Optimization Method of a Low Cost, High Performance Ceramic Proppant by Orthogonal Experimental Design

NASA Astrophysics Data System (ADS)

Zhou, Y.; Tian, Y. M.; Wang, K. Y.; Li, G.; Zou, X. W.; Chai, Y. S.

2017-09-01

This study focused on optimization method of a ceramic proppant material with both low cost and high performance that met the requirements of Chinese Petroleum and Gas Industry Standard (SY/T 5108-2006). The orthogonal experimental design of L9(34) was employed to study the significance sequence of three factors, including weight ratio of white clay to bauxite, dolomite content and sintering temperature. For the crush resistance, both the range analysis and variance analysis reflected the optimally experimental condition was weight ratio of white clay to bauxite=3/7, dolomite content=3 wt.%, temperature=1350°C. For the bulk density, the most important factor was the sintering temperature, followed by the dolomite content, and then the ratio of white clay to bauxite.

Crater palaeolakes in the Tibesti mountains (Central Sahara, North Chad) - New insights into past Saharan climates

NASA Astrophysics Data System (ADS)

Kröpelin, Stefan; Dinies, Michèle; Sylvestre, Florence; Hoelzmann, Philipp

2016-04-01

For the first time continuous lacustrine sections were sampled from the volcanic Tibesti Mountains (Chad): In the 900 m deep crater of Trou au Natron at Pic Toussidé (3,315 m a.s.l.) and from the 800 m deep Era Kohor, the major sub-caldera of Emi Koussi (3,445 m a.s.l.). The remnant diatomites on their slopes are located 360 m (Trou au Natron) and 125 m (Era Kohor) above the present day bottom of the calderas. These sediments from highly continental positions in the central Sahara are keys for the reconstruction of the last climatic cycles (Kröpelin et al. 2015). We report first results from sedimentary-geochemical (total organic and total inorganic carbon contents; total nitrogen; major elements; mineralogy) and palynological analyses for palaeo-environmental interpretations. The diatomites from the Trou au Natron comprise 330 cm of mostly calcitic sediments with relatively low organic carbon (<2.5 %) and strongly varying aragonite and gypsum contents. Major elements (Ca, Fe, K, Mg, Mn, Na, P, S, Sr), elemental ratios (Sr/Ca, Mg/Ca, Fe/Mn) and the mineralogy are used to interpret the lake's salinity, productivity and ecological conditions. Trilete spores are preserved throughout the sequence, probably reflecting local moss/fern stands. Regional pollen rain-e.g. grasses and wormwood-is scarcely represented. Golden algae dominate in the lower section. The results of the first palynological samples suggest a small sedimentation basin. Two 14C-dated charcoals out of the upper part of the section indicate mid-Holocene ages and a linear extrapolation based on a sediment accumulation rate of 1.4mma-1 would lead to tentative dates of ~8650 cal a BP for basal lacustrine sediments and ~4450 cal a BP for the cessation of this lacustrine sequence. The diatomites from the Era Kohor reflect a suite of sections that in total sum up to 145 cm of mostly silica-based sediments with very low carbon contents (< 2% TC). Calcite dominated sediments are only present in the topmost 15 cm. Grasses and wormword are dominating throughout the sequence, probably reflecting the main constituents of the regional vegetation. Cattail (Typha/Sparganium) and especially milfoil (Myriophyllum) are recorded abundantly and continuously throughout the sequence. In combination with green algae like Pediastrum the first pollen spectra indicate a lake shore and shallow fresh water vegetation. This seems to be in agreement with the preliminary observations of the fossil diatom contents, which show a diatom flora mainly composed of benthic and tychoplanktonic species, indicating a shallow freshwater lake. Both diatomite sequences thus suggest shallow lakes throughout their deposition-whether this is due to their marginal position within the large calderas and/or shallow waters covered the entire calderas is an outstanding question that will be addressed with planned additional investigations. Kröpelin, S. etal (2015): New data on the unresolved paradox of the Tibesti crater paleolakes (Central Sahara, North Chad). Abstract #64322 AGU-Fall-Meeting-2015.

enoLOGOS: a versatile web tool for energy normalized sequence logos

PubMed Central

Workman, Christopher T.; Yin, Yutong; Corcoran, David L.; Ideker, Trey; Stormo, Gary D.; Benos, Panayiotis V.

2005-01-01

enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a set of aligned sequences. Each position of the alignment is represented by a column of stacked symbols with its total height reflecting the information content in this position. Currently, the available web servers are able to create logo images from a set of aligned sequences, but none of them generates weighted sequence logos directly from energy measurements or other sources. With the advent of high-throughput technologies for estimating the contact energy of different DNA sequences, tools that can create logos directly from binding affinity data are useful to researchers. enoLOGOS generates sequence logos from a variety of input data, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence, a unique feature of this tool. Another web interface for our software, C2H2-enoLOGOS, generates logos for the DNA-binding preferences of the C2H2 zinc-finger transcription factor family members. enoLOGOS and C2H2-enoLOGOS are accessible over the web at . PMID:15980495

Lactobacillus buchneri genotyping on the basis of clustered regularly interspaced short palindromic repeat (CRISPR) locus diversity.

PubMed

Briner, Alexandra E; Barrangou, Rodolphe

2014-02-01

Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.

Revealing representational content with pattern-information fMRI--an introductory guide.

PubMed

Mur, Marieke; Bandettini, Peter A; Kriegeskorte, Nikolaus

2009-03-01

Conventional statistical analysis methods for functional magnetic resonance imaging (fMRI) data are very successful at detecting brain regions that are activated as a whole during specific mental activities. The overall activation of a region is usually taken to indicate involvement of the region in the task. However, such activation analysis does not consider the multivoxel patterns of activity within a brain region. These patterns of activity, which are thought to reflect neuronal population codes, can be investigated by pattern-information analysis. In this framework, a region's multivariate pattern information is taken to indicate representational content. This tutorial introduction motivates pattern-information analysis, explains its underlying assumptions, introduces the most widespread methods in an intuitive way, and outlines the basic sequence of analysis steps.

Inability of Prevotella bryantii to Form a Functional Shine-Dalgarno Interaction Reflects Unique Evolution of Ribosome Binding Sites in Bacteroidetes

PubMed Central

Accetto, Tomaž; Avguštin, Gorazd

2011-01-01

The Shine-Dalgarno (SD) sequence is a key element directing the translation to initiate at the authentic start codons and also enabling translation initiation to proceed in 5′ untranslated mRNA regions (5′-UTRs) containing moderately strong secondary structures. Bioinformatic analysis of almost forty genomes from the major bacterial phylum Bacteroidetes revealed, however, a general absence of SD sequence, drop in GC content and consequently reduced tendency to form secondary structures in 5′-UTRs. The experiments using the Prevotella bryantii TC1-1 expression system were in agreement with these findings: neither addition nor omission of SD sequence in the unstructured 5′-UTR affected the level of the reporter protein, non-specific nuclease NucB. Further, NucB level in P. bryantii TC1-1, contrary to hMGFP level in Escherichia coli, was five times lower when SD sequence formed part of the secondary structure with a folding energy -5,2 kcal/mol. Also, the extended SD sequences did not affect protein levels as in E. coli. It seems therefore that a functional SD interaction does not take place during the translation initiation in P. bryanttii TC1-1 and possibly other members of phylum Bacteroidetes although the anti SD sequence is present in 16S rRNA genes of their genomes. We thus propose that in the absence of the SD sequence interaction, the selection of genuine start codons in Bacteroidetes is accomplished by binding of ribosomal protein S1 to unstructured 5′-UTR as opposed to coding region which is inaccessible due to mRNA secondary structure. Additionally, we found that sequence logos of region preceding the start codons may be used as taxonomical markers. Depending on whether complete sequence logo or only part of it, such as information content and base proportion at specific positions, is used, bacterial genera or families and in some cases even bacterial phyla can be distinguished. PMID:21857964

Centennial-scale records of total organic carbon in sediment cores from the South Yellow Sea, China

NASA Astrophysics Data System (ADS)

Zhu, Qing; Lin, Jia; Hong, Yuehui; Yuan, Lirong; Liu, Jinzhong; Xu, Xiaoming; Wang, Jianghai

2018-01-01

Global carbon cycling is a significant factor that controls climate change. The centennial-scale variations in total organic carbon (TOC) contents and its sources in marginal sea sediments may reflect the influence of human activities on global climate change. In this study, two fine-grained sediment cores from the Yellow Sea Cold Water Mass of the South Yellow Sea were used to systematically determine TOC contents and stable carbon isotope ratios. These results were combined with previous data of black carbon and 210Pb dating from which we reconstructed the centennial-scale initial sequences of TOC, terrigenous TOC (TOCter) and marine autogenous TOC (TOCmar) after selecting suitable models to correct the measured TOC (TOCcor). These sequences showed that the TOCter decreased with time in the both cores while the TOCmar increased, particularly the rapid growth in core H43 since the late 1960s. According to the correlation between the Huanghe (Yellow) River discharge and the TOCcor, TOCter, or TOCmar, we found that the TOCter in the two cores mainly derived from the Huanghe River and was transported by it, and that higher Huanghe River discharge could strengthen the decomposition of TOCmar. The newly obtained initial TOC sequences provide important insights into the interaction between human activities and natural processes.

Correlation between MCAT biology content specifications and topic scope and sequence of general education college biology textbooks.

PubMed

Rissing, Steven W

2013-01-01

Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing general education (GE) graduation requirements. Biology textbooks for these three audiences present a topic scope and sequence that correlates with the topic scope and importance ratings of the biology content specifications for the MCAT regardless of the intended audience. Texts for "nonmajors," GE courses appear derived directly from their publisher's majors text. Topic scope and sequence of GE texts reflect those of "their" majors text and, indirectly, the MCAT. MCAT term density of GE texts equals or exceeds that of their corresponding majors text. Most American universities require a GE curriculum to promote a core level of academic understanding among their graduates. This includes civic scientific literacy, recognized as an essential competence for the development of public policies in an increasingly scientific and technological world. Deriving GE biology and related science texts from majors texts designed to meet very different learning objectives may defeat the scientific literacy goals of most schools' GE curricula.

Correlation between MCAT Biology Content Specifications and Topic Scope and Sequence of General Education College Biology Textbooks

PubMed Central

Rissing, Steven W.

2013-01-01

Most American colleges and universities offer gateway biology courses to meet the needs of three undergraduate audiences: biology and related science majors, many of whom will become biomedical researchers; premedical students meeting medical school requirements and preparing for the Medical College Admissions Test (MCAT); and students completing general education (GE) graduation requirements. Biology textbooks for these three audiences present a topic scope and sequence that correlates with the topic scope and importance ratings of the biology content specifications for the MCAT regardless of the intended audience. Texts for “nonmajors,” GE courses appear derived directly from their publisher's majors text. Topic scope and sequence of GE texts reflect those of “their” majors text and, indirectly, the MCAT. MCAT term density of GE texts equals or exceeds that of their corresponding majors text. Most American universities require a GE curriculum to promote a core level of academic understanding among their graduates. This includes civic scientific literacy, recognized as an essential competence for the development of public policies in an increasingly scientific and technological world. Deriving GE biology and related science texts from majors texts designed to meet very different learning objectives may defeat the scientific literacy goals of most schools’ GE curricula. PMID:24006392

Exploring the role of curriculum materials to support teachers in science education reform

NASA Astrophysics Data System (ADS)

Schneider, Rebecca M.

2001-07-01

For curriculum materials to succeed in promoting large-scale science education reform, teacher learning must be supported. Materials were designed to reflect desired reforms and to be educative by including detailed lesson descriptions that addressed necessary content, pedagogy, and pedagogical content knowledge for teachers. The goal of this research was to describe how such materials contributed to classroom practices. As part of an urban systemic reform effort, four middle school teachers' initial enactment of an inquiry-based science unit on force and motion were videotaped. Enactments focused on five lesson sequences containing experiences with phenomena, investigation, technology use, or artifact development. Each sequence spanned three to five days across the 10-week unit. For each lesson sequence, intended and actual enactment were compared using ratings of (1) accuracy and completeness of science ideas presented, (2) amount student learning opportunities, similarity of learning opportunities with those intended, and quality of adaptations , and (3) amount of instructional supports offered, appropriateness of instructional supports and source of ideas for instructional supports. Ratings indicated two teachers' enactments were consistent with intentions and two teachers' enactments were not. The first two were in school contexts supportive of the reform. They purposefully used the materials to guide enactment, which tended to be consistent with standards-based reform. They provided students opportunities to use technology tools, design investigations, and discuss ideas. However, enactment ratings were less reflective of curriculum intent when challenges were greatest, such as when teachers attempted to present challenging science ideas, respond to students' ideas, structure investigations, guide small-group discussions, or make adaptations. Moreover, enactment ratings were less consistent in parts of lessons where materials did not include lesson specific educative supports for teachers. Overall, findings indicate curriculum materials that include detailed descriptions of lessons accompanied by educative features can help teachers with enactment. Therefore, design principles to improve materials to support teachers in reform are suggested. However, results also demonstrate materials alone are not sufficient to create intended enactments; reform efforts must include professional development in content and pedagogy and efforts to create systemic change in context and policy to support teacher learning and classroom enactment.

Lactobacillus buchneri Genotyping on the Basis of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Locus Diversity

PubMed Central

Briner, Alexandra E.

2014-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel “spacers” that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5′-AAAA-3′. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri. PMID:24271175

Distribution and variation of the inorganic fraction of Devonian to Bashkirian black shales in the north-western part of the Dniepr-Donets Basin, Ukraine

NASA Astrophysics Data System (ADS)

Wegerer, Eva; Sachsenhofer, Reinhard; Misch, David; Aust, Nicolai

2016-04-01

Mineralogical data of 112 core samples from 12 wells are used to investigate lateral and vertical variations in the lithofacies of Devonian to Bashkirian black shales in the north-western part of the Dniepr-Donets-Basin. Sulphur and carbonate contents as well as organic geochemical parameters, including TOC and Hydrogen Index have been determined on the same sample set within the frame of an earlier study (Sachsenhofer et al. 2010). This allows the correlation of inorganic and organic composition of the black shales. Aims of the study are to distinguish between detrital and authigenic minerals, to relate the lithofacies of the black shales with the tectono-stratigraphic sequences of the Dniepr-Donets Basin, to contribute to the reconstruction of the depositional environment and to relate diagenetic processes with the thermal history of the basin. Mineral compositions were determined primarily using XRD-measurements applying several measurement procedures, e.g. chemical and temperature treatment, and specific standards. Major differences exist in the mineralogical composition of the black shales. For example, clay mineral contents range from less than 20 to more than 80 Vol%. Kaolinite contents are significantly higher in rocks with a Tournaisian or Early Visean age than in any other stratigraphic unit. This is also true for two Lower Visean coal samples from the shallow north-westernmost part of the basin. Chlorite contents reach maxima in uppermost Visean and overlying rocks. Quartz contents are often high in Upper Visean rocks and reach maxima in Bashkirian units. Feldspar-rich rocks are observed in Devonian sediments from the north-western part of the study area and may reflect the proximity to a sediment source. Carbonate contents are typically low, but reach very high values in some Tournaisian, Lower Visean and Serpukhovian samples. Pyrite contents reach maxima along the basin axis in Tournaisian and Visean rocks reflecting anoxic conditions. Mixed layer minerals are dominated by illite. Their presence in samples from depth exceeding 5 km reflects the low thermal overprint of Paleozoic rocks in the north-western Dniepr-Donets-Basin.

Covalent attachment of TAT peptides and thiolated alkyl molecules on GaAs surfaces.

PubMed

Cho, Youngnam; Ivanisevic, Albena

2005-07-07

Four TAT peptide fragments were used to functionalize GaAs surfaces by adsorption from solution. In addition, two well-studied alkylthiols, mercaptohexadecanoic acid (MHA) and 1-octadecanethiol (ODT) were utilized as references to understand the structure of the TAT peptide monolayer on GaAs. The different sequences of TAT peptides were employed in recognition experiments where a synthetic RNA sequence was tested to verify the specific interaction with the TAT peptide. The modified GaAs surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). AFM studies were used to compare the surface roughness before and after functionalization. XPS allowed us to characterize the chemical composition of the GaAs surface and conclude that the monolayers composed of different sequences of peptides have similar surface chemistries. Finally, FT-IRRAS experiments enabled us to deduce that the TAT peptide monolayers have a fairly ordered and densely packed alkyl chain structure. The recognition experiments showed preferred interaction of the RNA sequence toward peptides with high arginine content.

Geology of natural gas reservoir: Upper Travis Peak Formation, western flank of Sabine Uplift, east Texas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fracasso, M.A.

The Travis Peak Formation (Lower Cretaceous) in the eastern East Texas basin represents a sand-rich, fluvial-deltaic depositional system. This lobate, high-constructive deltaic system prograded radially to the southeast from an Upshur County locus. Regional studies of the Travis Peak established a threefold internal stratigraphic framework: a middle sand-rich fluvial and delta-plain sequence is gradationally overlain and underlain by a marine-influenced delta-fringe zone with a higher mud content. The entire Travis Peak succession thins over the Bethany dome on the western flank of the Sabine uplift. However, the delta-fringe sequences are relatively thicker over the structure because of a disproportionately greatermore » thinning of the middle sandy fluvial-deltaic sequence. Lesser sand deposition over the Bethany dome reflects an active structural control over facies distribution. Gas production in the Bethany field and surrounding area is concentrated in thin zones (5-15 ft) of the upper delta-fringe sequence. This distribution probably reflects the increased abundance of mudstone beds in the upper delta-fringe interval, which may have served as source rocks or barriers to upward gas migration, or as both. The predominant trapping mechanism in this region is stratigraphic sand pinch-out in a structurally updip direction on the flanks of major structures. Studies of core and closely spaced electric logs west of the Bethany dome help define the depositional systems in the upper delta-fringe producing interval. This sequence comprises a complex mosaic of continental and marine facies, and exhibits an overall upward trend of increasing marine influence that spans a gradual transition into transgressive carbonates of the Sligo Formation.« less

The association of personal semantic memory to identity representations: insight into higher-order networks of autobiographical contents.

PubMed

Grilli, Matthew D

2017-11-01

Identity representations are higher-order knowledge structures that organise autobiographical memories on the basis of personality and role-based themes of one's self-concept. In two experiments, the extent to which different types of personal semantic content are reflected in these higher-order networks of memories was investigated. Healthy, young adult participants generated identity representations that varied in remoteness of formation and verbally reflected on these themes in an open-ended narrative task. The narrative responses were scored for retrieval of episodic, experience-near personal semantic and experience-far (i.e., abstract) personal semantic contents. Results revealed that to reflect on remotely formed identity representations, experience-far personal semantic contents were retrieved more than experience-near personal semantic contents. In contrast, to reflect on recently formed identity representations, experience-near personal semantic contents were retrieved more than experience-far personal semantic contents. Although episodic memory contents were retrieved less than both personal semantic content types to reflect on remotely formed identity representations, this content type was retrieved at a similar frequency as experience-far personal semantic content to reflect on recently formed identity representations. These findings indicate that the association of personal semantic content to identity representations is robust and related to time since acquisition of these knowledge structures.

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes.

PubMed

Bazak, Lily; Haviv, Ami; Barak, Michal; Jacob-Hirsch, Jasmine; Deng, Patricia; Zhang, Rui; Isaacs, Farren J; Rechavi, Gideon; Li, Jin Billy; Eisenberg, Eli; Levanon, Erez Y

2014-03-01

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.

Using a color-coded ambigraphic nucleic acid notation to visualize conserved palindromic motifs within and across genomes

PubMed Central

2014-01-01

Background Ambiscript is a graphically-designed nucleic acid notation that uses symbol symmetries to support sequence complementation, highlight biologically-relevant palindromes, and facilitate the analysis of consensus sequences. Although the original Ambiscript notation was designed to easily represent consensus sequences for multiple sequence alignments, the notation’s black-on-white ambiguity characters are unable to reflect the statistical distribution of nucleotides found at each position. We now propose a color-augmented ambigraphic notation to encode the frequency of positional polymorphisms in these consensus sequences. Results We have implemented this color-coding approach by creating an Adobe Flash® application ( http://www.ambiscript.org) that shades and colors modified Ambiscript characters according to the prevalence of the encoded nucleotide at each position in the alignment. The resulting graphic helps viewers perceive biologically-relevant patterns in multiple sequence alignments by uniquely combining color, shading, and character symmetries to highlight palindromes and inverted repeats in conserved DNA motifs. Conclusion Juxtaposing an intuitive color scheme over the deliberate character symmetries of an ambigraphic nucleic acid notation yields a highly-functional nucleic acid notation that maximizes information content and successfully embodies key principles of graphic excellence put forth by the statistician and graphic design theorist, Edward Tufte. PMID:24447494

In Vivo Visualization of Alzheimer’s Amyloid Plaques by MRI in Transgenic Mice Without a Contrast Agent

PubMed Central

Jack, Clifford R.; Garwood, Michael; Wengenack, Thomas M.; Borowski, Bret; Curran, Geoffrey L.; Lin, Joseph; Adriany, Gregor; Grohn, Olli H.J.; Grimm, Roger; Poduslo, Joseph F.

2009-01-01

One of the cardinal pathologic features of Alzheimer’s disease (AD) is formation of senile, or amyloid, plaques. Transgenic mice have been developed that express one or more of the genes responsible for familial AD in humans. Doubly transgenic mice develop “human-like” plaques, providing a mechanism to study amyloid plaque biology in a controlled manner. Imaging of labeled plaques has been accomplished with other modalities, but only MRI has sufficient spatial and contrast resolution to visualize individual plaques non-invasively. Methods to optimize visualization of plaques in vivo in transgenic mice at 9.4 T using a spin echo sequence based on adiabatic pulses are described. Preliminary results indicate that a spin echo acquisition more accurately reflects plaque size, while a T2* weighted gradient echo sequence reflects plaque iron content not plaque size. In vivo MRI – ex vivo MRI – in vitro histological correlations are provided. Histologically verified plaques as small as 50 μm in diameter were visualized in the living animal. To our knowledge this work represents the first demonstration of non-invasive in vivo visualization of individual AD plaques without the use of a contrast agent. PMID:15562496

QTL mapping of soybean oil content for marker-assisted selection in plant breeding program.

PubMed

Leite, D C; Pinheiro, J B; Campos, J B; Di Mauro, A O; Unêda-Trevisoli, S H

2016-03-18

The present study was undertaken to detect and map the quantitative trait loci (QTL) related to soybean oil content. We used 244 progenies derived from a bi-parental cross of the Lineage 69 (from Universidade Estadual Paulista "Júlio de Mesquita Filho"/Faculdade de Ciências Agrárias e Veterinárias - Breeding Program) and Tucunaré cultivar. A total of 358 simple sequence repeat (SSR; microsatellite) markers were used to investigate the polymorphism between the parental lines, and for the polymorphic lines all the F2 individuals were tested. Evaluation of the oil content and phenotype was performed with the aid of a Tango equipment by near infra-red reflectance spectroscopy, using single F2 seeds and F2:3 progenies, in triplicate. The data were analyzed by QTL Cartographer program for 56 SSR polymorphic markers. Two oil-content related QTLs were detected on K and H linkage groups. The total phenotypic variation explained by QTLs ranged from 7.8 to 46.75% for oil content. New QTLs were identified for the oil content in addition to those previously identified in other studies. The results reported in this study show that regions different from those already known could be involved in the genetic control of soybean oil content.

Image Recommendation Algorithm Using Feature-Based Collaborative Filtering

NASA Astrophysics Data System (ADS)

Kim, Deok-Hwan

As the multimedia contents market continues its rapid expansion, the amount of image contents used in mobile phone services, digital libraries, and catalog service is increasing remarkably. In spite of this rapid growth, users experience high levels of frustration when searching for the desired image. Even though new images are profitable to the service providers, traditional collaborative filtering methods cannot recommend them. To solve this problem, in this paper, we propose feature-based collaborative filtering (FBCF) method to reflect the user's most recent preference by representing his purchase sequence in the visual feature space. The proposed approach represents the images that have been purchased in the past as the feature clusters in the multi-dimensional feature space and then selects neighbors by using an inter-cluster distance function between their feature clusters. Various experiments using real image data demonstrate that the proposed approach provides a higher quality recommendation and better performance than do typical collaborative filtering and content-based filtering techniques.

The evolving content of meals in Great Britain. Results of a survey in 2012 in comparison with the 1950s.

PubMed

Yates, Luke; Warde, Alan

2015-01-01

This paper examines food eaten at meals in Great Britain. It presents findings about contemporary meal content, reflecting on the relationship between meal content and occasion, and makes comparison with an earlier study. Drawing on an online survey (N = 2784), conducted in September 2012, it describes the food consumed at daily eating events in terms of content, volume and complexity, common components and combinations, and sequence. Socio-demographic and economic differences are examined. Conceptual tools for analysing the association between food content and meal occasions are refined. The paper first explores the regularity of meal patterns. This is followed by description of the contours of the three principal daily eating events, with a brief section on snacks. The paper interprets distinctive features of current patterns by way of comparison with a similar study of eating habits in the 1950s. Findings reveal morning and midday eating events as simple and homogeneous in content, particularly on weekdays, with respondents breakfasting on cereal or toast, and lunching on sandwiches. Evening meals are more complex, structured and varied in content. Common patterns and systematic differentiation can be discerned, particularly across age cohort. Significant historical change can also be observed in relation to meal content and, to a lesser extent, meal pattern. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recognition, correlation, and hierarchical stacking patterns of cycles in the Ferry Lake - Uppe Glen Rose, East Texas Basin: Implications for grainstone reservoir distribution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fitchen, W.M.; Bebout, D.G.; Hoffman, C.L.

1994-12-31

Core descriptions and regional log correlation/interpretation of Ferry Lake-Upper Glen Rose strata in the East Texas Basin exhibit the uniformity of cyclicity in these shelf units. The cyclicity is defined by an upward decrease in shale content within each cycle accompanied by an upward increase in anhydrite (Ferry Lake) or carbonate (Upper Glen Rose). Core-to-log calibration of facies indicates that formation resistivity is inversely proportional to shale content and thus is a potential proxy for facies identification beyond core control. Cycles (delineated by resistivity log patterns) were correlated for 90 mi across the shelf; they show little change in logmore » signature despite significant updip thinning due to the regional subsidence gradient. The Ferry-Lake-Upper Glen Rose intervals is interpreted as a composite sequence composed of 13 high-frequency sequences (4 in the Ferry Lake and 9 in the Upper Glen Rose). High-frequency sequences contain approximately 20 ({+-}5) cycles; in the Upper Glen Rose, successive cycles exhibit decreasing proportions of shale and increasing proportions of grain-rich carbonate. High-frequency sequences were terminated by terrigenous inundation, possibly preceded by subaerial exposure. Cycle and high-frequency sequence composition is interpreted to reflect composite, periodic(?) fluctuations is terrigeneous dilution from nearby source areas. Grainstones typically occur (stratigraphically) within the upper cycles of high-frequency sequences, where terrigeneous dilution and turbidity were least and potential for carbonate production and shoaling was greatest. Published mid-Cretaceous geographic reconstructions and climate models suggest that precipitation and runoff in the area were controlled by the seasonal amplitude in solar insolation. In this model, orbital variations, combined with subsidence, hydrography, and bathymetry, were in primary controls on Ferry Lake-Upper Glen Rose facies architecture and stratigraphic development.« less

Methods for sequencing GC-rich and CCT repeat DNA templates

DOEpatents

Robinson, Donna L.

2007-02-20

The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins.

PubMed

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N

2014-03-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea.

Molecular mechanisms of adaptation emerging from the physics and evolution of nucleic acids and proteins

PubMed Central

Goncearenco, Alexander; Ma, Bin-Guang; Berezovsky, Igor N.

2014-01-01

DNA, RNA and proteins are major biological macromolecules that coevolve and adapt to environments as components of one highly interconnected system. We explore here sequence/structure determinants of mechanisms of adaptation of these molecules, links between them, and results of their mutual evolution. We complemented statistical analysis of genomic and proteomic sequences with folding simulations of RNA molecules, unraveling causal relations between compositional and sequence biases reflecting molecular adaptation on DNA, RNA and protein levels. We found many compositional peculiarities related to environmental adaptation and the life style. Specifically, thermal adaptation of protein-coding sequences in Archaea is characterized by a stronger codon bias than in Bacteria. Guanine and cytosine load in the third codon position is important for supporting the aerobic life style, and it is highly pronounced in Bacteria. The third codon position also provides a tradeoff between arginine and lysine, which are favorable for thermal adaptation and aerobicity, respectively. Dinucleotide composition provides stability of nucleic acids via strong base-stacking in ApG dinucleotides. In relation to coevolution of nucleic acids and proteins, thermostability-related demands on the amino acid composition affect the nucleotide content in the second codon position in Archaea. PMID:24371267

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment.

PubMed

Kelley, Joanna L; Peyton, Justin T; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M; Yee, Muh-Ching; Johnston, J Spencer; Bustamante, Carlos D; Lee, Richard E; Denlinger, David L

2014-08-12

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment.

Reading the Second Code: Mapping Epigenomes to Understand Plant Growth, Development, and Adaptation to the Environment[OA

PubMed Central

2012-01-01

We have entered a new era in agricultural and biomedical science made possible by remarkable advances in DNA sequencing technologies. The complete sequence of an individual’s set of chromosomes (collectively, its genome) provides a primary genetic code for what makes that individual unique, just as the contents of every personal computer reflect the unique attributes of its owner. But a second code, composed of “epigenetic” layers of information, affects the accessibility of the stored information and the execution of specific tasks. Nature’s second code is enigmatic and must be deciphered if we are to fully understand and optimize the genetic potential of crop plants. The goal of the Epigenomics of Plants International Consortium is to crack this second code, and ultimately master its control, to help catalyze a new green revolution. PMID:22751210

Compact genome of the Antarctic midge is likely an adaptation to an extreme environment

PubMed Central

Kelley, Joanna L.; Peyton, Justin T.; Fiston-Lavier, Anna-Sophie; Teets, Nicholas M.; Yee, Muh-Ching; Johnston, J. Spencer; Bustamante, Carlos D.; Lee, Richard E.; Denlinger, David L.

2014-01-01

The midge, Belgica antarctica, is the only insect endemic to Antarctica, and thus it offers a powerful model for probing responses to extreme temperatures, freeze tolerance, dehydration, osmotic stress, ultraviolet radiation and other forms of environmental stress. Here we present the first genome assembly of an extremophile, the first dipteran in the family Chironomidae, and the first Antarctic eukaryote to be sequenced. At 99 megabases, B. antarctica has the smallest insect genome sequenced thus far. Although it has a similar number of genes as other Diptera, the midge genome has very low repeat density and a reduction in intron length. Environmental extremes appear to constrain genome architecture, not gene content. The few transposable elements present are mainly ancient, inactive retroelements. An abundance of genes associated with development, regulation of metabolism and responses to external stimuli may reflect adaptations for surviving in this harsh environment. PMID:25118180

Response of bacterial pdo1, nah, and C12O genes to aged soil PAH pollution in a coke factory area.

PubMed

Han, Xue-Mei; Liu, Yu-Rong; Zheng, Yuan-Ming; Zhang, Xiao-Xia; He, Ji-Zheng

2014-01-01

Soil pollution caused by polycyclic aromatic hydrocarbons (PAHs) is threatening human health and environmental safety. Investigating the relative prevalence of different PAH-degrading genes in PAH-polluted soils and searching for potential bioindicators reflecting the impact of PAH pollution on microbial communities are useful for microbial monitoring, risk evaluation, and potential bioremediation of soils polluted by PAHs. In this study, three functional genes, pdo1, nah, and C12O, which might be involved in the degradation of PAHs from a coke factory, were investigated by real-time quantitative PCR (qPCR) and clone library approaches. The results showed that the pdo1 and C12O genes were more abundant than the nah gene in the soils. There was a significantly positive relationship between the nah or pdo1 gene abundances and PAH content, while there was no correlation between C12O gene abundance and PAH content. Analyses of clone libraries showed that all the pdo1 sequences were grouped into Mycobacterium, while all the nah sequences were classified into three groups: Pseudomonas, Comamonas, and Polaromonas. These results indicated that the abundances of nah and pdo1 genes were positively influenced by levels of PAHs in soil and could be potential microbial indicators reflecting the impact of soil PAH pollution and that Mycobacteria were one of the most prevalent PAHs degraders in these PAH-polluted soils. Principal component analysis (PCA) and correlation analyses between microbial parameters and environmental factors revealed that total carbon (TC), total nitrogen (TN), and dissolved organic carbon (DOC) had positive effects on the abundances of all PAH-degrading genes. It suggests that increasing TC, TN, and DOC inputs could be a useful way to remediate PAH-polluted soils.

Prefrontal neural correlates of memory for sequences.

PubMed

Averbeck, Bruno B; Lee, Daeyeol

2007-02-28

The sequence of actions appropriate to solve a problem often needs to be discovered by trial and error and recalled in the future when faced with the same problem. Here, we show that when monkeys had to discover and then remember a sequence of decisions across trials, ensembles of prefrontal cortex neurons reflected the sequence of decisions the animal would make throughout the interval between trials. This signal could reflect either an explicit memory process or a sequence-planning process that begins far in advance of the actual sequence execution. This finding extended to error trials such that, when the neural activity during the intertrial interval specified the wrong sequence, the animal also attempted to execute an incorrect sequence. More specifically, we used a decoding analysis to predict the sequence the monkey was planning to execute at the end of the fore-period, just before sequence execution. When this analysis was applied to error trials, we were able to predict where in the sequence the error would occur, up to three movements into the future. This suggests that prefrontal neural activity can retain information about sequences between trials, and that regardless of whether information is remembered correctly or incorrectly, the prefrontal activity veridically reflects the animal's action plan.

Current robotic curricula for surgery residents: A need for additional cognitive and psychomotor focus.

PubMed

Green, Courtney A; Chern, Hueylan; O'Sullivan, Patricia S

2018-02-01

Current robot surgery curricula developed by industry were designed for expert surgeons. We sought to identify the robotic curricula that currently exist in general surgery residencies and describe their components. We identified 12 residency programs with robotic curricula. Using a structured coding form to identify themes including sequence, duration, emphasis and assessment, we generated a descriptive summary. Curricula followed a similar sequence: learners started with online modules and simulation exercises, followed by bedside experience during R2-R3 training years, and then operative opportunities on the console in the final years of training. Consistent portions of the curricula reflect a device-dependent training paradigm; they defined the sequence of instruction. Most curricula lacked specifics on duration and content of training activities. None clearly described cognitive or psychomotor skills needed by residents and none required a proficiency assessment before graduation. Resident-specific robotic curricula remain grounded in initial industrial efforts to train experienced surgeons, are non-specific regarding the type and nature of hands on experience, and do not include discussion of operative technique and surgical concepts. Copyright © 2017 Elsevier Inc. All rights reserved.

Method and apparatus for characterizing reflected ultrasonic pulses

NASA Technical Reports Server (NTRS)

Yost, William T. (Inventor); Cantrell, John H., Jr. (Inventor)

1991-01-01

The invention is a method of and apparatus for characterizing the amplitudes of a sequence of reflected pulses R1, R2, and R3 by converting them into corresponding electric signals E1, E2, and E3 to substantially the same value during each sequence thereby restoring the reflected pulses R1, R2, and R3 to their initial reflection values by timing means, an exponential generator, and a time gain compensator. Envelope and baseline reject circuits permit the display and accurate location of the time spaced sequence of electric signals having substantially the same amplitude on a measurement scale on a suitable video display or oscilloscope.

Teaching Research Methodology Using a Project-Based Three Course Sequence Critical Reflections on Practice

ERIC Educational Resources Information Center

Braguglia, Kay H.; Jackson, Kanata A.

2012-01-01

This article presents a reflective analysis of teaching research methodology through a three course sequence using a project-based approach. The authors reflect critically on their experiences in teaching research methods courses in an undergraduate business management program. The introduction of a range of specific techniques including student…

Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping.

PubMed

Mottawea, Walid; Duceppe, Marc-Olivier; Dupras, Andrée A; Usongo, Valentine; Jeukens, Julie; Freschi, Luca; Emond-Rheault, Jean-Guillaume; Hamel, Jeremie; Kukavica-Ibrulj, Irena; Boyle, Brian; Gill, Alexander; Burnett, Elton; Franz, Eelco; Arya, Gitanjali; Weadge, Joel T; Gruenheid, Samantha; Wiedmann, Martin; Huang, Hongsheng; Daigle, France; Moineau, Sylvain; Bekal, Sadjia; Levesque, Roger C; Goodridge, Lawrence D; Ogunremi, Dele

2018-01-01

Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella . In this study, the prophage sequence diversity in different Salmonella serovars and genetically related strains was investigated. Using whole genome sequences of 1,760 isolates of S. enterica representing 151 Salmonella serovars and 66 closely related bacteria, prophage sequences were identified from assembled contigs using PHASTER. We detected 154 different prophages in S. enterica genomes. Prophage sequences were highly variable among S. enterica serovars with a median ± interquartile range (IQR) of 5 ± 3 prophage regions per genome. While some prophage sequences were highly conserved among the strains of specific serovars, few regions were lineage specific. Therefore, strains belonging to each serovar could be clustered separately based on their prophage content. Analysis of S . Enteritidis isolates from seven outbreaks generated distinct prophage profiles for each outbreak. Taken altogether, the diversity of the prophage sequences correlates with genome diversity. Prophage repertoires provide an additional marker for differentiating S. enterica subtypes during foodborne outbreaks.

Colorstratigraphy; A New Stratigraphic Correlation Technique

NASA Astrophysics Data System (ADS)

Nanayakkara, N. U.; Ranasinghage, P. N.; Priyantha, C.; Abillapitiya, T.

2016-12-01

Here we introduce a novel stratigraphic technique namely colorstratigraphy for correlating sedimentary sequences. Minihagalkanda is about 1 km long amphitheater like sedimentary terrain, situated at the southeastern coast of Sri Lanka. It has Miocene sedimentary sequences, separated in to 10-12 m high small hillocks by erosion, and bounded by about 30 m high escarpment. Sandstone, yellowish sandy clay, greenish silty clay sequences are capped by 4-5 m limestone bed in these hillocks but not at the boundary escarpment. Stratigraphic profiles at two hillocks and the boundary escarpment, separated each other by 200-300 m, were selected to test the new colorstartigraphic correlation technique. Color reflectance (DSR) was measured at four samples in each sequence at every profile and hence altogether 36 reflectance measurements were taken using Minolta 2500D hand-held color spectrophotometer. The first-derivative of the reflectance spectra (dR/dλ) defines the "spectral shape" of the sample. Therefore, DSR data (360-740 nm) measured at 10 nm resolution were used to calculate a center-weighted, first-derivative spectra for each reflectance sample consisting of 39 channels. Particle size of each sequence was measured at all 03 profiles using laser particle size analyzer to verify the stratigraphic correlation. Mean reflectance spectrum for each sequence at all 03 profiles were plotted on the same graph for comparison. Same was done for the grain size spectrums. Discriminant function analysis was performed separately for dsr data and grain size data using a number assigned to each sedimentary sequence as the grouping variable Color spectrums of sandstone, yellowish sandy clay, and greenish silty clay sequences at all three profiles perfectly match showing clear stratigraphic correlation among these three stratigraphic profiles. Matching grain size distribution curves of the three sequence at the three profiles verify the stratigraphic correlation. Perfect 100 % discrimination of the three sequences with color reflectance data proves the accuracy of the correlation. Similar 100 % discrimination resulted with grain size data further verifies the results. Therefore, colorstratigraphy based on DSR can be introduced as a quick and easy technique for stratigraphic correlation of sedimentary sequences.

Relationships between leaf chlorophyll content and spectral reflectance and algorithms for non-destructive chlorophyll assessment in higher plant leaves.

PubMed

Gitelson, Anatoly A; Gritz, Yuri; Merzlyak, Mark N

2003-03-01

Leaf chlorophyll content provides valuable information about physiological status of plants. Reflectance measurement makes it possible to quickly and non-destructively assess, in situ, the chlorophyll content in leaves. Our objective was to investigate the spectral behavior of the relationship between reflectance and chlorophyll content and to develop a technique for non-destructive chlorophyll estimation in leaves with a wide range of pigment content and composition using reflectance in a few broad spectral bands. Spectral reflectance of maple, chestnut, wild vine and beech leaves in a wide range of pigment content and composition was investigated. It was shown that reciprocal reflectance (R lambda)-1 in the spectral range lambda from 520 to 550 nm and 695 to 705 nm related closely to the total chlorophyll content in leaves of all species. Subtraction of near infra-red reciprocal reflectance, (RNIR)-1, from (R lambda)-1 made index [(R lambda)(-1)-(RNIR)-1] linearly proportional to the total chlorophyll content in spectral ranges lambda from 525 to 555 nm and from 695 to 725 nm with coefficient of determination r2 > 0.94. To adjust for differences in leaf structure, the product of the latter index and NIR reflectance [(R lambda)(-1)-(RNIR)-1]*(RNIR) was used; this further increased the accuracy of the chlorophyll estimation in the range lambda from 520 to 585 nm and from 695 to 740 nm. Two independent data sets were used to validate the developed algorithms. The root mean square error of the chlorophyll prediction did not exceed 50 mumol/m2 in leaves with total chlorophyll ranged from 1 to 830 mumol/m2.

Distortion of genetically modified organism quantification in processed foods: influence of particle size compositions and heat-induced DNA degradation.

PubMed

Moreano, Francisco; Busch, Ulrich; Engel, Karl-Heinz

2005-12-28

Milling fractions from conventional and transgenic corn were prepared at laboratory scale and used to study the influence of sample composition and heat-induced DNA degradation on the relative quantification of genetically modified organisms (GMO) in food products. Particle size distributions of the obtained fractions (coarse grits, regular grits, meal, and flour) were characterized using a laser diffraction system. The application of two DNA isolation protocols revealed a strong correlation between the degree of comminution of the milling fractions and the DNA yield in the extracts. Mixtures of milling fractions from conventional and transgenic material (1%) were prepared and analyzed via real-time polymerase chain reaction. Accurate quantification of the adjusted GMO content was only possible in mixtures containing conventional and transgenic material in the form of analogous milling fractions, whereas mixtures of fractions exhibiting different particle size distributions delivered significantly over- and underestimated GMO contents depending on their compositions. The process of heat-induced nucleic acid degradation was followed by applying two established quantitative assays showing differences between the lengths of the recombinant and reference target sequences (A, deltal(A) = -25 bp; B, deltal(B) = +16 bp; values related to the amplicon length of the reference gene). Data obtained by the application of method A resulted in underestimated recoveries of GMO contents in the samples of heat-treated products, reflecting the favored degradation of the longer target sequence used for the detection of the transgene. In contrast, data yielded by the application of method B resulted in increasingly overestimated recoveries of GMO contents. The results show how commonly used food technological processes may lead to distortions in the results of quantitative GMO analyses.

[Spectral reflectance characteristics and modeling of typical Takyr Solonetzs water content].

PubMed

Zhang, Jun-hua; Jia, Ke-li

2015-03-01

Based on the analysis of the spectral reflectance of the typical Takyr Solonetzs soil in Ningxia, the relationship of soil water content and spectral reflectance was determined, and a quantitative model for the prediction of soil water content was constructed. The results showed that soil spectral reflectance decreased with the increasing soil water content when it was below the water holding capacity but increased with the increasing soil water content when it was higher than the water holding capacity. Soil water content presented significantly negative correlation with original reflectance (r), smooth reflectance (R), logarithm of reflectance (IgR), and positive correlation with the reciprocal of R and logarithm of reciprocal [lg (1/R)]. The correlation coefficient of soil water content and R in the whole wavelength was 0.0013, 0.0397 higher than r and lgR, respectively. Average correlation coefficient of soil water content with 1/R and [lg (1/R)] at the wavelength of 950-1000 nm was 0.2350 higher than that of 400-950 nm. The relationships of soil water content with the first derivate differential (R') , the first derivate differential of logarithm (lgR)' and the first derivate differential of logarithm of reciprocal [lg(1/R)]' were unstable. Base on the coefficients of r, lg(1/R), R' and (lgR)', different regression models were established to predict soil water content, and the coefficients of determination were 0.7610, 0.8184, 0.8524 and 0.8255, respectively. The determination coefficient for power function model of R'. reached 0.9447, while the fitting degree between the predicted value based on this model and on-site measured value was 0.8279. The model of R' had the highest fitted accuracy, while that of r had the lowest one. The results could provide a scientific basis for soil water content prediction and field irrigation in the Takyr Solonetzs region.

Research advances in reflectance spectra of plant leafs

NASA Astrophysics Data System (ADS)

Zhu, Taotao; Yang, Ting; Guo, Yanxin; Xu, Jingqi; Chang, Wandong; Fang, Siyi; Zhu, Kangkang; Xu, Tingyan

2018-02-01

Leaves are an important factor when we study plants because their water content, pigment content and nutrient content of leaves can reflect the current growth status of the whole plant. The methods of spectral diagnosis technology or image technology mainly are the pre-detection technique which can be used to invert the color, texture and spectral reflectance of the leaves. From this we can obtain the changes of the internal components and the external morphological characteristics of the plant leaves in different states changes. In this paper, the reflection spectral response mechanism of plant water content, pigment and nutrient elements at domestic and overseas are reviewed and compared.

High dimensional reflectance analysis of soil organic matter

NASA Technical Reports Server (NTRS)

Henderson, T. L.; Baumgardner, M. F.; Franzmeier, D. P.; Stott, D. E.; Coster, D. C.

1992-01-01

Recent breakthroughs in remote-sensing technology have led to the development of high spectral resolution imaging sensors for observation of earth surface features. This research was conducted to evaluate the effects of organic matter content and composition on narrowband soil reflectance across the visible and reflective infrared spectral ranges. Organic matter from four Indiana agricultural soils, ranging in organic C content from 0.99 to 1.72 percent, was extracted, fractionated, and purified. Six components of each soil were isolated and prepared for spectral analysis. Reflectance was measured in 210 narrow bands in the 400- to 2500-nm wavelength range. Statistical analysis of reflectance values indicated the potential of high dimensional reflectance data in specific visible, near-infrared, and middle-infrared bands to provide information about soil organic C content, but not organic matter composition. These bands also responded significantly to Fe- and Mn-oxide content.

Leaf Surface Effects on Retrieving Chlorophyll Content from Hyperspectral Remote Sensing

NASA Astrophysics Data System (ADS)

Qiu, Feng; Chen, JingMing; Ju, Weimin; Wang, Jun; Zhang, Qian

2017-04-01

Light reflected directly from the leaf surface without entering the surface layer is not influenced by leaf internal biochemical content. Leaf surface reflectance varies from leaf to leaf due to differences in the surface roughness features and is relatively more important in strong absorption spectral regions. Therefore it introduces dispersion of data points in the relationship between biochemical concentration and reflectance (especially in the visible region). Separation of surface from total leaf reflection is important to improve the link between leaf pigments content and remote sensing data. This study aims to estimate leaf surface reflectance from hyperspectral remote sensing data and retrieve chlorophyll content by inverting a modified PROSPECT model. Considering leaf surface reflectance is almost the same in the visible and near infrared spectral regions, a surface layer with a reflectance independent of wavelength but varying from leaf to leaf was added to the PROSPECT model. The specific absorption coefficients of pigments were recalibrated. Then the modified model was inverted on independent datasets to check the performance of the model in predicting the chlorophyll content. Results show that differences in estimated surface layer reflectance of various species are noticeable. Surface reflectance of leaves with epicuticular waxes and trichomes is usually higher than other samples. Reconstruction of leaf reflectance and transmittance in the 400-1000 nm wavelength region using the modified PROSPECT model is excellent with low root mean square error (RMSE) and bias. Improvements for samples with high surface reflectance (e.g. maize) are significant, especially for high pigment leaves. Moreover, chlorophyll retrieved from inversion of the modified model is consequently improved (RMSE from 5.9-13.3 ug/cm2 with mean value 8.1 ug/cm2, while mean correlation coefficient is 0.90) compared to results of PROSPECT-5 (RMSE from 9.6-20.2 ug/cm2 with mean value 13.1 ug/cm2, while mean correlation coefficient is 0.81). Underestimation of high chlorophyll content, which is due to underestimation of reflectance in the visible region of PROSPECT, is partially corrected or alleviated. Improvements are particularly noticeable for leaves with high surface reflectance or high chlorophyll content, which both lead to large proportions of surface reflectance to the total leaf reflectance.

Study on Hyperspectral Estimation Model of Total Nitrogen Content in Soil of Shaanxi Province

NASA Astrophysics Data System (ADS)

Liu, Jinbao; Dong, Zhenyu; Chen, Xi

2018-01-01

The development of hyperspectral remote sensing technology has been widely used in soil nutrient prediction. The soil is the representative soil type in Shaanxi Province. In this study, the soil total nitrogen content in Shaanxi soil was used as the research target, and the soil samples were measured by reflectance spectroscopy using ASD method. Pre-treatment, the first order differential, second order differential and reflectance logarithmic transformation of the reflected spectrum after pre-treatment, and the hyperspectral estimation model is established by using the least squares regression method and the principal component regression method. The results show that the correlation between the reflectance spectrum and the total nitrogen content of the soil is significantly improved. The correlation coefficient between the original reflectance and soil total nitrogen content is in the range of 350 ~ 2500nm. The correlation coefficient of soil total nitrogen content and first deviation of reflectance is more than 0.5 at 142nm, 1963nm, 2204nm and 2307nm, the second deviation has a significant positive correlation at 1114nm, 1470nm, 1967nm, 2372nm and 2402nm, respectively. After the reciprocal logarithmic transformation of the reflectance with the total nitrogen content of the correlation analysis found that the effect is not obvious. Rc2 = 0.7102, RMSEC = 0.0788; Rv2 = 0.8480, RMSEP = 0.0663, which can achieve the rapid prediction of the total nitrogen content in the region. The results show that the principal component regression model is the best.

Distinguishing cognitive state with multifractal complexity of hippocampal interspike interval sequences

PubMed Central

Fetterhoff, Dustin; Kraft, Robert A.; Sandler, Roman A.; Opris, Ioan; Sexton, Cheryl A.; Marmarelis, Vasilis Z.; Hampson, Robert E.; Deadwyler, Sam A.

2015-01-01

Fractality, represented as self-similar repeating patterns, is ubiquitous in nature and the brain. Dynamic patterns of hippocampal spike trains are known to exhibit multifractal properties during working memory processing; however, it is unclear whether the multifractal properties inherent to hippocampal spike trains reflect active cognitive processing. To examine this possibility, hippocampal neuronal ensembles were recorded from rats before, during and after a spatial working memory task following administration of tetrahydrocannabinol (THC), a memory-impairing component of cannabis. Multifractal detrended fluctuation analysis was performed on hippocampal interspike interval sequences to determine characteristics of monofractal long-range temporal correlations (LRTCs), quantified by the Hurst exponent, and the degree/magnitude of multifractal complexity, quantified by the width of the singularity spectrum. Our results demonstrate that multifractal firing patterns of hippocampal spike trains are a marker of functional memory processing, as they are more complex during the working memory task and significantly reduced following administration of memory impairing THC doses. Conversely, LRTCs are largest during resting state recordings, therefore reflecting different information compared to multifractality. In order to deepen conceptual understanding of multifractal complexity and LRTCs, these measures were compared to classical methods using hippocampal frequency content and firing variability measures. These results showed that LRTCs, multifractality, and theta rhythm represent independent processes, while delta rhythm correlated with multifractality. Taken together, these results provide a novel perspective on memory function by demonstrating that the multifractal nature of spike trains reflects hippocampal microcircuit activity that can be used to detect and quantify cognitive, physiological, and pathological states. PMID:26441562

Reflective Pedagogy: The Integration of Methodology and Subject-Matter Content in a Graduate-Level Course

ERIC Educational Resources Information Center

Jakeman, Rick C.; Henderson, Markesha M.; Howard, Lionel C.

2017-01-01

This article presents a critical reflection on how we, instructors of a graduate-level course in higher education administration, sought to integrate theoretical and subject-matter content and research methodology. Our reflection, guided by autoethnography and teacher reflection, challenged both our assumptions about curriculum design and our…

Student Reflective Writing: Cognition and Affect before, during, and after Study Abroad

ERIC Educational Resources Information Center

Savicki, Victor; Price, Michele V.

2015-01-01

Reflective thinking is an important feature of study-abroad learning, yet research on reflection in this context is sparse. The current study examined student reflection on 3 content areas (Academic Expectations, Cultural Expectations, and Psychological Issues) at 3 times (before, during, and after study abroad). A content analysis approach with…

Spectral reflectance relationships to leaf water stress

NASA Technical Reports Server (NTRS)

Ripple, William J.

1986-01-01

Spectral reflectance data were collected from detached snapbean leaves in the laboratory with a multiband radiometer. Four experiments were designed to study the spectral response resulting from changes in leaf cover, relative water content of leaves, and leaf water potential. Spectral regions included in the analysis were red (630-690 nm), NIR (760-900 nm), and mid-IR (2.08-2.35 microns). The red and mid-IR bands showed sensitivity to changes in both leaf cover and relative water content of leaves. The NIR was only highly sensitive to changes in leaf cover. Results provided evidence that mid-IR reflectance was governed primarily by leaf moisture content, although soil reflectance was an important factor when leaf cover was less than 100 percent. High correlations between leaf water potentials and reflectance were attributed to covariances with relative water content of leaves and leaf cover.

Interactions of multi-scale heterogeneity in the lithosphere: Australia

NASA Astrophysics Data System (ADS)

Kennett, B. L. N.; Yoshizawa, K.; Furumura, T.

2017-10-01

Understanding the complex heterogeneity of the continental lithosphere involves a wide variety of spatial scales and the synthesis of multiple classes of information. Seismic surface waves and multiply reflected body waves provide the main constraints on broad-scale structure, and bounds on the extent of the lithosphere-asthenosphere transition (LAT) can be found from the vertical gradients of S wavespeed. Information on finer-scale structures comes through body wave studies, including detailed seismic tomography and P-wave reflectivity extracted from stacked autocorrelograms of continuous component records. With the inclusion of deterministic large-scale structure and realistic medium-scale stochastic features fine-scale variations are subdued. The resulting multi-scale heterogeneity model for the Australian region gives a good representation of the character of observed seismograms and their geographic variations and matches the observations of P-wave reflectivity. P reflections in the 0.5-3.0 Hz band in the uppermost mantle suggest variations on vertical scales of a few hundred metres with amplitudes of the order of 1%. Interference of waves reflected or converted at sequences of such modest variations in physical properties produce relatively simple behaviour for lower frequencies, which can suggest simpler structures than are actually present. Vertical changes in the character of fine-scale heterogeneity can produce apparent discontinuities. In Central Australia a 'mid-lithospheric discontinuity' can be tracked via changes in frequency content of station reflectivity, with links to the broad-scale pattern of wavespeed gradients and, in particular, the gradients of radial anisotropy. Comparisons with xenolith results from southeastern Australia indicate a strong tie between geochemical stratification and P-wave reflectivity.

Personal Reflection: Pedagogical Content Knowledge and the Affective Domain of Scholarship of Teaching and Learning

ERIC Educational Resources Information Center

Garritz, Andoni

2010-01-01

The question of these reflections is if among those content-dependent instructional conditions necessary to attain conceptual understanding, those belonging to the affective domain of teaching and learning must be included in Pedagogical Content Knowledge (PCK), the special amalgam of content knowledge and knowledge of general pedagogy that a…

Site-specific ultrasound reflection properties and superficial collagen content of bovine knee articular cartilage

NASA Astrophysics Data System (ADS)

Laasanen, Mikko S.; Saarakkala, Simo; Töyräs, Juha; Rieppo, Jarno; Jurvelin, Jukka S.

2005-07-01

Previous quantitative 2D-ultrasound imaging studies have demonstrated that the ultrasound reflection measurement of articular cartilage surface sensitively detects degradation of the collagen network, whereas digestion of cartilage proteoglycans has no significant effect on the ultrasound reflection. In this study, the first aim was to characterize the ability of quantitative 2D-ultrasound imaging to detect site-specific differences in ultrasound reflection and backscattering properties of cartilage surface and cartilage-bone interface at visually healthy bovine knee (n = 30). As a second aim, we studied factors controlling ultrasound reflection properties of an intact cartilage surface. The ultrasound reflection coefficient was determined in time (R) and frequency domains (IRC) at medial femoral condyle, lateral patello-femoral groove, medial tibial plateau and patella using a 20 MHz ultrasound imaging instrument. Furthermore, cartilage surface roughness was quantified by calculating the ultrasound roughness index (URI). The superficial collagen content of the cartilage was determined using a FT-IRIS-technique. A significant site-dependent variation was shown in cartilage thickness, ultrasound reflection parameters, URI and superficial collagen content. As compared to R and IRC, URI was a more sensitive parameter in detecting differences between the measurement sites. Ultrasound reflection parameters were not significantly related to superficial collagen content, whereas the correlation between R and URI was high. Ultrasound reflection at the cartilage-bone interface showed insignificant site-dependent variation. The current results suggest that ultrasound reflection from the intact cartilage surface is mainly dependent on the cartilage surface roughness and the collagen content has a less significant role.

The distribution of organic carbon fractions in a typical loess-paleosol profile and its paleoenvironmental significance

PubMed Central

Hu, Feinan; Huo, Na; Shang, Yingni; Chang, Wenqian

2018-01-01

Background The loess-paleosol sequence on the Loess Plateau has been considered an important paleoclimatic archive to study global climatic and environmental changes in the Quaternary. So far, little attention has been paid to the characteristics of soil organic carbon fractions in loess-paleosol sequences, which may provide valuable information for exploring the evolution of climate and environment in the Quaternary on the Loess Plateau. Methods In order to explore the significance of mineral-associated organic carbon to total organic carbon (MOC/TOC) ratios in the loess-paleosol sequence for reconstructing paleoenvironmental and paleoclimatic evolution in the Quaternary on the Loess Plateau, we selected a typical loess-paleosol profile in Chunhua county, Xianyang city, Shaanxi province, as the research object. The content of total organic carbon (TOC) and MOC/TOC ratio in each loess and paleosol layers of the Chunhua loess-paleosol profile were analyzed, together with the paleoclimatic proxies, such as soil grain size, CaCO3 content and their correlations with organic carbon parameters. Results The main results were as follows: (1) the total content of soil organic carbon and MOC/TOC ratios were generally higher in paleosol layers than in the underlying loess layers of the Chunhua loess-paleosol profile. Compared to total organic carbon content, MOC/TOC ratios changed more obviously in soil layers below a paleosol layer S8; (2) soil clay content and median grain size (Md (ϕ)) were higher in paleosol than in the underlying loess, while CaCO3 content showed an opposite tendency. In the Chunhua profile, the distribution characteristics of the three paleoclimatic proxies showed good indications of paleoclimate changes in the Quaternary; (3) in the Chunhua loess-paleosol profile, MOC/TOC ratios were positively correlated with clay content and median grain size (ϕ), while negatively correlated with CaCO3 content, and the correlations were more significant in soil layers below S8. Discussion Our results indicated that MOC/TOC ratios in the Chunhua loess-paleosol profile correlated with the cold dry-warm wet paleoclimatic cycle in the Quaternary. The high MOC/TOC ratios in the loess-paleosol profile might reflect warm and humid climate, while lower ratios indicated relatively cold and dry climate. That is because when the climate changed from warm-humid to cold-dry, the vegetation coverage and pedogenesis intensity decreased, which increased soil CaCO3 content and decreased soil clay content and Md (ϕ), leading to decreased MOC/TOC ratios. Compared to TOC, MOC/TOC ratios had greater significance in indicating paleoenvironmental evolution in the Quaternary on the Loess Plateau. Therefore, investigating MOC/TOC ratios in loess-paleosol profile can offer new evidence to reconstructing paleoenvironmental changes, and also provide a basis for predicting responses of soil organic carbon pools to vegetation and climate changes in the future. PMID:29666763

Motility and Flagellar Glycosylation in Clostridium difficile▿ †

PubMed Central

Twine, Susan M.; Reid, Christopher W.; Aubry, Annie; McMullin, David R.; Fulton, Kelly M.; Austin, John; Logan, Susan M.

2009-01-01

In this study, intact flagellin proteins were purified from strains of Clostridium difficile and analyzed using quadrupole time of flight and linear ion trap mass spectrometers. Top-down studies showed the flagellin proteins to have a mass greater than that predicted from the corresponding gene sequence. These top-down studies revealed marker ions characteristic of glycan modifications. Additionally, diversity in the observed masses of glycan modifications was seen between strains. Electron transfer dissociation mass spectrometry was used to demonstrate that the glycan was attached to the flagellin protein backbone in O linkage via a HexNAc residue in all strains examined. Bioinformatic analysis of C. difficile genomes revealed diversity with respect to glycan biosynthesis gene content within the flagellar biosynthesis locus, likely reflected by the observed flagellar glycan diversity. In C. difficile strain 630, insertional inactivation of a glycosyltransferase gene (CD0240) present in all sequenced genomes resulted in an inability to produce flagellar filaments at the cell surface and only minor amounts of unmodified flagellin protein. PMID:19749038

Genomics of Actinobacteria: Tracing the Evolutionary History of an Ancient Phylum†

PubMed Central

Ventura, Marco; Canchaya, Carlos; Tauch, Andreas; Chandra, Govind; Fitzgerald, Gerald F.; Chater, Keith F.; van Sinderen, Douwe

2007-01-01

Summary: Actinobacteria constitute one of the largest phyla among Bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context. PMID:17804669

The relationship between leaf water status, gas exchange, and spectral reflectance in cotton leaves

NASA Technical Reports Server (NTRS)

Bowman, William D.

1989-01-01

Measurements of leaf spectral reflectance, the components of water potential, and leaf gas exchanges as a function of leaf water content were made to evaluate the use of NIR reflectance as an indicator of plant water status. Significant correlations were determined between spectral reflectance at 810 nm, 1665 nm, and 2210 nm and leaf relative water content, total water potential, and turgor pressure. However, the slopes of these relationships were relatively shallow and, when evaluated over the range of leaf water contents in which physiological activity occurs (e.g., photosynthesis), had lower r-squared values, and some relationships were not statistically significant. NIR reflectance varied primarily as a function of leaf water content, and not independently as a function of turgor pressure, which is a sensitive indicator of leaf water status. The limitations of this approach to measuring plant water stress are discussed.

Hidden Structural Codes in Protein Intrinsic Disorder.

PubMed

Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

2017-10-17

Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

Learning Portfolio Analysis and Mining for SCORM Compliant Environment

ERIC Educational Resources Information Center

Su, Jun-Ming; Tseng, Shian-Shyong; Wang, Wei; Weng, Jui-Feng; Yang, Jin Tan David; Tsai, Wen-Nung

2006-01-01

With vigorous development of the Internet, e-learning system has become more and more popular. Sharable Content Object Reference Model (SCORM) 2004 provides the Sequencing and Navigation (SN) Specification to define the course sequencing behavior, control the sequencing, selecting and delivering of course, and organize the content into a…

Flexible manipulation of terahertz wave reflection using polarization insensitive coding metasurfaces.

PubMed

Jiu-Sheng, Li; Ze-Jiang, Zhao; Jian-Quan, Yao

2017-11-27

In order to extend to 3-bit encoding, we propose notched-wheel structures as polarization insensitive coding metasurfaces to control terahertz wave reflection and suppress backward scattering. By using a coding sequence of "00110011…" along x-axis direction and 16 × 16 random coding sequence, we investigate the polarization insensitive properties of the coding metasurfaces. By designing the coding sequences of the basic coding elements, the terahertz wave reflection can be flexibly manipulated. Additionally, radar cross section (RCS) reduction in the backward direction is less than -10dB in a wide band. The present approach can offer application for novel terahertz manipulation devices.

What Medical Students Say about Psychiatry: Results of a Reflection Exercise

ERIC Educational Resources Information Center

Brenner, Adam M.

2011-01-01

Objective: The author describes the results of a reflection exercise for psychiatry clerkship students. Method: The author performed a qualitative analysis on 100 "reflection" papers written by medical students in their psychiatry clerkship and identified the most prominent thematic content. Results: The most common thematic content involved…

Comparing Traditional Journal Writing with Journal Writing Shared over E-mail List Serves as Tools for Facilitating Reflective Thinking: A Study of Preservice Teachers

ERIC Educational Resources Information Center

Kaplan, Diane S.; Rupley, William H.; Sparks, Joanne; Holcomb, Angelia

2007-01-01

To determine the conditions that would best encourage reflection in journal writing of preservice teachers in field-based reading internships, the degree of reflective content found in self-contained traditional journals was compared to the reflective content found in journal entries shared over e-mail list serves. Participants were 56 preservice…

Extracellular vesicle long noncoding RNA as potential biomarkers of liver cancer

PubMed Central

Mohankumar, Swathi

2016-01-01

Analysis of extracellular vesicles (EV) and their contents may be useful as disease biomarkers if they reflect the contents of cells of origin, differ between normal and diseased tissue and can be reliably detected. An increasing number of long noncoding RNA (lncRNA) are being reported to be aberrantly expressed in human cancers. These tumor-associated lncRNA may have potential as new biomarkers of disease. In this review, we highlight lncRNAs that are commonly associated with hepatocellular cancer, and summarize their potential biological roles and underlying molecular mechanisms. While lncRNA can be detected in the circulation, their low expression within circulating vesicles will require the use of highly sensitive detection technologies such as digital polymerase chain reaction or next-generation sequencing. While the integrity and functional role of tumor-specific lncRNAs within EV have yet to be established, their presence or enrichment within tumor cell-derived EV offers promise for their potential as disease biomarkers. PMID:26634812

Soundtrack contents and depicted sexual violence.

PubMed

Pfaus, J G; Myronuk, L D; Jacobs, W J

1986-06-01

Male undergraduates were exposed to a videotaped depiction of heterosexual rape accompanied by one of three soundtracks: the original soundtrack (featuring dialogue and background rock music), relaxing music, or no sound. Subjective reports of sexual arousal, general enjoyment, perceived erotic content, and perceived pornographic content of the sequence were then provided by each subject. Results indicated that males exposed to the videotape accompanied by the original soundtrack found the sequence significantly more pornographic than males exposed to the sequence accompanied by either relaxing background music or no sound. Ratings of sexual arousal, general enjoyment, and the perceived erotic content, however, did not differ significantly across soundtrack conditions. These results are compatible with the assertion that the content of a video soundtrack may influence the impact of depicted sexual violence.

The 'F-complex' and MMN tap different aspects of deviance.

PubMed

Laufer, Ilan; Pratt, Hillel

2005-02-01

To compare the 'F(fusion)-complex' with the Mismatch negativity (MMN), both components associated with automatic detection of changes in the acoustic stimulus flow. Ten right-handed adult native Hebrew speakers discriminated vowel-consonant-vowel (V-C-V) sequences /ada/ (deviant) and /aga/ (standard) in an active auditory 'Oddball' task, and the brain potentials associated with performance of the task were recorded from 21 electrodes. Stimuli were generated by fusing the acoustic elements of the V-C-V sequences as follows: base was always presented in front of the subject, and formant transitions were presented to the front, left or right in a virtual reality room. An illusion of a lateralized echo (duplex sensation) accompanied base fusion with the lateralized formant locations. Source current density estimates were derived for the net response to the fusion of the speech elements (F-complex) and for the MMN, using low-resolution electromagnetic tomography (LORETA). Statistical non-parametric mapping was used to estimate the current density differences between the brain sources of the F-complex and the MMN. Occipito-parietal regions and prefrontal regions were associated with the F-complex in all formant locations, whereas the vicinity of the supratemporal plane was bilaterally associated with the MMN, but only in case of front-fusion (no duplex effect). MMN is sensitive to the novelty of the auditory object in relation to other stimuli in a sequence, whereas the F-complex is sensitive to the acoustic features of the auditory object and reflects a process of matching them with target categories. The F-complex and MMN reflect different aspects of auditory processing in a stimulus-rich and changing environment: content analysis of the stimulus and novelty detection, respectively.

Prediction of protein secondary structure content for the twilight zone sequences.

PubMed

Homaeian, Leila; Kurgan, Lukasz A; Ruan, Jishou; Cios, Krzysztof J; Chen, Ke

2007-11-15

Secondary protein structure carries information about local structural arrangements, which include three major conformations: alpha-helices, beta-strands, and coils. Significant majority of successful methods for prediction of the secondary structure is based on multiple sequence alignment. However, multiple alignment fails to provide accurate results when a sequence comes from the twilight zone, that is, it is characterized by low (<30%) homology. To this end, we propose a novel method for prediction of secondary structure content through comprehensive sequence representation, called PSSC-core. The method uses a multiple linear regression model and introduces a comprehensive feature-based sequence representation to predict amount of helices and strands for sequences from the twilight zone. The PSSC-core method was tested and compared with two other state-of-the-art prediction methods on a set of 2187 twilight zone sequences. The results indicate that our method provides better predictions for both helix and strand content. The PSSC-core is shown to provide statistically significantly better results when compared with the competing methods, reducing the prediction error by 5-7% for helix and 7-9% for strand content predictions. The proposed feature-based sequence representation uses a comprehensive set of physicochemical properties that are custom-designed for each of the helix and strand content predictions. It includes composition and composition moment vectors, frequency of tetra-peptides associated with helical and strand conformations, various property-based groups like exchange groups, chemical groups of the side chains and hydrophobic group, auto-correlations based on hydrophobicity, side-chain masses, hydropathy, and conformational patterns for beta-sheets. The PSSC-core method provides an alternative for predicting the secondary structure content that can be used to validate and constrain results of other structure prediction methods. At the same time, it also provides useful insight into design of successful protein sequence representations that can be used in developing new methods related to prediction of different aspects of the secondary protein structure. (c) 2007 Wiley-Liss, Inc.

Imaging the Ferron Member of the Mancos Shale formation using reprocessed high-resolution 2-D seismic reflection data: Emery County, Utah

USGS Publications Warehouse

Taylor, D.J.

2003-01-01

Late in 1982 and early in 1983, Arco Exploration contracted with Rocky Mountain Geophysical to acquired four high-resolution 2-D multichannel seismic reflection lines in Emery County, Utah. The primary goal in acquiring this data was an attempt to image the Ferron Member of the Upper Cretaceous Mancos Shale. Design of the high-resolution 2-D seismic reflection data acquisition used both a short geophone group interval and a short sample interval. An explosive energy source was used which provided an input pulse with broad frequency content and higher frequencies than typical non-explosive Vibroseis?? sources. Reflections produced by using this high-frequency energy source when sampled at a short interval are usually able to resolve shallow horizons that are relatively thin compared to those that can be resolved using more typical oil and gas exploration seismic reflection methods.The U.S. Geological Survey-Energy Resources Program, Geophysical Processing Group used the processing sequence originally applied by Arco in 1984 as a guide and experimented with processing steps applied in a different order using slightly different parameters in an effort to improve imaging the Ferron Member horizon. As with the Arco processed data there are sections along all four seismic lines where the data quality cannot be improved upon, and in fact the data quality is so poor that the Ferron horizon cannot be imaged at all.Interpretation of the seismic and core hole data indicates that the Ferron Member in the study area represent a deltaic sequence including delta front, lower delta plain, and upper delta plain environments. Correlating the depositional environments for the Ferron Member as indicated in the core holes with the thickness of Ferron Member suggests the presence of a delta lobe running from the northwest to the southeast through the study area. The presence of a deltaic channel system within the delta lobe complex might prove to be an interesting conventional exploration target along with the coal-bed methane production already proven in the area. ?? 2003 Elsevier B.V. All rights reserved.

The Construct Validity of Higher Order Structure-of-Intellect Factors Reflecting Semantic and Symbolic Content Abilities.

ERIC Educational Resources Information Center

Khattab, Ali-Maher; Michael, William B.

1986-01-01

Based on reanalyses of correlational data obtained from the University of Southern California Aptitudes Research Project, this investigation examined the extent to which two higher order factors of semantic content and symbolic content form Guilford's structure-of-intellect model reflected distinct constructs. (Author/LMO)

Content, Structure, and Sequence of the Detailing Discipline at Kendall College of Art and Design.

ERIC Educational Resources Information Center

Mulder, Bruce E.

A study identified the appropriate general content, structure, and sequence for a detailing discipline that promoted student achievement to professional levels. Its focus was the detailing discipline, a sequence of studio courses within the furniture design program at Kendall College of Art and Design, Grand Rapids, Michigan. (Detailing, an…

Study on Hyperspectral Characteristics and Estimation Model of Soil Mercury Content

NASA Astrophysics Data System (ADS)

Liu, Jinbao; Dong, Zhenyu; Sun, Zenghui; Ma, Hongchao; Shi, Lei

2017-12-01

In this study, the mercury content of 44 soil samples in Guan Zhong area of Shaanxi Province was used as the data source, and the reflectance spectrum of soil was obtained by ASD Field Spec HR (350-2500 nm) Comparing the reflection characteristics of different contents and the effect of different pre-treatment methods on the establishment of soil heavy metal spectral inversion model. The first order differential, second order differential and reflectance logarithmic transformations were carried out after the pre-treatment of NOR, MSC and SNV, and the sensitive bands of reflectance and mercury content in different mathematical transformations were selected. A hyperspectral estimation model is established by regression method. The results of chemical analysis show that there is a serious Hg pollution in the study area. The results show that: (1) the reflectivity decreases with the increase of mercury content, and the sensitive regions of mercury are located at 392 ~ 455nm, 923nm ~ 1040nm and 1806nm ~ 1969nm. (2) The combination of NOR, MSC and SNV transformations combined with differential transformations can improve the information of heavy metal elements in the soil, and the combination of high correlation band can improve the stability and prediction ability of the model. (3) The partial least squares regression model based on the logarithm of the original reflectance is better and the precision is higher, Rc2 = 0.9912, RMSEC = 0.665; Rv2 = 0.9506, RMSEP = 1.93, which can achieve the mercury content in this region Quick forecast.

Clustering evolving proteins into homologous families.

PubMed

Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

2013-04-08

Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better choice, especially if computational resources are not limiting.

Soil moisture content estimation using ground-penetrating radar reflection data

NASA Astrophysics Data System (ADS)

Lunt, I. A.; Hubbard, S. S.; Rubin, Y.

2005-06-01

Ground-penetrating radar (GPR) reflection travel time data were used to estimate changes in soil water content under a range of soil saturation conditions throughout the growing season at a California winery. Data were collected during three data acquisition campaigns over an 80 by 180 m area using 100 MHz surface GPR antennas. GPR reflections were associated with a thin, low permeability clay layer located 0.8-1.3 m below the ground surface that was identified from borehole information and mapped across the study area. Field infiltration tests and neutron probe logs suggest that the thin clay layer inhibited vertical water flow, and was coincident with high volumetric water content (VWC) values. The GPR reflection two-way travel time and the depth of the reflector at the borehole locations were used to calculate an average dielectric constant for soils above the reflector. A site-specific relationship between the dielectric constant and VWC was then used to estimate the depth-averaged VWC of the soils above the reflector. Compared to average VWC measurements from calibrated neutron probe logs over the same depth interval, the average VWC estimates obtained from GPR reflections had an RMS error of 0.018 m 3 m -3. These results suggested that the two-way travel time to a GPR reflection associated with a geological surface could be used under natural conditions to obtain estimates of average water content when borehole control is available and the reflection strength is sufficient. The GPR reflection method therefore, has potential for monitoring soil water content over large areas and under variable hydrological conditions.

Context Becomes Content: Sensor Data for Computer-Supported Reflective Learning

ERIC Educational Resources Information Center

Muller, Lars; Divitini, Monica; Mora, Simone; Rivera-Pelayo, Veronica; Stork, Wilhelm

2015-01-01

Wearable devices and ambient sensors can monitor a growing number of aspects of daily life and work. We propose to use this context data as content for learning applications in workplace settings to enable employees to reflect on experiences from their work. Learning by reflection is essential for today's dynamic work environments, as employees…

Transformation of a Traditional, Freshman Biology, Three-Semester Sequence, to a Two-Semester, Integrated Thematically Organized, and Team-Taught Course

ERIC Educational Resources Information Center

Soto, Julio G.; Everhart, Jerry

2016-01-01

Biology faculty at San José State University developed, piloted, implemented, and assessed a freshmen course sequence based on the macro-to micro-teaching approach that was team-taught, and organized around unifying themes. Content learning assessment drove the conceptual framework of our course sequence. Content student learning increased…

Comparative genomics of the lactic acid bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarova, K.; Slesarev, A.; Wolf, Y.

Lactic acid-producing bacteria are associated with various plant and animal niches and play a key role in the production of fermented foods and beverages. We report nine genome sequences representing the phylogenetic and functional diversity of these bacteria. The small genomes of lactic acid bacteria encode a broad repertoire of transporters for efficient carbon and nitrogen acquisition from the nutritionally rich environments they inhabit and reflect a limited range of biosynthetic capabilities that indicate both prototrophic and auxotrophic strains. Phylogenetic analyses, comparison of gene content across the group, and reconstruction of ancestral gene sets indicate a combination of extensive genemore » loss and key gene acquisitions via horizontal gene transfer during the coevolution of lactic acid bacteria with their habitats.« less

Mineralogy, petrology, and surface features of lunar samples 10062,35, 10067,9, 10069,30, and 10085,16.

PubMed

Carter, J L; Macgregor, I D

1970-01-30

The primary rocks are a sequence of titanium-rich basic volcanics, composed of clinopyroxene, plagioclase, and ilmenite with minor olivine, troilite, and native iron. The soil and microbreccias are respectively loose and compacted mixtures of fragments and aggregates of similar rocks, minerals, and glassy fragments and spheres. Impact events are reflected by the presence of shock metamorphosed rock fragments, breccias, and glasses and their resulting compaction to form complex breccias, glass-spattered surfaces, and numerous glass-lined craters. Chemistry of the glasses formed by the impact events is highly variable, and the high iron and nickel content of a few moundlike features suggests that at least some of the projectiles are iron and nickel-rich meteorites.

Behaviour of Ni-PGE-Au-Cu in mafic-ultramafic volcanic suites of the 2.7 Ga Kambalda Sequence, Kalgoorlie Terrane, Yilgarn Craton

NASA Astrophysics Data System (ADS)

Said, Nuru; Kerrich, Robert; Maier, W. D.; McCuaig, Campbell

2011-05-01

The 2.7 Ga Kambalda Sequence comprises a mafic to ultramafic dominated volcanic rock sequence of the Kalgoorlie Terrane, Yilgarn Craton, Western Australia. The Sequence is divided into Lower and Upper Units separated by the Kambalda Komatiite Formation. Five basalt suites of the Lower Unit are tholeiitic where MgO spans 5-10 wt.% MgO, with minor assimilation-fractional crystallization (AFC), whereas six volcanic suites identified in the Upper Unit are tholeiitic to komatiitic-basalts with MgO 24-5 wt.% having generally greater degrees of AFC. Upper suites plot at Al 2O 3/TiO 2 (17-26) close to the primitive mantle ratio of 21, and Pt + Pd (19-31 ppb), whereas the PGE-depleted Lower basalts plot at generally lower Al 2O 3/TiO 2 (<16) and Pt + Pd (<10 ppb). Most suites have an average Pt/Pd ratio of 1.11, despite large variations in MgO contents, broadly consistent with the Pt/Pd ratio in the primitive mantle. On primitive mantle-normalised PGE plots, Upper suites generally display less fractionated patterns of the IPGE (Os, Ir, Ru and Rh) from the PPGE (Pt and Pd) relative to the Lower basalts. Most suites exhibit patterns with positive slopes reflecting relative enrichment of Pd, Pt, Au and Cu relative to Ni and IPGE. In suites of both Units, the concentrations of Ir and Ru fall with decreasing MgO contents, indicating their broadly compatible behaviour during magmatic evolution that involved AFC. Platinum and Pd behave as incompatible elements in the high-MgO suites, whereas Pt and Pd behave compatibly during crystallisation of the Lower basalt magmas, an interpretation consistent with progressively higher Cu/Pt and Cu/Pd ratios at decreasing MgO contents, and with falling Pt/Ti, collectively due to sulphur saturation induced by AFC as recorded in an antivariance of Pd/Ir with Nb/Th, a monitor of AFC. Collectively, the data suggest that several of the Lower Basalt suites crystallised under sulphide-saturated conditions, whereas most of the Upper Basalt Sequences remained sulphur undersaturated during magmatic evolution. Alteration, and fractional crystallisation of silicate and oxide phases, can be ruled out as factors governing PGE distribution in these mafic-ultramafic suites. Instead, the data suggest that discrete PGE-bearing phase (s) fractionated from the magmas. Such phases could be platinum group minerals (PGM; e.g., laurite) and/or alloys, or discrete PGE-rich nuggets or sulphides.

Effect of the reflectional symmetry on the coherent hole transport across DNA hairpins

NASA Astrophysics Data System (ADS)

Zarea, Mehdi; Berlin, Yuri; Ratner, Mark A.

2017-03-01

The coherent hole transfer in three types of DNA hairpins containing strands with adenine (A) and guanine (G) nucleobases has been studied. The investigated hairpins involve An+1GGAn, AnGAGAn, or (AG)2nA strands that connect the hole donor and hole acceptor located on opposite ends of hairpins. The positive charge transfer from the photo-excited donor to the acceptor is shown to be slower for An+1GGAn in comparison with AnGAGAn and (AG)2nA sequences. We have revealed that this is due to the reflectional symmetry of the last two sequences with respect to the axis passing through the middle base. As has been demonstrated, the symmetry of the sequence structure manifests itself in the reflectional symmetry of the energy eigenstates. In addition, it has been shown that (AG)2nA is the only symmetric sequence with a zero energy state in the middle of the LUMO tight-binding energy band. Based on our theoretical findings, we predict that the hairpin with this sequence should have the fastest coherent hole transfer rate among the class of base sequences studied.

Measurement of sugar content of watermelon using near-infrared reflectance spectroscopy in comparison with dielectric property

NASA Astrophysics Data System (ADS)

Tao, Xuemei; Bao, Yidan

2006-09-01

The sugar content of watermelon is important to its taste thus influences the market. It's difficult to know whether the melon is sweet or not for consumers. We tried to develop a convenient meter to determine the sugar of watermelon. The first objective of this paper was to demonstrate the feasibility of using a near-infrared reflectance spectrometer (NIRS) to investigate the relationship between sugar content of watermelon and absorption spectra. The NIRS reflectance of nondestructive watermelon was measured with a Visible/NIR spectrophotometer in 325-1075nm range. The sugar content of watermelon was obtained with a handhold sugar content meter. The second objective was to measure the watermelon's dielectric property, such as dielectric resistance, capacitance, quality factor and dielectric loss. A digital electric bridge instrument was used to get the dielectric property. The experimental results show that they were related to watermelon's sugar content. A comparison between the two methods was made in the paper. The model derived from NIRS reflection is useful for class identification of Zaochun Hongyu watermelon though it's not quite accurate in sweetness prediction (the max. deviation is 0.7). Electric property bears little relation to sugar content of watermelon at this experiment and it couldn't be used as non-destructive inspection method.

Optical Method for Estimating the Chlorophyll Contents in Plant Leaves.

PubMed

Pérez-Patricio, Madaín; Camas-Anzueto, Jorge Luis; Sanchez-Alegría, Avisaí; Aguilar-González, Abiel; Gutiérrez-Miceli, Federico; Escobar-Gómez, Elías; Voisin, Yvon; Rios-Rojas, Carlos; Grajales-Coutiño, Ruben

2018-02-22

This work introduces a new vision-based approach for estimating chlorophyll contents in a plant leaf using reflectance and transmittance as base parameters. Images of the top and underside of the leaf are captured. To estimate the base parameters (reflectance/transmittance), a novel optical arrangement is proposed. The chlorophyll content is then estimated by using linear regression where the inputs are the reflectance and transmittance of the leaf. Performance of the proposed method for chlorophyll content estimation was compared with a spectrophotometer and a Soil Plant Analysis Development (SPAD) meter. Chlorophyll content estimation was realized for Lactuca sativa L., Azadirachta indica , Canavalia ensiforme , and Lycopersicon esculentum . Experimental results showed that-in terms of accuracy and processing speed-the proposed algorithm outperformed many of the previous vision-based approach methods that have used SPAD as a reference device. On the other hand, the accuracy reached is 91% for crops such as Azadirachta indica , where the chlorophyll value was obtained using the spectrophotometer. Additionally, it was possible to achieve an estimation of the chlorophyll content in the leaf every 200 ms with a low-cost camera and a simple optical arrangement. This non-destructive method increased accuracy in the chlorophyll content estimation by using an optical arrangement that yielded both the reflectance and transmittance information, while the required hardware is cheap.

Soil Moisture Content Estimation using GPR Reflection Travel Time

NASA Astrophysics Data System (ADS)

Lunt, I. A.; Hubbard, S. S.; Rubin, Y.

2003-12-01

Ground-penetrating radar (GPR) reflection travel time data were used to estimate changes in soil water content under a range of soil saturation conditions throughout the growing season at a California winery. Data were collected during four data acquisition campaigns over an 80 by 180 m area using 100 MHz surface GPR antennae. GPR reflections were associated with a thin, low permeability clay layer located between 0.8 to 1.3 m below the ground surface that was calibrated with borehole information and mapped across the study area. Field infiltration tests and neutron probe logs suggest that the thin clay layer inhibited vertical water flow, and was coincident with high volumetric water content (VWC) values. The GPR reflection two-way travel time and the depth of the reflector at borehole locations were used to calculate an average dielectric constant for soils above the reflector. A site-specific relationship between the dielectric constant and VWC was then used to estimate the depth-averaged VWC of the soils above the reflector. Compared to average VWC measurements from calibrated neutron probe logs over the same depth interval, the average VWC estimates obtained from GPR reflections had an RMS error of 2 percent. We also investigated the estimation of VWC using reflections associated with an advancing water front, and found that estimates of average VWC to the water front could be obtained with similar accuracy. These results suggested that the two-way travel time to a GPR reflection associated with a geological surface or wetting front can be used under natural conditions to obtain estimates of average water content when borehole control is available. The GPR reflection method therefore has potential for monitoring soil water content over large areas and under variable hydrological conditions.

Application of near infrared spectroscopy (NIRS) to non-destructive internal quality inspection of tomatoes

NASA Astrophysics Data System (ADS)

Tao, Xuemei; He, Yong

2006-09-01

The internal quality of tomato such as acidity and sugar content is important to its taste thus influences the market. The objective of this paper was to demonstrate the feasibility of using a near-infrared spectroscopy (NIRS) to investigate the relationship between sugar content and acidity of tomato and absorption spectra. The N1RS reflectance of nondestructive tomatoes was measured with a Visible/NJR spectrophotometer in 325-1075 nm range. The sugar content and acidity of tomato were obtained with a handhold sugar content meter and a PH meter. The reflectance data set was recorded and analyzed with some mathematic methods. The PLS (Partial least squares) calibration method was developed for converting the NIRS reflectance of tomato into the data which determined the acidity value. BP (Back propagation) neural network was used to set up the relationship between the NIRS reflectance of tomato and sugar content. The acidity values were detected with an accuracy of 9O% and the sugar contents determined by the BP network were also very close to the measurements (coefficient of correlation r2=0.8764). NW spectra analysis would be very useful in the nondestructive internal quality inspecting of tomato.

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

PubMed Central

Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

2015-01-01

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. PMID:26698853

Chromosome-based survey sequencing reveals the genome organization of wild wheat progenitor Triticum dicoccoides.

PubMed

Akpinar, Bala Ani; Biyiklioglu, Sezgi; Alptekin, Burcu; Havránková, Miroslava; Vrána, Jan; Doležel, Jaroslav; Distelfeld, Assaf; Hernandez, Pilar; Budak, Hikmet

2018-05-04

Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Structure and evolution of the mitochondrial genome of Exorista sorbillans: the Tachinidae (Diptera: Calyptratae) perspective.

PubMed

Shao, Yuan-jun; Hu, Xian-qiong; Peng, Guang-da; Wang, Rui-xian; Gao, Rui-na; Lin, Chao; Shen, Wei-de; Li, Rui; Li, Bing

2012-12-01

The first complete mitochondrial genome (mitogenome) of Tachinidae Exorista sorbillans (Diptera) is sequenced by PCR-based approach. The circular mitogenome is 14,960 bp long and has the representative mitochondrial gene (mt gene) organization and order of Diptera. All protein-coding sequences are initiated with ATN codon; however, the only exception is Cox I gene, which has a 4-bp ATCG putative start codon. Ten of the thirteen protein-coding genes have a complete termination codon (TAA), but the rest are seated on the H strand with incomplete codons. The mitogenome of E. sorbillans is biased toward A+T content at 78.4 %, and the strand-specific bias is in reflection of the third codon positions of mt genes, and their T/C ratios as strand indictor are higher on the H strand more than those on the L strand pointing at any strain of seven Diptera flies. The length of the A+T-rich region of E. sorbillans is 106 bp, including a tandem triple copies of a13-bp fragment. Compared to Haematobia irritans, E. sorbillans holds distant relationship with Drosophila. Phylogenetic topologies based on the amino acid sequences, supporting that E. sorbillans (Tachinidae) is clustered with strains of Calliphoridae and Oestridae, and superfamily Oestroidea are polyphyletic groups with Muscidae in a clade.

Near-infrared diffuse reflection systems for chlorophyll content of tomato leaves measurement

NASA Astrophysics Data System (ADS)

Jiang, Huanyu; Ying, Yibin; Lu, Huishan

2006-10-01

In this study, two measuring systems for chlorophyll content of tomato leaves were developed based on near-infrared spectral techniques. The systems mainly consists of a FT-IR spectrum analyzer, optic fiber diffuses reflection accessories and data card. Diffuse reflectance of intact tomato leaves was measured by an optics fiber optic fiber diffuses reflection accessory and a smart diffuses reflection accessory. Calibration models were developed from spectral and constituent measurements. 90 samples served as the calibration sets and 30 samples served as the validation sets. Partial least squares (PLS) and principal component regression (PCR) technique were used to develop the prediction models by different data preprocessing. The best model for chlorophyll content had a high correlation efficient of 0.9348 and a low standard error of prediction RMSEP of 4.79 when we select full range (12500-4000 cm -1), MSC path length correction method by the log(1/R). The results of this study suggest that FT-NIR method can be feasible to detect chlorophyll content of tomato leaves rapidly and nondestructively.

Elementary teachers' perceptions about the effective features of explicit-reflective nature of science instruction

NASA Astrophysics Data System (ADS)

Adibelli-Sahin, Elif; Deniz, Hasan

2017-04-01

This qualitative study explored elementary teachers' perceptions about the effective features of explicit-reflective nature of science (NOS) instruction. Our participants were four elementary teachers from a public charter school located in the Southwestern U.S.A. The four elementary teachers participated in an academic year-long professional development about NOS which consisted of NOS training and NOS teaching phases. After each phase of the professional development, we specifically asked our participants which features of the explicit-reflective NOS instruction they found effective in improving their NOS conceptions by presenting pre- and post-profiles of their NOS conceptions. We identified nine features perceived by the participants as effective components of explicit-reflective NOS instruction: (1) specific focus on NOS content, (2) participation in hands-on NOS activities, (3) introductory NOS readings, (4) multiple types/forms of reflection, (5) multiple exposure to NOS content, (6) structural consistency in the presentation of NOS content, (7) the evaluation of secondary NOS data from elementary students, (8) the analysis of national and state science standards in terms of NOS content, and (9) NOS teaching experience.

Seismic stratigraphic characteristics of upper Louisiana continental slope: an area east of Green Canyon

USGS Publications Warehouse

Bouma, Arnold H.; Feeley, Mary H.; Kindinger, Jack G.; Stelting, Charles E.; Hilde, Thomas W.C.

1981-01-01

A high-resolution seismic reflection survey was conducted in a small area of the upper Louisiana Continental Slope known as Green Canyon Area. This area includes tracts 427, 428, 471, 472, 515, and 516, that will be offered for sale in March 1982 as part of Lease Sale 67.The sea floor of this region is, slightly hummocky and is underlain by salt diapirs that are mantled by early Tertiary shale. Most of the shale is overlain by younger Tertiary and Quaternary deposits, although locally some of the shale protrudes the sea floor. Because of proximity to older Mississippi River sources, the sediments are thick. The sediment cover shows an abundance of geologic phenomena such as horsts, grabens, growth faults, normal faults, and consolidation faults, zones with distinct and indistinct parallel reflections, semi-transparent zones, distorted zones, and angular unconformities.The major feature of this region is a N-S linear zone of uplifted and intruded sedimentary deposits formed due to diapiric intrusion.Small scale graben development over the crest of the structure can be attributed to extension and collapse. Large scale undulations of reflections well off the flanks of the uplifted structure suggest sediment creep and slumping. Dipping of parallel reflections show block faulting and tilting.Air gun (5 and 40 cubic inch) records reveal at least five major sequences that show masked onlap and slumping in their lower parts grading into more distinct parallel reflections in their upper parts. Such sequences can be related to local uplift and sea level changes. Minisparker records of this area show similar sequences but on a smaller scale. The distinct parallel reflections often onlap the diapir flanks. The highly reflective parts of these sequences may represent turbidite-type deposition, possibly at times of lower sea level. The acoustically more transparent parts of each sequence may represent deposits containing primarily hemipelagic and pelagic sediment.A complex ridge system is present along the west side of the area and distinct parallel reflections onlap onto this structure primarily from the east. Much of this deposition may be ascribed to sedimentation within a submarine canyon whose position is controlled by this ridge.

Light beam range finder

DOEpatents

McEwan, Thomas E.

1998-01-01

A "laser tape measure" for measuring distance which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%.

Light beam range finder

DOEpatents

McEwan, T.E.

1998-06-16

A ``laser tape measure`` for measuring distance is disclosed which includes a transmitter such as a laser diode which transmits a sequence of electromagnetic pulses in response to a transmit timing signal. A receiver samples reflections from objects within the field of the sequence of visible electromagnetic pulses with controlled timing, in response to a receive timing signal. The receiver generates a sample signal in response to the samples which indicates distance to the object causing the reflections. The timing circuit supplies the transmit timing signal to the transmitter and supplies the receive timing signal to the receiver. The receive timing signal causes the receiver to sample the reflection such that the time between transmission of pulses in the sequence in sampling by the receiver sweeps over a range of delays. The transmit timing signal causes the transmitter to transmit the sequence of electromagnetic pulses at a pulse repetition rate, and the received timing signal sweeps over the range of delays in a sweep cycle such that reflections are sampled at the pulse repetition rate and with different delays in the range of delays, such that the sample signal represents received reflections in equivalent time. The receiver according to one aspect of the invention includes an avalanche photodiode and a sampling gate coupled to the photodiode which is responsive to the received timing signal. The transmitter includes a laser diode which supplies a sequence of visible electromagnetic pulses. A bright spot projected on to the target clearly indicates the point that is being measured, and the user can read the range to that point with precision of better than 0.1%. 7 figs.

Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity.

PubMed

Andersen, Kenneth; Bird, Karen Lise; Rasmussen, Morten; Haile, James; Breuning-Madsen, Henrik; Kjaer, Kurt H; Orlando, Ludovic; Gilbert, M Thomas P; Willerslev, Eske

2012-04-01

DNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, the extent to which such 'dirt' DNA reflects taxonomic richness and structural diversity remains contentious. Here, we couple second generation high-throughput sequencing with 16S mitochondrial DNA (mtDNA) meta-barcoding, to explore the accuracy and sensitivity of 'dirt' DNA as an indicator of vertebrate diversity, from soil sampled at safari parks, zoological gardens and farms with known species compositions. PCR amplification was successful in the full pH range of the investigated soils (6.2 ± 0.2 to 8.3 ± 0.2), but inhibition was detected in extracts from soil of high organic content. DNA movement (leaching) through strata was evident in some sporadic cases and is influenced by soil texture and structure. We find that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species. However, one species that was recently introduced was not detected. Furthermore, animal behaviour was shown to influence DNA deposition rates. The approach potentially provides a quick methodological alternative to classical ecological surveys of biodiversity, and most reliable results are obtained with spatial sample replicates, while relative amounts of soil processed per site is of less importance. © 2011 Blackwell Publishing Ltd.

Sequence Composition and Gene Content of the Short Arm of Rye (Secale cereale) Chromosome 1

PubMed Central

Fluch, Silvia; Kopecky, Dieter; Burg, Kornel; Šimková, Hana; Taudien, Stefan; Petzold, Andreas; Kubaláková, Marie; Platzer, Matthias; Berenyi, Maria; Krainer, Siegfried; Doležel, Jaroslav; Lelley, Tamas

2012-01-01

Background The purpose of the study is to elucidate the sequence composition of the short arm of rye chromosome 1 (Secale cereale) with special focus on its gene content, because this portion of the rye genome is an integrated part of several hundreds of bread wheat varieties worldwide. Methodology/Principal Findings Multiple Displacement Amplification of 1RS DNA, obtained from flow sorted 1RS chromosomes, using 1RS ditelosomic wheat-rye addition line, and subsequent Roche 454FLX sequencing of this DNA yielded 195,313,589 bp sequence information. This quantity of sequence information resulted in 0.43× sequence coverage of the 1RS chromosome arm, permitting the identification of genes with estimated probability of 95%. A detailed analysis revealed that more than 5% of the 1RS sequence consisted of gene space, identifying at least 3,121 gene loci representing 1,882 different gene functions. Repetitive elements comprised about 72% of the 1RS sequence, Gypsy/Sabrina (13.3%) being the most abundant. More than four thousand simple sequence repeat (SSR) sites mostly located in gene related sequence reads were identified for possible marker development. The existence of chloroplast insertions in 1RS has been verified by identifying chimeric chloroplast-genomic sequence reads. Synteny analysis of 1RS to the full genomes of Oryza sativa and Brachypodium distachyon revealed that about half of the genes of 1RS correspond to the distal end of the short arm of rice chromosome 5 and the proximal region of the long arm of Brachypodium distachyon chromosome 2. Comparison of the gene content of 1RS to 1HS barley chromosome arm revealed high conservation of genes related to chromosome 5 of rice. Conclusions The present study revealed the gene content and potential gene functions on this chromosome arm and demonstrated numerous sequence elements like SSRs and gene-related sequences, which can be utilised for future research as well as in breeding of wheat and rye. PMID:22328922

An unbiased adaptive sampling algorithm for the exploration of RNA mutational landscapes under evolutionary pressure.

PubMed

Waldispühl, Jérôme; Ponty, Yann

2011-11-01

The analysis of the relationship between sequences and structures (i.e., how mutations affect structures and reciprocally how structures influence mutations) is essential to decipher the principles driving molecular evolution, to infer the origins of genetic diseases, and to develop bioengineering applications such as the design of artificial molecules. Because their structures can be predicted from the sequence data only, RNA molecules provide a good framework to study this sequence-structure relationship. We recently introduced a suite of algorithms called RNAmutants which allows a complete exploration of RNA sequence-structure maps in polynomial time and space. Formally, RNAmutants takes an input sequence (or seed) to compute the Boltzmann-weighted ensembles of mutants with exactly k mutations, and sample mutations from these ensembles. However, this approach suffers from major limitations. Indeed, since the Boltzmann probabilities of the mutations depend of the free energy of the structures, RNAmutants has difficulties to sample mutant sequences with low G+C-contents. In this article, we introduce an unbiased adaptive sampling algorithm that enables RNAmutants to sample regions of the mutational landscape poorly covered by classical algorithms. We applied these methods to sample mutations with low G+C-contents. These adaptive sampling techniques can be easily adapted to explore other regions of the sequence and structural landscapes which are difficult to sample. Importantly, these algorithms come at a minimal computational cost. We demonstrate the insights offered by these techniques on studies of complete RNA sequence structures maps of sizes up to 40 nucleotides. Our results indicate that the G+C-content has a strong influence on the size and shape of the evolutionary accessible sequence and structural spaces. In particular, we show that low G+C-contents favor the apparition of internal loops and thus possibly the synthesis of tertiary structure motifs. On the other hand, high G+C-contents significantly reduce the size of the evolutionary accessible mutational landscapes.

Use of high-dimensional spectral data to evaluate organic matter, reflectance relationships in soils

NASA Technical Reports Server (NTRS)

Henderson, T. L.; Baumgardner, M. F.; Coster, D. C.; Franzmeier, D. P.; Stott, D. E.

1990-01-01

Recent breakthroughs in remote sensing technology have led to the development of a spaceborne high spectral resolution imaging sensor, HIRIS, to be launched in the mid-1990s for observation of earth surface features. The effects of organic carbon content on soil reflectance over the spectral range of HIRIS, and to examine the contributions of humic and fulvic acid fractions to soil reflectance was evaluated. Organic matter from four Indiana agricultural soils was extracted, fractionated, and purified, and six individual components of each soil were isolated and prepared for spectral analysis. The four soils, ranging in organic carbon content from 0.99 percent, represented various combinations of genetic parameters such as parent material, age, drainage, and native vegetation. An experimental procedure was developed to measure reflectance of very small soil and organic component samples in the laboratory, simulating the spectral coverage and resolution of the HIRIS sensor. Reflectance in 210 narrow (10 nm) bands was measured using the CARY 17D spectrophotometer over the 400 to 2500 nm wavelength range. Reflectance data were analyzed statistically to determine the regions of the reflective spectrum which provided useful information about soil organic matter content and composition. Wavebands providing significant information about soil organic carbon content were located in all three major regions of the reflective spectrum: visible, near infrared, and middle infrared. The purified humic acid fractions of the four soils were separable in six bands in the 1600 to 2400 nm range, suggesting that longwave middle infrared reflectance may be useful as a non-destructive laboratory technique for humic acid characterization.

Qualitative Analysis of Written Reflections during a Teaching Certificate Program

PubMed Central

Castleberry, Ashley N.; Payakachat, Nalin; Ashby, Sarah; Nolen, Amanda; Carle, Martha; Neill, Kathryn K.

2016-01-01

Objective. To evaluate the success of a teaching certificate program by qualitatively evaluating the content and extent of participants’ reflections. Methods. Two investigators independently identified themes within midpoint and final reflection essays across six program years. Each essay was evaluated to determine the extent of reflection in prompted teaching-related topic areas (strengths, weaknesses, assessment, feedback). Results. Twenty-eight themes were identified within 132 essays. Common themes encompassed content delivery, student assessment, personal successes, and challenges encountered. Deep reflection was exhibited, with 48% of essays achieving the highest level of critical reflection. Extent of reflection trended higher from midpoint to final essays, with significant increases in the strengths and feedback areas. Conclusion. The teaching certificate program fostered critical reflection and self-reported positive behavior change in teaching, thus providing a high-quality professional development opportunity. Such programs should strongly consider emphasizing critical reflection through required reflective exercises at multiple points within program curricula. PMID:26941436

Visual Perceptual Echo Reflects Learning of Regularities in Rapid Luminance Sequences.

PubMed

Chang, Acer Y-C; Schwartzman, David J; VanRullen, Rufin; Kanai, Ryota; Seth, Anil K

2017-08-30

A novel neural signature of active visual processing has recently been described in the form of the "perceptual echo", in which the cross-correlation between a sequence of randomly fluctuating luminance values and occipital electrophysiological signals exhibits a long-lasting periodic (∼100 ms cycle) reverberation of the input stimulus (VanRullen and Macdonald, 2012). As yet, however, the mechanisms underlying the perceptual echo and its function remain unknown. Reasoning that natural visual signals often contain temporally predictable, though nonperiodic features, we hypothesized that the perceptual echo may reflect a periodic process associated with regularity learning. To test this hypothesis, we presented subjects with successive repetitions of a rapid nonperiodic luminance sequence, and examined the effects on the perceptual echo, finding that echo amplitude linearly increased with the number of presentations of a given luminance sequence. These data suggest that the perceptual echo reflects a neural signature of regularity learning.Furthermore, when a set of repeated sequences was followed by a sequence with inverted luminance polarities, the echo amplitude decreased to the same level evoked by a novel stimulus sequence. Crucially, when the original stimulus sequence was re-presented, the echo amplitude returned to a level consistent with the number of presentations of this sequence, indicating that the visual system retained sequence-specific information, for many seconds, even in the presence of intervening visual input. Altogether, our results reveal a previously undiscovered regularity learning mechanism within the human visual system, reflected by the perceptual echo. SIGNIFICANCE STATEMENT How the brain encodes and learns fast-changing but nonperiodic visual input remains unknown, even though such visual input characterizes natural scenes. We investigated whether the phenomenon of "perceptual echo" might index such learning. The perceptual echo is a long-lasting reverberation between a rapidly changing visual input and evoked neural activity, apparent in cross-correlations between occipital EEG and stimulus sequences, peaking in the alpha (∼10 Hz) range. We indeed found that perceptual echo is enhanced by repeatedly presenting the same visual sequence, indicating that the human visual system can rapidly and automatically learn regularities embedded within fast-changing dynamic sequences. These results point to a previously undiscovered regularity learning mechanism, operating at a rate defined by the alpha frequency. Copyright © 2017 the authors 0270-6474/17/378486-12$15.00/0.

Study on grain quality forecasting method and indicators by using hyperspectral data in wheat

NASA Astrophysics Data System (ADS)

Huang, Wenjiang; Wang, Jihua; Liu, Liangyun; Wang, Zhijie; Tan, Changwei; Song, Xiaoyu; Wang, Jingdi

2005-01-01

Field experiments were conducted to examine the influence factors of cultivar, nitrogen application and irrigation on grain protein content, gluten content and grain hardness in three winter wheat cultivars under four levels of nitrogen and irrigation treatments. Firstly, the influence of cultivars and environment factors on grain quality were studied, the effective factors were cultivars, irrigation, fertilization, et al. Secondly, total nitrogen content around winter wheat anthesis stage was proved to be significant correlative with grain protein content, and spectral vegetation index significantly correlated to total nitrogen content around anthesis stage were the potential indicators for grain protein content. Accumulation of total nitrogen content and its transfer to grain is the physical link to produce the final grain protein, and total nitrogen content at anthesis stage was proved to be an indicator of final grain protein content. The selected normalized photochemical reflectance index (NPRI) was proved to be able to predict of grain protein content on the close correlation between the ratio of total carotenoid to chlorophyll a and total nitrogen content. The method contributes towards developing optimal procedures for predicting wheat grain quality through analysis of their canopy reflected spectrum at anthesis stage. Regression equations were established for forecasting grain protein and dry gluten content by total nitrogen content at anthesis stage, so it is feasible for forecasting grain quality by establishing correlation equations between biochemical constitutes and canopy reflected spectrum.

Determining water content of fresh concrete by microwave reflection or transmission measurement.

DOT National Transportation Integrated Search

1987-01-01

In search of a rapid and accurate method for determining the water content of fresh concrete mixes, the microwave reflection and transmission properties of fresh concrete mixes were studied to determine the extent of correlation between each of these...

Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

PubMed

Wu, Zhikun; Wang, Bo; Chen, Xun; Wu, Jiangsheng; King, Graham J; Xiao, Yingjie; Liu, Kede

2016-01-01

High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.

Educative Mentoring: How a Mentor Supported a Preservice Biology Teacher's Pedagogical Content Knowledge Development

NASA Astrophysics Data System (ADS)

Barnett, Ellen; Friedrichsen, Patricia J.

2015-11-01

Research suggests discipline-specific, educative mentoring can help preservice teachers develop more sophisticated pedagogical content knowledge (PCK). However, there are few studies examining the nature of mentors' practice and how mentors influence preservice teacher's (PST) PCK. The purpose of this case study was to describe the strategies used by a secondary biology mentor teacher to support the development of a PST's PCK. The primary data sources were the transcripts of audio-recorded, daily meetings between the mentor and the PST during two curriculum units: DNA/Protein Synthesis and Evolution. The mentor influenced the PST's teaching orientation by repeatedly comparing teacher- and student-centered approaches, asking him to consider how students learn, and asking him to self-assess whether his instruction aligned with his teaching beliefs. The mentor helped the PST develop topic-specific knowledge of instructional strategies by sharing strategies she used previously, modeling critical reflection, and inviting him to critically reflect on his own instructional strategies. Topic-specific knowledge of students' understanding of science was developed by discussing common student misconceptions revealed in students' conversations and by sharing the results of test-item analysis from previous unit tests. The mentor helped develop the PST's topic-specific knowledge of assessment by helping him critically analyze and revise previous examinations to better align with the current curriculum units. Topic-specific knowledge of curricula was developed by jointly grappling with decisions about concept sequencing within units. The study includes implications for research, science teacher education, and professional development for mentors.

Contribution of pigment content, myoglobin forms and internal reflectance to the colour of pork loin and ham from pure breed pigs.

PubMed

Lindahl, G; Lundström, K; Tornberg, E

2001-10-01

The colour of loin, M. longissimus dorsi (LD), and ham, M. biceps femoris (BF), from pure breed Hampshire, Swedish Landrace and Swedish Yorkshire pigs was studied. The contribution of the pigment content, the myoglobin forms deoxymyoglobin (Mb), oxymyoglobin (MbO) and metmyoglobin (MetMb) and the internal reflectance to the colour of pork of normal meat quality was evaluated using partial least squares regression (PLS). The colour of LD and BF from the Hampshire breed was more red and yellow and more saturated than the colour of the same muscles from the Swedish Landrace and the Swedish Yorkshire breeds. Furthermore, BF from Hampshire was darker than BF from the other two breeds. These differences in colour were related to the lower pH in Hampshire, resulting in more blooming and in higher internal reflectance, and to the higher pigment content. The colour of BF was darker and more red than the colour of LD within each breed. No colour difference was found between gilts and castrates within each breed. Most of the variation (86-90%) in lightness (L* value), redness (a* value) and yellowness (b* value), chroma (saturation) and hue angle of pork of normal meat quality was explained by the pigment content, myoglobin forms and internal reflectance. The L* value, a* value, chroma and hue angle were influenced by both the pigment content and by the myoglobin forms to almost the same extent, while the internal reflectance was of no significance to these colour parameters. The b* value was influenced most by the myoglobin forms, less by the internal reflectance and almost not at all by the pigment content.

Fiber optic moisture sensor with moisture-absorbing reflective target

DOEpatents

Kirkham, Randy R.

1987-01-01

A method and apparatus for sensing moisture changes by utilizing optical fiber technology. One embodiment uses a reflective target at the end of an optical fiber. The reflectance of the target varies with its moisture content and can be detected by a remote unit at the opposite end of the fiber. A second embodiment utilizes changes in light loss along the fiber length. This can be attributed to changes in reflectance of cladding material as a function of its moisture content. It can also be affected by holes or inserts interposed in the cladding material and/or fiber. Changing light levels can also be coupled from one fiber to another in an assembly of fibers as a function of varying moisture content in their overlapping lengths of cladding material.

Study on preparation and mechanical performance of TPU/nonwoven composites

NASA Astrophysics Data System (ADS)

Sun, X. C.; Xi, B. J.

2016-07-01

In order to study the influence of resin content and layer sequence parameters on the mechanical properties of TPU/non-woven composite materials synthesized by moulding pressing technology. The effects of the resin content and layer sequence on composites were discussed. Through experiments and theoretical analysis, it was revealed how resin content, layer sequence impact on mechanical properties of composite. The mechanics properties of TPU/non-woven composite materials are improved. The process is pressure 0.5 MPa, temperature 110 °C and time 120s min. The melting of the TPU infiltrated into the fabric and filled the space between the fibers.

Ecophysiological Remote Sensing of Leaf-Canopy Photosynthetic Characteristics in a Cool-Temperate Deciduous Forest in Japan

NASA Astrophysics Data System (ADS)

Noda, H. M.; Muraoka, H.

2014-12-01

Satellite remote sensing of structure and function of canopy is crucial to detect temporal and spatial distributions of forest ecosystems dynamics in changing environments. The spectral reflectance of the canopy is determined by optical properties (spectral reflectance and transmittance) of single leaves and their spatial arrangements in the canopy. The optical properties of leaves reflect their pigments contents and anatomical structures. Thus detailed information and understandings of the consequence between ecophysiological traits and optical properties from single leaf to canopy level are essential for remote sensing of canopy ecophysiology. To develop the ecophysiological remote sensing of forest canopy, we have been promoting multiple and cross-scale measurements in "Takayama site" belonging to AsiaFlux and JaLTER networks, located in a cool-temperate deciduous broadleaf forest on a mountainous landscape in Japan. In this forest, in situ measurement of canopy spectral reflectance has been conducted continuously by a spectroradiometer as part of the "Phenological Eyes Network (PEN)" since 2004. To analyze the canopy spectral reflectance from leaf ecophysiological viewpoints, leaf mass per area, nitrogen content, chlorophyll contents, photosynthetic capacities and the optical properties have been measured for dominant canopy tree species Quercus crispla and Betula ermanii throughout the seasons for multiple years.Photosynthetic capacity was largely correlated with chlorophyll contents throughout the growing season in both Q. crispla and B. ermanii. In these leaves, the reflectance at "red edge" (710 nm) changed by corresponding to the changes of chlorophyll contents throughout the seasons. Our canopy-level examination showed that vegetation indices obtained by red edge reflectance have linear relationship with leaf chlorophyll contents and photosynthetic capacity. Finally we apply this knowledge to the Rapid Eye satellite imagery around Takayama site to scale-up the leaf-level findings to canopy and landscape levels on a mountainous landscape.

Estimation of canopy carotenoid content of winter wheat using multi-angle hyperspectral data

NASA Astrophysics Data System (ADS)

Kong, Weiping; Huang, Wenjiang; Liu, Jiangui; Chen, Pengfei; Qin, Qiming; Ye, Huichun; Peng, Dailiang; Dong, Yingying; Mortimer, A. Hugh

2017-11-01

Precise estimation of carotenoid (Car) content in crops, using remote sensing data, could be helpful for agricultural resources management. Conventional methods for Car content estimation were mostly based on reflectance data acquired from nadir direction. However, reflectance acquired at this direction is highly influenced by canopy structure and soil background reflectance. Off-nadir observation is less impacted, and multi-angle viewing data are proven to contain additional information rarely exploited for crop Car content estimation. The objective of this study was to explore the potential of multi-angle observation data for winter wheat canopy Car content estimation. Canopy spectral reflectance was measured from nadir as well as from a series of off-nadir directions during different growing stages of winter wheat, with concurrent canopy Car content measurements. Correlation analyses were performed between Car content and the original and continuum removed spectral reflectance. Spectral features and previously published indices were derived from data obtained at different viewing angles and were tested for Car content estimation. Results showed that spectral features and indices obtained from backscattering directions between 20° and 40° view zenith angle had a stronger correlation with Car content than that from the nadir direction, and the strongest correlation was observed from about 30° backscattering direction. Spectral absorption depth at 500 nm derived from spectral data obtained from 30° backscattering direction was found to reduce the difference induced by plant cultivars greatly. It was the most suitable for winter wheat canopy Car estimation, with a coefficient of determination 0.79 and a root mean square error of 19.03 mg/m2. This work indicates the importance of taking viewing geometry effect into account when using spectral features/indices and provides new insight in the application of multi-angle remote sensing for the estimation of crop physiology.

Effect of Multiangular Observations on Crop Chlorophyll Content Retrieval Using Field Top-Of Spectrometer Data

NASA Astrophysics Data System (ADS)

Jiao, Q.; Liu, L.; Zhang, B.

2017-12-01

Leaf chlorophyll content is an important indicator of crop growth condition that determines final crop yield. A lot of research on remote sensing of leaf chlorophyll content were based on reflectance data acquired from nadir direction. However, reflectance data at nadir may be affected by soil background. In fact, many satellite sensors with capability of chlorophyll retrieval, like the 68.5 degrees field-of-view MERIS, have produced large multiangular data. This study tries to assess the anisotropic effect on the retrieval of leaf chlorophyll content using field hyperspectral data of wheat canopy. The field multi-angle observation experiment of winter wheat was carried out in April 2017 in Xiaotangshan agriculture demonstration study site in Beijing. Field canopy spectra and leaf chlorophyll content of winter wheat were measured. The most used indices for chlorophyll content retrieval, such as CIred-edge, REP, MTCI, MCARI/OSAVI[705,750], TCARI/OSAVI[705,750], were calculated based on the filed multiangular reflectance. The ratio index TCARI/OSAVI owned the best results in estimating leaf chlorophyll content (R2 of 0.62) among all the selected indices, when using the top-of-canopy reflectance at nadir. The determination coefficient of the relationship of TCARI/OSAVI with chlorophyll content reached its peak (R2 of 0.70) at angle of 15 degrees, and the minimum R2 value of only 0.25 at angle of 60 degrees. The MTCI got the peak of determination coefficient (R2 of 0.63) at angle of 15 degrees and the minimum value (R2 of 0.57) for 60 degrees. Our results showed the MTCI could keep a more satisfactory correlation with leaf chlorophyll content of winter wheat, however the mean values of the MTCI basically decreased as the observation angle increases. This work shows the strong anisotropic effects of top-of-canopy reflectance which influences most of selected popular chlorophyll indices. If spectral index selection is proper, multiangular remote sensing could produce higher accuracy for leaf chlorophyll content retrieval than only using nadir observation. Multi-angular remote sensing has the potential of leaf chlorophyll content retrieval for diagnosis of crop nitrogen stress or water stress.

The role of linguistic experience in the processing of probabilistic information in production.

PubMed

Gustafson, Erin; Goldrick, Matthew

2018-01-01

Speakers track the probability that a word will occur in a particular context and utilize this information during phonetic processing. For example, content words that have high probability within a discourse tend to be realized with reduced acoustic/articulatory properties. Such probabilistic information may influence L1 and L2 speech processing in distinct ways (reflecting differences in linguistic experience across groups and the overall difficulty of L2 speech processing). To examine this issue, L1 and L2 speakers performed a referential communication task, describing sequences of simple actions. The two groups of speakers showed similar effects of discourse-dependent probabilistic information on production, suggesting that L2 speakers can successfully track discourse-dependent probabilities and use such information to modulate phonetic processing.

Genomic minimalism in the early diverging intestinal parasite Giardia lamblia.

PubMed

Morrison, Hilary G; McArthur, Andrew G; Gillin, Frances D; Aley, Stephen B; Adam, Rodney D; Olsen, Gary J; Best, Aaron A; Cande, W Zacheus; Chen, Feng; Cipriano, Michael J; Davids, Barbara J; Dawson, Scott C; Elmendorf, Heidi G; Hehl, Adrian B; Holder, Michael E; Huse, Susan M; Kim, Ulandt U; Lasek-Nesselquist, Erica; Manning, Gerard; Nigam, Anuranjini; Nixon, Julie E J; Palm, Daniel; Passamaneck, Nora E; Prabhu, Anjali; Reich, Claudia I; Reiner, David S; Samuelson, John; Svard, Staffan G; Sogin, Mitchell L

2007-09-28

The genome of the eukaryotic protist Giardia lamblia, an important human intestinal parasite, is compact in structure and content, contains few introns or mitochondrial relics, and has simplified machinery for DNA replication, transcription, RNA processing, and most metabolic pathways. Protein kinases comprise the single largest protein class and reflect Giardia's requirement for a complex signal transduction network for coordinating differentiation. Lateral gene transfer from bacterial and archaeal donors has shaped Giardia's genome, and previously unknown gene families, for example, cysteine-rich structural proteins, have been discovered. Unexpectedly, the genome shows little evidence of heterozygosity, supporting recent speculations that this organism is sexual. This genome sequence will not only be valuable for investigating the evolution of eukaryotes, but will also be applied to the search for new therapeutics for this parasite.

A genomic view of 500 million years of cnidarian evolution

PubMed Central

Steele, Robert E.; David, Charles N.; Technau, Ulrich

2010-01-01

Cnidarians (corals, anemones, jellyfish, and hydras) are a diverse group of animals of interest to evolutionary biologists, ecologists, and developmental biologists. With the publication of the genome sequences of Hydra and Nematostella, whose last common ancestor was the stem cnidarian, we are beginning to see the genomic underpinnings of cnidarian biology. Cnidarians are known for the remarkable plasticity of their morphology and life cycles. This plasticity is reflected in the Hydra and Nematostella genomes, which differ to an exceptional degree in size, base composition, transposable element content, and gene conservation. We now know what cnidarian genomes are capable of doing given 500 million years; the next challenge is to understand how this genomic history has led to the striking diversity we see in cnidarians. PMID:21047698

Normalization of Complete Genome Characteristics: Application to Evolution from Primitive Organisms to Homo sapiens.

PubMed

Sorimachi, Kenji; Okayasu, Teiji; Ohhira, Shuji

2015-04-01

Normalized nucleotide and amino acid contents of complete genome sequences can be visualized as radar charts. The shapes of these charts depict the characteristics of an organism's genome. The normalized values calculated from the genome sequence theoretically exclude experimental errors. Further, because normalization is independent of both target size and kind, this procedure is applicable not only to single genes but also to whole genomes, which consist of a huge number of different genes. In this review, we discuss the applications of the normalization of the nucleotide and predicted amino acid contents of complete genomes to the investigation of genome structure and to evolutionary research from primitive organisms to Homo sapiens. Some of the results could never have been obtained from the analysis of individual nucleotide or amino acid sequences but were revealed only after the normalization of nucleotide and amino acid contents was applied to genome research. The discovery that genome structure was homogeneous was obtained only after normalization methods were applied to the nucleotide or predicted amino acid contents of genome sequences. Normalization procedures are also applicable to evolutionary research. Thus, normalization of the contents of whole genomes is a useful procedure that can help to characterize organisms.

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

PubMed

Liu, Sophia S; Hockenberry, Adam J; Lancichinetti, Andrea; Jewett, Michael C; Amaral, Luís A N

2016-11-01

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. In order to accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. While many tools have been developed to create random nucleotide sequences, protein coding sequences are subject to a unique set of constraints that complicates the process of generating appropriate null models. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content for the purpose of hypothesis testing. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content, which we have developed into a python package. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. Furthermore, this approach can easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes as well as more effective engineering of biological systems.

College Students' Responses to Suicidal Content on Social Networking Sites: An Examination Using a Simulated Facebook Newsfeed.

PubMed

Corbitt-Hall, Darcy J; Gauthier, Jami M; Davis, Margaret T; Witte, Tracy K

2016-10-01

Although Facebook has a peer-initiated suicide prevention protocol, little is known about users' abilities to notice, recognize, and appropriately interpret suicidal content or about their willingness to intervene. In this study, 468 college students were randomly assigned to interact with a simulated Facebook newsfeed containing content reflecting various suicide risk levels. A larger proportion of those exposed to content reflecting moderate and severe suicide risk noticed, recognized, appropriately interpreted, and endorsed taking action to intervene, as compared to those exposed to content representing no or low risk. Overall, results indicate that college students are responsive to suicidal content on Facebook. © 2016 The American Association of Suicidology.

Opinion: Clarifying Two Controversies about Information Mapping's Method.

ERIC Educational Resources Information Center

Horn, Robert E.

1992-01-01

Describes Information Mapping, a methodology for the analysis, organization, sequencing, and presentation of information and explains three major parts of the method: (1) content analysis, (2) project life-cycle synthesis and integration of the content analysis, and (3) sequencing and formatting. Major criticisms of the methodology are addressed.…

Submarine fans: Characteristics, models, classification, and reservoir potential

NASA Astrophysics Data System (ADS)

Shanmugam, G.; Moiola, R. J.

1988-02-01

Submarine-fan sequences are important hydrocarbon reservoirs throughout the world. Submarine-fan sequences may be interpreted from bed-thickness trends, turbidite facies associations, log motifs, and seismic-reflection profiles. Turbidites occurring predominantly in channels and lobes (or sheet sands) constitute the major portion of submarine-fan sequences. Thinning- and thickening-upward trends are suggestive of channel and lobe deposition, respectively. Mounded seismic reflections are commonly indicative of lower-fan depositional lobes. Fan models are discussed in terms of modern and ancient fans, attached and detached lobes, highly efficient and poorly efficient systems, and transverse and longitudinal fans. In general, depositional lobes are considered to be attached to feeder channels. Submarine fans can be classified into four types based on their tectonic settings: (1) immature passive-margin fans (North Sea type); (2) mature passive-margin fans (Atlantic type); (3) active-margin fans (Pacific type); and (4) mixed-setting fans. Immature passive-margin fans (e.g., Balder, North Sea), and active-margin fans (e.g., Navy, Pacific Ocean) are usually small, sand-rich, and possess well developed lobes. Mature passive-margin fans (e.g., Amazon, Atlantic Ocean) are large, mud-rich, and do not develop typical lobes. However, sheet sands are common in the lower-fan regions of mature passive-margin fans. Mixed-setting fans display characteristics of either Atlantic type (e.g., Bengal, Bay of Bengal), or Pacific type (Orinoco, Caribbean), or both. Conventional channel-lobe models may not be applicable to fans associated with mature passive margins. Submarine fans develop primarily during periods of low sea level on both active- and passive-margin settings. Consequently, hydrocarbon-bearing fan sequences are associated generally with global lowstands of sea level. Channel-fill sandstones in most tectonic settings are potential reservoirs. Lobes exhibit the most favorable reservoir quality in terms of sand content, lateral continuity, and porosity development. Lower-fan sheet sands may also make good reservoirs. Quartz-rich sandstones of mature passive-margin fans are most likely to preserve depositional porosity, whereas lithic sandstones of active-margin fans may not.

TRAP: automated classification, quantification and annotation of tandemly repeated sequences.

PubMed

Sobreira, Tiago José P; Durham, Alan M; Gruber, Arthur

2006-02-01

TRAP, the Tandem Repeats Analysis Program, is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences. TRAP uses the results of the Tandem Repeats Finder program to perform a global analysis of the satellite content of DNA sequences, permitting researchers to easily assess the tandem repeat content for both individual sequences and whole genomes. The results can be generated in convenient formats such as HTML and comma-separated values. TRAP can also be used to automatically generate annotation data in the format of feature table and GFF files.

Density-independent algorithm for sensing moisture content of sawdust based on reflection measurements

USDA-ARS?s Scientific Manuscript database

A density-independent algorithm for moisture content determination in sawdust, based on a one-port reflection measurement technique is proposed for the first time. Performance of this algorithm is demonstrated through measurement of the dielectric properties of sawdust with an open-ended haft-mode s...

Event-related potentials in response to violations of content and temporal event knowledge.

PubMed

Drummer, Janna; van der Meer, Elke; Schaadt, Gesa

2016-01-08

Scripts that store knowledge of everyday events are fundamentally important for managing daily routines. Content event knowledge (i.e., knowledge about which events belong to a script) and temporal event knowledge (i.e., knowledge about the chronological order of events in a script) constitute qualitatively different forms of knowledge. However, there is limited information about each distinct process and the time course involved in accessing content and temporal event knowledge. Therefore, we analyzed event-related potentials (ERPs) in response to either correctly presented event sequences or event sequences that contained a content or temporal error. We found an N400, which was followed by a posteriorly distributed P600 in response to content errors in event sequences. By contrast, we did not find an N400 but an anteriorly distributed P600 in response to temporal errors in event sequences. Thus, the N400 seems to be elicited as a response to a general mismatch between an event and the established event model. We assume that the expectancy violation of content event knowledge, as indicated by the N400, induces the collapse of the established event model, a process indicated by the posterior P600. The expectancy violation of temporal event knowledge is assumed to induce an attempt to reorganize the event model in working memory, a process indicated by the frontal P600. Copyright © 2015 Elsevier Ltd. All rights reserved.

Chlorophyll content retrieval from hyperspectral remote sensing imagery.

PubMed

Yang, Xiguang; Yu, Ying; Fan, Wenyi

2015-07-01

Chlorophyll content is the essential parameter in the photosynthetic process determining leaf spectral variation in visible bands. Therefore, the accurate estimation of the forest canopy chlorophyll content is a significant foundation in assessing forest growth and stress affected by diseases. Hyperspectral remote sensing with high spatial resolution can be used for estimating chlorophyll content. In this study, the chlorophyll content was retrieved step by step using Hyperion imagery. Firstly, the spectral curve of the leaf was analyzed, 25 spectral characteristic parameters were identified through the correlation coefficient matrix, and a leaf chlorophyll content inversion model was established using a stepwise regression method. Secondly, the pixel reflectance was converted into leaf reflectance by a geometrical-optical model (4-scale). The three most important parameters of reflectance conversion, including the multiple scattering factor (M 0 ), and the probability of viewing the sunlit tree crown (P T ) and the background (P G ), were estimated by leaf area index (LAI), respectively. The results indicated that M 0 , P T , and P G could be described as a logarithmic function of LAI, with all R (2) values above 0.9. Finally, leaf chlorophyll content was retrieved with RMSE = 7.3574 μg/cm(2), and canopy chlorophyll content per unit ground surface area was estimated based on leaf chlorophyll content and LAI. Chlorophyll content mapping can be useful for the assessment of forest growth stage and diseases.

Spectral reflectance of surface soils: Relationships with some soil properties

NASA Technical Reports Server (NTRS)

Kiesewetter, C. H.

1983-01-01

Using a published atlas of reflectance curves and physicochemical properties of soils, a statistical analysis was carried out. Reflectance bands which correspond to five of the wavebands used by NASA's Thematic Mapper were examined for relationships to specific soil properties. The properties considered in this study include: Sand Content, Silt Content, Clay Content, Organic Matter Content, Cation Exchange Capacity, Iron Oxide Content and Moisture Content. Regression of these seven properties on the mean values of five TM bands produced results that indicate that the predictability of the properties can be increased by stratifying the data. The data was stratified by parent material, taxonomic order, temperature zone, moisture zone and climate (combined temperature and moisture). The best results were obtained when the sample was examined by climatic classes. The middle Infra-red bands, 5 and 7, as well as the visible bands, 2 and 3, are significant in the model. The near Infra-red band, band 4, is almost as useful and should be included in any studies. General linear modeling procedures examined relationships of the seven properties with certain wavebands in the stratified samples.

Three-Year High School Science Core Curriculum: A Framework.

ERIC Educational Resources Information Center

Bardeen, Marjorie; Freeman, Wade; Lederman, Leon; Marshall, Stephanie; Thompson, Bruce; Young, M. Jean

It is time to start a complete re-structuring of the high school science sequence: new content, new instructional materials, new laboratories, new assessment tools, and new teacher preparation. This white paper initiates re-structuring by proposing organization, pedagogy, and content for a new sequence of science courses. The proposal respects the…

Epistemic Search Sequences in Peer Interaction in a Content-Based Language Classroom

ERIC Educational Resources Information Center

Jakonen, Teppo; Morton, Tom

2015-01-01

Epistemics in interaction refers to how participants display, manage, and orient to their own and others' states of knowledge. This article applies recent conversation analytical work on epistemics to classrooms where language and content instruction are combined. It focuses on Epistemic Search Sequences (ESSs) through which students in peer…

Curriculum Mapping in Higher Education: A Case Study and Proposed Content Scope and Sequence Mapping Tool

ERIC Educational Resources Information Center

Arafeh, Sousan

2016-01-01

Best practice in curriculum development and implementation requires that discipline-based standards or requirements embody both curricular and programme scopes and sequences. Ensuring these are present and aligned in course/programme content, activities and assessments to support student success requires formalised and systematised review and…

Analysis of SINE and LINE repeat content of Y chromosomes in the platypus, Ornithorhynchus anatinus.

PubMed

Kortschak, R Daniel; Tsend-Ayush, Enkhjargal; Grützner, Frank

2009-01-01

Monotremes feature an extraordinary sex-chromosome system that consists of five X and five Y chromosomes in males. These sex chromosomes share homology with bird sex chromosomes but no homology with the therian X. The genome of a female platypus was recently completed, providing unique insights into sequence and gene content of autosomes and X chromosomes, but no Y-specific sequence has so far been analysed. Here we report the isolation, sequencing and analysis of approximately 700 kb of sequence of the non-recombining regions of Y2, Y3 and Y5, which revealed differences in base composition and repeat content between autosomes and sex chromosomes, and within the sex chromosomes themselves. This provides the first insights into repeat content of Y chromosomes in platypus, which overall show similar patterns of repeat composition to Y chromosomes in other species. Interestingly, we also observed differences between the various Y chromosomes, and in combination with timing and activity patterns we provide an approach that can be used to examine the evolutionary history of the platypus sex-chromosome chain.

Protein functional features are reflected in the patterns of mRNA translation speed.

PubMed

López, Daniel; Pazos, Florencio

2015-07-09

The degeneracy of the genetic code makes it possible for the same amino acid string to be coded by different messenger RNA (mRNA) sequences. These "synonymous mRNAs" may differ largely in a number of aspects related to their overall translational efficiency, such as secondary structure content and availability of the encoded transfer RNAs (tRNAs). Consequently, they may render different yields of the translated polypeptides. These mRNA features related to translation efficiency are also playing a role locally, resulting in a non-uniform translation speed along the mRNA, which has been previously related to some protein structural features and also used to explain some dramatic effects of "silent" single-nucleotide-polymorphisms (SNPs). In this work we perform the first large scale analysis of the relationship between three experimental proxies of mRNA local translation efficiency and the local features of the corresponding encoded proteins. We found that a number of protein functional and structural features are reflected in the patterns of ribosome occupancy, secondary structure and tRNA availability along the mRNA. One or more of these proxies of translation speed have distinctive patterns around the mRNA regions coding for certain protein local features. In some cases the three patterns follow a similar trend. We also show specific examples where these patterns of translation speed point to the protein's important structural and functional features. This support the idea that the genome not only codes the protein functional features as sequences of amino acids, but also as subtle patterns of mRNA properties which, probably through local effects on the translation speed, have some consequence on the final polypeptide. These results open the possibility of predicting a protein's functional regions based on a single genomic sequence, and have implications for heterologous protein expression and fine-tuning protein function.

Sedimentary evidence of landscape and climate history since the end of MIS 3 in the Krkonoše Mountains, Czech Republic

NASA Astrophysics Data System (ADS)

Engel, Zbyněk; Nývlt, Daniel; Křížek, Marek; Treml, Václav; Jankovská, Vlasta; Lisá, Lenka

2010-04-01

A sedimentary core recovered from the cirque basin of Labský důl valley (1039 m a.s.l.) in the Krkonoše Mountains reflects the environmental history for approximately the last 30,000 years. Analyses of magnetic susceptibility, carbon content, pollen assemblages and macrofossil data in a 15 m thick sediment sequence provide the first continuous record of Lateglacial and Holocene vegetation history in Sudetes region of the Czech Republic. The succession of sedimentary units in the lower part of the core suggests that the cirque was ice-free before the onset of the last glaciation at the beginning of marine isotope stage 2. Highly variable climate prevailed during this period with cold conditions culminating about 18 cal ka BP. Cold climates persisted until the Lateglacial period, evidenced by an identified warming and subsequent cooling event correlated with the Younger Dryas period. Sparse, treeless vegetation dominated in the catchment area at that time. The sequence of interrupted thinly laminated silts reflects the retreat and temporary readvance of a local glacier in the cirque during 12.5-10.8 cal ka BP. Subsequently, the alpine treeline ecotone gradually shifted above the cirque floor. Palaeoclimatic conditions in the early Holocene fluctuated strongly, whereas since 5.1 cal ka BP conditions have been more stable. Pollen-based climate reconstructions suggest significant cooling at around 9.8-9.3, 7.7-7.5 and 4.0-3.3 cal ka BP. Spruce forests have dominated the site since 5.0 cal ka BP when the vegetation became similar to the modern one. Two phases of increased sedimentation were identified within the Holocene culminating about 9.2-7.5 cal ka BP and 5.8-5.5 cal ka BP. Sediment yield was as high as 2.4 mm yr -1 during the period, reflecting environmental changes during the Atlantic/Sub-Boreal transition.

Geochemistry of Permian rocks from the margins of the Phosphoria Basin

USGS Publications Warehouse

Perkins, Robert B.; McIntyre, Brandie; Hein, James R.; Piper, David Z.

2003-01-01

The Permian Phosphoria Formation and interbedded units of the Park City Formation and Shedhorn Sandstone in western Wyoming represent deposition along a carbonate ramp at the eastern margin of the Phosphoria Basin, with portions of the Phosphoria units reflecting periods of upwelling and widespread phosphogenesis. Thickness-weighted slab-samples of these units were collected at a maximum interval of 3 m along an 80+ m-length of unweathered core and analyzed for major-, minor-, and trace-element contents. Interpretations of geochemistry were made within the confines of a previously recognized sequence stratigraphy framework. Major shifts in element ratios characteristic of terrigenous debris that occur at sequence boundaries at the base of the Meade Peak and Retort Members of the Phosphoria Formation are attributed to changing sediment sources. Inter-element relationships in the marine fraction indicate that bottom waters of the Phosphoria Basin were predominantly denitrifying during deposition of the Ervay, Grandeur, and Phosphoria sediments, although sulfate-reducing conditions may have existed during deposition of the lower Meade Peak sediments. Oxic conditions were prevalent during deposition of a large part of the Franson Member, which represents sedimentation in a shallow, inner- to back-ramp setting. Variations in sediment facies and organic matter and trace element contents largely reflect changes in Permian sea level. Changes in sea level in basin-margin areas, such as represented by the study section, may have affected the oxidation of settling organic matter, the foci of intersection of upwelling bottom waters with the photic zone, the rate of terrigenous sedimentation, and, ultimately, the overall environment of deposition. Our study suggests that phosphogenesis can occur under lowstand, transgressive, and highstand conditions in marginal areas, assuming water depths sufficient for upwelling to occur. Formation of phosphorite layers under upwelling conditions appears to have been most dependent on a lack of dilution by terrigenous sedimentation and carbonate shoaling. Differences in the geochemistry between two similar environments represented by the upper and lower Phosphoria units are largely attributed to higher rates of diluting terrigenous sediment during deposition of the upper unit. This is consistent with prior interpretations of a more shoreward setting for the upper Phosphoria.

TXESS Revolution: Utilizing TERC's EarthLabs Cryosphere Module to Support Professional Development of Texas Teachers

NASA Astrophysics Data System (ADS)

Odell, M.; Ellins, K. K.; Polito, E. J.; Castillo Comer, C. A.; Stocks, E.; Manganella, K.; Ledley, T. S.

2010-12-01

TERC’s EarthLabs project provides rigorous and engaging Earth and environmental science labs. Four existing modules illustrate sequences for learning science concepts through data analysis activities and hands-on experiments. A fifth module, developed with NSF, comprises a series of linked inquiry based activities focused on the cryosphere to help students understand concepts around change over time on multiple and embedded time scales. Teachers recruited from the NSF-OEDG-sponsored Texas Earth and Space Science (TXESS) Revolution teacher professional development program conducted a pedagogical review of the Cryosphere EarthLabs module and provided feedback on how well the materials matched high school needs in Texas and were aligned with state and national standards. Five TXESS Revolution teachers field tested the materials in their classrooms and then trained other TXESS Revolution teachers on their implementation during spring and summer 2010. Here we report on the results of PD delivery during the summer 2010 TXESS Revolution summer institute as determined by (1) a set of evaluation instruments that included a pre-post concept map activity to assess changes in workshop teachers’ understanding of the concepts presented, a pre-post test content knowledge test, and a pre-post survey of teachers’ comfort in teaching the Texas Earth and Space Science standards addressed by the module; (2) teacher reflections; and (3) focus group responses. The findings reveal that the teachers liked the module activities and felt they could use them to teach Environmental and Earth Science. They appreciated that the sequence of activities contributed to a deeper understanding and observed that the variety of methods used to present the information accommodates different learning styles. Information about the cryosphere was new to all the teachers. The content knowledge tests reveal that although teachers made appreciable gains, their understanding of cryosphere, how it changes over time, and it’s role in Earth’s climate system remains weak. Our results clearly reflect the challenges of addressing the complexity of climate science and critical need for climate literacy education.

Analysis of pedagogical content knowledge (PCK) ability of science teachers in planning and reflecting on environmental pollution content

NASA Astrophysics Data System (ADS)

Purwianingsih, W.; Mardiyah, A.

2018-05-01

Pedagogical Content Knowledge (PCK) is a blend of content knowledge and pedagogy knowledge, which can illustrate the ability of teachers to design and to teach a content by accessing what they knows about the material, students, curriculum and how best to teach the content. Description of PCK ability of science teachers can be accessed through an analysis of their ability to plan and reflect on learning. This study aims to provide an overview of teachers’ PCK skills on environmental pollution materials through use of Content Representation (CoRe) and Pedagogical and Professional-experience Repertoires (PaP-eRs). Descriptive method used in this study with six of science teachers on 7th class from three different schools as subject. The results show that teachers’ PCK skills in planning through CoRe and reflecting through PaP-eRs are in fairly good category. The teacher’s ability in implementing environmental pollution learning materials is in good category. However, there is still a discrepancy between planning through CoRe and the implementation of classroom learning. The teacher’s PCK is influenced by teaching experience and educational background.

Reflection as a component of formative assessment appears to be instrumental in promoting the use of feedback; an observational study.

PubMed

Pelgrim, E A M; Kramer, A W M; Mokkink, H G A; van der Vleuten, C P M

2013-09-01

Although the literature suggests that reflection has a positive impact on learning, there is a paucity of evidence to support this notion. We investigated feedback and reflection in relation to the likelihood that feedback will be used to inform action plans. We hypothesised that feedback and reflection present a cumulative sequence (i.e. trainers only pay attention to trainees' reflections when they provided specific feedback) and we hypothesised a supplementary effect of reflection. We analysed copies of assessment forms containing trainees' reflections and trainers' feedback on observed clinical performance. We determined whether the response patterns revealed cumulative sequences in line with the Guttman scale. We further examined the relationship between reflection, feedback and the mean number of specific comments related to an action plan (ANOVA) and we calculated two effect sizes. Both hypotheses were confirmed by the results. The response pattern found showed an almost perfect fit with the Guttman scale (0.99) and reflection seems to have supplementary effect on the variable action plan. Reflection only occurs when a trainer has provided specific feedback; trainees who reflect on their performance are more likely to make use of feedback. These results confirm findings and suggestions reported in the literature.

Feeding by Pseudocalanus copepods in the Bering Sea: Trophic linkages and a potential mechanism of niche partitioning

NASA Astrophysics Data System (ADS)

Cleary, Alison C.; Durbin, Edward G.; Rynearson, Tatiana A.; Bailey, Jennifer

2016-12-01

Pseudocalanus copepods are small, abundant zooplankton in the Bering Sea ecosystem that play an important role in transferring primary production to fish and other higher trophic-level predators. Four morphologically cryptic species, the primarily arctic Pseudocalanus minutus and Pseudocalanus acuspes, and the more temperate Pseudocalanus newmani and Pseudocalanus mimus, are found within the Bering Sea. Pseudocalanus are generally considered phytoplanktivores. However, their feeding is poorly known, despite their importance to the ecosystem. In situ feeding by the three most abundant Pseudocalanus congeners, P. minutus, P. newmani, and P. acuspes, was investigated by sequencing partial 18S rDNA (ribosomal Deoxyribonucleic Acid) of gut contents from 225 individuals sampled from 8 stations across the Bering Sea in May and June of 2010. The 28,456 prey 18S rDNA sequences obtained clustered into 138 distinct prey items with a 97% similarity cut-off, and included diatoms, dinoflagellates, microzooplankton, mesozooplankton, and vascular plants. Pseudocalanus diets reflected variations in the environment, with phytoplankton sequences relatively more abundant in copepods from stations with higher water-column chlorophyll a concentrations. Feeding differences were observed between species. P. acuspes diet contained relatively more heterotrophic dinoflagellate sequences, and was significantly different from that of P. minutus and P. newmani, both of which contained relatively more diatom sequences, and between which no significant difference was observed. Feeding differences between the two primarily arctic species may be a mechanism of niche partitioning between these spatially co-located congeners and may have implications for the effects of climate change on the success of these abundant zooplankters and their many predators in this ecosystem.

­Oligo-Miocene Monazite Ages in the Lesser Himalaya Sequence, Arunachal Pradesh, India; Geological Content of Age Variations

NASA Astrophysics Data System (ADS)

Clarke, G. L.; Bhowmik, S. K.; Ireland, T. R.; Aitchison, J. C.; Chapman, S. L.; Kent, L.

2016-12-01

A telescoped and inverted greenschist-upper amphibolite facies sequence in the in the Siyom Valley of eastern Arunachal Pradesh is tectonically overlain by an upright (grade decreasing upward) granulite to lower amphibolite facies sequence. Such grade relationships would normally attribute the boundary to a Main Central Thrust (MCT) structure, and predict a change from underlying Lesser Himalaya Sequence (LHS) to Greater Himalaya Sequence rocks across the boundary. However, all pelitic and psammitic samples have similar detrital zircon age spectra, involving c. 2500, 1750-1500, 1200 and 1000 Ma Gondwanan populations correlated with the LHS. Isograds are broadly parallel to a penetrative NW-dipping S2 foliation, developed contemporaneously with the inversion. Garnet growth in garnet, staurolite and kyanite zone schists beneath the thrust commenced at P>8 kbar and T≈550°C, before syn- to post-S2 heating of staurolite and kyanite zone rocks to T≈640°C at P≈8.5 kbar, most probably at c. 18.5 Ma. Kyanite-rutile-garnet migmatite immediately above the thrust records peak conditions of P≈10 kbar and T≈750°C and c. 21.5 Ma monazite ages. Complexity in c. 21-1000 Ma monazite ages in overlying amphibolite facies schists reflects the patchy recrystallization of detrital grains, intra-grain complexity being dependent on whole rock composition, metamorphic grade and evolition. Slip on a SE-propagating thrust was likely contemporaneous with early Miocene metamorphism, based on the distribution of structure, metamorphic textures, and overlap of age relationships. It is inferred to have initially controlled the uplift of granulite to mid-crustal levels between 22 and 19 Ma, thermal relaxation within a disrupted LHS metamorphic profile inducing a post-S2 thermal peak in lower grade footwall rocks.

Dialog detection in narrative video by shot and face analysis

NASA Astrophysics Data System (ADS)

Kroon, B.; Nesvadba, J.; Hanjalic, A.

2007-01-01

The proliferation of captured personal and broadcast content in personal consumer archives necessitates comfortable access to stored audiovisual content. Intuitive retrieval and navigation solutions require however a semantic level that cannot be reached by generic multimedia content analysis alone. A fusion with film grammar rules can help to boost the reliability significantly. The current paper describes the fusion of low-level content analysis cues including face parameters and inter-shot similarities to segment commercial content into film grammar rule-based entities and subsequently classify those sequences into so-called shot reverse shots, i.e. dialog sequences. Moreover shot reverse shot specific mid-level cues are analyzed augmenting the shot reverse shot information with dialog specific descriptions.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.

PubMed

Bizon, Chris; Spiegel, Michael; Chasse, Scott A; Gizer, Ian R; Li, Yun; Malc, Ewa P; Mieczkowski, Piotr A; Sailsbery, Josh K; Wang, Xiaoshu; Ehlers, Cindy L; Wilhelmsen, Kirk C

2014-01-30

The reduction in the cost of sequencing a human genome has led to the use of genotype sampling strategies in order to impute and infer the presence of sequence variants that can then be tested for associations with traits of interest. Low-coverage Whole Genome Sequencing (WGS) is a sampling strategy that overcomes some of the deficiencies seen in fixed content SNP array studies. Linkage-disequilibrium (LD) aware variant callers, such as the program Thunder, may provide a calling rate and accuracy that makes a low-coverage sequencing strategy viable. We examined the performance of an LD-aware variant calling strategy in a population of 708 low-coverage whole genome sequences from a community sample of Native Americans. We assessed variant calling through a comparison of the sequencing results to genotypes measured in 641 of the same subjects using a fixed content first generation exome array. The comparison was made using the variant calling routines GATK Unified Genotyper program and the LD-aware variant caller Thunder. Thunder was found to improve concordance in a coverage dependent fashion, while correctly calling nearly all of the common variants as well as a high percentage of the rare variants present in the sample. Low-coverage WGS is a strategy that appears to collect genetic information intermediate in scope between fixed content genotyping arrays and deep-coverage WGS. Our data suggests that low-coverage WGS is a viable strategy with a greater chance of discovering novel variants and associations than fixed content arrays for large sample association analyses.

Determining the Effects of Reflection Type and Cognitive Style on Students' Content Knowledge

ERIC Educational Resources Information Center

Blackburn, J. Joey; Robinson, J. Shane; Kacal, Amanda

2015-01-01

The purpose of this exploratory, experimental study was to determine the effects that the type of reflection-in-action and students' cognitive style had on content knowledge of preservice agriculture teachers (N = 57) at Oklahoma State University. Students' cognitive style was assessed using Kirton's Adaptation-Innovation Inventory (KAI). Students…

Examining the Content of Preservice Teachers' Reflections of Early Field Experiences

ERIC Educational Resources Information Center

Subramaniam, Karthigeyan

2013-01-01

This paper describes an exploratory study that examined the content of preservice elementary teachers' reflections of their documented early field experiences of science teaching in authentic contexts. The study used an early field experience model that was focused on the objective of profiling an elementary science teacher as the practical…

Published Views of Two-Year College English as Reflected in English Textbooks.

ERIC Educational Resources Information Center

Bowyer, Dolores LaVerna

This study answered four research questions: (1) Can textbook content for freshman English be determined from statements of leaders in two-year college English curriculum? (2) Do current textbooks reflect the content suggested by these leaders? (3) Are textbooks specifically designed for two-year college students? (4) How can publishers and…

76 FR 24926 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses Involving No...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-03

... addition, the requestor/petitioner shall provide a brief explanation of the bases for the contention and a... Bases changes which reflect the proposed changes and more accurately reflect the contents of the... qualification temperature of the control room equipment is not affected. Future changes to the Bases or licensee...

Characterization of metabolic network of oxalic acid biosynthesis through RNA seq data analysis of developing spikes of finger millet (Eleusine coracana): Deciphering the role of key genes involved in oxalate formation in relation to grain calcium accumulation.

PubMed

Akbar, Naved; Gupta, Supriya; Tiwari, Apoorv; Singh, K P; Kumar, Anil

2018-04-05

In the present study, we identified seven major genes of oxalic acid biosynthesis pathway (SGAT, GGAT, ICL, GLO, MHAR, APO and OXO) from developing spike transcriptome of finger millet using rice as a reference. Sequence alignment of identified genes showed high similarity with their respective homolog in rice except for OXO and GLO. Transcript abundance (FPKM) reflects the higher accumulation of identified genes in GP-1 (low calcium genotype) as compared to GP-45 (high calcium genotype) which was further confirmed by qRT-PCR analysis, indicating differential oxalate formation in both genotypes. Determination of oxalic acid and tartaric acid content in developing spikes explain that higher oxalic acid content in GP-1 however, tartaric acid content was more in GP-45. Higher calcium content in GP-45 and lower oxalate accumulation may be due to the diversion of more ascorbic acid into tartaric acid and may correspond to less formation of calcium oxalate. Our results suggest that more than one pathway for oxalic acid biosynthesis might be present in finger millet with probable predominance of ascorbate-tartarate pathway rather than glyoxalate-oxalate conversion. Thus, finger millet can be use as an excellent model system for understanding more specific role of nutrients-antinutrients interactions, as evident from the present study. Copyright © 2018 Elsevier B.V. All rights reserved.

Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping.

PubMed

Otto, Lars-Gernot; Mondal, Prodyut; Brassac, Jonathan; Preiss, Susanne; Degenhardt, Jörg; He, Sang; Reif, Jochen Christoph; Sharbel, Timothy Francis

2017-08-10

Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active. In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content. GBS analysis allowed the identification of 6495 high-quality SNP-markers in our panel of 91 M. recutita plants from 33 origins (2-4 genotypes each) and 4 M. discoidea plants as outgroup, grown in the greenhouse in Gatersleben, Germany. M. recutita proved to be clearly distinct from the outgroup, as was demonstrated by different cluster and principal coordinate analyses using the SNP-markers. Chamomile genotypes from the same origin were mostly genetically similar. Model-based cluster analysis revealed one large group of tetraploid genotypes with low genetic differentiation including 39 plants from 14 origins. Tetraploids tended to display lower genetic diversity than diploids, probably reflecting their origin by artificial polyploidisation from only a limited set of genetic backgrounds. Analyses of flowering time demonstrated that diploids generally flowered earlier than tetraploids, and the analysis of alpha-bisabolol identified several tetraploid genotypes with a high content. GWAS identified highly significant (P < 0.01) SNPs for flowering time (9) and alpha-bisabolol (71). One sequence harbouring SNPs associated with flowering time was described to play a role in self-pollination in Arabidopsis thaliana, whereas four sequences harbouring SNPs associated with alpha-bisabolol were identified to be involved in plant biotic and abiotic stress response in various plants species. The first genomic resource for future applications to enhance breeding in chamomile was created, andanalyses of diversity will facilitate the exploitation of these genetic resources. The GWAS data pave the way for future research towards the genetics underlying important traits in chamomile, the identification of marker-trait associations, and development of reliable markers for practical breeding.

An unusual plant triterpene synthase with predominant α-amyrin-producing activity identified by characterizing oxidosqualene cyclases from Malus × domestica.

PubMed

Brendolise, Cyril; Yauk, Yar-Khing; Eberhard, Ellen D; Wang, Mindy; Chagne, David; Andre, Christelle; Greenwood, David R; Beuning, Lesley L

2011-07-01

The pentacyclic triterpenes, in particular ursolic acid and oleanolic acid and their derivatives, exist abundantly in the plant kingdom, where they are well known for their anti-inflammatory, antitumour and antimicrobial properties. α-Amyrin and β-amyrin are the precursors of ursolic and oleanolic acids, respectively, formed by concerted cyclization of squalene epoxide by a complex synthase reaction. We identified three full-length expressed sequence tag sequences in cDNA libraries constructed from apple (Malus × domestica 'Royal Gala') that were likely to encode triterpene synthases. Two of these expressed sequence tag sequences were essentially identical (> 99% amino acid similarity; MdOSC1 and MdOSC3). MdOSC1 and MdOSC2 were expressed by transient expression in Nicotiana benthamiana leaves and by expression in the yeast Pichia methanolica. The resulting products were analysed by GC and GC-MS. MdOSC1 was shown to be a mixed amyrin synthase (a 5 : 1 ratio of α-amyrin to β-amyrin). MdOSC1 is the only triterpene synthase so far identified in which the level of α-amyrin produced is > 80% of the total product and is, therefore, primarily an α-amyrin synthase. No product was evident for MdOSC2 when expressed either transiently or in yeast, suggesting that this putative triterpene synthase is either encoded by a pseudogene or does not express well in these systems. Transcript expression analysis in Royal Gala indicated that the genes are mostly expressed in apple peel, and that the MdOSC2 expression level was much lower than that of MdOSC1 and MdOSC3 in all the tissues tested. Amyrin content analysis was undertaken by LC-MS, and demonstrated that levels and ratios differ between tissues, but that the true consequence of synthase activity is reflected in the ursolic/oleanolic acid content and in further triterpenoids derived from them. Phylogenetic analysis placed the three triterpene synthase sequences with other triterpene synthases that encoded either α-amyrin and/or β-amyrin synthase. MdOSC1 and MdOSC3 clustered with the multifunctional triterpene synthases, whereas MdOSC2 was most similar to the β-amyrin synthases. © 2011 The New Zealand Institute for Plant and Food Research Limited. Journal compilation © 2011 FEBS.

Myotonin protein-kinase [AGC]n trinucleotide repeat in seven nonhuman primates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novelli, G.; Sineo, L.; Pontieri, E.

Myotonic dystrophy (DM) is due to a genomic instability of a trinucleotide [AGC]n motif, located at the 3{prime} UTR region of a protein-kinase gene (myotonin protein kinase, MT-PK). The [AGC] repeat is meiotically and mitotically unstable, and it is directly related to the manifestations of the disorder. Although a gene dosage effect of the MT-PK has been demonstrated n DM muscle, the mechanism(s) by which the intragenic repeat expansion leads to disease is largely unknown. This non-standard mutational event could reflect an evolutionary mechanism widespread among animal genomes. We have isolated and sequenced the complete 3{prime}UTR region of the MT-PKmore » gene in seven primates (macaque, orangutan, gorilla, chimpanzee, gibbon, owl monkey, saimiri), and examined by comparative sequence nucleotide analysis the [AGC]n intragenic repeat and the surrounding nucleotides. The genomic organization, including the [AGC]n repeat structure, was conserved in all examined species, excluding the gibbon (Hylobates agilis), in which the [AGC]n upstream sequence (GGAA) is replaced by a GA dinucleotide. The number of [AGC]n in the examined species ranged between 7 (gorilla) and 13 repeats (owl monkeys), with a polymorphism informative content (PIC) similar to that observed in humans. These results indicate that the 3{prime}UTR [AGC] repeat within the MT-PK gene is evolutionarily conserved, supporting that this region has important regulatory functions.« less

The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs

PubMed Central

2010-01-01

Background The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari. Results The mitochondrial genome of P. citri is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs), a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for P. citri is the same as those for P. ulmi and Tetranychus urticae, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the P. citri mitochondrial genome has a high A + T content (85.28%), which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03). The Acari mitochondrial nad1 exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of P. citri are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp), lacking either the T- or D-arm, as found in P. ulmi, T. urticae, and other Acariform mites. Conclusions The P. citri mitochondrial gene order is markedly different from those of other chelicerates, but is conserved within the family Tetranychidae indicating that high rearrangements have occurred after Tetranychidae diverged from other Acari. Comparative analyses suggest that the genome size, gene order, gene content, codon usage, and base composition are strongly variable among Acari mitochondrial genomes. While extremely small and unusual tRNA genes seem to be common for Acariform mites, further experimental evidence is needed. PMID:20969792

Genomics dataset on unclassified published organism (patent US 7547531).

PubMed

Khan Shawan, Mohammad Mahfuz Ali; Hasan, Md Ashraful; Hossain, Md Mozammel; Hasan, Md Mahmudul; Parvin, Afroza; Akter, Salina; Uddin, Kazi Rasel; Banik, Subrata; Morshed, Mahbubul; Rahman, Md Nazibur; Rahman, S M Badier

2016-12-01

Nucleotide (DNA) sequence analysis provides important clues regarding the characteristics and taxonomic position of an organism. With the intention that, DNA sequence analysis is very crucial to learn about hierarchical classification of that particular organism. This dataset (patent US 7547531) is chosen to simplify all the complex raw data buried in undisclosed DNA sequences which help to open doors for new collaborations. In this data, a total of 48 unidentified DNA sequences from patent US 7547531 were selected and their complete sequences were retrieved from NCBI BioSample database. Quick response (QR) code of those DNA sequences was constructed by DNA BarID tool. QR code is useful for the identification and comparison of isolates with other organisms. AT/GC content of the DNA sequences was determined using ENDMEMO GC Content Calculator, which indicates their stability at different temperature. The highest GC content was observed in GP445188 (62.5%) which was followed by GP445198 (61.8%) and GP445189 (59.44%), while lowest was in GP445178 (24.39%). In addition, New England BioLabs (NEB) database was used to identify cleavage code indicating the 5, 3 and blunt end and enzyme code indicating the methylation site of the DNA sequences was also shown. These data will be helpful for the construction of the organisms' hierarchical classification, determination of their phylogenetic and taxonomic position and revelation of their molecular characteristics.

Intrusion Detection in Control Systems using Sequence Characteristics

NASA Astrophysics Data System (ADS)

Kiuchi, Mai; Onoda, Takashi

Intrusion detection is considered effective in control systems. Sequences of the control application behavior observed in the communication, such as the order of the control device to be controlled, are important in control systems. However, most intrusion detection systems do not effectively reflect sequences in the application layer into the detection rules. In our previous work, we considered utilizing sequences for intrusion detection in control systems, and demonstrated the usefulness of sequences for intrusion detection. However, manually writing the detection rules for a large system can be difficult, so using machine learning methods becomes feasible. Also, in the case of control systems, there have been very few observed cyber attacks, so we have very little knowledge of the attack data that should be used to train the intrusion detection system. In this paper, we use an approach that combines CRF (Conditional Random Field) considering the sequence of the system, thus able to reflect the characteristics of control system sequences into the intrusion detection system, and also does not need the knowledge of attack data to construct the detection rules.

Reflective terahertz (THz) imaging: system calibration using hydration phantoms

NASA Astrophysics Data System (ADS)

Bajwa, Neha; Garritano, James; Lee, Yoon Kyung; Tewari, Priyamvada; Sung, Shijun; Maccabi, Ashkan; Nowroozi, Bryan; Babakhanian, Meghedi; Sanghvi, Sajan; Singh, Rahul; Grundfest, Warren; Taylor, Zachary

2013-02-01

Terahertz (THz) hydration sensing continues to gain traction in the medical imaging community due to its unparalleled sensitivity to tissue water content. Rapid and accurate detection of fluid shifts following induction of thermal skin burns as well as remote corneal hydration sensing have been previously demonstrated in vivo using reflective, pulsed THz imaging. The hydration contrast sensing capabilities of this technology were recently confirmed in a parallel 7 Tesla Magnetic Resonance (MR) imaging study, in which burn areas are associated with increases in local mobile water content. Successful clinical translation of THz sensing, however, still requires quantitative assessments of system performance measurements, specifically hydration concentration sensitivity, with tissue substitutes. This research aims to calibrate the sensitivity of a novel, reflective THz system to tissue water content through the use of hydration phantoms for quantitative comparisons of THz hydration imagery.Gelatin phantoms were identified as an appropriate tissue-mimicking model for reflective THz applications, and gel composition, comprising mixtures of water and protein, was varied between 83% to 95% hydration, a physiologically relevant range. A comparison of four series of gelatin phantom studies demonstrated a positive linear relationship between THz reflectivity and water concentration, with statistically significant hydration sensitivities (p < .01) ranging between 0.0209 - 0.038% (reflectivity: %hydration). The THz-phantom interaction is simulated with a three-layer model using the Transfer Matrix Method with agreement in hydration trends. Having demonstrated the ability to accurately and noninvasively measure water content in tissue equivalent targets with high sensitivity, reflective THz imaging is explored as a potential tool for early detection and intervention of corneal pathologies.

Effect of the sequence data deluge on the performance of methods for detecting protein functional residues.

PubMed

Garrido-Martín, Diego; Pazos, Florencio

2018-02-27

The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. These results are informative for the methods' developers and final users, and may have implications in the design of new sequencing initiatives.

Improving Students' Conceptual Understanding of a Specific Content Learning: A Designed Teaching Sequence

ERIC Educational Resources Information Center

Ahmad, N. J.; Lah, Y. Che

2012-01-01

The efficacy of a teaching sequence designed for a specific content of learning of electrochemistry is described in this paper. The design of the teaching draws upon theoretical insights into perspectives on learning and empirical studies to improve the teaching of this topic. A case study involving two classes, the experimental and baseline…

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites.

PubMed

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO 2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO 2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO 2 levels (sample groups I and II) and one control site with low CO 2 content (group III). Samples from sites with elevated CO 2 had pH ranging from 6.2 to 4.5 and samples from the low-CO 2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO 2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae , and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO 2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO 2 leakage from geologic storage sites.

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites

PubMed Central

Ham, Baknoon; Choi, Byoung-Young; Chae, Gi-Tak; Kirk, Matthew F.; Kwon, Man Jae

2017-01-01

Microorganisms influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites. PMID:29170659

Geochemical imprint of depositional conditions on organic matter in laminated-Bioturbated interbeds from fine-grained marine sequences

USGS Publications Warehouse

Pratt, L.M.; Claypool, G.E.; King, J.D.

1986-01-01

Laminated organic-rich shales are interbedded at a scale of centimeters to a few meters with bioturbated organic-poor mudstones or limestones in some fine-grained marine sequences. We have analyzed the organic matter in pairs of laminated/bioturbated interbeds from Cretaceous and Devonian rocks deposited in epicontinental and oceanic settings for the purpose of studying the influence of depositional and early diagenetic environment on the organic geochemical properties of marine shales. Results of these analyses indicate that for rocks that are still in a diagenetic stage of thermal alteration, the relative abundance of biomarker compounds and specific biomarker indices can be useful indicators of depositional and early diagenetic conditions. Pristane/phytane ratios are generally highest for laminated rocks from epicontinental basins and appear to reflect the input of isoprenoid precursors more than oxygenated versus anoxic depositional conditions. The thermally immature laminated rocks are characterized by relatively high contents of 17??(H), 21??(H)-hopanes, hopenes, sterenes and diasterenes, and by strong predominance of the 22R over 22S homohopane isomers. Thermally immature bioturbated samples are characterized by absence of the ??,??-hopanes, by low contents of both saturated and unsaturated polycyclic hydrocarbons, and by slight or no predominance of the 22R over 22S homohopane isomers. There are less obvious compositional differences between the saturated hydrocarbons in the laminated and bioturbated units from the thermally mature sequences. For both the thermally mature and immature laminated samples, the degree of isomerization at the 22C position for hopanes and at the 20C position for steranes is generally consistent with the degree of thermal maturity interpreted from other properties of the organic matter. The bioturbated samples, however, exhibit inconsistent and anomalously high degrees of isomerization for the homohopanes, resulting either from reworking and oxidation of the primary organic matter or from the presence of older recycled organic matter. ?? 1986.

Observed reflectivities and liquid water content for marine stratocumulus

NASA Technical Reports Server (NTRS)

Coakley, J. A., Jr.; Snider, J. B.

1989-01-01

Simultaneous observations of cloud liquid water content and cloud reflectivity are used to verify their parametric relationship in a manner consistent with simple parameterizations often used in general-circulation climate models. The column amount of cloud liquid water was measured with a microwave radiometer on San Nicolas Island as described by Hogg et al., (1983). Cloud reflectivity was obtained through spatial coherence analysis of AVHRR imagery data as per Coakley and Baldwin (1984) and Coakley and Beckner (1988). The dependence of the observed reflectivity on the observed liquid water is discussed, and this empirical relationship is compared with the parameterization proposed by Stephens (1978).

Improving Inquiry Teaching through Reflection on Practice

NASA Astrophysics Data System (ADS)

Lotter, Christine R.; Miller, Cory

2017-08-01

In this paper, we explore middle school science teachers' learning of inquiry-based instructional strategies through reflection on practice teaching sessions during a summer enrichment program with middle level students. The reflection sessions were part of a larger year-long inquiry professional development program in which teachers learned science content and inquiry pedagogy. The program included a 2-week summer institute in which teachers participated in science content sessions, practice teaching to middle level students, and small group-facilitated reflection sessions on their teaching. For this study, data collection focused on teachers' recorded dialogue during the facilitator - run reflection sessions, the teachers' daily written reflections, a final written reflection, and a written reflection on a videotaped teaching session. We investigated the teachers' reflection levels and the themes teachers focused on during their reflection sessions. Teachers were found to reflect at various reflection levels, from simple description to a more sophisticated focus on how to improve student learning. Recurrent themes point to the importance of providing situated learning environments, such as the practice teaching with immediate reflection for teachers to have time to practice new instructional strategies and gain insight from peers and science educators on how to handle student learning issues.

A tale of phenocrysts: trace element contents of boninites and forearc basalts from IODP Expedition 352

NASA Astrophysics Data System (ADS)

Chapman, T.; Clarke, G. L.; Reagan, M. K.; Sakuyama, T.; Godard, M.; Shervais, J. W.; Prytulak, J.; Shimizu, K.; Nelson, W. R.; Heaton, D. E.; Whattam, S. A.; Li, H.; Pearce, J. A.

2016-12-01

The Izu-Bonin Mariana (IBM) forearc represents an ideal location to study the dynamics of subduction initiation and to reveal the volcanic sequences appropriate to assess ophiolite origins. The volcanic stratigraphy recovered on Expedition 352 illustrates an abrupt shift from forearc basalt (FAB) to boninite magmatism, with limited transitional rock types, as observed from submersible and previous drill work in the Izu-Bonin and Mariana sections. The transition represents a change from decompression melting to fluxed melting of the mantle wedge. The volcanic stratigraphy has several distinct boninite chemical evolution trends (basaltic boninite, low- and high-silica boninite). Mineral assemblages and phenocryst trace element compositions vary throughout the volcanic sequence providing an opportunity to explore more completely boninite and FAB transitions and petrogenesis. FABs are characterised by early plagioclase crystallization and HREE enriched clinopyroxene with high Ti contents. Basaltic boninite and some low-silica boninite lavas have overlapping REE concentrations consistent with early plagioclase growth preceded by clinopyroxene. In contrast, textures and HREE depleted concentrations of clinopyroxene in high-silica boninite imply late plagioclase growth relative to olivine and orthopyroxene. Variations in mineral compositions and paragenesis in boninites reflect changes in magma compositions and a progressive depletion of mantle sources over time. This is illustrated via key incompatible and compatible trace element ratios and concentrations (e.g. Zr/Ti & V or Cr). The transition from FAB to low-Si boninite was subtle in terms of mineral modes, but was more evident in terms of the phase and lava compositions.

Binocular video ophthalmoscope for simultaneous recording of sequences of the human retina to compare dynamic parameters

NASA Astrophysics Data System (ADS)

Tornow, Ralf P.; Milczarek, Aleksandra; Odstrcilik, Jan; Kolar, Radim

2017-07-01

A parallel video ophthalmoscope was developed to acquire short video sequences (25 fps, 250 frames) of both eyes simultaneously with exact synchronization. Video sequences were registered off-line to compensate for eye movements. From registered video sequences dynamic parameters like cardiac cycle induced reflection changes and eye movements can be calculated and compared between eyes.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota.

PubMed

Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

2016-01-01

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.

Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota

PubMed Central

Oton, Eduard Vico; Quince, Christopher; Nicol, Graeme W; Prosser, James I; Gubry-Rangin, Cécile

2016-01-01

Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota. PMID:26140533

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone.

PubMed

Lee, Kevin C; Stott, Matthew B; Dunfield, Peter F; Huttenhower, Curtis; McDonald, Ian R; Morgan, Xochitl C

2016-06-15

Chthonomonas calidirosea T49(T) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. Copyright © 2016 Lee et al.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

PubMed Central

Lee, Kevin C.; Stott, Matthew B.; Dunfield, Peter F.; Huttenhower, Curtis; McDonald, Ian R.

2016-01-01

ABSTRACT Chthonomonas calidirosea T49T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa. IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa. PMID:27060125

CRISPR Diversity and Microevolution in Clostridium difficile

PubMed Central

Andersen, Joakim M.; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E.P.; Barrangou, Rodolphe

2016-01-01

Abstract Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes. PMID:27576538

A genomic view of 500 million years of cnidarian evolution.

PubMed

Steele, Robert E; David, Charles N; Technau, Ulrich

2011-01-01

Cnidarians (corals, anemones, jellyfish and hydras) are a diverse group of animals of interest to evolutionary biologists, ecologists and developmental biologists. With the publication of the genome sequences of Hydra and Nematostella, whose last common ancestor was the stem cnidarian, researchers are beginning to see the genomic underpinnings of cnidarian biology. Cnidarians are known for the remarkable plasticity of their morphology and life cycles. This plasticity is reflected in the Hydra and Nematostella genomes, which differ to an exceptional degree in size, base composition, transposable element content and gene conservation. It is now known what cnidarian genomes, given 500 million years, are capable of; as we discuss here, the next challenge is to understand how this genomic history has led to the striking diversity seen in this group. Copyright © 2010 Elsevier Ltd. All rights reserved.

An Investigation into the Contents and Aspects of College Students' Reflective Thoughts during Field Experience

ERIC Educational Resources Information Center

Su, Yuling

2015-01-01

Field experience makes a strong contribution to the learning of students. However, the procedure for conducting training sessions based on experiential teaching methods is relatively unclear, and the contents and aspects of students' reflections during such training are not well known. This study applied experiential teaching methods in a college…

Online Problem-Based Learning in Postgraduate Medical Education--Content Analysis of Reflection Comments

ERIC Educational Resources Information Center

Gonzalez, Maria L.; Salmoni, Alan J.

2008-01-01

We developed the Med-e-Conference, an online tool to teach clinical skills to medical students, which integrated problem-based learning with collaborative group tasks. The final task asked students to consider what they had done (reflection). These comments were analysed using content analysis, and 10 themes were elicited. The number of agreements…

Fiber optic moisture sensor

DOEpatents

Kirkham, R.R.

1984-08-03

A method and apparatus for sensing moisture changes by utilizing optical fiber technology. One embodiment uses a reflective target at the end of an optical fiber. The reflectance of the target varies with its moisture content and can be detected by a remote unit at the opposite end of the fiber. A second embodiment utilizes changes in light loss along the fiber length. This can be attributed to changes in reflectance of cladding material as a function of its moisture content. It can also be affected by holes or inserts interposed in the cladding material and/or fiber. Changing light levels can also be coupled from one fiber to another in an assembly of fibers as a function of varying moisture content in their overlapping lengths of cladding material.

Components of Reflection: A Longitudinal Analysis of Study Abroad Student Blog Posts

ERIC Educational Resources Information Center

Savicki, Victor; Price, Michele V.

2017-01-01

Reflection supports actively transforming perspectives regarding study abroad experiences. The current study examines the "how" of reflection. Content of reflections is dictated by questions posed. The process of reflection is less prescribed yet revealing of paths to student understanding. Students posted to a web log (blog) over six…

Reflection during Portfolio-Based Conversations

ERIC Educational Resources Information Center

Oosterbaan, Anne E.; van der Schaaf, Marieke F.; Baartman, Liesbeth K. J.; Stokking, Karel M.

2010-01-01

This study aims to explore the relationship between the occurrence of reflection (and non-reflection) and thinking activities (e.g., orientating, selecting, analysing) during portfolio-based conversations. Analysis of 21 transcripts of portfolio-based conversations revealed that 20% of the segments were made up of reflection (content reflection…

Self-reflection and academic performance: is there a relationship?

PubMed

Lew, Magdeleine D N; Schmidt, Henk G

2011-10-01

The purposes of the present study were two-fold: first, to evaluate whether reflection journal writing was effective in promoting self-reflection and learning, and whether students become better at self-reflection if they engage continuously in reflection journal writing. To that end, the reflection journals of 690 first-year applied science students at a local polytechnic were studied by means of an automated coding procedures using software. Data was collected twice, once at the beginning and again towards the end of an academic year. Outcomes of the textual content analyses revealed that students reflected on both the process and contents of their learning: critical review of past learning experiences, learning strategies and summaries of what was learned. Correlational analyses showed weak to moderate inter-relationships between the textual categories and their classroom and knowledge acquisition test grades. Taken together, the findings suggest that self-reflection on both how and what students have learned does lead to improvements in academic performance, although to a limited extent.

Estimating soil water content from ground penetrating radar coarse root reflections

NASA Astrophysics Data System (ADS)

Liu, X.; Cui, X.; Chen, J.; Li, W.; Cao, X.

2016-12-01

Soil water content (SWC) is an indispensable variable for understanding the organization of natural ecosystems and biodiversity. Especially in semiarid and arid regions, soil moisture is the plants primary source of water and largely determine their strategies for growth and survival, such as root depth, distribution and competition between them. Ground penetrating radar (GPR), a kind of noninvasive geophysical technique, has been regarded as an accurate tool for measuring soil water content at intermediate scale in past decades. For soil water content estimation with surface GPR, fixed antenna offset reflection method has been considered to have potential to obtain average soil water content between land surface and reflectors, and provide high resolution and few measurement time. In this study, 900MHz surface GPR antenna was used to estimate SWC with fixed offset reflection method; plant coarse roots (with diameters greater than 5 mm) were regarded as reflectors; a kind of advanced GPR data interpretation method, HADA (hyperbola automatic detection algorithm), was introduced to automatically obtain average velocity by recognizing coarse root hyperbolic reflection signals on GPR radargrams during estimating SWC. In addition, a formula was deduced to determine interval average SWC between two roots at different depths as well. We examined the performance of proposed method on a dataset simulated under different scenarios. Results showed that HADA could provide a reasonable average velocity to estimate SWC without knowledge of root depth and interval average SWC also be determined. When the proposed method was applied to estimation of SWC on a real-field measurement dataset, a very small soil water content vertical variation gradient about 0.006 with depth was captured as well. Therefore, the proposed method could be used to estimate average soil water content from ground penetrating radar coarse root reflections and obtain interval average SWC between two roots at different depths. It is very promising for measuring root-zone-soil-moisture and mapping soil moisture distribution around a shrub or even in field plot scale.

Superstatistical model of bacterial DNA architecture

NASA Astrophysics Data System (ADS)

Bogachev, Mikhail I.; Markelov, Oleg A.; Kayumov, Airat R.; Bunde, Armin

2017-02-01

Understanding the physical principles that govern the complex DNA structural organization as well as its mechanical and thermodynamical properties is essential for the advancement in both life sciences and genetic engineering. Recently we have discovered that the complex DNA organization is explicitly reflected in the arrangement of nucleotides depicted by the universal power law tailed internucleotide interval distribution that is valid for complete genomes of various prokaryotic and eukaryotic organisms. Here we suggest a superstatistical model that represents a long DNA molecule by a series of consecutive ~150 bp DNA segments with the alternation of the local nucleotide composition between segments exhibiting long-range correlations. We show that the superstatistical model and the corresponding DNA generation algorithm explicitly reproduce the laws governing the empirical nucleotide arrangement properties of the DNA sequences for various global GC contents and optimal living temperatures. Finally, we discuss the relevance of our model in terms of the DNA mechanical properties. As an outlook, we focus on finding the DNA sequences that encode a given protein while simultaneously reproducing the nucleotide arrangement laws observed from empirical genomes, that may be of interest in the optimization of genetic engineering of long DNA molecules.

Genome structure of Rosa multiflora, a wild ancestor of cultivated roses

PubMed Central

Nakamura, Noriko; Hirakawa, Hideki; Sato, Shusei; Otagaki, Shungo; Matsumoto, Shogo; Tabata, Satoshi; Tanaka, Yoshikazu

2018-01-01

Abstract The draft genome sequence of a wild rose (Rosa multiflora Thunb.) was determined using Illumina MiSeq and HiSeq platforms. The total length of the scaffolds was 739,637,845 bp, consisting of 83,189 scaffolds, which was close to the 711 Mbp length estimated by k-mer analysis. N50 length of the scaffolds was 90,830 bp, and extent of the longest was 1,133,259 bp. The average GC content of the scaffolds was 38.9%. After gene prediction, 67,380 candidates exhibiting sequence homology to known genes and domains were extracted, which included complete and partial gene structures. This large number of genes for a diploid plant may reflect heterogeneity of the genome originating from self-incompatibility in R. multiflora. According to CEGMA analysis, 91.9% and 98.0% of the core eukaryotic genes were completely and partially conserved in the scaffolds, respectively. Genes presumably involved in flower color, scent and flowering are assigned. The results of this study will serve as a valuable resource for fundamental and applied research in the rose, including breeding and phylogenetic study of cultivated roses. PMID:29045613

Genome-wide comparative analysis of codon usage bias and codon context patterns among cyanobacterial genomes.

PubMed

Prabha, Ratna; Singh, Dhananjaya P; Sinha, Swati; Ahmad, Khurshid; Rai, Anil

2017-04-01

With the increasing accumulation of genomic sequence information of prokaryotes, the study of codon usage bias has gained renewed attention. The purpose of this study was to examine codon selection pattern within and across cyanobacterial species belonging to diverse taxonomic orders and habitats. We performed detailed comparative analysis of cyanobacterial genomes with respect to codon bias. Our analysis reflects that in cyanobacterial genomes, A- and/or T-ending codons were used predominantly in the genes whereas G- and/or C-ending codons were largely avoided. Variation in the codon context usage of cyanobacterial genes corresponded to the clustering of cyanobacteria as per their GC content. Analysis of codon adaptation index (CAI) and synonymous codon usage order (SCUO) revealed that majority of genes are associated with low codon bias. Codon selection pattern in cyanobacterial genomes reflected compositional constraints as major influencing factor. It is also identified that although, mutational constraint may play some role in affecting codon usage bias in cyanobacteria, compositional constraint in terms of genomic GC composition coupled with environmental factors affected codon selection pattern in cyanobacterial genomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Genomics dataset of unidentified disclosed isolates.

PubMed

Rekadwad, Bhagwan N

2016-09-01

Analysis of DNA sequences is necessary for higher hierarchical classification of the organisms. It gives clues about the characteristics of organisms and their taxonomic position. This dataset is chosen to find complexities in the unidentified DNA in the disclosed patents. A total of 17 unidentified DNA sequences were thoroughly analyzed. The quick response codes were generated. AT/GC content of the DNA sequences analysis was carried out. The QR is helpful for quick identification of isolates. AT/GC content is helpful for studying their stability at different temperatures. Additionally, a dataset on cleavage code and enzyme code studied under the restriction digestion study, which helpful for performing studies using short DNA sequences was reported. The dataset disclosed here is the new revelatory data for exploration of unique DNA sequences for evaluation, identification, comparison and analysis.

Relationship between leaf optical properties, chlorophyll fluorescence and pigment changes in senescing Acer saccharum leaves.

PubMed

Junker, Laura Verena; Ensminger, Ingo

2016-06-01

The ability of plants to sequester carbon is highly variable over the course of the year and reflects seasonal variation in photosynthetic efficiency. This seasonal variation is most prominent during autumn, when leaves of deciduous tree species such as sugar maple (Acer saccharum Marsh.) undergo senescence, which is associated with downregulation of photosynthesis and a change of leaf color. The remote sensing of leaf color by spectral reflectance measurements and digital repeat images is increasingly used to improve models of growing season length and seasonal variation in carbon sequestration. Vegetation indices derived from spectral reflectance measurements and digital repeat images might not adequately reflect photosynthetic efficiency of red-senescing tree species during autumn due to the changes in foliar pigment content associated with autumn phenology. In this study, we aimed to assess how effectively several widely used vegetation indices capture autumn phenology and reflect the changes in physiology and photosynthetic pigments during autumn. Chlorophyll fluorescence and pigment content of green, yellow, orange and red leaves were measured to represent leaf senescence during autumn and used as a reference to validate and compare vegetation indices derived from leaf-level spectral reflectance measurements and color analysis of digital images. Vegetation indices varied in their suitability to track the decrease of photosynthetic efficiency and chlorophyll content despite increasing anthocyanin content. Commonly used spectral reflectance indices such as the normalized difference vegetation index and photochemical reflectance index showed major constraints arising from a limited representation of gradual decreases in chlorophyll content and an influence of high foliar anthocyanin levels. The excess green index and green-red vegetation index were more suitable to assess the process of senescence. Similarly, digital image analysis revealed that vegetation indices such as Hue and normalized difference index are superior compared with the often-used green chromatic coordinate. We conclude that indices based on red and green color information generally represent autumn phenology most efficiently. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Estimating chlorophyll content of spartina alterniflora at leaf level using hyper-spectral data

NASA Astrophysics Data System (ADS)

Wang, Jiapeng; Shi, Runhe; Liu, Pudong; Zhang, Chao; Chen, Maosi

2017-09-01

Spartina alterniflora, one of most successful invasive species in the world, was firstly introduced to China in 1979 to accelerate sedimentation and land formation via so-called "ecological engineering", and it is now widely distributed in coastal saltmarshes in China. A key question is how to retrieve chlorophyll content to reflect growth status, which has important implication of potential invasiveness. In this work, an estimation model of chlorophyll content of S. alterniflora was developed based on hyper-spectral data in the Dongtan Wetland, Yangtze Estuary, China. The spectral reflectance of S. alterniflora leaves and their corresponding chlorophyll contents were measured, and then the correlation analysis and regression (i.e., linear, logarithmic, quadratic, power and exponential regression) method were established. The spectral reflectance was transformed and the feature parameters (i.e., "san bian", "lv feng" and "hong gu") were extracted to retrieve the chlorophyll content of S. alterniflora . The results showed that these parameters had a large correlation coefficient with chlorophyll content. On the basis of the correlation coefficient, mathematical models were established, and the models of power and exponential based on SDb had the least RMSE and larger R2 , which had a good performance regarding the inversion of chlorophyll content of S. alterniflora.

Gene: a gene-centered information resource at NCBI.

PubMed

Brown, Garth R; Hem, Vichet; Katz, Kenneth S; Ovetsky, Michael; Wallin, Craig; Ermolaeva, Olga; Tolstoy, Igor; Tatusova, Tatiana; Pruitt, Kim D; Maglott, Donna R; Murphy, Terence D

2015-01-01

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Content of intrinsic disorder influences the outcome of cell-free protein synthesis.

PubMed

Tokmakov, Alexander A; Kurotani, Atsushi; Ikeda, Mariko; Terazawa, Yumiko; Shirouzu, Mikako; Stefanov, Vasily; Sakurai, Tetsuya; Yokoyama, Shigeyuki

2015-09-11

Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yields with the contents of intrinsic disorder bioinformatically predicted in the expressed sequences. This analysis revealed strong relationships between intrinsic disorder and protein amenability to heterologous cell-free expression. On the one hand, elevated disorder content was associated with the increased ratio of soluble expression. On the other hand, overall propensity for detectable protein expression decreased with disorder content. We further demonstrated that these tendencies are rooted in some distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation, including sites of ubiquitination and PEST sequences. Our findings suggest that identification of intrinsically disordered regions in the expressed amino acid sequences can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

[Identification of common medicinal snakes in medicated liquor of Guangdong by COI barcode sequence].

PubMed

Liao, Jing; Chao, Zhi; Zhang, Liang

2013-11-01

To identify the common snakes in medicated liquor of Guangdong using COI barcode sequence,and to test the feasibility. The COI barcode sequences of collected medicinal snakes were amplified and sequenced. The sequences combined with the data from GenBank were analyzed for divergence and building a neighbor-joining(NJ) tree with MEGA 5.0. The genetic distance and NJ tree demonstrated that there were 241 variable sites in these species, and the average (A + T) content of 56.2% was higher than the average (G + C) content of 43.7%. The maximum interspecific genetic distance was 0.2568, and the minimum was 0. 1519. In the NJ tree,each species formed a monophyletic clade with bootstrap supports of 100%. DNA barcoding identification method based on the COI sequence is accurate and can be applied to identify the common medicinal snakes.

Assessing Student Teachers' Reflective Writing through Quantitative Content Analysis

ERIC Educational Resources Information Center

Poldner, Eric; Van der Schaaf, Marieke; Simons, P. Robert-Jan; Van Tartwijk, Jan; Wijngaards, Guus

2014-01-01

Students' reflective essay writing can be stimulated by the formative assessments provided to them by their teachers. Such assessments contain information about the quality of students' reflective writings and offer suggestions for improvement. Despite the importance of formatively assessing students' reflective writings in teacher education…

Sequence-Dependent Persistence Length of Long DNA

NASA Astrophysics Data System (ADS)

Chuang, Hui-Min; Reifenberger, Jeffrey G.; Cao, Han; Dorfman, Kevin D.

2017-12-01

Using a high-throughput genome-mapping approach, we obtained circa 50 million measurements of the extension of internal human DNA segments in a 41 nm ×41 nm nanochannel. The underlying DNA sequences, obtained by mapping to the reference human genome, are 2.5-393 kilobase pairs long and contain percent GC contents between 32.5% and 60%. Using Odijk's theory for a channel-confined wormlike chain, these data reveal that the DNA persistence length increases by almost 20% as the percent GC content increases. The increased persistence length is rationalized by a model, containing no adjustable parameters, that treats the DNA as a statistical terpolymer with a sequence-dependent intrinsic persistence length and a sequence-independent electrostatic persistence length.

The Sequence of Learning Cycle Activities in High School Chemistry.

ERIC Educational Resources Information Center

Abraham, Michael R.; Renner, John W.

1986-01-01

Different learning cycle sequences were investigated to determine factors accounting for success of the cycle, compared learning with conventional instruction, and examined relationships between Piaget's theory and learning cycles. Results show that the normal learning cycle sequence is the optimum sequence for achievement of content knowledge in…

Allochthonous 2.78 Ga oceanic plateau slivers in a 2.72 Ga continental arc sequence: Vizien greenstone belt, northeastern Superior Province, Canada

NASA Astrophysics Data System (ADS)

Skulski, T.; Percival, J. A.

1996-04-01

Embedded within the vast granitoid terrane of the Minto block of northeastern Superior Province are Late Archean greenstone belts of the Goudalie domain that preserve a long-lived record of continent-ocean interaction. The Vizien greenstone belt is one such belt and it contains four fault-bounded structural panels. The 2786 Ma mafic-ultramafic sequence is an allochthonous package of pillowed basaltic andesite, komatiite and volcaniclastic rocks cut by peridotite and gabbro sills. The mafic rocks are LREE-depleted tholeiites which have primitive mantle (PRIM)-normalized abundances of Th < Nb < La, and ɛNd values of +1.5 to + 3.2 reflecting extraction from a depleted mantle source. The 2724 Ma lac Lintelle continental calc-alkaline volcanic sequence consists of massive basalt, plagioclase-porphyritic andesite, dacite, rhyolite, capped by quartz-rich sandstones/conglomerates with 2.97 Ga Nd model ages. Lac Lintelle volcanic rocks are LREE enriched, with low TiO 2 (< 1%) and Zr (< 200 ppm), PRIM-normalized enrichment in Th > La > Nb, and a range of ɛNd values from -0.1 to +1.7. The ~ 2722 Ma lac Serindac bimodal, subaerial tholeiitic volcanic sequence contains andesite (locally with tonalite xenoliths), basalt, gabbro sills, lenses of quartz-rich sedimentary rocks and a thick, upper rhyolite sequence. The lac Serindac tholeiites are LREE-enriched, have PRIM-normalized Th > La > Nb, high Zr (to 300 ppm) and Ti contents, and low ɛNd values from +0.8 in basalt to -1.4 in rhyolite. The < 2718 Ma basement-cover sequence comprises 2.94 Ga tonalitic gneiss unconformably overlain by clastic sediments and a thin upper sequence of 2700 Ma gabbro, siliceous high-Mg basalt (SHMB) and andesite. The SHMB are characterised by LREE depletion and ɛNd values of +2.6, whereas the andesite is LREE-enriched and has ɛNd values of -0.3. The 2786 Ma mafic-ultramafic sequence is interpreted as a sliver of plume-related oceanic plateau crust. The 2724 lac Lintelle sequence represents a continental arc formed on the eastern protocraton. The ~ 2722 Ma lac Serindac volcanic sequence represents late continental rift deposits. The various 2.8-2.7 Ga supracrustal sequences were accreted, deformed and metamorphosed to mid-amphibolite facies during late-stage assembly of the Minto block between 2.718 and 2.693 Ga.

The relationship between shellbed type and sequence architecture: examples from Japan and New Zealand

NASA Astrophysics Data System (ADS)

Kondo, Yasuo; Abbott, Stephen T.; Kitamura, Akihisa; Kamp, Peter J. J.; Naish, Tim R.; Kamataki, Takanobu; Saul, Gordon S.

1998-12-01

Examples of lithology, fossil content and taphonomic features of shellbeds and intervening less fossiliferous intervals are presented from four Plio-Pleistocene successions (Shimosa Group, Boso Peninsula, Omma Formation, Hokuriku area, Japan, and Okehu, Kai-iwi, and Shakespeare groups in Wanganui, and the Rangitikei Group along the Rangitikei River in New Zealand). As for pre-Pliocene 3rd- and 4th-order depositional sequences, Plio-Pleistocene 5th- to 7th-order depositional sequences contain a variety of shellbeds which are often associated with surfaces or intervals that are characterized by sedimentary condensation, omission or erosion (e.g. sequence boundaries, ravinement surfaces, downlap surfaces and condensed sections). Stratigraphic patterns of shellbed type tend to be similar and repetitive within a basin and a locality. This demonstrates that a specific palaeogeography played an important role in determining the nature of shellbeds. For example, shellbeds formed in the context of toplap are common only in the Shimosa Group, which was deposited in a moderately sheltered sea, the palaeo-Tokyo Bay. Toplap shellbeds are rare in other sequences formed in more open conditions. Despite the variability resulting from such basin characteristics, common styles of shellbeds can be recognized that formed under conditions of marine onlap, backlap, downlap and toplap. Each type of shellbed has a characteristic fossil composition and taphonomy. Onlap and toplap shellbeds contain low-diversity macrobenthic associations including Glycymeris, Mercenaria, Paphies or other bivalves having robust shells, which are often abraded or fragmented. Backlap shellbeds, which are equivalent to the condensed section formed at the maximum transgression, are characterized by dominance of epifaunal macrobenthos such as bryozoa, brachiopoda, pectinid and ostreid bivalves, preserved in a slightly cemented, glauconitic muddy matrix. In contrast to fossils in such condensed sections, the shell density and species diversity of downlap shellbed associations are rather low, and in a few examples the macrobenthic association was buried rapidly in a lower unit of the highstand systems tract (HST) stratigraphically located above the condensed sections. Variations in the stratigraphic distribution of shellbed types are reflected in symmetrical and asymmetrical sequence architectures. Symmetrical sequences have roughly the same thickness of transgressive systems tracts (TST) and highstand systems tracts (HST), and have well segregated shellbeds that were formed during marine onlap and backlap. Asymmetrical cycles have very thin TSTs and much thicker HSTs, and are characterized by the amalgamation of condensed onlap and backlap shellbeds. Such contrasting cycle architectures are interpreted to reflect inner (symmetrical) and outer (asymmetrical) shelf palaeodepositional settings. The amalgamated onlap/backlap shellbeds appear to be common in Plio-Pleistocene sequences. Owing to the short duration of glacio-eustatic sea-level changes with dominant frequencies of 20,000, 40,000 or 100,000 years, shellbeds in the Plio-Pleistocene are relatively simple and thin compared to those formed in ordinary third-order depositional sequences. Infauna-dominated benthic associations are generally more common than in third-order cycles, and epifaunal associations facilitated by taphonomic feedback on sediment-starved shell-gravel substrates occur only in the condensed section corresponding to maximum transgression in most Plio-Pleistocene sequences.

A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.

PubMed

Reinharz, Vladimir; Ponty, Yann; Waldispühl, Jérôme

2013-07-01

The design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity. In this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. Supplementary data are available at Bioinformatics online.

Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals.

PubMed

Chow, S; Ueno, Y; Toyokawa, M; Oohara, I; Takeyama, H

2009-01-01

Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 sequences (118 to 422 bp) with lower GC content (35.8% to 61.7%) than the other animal taxa. Mollusca and Crustacea were diverse groups with respect to ITS1 length, ranging from 108 to 1,118 and 182 to 1,613 bp, respectively. No universal relationship between length and GC content was observed. Our data indicated that ITS1 has a limited utility for phylogenetic analysis as obtaining confident sequence alignment was often impossible between different genera of the same family and even between congeneric species.

Sensing of moisture content in in-shell peanuts by NIR (Near Infra Red) reflectance spectroscopy

USDA-ARS?s Scientific Manuscript database

It was found earlier that moisture content (MC) of intact kernels of grain and nuts could be determined by Near Infra Red (NIR) reflectance spectrometry. However, if the MC values can be determined while the nuts are in their shells, it would save lot of labor and money spent in shelling and cleanin...

The Content and Nature of Reflective Teaching: A Case of an Expert Middle School Science Teacher.

ERIC Educational Resources Information Center

Moallem, Mahnaz

1997-01-01

Explores the practical view of reflective teaching as it was revealed in the activities and thinking processes of an expert middle school science teacher. Discusses differences between types of reflection, importance of self-analysis by teachers, effect of social context on reflection, and having the opportunity to reflect. (RS)

High-Throughput Phenotyping of Maize Leaf Physiological and Biochemical Traits Using Hyperspectral Reflectance1[OPEN

PubMed Central

Yendrek, Craig R.; Tomaz, Tiago; Montes, Christopher M.; Cao, Youyuan; Morse, Alison M.; Brown, Patrick J.; McIntyre, Lauren M.; Leakey, Andrew D.B.

2017-01-01

High-throughput, noninvasive field phenotyping has revealed genetic variation in crop morphological, developmental, and agronomic traits, but rapid measurements of the underlying physiological and biochemical traits are needed to fully understand genetic variation in plant-environment interactions. This study tested the application of leaf hyperspectral reflectance (λ = 500–2,400 nm) as a high-throughput phenotyping approach for rapid and accurate assessment of leaf photosynthetic and biochemical traits in maize (Zea mays). Leaf traits were measured with standard wet-laboratory and gas-exchange approaches alongside measurements of leaf reflectance. Partial least-squares regression was used to develop a measure of leaf chlorophyll content, nitrogen content, sucrose content, specific leaf area, maximum rate of phosphoenolpyruvate carboxylation, [CO2]-saturated rate of photosynthesis, and leaf oxygen radical absorbance capacity from leaf reflectance spectra. Partial least-squares regression models accurately predicted five out of seven traits and were more accurate than previously used simple spectral indices for leaf chlorophyll, nitrogen content, and specific leaf area. Correlations among leaf traits and statistical inferences about differences among genotypes and treatments were similar for measured and modeled data. The hyperspectral reflectance approach to phenotyping was dramatically faster than traditional measurements, enabling over 1,000 rows to be phenotyped during midday hours over just 2 to 4 d, and offers a nondestructive method to accurately assess physiological and biochemical trait responses to environmental stress. PMID:28049858

Relative Water Content, Bidirectional Reflectance and Bidirectional Transmittance of the Interior of Detached Leaves During Dry Down.

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

2015-01-01

Remotely sensing the water status of plants and the water content of canopies remain long-term goals of remote sensing research [1]. Estimates of canopy water content commonly involve measurements in the 900nm to 2000nm portion of the optical spectrum [1]. We have used optical polarization techniques to remove leaf surface reflection and to demonstrate that the visible light reflected by the interior of green healthy corn leaves measured in situ inversely depends upon the leaf relative water content (RWC) [2]. In the research reported here, we again used optical polarization techniques in order to remove the leaf surface reflection from our measurements. This allowed us to monitor the interiors of detached corn leaf samples during leaf dry down measuring for each sample the RWC, bidirectional spectral reflectance and bidirectional spectral transmittance over the wavelength range 450nm to 2,500nm. Our new results like our earlier results show light scattered by the leaf interior measured in the visible wavelength region generally increased as leaf RWC decreased. However, the spectral character and the much improved signal noise of our new results shows the RWC-linked visible light scattering changes are due to leaf structural changes. Our new results show that scattering changes that occur with changing leaf RWC are not attributable to molecular configuration changes in cellular pigments.

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

DOE PAGES

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.; ...

2017-07-18

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diner, Rachel E.; Noddings, Chari M.; Lian, Nathan C.

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequencemore » features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.« less

Cultivating Reflective Practitioners in Technology Preparation: Constructing TPACK through Reflection

ERIC Educational Resources Information Center

Lu, Liangyue

2014-01-01

Teaching is a complex profession, which is further complicated by the integration of technology into classrooms. Reflection can help teachers unpack the complexity in their practice. Reflection can be an effective instructional strategy in helping preservice teachers develop technological pedagogical content knowledge (TPACK), the complex and…

Neural correlates of skill acquisition: decreased cortical activity during a serial interception sequence learning task.

PubMed

Gobel, Eric W; Parrish, Todd B; Reber, Paul J

2011-10-15

Learning of complex motor skills requires learning of component movements as well as the sequential structure of their order and timing. Using a Serial Interception Sequence Learning (SISL) task, participants learned a sequence of precisely timed interception responses through training with a repeating sequence. Following initial implicit learning of the repeating sequence, functional MRI data were collected during performance of that known sequence and compared with activity evoked during novel sequences of actions, novel timing patterns, or both. Reduced activity was observed during the practiced sequence in a distributed bilateral network including extrastriate occipital, parietal, and premotor cortical regions. These reductions in evoked activity likely reflect improved efficiency in visuospatial processing, spatio-motor integration, motor planning, and motor execution for the trained sequence, which is likely supported by nondeclarative skill learning. In addition, the practiced sequence evoked increased activity in the left ventral striatum and medial prefrontal cortex, while the posterior cingulate was more active during periods of better performance. Many prior studies of perceptual-motor skill learning have found increased activity in motor areas of the frontal cortex (e.g., motor and premotor cortex, SMA) and striatal areas (e.g., the putamen). The change in activity observed here (i.e., decreased activity across a cortical network) may reflect skill learning that is predominantly expressed through more accurate performance rather than decreased reaction time. Copyright © 2011 Elsevier Inc. All rights reserved.

Neural Correlates of Skill Acquisition: Decreased Cortical Activity During a Serial Interception Sequence Learning Task

PubMed Central

Gobel, Eric W.; Parrish, Todd B.; Reber, Paul J.

2011-01-01

Learning of complex motor skills requires learning of component movements as well as the sequential structure of their order and timing. Using a Serial Interception Sequence Learning (SISL) task, participants learned a sequence of precisely timed interception responses through training with a repeating sequence. Following initial implicit learning of the repeating sequence, functional MRI data were collected during performance of that known sequence and compared with activity evoked during novel sequences of actions, novel timing patterns, or both. Reduced activity was observed during the practiced sequence in a distributed bilateral network including extrastriate occipital, parietal, and premotor cortical regions. These reductions in evoked activity likely reflect improved efficiency in visuospatial processing, spatio-motor integration, motor planning, and motor execution for the trained sequence, which is likely supported by nondeclarative skill learning. In addition, the practiced sequence evoked increased activity in the left ventral striatum and medial prefrontal cortex, while the posterior cingulate was more active during periods of better performance. Many prior studies of perceptual-motor skill learning have found increased activity in motor areas of frontal cortex (e.g., motor and premotor cortex, SMA) and striatal areas (e.g., the putamen). The change in activity observed here (i.e., decreased activity across a cortical network) may reflect skill learning that is predominantly expressed through more accurate performance rather than decreased reaction time. PMID:21771663

Variations in Grain-Scale Sediment Structure in a Gravel-Bed Channel as a Function of Fine Sediment Content and Morphological Location

NASA Astrophysics Data System (ADS)

Voepel, H.; Ahmed, S. I.; Hodge, R. A.; Leyland, J.; Sear, D. A.

2016-12-01

One of the major causes of uncertainty in estimates of bedload transport rates in gravel bed rivers is a lack of understanding of grain-scale sediment structure, and the impact that this structure has on bed stability. Furthermore, grain-scale structure varies throughout a channel and over time in ways that have not been fully quantified. Our research aims to quantify variations in sediment structure caused by two key variables; morphological location within a riffle-pool sequence (reflecting variation in hydraulic conditions), and the fine sediment content of the gravel bed (sand and clay). We report results from a series of flume experiments in which we water-worked a gravel bed with a riffle-pool morphology. The fine sediment content of the bed was incrementally increased over a series of runs from gravel only, to coarse sand, fine sand and two concentrations of clay. After each experimental run intact samples of the bed at different locations were extracted and the internal structure of the bed was measured using non-destructive, micro-focus X-ray computed tomography (CT) imaging. The CT images were processed to measure the properties of individual grains, including volume, center of mass, dimension, and contact points. From these data we were able to quantify the sediment structure through metrics including measurement of grain pivot angles, grain exposure and protrusion, and vertical variation in bed porosity and fine sediment content. Metrics derived from the CT data were verified using data from grain counts and tilt-table measurements on co-located samples. Comparison of the metrics across different morphological locations and fine sediment content demonstrates how these factors affect the bed structure. These results have implications for the development of sediment entrainment models for gravel bed rivers.

Estimating the leaf nitrogen content of paddy rice by using the combined reflectance and laser-induced fluorescence spectra.

PubMed

Yang, Jian; Du, Lin; Sun, Jia; Zhang, Zhenbing; Chen, Biwu; Shi, Shuo; Gong, Wei; Song, Shalei

2016-08-22

Paddy rice is one of the most important crops in China, and leaf nitrogen content (LNC) serves as a significant indictor for monitoring crop status. A reliable method is needed for precise and fast quantification of LNC. Laser-induced fluorescence (LIF) technology and reflectance spectra of crops are widely used to monitor leaf biochemical content. However, comparison between the fluorescence and reflectance spectra has been rarely investigated in the monitoring of LNC. In this study, the performance of the fluorescence and reflectance spectra for LNC estimation was discussed based on principal component analysis (PCA) and back-propagation neural network (BPNN). The combination of fluorescence and reflectance spectra was also proposed to monitor paddy rice LNC. The fluorescence and reflectance spectra exhibited a high degree of multi-collinearity. About 95.38%, and 97.76% of the total variance included in the spectra were efficiently extracted by using the first three PCs in PCA. The BPNN was implemented for LNC prediction based on new variables calculated using PCA. The experimental results demonstrated that the fluorescence spectra (R² = 0.810, 0.804 for 2014 and 2015, respectively) are superior to the reflectance spectra (R² = 0.721, 0.671 for 2014 and 2015, respectively) for estimating LNC based on the PCA-BPNN model. The proposed combination of fluorescence and reflectance spectra can greatly improve the accuracy of LNC estimation (R² = 0.912, 0.890 for 2014 and 2015, respectively).

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

PubMed Central

Steczkiewicz, Kamil; Ginalski, Krzysztof

2017-01-01

Abstract Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a “cut-and-paste” fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species’ lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition. PMID:29228286

Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.

PubMed

Rius, Nuria; Guillén, Yolanda; Delprat, Alejandra; Kapusta, Aurélie; Feschotte, Cédric; Ruiz, Alfredo

2016-05-10

Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis. We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes. TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy.

Identification of genes in anonymous DNA sequences. Annual performance report, February 1, 1991--January 31, 1992

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fields, C.A.

1996-06-01

The objective of this project is the development of practical software to automate the identification of genes in anonymous DNA sequences from the human, and other higher eukaryotic genomes. A software system for automated sequence analysis, gm (gene modeler) has been designed, implemented, tested, and distributed to several dozen laboratories worldwide. A significantly faster, more robust, and more flexible version of this software, gm 2.0 has now been completed, and is being tested by operational use to analyze human cosmid sequence data. A range of efforts to further understand the features of eukaryoyic gene sequences are also underway. This progressmore » report also contains papers coming out of the project including the following: gm: a Tool for Exploratory Analysis of DNA Sequence Data; The Human THE-LTR(O) and MstII Interspersed Repeats are subfamilies of a single widely distruted highly variable repeat family; Information contents and dinucleotide compostions of plant intron sequences vary with evolutionary origin; Splicing signals in Drosophila: intron size, information content, and consensus sequences; Integration of automated sequence analysis into mapping and sequencing projects; Software for the C. elegans genome project.« less

Response to 'pervasive sequence patents cover the entire human genome' - authors' reply.

PubMed

Rosenfeld, Jeffrey; Mason, Christopher

2014-01-01

An author reply to the Letter to the Editor from Tu et al. regarding Pervasive sequence patents cover the entire human genome by J Rosenfeld and C Mason. Genome Med 2013, 5:27. See related Correspondence by Rosenfeld and Mason, http://genomemedicine.com/content/5/3/27, and related letter by Tu et al., http://genomemedicine.com/content/6/2/14.

The full mitochondrial genome sequence of Raillietina tetragona from chicken (Cestoda: Davaineidae).

PubMed

Liang, Jian-Ying; Lin, Rui-Qing

2016-11-01

In the present study, the complete mitochondrial DNA (mtDNA) sequence of Raillietina tetragona was sequenced and its gene contents and genome organizations was compared with that of other tapeworm. The complete mt genome sequence of R. tetragona is 14,444 bp in length. It contains 12 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and two non-coding region. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A + T of the complete mt genome are 71.4% for R. tetragona. The R. tetragona mt genome sequence provides novel mtDNA marker for studying the molecular epidemiology and population genetics of Raillietina and has implications for the molecular diagnosis of chicken cestodosis caused by Raillietina.

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.

PubMed

Lathe, R

1985-05-05

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

Do Scaffolding Tools Improve Reflective Writing in Professional Portfolios? A Content Analysis of Reflective Writing in an Advanced Preparation Program

ERIC Educational Resources Information Center

Houston, Cynthia R.

2016-01-01

Reflective practice is an important skill that teachers must develop to be able to assess the effectiveness of their teaching and modify their instructional behavior. In many education programs reflective narratives, which are often part of teaching portfolios, are intended to assess students' abilities in these areas. Research on reflectivity in…

Relative performance evaluation of a custom-made near infrared reflectance instrument and two commercial instruments (Foss and ASD) in the nondestructive moisture content measurement of in-shell peanuts

USDA-ARS?s Scientific Manuscript database

A custom made Near Infrared Reflectance (NIR) spectroscope was used to determine the moisture content of in-shell peanuts of Virginia type peanuts. Peanuts were conditioned to different moisture levels between 6 and 26 % (wet basis) and samples from different moisture levels were separated into two...

Personal Reflection: "Joy Ride" with SoTL Practice: The Investigation of the Effectiveness of Assistive Technology Course Contents on Student Learning

ERIC Educational Resources Information Center

Cho, Jeong il

2012-01-01

This reflection is based on my project that investigated the impact of new course content on student learning of basic knowledge and attitudes toward various assistive technology (AT) devices and services using multiple measures in an introductory-level course in a special education program at Indiana University-Purdue University Fort Wayne.…

Compositions and methods for xylem-specific expression in plant cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Han, Kyung-Hwan; Ko, Jae-Heung

The invention provides promoter sequences that regulate specific expression of operably linked sequences in developing xylem cells and/or in developing xylem tissue. The developing xylem-specific sequences are exemplified by the DX5, DX8, DX11, and DX15 promoters, portions thereof, and homologs thereof. The invention further provides expression vectors, cells, tissues and plants that contain the invention's sequences. The compositions of the invention and methods of using them are useful in, for example, improving the quantity (biomass) and/or the quality (wood density, lignin content, sugar content etc.) of expressed biomass feedstock products that may be used for bioenergy, biorefinary, and generating woodmore » products such as pulp, paper, and solid wood.« less

Critical Reflection as a Framework for Transformative Learning in Teacher Education

ERIC Educational Resources Information Center

Liu, Katrina

2015-01-01

This paper presents a framework for critical reflection that teacher educators can employ to analyze prospective teachers' reflection and support their transformative learning. The author argues that teacher educators should not only pay attention to the cognitive processes of prospective teachers (how they reflect), but also the content of their…

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

Desert soil clay content estimation using reflectance spectroscopy preprocessed by fractional derivative

PubMed Central

Tiyip, Tashpolat; Ding, Jianli; Zhang, Dong; Liu, Wei; Wang, Fei; Tashpolat, Nigara

2017-01-01

Effective pretreatment of spectral reflectance is vital to model accuracy in soil parameter estimation. However, the classic integer derivative has some disadvantages, including spectral information loss and the introduction of high-frequency noise. In this paper, the fractional order derivative algorithm was applied to the pretreatment and partial least squares regression (PLSR) was used to assess the clay content of desert soils. Overall, 103 soil samples were collected from the Ebinur Lake basin in the Xinjiang Uighur Autonomous Region of China, and used as data sets for calibration and validation. Following laboratory measurements of spectral reflectance and clay content, the raw spectral reflectance and absorbance data were treated using the fractional derivative order from the 0.0 to the 2.0 order (order interval: 0.2). The ratio of performance to deviation (RPD), determinant coefficients of calibration (Rc2), root mean square errors of calibration (RMSEC), determinant coefficients of prediction (Rp2), and root mean square errors of prediction (RMSEP) were applied to assess the performance of predicting models. The results showed that models built on the fractional derivative order performed better than when using the classic integer derivative. Comparison of the predictive effects of 22 models for estimating clay content, calibrated by PLSR, showed that those models based on the fractional derivative 1.8 order of spectral reflectance (Rc2 = 0.907, RMSEC = 0.425%, Rp2 = 0.916, RMSEP = 0.364%, and RPD = 2.484 ≥ 2.000) and absorbance (Rc2 = 0.888, RMSEC = 0.446%, Rp2 = 0.918, RMSEP = 0.383% and RPD = 2.511 ≥ 2.000) were most effective. Furthermore, they performed well in quantitative estimations of the clay content of soils in the study area. PMID:28934274

The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

PubMed

Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

2012-01-01

The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

Detection of sequence variation in parasite ribosomal DNA by electrophoresis in agarose gels supplemented with a DNA-intercalating agent.

PubMed

Zhu, X Q; Chilton, N B; Gasser, R B

1998-05-01

This study evaluated the use of a commercially available DNA intercalating agent (Resolver Gold) in agarose gels for the direct detection of sequence variation in ribosomal DNA (rDNA). This agent binds preferentially to AT sequence motifs in DNA. Regions of nuclear rDNA, known to provide genetic markers for the identification of species of parasitic ascarid nematodes (order Ascaridida), were amplified by polymerase chain reaction (PCR) and subjected to electrophoresis in standard agarose gels versus gels supplemented with Resolver Gold. Individual taxa examined could not be distinguished reliably based on the size of their amplicons in standard agarose gels, whereas they could be readily delineated based on mobility using Resolver Gold-supplemented gels. The latter was achieved because of differences (approximately 0.1-8.2%) in the AT content of the fragments among different taxa, which were associated with significant interspecific differences (approximately 11-39%) in the rDNA sequences employed. There was a tendency for fragments with higher AT content to migrate slower in supplemented agarose gels compared with those of lower AT content. The results indicate the usefulness of this electrophoretic approach to rapidly screen for sequence variability within or among PCR-amplified rDNA fragments of similar sizes but differing AT contents. Although evaluated on rDNA of parasites, the approach has potential to be applied to a range of genes of different groups of infectious organisms.

Creating photorealistic virtual model with polarization-based vision system

NASA Astrophysics Data System (ADS)

Shibata, Takushi; Takahashi, Toru; Miyazaki, Daisuke; Sato, Yoichi; Ikeuchi, Katsushi

2005-08-01

Recently, 3D models are used in many fields such as education, medical services, entertainment, art, digital archive, etc., because of the progress of computational time and demand for creating photorealistic virtual model is increasing for higher reality. In computer vision field, a number of techniques have been developed for creating the virtual model by observing the real object in computer vision field. In this paper, we propose the method for creating photorealistic virtual model by using laser range sensor and polarization based image capture system. We capture the range and color images of the object which is rotated on the rotary table. By using the reconstructed object shape and sequence of color images of the object, parameter of a reflection model are estimated in a robust manner. As a result, then, we can make photorealistic 3D model in consideration of surface reflection. The key point of the proposed method is that, first, the diffuse and specular reflection components are separated from the color image sequence, and then, reflectance parameters of each reflection component are estimated separately. In separation of reflection components, we use polarization filter. This approach enables estimation of reflectance properties of real objects whose surfaces show specularity as well as diffusely reflected lights. The recovered object shape and reflectance properties are then used for synthesizing object images with realistic shading effects under arbitrary illumination conditions.

Physiochemical, site, and bidirectional reflectance factor characteristics of uniformly moist soils. [Brazil, Spain and the United States of America

NASA Technical Reports Server (NTRS)

Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

1980-01-01

The author has identified the following significant results. The bidirectional reflectance factor (0.5 micron to 2.3 micron wavelength interval) and physiochemical properties of over 500 soils from 39 states, Brazil and Spain were measured. Site characteristics of soil temperature regime and moisture zone were used as selection criteria. Parent material and internal drainage were noted for each soil. At least five general types of soil reflectance curves were identified based primarily on the presence or absence of ferric iron absorption bands, organic matter content, and soil drainage characteristics. Reflectance in 10 bands across the spectrum was found to be negatively correlated with the natural log of organic matter content.

Whole-Genome Sequence of "Candidatus Profftella armatura" from Diaphorina citri in Guangdong, China.

PubMed

Wu, F; Deng, X; Liang, G; Huang, J; Cen, Y; Chen, J

2015-11-05

The genome of "Candidatus Profftella armatura" strain YCPA from Diaphorina citri in Guangdong, China, was sequenced. The strain has a chromosome of 457,565 bp, 24.3% G+C content, 364 predicted open reading frames (ORFs), and 38 RNAs, and a plasmid, pYCPA54, of 5,458 bp with 23.9% G+C content and 5 ORFs. Copyright © 2015 Wu et al.

Response to ‘pervasive sequence patents cover the entire human genome’ - authors’ reply

PubMed Central

2014-01-01

An author reply to the Letter to the Editor from Tu et al. regarding Pervasive sequence patents cover the entire human genome by J Rosenfeld and C Mason. Genome Med 2013, 5:27. See related Correspondence by Rosenfeld and Mason, http://genomemedicine.com/content/5/3/27, and related letter by Tu et al., http://genomemedicine.com/content/6/2/14 PMID:24764495

An information technology emphasis in biomedical informatics education.

PubMed

Kane, Michael D; Brewer, Jeffrey L

2007-02-01

Unprecedented growth in the interdisciplinary domain of biomedical informatics reflects the recent advancements in genomic sequence availability, high-content biotechnology screening systems, as well as the expectations of computational biology to command a leading role in drug discovery and disease characterization. These forces have moved much of life sciences research almost completely into the computational domain. Importantly, educational training in biomedical informatics has been limited to students enrolled in the life sciences curricula, yet much of the skills needed to succeed in biomedical informatics involve or augment training in information technology curricula. This manuscript describes the methods and rationale for training students enrolled in information technology curricula in the field of biomedical informatics, which augments the existing information technology curriculum and provides training on specific subjects in Biomedical Informatics not emphasized in bioinformatics courses offered in life science programs, and does not require prerequisite courses in the life sciences.

Hippocampal replay in the awake state: a potential physiological substrate of memory consolidation and retrieval

PubMed Central

Carr, Margaret F.; Jadhav, Shantanu P.; Frank, Loren M.

2011-01-01

The hippocampus is required for the encoding, consolidation, and retrieval of event memories. While the neural mechanisms that underlie these processes are only partially understood, a series of recent papers point to awake memory replay as a potential contributor to both consolidation and retrieval. Replay is the sequential reactivation of hippocampal place cells that represent previously experienced behavioral trajectories and occurs frequently in the awake state, particularly during periods of relative immobility. Awake replay may reflect trajectories through either the current environment or previously visited environments that are spatially remote. The repetition of learned sequences on a compressed time scale is well suited to promote memory consolidation in distributed circuits beyond the hippocampus, suggesting that consolidation occurs in both the awake and sleeping animal. Moreover, sensory information can influence the content of awake replay, suggesting a role for awake replay in memory retrieval. PMID:21270783

Endozoicomonas dominates the gill and intestinal content microbiomes of Mytilus edulis from Barnegat Bay, New Jersey

USGS Publications Warehouse

Schill, William B.; Iwanowicz, Deborah; Adams, Cynthia

2017-01-01

Blue mussels, Mytilus edulis, Linnaeus 1758 from southern Barnegat Bay, New Jersey were examined to determine the make-up of the normal blue mussel microbiome. Sequencing of 16S ribosomal DNA amplicons from gill and intestinal content microbiomes using the Illumina® MiSeq platform yielded 1,276,161 paired end sequence reads from the gill libraries and 1,092,333 paired end sequence reads from the intestinal content libraries. General bioinformatic analyses were conducted with the open-source packages Qiime and Mothur. Phylotype assignments to the genus level were made using the commercial One Codex platform. This resulted in 1,697,852 gill and 988,436 intestinal content sequences being classified to genus. A majority of these (67.6% and 37.2% respectively) were assigned to a single operational taxonomic unit (Mytilus edulis Symbiont, MeS) that has homologies with other recently described Endozoicomonas pathogens and symbionts of marine invertebrates. MeS shares 98% identity with an uncultured bacterium from the gill tissue of an invasive indo-Pacific oyster and with HQE1 and HQE2 isolated from the sea squirt, Styela clava. Other than MeS, most of the detected bacterial species are known from marine sediments and seawater.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

PubMed

Oyola, Samuel O; Otto, Thomas D; Gu, Yong; Maslen, Gareth; Manske, Magnus; Campino, Susana; Turner, Daniel J; Macinnis, Bronwyn; Kwiatkowski, Dominic P; Swerdlow, Harold P; Quail, Michael A

2012-01-03

Massively parallel sequencing technology is revolutionizing approaches to genomic and genetic research. Since its advent, the scale and efficiency of Next-Generation Sequencing (NGS) has rapidly improved. In spite of this success, sequencing genomes or genomic regions with extremely biased base composition is still a great challenge to the currently available NGS platforms. The genomes of some important pathogenic organisms like Plasmodium falciparum (high AT content) and Mycobacterium tuberculosis (high GC content) display extremes of base composition. The standard library preparation procedures that employ PCR amplification have been shown to cause uneven read coverage particularly across AT and GC rich regions, leading to problems in genome assembly and variation analyses. Alternative library-preparation approaches that omit PCR amplification require large quantities of starting material and hence are not suitable for small amounts of DNA/RNA such as those from clinical isolates. We have developed and optimized library-preparation procedures suitable for low quantity starting material and tolerant to extremely high AT content sequences. We have used our optimized conditions in parallel with standard methods to prepare Illumina sequencing libraries from a non-clinical and a clinical isolate (containing ~53% host contamination). By analyzing and comparing the quality of sequence data generated, we show that our optimized conditions that involve a PCR additive (TMAC), produces amplified libraries with improved coverage of extremely AT-rich regions and reduced bias toward GC neutral templates. We have developed a robust and optimized Next-Generation Sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due to low mass of DNA starting material.

Prediction of soil organic carbon in a coal mining area by Vis-NIR spectroscopy.

PubMed

Sun, Wenjuan; Li, Xinju; Niu, Beibei

2018-01-01

Coal mining has led to increasingly serious land subsidence, and the reclamation of the subsided land has become a hot topic of concern for governments and scholars. Soil quality of reclaimed land is the key indicator to the evaluation of the reclamation effect; hence, rapid monitoring and evaluation of reclaimed land is of great significance. Visible-near infrared (Vis-NIR) spectroscopy has been shown to be a rapid, timely and efficient tool for the prediction of soil organic carbon (SOC). In this study, 104 soil samples were collected from the Baodian mining area of Shandong province. Vis-NIR reflectance spectra and soil organic carbon content were then measured under laboratory conditions. The spectral data were first denoised using the Savitzky-Golay (SG) convolution smoothing method or the multiple scattering correction (MSC) method, after which the spectral reflectance (R) was subjected to reciprocal, reciprocal logarithm and differential transformations to improve spectral sensitivity. Finally, regression models for estimating the SOC content by the spectral data were constructed using partial least squares regression (PLSR). The results showed that: (1) The SOC content in the mining area was generally low (at the below-average level) and exhibited great variability. (2) The spectral reflectance increased with the decrease of soil organic carbon content. In addition, the sensitivity of the spectrum to the change in SOC content, especially that in the near-infrared band of the original reflectance, decreased when the SOC content was low. (3) The modeling results performed best when the spectral reflectance was preprocessed by Savitzky-Golay (SG) smoothing coupled with multiple scattering correction (MSC) and first-order differential transformation (modeling R2 = 0.86, RMSE = 2.00 g/kg, verification R2 = 0.78, RMSE = 1.81 g/kg, and RPD = 2.69). In addition, the first-order differential of R combined with SG, MSC with R, SG together with MSC and R also produced better modeling results than other pretreatment combinations. Vis-NIR modeling with specific spectral preprocessing methods could predict SOC content effectively.

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maas, R.; McCulloch, M.T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3,000 to 3,700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneissmore » terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. {epsilon}{sub Nd}(T{sub Dep}) values in Jack Hills metasediments vary widely (+5 to {minus}12) but have a smaller range in the Mt. Narryer belt ({minus}5 to {minus}9). The lowest {epsilon}{sub Nd} values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger ({ge} 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons ({approx}3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.« less

Automated detection of records in biological sequence databases that are inconsistent with the literature.

PubMed

Bouadjenek, Mohamed Reda; Verspoor, Karin; Zobel, Justin

2017-07-01

We investigate and analyse the data quality of nucleotide sequence databases with the objective of automatic detection of data anomalies and suspicious records. Specifically, we demonstrate that the published literature associated with each data record can be used to automatically evaluate its quality, by cross-checking the consistency of the key content of the database record with the referenced publications. Focusing on GenBank, we describe a set of quality indicators based on the relevance paradigm of information retrieval (IR). Then, we use these quality indicators to train an anomaly detection algorithm to classify records as "confident" or "suspicious". Our experiments on the PubMed Central collection show assessing the coherence between the literature and database records, through our algorithms, is an effective mechanism for assisting curators to perform data cleansing. Although fewer than 0.25% of the records in our data set are known to be faulty, we would expect that there are many more in GenBank that have not yet been identified. By automated comparison with literature they can be identified with a precision of up to 10% and a recall of up to 30%, while strongly outperforming several baselines. While these results leave substantial room for improvement, they reflect both the very imbalanced nature of the data, and the limited explicitly labelled data that is available. Overall, the obtained results show promise for the development of a new kind of approach to detecting low-quality and suspicious sequence records based on literature analysis and consistency. From a practical point of view, this will greatly help curators in identifying inconsistent records in large-scale sequence databases by highlighting records that are likely to be inconsistent with the literature. Copyright © 2017 Elsevier Inc. All rights reserved.

CRISPR Diversity and Microevolution in Clostridium difficile.

PubMed

Andersen, Joakim M; Shoup, Madelyn; Robinson, Cathy; Britton, Robert; Olsen, Katharina E P; Barrangou, Rodolphe

2016-09-19

Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Stratigraphic variations in the biomarker distribution of the Moreno Formation: Their correlation with San Joaquin basin oils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bac, M.G.; Schulein, B.J.

1990-05-01

Variability in the biomarker compositions of petroleums is typically employed in the recognition and distinction of contributions from different source rocks. We demonstrate that the fluctuations in the biomarker distributions of different intervals within a single source rock sequence appear to account for specific compositional differences in a suite of oils from the San Joaquin basin California. Rock-Eval pyrolysis studies of a 100-m-thick immature, laminated, marine shale sequence within the Upper Cretaceous lo lower Paleocene portion of the Moreno Formation reveals TOC (total organic carbon) contents consistently around 2% and moderate hydrogen indices (i.e., 175-300 mg HC/g org. C) characteristicsmore » suggestive of a uniform depositional sequence with source rock potential. Analyses of the extractable aliphatic hydrocarbons of cored samples taken at approximately 10-m intervals from the sequence reveal significant variability in biomarker distributions. Such differences are exemplified by the triterpenoids (as seen in m/z 191 chromatograms from GC-MS and GC-MS/MS analyses) where the dominant component fluctuates from a 17{alpha}(h),21{beta}(H)-30-norhopane to 28,30-l8{alpha}(H)-bisnorhopane to 20S and 20R danunar-13(17)-enes. Some components are dominant in one interval, but are not detected in others, suggesting discrete stratigraphic variations in the biomarker characteristics of the Moreno. Similar discrepancies in biomarker distributions are evident in the aliphatic hydrocarbons of the suite of oils. The three petroleums reservoired in the San Carlos sandstone member of the Lodo Formation which directly overlies the Moreno, reflect biomarker contributions from a Moreno source, including compound distributions, and the occurrence of both alkanes (e.g., 28.30-bisnorhopane) and alkenes (e.g.. danunarenes and diasterenes).« less

Soil moisture balance and magnetic enhancement in loess-paleosol sequences from the Tibetan Plateau and Chinese Loess Plateau

NASA Astrophysics Data System (ADS)

Hu, Pengxiang; Liu, Qingsong; Heslop, David; Roberts, Andrew P.; Jin, Chunsheng

2015-01-01

We present a first combined environmental magnetic and geochemical investigation of a loess-paleosol sequence (<55 ka) from the Chuanxi Plateau on the eastern margin of the Tibetan Plateau. Detailed comparison between the Ganzi section and the Luochuan section from the Chinese Loess Plateau (CLP) allows quantification of the effects of provenance and climate on pedogenic magnetic enhancement in Chinese loess. Rare earth element patterns and clay mineral compositions indicate that the Ganzi loess originates from the interior of the Tibetan Plateau. The different Ganzi and CLP loess provenances add complexity to interpretation of magnetic parameters in terms of the concentration and grain size of eolian magnetic minerals. Enhanced paleosol magnetism via pedogenic formation of ferrimagnetic nanoparticles is observed in both sections, but weaker ferrimagnetic contributions, finer superparamagnetic (SP) particles and stronger chemical weathering are found in the Ganzi loess, which indicates the action of multiple pedogenic processes that are dominated by the combined effects of mean annual precipitation (MAP), potential evapotranspiration (PET), organic matter and aluminium content. Under relatively high MAP and low PET conditions, high soil moisture favours transformation of ferrimagnetic minerals to hematite, which results in a relatively higher concentration of hematite but weaker ferrimagnetism of Ganzi loess. Initial growth of superparamagnetic (SP) particles is also documented in the incipient loess at Ganzi, which directly reflects the dynamic formation of nano-sized pedogenic ferrimagnets. A humid pedogenic environment with more organic matter and higher Al content also helps to form finer SP particles. We therefore propose that soil water balance, rather than solely rainfall, dominates the type, concentration and grain size of secondary ferrimagnetic minerals produced by pedogenesis.

HyperART: non-invasive quantification of leaf traits using hyperspectral absorption-reflectance-transmittance imaging.

PubMed

Bergsträsser, Sergej; Fanourakis, Dimitrios; Schmittgen, Simone; Cendrero-Mateo, Maria Pilar; Jansen, Marcus; Scharr, Hanno; Rascher, Uwe

2015-01-01

Combined assessment of leaf reflectance and transmittance is currently limited to spot (point) measurements. This study introduces a tailor-made hyperspectral absorption-reflectance-transmittance imaging (HyperART) system, yielding a non-invasive determination of both reflectance and transmittance of the whole leaf. We addressed its applicability for analysing plant traits, i.e. assessing Cercospora beticola disease severity or leaf chlorophyll content. To test the accuracy of the obtained data, these were compared with reflectance and transmittance measurements of selected leaves acquired by the point spectroradiometer ASD FieldSpec, equipped with the FluoWat device. The working principle of the HyperART system relies on the upward redirection of transmitted and reflected light (range of 400 to 2500 nm) of a plant sample towards two line scanners. By using both the reflectance and transmittance image, an image of leaf absorption can be calculated. The comparison with the dynamically high-resolution ASD FieldSpec data showed good correlation, underlying the accuracy of the HyperART system. Our experiments showed that variation in both leaf chlorophyll content of four different crop species, due to different fertilization regimes during growth, and fungal symptoms on sugar beet leaves could be accurately estimated and monitored. The use of leaf reflectance and transmittance, as well as their sum (by which the non-absorbed radiation is calculated) obtained by the HyperART system gave considerably improved results in classification of Cercospora leaf spot disease and determination of chlorophyll content. The HyperART system offers the possibility for non-invasive and accurate mapping of leaf transmittance and absorption, significantly expanding the applicability of reflectance, based on mapping spectroscopy, in plant sciences. Therefore, the HyperART system may be readily employed for non-invasive determination of the spatio-temporal dynamics of various plant properties.

Sequence learning in Parkinson's disease: Focusing on action dynamics and the role of dopaminergic medication.

PubMed

Ruitenberg, Marit F L; Duthoo, Wout; Santens, Patrick; Seidler, Rachael D; Notebaert, Wim; Abrahamse, Elger L

2016-12-01

Previous studies on movement sequence learning in Parkinson's disease (PD) have produced mixed results. A possible explanation for the inconsistent findings is that some studies have taken dopaminergic medication into account while others have not. Additionally, in previous studies the response modalities did not allow for an investigation of the action dynamics of sequential movements as they unfold over time. In the current study we investigated sequence learning in PD by specifically considering the role of medication status in a sequence learning task where mouse movements were performed. The focus on mouse movements allowed us to examine the action dynamics of sequential movement in terms of initiation time, movement time, movement accuracy, and velocity. PD patients performed the sequence learning task once on their regular medication, and once after overnight withdrawal from their medication. Results showed that sequence learning as reflected in initiation times was impaired when PD patients performed the task ON medication compared to OFF medication. In contrast, sequence learning as reflected in the accuracy of movement trajectories was enhanced when performing the task ON compared to OFF medication. Our findings suggest that while medication enhances execution processes of movement sequence learning, it may at the same time impair planning processes that precede actual execution. Overall, the current study extends earlier findings on movement sequence learning in PD by differentiating between various components of performance, and further refines previous dopamine overdose effects in sequence learning. Copyright © 2016 Elsevier Ltd. All rights reserved.

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content

PubMed Central

Joseph, Roy; Poschmann, Jeremie; Sukarieh, Rami; Too, Peh Gek; Julien, Sofi G.; Xu, Feng; Teh, Ai Ling; Holbrook, Joanna D.; Ng, Kai Lyn; Chong, Yap Seng; Gluckman, Peter D.; Prabhakar, Shyam

2015-01-01

Individuals who are born small for gestational age (SGA) have a risk to develop various metabolic diseases during their life course. The biological memory of the prenatal state of growth restricted individuals may be reflected in epigenetic alterations in stem cell populations. Mesenchymal stem cells (MSCs) from the Wharton's jelly of umbilical cord tissue are multipotent, and we generated primary umbilical cord MSC isolates from SGA and normal neonates, which were subsequently differentiated into adipocytes. We established chromatin state maps for histone marks H3K27 acetylation and H3K27 trimethylation and tested whether enrichment of these marks was associated with gene expression changes. After validating gene expression levels for 10 significant chromatin immunoprecipitation sequencing candidate genes, we selected acyl-coenzyme A synthetase 1 (ACSL1) for further investigations due to its key roles in lipid metabolism. The ACSL1 gene was found to be highly associated with histone acetylation in adipocytes differentiated from MSCs with SGA background. In SGA-derived adipocytes, the ACSL1 expression level was also found to be associated with increased lipid loading as well as higher insulin sensitivity. ACSL1 depletion led to changes in expression of candidate genes such as proinflammatory chemokines and down-regulated both, the amount of cellular lipids and glucose uptake. Increased ACSL1, as well as modulated downstream candidate gene expression, may reflect the obese state, as detected in mice fed a high-fat diet. In summary, we believe that ACSL1 is a programmable mediator of insulin sensitivity and cellular lipid content and adipocytes differentiated from Wharton's jelly MSCs recapitulate important physiological characteristics of SGA individuals. PMID:25915184

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content.

PubMed

Joseph, Roy; Poschmann, Jeremie; Sukarieh, Rami; Too, Peh Gek; Julien, Sofi G; Xu, Feng; Teh, Ai Ling; Holbrook, Joanna D; Ng, Kai Lyn; Chong, Yap Seng; Gluckman, Peter D; Prabhakar, Shyam; Stünkel, Walter

2015-06-01

Individuals who are born small for gestational age (SGA) have a risk to develop various metabolic diseases during their life course. The biological memory of the prenatal state of growth restricted individuals may be reflected in epigenetic alterations in stem cell populations. Mesenchymal stem cells (MSCs) from the Wharton's jelly of umbilical cord tissue are multipotent, and we generated primary umbilical cord MSC isolates from SGA and normal neonates, which were subsequently differentiated into adipocytes. We established chromatin state maps for histone marks H3K27 acetylation and H3K27 trimethylation and tested whether enrichment of these marks was associated with gene expression changes. After validating gene expression levels for 10 significant chromatin immunoprecipitation sequencing candidate genes, we selected acyl-coenzyme A synthetase 1 (ACSL1) for further investigations due to its key roles in lipid metabolism. The ACSL1 gene was found to be highly associated with histone acetylation in adipocytes differentiated from MSCs with SGA background. In SGA-derived adipocytes, the ACSL1 expression level was also found to be associated with increased lipid loading as well as higher insulin sensitivity. ACSL1 depletion led to changes in expression of candidate genes such as proinflammatory chemokines and down-regulated both, the amount of cellular lipids and glucose uptake. Increased ACSL1, as well as modulated downstream candidate gene expression, may reflect the obese state, as detected in mice fed a high-fat diet. In summary, we believe that ACSL1 is a programmable mediator of insulin sensitivity and cellular lipid content and adipocytes differentiated from Wharton's jelly MSCs recapitulate important physiological characteristics of SGA individuals.

Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

NASA Astrophysics Data System (ADS)

Kacar, Betul; Guy, Lionel; Smith, Eric; Baross, John

2017-11-01

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the beta-carbonic anhydrase protein. We assess how carbonic anhydrase proteins meet our selection criteria for reconstructing ancient biosignatures in the laboratory, which we term palaeophenotype reconstruction. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Response of some Thematic Mapper band ratios to variation in soil water content

NASA Technical Reports Server (NTRS)

Musick, H. Brad; Pelletier, Ramona E.

1986-01-01

Bidirectional reflectance to nadir in the reflective TM bands and the 1.15-1.3-micron band was measured in the laboratory as moisture content was varied in ten soils. Stronger absorption by water in TM5 and TM7 was expected to cause ratios of other bands to TM5 and TM7 to increase with water content, but in most cases these ratios were constant or decreased at low to intermediate water content and increased only at high moisture levels. Because these ratios were found to decrease as illumination elevation angle decreased, it was suggested that increased roughness resulting from the methods of moistening and mixing the soil may have tended to counteract the expected ratio increases.

Classification of community types, successional sequences, and landscapes of the Copper River Delta, Alaska.

Treesearch

Keith. Boggs

2000-01-01

A classification of community types, successional sequences, and landscapes is presented for the piedmont of the Copper River Delta. The classification was based on a sampling of 471 sites. A total of 75 community types, 42 successional sequences, and 6 landscapes are described. The classification of community types reflects the existing vegetation communities on the...

Laying-sequence-specific variation in yolk oestrogen levels, and relationship to plasma oestrogen in female zebra finches (Taeniopygia guttata)

PubMed Central

Williams, Tony D.; Ames, Caroline E.; Kiparissis, Yiannis; Wynne-Edwards, Katherine E.

2005-01-01

We investigated the relationship between plasma and yolk oestrogens in laying female zebra finches (Taeniopygia guttata) by manipulating plasma oestradiol (E2) levels, via injection of oestradiol-17β, in a sequence-specific manner to maintain chronically high plasma levels for later-developing eggs (contrasting with the endogenous pattern of decreasing plasma E2 concentrations during laying). We report systematic variation in yolk oestrogen concentrations, in relation to laying sequence, similar to that widely reported for androgenic steroids. In sham-manipulated females, yolk E2 concentrations decreased with laying sequence. However, in E2-treated females plasma E2 levels were higher during the period of rapid yolk development of later-laid eggs, compared with control females. As a consequence, we reversed the laying-sequence-specific pattern of yolk E2: in E2-treated females, yolk E2 concentrations increased with laying-sequence. In general therefore, yolk E2 levels were a direct reflection of plasma E2 levels. However, in control females there was some inter-individual variability in the endogenous pattern of plasma E2 levels through the laying cycle which could generate variation in sequence-specific patterns of yolk hormone levels even if these primarily reflect circulating steroid levels. PMID:15695208

When Talking Is Better Than Staying Quiet

NASA Astrophysics Data System (ADS)

Lasry, Nathaniel; Charles, Elizabeth; Whittaker, Chris; Lautman, Michael

2009-11-01

The effectiveness of Peer Instruction is often associated to the importance of in-class discussions between peers. Typically, a greater number of students have correct answers after peer discussions. However, other cognitive and metacognitive processes such as reflection or time-on-task may also explain this increase because students answering conceptual questions reflect more and spend more time thinking about their understanding. An identical sequence of conceptual questions was given to three groups of students. All groups were polled twice on each question. Between polls, students were asked either to discuss their choice with a peer, or to reflect for a minute (no discussion), or were given a distraction task (sequence of cartoons: no discussion and no reflection). Increases in the rates of correct answers between the first and the second poll were found across all conditions. The `Distract' condition had a small but positive increase (3.4%). The `Reflect' condition had a greater increase (9.7%) while the `Discuss' condition had the greatest (21.0%). All conditions showed gains, possibly because of `testing effects', though peer-discussions clearly yield greatest increases. Our findings show that learning gains through peer discussions cannot be explained only by additional time-on-task or self-reflection.

Complete Genome Sequence of Thiostrepton-Producing Streptomyces laurentii ATCC 31255

PubMed Central

Fujino, Yasuhiro; Nagayoshi, Yuko; Ohshima, Toshihisa; Ogata, Seiya

2016-01-01

Streptomyces laurentii ATCC 31255 produces thiostrepton, a thiopeptide class antibiotic. Here, we report the complete genome sequence for this strain, which contains a total of 8,032,664 bp, 7,452 predicted coding sequences, and a G+C content of 72.3%. PMID:27257211

Complete genome sequence of Enterobacter aerogenes KCTC 2190.

PubMed

Shin, Sang Heum; Kim, Sewhan; Kim, Jae Young; Lee, Soojin; Um, Youngsoon; Oh, Min-Kyu; Kim, Young-Rok; Lee, Jinwon; Yang, Kap-Seok

2012-05-01

This is the first complete genome sequence of the Enterobacter aerogenes species. Here we present the genome sequence of E. aerogenes KCTC 2190, which contains 5,280,350 bp with a G + C content of 54.8 mol%, 4,912 protein-coding genes, and 109 structural RNAs.

Evolving discriminators for querying video sequences

NASA Astrophysics Data System (ADS)

Iyengar, Giridharan; Lippman, Andrew B.

1997-01-01

In this paper we present a framework for content based query and retrieval of information from large video databases. This framework enables content based retrieval of video sequences by characterizing the sequences using motion, texture and colorimetry cues. This characterization is biologically inspired and results in a compact parameter space where every segment of video is represented by an 8 dimensional vector. Searching and retrieval is done in real- time with accuracy in this parameter space. Using this characterization, we then evolve a set of discriminators using Genetic Programming Experiments indicate that these discriminators are capable of analyzing and characterizing video. The VideoBook is able to search and retrieve video sequences with 92% accuracy in real-time. Experiments thus demonstrate that the characterization is capable of extracting higher level structure from raw pixel values.

[Study on correlation between ITS sequence of Arctium lappa and quality of Fructus Arctii].

PubMed

Xu, Liang; Dou, Deqiang; Wang, Bing; Yang, Yanyun; Kang, Tingguo

2011-07-01

To study the correlation between ITS sequence of Arctium lappa and Fructus Arctii quality of different origin. The samples of Fructu arctii materials were collected from 26 different producing areas. Their ITS sequence were determined after polymerase chain reaction (PCR) and quality were evaluated through the determination of arctiin content by HPLC. Genetic diversity, genotype and correlation were analyzed by ClustalX (1.81), Mage 4.0, SPSS 13.0 statistical software. ITS sequence of A. was obtained from 26 samples, and was registered in the GenBank. Corresponding arctiin content of Fructus arctii and 1000-grain weight were determined. A. lappa genotype correlated with Fructus arctii quality by statistical analysis. The research provided a foundation for revealing the molecular mechanism of Fructus arctii geoherbs.

The Main Sequence of Explosive Solar Active Regions: Comparison of Emerging and Mature Active Regions

NASA Technical Reports Server (NTRS)

Falconer, David; Moore, Ron

2011-01-01

For mature active regions, an active region s magnetic flux content determines the maximum free energy the active region can have. Most Large flares and CMEs occur in active regions that are near their free-energy limit. Active-region flare power radiated in the GOES 1-8 band increases steeply as the free-energy limit is approached. We infer that the free-energy limit is set by the rate of release of an active region s free magnetic energy by flares, CMEs and coronal heating balancing the maximum rate the Sun can put free energy into the active region s magnetic field. This balance of maximum power results in explosive active regions residing in a "mainsequence" in active-region (flux content, free energy content) phase space, which sequence is analogous to the main sequence of hydrogen-burning stars in (mass, luminosity) phase space.

TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence.

PubMed

Fortin, Connor H; Schulze, Katharina V; Babbitt, Gregory A

2015-01-01

It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in the genome (e.g. DNA shape, charge and intrinsic dynamics). However, these physical features of DNA polymer are not directly apparent when analyzing and viewing Shannon information content calculated at single nucleobases in a traditional sequence logo plot. Thus, sequence logos plots are severely limited in that they convey no explicit information regarding the structural dynamics of DNA backbone, a feature often critical to binding specificity. We present TRX-LOGOS, an R software package and Perl wrapper code that interfaces the JASPAR database for computational regulatory genomics. TRX-LOGOS extends the traditional sequence logo plot to include Shannon information content calculated with regard to the dinucleotide-based BI-BII conformation shifts in phosphate linkages on the DNA backbone, thereby adding a visual measure of intrinsic DNA flexibility that can be critical for many DNA-protein interactions. TRX-LOGOS is available as an R graphics module offered at both SourceForge and as a download supplement at this journal. To demonstrate the general utility of TRX logo plots, we first calculated the information content for 416 Saccharomyces cerevisiae transcription factor binding sites functionally confirmed in the Yeastract database and matched to previously published yeast genomic alignments. We discovered that flanking regions contain significantly elevated information content at phosphate linkages than can be observed at nucleobases. We also examined broader transcription factor classifications defined by the JASPAR database, and discovered that many general signatures of transcription factor binding are locally more information rich at the level of DNA backbone dynamics than nucleobase sequence. We used TRX-logos in combination with MEGA 6.0 software for molecular evolutionary genetics analysis to visually compare the human Forkhead box/FOX protein evolution to its binding site evolution. We also compared the DNA binding signatures of human TP53 tumor suppressor determined by two different laboratory methods (SELEX and ChIP-seq). Further analysis of the entire yeast genome, center aligned at the start codon, also revealed a distinct sequence-independent 3 bp periodic pattern in information content, present only in coding region, and perhaps indicative of the non-random organization of the genetic code. TRX-LOGOS is useful in any situation in which important information content in DNA can be better visualized at the positions of phosphate linkages (i.e. dinucleotides) where the dynamic properties of the DNA backbone functions to facilitate DNA-protein interaction.

Geochemical and Sulfur-Isotopic Signatures of Volcanogenic Massive Sulfide Deposits on Prince of Wales Island and Vicinity, Southeastern Alaska

USGS Publications Warehouse

Slack, John F.; Shanks, Wayne C.; Karl, Susan M.; Gemery, Pamela A.; Bittenbender, Peter E.; Ridley, W. Ian

2007-01-01

Stratabound volcanogenic massive sulfide (VMS) deposits on Prince of Wales Island and vicinity, southeastern Alaska, occur in two volcanosedimentary sequences of Late Proterozoic through Cambrian and of Ordovician through Early Silurian age. This study presents geochemical data on sulfide-rich samples, in situ laser-ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) of sulfide minerals, and sulfur-isotopic analyses of sulfides and sulfates (barite) for identifying and distinguishing between primary sea-floor signatures and later regional metamorphic overprints. These datasets are also used here in an attempt to discriminate the VMS deposits in the older Wales Group from those in the younger Moira Sound unit (new informal name). The Wales Group and its contained VMS deposits have been multiply deformed and metamorphosed from greenschist to amphibolite grade, whereas the Moira Sound unit and related VMS deposits are less deformed and generally less metamorphosed (lower to middle greenschist grade). Variations in the sulfide mineral assemblages and textures of the VMS deposits in both sequences reflect a combination of processes, including primary sea-floor mineralization and sub-sea-floor zone refining, followed by metamorphic recrystallization. Very coarse grained (>1 cm diam) sulfide minerals and abundant pyrrhotite are restricted to VMS deposits in a small area of the Wales Group, at Khayyam and Stumble-On, which record high-grade metamorphism of the sulfides. Geochemical and sulfur-isotopic data distinguish the VMS deposits in the Wales Group from those in the Moira Sound unit. Although base- and precious-metal contents vary widely in sulfide-rich samples from both sequences, samples from the Moira Sound generally have proportionately higher Ag contents relative to base metals and Au. In situ LA-ICP-MS analysis of trace elements in the sulfide minerals suggests that primary sea-floor hydrothermal signatures are preserved in some samples (for example, Mn, As, Sb, and Tl in pyrite from the Moira Sound unit), whereas in other samples the signatures are varyingly annealed, owing to metamorphic overprinting. A limited LA-ICP-MS database for sphalerite indicates that low-Fe sphalerite is preferentially associated with the most Au rich deposits, the Niblack and Nutkwa. Sulfur-isotopic values for sulfide minerals in the VMS deposits in the Wales Group range from 5.9 to 17.4 permil (avg 11.5?2.7 permil), about 5 to 6 permil higher than those in the Moira Sound unit, which range from -2.8 to 10.4 permil (avg 6.1?4.0 permil). This difference in 34Ssulfide values reflects a dominantly seawater sulfate source of the sulfides and is linked to the 34S values of contemporaneous seawater sulfate, which were slightly higher during the Late Proterozoic through Cambrian than during the Ordovician through Early Silurian.

Second-surface silvered glass solar mirrors of very high reflectance

NASA Astrophysics Data System (ADS)

Butel, Guillaume P.; Coughenour, Blake M.; Macleod, H. Angus; Kennedy, Cheryl E.; Olbert, Blain H.; Angel, J. Roger P.

2011-10-01

This paper reports methods developed to maximize the overall reflectance second-surface silvered glass. The reflectance at shorter wavelengths is increased with the aid of a dielectric enhancing layer between the silver and the glass, while at longer wavelengths it is enhanced by use of glass with negligible iron content. The calculated enhancement of reflectance, compared to unenhanced silver on standard low-iron float glass, corresponds to a 4.4% increase in reflectance averaged across the full solar spectrum, appropriate for CSP, and 2.7% for CPV systems using triple junction cells. An experimental reflector incorporating these improvements, of drawn crown glass and a silvered second-surface with dielectric boost, was measured at NREL to have 95.4% solar weighted reflectance. For comparison, non-enhanced, wetsilvered reflectors of the same 4 mm thickness show reflectance ranging from 91.6 - 94.6%, depending on iron content. A potential drawback of using iron-free drawn glass is reduced concentration in high concentration systems because of the inherent surface errors. This effect is largely mitigated for glass shaped by slumping into a concave mold, rather than by bending.

The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements.

PubMed

Horta-Valerdi, Guillermo; Sanchez-Alonso, Maria Patricia; Perez-Marquez, Victor M; Negrete-Abascal, Erasmo; Vaca-Pacheco, Sergio; Hernandez-Gonzalez, Ismael; Gomez-Lunar, Zulema; Olmedo-Álvarez, Gabriela; Vázquez-Cruz, Candelario

2017-04-13

The draft genome sequence of Avibacterium paragallinarum strain CL serovar C is reported here. The genome comprises 154 contigs corresponding to 2.4 Mb with 41% G+C content and many insertion sequence (IS) elements, a characteristic not previously reported in A. paragallinarum . Copyright © 2017 Horta-Valerdi et al.

Facilitating Co-Authoring: Reflections of Content and Language Lecturers

ERIC Educational Resources Information Center

Wright, J.

2010-01-01

During a content and language project at a University of Technology (UoT) in Cape Town, South Africa, pairs of language and content lecturers, whose broad definition of integration was "the provision of linguistic access to content knowledge", co-authored ten integrated textbooks. Their intention was to assist first year learners with…

Analyzing reflective narratives to assess the ethical reasoning of pediatric residents.

PubMed

Moon, Margaret; Taylor, Holly A; McDonald, Erin L; Hughes, Mark T; Beach, Mary Catherine; Carrese, Joseph A

2013-01-01

A limiting factor in ethics education in medical training has been difficulty in assessing competence in ethics. This study was conducted to test the concept that content analysis of pediatric residents' personal reflections about ethics experiences can identify changes in ethical sensitivity and reasoning over time. Analysis of written narratives focused on two of our ethics curriculum's goals: 1) To raise sensitivity to ethical issues in everyday clinical practice and 2) to enhance critical reflection on personal and professional values as they affect patient care. Content analysis of written reflections was guided by a tool developed to identify and assess the level of ethical reasoning in eight domains determined to be important aspects of ethical competence. Based on the assessment of narratives written at two times (12 to 16 months/apart) during their training, residents showed significant progress in two specific domains: use of professional values, and use of personal values. Residents did not show decline in ethical reasoning in any domain. This study demonstrates that content analysis of personal narratives may provide a useful method for assessment of developing ethical sensitivity and reasoning.

Using Maximum Entropy to Find Patterns in Genomes

NASA Astrophysics Data System (ADS)

Liu, Sophia; Hockenberry, Adam; Lancichinetti, Andrea; Jewett, Michael; Amaral, Luis

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. To accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. This approach can also be easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes. National Institute of General Medical Science, Northwestern University Presidential Fellowship, National Science Foundation, David and Lucile Packard Foundation, Camille Dreyfus Teacher Scholar Award.

Sequence Polishing Library (SPL) v10.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oberortner, Ernst

The Sequence Polishing Library (SPL) is a suite of software tools in order to automate "Design for Synthesis and Assembly" workflows. Specifically: The SPL "Converter" tool converts files among the following sequence data exchange formats: CSV, FASTA, GenBank, and Synthetic Biology Open Language (SBOL); The SPL "Juggler" tool optimizes the codon usages of DNA coding sequences according to an optimization strategy, a user-specific codon usage table and genetic code. In addition, the SPL "Juggler" can translate amino acid sequences into DNA sequences.:The SPL "Polisher" verifies NA sequences against DNA synthesis constraints, such as GC content, repeating k-mers, and restriction sites.more » In case of violations, the "Polisher" reports the violations in a comprehensive manner. The "Polisher" tool can also modify the violating regions according to an optimization strategy, a user-specific codon usage table and genetic code;The SPL "Partitioner" decomposes large DNA sequences into smaller building blocks with partial overlaps that enable an efficient assembly. The "Partitioner" enables the user to configure the characteristics of the overlaps, which are mostly determined by the utilized assembly protocol, such as length, GC content, or melting temperature.« less

Early event-related brain potentials that reflect interest for content information in the media.

PubMed

Adachi, Shinobu; Morikawa, Koji; Nittono, Hiroshi

2012-03-28

This study investigated the relationship between event-related brain potentials (ERPs) to abridged content information in the media and the subsequent decisions to view the full content. Student volunteers participated in a task that simulated information selection on the basis of the content information. Screenshots of television clips and headlines of news articles on the Web were used as content information for the image condition and the headline condition, respectively. Following presentation of a stimulus containing content information, participants decided whether or not they would view the full content by pressing a select or a reject button. When the select button was pressed, participants were presented with a television clip or a news article. When the reject button was pressed, participants continued on to the next trial, without viewing further. In comparison with rejected stimuli, selected stimuli elicited a larger negative component, with a peak latency of ∼250 ms. The increase in the negative component was independent of the type of visual stimulus. These results suggest that interest toward content information is reflected in early-stage event-related brain potential responses.

Draft genome sequences of two Bifidobacterium sp. from the honey bee (Apis mellifera)

USDA-ARS?s Scientific Manuscript database

We provide genome sequences for two strains of honey bee associated Bifidobacterium. Reflecting an oxygen-rich niche, both strains possessed catalase, peroxidase, superoxide-dismutase and respiratory chain enzymes indicative of oxidative metabolism. The strains show markedly different carbohydrate ...

ePortfolio as a Measure of Reflective Practice

ERIC Educational Resources Information Center

Parkes, Kelly A.; Dredger, Katie S.; Hicks, David

2013-01-01

This instructional article outlines the qualities of effective ePortfolios and how reflection and student growth is measured. Student exemplars and assessment rubrics show how, despite changing tools and evolving standards, sustained collaboration and student coaching yields reflective practitioners in content areas and in technological knowledge.…

The Late-Glacial and Holocene Marboré Lake sequence (2612 m a.s.l., Central Pyrenees, Spain): Testing high altitude sites sensitivity to millennial scale vegetation and climate variability

NASA Astrophysics Data System (ADS)

Leunda, Maria; González-Sampériz, Penélope; Gil-Romera, Graciela; Aranbarri, Josu; Moreno, Ana; Oliva-Urcia, Belén; Sevilla-Callejo, Miguel; Valero-Garcés, Blas

2017-10-01

This paper presents the environmental, climate and vegetation changes reconstructed for the last 14.6 kyr cal BP from the Marboré Lake sedimentary sequence, the highest altitude record (2612 m a.s.l.) in the Pyrenees studied up to date. We investigate the sensitivity of this high altitude site to vegetational and climate dynamics and altitudinal shifts during the Holocene by comparing palynological spectra of the fossil sequence and pollen rain content from current moss pollsters. We hypothesize that the input of sediments in lakes at such altitude is strongly controlled by ice phenology (ice-free summer months) and that during cold periods Pollen Accumulation Rate (PAR) and Pollen Concentration (PC) reflect changes in ice-cover and thus is linked to temperature changes. Low sedimentation rates and low PC and PAR occurred during colder periods as the Younger Dryas (GS-1) and the Holocene onset (12.6-10.2 kyr cal BP), suggesting that the lake-surface remained ice-covered for most of the year during these periods. Warmer conditions are not evident until 10.2 kyr cal BP, when an abrupt increase in sedimentation rate, PC and PAR occur, pointing to a delayed onset of the Holocene temperature increase at high altitude. Well-developed pinewoods and deciduous forest dominated the mid montane belt since 9.3 kyr cal BP until mid-Holocene (5.2 kyr cal BP). A downwards shift in the deciduous forest occurred after 5.2 kyr cal BP, in agreement with the aridity trend observed at a regional and Mediterranean context. The increase of herbaceous taxa during the late-Holocene (3.5 kyr cal BP-present) reflects a general trend to reduced montane forest, as anthropogenic disturbances were not evident until 1.3 kyr cal BP when Olea proportions from lowland areas and other anthropogenic indicators clearly expand. Our study demonstrates the need to perform local experimental approaches to check the effect of ice phenology on high altitude lakes sensitivity to vegetation changes to obtain more realistic reconstructions of mountain vegetation belts dynamics.

Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane

PubMed Central

Mukherjee, Udita; Kumar, Roshan; Mahato, Nitish Kumar; Khurana, J. P.

2013-01-01

Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%. PMID:24051321

Exploring the Relationship Between Reflectance Red Edge and Chlorophyll Content in Slash Pine

NASA Technical Reports Server (NTRS)

Curran, Paul J.; Dungan, Jennifer L.; Gholz, Henry L.

1990-01-01

Chlorophyll is a key indicator of the physiological status of a forest canopy. However, its distribution may vary greatly in time and space, so that the estimation of chlorophyll content of canopies or branches by extrapolation from leaf values obtained by destructive sampling is labor intensive and potentially inaccurate. Chlorophy11 content is related positively to the point of maximum slope in vegetation reflectance spectra which occurs at wavelengths between 690-740 nm and is known as the "red edge." The red edge of needles on individual slash pine (Piniis elliottii Engelm.) branches and in whole forest canopies was measured with a spectroradiometer. Branches were measured on the ground against a spectrally flat reflectance target and canopies were measured from observation towers against a spectrally variable understory and forest floor. There was a linear relationship between red edge and chlorophyll content of branches (R(exp 2) = 0.91). Measurements of the red edge and this relationship were used to estimate the chlorophyll content of other branches with an error that was lower than that associated with the colorimetric (laboratory) method. There was no relationship between the red edge and the chlorophyll content of whole canopies. This can be explained by the overriding influence of the understory and forest floor, an influence that was illustrated by spectral mixture modeling. The results suggest that the red edge could be used to estimate the chlorophyll content in branches but it is unlikely to be of value for the estimation of chlorophyll content in canopies unless the canopy cover is high.

[Design of plant leaf bionic camouflage materials based on spectral analysis].

PubMed

Yang, Yu-Jie; Liu, Zhi-Ming; Hu, Bi-Ru; Wu, Wen-Jian

2011-06-01

The influence of structure parameters and contents of plant leaves on their reflectance spectra was analyzed using the PROSPECT model. The result showed that the bionic camouflage materials should be provided with coarse surface and spongy inner structure, the refractive index of main content must be close to that of plant leaves, the contents of materials should contain chlorophyll and water, and the content of C-H bond must be strictly controlled. Based on the analysis above, a novel camouflage material, which was constituted by coarse transparent waterproof surface, chlorophyll, water and spongy material, was designed. The result of verifiable experiment showed that the reflectance spectra of camouflage material exhibited the same characteristics as those of plant leaves. The similarity coefficient of reflectance spectrum of the camouflage material and camphor leaves was 0.988 1, and the characteristics of camouflage material did not change after sunlight treatment for three months. The bionic camouflage material, who exhibited a high spectral similarity with plant leaves and a good weather resistance, will be an available method for reconnaissance of hyperspectral imaging hopefully.

Spectral characteristics of normal and nutrient-deficient maize leaves

NASA Technical Reports Server (NTRS)

Al-Abbas, A. H.; Barr, R.; Hall, J. D.; Crane, F. L.; Baumgardner, M. F.

1972-01-01

Reflectance, transmittance and absorbance spectra of normal and six types of mineral-deficient (N,P,K,S,Mg and Ca) maize (Zea mays L.) leaves were analyzed at 30 selected wavelengths along the electromagnetic spectrum from 500 to 2600 nm. Chlorophyll content and percent leaf moisture were also determined. Leaf thermograms were obtained for normal, N- and S- deficient leaves. The results of the analysis of variance showed significant differences in reflectance, transmittance and absorbance in the visible wavelengths among leaf numbers 3, 4, and 5, among the seven nutrient treatments, and among the interactions of leaves and treatments. In the reflective infrared wavelengths only treatments produced significant differences. The chlorophyll content of leaves was reduced in all deficiencies in comparison to controls. Percent moisture was increased in S-, Mg- and N- deficiencies. Positive correlation (r = 0.707) between moisture content and percent absorption at both 1450 and 1930 nm were obtained. Polynomial regression analysis of leaf thickness and leaf moisture content showed that these two variables were significantly and directly related (r = 0.894).

The provenance of Archean clastic metasediments in the Narryer Gneiss Complex, Western Australia: Trace element geochemistry, Nd isotopes, and U-Pb ages for detrital zircons

NASA Astrophysics Data System (ADS)

Maas, Roland; McCulloch, Malcolm T.

1991-07-01

Clastic metasedimentary rocks of mid-Archean age from the Mt. Narryer and Jack Hills metasedimentary belts have REE patterns resembling those of mid- to late-Archean pelitic-quartzitic cratonic sequences elsewhere, and post-Archean continental rocks in general. Detrital zircons in the metasediments range in age from ca. 3000 to 3700 Ma. This indicates a provenance from mature cratonic sources controlled by K-rich granitic rocks. Additional minor sediment sources were identified as older, mainly chemical sedimentary sequences, ultramafic rocks, and felsic rocks characterized by low HREE contents, perhaps of tonalitic affinity. The association of the near-shore/fluviatile clastic association studied here with extensive turbiditic and chemical sedimentary sequences indicates these sources formed part of a (rifted ?) cratonic margin ca. 3 Ga ago. Differences between sedimentary REE patterns and those in the surrounding 3.73-3.0 Ga orthogneiss terrain, and between detrital zircon ages and the age distribution in the gneisses, suggest that the present association of the metasedimentary belts with the orthogneiss terrain is of tectonic origin. The occurrence of detrital zircons with U-Pb ages > 4 Ga in certain quartzites and conglomerates of the Jack Hills and Mt. Narryer metasedimentary sequences indicates a further, most likely granitic, source. ɛNd( TDep) values in Jack Hills metasediments vary widely (+5 to -12) but have a smaller range in the Mt. Narryer belt (-5 to -9). The lowest ɛNd values of both sequences are interpreted to reflect the presence of detritus derived from 4.1-4.2 Ga old LREE-enriched continental crust in proportions considerably larger (≥ 10%) than estimated previously from the abundance of pre-4 Ga detrital zircons (≈3%). This would imply the former existence of significant volumes of pre-4 Ga continental crust in the provenance of the Mt. Narryer and Jack Hills metasediments.

Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.

PubMed

Wistow, Graeme; Bernstein, Steven L; Wyatt, M Keith; Behal, Amita; Touchman, Jeffrey W; Bouffard, Gerald; Smith, Don; Peterson, Katherine

2002-06-15

To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses. A cDNA library was constructed from two adult (40 year old) human lenses. Over two thousand clones were sequenced from the unamplified, un-normalized library. The library was then normalized and a further 2200 sequences were obtained. All the data were analyzed using GRIST (GRouping and Identification of Sequence Tags), a procedure for gene identification and clustering. The lens library (by) contains a low percentage of non-mRNA contaminants and a high fraction (over 75%) of apparently full length cDNA clones. Approximately 2000 reads from the unamplified library yields 810 clusters, potentially representing individual genes expressed in the lens. After normalization, the content of crystallins and other abundant cDNAs is markedly reduced and a similar number of reads from this library (fs) yields 1455 unique groups of which only two thirds correspond to named genes in GenBank. Among the most abundant cDNAs is one for a novel gene related to glutamine synthetase, which was designated "lengsin" (LGS). Analyses of ESTs also reveal examples of alternative transcripts, including a major alternative splice form for the lens specific membrane protein MP19. Variant forms for other transcripts, including those encoding the apoptosis inhibitor Livin and the armadillo repeat protein ARVCF, are also described. The lens cDNA libraries are a resource for gene discovery, full length cDNAs for functional studies and microarrays. The discovery of an abundant, novel transcript, lengsin, and a major novel splice form of MP19 reflect the utility of unamplified libraries constructed from dissected tissue. Many novel transcripts and splice forms are represented, some of which may be candidates for genetic diseases.

Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.

PubMed

Lu, Hong; Patil, Prabhu; Van Sluys, Marie-Anne; White, Frank F; Ryan, Robert P; Dow, J Maxwell; Rabinowicz, Pablo; Salzberg, Steven L; Leach, Jan E; Sonti, Ramesh; Brendel, Volker; Bogdanove, Adam J

2008-01-01

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown. To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage. Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or in non-coding sequences, and/or differences outside the clusters, potentially among regulatory targets or secretory substrates.

How Reflective are Teachers? A Study of Kindergarten Teachers' and Special Teachers' Levels of Reflection in Day Care

ERIC Educational Resources Information Center

Pihlaja, Paivi Marjo; Holst, Teija Kristiina

2013-01-01

The purpose of this study is to examine teachers' reflections of their early childhood special education work in Finnish day care. Work contents and work roles have faced many challenges in Early Childhood Special Education (ECSE), and therefore general reflection and research need to be developed. Teachers ("n"?=?218) evaluated, via an…

Examining Students' Reflective Thinking from Keywords Tagged to Blogs: Using Map Analysis as a Content Analysis Method

ERIC Educational Resources Information Center

Xie, Ying; Sharma, Priya

2013-01-01

Reflective learning refers to a learner's purposeful and conscious manipulation of ideas toward meaningful learning. Blogs have been used to support reflective thinking, but the commonly seen blog software usually does not provide overt mechanisms for students' high-level reflections. A new tool was designed to support the reflective…

Design of an All-Optical Network Based on LCoS Technologies

NASA Astrophysics Data System (ADS)

Cheng, Yuh-Jiuh; Shiau, Yhi

2016-06-01

In this paper, an all-optical network composed of the ROADMs (reconfigurable optical add-drop multiplexer), L2/L3 optical packet switches, and the fiber optical cross-connection for fiber scheduling and measurement based on LCoS (liquid crystal on silicon) technologies is proposed. The L2/L3 optical packet switches are designed with optical output buffers. Only the header of optical packets is converted to electronic signals to control the wavelength of input ports and the packet payloads can be transparently destined to their output ports. An optical output buffer is designed to queue the packets when more than one incoming packet should reach to the same destination output port. For preserving service-packet sequencing and fairness of routing sequence, a priority scheme and a round-robin algorithm are adopted at the optical output buffer. The wavelength of input ports is designed for routing incoming packets using LCoS technologies. Finally, the proposed OFS (optical flow switch) with input buffers can quickly transfer the big data to the output ports and the main purpose of the OFS is to reduce the number of wavelength reflections. The all-optical content delivery network is comprised of the OFSs for a large amount of audio and video data transmissions in the future.

Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.

PubMed

Yafremava, Liudmila S; Di Giulio, Massimo; Caetano-Anollés, Gustavo

2013-01-01

Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life. The pyrococcal proteomes are very similar and share a very early ancestor. Relative amino acid abundance analyses showed that biases in the use of amino acids are due to their shared fold superfamilies. Within these repertoires, only two of the five amino acids that are preferentially barophilic, aspartic acid and arginine, displayed this preference significantly and consistently across structure and in domains appearing in the ancestor. The more primordial asparagine, lysine and threonine displayed a consistent preference for nonbarophily across structure and in the ancestor. Since barophilic preferences are already evident in ancient domains that are at least ~3 billion year old, we conclude that barophily is a very ancient trait that unfolded concurrently with genetic idiosyncrasies in convergence towards a universal code.

Using assessments to investigate and compare the nature of learning in undergraduate science courses.

PubMed

Momsen, Jennifer; Offerdahl, Erika; Kryjevskaia, Mila; Montplaisir, Lisa; Anderson, Elizabeth; Grosz, Nate

2013-06-01

Assessments and student expectations can drive learning: students selectively study and learn the content and skills they believe critical to passing an exam in a given subject. Evaluating the nature of assessments in undergraduate science education can, therefore, provide substantial insight into student learning. We characterized and compared the cognitive skills routinely assessed by introductory biology and calculus-based physics sequences, using the cognitive domain of Bloom's taxonomy of educational objectives. Our results indicate that both introductory sequences overwhelmingly assess lower-order cognitive skills (e.g., knowledge recall, algorithmic problem solving), but the distribution of items across cognitive skill levels differs between introductory biology and physics, which reflects and may even reinforce student perceptions typical of those courses: biology is memorization, and physics is solving problems. We also probed the relationship between level of difficulty of exam questions, as measured by student performance and cognitive skill level as measured by Bloom's taxonomy. Our analyses of both disciplines do not indicate the presence of a strong relationship. Thus, regardless of discipline, more cognitively demanding tasks do not necessarily equate to increased difficulty. We recognize the limitations associated with this approach; however, we believe this research underscores the utility of evaluating the nature of our assessments.

Complete Genome Sequence of the Soil Actinomycete Kocuria rhizophila▿

PubMed Central

Takarada, Hiromi; Sekine, Mitsuo; Kosugi, Hiroki; Matsuo, Yasunori; Fujisawa, Takatomo; Omata, Seiha; Kishi, Emi; Shimizu, Ai; Tsukatani, Naofumi; Tanikawa, Satoshi; Fujita, Nobuyuki; Harayama, Shigeaki

2008-01-01

The soil actinomycete Kocuria rhizophila belongs to the suborder Micrococcineae, a divergent bacterial group for which only a limited amount of genomic information is currently available. K. rhizophila is also important in industrial applications; e.g., it is commonly used as a standard quality control strain for antimicrobial susceptibility testing. Sequencing and annotation of the genome of K. rhizophila DC2201 (NBRC 103217) revealed a single circular chromosome (2,697,540 bp; G+C content of 71.16%) containing 2,357 predicted protein-coding genes. Most of the predicted proteins (87.7%) were orthologous to actinobacterial proteins, and the genome showed fairly good conservation of synteny with taxonomically related actinobacterial genomes. On the other hand, the genome seems to encode much smaller numbers of proteins necessary for secondary metabolism (one each of nonribosomal peptide synthetase and type III polyketide synthase), transcriptional regulation, and lateral gene transfer, reflecting the small genome size. The presence of probable metabolic pathways for the transformation of phenolic compounds generated from the decomposition of plant materials, and the presence of a large number of genes associated with membrane transport, particularly amino acid transporters and drug efflux pumps, may contribute to the organism's utilization of root exudates, as well as the tolerance to various organic compounds. PMID:18408034

Using Assessments to Investigate and Compare the Nature of Learning in Undergraduate Science Courses

PubMed Central

Momsen, Jennifer; Offerdahl, Erika; Kryjevskaia, Mila; Montplaisir, Lisa; Anderson, Elizabeth; Grosz, Nate

2013-01-01

Assessments and student expectations can drive learning: students selectively study and learn the content and skills they believe critical to passing an exam in a given subject. Evaluating the nature of assessments in undergraduate science education can, therefore, provide substantial insight into student learning. We characterized and compared the cognitive skills routinely assessed by introductory biology and calculus-based physics sequences, using the cognitive domain of Bloom's taxonomy of educational objectives. Our results indicate that both introductory sequences overwhelmingly assess lower-order cognitive skills (e.g., knowledge recall, algorithmic problem solving), but the distribution of items across cognitive skill levels differs between introductory biology and physics, which reflects and may even reinforce student perceptions typical of those courses: biology is memorization, and physics is solving problems. We also probed the relationship between level of difficulty of exam questions, as measured by student performance and cognitive skill level as measured by Bloom's taxonomy. Our analyses of both disciplines do not indicate the presence of a strong relationship. Thus, regardless of discipline, more cognitively demanding tasks do not necessarily equate to increased difficulty. We recognize the limitations associated with this approach; however, we believe this research underscores the utility of evaluating the nature of our assessments. PMID:23737631

Adaptation, ecology, and evolution of the halophilic stromatolite archaeon Halococcus hamelinensis inferred through genome analyses.

PubMed

Gudhka, Reema K; Neilan, Brett A; Burns, Brendan P

2015-01-01

Halococcus hamelinensis was the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome of H. hamelinensis consisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of the H. hamelinensis genome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome of H. hamelinensis also revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes of H. hamelinensis against various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

Terahertz time-domain spectroscopy for non-invasive assessment of water content in biological samples.

PubMed

Borovkova, Mariia; Khodzitsky, Mikhail; Demchenko, Petr; Cherkasova, Olga; Popov, Alexey; Meglinski, Igor

2018-05-01

We apply terahertz time-domain spectroscopy for the quantitative non-invasive assessment of the water content in biological samples, such as Carpinus caroliniana tree leaves and pork muscles. The developed experimental terahertz time-domain spectroscopy system operates both in transmission and reflection modes. The Landau-Looyenga-Lifshitz-based model is used for the calculation of the water concentration within the samples. The results of the water concentration measurements are compared with the results of the gravimetric measurements. The obtained results show that the water content in biological samples can be measured non-invasively, with a high accuracy, utilizing terahertz waves in transmission and reflection modes.

Prediction of iron oxide contents using diffuse reflectance spectroscopy

NASA Astrophysics Data System (ADS)

Marques, José, Jr.; Arantes Camargo, Livia

2015-04-01

Determining soil iron oxides using conventional analysis is relatively unfeasible when large areas are mapped, with the aim of characterizing spatial variability. Diffuse reflectance spectroscopy (DRS) is rapid, less expensive, non-destructive and sometimes more accurate than conventional analysis. Furthermore, this technique allows the simultaneous characterization of many soil attributes with agronomic and environmental relevance. This study aims to assess the DRS capability to predict iron oxides content -hematite and goethite - , characterizing their spatial variability in soils of Brazil. Soil samples collected from an 800-hectare area were scanned in the visible and near-infrared spectral range. Moreover, chemometric calibration was obtained through partial least-squares regression (PLSR). Then, spatial distribution maps of the attributes were constructed using predicted values from calibrated models through geostatistical methods. The studied area presented soils with varied contents of iron oxides as examples for the Oxisols and Entisols. In the spectra of each soil is observed that the reflectance decreases with the content of iron oxides present in the soil. In soils with a high content of iron oxides can be observed more pronounced concavities between 380 and 1100 nm which are characteristic of the presence of these oxides. In soils with higher reflectance it were observed concavity characteristics due to the presence of kaolinite, in agreement with the low iron contents of those soils. The best accuracy of prediction models [residual prediction deviation (RPD) = 1.7] was obtained for goethite within the visible region (380-800 nm), and for hematite (RPD = 2.0) within the visible near infrared (380-2300 nm). The maps of goethite and hematite predicted showed the spatial distribution pattern similar to the maps of clay and iron extracted by dithionite-citrate-bicarbonate, being consistent with the iron oxide contents of soils present in the study area. These results confirm the value of DRS in the mapping of iron oxides in large areas at detailed scale.

Students' Appropriation, Rejection and Perceptions of Creativity in Reflective Journals

ERIC Educational Resources Information Center

O'Connell, Timothy S.; Dyment, Janet E.; Smith, Heidi A.

2015-01-01

This paper explores the intersection of reflection, journal writing and creativity. Undergraduate students who participated in a residential field camp were required to keep a creative reflective journal to demonstrate their theoretical and practical understandings of their experience. This study reports on the content analysis of 42 student…

Combining observations in the reflective solar and thermal domains for improved mapping of carbon, water and energy fluxes

USDA-ARS?s Scientific Manuscript database

The REGularized canopy reFLECtance (REGFLEC) modeling tool integrates leaf optics, canopy reflectance, and atmospheric radiative transfer model components, facilitating accurate retrieval of leaf area index (LAI) and leaf chlorophyll content (Cab) directly from at-sensor radiances in green, red and ...

Collaborative Learning through Formative Peer Review with Technology

ERIC Educational Resources Information Center

Eaton, Carrie Diaz; Wade, Stephanie

2014-01-01

This paper describes a collaboration between a mathematician and a compositionist who developed a sequence of collaborative writing assignments for calculus. This sequence of developmentally appropriate assignments presents peer review as a collaborative process that promotes reflection, deepens understanding, and improves exposition. First, we…

Oscillatory dynamics and place field maps reflect hippocampal ensemble processing of sequence and place memory under NMDA receptor control.

PubMed

Cabral, Henrique O; Vinck, Martin; Fouquet, Celine; Pennartz, Cyriel M A; Rondi-Reig, Laure; Battaglia, Francesco P

2014-01-22

Place coding in the hippocampus requires flexible combination of sensory inputs (e.g., environmental and self-motion information) with memory of past events. We show that mouse CA1 hippocampal spatial representations may either be anchored to external landmarks (place memory) or reflect memorized sequences of cell assemblies depending on the behavioral strategy spontaneously selected. These computational modalities correspond to different CA1 dynamical states, as expressed by theta and low- and high-frequency gamma oscillations, when switching from place to sequence memory-based processing. These changes are consistent with a shift from entorhinal to CA3 input dominance on CA1. In mice with a deletion of forebrain NMDA receptors, the ability of place cells to maintain a map based on sequence memory is selectively impaired and oscillatory dynamics are correspondingly altered, suggesting that oscillations contribute to selecting behaviorally appropriate computations in the hippocampus and that NMDA receptors are crucial for this function. Copyright © 2014 Elsevier Inc. All rights reserved.

A new molecular evolution model for limited insertion independent of substitution.

PubMed

Lèbre, Sophie; Michel, Christian J

2013-10-01

We recently introduced a new molecular evolution model called the IDIS model for Insertion Deletion Independent of Substitution [13,14]. In the IDIS model, the three independent processes of substitution, insertion and deletion of residues have constant rates. In order to control the genome expansion during evolution, we generalize here the IDIS model by introducing an insertion rate which decreases when the sequence grows and tends to 0 for a maximum sequence length nmax. This new model, called LIIS for Limited Insertion Independent of Substitution, defines a matrix differential equation satisfied by a vector P(t) describing the sequence content in each residue at evolution time t. An analytical solution is obtained for any diagonalizable substitution matrix M. Thus, the LIIS model gives an expression of the sequence content vector P(t) in each residue under evolution time t as a function of the eigenvalues and the eigenvectors of matrix M, the residue insertion rate vector R, the total insertion rate r, the initial and maximum sequence lengths n0 and nmax, respectively, and the sequence content vector P(t0) at initial time t0. The derivation of the analytical solution is much more technical, compared to the IDIS model, as it involves Gauss hypergeometric functions. Several propositions of the LIIS model are derived: proof that the IDIS model is a particular case of the LIIS model when the maximum sequence length nmax tends to infinity, fixed point, time scale, time step and time inversion. Using a relation between the sequence length l and the evolution time t, an expression of the LIIS model as a function of the sequence length l=n(t) is obtained. Formulas for 'insertion only', i.e. when the substitution rates are all equal to 0, are derived at evolution time t and sequence length l. Analytical solutions of the LIIS model are explicitly derived, as a function of either evolution time t or sequence length l, for two classical substitution matrices: the 3-parameter symmetric substitution matrix [12] (LIIS-SYM3) and the HKY asymmetric substitution matrix[9] (LIIS-HKY). An evaluation of the LIIS model (precisely, LIIS-HKY) based on four statistical analyses of the GC content in complete genomes of four prokaryotic taxonomic groups, namely Chlamydiae, Crenarchaeota, Spirochaetes and Thermotogae, shows the expected improvement from the theory of the LIIS model compared to the IDIS model. Copyright © 2013 Elsevier Inc. All rights reserved.

Method for determining shear direction using liquid crystal coatings

NASA Technical Reports Server (NTRS)

Reda, Daniel C.

1995-01-01

A method is provided for determining shear direction wherein a beam of white light is directed onto the surface of a liquid crystal coating to cause the white light to be dispersed (reflected) from the surface in a spectrum having bands of different colors in a fixed spatial 2 (angular) sequence. The system is calibrated by locating an observer, e.g., a video and movie camera, such that a particular color band (preferably at or near the center of the reflected spectrum) is observed to thereby provide a reference color band. Because the application of shear causes either clockwise or counterclockwise rotation of the reflected spectrum dependent on the direction of the shear, a determination is then made of the reflected color band observed by the observer when the surface of the liquid crystal is subjected to shear to thereby determine the direction of the shear based on the directional (rotation) relation of the observed color band with respect to the reference color band in the spatial sequence of color bands.

Sequence to Sequence - Video to Text

DTIC Science & Technology

2015-12-11

Saenko, and S. Guadarrama. Generating natural-language video descriptions using text - mined knowledge. In AAAI, July 2013. 2 [20] P. Kuznetsova, V...Sequence to Sequence – Video to Text Subhashini Venugopalan1 Marcus Rohrbach2,4 Jeff Donahue2 Raymond Mooney1 Trevor Darrell2 Kate Saenko3...1. Introduction Describing visual content with natural language text has recently received increased interest, especially describing images with a

The Summerville Formation: Evidence for a sub-horizontal stratigraphic sequence below the post-rift unconformity in the Middleton Place Summerville Seismic Zone

NASA Astrophysics Data System (ADS)

Getz, Joseph Edward

The Middleton Place Summerville Seismic Zone (MPSSZ) near Summerville, South Carolina was the site of renewed extensive investigation, beginning in the 1970's, for the source of the 1886 Charleston earthquake. Reactivation of faults associated with a putative fault-bounded Triassic rift basin through analysis of seismic reflection, seismic refraction, and well data has since become the favored interpretation for the source of MPSSZ seismicity. Critical to this interpretation is the association of continental redbed sedimentary rocks with Triassic basins identified throughout the North American Atlantic margin. Reanalysis of 18 seismic reflection profiles and 25 seismic refraction profiles within the MPSSZ suggests that the red beds found here are a thin, sub-horizontal, regionally extensive, generally unbroken subsurface stratigraphic sequence distinct from the sedimentary architecture observed in analog Triassic rift systems. In addition, this sequence appears to unconformably overly a structural depression (the Jedberg basin) previously interpreted as a Triassic rift basin in the vicinity of the MPSSZ. In addition to the geometries observed on seismic reflection profiles, seismic refraction velocities ranging from 4.2 to 6.1 km/s can be correlated with (1) Jurassic basalt flows, (2) the newly proposed Summerville Formation, and (3) the Basement (B) sequences respectively. The current study maps the Summerville red bed section and its bounding reflectors. In addition to mapping the regional extent of the newly proposed Summerville Formation, refraction velocities and changes in reflection character, the lateral extent of the basalt flows can be changed to a more localized flow rather than a regionally extensive flow of which was previously thought. Reanalysis of data in the MPSSZ suggests that the area may not be part of the Triassic South Georgia Rift system due to the sub-horizontal geometry of the red bed reflections, the apparent lack of faulting, and their regional extent.

Finite Element Analysis of Simple Rectangular Microstrip Sensor for Determination Moisture Content of Hevea Rubber Latex

NASA Astrophysics Data System (ADS)

Yahaya, NZ; Ramli, MR; Razak, NNANA; Abbas, Z.

2018-04-01

The Finite Element Method, FEM has been successfully used to model a simple rectangular microstrip sensor to determine the moisture content of Hevea rubber latex. The FEM simulation of sensor and samples was implemented by using COMSOL Multiphysics software. The simulation includes the calculation of magnitude and phase of reflection coefficient and was compared to analytical method. The results show a good agreement in finding the magnitude and phase of reflection coefficient when compared with analytical results. Field distributions of both the unloaded sensor as well as the sensor loaded with different percentages of moisture content were visualized using FEM in conjunction with COMSOL software. The higher the amount of moisture content in the sample the more the electric loops were observed.

Content-based fused off-axis object illumination direct-to-digital holography

DOEpatents

Price, Jeffery R.

2006-05-02

Systems and methods are described for content-based fused off-axis illumination direct-to-digital holography. A method includes calculating an illumination angle with respect to an optical axis defined by a focusing lens as a function of data representing a Fourier analyzed spatially heterodyne hologram; reflecting a reference beam from a reference mirror at a non-normal angle; reflecting an object beam from an object the object beam incident upon the object at the illumination angle; focusing the reference beam and the object beam at a focal plane of a digital recorder to from the content-based off-axis illuminated spatially heterodyne hologram including spatially heterodyne fringes for Fourier analysis; and digitally recording the content based off-axis illuminated spatially heterodyne hologram including spatially heterodyne fringes for Fourier analysis.

Reflective mulch enhances ripening and health compounds in apple fruit.

PubMed

Overbeck, Verena; Schmitz-Eiberger, Michaela A; Blanke, Michael M

2013-08-15

The objective of the study was to improve fruit quality, including health compounds, by improving light utilization for fruit crops under hail net. Four reflective mulches including plastics such as Extenday® and a bio-degradable paper were spread in the alleyways of a cv. 'Gala Mondial' apple orchard on 10 August 2010 5 weeks before anticipated harvest. Reflective mulch affected neither fruit firmness nor sugar, but accelerated starch breakdown, indicative of riper fruits (smaller Streif index), compared with the uncovered grass alleyway (control). Reflective mulches also improved fruit quality such as red coloration of cv. 'Gala Mondial' apples. This was due to significantly enhanced flavonoids and anthocyanins. Flavonoids increased up to 52.4% in the Extenday® treatment (29.2 nmol cm(-2) in the grass control versus 44.5 nmol cm(-2) fruit peel with reflective mulch). Similarly, reflective mulch improved anthocyanin content in cv. 'Gala Mondial' peel up to 66% compared to grass control (14.5 nmol cm(-2) in control fruit versus 24.1 nmol cm(-2) with reflective mulch). The reflective mulch did not affect chlorophyll and carotenoid content in the 'Gala' fruit peel. Overall, the application of reflective mulches improved fruit quality in terms of better coloration and health compounds and accelerated ripening, leading to higher market value. © 2013 Society of Chemical Industry.

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content.

PubMed

Goettel, Wolfgang; Xia, Eric; Upchurch, Robert; Wang, Ming-Li; Chen, Pengyin; An, Yong-Qiang Charles

2014-04-23

Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality.

Teaching Badminton through Play Practice in Physical Education

ERIC Educational Resources Information Center

Kim, Insook

2017-01-01

There is a strong belief that teachers' in-depth content knowledge is key for effective teaching. Teachers who possess specialized content knowledge uniquely needed for teaching are capable of appropriately selecting, sequencing, representing and adapting content applicable for students with different learning needs. Beyond teachers' content…

Calculation of vitrinite reflectance from thermal histories: A comparison of some methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morrow, D.W.; Issler, D.R.

1993-04-01

Vitrinite reflectance values (%R[sub o]) calculated from commonly used methods are compared with respect to time invariant temperatures and constant heating rates. Two monofunctional methods, one involving a time-temperature index to vitrinite reflectance correlation (TTI-%R[sub o]) to depth correlation, yield vitrinite reflectance values that are similar to those calculated by recently published Arrhenius-based methods, such as EASY%R[sub o]. The approximate agreement between these methods supports the perception that the EASY%R[sub o] algorithm is the most accurate method for the prediction of vitrinite reflectances throughout the range of organic maturity normally encountered. However, calibration of these methods against vitrinite reflectance datamore » from two basin sequences with well-documented geologic histories indicates that, although the EASY%R[sub o] method has wide applicability, it slightly overestimates vitrinite reflectances in strata of low to medium maturity up to a %R[sub o] value of 0.9%. The two monofunctional methods may be more accurate for prediction of vitrinite reflectances in similar sequences of low maturity. An older, but previously widely accepted TTI-%R[sub O] correlation consistently overestimates vitrinite reflectances with respect to other methods. Underestimation of paleogeothermal gradients in the original calibration of time-temperature history to vitrinite reflectance may have introduced a systematic bias to the TTI-%R[sub o] correlation used in this method. Also, incorporation of TAI (thermal alteration index) data and its conversion to %R[sub o]-equivalent values may have introduced inaccuracies. 36 refs., 7 figs.« less

Genome content analysis yields new insights into the relationship between the human malaria parasite Plasmodium falciparum and its anopheline vectors.

PubMed

Oppenheim, Sara J; Rosenfeld, Jeffrey A; DeSalle, Rob

2017-02-27

The persistent and growing gap between the availability of sequenced genomes and the ability to assign functions to sequenced genes led us to explore ways to maximize the information content of automated annotation for studies of anopheline mosquitos. Specifically, we use genome content analysis of a large number of previously sequenced anopheline mosquitos to follow the loss and gain of protein families over the evolutionary history of this group. The importance of this endeavor lies in the potential for comparative genomic studies between Anopheles and closely related non-vector species to reveal ancestral genome content dynamics involved in vector competence. In addition, comparisons within Anopheles could identify genome content changes responsible for variation in the vectorial capacity of this family of important parasite vectors. The competence and capacity of P. falciparum vectors do not appear to be phylogenetically constrained within the Anophelinae. Instead, using ancestral reconstruction methods, we suggest that a previously unexamined component of vector biology, anopheline nucleotide metabolism, may contribute to the unique status of anophelines as P. falciparum vectors. While the fitness effects of nucleotide co-option by P. falciparum parasites on their anopheline hosts are not yet known, our results suggest that anopheline genome content may be responding to selection pressure from P. falciparum. Whether this response is defensive, in an attempt to redress improper nucleotide balance resulting from P. falciparum infection, or perhaps symbiotic, resulting from an as-yet-unknown mutualism between anophelines and P. falciparum, is an open question that deserves further study. Clearly, there is a wealth of functional information to be gained from detailed manual genome annotation, yet the rapid increase in the number of available sequences means that most researchers will not have the time or resources to manually annotate all the sequence data they generate. We believe that efforts to maximize the amount of information obtained from automated annotation can help address the functional annotation deficit that most evolutionary biologists now face, and here demonstrate the value of such an approach.

An Evaluation of Total Solar Reflectance and Spectral Band Ratioing Techniques for Estimating Soil Water Content

NASA Technical Reports Server (NTRS)

Reginato, R. J.; Vedder, J. F.; Idso, S. B.; Jackson, R. D.; Blanchard, M. B.; Goettelman, R.

1977-01-01

For several days in March of 1975, reflected solar radiation measurements were obtained from smooth and rough surfaces of wet, drying, and continually dry Avondale loam at Phoenix, Arizona, with pyranometers located 50 cm above the ground surface and a multispectral scanner flown at a 300-m height. The simple summation of the different band radiances measured by the multispectral scanner proved equally as good as the pyranometer data for estimating surface soil water content if the multispectral scanner data were standardized with respect to the intensity of incoming solar radiation or the reflected radiance from a reference surface, such as the continually dry soil. Without this means of standardization, multispectral scanner data are most useful in a spectral band ratioing context. Our results indicated that, for the bands used, no significant information on soil water content could be obtained by band ratioing. Thus the variability in soil water content should insignificantly affect soil-type discrimination based on identification of type-specific spectral signatures. Therefore remote sensing, conducted in the 0.4- to 1.0-micron wavelength region of the solar spectrum, would seem to be much More suited to identifying crop and soil types than to estimating of soil water content.

Repeat-aware modeling and correction of short read errors.

PubMed

Yang, Xiao; Aluru, Srinivas; Dorman, Karin S

2011-02-15

High-throughput short read sequencing is revolutionizing genomics and systems biology research by enabling cost-effective deep coverage sequencing of genomes and transcriptomes. Error detection and correction are crucial to many short read sequencing applications including de novo genome sequencing, genome resequencing, and digital gene expression analysis. Short read error detection is typically carried out by counting the observed frequencies of kmers in reads and validating those with frequencies exceeding a threshold. In case of genomes with high repeat content, an erroneous kmer may be frequently observed if it has few nucleotide differences with valid kmers with multiple occurrences in the genome. Error detection and correction were mostly applied to genomes with low repeat content and this remains a challenging problem for genomes with high repeat content. We develop a statistical model and a computational method for error detection and correction in the presence of genomic repeats. We propose a method to infer genomic frequencies of kmers from their observed frequencies by analyzing the misread relationships among observed kmers. We also propose a method to estimate the threshold useful for validating kmers whose estimated genomic frequency exceeds the threshold. We demonstrate that superior error detection is achieved using these methods. Furthermore, we break away from the common assumption of uniformly distributed errors within a read, and provide a framework to model position-dependent error occurrence frequencies common to many short read platforms. Lastly, we achieve better error correction in genomes with high repeat content. The software is implemented in C++ and is freely available under GNU GPL3 license and Boost Software V1.0 license at "http://aluru-sun.ece.iastate.edu/doku.php?id = redeem". We introduce a statistical framework to model sequencing errors in next-generation reads, which led to promising results in detecting and correcting errors for genomes with high repeat content.

Gene Space Dynamics during the Evolution of Aegilops tauschii, Brachypodium distachyon, Oryza sativa, and Sorghum bicolor Genomes

USDA-ARS?s Scientific Manuscript database

Nine different regions totaling 9.7 Mb of the 4.02 Gb Aegilops tauschii genome were sequenced using the Sanger sequencing technology and compared with orthologous Brachypodium distachyon, Oryza sativa (rice) and Sorghum bicolor (sorghum) genomic sequences. The ancestral gene content in these regio...

Designing and Evaluating Research-Based Instructional Sequences for Introducing Magnetic Fields

ERIC Educational Resources Information Center

Guisasola, Jenaro; Almudi, Jose Manuel; Ceberio, Mikel; Zubimendi, Jose Luis

2009-01-01

This study examines the didactic suitability of introducing a teaching sequence when teaching the concept of magnetic fields within introductory physics courses at the university level. This instructional sequence was designed taking into account students' common conceptions, an analysis of the course content, and the history of the development of…

Complete genome sequence of ‘Candidatus Liberibacter africanus’

USDA-ARS?s Scientific Manuscript database

The complete genome sequence of ‘Candidatus Liberibacter africanus’ (Laf), strain ptsapsy, was obtained by an Illumina HiSeq 2000. The Laf genome comprises 1,192,232 nucleotides, 34.5% GC content, 1,141 predicted coding sequences, 44 tRNAs, 3 complete copies of ribosomal RNA genes (16S, 23S and 5S) ...

Genome Sequence of a Chromium-Reducing Strain, Bacillus cereus S612

DOE PAGES

Wang, Dongping; Boukhalfa, Hakim; Ware, Doug S.; ...

2015-12-10

We report here the genome sequence of an effective chromium-reducing bacterium,Bacillus cereusstrain S612. We found that the size of the draft genome sequence is approximately 5.4 Mb, with a G+C content of 35%, and it is predicted to contain 5,450 protein-coding genes.

An improved TCF sequence for biobleaching kenaf pulp: influence of the hexenuronic acid content and the use of xylanase.

PubMed

Andreu, Glòria; Vidal, Teresa

2014-01-01

Enzymatic delignification with laccase from Trametes villosa used in combination with chemical mediators (acetosyringone, acetovanillone and 1-hydroxybenzotriazole) to improve the totally chlorine-free (TCF) bleaching of kenaf pulp was studied. The best final pulp properties were obtained by using an LHBTQPo sequence developed by incorporating a laccase-mediator stage into an industrial bleaching sequence involving chelation and peroxide stages. The new sequence resulted in increased kenaf pulp delignification (90.4%) and brightness (77.2%ISO) relative to a conventional TCF chemical sequence (74.5% delignification and 74.5% brightness). Also, the sequence provided bleached kenaf fibers with high cellulose content (pulp viscosity of 890 g·mL(-1) vs 660 g·mL(-1)). Scanning electron micrographs revealed that xylanase altered fiber surfaces and facilitated reagent access as a result. However, the LHBTX (xylanase) stage removed 21% of hexenuronic acids in kenaf pulp. These recalcitrant compounds spent additional bleaching reagents and affected pulp properties after peroxide stage. Copyright © 2013 Elsevier Ltd. All rights reserved.

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

PubMed

Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

Combined effect of Pt and W alloying elements on Ni-silicide formation

NASA Astrophysics Data System (ADS)

Luo, T.; Mangelinck, D.; Descoins, M.; Bertoglio, M.; Mouaici, N.; Hallén, A.; Girardeaux, C.

2018-03-01

A combinatorial study of the combined effect of Pt and W on Ni silicide formation is performed. Ni(Pt, W) films with thickness and composition gradients were prepared by a co-deposition composition spread technique using sputtering deposition from Pt, W, and Ni targets. The deposited Ni(Pt,W) films were characterized by X-ray diffraction, X-ray reflectivity, Rutherford backscattering, and atom probe tomography. The maximum content of alloying elements is close to 27 at. %. Simulations of the thickness and composition were carried out and compared with experimental results. In situ X-ray diffraction and atom probe tomography were used to study the phase formation. Both additive alloying elements (Pt + W) slow down the Ni consumption and the effect of W is more pronounced than the one of Pt. Regarding the effect of alloying elements on Ni silicides formation, three regions could be distinguished in the Ni(Pt,W)/Si wafer. For the region close to the Ni target, the low contents of alloying elements (Pt + W) have little impact on the phase sequence (δ-Ni2Si is the first silicide and NiSi forms when Ni is entirely consumed) but the kinetics of silicide formation slows down. The region close to the Pt target has high contents of (Pt + W) and is rich in Pt and a simultaneous phase formation of δ-Ni2Si and NiSi is observed. For the high (Pt + W) contents and W-rich region, NiSi forms unexpectedly before δ-Ni2Si and the subsequent growth of δ-Ni2Si is accompanied by the NiSi consumption. When Ni is entirely consumed, NiSi regrows at the expense of δ-Ni2Si.

[Progress on molecular biology of Isaria farinosa, pathogen of host of Ophiocordyceps sinensis during the artificial culture].

PubMed

Liu, Fei; Wu, Xiao-Li; Liu, Ying; Chen, Da-Xia; Zhang, De-Li; Yang, Da-Jian

2016-02-01

Isaria farinosa is the pathogen of the host of Ophiocordyceps sinensis. The present research has analyzed the progress on the molecular biology according to the bibliometrics, the sequences (including the gene sequences) of I. farinosa in the NCBI. The results indicated that different country had published different number of the papers, and had landed different kinds and different number of the sequences (including the gene sequences). China had published the most number of the papers, and had landed the most number of the sequences (including the gene sequences). America had landed the most numbers of the function genes. The main content about the pathogen study was focus on the biological controlling. The main content about the molecular study concentrated on the phylogenies classification. In recent years some protease genes and chitinase genes had been researched. With the increase of the effect on the healthy of O. sinensis, and the whole sequence and more and more pharmacological activities of I. farinosa being made known to the public, the study on the molecular biology of the I. farinosa would be deeper and wider. Copyright© by the Chinese Pharmaceutical Association.

Light reflection by the cuticle of C. aurigans scarabs: a biological broadband reflector of left handed circularly polarized light

NASA Astrophysics Data System (ADS)

Libby, E.; Azofeifa, D. E.; Hernández-Jiménez, M.; Barboza-Aguilar, C.; Solís, A.; García-Aguilar, I.; Arce-Marenco, L.; Hernández, A.; Vargas, W. E.

2014-08-01

Measured reflection spectra from elytra of Chrysina aurigans scarabs are reported. They show a broad reflection band for wavelengths from 0.525 to 1.0 μm with a sequence of maxima and minima reflection values superimposed on a mean value of around 40% for the high reflection band. Different mechanisms contributing to the reflection spectra have been considered, with the dominant effect, reflection of left handed circularly polarized light, being produced by a laminated left handed twisted structure whose pitch changes with depth through the procuticle in a more complex way than that characterizing broad band circular polarizers based on cholesteric liquid crystals.

Understanding the Language Demands on Science Students from an Integrated Science and Language Perspective

NASA Astrophysics Data System (ADS)

Seah, Lay Hoon; Clarke, David John; Hart, Christina Eugene

2014-04-01

This case study of a science lesson, on the topic thermal expansion, examines the language demands on students from an integrated science and language perspective. The data were generated during a sequence of 9 lessons on the topic of 'States of Matter' in a Grade 7 classroom (12-13 years old students). We identify the language demands by comparing students' writings with the scientific account of expansion that the teacher intended the students to learn. The comparison involved both content analysis and lexicogrammatical (LG) analysis. The framework of Systemic Functional Linguistics was adopted for the LG analysis. Our analysis reveals differences in the meaning and the way LG resources were employed between the students' writings and the scientific account. From these differences, we found the notion of condition-of-use for LG resources to be a significant aspect of the language that students need to appropriate in order to employ the language of school science appropriately. This notion potentially provides a means by which teachers could concurrently address the conceptual and representational demands of science learning. Finally, we reflect on how the complementary use of content analysis and LG analysis provides a way for integrating the science and language perspectives in order to understand the demands of learning science through language.

Implementing technical refinement in high-level athletics: exploring the knowledge schemas of coaches.

PubMed

Kearney, Philip E; Carson, Howie J; Collins, Dave

2018-05-01

This paper explores the approaches adopted by high-level field athletics coaches when attempting to refine an athlete's already well-established technique (long and triple jump and javelin throwing). Six coaches, who had all coached multiple athletes to multiple major championships, took part in semi-structured interviews focused upon a recent example of technique refinement. Data were analysed using a thematic content analysis. The coaching tools reported were generally consistent with those advised by the existing literature, focusing on attaining "buy-in", utilising part-practice, restoring movement automaticity and securing performance under pressure. Five of the six coaches reported using a systematic sequence of stages to implement the refinement, although the number and content of these stages varied between them. Notably, however, there were no formal sources of knowledge (e.g., coach education or training) provided to inform coaches' decision making. Instead, coaches' decisions were largely based on experience both within and outside the sporting domain. Data offer a useful stimulus for reflection amongst sport practitioners confronted by the problem of technique refinement. Certainly the limited awareness of existing guidelines on technique refinement expressed by the coaches emphasises a need for further collaborative work by researchers and coach educators to disseminate best practice.

[Contents of total flavonoids in Rhizoma Arisaematis].

PubMed

Du, S S; Lin, H Y; Zhou, Y X; Wei, L X

2001-06-01

Comparing the contents of total flavonoides of Rhizoma Arisaematis, which collected in different time, regions, different varieties and processed. Determining the contents by ultraviolet spectro-photometry. The contents were found in the following sequence: 1. the end of July, the begin of July, August, September; 2. Beijing, Shanxi, Sichuan, Anhui; 3. Arisaema erubenscens, A. heterophyllum, A. amurense; 4. unprocessed product, processed product.

Registered nurses' reflections on bioscience courses during the undergraduate nursing programme: an exploratory study.

PubMed

Craft, Judy A; Hudson, Peter B; Plenderleith, Mark B; Gordon, Christopher J

2017-06-01

To explore new graduate registered nurses' reflections of bioscience courses during their nursing programme and the relationship between bioscience content and their clinical practice. Undergraduate nursing students internationally find bioscience courses challenging, which may be due to the volume of content and level of difficulty of these courses. Such challenges may be exacerbated by insufficient integration between bioscience theory and nursing clinical practice. A descriptive, cross-sectional mixed methods study was conducted. A 30-item questionnaire with five written response questions which explored recently registered nurses' reflections on bioscience courses during their nursing degree was employed. Descriptive analyses were reported for individual items. Thematic analysis of qualitative responses was grouped to reveal emerging themes. Registered nurses' (n = 22) reflections revealed that bioscience courses were a significant challenge during their undergraduate programme, and they lacked confidence explaining the biological basis of nursing. Participants would like improved knowledge of the relevant bioscience for nursing and agreed that bioscience courses should be extended into the undergraduate final year. The importance of relating bioscience content to nursing practice was elaborated extensively throughout written responses. Although registered nurses reflected that bioscience courses were difficult with large volumes of content, having more bioscience with greater relevance to nursing applications was considered important in their current clinical practice. It is suggested that bioscience academics develop greater contextual links between bioscience content and clinical practice relevant to nursing. After working as a registered nurse, there was appreciation of bioscience relevance for clinical practice, and the nurses believed they would have benefitted from more nursing-related bioscience during their undergraduate programme. Focussed integration of bioscience with clinical nursing courses should be driven by academics, nurse educators and clinical nurses to provide a biological basis for patient care to nursing students. © 2016 John Wiley & Sons Ltd.

Middle Tertiary stratigraphic sequences of the San Joaquin Basin, California: Chapter 6 in Petroleum systems and geologic assessment of oil and gas in the San Joaquin Basin Province, California

USGS Publications Warehouse

Johnson, Cari L.; Graham, Stephan A.

2007-01-01

An integrated database of outcrop studies, borehole logs, and seismic-reflection profiles is used to divide Eocene through Miocene strata of the central and southern San Joaquin Basin, California, into a framework of nine stratigraphic sequences. These third- and higher-order sequences (<3 m.y. duration) comprise the principal intervals for petroleum assessment for the basin, including key reservoir and source rock intervals. Important characteristics of each sequence are discussed, including distribution and stratigraphic relationships, sedimentary facies, regional correlation, and age relations. This higher-order stratigraphic packaging represents relatively short-term fluctuations in various forcing factors including climatic effects, changes in sediment supply, local and regional tectonism, and fluctuations in global eustatic sea level. These stratigraphic packages occur within the context of second-order stratigraphic megasequences, which mainly reflect long-term tectonic basin evolution. Despite more than a century of petroleum exploration in the San Joaquin Basin, many uncertainties remain regarding the age, correlation, and origin of the third- and higher-order sequences. Nevertheless, a sequence stratigraphic approach allows definition of key intervals based on genetic affinity rather than purely lithostratigraphic relationships, and thus is useful for reconstructing the multiphase history of this basin, as well as understanding its petroleum systems.

Attentional awakening: gradual modulation of temporal attention in rapid serial visual presentation.

PubMed

Ariga, Atsunori; Yokosawa, Kazuhiko

2008-03-01

Orienting attention to a point in time facilitates processing of an item within rapidly changing surroundings. We used a one-target RSVP task to look for differences in accuracy in reporting a target related to when the target temporally appeared in the sequence. The results show that observers correctly report a target early in the sequence less frequently than later in the sequence. Previous RSVP studies predicted equivalently accurate performances for one target wherever it appeared in the sequence. We named this new phenomenon attentional awakening, which reflects a gradual modulation of temporal attention in a rapid sequence.

The Development of Reflective Practice through Student Journals

ERIC Educational Resources Information Center

Pavlovich, Kathryn

2007-01-01

This paper explores the design and assessment of reflective journals in a course on spirituality and management in a tertiary institution. The purpose of reflection in education is to develop students' self-awareness and inner leadership. Yet, such assessment poses challenges in terms of design, content and grading. This paper explores the…

Characterization of four species of Trichuris (Nematoda: Enoplida) by their second internal transcribed spacer ribosomal DNA sequence.

PubMed

Oliveros, R; Cutillas, C; De Rojas, M; Arias, P

2000-12-01

Adult worms of Trichuris ovis and T. globulosa were collected from Ovis aries (sheep) and Capra hircus (goats). T. suis was isolated from Sus scrofa domestica (swine) and T. leporis was isolated from Lepus europaeus (rabbits) in Spain. Genomic DNA was isolated and a ribosomal internal transcribed spacer (ITS2) was amplified and sequenced using polymerase-chain-reaction (PCR) techniques. The ITS2 of T. ovis and T. globulosa was 407 nucleotides in length and had a GC content of about 62%. Furthermore, the ITS2 of T. suis and T. leporis was 534 and 418 nucleotides in length and had a GC content of about 64.8% and 62.4%, respectively. There was evidence of slight variation in the sequence within individuals of all species analyzed, indicating intraindividual variation in the sequence of different copies of the ribosomal DNA. Furthermore, low-level intraspecific variation was detected. Sequence analyses of ITS2 products of T. ovis and T. globulosa demonstrated no sequence difference between them. Nevertheless, differences were detected between the ITS2 sequences of T. suis, T. leporis, and T. ovis, indicating that Trichuris species can reliably be differentiated by their ITS2 sequences and PCR-linked restriction-fragment-length polymorphism (RFLP).

High-Throughput Block Optical DNA Sequence Identification.

PubMed

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Science teachers' utilization of Internet and inquiry-based laboratory lessons after an Internet-delivered professional development program

NASA Astrophysics Data System (ADS)

Lee, Kathryn Martell

Much of the professional development in the past decades has been single incident experiences. The heart of inservice growth is the sustained development of current knowledge and practices, vital in science education, as reflected in the National Science Education Standards' inquiry and telecommunications components. This study was an exploration of an Internet-delivered professional development experience, utilizing multiple session interactive real-time data sources and semester-long sustained telementoring. Two groups of inservice teachers participated in the study, with only one group receiving a telementored coaching component. Measures of the dependent variable (delivery of an inquiry-based laboratory lesson sequence) were obtained by videotape, and predictive variables (self-analysis of teaching style and content delivery interviews) were administered to the forty veteran secondary school science teacher volunteers. Results showed that teachers in the group receiving semester-long coaching performed significantly better on utilizing the Internet for content research and inquiry-based lesson sequence delivery than the group not receiving the coaching. Members of the coached group were able to select a dedicated listserv, e-mail, chatline or telephone as the medium of coaching. While the members of the coached group used the listserv, the overwhelming preference was to be coached via the telephone. Qualitative analysis indicated that the telephone was selected for its efficiency of time, immediacy of response, and richer dialogue. Perceived barriers to the implementation of the Internet as a real-time data source in science classrooms included time for access, obsolesce of equipment, and logistics of computer to student ratios. These findings suggest that the group of science teachers studied (1) benefited from a sustained coaching experience for inquiry-based lesson delivery, (2) perceived the Internet as a source of content for their curriculum rather than a communication source, and (3) preferred the telephone as a coaching tool for its efficiency and convenience. Utilizing current pedagogy in science and telecommunication tools has served to whet the appetite of the study teachers to develop utilization of the Internet in their classes for real-time data acquisition.

Curricular Guidelines in Gross Anatomy.

ERIC Educational Resources Information Center

Horn, Stanton D.; And Others

1981-01-01

An outline of AADS curricular guidelines for gross anatomy in dental education includes primary educational goals, prerequisites, core content, specific course objectives for each section of content, sequencing, faculty requirements, and facility and equipment needs. (MSE)

Characterization of bovine ruminal epithelial bacterial communities using 16S rRNA sequencing, PCR-DGGE, and qRT-PCR analysis.

PubMed

Li, Meiju; Zhou, Mi; Adamowicz, Elizabeth; Basarab, John A; Guan, Le Luo

2012-02-24

Currently, knowledge regarding the ecology and function of bacteria attached to the epithelial tissue of the rumen wall is limited. In this study, the diversity of the bacterial community attached to the rumen epithelial tissue was compared to the rumen content bacterial community using 16S rRNA gene sequencing, PCR-DGGE, and qRT-PCR analysis. Sequence analysis of 2785 randomly selected clones from six 16S rDNA (∼1.4kb) libraries showed that the community structures of three rumen content libraries clustered together and were separated from the rumen tissue libraries. The diversity index of each library revealed that ruminal content bacterial communities (4.12/4.42/4.88) were higher than ruminal tissue communities (2.90/2.73/3.23), based on 97% similarity. The phylum Firmicutes was predominant in the ruminal tissue communities, while the phylum Bacteroidetes was predominant in the ruminal content communities. The phyla Fibrobacteres, Planctomycetes, and Verrucomicrobia were only detected in the ruminal content communities. PCR-DGGE analysis of the bacterial profiles of the rumen content and ruminal epithelial tissue samples from 22 steers further confirmed that there is a distinct bacterial community that inhibits the rumen epithelium. The distinctive epimural bacterial communities suggest that Firmicutes, together with other epithelial-specific species, may have additional functions other than food digestion. Copyright © 2011 Elsevier B.V. All rights reserved.

From the Cover: Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features

NASA Astrophysics Data System (ADS)

Derelle, Evelyne; Ferraz, Conchita; Rombauts, Stephane; Rouzé, Pierre; Worden, Alexandra Z.; Robbens, Steven; Partensky, Frédéric; Degroeve, Sven; Echeynié, Sophie; Cooke, Richard; Saeys, Yvan; Wuyts, Jan; Jabbari, Kamel; Bowler, Chris; Panaud, Olivier; Piégu, Benoît; Ball, Steven G.; Ral, Jean-Philippe; Bouget, François-Yves; Piganeau, Gwenael; de Baets, Bernard; Picard, André; Delseny, Michel; Demaille, Jacques; van de Peer, Yves; Moreau, Hervé

2006-08-01

The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world's smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry. genome heterogeneity | genome sequence | green alga | Prasinophyceae | gene prediction

Thinking Allowed: Content and Language Integrated Learning--A Research Agenda

ERIC Educational Resources Information Center

Dalton-Puffer, Christiane; Smit, Ute

2013-01-01

While Content and Language Integrated Learning (CLIL) has received a considerable amount of research interest lately, its increasing popularity as an approach to teaching content subjects in a foreign language requires concerted investigation that reflects and recognises its fundamentally contextualised nature. In this contribution, we sketch…

An Integrated Developmental Model for Studying Identity Content in Context

ERIC Educational Resources Information Center

Galliher, Renee V.; McLean, Kate C.; Syed, Moin

2017-01-01

Historically, identity researchers have placed greater emphasis on processes of identity development ("how" people develop their identities) and less on the content of identity ("what" the identity is). The relative neglect of identity content may reflect the lack of a comprehensive framework to guide research. In this article,…

A Content Comparison of Six Physical Geography Textbooks Spanning a Century

ERIC Educational Resources Information Center

Jennings, Steven A.

2006-01-01

Six physical geography textbooks published between 1901 and 2002 were qualitatively analysed for content and compared to the National Geography Standards. General relationships to dominant approaches to geography, content, and pedagogy of these textbooks were analysed. These textbooks reflect dominant approaches to geography at the time they were…

Quantification of Cannabinoid Content in Cannabis

NASA Astrophysics Data System (ADS)

Tian, Y.; Zhang, F.; Jia, K.; Wen, M.; Yuan, Ch.

2015-09-01

Cannabis is an economically important plant that is used in many fields, in addition to being the most commonly consumed illicit drug worldwide. Monitoring the spatial distribution of cannabis cultivation and judging whether it is drug- or fiber-type cannabis is critical for governments and international communities to understand the scale of the illegal drug trade. The aim of this study was to investigate whether the cannabinoids content in cannabis could be spectrally quantified using a spectrometer and to identify the optimal wavebands for quantifying the cannabinoid content. Spectral reflectance data of dried cannabis leaf samples and the cannabis canopy were measured in the laboratory and in the field, respectively. Correlation analysis and the stepwise multivariate regression method were used to select the optimal wavebands for cannabinoid content quantification based on the laboratory-measured spectral data. The results indicated that the delta-9-tetrahydrocannabinol (THC) content in cannabis leaves could be quantified using laboratory-measured spectral reflectance data and that the 695 nm band is the optimal band for THC content quantification. This study provides prerequisite information for designing spectral equipment to enable immediate quantification of THC content in cannabis and to discriminate drug- from fiber-type cannabis based on THC content quantification in the field.

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

PubMed Central

Vuillemin, Aurèle; Horn, Fabian; Alawi, Mashal; Henny, Cynthia; Wagner, Dirk; Crowe, Sean A.; Kallmeyer, Jens

2017-01-01

Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted. PMID:28798742

Mechanisms behind the estimation of photosynthesis traits from leaf reflectance observations

NASA Astrophysics Data System (ADS)

Dechant, Benjamin; Cuntz, Matthias; Doktor, Daniel; Vohland, Michael

2016-04-01

Many studies have investigated the reflectance-based estimation of leaf chlorophyll, water and dry matter contents of plants. Only few studies focused on photosynthesis traits, however. The maximum potential uptake of carbon dioxide under given environmental conditions is determined mainly by RuBisCO activity, limiting carboxylation, or the speed of photosynthetic electron transport. These two main limitations are represented by the maximum carboxylation capacity, V cmax,25, and the maximum electron transport rate, Jmax,25. These traits were estimated from leaf reflectance before but the mechanisms underlying the estimation remain rather speculative. The aim of this study was therefore to reveal the mechanisms behind reflectance-based estimation of V cmax,25 and Jmax,25. Leaf reflectance, photosynthetic response curves as well as nitrogen content per area, Narea, and leaf mass per area, LMA, were measured on 37 deciduous tree species. V cmax,25 and Jmax,25 were determined from the response curves. Partial Least Squares (PLS) regression models for the two photosynthesis traits V cmax,25 and Jmax,25 as well as Narea and LMA were studied using a cross-validation approach. Analyses of linear regression models based on Narea and other leaf traits estimated via PROSPECT inversion, PLS regression coefficients and model residuals were conducted in order to reveal the mechanisms behind the reflectance-based estimation. We found that V cmax,25 and Jmax,25 can be estimated from leaf reflectance with good to moderate accuracy for a large number of species and different light conditions. The dominant mechanism behind the estimations was the strong relationship between photosynthesis traits and leaf nitrogen content. This was concluded from very strong relationships between PLS regression coefficients, the model residuals as well as the prediction performance of Narea- based linear regression models compared to PLS regression models. While the PLS regression model for V cmax,25 was fully based on the correlation to Narea, the PLS regression model for Jmax,25 was not entirely based on it. Analyses of the contributions of different parts of the reflectance spectrum revealed that the information contributing to the Jmax,25 PLS regression model in addition to the main source of information, Narea, was mainly located in the visible part of the spectrum (500-900 nm). Estimated chlorophyll content could be excluded as potential source of this extra information. The PLS regression coefficients of the Jmax,25 model indicated possible contributions from chlorophyll fluorescence and cytochrome f content. In summary, we found that the main mechanism behind the estimation of V cmax,25 and Jmax,25 from leaf reflectance observations is the correlation to Narea but that there is additional information related to Jmax,25 mainly in the visible part of the spectrum.

Starting with Worldviews: A Five-Step Preparatory Approach to Integrative Interdisciplinary Learning

ERIC Educational Resources Information Center

Augsburg, Tanya; Chitewere, Tendai

2013-01-01

In this article we propose a five-step sequenced approach to integrative interdisciplinary learning in undergraduate gateway courses. Drawing from the literature of interdisciplinarity, transformative learning theory, and theories of reflective learning, we utilize a sequence of five steps early in our respective undergraduate gateway courses to…

Critical thinking evaluation in reflective writing: Development and testing of Carter Assessment of Critical Thinking in Midwifery (Reflection).

PubMed

Carter, Amanda G; Creedy, Debra K; Sidebotham, Mary

2017-11-01

develop and test a tool designed for use by academics to evaluate pre-registration midwifery students' critical thinking skills in reflective writing. a descriptive cohort design was used. a random sample (n = 100) of archived student reflective writings based on a clinical event or experience during 2014 and 2015. a staged model for tool development was used to develop a fifteen item scale involving item generation; mapping of draft items to critical thinking concepts and expert review to test content validity; inter-rater reliability testing; pilot testing of the tool on 100 reflective writings; and psychometric testing. Item scores were analysed for mean, range and standard deviation. Internal reliability, content and construct validity were assessed. expert review of the tool revealed a high content validity index score of 0.98. Using two independent raters to establish inter-rater reliability, good absolute agreement of 72% was achieved with a Kappa coefficient K = 0.43 (p<0.0001). Construct validity via exploratory factor analysis revealed three factors: analyses context, reasoned inquiry, and self-evaluation. The mean total score for the tool was 50.48 (SD = 12.86). Total and subscale scores correlated significantly. The scale achieved good internal reliability with a Cronbach's alpha coefficient of .93. this study establishedthe reliability and validity of the CACTiM (reflection) for use by academics to evaluate midwifery students' critical thinking in reflective writing. Validation with large diverse samples is warranted. reflective practice is a key learning and teaching strategy in undergraduate Bachelor of Midwifery programmes and essential for safe, competent practice. There is the potential to enhance critical thinking development by assessingreflective writing with the CACTiM (reflection) tool to provide formative and summative feedback to students and inform teaching strategies. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Integrating motion, illumination, and structure in video sequences with applications in illumination-invariant tracking.

PubMed

Xu, Yilei; Roy-Chowdhury, Amit K

2007-05-01

In this paper, we present a theory for combining the effects of motion, illumination, 3D structure, albedo, and camera parameters in a sequence of images obtained by a perspective camera. We show that the set of all Lambertian reflectance functions of a moving object, at any position, illuminated by arbitrarily distant light sources, lies "close" to a bilinear subspace consisting of nine illumination variables and six motion variables. This result implies that, given an arbitrary video sequence, it is possible to recover the 3D structure, motion, and illumination conditions simultaneously using the bilinear subspace formulation. The derivation builds upon existing work on linear subspace representations of reflectance by generalizing it to moving objects. Lighting can change slowly or suddenly, locally or globally, and can originate from a combination of point and extended sources. We experimentally compare the results of our theory with ground truth data and also provide results on real data by using video sequences of a 3D face and the entire human body with various combinations of motion and illumination directions. We also show results of our theory in estimating 3D motion and illumination model parameters from a video sequence.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

PubMed

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

USGS Publications Warehouse

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

SNP in Chalcone Synthase gene is associated with variation of 6-gingerol content in contrasting landraces of Zingiber officinale.Roscoe.

PubMed

Ghosh, Subhabrata; Mandi, Swati Sen

2015-07-25

Zingiber officinale, medicinally the most important species within Zingiber genus, contains 6-gingerol as the active principle. This compound obtained from rhizomes of Z.officinale, has immense medicinal importance and is used in various herbal drug formulations. Our record of variation in content of this active principle, viz. 6-gingerol, in land races of this drug plant collected from different locations correlated with our Gene expression studies exhibiting high Chalcone Synthase gene (Chalcone Synthase is the rate limiting enzyme of 6-gingerol biosynthesis pathway) expression in high 6-gingerol containing landraces than in the low 6-gingerol containing landraces. Sequencing of Chalcone Synthase cDNA and subsequent multiple sequence alignment revealed seven SNPs between these contrasting genotypes. Converting this nucleotide sequence to amino acid sequence, alteration of two amino acids becomes evident; one amino acid change (asparagine to serine at position 336) is associated with base change (A→G) and another change (serine to leucine at position 142) is associated with the base change (C→T). Since asparagine at position 336 is one of the critical amino acids of the catalytic triad of Chalcone Synthase enzyme, responsible for substrate binding, our study suggests that landraces with a specific amino acid change viz. Asparagine (found in high 6-gingerol containing landraces) to serine causes low 6-gingerol content. This is probably due to a weak enzyme substrate association caused by the absence of asparagine in the catalytic triad. Detailed study of this finding could also help to understand molecular mechanism associated with variation in 6-gingerol content in Z.officinale genotypes and thereby strategies for developing elite genotypes containing high 6-gingerol content. Copyright © 2015 Elsevier B.V. All rights reserved.

Refining the structure and content of clinical genomic reports.

PubMed

Dorschner, Michael O; Amendola, Laura M; Shirts, Brian H; Kiedrowski, Lesli; Salama, Joseph; Gordon, Adam S; Fullerton, Stephanie M; Tarczy-Hornoch, Peter; Byers, Peter H; Jarvik, Gail P

2014-03-01

To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professionals, we developed separate indication-specific and incidental findings reports. Standard test report elements were supplemented with research study-specific language, which highlighted the limitations of exome sequencing and provided detailed, structured results, and interpretations. The report format we developed to communicate research results can easily be transformed for clinical use by removal of research-specific statements and disclaimers. The development of clinical reports for exome sequencing has shown that accurate and open communication between the clinician and laboratory is ideally an ongoing process to address the increasing complexity of molecular genetic testing. © 2014 Wiley Periodicals, Inc.

Refining the Structure and Content of Clinical Genomic Reports

PubMed Central

DORSCHNER, MICHAEL O.; AMENDOLA, LAURA M.; SHIRTS, BRIAN H.; KIEDROWSKI, LESLI; SALAMA, JOSEPH; GORDON, ADAM S.; FULLERTON, STEPHANIE M.; TARCZY-HORNOCH, PETER; BYERS, PETER H.; JARVIK, GAIL P.

2014-01-01

To effectively articulate the results of exome and genome sequencing we refined the structure and content of molecular test reports. To communicate results of a randomized control trial aimed at the evaluation of exome sequencing for clinical medicine, we developed a structured narrative report. With feedback from genetics and non-genetics professionals, we developed separate indication-specific and incidental findings reports. Standard test report elements were supplemented with research study-specific language, which highlighted the limitations of exome sequencing and provided detailed, structured results, and interpretations. The report format we developed to communicate research results can easily be transformed for clinical use by removal of research-specific statements and disclaimers. The development of clinical reports for exome sequencing has shown that accurate and open communication between the clinician and laboratory is ideally an ongoing process to address the increasing complexity of molecular genetic testing. PMID:24616401

Complete genome sequence of chinese strain of ‘Candidatus Liberibacter asiaticus’

USDA-ARS?s Scientific Manuscript database

The complete genome sequence of ‘Candidatus Liberibacter asiaticus’ strain (Las) Guangxi-1(GX-1) was obtained by an Illumina HiSeq 2000. The GX-1 genome comprises 1,268,237 nucleotides, 36.5 % GC content, 1,141 predicted coding sequences, 44 tRNAs, 3 complete copies of ribosomal RNA genes (16S, 23S ...

Complete mitochondrial genome of the fennec fox (Vulpes zerda).

PubMed

Yang, Xiufeng; Zhao, Chao; Zhang, Honghai; Zhang, Jin; Chen, Lei; Sha, Weilai; Liu, Guangshuai

2016-01-01

In this study, the complete mitochondrial genome of the fennec fox (Vulpes zerda) was sequenced using blood samples obtained from a female individual in Shanghai wildlife Park. Sequence analysis showed that the content of T (26.7%) in total composition was no more than C (27.2%), which is different from most of Canide individuals sequenced previously.

Draft Genome Sequence of Thiostrepton-Producing Streptomyces azureus ATCC 14921

PubMed Central

Sakihara, Kengo; Maeda, Jumpei; Tashiro, Kosuke; Fujino, Yasuhiro; Kuhara, Satoru; Ohshima, Toshihisa; Ogata, Seiya

2015-01-01

Streptomyces azureus ATCC 14921 belongs to the Streptomyces cyaneus cluster and is known to be a thiostrepton producer. Here, we report a draft genome sequence for this strain, consisting of 350 contigs containing a total of 8,790,525 bp, 8,164 predicted coding sequences, and a G+C content of 70.9%. PMID:26494661

Draft Genome Sequence of “Cohnella kolymensis” B-2846

PubMed Central

Kudryashova, Ekaterina B.; Ariskina, Elena V.

2016-01-01

A draft genome sequence of “Cohnella kolymensis” strain B-2846 was derived using IonTorrent sequencing technology. The size of the assembly and G+C content were in agreement with those of other species of this genus. Characterization of the genome of a novel species of Cohnella will assist in bacterial systematics. PMID:26769947

Algorithm for retrieving vegetative canopy and leaf parameters from multi- and hyperspectral imagery

NASA Astrophysics Data System (ADS)

Borel, Christoph

2009-05-01

In recent years hyper-spectral data has been used to retrieve information about vegetative canopies such as leaf area index and canopy water content. For the environmental scientist these two parameters are valuable, but there is potentially more information to be gained as high spatial resolution data becomes available. We developed an Amoeba (Nelder-Mead or Simplex) based program to invert a vegetative canopy radiosity model coupled with a leaf (PROSPECT5) reflectance model and modeled for the background reflectance (e.g. soil, water, leaf litter) to a measured reflectance spectrum. The PROSPECT5 leaf model has five parameters: leaf structure parameter Nstru, chlorophyll a+b concentration Cab, carotenoids content Car, equivalent water thickness Cw and dry matter content Cm. The canopy model has two parameters: total leaf area index (LAI) and number of layers. The background reflectance model is either a single reflectance spectrum from a spectral library() derived from a bare area pixel on an image or a linear mixture of soil spectra. We summarize the radiosity model of a layered canopy and give references to the leaf/needle models. The method is then tested on simulated and measured data. We investigate the uniqueness, limitations and accuracy of the retrieved parameters on canopy parameters (low, medium and high leaf area index) spectral resolution (32 to 211 band hyperspectral), sensor noise and initial conditions.

Application of a LED-based reflectance sensor for the assessing in situ the lycopene content of tomatoes (Lycopersicon esculentum Mill.)

NASA Astrophysics Data System (ADS)

Mignani, Anna G.; Ciaccheri, Leonardo; Mencaglia, Andrea A.; Tuccio, Lorenza; Agati, Giovanni

2015-05-01

Nondestructive in situ determination of the antioxidant lycopene of fresh tomato fruits is of large interest for the growers, willing to optimize the harvest time for high quality products. For this, we developed a portable LED-based colorimeter which was able to measure reflectance spectra of whole tomatoes in the 400-750 nm range. The tomato skins from the same samples were then frozen in liquid nitrogen, extracted with an acetone/ethanol/hexane mixture and analyzed by means of a spectrophotometer for their lycopene content. Concentration of lycopene was varying between 70 and 550 mg/Kg fresh weight skin. Partial Least Square regression was used to correlate spectral data to the tomato lycopene content. The multivariate processing of the reflectance data showed that lycopene content could be nicely predicted with a coefficient of determination R2=0.945 and a root mean square error of cross-validation RMSECV=57 mg/Kg skin fresh weight. These results suggest that portable, low-cost and compact LED-based sensors appear to be promising instruments for the nondestructive assessment of tomato lycopene even in the field.

Cue self-relevance affects autobiographical memory specificity in individuals with a history of major depression

PubMed Central

Crane, Catherine; Barnhofer, Thorsten; Williams, J. Mark G.

2007-01-01

Previously depressed and never-depressed individuals identified personal characteristics (self-guides) defining their ideal, ought, and feared selves. One week later they completed the autobiographical memory test (AMT). For each participant the number of AMT cues that reflected self-guide content was determined to produce an index of AMT cue self-relevance. Individuals who had never been depressed showed no significant relationship between cue self-relevance and specificity. In contrast, in previously depressed participants there was a highly significant negative correlation between cue self-relevance and specificity—the greater the number of AMT cues that reflected self-guide content, the fewer specific memories participants recalled. It is suggested that in individuals with a history of depression, cues reflecting self-guide content are more likely to prompt a shift to processing of information within the long-term self (Conway, Singer, & Tagini, 2004), increasing the likelihood that self-related semantic information will be provided in response to cues on the autobiographical memory test. PMID:17454667

Broadband superior electromagnetic absorption of a discrete-structure microwave coating

NASA Astrophysics Data System (ADS)

Duan, Yuping; Xi, Qun; Liu, Wei; Wang, Tongmin

2016-10-01

A method of improving the electromagnetic (EM) absorption property of conventional microwave absorber (CMA) is proposed here. The structural design process was mainly concerned with systematic analysis and research into the impedance matching characteristic and induced current. By processing a CMA-carbonyl-iron powder (CIP) coating into many isolated regions, the discrete-structure microwave absorber (DMA) had a much better absorption property than the corresponding CMA. When the thickness was only 2.0 mm and the component content was 33 wt%, the loss of reflection was less than -10 dB shifted from 6-7 GHz to 7-13 GHz and the loss of minimum reflection decreased from 12.5 dB lost to 32 dB lost through a discrete-structure process. The microwave absorption properties of coatings with different component contents and thicknesses were investigated. The minimum reflection peaks tended to shift towards the lower frequency region as CIP content or coating thickness increased. By adjusting these three factors, a high-performance broadband absorber was produced.

Cue self-relevance affects autobiographical memory specificity in individuals with a history of major depression.

PubMed

Crane, Catherine; Barnhofer, Thorsten; Mark, J; Williams, G

2007-04-01

Previously depressed and never-depressed individuals identified personal characteristics (self-guides) defining their ideal, ought, and feared selves. One week later they completed the autobiographical memory test (AMT). For each participant the number of AMT cues that reflected self-guide content was determined to produce an index of AMT cue self-relevance. Individuals who had never been depressed showed no significant relationship between cue self-relevance and specificity. In contrast, in previously depressed participants there was a highly significant negative correlation between cue self-relevance and specificity--the greater the number of AMT cues that reflected self-guide content, the fewer specific memories participants recalled. It is suggested that in individuals with a history of depression, cues reflecting self-guide content are more likely to prompt a shift to processing of information within the long-term self (Conway, Singer, & Tagini, 2004), increasing the likelihood that self-related semantic information will be provided in response to cues on the autobiographical memory test.

Prediction of Soil Organic Carbon at the European Scale by Visible and Near InfraRed Reflectance Spectroscopy.

PubMed

Stevens, Antoine; Nocita, Marco; Tóth, Gergely; Montanarella, Luca; van Wesemael, Bas

2013-01-01

Soil organic carbon is a key soil property related to soil fertility, aggregate stability and the exchange of CO2 with the atmosphere. Existing soil maps and inventories can rarely be used to monitor the state and evolution in soil organic carbon content due to their poor spatial resolution, lack of consistency and high updating costs. Visible and Near Infrared diffuse reflectance spectroscopy is an alternative method to provide cheap and high-density soil data. However, there are still some uncertainties on its capacity to produce reliable predictions for areas characterized by large soil diversity. Using a large-scale EU soil survey of about 20,000 samples and covering 23 countries, we assessed the performance of reflectance spectroscopy for the prediction of soil organic carbon content. The best calibrations achieved a root mean square error ranging from 4 to 15 g C kg(-1) for mineral soils and a root mean square error of 50 g C kg(-1) for organic soil materials. Model errors are shown to be related to the levels of soil organic carbon and variations in other soil properties such as sand and clay content. Although errors are ∼5 times larger than the reproducibility error of the laboratory method, reflectance spectroscopy provides unbiased predictions of the soil organic carbon content. Such estimates could be used for assessing the mean soil organic carbon content of large geographical entities or countries. This study is a first step towards providing uniform continental-scale spectroscopic estimations of soil organic carbon, meeting an increasing demand for information on the state of the soil that can be used in biogeochemical models and the monitoring of soil degradation.

Prediction of Soil Organic Carbon at the European Scale by Visible and Near InfraRed Reflectance Spectroscopy

PubMed Central

Stevens, Antoine; Nocita, Marco; Tóth, Gergely; Montanarella, Luca; van Wesemael, Bas

2013-01-01

Soil organic carbon is a key soil property related to soil fertility, aggregate stability and the exchange of CO2 with the atmosphere. Existing soil maps and inventories can rarely be used to monitor the state and evolution in soil organic carbon content due to their poor spatial resolution, lack of consistency and high updating costs. Visible and Near Infrared diffuse reflectance spectroscopy is an alternative method to provide cheap and high-density soil data. However, there are still some uncertainties on its capacity to produce reliable predictions for areas characterized by large soil diversity. Using a large-scale EU soil survey of about 20,000 samples and covering 23 countries, we assessed the performance of reflectance spectroscopy for the prediction of soil organic carbon content. The best calibrations achieved a root mean square error ranging from 4 to 15 g C kg−1 for mineral soils and a root mean square error of 50 g C kg−1 for organic soil materials. Model errors are shown to be related to the levels of soil organic carbon and variations in other soil properties such as sand and clay content. Although errors are ∼5 times larger than the reproducibility error of the laboratory method, reflectance spectroscopy provides unbiased predictions of the soil organic carbon content. Such estimates could be used for assessing the mean soil organic carbon content of large geographical entities or countries. This study is a first step towards providing uniform continental-scale spectroscopic estimations of soil organic carbon, meeting an increasing demand for information on the state of the soil that can be used in biogeochemical models and the monitoring of soil degradation. PMID:23840459

Earth Science Content Guidelines Grades K-12.

ERIC Educational Resources Information Center

American Geological Inst., Alexandria, VA.

Teams of teachers, other science educators, and scientists selected from a national search for project writers have proposed using the following set of questions to guide the inclusion of earth science content into the kindergarten through grade 12 curriculum. The Essential Questions are organized in a K-12 sequence by six content areas: (1) Solid…

Single molecule sequencing of the M13 virus genome without amplification

PubMed Central

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X.; Yan, Qin; Deem, Michael W.; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias. PMID:29253901

Single molecule sequencing of the M13 virus genome without amplification.

PubMed

Zhao, Luyang; Deng, Liwei; Li, Gailing; Jin, Huan; Cai, Jinsen; Shang, Huan; Li, Yan; Wu, Haomin; Xu, Weibin; Zeng, Lidong; Zhang, Renli; Zhao, Huan; Wu, Ping; Zhou, Zhiliang; Zheng, Jiao; Ezanno, Pierre; Yang, Andrew X; Yan, Qin; Deem, Michael W; He, Jiankui

2017-01-01

Next generation sequencing (NGS) has revolutionized life sciences research. However, GC bias and costly, time-intensive library preparation make NGS an ill fit for increasing sequencing demands in the clinic. A new class of third-generation sequencing platforms has arrived to meet this need, capable of directly measuring DNA and RNA sequences at the single-molecule level without amplification. Here, we use the new GenoCare single-molecule sequencing platform from Direct Genomics to sequence the genome of the M13 virus. Our platform detects single-molecule fluorescence by total internal reflection microscopy, with sequencing-by-synthesis chemistry. We sequenced the genome of M13 to a depth of 316x, with 100% coverage. We determined a consensus sequence accuracy of 100%. In contrast to GC bias inherent to NGS results, we demonstrated that our single-molecule sequencing method yields minimal GC bias.

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium

PubMed Central

Kohli, Puneet; Dua, Ankita; Sangwan, Naseer; Oldach, Phoebe; Khurana, J. P.

2013-01-01

Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00′N and 81°09′E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content. PMID:24233594

Aromatic claw: A new fold with high aromatic content that evades structural prediction: Aromatic Claw

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sachleben, Joseph R.; Adhikari, Aashish N.; Gawlak, Grzegorz

2016-11-10

We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet withmore » a novel fold that we have termed an Aromatic Claw. As this fold was previously unknown and the sequence unique, we submitted the sequence to CASP10 as a target for blind structural prediction. At the end of the competition, the sequence was classified a hard template based model; the structural relationship between the template and the experimental structure was small and the predictions all failed to predict the structure. CSRosetta was found to predict the secondary structure and its packing; however, it was found that there was little correlation between CSRosetta score and the RMSD between the CSRosetta structure and the NMR determined one. This work demonstrates that even in relatively small proteins, we do not yet have the capacity to accurately predict the fold for all primary sequences. The experimental discovery of new folds helps guide the improvement of structural prediction methods.« less

Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content

PubMed Central

2014-01-01

Background Variation in seed oil composition and content among soybean varieties is largely attributed to differences in transcript sequences and/or transcript accumulation of oil production related genes in seeds. Discovery and analysis of sequence and expression variations in these genes will accelerate soybean oil quality improvement. Results In an effort to identify these variations, we sequenced the transcriptomes of soybean seeds from nine lines varying in oil composition and/or total oil content. Our results showed that 69,338 distinct transcripts from 32,885 annotated genes were expressed in seeds. A total of 8,037 transcript expression polymorphisms and 50,485 transcript sequence polymorphisms (48,792 SNPs and 1,693 small Indels) were identified among the lines. Effects of the transcript polymorphisms on their encoded protein sequences and functions were predicted. The studies also provided independent evidence that the lack of FAD2-1A gene activity and a non-synonymous SNP in the coding sequence of FAB2C caused elevated oleic acid and stearic acid levels in soybean lines M23 and FAM94-41, respectively. Conclusions As a proof-of-concept, we developed an integrated RNA-seq and bioinformatics approach to identify and functionally annotate transcript polymorphisms, and demonstrated its high effectiveness for discovery of genetic and transcript variations that result in altered oil quality traits. The collection of transcript polymorphisms coupled with their predicted functional effects will be a valuable asset for further discovery of genes, gene variants, and functional markers to improve soybean oil quality. PMID:24755115

Fostering Self-Reflection and Meaningful Learning: Earth Science Professional Development for Middle School Science Teachers

ERIC Educational Resources Information Center

Monet, Julie A.; Etkina, Eugenia

2008-01-01

This paper describes the analysis of teachers' journal reflections during an inquiry-based professional development program. As a part of their learning experience, participants reflected on what they learned and how they learned. Progress of subject matter and pedagogical content knowledge was assessed though surveys and pre- and posttests. We…

Using Reflective Learning to Improve the Impact of Continuing Education in the Context of Work Rehabilitation

ERIC Educational Resources Information Center

Vachon, Brigitte; Durand, Marie-Jose; LeBlanc, Jeannette

2010-01-01

Reflective learning has been described as a promising approach for ameliorating the impact of continuing education (CE) programs. However, there are still very few studies that have investigated how occupational therapists use reflection to improve the integration of CE program content in their decision-making processes. The study objectives were…

The Impact of Incorrect Examples on Learning Fractions: A Field Experiment with 6th Grade Students

ERIC Educational Resources Information Center

Heemsoth, Tim; Heinze, Aiso

2014-01-01

Educational research indicates that error reflection, especially reflection on incorrect examples, has a positive effect on knowledge acquisition. The benefit of error reflections might be explained by the extended knowledge of incorrect strategies and concepts (negative knowledge) which fosters the learning of new content. In a field experiment…

What You Can Learn from the 1979 Pacemakers.

ERIC Educational Resources Information Center

Brasler, Wayne

1980-01-01

Indicates that prizewinning school publications differ from good publications in having three qualities: wide-ranging content reflecting organized, creative approaches to coverage; intelligence and sensitivity in content; and thoughtful design. Includes illustrations from prizewinners. (TJ)

Modular and configurable optimal sequence alignment software: Cola.

PubMed

Zamani, Neda; Sundström, Görel; Höppner, Marc P; Grabherr, Manfred G

2014-01-01

The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignment does not always reflect the patterns by which nucleotides mutate. Efficiently implemented algorithms that can be parameterised to accommodate more complex non-linear scoring schemes are thus desirable. We present Cola, alignment software that implements different optimal alignment algorithms, also allowing for scoring contiguous matches of nucleotides in a nonlinear manner. The latter places more emphasis on short, highly conserved motifs, and less on the surrounding nucleotides, which can be more diverged. To illustrate the differences, we report results from aligning 14,100 sequences from 3' untranslated regions of human genes to 25 of their mammalian counterparts, where we found that a nonlinear scoring scheme is more consistent than a linear scheme in detecting short, conserved motifs. Cola is freely available under LPGL from https://github.com/nedaz/cola.

Curriculum coherence: A comparative analysis of elementary science content standards in People's Republic of China and the USA

NASA Astrophysics Data System (ADS)

Huang, Fang

This study examines elementary science content standards curriculum coherence between the People's Republic of China and the United States of America. Three aspects of curriculum coherence are examined in this study: topic inclusion, topic duration, and curriculum structure. Specifically this study centers on the following research questions: (1) What science knowledge is intended for elementary students in each country? (2) How long each topic stays in the curriculum? (3) How these topics sequence and connect with each other? (4) And finally, what is the implication for elementary science curriculum development? Four intended science curriculum frameworks were selected respectively for each country. A technique of General Topic Trace Mapping (GTTM) was applied to generate the composite science content standards out of the selected curriculum for each country. In comparison, the composite USA and Chinese elementary science content standards form a stark contrast: a bunch of broad topics vs. a focus on a set of key topics at each grade; an average of 3.4 year topic duration vs. an average of 1.68 year topic duration; a stress on connections among related ideas vs. a discrete disposition of related ideas; laundry list topic organization vs. hierarchical organization of science topics. In analyzing the interrelationships among these characteristics, this study reached implications for developing coherent science content standards: First, for the overall curriculum, the topic inclusion should reflect the logical and sequential nature of knowledge in science. Second, for each grade level, less, rather than more science topics should be focused. Third, however, it should be clarified that a balance should be made between curriculum breadth and depth by considering student needs, subject matter, and child development. Fourth, the topic duration should not be too long. The lengthy topic duration tends to undermine links among ideas as well as lead to superficial treatment of topics.

Cocoa/Cotton Comparative Genomics

USDA-ARS?s Scientific Manuscript database

With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

A frequency-domain seismic blind deconvolution based on Gini correlations

NASA Astrophysics Data System (ADS)

Wang, Zhiguo; Zhang, Bing; Gao, Jinghuai; Huo Liu, Qing

2018-02-01

In reflection seismic processing, the seismic blind deconvolution is a challenging problem, especially when the signal-to-noise ratio (SNR) of the seismic record is low and the length of the seismic record is short. As a solution to this ill-posed inverse problem, we assume that the reflectivity sequence is independent and identically distributed (i.i.d.). To infer the i.i.d. relationships from seismic data, we first introduce the Gini correlations (GCs) to construct a new criterion for the seismic blind deconvolution in the frequency-domain. Due to a unique feature, the GCs are robust in their higher tolerance of the low SNR data and less dependent on record length. Applications of the seismic blind deconvolution based on the GCs show their capacity in estimating the unknown seismic wavelet and the reflectivity sequence, whatever synthetic traces or field data, even with low SNR and short sample record.

Evaluation Criterion for Quality Assessment of E-Learning Content

ERIC Educational Resources Information Center

Al-Alwani, Abdulkareem

2014-01-01

Research trends related to e-learning systems are oriented towards increasing the efficiency and capacity of the systems, thus they reflect a large variance in performance when considering content conformity and quality standards. The Framework related to standardisation of digital content for e-learning systems is likely to play a significant…

Estimating cadmium concentration in the edible part of Capsicum annuum using hyperspectral models.

PubMed

Wang, Ting; Wei, Hong; Zhou, Cui; Gu, Yanwen; Li, Rui; Chen, Hongchun; Ma, Wenchao

2017-10-09

Hyperspectral remote sensing can be applied to the rapid and nondestructive monitoring of heavy-metal pollution in crops. To realize the rapid and real-time detection of cadmium in the edible part (fruit) of Capsicum annuum, the leaf spectral reflectance of plants exposed to different levels of cadmium stress was measured using hyperspectral remote sensing during four growth stages. The spectral indices or bands sensitive to cadmium stress were determined by correlation analysis, and hyperspectral estimation models for predicting the cadmium content in the fruit of C. annuum during the mature growth stage were established. The models were cross validated by taking the sensitive spectral indices in the bud stage and the sensitive spectral bands in the flowering stage as the input variables. The results indicated that cadmium accumulated in the leaves and fruit of C. annuum and leaf cadmium content in the three early growth stages were correlated with the cadmium content of the pepper in the mature stage. Leaf spectral reflectance was sensitive to cadmium stress, and the first derivative of the original spectral reflectance was strongly correlated with leaf cadmium content during all growth stages. Among the established models, the multiple regression model based on the sensitive spectral bands in the flowering stage was optimal for predicting fruit cadmium content of the pepper. This model provides a promising method to ensure food safety during the early growth stage of the plant.

Elementary student teachers' science content representations

NASA Astrophysics Data System (ADS)

Zembal-Saul, Carla; Krajcik, Joseph; Blumenfeld, Phyllis

2002-08-01

This purpose of this study was to examine the ways in which three prospective teachers who had early opportunities to teach science would approach representing science content within the context of their student teaching experiences. The study is framed in the literature on pedagogical content knowledge and learning to teach. A situated perspective on cognition is applied to better understand the influence of context and the role of the cooperating teacher. The three participants were enrolled in an experimental teacher preparation program designed to enhance the teaching of science at the elementary level. Qualitative case study design guided the collection, organization, and analysis of data. Multiple forms of data associated with student teachers' content representations were collected, including audiotaped planning and reflection interviews, written lesson plans and reflections, and videotaped teaching experiences. Broad analysis categories were developed and refined around the subconstructs of content representation (i.e., knowledge of instructional strategies that promote learning and knowledge of students and their requirements for meaningful science learning). Findings suggest that when prospective teachers are provided with opportunities to apply and reflect substantively on their developing considerations for supporting children's science learning, they are able to maintain a subject matter emphasis. However, in the absence of such opportunities, student teachers abandon their subject matter emphasis, even when they have had extensive background and experiences addressing subject-specific considerations for teaching and learning.

The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance.

PubMed

Molin, William T; Wright, Alice A; Lawton-Rauh, Amy; Saski, Christopher A

2017-01-17

The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene. By sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the "EPSPS cassette." This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette. Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content. The adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri, the amplification of the EPSPS cassette, characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion.

WebLogo: A Sequence Logo Generator

PubMed Central

Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc; Brenner, Steven E.

2004-01-01

WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Each logo consists of stacks of letters, one stack for each position in the sequence. The overall height of each stack indicates the sequence conservation at that position (measured in bits), whereas the height of symbols within the stack reflects the relative frequency of the corresponding amino or nucleic acid at that position. WebLogo has been enhanced recently with additional features and options, to provide a convenient and highly configurable sequence logo generator. A command line interface and the complete, open WebLogo source code are available for local installation and customization. PMID:15173120

Reflectance measurements of cotton leaf senescence altered by mepiquat chloride

NASA Technical Reports Server (NTRS)

Gausman, H. W.; Escobar, D. E.; Rodriguez, R. R. (Principal Investigator)

1982-01-01

Spectrophotometric reflectance measurements were made on plant-attached leaves to evaluate growth chamber-grown cotton leaf (Gossypium hirsutum L.) senescence (chlorophyll degradation as criterion) that was delayed by mepiquat chloride (1,1-dimethylpiperidinium chloride) rates of 0, 10, 40, 70, and 100 g a.i./ha. Mepiquat chloride (MC increased both chlorophyll and leaf water contents as compared with that of untreated leaves. Reflectance was inversely and linearly correlated (r = -0.873**) with eater content at the 1.65 micrometer wavelength and was inversely correlated (r = -0.812**) with chlorophyll concentration at the 0.55 micrometer wavelength but best fit a quadratic equation. Either wavelength measurement might be useful to remotely detect cotton leaf senescence or fields of MC-treated cotton plants.

[Increased content of nucleotide sequences in transcriptionally active DNA and poly(A)+-mRNA of the rat liver and a rise in its translation activity as affected by inducers].

PubMed

Dashkevich, V S; Vishnivetskiĭ, S N; Skobel'tsina, L M; Luk'ianchikova, N L; Kaledin, V I

1986-12-01

Cortisol and 3'-methyl-4-dimethyl-amino-azobenzene induce an increase in the content of repeated sequences (RS) in transcriptionally active (TA) DNA, while the content of respective RS in potentially active DNA fractions enriched with regulatory regions of the genome decreases. RS content in induced poly A+-mRNA also rises, as determined by the nature of hybridization of respective c DNA with total DNA. The translation of induced poly A+-mRNA rises essentially, with the qualitative distinctions in in vitro synthesized protein product spectrum being absent. Inducible RS with unstable chromatine conformation are thought to provide a universal system of rapid response of the genetic apparatus to extreme situations, serving as transcription intensifiers in TA DNA and as translation intensifiers in induced poly A+-mRNA.

A Teaching--Learning Sequence on Free Fall Motion

ERIC Educational Resources Information Center

Borghi, L.; De Ambrosis, A.; Lamberti, N.; Mascheretti, P.

2005-01-01

A teaching--learning sequence is presented that is designed to help high school pupils gain awareness about the independence of the vertical and horizontal components of free fall motion. The approach we propose is based on the use of experimental activities and computer simulations designed specifically to help pupils reflect on the experiments…

Biosensing of BCR/ABL fusion gene using an intensity-interrogation surface plasmon resonance imaging system

NASA Astrophysics Data System (ADS)

Wu, Jiangling; Huang, Yu; Bian, Xintong; Li, DanDan; Cheng, Quan; Ding, Shijia

2016-10-01

In this work, a custom-made intensity-interrogation surface plasmon resonance imaging (SPRi) system has been developed to directly detect a specific sequence of BCR/ABL fusion gene in chronic myelogenous leukemia (CML). The variation in the reflected light intensity detected from the sensor chip composed of gold islands array is proportional to the change of refractive index due to the selective hybridization of surface-bound DNA probes with target ssDNA. SPRi measurements were performed with different concentrations of synthetic target DNA sequence. The calibration curve of synthetic target sequence shows a good relationship between the concentration of synthetic target and the change of reflected light intensity. The detection limit of this SPRi measurement could approach 10.29 nM. By comparing SPRi images, the target ssDNA and non-complementary DNA sequence are able to be distinguished. This SPRi system has been applied for assay of BCR/ABL fusion gene extracted from real samples. This nucleic acid-based SPRi biosensor therefore offers an alternative high-effective, high-throughput label-free tool for DNA detection in biomedical research and molecular diagnosis.

Enhancing the Skill-Building Phase of Introductory Organic Chemistry Lab through a Reflective Peer Review Structure

ERIC Educational Resources Information Center

Pontrello, Jason K.

2016-01-01

Introductory organic laboratory courses frequently begin with a set of activities built around developing basic experimental skills and techniques, often with guided-inquiry components. A sequence of skill-based activities is described to promote reflection, analysis of, and interpersonal communication around science. A multistage process was used…

The Complexity of Bit Retrieval

DOE PAGES

Elser, Veit

2018-09-20

Bit retrieval is the problem of reconstructing a periodic binary sequence from its periodic autocorrelation, with applications in cryptography and x-ray crystallography. After defining the problem, with and without noise, we describe and compare various algorithms for solving it. A geometrical constraint satisfaction algorithm, relaxed-reflect-reflect, is currently the best algorithm for noisy bit retrieval.

The Complexity of Bit Retrieval

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elser, Veit

Bit retrieval is the problem of reconstructing a periodic binary sequence from its periodic autocorrelation, with applications in cryptography and x-ray crystallography. After defining the problem, with and without noise, we describe and compare various algorithms for solving it. A geometrical constraint satisfaction algorithm, relaxed-reflect-reflect, is currently the best algorithm for noisy bit retrieval.

Students' Socio-Scientific Reasoning in an Astrobiological Context during Work with a Digital Learning Environment

ERIC Educational Resources Information Center

Hansson, Lena; Redfors, Andreas; Rosberg, Maria

2011-01-01

In a European project--CoReflect--researchers in seven countries are developing, implementing and evaluating teaching sequences using a web-based platform (STOCHASMOS). The interactive web-based inquiry materials support collaborative and reflective work. The learning environments will be iteratively tested and refined, during different phases of…

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Louati, Moussa

Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content and 7,307 predicted protein-coding genes.

Draft Genome Sequence of Pediococcus lolii NGRI 0510QT Isolated from Ryegrass Silage

PubMed Central

Mori, Kazuki; Tashiro, Kosuke; Fujino, Yasuhiro; Nagayoshi, Yuko; Hayashi, Yoshiharu; Kuhara, Satoru; Ohshima, Toshihisa

2013-01-01

Pediococcus lolii NGRI 0510QT was isolated from ryegrass silage produced on Ishigaki Island, Okinawa Prefecture, Japan. Here we present a draft genome sequence for this strain, consisting of 103 contigs for a total of 2,047,078 bp, 2,154 predicted coding sequences, and a G+C content of 42.1%. PMID:23405350

Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera

PubMed Central

Malhotra, Jaya; Dua, Ankita; Saxena, Anjali; Sangwan, Naseer; Mukherjee, Udita; Pandey, Neeti; Rajagopal, Raman; Khurana, Paramjit; Khurana, Jitendra P.

2012-01-01

In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%. PMID:22933775

Permanent Improved High-Quality Draft Genome Sequence of Nocardia casuarinae Strain BMG51109, an Endophyte of Actinorhizal Root Nodules of Casuarina glauca

DOE PAGES

Ghodhbane-Gtari, Faten; Beauchemin, Nicholas; Louati, Moussa; ...

2016-08-04

Here, we report the first genome sequence of a Nocardia plant endophyte, N. casuarinae strain BMG51109, isolated from Casuarina glauca root nodules. The improved high-quality draft genome sequence contains 8,787,999 bp with a 68.90% GC content and 7,307 predicted protein-coding genes.

On the recovery of missing low and high frequency information from bandlimited reflectivity data

NASA Astrophysics Data System (ADS)

Sacchi, M. D.; Ulrych, T. J.

2007-12-01

During the last two decades, an important effort in the seismic exploration community has been made to retrieve broad-band seismic data by means of deconvolution and inversion. In general, the problem can be stated as a spectral reconstruction problem. In other words, given limited spectral information about the earth's reflectivity sequence, one attempts to create a broadband estimate of the Fourier spectra of the unknown reflectivity. Techniques based on the principle of parsimony can be effectively used to retrieve a sparse spike sequence and, consequently, a broad band signal. Alternatively, continuation methods, e.g., autoregressive modeling, can be used to extrapolate the recorded bandwidth of the seismic signal. The goal of this paper is to examine under what conditions the recovery of low and high frequencies from band-limited and noisy signals is possible. At the heart of the methods we discuss, is the celebrated non-Gaussian assumption so important in many modern signal processing methods, such as ICA, for example. Spectral recovery from limited information tends to work when the reflectivity consist of a few well isolated events. Results degrade with the number of reflectors, decreasing SNR and decreasing bandwidth of the source wavelet. Constrains and information-based priors can be used to stabilize the recovery but, as in all inverse problems, the solution is nonunique and effort is required to understand the level of recovery that is achievable, always keeping the physics of the problem in mind. We provide in this paper, a survey of methods to recover broad-band reflectivity sequences and examine the role that these techniques can play in the processing and inversion as applied to exploration and global seismology.

Optoelectronic system of online measurements of unburned carbon in coal fly ash

NASA Astrophysics Data System (ADS)

Golas, Janusz; Jankowski, Henryk; Niewczas, Bogdan; Piechna, Janusz; Skiba, Antoni; Szkutnik, Wojciech; Szkutnik, Zdzislaw P.; Wartak, Ryszarda; Worek, Cezary

2001-08-01

Carbon-in-ash level is an important consideration for combustion efficiency as well as ash marketing. The optoelectronic analyzing system for on-line determination and monitoring of the u burned carbon content of ash samples is presented. The apparatus operates on the principle that carbon content is proportional to the reflectance of IR light. Ash samples are collected iso kinetically from the flue gas duct and placed in a sample tube with a flat glass bottom. The same is then exposed to a light. The reflectance intensity is used by the system's computer to determine residual carbon content from correlation curves. The sample is then air purged back to the duct or to the attached sample canister to enable laboratory check analysis. The total cycle time takes between 5 and 10 minutes. Real time result of carbon content with accuracy 0.3-0.7 percent are reported and can be used for boiler controlling.

Draft Genome Sequence of Thermus sp. Strain RL, Isolated from a Hot Water Spring Located atop the Himalayan Ranges at Manikaran, India

PubMed Central

Dwivedi, Vatsala; Sangwan, Naseer; Nigam, Aeshna; Garg, Nidhi; Niharika, Neha; Khurana, Paramjit; Khurana, Jitendra P.

2012-01-01

Thermus sp. strain RL was isolated from a hot water spring (90°C to 98°C) at Manikaran, Himachal Pradesh, India. Here we report the draft genome sequence (20,36,600 bp) of this strain. The draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average G+C content of 68.77%. PMID:22689228

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

PubMed Central

Li, Yushuang; Yang, Jiasheng; Zhang, Yi

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector. PMID:27918587

HIV Sequence Compendium 2015

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian

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 ismore » 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.« less

Does the Genetic Code Have A Eukaryotic Origin?

PubMed Central

Zhang, Zhang; Yu, Jun

2013-01-01

In the RNA world, RNA is assumed to be the dominant macromolecule performing most, if not all, core “house-keeping” functions. The ribo-cell hypothesis suggests that the genetic code and the translation machinery may both be born of the RNA world, and the introduction of DNA to ribo-cells may take over the informational role of RNA gradually, such as a mature set of genetic code and mechanism enabling stable inheritance of sequence and its variation. In this context, we modeled the genetic code in two content variables—GC and purine contents—of protein-coding sequences and measured the purine content sensitivities for each codon when the sensitivity (% usage) is plotted as a function of GC content variation. The analysis leads to a new pattern—the symmetric pattern—where the sensitivity of purine content variation shows diagonally symmetry in the codon table more significantly in the two GC content invariable quarters in addition to the two existing patterns where the table is divided into either four GC content sensitivity quarters or two amino acid diversity halves. The most insensitive codon sets are GUN (valine) and CAN (CAR for asparagine and CAY for aspartic acid) and the most biased amino acid is valine (always over-estimated) followed by alanine (always under-estimated). The unique position of valine and its codons suggests its key roles in the final recruitment of the complete codon set of the canonical table. The distinct choice may only be attributable to sequence signatures or signals of splice sites for spliceosomal introns shared by all extant eukaryotes. PMID:23402863

Chemical characteristics and origin of H chondrite regolith breccias

NASA Technical Reports Server (NTRS)

Lipschutz, M. E.; Biswas, S.; Mcsween, H. Y., Jr.

1983-01-01

Petrologic data and contents of Ag, Bi, Cd, Co, Cs, Ga, In, Rb, Se, Te, Tl and Zn-trace elements spanning the volatility/mobility range-in light and dark portions of H chondrite regolith breccias and L chondrite fragmental breccias are reported. The chemical/petrologic characteristics of H chondrite regolith breccias differ from those of nonbrecciated chondrites or fragmental breccias. Petrologic characteristics and at least some trace element contents of H chondrite regolith breccias reflect primary processes; contents of the most volatile/mobile elements may reflect either primary or secondary processing, possibly within layered H chondrite parent object(s). Chemical/petrologic differences existed in different regions of the parent(s). Regoligh formation and gardening and meteoroid compaction were not so severe as to alter compositions markedly.

Leaf Relative Water Content Estimated from Leaf Reflectance and Transmittance

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

2016-01-01

Remotely sensing the water status of plants and the water content of canopies remain long term goals of remote sensing research. In the research we report here, we used optical polarization techniques to monitor the light reflected from the leaf interior, R, as well as the leaf transmittance, T, as the relative water content (RWC) of corn (Zea mays) leaves decreased. Our results show that R and T both change nonlinearly. The result show that the nonlinearities cancel in the ratio R/T, which appears linearly related to RWC for RWC less than 90%. The results suggest that potentially leaf water status and perhaps even canopy water status could be monitored starting from leaf and canopy optical measurements.

Criteria for the recognition and correlation of sandstone units in the Precambrian and Paleozoic-Mesozoic clastic sequence in the near east

NASA Astrophysics Data System (ADS)

Weissbrod, T.; Perath, I.

A systematic study of the Precambrian and Paleozoic-Mesozoic clastic sequences (Nubian Sandstone) in Israel and Sinai, and a comparative analysis of its stratigraphy in neighbouring countries, has shown that besides the conventional criteria of subdivision (lithology, field appearance, photogeological features, fossil content), additional criteria can be applied, which singly or in mutual conjuction enable the recognition of widespread units and boundaries. These criteria show lateral constancy, and recurrence of a similar vertical sequence over great distances, and are therefore acceptable for the identification of synchronous, region-wide sedimentary units (and consequently, major unconformities). They also enable, once the units are established, to identify detached (not in situ) samples, samples from isolated or discontinous outcrops, borehole material or archive material. The following rock properties were tested and found to be usefuls in stratigraphic interpretation, throughout large distribution areas of the clastic sequence: Landscape, which is basically the response of a particular textural-chemic al aggregate to atmospheric weathering. Characteristic outcrop feature — styles of roundness or massivity, fissuring or fliatin, slope profile, bedding — express a basic uniformity of these platform-type clastics. Colors are often stratigraphically constant over hundreds of kilometers, through various climates and topographies, and express some intrinsic unity of the rock bodies. Grain size and sorting, when cross-plotted, enable to differentiate existing unit. The method requires the analysis of representative numbers of samples. Vertical trends of median grain size and sorting show reversals, typically across unconformities. Feldstar content diminishes from 15-50% in Precambrian-Paleozoic rocks to a mere 5% or less in Mesozoic sandstones — a distinctive regionwide time trend. Dominance of certain feldstar types characterizes Precambrian and Paleozoic units. Clay minerals, though subordinate, characterize certain units. Illite is usually the dominant clay mineral in the Precambrain-Paleozoic sediments, showing different degress of crystallization in different units. Kaolinite is the main, often the only clay mineral in Mesozoic units. Heavy minerals, whose species spectra reflect on parent rock and provenance terrain and whose differential response to degradation points to the sedimentary history of the deposit, show certain vertical regularities, such as the abrupt disappearance of species or whole assemblages at certain levels, indicating unconformities. Trace metals, which in places reach ore concentrations (e.g. copper), are often extensive, though of well-defined vertical distribution. They express adsorptive capacity of specific widespread lithologies, enabling the discrimination of units. Even though each of these criteria is not always by itself diagnostic, they may in conjuction with one or more other criteria amount to a petrographic fingerprint that enables fairly accurate identification of the age interval of the unit, and its relation both to the regional and the local stratigraphic sequence.

Abrupt climate warming in East Antarctica during the early Holocene

NASA Astrophysics Data System (ADS)

Cremer, Holger; Heiri, Oliver; Wagner, Bernd; Wagner-Cremer, Friederike

2007-08-01

We report a centennial-scale warming event between 8600 and 8400 cal BP from Amery Oasis, East Antarctica, that is documented by the geochemical record in a lacustrine sediment sequence. The organic carbon content, the C/S ratio, and the sedimentation rate in this core have distinctly elevated values around 8500 y ago reflecting relatively warm and ice-free conditions that led to well-ventilated conditions in the lake and considerable sedimentation of both autochthonous and allochthonous organic matter on the lake bottom. This abrupt warming event occurred concurrently with reported warm climatic conditions in the Southern Ocean while the climate in central East Antarctic remained cold. The comparison of the spatial and temporal variability of warm climatic periods documented in various terrestrial, marine, and glacial archives from East Antarctica elucidates the uniqueness of the centennial-scale warming event in the Amery Oasis. We also discuss a possible correlation of the Amery warming event with the abrupt climatic deterioration around 8200 cal BP on the Northern Hemisphere.

Learning and memory for sequences of pictures, words, and spatial locations: an exploration of serial position effects.

PubMed

Bonk, William J; Healy, Alice F

2010-01-01

A serial reproduction of order with distractors task was developed to make it possible to observe successive snapshots of the learning process at each serial position. The new task was used to explore the effect of several variables on serial memory performance: stimulus content (words, blanks, and pictures), presentation condition (spatial information vs. none), semantically categorized item clustering (grouped vs. ungrouped), and number of distractors relative to targets (none, equal, double). These encoding and retrieval variables, along with learning attempt number, affected both overall performance levels and the shape of the serial position function, although a large and extensive primacy advantage and a small 1-item recency advantage were found in each case. These results were explained well by a version of the scale-independent memory, perception, and learning model that accounted for improved performance by increasing the value of only a single parameter that reflects reduced interference from distant items.

Preventing distraction: Assessing stimulus-specific and general effects of the predictive cueing of deviant auditory events

PubMed Central

Horváth, János; Sussman, Elyse; Winkler, István; Schröger, Erich

2011-01-01

Rare irregular sounds (deviants) embedded into a regular sound sequence have large potential to draw attention to themselves (distraction). It has been previously shown that distraction, as manifested by behavioral response delay, and the P3a and reorienting negativity (RON) event-related potentials, could be reduced when the forthcoming deviant was signaled by visual cues preceding the sounds. In the present study, we investigated the type of information used in the prevention of distraction by manipulating the information content of the visual cues preceding the sounds. Cues could signal the specific variant of the forthcoming deviant, or they could just signal that the next tone was a deviant. We found that stimulus-specific cue information was used in reducing distraction. The results also suggest that early P3a and RON index processes related to the specific deviating stimulus feature, whereas late P3a reflects a general distraction-related process. PMID:21310210

The Suppression of Beta Oscillations in the Primate Supplementary Motor Complex Reflects a Volatile State During the Updating of Action Sequences.

PubMed

Hosaka, Ryosuke; Nakajima, Toshi; Aihara, Kazuyuki; Yamaguchi, Yoko; Mushiake, Hajime

2016-08-01

The medial motor areas play crucial but flexible roles in the temporal organizations of multiple movements. The beta oscillation of local field potentials is the predominant oscillatory activity in the motor areas, but the manner in which increases and decreases in beta power contribute to updating of multiple action plans is not yet fully understood. In the present study, beta and high-gamma activities in the supplementary motor area (SMA) and pre-SMA of monkeys were analyzed during performance of a bimanual motor sequence task that required updating and maintenance of the memory of action sequences. Beta power was attenuated during early delay periods of updating trials but was increased during maintenance trials, while there was a reciprocal increase in high-gamma power during updating trials. Moreover, transient attenuation of beta power during maintenance trials resulted in the erroneous selection of an action sequence. Therefore, it was concluded that the suppression of beta power during the early delay period reflects volatility of neural representation of the action sequence. This neural representation would be properly updated to the appropriate instructed action sequence via increases in high-gamma power in updating trials whereas it would be erroneously updated without the appropriate updating signal in maintenance trials. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Tectonic sequence stratigraphy, Early Permian Dry Mountain trough, east-central Nevada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Snyder, W.S.; Gallegos, D.M.; Spinosa, C.

1991-06-01

The Early Permian Dry Mountain trough (DMT) of east-central Nevada is one of several tectonic basins and associated uplifts that developed along the continenetal margin during the latest Pennsylvanian-Early Permian Dry Mountain tectonic phase. The sequence stratigraphy reflects a combination of eustatic sea level changes and tectonic uplift or subsidence. Fewer than one to only a few million years separate the development of sequence boundaries within the DMT. At this scale, differences among published eustasy curves preclude their use as definitive tools to identify eustatically controlled sequence boundaries. Nevertheless, available data indicate several pulses of tectonism affected sedimentation within themore » DMT. The authors are attempting to develop criteria to distinguish tectonic from eustatic sequence boundaries. Detailed biostratigraphic data are required to provide an independent check on the correlation of sequence boundaries between measured sections. For example, the same age boundary may reflect tectonic uplift in one part of the basin and subsidence in another. The uplift may or may not result in subaerial exposure and erosion. For those boundaries that do not result from subaerial exposure, lithofacies and biofacies analyses are required to infer relative uplift (water depth decrease) or subsidence (water depth increase). There are inherent resolution limitations in both the paleontologic and sedimentologic methodologies. These limitations, combined with those of eustasy curves, dictate the preliminary nature of their results.« less

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure.

PubMed

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: [Formula: see text] (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

PubMed Central

Li, Jiabao; Rui, Junpeng; Yao, Minjie; Zhang, Shiheng; Yan, Xuefeng; Wang, Yuanpeng; Yan, Zhiying; Li, Xiangzhen

2015-01-01

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters. PMID:26648921

Retrieval of optical properties of skin from measurement and modeling the diffuse reflectance

NASA Astrophysics Data System (ADS)

Douven, Lucien F. A.; Lucassen, Gerald W.

2000-06-01

We present results on the retrieval of skin optical properties obtained by fitting of measurements of the diffuse reflectance of human skin. Reflectance spectra are simulated using an analytical model based on the diffusion approximation. This model is implemented in a simplex fit routine. The skin optical model used consists of five layers representing epidermis, capillary blood plexus, dermis, deep blood plexus and hypodermis. The optical properties of each layer are assumed homogeneously distributed. The main optical absorbers included are melanin in epidermis and blood. The experimental setup consists of a HP photospectrometer equipped with a remote fiber head. Total reflectance spectra were measured in the 400 - 820 nm wavelength range on the volar underarm of 19 volunteers under various conditions influencing the blood content and oxygenation degree. Changes in the reflectance spectra were observed. Using the fit routine changes in blood content in the capillary blood plexus and in the deep blood plexus could be quantified. These showed different influences on the total reflectance. The method can be helpful to quantitatively assess changes in skin color appearance such as occurs in the treatment of port wine stains, blanching, skin irritation and tanning.

Cenozoic global sea level, sequences, and the New Jersey transect: Results from coastal plain and continental slope drilling

USGS Publications Warehouse

Miller, K.G.; Mountain, Gregory S.; Browning, J.V.; Kominz, M.; Sugarman, P.J.; Christie-Blick, N.; Katz, M.E.; Wright, J.D.

1998-01-01

The New Jersey Sea Level Transect was designed to evaluate the relationships among global sea level (eustatic) change, unconformity-bounded sequences, and variations in subsidence, sediment supply, and climate on a passive continental margin. By sampling and dating Cenozoic strata from coastal plain and continental slope locations, we show that sequence boundaries correlate (within ??0.5 myr) regionally (onshore-offshore) and interregionally (New Jersey-Alabama-Bahamas), implicating a global cause. Sequence boundaries correlate with ??18O increases for at least the past 42 myr, consistent with an ice volume (glacioeustatic) control, although a causal relationship is not required because of uncertainties in ages and correlations. Evidence for a causal connection is provided by preliminary Miocene data from slope Site 904 that directly link ??18O increases with sequence boundaries. We conclude that variation in the size of ice sheets has been a primary control on the formation of sequence boundaries since ~42 Ma. We speculate that prior to this, the growth and decay of small ice sheets caused small-amplitude sea level changes (<20 m) in this supposedly ice-free world because Eocene sequence boundaries also appear to correlate with minor ??18O increases. Subsidence estimates (backstripping) indicate amplitudes of short-term (million-year scale) lowerings that are consistent with estimates derived from ??18O studies (25-50 m in the Oligocene-middle Miocene and 10-20 m in the Eocene) and a long-term lowering of 150-200 m over the past 65 myr, consistent with estimates derived from volume changes on mid-ocean ridges. Although our results are consistent with the general number and timing of Paleocene to middle Miocene sequences published by workers at Exxon Production Research Company, our estimates of sea level amplitudes are substantially lower than theirs. Lithofacies patterns within sequences follow repetitive, predictable patterns: (1) coastal plain sequences consist of basal transgressive sands overlain by regressive highstand silts and quartz sands; and (2) although slope lithofacies variations are subdued, reworked sediments constitute lowstand deposits, causing the strongest, most extensive seismic reflections. Despite a primary eustatic control on sequence boundaries, New Jersey sequences were also influenced by changes in tectonics, sediment supply, and climate. During the early to middle Eocene, low siliciclastic and high pelagic input associated with warm climates resulted in widespread carbonate deposition and thin sequences. Late middle Eocene and earliest Oligocene cooling events curtailed carbonate deposition in the coastal plain and slope, respectively, resulting in a switch to siliciclastic sedimentation. In onshore areas, Oligocene sequences are thin owing to low siliciclastic and pelagic input, and their distribution is patchy, reflecting migration or progradation of depocenters; in contrast, Miocene onshore sequences are thicker, reflecting increased sediment supply, and they are more complete downdip owing to simple tectonics. We conclude that the New Jersey margin provides a natural laboratory for unraveling complex interactions of eustasy, tectonics, changes in sediment supply, and climate change.

Factors confounding the assessment of reflection: a critical review

PubMed Central

2011-01-01

Background Reflection on experience is an increasingly critical part of professional development and lifelong learning. There is, however, continuing uncertainty about how best to put principle into practice, particularly as regards assessment. This article explores those uncertainties in order to find practical ways of assessing reflection. Discussion We critically review four problems: 1. Inconsistent definitions of reflection; 2. Lack of standards to determine (in)adequate reflection; 3. Factors that complicate assessment; 4. Internal and external contextual factors affecting the assessment of reflection. Summary To address the problem of inconsistency, we identified processes that were common to a number of widely quoted theories and synthesised a model, which yielded six indicators that could be used in assessment instruments. We arrived at the conclusion that, until further progress has been made in defining standards, assessment must depend on developing and communicating local consensus between stakeholders (students, practitioners, teachers, supervisors, curriculum developers) about what is expected in exercises and formal tests. Major factors that complicate assessment are the subjective nature of reflection's content and the dependency on descriptions by persons being assessed about their reflection process, without any objective means of verification. To counter these validity threats, we suggest that assessment should focus on generic process skills rather than the subjective content of reflection and where possible to consider objective information about the triggering situation to verify described reflections. Finally, internal and external contextual factors such as motivation, instruction, character of assessment (formative or summative) and the ability of individual learning environments to stimulate reflection should be considered. PMID:22204704

Mineralogical and geochemical evolution of micas from miarolitic pegmatites of the anorogenic pikes peak batholith, Colorado

USGS Publications Warehouse

Foord, E.E.; Cerny, P.; Jackson, L.L.; Sherman, David M.; Eby, R.K.

1995-01-01

A suite of 29 micas from miarolitic pegmatites associated with granitic units of the anorogenic Pikes Peak batholith (1.08-1.02 Ga), Colorado range in composition, and follow in paragenetic sequence, from 1M siderophyllite (N = 1), and 3T or 2M1 lithian biotite (N = 5) to 1M zinnwaldite (N = 20) and 1M ferroan lepidolite (N = 1). Locally, 1M (?) phlogopite (N = 1) and ferroan 2M1 muscovite (N = 1) are also present. Pervasive, late-stage hydrothermal alteration along with possible supergene weathering of many of these micas produced vermiculite. Additionally, some vugs and cavities were filled with chlorite and/or smectite. Early crystallized micas form tapered columnar crystals in graphic pegmatite, growing toward, and adjacent to the miarolitic cavity zone which contains the later crystallized micas. Principal associated minerals are quartz, microcline perthite (mostly amazonite), and albite, with local topaz or fluorite, and rarely tourmaline (schorl-elbaite). Progressively younger micas of the main crystallization sequence display increasing Si, Li, F, and Al/Ga, and decreasing total Fe, Mg, and octahedral occupancy. The zinc content of all micas is considerably elevated, whereas Mn, Rb, Cs, and Sc are moderate and T1 is very low. Early siderophyllite and lithian biotite show a narrow range of FeO/Fe2O3 (5.6-8.0), whereas later zinnwaldite is much more variable (2.4-40.3). Annite of the host granite and early graphic pegmatite is compositionally homogeneous, but most mica crystals from cavities show remarkable compositional and abrupt, sharp and distinct color zoning. Most cavity-grown zinnwaldite crystals show a decrease, from core to rim, in total Fe and Mg, whereas Si, Li and F increase and Mn, Rb, Cs and Na are essentially constant. A few to more than 100 color zones have been identified in some mica crystals. The zones are well correlated with the Ti content (<0.2 wt. % TiO2 colorless, 0.4-0.6 wt.% TiO2 red-brown). The total Fe content may or may not correlate with color zoning, whereas Zn variations (up to 1.1 wt. %) are entirely independent. The dark color zones probably reflect Fe-Ti charge transfer. The mica composition sequence described here is typical of the extreme fractionation observed in pegmatites of the NYF family, associated with anorogenec granites. Elevated Fe, Zn, and enhanced Sc contents are characteristic of this family. Strong enrichment in Li, Rb, and F is present, particularly in the micas of the miarolitic cavities. Sharp color zonation and compositional variation in cavity-grown zinnwaldite and ferroan lepidolite crystals suggest rapid changes in the intensive parameters, particularly the f(O2), of the parent fluid during the final stages of pegmatite consolidation ?? 1995 Springer-Verlag.

Microwave reflection measurements of the dielectric properties of concrete : final report.

DOT National Transportation Integrated Search

1983-01-01

The use of microwave reflection measurements to continuously and nondestructively monitor the hydration of concrete is described. The method relies upon the influence of the free-water content on the dielectric properties of the concrete. Use of the ...

Comparative Sequence Analysis of Plasmids from Lactobacillus delbrueckii and Construction of a Shuttle Cloning Vector▿

PubMed Central

Lee, Ju-Hoon; Halgerson, Jamie S.; Kim, Jeong-Hwan; O'Sullivan, Daniel J.

2007-01-01

While plasmids are very commonly associated with the majority of the lactic acid bacteria, they are only very rarely associated with Lactobacillus delbrueckii, with only four characterized to date. In this study, the complete sequence of a native plasmid, pDOJ1, from a strain of Lactobacillus delbrueckii subsp. bulgaricus was determined. It consisted of a circular DNA molecule of 6,220 bp with a G+C content of 44.6% and a characteristic ori and encoded six open reading frames (ORFs), of which functions could be predicted for three—a mobilization (Mob) protein, a transposase, and a fused primase-helicase replication protein. Comparative analysis of pDOJ1 and the other available L. delbrueckii plasmids (pLBB1, pJBL2, pN42, and pLL1212) revealed a very similar organization and amino acid identities between 85 and 98% for the putative proteins of all six predicted ORFs from pDOJ1, reflecting a common origin for L. delbrueckii plasmids. Analysis of the fused primase-helicase replication gene found a similar fused organization only in the theta replicating group B plasmids from Streptococcus thermophilus. This observation and the ability of the replicon to function in S. thermophilus support the idea that the origin of plasmids in L. delbrueckii was likely from S. thermophilus. This may reflect the close association of these two species in dairy fermentations, particularly yogurt production. As no vector based on plasmid replicons from L. delbrueckii has previously been constructed, an Escherichia coli-L. delbrueckii shuttle cloning vector, pDOJ4, was constructed from pDOJ1, the p15A ori, the chloramphenicol resistance gene of pCI372, and the lacZ polylinker from pUC18. This cloning vector was successfully introduced into E. coli, L. delbrueckii subsp. bulgaricus, S. thermophilus, and Lactococcus lactis. This shuttle cloning vector provides a new tool for molecular analysis of Lactobacillus delbrueckii and other lactic acid bacteria. PMID:17526779

Measuring third year undergraduate nursing students' reflective thinking skills and critical reflection self-efficacy following high fidelity simulation: A pilot study.

PubMed

Tutticci, Naomi; Lewis, Peter A; Coyer, Fiona

2016-05-01

Critical reflection underpins critical thinking, a highly desirable generic nursing graduate capability. To improve the likelihood of critical thinking transferring to clinical practice, reflective thinking needs to be measured within the learning space of simulation. This study was divided into two phases to address the reliability and validity measures of previously untested surveys. Phase One data was collected from individuals (n = 6) using a 'think aloud' approach and an expert panel to review content validity, and verbatim comment analysis was undertaken. The Reflective Thinking Instrument and Critical Reflection Self-Efficacy Visual Analogue Scale items were contextualised to simulation. The expert review confirmed these instruments exhibited content validity. Phase Two data was collected through an online survey (n = 58). Cronbach's alpha measured internal consistency and was demonstrated by all subscales and the Instrument as a whole (.849). There was a small to medium positive correlation between critical reflection self-efficacy and general self-efficacy (r = .324, n = 56, p = .048). Participant responses were positive regarding the simulation experience. The research findings demonstrated that the Reflective Thinking and Simulation Satisfaction survey is reliable. Further development of this survey to establish validity is recommended to make it viable. Copyright © 2016 Elsevier Ltd. All rights reserved.

Assessing White Matter Microstructure in Brain Regions with Different Myelin Architecture Using MRI.

PubMed

Groeschel, Samuel; Hagberg, Gisela E; Schultz, Thomas; Balla, Dávid Z; Klose, Uwe; Hauser, Till-Karsten; Nägele, Thomas; Bieri, Oliver; Prasloski, Thomas; MacKay, Alex L; Krägeloh-Mann, Ingeborg; Scheffler, Klaus

2016-01-01

We investigate how known differences in myelin architecture between regions along the cortico-spinal tract and frontal white matter (WM) in 19 healthy adolescents are reflected in several quantitative MRI parameters that have been proposed to non-invasively probe WM microstructure. In a clinically feasible scan time, both conventional imaging sequences as well as microstructural MRI parameters were assessed in order to quantitatively characterise WM regions that are known to differ in the thickness of their myelin sheaths, and in the presence of crossing or parallel fibre organisation. We found that diffusion imaging, MR spectroscopy (MRS), myelin water fraction (MWF), Magnetization Transfer Imaging, and Quantitative Susceptibility Mapping were myelin-sensitive in different ways, giving complementary information for characterising WM microstructure with different underlying fibre architecture. From the diffusion parameters, neurite density (NODDI) was found to be more sensitive than fractional anisotropy (FA), underlining the limitation of FA in WM crossing fibre regions. In terms of sensitivity to different myelin content, we found that MWF, the mean diffusivity and chemical-shift imaging based MRS yielded the best discrimination between areas. Multimodal assessment of WM microstructure was possible within clinically feasible scan times using a broad combination of quantitative microstructural MRI sequences. By assessing new microstructural WM parameters we were able to provide normative data and discuss their interpretation in regions with different myelin architecture, as well as their possible application as biomarker for WM disorders.

The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 °C

PubMed Central

Brügger, Kim; Chen, Lanming; Stark, Markus; Zibat, Arne; Redder, Peter; Ruepp, Andreas; Awayez, Mariana; She, Qunxin; Garrett, Roger A.; Klenk, Hans-Peter

2007-01-01

Hyperthermus butylicus, a hyperthermophilic neutrophile and anaerobe, is a member of the archaeal kingdom Crenarchaeota. Its genome consists of a single circular chromosome of 1,667,163 bp with a 53.7% G+C content. A total of 1672 genes were annotated, of which 1602 are protein-coding, and up to a third are specific to H. butylicus. In contrast to some other crenarchaeal genomes, a high level of GUG and UUG start codons are predicted. Two cdc6 genes are present, but neither could be linked unambiguously to an origin of replication. Many of the predicted metabolic gene products are associated with the fermentation of peptide mixtures including several peptidases with diverse specificities, and there are many encoded transporters. Most of the sulfur-reducing enzymes, hydrogenases and electron-transfer proteins were identified which are associated with energy production by reducing sulfur to H2S. Two large clusters of regularly interspaced repeats (CRISPRs) are present, one of which is associated with a crenarchaeal-type cas gene superoperon; none of the spacer sequences yielded good sequence matches with known archaeal chromosomal elements. The genome carries no detectable transposable or integrated elements, no inteins, and introns are exclusive to tRNA genes. This suggests that the genome structure is quite stable, possibly reflecting a constant, and relatively uncompetitive, natural environment. PMID:17350933

Sensitivity of Cross-State Assessment Item Difficulty to Differences in State Curricular Content Standards

ERIC Educational Resources Information Center

Traynor, Anne

2017-01-01

It has long been argued that U.S. states' differential performance on nationwide assessments may reflect differences in students' opportunity to learn the tested content that is primarily due to variation in curricular content standards, rather than in instructional quality or educational investment. To quantify the effect of differences in…

Prospective Elementary Teachers' Analysis of Children's Science Talk in an Undergraduate Physics Course

ERIC Educational Resources Information Center

Harlow, Danielle B.; Swanson, Lauren H.; Otero, Valerie K.

2014-01-01

We investigated how prospective teachers used physics content knowledge when analyzing the talk of elementary children during special activities in an undergraduate physics content course designed for prospective teachers. We found that prospective teachers used content knowledge to reflect on their own learning and to identify students'…

Content Validity of Standardized Achievement Tests and Test Curriculum Overlap.

ERIC Educational Resources Information Center

Green, Donald Ross

Discussions of "test curriculum overlap" that focus on the term "mismatch" tend to be based on several untenable premises. This paper addresses the issue of the degree to which standardized tests should reflect the specific content of a given school curriculum with regard to three points: (1) The idea of matching the content of…

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

PubMed Central

Kurotani, Atsushi; Sakurai, Tetsuya

2015-01-01

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups. PMID:26307970

In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

PubMed

Kurotani, Atsushi; Sakurai, Tetsuya

2015-08-20

Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bragaglia, A.; Carretta, E.; Gratton, R. G.

We present the first chemical composition study of two unevolved stars in the globular cluster NGC 2808, obtained with the X-shooter spectrograph at VLT. NGC 2808 shows three discrete, well-separated main sequences. The most accepted explanation for this phenomenon is that their stars have different helium contents. We observed one star on the bluest main sequence (bMS, claimed to have a high helium content, Y {approx}0.4) and the other on the reddest main sequence (rMS, consistent with a canonical helium content, Y = 0.245). We analyzed features of NH, CH, Na, Mg, Al, and Fe. While Fe, Ca, and othermore » elements have the same abundances in the two stars, the bMS star shows a huge enhancement of N, a depletion of C, an enhancement of Na and Al, and a small depletion of Mg with respect to the rMS star. This is exactly what is expected if stars on the bMS formed from the ejecta produced by an earlier stellar generation in the complete CNO and MgAl cycles whose main product is helium. The elemental abundance pattern differences in these two stars are consistent with the differences in the helium content suggested by the color-magnitude diagram positions of the stars.« less

Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B-24224

PubMed Central

Ali, Ilzat; Jones, Acacia Eleri; Mohamed, Aleem

2018-01-01

ABSTRACT Bacteriophages Ilzat and Eleri are newly isolated Siphoviridae infecting Microbacterium foliorum NRRL B-24224. The phage genomes are similar in length, G+C content, and architecture and share 62.9% nucleotide sequence identity. PMID:29650566

A model for mentoring newly-appointed nurse educators in nursing education institutions in South Africa.

PubMed

Seekoe, Eunice

2014-04-24

South Africa transformed higher education through the enactment of the Higher Education Act (No. 101 of 1997). The researcher identified the need to develop a model for the mentoring of newly-appointed nurse educators in nursing education institutions in South Africa.  To develop and describe the model for mentoring newly-appointed nurse educators in nursing education institutions in South Africa.  A qualitative and theory-generating design was used (following empirical findings regarding needs analysis) in order to develop the model. The conceptualisation of the framework focused on the context, content, process and the theoretical domains that influenced the model. Ideas from different theories were borrowed from and integrated with the literature and deductive and inductive strategies were applied.  The structure of the model is multidimensional and complex in nature (macro, mesoand micro) based on the philosophy of reflective practice, competency-based practice andcritical learning theories. The assumptions are in relation to stakeholders, context, mentoring, outcome, process and dynamic. The stakeholders are the mentor and mentee within an interactive participatory relationship. The mentoring takes place within the process with a sequence of activities such as relationship building, development, engagement, reflective process and assessment. Capacity building and empowerment are outcomes of mentoring driven by motivation.  The implication for nurse managers is that the model can be used to develop mentoring programmes for newly-appointed nurse educators.

Microwave limb sounder. [measuring trace gases in the upper atmosphere

NASA Technical Reports Server (NTRS)

Gustincic, J. J. (Inventor)

1981-01-01

Trace gases in the upper atmosphere can be measured by comparing spectral noise content of limb soundings with the spectral noise content of cold space. An offset Cassegrain antenna system and tiltable input mirror alternately look out at the limb and up at cold space at an elevation angle of about 22. The mirror can also be tilted to look at a black body calibration target. Reflection from the mirror is directed into a radiometer whose head functions as a diplexer to combine the input radiation and a local ocillator (klystron) beam. The radiometer head is comprised of a Fabry-Perot resonator consisting of two Fabry-Perot cavities spaced a number of half wavelengths apart. Incoming radiation received on one side is reflected and rotated 90 deg in polarization by the resonator so that it will be reflected by an input grid into a mixer, while the klystron beam received on the other side is also reflected and rotated 90 deg, but not without passing some energy to be reflected by the input grid into the mixer.

Complete cDNA sequence and amino acid analysis of a bovine ribonuclease K6 gene.

PubMed

Pietrowski, D; Förster, M

2000-01-01

The complete cDNA sequence of a ribonuclease k6 gene of Bos Taurus has been determined. It codes for a protein with 154 amino acids and contains the invariant cysteine, histidine and lysine residues as well as the characteristic motifs specific to ribonuclease active sites. The deduced protein sequence is 27 residues longer than other known ribonucleases k6 and shows amino acids exchanges which could reflect a strain specificity or polymorphism within the bovine genome. Based on sequence similarity we have termed the identified gene bovine ribonuclease k6 b (brk6b).

Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments.

PubMed

Jang, Hyein; Addy, Nicole; Ewing, Laura; Jean-Gilles Beaubrun, Junia; Lee, YouYoung; Woo, JungHa; Negrete, Flavia; Finkelstein, Samantha; Tall, Ben D; Lehner, Angelika; Eshwar, Athmanya; Gopinath, Gopal R

2018-04-12

Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from foods of plant origin and dried-food manufacturing facilities. Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb and 3,977 to 4,256 gene-coding sequences with G+C contents of ∼57.0%.

Sequencing, De Novo Assembly, and Annotation of the Complete Genome of a New Thraustochytrid Species, Strain CCAP_4062/3

PubMed Central

Seddiki, Khawla; Godart, François; Aiese Cigliano, Riccardo; Sanseverino, Walter; Barakat, Mohamed; Ortet, Philippe; Rébeillé, Fabrice; Maréchal, Eric

2018-01-01

ABSTRACT Thraustochytrids are ecologically and biotechnologically relevant marine species. We report here the de novo assembly and annotation of the whole-genome sequence of a new thraustochytrid strain, CCAP_4062/3. The genome size was estimated at 38.7 Mb with 11,853 predicted coding sequences, and the GC content was scored at 57%. PMID:29545303

Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite

PubMed Central

Kumar, Roshan; Dwivedi, Vatsala; Negi, Vivek; Khurana, J. P.

2013-01-01

Sphingobium lactosutens DS20T has been isolated from the hexachlorocyclohexane (HCH) dumpsite in Lucknow, India, but does not degrade any of the HCH isomers. Here, we present the ~5.36-Mb draft genome sequence of strain DS20T, which consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%. PMID:24051323

Draft Genome Sequence of Lactobacillus reuteri Strain CRL 1098, an Interesting Candidate for Functional Food Development.

PubMed

Torres, Andrea C; Suárez, Nadia E; Font, Graciela; Saavedra, Lucila; Taranto, María Pía

2016-08-25

We report here the draft genome sequence of Lactobacillus reuteri strain CRL 1098. This strain represents an interesting candidate for functional food development because of its proven probiotic properties. The draft genome sequence is composed of 1,969,471 bp assembled into 45 contigs and an average G+C content of 38.8%. Copyright © 2016 Torres et al.

Predoctoral Curriculum Guidelines for Biomaterials.

ERIC Educational Resources Information Center

Journal of Dental Education, 1986

1986-01-01

The American Association of Dental Schools' predoctoral guidelines for biomaterials curricula includes notes on interrelationships between this and other fields, a curriculum overview, primary educational goals, prerequisites, a core content outline, specific behavioral objectives for each content area, and information on sequencing, faculty and…

How Can Magnetic Forces Do Work? Investigating the Problem with Students

ERIC Educational Resources Information Center

Onorato, Pasquale; De Ambrosis, Anna

2013-01-01

We present a sequence of activities aimed at promoting both learning about magnetic forces and students' reflection about the conceptual bridge between magnetic forces on a moving charge and on a current-carrying wire in a magnetic field. The activity sequence, designed for students in high school or on introductory physics courses, has been…

Exploring the Presence of microDNAs in Prostate Cancer Cell Lines, Tissue, and Sera of Prostate Cancer Patients and its Possible Application as Biomarker

DTIC Science & Technology

2015-08-01

Sequence tags were mapped on the human reference genome using the Novoalign software. Only those tags... the linear islands to create a novel junctional sequence that does not exist in the genome . Thus the PE- sequence of a fragment that breaks at or...identified in cancer cell lines. (b) Median percent GC content of microDNAs and the genomic sequences up- or downstream of the source loci are

Method and apparatus for measuring butterfat and protein content using microwave absorption techniques

DOEpatents

Fryer, Michael O.; Hills, Andrea J.; Morrison, John L.

2000-01-01

A self calibrating method and apparatus for measuring butterfat and protein content based on measuring the microwave absorption of a sample of milk at several microwave frequencies. A microwave energy source injects microwave energy into the resonant cavity for absorption and reflection by the sample undergoing evaluation. A sample tube is centrally located in the resonant cavity passing therethrough and exposing the sample to the microwave energy. A portion of the energy is absorbed by the sample while another portion of the microwave energy is reflected back to an evaluation device such as a network analyzer. The frequency at which the reflected radiation is at a minimum within the cavity is combined with the scatter coefficient S.sub.11 as well as a phase change to calculate the butterfat content in the sample. The protein located within the sample may also be calculated in a likewise manner using the frequency, S.sub.11 and phase variables. A differential technique using a second resonant cavity containing a reference standard as a sample will normalize the measurements from the unknown sample and thus be self-calibrating. A shuttered mechanism will switch the microwave excitation between the unknown and the reference cavities. An integrated apparatus for measuring the butterfat content in milk using microwave absorption techniques is also presented.

Reflective Course Design: An Interplay between Pedagogy and Technology in a Language Teacher Education Course

ERIC Educational Resources Information Center

Firdyiwek, Yitna; Scida, Emily E.

2014-01-01

This study reports on a sequence of iterative redesigns of a graduate-level foreign language teacher education course. The study describes the interplay between technology and pedagogy that resulted in important curricular changes, from a focus on individual to social and then holistic reflection. Using a team-based design model, instructional…

Enhanced Passive and Active Processing of Syllables in Musician Children

ERIC Educational Resources Information Center

Chobert, Julie; Marie, Celine; Francois, Clement; Schon, Daniele; Besson, Mireille

2011-01-01

The aim of this study was to examine the influence of musical expertise in 9-year-old children on passive (as reflected by MMN) and active (as reflected by discrimination accuracy) processing of speech sounds. Musician and nonmusician children were presented with a sequence of syllables that included standards and deviants in vowel frequency,…

The Thermal Infrared Sensor on the Landsat Data Continutiy Mission

USDA-ARS?s Scientific Manuscript database

The REGularized canopy reFLECtance (REGFLEC) modeling tool integrates leaf optics, canopy reflectance, and atmospheric radiative transfer model components, facilitating accurate retrieval of leaf area index (LAI) and leaf chlorophyll content (Cab) directly from at-sensor radiances in green, red and ...

Plant Chlorophyll Content Imager with Reference Detection Signals

NASA Technical Reports Server (NTRS)

Spiering, Bruce A. (Inventor); Carter, Gregory A. (Inventor)

2000-01-01

A portable plant chlorophyll imaging system is described which collects light reflected from a target plant and separates the collected light into two different wavelength bands. These wavelength bands, or channels, are described as having center wavelengths of 700 nm and 840 nm. The light collected in these two channels is processed using synchronized video cameras. A controller provided in the system compares the level of light of video images reflected from a target plant with a reference level of light from a source illuminating the plant. The percent of reflection in the two separate wavelength bands from a target plant are compared to provide a ratio video image which indicates a relative level of plant chlorophyll content and physiological stress. Multiple display modes are described for viewing the video images.

Minimal Absent Words in Four Human Genome Assemblies

PubMed Central

Garcia, Sara P.; Pinho, Armando J.

2011-01-01

Minimal absent words have been computed in genomes of organisms from all domains of life. Here, we aim to contribute to the catalogue of human genomic variation by investigating the variation in number and content of minimal absent words within a species, using four human genome assemblies. We compare the reference human genome GRCh37 assembly, the HuRef assembly of the genome of Craig Venter, the NA12878 assembly from cell line GM12878, and the YH assembly of the genome of a Han Chinese individual. We find the variation in number and content of minimal absent words between assemblies more significant for large and very large minimal absent words, where the biases of sequencing and assembly methodologies become more pronounced. Moreover, we find generally greater similarity between the human genome assemblies sequenced with capillary-based technologies (GRCh37 and HuRef) than between the human genome assemblies sequenced with massively parallel technologies (NA12878 and YH). Finally, as expected, we find the overall variation in number and content of minimal absent words within a species to be generally smaller than the variation between species. PMID:22220210

Two Low Coverage Bird Genomes and a Comparison of Reference-Guided versus De Novo Genome Assemblies

PubMed Central

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthew K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies. PMID:25192061

Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus.

PubMed

Ouwerkerk, D; Klieve, A V; Forster, R J; Templeton, J M; Maguire, A J

2005-01-01

To determine the culturable biodiversity of anaerobic bacteria isolated from the forestomach contents of an eastern grey kangaroo, Macropus giganteus, using phenotypic characterization and 16S rDNA sequence analysis. Bacteria from forestomach contents of an eastern grey kangaroo were isolated using anaerobic media containing milled curly Mitchell grass (Astrebla lappacea). DNA was extracted and the 16S rDNA sequenced for phylogenetic analysis. Forty bacterial isolates were obtained and placed in 17 groups based on phenotypic characteristics and restriction enzyme digestion of 16S rDNA PCR products. DNA sequencing revealed that the 17 groups comprised five known species (Clostridium butyricum, Streptococcus bovis, Clostridium sporogenes, Clostridium paraputrificum and Enterococcus avium) and 12 groups apparently representing new species, all within the phylum Firmicutes. Foregut contents from Australian macropod marsupials contain a microbial ecosystem with a novel bacterial biodiversity comprising a high percentage of previously unrecognized species. This study adds to knowledge of Australia's unique biodiversity, which may provide a future bioresource of genetic information and bacterial species of benefit to agriculture.

The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition

PubMed Central

Yin, Shuang; Jensen, Mark A.; Bai, Jiawei; DebRoy, Chitrita; Barrangou, Rodolphe

2013-01-01

The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the “big six” serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity. PMID:23851088

The evolutionary divergence of Shiga toxin-producing Escherichia coli is reflected in clustered regularly interspaced short palindromic repeat (CRISPR) spacer composition.

PubMed

Yin, Shuang; Jensen, Mark A; Bai, Jiawei; Debroy, Chitrita; Barrangou, Rodolphe; Dudley, Edward G

2013-09-01

The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the "big six" serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity.

A Study on Spectral Signature Analysis of Wetland Vegetation Based on Ground Imaging Spectrum Data

NASA Astrophysics Data System (ADS)

Ling, Chengxing; Liu, Hua; Ju, Hongbo; Zhang, Huaiqing; You, Jia; Li, Weina

2017-10-01

The objective of this study was to verify the application of imaging spectrometer in wetland vegetation remote sensing monitoring, based on analysis of wetland vegetation spectral features. Spectral information of Carex vegetation spectral data under different water environment was collected bySOC710VP and ASD FieldSpec 3; Meanwhile, the chlorophyll contents of wheat leaves were tested in the lab. A total 9 typical vegetation indices were calculated by using two instruments’ data which were spectral values from 400nm to 1000 nm. Then features between the same vegetation indices and soil water contents for two applications were analyzed and compared. The results showed that there were same spectrum curve trends of Carex vegetation (soil moisture content of 51%, 32%, 14% and three regional comparative analysis)reflectance between SOC710VP and ASD FieldSpec 3, including the two reflectance peak of 550nm and 730 nm, two reflectance valley of 690 nm and 970nm, and continuous near infrared reflectance platform. However, The two also have a very clear distinction: (1) The reflection spectra of SOC710VP leaves of Carex Carex leaf spectra in the three soil moisture environment values are greater than ASD FieldSpec 3 collected value; (2) The SOC710VP reflectivity curve does not have the smooth curve of the original spectrum measured by the ASD FieldSpec 3, the amplitude of fluctuation is bigger, and it is more obvious in the near infrared band. It is concluded that SOC710VP spectral data are reliable, with the image features, spectral curve features reliable. It has great potential in the research of hyperspectral remote sensing technology in the development of wetland near earth, remote sensing monitoring of wetland resources.

Genome-wide association mapping of soybean chlorophyll traits based on canopy spectral reflectance and leaf extracts.

PubMed

Dhanapal, Arun Prabhu; Ray, Jeffery D; Singh, Shardendu K; Hoyos-Villegas, Valerio; Smith, James R; Purcell, Larry C; Fritschi, Felix B

2016-08-04

Chlorophyll is a major component of chloroplasts and a better understanding of the genetic basis of chlorophyll in soybean [Glycine max (L.) Merr.] might contribute to improving photosynthetic capacity and yield in regions with adverse environmental conditions. A collection of 332 diverse soybean genotypes were grown in 2 years (2009 and 2010) and chlorophyll a (eChl_A), chlorophyll b (eChl_B), and total chlorophyll (eChl_T) content as well as chlorophyll a/b ratio (eChl_R) in leaf tissues were determined by extraction and spectrometric determination. Total chlorophyll was also derived from canopy spectral reflectance measurements using a model of wavelet transformed spectra (tChl_T) as well as with a spectral reflectance index (iChl_T). A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches. Results presented here show that markers for chlorophyll traits can be identified in soybean using both extract-based and canopy spectral reflectance-based phenotypes, and confirm that high-throughput phenotyping-amenable canopy spectral reflectance measurements can be used for association mapping.

Using Personal Ads and Online Self-Help Groups to Teach Content Analysis in a Research Methods Course

ERIC Educational Resources Information Center

Finn, Jerry; Dillon, Caroline

2007-01-01

This paper describes methods for teaching content analysis as part of the Research sequence in social work education. Teaching content analysis is used to develop research skills as well as to promote students' knowledge and critical thinking and about new information technology resources that are being increasingly used by the general public. The…

[Microelement contents of litter, soil fauna and soil in Pinus koraiensis and broad-leaved mixed forest].

PubMed

Yin, Xiu-qin; Li, Jin-xia; Dong, Wei-hua

2007-02-01

The analysis on the Mn, Zn and Cu contents of litter, soil fauna and soil in Pinus korazenszis and broad-leaved mixed forest in Liangshui Natural Reserve of Xiaoxing' an Mountains showed that the test microelement contents in the litter, soil fauna and soil all followed the sequence of Mn > Zn > Cu, but varied with these environmental components, being in the sequence of soil > litter > soil fauna for Mn, soil fauna > litter and soil for Zn, and soil fauna > soil > litter for Cu. The change range of test microelement contents in litter was larger in broad-leaved forest than in coniferous forest. Different soil fauna differed in their microelement-enrichment capability, e. g. , earthworm, centipede, diplopod had the highest content of Mn, Zn and Cu, respectively. The contents of test microelements in soil fauna had significant correlations with their environmental background values, litter decomposition rate, food habit of soil fauna, and its absorbing selectivity and enrichment to microelements. The microelements contained in 5-20 cm soil layer were more than those in 0-5 cm soil layer, and their dynamics differed in various soil layers.

Dependence of marine stratocumulus reflectivities on liquid water paths

NASA Technical Reports Server (NTRS)

Coakley, James A., Jr.; Snider, Jack B.

1990-01-01

Simple parameterizations that relate cloud liquid water content to cloud reflectivity are often used in general circulation climate models to calculate the effect of clouds in the earth's energy budget. Such parameterizations have been developed by Stephens (1978) and by Slingo and Schrecker (1982) and others. Here researchers seek to verify the parametric relationship through the use of simultaneous observations of cloud liquid water content and cloud reflectivity. The column amount of cloud liquid was measured using a microwave radiometer on San Nicolas Island following techniques described by Hogg et al., (1983). Cloud reflectivity was obtained through spatial coherence analysis of Advanced Very High Resolution Radiometer (AVHRR) imagery data (Coakley and Beckner, 1988). They present the dependence of the observed reflectivity on the observed liquid water path. They also compare this empirical relationship with that proposed by Stephens (1978). Researchers found that by taking clouds to be isotropic reflectors, the observed reflectivities and observed column amounts of cloud liquid water are related in a manner that is consistent with simple parameterizations often used in general circulation climate models to determine the effect of clouds on the earth's radiation budget. Attempts to use the results of radiative transfer calculations to correct for the anisotropy of the AVHRR derived reflectivities resulted in a greater scatter of the points about the relationship expected between liquid water path and reflectivity. The anisotropy of the observed reflectivities proved to be small, much smaller than indicated by theory. To critically assess parameterizations, more simultaneous observations of cloud liquid water and cloud reflectivities and better calibration of the AVHRR sensors are needed.

Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man

PubMed Central

Mallon, A.-M.; Platzer, M.; Bate, R.; Gloeckner, G.; Botcherby, M.R.M.; Nordsiek, G.; Strivens, M.A.; Kioschis, P.; Dangel, A.; Cunningham, D.; Straw, R.N.A.; Weston, P.; Gilbert, M.; Fernando, S.; Goodall, K.; Hunter, G.; Greystrong, J.S.; Clarke, D.; Kimberley, C.; Goerdes, M.; Blechschmidt, K.; Rump, A.; Hinzmann, B.; Mundy, C.R.; Miller, W.; Poustka, A.; Herman, G.E.; Rhodes, M.; Denny, P.; Rosenthal, A.; Brown, S.D.M.

2000-01-01

The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions. [The sequence data described in this paper have been submitted to EMBL under the following accession nos.: Mouse Genomic Sequence: Mouse contig A (AL021127), Mouse contig B (AL049866), BAC41M10 (AL136328), PAC303O11(AL136329). Human Genomic Sequence: Human contig 1 (U82671, U82670), Human contig 2 (U82695).] PMID:10854409

Terrestrial mollusk records from Chinese loess sequences and changes in the East Asian monsoonal environment

NASA Astrophysics Data System (ADS)

Wu, Naiqin; Li, Fengjiang; Rousseau, Denis-Didier

2018-04-01

The terrestrial mollusk fossils found in Chinese loess strata have been studied for over one hundred years. However, the greatest progress in these studies has been made only in the last two decades. In this paper, we review the advancements, advantages and limitations of terrestrial mollusk studies in Chinese loess deposits. Improvements in research methods and approaches have allowed the extraction of more detailed paleoenvironmental and paleoclimatic information from mollusk assemblages. The broadened research scope and content have yielded many new findings and results. The mollusk record has thus become one of the most important proxies in the paleoenvironmental and paleoclimatic reconstruction of loess-paleosol sequences in China. The greatest progress in the studies of terrestrial mollusks in Chinese loess sequences can be summarized as follows: (1) modern mollusk assemblages can be classified into four ecotypes, based on their temperature and humidity requirements, including eurytopic, semi-aridiphilous and sub-humidiphilous, cold-aridiphilous, and thermo-humidiphilous types; (2) Quaternary mollusk assemblages can be modified into the following three ecological types: glacial loess, interglacial paleosol, and interstadial weakly-developed paleosol assemblages; (3) mollusk records successfully reveal long-term climatic and environmental changes reflective of the history of East Asian monsoonal variations since the Late Cenozoic, and the succession of mollusk species also indicate short-term environmental changes such as millennial climate variability during Last Glacial Maximum and unstable climatic fluctuations during glacial and interglacial periods; and (4) more recently, new analytical approaches have offered increased research potential in areas such as paleotemperature reconstruction using the isotopic compositions of modern and fossil mollusk shells, combined with higher accuracy 14C dating of Quaternary loess deposits, which will greatly improve future loess paleoenvironmental research.

"3D Depositional Model in a Complex Incised Valley Fill: An example from the late Messinian Abu Madi Formation, Nile Delta Basin, Egypt"

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.; Abu El-Ata, A. S. A.

2016-12-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

3D Depositional Model in a Complex Incised Valley Fill: An Example from the Late Messinian Abu Madi Formation, Nile Delta Basin, Egypt

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.

2015-12-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

3D Depositional Model in a Complex Incised Valley Fill: An Example from the Late Messinian Abu Madi Formation, Nile Delta Basin, Egypt

NASA Astrophysics Data System (ADS)

Nasr El-Deen Badawy, A. M. E. S.

2016-02-01

The study area lies in the Central Marine Delta, which is located in the Baltim offshore concession, about 25 kms from the shoreline and 40 kms North Abu Madi-El Qara fields. The current study is aiming to give a comprehensive combined and conjugated study between well data and seismic survey interpretations. The former includes well logging data, acquired results of actual drilling and biostratigraphic study, to give an integrated picture for the considered area in a true attempt to visualize the geological and geophysical data given from both wells and seismic reflection surveys, and hence introduce an updated sequence stratigraphic framework for the Messinian sequence at the offshore Nile Delta area. The 3D geological model, based on all the available well data (faunal contents, litho-facies, log signatures…...etc.) and the seismic expressions (facies and geometry), has been constructed for the study area. This model shows that, the study area was changed from shelf (considered as erosional), to delta channels and then directed to the north. It changed to delta front mouth bars on the shoreface and affected by the main Rosetta fault to collect deposits as sand bars in the southern part on the downthrown side of the fault. Most deposits on this face were highstand system tracts. This deduced from the sequence stratigraphy study. The area was then sloped to the north, as shelf slope with the deposition of slumps, which was formed during erosions and mass flows. Some mud diapers also formed upon this slope. After dropping the sea level with the activity of some syn-sedimentary faults, some channels with sediment supply started their activities to dig their ways to the north.

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

PubMed Central

Chen, Ming; Henry, Nathan; Almsaeed, Abdullah; Zhou, Xiao; Wegrzyn, Jill; Ficklin, Stephen

2017-01-01

Abstract Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression PMID:29220446

A High Resolution Genome-Wide Scan for Significant Selective Sweeps: An Application to Pooled Sequence Data in Laying Chickens

PubMed Central

Qanbari, Saber; Strom, Tim M.; Haberer, Georg; Weigend, Steffen; Gheyas, Almas A.; Turner, Frances; Burt, David W.; Preisinger, Rudolf; Gianola, Daniel; Simianer, Henner

2012-01-01

In most studies aimed at localizing footprints of past selection, outliers at tails of the empirical distribution of a given test statistic are assumed to reflect locus-specific selective forces. Significance cutoffs are subjectively determined, rather than being related to a clear set of hypotheses. Here, we define an empirical p-value for the summary statistic by means of a permutation method that uses the observed SNP structure in the real data. To illustrate the methodology, we applied our approach to a panel of 2.9 million autosomal SNPs identified from re-sequencing a pool of 15 individuals from a brown egg layer line. We scanned the genome for local reductions in heterozygosity, suggestive of selective sweeps. We also employed a modified sliding window approach that accounts for gaps in the sequence and increases scanning resolution by moving the overlapping windows by steps of one SNP only, and suggest to call this a “creeping window” strategy. The approach confirmed selective sweeps in the region of previously described candidate genes, i.e. TSHR, PRL, PRLHR, INSR, LEPR, IGF1, and NRAMP1 when used as positive controls. The genome scan revealed 82 distinct regions with strong evidence of selection (genome-wide p-value<0.001), including genes known to be associated with eggshell structure and immune system such as CALB1 and GAL cluster, respectively. A substantial proportion of signals was found in poor gene content regions including the most extreme signal on chromosome 1. The observation of multiple signals in a highly selected layer line of chicken is consistent with the hypothesis that egg production is a complex trait controlled by many genes. PMID:23209582

[Study on predicting sugar content and valid acidity of apples by near infrared diffuse reflectance technique].

PubMed

Liu, Yan-de; Ying, Yi-bin; Fu, Xia-ping

2005-11-01

The nondestructive method for quantifying sugar content (SC) and available acid (VA) of intact apples using diffuse near infrared reflectance and optical fiber sensing techniques were explored in the present research. The standard sample sets and prediction models were established by partial least squares analysis (PLS). A total of 120 Shandong Fuji apples were tested in the wave number of 12,500 - 4000 cm(-1) using Fourier transform near infrared spectroscopy. The results of the research indicated that the nondestructive quantification of SC and VA, gave a high correlation coefficient 0.970 and 0.906, a low root mean square error of prediction (RMSEP) 0.272 and 0.056 2, a low root mean square error of calibration (RMSEC) 0.261 and 0.0677, and a small difference between RMSEP and RMSEC 0.011 a nd 0.0115. It was suggested that the diffuse nearinfrared reflectance technique be feasible for nondestructive determination of apple sugar content in the wave number range of 10,341 - 5461 cm(-1) and for available acid in the wave number range of 10,341 - 3818 cm(-1).

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

PubMed

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus

PubMed Central

Niu, Zhitao; Xue, Qingyun; Wang, Hui; Xie, Xuezhu; Zhu, Shuying; Liu, Wei; Ding, Xiaoyu

2017-01-01

The variation of GC content is a key genome feature because it is associated with fundamental elements of genome organization. However, the reason for this variation is still an open question. Different kinds of hypotheses have been proposed to explain the variation of GC content during genome evolution. However, these hypotheses have not been explicitly investigated in whole plastome sequences. Dendrobium is one of the largest genera in the orchid species. Evolutionary studies of the plastomic organization and base composition are limited in this genus. In this study, we obtained the high-quality plastome sequences of D. loddigesii and D. devonianum. The comparison results showed a nearly identical organization in Dendrobium plastomes, indicating that the plastomic organization is highly conserved in Dendrobium genus. Furthermore, the impact of three evolutionary forces—selection, mutational biases, and GC-biased gene conversion (gBGC)—on the variation of GC content in Dendrobium plastomes was evaluated. Our results revealed: (1) consistent GC content evolution trends and mutational biases in single-copy (SC) and inverted repeats (IRs) regions; and (2) that gBGC has influenced the plastome-wide GC content evolution. These results suggest that both mutational biases and gBGC affect GC content in the plastomes of Dendrobium genus. PMID:29099062

Using 'How People Learn' as a Blueprint for Developing Teaching Strategies in an Introductory Geology Course

NASA Astrophysics Data System (ADS)

Debari, S. M.; Bachmann, J.; Dougan, B.; Fackler-Adams, B.; Kratz, R.; Linneman, S.; Plake, T.; Smith, B.

2008-12-01

A new curriculum for an introductory geology course, Geology and Everyday Thinking (GET), incorporates the key research findings of How People Learn (NAS, 1999), and is based on the pedagogical approach of Physics and Everyday Thinking (PET; http://petproject.sdsu.edu/). These key findings have profound implications for developing teaching strategies that promote student learning. They suggest that for learning to occur: 1) students' preconceptions must be engaged, 2) students must be able to build their own conceptual framework, and 3) students must be given an opportunity to reflect on their learning (metacognition). Our curriculum has been carefully constructed into cycles that apply these key findings while exploring a key geologic concept. Each cycle engages students' 'Initial Ideas' about these concepts (and continuously revisits those Initial Ideas), sequentially builds upon concepts in a logical framework, and requires reflective writing. The curriculum employs questioning, small group work, and small and large class discussions. Students construct concepts by doing inquiry lab activities, but embedded group discussions that promote discourse and questioning among students is a crucial tool in the sense-making and solidification of those concepts. The questioning and discourse occur throughout each module so that students' preconceptions about a particular concept are brought out early on, and are revisited and challenged again as students construct their new understanding. Whiteboarding, or the process of sharing small-group ideas to a larger group, is the primary method of generating discussion. The instructor's role as facilitator and questioner is the cornerstone in this process. The primary audience for this course is future elementary teachers, who are required take a year-long science sequence. The year-long sequence includes physics (PET), geology (GET), and a correlative new curriculum in biology (BET). Class size is limited to 24 students, and the sequence is taught at a 4-year university as well as at four regional feeder community colleges. These courses model an inquiry-based teaching methodology that our pre-service teachers will use to teach science to their future students. Both quantitative and qualitative assessment data collected from our students show impressive gains both in attitudes about science and science content, especially compared to larger lecture-based introductory courses.

LIFETIME AND SPECTRAL EVOLUTION OF A MAGMA OCEAN WITH A STEAM ATMOSPHERE: ITS DETECTABILITY BY FUTURE DIRECT IMAGING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamano, Keiko; Kawahara, Hajime; Abe, Yutaka

2015-06-20

We present the thermal evolution and emergent spectra of solidifying terrestrial planets along with the formation of steam atmospheres. The lifetime of a magma ocean and its spectra through a steam atmosphere depends on the orbital distance of the planet from the host star. For a Type I planet, which is formed beyond a certain critical distance from the host star, the thermal emission declines on a timescale shorter than approximately 10{sup 6} years. Therefore, young stars should be targets when searching for molten planets in this orbital region. In contrast, a Type II planet, which is formed inside themore » critical distance, will emit significant thermal radiation from near-infrared atmospheric windows during the entire lifetime of the magma ocean. The K{sub s} and L bands will be favorable for future direct imaging because the planet-to-star contrasts of these bands are higher than approximately 10{sup −7}–10{sup −8}. Our model predicts that, in the Type II orbital region, molten planets would be present over the main sequence of the G-type host star if the initial bulk content of water exceeds approximately 1 wt%. In visible atmospheric windows, the contrasts of the thermal emission drop below 10{sup −10} in less than 10{sup 5} years, whereas those of the reflected light remain 10{sup −10} for both types of planets. Since the contrast level is comparable to those of reflected light from Earth-sized planets in the habitable zone, the visible reflected light from molten planets also provides a promising target for direct imaging with future ground- and space-based telescopes.« less

Adaptation of pelage color and pigment variations in Israeli subterranean blind mole rats, Spalax ehrenbergi [corrected].

PubMed

Singaravelan, Natarajan; Raz, Shmuel; Tzur, Shay; Belifante, Shirli; Pavlicek, Tomas; Beiles, Avigdor; Ito, Shosuke; Wakamatsu, Kazumasa; Nevo, Eviatar

2013-01-01

Concealing coloration in rodents is well established. However, only a few studies examined how soil color, pelage color, hair-melanin content, and genetics (i.e., the causal chain) synergize to configure it. This study investigates the causal chain of dorsal coloration in Israeli subterranean blind mole rats, Spalax ehrenbergi. We examined pelage coloration of 128 adult animals from 11 populations belonging to four species of Spalax ehrenbergi superspecies (Spalax galili, Spalax golani, Spalax carmeli, and Spalax judaei) and the corresponding coloration of soil samples from the collection sites using a digital colorimeter. Additionally, we quantified hair-melanin contents of 67 animals using HPLC and sequenced the MC1R gene in 68 individuals from all four mole rat species. Due to high variability of soil colors, the correlation between soil and pelage color coordinates was weak and significant only between soil hue and pelage lightness. Multiple stepwise forward regression revealed that soil lightness was significantly associated with all pelage color variables. Pelage color lightness among the four species increased with the higher southward aridity in accordance to Gloger's rule (darker in humid habitats and lighter in arid habitats). Darker and lighter pelage colors are associated with darker basalt and terra rossa, and lighter rendzina soils, respectively. Despite soil lightness varying significantly, pelage lightness and eumelanin converged among populations living in similar soil types. Partial sequencing of the MC1R gene identified three allelic variants, two of which were predominant in northern species (S. galili and S. golani), and the third was exclusive to southern species (S. carmeli and S. judaei), which might have caused the differences found in pheomelanin/eumelanin ratio. Darker dorsal pelage in darker basalt and terra rossa soils in the north and lighter pelage in rendzina and loess soils in the south reflect the combined results of crypsis and thermoregulatory function following Gloger's rule.

Assessing uncertainty in radar measurements on simplified meteorological scenarios

NASA Astrophysics Data System (ADS)

Molini, L.; Parodi, A.; Rebora, N.; Siccardi, F.

2006-02-01

A three-dimensional radar simulator model (RSM) developed by Haase (1998) is coupled with the nonhydrostatic mesoscale weather forecast model Lokal-Modell (LM). The radar simulator is able to model reflectivity measurements by using the following meteorological fields, generated by Lokal Modell, as inputs: temperature, pressure, water vapour content, cloud water content, cloud ice content, rain sedimentation flux and snow sedimentation flux. This work focuses on the assessment of some uncertainty sources associated with radar measurements: absorption by the atmospheric gases, e.g., molecular oxygen, water vapour, and nitrogen; attenuation due to the presence of a highly reflecting structure between the radar and a "target structure". RSM results for a simplified meteorological scenario, consisting of a humid updraft on a flat surface and four cells placed around it, are presented.

Knowledge Growth in Teaching Mathematics/Science with Spreadsheets: Moving PCK to TPACK through Online Professional Development

ERIC Educational Resources Information Center

Niess, Margaret L.; van Zee, Emily H.; Gillow-Wiles, Henry

2011-01-01

Inservice teachers need ways to gain an integrated knowledge of content, pedagogy, and technologies that reflects new ways of teaching and learning in the 21st century. This interpretive study examined inservice K-8 teachers' growth in their pedagogical content knowledge (PCK) toward technology, pedagogy, and content knowledge (TPACK) in an online…

[Inversion of organic matter content of the north fluvo-aquic soil based on hyperspectral and multi-spectra].

PubMed

Wang, Yan-Cang; Gu, Xiao-He; Zhu, Jin-Shan; Long, Hui-Ling; Xu, Peng; Liao, Qin-Hong

2014-01-01

The present study aims to assess the feasibility of multi-spectral data in monitoring soil organic matter content. The data source comes from hyperspectral measured under laboratory condition, and simulated multi-spectral data from the hyperspectral. According to the reflectance response functions of Landsat TM and HJ-CCD (the Environment and Disaster Reduction Small Satellites, HJ), the hyperspectra were resampled for the corresponding bands of multi-spectral sensors. The correlation between hyperspectral, simulated reflectance spectra and organic matter content was calculated, and used to extract the sensitive bands of the organic matter in the north fluvo-aquic soil. The partial least square regression (PLSR) method was used to establish experiential models to estimate soil organic matter content. Both root mean squared error (RMSE) and coefficient of the determination (R2) were introduced to test the precision and stability of the modes. Results demonstrate that compared with the hyperspectral data, the best model established by simulated multi-spectral data gives a good result for organic matter content, with R2=0.586, and RMSE=0.280. Therefore, using multi-spectral data to predict tide soil organic matter content is feasible.

Sequence variations of the alpha-globin genes: scanning of high CG content genes with DHPLC and DG-DGGE.

PubMed

Lacerra, Giuseppina; Fiorito, Mirella; Musollino, Gennaro; Di Noce, Francesca; Esposito, Maria; Nigro, Vincenzo; Gaudiano, Carlo; Carestia, Clementina

2004-10-01

The alpha-globin chains are encoded by two duplicated genes (HBA2 and HBA1, 5'-3') showing overall sequence homology >96% and average CG content >60%. alpha-Thalassemia, the most prevalent worldwide autosomal recessive disorder, is a hereditary anemia caused by sequence variations of these genes in about 25% of carriers. We evaluated the overall sensitivity and suitability of DHPLC and DG-DGGE in scanning both the alpha-globin genes by carrying out a retrospective analysis of 19 variant alleles in 29 genotypes. The HBA2 alleles c.1A>G, c.79G>A, and c.281T>G, and the HBA1 allele c.475C>A were new. Three pathogenic sequence variations were associated in cis with nonpathogenic variations in all families studied; they were the HBA2 variation c.2T>C associated with c.-24C>G, and the HBA2 variations c.391G>C and c.427T>C, both associated with c.565G>A. We set up original experimental conditions for DHPLC and DG-DGGE and analyzed 10 normal subjects, 46 heterozygotes, seven homozygotes, seven compound heterozygotes, and six compound heterozygotes for a hybrid gene. Both the methodologies gave reproducible results and no false-positive was detected. DHPLC showed 100% sensitivity and DG-DGGE nearly 90%. About 100% of the sequence from the cap site to the polyA addition site could be scanned by DHPLC, about 87% by DG-DGGE. It is noteworthy that the three most common pathogenic sequence variations (HBA2 alleles c.2T>C, c.95+2_95+6del, and c.523A>G) were unambiguously detected by both the methodologies. Genotype diagnosis must be confirmed with PCR sequencing of single amplicons or with an allele-specific method. This study can be helpful for scanning genes with high CG content and offers a model suitable for duplicated genes with high homology. Copyright 2004 Wiley-Liss, Inc.

Symbiotic interaction between dinoflagellates and the demosponge Lubomirskia baicalensis: aquaporin-mediated glycerol transport.

PubMed

Müller, Werner E G; Belikov, Sergey I; Kaluzhnaya, Oxana V; Chernogor, L; Krasko, Anatoli; Schröder, Heinz C

2009-01-01

Lake Baikal is rich in endemic sponge species, among them the arborescently growing species Lubomirskia baicalensis. During winter when the lake is covered by ice, this species reproduces sexually, reflecting a high metabolic activity. Throughout the year, L. baicalensis lives in association with dinoflagellates, which - according to the data presented herein - are symbiotic. The dinoflagellates have been determined on the basis of their rDNA/ITS characteristics and were found to display high sequence similarity to Gymnodinium sanguineum. The dinoflagellates give the sponge its characteristic green color, reflecting the high chlorophyll content (chlorophyll-a content in March and September of 3.2 +/- 0.6 microg/g and 1.9 +/- 0.5 microg/g of protein, respectively). With the in vitro cell culture system for sponges, the primmorphs, it could be demonstrated that [(14)C] glycerol is readily taken up by sponge cells; this process can be inhibited by phloretin, an aquaporin channel blocker. In order to prove the effect of cholesterol on the intermediate metabolism of the sponge cells, molecule probes, cDNAs for key enzymes in gluconeogenesis, glycolysis, and citric acid, have been applied in Northern blot studies. The data revealed that the genes coding for the enzymes citrate synthase and fructose-1,6-bisphosphatase are strongly upregulated after exposure of primmorphs to glycerol. This effect is abolished by phloretin. The genes encoding the phosphoglucose isomerase and pyruvate dehydrogenase do not respond to glycerol supply, suggesting that their expression is not under genetic control in L. baicalensis. To prove the assumption that the aquaporin channel is involved in the influx of glycerol in sponge cells, this cDNA was cloned and applied for in situ hybridization studies. The results obtained show that cells surrounding the dinoflagellates become brightly stained after hybridization with the aquaporin this probe. This demonstrates that L. baicalensis cells respond to glycerol, a metabolite which might be supplied by the dinoflagellates and imported via the aquaporin channel into the sponge cells.

Reflectance and internal structure of leaves from several crops during a growing season.

NASA Technical Reports Server (NTRS)

Sinclair, T. R.; Hoffer, R. M.; Schreiber, M. M.

1971-01-01

Measurements of spectral reflectance characteristics during a growing season of leaves from six crops are reported. These crops include soybeans, wheat, oats, sorghum, corn, and sudangrass. The characteristics measured are related to changes in leaf structure and water content.

The Yoga of Critical Discourse

ERIC Educational Resources Information Center

Hyde, Andrea M.

2013-01-01

This article offers a comparative self-reflection on two seemingly disparate teaching practices: hatha yoga and critical social theories of education. As some have already discovered, the two enacted fields share many core principles and practices; deal with strikingly similar content; and are primarily self-reflective. As an…

Reflectance calibration and shadow effect of VNIS spectra acquired by the Yutu rover

NASA Astrophysics Data System (ADS)

Hu, Sen; Lin, Yang-Ting; Liu, Bin; Yang, Wei; He, Zhi-Ping; Xing, Wei-Fan

2015-09-01

Yutu is the first lunar rover after the Apollo program and Luna missions. One of the payloads on the Yutu rover, the Visible and Near-infrared Imaging Spectrometer (VNIS), has acquired four VIS/NIR images and SWIR spectra near its landing site in Mare Imbrium. The radiance images were reduced through repairing bad lines and bad points, and applying flat field correction, and then were converted into reflectance values based on the solar irradiance and angles of incidence. A significant shadow effect was observed in the VIS/NIR image. The shadowed regions show lower reflectance with a darkening trend compared with illuminated regions. The reflectance increased by up to 24% for entire images and 17% for the VIS/NIR-SWIR overlapping regions after shadow correction. The correction for the shadow effect will remarkably decrease the estimate of FeO content, by up to 4.9 wt.% in this study. The derived FeO contents of CD-005∼008 after shadow correction are around 18.0 wt.%.

Do Facebook Status Updates Reflect Subjective Well-Being?

PubMed

Liu, Pan; Tov, William; Kosinski, Michal; Stillwell, David J; Qiu, Lin

2015-07-01

Nowadays, millions of people around the world use social networking sites to express everyday thoughts and feelings. Many researchers have tried to make use of social media to study users' online behaviors and psychological states. However, previous studies show mixed results about whether self-generated contents on Facebook reflect users' subjective well-being (SWB). This study analyzed Facebook status updates to determine the extent to which users' emotional expression predicted their SWB-specifically their self-reported satisfaction with life. It was found that positive emotional expressions on Facebook did not correlate with life satisfaction, whereas negative emotional expressions within the past 9-10 months (but not beyond) were significantly related to life satisfaction. These findings suggest that both the type of emotional expressions and the time frame of status updates determine whether emotional expressions in Facebook status updates can effectively reflect users' SWB. The findings shed light on the characteristics of online social media and improve the understanding of how user-generated contents reflect users' psychological states.

Response of Thematic Mapper bands to plant water stress

NASA Technical Reports Server (NTRS)

Cibula, W. G.; Zetka, E. F.; Rickman, D. L.

1992-01-01

Changes in leaf reflectance as water content decreases have been hypothesized to occur in the 1.55-1.75 and 2.08-2.35 micron wavelength regions. To evaluate this hypothesis, studies were conducted on ryegrass (Lolium multiflorum Lam.) and oats (Avena sativa L.), which were grown in a controlled, outdoor situation. Both fully-watered control beds and water-stressed beds were periodically examined with a spectroradiometer calibrated against a reflectance reference of polytetrafluoroethylene. The observed changes correspond to those predicted by stochastic leaf models employed by other investigators (leaf reflection increases in the 1.55-1.75 micron region as leaf water content decreases). Although the percentage changes in TM bands 1-3 are nearly as great as those found in TM bands 5 and 7, the absolute values of reflectance change are much lower. It is believed that these patterns are probably characteristic of a broad range of vegetation types. In terms of phenomena detection, these patterns should be considered in any practical remote sensing sensor scenario.

High-Si content BARC for dual-BARC systems such as trilayer patterning

NASA Astrophysics Data System (ADS)

Kennedy, Joseph; Xie, Song-Yuan; Wu, Ze-Yu; Katsanes, Ron; Flanigan, Kyle; Lee, Kevin; Slezak, Mark; Liu, Zhi; Lin, Shang-Ho

2009-03-01

This work discusses the requirements and performance of Honeywell's middle layer material, UVAS, for tri-layer patterning. UVAS is a high Si content polymer synthesized directly from Si containing starting monomer components. The monomers are selected to produce a film that meets the requirements as a middle layer for tri-layer patterning (TLP) and gives us a level of flexibility to adjust the properties of the film to meet the customer's specific photoresist and patterning requirements. Results of simulations of the substrate reflectance versus numerical aperture, UVAS thickness, and under layer film are presented. ArF photoresist line profiles and process latitude versus UVAS bake at temperatures as low as 150ºC are presented and discussed. Immersion lithographic patterning of ArF photoresist line space and contact hole features will be presented. A sequence of SEM images detailing the plasma etch transfer of line space photoresist features through the middle and under layer films comprising the TLP film stack will be presented. Excellent etch selectivity between the UVAS and the organic under layer film exists as no edge erosion or faceting is observed as a result of the etch process. A detailed study of the impact of a PGMEA solvent photoresist rework process on the lithographic process window of a TLP film stack was performed with the results indicating that no degradation to the UVAS film occurs.

Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa.

PubMed

Karlsen, Christian; Hjerde, Erik; Klemetsen, Terje; Willassen, Nils Peder

2017-04-20

Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs. The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles. Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.

HU content and dynamics in Escherichia coli during the cell cycle and at different growth rates.

PubMed

Abebe, Anteneh Hailu; Aranovich, Alexander; Fishov, Itzhak

2017-10-16

DNA-binding proteins play an important role in maintaining bacterial chromosome structure and functions. Heat-unstable (HU) histone-like protein is one of the most abundant of these proteins and participates in all major chromosome-related activities. Owing to its low sequence specificity, HU fusions with fluorescent proteins were used for general staining of the nucleoid, aiming to reveal its morphology and dynamics. We have exploited a single chromosomal copy of hupA-egfp fusion under the native promoter and used quantitative microscopy imaging to investigate the amount and dynamics of HUα in Escherichia coli cells. We found that in steady-state growing populations the cellular HUα content is proportional to the cell size, whereas its concentration is size independent. Single-cell live microscopy imaging confirmed that the amount of HUα exponentially increases during the cell cycle, but its concentration is maintained constant. This supports the existence of an auto-regulatory mechanism underlying the HUα cellular level, in addition to reflecting the gene copy number. Both the HUα amount and concentration strongly increase with the cell growth rate in different culture media. Unexpectedly, the HU/DNA stoichiometry also remarkably increases with the growth rate. This last finding may be attributed to a higher requirement for maintaining the chromosome structure in nucleoids with higher complexity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Multiple alignment-free sequence comparison

PubMed Central

Ren, Jie; Song, Kai; Sun, Fengzhu; Deng, Minghua; Reinert, Gesine

2013-01-01

Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k-tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k-tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis-regulatory module data where the task is to identify cis-regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/∼fsun/Programs/multiAlignFree/multiAlignFreemain.html. Contact: reinert@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23990418

Processing of Natural Echolocation Sequences in the Inferior Colliculus of Seba’s Fruit Eating Bat, Carollia perspicillata

PubMed Central

Kordes, Sebastian; Kössl, Manfred

2017-01-01

Abstract For the purpose of orientation, echolocating bats emit highly repetitive and spatially directed sonar calls. Echoes arising from call reflections are used to create an acoustic image of the environment. The inferior colliculus (IC) represents an important auditory stage for initial processing of echolocation signals. The present study addresses the following questions: (1) how does the temporal context of an echolocation sequence mimicking an approach flight of an animal affect neuronal processing of distance information to echo delays? (2) how does the IC process complex echolocation sequences containing echo information from multiple objects (multiobject sequence)? Here, we conducted neurophysiological recordings from the IC of ketamine-anaesthetized bats of the species Carollia perspicillata and compared the results from the IC with the ones from the auditory cortex (AC). Neuronal responses to an echolocation sequence was suppressed when compared to the responses to temporally isolated and randomized segments of the sequence. The neuronal suppression was weaker in the IC than in the AC. In contrast to the cortex, the time course of the acoustic events is reflected by IC activity. In the IC, suppression sharpens the neuronal tuning to specific call-echo elements and increases the signal-to-noise ratio in the units’ responses. When presenting multiple-object sequences, despite collicular suppression, the neurons responded to each object-specific echo. The latter allows parallel processing of multiple echolocation streams at the IC level. Altogether, our data suggests that temporally-precise neuronal responses in the IC could allow fast and parallel processing of multiple acoustic streams. PMID:29242823

Processing of Natural Echolocation Sequences in the Inferior Colliculus of Seba's Fruit Eating Bat, Carollia perspicillata.

PubMed

Beetz, M Jerome; Kordes, Sebastian; García-Rosales, Francisco; Kössl, Manfred; Hechavarría, Julio C

2017-01-01

For the purpose of orientation, echolocating bats emit highly repetitive and spatially directed sonar calls. Echoes arising from call reflections are used to create an acoustic image of the environment. The inferior colliculus (IC) represents an important auditory stage for initial processing of echolocation signals. The present study addresses the following questions: (1) how does the temporal context of an echolocation sequence mimicking an approach flight of an animal affect neuronal processing of distance information to echo delays? (2) how does the IC process complex echolocation sequences containing echo information from multiple objects (multiobject sequence)? Here, we conducted neurophysiological recordings from the IC of ketamine-anaesthetized bats of the species Carollia perspicillata and compared the results from the IC with the ones from the auditory cortex (AC). Neuronal responses to an echolocation sequence was suppressed when compared to the responses to temporally isolated and randomized segments of the sequence. The neuronal suppression was weaker in the IC than in the AC. In contrast to the cortex, the time course of the acoustic events is reflected by IC activity. In the IC, suppression sharpens the neuronal tuning to specific call-echo elements and increases the signal-to-noise ratio in the units' responses. When presenting multiple-object sequences, despite collicular suppression, the neurons responded to each object-specific echo. The latter allows parallel processing of multiple echolocation streams at the IC level. Altogether, our data suggests that temporally-precise neuronal responses in the IC could allow fast and parallel processing of multiple acoustic streams.

Effect of temperature, high pressure and freezing/thawing of dry-cured ham slices on dielectric time domain reflectometry response.

PubMed

Rubio-Celorio, Marc; Garcia-Gil, Núria; Gou, Pere; Arnau, Jacint; Fulladosa, Elena

2015-02-01

Dielectric Time Domain Reflectometry (TDR) is a useful technique for the characterization and classification of dry-cured ham according to its composition. However, changes in the behavior of dielectric properties may occur depending on environmental factors and processing. The effect of temperature, high pressure (HP) and freezing/thawing of dry-cured ham slices on the obtained TDR curves and on the predictions of salt and water contents when using previously developed predictive models, was evaluated in three independent experiments. The results showed that at temperatures below 20 °C there is an increase of the predicted salt content error, being more important in samples with higher water content. HP treatment caused a decrease of the reflected signal intensity due to the major mobility of available ions promoting an increase of the predicted salt content. Freezing/thawing treatment caused an increase of the reflected signal intensity due to the microstructural damages and the loss of water and ions, promoting a decrease of the predicted salt content.

Metagenomic ventures into outer sequence space.

PubMed

Dutilh, Bas E

Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as "unknowns," and reflect the vast unexplored microbial sequence space of our biosphere, also known as "biological dark matter." However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.

Multiplex analysis of DNA

DOEpatents

Church, George M.; Kieffer-Higgins, Stephen

1992-01-01

This invention features vectors and a method for sequencing DNA. The method includes the steps of: a) ligating the DNA into a vector comprising a tag sequence, the tag sequence includes at least 15 bases, wherein the tag sequence will not hybridize to the DNA under stringent hybridization conditions and is unique in the vector, to form a hybrid vector, b) treating the hybrid vector in a plurality of vessels to produce fragments comprising the tag sequence, wherein the fragments differ in length and terminate at a fixed known base or bases, wherein the fixed known base or bases differs in each vessel, c) separating the fragments from each vessel according to their size, d) hybridizing the fragments with an oligonucleotide able to hybridize specifically with the tag sequence, and e) detecting the pattern of hybridization of the tag sequence, wherein the pattern reflects the nucleotide sequence of the DNA.

Sedimentological indicators of paleoenvironments and siliciclastic stratigraphic sequences in some Miocene deposits of the Calvert Cliffs, southern Maryland

USGS Publications Warehouse

Shideler, G.L.

1994-01-01

Middle Miocene siliciclastic deposits comprising the Calvert Cliffs section at the Baltimore Gas and Electric Company's (BG&E) nuclear power plant site in southern Maryland were analyzed in terms of lithostratigraphy, sedimentary structures, and granulometric parameters, to interprete paleo-environments within a sequence-stratigraphic framework. In terms of sequence-stratigraphic models, the BG&E section can be interpreted as consisting of two genetic stratigraphic sequences (Galloway model), namely, a shelf sequence and an overlying deltaic sequence. Using the Exxon model, the section consists of two third-order (1-5 m.y. duration) depositional sequences. The stratigraphic sequences of the BG&E section reflect both relatively short-term eustatic transgressive events, as well as a long-term regressive trend with associated local deltation and coastal progradation. The regression probably signified a regional basinward shift of depocenters within the Salisbury embayment during Miocene time. -from Author

[Progressive damage monitoring of corrugated composite skins by the FBG spectral characteristics].

PubMed

Zhang, Yong; Wang, Bang-Feng; Lu, Ji-Yun; Gu, Li-Li; Su, Yong-Gang

2014-03-01

In the present paper, a method of monitoring progressive damage of composite structures by non-uniform fiber Bragg grating (FBG) reflection spectrum is proposed. Due to the finite element analysis of corrugated composite skins specimens, the failure process under tensile load and corresponding critical failure loads of corrugated composite skin was predicated. Then, the non-uniform reflection spectrum of FBG sensor could be reconstructed and the corresponding relationship between layer failure order sequence of corrugated composite skin and FBG sensor reflection spectrums was acquired. A monitoring system based on FBG non-uniform reflection spectrum, which can be used to monitor progressive damage of corrugated composite skins, was built. The corrugated composite skins were stretched under this FBG non-uniform reflection spectrum monitoring system. The results indicate that real-time spectrums acquired by FBG non-uniform reflection spectrum monitoring system show the same trend with the reconstruction reflection spectrums. The maximum error between the corresponding failure and the predictive value is 8.6%, which proves the feasibility of using FBG sensor to monitor progressive damage of corrugated composite skin. In this method, the real-time changes in the FBG non-uniform reflection spectrum within the scope of failure were acquired through the way of monitoring and predicating, and at the same time, the progressive damage extent and layer failure sequence of corru- gated composite skin was estimated, and without destroying the structure of the specimen, the method is easy and simple to operate. The measurement and transmission section of the system are completely composed of optical fiber, which provides new ideas and experimental reference for the field of dynamic monitoring of smart skin.

Draft genome sequence of rice orange leaf phytoplasma from Guangdong, China

USDA-ARS?s Scientific Manuscript database

The genome of rice orange leaf phytoplasma strain LD1 from Luoding City, Guangdong, P. R. China, was sequenced. The draft LD1genome is 599,264 bp with GC content of 28.2%, 647 predicted open reading frames and 33 RNA genes....

Draft Genome Sequence of Pseudomonas oceani DSM 100277T, a Deep-Sea Bacterium

PubMed Central

2018-01-01

ABSTRACT Pseudomonas oceani DSM 100277T was isolated from deep seawater in the Okinawa Trough at 1390 m. P. oceani belongs to the Pseudomonas pertucinogena group. Here, we report the draft genome sequence of P. oceani, which has an estimated size of 4.1 Mb and exhibits 3,790 coding sequences, with a G+C content of 59.94 mol%. PMID:29650573

Whole-Genome Sequences of Cronobacter sakazakii Isolates Obtained from Foods of Plant Origin and Dried-Food Manufacturing Environments

PubMed Central

Addy, Nicole; Ewing, Laura; Jean-Gilles Beaubrun, Junia; Lee, YouYoung; Woo, JungHa; Negrete, Flavia; Finkelstein, Samantha; Tall, Ben D.; Lehner, Angelika; Eshwar, Athmanya; Gopinath, Gopal R.

2018-01-01

ABSTRACT Here, we present draft genome sequences of 29 Cronobacter sakazakii isolates obtained from foods of plant origin and dried-food manufacturing facilities. Assemblies and annotations resulted in genome sizes ranging from 4.3 to 4.5 Mb and 3,977 to 4,256 gene-coding sequences with G+C contents of ∼57.0%. PMID:29650569

Draft Genome Sequence of Algoriphagus sp. Strain NH1, a Multidrug-Resistant Bacterium Isolated from Coastal Sediments of the Northern Yellow Sea in China

PubMed Central

Mu, Dashuai; Zhao, Jinxin; Wang, Zongjie; Chen, Guanjun

2016-01-01

Algoriphagus sp. NH1 is a multidrug-resistant bacterium isolated from coastal sediments of the northern Yellow Sea in China. Here, we report the draft genome sequence of NH1, with a size of 6,131,579 bp, average G+C content of 42.68%, and 5,746 predicted protein-coding sequences. PMID:26769940

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Draft Genome Sequence of Lactobacillus sp. Strain TCF032-E4, Isolated from Fermented Radish.

PubMed

Mao, Yuejian; Chen, Meng; Horvath, Philippe

2015-07-30

Here, we report the draft genome sequence of Lactobacillus sp. strain TCF032-E4 (= CCTCC AB2015090 = DSM 100358), isolated from a Chinese fermented radish. The total length of the 57 contigs is about 2.9 Mb, with a G+C content of 43.5 mol% and 2,797 predicted coding sequences (CDSs). Copyright © 2015 Mao et al.

Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil.

PubMed

Lemos, Leandro Nascimento; de Souza, Rosineide Cardoso; de Souza Cannavan, Fabiana; Patricio, André; Pylro, Victor Satler; Hanada, Rogério Eiji; Mui, Tsai Siu

2016-12-01

The Anthropogenic Amazon Dark Earth soil is considered one of the world's most fertile soils. These soils differs from conventional Amazon soils because its higher organic content concentration. Here we describe the metagenome sequencing of microbial communities of two sites of Anthropogenic Amazon Dark Earth soils from Amazon Rainforest, Brazil. The raw sequence data are stored under Short Read Accession number: PRJNA344917.

Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with Bacteriophage ϕOH2

PubMed Central

Mori, Kazuki; Martono, Hindra; Nagayoshi, Yuko; Fujino, Yasuhiro; Tashiro, Kosuke; Kuhara, Satoru; Ohshima, Toshihisa

2013-01-01

Geobacillus kaustophilus strain GBlys was isolated along with the bacteriophage ϕOH2, which infects G. kaustophilus NBRC 102445T. Here we present a draft sequence of this strain’s genome, which consists of 216 contigs for a total of 3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%. PMID:23950135

Draft Genome Sequence of Cellulolytic and Xylanolytic Cellulomonas sp. Strain B6 Isolated from Subtropical Forest Soil

PubMed Central

Piccinni, Florencia; Murua, Yanina; Ghio, Silvina; Talia, Paola; Rivarola, Máximo

2016-01-01

Cellulomonas sp. strain B6 was isolated from a subtropical forest soil sample and presented (hemi)cellulose-degrading activity. We report here its draft genome sequence, with an estimated genome size of 4 Mb, a G+C content of 75.1%, and 3,443 predicted protein-coding sequences, 92 of which are glycosyl hydrolases involved in polysaccharide degradation. PMID:27563050

Complete Genome Sequence of Petrimonas sp. Strain IBARAKI, Assembled from the Metagenome Data of a Culture Containing Dehalococcoides spp.

PubMed

Ikegami, Kentaro; Aita, Yuto; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Shinzato, Misuzu; Ohki, Shun; Nakano, Kazuma; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi; Yohda, Masafumi

2018-05-03

The complete genome sequence of Petrimonas sp. strain IBARAKI in a Dehalococcoides -containing culture was determined using the PacBio RS II platform. The genome is a single circular chromosome of 3,693,233 nucleotides (nt), with a GC content of 44%. This is the first genome sequence of a Petrimonas species. Copyright © 2018 Ikegami et al.

Draft Genome Sequence of Photorhabdus luminescens Strain DSPV002N Isolated from Santa Fe, Argentina

PubMed Central

Del Valle, Eleodoro E.; Frizzo, Laureano; Berry, Colin; Caballero, Primitivo

2016-01-01

Here, we report the draft genome sequence of Photorhabdus luminescens strain DSPV002N, which consists of 177 contig sequences accounting for 5,518,143 bp, with a G+C content of 42.3% and 4,701 predicted protein-coding genes (CDSs). From these, 27 CDSs exhibited significant similarity with insecticidal toxin proteins from Photorhabdus luminescens subsp. laumondii TT01. PMID:27469965

Draft Genome Sequence of Agrobacterium sp. Strain UHFBA-218, Isolated from Rhizosphere Soil of Crown Gall-Infected Cherry Rootstock Colt

PubMed Central

Dua, Ankita; Sangwan, Naseer; Kaur, Jasvinder; Saxena, Anjali; Kohli, Puneet; Gupta, A. K.

2013-01-01

We report here the draft genome sequence of the alphaproteobacterium Agrobacterium sp. strain UHFBA-218, which was isolated from rhizosphere soil of crown gall-infected cherry rootstock Colt. The draft genome of strain UHFBA-218 consists of 112 contigs (5,425,303 bp) and 5,063 coding sequences with a G+C content of 59.8%. PMID:23723402

Draft Genome Sequence of Pseudomonas sp. Strain B1, Isolated from a Contaminated Sediment

DOE PAGES

Pathak, Ashish; Jaswal, Rajneesh; Stothard, Paul; ...

2018-06-21

ABSTRACT The draft genome sequence of Pseudomonas sp. strain B1, isolated from a contaminated soil, is reported. The genome comprises 6,706,934 bases, 6,059 coding sequences, and 70 RNAs and has a G+C content of 60.3%. A suite of biodegradative genes, many located on genomic islands, were identified from strain B1, further enhancing our understanding of the versatile pseudomonads.

Georgia's Teacher Performance Assessment

ERIC Educational Resources Information Center

Fenton, Anne Marie; Wetherington, Pamela

2016-01-01

Like most states, Georgia until recently depended on an assessment of content knowledge to award teaching licenses, along with a licensure recommendation from candidates' educator preparation programs. While the content assessment reflected candidates' grasp of subject matter, licensure decisions did not hinge on direct, statewide assessment of…

Distinguishing succulent plants from crop and woody plants

NASA Technical Reports Server (NTRS)

Gausman, H. W.; Escobar, D. E.; Everitt, J. H.; Richardson, A. J.; Rodriguez, R. R.

1978-01-01

We compared laboratory spectrophotometrically measured leaf reflectances of six succulents (peperomia, possum-grape, prickly pear, spiderwort, Texas tuberose, wolfberry) with those of four nonsucculents (cenizo, honey mesquite, cotton, sugarcane) for plant species discrimination. Succulents (average leaf water content of 92.2 percent) could be distinguished from nonsucculents (average leaf water content of 71.2 percent) within the near-infrared water absorption waveband (1.35 to 2.5 microns). This was substantiated by field spectrophotometric reflectances of plant canopies. Sensor bands encompassing either the 1.6- or 2.2-wavelengths may be useful to distinguish succulent from nonsucculent plant species.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.

PubMed

Haiminen, Niina; Feltus, F Alex; Parida, Laxmi

2011-04-15

We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using in silico simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence. The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on Arabidopsis. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most. BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Robasky, Kimberly; Bulyk, Martha L

2011-01-01

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

[Hydrologic variability and sensitivity based on Hurst coefficient and Bartels statistic].

PubMed

Lei, Xu; Xie, Ping; Wu, Zi Yi; Sang, Yan Fang; Zhao, Jiang Yan; Li, Bin Bin

2018-04-01

Due to the global climate change and frequent human activities in recent years, the pure stochastic components of hydrological sequence is mixed with one or several of the variation ingredients, including jump, trend, period and dependency. It is urgently needed to clarify which indices should be used to quantify the degree of their variability. In this study, we defined the hydrological variability based on Hurst coefficient and Bartels statistic, and used Monte Carlo statistical tests to test and analyze their sensitivity to different variants. When the hydrological sequence had jump or trend variation, both Hurst coefficient and Bartels statistic could reflect the variation, with the Hurst coefficient being more sensitive to weak jump or trend variation. When the sequence had period, only the Bartels statistic could detect the mutation of the sequence. When the sequence had a dependency, both the Hurst coefficient and the Bartels statistics could reflect the variation, with the latter could detect weaker dependent variations. For the four variations, both the Hurst variability and Bartels variability increased with the increases of variation range. Thus, they could be used to measure the variation intensity of the hydrological sequence. We analyzed the temperature series of different weather stations in the Lancang River basin. Results showed that the temperature of all stations showed the upward trend or jump, indicating that the entire basin had experienced warming in recent years and the temperature variability in the upper and lower reaches was much higher. This case study showed the practicability of the proposed method.

Reflective practice and daily ward reality: a covert power game.

PubMed

Mantzoukas, Stefanos; Jasper, Melanie A

2004-11-01

The concept of reflection is propounded in the literature as an epistemology for practice that enables practitioners to solve their daily problematic situations through conscious thought processes which eventually leads to practice-based knowledge. Hence, reflection became a central tenet of both theory development and educational provision in nursing. Furthermore, this centrality of reflection was reinforced by statutory nursing bodies and service providers by adopting it as the means for carrying out adequate professional practice. Although this may be the case, issues of implementation of reflection within the daily reality of practitioners are frequently overlooked within the literature. Moreover, little consideration appears to be given on the impact that the organizational culture and the politics of power may exert on the implementation of reflective practices within daily ward reality. This paper explores how reflection is viewed by nurses within their daily reality in the medical wards, examines the relationships between the organizational culture of these wards and the practitioners and investigates whether reflective methods of practice were being implemented when the study was conducted. An interpretative ethnographical methodology was implemented and the data collecting methods used were observation, interviews and qualitative content analysis with a group of 16 practising nurses from four medical wards of one NHS Trust in England. Two interviews were conducted with each nurse within 3-week intervals. The content of these interviews evolved from the analysis of episodes of practice observed when the nurses were giving nursing care. These data were supplemented by narratives from the nurses' in the form of written reflective accounts that were analysed via qualitative content analysis techniques. Four themes were generated: (i) relationships between nurses and doctors; (ii) relationships between nurses and managers; (iii) nursing practice; and (iv) nurses' input in the outcome of a clinical situation. The concept of reflection appears to be invalidated by the organizational hierarchy of the wards on the basis of a power struggle game. The ward structure portrays reflection as an abnormal method of practice and knowledge development. This belittlement of reflection does not mirror the practitioners' reality. Instead, it is an intelligent and intentional act on behalf of the dominant professional groups in the wards to create an illusionary picture of ward reality to allow them to survey and define nursing practice and thus maintain and remain in power. This is explicated by using Foucault's analysis and critical social theory framework. Hence, reflective processes are constrained by this covert power game; reflection, where used, is confined to nurses' personal time and space. The realization of this covert power game by individual clinical nurses can become the incipient point for formally using reflective methods in the practice setting.

Range-gated field disturbance sensor with range-sensitivity compensation

DOEpatents

McEwan, T.E.

1996-05-28

A field disturbance sensor operates with relatively low power, provides an adjustable operating range, is not hypersensitive at close range, allows co-location of multiple sensors, and is inexpensive to manufacture. The sensor includes a transmitter that transmits a sequence of transmitted bursts of electromagnetic energy. The transmitter frequency is modulated at an intermediate frequency. The sequence of bursts has a burst repetition rate, and each burst has a burst width and comprises a number of cycles at a transmitter frequency. The sensor includes a receiver which receives electromagnetic energy at the transmitter frequency, and includes a mixer which mixes a transmitted burst with reflections of the same transmitted burst to produce an intermediate frequency signal. Circuitry, responsive to the intermediate frequency signal indicates disturbances in the sensor field. Because the mixer mixes the transmitted burst with reflections of the transmitted burst, the burst width defines the sensor range. The burst repetition rate is randomly or pseudorandomly modulated so that bursts in the sequence of bursts have a phase which varies. 8 figs.

Range-gated field disturbance sensor with range-sensitivity compensation

DOEpatents

McEwan, Thomas E.

1996-01-01

A field disturbance sensor operates with relatively low power, provides an adjustable operating range, is not hypersensitive at close range, allows co-location of multiple sensors, and is inexpensive to manufacture. The sensor includes a transmitter that transmits a sequence of transmitted bursts of electromagnetic energy. The transmitter frequency is modulated at an intermediate frequency. The sequence of bursts has a burst repetition rate, and each burst has a burst width and comprises a number of cycles at a transmitter frequency. The sensor includes a receiver which receives electromagnetic energy at the transmitter frequency, and includes a mixer which mixes a transmitted burst with reflections of the same transmitted burst to produce an intermediate frequency signal. Circuitry, responsive to the intermediate frequency signal indicates disturbances in the sensor field. Because the mixer mixes the transmitted burst with reflections of the transmitted burst, the burst width defines the sensor range. The burst repetition rate is randomly or pseudorandomly modulated so that bursts in the sequence of bursts have a phase which varies.

Development of Overarm Throwing Technique Reflects Throwing Ability during Childhood

PubMed Central

KASUYAMA, Tatsuya; MUTOU, Ikuo; SASAMOTO, Hitoshi

2016-01-01

Background: It is important to acquire fundamental movement skills during childhood. Throwing is a representative manipulative skill required for various intrinsic factors. However, the relationship between intrinsic factors and throwing ability in childhood is unclear. The purpose of this study was to investigate intrinsic factors related to the ball throwing distance of Japanese elementary school children. Methods: Japanese elementary school children from grades 1-6 (aged 6-12 years; n=112) participated in this study. The main outcome was throwing ability, which was measured as the ball throwing distance. We measured five general anthropometric parameters, seven physical fitness parameters, and the Roberton's developmental sequence for all subjects. The relationships between the throwing ability and the 13 parameters were analysed. Results: The Roberton's developmental sequence was the best predictor of ball throwing distance (r=0.80, p≤0.01). The best multiple regression model, which included sex, handgrip strength, shuttle run test, and the Roberton's developmental sequence, accounted for 81% of the total variance. Conclusions: The development of correct throwing technique reflects throwing abilities in childhood. In addition to the throwing sequence, enhancement of grip strength and aerobic capacity are also required for children's throwing ability. PMID:28289578

Fostering Critical Reflection: Moving From a Service to a Social Justice Paradigm.

PubMed

Owen, Julie E

2016-06-01

This chapter explores how community engagement creates opportunities to facilitate meaningful discussions about issues including: the nature and sources of power; who benefits and who is silenced by service and leadership efforts; which community actions result in change rather than charity; and how to developmentally sequence reflective practice. © 2016 Wiley Periodicals, Inc., A Wiley Company.

Characterizing partial AZFc deletions of the Y chromosome with amplicon-specific sequence markers

PubMed Central

Navarro-Costa, Paulo; Pereira, Luísa; Alves, Cíntia; Gusmão, Leonor; Proença, Carmen; Marques-Vidal, Pedro; Rocha, Tiago; Correia, Sónia C; Jorge, Sónia; Neves, António; Soares, Ana P; Nunes, Joaquim; Calhaz-Jorge, Carlos; Amorim, António; Plancha, Carlos E; Gonçalves, João

2007-01-01

Background The AZFc region of the human Y chromosome is a highly recombinogenic locus containing multi-copy male fertility genes located in repeated DNA blocks (amplicons). These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. Yet, partial AZFc deletions yield phenotypes ranging from normospermia to azoospermia, thwarting definite conclusions on their real impact on fertility. Results The amplicon content of partial AZFc deletion products was characterized with novel amplicon-specific sequence markers. Data indicate that partial AZFc deletions are a male infertility risk [odds ratio: 5.6 (95% CI: 1.6–30.1)] and although high diversity of partial deletion products and sequence conversion profiles were recorded, the AZFc marker profiles detected in fertile men were also observed in infertile men. Additionally, the assessment of rearrangement recurrence by Y-lineage analysis indicated that while partial AZFc deletions occurred in highly diverse samples, haplotype diversity was minimal in fertile men sharing identical marker profiles. Conclusion Although partial AZFc deletion products are highly heterogeneous in terms of amplicon content, this plasticity is not sufficient to account for the observed phenotypical variance. The lack of causative association between the deletion of specific gene copies and infertility suggests that AZFc gene content might be part of a multifactorial network, with Y-lineage evolution emerging as a possible phenotype modulator. PMID:17903263

BAC sequencing using pooled methods.

PubMed

Saski, Christopher A; Feltus, F Alex; Parida, Laxmi; Haiminen, Niina

2015-01-01

Shotgun sequencing and assembly of a large, complex genome can be both expensive and challenging to accurately reconstruct the true genome sequence. Repetitive DNA arrays, paralogous sequences, polyploidy, and heterozygosity are main factors that plague de novo genome sequencing projects that typically result in highly fragmented assemblies and are difficult to extract biological meaning. Targeted, sub-genomic sequencing offers complexity reduction by removing distal segments of the genome and a systematic mechanism for exploring prioritized genomic content through BAC sequencing. If one isolates and sequences the genome fraction that encodes the relevant biological information, then it is possible to reduce overall sequencing costs and efforts that target a genomic segment. This chapter describes the sub-genome assembly protocol for an organism based upon a BAC tiling path derived from a genome-scale physical map or from fine mapping using BACs to target sub-genomic regions. Methods that are described include BAC isolation and mapping, DNA sequencing, and sequence assembly.

Exploring the perception of nursing students about consequences of reflection in clinical settings

PubMed Central

Karimi, Shahnaz; Haghani, Fariba; Yamani, Nikoo; Kalyani, Majid Najafi

2017-01-01

Background Reflection on practical experiences is a key element that enables students to recognize their own strengths and weaknesses and develop nursing skills. Whilst reflection may enhance students’ learning in practice, there is little evidence about nursing students’ perception of the consequences of reflection in clinical settings. Objective This study aimed to explore Iranian nursing students’ perception regarding the consequences of reflection during clinical practices. Methods This qualitative study was conducted by a conventional content analysis approach in two nursing schools at Shiraz and Fasa Universities of Medical Sciences in Iran. Data were collected through in-depth semi-structured interviews during 2015–2016, from 20 students selected by purposive sampling. All the interviews were tape-recorded, transcribed verbatim, and analyzed by content analysis method. Rigor of this study was approved by member check and external audit. Results Two categories emerged from the data analysis, including movement toward professionalism and self-actualization of emotions. The former consisted of three subcategories of function modification, sharing experiences and generalizing experiences. The latter consisted of two subcategories of inner satisfaction and peace of mind. Conclusion The results indicated that nursing students’ reflection in clinical settings is effective in personal and professional levels. Reflection in a personal level led to positive emotions that increased the quality of care in patients. Accordingly, nursing educators need to create a nurturing climate as well as supporting reflective behaviors of nursing students. PMID:29038696

The development of pedagogical content knowledge in science teachers: New opportunities through technology-mediated reflection and peer-exchange

NASA Astrophysics Data System (ADS)

Madeira, M. Cheryl-Ann

This design-based research study investigates the development of pedagogical content knowledge among nine teacher-participants (N = 9) in three design phases. PCK is a particular type of teacher knowledge that addresses not only the teacher's understanding of the content to be instructed, but also ways of how to teach that content effectively. This knowledge has been well documented over several decades, and is seen as central to teacher expertise. However, its actual development has been difficult for researchers to investigate. This study offers a detailed perspective on how teachers developed PCK with their engagement in lesson planning and enactment of a project-based technology-enhanced lesson. The study includes two specific interventions designed to enhance teachers' development of PCK: (1) scaffolded reflection that occurs throughout the practices; and (2) peer-exchange of lesson plans, enactment ideas, and completed reflections. The findings demonstrate that teachers improve their planning and enactment of project-based technology-enhanced lessons with scaffolded reflection and peer exchange. Positive correlations were seen between teachers' engagement in the reflections and the quality of their lesson planning. Teachers who participated more deeply in the scaffolded reflections were able to understand how their lesson plans and enactment patterns fostered student understanding of relevant science concepts. Positive correlations were also seen between community influence and teacher lesson plans and enactment. Additionally, positive correlations were confirmed between teachers' level of participation in the peer exchange activities and the quality of their lesson planning and enactments. Teachers who contributed more deeply within the online and face-to-face peer community meetings benefited from the different perspectives of their peers about student learning and the best ways to succeed with project-based instruction. This study allowed some insight into how PCK develops as a result of teachers' engagement in the complex set of activities that constitute the practices of lesson planning and enactment. The primary implication of this study is that engaging teachers in scaffolded reflections and peer exchange can be a valuable in-service professional development activity. A methodological strength is derived from an approach to coding teachers' lesson planning and enactment according to an activity systems perspective, drawing on a spectrum of data sources (e.g., wiki-based reflections, planning artefacts, videotaped classroom enactments). Teacher learning---particularly the development of PCK---is recognized as critical in promoting student understanding of science concepts. This dissertation lays out a possible foundation for professional development models that promote effective teacher learning.

Study on the prediction of soil heavy metal elements content based on visible near-infrared spectroscopy.

PubMed

Liu, Jinbao; Zhang, Yang; Wang, Huanyuan; Du, Yichun

2018-06-15

The estimation of soils heavy metal content can reflect the impending surroundings of surface, which lays theoretical foundation for using covered vegetation to monitor environment and investigate resource. In this study, the contents of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb in 44 soil samples were collected from Fufeng County, Yangling County and Wugong County, Shaanxi Province and were used as data sources. ASD FieldSpec HR (350-2500nm), and then the NOR, MSC and SNV of the reflectance were pretreated, the first deviation, second deviation and reflectance reciprocal logarithmic transformation were carried out. The optimal spectroscopy estimation model of nine heavy metal elements of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb was established by regression method. Comparing the diffuse reflectance characteristics of different heavy metal contents and the effect of different pretreatment methods on the establishment of soil heavy metal spectral inversion model. The results of chemical analysis show that there was a serious Hg pollution in the study area, and the Cd content was close to the critical value. The results show that: (1) NOR, MSC and SNV were adopted for the acquisition of visible near-infrared. Combining differential transformation can improve the information of heavy metal elements in the soil, and use the correlation band energy Significantly improve the stability and predictability of the model. (2) The modeling accuracy of the optimal model of nine heavy metal spectra of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb by PLSR method were 0.70, 0.79, 0.69, 0.81, 0.86, 0.58, 0.55, 0.99, 0.62. (3) The optimal estimation model of different elements using different treatment methods has better stability and higher precision, and can realize the rapid prediction of nine kinds of heavy metal elements in this region. Copyright © 2018 Elsevier B.V. All rights reserved.

Study on the prediction of soil heavy metal elements content based on visible near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Liu, Jinbao; Zhang, Yang; Wang, Huanyuan; Du, Yichun

2018-06-01

The estimation of soils heavy metal content can reflect the impending surroundings of surface, which lays theoretical foundation for using covered vegetation to monitor environment and investigate resource. In this study, the contents of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb in 44 soil samples were collected from Fufeng County, Yangling County and Wugong County, Shaanxi Province and were used as data sources. ASD FieldSpec HR (350-2500 nm), and then the NOR, MSC and SNV of the reflectance were pretreated, the first deviation, second deviation and reflectance reciprocal logarithmic transformation were carried out. The optimal spectroscopy estimation model of nine heavy metal elements of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb was established by regression method. Comparing the diffuse reflectance characteristics of different heavy metal contents and the effect of different pretreatment methods on the establishment of soil heavy metal spectral inversion model. The results of chemical analysis show that there was a serious Hg pollution in the study area, and the Cd content was close to the critical value. The results show that: (1) NOR, MSC and SNV were adopted for the acquisition of visible near-infrared. Combining differential transformation can improve the information of heavy metal elements in the soil, and use the correlation band energy Significantly improve the stability and predictability of the model. (2) The modeling accuracy of the optimal model of nine heavy metal spectra of Cr, Mn, Ni, Cu, Zn, As, Cd, Hg and Pb by PLSR method were 0.70, 0.79, 0.69, 0.81, 0.86, 0.58, 0.55, 0.99, 0.62. (3) The optimal estimation model of different elements using different treatment methods has better stability and higher precision, and can realize the rapid prediction of nine kinds of heavy metal elements in this region.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

PubMed

Quail, Michael A; Smith, Miriam; Coupland, Paul; Otto, Thomas D; Harris, Simon R; Connor, Thomas R; Bertoni, Anna; Swerdlow, Harold P; Gu, Yong

2012-07-24

Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.

The processing of images of biological threats in visual short-term memory.

PubMed

Quinlan, Philip T; Yue, Yue; Cohen, Dale J

2017-08-30

The idea that there is enhanced memory for negatively, emotionally charged pictures was examined. Performance was measured under rapid, serial visual presentation (RSVP) conditions in which, on every trial, a sequence of six photo-images was presented. Briefly after the offset of the sequence, two alternative images (a target and a foil) were presented and participants attempted to choose which image had occurred in the sequence. Images were of threatening and non-threatening cats and dogs. The target depicted either an animal expressing an emotion distinct from the other images, or the sequences contained only images depicting the same emotional valence. Enhanced memory was found for targets that differed in emotional valence from the other sequence images, compared to targets that expressed the same emotional valence. Further controls in stimulus selection were then introduced and the same emotional distinctiveness effect obtained. In ruling out possible visual and attentional accounts of the data, an informal dual route topic model is discussed. This places emphasis on how visual short-term memory reveals a sensitivity to the emotional content of the input as it unfolds over time. Items that present with a distinctive emotional content stand out in memory. © 2017 The Author(s).

Iterative dictionary construction for compression of large DNA data sets.

PubMed

Kuruppu, Shanika; Beresford-Smith, Bryan; Conway, Thomas; Zobel, Justin

2012-01-01

Genomic repositories increasingly include individual as well as reference sequences, which tend to share long identical and near-identical strings of nucleotides. However, the sequential processing used by most compression algorithms, and the volumes of data involved, mean that these long-range repetitions are not detected. An order-insensitive, disk-based dictionary construction method can detect this repeated content and use it to compress collections of sequences. We explore a dictionary construction method that improves repeat identification in large DNA data sets. Our adaptation, COMRAD, of an existing disk-based method identifies exact repeated content in collections of sequences with similarities within and across the set of input sequences. COMRAD compresses the data over multiple passes, which is an expensive process, but allows COMRAD to compress large data sets within reasonable time and space. COMRAD allows for random access to individual sequences and subsequences without decompressing the whole data set. COMRAD has no competitor in terms of the size of data sets that it can compress (extending to many hundreds of gigabytes) and, even for smaller data sets, the results are competitive compared to alternatives; as an example, 39 S. cerevisiae genomes compressed to 0.25 bits per base.