, Michael R; Arrese, Estela L; Cao, Xiaolong; Chen, Yun-Ru; Chellapilla, Sanjay; Goldsmith, Marian R; Grosse-Wilde, Ewald; Heckel, David G; Herndon, Nicolae; Jiang, Haobo; Papanicolaou, Alexie; Qu, Jiaxin; Soulages, Jose L; Vogel, Heiko; Walters, James; Waterhouse, Robert M; Ahn, Seung-Joon; Almeida, Francisca C; An, Chunju; Aqrawi, Peshtewani; Bretschneider, Anne; Bryant, William B; Bucks, Sascha; Chao, Hsu; Chevignon, Germain; Christen, Jayne M; Clarke, David F; Dittmer, Neal T; Ferguson, Laura C F; Garavelou, Spyridoula; Gordon, Karl H J; Gunaratna, Ramesh T; Han, Yi; Hauser, Frank; He, Yan; Heidel-Fischer, Hanna; Hirsh, Ariana; Hu, Yingxia; Jiang, Hongbo; Kalra, Divya; Klinner, Christian; König, Christopher; Kovar, Christie; Kroll, Ashley R; Kuwar, Suyog S; Lee, Sandy L; Lehman, Rüdiger; Li, Kai; Li, Zhaofei; Liang, Hanquan; Lovelace, Shanna; Lu, Zhiqiang; Mansfield, Jennifer H; McCulloch, Kyle J; Mathew, Tittu; Morton, Brian; Muzny, Donna M; Neunemann, David; Ongeri, Fiona; Pauchet, Yannick; Pu, Ling-Ling; Pyrousis, Ioannis; Rao, Xiang-Jun; Redding, Amanda; Roesel, Charles; Sanchez-Gracia, Alejandro; Schaack, Sarah; Shukla, Aditi; Tetreau, Guillaume; Wang, Yang; Xiong, Guang-Hua; Traut, Walther; Walsh, Tom K; Worley, Kim C; Wu, Di; Wu, Wenbi; Wu, Yuan-Qing; Zhang, Xiufeng; Zou, Zhen; Zucker, Hannah; Briscoe, Adriana D; Burmester, Thorsten; Clem, Rollie J; Feyereisen, René; Grimmelikhuijzen, Cornelis J P; Hamodrakas, Stavros J; Hansson, Bill S; Huguet, Elisabeth; Jermiin, Lars S; Lan, Que; Lehman, Herman K; Lorenzen, Marce; Merzendorfer, Hans; Michalopoulos, Ioannis; Morton, David B; Muthukrishnan, Subbaratnam; Oakeshott, John G; Palmer, Will; Park, Yoonseong; Passarelli, A Lorena; Rozas, Julio; Schwartz, Lawrence M; Smith, Wendy; Southgate, Agnes; Vilcinskas, Andreas; Vogt, Richard; Wang, Ping; Werren, John; Yu, Xiao-Qiang; Zhou, Jing-Jiang; Brown, Susan J; Scherer, Steven E; Richards, Stephen; Blissard, Gary W

    2016-09-01

    Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.

  14. Insights in metabolism and toxin production from the complete genome sequence of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Gottschalk, Gerhard

    2004-04-01

    The decryption of prokaryotic genome sequences progresses rapidly and provides the scientific community with an enormous amount of information. Clostridial genome sequencing projects have been finished only recently, starting with the genome of the solvent-producing Clostridium acetobutylicum in 2001. A lot of attention has been devoted to the genomes of pathogenic clostridia. In 2002, the genome sequence of C. perfringens, the causative agent of gas gangrene, has been released. Currently in the finishing stage and prior to publication are the genomes of the foodborne botulism-causing C. botulinum and of C. difficile, the causative agent of a wide spectrum of clinical manifestations such as antibiotic-associated diarrhea. Our team sequenced the genome of neuropathogenic C. tetani, a Gram-positive spore-forming bacterium predominantly found in the soil. In deep wound infections it occasionally causes spastic paralysis in humans and vertebrate animals, known as tetanus disease, by the secretion of potent neurotoxin, designated tetanus toxin. The toxin blocks the release of neurotransmitters from presynaptic membranes of interneurons of the spinal cord and the brainstem, thus preventing muscle relaxation. Fortunately, this disease is successfully controlled through immunization with tetanus toxoid, a formaldehyde-treated tetanus toxin, but nevertheless, an estimated 400,000 cases still occur each year, mainly of neonatal tetanus. The World Health Organization has stated that neonatal tetanus is the second leading cause of death from vaccine preventable diseases among children worldwide. This minireview focuses on an analysis of the genome sequence of C. tetani E88, a vaccine production strain, which is a toxigenic non-sporulating variant of strain Massachusetts. The genome consists of a 2,799,250 bp chromosome encoding 2618 open reading frames. The tetanus toxin is encoded on a 74,082 kb plasmid, containing 61 genes. Additional virulence-related factors as well as an

  15. Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

    Science.gov (United States)

    Guo, Michael H.; Nandakumar, Satish K.; Ulirsch, Jacob C.; Zekavat, Seyedeh M.; Buenrostro, Jason D.; Natarajan, Pradeep; Salem, Rany M.; Chiarle, Roberto; Mitt, Mario; Kals, Mart; Pärn, Kalle; Fischer, Krista; Milani, Lili; Mägi, Reedik; Palta, Priit; Gabriel, Stacey B.; Metspalu, Andres; Lander, Eric S.; Kathiresan, Sekar; Hirschhorn, Joel N.; Esko, Tõnu; Sankaran, Vijay G.

    2017-01-01

    Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA. The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance. PMID:28031487

  16. Deep Sequencing of HIV-Infected Cells: Insights into Nascent Transcription and Host-Directed Therapy

    Science.gov (United States)

    Peng, Xinxia; Sova, Pavel; Green, Richard R.; Thomas, Matthew J.; Korth, Marcus J.; Proll, Sean; Xu, Jiabao; Cheng, Yanbing; Yi, Kang; Chen, Li; Peng, Zhiyu; Wang, Jun; Palermo, Robert E.

    2014-01-01

    ABSTRACT Polyadenylated mature mRNAs are the focus of standard transcriptome analyses. However, the profiling of nascent transcripts, which often include nonpolyadenylated RNAs, can unveil novel insights into transcriptional regulation. Here, we separately sequenced total RNAs (Total RNAseq) and mRNAs (mRNAseq) from the same HIV-1-infected human CD4+ T cells. We found that many nonpolyadenylated RNAs were differentially expressed upon HIV-1 infection, and we identified 8 times more differentially expressed genes at 12 h postinfection by Total RNAseq than by mRNAseq. These expression changes were also evident by concurrent changes in introns and were recapitulated by later mRNA changes, revealing an unexpectedly significant delay between transcriptional initiation and mature mRNA production early after HIV-1 infection. We computationally derived and validated the underlying regulatory programs, and we predicted drugs capable of reversing these HIV-1-induced expression changes followed by experimental confirmation. Our results show that combined total and mRNA transcriptome analysis is essential for fully capturing the early host response to virus infection and provide a framework for identifying candidate drugs for host-directed therapy against HIV/AIDS. IMPORTANCE In this study, we used mass sequencing to identify genes differentially expressed in CD4+ T cells during HIV-1 infection. To our surprise, we found many differentially expressed genes early after infection by analyzing both newly transcribed unprocessed pre-mRNAs and fully processed mRNAs, but not by analyzing mRNAs alone, indicating a significant delay between transcription initiation and mRNA production early after HIV-1 infection. These results also show that important findings could be missed by the standard practice of analyzing mRNAs alone. We then derived the regulatory mechanisms driving the observed expression changes using integrative computational analyses. Further, we predicted drugs that

  17. 斜井施工中红黏土层高效钻眼爆破试验%Experiment on High Efficient Drilling and Blasting Construction for Mine Inclined Shaft in Red Clay

    Institute of Scientific and Technical Information of China (English)

    杨仁树; 杨立云; 李清; 方体利

    2011-01-01

    According to the mine gateway driving operation in red clay, the drilling and blasting construction technique applied would often have the borehole drilling difficulty, the serious requirement of the borehole parameter design, the driving speed low and other problems. The paper had the analysis and study on the borehole drilling and blasting mechanism in the red clay individually. With the improvement of the borehole drilling tools, the EZ1-21/2 hand type pneumatic drill with anger bit and auger rod was applied to the borehole drilling operation and the borehole drilling quality and speed could be highly increased. With the optimization of the borehole pattern, angle, depth, explosive loading and other blasting parameters and the twice and two sectional millisecond delay blasting technology, the utilization rate of the blasting boreholes was improved from previous 70% to over 90%. The driving rate of the single circulation was improved from 1.30 m to 1.75 m. The missed blasting rate was reduced from 24% to about 3%. Thus the profile shape results would be good and the driving speed could be highly increased.%在红黏土层中进行巷道掘进作业时,采用钻眼爆破施工工艺经常遇到钻孔困难、炮孔参数设计要求严格、掘进速度慢等问题,基于此分别对红黏土层中的钻眼成孔和爆破机理进行分析研究.通过改进钻眼成孔机具,采用EZ1-21/2手持式气动钻机配梅花钻头和麻花钻杆进行成孔作业,大幅加快了成孔质量和速度;通过优化炮眼排列、角度、深度、装药量等爆破参数和采用两次两段微差爆破技术,炮眼利用率从原来的70%提高到90%以上,单循环进尺从1.30 m提高到1.75m,拒爆率由24%降到3%左右,而且周边成形效果好,掘进速度有了较大提高.

  18. Structural insights of microbial community of Deulajhari (India hot spring using 16s-rRNA based metagenomic sequencing

    Directory of Open Access Journals (Sweden)

    Archana Singh

    2016-03-01

    Full Text Available Insights about the distribution of the microbial community prove to be the major goal of understanding microbial ecology which remains to be fully deciphered. Hot springs being hub for the thermophilic microbiota attract the attention of the microbiologists. Deulajhari hot spring cluster is located in the Angul district of Odisha. Covered within a wooded area, Deulajhari hot spring is also fed by the plant litter resulting in a relatively high amount of total organic content (TOC. For the first time, Illumina sequencing based biodiversity analysis of microbial composition is studied through amplicon metagenome sequencing of 16s rRNA targeting V3‐V4 region using metagenomic DNA from the hot spring sediment. Over 28 phyla were detected through the amplicon metagenome sequencing of which the most dominating phyla at the existing physiochemical parameters like; temperature 69 °C, pH 8.09, electroconductivity 0.025 dSm−1 and total organic carbon 0.356%, were Proteobacteria (88.12%, Bacteriodetes (10.76%, Firmicutes (0.35%, Spirochetes (0.18% and chloroflexi (0.11%. Approximately 713 species were observed at the above physiochemical parameters. The analysis of the metagenome provides the quantitative insights into microbial populations based on the sequence data in Deulajhari hot spring. Metagenome sequence is deposited to SRA database which is available at NCBI with accession no. SRX1459736.

  19. Research on the Characteristic and Genesis of Q2 Vermicular Red Clay in Ningxiang of Changsha -Yiyang Railway%长益城际宁乡 Q2网纹黏土特征及成因分析

    Institute of Scientific and Technical Information of China (English)

    汪莹鹤

    2015-01-01

    研究目的:长益城际沿线广泛分布 Q2棕红色网纹黏土,土层厚度达5~30 m。城际铁路对路基的沉降变形控制十分严格,针对此种路基如何进行合理处理是一个关键问题。由于土体的成分、结构、成因对工程性能有着很大的影响,本文结合现场调查、颗粒分析、化学成分分析、X 射线分析及微观图像,对网纹土体的成分、结构、成因进行系统研究,为地基处理方案选择提供参考。研究结论:(1)宁乡红白网纹土均以黏粒为第一优势粒级,含量在65%以上,红网纹黏粒含量大于白网纹土;(2)网纹土中 SiO2含量占总含量的60%左右,其次为 Al2 O3和 TFe2 O3,这三种物质的总含量超过85%;(3)红土中铁的含量差不多是白土的三倍,SiO2含量相对减少;(4)白土的颗粒形状多为片状,排列较为规则,颗粒之间的接触主要为面-面、面-边接触;(5)红土颗粒结构单元体排列较白土紊乱,无明显定向排列且结构比白土小;(6)网纹土不是在单一气候条件下形成的,而是经历了多阶段的气候波动,因而是一种复合型的古土壤;(7)本研究成果可供网纹土成因研究提供参考。%Research purposes:The Q2 vermicular red clay was widely distributed along the Changsha -Yiyang railway where soil thickness is 5 ~30 m.It is the key problem to choose proper method to treat this type of soil because the settlement of intercity railway subgrade must be controlled strictly.Based on the site survey,particle -size analysis, chemical component analysis,X -ray spectrometry analysis and microstructure,the material composition,structure and genesis of the Q2 vermicular red clay were studied systematically,which can provide a reference to choose the foundation treatment method. Research conclusions:(1 )The clay was the preponderant particle in which the content was about 65% in the soil of

  20. Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

    Directory of Open Access Journals (Sweden)

    Wang Jintu

    2011-04-01

    Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

  1. Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

    Directory of Open Access Journals (Sweden)

    Le Provost Grégoire

    2011-06-01

    Full Text Available Abstract Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be

  2. Genome sequence of the Brown Norway rat yields insights into mammalian evolution

    NARCIS (Netherlands)

    Gibbs, RA; Weinstock, GM; Metzker, ML; Muzny, DM; Sodergren, EJ; Scherer, S; Scott, G; Steffen, D; Worley, KC; Burch, PE; Okwuonu, G; Hines, S; Lewis, L; DeRamo, C; Delgado, O; Dugan-Rocha, S; Miner, G; Morgan, M; Hawes, A; Gill, R; Holt, RA; Adams, MD; Amanatides, PG; Baden-Tillson, H; Barnstead, M; Chin, S; Evans, CA; Ferriera, S; Fosler, C; Glodek, A; Gu, ZP; Jennings, D; Kraft, CL; Nguyen, T; Pfannkoch, CM; Sitter, C; Sutton, GG; Venter, JC; Woodage, T; Smith, D; Lee, HM; Gustafson, E; Cahill, P; Kana, A; Doucette-Stamm, L; Weinstock, K; Fechtel, K; Weiss, RB; Dunn, DM; Green, ED; Blakesley, RW; Bouffard, GG; de Jong, J; Osoegawa, K; Zhu, BL; Marra, M; Schein, J; Bosdet, [No Value; Fjell, C; Jones, S; Krzywinski, M; Mathewson, C; Siddiqui, A; Wye, N; McPherson, J; Zhao, SY; Fraser, CM; Shetty, J; Shatsman, S; Geer, K; Chen, YX; Abramzon, S; Nierman, WC; Gibbs, RA; Weinstock, GM; Havlak, PH; Durbin, KJ; Egan, A; Ren, YR; Song, XZ; Li, BS; Qin, [No Value; Cawley, S; Weinstock, GM; Worley, KC; Cooney, AJ; Gibbs, RA; D'Souza, LM; Martin, K; Wu, JQ; Gonzalez-Garay, ML; Jackson, AR; Kalafus, KJ; McLeod, MP; Milosavljevic, A; Virk, D; Volkov, A; Wheeler, DA; Zhang, ZD; Bailey, JA; Eichler, EE; Tuzun, E; Birney, E; Mongin, E; Ureta-Vidal, A; Woodwark, C; Zdobnov, E; Bork, P; Suyama, M; Torrents, D; Alexandersson, M; Trask, BJ; Young, JM; Smith, D; Huang, H; Fechtel, K; Wang, HJ; Xing, HM; Weinstock, K; Gietzen, D; Schmidt, J; Stevens, K; Vitt, U; Wingrove, J; Camara, F; Schmidt, J; Stevens, K; Vitt, U; Wingrove, J; Camara, F; Alba, MM; Abril, JF; Guigo, R; Smit, A; Dubchak, [No Value; Rubin, EM; Couronne, O; Poliakov, A; Hubner, N; Ganten, D; Goesele, C; Hummel, O; Kreitler, T; Lee, YA; Monti, J; Schulz, H; Zimdahl, H; Himmelbauer, H; Lehrach, H; Jacob, HJ; Bromberg, S; Gullings-Handley, J; Jensen-Seaman, MI; Kwitek, AE; Lazar, J; Pasko, D; Tonellato, PJ; Twigger, S; Ponting, P; Duarte, JM; Rice, S; Goodstadt, L; Beatson, SA; Emes, RD; Winter, EE; Webber, C; Brandt, P; Nyakatura, G; Adetobi, M; Chiaromonte, F; Elnitski, L; Eswara, P; Hardison, RC; Hou, MM; Kolbe, D; Makova, K; Miller, W; Nekrutenko, A; Riemer, C; Schwartz, S; Taylor, J; Zhang, Y; Lindpaintner, K; Andrews, TD; Caccamo, M; Clamp, M; Clarke, L; Curwen, [No Value; Durbin, R; Eyras, E; Searle, SM; Cooper, GM; Batzoglou, S; Brudno, M; Sidow, A; Stone, EA; Venter, JC; Payseur, BA; Bourque, G; Lopez-Otin, C; Puente, XS; Chakrabarti, K; Chatterji, S; Dewey, C; Pachter, L; Bray, N; Yap, VB; Caspi, A; Tesler, G; Pevzner, PA; Haussler, D; Roskin, KM; Baertsch, R; Clawson, H; Furey, TS; Hinrichs, AS; Karolchik, D; Kent, WJ; Rosenbloom, KR; Trumbower, H; Weirauch, M; Cooper, DN; Stenson, PD; Ma, B; Brent, M; Arumugam, M; Shteynberg, D; Copley, RR; Taylor, MS; Riethman, H; Mudunuri, U; Peterson, J; Guyer, M; Felsenfeld, A; Old, S; Mockrin, S; Collins, F; Daniels, S.

    2004-01-01

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 9

  3. Control of automated behavior: insights from the discrete sequence production task

    NARCIS (Netherlands)

    Abrahamse, E.L.; Ruitenberg, M.F.L.; de Kleine, Elian; Verwey, Willem B.

    2013-01-01

    Work with the discrete sequence production (DSP) task has provided a substantial literature on discrete sequencing skill over the last decades. The purpose of the current article is to provide a comprehensive overview of this literature and of the theoretical progress that it has prompted. We start

  4. Genome sequence of the Brown Norway rat yields insights into mammalian evolution

    DEFF Research Database (Denmark)

    Gibbs, Richard A; Weinstock, George M; Metzker, Michael L

    2004-01-01

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering ove...

  5. Highly sulfated hexasaccharide sequences isolated from chondroitin sulfate of shark fin cartilage: insights into the sugar sequences with bioactivities.

    Science.gov (United States)

    Mizumoto, Shuji; Murakoshi, Saori; Kalayanamitra, Kittiwan; Deepa, Sarama Sathyaseelan; Fukui, Shigeyuki; Kongtawelert, Prachya; Yamada, Shuhei; Sugahara, Kazuyuki

    2013-02-01

    Chondroitin sulfate (CS) chains regulate the development of the central nervous system in vertebrates and are linear polysaccharides consisting of variously sulfated repeating disaccharides, [-4GlcUAβ1-3GalNAcβ1-](n), where GlcUA and GalNAc represent D-glucuronic acid and N-acetyl-D-galactosamine, respectively. CS chains containing D-disaccharide units [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)] are involved in the development of cerebellar Purkinje cells and neurite outgrowth-promoting activity through interaction with a neurotrophic factor, pleiotrophin, resulting in the regulation of signaling. In this study, to obtain further structural information on the CS chains containing d-disaccharide units involved in brain development, oligosaccharides containing D-units were isolated from a shark fin cartilage. Seven novel hexasaccharide sequences, ΔO-D-D, ΔA-D-D, ΔC-D-D, ΔE-A-D, ΔD-D-C, ΔE-D-D and ΔA-B-D, in addition to three previously reported sequences, ΔC-A-D, ΔC-D-C and ΔA-D-A, were isolated from a CS preparation of shark fin cartilage after exhaustive digestion with chondroitinase AC-I, which cannot act on the galactosaminidic linkages bound to D-units. The symbol Δ stands for a 4,5-unsaturated bond of uronic acids, whereas A, B, C, D, E and O represent [GlcUA-GalNAc(4-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(4-O-sulfate)], [GlcUA-GalNAc(6-O-sulfate)], [GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)], [GlcUA-GalNAc(4-O-, 6-O-sulfate)] and [GlcUA-GalNAc], respectively. In binding studies using an anti-CS monoclonal antibody, MO-225, the epitopes of which are involved in cerebellar development in mammals, novel epitope structures, ΔA-D-A, ΔA-D-D and ΔA-B-D, were revealed. Hexasaccharides containing two consecutive D-units or a B-unit will be useful for the structural and functional analyses of CS chains particularly in the neuroglycobiological fields.

  6. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    Energy Technology Data Exchange (ETDEWEB)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  7. Genome sequence of the brown Norway rat yields insights into mammalian evolution

    Energy Technology Data Exchange (ETDEWEB)

    Gibbs, Richard A.; Weinstock, George M.; Metzker, Michael L.; Muzny, Donna M.; Sodergren, Erica J.; Scherer, Steven; Scott, Graham; Steffen, David; Worley, Kim C.; Burch, Paula E.; Okwuonu, Geoffrey; Hines, Sandra; Lewis, Lora; DeRamo, Christine; Delgado, Oliver; Dugan-Rocha, Shannon; Miner, George; Morgan, Margaret; Hawes, Alicia; Gill, Rachel; Holt, Robert A.; Adams, Mark D.; Amanatides, Peter G.; Baden-Tillson, Holly; Barnstead, Mary; Chin, Soo; Evans, Cheryl A.; Ferriera, Steven; Fosler, Carl; Glodek, Anna; Gu, Zhiping; Jennings, Don; Kraft, Cheryl L.; Nguyen, Trixie; Pfannkoch, Cynthia M.; Sitter, Cynthia; Sutton, Granger G.; Venter, J. Craig; Woodage, Trevor; Smith, Douglas; Lee, Hong-Maei; Gustafson, Erik; Cahill, Patrick; Kana, Arnold; Doucette-Stamm, Lynn; Weinstock, Keith; Fechtel, Kim; Weiss, Robert B.; Dunn, Diane M.; Green, Eric D.; Blakesley, Robert W.; Bouffard, Gerard G.; de Jong, Pieter J.; Osoegawa, Kazutoyo; Zhu, Baoli; Marra, Marco; Schein, Jacqueline; Bosdet, Ian; Fjell, Chris; Jones, Steven; Krzywinski, Martin; Mathewson, Carrie; Siddiqui, Asim; Wye, Natasja; McPherson, John; Zhao, Shaying; Fraser, Claire M.; Shetty, Jyoti; Shatsman, Sofiya; Geer, Keita; Chen, Yixin; Abramzon, Sofyia; Nierman, William C.; Havlak, Paul H.; Chen, Rui; Durbin, K. James; Egan, Amy; Ren, Yanru; Song, Xing-Zhi; Li, Bingshan; Liu, Yue; Qin, Xiang; Cawley, Simon; Cooney, A.J.; D' Souza, Lisa M.; Martin, Kirt; Wu, Jia Qian; Gonzalez-Garay, Manuel L.; Jackson, Andrew R.; Kalafus, Kenneth J.; McLeod, Michael P.; Milosavljevic, Aleksandar; Virk, Davinder; Volkov, Andrei; Wheeler, David A.; Zhang, Zhengdong; Bailey, Jeffrey A.; Eichler, Evan E.; Tuzun, Eray; Birney, Ewan; Mongin, Emmanuel; Ureta-Vidal, Abel; Woodwark, Cara; Zdobnov, Evgeny; Bork, Peer; Suyama, Mikita; Torrents, David; Alexandersson, Marina; Trask, Barbara J.; Young, Janet M.; et al.

    2004-02-02

    The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90 percent of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

  8. New insights into statistical learning and chunk learning in implicit sequence acquisition.

    Science.gov (United States)

    Du, Yue; Clark, Jane E

    2016-11-03

    Implicit sequence learning is ubiquitous in our daily life. However, it is unclear whether the initial acquisition of sequences results from learning to chunk items (i.e., chunk learning) or learning the underlying statistical regularities (i.e., statistical learning). By grouping responses with or without a distinct chunk or statistical structure into segments and comparing these responses, previous studies have demonstrated both chunk and statistical learning. However, few studies have considered the response sequence as a whole and examined the temporal dependency of the entire sequence, where the temporal dependencies could disclose the internal representations of chunk and statistical learning. Participants performed a serial reaction time (SRT) task under different stimulus interval conditions. We found that sequence learning reflected by reaction time (RT) rather than motor improvements represented by movement time (MT). The temporal dependency of RT and MT revealed that both RT and MT displayed recursive patterns caused by biomechanical effects of response locations and foot transitions. Chunking was noticeable only in the presence of the recurring RT or MT but vanished after the recursive component was removed, implying that chunk formation may result from biomechanical constraints rather than learning itself. In addition, we observed notable first-order autocorrelations in RT. This trial-to-trial association enhanced as learning progressed regardless of stimulus intervals, reflecting the internal cognitive representation of the first-order stimulus contingencies. Our results suggest that initial acquisition of implicit sequences may arise from first-order statistical learning rather than chunk learning.

  9. Two New Complete Genome Sequences Offer Insight into Host and Tissue Specificity of Plant Pathogenic Xanthomonas spp.▿†

    Science.gov (United States)

    Bogdanove, Adam J.; Koebnik, Ralf; Lu, Hong; Furutani, Ayako; Angiuoli, Samuel V.; Patil, Prabhu B.; Van Sluys, Marie-Anne; Ryan, Robert P.; Meyer, Damien F.; Han, Sang-Wook; Aparna, Gudlur; Rajaram, Misha; Delcher, Arthur L.; Phillippy, Adam M.; Puiu, Daniela; Schatz, Michael C.; Shumway, Martin; Sommer, Daniel D.; Trapnell, Cole; Benahmed, Faiza; Dimitrov, George; Madupu, Ramana; Radune, Diana; Sullivan, Steven; Jha, Gopaljee; Ishihara, Hiromichi; Lee, Sang-Won; Pandey, Alok; Sharma, Vikas; Sriariyanun, Malinee; Szurek, Boris; Vera-Cruz, Casiana M.; Dorman, Karin S.; Ronald, Pamela C.; Verdier, Valérie; Dow, J. Maxwell; Sonti, Ramesh V.; Tsuge, Seiji; Brendel, Volker P.; Rabinowicz, Pablo D.; Leach, Jan E.; White, Frank F.; Salzberg, Steven L.

    2011-01-01

    Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity. PMID:21784931

  10. Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.

    Science.gov (United States)

    Bogdanove, Adam J; Koebnik, Ralf; Lu, Hong; Furutani, Ayako; Angiuoli, Samuel V; Patil, Prabhu B; Van Sluys, Marie-Anne; Ryan, Robert P; Meyer, Damien F; Han, Sang-Wook; Aparna, Gudlur; Rajaram, Misha; Delcher, Arthur L; Phillippy, Adam M; Puiu, Daniela; Schatz, Michael C; Shumway, Martin; Sommer, Daniel D; Trapnell, Cole; Benahmed, Faiza; Dimitrov, George; Madupu, Ramana; Radune, Diana; Sullivan, Steven; Jha, Gopaljee; Ishihara, Hiromichi; Lee, Sang-Won; Pandey, Alok; Sharma, Vikas; Sriariyanun, Malinee; Szurek, Boris; Vera-Cruz, Casiana M; Dorman, Karin S; Ronald, Pamela C; Verdier, Valérie; Dow, J Maxwell; Sonti, Ramesh V; Tsuge, Seiji; Brendel, Volker P; Rabinowicz, Pablo D; Leach, Jan E; White, Frank F; Salzberg, Steven L

    2011-10-01

    Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.

  11. Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism.

    Science.gov (United States)

    Rozemuller, E H; Bouwens, A G; van Oort, E; Versluis, L F; Marsh, S G; Bodmer, J G; Tilanus, M G

    1995-01-01

    An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)

  12. The first insight into the tissue specific taxus transcriptome via Illumina second generation sequencing.

    Directory of Open Access Journals (Sweden)

    Da Cheng Hao

    Full Text Available BACKGROUND: Illumina second generation sequencing is now an efficient route for generating enormous sequence collections that represent expressed genes and quantitate expression level. Taxus is a world-wide endangered gymnosperm genus and forms an important anti-cancer medicinal resource, but the large and complex genomes of Taxus have hindered the development of genomic resources. The research of its tissue-specific transcriptome is absent. There is also no study concerning the association between the plant transcriptome and metabolome with respect to the plant tissue type. METHODOLOGY/PRINCIPAL FINDINGS: We performed the de novo assembly of Taxus mairei transcriptome using Illumina paired-end sequencing technology. In a single run, we produced 13,737,528 sequencing reads corresponding to 2.03 Gb total nucleotides. These reads were assembled into 36,493 unique sequences. Based on similarity search with known proteins, 23,515 Unigenes were identified to have the Blast hit with a cut-off E-value above 10⁻⁵. Furthermore, we investigated the transcriptome difference of three Taxus tissues using a tag-based digital gene expression system. We obtained a sequencing depth of over 3.15 million tags per sample and identified a large number of genes associated with tissue specific functions and taxane biosynthetic pathway. The expression of the taxane biosynthetic genes is significantly higher in the root than in the leaf and the stem, while high activity of taxane-producing pathway in the root was also revealed via metabolomic analyses. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and enriched metabolic pathways with regard to the differentially expressed genes were revealed for the first time. CONCLUSIONS/SIGNIFICANCE: Our data provides the most comprehensive sequence resource available for Taxus study and will help define mechanisms of tissue

  13. Large Scale Sequencing of Dothideomycetes Provides Insights into Genome Evolution and Adaptation

    Energy Technology Data Exchange (ETDEWEB)

    Haridas, Sajeet; Crous, Pedro; Binder, Manfred; Spatafora, Joseph; Grigoriev, Igor

    2015-03-16

    Dothideomycetes is the largest and most diverse class of ascomycete fungi with 23 orders 110 families, 1300 genera and over 19,000 known species. We present comparative analysis of 70 Dothideomycete genomes including over 50 that we sequenced and are as yet unpublished. This extensive sampling has almost quadrupled the previous study of 18 species and uncovered a 10 fold range of genome sizes. We were able to clarify the phylogenetic positions of several species whose origins were unclear in previous morphological and sequence comparison studies. We analyzed selected gene families including proteases, transporters and small secreted proteins and show that major differences in gene content is influenced by speciation.

  14. An atlas of over 90.000 conserved noncoding sequences provides insight into crucifer regulatory regions

    NARCIS (Netherlands)

    Haudry, A.; Platts, A.E.; Vello, E.; Hoen, D.R.; Leclerq, M.; Williamson, R.J.; Forczek, E.; Joly-Lopez, Z.; Steffen, J.G.; Hazzouri, K.M.; Dewar, K.; Stinchcombe, J.R.; Schoen, D.J.; Wang, X.; Schmutz, J.; Town, C.D.; Edger, P.P.; Pires, J.C.; Schumaker, K.S.; Jarvis, D.E.; Mandakova, T.; Lysak, M.; Bergh, van den E.; Schranz, M.E.; Harrison, P.M.

    2013-01-01

    Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymb

  15. Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis

    DEFF Research Database (Denmark)

    Gilbert, M Thomas P; Binladen, Jonas; Miller, Webb;

    2007-01-01

    , and subsequently be interpreted to enable characterization of the aDNA damage behind the observed phenotypes. Through comparative analyses on 390,965 bp of modern chloroplast and 131,474 bp of ancient woolly mammoth GS20 sequence data we conclusively demonstrate that in this sample at least, a permafrost preserved...

  16. 18S ribosomal DNA sequences provide insight into the phylogeny of patellogastropod limpets (Mollusca: Gastropoda).

    Science.gov (United States)

    Yoon, Sook Hee; Kim, Won

    2007-02-28

    To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.

  17. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

    Science.gov (United States)

    Wambui Njunguna; Aaron Liston; Richard Cronn; Tia-Lynn Ashman; Nahla Bassil

    2013-01-01

    The cultivated strawberry is one of the youngest domesticated plants, developed in France in the 1700s from chance hybridization between two western hemisphere octoploid species. However, little is known about the evolution of the species that gave rise to this important fruit crop. Phylogenetic analysis of chloroplast genome sequences of 21 Fragaria...

  18. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts

    Science.gov (United States)

    Liu, Zhanjiang; Liu, Shikai; Yao, Jun; Bao, Lisui; Zhang, Jiaren; Li, Yun; Jiang, Chen; Sun, Luyang; Wang, Ruijia; Zhang, Yu; Zhou, Tao; Zeng, Qifan; Fu, Qiang; Gao, Sen; Li, Ning; Koren, Sergey; Jiang, Yanliang; Zimin, Aleksey; Xu, Peng; Phillippy, Adam M.; Geng, Xin; Song, Lin; Sun, Fanyue; Li, Chao; Wang, Xiaozhu; Chen, Ailu; Jin, Yulin; Yuan, Zihao; Yang, Yujia; Tan, Suxu; Peatman, Eric; Lu, Jianguo; Qin, Zhenkui; Dunham, Rex; Li, Zhaoxia; Sonstegard, Tad; Feng, Jianbin; Danzmann, Roy G.; Schroeder, Steven; Scheffler, Brian; Duke, Mary V.; Ballard, Linda; Kucuktas, Huseyin; Kaltenboeck, Ludmilla; Liu, Haixia; Armbruster, Jonathan; Xie, Yangjie; Kirby, Mona L.; Tian, Yi; Flanagan, Mary Elizabeth; Mu, Weijie; Waldbieser, Geoffrey C.

    2016-01-01

    Catfish represent 12% of teleost or 6.3% of all vertebrate species, and are of enormous economic value. Here we report a high-quality reference genome sequence of channel catfish (Ictalurus punctatus), the major aquaculture species in the US. The reference genome sequence was validated by genetic mapping of 54,000 SNPs, and annotated with 26,661 predicted protein-coding genes. Through comparative analysis of genomes and transcriptomes of scaled and scaleless fish and scale regeneration experiments, we address the genomic basis for the most striking physical characteristic of catfish, the evolutionary loss of scales and provide evidence that lack of secretory calcium-binding phosphoproteins accounts for the evolutionary loss of scales in catfish. The channel catfish reference genome sequence, along with two additional genome sequences and transcriptomes of scaled catfishes, provide crucial resources for evolutionary and biological studies. This work also demonstrates the power of comparative subtraction of candidate genes for traits of structural significance. PMID:27249958

  19. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Science.gov (United States)

    Howard, James B; Kechris, Katerina J; Rees, Douglas C; Glazer, Alexander N

    2013-01-01

    Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf) yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification provides the bases for

  20. Multiple amino acid sequence alignment nitrogenase component 1: insights into phylogenetics and structure-function relationships.

    Directory of Open Access Journals (Sweden)

    James B Howard

    Full Text Available Amino acid residues critical for a protein's structure-function are retained by natural selection and these residues are identified by the level of variance in co-aligned homologous protein sequences. The relevant residues in the nitrogen fixation Component 1 α- and β-subunits were identified by the alignment of 95 protein sequences. Proteins were included from species encompassing multiple microbial phyla and diverse ecological niches as well as the nitrogen fixation genotypes, anf, nif, and vnf, which encode proteins associated with cofactors differing at one metal site. After adjusting for differences in sequence length, insertions, and deletions, the remaining >85% of the sequence co-aligned the subunits from the three genotypes. Six Groups, designated Anf, Vnf , and Nif I-IV, were assigned based upon genetic origin, sequence adjustments, and conserved residues. Both subunits subdivided into the same groups. Invariant and single variant residues were identified and were defined as "core" for nitrogenase function. Three species in Group Nif-III, Candidatus Desulforudis audaxviator, Desulfotomaculum kuznetsovii, and Thermodesulfatator indicus, were found to have a seleno-cysteine that replaces one cysteinyl ligand of the 8Fe:7S, P-cluster. Subsets of invariant residues, limited to individual groups, were identified; these unique residues help identify the gene of origin (anf, nif, or vnf yet should not be considered diagnostic of the metal content of associated cofactors. Fourteen of the 19 residues that compose the cofactor pocket are invariant or single variant; the other five residues are highly variable but do not correlate with the putative metal content of the cofactor. The variable residues are clustered on one side of the cofactor, away from other functional centers in the three dimensional structure. Many of the invariant and single variant residues were not previously recognized as potentially critical and their identification

  1. Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing

    Directory of Open Access Journals (Sweden)

    Gan Xiaoni

    2010-06-01

    Full Text Available Abstract Background Variations in genome size within and between species have been observed since the 1950 s in diverse taxonomic groups. Serving as model organisms, smooth pufferfish possess the smallest vertebrate genomes. Interestingly, spiny pufferfish from its sister family have genome twice as large as smooth pufferfish. Therefore, comparative genomic analysis between smooth pufferfish and spiny pufferfish is useful for our understanding of genome size evolution in pufferfish. Results Ten BAC clones of a spiny pufferfish Diodon holocanthus were randomly selected and shotgun sequenced. In total, 776 kb of non-redundant sequences without gap representing 0.1% of the D. holocanthus genome were identified, and 77 distinct genes were predicted. In the sequenced D. holocanthus genome, 364 kb is homologous with 265 kb of the Takifugu rubripes genome, and 223 kb is homologous with 148 kb of the Tetraodon nigroviridis genome. The repetitive DNA accounts for 8% of the sequenced D. holocanthus genome, which is higher than that in the T. rubripes genome (6.89% and that in the Te. nigroviridis genome (4.66%. In the repetitive DNA, 76% is retroelements which account for 6% of the sequenced D. holocanthus genome and belong to known families of transposable elements. More than half of retroelements were distributed within genes. In the non-homologous regions, repeat element proportion in D. holocanthus genome increased to 10.6% compared with T. rubripes and increased to 9.19% compared with Te. nigroviridis. A comparison of 10 well-defined orthologous genes showed that the average intron size (566 bp in D. holocanthus genome is significantly longer than that in the smooth pufferfish genome (435 bp. Conclusion Compared with the smooth pufferfish, D. holocanthus has a low gene density and repeat elements rich genome. Genome size variation between D. holocanthus and the smooth pufferfish exhibits as length variation between homologous region and different

  2. Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species.

    Science.gov (United States)

    Kim, Seungill; Park, Minkyu; Yeom, Seon-In; Kim, Yong-Min; Lee, Je Min; Lee, Hyun-Ah; Seo, Eunyoung; Choi, Jaeyoung; Cheong, Kyeongchae; Kim, Ki-Tae; Jung, Kyongyong; Lee, Gir-Won; Oh, Sang-Keun; Bae, Chungyun; Kim, Saet-Byul; Lee, Hye-Young; Kim, Shin-Young; Kim, Myung-Shin; Kang, Byoung-Cheorl; Jo, Yeong Deuk; Yang, Hee-Bum; Jeong, Hee-Jin; Kang, Won-Hee; Kwon, Jin-Kyung; Shin, Chanseok; Lim, Jae Yun; Park, June Hyun; Huh, Jin Hoe; Kim, June-Sik; Kim, Byung-Dong; Cohen, Oded; Paran, Ilan; Suh, Mi Chung; Lee, Saet Buyl; Kim, Yeon-Ki; Shin, Younhee; Noh, Seung-Jae; Park, Junhyung; Seo, Young Sam; Kwon, Suk-Yoon; Kim, Hyun A; Park, Jeong Mee; Kim, Hyun-Jin; Choi, Sang-Bong; Bosland, Paul W; Reeves, Gregory; Jo, Sung-Hwan; Lee, Bong-Woo; Cho, Hyung-Taeg; Choi, Hee-Seung; Lee, Min-Soo; Yu, Yeisoo; Do Choi, Yang; Park, Beom-Seok; van Deynze, Allen; Ashrafi, Hamid; Hill, Theresa; Kim, Woo Taek; Pai, Hyun-Sook; Ahn, Hee Kyung; Yeam, Inhwa; Giovannoni, James J; Rose, Jocelyn K C; Sørensen, Iben; Lee, Sang-Jik; Kim, Ryan W; Choi, Ik-Young; Choi, Beom-Soon; Lim, Jong-Sung; Lee, Yong-Hwan; Choi, Doil

    2014-03-01

    Hot pepper (Capsicum annuum), one of the oldest domesticated crops in the Americas, is the most widely grown spice crop in the world. We report whole-genome sequencing and assembly of the hot pepper (Mexican landrace of Capsicum annuum cv. CM334) at 186.6× coverage. We also report resequencing of two cultivated peppers and de novo sequencing of the wild species Capsicum chinense. The genome size of the hot pepper was approximately fourfold larger than that of its close relative tomato, and the genome showed an accumulation of Gypsy and Caulimoviridae family elements. Integrative genomic and transcriptomic analyses suggested that change in gene expression and neofunctionalization of capsaicin synthase have shaped capsaicinoid biosynthesis. We found differential molecular patterns of ripening regulators and ethylene synthesis in hot pepper and tomato. The reference genome will serve as a platform for improving the nutritional and medicinal values of Capsicum species.

  3. Insights into the Evolution of Cotton Diploids and Polyploids from Whole-Genome Re-sequencing

    OpenAIRE

    Page, Justin T.; Huynh, Mark D; Zach S Liechty; Grupp, Kara; Stelly, David; Hulse, Amanda M; Ashrafi, Hamid; Van Deynze, Allen; Wendel, Jonathan F.; Udall, Joshua A.

    2013-01-01

    Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton) genome is complicated by the joint presence of two genomes in its nucleus (AT and DT genomes). These two genomes were derived from progenitor A-genome and D-genome diploids involved in ancestral allopolyploidization. To better understand the allopolyploid genome, we re-sequenced the genomes of extant diploid relatives that contain the A1 (Gossypium herbaceum), A2 (Gossypium arboreum), or D5 (Gossypium ra...

  4. Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients

    DEFF Research Database (Denmark)

    Marvig, Rasmus Lykke; Madsen Sommer, Lea Mette; Jelsbak, Lars;

    2015-01-01

    is suggested to be due to the large genetic repertoire of P. aeruginosa and its ability to genetically adapt to the host environment. Here, we review the recent work that has applied whole-genome sequencing to understand P. aeruginosa population genomics, within-host microevolution and diversity, mutational...... mechanisms, genetic adaptation and transmission events. Finally, we summarize the advances in relation to medical applications and laboratory evolution experiments....

  5. Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

    Science.gov (United States)

    Singh, Pushpendra; Benjak, Andrej; Schuenemann, Verena J.; Herbig, Alexander; Avanzi, Charlotte; Busso, Philippe; Nieselt, Kay; Krause, Johannes; Vera-Cabrera, Lucio; Cole, Stewart T.

    2015-01-01

    Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequence of M. lepromatosis present in a skin biopsy from a Mexican patient, and compared it with that of Mycobacterium leprae, which has undergone extensive reductive evolution. The genomes display extensive synteny and are similar in size (∼3.27 Mb). Protein-coding genes share 93% nucleotide sequence identity, whereas pseudogenes are only 82% identical. The events that led to pseudogenization of 50% of the genome likely occurred before divergence from their most recent common ancestor (MRCA), and both M. lepromatosis and M. leprae have since accumulated new pseudogenes or acquired specific deletions. Functional comparisons suggest that M. lepromatosis has lost several enzymes required for amino acid synthesis whereas M. leprae has a defective heme pathway. M. lepromatosis has retained all functions required to infect the Schwann cells of the peripheral nervous system and therefore may also be neuropathogenic. A phylogeographic survey of 227 leprosy biopsies by differential PCR revealed that 221 contained M. leprae whereas only six, all from Mexico, harbored M. lepromatosis. Phylogenetic comparisons indicate that M. lepromatosis is closer than M. leprae to the MRCA, and a Bayesian dating analysis suggests that they diverged from their MRCA approximately 13.9 Mya. Thus, despite their ancient separation, the two leprosy bacilli are remarkably conserved and still cause similar pathologic conditions. PMID:25831531

  6. Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.

    Science.gov (United States)

    Tachibana, Shin-Ichiro; Sullivan, Steven A; Kawai, Satoru; Nakamura, Shota; Kim, Hyunjae R; Goto, Naohisa; Arisue, Nobuko; Palacpac, Nirianne M Q; Honma, Hajime; Yagi, Masanori; Tougan, Takahiro; Katakai, Yuko; Kaneko, Osamu; Mita, Toshihiro; Kita, Kiyoshi; Yasutomi, Yasuhiro; Sutton, Patrick L; Shakhbatyan, Rimma; Horii, Toshihiro; Yasunaga, Teruo; Barnwell, John W; Escalante, Ananias A; Carlton, Jane M; Tanabe, Kazuyuki

    2012-09-01

    P. cynomolgi, a malaria-causing parasite of Asian Old World monkeys, is the sister taxon of P. vivax, the most prevalent malaria-causing species in humans outside of Africa. Because P. cynomolgi shares many phenotypic, biological and genetic characteristics with P. vivax, we generated draft genome sequences for three P. cynomolgi strains and performed genomic analysis comparing them with the P. vivax genome, as well as with the genome of a third previously sequenced simian parasite, Plasmodium knowlesi. Here, we show that genomes of the monkey malaria clade can be characterized by copy-number variants (CNVs) in multigene families involved in evasion of the human immune system and invasion of host erythrocytes. We identify genome-wide SNPs, microsatellites and CNVs in the P. cynomolgi genome, providing a map of genetic variation that can be used to map parasite traits and study parasite populations. The sequencing of the P. cynomolgi genome is a critical step in developing a model system for P. vivax research and in counteracting the neglect of P. vivax.

  7. Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis

    Directory of Open Access Journals (Sweden)

    Susan eJoseph

    2012-11-01

    Full Text Available Cronobacter spp. (previously known as Enterobacter sakazakii is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. One recognised route of infection being the consumption of contaminated infant formula. As a recently recognised bacterial pathogen of considerable importance and regulatory control, appropriate detection and identification schemes are required. The application of multilocus sequence typing (MLST and analysis (MLSA of the seven alleles atpD, fusA, glnS, gltB, gyrB, infB and ppsA (concatenated length 3036 base pairs has led to considerable advances in our understanding of the genus. This approach is supported by both the reliability of DNA sequencing over subjective phenotyping and the establishment of a MLST database which has open access and is also curated; http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of the newly recognised genus, instrumental in the formal recognition of new Cronobacter species (C. universalis and C. condimenti and revealed the high clonality of strains and the association of clonal complex 4 with neonatal meningitis cases. Clearly the MLST approach has considerable benefits over the use of non-DNA sequence based methods of analysis for newly emergent bacterial pathogens. The application of MLST and MLSA has dramatically enabled us to better understand this opportunistic bacterium which can cause irreparable damage to a newborn baby’s brain, and has contributed to improved control measures to protect neonatal health.

  8. Insights into three whole-genome duplications gleaned from the Paramecium caudatum genome sequence.

    Science.gov (United States)

    McGrath, Casey L; Gout, Jean-Francois; Doak, Thomas G; Yanagi, Akira; Lynch, Michael

    2014-08-01

    Paramecium has long been a model eukaryote. The sequence of the Paramecium tetraurelia genome reveals a history of three successive whole-genome duplications (WGDs), and the sequences of P. biaurelia and P. sexaurelia suggest that these WGDs are shared by all members of the aurelia species complex. Here, we present the genome sequence of P. caudatum, a species closely related to the P. aurelia species group. P. caudatum shares only the most ancient of the three WGDs with the aurelia complex. We found that P. caudatum maintains twice as many paralogs from this early event as the P. aurelia species, suggesting that post-WGD gene retention is influenced by subsequent WGDs and supporting the importance of selection for dosage in gene retention. The availability of P. caudatum as an outgroup allows an expanded analysis of the aurelia intermediate and recent WGD events. Both the Guanine+Cytosine (GC) content and the expression level of preduplication genes are significant predictors of duplicate retention. We find widespread asymmetrical evolution among aurelia paralogs, which is likely caused by gradual pseudogenization rather than by neofunctionalization. Finally, cases of divergent resolution of intermediate WGD duplicates between aurelia species implicate this process acts as an ongoing reinforcement mechanism of reproductive isolation long after a WGD event.

  9. Insights into the Emergent Bacterial Pathogen Cronobacter spp., Generated by Multilocus Sequence Typing and Analysis.

    Science.gov (United States)

    Joseph, Susan; Forsythe, Stephen J

    2012-01-01

    Cronobacter spp. (previously known as Enterobacter sakazakii) is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. One recognized route of infection being the consumption of contaminated infant formula. As a recently recognized bacterial pathogen of considerable importance and regulatory control, appropriate detection, and identification schemes are required. The application of multilocus sequence typing (MLST) and analysis (MLSA) of the seven alleles atpD, fusA, glnS, gltB, gyrB, infB, and ppsA (concatenated length 3036 base pairs) has led to considerable advances in our understanding of the genus. This approach is supported by both the reliability of DNA sequencing over subjective phenotyping and the establishment of a MLST database which has open access and is also curated; http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of the newly recognized genus, instrumental in the formal recognition of new Cronobacter species (C. universalis and C. condimenti) and revealed the high clonality of strains and the association of clonal complex 4 with neonatal meningitis cases. Clearly the MLST approach has considerable benefits over the use of non-DNA sequence based methods of analysis for newly emergent bacterial pathogens. The application of MLST and MLSA has dramatically enabled us to better understand this opportunistic bacterium which can cause irreparable damage to a newborn baby's brain, and has contributed to improved control measures to protect neonatal health.

  10. Inherited platelet disorders: Insight from platelet genomics using next-generation sequencing.

    Science.gov (United States)

    Maclachlan, Annabel; Watson, Steve P; Morgan, Neil V

    2017-01-01

    Inherited platelet disorders (IPDs) are a heterogeneous group of disorders associated with normal or reduced platelet counts and bleeding diatheses of varying severities. The identification of the underlying cause of IPDs is clinically challenging due to the absence of a gold-standard platelet test, and is often based on a clinical presentation and normal values in other hematology assays. As a consequence, a DNA-based approach has a potentially important role in the investigation of these patients. Next-generation sequencing (NGS) technologies are allowing the rapid analysis of genes that have been previously implicated in IPDs or that are known to have a key role in platelet regulation, as well as novel genes that have not been previously implicated in platelet dysfunction. The potential limitations of NGS arise with the interpretation of the sheer volume of genetic information obtained from whole exome sequencing (WES) or whole genome sequencing (WGS) in order to identify function-disrupting variants. Following on from bioinformatic analysis, a number of candidate genetic variants usually remain, therefore adding to the difficulty of phenotype-genotype segregation verification. Linking genetic changes to an underlying bleeding disorder is an ongoing challenge and may not always be feasible due to the multifactorial nature of IPDs. Nevertheless, NGS will play a key role in our understanding of the mechanisms of platelet function and the genetics involved.

  11. De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

    Science.gov (United States)

    Meena, Seema; Kumar, Sarma R.; Venkata Rao, D. K.; Dwivedi, Varun; Shilpashree, H. B.; Rastogi, Shubhra; Shasany, Ajit K.; Nagegowda, Dinesh A.

    2016-01-01

    Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition. PMID:27516768

  12. Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath.

    Directory of Open Access Journals (Sweden)

    Naomi Ward

    2004-10-01

    Full Text Available Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere. Despite their importance, and in contrast to organisms that play roles in other major parts of the carbon cycle such as photosynthesis, no genome-level studies have been published on the biology of methanotrophs. We report the first complete genome sequence to our knowledge from an obligate methanotroph, Methylococcus capsulatus (Bath, obtained by the shotgun sequencing approach. Analysis revealed a 3.3-Mb genome highly specialized for a methanotrophic lifestyle, including redundant pathways predicted to be involved in methanotrophy and duplicated genes for essential enzymes such as the methane monooxygenases. We used phylogenomic analysis, gene order information, and comparative analysis with the partially sequenced methylotroph Methylobacterium extorquens to detect genes of unknown function likely to be involved in methanotrophy and methylotrophy. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear. One of the most surprising outcomes of the project is evidence suggesting the existence of previously unsuspected metabolic flexibility in M. capsulatus, including an ability to grow on sugars, oxidize chemolithotrophic hydrogen and sulfur, and live under reduced oxygen tension, all of which have implications for methanotroph ecology. The availability of the complete genome of M. capsulatus (Bath deepens our understanding of methanotroph biology and its relationship to global carbon cycles. We have gained evidence for greater metabolic flexibility than was previously known, and for

  13. Structural insights into DNA sequence recognition by Type ISP restriction-modification enzymes.

    Science.gov (United States)

    Kulkarni, Manasi; Nirwan, Neha; van Aelst, Kara; Szczelkun, Mark D; Saikrishnan, Kayarat

    2016-05-19

    Engineering restriction enzymes with new sequence specificity has been an unaccomplished challenge, presumably because of the complexity of target recognition. Here we report detailed analyses of target recognition by Type ISP restriction-modification enzymes. We determined the structure of the Type ISP enzyme LlaGI bound to its target and compared it with the previously reported structure of a close homologue that binds to a distinct target, LlaBIII. The comparison revealed that, although the two enzymes use almost a similar set of structural elements for target recognition, the residues that read the bases vary. Change in specificity resulted not only from appropriate substitution of amino acids that contacted the bases but also from new contacts made by positionally distinct residues directly or through a water bridge. Sequence analyses of 552 Type ISP enzymes showed that the structural elements involved in target recognition of LlaGI and LlaBIII were structurally well-conserved but sequentially less-conserved. In addition, the residue positions within these structural elements were under strong evolutionary constraint, highlighting the functional importance of these regions. The comparative study helped decipher a partial consensus code for target recognition by Type ISP enzymes.

  14. Molecular phylogeny of Lathyrus species: insights from sequence-related amplified polymorphism markers.

    Science.gov (United States)

    Marghali, S; Touati, A; Gharbi, M; Sdouga, D; Trifi-Farah, N

    2016-03-31

    Sequence-related amplified polymorphism (SRAP) markers were used to evaluate the intra- and interspecific variation among 40 Lathyrus genotypes (four species) (Fabaceae). Ten SRAP primer combinations resulted in a total of 94 bands, and they exhibited high interspecific variability. The genetic differentiation among Lathyrus, estimated using AMOVA, was highly significant. The results indicated that 58% of the total genetic variation existed among species, and 42% of the differentiation was within species. This was explained by the high level of genome conservation of these species as well as the recent and slow evolution of this genus. These results were confirmed by the topology of the neighbor-joining cladogram and the results of the principal coordinate analysis. Our data support previous results based on seed protein diversity. These results make SRAP markers choice markers for the study of functional polymorphism that is directly related to the transcriptomic data. The SRAP markers used in this study provide an accurate picture of the population structure within Lathyrus germplasm, which is critically important information for the design of genetic diversity and structure analyses. Moreover, further extensive studies are necessary to fully examine other Lathyrus species and tests that adopt the SRAP technique to enrich the Lathyrus library for next-generation sequencing, thus providing a potent protocol for the study of polymorphism.

  15. Insights into fluorometabolite biosynthesis in Streptomyces cattleya DSM46488 through genome sequence and knockout mutants.

    Science.gov (United States)

    Zhao, Chunhua; Li, Peng; Deng, Zixin; Ou, Hong-Yu; McGlinchey, Ryan P; O'Hagan, David

    2012-10-01

    Streptomyces cattleya DSM 46488 is unusual in its ability to biosynthesise fluorine containing natural products, where it can produce fluoroacetate and 4-fluorothreonine. The individual enzymes involved in fluorometabolite biosynthesis have already been demonstrated in in vitro investigations. Candidate genes for the individual biosynthetic steps were located from recent genome sequences. In vivo inactivation of individual genes including those encoding the S-adenosyl-l-methionine:fluoride adenosyltransferase (fluorinase, SCATT_41540), 5'-fluoro-5'-deoxyadenosine phosphorylase (SCATT_41550), fluoroacetyl-CoA thioesterase (SCATT_41470), 5-fluoro-5-deoxyribose-1-phosphate isomerase (SCATT_20080) and a 4-fluorothreonine acetaldehyde transaldolase (SCATT_p11780) confirm that they are essential for fluorometabolite production. Notably gene disruption of the transaldolase (SCATT_p11780) resulted in a mutant which could produce fluoroacetate but was blocked in its ability to biosynthesise 4-fluorothreonine, revealing a branchpoint role for the PLP-transaldolase.

  16. High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species

    DEFF Research Database (Denmark)

    Razgour, Orly; Clare, Elizabeth L.; Zeale, Matt R.K.

    2011-01-01

    cryptic bat species that are sympatric in southern England (Plecotus austriacus and P. auritus) (Fig. 1). Using Roche FLX 454 (Roche, Basel, CH) high-throughput sequencing (HTS) and uniquely tagged generic arthropod primers, we identified 142 prey Molecular Operational Taxonomic Units (MOTUs) in the diet...... of the cryptic bats, 60% of which were assigned to a likely species or genus. The findings from the molecular study supported the results of microscopic analyses in showing that the diets of both species were dominated by lepidopterans. However, HTS provided a sufficiently high resolution of prey identification...... to determine fine-scale differences in resource use. Although both bat species appeared to have a generalist diet, eared-moths from the family Noctuidae were the main prey consumed. Interspecific niche overlap was greater than expected by chance (O(jk) = 0.72, P

  17. RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

    DEFF Research Database (Denmark)

    Suárez-Fariñas, Mayte; Ungar, Benjamin; Correa da Rosa, Joel

    2015-01-01

    . These limitations might be lessened with next-generation RNA sequencing (RNA-seq). Objective: We sought to define the lesional AD transcriptome using RNA-seq and compare it using microarrays performed on the same cohort. Methods: RNA-seq and microarrays were performed to identify differentially expressed genes...... RNA-seq showed somewhat better agreement with RT-PCR (intraclass correlation coefficient, 0.57 and 0.70 for microarrays and RNA-seq vs RT-PCR, respectively), bias was not eliminated. Among genes uniquely identified by using RNA-seq were triggering receptor expressed on myeloid cells 1 (TREM-1......) signaling (eg, CCL2, CCL3, and single immunoglobulin domain IL1R1 related [SIGIRR]) and IL-36 isoform genes. TREM-1 is a surface receptor implicated in innate and adaptive immunity that amplifies infection-related inflammation. Conclusions: This is the first report of a lesional AD phenotype using RNA-seq...

  18. Revisiting the mitogenomic phylogeny of Salmoninae: new insights thanks to recent sequencing advances

    Directory of Open Access Journals (Sweden)

    Jose L. Horreo

    2017-09-01

    Full Text Available The phylogeny of the Salmonidae family, the only living one of the Order Salmoniformes, remains still unclear because of several reasons. Such reasons include insufficient taxon sampling and/or DNA information. The use of complete mitochondrial genomes (mitogenomics could provide some light on it, but despite the high number of mitogenomes of species belonging to this family published during last years, an integrative work containing all this information has not been done. In this work, the phylogeny of 46 Salmonidae species was inferred from their mitogenomic sequences. Results include a Bayesian molecular-dated phylogenetic tree with very high statistical support showing Coregoninae and Salmoninae as sister subfamilies, as well as several new phylogenetic relationships among species and genus of the family. All these findings contribute to improve our understanding of the Salmonidae systematics and could have consequences on related evolutionary studies, as well as highlight the importance of revisiting phylogenies with integrative studies.

  19. Genome sequence of mungbean and insights into evolution within Vigna species

    Science.gov (United States)

    Kang, Yang Jae; Kim, Sue K.; Kim, Moon Young; Lestari, Puji; Kim, Kil Hyun; Ha, Bo-Keun; Jun, Tae Hwan; Hwang, Won Joo; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Yoon, Min Young; Jang, Young Eun; Han, Kwang Soo; Taeprayoon, Puntaree; Yoon, Na; Somta, Prakit; Tanya, Patcharin; Kim, Kwang Soo; Gwag, Jae-Gyun; Moon, Jung-Kyung; Lee, Yeong-Ho; Park, Beom-Seok; Bombarely, Aureliano; Doyle, Jeffrey J.; Jackson, Scott A.; Schafleitner, Roland; Srinives, Peerasak; Varshney, Rajeev K.; Lee, Suk-Ha

    2014-01-01

    Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis. PMID:25384727

  20. The August 2002 earthquake sequence in north Afar: Insights into the neotectonics of the Danakil microplate

    Science.gov (United States)

    Ayele, Atalay; Stuart, Graham; Bastow, Ian; Keir, Derek

    2007-06-01

    In August 2002, there was high seismic activity in Afar concentrated at the plateau margin of the northern Ethiopian rift east of Mekele, near the western part of the Danakil microplate. The spatial and temporal distributions of this seismic activity over four weeks indicate the NNW propagation of the Gulf of Aden rift across the Afar Depression towards the western Ethiopian plateau. Fault plane solutions for six larger earthquakes from the August 2002 sequence are estimated from moment tensor inversion of local broadband waveform data. The results show only normal faulting on NNW trending and NE dipping faults, which agree with tectonics of the area and distribution of aftershocks. No strike-slip component is observed in any of our fault plane solutions or those of other workers including Harvard CMT solutions in the region. Such motion would be indicative of oblique-slip deformation between the Nubian plate and the Danakil microplate consistent with counter-clockwise rotation of the microplate. Hypocentral depths of well-constrained events are 5-7 km, which is the approximate elastic plate thickness in the Main Ethiopian rift, possibly indicating the depth to the brittle-ductile transition zone in this part of the Afar Depression. The shallowness of the depth estimates agree with the macroseismic reports available from a wide area in northern Ethiopia. Potential future shallow crustal deformation may cause significant loss of human life and damage to property in the densely populated highland region around Mekele unless measures are taken in improving building standards. The b-value for this sequence is estimated to be 0.66 using a least squares fit, while it is 0.67 ± 0.16 from a maximum-likelihood approach. This estimated b-value is low or the frequency of occurrence of relatively larger magnitude events is high indicating that it is a highly stressed region as evidenced by the recent increase of the seismicity in the area.

  1. Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.

    Science.gov (United States)

    Perry, George H; Kistler, Logan; Kelaita, Mary A; Sams, Aaron J

    2015-02-01

    Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in the TAS2R62 and TAS2R64 bitter taste receptor genes and the MYH16 masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the TAS2R38 bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC

  2. Molecular Mechanisms of Mild and Severe Pneumonia: Insights from RNA Sequencing.

    Science.gov (United States)

    Huang, Sai; Feng, Cong; Chen, Li; Huang, Zhi; Zhou, Xuan; Li, Bei; Wang, Li-Li; Chen, Wei; Lv, Fa-Qin; Li, Tan-Shi

    2017-04-06

    BACKGROUND This study aimed to uncover the molecular mechanisms underlying mild and severe pneumonia by use of mRNA sequencing (RNA-seq). MATERIAL AND METHODS RNA was extracted from the peripheral blood of patients with mild pneumonia, severe pneumonia, and healthy controls. Sequencing was performed on the HiSeq4000 platform. After filtering, clean reads were mapped to the human reference genome hg19. Differentially expressed genes (DEGs) were identified between the control group and the mild or severe group. A transcription factor-gene network was constructed for each group. Biological process (BP) terms enriched by DEGs in the network were analyzed and these genes were also mapped to the Connectivity map to search for small-molecule drugs. RESULTS A total of 199 and 560 DEGs were identified from the mild group and severe group, respectively. A transcription factor-gene network consisting of 215 nodes and another network consisting of 451 nodes were constructed in the mild group and severe group, respectively, and 54 DEGs (e.g., S100A9 and S100A12) were found to be common, with consistent differential expression changes in the 2 groups. Genes in the transcription factor-gene network for the mild group were mainly enriched in 13 BP terms, especially defense and inflammatory response (e.g., S100A8) and spermatogenesis, while the top BP terms enriched by genes in the severe group include response to oxidative stress (CCL5), wound healing, and regulation of cell differentiation (CCL5), and of the cellular protein metabolic process. CONCLUSIONS S100A9 and S100A12 may have a role in the pathogenesis of pneumonia: S100A9 and CXCL1 may contribute solely in mild pneumonia, and CCL5 and CXCL11 may contribute in severe pneumonia.

  3. Small RNA and transcriptome deep sequencing proffers insight into floral gene regulation in Rosa cultivars

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    Kim Jungeun

    2012-11-01

    Full Text Available Abstract Background Roses (Rosa sp., which belong to the family Rosaceae, are the most economically important ornamental plants—making up 30% of the floriculture market. However, given high demand for roses, rose breeding programs are limited in molecular resources which can greatly enhance and speed breeding efforts. A better understanding of important genes that contribute to important floral development and desired phenotypes will lead to improved rose cultivars. For this study, we analyzed rose miRNAs and the rose flower transcriptome in order to generate a database to expound upon current knowledge regarding regulation of important floral characteristics. A rose genetic database will enable comprehensive analysis of gene expression and regulation via miRNA among different Rosa cultivars. Results We produced more than 0.5 million reads from expressed sequences, totalling more than 110 million bp. From these, we generated 35,657, 31,434, 34,725, and 39,722 flower unigenes from Rosa hybrid: ‘Vital’, ‘Maroussia’, and ‘Sympathy’ and Rosa rugosa Thunb. , respectively. The unigenes were assigned functional annotations, domains, metabolic pathways, Gene Ontology (GO terms, Plant Ontology (PO terms, and MIPS Functional Catalogue (FunCat terms. Rose flower transcripts were compared with genes from whole genome sequences of Rosaceae members (apple, strawberry, and peach and grape. We also produced approximately 40 million small RNA reads from flower tissue for Rosa, representing 267 unique miRNA tags. Among identified miRNAs, 25 of them were novel and 242 of them were conserved miRNAs. Statistical analyses of miRNA profiles revealed both shared and species-specific miRNAs, which presumably effect flower development and phenotypes. Conclusions In this study, we constructed a Rose miRNA and transcriptome database, and we analyzed the miRNAs and transcriptome generated from the flower tissues of four Rosa cultivars. The database provides a

  4. Expanding the diversity of oenococcal bacteriophages: insights into a novel group based on the integrase sequence.

    Science.gov (United States)

    Jaomanjaka, Fety; Ballestra, Patricia; Dols-lafargue, Marguerite; Le Marrec, Claire

    2013-09-01

    Temperate bacteriophages are a contributor of the genetic diversity in the lactic acid bacterium Oenococcus oeni. We used a classification scheme for oenococcal prophages based on integrase gene polymorphism, to analyze a collection of Oenococcus strains mostly isolated in the area of Bordeaux, which represented the major lineages identified through MLST schemes in the species. Genome sequences of oenococcal prophages were clustered into four integrase groups (A to D) which were related to the chromosomal integration site. The prevalence of each group was determined and we could show that members of the intB- and intC-prophage groups were rare in our panel of strains. Our study focused on the so far uncharacterized members of the intD-group. Various intD viruses could be easily isolated from wine samples, while intD lysogens could be induced to produce phages active against two permissive O. oeni isolates. These data support the role of this prophage group in the biology of O. oeni. Global alignment of three relevant intD-prophages revealed significant conservation and highlighted a number of unique ORFs that may contribute to phage and lysogen fitness.

  5. Polyphyly of the fern family Tectariaceae sensu Ching: Insights from cpDNA sequence data

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  6. Polyphyly of the fern family Tectariaceae sensu Ching: insights from cpDNA sequence data.

    Science.gov (United States)

    Liu, HongMei; Zhang, XianChun; Chen, ZhiDuan; Dong, ShiYong; Qiu, YinLong

    2007-12-01

    Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.

  7. The genome sequence and insights into the immunogenetics of the bananaquit (Passeriformes: Coereba flaveola).

    Science.gov (United States)

    Antonides, Jennifer; Ricklefs, Robert; DeWoody, J Andrew

    2017-03-01

    Avian genomics, especially of non-model species, is in its infancy relative to mammalian genomics. Here, we describe the sequencing, assembly, and annotation of a new avian genome, that of the bananaquit Coereba flaveola (Passeriformes: Thraupidae). We produced ∼30-fold coverage of the genome with an assembly size of ca. 1.2 Gb, including approximately 16,500 annotated genes. Passerine birds, such as the bananaquit, are commonly infected by avian malarial parasites (Haemosporida), which presumably drive adaptive evolution of immunogenetic loci within the host genome. In the context of our research on the distribution of avian Haemosporida, we specifically characterized immune loci, including toll-like receptor (TLR) and major histocompatibility complex (MHC) genes. Additionally, we identified novel molecular markers in the form of single nucleotide polymorphisms (SNPs), both genome-wide and within identified immune loci. We discovered nine TLR genes and four MHC genes and identified five other TLR- or MHC- associated genes. Genome-wide, over 6 million high-quality SNPs were annotated, including 568 within TLR genes and 102 in MHC genes. This newly described genome and immune characterization expands the knowledge base for avian genomics and phylogenetics and allows for immune genotyping in the bananaquit, providing tools for the investigation of host-parasite coevolution.

  8. Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma

    Directory of Open Access Journals (Sweden)

    Gartner Jared J

    2012-09-01

    Full Text Available Abstract Background Metastasis is characterized by spreading of neoplastic cells to an organ other than where they originated and is the predominant cause of death among cancer patients. This holds true for melanoma, whose incidence is increasing more rapidly than any other cancer and once disseminated has few therapeutic options. Here we performed whole exome sequencing of two sets of matched normal and metastatic tumor DNAs. Results Using stringent criteria, we evaluated the similarities and differences between the lesions. We find that in both cases, 96% of the single nucleotide variants are shared between the two metastases indicating that clonal populations gave rise to the distant metastases. Analysis of copy number variation patterns of both metastatic sets revealed a trend similar to that seen with our single nucleotide variants. Analysis of pathway enrichment on tumor sets shows commonly mutated pathways enriched between individual sets of metastases and all metastases combined. Conclusions These data provide a proof-of-concept suggesting that individual metastases may have sufficient similarity for successful targeting of driver mutations.

  9. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.

    Science.gov (United States)

    Zhang, Guo-Qiang; Xu, Qing; Bian, Chao; Tsai, Wen-Chieh; Yeh, Chuan-Ming; Liu, Ke-Wei; Yoshida, Kouki; Zhang, Liang-Sheng; Chang, Song-Bin; Chen, Fei; Shi, Yu; Su, Yong-Yu; Zhang, Yong-Qiang; Chen, Li-Jun; Yin, Yayi; Lin, Min; Huang, Huixia; Deng, Hua; Wang, Zhi-Wen; Zhu, Shi-Lin; Zhao, Xiang; Deng, Cao; Niu, Shan-Ce; Huang, Jie; Wang, Meina; Liu, Guo-Hui; Yang, Hai-Jun; Xiao, Xin-Ju; Hsiao, Yu-Yun; Wu, Wan-Lin; Chen, You-Yi; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Luo, Yi-Bo; Van de Peer, Yves; Liu, Zhong-Jian

    2016-01-12

    Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.

  10. Whole-genome duplication and molecular evolution in Cornus L. (Cornaceae) – Insights from transcriptome sequences

    Science.gov (United States)

    Yu, Yan; Xiang, Qiuyun; Manos, Paul S.; Soltis, Douglas E.; Soltis, Pamela S.; Song, Bao-Hua; Cheng, Shifeng; Liu, Xin; Wong, Gane

    2017-01-01

    The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework. Here we compare ten de novo-assembled transcriptomes representing the major lineages of the angiosperm genus Cornus (dogwood) and relevant outgroups using a customized pipeline for analyses. Using three distinct approaches, molecular dating of orthologous genes, analyses of the distribution of synonymous substitutions between paralogous genes, and examination of substitution rates through time, we detected a shared WGD event in the late Cretaceous across all taxa sampled. The inferred doubling event coincides temporally with the paleoclimatic changes associated with the initial divergence of the genus into three major lineages. Analyses also showed an acceleration of rates of molecular evolution after WGD. The highest rates of molecular evolution were observed in the transcriptome of the herbaceous lineage, C. canadensis, a species commonly found at higher latitudes, including the Arctic. Our study demonstrates the value of transcriptome data for understanding genome evolution in closely related species. The results suggest dramatic increase in sea surface temperature in the late Cretaceous may have contributed to the evolution and diversification of flowering plants. PMID:28225773

  11. De novo Sequencing and Analysis of Lemongrass Transcriptome Provides First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

    Directory of Open Access Journals (Sweden)

    Seema Meena

    2016-07-01

    Full Text Available Aromatic grasses of the genus Cymbopogon (Poaceae family represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavour, fragrance, cosmetic and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step towards understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases (TPS, pyrophosphatases (PPase, alcohol dehydrogenases (ADH, aldo-keto reductases (AKR, carotenoid cleavage dioxygenases (CCD, alcohol acetyltransferases (AAT and aldehyde dehydrogenases (ALDH, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes and acetates. Molecular modeling and docking further supported the role of identified enzymes in aroma formation in Cymbopogon. Also, simple sequence repeats (SSRs were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

  12. Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle, and koalas.

    Science.gov (United States)

    Jelocnik, Martina; Frentiu, Francesca D; Timms, Peter; Polkinghorne, Adam

    2013-08-01

    Chlamydia pecorum is a significant pathogen of domestic livestock and wildlife. We have developed a C. pecorum-specific multilocus sequence analysis (MLSA) scheme to examine the genetic diversity of and relationships between Australian sheep, cattle, and koala isolates. An MLSA of seven concatenated housekeeping gene fragments was performed using 35 isolates, including 18 livestock isolates (11 Australian sheep, one Australian cow, and six U.S. livestock isolates) and 17 Australian koala isolates. Phylogenetic analyses showed that the koala isolates formed a distinct clade, with limited clustering with C. pecorum isolates from Australian sheep. We identified 11 MLSA sequence types (STs) among Australian C. pecorum isolates, 10 of them novel, with koala and sheep sharing at least one identical ST (designated ST2013Aa). ST23, previously identified in global C. pecorum livestock isolates, was observed here in a subset of Australian bovine and sheep isolates. Most notably, ST23 was found in association with multiple disease states and hosts, providing insights into the transmission of this pathogen between livestock hosts. The complexity of the epidemiology of this disease was further highlighted by the observation that at least two examples of sheep were infected with different C. pecorum STs in the eyes and gastrointestinal tract. We have demonstrated the feasibility of our MLSA scheme for understanding the host relationship that exists between Australian C. pecorum strains and provide the first molecular epidemiological data on infections in Australian livestock hosts.

  13. Metagenomic Sequencing of Marine Periphyton: Taxonomic and Functional Insights into Biofilm Communities

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    Kemal eSanli

    2015-10-01

    Full Text Available Periphyton communities are complex phototrophic, multispecies biofilms that develop on surfaces in aquatic environments. These communities harbor a large diversity of organisms comprising viruses, bacteria, algae, fungi, protozoans and metazoans. However, thus far the total biodiversity of periphyton has not been described. In this study, we use metagenomics to characterize periphyton communities from the marine environment of the Swedish west coast. Although we found approximately ten times more eukaryotic rRNA marker gene sequences compared to prokaryotic, the whole metagenome-based similarity searches showed that bacteria constitute the most abundant phyla in these biofilms. We show that marine periphyton encompass a range of heterotrophic and phototrophic organisms. Heterotrophic bacteria, including the majority of proteobacterial clades and Bacteroidetes, and eukaryotic macro-invertebrates were found to dominate periphyton. The phototrophic groups comprise Cyanobacteria and the alpha-proteobacterial genus Roseobacter, followed by different micro- and macro-algae. We also assess the metabolic pathways that predispose these communities to an attached lifestyle. Functional indicators of the biofilm form of life in periphyton involve genes coding for enzymes that catalyze the production and degradation of extracellular polymeric substances, mainly in the form of complex sugars such as starch and glycogen-like meshes together with chitin. Genes for 278 different transporter proteins were detected in the metagenome, constituting the most abundant protein complexes. Finally, genes encoding enzymes that participate in anaerobic pathways, such as denitrification and methanogenesis, were detected suggesting the presence of anaerobic or low-oxygen micro-zones within the biofilms.

  14. Controls on solid-phase inclusion during porphyroblast growth: insights from the Barrovian sequence (Scottish Dalradian)

    Science.gov (United States)

    Farber, Katja; Caddick, Mark J.; John, Timm

    2014-12-01

    A series of Barrovian sequence samples ranging from garnet to sillimanite zones were investigated to infer their porphyroblast-forming reactions and mineral inclusion histories. Quartz is overgrown and partly consumed during garnet formation and remains as inclusion-rich layers in porphyroblasts of the garnet zone. Staurolite crystals in the staurolite zone display sharp transitions between inclusion-rich and inclusion-free areas, suggesting two stages of growth with a different role of quartz in each. The inclusion-rich domains formed similarly to those in garnet by simple overgrowth and resorption of matrix minerals, with thermodynamic constraints suggesting that this staurolite-forming reaction required the presence of chloritoid that is now absent from the examined samples. The participation of garnet was limited in staurolite formation, with chloritoid breakdown supplying sufficient material to form the large amounts (c. 25 vol%) of staurolite found in the rock. This reaction produces an excess of SiO2, which leaves the crystal domain as SiO2aq and thus caused the formation of the inclusion-free areas in the staurolite and precipitation of quartz in the matrix. In the sillimanite zone, staurolite is consumed forming new garnet. The newly formed garnet has less quartz inclusions than its core due to a proportionally greater consumption of quartz by the second garnet-forming reaction than by the initial, garnet-grade reactions. Textural and thermodynamic data both suggest that inclusions in these porphyroblasts represent leftovers of a preferentially overgrown matrix than co-products of the porphyroblast-forming reaction.

  15. New insights into Holocene eruption episodes from proximal deposit sequences at Mt. Taranaki (Egmont), New Zealand

    Science.gov (United States)

    Torres-Orozco, Rafael; Cronin, Shane J.; Pardo, Natalia; Palmer, Alan S.

    2017-01-01

    Upper stratovolcano flanks contain the most nuanced depositional record of long eruption episodes, but steep, irregular terrain makes these sequences difficult to correlate and interpret. This necessitates development of a detailed and systematic approach to describing localized depositional facies and relating these to eruptive processes. In this work, the late-Holocene eruption history of Mt. Taranaki/Egmont, New Zealand, was re-assessed based on a study of proximal deposits spanning the 14C-dated age range of 5.0-0.3 cal ka B.P. Mt. Taranaki is a textbook-example stratovolcano, with geological evidence pointing to sudden switches in scale, type and frequency of eruptions over its 130 ka history. The proximal stratigraphy presented here almost doubles the number of eruptions recognized from previous soil-stratigraphy studies. A total of 53 lithostratigraphic bed-sets record eruptions of the summit crater and parasitic vents like Fanthams Peak (the latter between 3.0 and 1.5 cal ka B.P.). At least 12 of the eruptions represented by these bed-sets comprise deposits comparable with or thicker than those of the latest sub-Plinian eruption of AD 1655. The largest eruption episode represented is the 4.6-4.7-cal ka B.P. Kokowai. Contrasting eruption styles were identified, from stable basaltic-andesite eruption columns at Fanthams Peak, to andesitic lava-dome extrusion, blasts and partial collapse of unstable eruption columns at Mt. Taranaki's summit. The centemetre-scale proximal deposit descriptions were used to identify several previously unknown, smaller eruption events. These details are indispensable for building a comprehensive probabilistic event record and in the development of realistic eruptive scenarios for complex eruption episodes prior to re-awakening of a volcano.

  16. Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing.

    Science.gov (United States)

    Christie, Andrew E; Chi, Megan; Lameyer, Tess J; Pascual, Micah G; Shea, Devlin N; Stanhope, Meredith E; Schulz, David J; Dickinson, Patsy S

    2015-01-01

    Peptides are the largest and most diverse class of molecules used for neurochemical communication, playing key roles in the control of essentially all aspects of physiology and behavior. The American lobster, Homarus americanus, is a crustacean of commercial and biomedical importance; lobster growth and reproduction are under neuropeptidergic control, and portions of the lobster nervous system serve as models for understanding the general principles underlying rhythmic motor behavior (including peptidergic neuromodulation). While a number of neuropeptides have been identified from H. americanus, and the effects of some have been investigated at the cellular/systems levels, little is currently known about the molecular components of neuropeptidergic signaling in the lobster. Here, a H. americanus neural transcriptome was generated and mined for sequences encoding putative peptide precursors and receptors; 35 precursor- and 41 receptor-encoding transcripts were identified. We predicted 194 distinct neuropeptides from the deduced precursor proteins, including members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FLRFamide, GSEFLamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, proctolin, pyrokinin, SIFamide, sulfakinin and tachykinin-related peptide families. While some of the predicted peptides are known H. americanus isoforms, most are novel identifications, more than doubling the extant lobster neuropeptidome. The deduced receptor proteins are the first descriptions of H. americanus neuropeptide receptors, and include ones for most of the peptide groups mentioned earlier, as well as those for ecdysis-triggering hormone, red pigment concentrating hormone

  17. Insight into Shiga toxin genes encoded by Escherichia coli O157 from whole genome sequencing

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    Philip M. Ashton

    2015-02-01

    Full Text Available The ability of Shiga toxin-producing Escherichia coli (STEC to cause severe illness in humans is determined by multiple host factors and bacterial characteristics, including Shiga toxin (Stx subtype. Given the link between Stx2a subtype and disease severity, we sought to identify the stx subtypes present in whole genome sequences (WGS of 444 isolates of STEC O157. Difficulties in assembling the stx genes in some strains were overcome by using two complementary bioinformatics methods: mapping and de novo assembly. We compared the WGS analysis with the results obtained using a PCR approach and investigated the diversity within and between the subtypes. All strains of STEC O157 in this study had stx1a, stx2a or stx2c or a combination of these three genes. There was over 99% (442/444 concordance between PCR and WGS. When common source strains were excluded, 236/349 strains of STEC O157 had multiple copies of different Stx subtypes and 54 had multiple copies of the same Stx subtype. Of those strains harbouring multiple copies of the same Stx subtype, 33 had variants between the alleles while 21 had identical copies. Strains harbouring Stx2a only were most commonly found to have multiple alleles of the same subtype (42%. Both the PCR and WGS approach to stx subtyping provided a good level of sensitivity and specificity. In addition, the WGS data also showed there were a significant proportion of strains harbouring multiple alleles of the same Stx subtype associated with clinical disease in England.

  18. Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing.

    Directory of Open Access Journals (Sweden)

    Andrew E Christie

    Full Text Available Peptides are the largest and most diverse class of molecules used for neurochemical communication, playing key roles in the control of essentially all aspects of physiology and behavior. The American lobster, Homarus americanus, is a crustacean of commercial and biomedical importance; lobster growth and reproduction are under neuropeptidergic control, and portions of the lobster nervous system serve as models for understanding the general principles underlying rhythmic motor behavior (including peptidergic neuromodulation. While a number of neuropeptides have been identified from H. americanus, and the effects of some have been investigated at the cellular/systems levels, little is currently known about the molecular components of neuropeptidergic signaling in the lobster. Here, a H. americanus neural transcriptome was generated and mined for sequences encoding putative peptide precursors and receptors; 35 precursor- and 41 receptor-encoding transcripts were identified. We predicted 194 distinct neuropeptides from the deduced precursor proteins, including members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH, CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FLRFamide, GSEFLamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, proctolin, pyrokinin, SIFamide, sulfakinin and tachykinin-related peptide families. While some of the predicted peptides are known H. americanus isoforms, most are novel identifications, more than doubling the extant lobster neuropeptidome. The deduced receptor proteins are the first descriptions of H. americanus neuropeptide receptors, and include ones for most of the peptide groups mentioned earlier, as well as those for ecdysis-triggering hormone, red pigment

  19. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis.

    Science.gov (United States)

    Wang, Linhai; Yu, Sheng; Tong, Chaobo; Zhao, Yingzhong; Liu, Yan; Song, Chi; Zhang, Yanxin; Zhang, Xudong; Wang, Ying; Hua, Wei; Li, Donghua; Li, Dan; Li, Fang; Yu, Jingyin; Xu, Chunyan; Han, Xuelian; Huang, Shunmou; Tai, Shuaishuai; Wang, Junyi; Xu, Xun; Li, Yingrui; Liu, Shengyi; Varshney, Rajeev K; Wang, Jun; Zhang, Xiurong

    2014-02-27

    Sesame, Sesamum indicum L., is considered the queen of oilseeds for its high oil content and quality, and is grown widely in tropical and subtropical areas as an important source of oil and protein. However, the molecular biology of sesame is largely unexplored. Here, we report a high-quality genome sequence of sesame assembled de novo with a contig N50 of 52.2 kb and a scaffold N50 of 2.1 Mb, containing an estimated 27,148 genes. The results reveal novel, independent whole genome duplication and the absence of the Toll/interleukin-1 receptor domain in resistance genes. Candidate genes and oil biosynthetic pathways contributing to high oil content were discovered by comparative genomic and transcriptomic analyses. These revealed the expansion of type 1 lipid transfer genes by tandem duplication, the contraction of lipid degradation genes, and the differential expression of essential genes in the triacylglycerol biosynthesis pathway, particularly in the early stage of seed development. Resequencing data in 29 sesame accessions from 12 countries suggested that the high genetic diversity of lipid-related genes might be associated with the wide variation in oil content. Additionally, the results shed light on the pivotal stage of seed development, oil accumulation and potential key genes for sesamin production, an important pharmacological constituent of sesame. As an important species from the order Lamiales and a high oil crop, the sesame genome will facilitate future research on the evolution of eudicots, as well as the study of lipid biosynthesis and potential genetic improvement of sesame.

  20. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.

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    Garret Suen

    Full Text Available Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to cultivate a fungus that serves as the colony's primary food source. This obligate ant-fungus mutualism is one of the few occurrences of farming by non-humans and likely facilitated the formation of their massive colonies. Mature leaf-cutter ant colonies contain millions of workers ranging in size from small garden tenders to large soldiers, resulting in one of the most complex polymorphic caste systems within ants. To begin uncovering the genomic underpinnings of this system, we sequenced the genome of Atta cephalotes using 454 pyrosequencing. One prediction from this ant's lifestyle is that it has undergone genetic modifications that reflect its obligate dependence on the fungus for nutrients. Analysis of this genome sequence is consistent with this hypothesis, as we find evidence for reductions in genes related to nutrient acquisition. These include extensive reductions in serine proteases (which are likely unnecessary because proteolysis is not a primary mechanism used to process nutrients obtained from the fungus, a loss of genes involved in arginine biosynthesis (suggesting that this amino acid is obtained from the fungus, and the absence of a hexamerin (which sequesters amino acids during larval development in other insects. Following recent reports of genome sequences from other insects that engage in symbioses with beneficial microbes, the A. cephalotes genome provides new insights into the symbiotic lifestyle of this ant and advances our understanding of host-microbe symbioses.

  1. Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution

    Science.gov (United States)

    Thiele, Kevin R.; Krauss, Siegfried L.; Barrett, Matthew D.

    2017-01-01

    Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set is still being explored. We present a case study for the use of genotyping-by-sequencing (GBS) to resolve relationships in a species complex of Australian arid and semi-arid grasses (Triodia R.Br.), highlighting our solutions to methodological challenges in the use of GBS data. We merged overlapping paired-end reads then optimised locus assembly in the program PyRAD to generate GBS data sets for phylogenetic and distance-based analyses. In addition to traditional concatenation analyses in RAxML, we also demonstrate the novel use of summary species tree analyses (taking gene trees as input) with GBS loci. We found that while species tree analyses were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses resulted in well-supported but conflicting topologies under different assembly settings. Despite this conflict, multiple clades in the complex were consistently supported as distinct across analyses. Our GBS data assembly and analyses improve the resolution of taxa and phylogenetic relationships in the Triodia basedowii complex compared to our previous study based on Sanger sequencing of nuclear (ITS/ETS) and chloroplast (rps16-trnK spacer) markers. The genomic results also partly support previous evidence for hybridization between species in the complex. Our methodological insights for analysing GBS data will assist researchers using similar data to resolve phylogenetic relationships within species complexes. PMID:28135342

  2. Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution.

    Science.gov (United States)

    Anderson, Benjamin M; Thiele, Kevin R; Krauss, Siegfried L; Barrett, Matthew D

    2017-01-01

    Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set is still being explored. We present a case study for the use of genotyping-by-sequencing (GBS) to resolve relationships in a species complex of Australian arid and semi-arid grasses (Triodia R.Br.), highlighting our solutions to methodological challenges in the use of GBS data. We merged overlapping paired-end reads then optimised locus assembly in the program PyRAD to generate GBS data sets for phylogenetic and distance-based analyses. In addition to traditional concatenation analyses in RAxML, we also demonstrate the novel use of summary species tree analyses (taking gene trees as input) with GBS loci. We found that while species tree analyses were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses resulted in well-supported but conflicting topologies under different assembly settings. Despite this conflict, multiple clades in the complex were consistently supported as distinct across analyses. Our GBS data assembly and analyses improve the resolution of taxa and phylogenetic relationships in the Triodia basedowii complex compared to our previous study based on Sanger sequencing of nuclear (ITS/ETS) and chloroplast (rps16-trnK spacer) markers. The genomic results also partly support previous evidence for hybridization between species in the complex. Our methodological insights for analysing GBS data will assist researchers using similar data to resolve phylogenetic relationships within species complexes.

  3. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction.

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    Kathryn Winglee

    2016-01-01

    Full Text Available Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC, causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system.We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes.This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity.

  4. Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction

    Science.gov (United States)

    Maiga, Mamoudou; Abeel, Thomas; Shea, Terrance; Desjardins, Christopher A.; Diarra, Bassirou; Baya, Bocar; Sanogo, Moumine; Diallo, Souleymane; Earl, Ashlee M.; Bishai, William R.

    2016-01-01

    Background Mycobacterium africanum, made up of lineages 5 and 6 within the Mycobacterium tuberculosis complex (MTC), causes up to half of all tuberculosis cases in West Africa, but is rarely found outside of this region. The reasons for this geographical restriction remain unknown. Possible reasons include a geographically restricted animal reservoir, a unique preference for hosts of West African ethnicity, and an inability to compete with other lineages outside of West Africa. These latter two hypotheses could be caused by loss of fitness or altered interactions with the host immune system. Methodology/Principal Findings We sequenced 92 MTC clinical isolates from Mali, including two lineage 5 and 24 lineage 6 strains. Our genome sequencing assembly, alignment, phylogeny and average nucleotide identity analyses enabled us to identify features that typify lineages 5 and 6 and made clear that these lineages do not constitute a distinct species within the MTC. We found that in Mali, lineage 6 and lineage 4 strains have similar levels of diversity and evolve drug resistance through similar mechanisms. In the process, we identified a putative novel streptomycin resistance mutation. In addition, we found evidence of person-to-person transmission of lineage 6 isolates and showed that lineage 6 is not enriched for mutations in virulence-associated genes. Conclusions This is the largest collection of lineage 5 and 6 whole genome sequences to date, and our assembly and alignment data provide valuable insights into what distinguishes these lineages from other MTC lineages. Lineages 5 and 6 do not appear to be geographically restricted due to an inability to transmit between West African hosts or to an elevated number of mutations in virulence-associated genes. However, lineage-specific mutations, such as mutations in cell wall structure, secretion systems and cofactor biosynthesis, provide alternative mechanisms that may lead to host specificity. PMID:26751217

  5. The road to the red sequence via secular and environmental processes: insights from the local Universe

    Science.gov (United States)

    Consolandi, Guido

    2017-04-01

    The evolution of galaxies can be thought as the result of the cumulative effects of two broad classes of processes: (i) secular (internal) processes determined by the very nature of the galaxy, and (ii) external processes that are determined by the environment in which the object is embedded. In this thesis I face both aspects of galaxy evolution. Among secular processes, I investigated the effects of stellar bars on the gaseous components of galaxies and their consequences on their evolution. In particular I show how bars affect both the ionized and cold gas in two different samples: the sample of the Halpha3 survey, an Halpha imaging survey of galaxies selected from ALFALFA in the Local and Coma superclusters; the Herschel Reference Sample, a representative sample of 323 local galaxies observed with the space-based Herschel observatory sensitive to the far-infrared emission of dust, a good tracer of cold gas. Owing to the Halpha3 data I demonstrate that main sequence barred galaxies have specific star formation rate suppressed with respect to pure disks. Here I propose a simple model in which bars drive the evolution of disk galaxies. Hydrodynamical simulations indeed show that a barred potential funnels the gas inside the corotation radius toward the center of the galaxy where it reaches high densities, cools and can be consumed by a burst of star formation. At the same time the dynamical torque of the bar keeps the gas outside the corotation radius in place, cutting the gas supply to the central region that consequently stops its star formation activity. Taking advantage of the images of the HRS sample, we show the evidences of such quenching. The aforementioned model is further tested by studying the stellar population properties of galaxies belonging to a sample of 6000 galaxies extracted from SDSS. To this aim, I designed in-house IDL codes that automatically perform aperture photometry and isophotal fitting recovering reliable magnitudes, colors

  6. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

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    Cloutier Sylvie

    2011-05-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

  7. Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism.

    Science.gov (United States)

    Liu, Tao; Wang, Kai-Yu; Wang, Jun; Chen, De-Fang; Huang, Xiao-Li; Ouyang, Ping; Geng, Yi; He, Yang; Zhou, Yi; Min, Jie

    2016-04-14

    Yersinia ruckeri is the etiologic agent of enteric red mouth disease (ERM), a severe fish disease prevailing in worldwide aquaculture industries. Here we report for the first time the complete genome of Y. ruckeri (Yersinia ruckeri) SC09, a highly virulent strain isolated from Ictalurus punctatus with severe septicemia. SC09 possesses a single chromosome of 3,923,491 base pairs, which contains 3651 predicted protein coding sequences (CDS), 19 rRNA genes, and 79 tRNA genes. Among the CDS, we have identified a Ysa locus containing genes encoding all the components of a type III secretion system (T3SS). Comparative analysis suggest that SC09-Ysa share extensive similarity in sequence, gene content, and gene arrangement with Salmonella enterica pathogenicity island 1 (SPI1) and chromosome-encoded T3SS from Yersinia enterocolitica biotype 1B. Furthermore, phylogenetic analysis shown that SC09-Ysa and SPI1-T3SS belong on the same branch of the phylogenetic tree. These results suggest that SC09-Ysa and SPI1-T3SS appear to mediate biological function to adapt to specific hosts with a similar niche, and both of them are likely to facilitate the development of an intracellular niche. In addition, our analysis also indicated that a substantial part of the SC09 genome might contribute to adaption in the intestinal microenvironment, including a number of proteins associated with aerobic or anaerobic respiration, signal transduction, and various stress reactions. Genomic analysis of the bacterium offered insights into the pathogenic mechanism associated with intracellular infection and intestinal survivability, which constitutes an important first step in understanding the pathogenesis of Y. ruckeri.

  8. Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa.

    Science.gov (United States)

    Vandelannoote, Koen; Jordaens, Kurt; Bomans, Pieter; Leirs, Herwig; Durnez, Lies; Affolabi, Dissou; Sopoh, Ghislain; Aguiar, Julia; Phanzu, Delphin Mavinga; Kibadi, Kapay; Eyangoh, Sara; Manou, Louis Bayonne; Phillips, Richard Odame; Adjei, Ohene; Ablordey, Anthony; Rigouts, Leen; Portaels, Françoise; Eddyani, Miriam; de Jong, Bouke C

    2014-02-01

    Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the phylogeographic relationships within the genetically conserved cluster of African M. ulcerans. Our analyses identified 23 different African insertion sequence element single nucleotide polymorphism (ISE-SNP) types that dominate in different areas where Buruli ulcer is endemic. These ISE-SNP types appear to be the initial stages of clonal diversification from a common, possibly ancestral ISE-SNP type. ISE-SNP types were found unevenly distributed over the greater West African hydrological drainage basins. Our findings suggest that geographical barriers bordering the basins to some extent prevented bacterial gene flow between basins and that this resulted in independent focal transmission clusters associated with the hydrological drainage areas. Different phylogenetic methods yielded two well-supported sister clades within the African ISE-SNP types. The ISE-SNP types from the "pan-African clade" were found to be widespread throughout Africa, while the ISE-SNP types of the "Gabonese/Cameroonian clade" were much rarer and found in a more restricted area, which suggested that the latter clade evolved more recently. Additionally, the Gabonese/Cameroonian clade was found to form a strongly supported monophyletic group with Papua New Guinean ISE-SNP type 8, which is unrelated to other Southeast Asian ISE-SNP types.

  9. CARBON-OXYGEN ISOTOPE RECORDS OF PEDOGENIC CARBONATE FROM THE EARLY MIOCENE-PLEISTOCENE LOESS-RED CLAY IN THE VICINITY OF THE LIUPANSHAN REGION AND ITS IMPLICATIONS FOR THE EARLY ORIGIN OF C4 PLANTS IN THE CHINESE LOESS PLATEAU%中新世以来六盘山邻区黄土-红粘土成土碳酸盐碳氧同位素记录及其对C4植物早期扩张的指示

    Institute of Scientific and Technical Information of China (English)

    张瑜; 熊尚发; 丁仲礼; 卢海建; 姜文英

    2011-01-01

    sites in the world have revealed that the timing of C4 plants origin and expansion was not globally synchronous, and different proxy records documented different timing features of C4 expansion. The history of C4 plants in Asia is an important component in reconstructing the globally geographical patterns of C4 expansion. Records from South Asia indicate C4 plants expanded abruptly during ca. 8 ~4Ma,and several localities in the Chinese Loess Plateau document a δ13C peak at ca. 6Ma,3Ma and from 1 Ma,respectively. Previous studies have demonstrated that during ca. 7 ~ 4Ma,soil carbonate records ( δ13Csc) in the Chinese Loess Plateau display a southern-ward negative trend, indicative of a southern-ward expansion of C4 plants during the Late Miocene and the Early Pliocene. It is remained unclear, however, that if the C4 plants expansion over the Chinese Loess Plateau occurred earlier than during the Late Miocene.Here we report a study based on δ13Csc of loess-red clay sequence from the Baishui and Zhuanglang sections near the Liupanshan region,and the result shows that C4 plants expansion may have initiated as early as at ca. 20Ma with C4 component up to 15% -40% during the Miocene. The Baishui section(35°24'10"N,106°54'43"E) is located in the southeastern part of the Liupanshan region,Central Loess Plateau. This section contains an upper 214m loess-paleosol sequence and a lower 82m red clay deposit. The Zhuanglang section ( 35°13'34"N, 106°4'11"E) lies at the southwestern part of the Liupanshan region,ca.80km to the Baishui section,and consists of 183. 4m red clay deposit. A total 2729 paleomagnetic samples (1026 samples for the Baishui section, 1703 for the Zhuanglang section) were analyzed by using thermal demagnetization at the Laboratory of Piaeomagnetism of the Institute of Geology and Geophysics, Chinese Academy of Sciences and at Lanzhou University. The specimens that exhibit stable component two vectors (91% for the Baishui section and 83.5% for the

  10. Complete metagenome sequencing based bacterial diversity and functional insights from basaltic hot spring of Unkeshwar, Maharashtra, India

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    Gajanan T. Mehetre

    2016-03-01

    Full Text Available Unkeshwar hot springs are located at geographical South East Deccan Continental basalt of India. Here, we report the microbial community analysis of this hot spring using whole metagenome shotgun sequencing approach. The analysis revealed a total of 848,096 reads with 212.87 Mbps with 50.87% G + C content. Metagenomic sequences were deposited in SRA database with accession number (SUB1242219. Community analysis revealed 99.98% sequences belonging to bacteria and 0.01% to archaea and 0.01% to Viruses. The data obtained revealed 41 phyla including bacteria and Archaea and including 719 different species. In taxonomic analysis, the dominant phyla were found as, Actinobacteria (56%, Verrucomicrobia (24%, Bacteriodes (13%, Deinococcus-Thermus (3% and firmicutes (2% and Viruses (2%. Furthermore, functional annotation using pathway information revealed dynamic potential of hot spring community in terms of metabolism, environmental information processing, cellular processes and other important aspects. Kyoto Encyclopedia of Genes and Genomes (KEGG pathway analysis of each contig sequence by assigning KEGG Orthology (KO numbers revealed contig sequences that were assigned to metabolism, organismal system, Environmental Information Processing, cellular processes and human diseases with some unclassified sequences. The Unkeshwar hot springs offer rich phylogenetic diversity and metabolic potential for biotechnological applications.

  11. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution

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    Purves Joanne

    2012-09-01

    Full Text Available Abstract Background Staphylococcus aureus Repeat (STAR elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.

  12. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution.

    Science.gov (United States)

    Purves, Joanne; Blades, Matthew; Arafat, Yasrab; Malik, Salman A; Bayliss, Christopher D; Morrissey, Julie A

    2012-09-28

    Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis.

  13. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

    Science.gov (United States)

    Bertelli, Claire; Aeby, Sébastien; Chassot, Bérénice; Clulow, James; Hilfiker, Olivier; Rappo, Samuel; Ritzmann, Sébastien; Schumacher, Paolo; Terrettaz, Céline; Benaglio, Paola; Falquet, Laurent; Farinelli, Laurent; Gharib, Walid H; Goesmann, Alexander; Harshman, Keith; Linke, Burkhard; Miyazaki, Ryo; Rivolta, Carlo; Robinson-Rechavi, Marc; van der Meer, Jan Roelof; Greub, Gilbert

    2015-01-01

    With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

  14. Assessing the ability of sequence-based methods to provide functional insight within membrane integral proteins: a case study analyzing the neurotransmitter/Na+ symporter family

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    Eskandari Sepehr

    2007-10-01

    Full Text Available Abstract Background Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent technological advances, structural coverage of membrane integral proteins continues to be sparse. ConSequently, sequence-based methods represent an important alternative to illuminate functional roles. In this report, we critically examine the ability of several computational methods to provide functional insight within two specific areas. First, can phylogenomic methods accurately describe the functional diversity across a membrane integral protein family? And second, can sequence-based strategies accurately predict key functional sites? Due to the presence of a recently solved structure and a vast amount of experimental mutagenesis data, the neurotransmitter/Na+ symporter (NSS family is an ideal model system to assess the quality of our predictions. Results The raw NSS sequence dataset contains 181 sequences, which have been aligned by various methods. The resultant phylogenetic trees always contain six major subfamilies are consistent with the functional diversity across the family. Moreover, in well-represented subfamilies, phylogenetic clustering recapitulates several nuanced functional distinctions. Functional sites are predicted using six different methods (phylogenetic motifs, two methods that identify subfamily-specific positions, and three different conservation scores. A canonical set of 34 functional sites identified by Yamashita et al. within the recently solved LeuTAa structure is used to assess the quality of the predictions, most of which are predicted by the bioinformatic methods. Remarkably, the importance of these sites is largely confirmed by experimental mutagenesis. Furthermore, the collective set of functional site predictions qualitatively clusters along the proposed transport pathway, further

  15. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

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    Tongwu Zhang

    Full Text Available The complete nucleotide sequences of the chloroplast (cp and mitochondrial (mt genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147 with a 72% coding sequence, and the larger mitochondrial genome have less genes (65 with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

  16. The complete chloroplast and mitochondrial genome sequences of Boea hygrometrica: insights into the evolution of plant organellar genomes.

    Science.gov (United States)

    Zhang, Tongwu; Fang, Yongjun; Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage.

  17. Global Transcriptome Analysis of the Tentacle of the Jellyfish Cyanea capillata Using Deep Sequencing and Expressed Sequence Tags: Insight into the Toxin- and Degenerative Disease-Related Transcripts.

    Directory of Open Access Journals (Sweden)

    Guoyan Liu

    Full Text Available Jellyfish contain diverse toxins and other bioactive components. However, large-scale identification of novel toxins and bioactive components from jellyfish has been hampered by the low efficiency of traditional isolation and purification methods.We performed de novo transcriptome sequencing of the tentacle tissue of the jellyfish Cyanea capillata. A total of 51,304,108 reads were obtained and assembled into 50,536 unigenes. Of these, 21,357 unigenes had homologues in public databases, but the remaining unigenes had no significant matches due to the limited sequence information available and species-specific novel sequences. Functional annotation of the unigenes also revealed general gene expression profile characteristics in the tentacle of C. capillata. A primary goal of this study was to identify putative toxin transcripts. As expected, we screened many transcripts encoding proteins similar to several well-known toxin families including phospholipases, metalloproteases, serine proteases and serine protease inhibitors. In addition, some transcripts also resembled molecules with potential toxic activities, including cnidarian CfTX-like toxins with hemolytic activity, plancitoxin-1, venom toxin-like peptide-6, histamine-releasing factor, neprilysin, dipeptidyl peptidase 4, vascular endothelial growth factor A, angiotensin-converting enzyme-like and endothelin-converting enzyme 1-like proteins. Most of these molecules have not been previously reported in jellyfish. Interestingly, we also characterized a number of transcripts with similarities to proteins relevant to several degenerative diseases, including Huntington's, Alzheimer's and Parkinson's diseases. This is the first description of degenerative disease-associated genes in jellyfish.We obtained a well-categorized and annotated transcriptome of C. capillata tentacle that will be an important and valuable resource for further understanding of jellyfish at the molecular level and information

  18. Whole-exome sequencing and targeted gene sequencing provide insights into the role of PALB2 as a male breast cancer susceptibility gene.

    Science.gov (United States)

    Silvestri, Valentina; Zelli, Veronica; Valentini, Virginia; Rizzolo, Piera; Navazio, Anna Sara; Coppa, Anna; Agata, Simona; Oliani, Cristina; Barana, Daniela; Castrignanò, Tiziana; Viel, Alessandra; Russo, Antonio; Tibiletti, Maria Grazia; Zanna, Ines; Masala, Giovanna; Cortesi, Laura; Manoukian, Siranoush; Azzollini, Jacopo; Peissel, Bernard; Bonanni, Bernardo; Peterlongo, Paolo; Radice, Paolo; Palli, Domenico; Giannini, Giuseppe; Chillemi, Giovanni; Montagna, Marco; Ottini, Laura

    2017-01-01

    Male breast cancer (MBC) is a rare disease whose etiology appears to be largely associated with genetic factors. BRCA1 and BRCA2 mutations account for about 10% of all MBC cases. Thus, a fraction of MBC cases are expected to be due to genetic factors not yet identified. To further explain the genetic susceptibility for MBC, whole-exome sequencing (WES) and targeted gene sequencing were applied to high-risk, BRCA1/2 mutation-negative MBC cases. Germ-line DNA of 1 male and 2 female BRCA1/2 mutation-negative breast cancer (BC) cases from a pedigree showing a first-degree family history of MBC was analyzed with WES. Targeted gene sequencing for the validation of WES results was performed for 48 high-risk, BRCA1/2 mutation-negative MBC cases from an Italian multicenter study of MBC. A case-control series of 433 BRCA1/2 mutation-negative MBC and female breast cancer (FBC) cases and 849 male and female controls was included in the study. WES in the family identified the partner and localizer of BRCA2 (PALB2) c.419delA truncating mutation carried by the proband, her father, and her paternal uncle (all affected with BC) and the N-acetyltransferase 1 (NAT1) c.97C>T nonsense mutation carried by the proband's maternal aunt. Targeted PALB2 sequencing detected the c.1984A>T nonsense mutation in 1 of the 48 BRCA1/2 mutation-negative MBC cases. NAT1 c.97C>T was not found in the case-control series. These results add strength to the evidence showing that PALB2 is involved in BC risk for both sexes and indicate that consideration should be given to clinical testing of PALB2 for BRCA1/2 mutation-negative families with multiple MBC and FBC cases. Cancer 2017;123:210-218. © 2016 American Cancer Society. © 2016 American Cancer Society.

  19. Taxonomy of the African army ant Dorylus gribodoi Emery, 1892 (Hymenoptera, Formicidae) - new insights from DNA sequence data and morphology

    DEFF Research Database (Denmark)

    Schöning, Caspar; Gotwald, William H.; Kronauer, Daniel Jan Christoph

    2008-01-01

    Numerous species in the Old World army ant genus Dorylus have been described based on a single sex or caste. Our analysis of mitochondrial cytochrome oxidase II gene sequences of specimens from the same population reveals that D. gribodoi Emery males are conspecific with D. gerstaeckeri Emery...

  20. Draft genome sequence of Karnal bunt pathogen (Tilletia indica) of wheat provides insights into the pathogenic mechanisms of quarantined fungus

    Science.gov (United States)

    Singh, Manoj; Pandey, Dinesh; Saharan, M. S.; Marla, Soma S.

    2017-01-01

    Karnal bunt disease in wheat is caused by hemibiotrophic fungus, Tilletia indica that has been placed as quarantine pest in more than 70 countries. Despite its economic importance, little knowledge about the molecular components of fungal pathogenesis is known. In this study, first time the genome sequence of T. indica has been deciphered for unraveling the effectors’ functions of molecular pathogenesis of Karnal bunt disease. The T. indica genome was sequenced employing hybrid approach of PacBio Single Molecule Real Time (SMRT) and Illumina HiSEQ 2000 sequencing platforms. The genome was assembled into 10,957 contigs (N50 contig length 3 kb) with total size of 26.7 Mb and GC content of 53.99%. The number of predicted putative genes were 11,535, which were annotated with Gene Ontology databases. Functional annotation of Karnal bunt pathogen genome and classification of identified effectors into protein families revealed interesting functions related to pathogenesis. Search for effectors’ genes using pathogen host interaction database identified 135 genes. The T. indica genome sequence and putative genes involved in molecular pathogenesis would further help in devising novel and effective disease management strategies including development of resistant wheat genotypes, novel biomarkers for pathogen detection and new targets for fungicide development. PMID:28152050

  1. A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing.

    Science.gov (United States)

    Huang, Kailong; Zhang, Xu-Xiang; Shi, Peng; Wu, Bing; Ren, Hongqiang

    2014-11-01

    In order to comprehensively investigate bacterial virulence in drinking water, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential pathogenic bacteria and virulence factors (VFs) in a full-scale drinking water treatment and distribution system. 16S rRNA gene pyrosequencing revealed high bacterial diversity in the drinking water (441-586 operational taxonomic units). Bacterial diversity decreased after chlorine disinfection, but increased after pipeline distribution. α-Proteobacteria was the most dominant taxonomic class. Alignment against the established pathogen database showed that several types of putative pathogens were present in the drinking water and Pseudomonas aeruginosa had the highest abundance (over 11‰ of total sequencing reads). Many pathogens disappeared after chlorine disinfection, but P. aeruginosa and Leptospira interrogans were still detected in the tap water. High-throughput sequencing revealed prevalence of various pathogenicity islands and virulence proteins in the drinking water, and translocases, transposons, Clp proteases and flagellar motor switch proteins were the predominant VFs. Both diversity and abundance of the detectable VFs increased after the chlorination, and decreased after the pipeline distribution. This study indicates that joint use of 454 pyrosequencing and Illumina sequencing can comprehensively characterize environmental pathogenesis, and several types of putative pathogens and various VFs are prevalent in drinking water.

  2. The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

    Science.gov (United States)

    Aversano, Riccardo; Contaldi, Felice; Ercolano, Maria Raffaella; Grosso, Valentina; Iorizzo, Massimo; Tatino, Filippo; Xumerle, Luciano; Dal Molin, Alessandra; Avanzato, Carla; Ferrarini, Alberto; Delledonne, Massimo; Sanseverino, Walter; Cigliano, Riccardo Aiese; Capella-Gutierrez, Salvador; Gabaldón, Toni; Frusciante, Luigi; Bradeen, James M.; Carputo, Domenico

    2015-01-01

    Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes. PMID:25873387

  3. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution

    NARCIS (Netherlands)

    Chena, X.G.; Jiang, X.; Gu, J.; Xu, M.; Wu, Y.; Deng, Y.; Zhang, C.; Bonizzoni, M.; Dermauw, W.; Vontas, J.; Armbruster, P.; Huang, X.; Yang, Y.; Zhang, H.; He, W.; Peng, H.; Liu, Y.; Wu, K.; Chen, J.; Lirakis, M.; Topalis, P.; Van Leeuwen, T.; Hall, B.A.; Thorpe, C.; Mueller, R.L.; Sun, C.; Waterhouse, R.M.; Yan, G.; Tu, Z.J.; Fang, X.; James, A.A.

    2015-01-01

    The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined

  4. Insight into the First Draft Genome Sequence of the Genus Sediminibacillus, Sediminibacillus halophilus Strain NSP9.3

    Science.gov (United States)

    Pal, Kamal Krishna; Sherathia, Dharmesh; Sukhadiya, Bhoomika; Dalsania, Trupti; Patel, Ilaxi; Savsani, Kinjal; Thomas, Manesh; Vanpariya, Sejal; Mandaliya, Mona; Rupapara, Rupal; Rawal, Priya; Ghorai, Sucheta; Bhayani, Sharmila; Shah, Abhi; Saxena, Anil Kumar

    2014-01-01

    We report the 3.98-Mbp first draft genome sequence of Sediminibacillus halophilus strain NSP9.3, a moderate halophile isolated from a seasonal salt marsh of the Great Rann of Kutch, India. Exploring the genome of this organism will facilitate the understanding of the mechanism(s) of osmotolerance and survival in differential osmolarity. PMID:24407641

  5. First Insights into the Genome Sequence of the Strictly Anaerobic Homoacetogenic Sporomusa sphaeroides Strain E (DSM 2875)

    Science.gov (United States)

    Villamizar, Genis Andrés Castillo; Daniel, Rolf

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of Sporomusa sphaeroides strain E (DSM 2875), a strict anaerobic homoacetogenic bacterium. It is able to grow autotrophically on different one-carbon compounds. The strain possesses several genes of the Wood-Ljungdahl pathway. The genome consists of a single chromosome (4.98 Mb). PMID:28336590

  6. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

    Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite

  7. Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0

    Directory of Open Access Journals (Sweden)

    Blakely Emma L

    2011-10-01

    Full Text Available Abstract Background Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA sequencing and mutation detection. Failure by the microarray to identify a base, compared to the reference sequence, is designated an 'N-call.' This study re-examined the N-call distribution of mtDNA samples sequenced by the Affymetrix MitoChip v.2.0, based on the hypothesis that N-calls may represent insertions or deletions (indels in mtDNA. Findings We analysed 16 patient mtDNA samples using MitoChip. N-calls by the proprietary GSEQ software were significantly reduced when either of the freeware on-line algorithms ResqMi or sPROFILER was utilized. With sPROFILER, this decrease in N-calls had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software, but ResqMi produced a significant change in mutation load, as well as producing longer N-cell stretches. For these reasons, further analysis using ResqMi was not attempted. Conventional DNA sequencing of the longer N-calls stretches from sPROFILER revealed 7 insertions and 12 point mutations. Moreover, analysis of single-base N-calls of one mtDNA sample found 3 other point mutations. Conclusions Our study is the first to analyse N-calls produced from GSEQ software for the MitoChipv2.0. By narrowing the focus to longer stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique insertions and point mutations. Shorter N-calls also harboured point mutations, but the absence of deletions among N-calls suggests that probe confirmation affects binding and thus N-calling. This study supports the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER.

  8. Genomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population.

    Science.gov (United States)

    Clark, Clifford G; Berry, Chrystal; Walker, Matthew; Petkau, Aaron; Barker, Dillon O R; Guan, Cai; Reimer, Aleisha; Taboada, Eduardo N

    2016-12-03

    Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates. Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain. The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression

  9. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages.

    Science.gov (United States)

    Chen, Feng; Lu, Jingrang

    2002-05-01

    The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for nucleotide metabolism were found between cyanophage P60 and marine unicellular cyanobacteria.

  10. Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing.

    Directory of Open Access Journals (Sweden)

    Lai-Ping Wong

    2014-05-01

    Full Text Available South Asia possesses a significant amount of genetic diversity due to considerable intergroup differences in culture and language. There have been numerous reports on the genetic structure of Asian Indians, although these have mostly relied on genotyping microarrays or targeted sequencing of the mitochondria and Y chromosomes. Asian Indians in Singapore are primarily descendants of immigrants from Dravidian-language-speaking states in south India, and 38 individuals from the general population underwent deep whole-genome sequencing with a target coverage of 30X as part of the Singapore Sequencing Indian Project (SSIP. The genetic structure and diversity of these samples were compared against samples from the Singapore Sequencing Malay Project and populations in Phase 1 of the 1,000 Genomes Project (1 KGP. SSIP samples exhibited greater intra-population genetic diversity and possessed higher heterozygous-to-homozygous genotype ratio than other Asian populations. When compared against a panel of well-defined Asian Indians, the genetic makeup of the SSIP samples was closely related to South Indians. However, even though the SSIP samples clustered distinctly from the Europeans in the global population structure analysis with autosomal SNPs, eight samples were assigned to mitochondrial haplogroups that were predominantly present in Europeans and possessed higher European admixture than the remaining samples. An analysis of the relative relatedness between SSIP with two archaic hominins (Denisovan, Neanderthal identified higher ancient admixture in East Asian populations than in SSIP. The data resource for these samples is publicly available and is expected to serve as a valuable complement to the South Asian samples in Phase 3 of 1 KGP.

  11. Exploring the correlations between sequence evolution rate and phenotypic divergence across the Mammalian tree provides insights into adaptive evolution

    Indian Academy of Sciences (India)

    Jan Janecka; Bhanu Chowdhary; William Murphy

    2012-11-01

    Sequence evolution behaves in a relatively consistent manner, leading to one of the fundamental paradigms in biology, the existence of a `molecular clock’. The molecular clock can be distilled to the concept of accumulation of substitutions, through time yielding a stable rate from which we can estimate lineage divergence. Over the last 50 years, evolutionary biologists have obtained an in-depth understanding of this clock’s nuances. It has been fine-tuned by taking into account the vast heterogeneity in rates across lineages and genes, leading to `relaxed’ molecular clock methods for timetree reconstruction. Sequence rate varies with life history traits including body size, generation time and metabolic rate, and we review recent studies on this topic. However, few studies have explicitly examined correlates between molecular evolution and morphological evolution. The patterns observed across diverse lineages suggest that rates of molecular and morphological evolution are largely decoupled. We discuss how identifying the molecular mechanisms behind rapid functional radiations are central to understanding evolution. The vast functional divergence within mammalian lineages that have relatively `slow’ sequence evolution refutes the hypotheses that pulses in diversification yielding major phenotypic change are the result of steady accumulation of substitutions. Patterns rather suggest phenotypic divergence is likely caused by regulatory alterations mediated through mechanisms such as insertions/deletions in functional regions. These can rapidly arise and sweep to fixation faster than predicted from a lineage’s sequence neutral substitution rate, enabling species to leapfrog between phenotypic `islands’. We suggest research directions that could illuminate mechanisms behind the functional diversity we see today.

  12. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

    Science.gov (United States)

    Alverson, Andrew J; Wei, XiaoXin; Rice, Danny W; Stern, David B; Barry, Kerrie; Palmer, Jeffrey D

    2010-06-01

    The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

  13. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations.

    Science.gov (United States)

    Manara, Richard M A; Tomasio, Susana; Khalid, Syma

    2015-01-27

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is "exonuclease sequencing", in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  14. Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche.

    Directory of Open Access Journals (Sweden)

    Ana M S Guimaraes

    Full Text Available Mycoplasma suis, the causative agent of porcine infectious anemia, has never been cultured in vitro and mechanisms by which it causes disease are poorly understood. Thus, the objective herein was to use whole genome sequencing and analysis of M. suis to define pathogenicity mechanisms and biochemical pathways. M. suis was harvested from the blood of an experimentally infected pig. Following DNA extraction and construction of a paired end library, whole-genome sequencing was performed using GS-FLX (454 and Titanium chemistry. Reads on paired-end constructs were assembled using GS De Novo Assembler and gaps closed by primer walking; assembly was validated by PFGE. Glimmer and Manatee Annotation Engine were used to predict and annotate protein-coding sequences (CDS. The M. suis genome consists of a single, 742,431 bp chromosome with low G+C content of 31.1%. A total of 844 CDS, 3 single copies, unlinked rRNA genes and 32 tRNAs were identified. Gene homologies and GC skew graph show that M. suis has a typical Mollicutes oriC. The predicted metabolic pathway is concise, showing evidence of adaptation to blood environment. M. suis is a glycolytic species, obtaining energy through sugars fermentation and ATP-synthase. The pentose-phosphate pathway, metabolism of cofactors and vitamins, pyruvate dehydrogenase and NAD(+ kinase are missing. Thus, ribose, NADH, NADPH and coenzyme A are possibly essential for its growth. M. suis can generate purines from hypoxanthine, which is secreted by RBCs, and cytidine nucleotides from uracil. Toxins orthologs were not identified. We suggest that M. suis may cause disease by scavenging and competing for host' nutrients, leading to decreased life-span of RBCs. In summary, genome analysis shows that M. suis is dependent on host cell metabolism and this characteristic is likely to be linked to its pathogenicity. The prediction of essential nutrients will aid the development of in vitro cultivation systems.

  15. Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections.

    Directory of Open Access Journals (Sweden)

    Ehtesham Mofiz

    2016-02-01

    Full Text Available The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis and two human patients (S. scabiei var. hominis living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1-3 distinct haplotypes per infestation.

  16. Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae at a Single Institution: Insights into Endemicity from Whole-Genome Sequencing

    Science.gov (United States)

    Stoesser, Nicole; Sheppard, Anna E.; Pankhurst, Louise; Giess, Adam; Yeh, Anthony J.; Didelot, Xavier; Turner, Stephen D.; Sebra, Robert; Kasarskis, Andrew; Peto, Tim; Crook, Derrick; Sifri, Costi D.

    2015-01-01

    The global emergence of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) multilocus sequence type ST258 is widely recognized. Less is known about the molecular and epidemiological details of non-ST258 K. pneumoniae in the setting of an outbreak mediated by an endemic plasmid. We describe the interplay of blaKPC plasmids and K. pneumoniae strains and their relationship to the location of acquisition in a U.S. health care institution. Whole-genome sequencing (WGS) analysis was applied to KPC-Kp clinical isolates collected from a single institution over 5 years following the introduction of blaKPC in August 2007, as well as two plasmid transformants. KPC-Kp from 37 patients yielded 16 distinct sequence types (STs). Two novel conjugative blaKPC plasmids (pKPC_UVA01 and pKPC_UVA02), carried by the hospital index case, accounted for the presence of blaKPC in 21/37 (57%) subsequent cases. Thirteen (35%) isolates represented an emergent lineage, ST941, which contained pKPC_UVA01 in 5/13 (38%) and pKPC_UVA02 in 6/13 (46%) cases. Seven (19%) isolates were the epidemic KPC-Kp strain, ST258, mostly imported from elsewhere and not carrying pKPC_UVA01 or pKPC_UVA02. Using WGS-based analysis of clinical isolates and plasmid transformants, we demonstrate the unexpected dispersal of blaKPC to many non-ST258 lineages in a hospital through spread of at least two novel blaKPC plasmids. In contrast, ST258 KPC-Kp was imported into the institution on numerous occasions, with other blaKPC plasmid vectors and without sustained transmission. Instead, a newly recognized KPC-Kp strain, ST941, became associated with both novel blaKPC plasmids and spread locally, making it a future candidate for clinical persistence and dissemination. PMID:25561339

  17. New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing.

    Science.gov (United States)

    Burroughs, Alexander Maxwell; Ando, Yoshinari; Aravind, L

    2014-01-01

    Our understanding of the pervasive involvement of small RNAs in regulating diverse biological processes has been greatly augmented by recent application of deep-sequencing technologies to small RNA across diverse eukaryotes. We review the currently known small RNA classes and place them in context of the reconstructed evolutionary history of the RNA interference (RNAi) protein machinery. This synthesis indicates that the earliest versions of eukaryotic RNAi systems likely utilized small RNA processed from three types of precursors: (1) sense-antisense transcriptional products, (2) genome-encoded, imperfectly complementary hairpin sequences, and (3) larger noncoding RNA precursor sequences. Structural dissection of PIWI proteins along with recent discovery of novel families (including Med13 of the Mediator complex) suggest that emergence of a distinct architecture with the N-terminal domains (also occurring separately fused to endoDNases in prokaryotes) formed via duplication of an ancestral unit was key to their recruitment as primary RNAi effectors and use of small RNAs of certain preferred lengths. Prokaryotic PIWI proteins are typically components of several RNA-directed DNA restriction or CRISPR/Cas systems. However, eukaryotic versions appear to have emerged from a subset that evolved RNA-directed RNAi. They were recruited alongside RNaseIII domains and RNA-dependent RNA polymerase (RdRP) domains, also from prokaryotic systems, to form the core eukaryotic RNAi system. Like certain regulatory systems, RNAi diversified into two distinct but linked arms concomitant with eukaryotic nucleocytoplasmic compartmentalization. Subsequent elaboration of RNAi proceeded via diversification of the core protein machinery through lineage-specific expansions and recruitment of new components from prokaryotes (nucleases and small RNA-modifying enzymes), allowing for diversification of associating small RNAs. © 2013 John Wiley & Sons, Ltd.

  18. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

    OpenAIRE

    Dereeper, Alexis; Guyot, Romain; Dubreuil Tranchant, Christine; Anthony, François; Argout, X.; Bellis, F; Combes, Marie-Christine; Gavory, F.; De Kochko, Alexandre; Kudrna, D.; Leroy, T.; Poulain, J.; Rondeau, M.; Song, X; Wing, R

    2013-01-01

    Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,41...

  19. A Comprehensive Insight into Tetracycline Resistant Bacteria and Antibiotic Resistance Genes in Activated Sludge Using Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Kailong Huang

    2014-06-01

    Full Text Available In order to comprehensively investigate tetracycline resistance in activated sludge of sewage treatment plants, 454 pyrosequencing and Illumina high-throughput sequencing were used to detect potential tetracycline resistant bacteria (TRB and antibiotic resistance genes (ARGs in sludge cultured with different concentrations of tetracycline. Pyrosequencing of 16S rRNA gene revealed that tetracycline treatment greatly affected the bacterial community structure of the sludge. Nine genera consisting of Sulfuritalea, Armatimonas, Prosthecobacter, Hyphomicrobium, Azonexus, Longilinea, Paracoccus, Novosphingobium and Rhodobacter were identified as potential TRB in the sludge. Results of qPCR, molecular cloning and metagenomic analysis consistently indicated that tetracycline treatment could increase both the abundance and diversity of the tet genes, but decreased the occurrence and diversity of non-tetracycline ARG, especially sulfonamide resistance gene sul2. Cluster analysis showed that tetracycline treatment at subinhibitory concentrations (5 mg/L was found to pose greater effects on the bacterial community composition, which may be responsible for the variations of the ARGs abundance. This study indicated that joint use of 454 pyrosequencing and Illumina high-throughput sequencing can be effectively used to explore ARB and ARGs in the environment, and future studies should include an in-depth investigation of the relationship between microbial community, ARGs and antibiotics in sewage treatment plant (STP sludge.

  20. The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

    Science.gov (United States)

    Manara, Richard M. A.; Tomasio, Susana; Khalid, Syma

    2015-01-01

    Nanopore technology for DNA sequencing is constantly being refined and improved. In strand sequencing a single strand of DNA is fed through a nanopore and subsequent fluctuations in the current are measured. A major hurdle is that the DNA is translocated through the pore at a rate that is too fast for the current measurement systems. An alternative approach is “exonuclease sequencing”, in which an exonuclease is attached to the nanopore that is able to process the strand, cleaving off one base at a time. The bases then flow through the nanopore and the current is measured. This method has the advantage of potentially solving the translocation rate problem, as the speed is controlled by the exonuclease. Here we consider the practical details of exonuclease attachment to the protein alpha hemolysin. We employ molecular dynamics simulations to determine the ideal (a) distance from alpha-hemolysin, and (b) the orientation of the monophosphate nucleotides upon release from the exonuclease such that they will enter the protein. Our results indicate an almost linear decrease in the probability of entry into the protein with increasing distance of nucleotide release. The nucleotide orientation is less significant for entry into the protein.

  1. Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution.

    Science.gov (United States)

    Chen, Xiao-Guang; Jiang, Xuanting; Gu, Jinbao; Xu, Meng; Wu, Yang; Deng, Yuhua; Zhang, Chi; Bonizzoni, Mariangela; Dermauw, Wannes; Vontas, John; Armbruster, Peter; Huang, Xin; Yang, Yulan; Zhang, Hao; He, Weiming; Peng, Hongjuan; Liu, Yongfeng; Wu, Kun; Chen, Jiahua; Lirakis, Manolis; Topalis, Pantelis; Van Leeuwen, Thomas; Hall, Andrew Brantley; Jiang, Xiaofang; Thorpe, Chevon; Mueller, Rachel Lockridge; Sun, Cheng; Waterhouse, Robert Michael; Yan, Guiyun; Tu, Zhijian Jake; Fang, Xiaodong; James, Anthony A

    2015-11-03

    The Asian tiger mosquito, Aedes albopictus, is a highly successful invasive species that transmits a number of human viral diseases, including dengue and Chikungunya fevers. This species has a large genome with significant population-based size variation. The complete genome sequence was determined for the Foshan strain, an established laboratory colony derived from wild mosquitoes from southeastern China, a region within the historical range of the origin of the species. The genome comprises 1,967 Mb, the largest mosquito genome sequenced to date, and its size results principally from an abundance of repetitive DNA classes. In addition, expansions of the numbers of members in gene families involved in insecticide-resistance mechanisms, diapause, sex determination, immunity, and olfaction also contribute to the larger size. Portions of integrated flavivirus-like genomes support a shared evolutionary history of association of these viruses with their vector. The large genome repertory may contribute to the adaptability and success of Ae. albopictus as an invasive species.

  2. Protein sequences insight into heavy metal tolerance in Cronobacter sakazakii BAA-894 encoded by plasmid pESA3.

    Science.gov (United States)

    Chaturvedi, Navaneet; Kajsik, Michal; Forsythe, Stephen; Pandey, Paras Nath

    2015-12-01

    The recently annotated genome of the bacterium Cronobacter sakazakii BAA-894 suggests that the organism has the ability to bind heavy metals. This study demonstrates heavy metal tolerance in C. sakazakii, in which proteins with the heavy metal interaction were recognized by computational and experimental study. As the result, approximately one-fourth of proteins encoded on the plasmid pESA3 are proposed to have potential interaction with heavy metals. Interaction between heavy metals and predicted proteins was further corroborated using protein crystal structures from protein data bank database and comparison of metal-binding ligands. In addition, a phylogenetic study was undertaken for the toxic heavy metals, arsenic, cadmium, lead and mercury, which generated relatedness clustering for lead, cadmium and arsenic. Laboratory studies confirmed the organism's tolerance to tellurite, copper and silver. These experimental and computational study data extend our understanding of the genes encoding for proteins of this important neonatal pathogen and provide further insights into the genotypes associated with features that can contribute to its persistence in the environment. The information will be of value for future environmental protection from heavy toxic metals.

  3. Sequence-based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families.

    Directory of Open Access Journals (Sweden)

    Janine Maimanakos

    2016-08-01

    Full Text Available Arylmalonate-Decarboxylases (AMDases, EC 4.1.1.76 are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta- and Gammaproteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the TTT family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99% of the (R-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes.

  4. Sequence-Based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families

    Science.gov (United States)

    Maimanakos, Janine; Chow, Jennifer; Gaßmeyer, Sarah K.; Güllert, Simon; Busch, Florian; Kourist, Robert; Streit, Wolfgang R.

    2016-01-01

    Arylmalonate Decarboxylases (AMDases, EC 4.1.1.76) are very rare and mostly underexplored enzymes. Currently only four known and biochemically characterized representatives exist. However, their ability to decarboxylate α-disubstituted malonic acid derivatives to optically pure products without cofactors makes them attractive and promising candidates for the use as biocatalysts in industrial processes. Until now, AMDases could not be separated from other members of the aspartate/glutamate racemase superfamily based on their gene sequences. Within this work, a search algorithm was developed that enables a reliable prediction of AMDase activity for potential candidates. Based on specific sequence patterns and screening methods 58 novel AMDase candidate genes could be identified in this work. Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta-, and Gamma-proteobacteria. Amino acid homologies and comparison of gene surrounding sequences enabled the classification of eight enzyme clusters. Particularly striking is the accumulation of genes coding for different transporters of the tripartite tricarboxylate transporters family, TRAP transporters and ABC transporters as well as genes coding for mandelate racemases/muconate lactonizing enzymes that might be involved in substrate uptake or degradation of AMDase products. Further, three novel AMDases were characterized which showed a high enantiomeric excess (>99%) of the (R)-enantiomer of flurbiprofen. These are the recombinant AmdA and AmdV from Variovorax sp. strains HH01 and HH02, originated from soil, and AmdP from Polymorphum gilvum found by a data base search. Altogether our findings give new insights into the class of AMDases and reveal many previously unknown enzyme candidates with high potential for bioindustrial processes. PMID:27610105

  5. New insights into flavivirus evolution, taxonomy and biogeographic history, extended by analysis of canonical and alternative coding sequences.

    Directory of Open Access Journals (Sweden)

    Gregory Moureau

    Full Text Available To generate the most diverse phylogenetic dataset for the flaviviruses to date, we determined the genomic sequences and phylogenetic relationships of 14 flaviviruses, of which 10 are primarily associated with Culex spp. mosquitoes. We analyze these data, in conjunction with a comprehensive collection of flavivirus genomes, to characterize flavivirus evolutionary and biogeographic history in unprecedented detail and breadth. Based on the presumed introduction of yellow fever virus into the Americas via the transatlantic slave trade, we extrapolated a timescale for a relevant subset of flaviviruses whose evolutionary history, shows that different Culex-spp. associated flaviviruses have been introduced from the Old World to the New World on at least five separate occasions, with 2 different sets of factors likely to have contributed to the dispersal of the different viruses. We also discuss the significance of programmed ribosomal frameshifting in a central region of the polyprotein open reading frame in some mosquito-associated flaviviruses.

  6. The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

    Energy Technology Data Exchange (ETDEWEB)

    Copley, Shelley D. [University of Colorado; Rokicki, Joseph [University of Colorado; Turner, Pernilla [University of Colorado; Daligault, Hajnalka E. [Los Alamos National Laboratory (LANL); Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL

    2012-01-01

    Sphingobium chlorophenolicum Strain L-1 can mineralize the toxic pesticide pentachlorophenol (PCP). We have sequenced the genome of S. chlorophenolicum Strain L-1. The genome consists of a primary chromosome that encodes most of the genes for core processes, a secondary chromosome that encodes primarily genes that appear to be involved in environmental adaptation, and a small plasmid. The genes responsible for degradation of PCP are found on chromosome 2. We have compared the genomes of S. chlorophenolicum Strain L-1 and Sphingobium japonicum, a closely related Sphingomonad that degrades lindane. Our analysis suggests that the genes encoding the first three enzymes in the PCP degradation pathway were acquired via two different horizontal gene transfer events, and the genes encoding the final two enzymes in the pathway were acquired from the most recent common ancestor of these two bacteria.

  7. A novel hemoglobin variant beta135(H13) Ala > Asp identified in an asymptomatic Korean family by direct sequencing: suggesting a new insight into Hb Beckman mutation.

    Science.gov (United States)

    Kim, S Y; Kim, G Y J; Jo, S A; Lee, E H; Cho, E H; Hwang, S H; Lee, E Y

    2010-02-01

    This article describes the clinical observation of a novel hemoglobin (Hb) variant found during the course of routine blood testing on a 61-year-old subject. The Hb variant was observed during HbA1c testing by ion-exchange high-performance liquid chromatography. Alkaline electrophoresis and DNA sequencing confirmed the presence of a new Hb variant, HBB:c.407C > A (p.Ala136Asp). This mutation has been reported to induce Hb Beckman variant in the Globin Gene Server. However, it was different from the only experimental report for Hb Beckman by Rahbar, Lee & Asmeron (p.Ala136Glu; Hb Beckman alpha2 beta2 135(H13) ala-to-glu: a new unstable variant and reduced oxygen affinity. Blood 78, 204a). And our case was asymptomatic with normal lab findings, while Rahbar et al.'s case showed the clinical manifestations of chronic anemia. This would be a report for a novel Hb variant suggesting new insight of Hb Beckman variant. This would be a report of a novel Hb variant suggesting new insights into Hb Beckman variant.

  8. Coding potential and transcript analysis of fowl adenovirus 4: insight into upstream ORFs as common sequence features in adenoviral transcripts.

    Science.gov (United States)

    Griffin, Bryan D; Nagy, Eva

    2011-06-01

    Recombinant fowl adenoviruses (FAdVs) have been successfully used as veterinary vaccine vectors. However, insufficient definitions of the protein-coding and non-coding regions and an incomplete understanding of virus-host interactions limit the progress of next-generation vectors. FAdVs are known to cause several diseases of poultry. Certain isolates of species FAdV-C are the aetiological agent of inclusion body hepatitis/hydropericardium syndrome (IBH/HPS). In this study, we report the complete 45667 bp genome sequence of FAdV-4 of species FAdV-C. Assessment of the protein-coding potential of FAdV-4 was carried out with the Bio-Dictionary-based Gene Finder together with an evaluation of sequence conservation among species FAdV-A and FAdV-D. On this basis, 46 potentially protein-coding ORFs were identified. Of these, 33 and 13 ORFs were assigned high and low protein-coding potential, respectively. Homologues of the ancestral adenoviral genes were, with few exceptions, assigned high protein-coding potential. ORFs that were unique to the FAdVs were differentiated into high and low protein-coding potential groups. Notable putative genes with high protein-coding capacity included the previously unreported fiber 1, hypothetical 10.3K and hypothetical 10.5K genes. Transcript analysis revealed that several of the small ORFs less than 300 nt in length that were assigned low coding potential contributed to upstream ORFs (uORFs) in important mRNAs, including the ORF22 mRNA. Subsequent analysis of the previously reported transcripts of FAdV-1, FAdV-9, human adenovirus 2 and bovine adenovirus 3 identified widespread uORFs in AdV mRNAs that have the potential to act as important translational regulatory elements.

  9. Insights into SCP/TAPS proteins of liver flukes based on large-scale bioinformatic analyses of sequence datasets.

    Directory of Open Access Journals (Sweden)

    Cinzia Cantacessi

    Full Text Available BACKGROUND: SCP/TAPS proteins of parasitic helminths have been proposed to play key roles in fundamental biological processes linked to the invasion of and establishment in their mammalian host animals, such as the transition from free-living to parasitic stages and the modulation of host immune responses. Despite the evidence that SCP/TAPS proteins of parasitic nematodes are involved in host-parasite interactions, there is a paucity of information on this protein family for parasitic trematodes of socio-economic importance. METHODOLOGY/PRINCIPAL FINDINGS: We conducted the first large-scale study of SCP/TAPS proteins of a range of parasitic trematodes of both human and veterinary importance (including the liver flukes Clonorchis sinensis, Opisthorchis viverrini, Fasciola hepatica and F. gigantica as well as the blood flukes Schistosoma mansoni, S. japonicum and S. haematobium. We mined all current transcriptomic and/or genomic sequence datasets from public databases, predicted secondary structures of full-length protein sequences, undertook systematic phylogenetic analyses and investigated the differential transcription of SCP/TAPS genes in O. viverrini and F. hepatica, with an emphasis on those that are up-regulated in the developmental stages infecting the mammalian host. CONCLUSIONS: This work, which sheds new light on SCP/TAPS proteins, guides future structural and functional explorations of key SCP/TAPS molecules associated with diseases caused by flatworms. Future fundamental investigations of these molecules in parasites and the integration of structural and functional data could lead to new approaches for the control of parasitic diseases.

  10. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity

    Directory of Open Access Journals (Sweden)

    Frey Jürg E

    2010-01-01

    Full Text Available Abstract Background Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora. Results The genome of the type strain of E. pyrifoliae strain DSM 12163T, was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome. Conclusions The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.

  11. Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.

    Science.gov (United States)

    Tanca, Alessandro; Palomba, Antonio; Deligios, Massimo; Cubeddu, Tiziana; Fraumene, Cristina; Biosa, Grazia; Pagnozzi, Daniela; Addis, Maria Filippa; Uzzau, Sergio

    2013-01-01

    Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database enabled a slight increment in respect to public databases. Then, database behavior in terms of false discovery rate and peptide degeneracy was critically evaluated. Public databases with generic taxonomy exhibited a markedly different trend compared to the counterparts. Finally, the reliability of taxonomic attribution according to the lowest common ancestor approach (using MEGAN and Unipept software) was assessed. The level of misassignments varied among the different databases, and specific thresholds based on the number of taxon-specific peptides were established to minimize false positives. This study confirms that database selection has a significant impact in metaproteomics, and provides critical indications for improving depth and

  12. Revisiting bovine pyometra--new insights into the disease using a culture-independent deep sequencing approach.

    Science.gov (United States)

    Knudsen, Lif Rødtness Vesterby; Karstrup, Cecilia Christensen; Pedersen, Hanne Gervi; Agerholm, Jørgen Steen; Jensen, Tim Kåre; Klitgaard, Kirstine

    2015-02-25

    The bacteria present in the uterus during pyometra have previously been studied using bacteriological culturing. These studies identified Fusobacterium necrophorum and Trueperella pyogenes as the major contributors to the pathogenesis of pyometra. However, an increasing number of culture-independent studies have demonstrated that the bacterial diversity in most environments is underestimated in culture-based studies. Consequently, fastidious pyometra-associated pathogens may have been overlooked. Therefore, the primary purpose of this study was to investigate the diversity of bacteria in the uterus of cows with pyometra by using culture-independent 16S rRNA PCR combined with next generation sequencing. We investigated the microbial composition in the uterus of 21 cows with pyometra, which were obtained from a Danish slaughterhouse. Similar to the observations from the culture studies, Fusobacteriaceae, the family that F. necrophorum belongs to, was the operational taxonomic unit (OTU) observed in the largest quantities. By contrast, the Actinomycetaceae family, which includes T. pyogenes, constituted only 1% of the total number of reads. Thus we cannot confirm the previously reported role of species from this family in the pathogenesis of pyometra. Finally, we identified a large number of sequences representing three families of Gram-negative bacteria in the pyometra samples: Porphyromonadaceae, Mycoplasmataceae, and Pasteurellaceae. It is likely that these families comprise potential pathogenic species of a fastidious nature, which have been overlooked in previous studies. Our results increase the knowledge of the complexity of the pyometra microbiota and suggest that pathogens in addition to F. necrophorum may be involved in the pathogenesis of pyometra.

  13. Supplementary Material for: Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

    KAUST Repository

    Phelan, Jody

    2016-01-01

    Abstract Background Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. Methods To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. Results The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. Conclusions Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel

  14. Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance

    KAUST Repository

    Phelan, Jody

    2016-03-23

    Background Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance. Methods To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods. Results The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites. Conclusions Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance

  15. Genome sequence of Perigonia lusca single nucleopolyhedrovirus: insights into the evolution of a nucleotide metabolism enzyme in the family Baculoviridae

    Science.gov (United States)

    Ardisson-Araújo, Daniel M. P.; Lima, Rayane Nunes; Melo, Fernando L.; Clem, Rollie J.; Huang, Ning; Báo, Sônia Nair; Sosa-Gómez, Daniel R.; Ribeiro, Bergmann M.

    2016-01-01

    The genome of a novel group II alphabaculovirus, Perigonia lusca single nucleopolyhedrovirus (PeluSNPV), was sequenced and shown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids. An interesting feature of this novel genome was the presence of a putative nucleotide metabolism enzyme-encoding gene (pelu112). The pelu112 gene was predicted to encode a fusion of thymidylate kinase (tmk) and dUTP diphosphatase (dut). Phylogenetic analysis indicated that baculoviruses have independently acquired tmk and dut several times during their evolution. Two homologs of the tmk-dut fusion gene were separately introduced into the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) genome, which lacks tmk and dut. The recombinant baculoviruses produced viral DNA, virus progeny, and some viral proteins earlier during in vitro infection and the yields of viral occlusion bodies were increased 2.5-fold when compared to the parental virus. Interestingly, both enzymes appear to retain their active sites, based on separate modeling using previously solved crystal structures. We suggest that the retention of these tmk-dut fusion genes by certain baculoviruses could be related to accelerating virus replication and to protecting the virus genome from deleterious mutation. PMID:27273152

  16. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop.

    Science.gov (United States)

    Hazzouri, Khaled M; Flowers, Jonathan M; Visser, Hendrik J; Khierallah, Hussam S M; Rosas, Ulises; Pham, Gina M; Meyer, Rachel S; Johansen, Caryn K; Fresquez, Zoë A; Masmoudi, Khaled; Haider, Nadia; El Kadri, Nabila; Idaghdour, Youssef; Malek, Joel A; Thirkhill, Deborah; Markhand, Ghulam S; Krueger, Robert R; Zaid, Abdelouahhab; Purugganan, Michael D

    2015-11-09

    Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.

  17. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop

    Science.gov (United States)

    Hazzouri, Khaled M.; Flowers, Jonathan M.; Visser, Hendrik J.; Khierallah, Hussam S. M.; Rosas, Ulises; Pham, Gina M.; Meyer, Rachel S.; Johansen, Caryn K.; Fresquez, Zoë A.; Masmoudi, Khaled; Haider, Nadia; El Kadri, Nabila; Idaghdour, Youssef; Malek, Joel A.; Thirkhill, Deborah; Markhand, Ghulam S.; Krueger, Robert R.; Zaid, Abdelouahhab; Purugganan, Michael D.

    2015-01-01

    Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop. PMID:26549859

  18. New insights on the genetic diversity of the honeybee parasite Nosema ceranae based on multilocus sequence analysis.

    Science.gov (United States)

    Roudel, Mathieu; Aufauvre, Julie; Corbara, Bruno; Delbac, Frederic; Blot, Nicolas

    2013-09-01

    The microsporidian parasite Nosema ceranae is a common pathogen of the Western honeybee (Apis mellifera) whose variable virulence could be related to its genetic polymorphism and/or its polyphenism responding to environmental cues. Since the genotyping of N. ceranae based on unique marker sequences had been unsuccessful, we tested whether a multilocus approach, assessing the diversity of ten genetic markers – encoding nine proteins and the small ribosomal RNA subunit – allowed the discrimination between N. ceranae variants isolated from single A. mellifera individuals in four distant locations. High nucleotide diversity and allele content were observed for all genes. Most importantly, the diversity was mainly present within parasite populations isolated from single honeybee individuals. In contrast the absence of isolate differentiation precluded any taxa discrimination, even through a multilocus approach, but suggested that similar populations of parasites seem to infect honeybees in distant locations. As statistical evolutionary analyses showed that the allele frequency is under selective pressure, we discuss the origin and consequences of N. ceranae heterozygosity in a single host and lack of population divergence in the context of the parasite natural and evolutionary history.

  19. Whole Genome Sequencing of the Asian Arowana (Scleropages formosus) Provides Insights into the Evolution of Ray-Finned Fishes.

    Science.gov (United States)

    Austin, Christopher M; Tan, Mun Hua; Croft, Larry J; Hammer, Michael P; Gan, Han Ming

    2015-10-06

    The Asian arowana (Scleropages formosus) is of commercial importance, conservation concern, and is a representative of one of the oldest lineages of ray-finned fish, the Osteoglossomorpha. To add to genomic knowledge of this species and the evolution of teleosts, the genome of a Malaysian specimen of arowana was sequenced. A draft genome is presented consisting of 42,110 scaffolds with a total size of 708 Mb (2.85% gaps) representing 93.95% of core eukaryotic genes. Using a k-mer-based method, a genome size of 900 Mb was also estimated. We present an update on the phylogenomics of fishes based on a total of 27 species (23 fish species and 4 tetrapods) using 177 orthologous proteins (71,360 amino acid sites), which supports established relationships except that arowana is placed as the sister lineage to all teleost clades (Bayesian posterior probability 1.00, bootstrap replicate 93%), that evolved after the teleost genome duplication event rather than the eels (Elopomorpha). Evolutionary rates are highly heterogeneous across the tree with fishes represented by both slowly and rapidly evolving lineages. A total of 94 putative pigment genes were identified, providing the impetus for development of molecular markers associated with the spectacular colored phenotypes found within this species.

  20. Trypanosoma cruzi IIc: Phylogenetic and Phylogeographic Insights from Sequence and Microsatellite Analysis and Potential Impact on Emergent Chagas Disease

    Science.gov (United States)

    Llewellyn, Martin S.; Lewis, Michael D.; Acosta, Nidia; Yeo, Matthew; Carrasco, Hernan J.; Segovia, Maikell; Vargas, Jorge; Torrico, Faustino; Miles, Michael A.; Gaunt, Michael W.

    2009-01-01

    Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe. PMID:19721699

  1. Trypanosoma cruzi IIc: phylogenetic and phylogeographic insights from sequence and microsatellite analysis and potential impact on emergent Chagas disease.

    Directory of Open Access Journals (Sweden)

    Martin S Llewellyn

    Full Text Available Trypanosoma cruzi, the etiological agent of Chagas disease, is highly genetically diverse. Numerous lines of evidence point to the existence of six stable genetic lineages or DTUs: TcI, TcIIa, TcIIb, TcIIc, TcIId, and TcIIe. Molecular dating suggests that T. cruzi is likely to have been an endemic infection of neotropical mammalian fauna for many millions of years. Here we have applied a panel of 49 polymorphic microsatellite markers developed from the online T. cruzi genome to document genetic diversity among 53 isolates belonging to TcIIc, a lineage so far recorded almost exclusively in silvatic transmission cycles but increasingly a potential source of human infection. These data are complemented by parallel analysis of sequence variation in a fragment of the glucose-6-phosphate isomerase gene. New isolates confirm that TcIIc is associated with terrestrial transmission cycles and armadillo reservoir hosts, and demonstrate that TcIIc is far more widespread than previously thought, with a distribution at least from Western Venezuela to the Argentine Chaco. We show that TcIIc is truly a discrete T. cruzi lineage, that it could have an ancient origin and that diversity occurs within the terrestrial niche independently of the host species. We also show that spatial structure among TcIIc isolates from its principal host, the armadillo Dasypus novemcinctus, is greater than that among TcI from Didelphis spp. opossums and link this observation to differences in ecology of their respective niches. Homozygosity in TcIIc populations and some linkage indices indicate the possibility of recombination but cannot yet be effectively discriminated from a high genome-wide frequency of gene conversion. Finally, we suggest that the derived TcIIc population genetic data have a vital role in determining the origin of the epidemiologically important hybrid lineages TcIId and TcIIe.

  2. Genome Sequencing of the Perciform Fish Larimichthys crocea Provides Insights into Molecular and Genetic Mechanisms of Stress Adaptation

    Science.gov (United States)

    Shi, Qiong; Zhu, Lv-Yun; Li, Ting; Ding, Yang; Nie, Li; Li, Qiuhua; Dong, Wei-ren; Jiang, Liang; Sun, Bing; Zhang, XinHui; Li, Mingyu; Zhang, Hai-Qi; Xie, ShangBo; Zhu, YaBing; Jiang, XuanTing; Wang, Xianhui; Mu, Pengfei; Chen, Wei; Yue, Zhen; Wang, Zhuo; Wang, Jun; Shao, Jian-Zhong; Chen, Xinhua

    2015-01-01

    The large yellow croaker Larimichthys crocea (L. crocea) is one of the most economically important marine fish in China and East Asian countries. It also exhibits peculiar behavioral and physiological characteristics, especially sensitive to various environmental stresses, such as hypoxia and air exposure. These traits may render L. crocea a good model for investigating the response mechanisms to environmental stress. To understand the molecular and genetic mechanisms underlying the adaptation and response of L. crocea to environmental stress, we sequenced and assembled the genome of L. crocea using a bacterial artificial chromosome and whole-genome shotgun hierarchical strategy. The final genome assembly was 679 Mb, with a contig N50 of 63.11 kb and a scaffold N50 of 1.03 Mb, containing 25,401 protein-coding genes. Gene families underlying adaptive behaviours, such as vision-related crystallins, olfactory receptors, and auditory sense-related genes, were significantly expanded in the genome of L. crocea relative to those of other vertebrates. Transcriptome analyses of the hypoxia-exposed L. crocea brain revealed new aspects of neuro-endocrine-immune/metabolism regulatory networks that may help the fish to avoid cerebral inflammatory injury and maintain energy balance under hypoxia. Proteomics data demonstrate that skin mucus of the air-exposed L. crocea had a complex composition, with an unexpectedly high number of proteins (3,209), suggesting its multiple protective mechanisms involved in antioxidant functions, oxygen transport, immune defence, and osmotic and ionic regulation. Our results reveal the molecular and genetic basis of fish adaptation and response to hypoxia and air exposure. The data generated by this study will provide valuable resources for the genetic improvement of stress resistance and yield potential in L. crocea. PMID:25835551

  3. New Insights into the Anti-pathogenic Potential of Lactococcus garvieae against Staphylococcus aureus Based on RNA Sequencing Profiling

    Science.gov (United States)

    Delpech, Pierre; Rifa, Etienne; Ball, Graham; Nidelet, Sabine; Dubois, Emeric; Gagne, Geneviève; Montel, Marie-Christine; Delbès, Céline; Bornes, Stéphanie

    2017-01-01

    The bio-preservation potential of Lactococcus garvieae lies in its capacity to inhibit the growth of staphylococci, especially Staphylococcus aureus, in dairy products and in vitro. In vitro, inhibition is modulated by the level of aeration, owing to hydrogen peroxide (H2O2) production by L. garvieae under aeration. The S. aureus response to this inhibition has already been studied. However, the molecular mechanisms of L. garvieae underlying the antagonism against S. aureus have never been explored. This study provides evidence of the presence of another extracellular inhibition effector in vitro. This effector was neither a protein, nor a lipid, nor a polysaccharide, nor related to an L-threonine deficiency. To better understand the H2O2-related inhibition mechanism at the transcriptome level and to identify other mechanisms potentially involved, we used RNA sequencing to determine the transcriptome response of L. garvieae to different aeration levels and to the presence or absence of S. aureus. The L. garvieae transcriptome differed radically between different aeration levels mainly in biological processes related to fundamental functions and nutritional adaptation. The transcriptomic response of L. garvieae to aeration level differed according to the presence or absence of S. aureus. The higher concentration of H2O2 with high aeration was not associated with a higher expression of L. garvieae H2O2-synthesis genes (pox, sodA, and spxA1) but rather with a repression of L. garvieae H2O2-degradation genes (trxB1, ahpC, ahpF, and gpx). We showed that L. garvieae displayed an original, previously undiscovered, H2O2 production regulation mechanism among bacteria. In addition to the key factor H2O2, the involvement of another extracellular effector in the antagonism against S. aureus was shown. Future studies should explore the relation between H2O2-metabolism, H2O2-producing LAB and the pathogen they inhibit. The nature of the other extracellular effector should also

  4. Element geochemical characteristics of the reticulate red clay in southern China and its significance for the formation proccess of reticulated mottles%中国南方网纹红土元素地球化学特征及其对网纹化过程的指示意义

    Institute of Scientific and Technical Information of China (English)

    徐传奇; 廖富强; 贾玉连; 黄思源; 连丽聪; 凌超豪; 龙进

    2016-01-01

    中国南方网纹红土是在季风气候条件下形成的一种特殊地层,对重建南方第四纪气候环境具有特殊重要的意义,但长期以来对网纹化过程的物化特点缺乏足够的认识。对江西九江、彭泽与湖南岳阳3个剖面的黏土质网纹红土中白色网纹和红色基质分离后进行了地球化学元素、游离铁含量等测试,结果表明:(1)白色网纹中,发生了 Fe、Mn、Th、Ga、Cu、Zn、Co、Ni、Cr、V 等元素的显著亏损,SiO2、Zr、Hf及轻稀土元素的显著富集,游离铁含量较低;红色基质中则完全相反;(2)网纹中 Fe2+含量较高,基质中含量较低,揭示了网纹倾向于还原环境,基质倾向于氧化环境。研究认为网纹和基质这种氧化还原差异,是 Fe、Mn、Co、Ni、Cr、V、Zn、Th、Ga、Cu等元素在网纹中游离淋失,并在基质中的沉淀富集,造成 Zr、SiO2及轻稀土等在网纹中的相对富集、在基质中“稀释”而呈现亏损的主要原因。%Reticulate red clay in southern China is a kind of special stratum that formed in a monsoon climate condition,which is of great significance to reconstruct the Quaternary climate environment.For a long time,there is a lack of adequate understanding of physical and chemical characteristics of the forma-tion process of reticulated mottles.Three sections of reticulate red clay,which were located in the Jiujiang and Pengze of Jiangxi Province,and Yueyang of Hunan Province,were studied,and the red matrix and the white reticulated mottles were separated and the geochemical elements, free iron content and so on were analysed.The results show that: (1 ) In the white reticulated mottles,Fe,Mn,Th,Ga,Cu, Zn,Co,Ni,Cr,V elements are outstanding leaching,while Zr,SiO2,Hf and light rare earth ele-ments are obvious enriched,and the content of free iron are low;in the red matrix,they are reversed. (2) Fe2+content is higher in the white reticulate,while lower

  5. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium.

    Science.gov (United States)

    Eppinger, Mark; Worsham, Patricia L; Nikolich, Mikeljon P; Riley, David R; Sebastian, Yinong; Mou, Sherry; Achtman, Mark; Lindler, Luther E; Ravel, Jacques

    2010-03-01

    To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.

  6. The whole genome sequence of the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), reveals insights into the biology and adaptive evolution of a highly invasive pest species.

    Science.gov (United States)

    Papanicolaou, Alexie; Schetelig, Marc F; Arensburger, Peter; Atkinson, Peter W; Benoit, Joshua B; Bourtzis, Kostas; Castañera, Pedro; Cavanaugh, John P; Chao, Hsu; Childers, Christopher; Curril, Ingrid; Dinh, Huyen; Doddapaneni, HarshaVardhan; Dolan, Amanda; Dugan, Shannon; Friedrich, Markus; Gasperi, Giuliano; Geib, Scott; Georgakilas, Georgios; Gibbs, Richard A; Giers, Sarah D; Gomulski, Ludvik M; González-Guzmán, Miguel; Guillem-Amat, Ana; Han, Yi; Hatzigeorgiou, Artemis G; Hernández-Crespo, Pedro; Hughes, Daniel S T; Jones, Jeffery W; Karagkouni, Dimitra; Koskinioti, Panagiota; Lee, Sandra L; Malacrida, Anna R; Manni, Mosè; Mathiopoulos, Kostas; Meccariello, Angela; Murali, Shwetha C; Murphy, Terence D; Muzny, Donna M; Oberhofer, Georg; Ortego, Félix; Paraskevopoulou, Maria D; Poelchau, Monica; Qu, Jiaxin; Reczko, Martin; Robertson, Hugh M; Rosendale, Andrew J; Rosselot, Andrew E; Saccone, Giuseppe; Salvemini, Marco; Savini, Grazia; Schreiner, Patrick; Scolari, Francesca; Siciliano, Paolo; Sim, Sheina B; Tsiamis, George; Ureña, Enric; Vlachos, Ioannis S; Werren, John H; Wimmer, Ernst A; Worley, Kim C; Zacharopoulou, Antigone; Richards, Stephen; Handler, Alfred M

    2016-09-22

    The Mediterranean fruit fly (medfly), Ceratitis capitata, is a major destructive insect pest due to its broad host range, which includes hundreds of fruits and vegetables. It exhibits a unique ability to invade and adapt to ecological niches throughout tropical and subtropical regions of the world, though medfly infestations have been prevented and controlled by the sterile insect technique (SIT) as part of integrated pest management programs (IPMs). The genetic analysis and manipulation of medfly has been subject to intensive study in an effort to improve SIT efficacy and other aspects of IPM control. The 479 Mb medfly genome is sequenced from adult flies from lines inbred for 20 generations. A high-quality assembly is achieved having a contig N50 of 45.7 kb and scaffold N50 of 4.06 Mb. In-depth curation of more than 1800 messenger RNAs shows specific gene expansions that can be related to invasiveness and host adaptation, including gene families for chemoreception, toxin and insecticide metabolism, cuticle proteins, opsins, and aquaporins. We identify genes relevant to IPM control, including those required to improve SIT. The medfly genome sequence provides critical insights into the biology of one of the most serious and widespread agricultural pests. This knowledge should significantly advance the means of controlling the size and invasive potential of medfly populations. Its close relationship to Drosophila, and other insect species important to agriculture and human health, will further comparative functional and structural studies of insect genomes that should broaden our understanding of gene family evolution.

  7. Complete genome sequence of Corynebacterium variabile DSM 44702 isolated from the surface of smear-ripened cheeses and insights into cheese ripening and flavor generation

    Science.gov (United States)

    2011-01-01

    Background Corynebacterium variabile is part of the complex microflora on the surface of smear-ripened cheeses and contributes to the development of flavor and textural properties during cheese ripening. Still little is known about the metabolic processes and microbial interactions during the production of smear-ripened cheeses. Therefore, the gene repertoire contributing to the lifestyle of the cheese isolate C. variabile DSM 44702 was deduced from the complete genome sequence to get a better understanding of this industrial process. Results The chromosome of C. variabile DSM 44702 is composed of 3, 433, 007 bp and contains 3, 071 protein-coding regions. A comparative analysis of this gene repertoire with that of other corynebacteria detected 1, 534 predicted genes to be specific for the cheese isolate. These genes might contribute to distinct metabolic capabilities of C. variabile, as several of them are associated with metabolic functions in cheese habitats by playing roles in the utilization of alternative carbon and sulphur sources, in amino acid metabolism, and fatty acid degradation. Relevant C. variabile genes confer the capability to catabolize gluconate, lactate, propionate, taurine, and gamma-aminobutyric acid and to utilize external caseins. In addition, C. variabile is equipped with several siderophore biosynthesis gene clusters for iron acquisition and an exceptional repertoire of AraC-regulated iron uptake systems. Moreover, C. variabile can produce acetoin, butanediol, and methanethiol, which are important flavor compounds in smear-ripened cheeses. Conclusions The genome sequence of C. variabile provides detailed insights into the distinct metabolic features of this bacterium, implying a strong adaption to the iron-depleted cheese surface habitat. By combining in silico data obtained from the genome annotation with previous experimental knowledge, occasional observations on genes that are involved in the complex metabolic capacity of C. variabile

  8. New insights into the tectonic inversion of North Canterbury and the regional structural context of the 2010-2011 Canterbury earthquake sequence, New Zealand

    Science.gov (United States)

    Barnes, Philip M.; Ghisetti, Francesca C.; Gorman, Andrew R.

    2016-02-01

    The 2010-2011 Canterbury earthquake sequence highlighted the existence of previously unknown active faults beneath the North Canterbury plains and Pegasus Bay, South Island, New Zealand. We provide new insights into the geometry and kinematics of ongoing deformation by analyzing marine seismic data to produce new maps of regional faults and cross-sectional reconstructions of deformation history. Active faulting and folding extends up to 30 km offshore, and involves reactivation of sets of Late Cretaceous-Paleogene normal faults under NW-SE tectonic compression. The active faults consist predominantly of NE-SW striking, SE-dipping reverse faults, and less commonly E-W to NW-SE faults suitably oriented for strike-slip reactivation. Additionally, newly developing reverse faults obliquely segment and overprint the inherited basement fabric and impose geometric and kinematic complexities revealed by mapping and reverse displacement profiles of markers. The Quaternary reverse slip rates decrease from 0.1-0.3 mm/yr beneath northern Pegasus Bay to Tectonic inversion and overprinting processes beneath Pegasus Bay are immature and tectonics, in which selective fault reactivation results from compressive stress imposed across a complex network of inherited faults.

  9. A modification to the SCAR (Sequence Characterized Amplified Region method provides phylogenetic insights within Ceratozamia (Zamiaceae Una modificación al método SCAR (Sequence Characterized Amplified Region aporta entendimiento filogenético en Ceratozamia (Zamiaceae

    Directory of Open Access Journals (Sweden)

    Dolores González

    2012-12-01

    Full Text Available Phylogenetic relationships among closely related plant species are still problematic. DNA intergenic regions often are insufficiently variable to provide desired resolution or support. In this study, a modification to the Sequence Characterized Amplified Region (SCAR method was used to find polymorphic loci for phylogenetic analyses within Ceratozamia. RAPD markers were first used to detect variation in 5 species. Then, equal length fragments found in 2 or more species were excised from the gel, purified and digested with frequent cutter restriction enzymes for isolating both ends, which have the same primer site. Digested fragments were sequenced with the RAPD primer. Variable sequences were used to design specific primers for amplifying and sequencing in all species for phylogenetic analyses. Our results confirmed the previously known high genome sequence resemblance within this genus that contrasts with its high morphological variation. Only 7 parsimony informative characters were found with this approach. Nonetheless, the Digested-SCAR (D-SCAR method provided some phylogenetic insights. Four main clades consistent with distribution ranges of the species were detected. The approach presented here was effective to solve some relationships within the genus and can potentially be implemented in other organisms to find polymorphic loci for phylogenetic studies at any taxonomic level.Las relaciones filogenéticas entre especies de plantas cercanamente relacionadas es aún problemático. Las regiones intergénicas del ADN son a menudo insuficientemente variables para proveer los niveles de resolución y soporte deseados. En este estudio, se usó una modificación al método Sequence Characterized Amplified Region (SCAR para encontrar loci polimórficos para análisis filogenéticos en Ceratozamia. Primero se usaron marcadores RAPD para detectar variación en 5 especies; luego, se cortaron del gel los fragmentos de la misma longitud en 2 o m

  10. Fluorescence and structure of methyl red-clay nanocomposites.

    Science.gov (United States)

    Martynková, Grazyna Simha; Kulhánková, Lenka; Malý, Petr; Capková, Pavla

    2008-04-01

    Two types of clay minerals-montmorillonite and vermiculite have been chosen as a host matrix for the intercalation of methyl red (MR) in order to investigate a possible fluorescence tuning via dye-clay interactions. The effect of silicate layer charge on the structure and fluorescence of dye-clay intercalated hybrid nanostructures was investigated using combination of molecular modeling with experiment. Structure of both intercalates MR-vermiculite (MR-VER) and MR-montmorillonite (MR-MMT) exhibits high degree of structural disorder resulting in broaden emission band. The fluorescence wavelength range of MR intercalated in clays is shifted to lower wavelengths compared with the pristine MR polycrystalline sample (800 nm). Results showed the strong dependence of fluorescence band maximum on the silicate layer charge, lambda(max) = 565 nm for MR-MMT, 645 nm for MR-VER and 800 nm for the methyl red fine crystalline powder, whereas the structural disorder in the arrangement of dye molecules affects the emission band broadening.

  11. Deep sequencing-based transcriptome profiling reveals comprehensive insights into the responses of Nicotiana benthamiana to beet necrotic yellow vein virus infections containing or lacking RNA4.

    Directory of Open Access Journals (Sweden)

    Huiyan Fan

    Full Text Available BACKGROUND: Beet necrotic yellow vein virus (BNYVV, encodes either four or five plus-sense single stranded RNAs and is the causal agent of sugar beet rhizomania disease, which is widely distributed in most regions of the world. BNYVV can also infect Nicotiana benthamiana systemically, and causes severe curling and stunting symptoms in the presence of RNA4 or mild symptoms in the absence of RNA4. RESULTS: Confocal laser scanning microscopy (CLSM analyses showed that the RNA4-encoded p31 protein fused to the red fluorescent protein (RFP accumulated mainly in the nuclei of N. benthamiana epidermal cells. This suggested that severe RNA4-induced symptoms might result from p31-dependent modifications of the transcriptome. Therefore, we used next-generation sequencing technologies to analyze the transcriptome profile of N. benthamiana in response to infection with different isolates of BNYVV. Comparisons of the transcriptomes of mock, BN3 (RNAs 1+2+3, and BN34 (RNAs 1+2+3+4 infected plants identified 3,016 differentially expressed transcripts, which provided a list of candidate genes that potentially are elicited in response to virus infection. Our data indicate that modifications in the expression of genes involved in RNA silencing, ubiquitin-proteasome pathway, cellulose synthesis, and metabolism of the plant hormone gibberellin may contribute to the severe symptoms induced by RNA4 from BNYVV. CONCLUSIONS: These results expand our understanding of the genetic architecture of N. benthamiana as well as provide valuable clues to identify genes potentially involved in resistance to BNYVV infection. Our global survey of gene expression changes in infected plants reveals new insights into the complicated molecular mechanisms underlying symptom development, and aids research into new strategies to protect crops against viruses.

  12. A new high-resolution pollen sequence at Lake Van, Turkey: insights into penultimate interglacial-glacial climate change on vegetation history

    Science.gov (United States)

    Pickarski, Nadine; Litt, Thomas

    2017-06-01

    -157 ka) with higher oscillations in tree percentages and a later stage (ca. 157-131 ka) with lower tree percentages and subdued oscillations. This subdivision of the penultimate glacial is also seen in other pollen records from southern Europe (e.g., MD01-2444 and I-284; Margari et al., 2010; Roucoux et al., 2011). The occurring vegetation pattern is analogous to the division of MIS 3 and MIS 2 during the last glacial in the same sediment sequence. Furthermore, we are able to identify the MIS 6e event (ca. 179-159 ka) as described in marine pollen records, which reveals clear climate variability due to rapid alternation in the vegetation cover.In comparison with long European pollen archives, speleothem isotope records from the Near East, and global climate parameters (e.g., insolation, atmospheric CO2 content), the new high-resolution Lake Van record presents an improved insight into regional vegetation dynamics and climate variability in the eastern Mediterranean region.

  13. Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.

    Science.gov (United States)

    Lie, Alle A Y; Liu, Zhenfeng; Hu, Sarah K; Jones, Adriane C; Kim, Diane Y; Countway, Peter D; Amaral-Zettler, Linda A; Cary, S Craig; Sherr, Evelyn B; Sherr, Barry F; Gast, Rebecca J; Caron, David A

    2014-07-01

    Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

  14. Insights into deep-sea sediment fungal communities from the East Indian Ocean using targeted environmental sequencing combined with traditional cultivation

    National Research Council Canada - National Science Library

    Zhang, Xiao-yong; Tang, Gui-ling; Xu, Xin-ya; Nong, Xu-hua; Qi, Shu-hua

    2014-01-01

    .... We investigated the fungal community structure in five sediments from a depth of ∼ 4000 m in the East India Ocean using a combination of targeted environmental sequencing and traditional cultivation...

  15. Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing.

    Science.gov (United States)

    Solomon, Kevin V; Haitjema, Charles H; Thompson, Dawn A; O'Malley, Michelle A

    2014-08-01

    It is becoming increasingly clear that microbes within microbial communities, for which cultured isolates have not yet been obtained, have an immense, untapped reservoir of enzymes that could help address grand challenges in human health, energy, and sustainability. Despite the obstacles associated with culturing these microbes, recent advances in next-generation sequencing (NGS) have made it possible to explore complex microbial communities in their native context for the first time. Key to extracting meaning from rapidly growing NGS datasets are bioinformatics tools that assemble the sequence data, annotate homologous sequences and interrogate it to reveal regulatory patterns. Complementing this are advances in proteomics that can link NGS data to biological function. This combination of next generation sequencing, proteomics and bioinformatic analysis forms a powerful tool to study non-model microbes, which will transform what we know about these dynamic systems.

  16. Insights into the phylogenetic positions of photosynthetic bacteria obtained from 5S rRNA and 16S rRNA sequence data

    Science.gov (United States)

    Fox, G. E.

    1985-01-01

    Comparisons of complete 16S ribosomal ribonucleic acid (rRNA) sequences established that the secondary structure of these molecules is highly conserved. Earlier work with 5S rRNA secondary structure revealed that when structural conservation exists the alignment of sequences is straightforward. The constancy of structure implies minimal functional change. Under these conditions a uniform evolutionary rate can be expected so that conditions are favorable for phylogenetic tree construction.

  17. 黄土高原西部红粘土岩石磁学性质及其指示的亚洲内陆中中新世气候变化特征%MID-MIOCENE CLIMATE IN THE ASIAN INTERIOR ,BASED ON THE MINERAL-MAGNETIC RECORD OF THE RED CLAY SEQUENCE ON THE WESTERN CHINESE LOESS PLATEAU

    Institute of Scientific and Technical Information of China (English)

    赵辉; 强小科; 敖红; 徐新文; 孙玉芳; 陈艇

    2012-01-01

    对黄土高原西部庄浪红粘土进行详细岩石磁学分析表明,沉积物磁性由磁铁矿和赤铁矿主导,并且含有一定量的磁赤铁矿.中中新世大暖期红粘土中磁铁矿、磁赤铁矿含量显著升高;中中新世大暖期前后红粘土中的磁铁矿含量相对较低,赤铁矿相对含量较高,但并未显示较强的磁赤铁矿信息.磁性矿物的整体粒径表现为以SP,SD和PSD颗粒为主,MD颗粒较少.庄浪红粘土磁化率在16.5 ~ 13.8Ma出现峰值,与当时的夏季风强盛、降水丰富、成壤作用较强造成的亚铁磁性矿物相对含量增加密切相关.在全球气候变暖的中中新世大暖期,综合庄浪岩石磁学特征以及陆地和海洋的其他证据可以推测当时东亚冬、夏季风可能同时增强.%Heqing Basin(26°27' - 26°46'N, 100°08' ~ 100°17'E) is a Late Cenozoic north-south oriented pull-apart basin near the northwestern margin of the Yunnan-Guizhou Plateau. The Basin is located at the southeastern margin of the Tibetan Plateau and belongs to the terminal of Hengduan Mountains. The local climate is dominated by Indian monsoon. Therefore,the continuous and thick sediments in the basin make it a perfect continental record for evolution of Indian summer monsoon. The Heqing drill core was obtained in the centre of the Heqing Basin. Using the internal lining method, recovery of the HQ drill core (26°33'43. 1"N, 100°10'14. 2"E;2200m) which has an accumulative depth of 665. 83m reaches up to 96. 7%. The lake sediments mainly consist of horizontally laminated greyish-green calcareous clay and silty clay with thin-bedded silt and fine sand layers, except two intervals of sand layers with fine gravels. With the equal interval of 50cm, we obtained 1368 samples from the drill core and chose 108 from different depositional units for detailed rock magnetic measurements. Based on detailed rock magnetic measurements like magnetic susceptibility versus high/low temperature curves, thermal demagnetization curve, hysteresis loops and FORC diagrams, we have investigated the magnetic properties of Heqing core lacustrine sediments. Magnetic measurements showed that sediments from the lower section (before 1.8Ma) of the core contain both magnetite and greigite while sediments from the upper section ( after 1. 8Ma) contain magnetite only.

  18. Transcriptional Slippage and RNA Editing Increase the Diversity of Transcripts in Chloroplasts: Insight from Deep Sequencing of Vigna radiata Genome and Transcriptome.

    Directory of Open Access Journals (Sweden)

    Ching-Ping Lin

    Full Text Available We performed deep sequencing of the nuclear and organellar genomes of three mungbean genotypes: Vigna radiata ssp. sublobata TC1966, V. radiata var. radiata NM92 and the recombinant inbred line RIL59 derived from a cross between TC1966 and NM92. Moreover, we performed deep sequencing of the RIL59 transcriptome to investigate transcript variability. The mungbean chloroplast genome has a quadripartite structure including a pair of inverted repeats separated by two single copy regions. A total of 213 simple sequence repeats were identified in the chloroplast genomes of NM92 and RIL59; 78 single nucleotide variants and nine indels were discovered in comparing the chloroplast genomes of TC1966 and NM92. Analysis of the mungbean chloroplast transcriptome revealed mRNAs that were affected by transcriptional slippage and RNA editing. Transcriptional slippage frequency was positively correlated with the length of simple sequence repeats of the mungbean chloroplast genome (R2=0.9911. In total, 41 C-to-U editing sites were found in 23 chloroplast genes and in one intergenic spacer. No editing site that swapped U to C was found. A combination of bioinformatics and experimental methods revealed that the plastid-encoded RNA polymerase-transcribed genes psbF and ndhA are affected by transcriptional slippage in mungbean and in main lineages of land plants, including three dicots (Glycine max, Brassica rapa, and Nicotiana tabacum, two monocots (Oryza sativa and Zea mays, two gymnosperms (Pinus taeda and Ginkgo biloba and one moss (Physcomitrella patens. Transcript analysis of the rps2 gene showed that transcriptional slippage could affect transcripts at single sequence repeat regions with poly-A runs. It showed that transcriptional slippage together with incomplete RNA editing may cause sequence diversity of transcripts in chloroplasts of land plants.

  19. Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants.

    Science.gov (United States)

    Maus, Irena; Wibberg, Daniel; Stantscheff, Robbin; Stolze, Yvonne; Blom, Jochen; Eikmeyer, Felix-Gregor; Fracowiak, Jochen; König, Helmut; Pühler, Alfred; Schlüter, Andreas

    2015-05-10

    The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed significant similarities. The absence of genes for a putative ammonium uptake system may indicate that M. bourgensis MS2(T) is adapted to environments rich in ammonium/ammonia. Specific genes featuring predicted functions in the context of osmolyte production were detected in the genome of M. bourgensis MS2(T). Mapping of metagenome sequences derived from a production-scale biogas plant revealed that M. bourgensis MS2(T) almost completely comprises the genetic information of dominant methanogens present in the biogas reactor analyzed. Hence, availability of the M. bourgensis MS2(T) genome sequence may be valuable regarding further research addressing the performance of Methanoculleus species in agricultural biogas plants.

  20. Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus.

    Science.gov (United States)

    Valdes, Jorge; Ossandon, Francisco; Quatrini, Raquel; Dopson, Mark; Holmes, David S

    2011-12-01

    Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

  1. Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus

    OpenAIRE

    Valdes, Jorge; Ossandon, Francisco; Quatrini, Raquel; Dopson, Mark; Holmes, David S

    2011-01-01

    Acidithiobacillus thiooxidans is a mesophilic, extremely acidophilic, chemolithoautotrophic gammaproteobacterium that derives energy from the oxidation of sulfur and inorganic sulfur compounds. Here we present the draft genome sequence of A. thiooxidans ATCC 19377, which has allowed the identification of genes for survival and colonization of extremely acidic environments.

  2. Draft genome sequence and transcriptome analysis of the wine spoilage yeast Dekkera bruxellensis LAMAP2480 provides insights into genetic diversity, metabolism and survival.

    Science.gov (United States)

    Valdes, Jorge; Tapia, Paz; Cepeda, Victoria; Varela, Javier; Godoy, Liliana; Cubillos, Francisco A; Silva, Evelyn; Martinez, Claudio; Ganga, Maria Angélica

    2014-12-01

    Dekkera bruxellensis is the major contaminant yeast in the wine industry worldwide. Here, we present the draft genome sequence of D. bruxellensis LAMAP2480 isolated from a Chilean wine. Genomic evidence reveals shared and exclusive genes potentially involved in colonization and survival during alcoholic fermentation.

  3. Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.

    Directory of Open Access Journals (Sweden)

    Brian M Shamblin

    Full Text Available Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for

  4. New insights into the molecular phylogeny of Balantidium (Ciliophora, Vetibuliferida) based on the analysis of new sequences of species from fish hosts.

    Science.gov (United States)

    Li, Ming; Ponce-Gordo, Francisco; Grim, J Norman; Wang, Chong; Nilsen, Frank

    2014-12-01

    We obtained sequences of the small subunit ribosomal RNA (rRNA) for two new isolates of Balantidium from fishes, Balantidium polyvacuolum and Balantidium ctenopharingodoni. This is the first introduction of molecular data of Balantidium species from fish hosts in the phylogenetic analyses of the ciliate subclass Trichostomatia. Despite the fact that these species share morphological characteristics common to other species of Balantidium, the phylogenetic analysis of their sequences has shown that they are to be placed in a different branch closely related to the so-called Australian clade. Thus, our results indicate that the genus Balantidium is polyphyletic and possibly should be represented by two different genera; however, the analysis of more species from other poikilothermic hosts (amphibians, reptiles) should be made before a revised taxonomical proposal could be made.

  5. Population Parameters of Intermediate-Age Star Clusters in the Large Magellanic Cloud. II. New Insights from Extended Main Sequence Turnoffs in 7 Star Clusters

    CERN Document Server

    Goudfrooij, Paul; Kozhurina-Platais, Vera; Chandar, Rupali

    2011-01-01

    We discuss new photometry from high-resolution images of 7 intermediate-age (1-2 Gyr) star clusters in the Large Magellanic Cloud taken with the Advanced Camera for Surveys on board the Hubble Space Telescope. We fit color-magnitude diagrams (CMDs) with several different sets of theoretical isochrones, and determine systematic uncertainties for population parameters when derived using any one set of isochrones. The cluster CMDs show several interesting features, including extended main sequence turnoff (MSTO) regions, narrow red giant branches, and clear sequences of unresolved binary stars. We show that the extended MSTOs are not caused by photometric uncertainties, contamination by field stars, or the presence of binary stars. Enhanced helium abundances in a fraction of cluster stars are also ruled out as the reason for the extended MSTOs. Quantitative comparisons with simulations indicate that the MSTO regions are better described by a spread in ages than by a bimodal age distribution, although we can not ...

  6. Insights into Protein Sequence and Structure-Derived Features Mediating 3D Domain Swapping Mechanism using Support Vector Machine Based Approach

    Directory of Open Access Journals (Sweden)

    Khader Shameer

    2010-06-01

    Full Text Available 3-dimensional domain swapping is a mechanism where two or more protein molecules form higher order oligomers by exchanging identical or similar subunits. Recently, this phenomenon has received much attention in the context of prions and neuro-degenerative diseases, due to its role in the functional regulation, formation of higher oligomers, protein misfolding, aggregation etc. While 3-dimensional domain swap mechanism can be detected from three-dimensional structures, it remains a formidable challenge to derive common sequence or structural patterns from proteins involved in swapping. We have developed a SVM-based classifier to predict domain swapping events using a set of features derived from sequence and structural data. The SVM classifier was trained on features derived from 150 proteins reported to be involved in 3D domain swapping and 150 proteins not known to be involved in swapped conformation or related to proteins involved in swapping phenomenon. The testing was performed using 63 proteins from the positive dataset and 63 proteins from the negative dataset. We obtained 76.33% accuracy from training and 73.81% accuracy from testing. Due to high diversity in the sequence, structure and functions of proteins involved in domain swapping, availability of such an algorithm to predict swapping events from sequence and structure-derived features will be an initial step towards identification of more putative proteins that may be involved in swapping or proteins involved in deposition disease. Further, the top features emerging in our feature selection method may be analysed further to understand their roles in the mechanism of domain swapping.

  7. Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle

    OpenAIRE

    Lingzhao Fang; Goutam Sahana; Guosheng Su; Ying Yu; Shengli Zhang; Mogens Sandø Lund; Peter Sørensen

    2017-01-01

    Connecting genome-wide association study (GWAS) to biological mechanisms underlying complex traits is a major challenge. Mastitis resistance and milk production are complex traits of economic importance in the dairy sector and are associated with intra-mammary infection (IMI). Here, we integrated IMI-relevant RNA-Seq data from Holstein cattle and sequence-based GWAS data from three dairy cattle breeds (i.e., Holstein, Nordic red cattle, and Jersey) to explore the genetic basis of mastitis res...

  8. Complete nucleotide sequence of the self-transmissible TOL plasmid pD2RT provides new insight into arrangement of toluene catabolic plasmids

    DEFF Research Database (Denmark)

    Jutkina, Jekaterina; Hansen, Lars Hestbjerg; Li, Lili

    2013-01-01

    In the present study we report the complete nucleotide sequence of the toluene catabolic plasmid pD2RT of Pseudomonas migulae strain D2RT isolated from Baltic Sea water. The pD2RT is 129,894 base pairs in size with an average G+ C content of 53.75%. A total of 135 open reading frames (ORFs) were ...

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

    Directory of Open Access Journals (Sweden)

    Jung Sung Kim

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  11. Involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of Gordonia polyisoprenivorans strain VH2.

    Science.gov (United States)

    Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Halbsguth, Tobias; Bröker, Daniel; Angelov, Angel; Liebl, Wolfgang; Daniel, Rolf; Steinbüchel, Alexander

    2012-04-01

    The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search.

  12. Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca ssp. bracteata (Rosaceae).

    Science.gov (United States)

    Tennessen, Jacob A; Govindarajulu, Rajanikanth; Liston, Aaron; Ashman, Tia-Lynn

    2013-08-07

    Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild strawberry, Fragaria vesca ssp. bracteata (Rosaceae), is a member of a clade with both dioecious and cultivated species, making it an ideal model in which to study the genetics of male sterility. To create a genetic map of F. v. ssp. bracteata, we identified informative polymorphisms from genomic sequencing (3-5x coverage) of two outbred plants from the same population. Using targeted enrichment, we sequenced 200 bp surrounding each of 6575 polymorphisms in 48 F1 offspring, yielding genotypes at 98% of targeted sites with mean coverage >100x, plus more than 600-kb high-coverage nontargeted sequence. With the resulting linkage map of 7802 stringently filtered markers (5417 targeted), we assessed recombination rates and genomic incongruities. Consistent with past work in strawberries, male sterility is dominant, segregates 1:1, and maps to a single location in the female. Further mapping an additional 55 offspring places male sterility in a gene-dense, 338-kb region of chromosome 4. The region is not syntenic with the sex-determining regions in the closely related octoploids, F. chiloensis and F. virginiana, suggesting either independent origins or translocation. The 57 genes in this region do not include protein families known to control male sterility and thus suggest alternate mechanisms for the suppression of male function.

  13. Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe.

    Directory of Open Access Journals (Sweden)

    Christopher P Middleton

    Full Text Available Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8-9 million years ago (MYA. The genome donors of hexaploid wheat diverged between 2.1-2.9 MYA, while rye diverged from Triticum aestivum approximately 3-4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

  14. Sequencing, De Novo Assembly, and Annotation of the Transcriptome of the Endangered Freshwater Pearl Bivalve, Cristaria plicata, Provides Novel Insights into Functional Genes and Marker Discovery.

    Directory of Open Access Journals (Sweden)

    Bharat Bhusan Patnaik

    Full Text Available The freshwater mussel Cristaria plicata (Bivalvia: Eulamellibranchia: Unionidae, is an economically important species in molluscan aquaculture due to its use in pearl farming. The species have been listed as endangered in South Korea due to the loss of natural habitats caused by anthropogenic activities. The decreasing population and a lack of genomic information on the species is concerning for environmentalists and conservationists. In this study, we conducted a de novo transcriptome sequencing and annotation analysis of C. plicata using Illumina HiSeq 2500 next-generation sequencing (NGS technology, the Trinity assembler, and bioinformatics databases to prepare a sustainable resource for the identification of candidate genes involved in immunity, defense, and reproduction.The C. plicata transcriptome analysis included a total of 286,152,584 raw reads and 281,322,837 clean reads. The de novo assembly identified a total of 453,931 contigs and 374,794 non-redundant unigenes with average lengths of 731.2 and 737.1 bp, respectively. Furthermore, 100% coverage of C. plicata mitochondrial genes within two unigenes supported the quality of the assembler. In total, 84,274 unigenes showed homology to entries in at least one database, and 23,246 unigenes were allocated to one or more Gene Ontology (GO terms. The most prominent GO biological process, cellular component, and molecular function categories (level 2 were cellular process, membrane, and binding, respectively. A total of 4,776 unigenes were mapped to 123 biological pathways in the KEGG database. Based on the GO terms and KEGG annotation, the unigenes were suggested to be involved in immunity, stress responses, sex-determination, and reproduction. A total of 17,251 cDNA simple sequence repeats (cSSRs were identified from 61,141 unigenes (size of >1 kb with the most abundant being dinucleotide repeats.This dataset represents the first transcriptome analysis of the endangered mollusc, C. plicata

  15. New evidence for the catastrophic demise of a prehistoric settlement (the Lajia Ruins) in the Guanting Basin, upper Yellow River, NW China

    Science.gov (United States)

    Zhao, Hui; Huang, Chun Chang; Zheng, Zixing; Hu, Ying; Zhang, Yuzhu; Guo, Yongqiang; Zhou, Qiang

    2017-09-01

    The Lajia Ruins in the Guanting Basin, NW China, are a product of the prehistoric Qijia Culture. Like Pompeii, they are a rare example of an archaeological site preserved by a natural disaster and are therefore important in archaeology, anthropology and geology. However, the nature of the disaster(s) responsible for the destruction of the site remains controversial. Most studies have focused on an earthquake and a red clay layer directly overlying the site and a detailed stratigraphic study of the mid-Holocene sedimentary strata combined with other intervals of red clay deposition (hence possible disasters) is lacking. We identified a mid-Holocene paleosol sequence (the Shanglajia section) at the site which contains two layers of red clay, dated to 3950 a BP and 3500 a BP, intercalated within the mid-Holocene paleosol (S0). Subsequent multi-proxy analysis indicated that the characteristics of the two red clay layers resemble those of typical Tertiary red clay deposits and the modern gully deposit at the foot of the Great Red Hills, but are distinctly different from those of the slackwater deposits of the Yellow River and the mid-Holocene paleosol. Our results suggest that, at 3950 a BP and 3500 a BP, two large-scale rainstorm-induced mudflow events, originating from the gullies to the north, flooded the Lajia area on the second terrace of the Yellow River, devastating and burying the human settlements. We infer that the intensified erosion and mass wasting were caused by human activity; in addition, natural factors such as rainstorms and earthquakes, may also have played an important role in triggering catastrophic mudflow events in the Tertiary Red Clay deposits. Overall, our results provide further insights into prehistoric man-land relationships in this environmentally sensitive region which may have implications for modern land use in this region of China and elsewhere.

  16. What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences.

    Science.gov (United States)

    Yonetani, Yoshiteru; Kono, Hidetoshi

    2012-01-01

    The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern in the DNA minor groove, the water bridge, for various DNA sequences to show that the water-bridge lifetime varies from 1 to ~300ps in a sequence-dependent manner. We find that it follows 1/k(V(step))P(m), where P(m) and V(step) are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of DNA, respectively. This relationship provides a picture of the water kinetics with atomistic detail and shows that water dissociation occurs when a particular hydrogen-bonding pattern appears. The rate constant of water dissociation k can be described as a function of the structural fluctuations of DNA. This picture is consistent with the model of Laage and Hynes proposing that hydrogen-bond switching occurs when an unusual number of hydrogen bonds are formed. The two new factors suggested here are discussed in the context of the surface's geometry and electrostatic nature, which were previously proposed as the determinants of water lifetimes.

  17. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

    Science.gov (United States)

    Yi, Xuan; Gao, Lei; Wang, Bo; Su, Ying-Juan; Wang, Ting

    2013-01-01

    We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

  18. Unveiling the Important Role of Groups in the Evolution of Massive Galaxies: Insights from an Infrared Passive Sequence at Intermediate Redshift

    CERN Document Server

    Wilman, D J; Tyler, K; McGee, S L; Oemler, A; Morris, S L; Balogh, M L; Bower, R G; Mulchaey, J S

    2008-01-01

    The most massive galaxies in the Universe are also the oldest. To overturn this apparent contradiction with hierarchical growth models, we focus on the group scale haloes which host most of these galaxies. A stellar mass selected M_* >~ 2x10^10M_sol sample at z~0.4 is constructed within the CNOC2 redshift survey. A sensitive Mid InfraRed (MIR) IRAC colour is used to isolate passive galaxies. It produces a bimodal distribution, in which passive galaxies (highlighted by morphological early-types) define a tight MIR colour sequence (Infrared Passive Sequence, IPS). This is due to stellar atmospheric emission from old stellar populations. Significantly offset from the IPS are galaxies where reemission by dust boosts emission at 8microns (InfraRed-Excess or IRE galaxies). They include all known morphological late-types. Comparison with EW[OII] shows that MIR colour is highly sensitive to low levels of activity, and allows us to separate dusty-active from passive galaxies. The fraction of IRE galaxies, f(IRE) drops...

  19. Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.

    Science.gov (United States)

    Kosa, Peter; Valach, Matus; Tomaska, Lubomir; Wolfe, Kenneth H; Nosek, Jozef

    2006-01-01

    We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.

  20. Rapid determination of P-wave-based Energy Magnitude: Insights on source parameter scaling of the 2016 Central Italy earthquake sequence

    Science.gov (United States)

    Picozzi, Matteo; Bindi, Dino; Brondi, Piero; Di Giacomo, Domenico; Parolai, Stefano; Zollo, Aldo

    2017-04-01

    In this study, we proposed a novel methodology for the rapid estimation of the earthquake size from the seismic radiated energy. Two relationships have been calibrated using recordings from 29 earthquakes of the 2009 L'Aquila and the 2012 Emilia seismic sequences in Italy. The first relation allows obtaining seismic radiated energy ER estimates using as proxy the time integral of squared P-waves velocities measured over vertical components, including regional attributes for describing the attenuation with distance. The second relation is a regression between the local magnitude and the radiated energy, which allows defining an energy-based local magnitude (MLe) compatible with ML for small earthquakes. We have applied the new procedure to the seismic sequence that struck central Italy in 2016. Scaling relationships involving seismic moment and radiated energy are discussed considering the Mw 6.0 Amatrice, Mw 5.9 Ussita and Mw 6.5 Norcia earthquakes and their ML >4 aftershocks, in total 38 events. The Mw 6.0 Amatrice earthquake presents the highest apparent stress, and the observed differences among the three larger shocks highlight the dynamic heterogeneity with which large earthquakes can occur in central Italy. Differences between MLe and Mw measures allows to identify events characterized by a higher amount of energy transferred to seismic waves, providing important constraints for the real-time evaluation of an earthquake shaking potential.

  1. Diversity of the luciferin binding protein gene in bioluminescent dinoflagellates--insights from a new gene in Noctiluca scintillans and sequences from gonyaulacoid genera.

    Science.gov (United States)

    Valiadi, Martha; Iglesias-Rodriguez, Maria Debora

    2014-01-01

    Dinoflagellate bioluminescence systems operate with or without a luciferin binding protein, representing two distinct modes of light production. However, the distribution, diversity, and evolution of the luciferin binding protein gene within bioluminescent dinoflagellates are not well known. We used PCR to detect and partially sequence this gene from the heterotrophic dinoflagellate Noctiluca scintillans and a group of ecologically important gonyaulacoid species. We report an additional luciferin binding protein gene in N. scintillans which is not attached to luciferase, further to its typical combined bioluminescence gene. This supports the hypothesis that a profound re-organization of the bioluminescence system has taken place in this organism. We also show that the luciferin binding protein gene is present in the genera Ceratocorys, Gonyaulax, and Protoceratium, and is prevalent in bioluminescent species of Alexandrium. Therefore, this gene is an integral component of the standard molecular bioluminescence machinery in dinoflagellates. Nucleotide sequences showed high within-strain variation among gene copies, revealing a highly diverse gene family comprising multiple gene types in some organisms. Phylogenetic analyses showed that, in some species, the evolution of the luciferin binding protein gene was different from the organism's general phylogenies, highlighting the complex evolutionary history of dinoflagellate bioluminescence systems.

  2. Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus.

    Science.gov (United States)

    Wu, Wei; Yang, Yu-Lan; He, Wei-Ming; Rouard, Mathieu; Li, Wei-Ming; Xu, Meng; Roux, Nicolas; Ge, Xue-Jun

    2016-08-17

    Crop wild relatives are valuable resources for future genetic improvement. Here, we report the de novo genome assembly of Musa itinerans, a disease-resistant wild banana relative in subtropical China. The assembled genome size was 462.1 Mb, covering 75.2% of the genome (615.2Mb) and containing 32, 456 predicted protein-coding genes. Since the approximate divergence around 5.8 million years ago, the genomes of Musa itinerans and Musa acuminata have shown conserved collinearity. Gene family expansions and contractions enrichment analysis revealed that some pathways were associated with phenotypic or physiological innovations. These include a transition from wood to herbaceous in the ancestral Musaceae, intensification of cold and drought tolerances, and reduced diseases resistance genes for subtropical marginally distributed Musa species. Prevalent purifying selection and transposed duplications were found to facilitate the diversification of NBS-encoding gene families for two Musa species. The population genome history analysis of M. itinerans revealed that the fluctuated population sizes were caused by the Pleistocene climate oscillations, and that the formation of Qiongzhou Strait might facilitate the population downsizing on the isolated Hainan Island about 10.3 Kya. The qualified assembly of the M. itinerans genome provides deep insights into the lineage-specific diversification and also valuable resources for future banana breeding.

  3. On the origins of the tetraploid Bromus species (section Bromus, Poaceae): insights from internal transcribed spacer sequences of nuclear ribosomal DNA.

    Science.gov (United States)

    Ainouche, M L; Bayer, R J

    1997-10-01

    The internal transcribed spacer (ITS) region of nuclear ribosomal DNA from 22 diploid and tetraploid annual Bromus species of section Bromus (Poaceae) and three species belonging to other Bromus sections, Bromus catharticus (section Ceratochloa), Bromus anomalus (section Pnigma), and Bromus sterilis (section Genea), were investigated by PCR amplification and direct sequencing. The length of the ITS-1 region varied from 215 to 218 bp, and that of the ITS-2 region from 215 to 216 bp, in the species analyzed. ITS-1 was more variable and provided more informative sites (49) than ITS-2 (32). No variation was encountered within species. In pairwise comparison among species of section Bromus, sequence divergence ranged from 0.0 to 8.0% for the combined ITS-1 and ITS-2 regions. Parsimony analysis using Avena longiglumis and Hordeum vulgare as outgroups resulted in well-resolved phylogenetic trees and showed that section Bromus is monophyletic according to the species analyzed outside of the section. The analysis clarified the phylogenetic relationships among monogenomic (diploid) species. Introduction of the allotetraploid species did not change the general topology of the trees obtained using only the diploid species. Although some tetraploid-diploid species relationships will have to be clarified with faster evolving markers, the ITS sequences are shown to be useful for assessing evolutionary relationships among closely related Bromus species, as well as for clarifying taxonomic problems in previously controversial cases (e.g., Bromus alopecuros and Bromus caroli-henrici). New hypotheses are proposed concerning the origin of several allotetraploid species. For example, it is shown that the tetraploid Bromus hordeaceus diverged earlier than all other species of section Bromus, excluding the diploid B. caroli-henrici, which is found to be basal in this group. The tetraploid Bromus arenarius, which was considered a hybrid between sections Bromus and Genea, and the

  4. Rapid determination of P wave-based energy magnitude: Insights on source parameter scaling of the 2016 Central Italy earthquake sequence

    Science.gov (United States)

    Picozzi, Matteo; Bindi, Dino; Brondi, Piero; Di Giacomo, Domenico; Parolai, Stefano; Zollo, Aldo

    2017-05-01

    We propose a P wave based procedure for the rapid estimation of the radiated seismic energy, and a novel relationship for obtaining an energy-based local magnitude (MLe) measure of the earthquake size. We apply the new procedure to the seismic sequence that struck Central Italy in 2016. Scaling relationships involving seismic moment and radiated energy are discussed for the Mw 6.0 Amatrice, Mw 5.9 Ussita, and Mw 6.5 Norcia earthquakes, including 35 ML > 4 aftershocks. The Mw 6.0 Amatrice earthquake shows the highest apparent stress, and the observed differences among the three main events highlight the dynamic heterogeneity with which large earthquakes can occur in Central Italy. Differences between estimates of MLe and Mw allows identification of events which are characterized by a higher proportion of energy being transferred to seismic waves, providing important real-time indications of earthquakes shaking potential.

  5. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii.

    Science.gov (United States)

    Moreira, Leandro M; Almeida, Nalvo F; Potnis, Neha; Digiampietri, Luciano A; Adi, Said S; Bortolossi, Julio C; da Silva, Ana C; da Silva, Aline M; de Moraes, Fabrício E; de Oliveira, Julio C; de Souza, Robson F; Facincani, Agda P; Ferraz, André L; Ferro, Maria I; Furlan, Luiz R; Gimenez, Daniele F; Jones, Jeffrey B; Kitajima, Elliot W; Laia, Marcelo L; Leite, Rui P; Nishiyama, Milton Y; Rodrigues Neto, Julio; Nociti, Letícia A; Norman, David J; Ostroski, Eric H; Pereira, Haroldo A; Staskawicz, Brian J; Tezza, Renata I; Ferro, Jesus A; Vinatzer, Boris A; Setubal, João C

    2010-04-13

    Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

  6. Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii

    Directory of Open Access Journals (Sweden)

    Nociti Letícia A

    2010-04-01

    Full Text Available Abstract Background Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C. Results We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein. Conclusion We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

  7. Late Paleozoic tectonics of the Solonker Zone in the Wuliji area, Inner Mongolia, China: Insights from stratigraphic sequence, chronology, and sandstone geochemistry

    Science.gov (United States)

    Shi, Guanzhong; Song, Guangzeng; Wang, Hua; Huang, Chuanyan; Zhang, Lidong; Tang, Jianrong

    2016-09-01

    The geology in the Wuliji area (including the Enger Us and Quagan Qulu areas) is important for understanding the Late Paleozoic tectonics of the Solonker Zone. Ultramafic/mafic rocks in the Enger Us area, previously interpreted as an ophiolitic suture, are actually lava flows and sills in a Permian turbiditic sequence and a small body of fault breccia containing serpentinite. Subduction zone features, such as accretionary complexes, magmatic arc volcanics or LP/HP metamorphism are absent. Early Permian N-MORB mafic rocks and Late Permian radiolarian cherts accompanied by turbidites and tuffeous rocks indicate a deep water setting. In the Quagan Qulu area, outcrops of the Late Carboniferous to Permian Amushan Formation are composed of volcano-sedimenary rocks and guyot-like reef limestone along with a Late Permian volcano-sedimentary unit. A dacite lava in the Late Permian volcano-sedimentary unit yields a zircon U-Pb age of 254 Ma. The gabbros in the Quagan Qulu area are intruded into the Amushan Formation and caused contact metamorphism of country rocks. Sandstones in the Upper Member of the Amushan Formation contain detrital clasts of volcanic fragments and mineral clasts of crystalline basement rocks (i.e. biotite, muscovite and garnet). Geochemical analysis of volcaniclastic sandstones shows a magmatic affinity to both continental island arc (CIA) and active continental margin (ACM) tectonic settings. A Late Permian incipient rift setting is suggested by analyzing the lithostratigraphic sequence and related magmatism in the Wuliji area. The volcano-sedimentary rocks in the Wuliji area experienced a nearly N-S shortening that was probably related to the Early Mesozoic nearly N-S compression well developed in other areas close to the Wuliji area.

  8. Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate.

    Science.gov (United States)

    Wübbeler, Jan Hendrik; Hiessl, Sebastian; Schuldes, Jörg; Thürmer, Andrea; Daniel, Rolf; Steinbüchel, Alexander

    2014-07-01

    Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.

  9. Transcriptome-based gene profiling provides novel insights into the characteristics of radish root response to Cr stress with next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Yang eXie

    2015-03-01

    Full Text Available Radish (Raphanus sativus L. is an important worldwide root vegetable crop with high nutrient values and is adversely affected by non-essential heavy metals including chromium (Cr. Little is known about the molecular mechanism underlying Cr stress response in radish. In this study, RNA-Seq technique was employed to identify differentially expressed genes (DEGs under Cr stress. Based on de novo transcriptome assembly, there were 30,676 unigenes representing 60,881 transcripts isolated from radish root under Cr stress. Differential gene analysis revealed that 2,985 uingenes were significantly differentially expressed between Cr-free (CK and Cr-treated (Cr600 libraries, among which 1,424 were up-regulated and 1,561 down-regulated. Gene ontology (GO analysis revealed that these DEGs were mainly involved in primary metabolic process, response to abiotic stimulus, cellular metabolic process and small molecule metabolic process. Kyoto encyclopedia of genes and genomes (KEGG enrichment analysis showed that the DEGs were mainly involved in protein processing in endoplasmic reticulum, starch and sucrose metabolism, amino acid metabolism, glutathione metabolism, drug and xenobiotics by cytochrome P450 metabolism. RT-qPCR analysis showed that the expression patterns of 12 randomly selected DEGs were highly accordant with the results from RNA-seq. Furthermore, many candidate genes including signaling protein kinases, transcription factors and metal transporters, chelate compound biosynthesis and antioxidant system, were involved in defense and detoxification mechanisms of Cr stress response regulatory networks. These results would provide novel insight into molecular mechanism underlying plant responsiveness to Cr stress and facilitate further genetic manipulation on Cr uptake and accumulation in radish.

  10. Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4–55 PHA synthase and an insight into its catalytic mechanism

    Directory of Open Access Journals (Sweden)

    Ahmad Khairudin Nurul

    2006-11-01

    Full Text Available Abstract Background Polyhydroxyalkanoates (PHA, are biodegradable polyesters derived from many microorganisms such as the pseudomonads. These polyesters are in great demand especially in the packaging industries, the medical line as well as the paint industries. The enzyme responsible in catalyzing the formation of PHA is PHA synthase. Due to the limited structural information, its functional properties including catalysis are lacking. Therefore, this study seeks to investigate the structural properties as well as its catalytic mechanism by predicting the three-dimensional (3D model of the Type II Pseudomonas sp. USM 4–55 PHA synthase 1 (PhaC1P.sp USM 4–55. Results Sequence analysis demonstrated that PhaC1P.sp USM 4–55 lacked similarity with all known structures in databases. PSI-BLAST and HMM Superfamily analyses demonstrated that this enzyme belongs to the alpha/beta hydrolase fold family. Threading approach revealed that the most suitable template to use was the human gastric lipase (PDB ID: 1HLG. The superimposition of the predicted PhaC1P.sp USM 4–55 model with 1HLG covering 86.2% of the backbone atoms showed an RMSD of 1.15 Å. The catalytic residues comprising of Cys296, Asp451 and His479 were found to be conserved and located adjacent to each other. In addition to this, an extension to the catalytic mechanism was also proposed whereby two tetrahedral intermediates were believed to form during the PHA biosynthesis. These transition state intermediates were further postulated to be stabilized by the formation of oxyanion holes. Based on the sequence analysis and the deduced model, Ser297 was postulated to contribute to the formation of the oxyanion hole. Conclusion The 3D model of the core region of PhaC1P.sp USM 4–55 from residue 267 to residue 484 was developed using computational techniques and the locations of the catalytic residues were identified. Results from this study for the first time highlighted Ser297 potentially

  11. Tracing the evolutionary lineage of pattern recognition receptor homologues in vertebrates: An insight into reptilian immunity via de novo sequencing of the wall lizard splenic transcriptome.

    Science.gov (United States)

    Priyam, Manisha; Tripathy, Mamta; Rai, Umesh; Ghorai, Soma Mondal

    2016-04-01

    Reptiles remain a deprived class in the area of genomic and molecular resources for the vertebrate classes. The transition of squamates from aquatic to terrestrial mode of life caused profound changes in their immune system to combat the altered variety of pathogens on land. The current study aims at delineating the evolution of defence mechanisms in wall lizard, Hemidactylus flaviviridis, by exploring its immunome. De novo sequencing of splenic transcriptome from wall lizard on the Illumina Hi-Seq platform generated 258,128 unique transcripts with an average GC content of 45%. Annotation of 555,557 and 6812 transcripts was carried out against NCBI (non-redundant database) and UniProt databases, respectively. The KEGG pathway annotation of transcripts classified them into 39 processes of six pathway function categories. A total of 3824 transcripts, involved in 23 immune-related pathways, were identified in the immune-relevant cluster built by harvesting the genes under KEGG pathways of immune system and immune diseases. Forty-two percent of the immune-relevant cluster was represented by pattern-recognition receptors (PRRs), of which the maximum number of transcripts was attributed to the Toll-like receptor (TLR) signalling pathway. Nine PRRs with potential full-length coding sequences were sorted for phylogenetic analysis and comparative domain analysis across the vertebrate lineage. They included DEC205/lymphocyte antigen 75 (ly75), nucleotide-binding oligomerisation domain-containing protein 1 (NOD1), NOD-like receptor family CARD domain-containing 3 (NLRC3), nucleotide-binding oligomerisation domain, leucine-rich repeat-containing X1 (NLRX1), DDX58/retinoic acid-inducible gene 1 (RIG-1), Toll-like receptor 3 (TLR3), TLR4, TLR5 and TLR7. From selection studies of these genes, we inferred positive selection for ly75, NOD1, RIG-1, TLR3 and TLR4. Apart from contributing to the scarce genomic resources available for reptiles and giving a broad scope for the immune

  12. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Directory of Open Access Journals (Sweden)

    Victor González

    2012-09-01

    Full Text Available Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510. The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis, and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

  13. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Science.gov (United States)

    Wisniewski-Dyé, Florence; Lozano, Luis; Acosta-Cruz, Erika; Borland, Stéphanie; Drogue, Benoît; Prigent-Combaret, Claire; Rouy, Zoé; Barbe, Valérie; Mendoza Herrera, Alberto; González, Victor; Mavingui, Patrick

    2012-01-01

    Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. PMID:24705077

  14. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

    Science.gov (United States)

    Yuan, Daojun; Tang, Zhonghui; Wang, Maojun; Gao, Wenhui; Tu, Lili; Jin, Xin; Chen, Lingling; He, Yonghui; Zhang, Lin; Zhu, Longfu; Li, Yang; Liang, Qiqi; Lin, Zhongxu; Yang, Xiyan; Liu, Nian; Jin, Shuangxia; Lei, Yang; Ding, Yuanhao; Li, Guoliang; Ruan, Xiaoan; Ruan, Yijun; Zhang, Xianlong

    2015-01-01

    Gossypium hirsutum contributes the most production of cotton fibre, but G. barbadense is valued for its better comprehensive resistance and superior fibre properties. However, the allotetraploid genome of G. barbadense has not been comprehensively analysed. Here we present a high-quality assembly of the 2.57 gigabase genome of G. barbadense, including 80,876 protein-coding genes. The double-sized genome of the A (or At) (1.50 Gb) against D (or Dt) (853 Mb) primarily resulted from the expansion of Gypsy elements, including Peabody and Retrosat2 subclades in the Del clade, and the Athila subclade in the Athila/Tat clade. Substantial gene expansion and contraction were observed and rich homoeologous gene pairs with biased expression patterns were identified, suggesting abundant gene sub-functionalization occurred by allopolyploidization. More specifically, the CesA gene family has adapted differentially temporal expression patterns, suggesting an integrated regulatory mechanism of CesA genes from At and Dt subgenomes for the primary and secondary cellulose biosynthesis of cotton fibre in a “relay race”-like fashion. We anticipate that the G. barbadense genome sequence will advance our understanding the mechanism of genome polyploidization and underpin genome-wide comparison research in this genus. PMID:26634818

  15. Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle.

    Science.gov (United States)

    Fang, Lingzhao; Sahana, Goutam; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

    2017-03-30

    Connecting genome-wide association study (GWAS) to biological mechanisms underlying complex traits is a major challenge. Mastitis resistance and milk production are complex traits of economic importance in the dairy sector and are associated with intra-mammary infection (IMI). Here, we integrated IMI-relevant RNA-Seq data from Holstein cattle and sequence-based GWAS data from three dairy cattle breeds (i.e., Holstein, Nordic red cattle, and Jersey) to explore the genetic basis of mastitis resistance and milk production using post-GWAS analyses and a genomic feature linear mixed model. At 24 h post-IMI, genes responsive to IMI in the mammary gland were preferentially enriched for genetic variants associated with mastitis resistance rather than milk production. Response genes in the liver were mainly enriched for variants associated with mastitis resistance at an early time point (3 h) post-IMI, whereas responsive genes at later stages were enriched for associated variants with milk production. The up- and down-regulated genes were enriched for associated variants with mastitis resistance and milk production, respectively. The patterns were consistent across breeds, indicating that different breeds shared similarities in the genetic basis of these traits. Our approaches provide a framework for integrating multiple layers of data to understand the genetic architecture underlying complex traits.

  16. Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle

    Science.gov (United States)

    Fang, Lingzhao; Sahana, Goutam; Su, Guosheng; Yu, Ying; Zhang, Shengli; Lund, Mogens Sandø; Sørensen, Peter

    2017-01-01

    Connecting genome-wide association study (GWAS) to biological mechanisms underlying complex traits is a major challenge. Mastitis resistance and milk production are complex traits of economic importance in the dairy sector and are associated with intra-mammary infection (IMI). Here, we integrated IMI-relevant RNA-Seq data from Holstein cattle and sequence-based GWAS data from three dairy cattle breeds (i.e., Holstein, Nordic red cattle, and Jersey) to explore the genetic basis of mastitis resistance and milk production using post-GWAS analyses and a genomic feature linear mixed model. At 24 h post-IMI, genes responsive to IMI in the mammary gland were preferentially enriched for genetic variants associated with mastitis resistance rather than milk production. Response genes in the liver were mainly enriched for variants associated with mastitis resistance at an early time point (3 h) post-IMI, whereas responsive genes at later stages were enriched for associated variants with milk production. The up- and down-regulated genes were enriched for associated variants with mastitis resistance and milk production, respectively. The patterns were consistent across breeds, indicating that different breeds shared similarities in the genetic basis of these traits. Our approaches provide a framework for integrating multiple layers of data to understand the genetic architecture underlying complex traits. PMID:28358110

  17. The closest relatives of cacti: insights from phylogenetic analyses of chloroplast and mitochondrial sequences with special emphasis on relationships in the tribe Anacampseroteae.

    Science.gov (United States)

    Nyffeler, Reto

    2007-01-01

    Recent molecular and morphological systematic investigations revealed that the cacti are most closely related to Anacampseroteae, Portulaca and Talinum of the family Portulacaceae (ACPT clade of suborder Portulacineae). A combined analysis of ndhF, matK, and nad1 sequence data from the chloroplast and the mitochondrial genomes indicates that the tribe Anacampseroteae is the sister group of the family Cactaceae. This clade, together with Portulaca, is well characterized by the presence of axillary hairs or scales. Relationships within Anacampseroteae are characterized by a grade of five species of Grahamia s.l. from North and South America, and Grahamia australiana is found to be sister to the genera Anacampseros and Avonia. A comparison of vegetative characteristics indicates an evolutionary transition from woody subshrubs to dwarf perennial and highly succulent herbs during the diversification of Anacampseroteae. Available evidence from the present investigation as well as from previously published studies suggests that a revised classification of Portulacineae on the basis of inferred phylogenetic relationships might consist of a superfamily that includes Cactaceae and the three genera Anacampseros s.l. (including Avonia and Grahamia s.l.), Portulaca, and Talinum (including Talinella), either referred to three monogeneric families or to a paraphyletic family Portulacaceae*.

  18. Biogenic hydrogen conversion of de-oiled jatropha waste via anaerobic sequencing batch reactor operation: process performance, microbial insights, and CO2 reduction efficiency.

    Science.gov (United States)

    Kumar, Gopalakrishnan; Lin, Chiu-Yue

    2014-01-01

    We report the semicontinuous, direct (anaerobic sequencing batch reactor operation) hydrogen fermentation of de-oiled jatropha waste (DJW). The effect of hydraulic retention time (HRT) was studied and results show that the stable and peak hydrogen production rate of 1.48 L/L ∗ d and hydrogen yield of 8.7 mL H2/g volatile solid added were attained when the reactor was operated at HRT 2 days (d) with a DJW concentration of 200 g/L, temperature 55 °C, and pH 6.5. Reduced HRT enhanced the production performance until 1.75 d. Further reduction has lowered the process efficiency in terms of biogas production and hydrogen gas content. The effluent from hydrogen fermentor was utilized for methane fermentation in batch reactors using pig slurry and cow dung as seed sources. The results revealed that pig slurry was a feasible seed source for methane generation. Peak methane production rate of 0.43 L CH4/L ∗ d and methane yield of 20.5 mL CH4/g COD were observed at substrate concentration of 10 g COD/L, temperature 30 °C, and pH 7.0. PCR-DGGE analysis revealed that combination of cellulolytic and fermentative bacteria were present in the hydrogen producing ASBR.

  19. Biogenic Hydrogen Conversion of De-Oiled Jatropha Waste via Anaerobic Sequencing Batch Reactor Operation: Process Performance, Microbial Insights, and CO2 Reduction Efficiency

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Kumar

    2014-01-01

    Full Text Available We report the semicontinuous, direct (anaerobic sequencing batch reactor operation hydrogen fermentation of de-oiled jatropha waste (DJW. The effect of hydraulic retention time (HRT was studied and results show that the stable and peak hydrogen production rate of 1.48 L/L*d and hydrogen yield of 8.7 mL H2/g volatile solid added were attained when the reactor was operated at HRT 2 days (d with a DJW concentration of 200 g/L, temperature 55°C, and pH 6.5. Reduced HRT enhanced the production performance until 1.75 d. Further reduction has lowered the process efficiency in terms of biogas production and hydrogen gas content. The effluent from hydrogen fermentor was utilized for methane fermentation in batch reactors using pig slurry and cow dung as seed sources. The results revealed that pig slurry was a feasible seed source for methane generation. Peak methane production rate of 0.43 L CH4/L*d and methane yield of 20.5 mL CH4/g COD were observed at substrate concentration of 10 g COD/L, temperature 30°C, and pH 7.0. PCR-DGGE analysis revealed that combination of celluloytic and fermentative bacteria were present in the hydrogen producing ASBR.

  20. Origin of temporal compositional trends in monogenetic vent eruptions: Insights from the crystal cargo in the Papoose Canyon sequence, Big Pine Volcanic Field, CA

    Science.gov (United States)

    Gao, Ruohan; Lassiter, John C.; Ramirez, Gabrielle

    2017-01-01

    Many monogenetic vents display systematic temporal-compositional variations over the course of eruption. Previous studies have proposed that these trends may reflect variable degrees of crustal assimilation, or melting and mixing of heterogeneous mantle source(s). Discrimination between these two endmember hypotheses is critical for understanding the plumbing systems of monogenetic volcanoes, which pose a significant volcanic hazard in many areas. In this study, we examine the Papoose Canyon (PC) monogenetic vent in the Big Pine Volcanic Field (BPVF), which had been well characterized for temporal-compositional variations in erupted basalts. We present new major and trace element and Sr-Nd-Pb-O isotopic data from the PC "crystal cargo" (phenocrysts and xenoliths). Comparison of "crystal cargo" and host basalt provides new constraints on the history of magma storage, fractionation, and crustal contamination that are obscured in the bulk basalts due to pre- and syn-eruptive magma mixing processes. The abundances of phenocrysts and ultramafic xenoliths in the PC sequence decrease up-section. Olivine and clinopyroxene phenocrysts span a wide range of Mg# (77-89). The majority of phenocrysts are more evolved than olivine or clinopyroxene in equilibrium with their host basalts (Mg# = 68- 71, equilibrium Fo ≈ 85- 89). In addition, the ultramafic xenoliths display cumulate textures. Olivine and clinopyroxene from ultramafic xenoliths have Mg# (73-87) similar to the phenocrysts, and lower than typical mantle peridotites. Sr-Nd-Pb isotope compositions of the xenoliths are similar to early PC basalts. Finally, many clinopyroxene phenocrysts and clinopyroxene in xenoliths have trace element abundances in equilibrium with melts that are more enriched than the erupted basalts. These features suggest that the phenocrysts and xenoliths derive from melt that is more fractionated and enriched than erupted PC basalts. Pressure constraints suggest phenocrysts and ultramafic

  1. Insights into the relationships of Palearctic and Nearctic lymnaeids (Mollusca : Gastropoda by rDNA ITS-2 sequencing and phylogeny of stagnicoline intermediate host species of Fasciola hepatica

    Directory of Open Access Journals (Sweden)

    Bargues M.D.

    2003-09-01

    Full Text Available Fascioliasis by Fasciola hepatica is the vector-borne disease presenting the widest latitudinal, longitudinal and altitudinal distribution known. F. hepatica shows a great adaptation power to new environmental conditions which is the consequence of its own capacities together with the adaptation and colonization abilities of its specific vector hosts, freshwater snails of the family Lymnaeidae. Several lymnaeid species only considered as secondary contributors to the liver fluke transmission have, however, played a very important role in the geographic expansion of this disease. Many of them belong to the so-called "stagnicoline" type group. Stagnicolines have, therefore, a very important applied interest in the Holarctic region, to which they are geographically restricted. The present knowledge on the genetics of stagnicolines and on their parasite-host interrelationships is, however, far from being sufficient. The present paper analyses the relationships between Palaearctic and Nearctic stagnicoline species on the base of the new light furnished by the results obtained in nuclear rDNA ITS-2 sequencing and corresponding phylogenetic studies of the lymnaeid taxa Lymnaea (Stagnicola occulta, L. (S. palustris palustris (topotype specimens and L.(S. p. turricula from Europe. Natural infections with F. hepatica have been reported in all of them. Surprisingly, ITS-2 length and G C content of L. occulta were similar and perfectly fitted within the respective ranges known in North American stagnicolines. Nucleotide differences and genetic distances were higher between L. occulta and the other European stagnicolines than between L. occulta and the North American ones. The ITS-2 sequence of L. p. turricula from Poland differed from the other genotypes known from turricula in Europe. The phylogenetic trees using the maximum-parsimony, distance and maximum-likelihood methods confirmed (i the inclusion of L. occulta in the branch of North American

  2. Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus

    Science.gov (United States)

    Wollenberg, Kurt R.; Desjardins, Christopher A.; Zalutskaya, Aksana; Slodovnikova, Vervara; Oler, Andrew J.; Quiñones, Mariam; Abeel, Thomas; Chapman, Sinead B.; Tartakovsky, Michael; Gabrielian, Andrei; Hoffner, Sven; Skrahin, Aliaksandr; Birren, Bruce W.; Rosenthal, Alexander

    2016-01-01

    ABSTRACT The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB. Using a phylogenomic approach, we estimated that the majority of MDR-TB was due to the recent transmission of already-resistant M. tuberculosis strains rather than repeated de novo evolution of resistance within patients, while XDR-TB was acquired through both routes. Longitudinal sampling of M. tuberculosis from 34 patients with treatment failure showed that most strains persisted genetically unchanged during treatment or acquired resistance to fluoroquinolones. HIV+ patients were significantly more likely to have multiple infections over time than HIV− patients, highlighting a specific need for careful infection control in these patients. These data provide a better understanding of the genomic composition, transmission, and evolution of MDR- and XDR-TB in Belarus and will enable improved diagnostics, treatment protocols, and prognostic decision-making. PMID:27903602

  3. Fast, cheap and out of control--Insights into thermodynamic and informatic constraints on natural protein sequences from de novo protein design.

    Science.gov (United States)

    Brisendine, Joseph M; Koder, Ronald L

    2016-05-01

    The accumulated results of thirty years of rational and computational de novo protein design have taught us important lessons about the stability, information content, and evolution of natural proteins. First, de novo protein design has complicated the assertion that biological function is equivalent to biological structure - demonstrating the capacity to abstract active sites from natural contexts and paste them into non-native topologies without loss of function. The structure-function relationship has thus been revealed to be either a generality or strictly true only in a local sense. Second, the simplification to "maquette" topologies carried out by rational protein design also has demonstrated that even sophisticated functions such as conformational switching, cooperative ligand binding, and light-activated electron transfer can be achieved with low-information design approaches. This is because for simple topologies the functional footprint in sequence space is enormous and easily exceeds the number of structures which could have possibly existed in the history of life on Earth. Finally, the pervasiveness of extraordinary stability in designed proteins challenges accepted models for the "marginal stability" of natural proteins, suggesting that there must be a selection pressure against highly stable proteins. This can be explained using recent theories which relate non-equilibrium thermodynamics and self-replication. This article is part of a Special Issue entitled Biodesign for Bioenergetics--The design and engineering of electronc transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula1[W

    Science.gov (United States)

    Cabeza, Ricardo; Koester, Beke; Liese, Rebecca; Lingner, Annika; Baumgarten, Vanessa; Dirks, Jan; Salinas-Riester, Gabriela; Pommerenke, Claudia; Dittert, Klaus; Schulze, Joachim

    2014-01-01

    The mechanism through which nitrate reduces the activity of legume nodules is controversial. The objective of the study was to follow Medicago truncatula nodule activity after nitrate provision continuously and to identify molecular mechanisms, which down-regulate the activity of the nodules. Nodule H2 evolution started to decline after about 4 h of nitrate application. At that point in time, a strong shift in nodule gene expression (RNA sequencing) had occurred (1,120 differentially expressed genes). The most pronounced effect was the down-regulation of 127 genes for nodule-specific cysteine-rich peptides. Various other nodulins were also strongly down-regulated, in particular all the genes for leghemoglobins. In addition, shifts in the expression of genes involved in cellular iron allocation and mitochondrial ATP synthesis were observed. Furthermore, the expression of numerous genes for the formation of proteins and glycoproteins with no obvious function in nodules (e.g. germins, patatin, and thaumatin) was strongly increased. This occurred in conjunction with an up-regulation of genes for proteinase inhibitors, in particular those containing the Kunitz domain. The additionally formed proteins might possibly be involved in reducing nodule oxygen permeability. Between 4 and 28 h of nitrate exposure, a further reduction in nodule activity occurred, and the number of differentially expressed genes almost tripled. In particular, there was a differential expression of genes connected with emerging senescence. It is concluded that nitrate exerts rapid and manifold effects on nitrogenase activity. A certain degree of nitrate tolerance might be achieved when the down-regulatory effect on late nodulins can be alleviated. PMID:24285852

  5. MicroRNA roles in signalling during lactation: an insight from differential expression, time course and pathway analyses of deep sequence data

    Science.gov (United States)

    Do, Duy N.; Li, Ran; Dudemaine, Pier-Luc; Ibeagha-Awemu, Eveline M.

    2017-01-01

    The study examined microRNA (miRNA) expression and regulatory patterns during an entire bovine lactation cycle. Total RNA from milk fat samples collected at the lactogenesis (LAC, day1 [D1] and D7), galactopoiesis (GAL, D30, D70, D130, D170 and D230) and involution (INV, D290 and when milk production dropped to 5 kg/day) stages from 9 cows was used for miRNA sequencing. A total of 475 known and 238 novel miRNAs were identified. Fifteen abundantly expressed miRNAs across lactation stages play regulatory roles in basic metabolic, cellular and immunological functions. About 344, 366 and 209 miRNAs were significantly differentially expressed (DE) between GAL and LAC, INV and GAL, and INV and LAC stages, respectively. MiR-29b/miR-363 and miR-874/miR-6254 are important mediators for transition signals from LAC to GAL and from GAL to INV, respectively. Moreover, 58 miRNAs were dynamically DE in all lactation stages and 19 miRNAs were significantly time-dependently DE throughout lactation. Relevant signalling pathways for transition between lactation stages are involved in apoptosis (PTEN and SAPK/JNK), intracellular signalling (protein kinase A, TGF-β and ERK5), cell cycle regulation (STAT3), cytokines, hormones and growth factors (prolactin, growth hormone and glucocorticoid receptor). Overall, our data suggest diverse, temporal and physiological signal-dependent regulatory and mediator functions for miRNAs during lactation. PMID:28317898

  6. Sequence-specific binding of recombinant Zbed4 to DNA: insights into Zbed4 participation in gene transcription and its association with other proteins.

    Science.gov (United States)

    Mokhonov, Vladislav V; Theendakara, Veena P; Gribanova, Yekaterina E; Ahmedli, Novruz B; Farber, Debora B

    2012-01-01

    Zbed4, a member of the BED subclass of Zinc-finger proteins, is expressed in cone photoreceptors and glial Müller cells of human retina whereas it is only present in Müller cells of mouse retina. To characterize structural and functional properties of Zbed4, enough amounts of purified protein were needed. Thus, recombinant Zbed4 was expressed in E. coli and its refolding conditions optimized for the production of homogenous and functionally active protein. Zbed4's secondary structure, determined by circular dichroism spectroscopy, showed that this protein contains 32% α-helices, 18% β-sheets, 20% turns and 30% unordered structures. CASTing was used to identify the target sites of Zbed4 in DNA. The majority of the DNA fragments obtained contained poly-Gs and some of them had, in addition, the core signature of GC boxes; a few clones had only GC-boxes. With electrophoretic mobility shift assays we demonstrated that Zbed4 binds both not only to DNA and but also to RNA oligonucleotides with very high affinity, interacting with poly-G tracts that have a minimum of 5 Gs; its binding to and GC-box consensus sequences. However, the latter binding depends on the GC-box flanking nucleotides. We also found that Zbed4 interacts in Y79 retinoblastoma cells with nuclear and cytoplasmic proteins Scaffold Attachment Factor B1 (SAFB1), estrogen receptor alpha (ERα), and cellular myosin 9 (MYH9), as shown with immunoprecipitation and mass spectrometry studies as well as gel overlay assays. In addition, immunostaining corroborated the co-localization of Zbed4 with these proteins. Most importantly, in vitro experiments using constructs containing promoters of genes directing expression of the luciferase gene, showed that Zbed4 transactivates the transcription of those promoters with poly-G tracts.

  7. Coupling channel evolution monitoring and RFID tracking in a large, wandering, gravel-bed river: Insights into sediment routing on geomorphic continuity through a riffle-pool sequence

    Science.gov (United States)

    Chapuis, Margot; Dufour, Simon; Provansal, Mireille; Couvert, Bernard; de Linares, Matthieu

    2015-02-01

    -pool sequence.

  8. 泥河湾盆地上新世生物地层序列与环境%PLIOCENE BIOSTRATIGRAPHIC SEQUENCE IN THE NIHEWAN BASIN, HEBEI, CHINA

    Institute of Scientific and Technical Information of China (English)

    李强; 郑绍华; 蔡保全

    2008-01-01

    总结了泥河湾盆地晚上新世生物地层,讨论了12个剖面含哺乳动物化石层位的相互关系,以稻地老窝沟剖面的地层顺序为基础排列出约3.7~2.6 Ma时段内的9个代表性的生物地层单位.哺乳动物以Paenelimnoecus chinensis、Lunanosorex cf.L. lii、Trischizolagus、Pliopentdagus nihewanicus、Ungaromys、Mimomys sp.、Chardina truncatus、Mesosiphneus praetingi、M. paratingi、Pliosiphneus lyratus、Pseudomeriones complicidens、Castor anderssoni、Huaxiamys downsi、Chardinomys yusheensis、C. nihowanicus、Hipparion houfenense和Gazella blacki组合为特征.动物群在时代上与榆社麻则沟动物组合、静乐红土动物群、灵台雷家河剖面V带及任家沟静乐红粘土动物组合、宁县水磨沟动物组合、游河动物群及沂南棋盘山洞穴动物组合相当.动物群所反映的是温带草原为主、间有树林和干草原的稀树草原环境.%A sequence of fluvio-lacustrine and paludine deposits with thickness over 150 meters occurs in the Nihewan Basin, Hebei, China (Yuan et al., 1996; Min et al., 2006). A series of ~ 30 m ( = "90 feet" ) thick red homogeneous clay exposured near the Sanggan River Gorge ( = Shixia) was originally considered as the weathering matter of the base rocks (Barbour et al.,1926). Due to the absence of fossils, its age once was speculated to belong to the Pontian (Teilhard and Piveteau, 1930) or the Late Miocene Baodean (Black et al., 1933). However,a sequence of ~ 30 m thick red gravel-bearing clay at the bottom of the section of Dabonggou in Shixia was named as "Dabonggou Formation" by Chen( 1988 ). At the same time, the ~ 12 m and ~ 7 m thick red clays in the lower part of the Hongya Nangou and Pump Station, respec-tively, were also included into this Pliocene formation. A series of 20 ~ 30 m thick redish or yellow-redish alternating sandy clay and gravel beds are exposed in the Luanshigedagou near Hongya village. Yielding Hipparion and

  9. Tectonic uplift-influenced monsoonal changes promoted hominin occupation of the Luonan Basin: Insights from a loess-paleosol sequence, eastern Qinling Mountains, central China

    Science.gov (United States)

    Fang, Qian; Hong, Hanlie; Zhao, Lulu; Furnes, Harald; Lu, Huayu; Han, Wen; Liu, Yao; Jia, Zhuoyue; Wang, Chaowen; Yin, Ke; Algeo, Thomas J.

    2017-08-01

    Quaternary soil deposits from northern and southern China are distinctly different, reflecting variability of the East Asian monsoon north and south of the Qinling Mountains. Coeval sediments from the transitional climatic zone of central China, which are little studied to date, have the potential to improve our understanding of Quaternary monsoon changes and associated influences on hominin occupation of this region. Here, we investigate in detail a well-preserved and continuous Quaternary loess-paleosol sequence (Shangbaichuan) from the Luonan Basin, using a variety of weathering indices including major and trace element ratios, clay mineralogy, and Fe-oxide mineralogy. The whole-rock samples display similar rare earth element patterns characterized by upper continental crustal ratios: (La/Yb)N ≈ 9.5 and Eu/Eu* ≈ 0.65. Elemental data such as (La/Yb)N, La/Th and Eu/Eu* ratios show a high degree of homogeneity, suggesting that dust in the source region may have been thoroughly mixed and recycled, resulting in all samples having a uniform initial composition. Indices for pedogenic weathering such as Na/K, Ba/Sr, Rb/Sr, CIA, CIW, CPA, PIA, kaolinite/illite, (kaolinite + smectite)/illite, and hematite/(hematite + goethite) exhibit similar secular trends and reveal a four-stage accumulation history. The indices also indicate that the climate was warmer and wetter during the most recent interglacial stage, compared with coeval environments of the Chinese Loess Plateau. Secular changes in weathering intensity can be related to stepwise uplift of the Qinling Mountains and variation in East Asian monsoon intensity, both of which played significant roles in controlling climate evolution in the Luonan Basin. Furthermore, intensified aridity and winter monsoon strength in dust source areas, as evidenced by mineralogic and geochemical changes, may have been due to the mid-Pleistocene climate transition. Based on temporal correlation of warmer and wetter climatic conditions

  10. Whole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans

    Science.gov (United States)

    Ayers, Sherry; Barreto, Marlen; Allard, Marc; Brown, Eric W.

    2016-01-01

    ABSTRACT Salmonella enterica subsp. enterica serotype Enteritidis is a major cause of human salmonellosis worldwide; however, little is known about the genetic relationships between S. Enteritidis clinical strains and S. Enteritidis strains from other sources in Chile. We compared the whole genomes of 30 S. Enteritidis strains isolated from gulls, domestic chicken eggs, and humans in Chile, to investigate their phylogenetic relationships and to establish their relatedness to international strains. Core genome multilocus sequence typing (cgMLST) analysis showed that only 246/4,065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II being further divided into five subclusters. One subcluster (subcluster 2) contained strains from all surveyed sources that differed at 1 to 18 loci (of 4,065 loci) with 1 to 18 single-nucleotide polymorphisms (SNPs), suggesting interspecies transmission of S. Enteritidis in Chile. Moreover, clusters were formed by strains that were distant geographically, which could imply that gulls might be spreading the pathogen throughout the country. Our cgMLST analysis, using other S. Enteritidis genomes available in the National Center for Biotechnology Information (NCBI) database, showed that S. Enteritidis strains from Chile and the United States belonged to different lineages, which suggests that S. Enteritidis regional markers might exist and could be used for trace-back investigations. IMPORTANCE This study highlights the importance of gulls in the spread of Salmonella Enteritidis in Chile. We revealed a close genetic relationship between some human and gull S. Enteritidis strains (with as few as 2 of 4,065 genes being different), and we also found that gull strains were present in clusters formed by strains isolated from other sources or distant locations. Together with previously published evidence, this suggests that gulls might be spreading this pathogen between different regions

  11. Consumer Insights

    Institute of Scientific and Technical Information of China (English)

    JANKOT

    2004-01-01

    Fang Jun, the head of consumer and market insights of Unilever Shanghai, has summarized his early life as a market in two sentences: rush about to study market changes;act all day to observe consumer behavior. And now?"Tell stories, conduct interviews and piece together different data; calculate numbers,build models and write reports."

  12. Sequence of the Cenozoic Mammalian Faunas of the Linxia Basin in Gansu, China

    Institute of Scientific and Technical Information of China (English)

    DENG Tao; WANG Xiaoming; NI Xijun; LIU Liping

    2004-01-01

    In the Linxia Basin on the northeast margin of the Tibetan Plateau, the Cenozoic strata are very thick and well exposed. Abundant mammalian fossils are discovered in the deposits from the Late Oligocene to the Early Pleistocene.The Dzungariotheriurn fauna comes from the sandstones of the Jiaozigou Formation, including many representative Late Oligocene taxa. The Platybelodon fauna comes from the sandstones of the Dongxiang Formation and the conglomerates of the Laogou Formation, and its fossils are typical Middle Miocene forms, such as Hemicyon, Amphicyon, Platybelodon,Choerolophodon, Anchitherium, and Hispanotherium. The Hipparion fauna comes from the red clay of the Liushu and Hewangjia Formations, and its fossils can be distinctly divided into four levels, including three Late Miocene levels and one Early Pliocene level. In the Linxia Basin, the Hipparion fauna has the richest mammalian fossils. The Equus fauna comes from the Wucheng Loess, and it is slightly older than that of the classical Early Pleistocene Nihewan Fauna. The mammalian faunas from the Linxia Basin provide the reliable evidence to divide the Cenozoic strata of this basin and correlate them with European mammalian sequence.

  13. Targeted isolation, sequence assembly and characterization of two white spruce (Picea glauca BAC clones for terpenoid synthase and cytochrome P450 genes involved in conifer defence reveal insights into a conifer genome

    Directory of Open Access Journals (Sweden)

    Ritland Carol

    2009-08-01

    Full Text Available Abstract Background Conifers are a large group of gymnosperm trees which are separated from the angiosperms by more than 300 million years of independent evolution. Conifer genomes are extremely large and contain considerable amounts of repetitive DNA. Currently, conifer sequence resources exist predominantly as expressed sequence tags (ESTs and full-length (FLcDNAs. There is no genome sequence available for a conifer or any other gymnosperm. Conifer defence-related genes often group into large families with closely related members. The goals of this study are to assess the feasibility of targeted isolation and sequence assembly of conifer BAC clones containing specific genes from two large gene families, and to characterize large segments of genomic DNA sequence for the first time from a conifer. Results We used a PCR-based approach to identify BAC clones for two target genes, a terpene synthase (3-carene synthase; 3CAR and a cytochrome P450 (CYP720B4 from a non-arrayed genomic BAC library of white spruce (Picea glauca. Shotgun genomic fragments isolated from the BAC clones were sequenced to a depth of 15.6- and 16.0-fold coverage, respectively. Assembly and manual curation yielded sequence scaffolds of 172 kbp (3CAR and 94 kbp (CYP720B4 long. Inspection of the genomic sequences revealed the intron-exon structures, the putative promoter regions and putative cis-regulatory elements of these genes. Sequences related to transposable elements (TEs, high complexity repeats and simple repeats were prevalent and comprised approximately 40% of the sequenced genomic DNA. An in silico simulation of the effect of sequencing depth on the quality of the sequence assembly provides direction for future efforts of conifer genome sequencing. Conclusion We report the first targeted cloning, sequencing, assembly, and annotation of large segments of genomic DNA from a conifer. We demonstrate that genomic BAC clones for individual members of multi-member gene

  14. Insights from Human/Mouse genome comparisons

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.

    2003-03-30

    Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish (Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.

  15. Field corrosion characterization of soil corrosion of X70 pipeline steel in a red clay soil

    Institute of Scientific and Technical Information of China (English)

    Shengrong Wang; Cuiwei Dun; Xiaogang Li; Zhiyong Liunn; Min Zhu; Dawei Zhang

    2015-01-01

    The corrosion behavior of X70 pipeline steel buried in red soil environment has been studied. The surface morphology and elemental distribution were determined by scanning electron microscopy (SEM),energy dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD). The corrosion kinetics was evaluated by weight loss measurement. The results show that in red soil, the corrosion rate of X70 steel decreases with time, and follows the exponential decay law. General corrosion with non-uniform and localized pitting occurred on the steel surface.α-FeOOH was the dominate products during corrosion in whole buried periods, and the corrosion products exhibited well protective properties. The potentiodynamic polarization tests revealed that icorr decreased with time, indicating the improvement of corrosion resistance. The results of Electrochemical impendence spectroscopy (EIS) are consistent with potentiodynamic polarization tests.

  16. Field corrosion characterization of soil corrosion of X70 pipeline steel in a red clay soil

    Directory of Open Access Journals (Sweden)

    Shengrong Wang

    2015-06-01

    Full Text Available The corrosion behavior of X70 pipeline steel buried in red soil environment has been studied. The surface morphology and elemental distribution were determined by scanning electron microscopy (SEM,energy dispersive X-ray spectroscopy (EDS, and X-ray diffraction (XRD. The corrosion kinetics was evaluated by weight loss measurement. The results show that in red soil, the corrosion rate of X70 steel decreases with time, and follows the exponential decay law. General corrosion with non-uniform and localized pitting occurred on the steel surface. α-FeOOH was the dominate products during corrosion in whole buried periods, and the corrosion products exhibited well protective properties. The potentiodynamic polarization tests revealed that icorr decreased with time, indicating the improvement of corrosion resistance. The results of Electrochemical impendence spectroscopy (EIS are consistent with potentiodynamic polarization tests.

  17. Chemosynthesis in deep-sea red-clay: Linking concepts to probable martian life

    Digital Repository Service at National Institute of Oceanography (India)

    Das, A.; Mourya, B.S.; Mamatha, S.S.; Khadge, N.H.; LokaBharathi, P.A.

    ) is exam- ined. The greater part of Mars is arid and shows evidences for volcanic activity [2]. Some of the other characteris- tics that could resemble life on Mars include oligotrophy and chemosynthesis based on redox chemistry of metals in Central...

  18. Aerobic microbial respiration in 86-million-year-old deep-sea red clay.

    Science.gov (United States)

    Røy, Hans; Kallmeyer, Jens; Adhikari, Rishi Ram; Pockalny, Robert; Jørgensen, Bo Barker; D'Hondt, Steven

    2012-05-18

    Microbial communities can subsist at depth in marine sediments without fresh supply of organic matter for millions of years. At threshold sedimentation rates of 1 millimeter per 1000 years, the low rates of microbial community metabolism in the North Pacific Gyre allow sediments to remain oxygenated tens of meters below the sea floor. We found that the oxygen respiration rates dropped from 10 micromoles of O(2) liter(-1) year(-1) near the sediment-water interface to 0.001 micromoles of O(2) liter(-1) year(-1) at 30-meter depth within 86 million-year-old sediment. The cell-specific respiration rate decreased with depth but stabilized at around 10(-3) femtomoles of O(2) cell(-1) day(-1) 10 meters below the seafloor. This result indicated that the community size is controlled by the rate of carbon oxidation and thereby by the low available energy flux.

  19. Effect of Crushed Glass Cullet Sizes on Physical and Mechanical Properties of Red Clay Bricks

    Directory of Open Access Journals (Sweden)

    Patricia Ponce Peña

    2016-01-01

    Full Text Available This study reports the effect of clear waste glass from bottles added on 20 to 30 wt.% and variable particle size (<500, <300, and <212 μm, into clay mixtures for the handmade brick manufacturing process. The bricks were manufactured with mixtures of clay, crushed glass, and water in different proportions, homogenized, casted in wooden molds, air-dried at room temperature for 72 h, and sintered at 1000°C for 12 h. Total shrinkage, water absorption, compressive strength, microstructure, and phase composition are discussed with respect to glass content and its particle size. The results indicate that increasing the content of glass and decreasing its particle size enhanced significantly the brick properties of water absorption and compressive strength by up to 18.5% and 6.8 MPa, for bricks with 30 wt% and particle size lower than 212 μm. It is proposed that decreasing the glass particle size its surface area increases allowing easier melting of glass by lower energy consumption, reducing porosity and enhancing brick properties.

  20. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  1. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies...

  2. Controls on dryland mountain landscape development along the NW Saharan desert margin: Insights from Quaternary river terrace sequences (Dadès River, south-central High Atlas, Morocco)

    DEFF Research Database (Denmark)

    Stokes, M.; Mather, A.E.; Belfoul, M.

    2017-01-01

    between 50 and 140 m. The rock strength, stratigraphy and structure of the mountain belt influences terrace distribution. Terraces are absent in river gorges of structurally thickened limestone; whilst well-developed, laterally continuous terraces (T1-T4) form along wide valleys occupying syncline...... sands and colluvium. This sequence with some OSL/IRSL age control, suggests terrace formation over a 100 ka climate cycle with valley floor aggradation during full glacials and incision during glacial-interglacial transitions. This integrates with other archives (e.g. lakes, glaciers, dunes), appearing...... typical of landscape development along the NW Saharan margin south of the High Atlas, and similar to patterns in the western-southern Mediterranean. The 100 ka climate cycle relationship suggests that the terrace sequence documents Late-Middle Pleistocene landscape development. Consistent altitudinal...

  3. Complete sequences of IncHI1 plasmids carrying blasub>CTX-M-1sub> and qnrS1 in equine Escherichia coli provide new insights into plasmid evolution

    DEFF Research Database (Denmark)

    Dolejska, Monika; Villa, Laura; Minoia, Marco;

    2014-01-01

    OBJECTIVES: To determine the structure of two multidrug-resistant IncHI1 plasmids carrying blaCTX-M-1 in Escherichia coli isolates disseminated in an equine clinic in the Czech Republic. METHODS: A complete nucleotide sequencing of 239 kb IncHI1 (pEQ1) and 287 kb IncHI1/X1 (pEQ2) plasmids was per...

  4. Exploring Insight: Focus on Shifts of Attention

    Science.gov (United States)

    Palatnik, Alik; Koichu, Boris

    2015-01-01

    The paper presents and analyses a sequence of events that preceded an insight solution to a challenging problem in the context of numerical sequences. A three­week long solution process by a pair of ninth­-grade students is analysed by means of the theory of shifts of attention. The goal for this article is to reveal the potential of this theory…

  5. A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus

    Directory of Open Access Journals (Sweden)

    Biao Tang

    2016-09-01

    Full Text Available The complete genome of methanol-utilizing Amycolatopsis methanolica strain 239T was generated, revealing a single 7,237,391 nucleotide circular chromosome with 7074 annotated protein-coding sequences (CDSs. Comparative analyses against the complete genome sequences of Amycolatopsis japonica strain MG417-CF17T, Amycolatopsis mediterranei strain U32 and Amycolatopsis orientalis strain HCCB10007 revealed a broad spectrum of genomic structures, including various genome sizes, core/quasi-core/non-core configurations and different kinds of episomes. Although polyketide synthase gene clusters were absent from the A. methanolica genome, 12 gene clusters related to the biosynthesis of other specialized (secondary metabolites were identified. Complete pathways attributable to the facultative methylotrophic physiology of A. methanolica strain 239T, including both the mdo/mscR encoded methanol oxidation and the hps/hpi encoded formaldehyde assimilation via the ribulose monophosphate cycle, were identified together with evidence that the latter might be the result of horizontal gene transfer. Phylogenetic analyses based on 16S rDNA or orthologues of AMETH_3452, a novel actinobacterial class-specific conserved gene against 62 or 18 Amycolatopsis type strains, respectively, revealed three major phyletic lineages, namely the mesophilic or moderately thermophilic A. orientalis subclade (AOS, the mesophilic Amycolatopsis taiwanensis subclade (ATS and the thermophilic A. methanolica subclade (AMS. The distinct growth temperatures of members of the subclades correlated with corresponding genetic variations in their encoded compatible solutes. This study shows the value of integrating conventional taxonomic with whole genome sequence data.

  6. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

    Science.gov (United States)

    Hamon, Perla; Grover, Corrinne E; Davis, Aaron P; Rakotomalala, Jean-Jacques; Raharimalala, Nathalie E; Albert, Victor A; Sreenath, Hosahalli L; Stoffelen, Piet; Mitchell, Sharon E; Couturon, Emmanuel; Hamon, Serge; de Kochko, Alexandre; Crouzillat, Dominique; Rigoreau, Michel; Sumirat, Ucu; Akaffou, Sélastique; Guyot, Romain

    2017-04-01

    A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Kohler's Insight Revisited.

    Science.gov (United States)

    Windholtz, George

    1985-01-01

    Psychology textbooks frequently present Wolfgang Kohler's two-stick experiment with chimpanzees as having demonstrated insight in learning. Studies that replicated Kohler's work support his findings but not his interpretation in terms of insightful solution. The uncritical inclusion of Kohler's insight interpretation in texts is not warranted in…

  8. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  9. Gestures and Insight in Advanced Mathematical Thinking

    Science.gov (United States)

    Yoon, Caroline; Thomas, Michael O. J.; Dreyfus, Tommy

    2011-01-01

    What role do gestures play in advanced mathematical thinking? We argue that the role of gestures goes beyond merely communicating thought and supporting understanding--in some cases, gestures can help generate new mathematical insights. Gestures feature prominently in a case study of two participants working on a sequence of calculus activities.…

  10. Gestures and Insight in Advanced Mathematical Thinking

    Science.gov (United States)

    Yoon, Caroline; Thomas, Michael O. J.; Dreyfus, Tommy

    2011-01-01

    What role do gestures play in advanced mathematical thinking? We argue that the role of gestures goes beyond merely communicating thought and supporting understanding--in some cases, gestures can help generate new mathematical insights. Gestures feature prominently in a case study of two participants working on a sequence of calculus activities.…

  11. Controls on dryland mountain landscape development along the NW Saharan desert margin: Insights from Quaternary river terrace sequences (Dadès River, south-central High Atlas, Morocco)

    Science.gov (United States)

    Stokes, M.; Mather, A. E.; Belfoul, M.; Faik, F.; Bouzid, S.; Geach, M. R.; Cunha, P. P.; Boulton, S. J.; Thiel, C.

    2017-06-01

    This study documents river terraces from upstream reaches of the Dadès River, a major fluvial system draining the south-central High Atlas Mountains. Terraces occur as straths with bedrock bases positioned at 10 m altitudinal intervals up to 40 m (T1-T5) above the valley floor, becoming less common between 50 and 140 m. The rock strength, stratigraphy and structure of the mountain belt influences terrace distribution. Terraces are absent in river gorges of structurally thickened limestone; whilst well-developed, laterally continuous terraces (T1-T4) form along wide valleys occupying syncline structures dominated by weaker interbedded limestone-mudstone. Terrace staircases develop in confined canyons associated with weaker lithologies and influence from structural dip and stratigraphic configuration. Terraces comprise a bedrock erosion surface overlain by fluvial conglomerates, rare overbank sands and colluvium. This sequence with some OSL/IRSL age control, suggests terrace formation over a 100 ka climate cycle with valley floor aggradation during full glacials and incision during glacial-interglacial transitions. This integrates with other archives (e.g. lakes, glaciers, dunes), appearing typical of landscape development along the NW Saharan margin south of the High Atlas, and similar to patterns in the western-southern Mediterranean. The 100 ka climate cycle relationship suggests that the terrace sequence documents Late-Middle Pleistocene landscape development. Consistent altitudinal spacing of terraces and their distribution throughout the orogen suggests sustained base-level lowering linked to uplift-exhumation of the High Atlas. Low incision rates (<0.2 mm a-1) and general absence of terrace deformation suggests dominance of isostatically driven base-level lowering with relief generation being Early Pleistocene or older.

  12. Whole Genome Sequencing Investigation of a Tuberculosis Outbreak in Port-au-Prince, Haiti Caused by a Strain with a "Low-Level" rpoB Mutation L511P - Insights into a Mechanism of Resistance Escalation.

    Directory of Open Access Journals (Sweden)

    Oksana Ocheretina

    Full Text Available The World Health Organization recommends diagnosing Multidrug-Resistant Tuberculosis (MDR-TB in high burden countries by detection of mutations in Rifampin (RIF Resistance Determining Region of Mycobacterium tuberculosis rpoB gene with rapid molecular tests GeneXpert MTB/RIF and Hain MTBDRplus. Such mutations are found in >95% of Mycobacterium tuberculosis strains resistant to RIF by conventional culture-based drug susceptibility testing (DST. However routine diagnostic screening with molecular tests uncovered specific "low level" rpoB mutations conferring resistance to RIF below the critical concentration of 1 μg/ml in some phenotypically susceptible strains. Cases with discrepant phenotypic (susceptible and genotypic (resistant results for resistance to RIF account for at least 10% of resistant diagnoses by molecular tests and urgently require new guidelines to inform therapeutic decision making. Eight strains with a "low level" rpoB mutation L511P were isolated by GHESKIO laboratory between 2008 and 2012 from 6 HIV-negative and 2 HIV-positive patients during routine molecular testing. Five isolates with a single L511P mutation and two isolates with double mutation L511P&M515T had MICs for RIF between 0.125 and 0.5 μg/ml and tested susceptible in culture-based DST. The eighth isolate carried a double mutation L511P&D516C and was phenotypically resistant to RIF. All eight strains shared the same spoligotype SIT 53 commonly found in Haiti but classic epidemiological investigation failed to uncover direct contacts between the patients. Whole Genome Sequencing (WGS revealed that L511P cluster isolates resulted from a clonal expansion of an ancestral strain resistant to Isoniazid and to a very low level of RIF. Under the selective pressure of RIF-based therapy the strain acquired mutation in the M306 codon of embB followed by secondary mutations in rpoB and escalation of resistance level. This scenario highlights the importance of subcritical

  13. Out-of-sequence reactivation of the Munsiari thrust in the Relli River basin, Darjiling Himalaya, India: Insights from Shuttle Radar Topography Mission digital elevation model-based geomorphic indices

    Science.gov (United States)

    Mukul, Manas; Srivastava, Vinee; Mukul, Malay

    2017-05-01

    Quantitative tectonic geomorphology has emerged as a powerful discipline for studying evolution of topography, landscapes, and neotectonics using geomorphic indices computed from digital elevation data such as the Shuttle Radar Topography Mission (SRTM) data. We computed SRTM-based geomorphic indices to study neotectonics in the Relli River basin in the Darjiling Himalaya. We also used Real Time Kinematic Global Positioning System (RTKGPS) independent checkpoints to assess the quality of the SRTM data used to compute the geomorphic indices along with their uncertainties. Our analysis revealed that though the SRTM C-Band 90-m resolution (C90) digital elevation data has been used extensively for geomorphic studies, the 30-m resolution (C30) data were significantly more accurate. Moreover, geomorphic indices computed using SRTM C30 and C90 elevations in the Relli basin indicate that normalized, nondimensional indices such as the relief ratio (Rh), hypsometric integral (HI), basin elongation (Re), and valley floor width-to-height ratio (Vf) are statistically indistinguishable with uncertainty (1σ) at least an order of magnitude below the index value. The geomorphic indices in the Relli basin reveal neotectonic activity in the Munsiari thrust (MT) fault zone and intraformational faults in its footwall in the Lesser Himalayan rocks and also indicate that the basin is at an early mature stage close to equilibrium between tectonic and erosional process. However, analysis of the uncertainties associated with the indices suggest that the normalized or nondimensional geomorphic indices have the lowest uncertainties and that neotectonics in the Relli basin may only be confined to reactivation in the MT. The reactivation in the MT fault zone by out-of-sequence neotectonics implies the possibility of large earthquake events in the Darjiling Himalaya and significant seismic and landslide hazard for populations in large towns specifically located on the MT. Our new approach of

  14. Whole Genome Sequencing Investigation of a Tuberculosis Outbreak in Port-au-Prince, Haiti Caused by a Strain with a "Low-Level" rpoB Mutation L511P - Insights into a Mechanism of Resistance Escalation.

    Science.gov (United States)

    Ocheretina, Oksana; Shen, Lishuang; Escuyer, Vincent E; Mabou, Marie-Marcelle; Royal-Mardi, Gertrude; Collins, Sean E; Pape, Jean W; Fitzgerald, Daniel W

    2015-01-01

    The World Health Organization recommends diagnosing Multidrug-Resistant Tuberculosis (MDR-TB) in high burden countries by detection of mutations in Rifampin (RIF) Resistance Determining Region of Mycobacterium tuberculosis rpoB gene with rapid molecular tests GeneXpert MTB/RIF and Hain MTBDRplus. Such mutations are found in >95% of Mycobacterium tuberculosis strains resistant to RIF by conventional culture-based drug susceptibility testing (DST). However routine diagnostic screening with molecular tests uncovered specific "low level" rpoB mutations conferring resistance to RIF below the critical concentration of 1 μg/ml in some phenotypically susceptible strains. Cases with discrepant phenotypic (susceptible) and genotypic (resistant) results for resistance to RIF account for at least 10% of resistant diagnoses by molecular tests and urgently require new guidelines to inform therapeutic decision making. Eight strains with a "low level" rpoB mutation L511P were isolated by GHESKIO laboratory between 2008 and 2012 from 6 HIV-negative and 2 HIV-positive patients during routine molecular testing. Five isolates with a single L511P mutation and two isolates with double mutation L511P&M515T had MICs for RIF between 0.125 and 0.5 μg/ml and tested susceptible in culture-based DST. The eighth isolate carried a double mutation L511P&D516C and was phenotypically resistant to RIF. All eight strains shared the same spoligotype SIT 53 commonly found in Haiti but classic epidemiological investigation failed to uncover direct contacts between the patients. Whole Genome Sequencing (WGS) revealed that L511P cluster isolates resulted from a clonal expansion of an ancestral strain resistant to Isoniazid and to a very low level of RIF. Under the selective pressure of RIF-based therapy the strain acquired mutation in the M306 codon of embB followed by secondary mutations in rpoB and escalation of resistance level. This scenario highlights the importance of subcritical resistance to RIF

  15. Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence.

    Science.gov (United States)

    Yang, Zhixiu; Guo, Qiang; Goto, Simon; Chen, Yuling; Li, Ningning; Yan, Kaige; Zhang, Yixiao; Muto, Akira; Deng, Haiteng; Himeno, Hyouta; Lei, Jianlin; Gao, Ning

    2014-05-01

    The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3' domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5' end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation.

  16. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  17. Atrial and ventricular activation sequence after ventricular induction/entrainment pacing during fast-slow atrioventricular nodal reentrant tachycardia: New insight into the use of V-A-A-V for the differential diagnosis of supraventricular tachycardia.

    Science.gov (United States)

    Kaneko, Yoshiaki; Nakajima, Tadashi; Irie, Tadanobu; Iizuka, Takashi; Tamura, Shuntaro; Kurabayashi, Masahiko

    2017-06-10

    The atrial and ventricular response observed immediately after cessation of ventricular induction/entrainment pacing is commonly analyzed to discriminate atrial tachycardia from other supraventricular tachycardias during electrophysiologic studies. However, the response in fast-slow atrioventricular nodal reentrant tachycardia (F/S-AVNRT) remains poorly investigated. The purpose of this study was to analyze the atrial and ventricular activation patterns after ventricular pacing in F/S-AVNRT. We enrolled 28 patients with F/S-AVNRT incorporating a typical slow pathway (typ-F/S-AVNRT) and 9 patients with F/S-AVNRT incorporating a superior slow pathway (sup-F/S-AVNRT). The V-A-A-V response was observed in 14 patients (38%) with F/S-AVNRT, more commonly in patients with sup-F/S-AVNRT than in those with typ-F/S-AVNRT (89% vs 21%, P = .0003). The underlying mechanisms included (1) a double atrial response (DAR) in 13 patients; (2) an anterograde block at the lower common pathway once after ventricular pacing in 2 patients; and (3) a pseudo-A-A-V response in 2 patients. The DAR was characterized by a V-A-A-V interatrial interval that was 55 ± 60 ms shorter than the tachycardia cycle length, whereas the block at the lower common pathway or infrahisian block had a V-A-A-V interatrial interval that was almost equal to or longer than the tachycardia cycle length. The V-A-A-V activation sequence immediately after ventricular induction/entrainment pacing is observed in patients with F/S-AVNRT, particularly in patients with sup-F/S-AVNRT, and is caused by multiple mechanisms, including a DAR, which is the major etiology. Copyright © 2017 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  18. A taxonomic re-assessment in the Chinese Bupleurum (Apiaceae):Insights from morphology, nuclear ribosomal internal transcribed spacer, and chloroplast (trnH-psbA, matK) sequences

    Institute of Scientific and Technical Information of China (English)

    Chang-Bao WANG; Xiang-GuangMA; Xing-Jin HE

    2011-01-01

    As one of the big genera in Apiaceae,Bupleurum L.has received considerable attention from plant taxonomists.Nevertheless,there are still many gaps in our knowledge of this genus,especially of those species endemic to China that have often been excluded from previous studies.In spite of a few recent studies on the phylogeny and classification of the Chinese Bupleurum,the most essential problem of species delimitation still remains unresolved.We re-evaluate the taxonomy of the Chinese Bupleurum using morphological and molecular evidence.Careful observations of living plants growing the field and herbarium specimens were made to understand the morphological variation and to ensure species identification for the molecular analysis.Phylogenetic analyses were carried out on sequence data of nuclear ribosomal intemal transcribed spacer (nrlTS),trnH-psbA,and matK,using parsimony and Bayesian approaches to evaluate species relationships.Analyses of both nrlTS and combined datasets of the three regions revealed the following results:(i) the Chinese Bupleurum species were divided into two major lineages; and (ii) most species were well defined,but some traditional inter- and infraspecific relationships were not supported.Our results,along with the results of previous works support that the Chinese Bupleurum species were derived from two different lineages and should be placed in Neves and Watson’s subgenus Bupleurum.Our detailed taxonomic re-assessment of several Chinese species resulted in new taxonomic recombinations with rank changes for three species:Bupleurum tenerum,B.amplexicaule,and B.franchetii; new combination for one variety,B.smithii var.flaviflorum; and the description of one variety and one species,B.stenophyllum vat.leiocarpum and B.sikangense.

  19. A bioinformatics insight to rhizobial globins: gene identification and mapping, polypeptide sequence and phenetic analysis, and protein modeling. [v1; ref status: indexed, http://f1000r.es/5ai

    Directory of Open Access Journals (Sweden)

    Reinier Gesto-Borroto

    2015-05-01

    Full Text Available Globins (Glbs are proteins widely distributed in organisms. Three evolutionary families have been identified in Glbs: the M, S and T Glb families. The M Glbs include flavohemoglobins (fHbs and single-domain Glbs (SDgbs; the S Glbs include globin-coupled sensors (GCSs, protoglobins and sensor single domain globins, and the T Glbs include truncated Glbs (tHbs. Structurally, the M and S Glbs exhibit 3/3-folding whereas the T Glbs exhibit 2/2-folding. Glbs are widespread in bacteria, including several rhizobial genomes. However, only few rhizobial Glbs have been characterized. Hence, we characterized Glbs from 62 rhizobial genomes using bioinformatics methods such as data mining in databases, sequence alignment, phenogram construction and protein modeling. Also, we analyzed soluble extracts from Bradyrhizobium japonicum USDA38 and USDA58 by (reduced + carbon monoxide (CO minus reduced differential spectroscopy. Database searching showed that only fhb, sdgb, gcs and thb genes exist in the rhizobia analyzed in this work. Promoter analysis revealed that apparently several rhizobial glb genes are not regulated by a -10 promoter but might be regulated by -35 and Fnr (fumarate-nitrate reduction regulator-like promoters. Mapping analysis revealed that rhizobial fhbs and thbs are flanked by a variety of genes whereas several rhizobial sdgbs and gcss are flanked by genes coding for proteins involved in the metabolism of nitrates and nitrites and chemotaxis, respectively. Phenetic analysis showed that rhizobial Glbs segregate into the M, S and T Glb families, while structural analysis showed that predicted rhizobial SDgbs and fHbs and GCSs globin domain and tHbs fold into the 3/3- and 2/2-folding, respectively. Spectra from B. japonicum USDA38 and USDA58 soluble extracts exhibited peaks and troughs characteristic of bacterial and vertebrate Glbs thus indicating that putative Glbs are synthesized in B. japonicum USDA38 and USDA58.

  20. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    Directory of Open Access Journals (Sweden)

    Jia Yi Har

    2015-09-01

    Full Text Available We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e. Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P, polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins. We hypothesize that such activities may mediate acclimation and persistence of bacteria in N. vectensis.

  1. Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression

    Science.gov (United States)

    Har, Jia Y.; Helbig, Tim; Lim, Ju H.; Fernando, Samodha C.; Reitzel, Adam M.; Penn, Kevin; Thompson, Janelle R.

    2015-01-01

    We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing 99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and

  2. Different RNA splicing mechanisms contribute to diverse infective outcome of classical swine fever viruses of differing virulence: insights from the deep sequencing data in swine umbilical vein endothelial cells.

    Science.gov (United States)

    Ning, Pengbo; Zhou, Yulu; Liang, Wulong; Zhang, Yanming

    2016-01-01

    Molecular mechanisms underlying RNA splicing regulation in response to viral infection are poorly understood. Classical swine fever (CSF), one of the most economically important and highly contagious swine diseases worldwide, is caused by classical swine fever virus (CSFV). Here, we used high-throughput sequencing to obtain the digital gene expression (DGE) profile in swine umbilical vein endothelial cells (SUVEC) to identify different response genes for CSFV by using both Shimen and C strains. The numbers of clean tags obtained from the libraries of the control and both CSFV-infected libraries were 3,473,370, 3,498,355, and 3,327,493 respectively. In the comparison among the control, CSFV-C, and CSFV-Shimen groups, 644, 158, and 677 differentially expressed genes (DEGs) were confirmed in the three groups. Pathway enrichment analysis showed that many of these DEGs were enriched in spliceosome, ribosome, proteasome, ubiquitin-mediated proteolysis, cell cycle, focal adhesion, Wnt signalling pathway, etc., where the processes differ between CSFV strains of differing virulence. To further elucidate important mechanisms related to the differential infection by the CSFV Shimen and C strains, we identified four possible profiles to assess the significantly expressed genes only by CSFV Shimen or CSFV C strain. GO analysis showed that infection with CSFV Shimen and C strains disturbed 'RNA splicing' of SUVEC, resulting in differential 'gene expression' in SUVEC. Mammalian target of rapamycin (mTOR) was identified as a significant response regulator contributed to impact on SUVEC function for CSFV Shimen. This computational study suggests that CSFV of differing virulence could induce alterations in RNA splicing regulation in the host cell to change cell metabolism, resulting in acute haemorrhage and pathological damage or infectious tolerance.

  3. 基于13个内含子的序列探讨鲸目的系统发育关系%Molecular phylogenetics of cetaceans: an insight from 13 nuclear intron sequences

    Institute of Scientific and Technical Information of China (English)

    熊晔; 周旭明; 杨梅; 张盼; 杨云霞; 杨光

    2011-01-01

    本文基于实验室筛选得到的13对内含子标记,在鲸偶蹄目的15个物种中进行有效扩增,并重建了这15个物种的系统发育关系.结果表明,抹香鲸总科(Physeteroidea)位于齿鲸亚目(Odontoceti)的基部,从而支持了传统的齿鲸亚目的单系性.在海豚总科(Delphinoidea)内部,贝斯分析结果支持了鼠海豚科(Phocoenidae)和一角鲸科(Monodontidae)的姐妹群关系,而后再与海豚科(Delphinidae)相聚.系统发育分析同时还强烈支持了海豚科的四个属(Sousa,Tursiops,Stenella,Delphinus)组成一个单系的"复合体".另外,我们的分析结果并不支持瓶鼻海豚属(Tursiops)和原海豚属(Stenella)的单系性.基于松散分子钟的分歧时间估算与以往文献中的结果没有明显差异.这些研究结果提示,核基因内含子序列有希望解决一些长期存在的鲸类系统发育问题.%Sequences of 13 introns from 15 Cetartiodactyla species were determined to reveal the phylogeny of cetaceans.Our results support the monophyly of the traditionally accepted suborder Odontoceti ( toothed whales ), placing the dwarf sperm whale ( Kogia sima), a representative species of superfamily Physeteroidea, as sister to other toothed whales. Within the superfamily Delphinoidea, phylogenetic analyses identified a sister relationship between Delphinidae and Monodontidae + Phocoenidae. A close relationship among four genera ( Sousa, Tursiops, Stenella, and Delphinus) is strongly supported,which suggested the monophyly of the Sousa-Stenella-Tursiops-Delphinus complex. Neither the two Tursiops species ( T.truncates and T. aduncus ) nor the two Stenella species (S. coeruleoalba and S. attenuata ) examined in present study clustered together, which strongly supported the paraphyly of these two genera as suggested in previous studies. Furthermore,the present Bayesian inference with a lognormal relaxed molecular clock provided divergence time for each clade, which is consistent with

  4. Theory of Mind in Schizophrenia: Associations With Clinical and Cognitive Insight Controlling for Levels of Psychopathology.

    Science.gov (United States)

    Popolo, Raffaele; Dimaggio, Giancarlo; Luther, Lauren; Vinci, Giancarlo; Salvatore, Giampaolo; Lysaker, Paul H

    2016-03-01

    Poor insight in schizophrenia is a risk factor for both poor outcomes and treatment adherence. Accordingly, interest in identifying causes of poor insight has increased. This study explored whether theory of mind (ToM) impairments are linked to poor clinical and cognitive insight independent of psychopathology. Participants with schizophrenia (n = 37) and control subjects (n = 40) completed assessments of ToM with the Hinting Task and the Brüne Picture Sequencing Task, clinical insight and psychopathology with the Positive and Negative Syndrome Scale, and cognitive insight with the Beck Cognitive Insight Scale. Results indicated that the schizophrenia group had greater impairments in ToM relative to control subjects. In the schizophrenia group, the Hinting Task performance was related to both cognitive and clinical insight, with only the relationship with cognitive insight persisting after controlling for psychopathology. Picture Sequencing Task performance was related to cognitive insight only. Future research directions and clinical implications are discussed.

  5. Gestures and insight in advanced mathematical thinking

    Science.gov (United States)

    Yoon, Caroline; Thomas, Michael O. J.; Dreyfus, Tommy

    2011-10-01

    What role do gestures play in advanced mathematical thinking? We argue that the role of gestures goes beyond merely communicating thought and supporting understanding - in some cases, gestures can help generate new mathematical insights. Gestures feature prominently in a case study of two participants working on a sequence of calculus activities. One participant uses gestures to clarify the relationships between a function, its derivative and its antiderivative. We show how these gestures help create a virtual mathematical construct, which in turn leads to a new problem-solving strategy. These results suggest that gestures are a productive, but potentially undertapped resource for generating new insights in advanced levels of mathematics.

  6. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  7. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  8. Genomic insights into the marine sponge microbiome.

    Science.gov (United States)

    Hentschel, Ute; Piel, Jörn; Degnan, Sandie M; Taylor, Michael W

    2012-09-01

    Marine sponges (phylum Porifera) often contain dense and diverse microbial communities, which can constitute up to 35% of the sponge biomass. The genome of one sponge, Amphimedon queenslandica, was recently sequenced, and this has provided new insights into the origins of animal evolution. Complementary efforts to sequence the genomes of uncultivated sponge symbionts have yielded the first glimpse of how these intimate partnerships are formed. The remarkable microbial and chemical diversity of the sponge-microorganism association, coupled with its postulated antiquity, makes sponges important model systems for the study of metazoan host-microorganism interactions, and their evolution, as well as for enabling access to biotechnologically important symbiont-derived natural products. In this Review, we discuss our current understanding of the interactions between marine sponges and their microbial symbiotic consortia, and highlight recent insights into these relationships from genomic studies.

  9. Inside PixInsight

    CERN Document Server

    Keller, Warren A

    2016-01-01

    In this book, Warren Keller reveals the secrets of astro-image processing software PixInsight in a practical and easy to follow manner, allowing the reader to produce stunning astrophotographs from even mediocre data. As the first comprehensive post-processing platform to be created by astro-imagers for astro-imagers, it has for many, replaced the generic graphics editors as the software of choice. With clear instructions from Keller, astrophotographers can get the most from its tools to create amazing images. Capable of complex post-processing routines, PixInsight is also an advanced pre-processing software, through which astrophotographers calibrate and stack their exposures into completed master files.This is the most comprehensive resource on PixInsight to date. With screenshots to help illustrate the process, it is a vital guide.

  10. Dreaming and insight

    Directory of Open Access Journals (Sweden)

    Christopher L Edwards

    2013-12-01

    Full Text Available This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years. Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996 therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams. The need to distinguish ‘aha’ experiences as a result of discovering a waking life source for part of a dream, from ‘aha’ experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared.

  11. Dreaming and insight.

    Science.gov (United States)

    Edwards, Christopher L; Ruby, Perrine M; Malinowski, Josie E; Bennett, Paul D; Blagrove, Mark T

    2013-01-01

    This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish "aha" experiences as a result of discovering a waking life source for part of a dream, from "aha" experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared.

  12. Dreaming and insight

    Science.gov (United States)

    Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

    2013-01-01

    This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

  13. OpenGL Insights

    CERN Document Server

    Cozzi, Patrick

    2012-01-01

    Get Real-World Insight from Experienced Professionals in the OpenGL Community With OpenGL, OpenGL ES, and WebGL, real-time rendering is becoming available everywhere, from AAA games to mobile phones to web pages. Assembling contributions from experienced developers, vendors, researchers, and educators, OpenGL Insights presents real-world techniques for intermediate and advanced OpenGL, OpenGL ES, and WebGL developers. Go Beyond the Basics The book thoroughly covers a range of topics, including OpenGL 4.2 and recent extensions. It explains how to optimize for mobile devices, explores the design

  14. Comparing the Statistical Fate of Paralogous and Orthologous Sequences

    OpenAIRE

    Massip, F.; Sheinman, M.; Schbath, S.; Arndt, P.

    2016-01-01

    Since several decades, sequence alignment is a widely used tool in bioinformatics. For instance, finding homologous sequences with known function in large databases is used to get insight into the function of non-annotated genomic regions. Very efficient tools, like BLAST have been developed to identify and rank possible homologous sequences. To estimate the significance of the homology, the ranking of alignment scores takes a background model for random sequences into account. Using this mod...

  15. Coarse fraction components in a red-clay sedimemt core, Central Indian Ocean Basin: Their occurrence and significance

    Digital Repository Service at National Institute of Oceanography (India)

    Iyer, S.D.; Fernandes, G.Q.; Mahender, K.

    , phillipsite, clinoptilolite and nontronite also occur (Kastner and Stonecipher, 1978; Iyer et al., 1997; Mascarenhas-Pereira and Nath, 2010). Diagenetically, well-formed phillipsite crystals form within manganese micronodules of the CIOB (Banerjee and Iyer... twinned crystals that show 2 or more intersecting twin planes. The crystals are either fresh and while a few show features of dissolution in the form of pores or pits. The pumices have ellipsoidal, elongated and spherical vesicles and also form nuclei...

  16. Preparation of Terracotta with Red Clay%利用赤泥制备琉璃瓦的研究

    Institute of Scientific and Technical Information of China (English)

    贺深阳; 蒋述兴

    2007-01-01

    利用赤泥及其他陶瓷原料,采用一次烧成工艺制备出达到国家建筑琉璃制品标准GB9197-88要求及国家建材行业建筑琉璃制品标准JC/T765-2006要求的无铅琉璃瓦.

  17. Outsourcing/Offshoring Insights

    DEFF Research Database (Denmark)

    Tate, Wendy; Bals, Lydia

    2017-01-01

    Findings: Both the geographical and governance dimensions are part of the rightshoring decision which is an important conceptual foundation for this special issue, as it invited insightful pieces on all of these phenomena (e.g. outsourcing, insourcing, offshoring, reshoring), acknowledging that t...

  18. Death: 'nothing' gives insight.

    Science.gov (United States)

    Ettema, Eric J

    2013-08-01

    According to a widely accepted belief, we cannot know our own death--death means 'nothing' to us. At first sight, the meaning of 'nothing' just implies the negation or absence of 'something'. Death then simply refers to the negation or absence of life. As a consequence, however, death has no meaning of itself. This leads to an ontological paradox in which death is both acknowledged and denied: death is … nothing. In this article, I investigate whether insight into the ontological paradox of the nothingness of death can contribute to a good end-of-life. By analysing Aquinas', Heidegger's and Derrida's understanding of death as nothingness, I explore how giving meaning to death on different ontological levels connects to, and at the same time provides resistance against, the harsh reality of death. By doing so, I intend to demonstrate that insight into the nothingness of death can count as a framework for a meaningful dealing with death.

  19. World energy insight 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-11-15

    The World Energy Insight 2011 is the official publication of the World Energy Council. It includes interviews, articles and case studies from a distinguished panel of World Energy Council Officers, CEOs, government ministers, academics and opinion formers from all areas of the energy sector and provides perspectives from around the globe. Government, industry and NGO's offer both policy and technology perspectives. The insights within this publication add to the work that WEC is doing to provide the forum for energy leaders, along with the on-going WEC studies and programmes on Energy Policies, 2050 Energy Scenarios, Energy Resources & Technologies, Energy for Urban Innovation, Rules Of Energy Trade and Global Energy Access.

  20. The politics of insight.

    Science.gov (United States)

    Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

    2016-01-01

    Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.

  1. Spot-Based Generations for Meta-Fibonacci Sequences

    CERN Document Server

    Dalton, Barnaby; Tanny, Stephen

    2011-01-01

    For many meta-Fibonacci sequences it is possible to identify a partition of the sequence into successive intervals (sometimes called blocks) with the property that the sequence behaves "similarly" in each block. This partition provides insights into the sequence properties. To date, for any given sequence, only ad hoc methods have been available to identify this partition. We apply a new concept - the spot-based generation sequence - to derive a general methodology for identifying this partition for a large class of meta-Fibonacci sequences. This class includes the Conolly and Conway sequences and many of their well-behaved variants, and even some highly chaotic sequences, such as Hofstadter's famous Q-sequence.

  2. Randomness in Sequence Evolution Increases over Time.

    Directory of Open Access Journals (Sweden)

    Guangyu Wang

    Full Text Available The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.

  3. Initial sequencing and analysis of the human genome.

    Science.gov (United States)

    Lander, E S; Linton, L M; Birren, B; Nusbaum, C; Zody, M C; Baldwin, J; Devon, K; Dewar, K; Doyle, M; FitzHugh, W; Funke, R; Gage, D; Harris, K; Heaford, A; Howland, J; Kann, L; Lehoczky, J; LeVine, R; McEwan, P; McKernan, K; Meldrim, J; Mesirov, J P; Miranda, C; Morris, W; Naylor, J; Raymond, C; Rosetti, M; Santos, R; Sheridan, A; Sougnez, C; Stange-Thomann, Y; Stojanovic, N; Subramanian, A; Wyman, D; Rogers, J; Sulston, J; Ainscough, R; Beck, S; Bentley, D; Burton, J; Clee, C; Carter, N; Coulson, A; Deadman, R; Deloukas, P; Dunham, A; Dunham, I; Durbin, R; French, L; Grafham, D; Gregory, S; Hubbard, T; Humphray, S; Hunt, A; Jones, M; Lloyd, C; McMurray, A; Matthews, L; Mercer, S; Milne, S; Mullikin, J C; Mungall, A; Plumb, R; Ross, M; Shownkeen, R; Sims, S; Waterston, R H; Wilson, R K; Hillier, L W; McPherson, J D; Marra, M A; Mardis, E R; Fulton, L A; Chinwalla, A T; Pepin, K H; Gish, W R; Chissoe, S L; Wendl, M C; Delehaunty, K D; Miner, T L; Delehaunty, A; Kramer, J B; Cook, L L; Fulton, R S; Johnson, D L; Minx, P J; Clifton, S W; Hawkins, T; Branscomb, E; Predki, P; Richardson, P; Wenning, S; Slezak, T; Doggett, N; Cheng, J F; Olsen, A; Lucas, S; Elkin, C; Uberbacher, E; Frazier, M; Gibbs, R A; Muzny, D M; Scherer, S E; Bouck, J B; Sodergren, E J; Worley, K C; Rives, C M; Gorrell, J H; Metzker, M L; Naylor, S L; Kucherlapati, R S; Nelson, D L; Weinstock, G M; Sakaki, Y; Fujiyama, A; Hattori, M; Yada, T; Toyoda, A; Itoh, T; Kawagoe, C; Watanabe, H; Totoki, Y; Taylor, T; Weissenbach, J; Heilig, R; Saurin, W; Artiguenave, F; Brottier, P; Bruls, T; Pelletier, E; Robert, C; Wincker, P; Smith, D R; Doucette-Stamm, L; Rubenfield, M; Weinstock, K; Lee, H M; Dubois, J; Rosenthal, A; Platzer, M; Nyakatura, G; Taudien, S; Rump, A; Yang, H; Yu, J; Wang, J; Huang, G; Gu, J; Hood, L; Rowen, L; Madan, A; Qin, S; Davis, R W; Federspiel, N A; Abola, A P; Proctor, M J; Myers, R M; Schmutz, J; Dickson, M; Grimwood, J; Cox, D R; Olson, M V; Kaul, R; Raymond, C; Shimizu, N; Kawasaki, K; Minoshima, S; Evans, G A; Athanasiou, M; Schultz, R; Roe, B A; Chen, F; Pan, H; Ramser, J; Lehrach, H; Reinhardt, R; McCombie, W R; de la Bastide, M; Dedhia, N; Blöcker, H; Hornischer, K; Nordsiek, G; Agarwala, R; Aravind, L; Bailey, J A; Bateman, A; Batzoglou, S; Birney, E; Bork, P; Brown, D G; Burge, C B; Cerutti, L; Chen, H C; Church, D; Clamp, M; Copley, R R; Doerks, T; Eddy, S R; Eichler, E E; Furey, T S; Galagan, J; Gilbert, J G; Harmon, C; Hayashizaki, Y; Haussler, D; Hermjakob, H; Hokamp, K; Jang, W; Johnson, L S; Jones, T A; Kasif, S; Kaspryzk, A; Kennedy, S; Kent, W J; Kitts, P; Koonin, E V; Korf, I; Kulp, D; Lancet, D; Lowe, T M; McLysaght, A; Mikkelsen, T; Moran, J V; Mulder, N; Pollara, V J; Ponting, C P; Schuler, G; Schultz, J; Slater, G; Smit, A F; Stupka, E; Szustakowki, J; Thierry-Mieg, D; Thierry-Mieg, J; Wagner, L; Wallis, J; Wheeler, R; Williams, A; Wolf, Y I; Wolfe, K H; Yang, S P; Yeh, R F; Collins, F; Guyer, M S; Peterson, J; Felsenfeld, A; Wetterstrand, K A; Patrinos, A; Morgan, M J; de Jong, P; Catanese, J J; Osoegawa, K; Shizuya, H; Choi, S; Chen, Y J; Szustakowki, J

    2001-02-15

    The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

  4. Modeling for Insights

    Energy Technology Data Exchange (ETDEWEB)

    Jacob J. Jacobson; Gretchen Matthern

    2007-04-01

    System Dynamics is a computer-aided approach to evaluating the interrelationships of different components and activities within complex systems. Recently, System Dynamics models have been developed in areas such as policy design, biological and medical modeling, energy and the environmental analysis, and in various other areas in the natural and social sciences. The real power of System Dynamic modeling is gaining insights into total system behavior as time, and system parameters are adjusted and the effects are visualized in real time. System Dynamic models allow decision makers and stakeholders to explore long-term behavior and performance of complex systems, especially in the context of dynamic processes and changing scenarios without having to wait decades to obtain field data or risk failure if a poor management or design approach is used. The Idaho National Laboratory recently has been developing a System Dynamic model of the US Nuclear Fuel Cycle. The model is intended to be used to identify and understand interactions throughout the entire nuclear fuel cycle and suggest sustainable development strategies. This paper describes the basic framework of the current model and presents examples of useful insights gained from the model thus far with respect to sustainable development of nuclear power.

  5. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  6. Insights from genomics into bacterial pathogen populations.

    Directory of Open Access Journals (Sweden)

    Daniel J Wilson

    2012-09-01

    Full Text Available Bacterial pathogens impose a heavy burden of disease on human populations worldwide. The gravest threats are posed by highly virulent respiratory pathogens, enteric pathogens, and HIV-associated infections. Tuberculosis alone is responsible for the deaths of 1.5 million people annually. Treatment options for bacterial pathogens are being steadily eroded by the evolution and spread of drug resistance. However, population-level whole genome sequencing offers new hope in the fight against pathogenic bacteria. By providing insights into bacterial evolution and disease etiology, these approaches pave the way for novel interventions and therapeutic targets. Sequencing populations of bacteria across the whole genome provides unprecedented resolution to investigate (i within-host evolution, (ii transmission history, and (iii population structure. Moreover, advances in rapid benchtop sequencing herald a new era of real-time genomics in which sequencing and analysis can be deployed within hours in response to rapidly changing public health emergencies. The purpose of this review is to highlight the transformative effect of population genomics on bacteriology, and to consider the prospects for answering abiding questions such as why bacteria cause disease.

  7. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  8. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  9. Insights on STEM Careers

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, Joanne Roth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-11-05

    This presentation will provide career advice for individuals seeking to go beyond just having a job to building a successful career in the areas of Science, Technology, Engineering, and Mathematics. Careful planning can be used to turn a job into a springboard for professional advancement and personal satisfaction. Topics to be addressed include setting priorities, understanding career ladders, making tough choices, overcoming stereotypes and assumptions by others, networking, developing a professional identify, and balancing a career with family and other personal responsibilities. Insights on the transition from individual technical work to leadership will also be provided. The author will draw upon experiences gained in academic, industrial, and government laboratory settings, as well as extensive professional service and community involvement.

  10. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  11. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  12. Complete genome sequence of Streptococcus pyogenes M1 476, isolated from a patient with streptococcal toxic shock syndrome.

    Science.gov (United States)

    Miyoshi-Akiyama, Tohru; Watanabe, Shinya; Kirikae, Teruo

    2012-10-01

    Here, we report the completely annotated genome sequence of Streptococcus pyogenes M1 476 isolated from a patient with streptococcal toxic shock syndrome (STSS) during pregnancy. The genome sequence will provide new insights into the mechanisms underlying STSS.

  13. Complete Genome Sequence of Streptococcus pyogenes M1 476, Isolated from a Patient with Streptococcal Toxic Shock Syndrome

    OpenAIRE

    Miyoshi-Akiyama, Tohru; WATANABE, Shinya; Kirikae, Teruo

    2012-01-01

    Here, we report the completely annotated genome sequence of Streptococcus pyogenes M1 476 isolated from a patient with streptococcal toxic shock syndrome (STSS) during pregnancy. The genome sequence will provide new insights into the mechanisms underlying STSS.

  14. Insights into business student's book

    CERN Document Server

    Lannon, Michael; Trappe, Tonya

    1993-01-01

    With Challenging reading and listening texts from a range of authentic business sources, New Insights into Business will really engage your students. The thorough language and vocabulary syllabus together with the strong focus on business skills development gives students everything they need to function effectively in the workplace. New Insights into Business is a self-contained course and is also an ideal follow-on to First Insights into Business.

  15. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  17. Insight with hands and things

    DEFF Research Database (Denmark)

    Vallée-Tourangeau, Frédéric; Steffensen, S. V.; Vallée-Tourangeau, Gaëlle

    2016-01-01

    Two experiments examined whether different task ecologies influenced insight problem solving. The 17 animals problem was employed, a pure insight problem. Its initial formulation encourages the application of a direct arithmetic solution, but its solution requires the spatial arrangement of sets...

  18. Cognitive insight: A systematic review.

    Science.gov (United States)

    Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

    2017-07-01

    Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

  19. Systemic sclerosis: Recent insights.

    Science.gov (United States)

    Elhai, Muriel; Avouac, Jérôme; Kahan, André; Allanore, Yannick

    2015-05-01

    Systemic sclerosis is an orphan connective tissue disease characterized by alterations of the microvasculature, disturbances of the immune system and massive deposition of collagen and other matrix substances in the skin and internal organs. A major achievement of the recent years has been the validation of new classification criteria, allowing earlier diagnosis and earlier treatment of systemic sclerosis, before irreversible fibrosis and organ damage appeared ("window of opportunity"). Raynaud's phenomenon is usually the first sign of the disease and is considered as the main sentinel sign for the identification of very early systemic sclerosis. Systemic sclerosis is clinically heterogeneous and disease course remains unpredictable. Its prognosis depends on cardiopulmonary involvement and recent studies aim to identify serum or genetic biomarkers predictive of severe organ involvement. Moreover, the prospective follow-up of large cohorts has provided and will offer critical material to identify strong prognostic factors. Whereas the outcomes of vascular manifestations of the disease has been recently improved due to targeted therapy, recent data have highlighted that mortality has not changed over the past 40 years. This reflects the absence of efficacy of current available drugs to counteract the fibrotic process. Nevertheless, several targeted immunity therapies, commonly with proven efficacy in other immune diseases, are about to be investigated in systemic sclerosis. Indeed, promising results in small and open studies have been reported. This article deals with recent insights into classification criteria, pathogenesis, organ involvements, outcome and current and possible future therapeutic options in systemic sclerosis.

  20. O insight em psiquiatria

    Directory of Open Access Journals (Sweden)

    Ana Margarida P. Cardoso

    2008-12-01

    Full Text Available O sinal de que algo está a acontecer contribui para que o paciente reconheça que alguma coisa de estranho se está a passar consigo. Este reconhecimento faz com que o sujeito possa desempenhar uma função activa e seja um elemento colaborante do seu processo de recuperação. Cada doença apresenta, contudo, diferentes sintomas, uma vez que cada doença psiquiátrica consiste em diferentes perturbações com diversos efeitos sobre o funcionamento mental. Desta maneira, o fenómeno do insight que é registado em cada doença é diferente e expressa-se sob diferentes formas, não somente devido às manifestações clínicas da doença mas também devido às características individuais do sujeito.

  1. Draft Genome Sequence of Rubrivivax gelatinosus CBS

    Energy Technology Data Exchange (ETDEWEB)

    Hu, P. S.; Lang, J.; Wawrousek, K.; Yu, J. P.; Maness, P. C.; Chen, J.

    2012-06-01

    Rubrivivax gelatinosus CBS, a purple nonsulfur photosynthetic bacterium, can grow photosynthetically using CO and N{sub 2} as the sole carbon and nitrogen nutrients, respectively. R. gelatinosus CBS is of particular interest due to its ability to metabolize CO and yield H{sub 2}. We present the 5-Mb draft genome sequence of R. gelatinosus CBS with the goal of providing genetic insight into the metabolic properties of this bacterium.

  2. Supercomputers and biological sequence comparison algorithms.

    Science.gov (United States)

    Core, N G; Edmiston, E W; Saltz, J H; Smith, R M

    1989-12-01

    Comparison of biological (DNA or protein) sequences provides insight into molecular structure, function, and homology and is increasingly important as the available databases become larger and more numerous. One method of increasing the speed of the calculations is to perform them in parallel. We present the results of initial investigations using two dynamic programming algorithms on the Intel iPSC hypercube and the Connection Machine as well as an inexpensive, heuristically-based algorithm on the Encore Multimax.

  3. Complete Genome Sequence of Bradyrhizobium diazoefficiens USDA 122, a Nitrogen-Fixing Soybean Symbiont

    Science.gov (United States)

    Sugawara, Masayuki; Tsukui, Takahiro; Kaneko, Takakazu; Ohtsubo, Yoshiyuki; Sato, Shusei; Nagata, Yuji; Tsuda, Masataka; Mitsui, Hisayuki

    2017-01-01

    ABSTRACT We report the complete genome sequence of Bradyrhizobium diazoefficiens USDA 122, a nitrogen-fixing soybean symbiont. The genome consists of a 9.1 Mb circular chromosome, and 8,551 coding sequences (CDSs) were predicted on the genome. The sequence will provide insight into the evolution of rhizobial genome, and the symbiotic compatibility with host plants. PMID:28254989

  4. Recent Neurobiological Insights into the Concept of Insight in Psychosis.

    Science.gov (United States)

    Mythri, Starlin Vijay; Sanjay, Y

    2016-01-01

    The concept of insight in psychosis has been an interesting area in clinical psychiatry for well over a century with a surge in research interest over the past 25 years. Moreover, the past 5 years have been particularly fruitful in deciphering its neurobiological underpinnings. This article presents the development of the concept of insight in psychosis and reviews the current neurobiological research findings in this area.

  5. Recent Neurobiological Insights into the Concept of Insight in Psychosis

    Science.gov (United States)

    Mythri, Starlin Vijay; Sanjay, Y

    2016-01-01

    The concept of insight in psychosis has been an interesting area in clinical psychiatry for well over a century with a surge in research interest over the past 25 years. Moreover, the past 5 years have been particularly fruitful in deciphering its neurobiological underpinnings. This article presents the development of the concept of insight in psychosis and reviews the current neurobiological research findings in this area. PMID:27335512

  6. The sequence of learning cycle activities in high school chemistry

    Science.gov (United States)

    Abraham, Michael R.; Renner, John W.

    The sequence of the three phases of two high school learning cycles in chemistry was altered in order to: (I ) give insights into the factors which account for the success of the learning cycle, (2) serve as an indirect test of the association between Piaget's theory and the learning cycle, and (3) to compare the learning cycle with traditional instruction. Each of the six sequences (one n o d and five altered) was studied with content and atritudc measures. The outcomes of the study supported the contention that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge.

  7. Reading biological processes from nucleotide sequences

    Science.gov (United States)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  8. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  9. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  10. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  11. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  12. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  13. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  14. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  15. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  16. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  17. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  18. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  19. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence $(L_n^{(2)})_n$. In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences and occur in formulae simultaneously with the latter.

  20. Psychophysiological prediction of choice: relevance to insight and drug addiction

    Science.gov (United States)

    Moeller, Scott J.; Hajcak, Greg; Parvaz, Muhammad A.; Dunning, Jonathan P.; Volkow, Nora D.

    2012-01-01

    An important goal of addiction research and treatment is to predict behavioural responses to drug-related stimuli. This goal is especially important for patients with impaired insight, which can interfere with therapeutic interventions and potentially invalidate self-report questionnaires. This research tested (i) whether event-related potentials, specifically the late positive potential, predict choice to view cocaine images in cocaine addiction; and (ii) whether such behaviour prediction differs by insight (operationalized in this study as self-awareness of image choice). Fifty-nine cocaine abusers and 32 healthy controls provided data for the following laboratory components that were completed in a fixed-sequence (to establish prediction): (i) event-related potential recordings while passively viewing pleasant, unpleasant, neutral and cocaine images, during which early (400–1000 ms) and late (1000–2000 ms) window late positive potentials were collected; (ii) self-reported arousal ratings for each picture; and (iii) two previously validated tasks: one to assess choice for viewing these same images, and the other to group cocaine abusers by insight. Results showed that pleasant-related late positive potentials and arousal ratings predicted pleasant choice (the choice to view pleasant pictures) in all subjects, validating the method. In the cocaine abusers, the predictive ability of the late positive potentials and arousal ratings depended on insight. Cocaine-related late positive potentials better predicted cocaine image choice in cocaine abusers with impaired insight. Another emotion-relevant event-related potential component (the early posterior negativity) did not show these results, indicating specificity of the late positive potential. In contrast, arousal ratings better predicted respective cocaine image choice (and actual cocaine use severity) in cocaine abusers with intact insight. Taken together, the late positive potential could serve as a biomarker

  1. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  2. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

    OpenAIRE

    Niels Grarup; Patrick Sulem; Sandholt, Camilla H.; Gudmar Thorleifsson; Ahluwalia, Tarunveer S.; Valgerdur Steinthorsdottir; Helgi Bjarnason; Gudbjartsson, Daniel F; Magnusson, Olafur T; Thomas Sparsø, [No Value; Anders Albrechtsen; Augustine Kong; Gisli Masson; Geng Tian; Hongzhi Cao

    2013-01-01

    Genome-wide association studies have mainly relied on common HapMap sequence variations. Recently, sequencing approaches have allowed analysis of low frequency and rare variants in conjunction with common variants, thereby improving the search for functional variants and thus the understanding of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architectu...

  3. Origin of the NEFA and Nuc signal sequences.

    Science.gov (United States)

    Karabinos, A; Bhattacharya, D; Kratzin, H D; Hilschmann, N

    1998-03-01

    The human protein NEFA binds calcium, contains a leucine zipper repeat that does not form a homodimer, and is proposed (along with the homologous Nuc protein) to have a common evolutionary history with an EF-hand ancestor. We have isolated and characterized the N-terminal domain of NEFA that contains a signal sequence inferred from both endoproteinase Asp-N (Asp-N) and tryptic digests. Analysis of this N-terminal sequence shows significant similarity to the conserved multiple domains of the mitochondrial carrier family (MCF) proteins. The leader sequence of Nuc is, however, most similar to the signal sequences of membrane and/or secreted proteins (e.g., mouse insulin-like growth factor receptor). We suggest that the divergent NEFA and Nuc N-terminal sequences may have independent origins and that the common high hydrophobicity governs their targeting to the ER. These results provide insights into signal sequence evolution and the multiple origins of protein targeting.

  4. Probabilistic Methods for Processing High-Throughput Sequencing Signals

    DEFF Research Database (Denmark)

    Sørensen, Lasse Maretty

    for reconstructing transcript sequences from RNA sequencing data. The method is based on a novel sparse prior distribution over transcript abundances and is markedly more accurate than existing approaches. The second chapter describes a new method for calling genotypes from a fixed set of candidate variants...... insights is far from trivial. A key challenge is that these methods cannot read the input sequences in their entirety. Due to technological constraints, they instead provide the sequences of very many fragments of the input molecules. Furthermore, not all nucleotides in these fragments are measured...... correctly and the final output of a typical experiment thus consists of hundreds of millions of error-containing sequence fragments. This thesis concerns the development of methods for transforming such a raw sequencing signal into a simpler representation from which biological inferences can then be made...

  5. Understanding Insight in the Context of Q

    Science.gov (United States)

    Coghlan, David

    2012-01-01

    In Revans' learning formula, L = P + Q, Q represents "questioning insight", by which Revans means that insight comes out of the process of questioning programmed knowledge (P) in the light of experience. We typically focus on the content of an insight rather than on the act of insight. Drawing primarily on the work of Bernard Lonergan this paper…

  6. Approaching the Distinction between Intuition and Insight.

    Science.gov (United States)

    Zhang, Zhonglu; Lei, Yi; Li, Hong

    2016-01-01

    Intuition and insight share similar cognitive and neural basis. Though, there are still some essential differences between the two. Here in this short review, we discriminated between intuition, and insight in two aspects. First, intuition, and insight are toward different aspects of information processing. Whereas intuition involves judgment about "yes or no," insight is related to "what" is the solution. Second, tacit knowledge play different roles in between intuition and insight. On the one hand, tacit knowledge is conducive to intuitive judgment. On the other hand, tacit knowledge may first impede but later facilitate insight occurrence. Furthermore, we share theoretical, and methodological views on how to access the distinction between intuition and insight.

  7. Draft genome sequences of 10 strains of the genus exiguobacterium.

    Science.gov (United States)

    Vishnivetskaya, Tatiana A; Chauhan, Archana; Layton, Alice C; Pfiffner, Susan M; Huntemann, Marcel; Copeland, Alex; Chen, Amy; Kyrpides, Nikos C; Markowitz, Victor M; Palaniappan, Krishna; Ivanova, Natalia; Mikhailova, Natalia; Ovchinnikova, Galina; Andersen, Evan W; Pati, Amrita; Stamatis, Dimitrios; Reddy, T B K; Shapiro, Nicole; Nordberg, Henrik P; Cantor, Michael N; Hua, X Susan; Woyke, Tanja

    2014-10-16

    High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation. The selected genomes include psychrotrophic and thermophilic species from a range of habitats, which will allow for a comparison of metabolic pathways and stress response genes.

  8. Complete Genome Sequence of the Haloalkaliphilic, Hydrogen Producing Halanaerobium hydrogenoformans

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Steven D [ORNL; Begemann, Matthew B [University of Wisconsin, Madison; Mormile, Dr. Melanie R. [Missouri University of Science and Technology; Wall, Judy D. [University of Missouri; Han, Cliff [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Samual [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Elias, Dwayne A [ORNL

    2011-01-01

    Halanaerobium hydrogenoformans is an alkaliphilic bacterium capable of biohydrogen production at pH 11 and 7% (w/v) salt. We present the 2.6 Mb genome sequence to provide insights into its physiology and potential for bioenergy applications.

  9. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  10. Insights from a Math Phobic.

    Science.gov (United States)

    Dodd, Anne Wescott

    1992-01-01

    The author's personal experiences in overcoming mathematics anxiety provide insights into how teachers can create a classroom environment to help students develop self-confidence by assessing students' feelings, using cooperative-learning techniques, showing more patience, and having students write about their experiences. (MDH)

  11. Global China Insights December 2013

    NARCIS (Netherlands)

    Segers, Rien T.; Havinga, Marieke; Fischer, Ingrid

    2013-01-01

    Journal in which the Groningen Confucius Institute (GCI) shares different perspectives on China and provides insights into China from as many different aspects as possible. GCI aims to provide a full view of real China to the readers as well as featuring international and comprehensive perspectives,

  12. New Insights into Behavioral Finance

    NARCIS (Netherlands)

    G. Baltussen (Guido)

    2008-01-01

    textabstractThis thesis applies insights from psychology and other behavioral sciences to overcome the shortcomings of the traditional finance approach (which assumes that agents and markets are rational) and improves our understanding of financial markets and its participants. More specific, this t

  13. Investigating Insight as Sudden Learning

    Science.gov (United States)

    Ash, Ivan K.; Jee, Benjamin D.; Wiley, Jennifer

    2012-01-01

    Gestalt psychologists proposed two distinct learning mechanisms. Associative learning occurs gradually through the repeated co-occurrence of external stimuli or memories. Insight learning occurs suddenly when people discover new relationships within their prior knowledge as a result of reasoning or problem solving processes that re-organize or…

  14. Global China Insights June 2014

    NARCIS (Netherlands)

    Ingrid Fischer; Rien T. Segers

    2013-01-01

    Journal in which the Groningen Confucius Institute (GCI) shares different perspectives on China and provides insights into China from as many different aspects as possible. GCI aims to provide a full view of real China to the readers as well as featuring international and comprehensive perspectives,

  15. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  16. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  17. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.

  18. Protein comparative sequence analysis and computer modeling.

    Science.gov (United States)

    Hambly, Brett D; Oakley, Cecily E; Fajer, Piotr G

    2008-01-01

    A problem frequently encountered by the biological scientist is the identification of a previously unknown gene or protein sequence, where there are few or no clues as to the biochemical function, ligand specificity, gene regulation, protein-protein interactions, tissue specificity, cellular localization, developmental phase of activity, or biological role. Through the process of bioinformatics there are now many approaches for predicting answers to at least some of these questions, often then allowing the design of more insightful experiments to characterize more definitively the new protein.

  19. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  20. Music and language perception: expectations, structural integration, and cognitive sequencing.

    Science.gov (United States)

    Tillmann, Barbara

    2012-10-01

    Music can be described as sequences of events that are structured in pitch and time. Studying music processing provides insight into how complex event sequences are learned, perceived, and represented by the brain. Given the temporal nature of sound, expectations, structural integration, and cognitive sequencing are central in music perception (i.e., which sounds are most likely to come next and at what moment should they occur?). This paper focuses on similarities in music and language cognition research, showing that music cognition research provides insight into the understanding of not only music processing but also language processing and the processing of other structured stimuli. The hypothesis of shared resources between music and language processing and of domain-general dynamic attention has motivated the development of research to test music as a means to stimulate sensory, cognitive, and motor processes. Copyright © 2012 Cognitive Science Society, Inc.

  1. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  2. A Genetic Algorithm on Multiple Sequences Alignment Problems in Biology

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The study and comparison of sequences of characters from a finite alphabet is relevant to various areas of science, notably molecular biology. The measurement of sequence similarity involves the consideration of the possible sequence alignments in order to find an optimal one for which the "distance" between sequences is minimum. In biology informatics area, it is a more important and difficult problem due to the long length (100 at least) of sequence, this cause the compute complexity and large memory require. By associating a path in a lattice to each alignment, a geometric insight can be brought into the problem of finding an optimal alignment, this give an obvious encoding of each path. This problem can be solved by applying genetic algorithm, which is more efficient than dynamic programming and hidden Markov model using commomly now.

  3. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  4. Rapid detection of a norovirus pseudo-outbreak by using real-time sequence based information

    NARCIS (Netherlands)

    Rahamat-Langendoen, J. C.; Lokate, M.; Scholvinck, E. H.; Friedrich, A. W.; Niesters, H. G. M.

    2013-01-01

    Background: Sequence based information is increasingly used to study the epidemiology of viruses, not only to provide insight in viral evolution, but also to understand transmission patterns during outbreaks. However, sequence analysis is not yet routinely performed by diagnostic laboratories, limit

  5. Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231

    OpenAIRE

    Ivshina, Irena B.; Kuyukina, Maria S.; Krivoruchko, Anastasiya V.; Barbe, Valérie; Fischer, Cécile

    2014-01-01

    We report a draft genome sequence of Rhodococcus ruber IEGM 231, isolated from a water spring near an oil-extracting enterprise (Perm region, Russian Federation). This sequence provides important insights into the genetic mechanisms of propane and n-butane metabolism, organic sulfide and beta-sitosterol biotransformation, glycolipid biosurfactant production, and heavy metal resistance in actinobacteria.

  6. Draft Genome Sequence of Propane- and Butane-Oxidizing Actinobacterium Rhodococcus ruber IEGM 231.

    Science.gov (United States)

    Ivshina, Irena B; Kuyukina, Maria S; Krivoruchko, Anastasiya V; Barbe, Valérie; Fischer, Cécile

    2014-12-11

    We report a draft genome sequence of Rhodococcus ruber IEGM 231, isolated from a water spring near an oil-extracting enterprise (Perm region, Russian Federation). This sequence provides important insights into the genetic mechanisms of propane and n-butane metabolism, organic sulfide and beta-sitosterol biotransformation, glycolipid biosurfactant production, and heavy metal resistance in actinobacteria.

  7. Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan

    NARCIS (Netherlands)

    Smit, S.; Derks, M.F.L.; Bervoets, Sander; Fahal, Ahmed; Leeuwen, van Willem; Belkum, van Alex; Sande, van de Wendy W.J.

    2016-01-01

    We present the first genome sequence for a strain of the main mycetoma causative agent, Madurella mycetomatis. This 36.7-Mb genome sequence will offer new insights into the pathogenesis of mycetoma, and it will contribute to the development of better therapies for this neglected tropical disease.

  8. Genome sequence of Madurella mycetomatis mm55, isolated from a human mycetoma case in Sudan

    NARCIS (Netherlands)

    Smit, S. (Sandra); Derks, M.F.L. (Martijn F.L.); Bervoets, S. (Sander); A.H. Fahal (Ahmed); W.B. van Leeuwen (Willem); A.F. van Belkum (Alex); W.W.J. van de Sande (Wendy)

    2016-01-01

    textabstractWe present the first genome sequence for a strain of the main mycetoma causative agent, Madurella mycetomatis. This 36.7-Mb genome sequence will offer new insights into the pathogenesis of mycetoma, and it will contribute to the development of better therapies for this neglected tropical

  9. Whole-Genome Sequence of Starmerella bacillaris PAS13, a Nonconventional Enological Yeast with Antifungal Activity.

    Science.gov (United States)

    Lemos Junior, Wilson José Fernandes; Treu, Laura; da Silva Duarte, Vinícius; Carlot, Milena; Nadai, Chiara; Campanaro, Stefano; Giacomini, Alessio; Corich, Viviana

    2017-08-10

    Starmerella bacillaris is a fermentative yeast commonly found in vineyards. Here, we present the draft genome sequence of S. bacillaris PAS13, a nonconventional enological yeast with a potential role as a biocontrol agent. This gene sequence will provide insights into the genetic basis of yeast activity against gray mold disease (Botrytis cinerea). Copyright © 2017 Lemos Junior et al.

  10. Draft Genome Sequence of Kluyveromyces marxianus Strain DMB1, Isolated from Sugarcane Bagasse Hydrolysate.

    Science.gov (United States)

    Suzuki, Toshihiro; Hoshino, Tamotsu; Matsushika, Akinori

    2014-07-24

    We determined the genome sequence of a thermotolerant yeast, Kluyveromyces marxianus strain DMB1, isolated from sugarcane bagasse hydrolysate, and the sequence provides further insights into the genomic differences between this strain and other reported K. marxianus strains. The genome described here is composed of 11,165,408 bases and has 4,943 protein-coding genes.

  11. SCIENCE CHINA In-Sight

    Institute of Scientific and Technical Information of China (English)

    HE ShiGang

    2010-01-01

    @@ 2010 celebrates the 60th anniversary of this journal.From this issue, the journal features a brand new section: 'In-Sight'.Equivalent to the Cutting Edge of the Cell, News and Views of the Nature and Perspective of the Science, 'In-Sight' provides a forum for discussions about science and science policies in China, the history and future development of this journal and the highlights of scientific progresses published in the current issue.

  12. Theoretical Insight into Shocked Gases

    Energy Technology Data Exchange (ETDEWEB)

    Leiding, Jeffery Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-09-29

    I present the results of statistical mechanical calculations on shocked molecular gases. This work provides insight into the general behavior of shock Hugoniots of gas phase molecular targets with varying initial pressures. The dissociation behavior of the molecules is emphasized. Impedance matching calculations are performed to determine the maximum degree of dissociation accessible for a given flyer velocity as a function of initial gas pressure.

  13. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  14. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  15. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  16. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  17. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  18. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  19. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  20. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  1. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  2. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  3. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  4. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  5. Quantifying the Qualitative: Measuring the Insight Experience

    Science.gov (United States)

    Jarman, Matthew S.

    2014-01-01

    No scales currently exist that measure variability in the insight experience. Two scales were created to measure two factors hypothesized to be key drivers of the insight experience: insight radicality (i.e., perceived deviation between previous and new problem representations) and restructuring experience (i.e., the subjective experience of the…

  6. Rare variant detection using family-based sequencing analysis.

    Science.gov (United States)

    Peng, Gang; Fan, Yu; Palculict, Timothy B; Shen, Peidong; Ruteshouser, E Cristy; Chi, Aung-Kyaw; Davis, Ronald W; Huff, Vicki; Scharfe, Curt; Wang, Wenyi

    2013-03-05

    Next-generation sequencing is revolutionizing genomic analysis, but this analysis can be compromised by high rates of missing true variants. To develop a robust statistical method capable of identifying variants that would otherwise not be called, we conducted sequence data simulations and both whole-genome and targeted sequencing data analysis of 28 families. Our method (Family-Based Sequencing Program, FamSeq) integrates Mendelian transmission information and raw sequencing reads. Sequence analysis using FamSeq reduced the number of false negative variants by 14-33% as assessed by HapMap sample genotype confirmation. In a large family affected with Wilms tumor, 84% of variants uniquely identified by FamSeq were confirmed by Sanger sequencing. In children with early-onset neurodevelopmental disorders from 26 families, de novo variant calls in disease candidate genes were corrected by FamSeq as mendelian variants, and the number of uniquely identified variants in affected individuals increased proportionally as additional family members were included in the analysis. To gain insight into maximizing variant detection, we studied factors impacting actual improvements of family-based calling, including pedigree structure, allele frequency (common vs. rare variants), prior settings of minor allele frequency, sequence signal-to-noise ratio, and coverage depth (∼20× to >200×). These data will help guide the design, analysis, and interpretation of family-based sequencing studies to improve the ability to identify new disease-associated genes.

  7. Comparing the Statistical Fate of Paralogous and Orthologous Sequences.

    Science.gov (United States)

    Massip, Florian; Sheinman, Michael; Schbath, Sophie; Arndt, Peter F

    2016-10-01

    For several decades, sequence alignment has been a widely used tool in bioinformatics. For instance, finding homologous sequences with a known function in large databases is used to get insight into the function of nonannotated genomic regions. Very efficient tools like BLAST have been developed to identify and rank possible homologous sequences. To estimate the significance of the homology, the ranking of alignment scores takes a background model for random sequences into account. Using this model we can estimate the probability to find two exactly matching subsequences by chance in two unrelated sequences. For two homologous sequences, the corresponding probability is much higher, which allows us to identify them. Here we focus on the distribution of lengths of exact sequence matches between protein-coding regions of pairs of evolutionarily distant genomes. We show that this distribution exhibits a power-law tail with an exponent [Formula: see text] Developing a simple model of sequence evolution by substitutions and segmental duplications, we show analytically and computationally that paralogous and orthologous gene pairs contribute differently to this distribution. Our model explains the differences observed in the comparison of coding and noncoding parts of genomes, thus providing a better understanding of statistical properties of genomic sequences and their evolution.

  8. The INSIGHT SEIS VBB Experiment

    Science.gov (United States)

    Tillier, S.; De Raucourt, S.; Lognonne, P. H.; Banerdt, B.; Mimoun, D.; Giardini, D.; Christensen, U. R.; Pike, W. T.; Zweifel, P.; Mance, D.; Bierwirth, M.; Laudet, P.; Perez, R.; Kerjean, L.; Hurst, K. J.; Mocquet, A.; Garcia, R. F.

    2012-12-01

    The SEIS experiment is the primary payload of the Interior Structure investigation using Seismology and Heat Transport (INSIGHT) Mission Proposal, submitted to NASA in the frame of the 2010 Discovery program, and selected for a competitive phase A study, together with two other projects. The objective of the INSIGHT SEIS experiment is the determination of the deep internal structure of Mars. In particular, geophysical parameters of first importance, such as the state (liquid/solid) and size of the core, structure of the mantle, shape of discontinuities, thickness of the crust will be determined by the experiment. It will measure seismic activity in a very broad band of signal, from the tidal frequencies (0.05 mHz) up to the short period frequencies (50 Hz), to address the widest range of scientific questions, from the state of the core to the meteoritic impact and quake rates. The instrument integrates a Very Broad Band (VBB) 3 axis seismometer, completed by another trihedron of MEMS short period seismometers, environmental sensors for pressure, wind and temperature, The sensors will be deployed on the Martian ground by a robotic arm from a Phoenix-type lander platform and protected by a wind and thermal shield. The sensor assembly, which contains all seismic sensors, the leveling system, as well as house-keeping and temperature measurements, will be deployed on the soil in order to allow the best possible mechanical coupling with the ground motion. The wind and thermal shield, the sensors' specific containers (vacuum sphere for VBBs) and a passive thermal compensation system will achieve a very high protection of the VBB against temperature and pressure variations, allowing the sensor to operate in the rough Martian thermal environment while reaching a deection threshold below 10-9 ms-2 Hz-1/2 in the VBB bandwidth. A dedicated electronics will manage the overall experiment and ultra-low noise, space qualified 24 bits A/D converters will perform the acquisition

  9. Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles

    Science.gov (United States)

    Farré, Marta; Narayan, Jitendra; Slavov, Gancho T.; Damas, Joana; Auvil, Loretta; Li, Cai; Jarvis, Erich D.; Burt, David W.; Griffin, Darren K.; Larkin, Denis M.

    2016-01-01

    Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes. PMID:27401172

  10. Takotsubo Syndrome: Insights from Japan.

    Science.gov (United States)

    Akashi, Yoshihiro J; Ishihara, Masaharu

    2016-10-01

    We report the history and new insights of takotsubo syndrome based on the achievements that Japanese researchers have contributed and summarize the evidence originally presented from Japan. Takotsubo syndrome is a newly described heart failure characterized by transient left ventricular dysfunction. We should be aware of this entity as a syndrome, not actual cardiomyopathy. Japanese researchers focus on the experimental approaches for clinical diagnosis and treatment of takotsubo syndrome. As representatives from a country originally naming this syndrome takotsubo, a global registry for takotsubo syndrome including Japan should be established. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  12. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  13. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  14. Oxygen isotope compositions of quartz grains(4-16 μm) from Chinese eolian deposits and their implications for provenance

    Institute of Scientific and Technical Information of China (English)

    HOU; Shengshan(侯圣山); YANG; Shiling(杨石岭); SUN; Jimin(孙继敏); DING; Zhongli(丁仲礼)

    2003-01-01

    Oxygen isotope compositions were measured in quartz grains extracted from a 7.0 Ma red clay-loess sequence at Lingtai and six late Pleistocene loess sediments(Malan loess). Results show that the changes in oxygen isotope compositions of Malan loess are basically controlled by the geochemical characteristics of the source materials, while the effect of weathering process after dust deposition could be minor. The oxygen isotope distribution of quartz grains from red clay at Lingtai is similar to that of the overlying loess-paleosol sequence, thus indicating that the red clay at Lingtai has the same eolian origin as the loess-paleosol deposits. Furthermore, the oscillations of the isotope compositions in 4-16 μm-sized quartz grains may reflect the changes, to some extent, of the climatic systems of the source region.

  15. Application of Bayesian theory in ground settlement of red clay%贝叶斯理论在红粘土地基沉降中的应用

    Institute of Scientific and Technical Information of China (English)

    李珍玉; 李海洋; 王永和; 杨果林

    2009-01-01

    通过对实测样本进行直方图分析和假设检验,得到样本的概率分布,结合先验分布,基于贝叶斯方法得到沉降修正系数的后验分布,对传统的沉降修正系数进行优化.实例分析结果表明:当先验分布为无信息分布时,其后验分布受样本信息的影响较大;当样本信息服从高斯分布时,其后验分布也服从参数为μ和σ的高斯分布,μ值随外荷载增大而减小,σ值呈无明显规律变化;通过贝叶斯方法的优化,修正经验系数考虑了荷载的影响,并且取值的区间明显缩小.%The probability distributions of samples measured are obtained through histogram analysis and hypothesis testing. The posterior distribution coefficients can be gotten based on the Bayesian approach and combined with priori distributions of the settlement modification coefficients. The analysis results show that when the prior distributions are the non-information, the posterior distributions of coefficients are greatly influenced by samples information. When the distributions of samples are approved to obey Gaussian distributions, the posterior distributions of coefficients also obey these distributions, whose parameters are μ and σ, the values of μ are decreased with external loads increasing, and the values of σ have no significant change law. Through the optimization by Bayesian methods, the range of settlement modification coefficients is narrowed, which the influence of external loads are taken into account. 3 tabs, 4 figs, 10 refs.

  16. 高液限红黏土回弹模量试验%Resilent Modulus Test of High Liquid Red Clay

    Institute of Scientific and Technical Information of China (English)

    陈开圣; 胡鑫

    2010-01-01

    土基回弹模量是路面结构设计中一个非常重要的参数,直接关系到路面结构的安全性和经济性.采用室内承载板法分析了高液限红黏土回弹模量与压实度、含水率、稠度和压实度、龄期以及最不利条件下回弹模量与压实度关系.结果表明回弹模量与含水率关系可以用幂函数E=Aw-n形式拟合;回弹模量随压实度的增大而增大;回弹模量与压实度和稠度指标具有良好的相关关系,不同地区不同土质其回归关系是不相同的;回弹模量随着龄期的增长有一定提高.同一压实度时,最不利条件下与最佳含水率条件下高液限红黏土回弹模量的相关关系为:E最不利条件=0.461 5E最佳含水率条件+21.041,R2=0.996 1.

  17. Corrosion Behavior of Copper-Clad Steel Bars with Unclad Two-End Faces for Grounding Grids in the Red Clay Soil

    Science.gov (United States)

    Shao, Yupei; Mu, Miaomiao; Zhang, Bing; Nie, Kaibin; Liao, Qiangqiang

    2017-02-01

    Iron-aluminum oxides in the red soil have a significant impact on the corrosion behavior of the metal for grounding grids. Effects of iron-aluminum oxides on the corrosion behavior of the cross section of copper-clad steel in the red soil have been investigated using electrochemical impedance spectroscopy and Tafel polarization. All the data indicate that the iron-aluminum oxides can promote the corrosion of copper-clad steel in the red soil. The corrosivity of the red soil greatly increases after iron-aluminum oxides are added into the soil. Iron-aluminum oxides promote galvanic corrosion of copper-clad steel and increase the corrosion degree of the center steel layer. The iron-aluminum oxides stimulate corrosion process of copper-clad steel acting as a cathodic depolarizing agent. XRD results further validate that the corrosion products of the copper-clad steel bar mainly consist of Fe3O4 and Cu2O.

  18. Corrosion Behavior of Copper-Clad Steel Bars with Unclad Two-End Faces for Grounding Grids in the Red Clay Soil

    Science.gov (United States)

    Shao, Yupei; Mu, Miaomiao; Zhang, Bing; Nie, Kaibin; Liao, Qiangqiang

    2017-04-01

    Iron-aluminum oxides in the red soil have a significant impact on the corrosion behavior of the metal for grounding grids. Effects of iron-aluminum oxides on the corrosion behavior of the cross section of copper-clad steel in the red soil have been investigated using electrochemical impedance spectroscopy and Tafel polarization. All the data indicate that the iron-aluminum oxides can promote the corrosion of copper-clad steel in the red soil. The corrosivity of the red soil greatly increases after iron-aluminum oxides are added into the soil. Iron-aluminum oxides promote galvanic corrosion of copper-clad steel and increase the corrosion degree of the center steel layer. The iron-aluminum oxides stimulate corrosion process of copper-clad steel acting as a cathodic depolarizing agent. XRD results further validate that the corrosion products of the copper-clad steel bar mainly consist of Fe3O4 and Cu2O.

  19. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  20. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  1. Theory of mind correlates with clinical insight but not cognitive insight in patients with schizophrenia.

    Science.gov (United States)

    Zhang, Qi; Li, Xu; Parker, Giverny J; Hong, Xiao-Hong; Wang, Yi; Lui, Simon S Y; Neumann, David L; Cheung, Eric F C; Shum, David H K; Chan, Raymond C K

    2016-03-30

    Research on the relationship between insight and social cognition, in particular Theory of Mind (ToM), in schizophrenia has yielded mixed findings to date. Very few studies, however, have assessed both clinical insight and cognitive insight when examining their relationships with ToM in schizophrenia. The current study thus investigated the relationship between clinical insight, cognitive insight, and ToM in a sample of 56 patients with schizophrenia and 30 healthy controls. Twenty-seven patients were classified as low in clinical insight according to their scores on the 'insight' item (G12) of the Positive and Negative Syndrome Scale (PANSS). Moreover, cognitive insight and ToM were assessed with the Beck Cognitive Insight Scale (BCIS) and the Yoni task, respectively. The results indicated that patients with poor clinical insight performed worse on tasks of second-order cognitive and affective ToM, while the ToM performance of patients with high clinical insight was equivalent to that of healthy controls. Furthermore, while clinical insight was correlated with ToM and clinical symptoms, cognitive insight did not correlate with clinical insight, ToM, or clinical symptoms. Clinical insight thus appears to be an important factor related to ToM in schizophrenia.

  2. Insight with hands and things.

    Science.gov (United States)

    Vallée-Tourangeau, Frédéric; Steffensen, Sune Vork; Vallée-Tourangeau, Gaëlle; Sirota, Miroslav

    2016-10-01

    Two experiments examined whether different task ecologies influenced insight problem solving. The 17 animals problem was employed, a pure insight problem. Its initial formulation encourages the application of a direct arithmetic solution, but its solution requires the spatial arrangement of sets involving some degree of overlap. Participants were randomly allocated to either a tablet condition where they could use a stylus and an electronic tablet to sketch a solution or a model building condition where participants were given material with which to build enclosures and figurines. In both experiments, participants were much more likely to develop a working solution in the model building condition. The difference in performance elicited by different task ecologies was unrelated to individual differences in working memory, actively open-minded thinking, or need for cognition (Experiment 1), although individual differences in creativity were correlated with problem solving success in Experiment 2. The discussion focuses on the implications of these findings for the prevailing metatheoretical commitment to methodological individualism that places the individual as the ontological locus of cognition.

  3. GOES-R: Satellite Insight

    Science.gov (United States)

    Fitzpatrick, Austin J.; Leon, Nancy J.; Novati, Alexander; Lincoln, Laura K.; Fisher, Diane K.

    2012-01-01

    GOES-R: Satellite Insight seeks to bring awareness of the GOES-R (Geostationary Operational Environmental Satellite -- R Series) satellite currently in development to an audience of all ages on the emerging medium of mobile games. The iPhone app (Satellite Insight) was created for the GOES-R Program. The app describes in simple terms the types of data products that can be produced from GOES-R measurements. The game is easy to learn, yet challenging for all audiences. It includes educational content and a path to further information about GOESR, its technology, and the benefits of the data it collects. The game features action-puzzle game play in which the player must prevent an overflow of data by matching falling blocks that represent different types of GOES-R data. The game adds more different types of data blocks over time, as long as the player can prevent a data overflow condition. Points are awarded for matches, and players can compete with themselves to beat their highest score.

  4. Inferring short-range linkage information from sequencing chromatograms.

    Directory of Open Access Journals (Sweden)

    Bastian Beggel

    Full Text Available Direct Sanger sequencing of viral genome populations yields multiple ambiguous sequence positions. It is not straightforward to derive linkage information from sequencing chromatograms, which in turn hampers the correct interpretation of the sequence data. We present a method for determining the variants existing in a viral quasispecies in the case of two nearby ambiguous sequence positions by exploiting the effect of sequence context-dependent incorporation of dideoxynucleotides. The computational model was trained on data from sequencing chromatograms of clonal variants and was evaluated on two test sets of in vitro mixtures. The approach achieved high accuracies in identifying the mixture components of 97.4% on a test set in which the positions to be analyzed are only one base apart from each other, and of 84.5% on a test set in which the ambiguous positions are separated by three bases. In silico experiments suggest two major limitations of our approach in terms of accuracy. First, due to a basic limitation of Sanger sequencing, it is not possible to reliably detect minor variants with a relative frequency of no more than 10%. Second, the model cannot distinguish between mixtures of two or four clonal variants, if one of two sets of linear constraints is fulfilled. Furthermore, the approach requires repetitive sequencing of all variants that might be present in the mixture to be analyzed. Nevertheless, the effectiveness of our method on the two in vitro test sets shows that short-range linkage information of two ambiguous sequence positions can be inferred from Sanger sequencing chromatograms without any further assumptions on the mixture composition. Additionally, our model provides new insights into the established and widely used Sanger sequencing technology. The source code of our method is made available at http://bioinf.mpi-inf.mpg.de/publications/beggel/linkageinformation.zip.

  5. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity......, Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...

  6. Learning of Chunking Sequences in Cognition and Behavior.

    Science.gov (United States)

    Fonollosa, Jordi; Neftci, Emre; Rabinovich, Mikhail

    2015-11-01

    We often learn and recall long sequences in smaller segments, such as a phone number 858 534 22 30 memorized as four segments. Behavioral experiments suggest that humans and some animals employ this strategy of breaking down cognitive or behavioral sequences into chunks in a wide variety of tasks, but the dynamical principles of how this is achieved remains unknown. Here, we study the temporal dynamics of chunking for learning cognitive sequences in a chunking representation using a dynamical model of competing modes arranged to evoke hierarchical Winnerless Competition (WLC) dynamics. Sequential memory is represented as trajectories along a chain of metastable fixed points at each level of the hierarchy, and bistable Hebbian dynamics enables the learning of such trajectories in an unsupervised fashion. Using computer simulations, we demonstrate the learning of a chunking representation of sequences and their robust recall. During learning, the dynamics associates a set of modes to each information-carrying item in the sequence and encodes their relative order. During recall, hierarchical WLC guarantees the robustness of the sequence order when the sequence is not too long. The resulting patterns of activities share several features observed in behavioral experiments, such as the pauses between boundaries of chunks, their size and their duration. Failures in learning chunking sequences provide new insights into the dynamical causes of neurological disorders such as Parkinson's disease and Schizophrenia.

  7. A deeper understanding of sequence in narrative visualization.

    Science.gov (United States)

    Hullman, Jessica; Drucker, Steven; Henry Riche, Nathalie; Lee, Bongshin; Fisher, Danyel; Adar, Eytan

    2013-12-01

    Conveying a narrative with visualizations often requires choosing an order in which to present visualizations. While evidence exists that narrative sequencing in traditional stories can affect comprehension and memory, little is known about how sequencing choices affect narrative visualization. We consider the forms and reactions to sequencing in narrative visualization presentations to provide a deeper understanding with a focus on linear, 'slideshow-style' presentations. We conduct a qualitative analysis of 42 professional narrative visualizations to gain empirical knowledge on the forms that structure and sequence take. Based on the results of this study we propose a graph-driven approach for automatically identifying effective sequences in a set of visualizations to be presented linearly. Our approach identifies possible transitions in a visualization set and prioritizes local (visualization-to-visualization) transitions based on an objective function that minimizes the cost of transitions from the audience perspective. We conduct two studies to validate this function. We also expand the approach with additional knowledge of user preferences for different types of local transitions and the effects of global sequencing strategies on memory, preference, and comprehension. Our results include a relative ranking of types of visualization transitions by the audience perspective and support for memory and subjective rating benefits of visualization sequences that use parallelism as a structural device. We discuss how these insights can guide the design of narrative visualization and systems that support optimization of visualization sequence.

  8. Deep whole-genome sequencing of 100 southeast Asian Malays.

    Science.gov (United States)

    Wong, Lai-Ping; Ong, Rick Twee-Hee; Poh, Wan-Ting; Liu, Xuanyao; Chen, Peng; Li, Ruoying; Lam, Kevin Koi-Yau; Pillai, Nisha Esakimuthu; Sim, Kar-Seng; Xu, Haiyan; Sim, Ngak-Leng; Teo, Shu-Mei; Foo, Jia-Nee; Tan, Linda Wei-Lin; Lim, Yenly; Koo, Seok-Hwee; Gan, Linda Seo-Hwee; Cheng, Ching-Yu; Wee, Sharon; Yap, Eric Peng-Huat; Ng, Pauline Crystal; Lim, Wei-Yen; Soong, Richie; Wenk, Markus Rene; Aung, Tin; Wong, Tien-Yin; Khor, Chiea-Chuen; Little, Peter; Chia, Kee-Seng; Teo, Yik-Ying

    2013-01-10

    Whole-genome sequencing across multiple samples in a population provides an unprecedented opportunity for comprehensively characterizing the polymorphic variants in the population. Although the 1000 Genomes Project (1KGP) has offered brief insights into the value of population-level sequencing, the low coverage has compromised the ability to confidently detect rare and low-frequency variants. In addition, the composition of populations in the 1KGP is not complete, despite the fact that the study design has been extended to more than 2,500 samples from more than 20 population groups. The Malays are one of the Austronesian groups predominantly present in Southeast Asia and Oceania, and the Singapore Sequencing Malay Project (SSMP) aims to perform deep whole-genome sequencing of 100 healthy Malays. By sequencing at a minimum of 30× coverage, we have illustrated the higher sensitivity at detecting low-frequency and rare variants and the ability to investigate the presence of hotspots of functional mutations. Compared to the low-pass sequencing in the 1KGP, the deeper coverage allows more functional variants to be identified for each person. A comparison of the fidelity of genotype imputation of Malays indicated that a population-specific reference panel, such as the SSMP, outperforms a cosmopolitan panel with larger number of individuals for common SNPs. For lower-frequency (population-level sequencing versus low-pass sequencing, especially in populations that are poorly represented in population-genetics studies.

  9. Learning of Chunking Sequences in Cognition and Behavior.

    Directory of Open Access Journals (Sweden)

    Jordi Fonollosa

    2015-11-01

    Full Text Available We often learn and recall long sequences in smaller segments, such as a phone number 858 534 22 30 memorized as four segments. Behavioral experiments suggest that humans and some animals employ this strategy of breaking down cognitive or behavioral sequences into chunks in a wide variety of tasks, but the dynamical principles of how this is achieved remains unknown. Here, we study the temporal dynamics of chunking for learning cognitive sequences in a chunking representation using a dynamical model of competing modes arranged to evoke hierarchical Winnerless Competition (WLC dynamics. Sequential memory is represented as trajectories along a chain of metastable fixed points at each level of the hierarchy, and bistable Hebbian dynamics enables the learning of such trajectories in an unsupervised fashion. Using computer simulations, we demonstrate the learning of a chunking representation of sequences and their robust recall. During learning, the dynamics associates a set of modes to each information-carrying item in the sequence and encodes their relative order. During recall, hierarchical WLC guarantees the robustness of the sequence order when the sequence is not too long. The resulting patterns of activities share several features observed in behavioral experiments, such as the pauses between boundaries of chunks, their size and their duration. Failures in learning chunking sequences provide new insights into the dynamical causes of neurological disorders such as Parkinson's disease and Schizophrenia.

  10. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  11. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak Syst

  12. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  13. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  14. The neural basis of implicit perceptual sequence learning

    Directory of Open Access Journals (Sweden)

    Freja eGheysen

    2011-11-01

    Full Text Available The present fMRI study investigated the neural areas involved in implicit perceptual sequence learning. To obtain more insight in the functional contributions of the brain areas, we tracked both the behavioral and neural time course of the learning process, using a perceptual serial color matching task. Next, to investigate whether the neural time course was specific for perceptual information, imaging results were compared to the results of implicit motor sequence learning, previously investigated using an identical serial color matching task. Results indicated that implicit sequences can be acquired by at least two neural systems: the caudate nucleus and the hippocampus, having different operating principles. The caudate nucleus contributed to the implicit sequence learning process for perceptual as well as motor information in a similar and gradual way. The hippocampus, on the other hand, was engaged in a much faster learning process which was more pronounced for the motor compared to the perceptual task. Interestingly, the perceptual and motor learning process occurred on a comparable implicit level, suggesting that consciousness is not the main determinant factor dissociating the hippocampal from the caudate learning system. This study is not only the first to successfully and unambiguously compare brain activation between perceptual and motor levels of implicit sequence learning, it also provides new insights into the specific hippocampal and caudate learning function.

  15. Learning the sequence determinants of alternative splicing from millions of random sequences.

    Science.gov (United States)

    Rosenberg, Alexander B; Patwardhan, Rupali P; Shendure, Jay; Seelig, Georg

    2015-10-22

    Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Toward better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of over two million (M) synthetic mini-genes, which include degenerate subsequences totaling over 100 M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing, as well as to gain new mechanistic insights. Our results show that the vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5' splicing also enhance (suppress) exon inclusion in alternative 3' or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.

  16. Topological Pressure and Coding Sequence Density Estimation in the Human Genome

    CERN Document Server

    Koslicki, David

    2011-01-01

    Inspired by concepts from ergodic theory, we give new insight into coding sequence (CDS) density estimation for the human genome. Our approach is based on the introduction and study of topological pressure: a numerical quantity assigned to any finite sequence based on an appropriate notion of `weighted information content'. For human DNA sequences, each codon is assigned a suitable weight, and using a window size of approximately 60,000bp, we obtain a very strong positive correlation between CDS density and topological pressure. The weights are selected by an optimization procedure, and can be interpreted as quantitative data on the relative importance of different codons for the density estimation of coding sequences. This gives new insight into codon usage bias which is an important subject where long standing questions remain open. Inspired again by ergodic theory, we use the weightings on the codons to define a probability measure on finite sequences. We demonstrate that this measure is effective in disti...

  17. Managing complexity insights, concepts, applications

    CERN Document Server

    Helbing, Dirk

    2007-01-01

    Each chapter in Managing Complexity focuses on analyzing real-world complex systems and transferring knowledge from the complex-systems sciences to applications in business, industry and society. The interdisciplinary contributions range from markets and production through logistics, traffic control, and critical infrastructures, up to network design, information systems, social conflicts and building consensus. They serve to raise readers' awareness concerning the often counter-intuitive behavior of complex systems and to help them integrate insights gained in complexity research into everyday planning, decision making, strategic optimization, and policy. Intended for a broad readership, the contributions have been kept largely non-technical and address a general, scientifically literate audience involved in corporate, academic, and public institutions.

  18. Illness Insight and Recovery: How Important is Illness Insight in Peoples’ Recovery Process?

    DEFF Research Database (Denmark)

    Korsbek, Lisa

    2013-01-01

    Topic: This account reflects on the topic of illness insight and recovery. Purpose: The purpose of the account is to clarify our understanding about the importance of illness insight in peoples’ recovery process, especially when relating the question of illness insight to the question of identity....... Sources Used:The writing is based on research literature related to illness insight and on personal recovery experiences.Conclusions and Implications for Practice: It is helpful to consider the integration of the issue of illness insight when addressing the questions and consequences of diagnosis...... in relation to the importance of illness insight in the recovery process....

  19. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  20. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  1. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  2. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  3. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  4. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  5. Sequencing BPS spectra

    Science.gov (United States)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-03-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  6. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  7. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  8. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  9. Evaluation of ddRADseq for reduced representation metagenome sequencing

    Directory of Open Access Journals (Sweden)

    Michael Y. Liu

    2017-09-01

    Full Text Available Background Profiling of microbial communities via metagenomic shotgun sequencing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq protocol for reduced representation metagenome profiling. Methods This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containing DNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

  10. CRISPR interference and priming varies with individual spacer sequences.

    Science.gov (United States)

    Xue, Chaoyou; Seetharam, Arun S; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J J; Severin, Andrew J; Sashital, Dipali G

    2015-12-15

    CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid 'primed' adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR-Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed 'naïve' adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection.

  11. First insights into disassembled "evapotranspiration"

    Science.gov (United States)

    Chormański, Jarosław; Kleniewska, Małgorzata; Berezowski, Tomasz; Szporak-Wasilewska, Sylwia; Okruszko, Tomasz; Szatyłowicz, Jan; Batelaan, Okke

    2015-04-01

    In this work we present an initial data analysis obtained from a complex tool for measuring water fluxes in wetland ecosystems. The tool was designed to quantify processes related to interception storage on plants leafs. The measurements are conducted by combining readings from various instruments, including: eddy covariance tower (EC), field spectrometer, SapFlow system, rain gauges above and under canopy, soil moisture probes and other. The idea of this set-up is to provide continuous measurement of overall water flux from the ecosystem (EC tower), intercepted water volume and timing (field spectrometers), through-fall (rain gauges above and under canopy), transpiration (SapFlow), evaporation and soil moisture (soil moisture probes). Disassembling the water flux to the above components allows giving more insight to the interception related processes and differentiates them fromthe total evapotranspiration. The measurements are conducted in the Upper Biebrza Basin (NE Poland). The study area is part of the valley and is covered by peat soils (mainly peat moss with the exception of areas near the river) and receives no inundations waters of the Biebrza. The plant community of Agrostietum-Carici caninae has a dominant share here creating an up to 0.6 km wide belt along the river. The area is covered also by Caricion lasiocarpae as well as meadows and pastures Molinio-Arrhenatheretea, Phragmitetum communis. Sedges form a hummock pattern characteristic for the sedge communities in natural river valleys with wetland vegetation. The main result of the measurement set-up will be the analyzed characteristics and dynamics of interception storage for sedge ecosystems and a developed methodology for interception monitoring by use spectral reflectance technique. This will give a new insight to processes of evapotranspiration in wetlands and its component transpiration, evaporation from interception and evaporation from soil. Moreover, other important results of this project

  12. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  13. Generic risk insights for Westinghouse and Combustion Engineering pressurized water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Travis, R.; Taylor, J.; Fresco, A. (Brookhaven National Lab., Upton, NY (USA)); Chung, J. (Nuclear Regulatory Commission, Washington, DC (USA))

    1990-11-01

    A methodology has been developed to extract generic risk-based information from probabilistic risk assessments (PRAs) of Westinghouse and Combustion Engineering (CE) pressurized water reactors (PWRs) and apply the insights gained to Westinghouse and Ce plants have not been subjected to a PRA. The available PRAs (five Westinghouse plants and one CE plant) were examined to identify the most probable, i.e., dominant accident sequences at each plant. The goal was to include all sequences which represented at least 80% of core damage frequency. If the same plant specific dominant accident sequence appeared within this boundary in at least two plant PRAs, the sequence was considered to be a representative sequence. Eleven sequences met this definition. From these sequences, the most important component failures and human errors that contributed to each sequence have been prioritized. Guidance is provided to prioritize the representative sequences and modify selected basic events that have been shown to be sensitive to the plant specific design or operating variations of the contributing PRAs. This risk-based guidance can be used for utility and NRC activities including operator training maintenance, design review, and inspections.

  14. Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets

    DEFF Research Database (Denmark)

    Grarup, Niels; Sulem, Patrick; Sandholt, Camilla H;

    2013-01-01

    of the underlying biology of human traits and diseases. Here, we used a large Icelandic whole genome sequence dataset combined with Danish exome sequence data to gain insight into the genetic architecture of serum levels of vitamin B12 (B12) and folate. Up to 22.9 million sequence variants were analyzed in combined...... in serum B12 or folate levels do not modify the risk of developing these conditions. Yet, the study demonstrates the value of combining whole genome and exome sequencing approaches to ascertain the genetic and molecular architectures underlying quantitative trait associations....

  15. Working wonders? investigating insight with magic tricks.

    Science.gov (United States)

    Danek, Amory H; Fraps, Thomas; von Müller, Albrecht; Grothe, Benedikt; Ollinger, Michael

    2014-02-01

    We propose a new approach to differentiate between insight and noninsight problem solving, by introducing magic tricks as problem solving domain. We argue that magic tricks are ideally suited to investigate representational change, the key mechanism that yields sudden insight into the solution of a problem, because in order to gain insight into the magicians' secret method, observers must overcome implicit constraints and thus change their problem representation. In Experiment 1, 50 participants were exposed to 34 different magic tricks, asking them to find out how the trick was accomplished. Upon solving a trick, participants indicated if they had reached the solution either with or without insight. Insight was reported in 41.1% of solutions. The new task domain revealed differences in solution accuracy, time course and solution confidence with insight solutions being more likely to be true, reached earlier, and obtaining higher confidence ratings. In Experiment 2, we explored which role self-imposed constraints actually play in magic tricks. 62 participants were presented with 12 magic tricks. One group received verbal cues, providing solution relevant information without giving the solution away. The control group received no informative cue. Experiment 2 showed that participants' constraints were suggestible to verbal cues, resulting in higher solution rates. Thus, magic tricks provide more detailed information about the differences between insightful and noninsightful problem solving, and the underlying mechanisms that are necessary to have an insight. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Mining Login Data for Actionable Student Insight

    Science.gov (United States)

    Agnihotri, Lalitha; Aghababyan, Ani; Mojarad, Shirin; Riedesel, Mark; Essa, Alfred

    2015-01-01

    Student login data is a key resource for gaining insight into their learning experience. However, the scale and the complexity of this data necessitate a thorough exploration to identify potential actionable insights, thus rendering it less valuable compared to student achievement data. To compensate for the underestimation of login data…

  17. Course of insight in manic episode

    Directory of Open Access Journals (Sweden)

    A Kumar

    2013-01-01

    Full Text Available Background: Insight is an important factor associated with non compliance and poor outcome. Poor level of insight has been described as a characteristic in patients with acute bipolar disorder with more unawareness in social consequences with increasing severity in manic episode. Aim: Main aim of study was to see the baseline and longitudinal relationship between dimensions of insight with improvement in psychopathology. Setting and Design: Forty four patients diagnosed with mania, were selected from an inpatient setting at Institute of Mental Health and Hospital, Agra with mean age of 31.07(±9.00 years. They were assessed at base line and were followed up weekly or psychopathology and insight. Materials and Methods: The Young′s mania rating scale for psychopathology and insight was assessed on three dimensions of SUMD. Results: Twenty five patients eventually completed the study. There was a positive correlation with global insight and with psychopathology consistent in longitudinal follow-up (P<0.05, but not correlating for awareness for achieved effect of medication and social consequences. Linear regression showed a positive relationship at the first and second week of assessment of SUMD and YMRS scores (P=0.001; 0.019. Conclusion: Improvement in insight is graded in a manic episode as compared to psychopathology. There is slower improvement in awareness of social consequences of mental disorder. It means that improvement in psychopathology may not necessarily indicate remission and need further supervision to improve insight and hence monitoring.

  18. Towards Responsible Steel: Preliminary Insights

    Directory of Open Access Journals (Sweden)

    Suzanne Benn

    2014-03-01

    Full Text Available This paper examines the structures and processes underpinning the attempt of the Australian steel industry to establish a certification scheme for Responsible Steel. We take it as a case example of how collective action and collaboration along a supply chain has the potential to be a win-win situation for the environment and for the competitiveness of an industry sector. The paper identifies the drivers that have prompted key stakeholders from all major sectors of the Australian steel product life cycle from mining through steel manufacturing, processing, product fabrication, use and re-use, and recycling to collaborate in the establishment of the Steel Stewardship Forum (SSF, the structure established to lead the development of the certification scheme. The development of this initiative is indicative of the wider shift to sustainability-related certification schemes as a means of garnering legitimacy and market advantage and provides detailed insights into both the drivers for and the challenges associated with such initiatives. Findings from the paper contribute to our understanding of the shift to sustainable supply chains as it is interpreted through institutional and institutional entrepreneurship theory.

  19. A