Community Involvement in School Management in Portugal

ERIC Educational Resources Information Center

Veloso, Luísa; Craveiro, Daniela; Rufino, Isabel

2013-01-01

This article discusses the ways in which the community is involved in Portuguese school management. It is based on an analysis of the external evaluation reports of 298 Portuguese schools for the academic years 2006-07, 2007-08 and 2008-09. The corpus analysed allowed the identification of two main aspects of the participation processes: (1) local…

FY 1987 current fiscal year work plan

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

Not Available

This Current Year Work Plan presents a detailed description of the activities to be performed by the Joint Integration Office during FY87. It breaks down the activities into two major work areas: Program Management and Program Analysis. Program Management is performed by the JIO by providing technical planning and guidance for the development of advanced TRU waste management capabilities. This includes equipment/facility design, engineering, construction, and operations. These functions are integrated to allow transition from interim storage to final disposition. JIO tasks include program requirements identification, long-range technical planning, budget development, program planning document preparation, task guidance, task monitoring, informationmore » gathering and task reporting to DOE, interfacing with other agencies and DOE lead programs, integrating public involvement with program efforts, and preparation of program status reports for DOE. Program Analysis is performed by the JIO to support identification and assessment of alternatives, and development of long-term TRU waste program capabilities. This work plan includes: system analyses, requirements analyses, interim and procedure development, legislative and regulatory analyses, dispatch and traffic analyses, and data bases.« less

Analysing photonic structures in plants

PubMed Central

Vignolini, Silvia; Moyroud, Edwige; Glover, Beverley J.; Steiner, Ullrich

2013-01-01

The outer layers of a range of plant tissues, including flower petals, leaves and fruits, exhibit an intriguing variation of microscopic structures. Some of these structures include ordered periodic multilayers and diffraction gratings that give rise to interesting optical appearances. The colour arising from such structures is generally brighter than pigment-based colour. Here, we describe the main types of photonic structures found in plants and discuss the experimental approaches that can be used to analyse them. These experimental approaches allow identification of the physical mechanisms producing structural colours with a high degree of confidence. PMID:23883949

Endodontic Microbiology and Pathobiology: Current State of Knowledge.

PubMed

Fouad, Ashraf F

2017-01-01

Newer research tools and basic science knowledge base have allowed the exploration of endodontic diseases in the pulp and periapical tissues in novel ways. The use of next generation sequencing, bioinformatics analyses, genome-wide association studies, to name just a few of these innovations, has allowed the identification of hundreds of microorganisms and of host response factors. This review addresses recent advances in endodontic microbiology and the host response and discusses the potential for future innovations in this area. Copyright © 2016 Elsevier Inc. All rights reserved.

Proposed Confidence Scale and ID Score in the Identification of Known-Unknown Compounds Using High Resolution MS Data

NASA Astrophysics Data System (ADS)

Rochat, Bertrand

2017-04-01

High-resolution (HR) MS instruments recording HR-full scan allow analysts to go further beyond pre-acquisition choices. Untargeted acquisition can reveal unexpected compounds or concentrations and can be performed for preliminary diagnosis attempt. Then, revealed compounds will have to be identified for interpretations. Whereas the need of reference standards is mandatory to confirm identification, the diverse information collected from HRMS allows identifying unknown compounds with relatively high degree of confidence without reference standards injected in the same analytical sequence. However, there is a necessity to evaluate the degree of confidence in putative identifications, possibly before further targeted analyses. This is why a confidence scale and a score in the identification of (non-peptidic) known-unknown, defined as compounds with entries in database, is proposed for (LC-) HRMS data. The scale is based on two representative documents edited by the European Commission (2007/657/EC) and the Metabolomics Standard Initiative (MSI), in an attempt to build a bridge between the communities of metabolomics and screening labs. With this confidence scale, an identification (ID) score is determined as [a number, a letter, and a number] (e.g., 2D3), from the following three criteria: I, a General Identification Category (1, confirmed, 2, putatively identified, 3, annotated compounds/classes, and 4, unknown); II, a Chromatography Class based on the relative retention time (from the narrowest tolerance, A, to no chromatographic references, D); and III, an Identification Point Level (1, very high, 2, high, and 3, normal level) based on the number of identification points collected. Three putative identification examples of known-unknown will be presented.

CEQer: a graphical tool for copy number and allelic imbalance detection from whole-exome sequencing data.

PubMed

Piazza, Rocco; Magistroni, Vera; Pirola, Alessandra; Redaelli, Sara; Spinelli, Roberta; Redaelli, Serena; Galbiati, Marta; Valletta, Simona; Giudici, Giovanni; Cazzaniga, Giovanni; Gambacorti-Passerini, Carlo

2013-01-01

Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data.

Identification of Lactobacillus alimentarius and Lactobacillus farciminis with 16S-23S rDNA intergenic spacer region polymorphism and PCR amplification using species-specific oligonucleotide.

PubMed

Rachman, C N; Kabadjova, P; Prévost, H; Dousset, X

2003-01-01

The restriction fragment length polymorphism (RFLP) method was used to differentiate Lactobacillus species having closely related identities in the 16S-23S rDNA intergenic spacer region (ISR). Species-specific primers for Lact. farciminis and Lact. alimentarius were designed and allowed rapid identification of these species. The 16S-23S rDNA spacer region was amplified by primers tAla and 23S/p10, then digested by HinfI and TaqI enzymes and analysed by electrophoresis. Digestion by HinfI was not sufficient to differentiate Lact. sakei, Lact. curvatus, Lact. farciminis, Lact. alimentarius, Lact. plantarum and Lact. paraplantarum. In contrast, digestion carried out by TaqI revealed five different patterns allowing these species to be distinguished, except for Lact. plantarum from Lact. paraplantarum. The 16S-23S rDNA spacer region of Lact. farciminis and Lact. alimentarius were amplified and then cloned into vector pCR(R)2.1 and sequenced. The DNA sequences obtained were analysed and species-specific primers were designed from these sequences. The specificity of these primers was positively demonstrated as no response was obtained for 14 other species tested. The species-specific primers for Lact. farciminis and Lact. alimentarius were shown to be useful for identifying these species among other lactobacilli. The RFLP profile obtained upon digestion with HinfI and TaqI enzymes can be used to discriminate Lact. farciminis, Lact. alimentarius, Lact. sakei, Lact. curvatus and Lact. plantarum. In this paper, we have established the first species-specific primer for PCR identification of Lact. farciminis and Lact. alimentarius. Both species-specific primer and RFLP, could be used as tools for rapid identification of lactobacilli up to species level.

Wound Healing Finally Enters the Age of Molecular Diagnostic Medicine

PubMed Central

Tatum, Owatha L.; Dowd, Scot E.

2012-01-01

Background Many wounds are difficult to heal because of the large, complex community of microbes present within the wound. The Problem Classical laboratory culture methods do not provide an accurate picture of the microbial interactions or representation of microorganisms within a wound. There is an inherent bias in diagnosis based upon classical culture stemming from the ability of certain organisms to thrive in culture while others are underrepresented or fail to be identified in culture altogether. Chronic wounds also contain polymicrobial infections existing as a cooperative community that is resistant to antibiotic therapy. Basic/Clinical Science Advances New methods in molecular diagnostic medicine allow the identification of nearly all organisms present in a wound irrespective of the ability of these organisms to be grown in culture. Advances in DNA analyses allow absolute identification of microorganisms from very small clinical specimens. These new methods also provide a quantitative representation of all microorganisms contributing to these polymicrobial infections. Clinical Care Relevance Technological advances in laboratory diagnostics can significantly shorten the time required to heal chronic wounds. Identification of the genetic signatures of organisms present within a wound allows clinicians to identify and treat the primary organisms responsible for nonhealing wounds. Conclusion Advanced genetic technologies targeting the specific needs of wound care patients are now accessible to all wound care clinicians. PMID:24527290

[The state legal and expert identification aspects of protecting the right of the person for citizens of the Russian Federation].

PubMed

Bykov, I Iu; Kolkutin, V V; Tolmachev, I A; Dmitriev, E G

2000-04-01

The article deals with the questions concerning the problem of person identification, different extreme situations. This problem is closely connected with ensuring of national security of Russia. The authors give the definition of person's right in contact with constant threat to violate this right. Two categories of person's properties are analysed (material and not material) with the help of which it is possible to establish identity of man and his personality. It is noted that protection of person's rights is carried out in six forms. For the first time the possibilities to create organisational system of person identification in the form of Federal service are discussed that must be legislatively secured. Scientific investigation of this problem allowed the authors to submit concrete proposals concerning the question of organisation of state service for person identification.

Development of an optimal filter substrate for the identification of small microplastic particles in food by micro-Raman spectroscopy.

PubMed

Oßmann, Barbara E; Sarau, George; Schmitt, Sebastian W; Holtmannspötter, Heinrich; Christiansen, Silke H; Dicke, Wilhelm

2017-06-01

When analysing microplastics in food, due to toxicological reasons it is important to achieve clear identification of particles down to a size of at least 1 μm. One reliable, optical analytical technique allowing this is micro-Raman spectroscopy. After isolation of particles via filtration, analysis is typically performed directly on the filter surface. In order to obtain high qualitative Raman spectra, the material of the membrane filters should not show any interference in terms of background and Raman signals during spectrum acquisition. To facilitate the usage of automatic particle detection, membrane filters should also show specific optical properties. In this work, beside eight different, commercially available membrane filters, three newly designed metal-coated polycarbonate membrane filters were tested to fulfil these requirements. We found that aluminium-coated polycarbonate membrane filters had ideal characteristics as a substrate for micro-Raman spectroscopy. Its spectrum shows no or minimal interference with particle spectra, depending on the laser wavelength. Furthermore, automatic particle detection can be applied when analysing the filter surface under dark-field illumination. With this new membrane filter, analytics free of interference of microplastics down to a size of 1 μm becomes possible. Thus, an important size class of these contaminants can now be visualized and spectrally identified. Graphical abstract A newly developed aluminium coated polycarbonate membrane filter enables automatic particle detection and generation of high qualitative Raman spectra allowing identification of small microplastics.

Development of sampling method and chromatographic analysis of volatile organic compounds emitted from human skin.

PubMed

Grabowska-Polanowska, Beata; Miarka, Przemysław; Skowron, Monika; Sułowicz, Joanna; Wojtyna, Katarzyna; Moskal, Karolina; Śliwka, Ireneusz

2017-10-01

The studies on volatile organic compounds emitted from skin are an interest for chemists, biologists and physicians due to their role in development of different scientific areas, including medical diagnostics, forensic medicine and the perfume design. This paper presents a proposal of two sampling methods applied to skin odor collection: the first one uses a bag of cellulose film, the second one, using cellulose sachets filled with active carbon. Volatile organic compounds were adsorbed on carbon sorbent, removed via thermal desorption and analyzed using gas chromatograph with mass spectrometer. The first sampling method allowed identification of more compounds (52) comparing to the second one (30). Quantitative analyses for acetone, butanal, pentanal and hexanal were done. The skin odor sampling method using a bag of cellulose film, allowed the identification of many more compounds when compared with the method using a sachet filled with active carbon.

Tools for phospho- and glycoproteomics of plasma membranes.

PubMed

Wiśniewski, Jacek R

2011-07-01

Analysis of plasma membrane proteins and their posttranslational modifications is considered as important for identification of disease markers and targets for drug treatment. Due to their insolubility in water, studying of plasma membrane proteins using mass spectrometry has been difficult for a long time. Recent technological developments in sample preparation together with important improvements in mass spectrometric analysis have facilitated analysis of these proteins and their posttranslational modifications. Now, large scale proteomic analyses allow identification of thousands of membrane proteins from minute amounts of sample. Optimized protocols for affinity enrichment of phosphorylated and glycosylated peptides have set new dimensions in the depth of characterization of these posttranslational modifications of plasma membrane proteins. Here, I summarize recent advances in proteomic technology for the characterization of the cell surface proteins and their modifications. In the focus are approaches allowing large scale mapping rather than analytical methods suitable for studying individual proteins or non-complex mixtures.

Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse.

PubMed

Horta, Maria Augusta Crivelente; Vicentini, Renato; Delabona, Priscila da Silva; Laborda, Prianda; Crucello, Aline; Freitas, Sindélia; Kuroshu, Reginaldo Massanobu; Polikarpov, Igor; Pradella, José Geraldo da Cruz; Souza, Anete Pereira

2014-01-01

Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

Efficient identification of Malassezia yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

PubMed

Kolecka, A; Khayhan, K; Arabatzis, M; Velegraki, A; Kostrzewa, M; Andersson, A; Scheynius, A; Cafarchia, C; Iatta, R; Montagna, M T; Youngchim, S; Cabañes, F J; Hoopman, P; Kraak, B; Groenewald, M; Boekhout, T

2014-02-01

Infections caused by Malassezia yeasts are most likely underdiagnosed, because fatty acid supplementation is needed for growth. Rapid identification of Malassezia species is essential for appropriate treatment of Malassezia-related skin infections, fungaemia and nosocomial outbreaks in neonates, children and adults and can be life-saving for those patients. Ma-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a rapid and reliable diagnostic tool to identify clinically important yeasts, but so far no data have been reported on identification of Malassezia isolates with this technique. To create an extensive database of main mass spectra (MSPs) that will allow quick identification of Malassezia species by MALDI-TOF MS. An in-house library of 113 MSPs was created from 48 reference strains from the CBS-KNAW yeast collection. The in-house library was challenged with two test sets of Malassezia strains, namely 165 reference strains from the CBS collection and 338 isolates collected in Greece, Italy, Sweden and Thailand. MALDI-TOF MS allowed correct identification of all 14 Malassezia spp. MALDI-TOF MS results were concordant with those of sequence analyses of the internal transcribed spacers (ITS1/ITS2) and the D1/D2 domains of the large subunit of the ribosomal DNA. Implementation of the MALDI-TOF MS system as a routine identification tool will contribute to correct identification of Malassezia yeasts with minimal effort and in a short turnaround time, which is especially important for the rapid identification of Malassezia in skin diseases and nosocomial outbreaks. © 2013 British Association of Dermatologists.

Targeting Anti-Cancer Active Compounds: Affinity-Based Chromatographic Assays

PubMed Central

de Moraes, Marcela Cristina; Cardoso, Carmen Lucia; Seidl, Claudia; Moaddel, Ruin; Cass, Quezia Bezerra

2016-01-01

Affinity-based chromatography assays encompass the use of solid supports containing immobilized biological targets to monitor binding events in the isolation , identification and/or characterization of bioactive compounds. This powerful bioanalytical technique allows the screening of potential binders through fast analyses that can be directly performed using isolated substances or complex matrices. An overview of the recent researches in frontal and zonal affinity-based chromatography screening assays, which has been used as a tool in the identification and characterization of new anti-cancer agents, is discussed. In addition, a critical evaluation of the recently emerged ligands fishing assays in complex mixtures is also discussed. PMID:27306095

Forecasting volcanic unrest using seismicity: The good, the bad and the time consuming

NASA Astrophysics Data System (ADS)

Salvage, Rebecca; Neuberg, Jurgen W.

2013-04-01

Volcanic eruptions are inherently unpredictable in nature, with scientists struggling to forecast the type and timing of events, in particular in real time scenarios. Current understanding suggests that the use of statistical patterns within precursory datasets of seismicity prior to eruptive events could hold the potential to be used as real time forecasting tools. They allow us to determine times of clear deviation in data, which might be indicative of volcanic unrest. The identification of low frequency seismic swarms and the acceleration of this seismicity prior to observed volcanic unrest may be key in developing forecasting tools. The development of these real time forecasting models which can be implemented at volcano observatories is of particular importance since the identification of early warning signals allows danger to the proximal population to be minimized. We concentrate on understanding the significance and development of these seismic swarms as unrest develops at the volcano. In particular, analysis of accelerations in event rate, amplitude and energy rates released by seismicity prior to eruption suggests that these are important indicators of developing unrest. Real time analysis of these parameters simultaneously allows possible improvements to forecasting models. Although more time and computationally intense, cross correlation techniques applied to continuous seismicity prior to volcanic unrest scenarios allows all significant seismic events to be analysed, rather than only those which can be detected by an automated identification system. This may allow a more accurate forecast since all precursory seismicity can be taken into account. In addition, the classification of seismic events based on spectral characteristics may allow us to isolate individual types of signals which are responsible for certain types of unrest. In this way, we may be able to better forecast the type of eruption that may ensue, or at least some of its prevailing characteristics.

Isolation and molecular identification of endophytic diazotrophs from seeds and stems of three cereal crops.

PubMed

Liu, Huawei; Zhang, Lei; Meng, Aihua; Zhang, Junbiao; Xie, Miaomiao; Qin, Yaohong; Faulk, Dylan Chase; Zhang, Baohong; Yang, Shushen; Qiu, Li

2017-01-01

Ten strains of endophytic diazotroph were isolated and identified from the plants collected from three different agricultural crop species, wheat, rice and maize, using the nitrogen-free selective isolation conditions. The nitrogen-fixing ability of endophytic diazotroph was verified by the nifH-PCR assay that showed positive nitrogen fixation ability. These identified strains were classified by 879F-RAPD and 16S rRNA sequence analysis. RAPD analyses revealed that the 10 strains were clustered into seven 879F-RAPD groups, suggesting a clonal origin. 16S rRNA sequencing analyses allowed the assignment of the 10 strains to known groups of nitrogen-fixing bacteria, including organisms from the genera Paenibacillus, Enterobacter, Klebsiella and Pantoea. These representative genus are not endophytic diazotrophs in the conventional sense. They may have obtained nitrogen fixation ability through lateral gene transfer, however, the evolutionary forces of lateral gene transfer are not well known. Molecular identification results from 16S rRNA analyses were also confirmed by morphological and biochemical data. The test strains SH6A and MZB showed positive effect on the growth of plants.

A Sparse Matrix Approach for Simultaneous Quantification of Nystagmus and Saccade

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Stone, Lee; Boyle, Richard D.

2012-01-01

The vestibulo-ocular reflex (VOR) consists of two intermingled non-linear subsystems; namely, nystagmus and saccade. Typically, nystagmus is analysed using a single sufficiently long signal or a concatenation of them. Saccade information is not analysed and discarded due to insufficient data length to provide consistent and minimum variance estimates. This paper presents a novel sparse matrix approach to system identification of the VOR. It allows for the simultaneous estimation of both nystagmus and saccade signals. We show via simulation of the VOR that our technique provides consistent and unbiased estimates in the presence of output additive noise.

Dispersive Raman spectroscopy allows the identification and quantification of melanin types

PubMed Central

Galván, Ismael; Jorge, Alberto

2015-01-01

Melanins are the most prevalent pigments in animals and are involved in visual communication by producing colored traits that often evolve as intraspecific signals of quality. Identifying and quantifying melanins are therefore essential to understand the function and evolution of melanin-based signals. However, the analysis of melanins is difficult due to their insolubility and the lack of simple methods that allow the identification of their chemical forms. We recently proposed the use of Raman spectroscopy as a simple, noninvasive technique that can be used to identify and quantify melanins in feathers and hairs. Contrarily, other authors later stated that melanins are characterized by a lack of defined Raman signals. Here, we use confocal Raman microscopy to confirm previous analyses showing that the two main chemical forms of melanins (eumelanin and pheomelanin) exhibit distinct Raman signal and compare different excitation wavelengths to analyze synthetic pheomelanin and natural melanins in feathers of different species of birds. Our analyses indicate that only laser excitation wavelengths below 1064 nm are useful for the analysis of melanins by Raman spectroscopy, and only 780-nm laser in the case of melanins in feathers. These findings show that the capacity of Raman spectroscopy to distinguish different chemical forms of melanins depends on laser power and integration time. As a consequence, Raman spectroscopy should be applied after preliminar analyses using a range of these parameters, especially in fragile biological tissues such as feathers. PMID:25897382

LANDSAT-4 Science Characterization Early Results. Volume 4: Applications. [agriculture, soils land use, geology, hydrology, wetlands, water quality, biomass identification, and snow mapping

NASA Technical Reports Server (NTRS)

Barker, J. L. (Editor)

1985-01-01

The excellent quality of TM data allows researchers to proceed directly with applications analyses, without spending a significant amount of time applying various corrections to the data. The early results derived of TM data are discussed for the following applications: agriculture, land cover/land use, soils, geology, hydrology, wetlands biomass, water quality, and snow.

Invasive candidiasis: future directions in non-culture based diagnosis.

PubMed

Posch, Wilfried; Heimdörfer, David; Wilflingseder, Doris; Lass-Flörl, Cornelia

2017-09-01

Delayed initial antifungal therapy is associated with high mortality rates caused by invasive candida infections, since accurate detection of the opportunistic pathogenic yeast and its identification display a diagnostic challenge. diagnosis of candida infections relies on time-consuming methods such as blood cultures, serologic and histopathologic examination. to allow for fast detection and characterization of invasive candidiasis, there is a need to improve diagnostic tools. trends in diagnostics switch to non-culture-based methods, which allow specified diagnosis within significantly shorter periods of time in order to provide early and appropriate antifungal treatment. Areas covered: within this review comprise novel pathogen- and host-related testing methods, e.g. multiplex-PCR analyses, T2 magnetic resonance, fungus-specific DNA microarrays, microRNA characterization or analyses of IL-17 as biomarker for early detection of invasive candidiasis. Expert commentary: Early recognition and diagnosis of fungal infections is a key issue for improved patient management. As shown in this review, a broad range of novel molecular based tests for the detection and identification of Candida species is available. However, several assays are in-house assays and lack standardization, clinical validation as well as data on sensitivity and specificity. This underscores the need for the development of faster and more accurate diagnostic tests.

CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data

PubMed Central

Piazza, Rocco; Magistroni, Vera; Pirola, Alessandra; Redaelli, Sara; Spinelli, Roberta; Redaelli, Serena; Galbiati, Marta; Valletta, Simona; Giudici, Giovanni; Cazzaniga, Giovanni; Gambacorti-Passerini, Carlo

2013-01-01

Copy number alterations (CNA) are common events occurring in leukaemias and solid tumors. Comparative Genome Hybridization (CGH) is actually the gold standard technique to analyze CNAs; however, CGH analysis requires dedicated instruments and is able to perform only low resolution Loss of Heterozygosity (LOH) analyses. Here we present CEQer (Comparative Exome Quantification analyzer), a new graphical, event-driven tool for CNA/allelic-imbalance (AI) coupled analysis of exome sequencing data. By using case-control matched exome data, CEQer performs a comparative digital exonic quantification to generate CNA data and couples this information with exome-wide LOH and allelic imbalance detection. This data is used to build mixed statistical/heuristic models allowing the identification of CNA/AI events. To test our tool, we initially used in silico generated data, then we performed whole-exome sequencing from 20 leukemic specimens and corresponding matched controls and we analyzed the results using CEQer. Taken globally, these analyses showed that the combined use of comparative digital exon quantification and LOH/AI allows generating very accurate CNA data. Therefore, we propose CEQer as an efficient, robust and user-friendly graphical tool for the identification of CNA/AI in the context of whole-exome sequencing data. PMID:24124457

Structure of Enhanced Cued Recall Task in the 7 Minute Screen Test.

PubMed

Mora-Simon, Sara; Ladera-Fernandez, Valentina; Garcia-Garcia, Ricardo; Patino-Alonso, María C; Perea-Bartolome, M Victoria; Unzueta-Arce, Jaime; Perez-Arechaederra, Diana; Rodriguez-Sanchez, Emiliano

2017-01-01

Episodic memory in the 7 Minute Screen is assessed by the Enhanced Cued Recall (ECR) test. The ECR test is composed of three phases, Identification, Immediate Recall, and Free and Cued Recall. However, just the last phase is considered for the total score. We believe that collecting the performance data of the Identification and Immediate Recall phases could provide information regarding possible difficulties or impairments in the different aspects involved in the temporal mnesic process of acquisition of new information, such as in working memory or visual identification. The objective was to assess the goodness of fit for the three phases of the ECR test using a Confirmatory Factor Analysis (CFA) to show if each phase is separated from each other as a different aspect that participates in the mnesic process. A total of 311 participants greater than 65 years were included in this study. Confirmatory factor analyses were conducted for each individual phase. The analyses show that the ECR test consists of three separate phases that identify different steps of the mnesic process. Individual scores for each phase could allow for investigation of patient performance in different aspects of the memory process and could help in further neuropsychological assessment.

MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: application to the identification of Lupinus nodulating strains.

PubMed

Sánchez-Juanes, Fernando; Ferreira, Laura; Alonso de la Vega, Pablo; Valverde, Angel; Barrios, Milagros León; Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; González-Buitrago, José Manuel; Trujillo, Martha E; Velázquez, Encarna

2013-12-01

Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species. Copyright © 2013. Published by Elsevier GmbH.

Computer aided manual validation of mass spectrometry-based proteomic data.

PubMed

Curran, Timothy G; Bryson, Bryan D; Reigelhaupt, Michael; Johnson, Hannah; White, Forest M

2013-06-15

Advances in mass spectrometry-based proteomic technologies have increased the speed of analysis and the depth provided by a single analysis. Computational tools to evaluate the accuracy of peptide identifications from these high-throughput analyses have not kept pace with technological advances; currently the most common quality evaluation methods are based on statistical analysis of the likelihood of false positive identifications in large-scale data sets. While helpful, these calculations do not consider the accuracy of each identification, thus creating a precarious situation for biologists relying on the data to inform experimental design. Manual validation is the gold standard approach to confirm accuracy of database identifications, but is extremely time-intensive. To palliate the increasing time required to manually validate large proteomic datasets, we provide computer aided manual validation software (CAMV) to expedite the process. Relevant spectra are collected, catalogued, and pre-labeled, allowing users to efficiently judge the quality of each identification and summarize applicable quantitative information. CAMV significantly reduces the burden associated with manual validation and will hopefully encourage broader adoption of manual validation in mass spectrometry-based proteomics. Copyright © 2013 Elsevier Inc. All rights reserved.

Readability of branding symbols in horses and histomorphological alterations at the branding site.

PubMed

Aurich, J E; Wohlsein, P; Wulf, M; Nees, M; Baumgärtner, W; Becker-Birck, M; Aurich, C

2013-03-01

Identification of horses has traditionally been facilitated by hot iron branding, but the extent by which branding symbols and numbers can be identified has not been investigated. The local pathological changes induced by branding are also unknown. This study analysed the readability of branding symbols and histomorphological alterations at the branding sites. A total of 248 horses in an equestrian championship were available for identification of symbols and numbers. A further 28 horses, euthanased for other reasons, provided histological examination of the branding site. All except one horse had evidence of histological changes at the brand site, including epidermal hyperplasia, increase of dermal collagenous fibrous tissue and loss of adnexal structures. In two foals, an ulcerative to necrotizing dermatitis was observed and interpreted as a complication of recent branding lesions. Despite the fact that hot iron branding caused lesions compatible with third degree thermal injury, it did not allow unambiguous identification of a large proportion of older horses. While the breed-specific symbol was consistently identified by three independent investigators in 84% of the horses, the double-digit branding number was read correctly by all three investigators in less than 40%. In conclusion, hot iron branding in horses causes lesions compatible with third degree thermal injury but does not always allow identification of horses. Copyright © 2012 Elsevier Ltd. All rights reserved.

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

PubMed

Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I; Marcotte, Edward M

2011-07-01

Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for every possible PSM and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for most proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses.

MSblender: a probabilistic approach for integrating peptide identifications from multiple database search engines

PubMed Central

Kwon, Taejoon; Choi, Hyungwon; Vogel, Christine; Nesvizhskii, Alexey I.; Marcotte, Edward M.

2011-01-01

Shotgun proteomics using mass spectrometry is a powerful method for protein identification but suffers limited sensitivity in complex samples. Integrating peptide identifications from multiple database search engines is a promising strategy to increase the number of peptide identifications and reduce the volume of unassigned tandem mass spectra. Existing methods pool statistical significance scores such as p-values or posterior probabilities of peptide-spectrum matches (PSMs) from multiple search engines after high scoring peptides have been assigned to spectra, but these methods lack reliable control of identification error rates as data are integrated from different search engines. We developed a statistically coherent method for integrative analysis, termed MSblender. MSblender converts raw search scores from search engines into a probability score for all possible PSMs and properly accounts for the correlation between search scores. The method reliably estimates false discovery rates and identifies more PSMs than any single search engine at the same false discovery rate. Increased identifications increment spectral counts for all detected proteins and allow quantification of proteins that would not have been quantified by individual search engines. We also demonstrate that enhanced quantification contributes to improve sensitivity in differential expression analyses. PMID:21488652

Building model analysis applications with the Joint Universal Parameter IdenTification and Evaluation of Reliability (JUPITER) API

USGS Publications Warehouse

Banta, E.R.; Hill, M.C.; Poeter, E.; Doherty, J.E.; Babendreier, J.

2008-01-01

The open-source, public domain JUPITER (Joint Universal Parameter IdenTification and Evaluation of Reliability) API (Application Programming Interface) provides conventions and Fortran-90 modules to develop applications (computer programs) for analyzing process models. The input and output conventions allow application users to access various applications and the analysis methods they embody with a minimum of time and effort. Process models simulate, for example, physical, chemical, and (or) biological systems of interest using phenomenological, theoretical, or heuristic approaches. The types of model analyses supported by the JUPITER API include, but are not limited to, sensitivity analysis, data needs assessment, calibration, uncertainty analysis, model discrimination, and optimization. The advantages provided by the JUPITER API for users and programmers allow for rapid programming and testing of new ideas. Application-specific coding can be in languages other than the Fortran-90 of the API. This article briefly describes the capabilities and utility of the JUPITER API, lists existing applications, and uses UCODE_2005 as an example.

Tissue microarrays and quantitative tissue-based image analysis as a tool for oncology biomarker and diagnostic development.

PubMed

Dolled-Filhart, Marisa P; Gustavson, Mark D

2012-11-01

Translational oncology has been improved by using tissue microarrays (TMAs), which facilitate biomarker analysis of large cohorts on a single slide. This has allowed for rapid analysis and validation of potential biomarkers for prognostic and predictive value, as well as for evaluation of biomarker prevalence. Coupled with quantitative analysis of immunohistochemical (IHC) staining, objective and standardized biomarker data from tumor samples can further advance companion diagnostic approaches for the identification of drug-responsive or resistant patient subpopulations. This review covers the advantages, disadvantages and applications of TMAs for biomarker research. Research literature and reviews of TMAs and quantitative image analysis methodology have been surveyed for this review (with an AQUA® analysis focus). Applications such as multi-marker diagnostic development and pathway-based biomarker subpopulation analyses are described. Tissue microarrays are a useful tool for biomarker analyses including prevalence surveys, disease progression assessment and addressing potential prognostic or predictive value. By combining quantitative image analysis with TMAs, analyses will be more objective and reproducible, allowing for more robust IHC-based diagnostic test development. Quantitative multi-biomarker IHC diagnostic tests that can predict drug response will allow for greater success of clinical trials for targeted therapies and provide more personalized clinical decision making.

Raman spectroscopic analysis of real samples: Brazilian bauxite mineralogy

NASA Astrophysics Data System (ADS)

Faulstich, Fabiano Richard Leite; Castro, Harlem V.; de Oliveira, Luiz Fernando Cappa; Neumann, Reiner

2011-10-01

In this investigation, Raman spectroscopy with 1064 and 632.8 nm excitation was used to investigate real mineral samples of bauxite ore from mines of Northern Brazil, together with Raman mapping and X-rays diffraction. The obtained results show clearly that the use of microRaman spectroscopy is a powerful tool for the identification of all the minerals usually found in bauxites: gibbsite, kaolinite, goethite, hematite, anatase and quartz. Bulk samples can also be analysed, and FT-Raman is more adequate due to better signal-to-noise ratio and representativity, although not efficient for kaolinite. The identification of fingerprinting vibrations for all the minerals allows the acquisition of Raman-based chemical maps, potentially powerful tools for process mineralogy applied to bauxite ores.

A simple algorithm for the identification of clinical COPD phenotypes.

PubMed

Burgel, Pierre-Régis; Paillasseur, Jean-Louis; Janssens, Wim; Piquet, Jacques; Ter Riet, Gerben; Garcia-Aymerich, Judith; Cosio, Borja; Bakke, Per; Puhan, Milo A; Langhammer, Arnulf; Alfageme, Inmaculada; Almagro, Pere; Ancochea, Julio; Celli, Bartolome R; Casanova, Ciro; de-Torres, Juan P; Decramer, Marc; Echazarreta, Andrés; Esteban, Cristobal; Gomez Punter, Rosa Mar; Han, MeiLan K; Johannessen, Ane; Kaiser, Bernhard; Lamprecht, Bernd; Lange, Peter; Leivseth, Linda; Marin, Jose M; Martin, Francis; Martinez-Camblor, Pablo; Miravitlles, Marc; Oga, Toru; Sofia Ramírez, Ana; Sin, Don D; Sobradillo, Patricia; Soler-Cataluña, Juan J; Turner, Alice M; Verdu Rivera, Francisco Javier; Soriano, Joan B; Roche, Nicolas

2017-11-01

This study aimed to identify simple rules for allocating chronic obstructive pulmonary disease (COPD) patients to clinical phenotypes identified by cluster analyses.Data from 2409 COPD patients of French/Belgian COPD cohorts were analysed using cluster analysis resulting in the identification of subgroups, for which clinical relevance was determined by comparing 3-year all-cause mortality. Classification and regression trees (CARTs) were used to develop an algorithm for allocating patients to these subgroups. This algorithm was tested in 3651 patients from the COPD Cohorts Collaborative International Assessment (3CIA) initiative.Cluster analysis identified five subgroups of COPD patients with different clinical characteristics (especially regarding severity of respiratory disease and the presence of cardiovascular comorbidities and diabetes). The CART-based algorithm indicated that the variables relevant for patient grouping differed markedly between patients with isolated respiratory disease (FEV 1 , dyspnoea grade) and those with multi-morbidity (dyspnoea grade, age, FEV 1 and body mass index). Application of this algorithm to the 3CIA cohorts confirmed that it identified subgroups of patients with different clinical characteristics, mortality rates (median, from 4% to 27%) and age at death (median, from 68 to 76 years).A simple algorithm, integrating respiratory characteristics and comorbidities, allowed the identification of clinically relevant COPD phenotypes. Copyright ©ERS 2017.

Current genetic methodologies in the identification of disaster victims and in forensic analysis.

PubMed

Ziętkiewicz, Ewa; Witt, Magdalena; Daca, Patrycja; Zebracka-Gala, Jadwiga; Goniewicz, Mariusz; Jarząb, Barbara; Witt, Michał

2012-02-01

This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).

Profiling oil sands mixtures from industrial developments and natural groundwaters for source identification.

PubMed

Frank, Richard A; Roy, James W; Bickerton, Greg; Rowland, Steve J; Headley, John V; Scarlett, Alan G; West, Charles E; Peru, Kerry M; Parrott, Joanne L; Conly, F Malcolm; Hewitt, L Mark

2014-01-01

The objective of this study was to identify chemical components that could distinguish chemical mixtures in oil sands process-affected water (OSPW) that had potentially migrated to groundwater in the oil sands development area of northern Alberta, Canada. In the first part of the study, OSPW samples from two different tailings ponds and a broad range of natural groundwater samples were assessed with historically employed techniques as Level-1 analyses, including geochemistry, total concentrations of naphthenic acids (NAs) and synchronous fluorescence spectroscopy (SFS). While these analyses did not allow for reliable source differentiation, they did identify samples containing significant concentrations of oil sands acid-extractable organics (AEOs). In applying Level-2 profiling analyses using electrospray ionization high resolution mass spectrometry (ESI-HRMS) and comprehensive multidimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOF/MS) to samples containing appreciable AEO concentrations, differentiation of natural from OSPW sources was apparent through measurements of O2:O4 ion class ratios (ESI-HRMS) and diagnostic ions for two families of suspected monoaromatic acids (GC × GC-TOF/MS). The resemblance between the AEO profiles from OSPW and from 6 groundwater samples adjacent to two tailings ponds implies a common source, supporting the use of these complimentary analyses for source identification. These samples included two of upward flowing groundwater collected <1 m beneath the Athabasca River, suggesting OSPW-affected groundwater is reaching the river system.

Point-by-point compositional analysis for atom probe tomography.

PubMed

Stephenson, Leigh T; Ceguerra, Anna V; Li, Tong; Rojhirunsakool, Tanaporn; Nag, Soumya; Banerjee, Rajarshi; Cairney, Julie M; Ringer, Simon P

2014-01-01

This new alternate approach to data processing for analyses that traditionally employed grid-based counting methods is necessary because it removes a user-imposed coordinate system that not only limits an analysis but also may introduce errors. We have modified the widely used "binomial" analysis for APT data by replacing grid-based counting with coordinate-independent nearest neighbour identification, improving the measurements and the statistics obtained, allowing quantitative analysis of smaller datasets, and datasets from non-dilute solid solutions. It also allows better visualisation of compositional fluctuations in the data. Our modifications include:.•using spherical k-atom blocks identified by each detected atom's first k nearest neighbours.•3D data visualisation of block composition and nearest neighbour anisotropy.•using z-statistics to directly compare experimental and expected composition curves. Similar modifications may be made to other grid-based counting analyses (contingency table, Langer-Bar-on-Miller, sinusoidal model) and could be instrumental in developing novel data visualisation options.

GOexpress: an R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data.

PubMed

Rue-Albrecht, Kévin; McGettigan, Paul A; Hernández, Belinda; Nalpas, Nicolas C; Magee, David A; Parnell, Andrew C; Gordon, Stephen V; MacHugh, David E

2016-03-11

Identification of gene expression profiles that differentiate experimental groups is critical for discovery and analysis of key molecular pathways and also for selection of robust diagnostic or prognostic biomarkers. While integration of differential expression statistics has been used to refine gene set enrichment analyses, such approaches are typically limited to single gene lists resulting from simple two-group comparisons or time-series analyses. In contrast, functional class scoring and machine learning approaches provide powerful alternative methods to leverage molecular measurements for pathway analyses, and to compare continuous and multi-level categorical factors. We introduce GOexpress, a software package for scoring and summarising the capacity of gene ontology features to simultaneously classify samples from multiple experimental groups. GOexpress integrates normalised gene expression data (e.g., from microarray and RNA-seq experiments) and phenotypic information of individual samples with gene ontology annotations to derive a ranking of genes and gene ontology terms using a supervised learning approach. The default random forest algorithm allows interactions between all experimental factors, and competitive scoring of expressed genes to evaluate their relative importance in classifying predefined groups of samples. GOexpress enables rapid identification and visualisation of ontology-related gene panels that robustly classify groups of samples and supports both categorical (e.g., infection status, treatment) and continuous (e.g., time-series, drug concentrations) experimental factors. The use of standard Bioconductor extension packages and publicly available gene ontology annotations facilitates straightforward integration of GOexpress within existing computational biology pipelines.

Rapid identification of acetic acid bacteria using MALDI-TOF mass spectrometry fingerprinting.

PubMed

Andrés-Barrao, Cristina; Benagli, Cinzia; Chappuis, Malou; Ortega Pérez, Ruben; Tonolla, Mauro; Barja, François

2013-03-01

Acetic acid bacteria (AAB) are widespread microorganisms characterized by their ability to transform alcohols and sugar-alcohols into their corresponding organic acids. The suitability of matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) for the identification of cultured AAB involved in the industrial production of vinegar was evaluated on 64 reference strains from the genera Acetobacter, Gluconacetobacter and Gluconobacter. Analysis of MS spectra obtained from single colonies of these strains confirmed their basic classification based on comparative 16S rRNA gene sequence analysis. MALDI-TOF analyses of isolates from vinegar cross-checked by comparative sequence analysis of 16S rRNA gene fragments allowed AAB to be identified, and it was possible to differentiate them from mixed cultures and non-AAB. The results showed that MALDI-TOF MS analysis was a rapid and reliable method for the clustering and identification of AAB species. Copyright © 2012 Elsevier GmbH. All rights reserved.

Species identification in meat products: A new screening method based on high resolution melting analysis of cyt b gene.

PubMed

Lopez-Oceja, A; Nuñez, C; Baeta, M; Gamarra, D; de Pancorbo, M M

2017-12-15

Meat adulteration by substitution with lower value products and/or mislabeling involves economic, health, quality and socio-religious issues. Therefore, identification and traceability of meat species has become an important subject to detect possible fraudulent practices. In the present study the development of a high resolution melt (HRM) screening method for the identification of eight common meat species is reported. Samples from Bos taurus, Ovis aries, Sus scrofa domestica, Equus caballus, Oryctolagus cuniculus, Gallus gallus domesticus, Meleagris gallopavo and Coturnix coturnix were analyzed through the amplification of a 148 bp fragment from the cyt b gene with a universal primer pair in HRM analyses. Melting profiles from each species, as well as from several DNA mixtures of these species and blind samples, allowed a successful species differentiation. The results demonstrated that the HRM method here proposed is a fast, reliable, and low-cost screening technique. Copyright © 2017 Elsevier Ltd. All rights reserved.

On the identification of folium and orchil on illuminated manuscripts

NASA Astrophysics Data System (ADS)

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-01

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books.

[Feasibility and acceptance of computer-based assessment for the identification of psychosocially distressed patients in routine clinical care].

PubMed

Sehlen, Susanne; Ott, Martin; Marten-Mittag, Birgitt; Haimerl, Wolfgang; Dinkel, Andreas; Duehmke, Eckhart; Klein, Christian; Schaefer, Christof; Herschbach, Peter

2012-07-01

This study investigated feasibility and acceptance of computer-based assessment for the identification of psychosocial distress in routine radiotherapy care. 155 cancer patients were assessed using QSC-R10, PO-Bado-SF and Mach-9. The congruence between computerized tablet PC and conventional paper assessment was analysed in 50 patients. The agreement between the 2 modes was high (ICC 0.869-0.980). Acceptance of computer-based assessment was very high (>95%). Sex, age, education, distress and Karnofsky performance status (KPS) did not influence acceptance. Computerized assessment was rated more difficult by older patients (p = 0.039) and patients with low KPS (p = 0.020). 75.5% of the respondents supported referral for psycho-social intervention for distressed patients. The prevalence of distress was 27.1% (QSC-R10). Computer-based assessment allows easy identification of distressed patients. Level of staff involvement is low, and the results are quickly available for care providers. © Georg Thieme Verlag KG Stuttgart · New York.

Direct identification of bacteria in positive blood culture bottles by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry.

PubMed

La Scola, Bernard; Raoult, Didier

2009-11-25

With long delays observed between sampling and availability of results, the usefulness of blood cultures in the context of emergency infectious diseases has recently been questioned. Among methods that allow quicker bacterial identification from growing colonies, matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) mass spectrometry was demonstrated to accurately identify bacteria routinely isolated in a clinical biology laboratory. In order to speed up the identification process, in the present work we attempted bacterial identification directly from blood culture bottles detected positive by the automate. We prospectively analysed routine MALDI-TOF identification of bacteria detected in blood culture by two different protocols involving successive centrifugations and then lysis by trifluoroacetic acid or formic acid. Of the 562 blood culture broths detected as positive by the automate and containing one bacterial species, 370 (66%) were correctly identified. Changing the protocol from trifluoroacetic acid to formic acid improved identification of Staphylococci, and overall correct identification increased from 59% to 76%. Lack of identification was observed mostly with viridans streptococci, and only one false positive was observed. In the 22 positive blood culture broths that contained two or more different species, only one of the species was identified in 18 samples, no species were identified in two samples and false species identifications were obtained in two cases. The positive predictive value of bacterial identification using this procedure was 99.2%. MALDI-TOF MS is an efficient method for direct routine identification of bacterial isolates in blood culture, with the exception of polymicrobial samples and viridans streptococci. It may replace routine identification performed on colonies, provided improvement for the specificity of blood culture broths growing viridans streptococci is obtained in the near future.

Ear biometrics for patient identification in global health: a cross-sectional study to test the feasibility of a simplified algorithm.

PubMed

Ragan, Elizabeth J; Johnson, Courtney; Milton, Jacqueline N; Gill, Christopher J

2016-11-02

One of the greatest public health challenges in low- and middle-income countries (LMICs) is identifying people over time and space. Recent years have seen an explosion of interest in developing electronic approaches to addressing this problem, with mobile technology at the forefront of these efforts. We investigate the possibility of biometrics as a simple, cost-efficient, and portable solution. Common biometrics approaches include fingerprinting, iris scanning and facial recognition, but all are less than ideal due to complexity, infringement on privacy, cost, or portability. Ear biometrics, however, proved to be a unique and viable solution. We developed an identification algorithm then conducted a cross sectional study in which we photographed left and right ears from 25 consenting adults. We then conducted re-identification and statistical analyses to identify the accuracy and replicability of our approach. Through principal component analysis, we found the curve of the ear helix to be the most reliable anatomical structure and the basis for re-identification. Although an individual ear allowed for high re-identification rate (88.3%), when both left and right ears were paired together, our rate of re-identification amidst the pool of potential matches was 100%. The results of this study have implications on future efforts towards building a biometrics solution for patient identification in LMICs. We provide a conceptual platform for further investigation into the development of an ear biometrics identification mobile application.

New paleoradiological investigations of ancient human remains from North West Lombardy archaeological excavations.

PubMed

Licata, Marta; Borgo, Melania; Armocida, Giuseppe; Nicosia, Luca; Ferioli, Elena

2016-03-01

Since its birth in 1895, radiology has been used to study ancient mummies. The purpose of this article is to present paleoradiological investigations conducted on several medieval human remains in Varese province. Anthropological (generic identification) and paleopathological analyses were carried out with the support of diagnostic imaging (X-ray and CT scans). Human remains were discovered during excavations of medieval archaeological sites in northwest Lombardy. Classical physical anthropological methods were used for the macroscopic identification of the human remains. X-ray and CT scans were performed on the same scanner (16-layer Hitachi Eclos 16 X-ray equipment). Results Radiological analysis permitted investigating (1) the sex, (2) age of death, (3) type of trauma, (4) therapeutic interventions and (5) osteomas in ancient human remains. In particular, X-ray and CT examinations showed dimorphic facial traits on the mummified skull, and the same radiological approaches allowed determining the age at death from a mummified lower limb. CT analyses allow investigating different types of traumatic lesions in skulls and postcranial skeleton portions and reconstructing the gait and functional outcomes of a fractured femur. Moreover, one case of possible Gardner’s syndrome (GS) was postulated from observing multiple osteomas in an ancient skull. Among the medical tests available to the clinician, radiology is the most appropriate first-line procedure for a diagnostic approach to ancient human remains because it can be performed without causing any significant damage to the specimen.

Multivariate analyses of individual variation in soccer skill as a tool for talent identification and development: utilising evolutionary theory in sports science.

PubMed

Wilson, Robbie S; James, Rob S; David, Gwendolyn; Hermann, Ecki; Morgan, Oliver J; Niehaus, Amanda C; Hunter, Andrew; Thake, Doug; Smith, Michelle D

2016-11-01

The development of a comprehensive protocol for quantifying soccer-specific skill could markedly improve both talent identification and development. Surprisingly, most protocols for talent identification in soccer still focus on the more generic athletic attributes of team sports, such as speed, strength, agility and endurance, rather than on a player's technical skills. We used a multivariate methodology borrowed from evolutionary analyses of adaptation to develop our quantitative assessment of individual soccer-specific skill. We tested the performance of 40 individual academy-level players in eight different soccer-specific tasks across an age range of 13-18 years old. We first quantified the repeatability of each skill performance then explored the effects of age on soccer-specific skill, correlations between each of the pairs of skill tasks independent of age, and finally developed an individual metric of overall skill performance that could be easily used by coaches. All of our measured traits were highly repeatable when assessed over a short period and we found that an individual's overall skill - as well as their performance in their best task - was strongly positively correlated with age. Most importantly, our study established a simple but comprehensive methodology for assessing skill performance in soccer players, thus allowing coaches to rapidly assess the relative abilities of their players, identify promising youths and work on eliminating skill deficits in players.

Association Studies of Sporadic Parkinson’s Disease in the Genomic Era

PubMed Central

Labbé, Catherine; Ross, Owen A

2014-01-01

Parkinson’s disease is a common age-related progressive neurodegenerative disorder. Over the last 10 years, advances have been made in our understanding of the etiology of the disease with the greatest insights perhaps coming from genetic studies, including genome-wide association approaches. These large scale studies allow the identification of genomic regions harboring common variants associated to disease risk. Since the first genome-wide association study on sporadic Parkinson’s disease performed in 2005, improvements in study design, including the advent of meta-analyses, have allowed the identification of ~21 susceptibility loci. The first loci to be nominated were previously associated to familial PD (SNCA, MAPT, LRRK2) and these have been extensively replicated. For other more recently identified loci (SREBF1, SCARB2, RIT2) independent replication is still warranted. Cumulative risk estimates of associated variants suggest that more loci are still to be discovered. Additional association studies combined with deep re-sequencing of known genome-wide association study loci are necessary to identify the functional variants that drive disease risk. As each of these associated genes and variants are identified they will give insight into the biological pathways involved the etiology of Parkinson’s disease. This will ultimately lead to the identification of molecules that can be used as biomarkers for diagnosis and as targets for the development of better, personalized treatment. PMID:24653658

Identification of Novel Placentally Expressed Aspartic Proteinase in Humans

PubMed Central

Majewska, Marta; Lipka, Aleksandra; Panasiewicz, Grzegorz; Gowkielewicz, Marek; Jozwik, Marcin; Majewski, Mariusz Krzysztof; Szafranska, Bozena

2017-01-01

This study presents pioneering data concerning the human pregnancy-associated glycoprotein-Like family, identified in the genome, of the term placental transcriptome and proteome. RNA-seq allowed the identification of 1364 bp hPAG-L/pep cDNA with at least 56.5% homology with other aspartic proteinases (APs). In silico analyses revealed 388 amino acids (aa) of full-length hPAG-L polypeptide precursor, with 15 aa-signal peptide, 47 aa-blocking peptide and 326 aa-mature protein, and two Asp residues (D), specific for a catalytic cleft of the APs (VVFDTGSSNLWV91-102 and AIVDTGTSLLTG274-285). Capillary sequencing identified 9330 bp of the hPAG-L gene (Gen Bank Acc. No. KX533473), composed of nine exons and eight introns. Heterologous Western blotting revealed the presence of one dominant 60 kDa isoform of the hPAG-L amongst cellular placental proteins. Detection with anti-pPAG-P and anti-Rec pPAG2 polyclonals allowed identification of the hPAG-L proteins located within regions of chorionic villi, especially within the syncytiotrophoblast of term singleton placentas. Our novel data extend the present knowledge about the human genome, as well as placental transcriptome and proteome during term pregnancy. Presumably, this may contribute to establishing a new diagnostic tool for examination of some disturbances during human pregnancy, as well as growing interest from both scientific and clinical perspectives. PMID:28594357

Identification of Novel Placentally Expressed Aspartic Proteinase in Humans.

PubMed

Majewska, Marta; Lipka, Aleksandra; Panasiewicz, Grzegorz; Gowkielewicz, Marek; Jozwik, Marcin; Majewski, Mariusz Krzysztof; Szafranska, Bozena

2017-06-08

This study presents pioneering data concerning the human pregnancy-associated glycoprotein-Like family, identified in the genome, of the term placental transcriptome and proteome. RNA-seq allowed the identification of 1364 bp hPAG-L/pep cDNA with at least 56.5% homology with other aspartic proteinases (APs). In silico analyses revealed 388 amino acids (aa) of full-length hPAG-L polypeptide precursor, with 15 aa-signal peptide, 47 aa-blocking peptide and 326 aa-mature protein, and two Asp residues (D), specific for a catalytic cleft of the APs (VVFDTGSSNLWV91-102 and AIVDTGTSLLTG274-285). Capillary sequencing identified 9330 bp of the hPAG-L gene (Gen Bank Acc. No. KX533473), composed of nine exons and eight introns. Heterologous Western blotting revealed the presence of one dominant 60 kDa isoform of the hPAG-L amongst cellular placental proteins. Detection with anti-pPAG-P and anti-Rec pPAG2 polyclonals allowed identification of the hPAG-L proteins located within regions of chorionic villi, especially within the syncytiotrophoblast of term singleton placentas. Our novel data extend the present knowledge about the human genome, as well as placental transcriptome and proteome during term pregnancy. Presumably, this may contribute to establishing a new diagnostic tool for examination of some disturbances during human pregnancy, as well as growing interest from both scientific and clinical perspectives.

A signal-detection-based diagnostic-feature-detection model of eyewitness identification.

PubMed

Wixted, John T; Mickes, Laura

2014-04-01

The theoretical understanding of eyewitness identifications made from a police lineup has long been guided by the distinction between absolute and relative decision strategies. In addition, the accuracy of identifications associated with different eyewitness memory procedures has long been evaluated using measures like the diagnosticity ratio (the correct identification rate divided by the false identification rate). Framed in terms of signal-detection theory, both the absolute/relative distinction and the diagnosticity ratio are mainly relevant to response bias while remaining silent about the key issue of diagnostic accuracy, or discriminability (i.e., the ability to tell the difference between innocent and guilty suspects in a lineup). Here, we propose a signal-detection-based model of eyewitness identification, one that encourages the use of (and helps to conceptualize) receiver operating characteristic (ROC) analysis to measure discriminability. Recent ROC analyses indicate that the simultaneous presentation of faces in a lineup yields higher discriminability than the presentation of faces in isolation, and we propose a diagnostic feature-detection hypothesis to account for that result. According to this hypothesis, the simultaneous presentation of faces allows the eyewitness to appreciate that certain facial features (viz., those that are shared by everyone in the lineup) are non-diagnostic of guilt. To the extent that those non-diagnostic features are discounted in favor of potentially more diagnostic features, the ability to discriminate innocent from guilty suspects will be enhanced.

Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing

PubMed Central

Bohmann, Kristine; Monadjem, Ara; Lehmkuhl Noer, Christina; Rasmussen, Morten; Zeale, Matt R. K.; Clare, Elizabeth; Jones, Gareth; Willerslev, Eske; Gilbert, M. Thomas P.

2011-01-01

Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep-sequence uniquely 5′ tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI sequences in the GenBank and BOLD databases, similarity to existing collections allowed the preliminary identification of 25 prey families from six orders of insects within the diet of C. pumilus, and 24 families from seven orders within the diet of M. condylurus. Insects identified to families within the orders Lepidoptera and Diptera were widely present among the faecal samples analysed. The two families that were observed most frequently were Noctuidae and Nymphalidae (Lepidoptera). Species-level analysis of the data was accomplished using novel bioinformatics techniques for the identification of molecular operational taxonomic units (MOTU). Based on these analyses, our data provide little evidence of resource partitioning between sympatric M. condylurus and C. pumilus in the Simunye region of Swaziland at the time of year when the samples were collected, although as more complete databases against which to compare the sequences are generated this may have to be re-evaluated. PMID:21731749

Regularities in eyewitness identification.

PubMed

Clark, Steven E; Howell, Ryan T; Davey, Sherrie L

2008-06-01

What do eyewitness identification experiments typically show? We address this question through a meta-analysis of 94 comparisons between target-present and target-absent lineups. The analyses showed that: (a) correct identifications and correct-nonidentifications were uncorrelated, (b) suspect identifications were more diagnostic with respect to the suspect's guilt or innocence than any other response, (c) nonidentifications were diagnostic of the suspect's innocence, (d) the diagnosticity of foil identifications depended on lineup composition, and (e) don't know responses were nondiagnostic with respect to guilt or innocence. Results of diagnosticity analyses for simultaneous and sequential lineups varied for full-sample versus direct-comparison analyses. Diagnosticity patterns also varied as a function of lineup composition. Theoretical, forensic, and legal implications are discussed.

Genetic identification of the main opportunistic Mucorales by PCR-restriction fragment length polymorphism.

PubMed

Machouart, M; Larché, J; Burton, K; Collomb, J; Maurer, P; Cintrat, A; Biava, M F; Greciano, S; Kuijpers, A F A; Contet-Audonneau, N; de Hoog, G S; Gérard, A; Fortier, B

2006-03-01

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera Absidia, Mucor, Rhizopus, and Rhizomucor, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis.

Genetic Identification of the Main Opportunistic Mucorales by PCR-Restriction Fragment Length Polymorphism

PubMed Central

Machouart, M.; Larché, J.; Burton, K.; Collomb, J.; Maurer, P.; Cintrat, A.; Biava, M. F.; Greciano, S.; Kuijpers, A. F. A.; Contet-Audonneau, N.; de Hoog, G. S.; Gérard, A.; Fortier, B.

2006-01-01

Mucormycosis is a rare and opportunistic infection caused by fungi belonging to the order Mucorales. Recent reports have demonstrated an increasing incidence of mucormycosis, which is frequently lethal, especially in patients suffering from severe underlying conditions such as immunodeficiency. In addition, even though conventional mycology and histopathology assays allow for the identification of Mucorales, they often fail in offering a species-specific diagnosis. Due to the lack of other laboratory tests, a precise identification of these molds is thus notoriously difficult. In this study we aimed to develop a molecular biology tool to identify the main Mucorales involved in human pathology. A PCR strategy selectively amplifies genomic DNA from molds belonging to the genera Absidia, Mucor, Rhizopus, and Rhizomucor, excluding human DNA and DNA from other filamentous fungi and yeasts. A subsequent digestion step identified the Mucorales at genus and species level. This technique was validated using both fungal cultures and retrospective analyses of clinical samples. By enabling a rapid and precise identification of Mucorales strains in infected patients, this PCR-restriction fragment length polymorphism-based method should help clinicians to decide on the appropriate treatment, consequently decreasing the mortality of mucormycosis. PMID:16517858

Provenance Challenges for Earth Science Dataset Publication

NASA Technical Reports Server (NTRS)

Tilmes, Curt

2011-01-01

Modern science is increasingly dependent on computational analysis of very large data sets. Organizing, referencing, publishing those data has become a complex problem. Published research that depends on such data often fails to cite the data in sufficient detail to allow an independent scientist to reproduce the original experiments and analyses. This paper explores some of the challenges related to data identification, equivalence and reproducibility in the domain of data intensive scientific processing. It will use the example of Earth Science satellite data, but the challenges also apply to other domains.

Hydrological information system based on on-line monitoring--from strategy to implementation in the Brantas River Basin, East Java, Indonesia.

PubMed

Marini, G W; Wellguni, H

2003-01-01

The worsening environmental situation of the Brantas River, East Java, is addressed by a comprehensive basin management strategy which relies on accurate water quantity and quality data retrieved from a newly installed online monitoring network. Integrated into a Hydrological Information System, the continuously measured indicative parameters allow early warning, control and polluter identification. Additionally, long-term analyses have been initiated for improving modelling applications like flood forecasting, water resource management and pollutant propagation. Preliminary results illustrate the efficiency of the installed system.

Comparing efficacy of different taxonomic resolutions and surrogates in detecting changes in soft bottom assemblages due to coastal defence structures.

PubMed

Bertasi, Fabio; Colangelo, Marina Antonia; Colosio, Francesco; Gregorio, Gianni; Abbiati, Marco; Ceccherelli, Victor Ugo

2009-05-01

Sandy shores on the West coast of the North Adriatic Sea are extensively protected by different types of defence structures to prevent coastal erosion. Coastal defence schemes modify the hydrodynamic regime, the sediment structure and composition thus affecting the benthic assemblages. This study examines the effectiveness in detecting changes in soft bottom assemblages caused by coastal defence structures by using different levels of taxonomic resolution, polychaetes and/or bivalves as surrogates and different data transformations. A synoptic analyses of three datasets of subtidal benthic macrofauna used in studies aimed at assessing the impact of breakwaters along the North Adriatic coast has been done. Analyses of similarities and correlations between distance matrices were done using matrices with different levels of taxonomic resolution, and with polychaetes or bivalves data alone. Lentidium mediterraneum was the most abundant species in all datasets. Its abundance was not consistently related to the presence of defence structures. Moreover, distribution patterns of L. mediterraneum were masking the structure of the whole macrofaunal assemblages. Removal of L. mediterraneum from the datasets allowed the detection of changes in benthic assemblages due to coastal defences. Analyses on different levels of taxonomic resolution showed that the level of family maintained sufficient information to detect the impacts of coastal defence structures on benthic assemblages. Moreover, the outcomes depended on the transformation used. Patterns of distribution of bivalves, used as surrogates, showed low correlations with the patterns of the total macrofaunal species assemblages. Patterns of polychaetes, if identified to the species or genus level showed higher correlations with the whole dataset. However, the identification of polychaetes to species and genus level is as costly as the identification of all macrobenthic taxa at family level. This study provided additional evidences that taxonomic sufficiency is a useful tool in environmental monitoring, also in investigations on the impacts of coastal defence structures on subtidal macrofauna. The use of coarser taxonomic level, being time-efficient, would allow improving sampling designs of monitoring programs by increasing replication in space and time and by allowing long term monitoring studies.

Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.

PubMed

Barghini, Elena; Mascagni, Flavia; Natali, Lucia; Giordani, Tommaso; Cavallini, Andrea

2017-02-01

Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.

MALDI-TOF mass spectrometry as a potential tool for Trichomonas vaginalis identification.

PubMed

Calderaro, Adriana; Piergianni, Maddalena; Montecchini, Sara; Buttrini, Mirko; Piccolo, Giovanna; Rossi, Sabina; Arcangeletti, Maria Cristina; Medici, Maria Cristina; Chezzi, Carlo; De Conto, Flora

2016-06-10

Trichomonas vaginalis is a flagellated protozoan causing trichomoniasis, a sexually transmitted human infection, with around 276.4 million new cases estimated by World Health Organization. Culture is the gold standard method for the diagnosis of T. vaginalis infection. Recently, immunochromatographic assays as well as PCR assays for the detection of T. vaginalis antigen or DNA, respectively, have been also available. Although the well-known genome sequence of T. vaginalis has made possible the application of proteomic studies, few data are available about the overall proteomic expression profiling of T. vaginalis. The aim of this study was to investigate the potential application of MALDI-TOF MS as a new tool for the identification of T. vaginalis. Twenty-one isolates were analysed by MALDI-TOF MS after the creation of a Main Spectrum Profile (MSP) from a T. vaginalis reference strain (G3) and its subsequent supplementation in the Bruker Daltonics database, not including any profile of protozoa. This was achieved after the development of a new identification method created by modifying the range setting (6-10 kDa) for the MALDI-TOF MS analysis in order to exclude the overlapping of peaks derived from the culture media used in this study. Two MSP reference spectra were created in 2 different range: 3-15 kDa (standard range setting) and 6-10 kDa (new range setting). Both MSP spectra were deposited in the MALDI BioTyper database for further identification of additional T. vaginalis strains. All the 21 strains analysed in this study were correctly identified by using the new identification method. In this study it was demonstrated that changes in the MALDI-TOF MS standard parameters usually used to identify bacteria and fungi allowed the identification of the protozoan T. vaginalis. This study shows the usefulness of MALDI-TOF MS in the reliable identification of microorganism grown on complex liquid media such as the protozoan T. vaginalis, on the basis of the proteic profile and not on the basis of single markers, by using a "new range setting" different from that developed for bacteria and fungi.

Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples

PubMed Central

Williamson, Charles H. D.; Sanchez, Daniel E.; Sobek, Colin J.; Chambers, Carol L.

2016-01-01

Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa. PMID:27654850

Species From Feces: Order-Wide Identification of Chiroptera From Guano and Other Non-Invasive Genetic Samples.

PubMed

Walker, Faith M; Williamson, Charles H D; Sanchez, Daniel E; Sobek, Colin J; Chambers, Carol L

Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sanger and Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.

hEIDI: An Intuitive Application Tool To Organize and Treat Large-Scale Proteomics Data.

PubMed

Hesse, Anne-Marie; Dupierris, Véronique; Adam, Claire; Court, Magali; Barthe, Damien; Emadali, Anouk; Masselon, Christophe; Ferro, Myriam; Bruley, Christophe

2016-10-07

Advances in high-throughput proteomics have led to a rapid increase in the number, size, and complexity of the associated data sets. Managing and extracting reliable information from such large series of data sets require the use of dedicated software organized in a consistent pipeline to reduce, validate, exploit, and ultimately export data. The compilation of multiple mass-spectrometry-based identification and quantification results obtained in the context of a large-scale project represents a real challenge for developers of bioinformatics solutions. In response to this challenge, we developed a dedicated software suite called hEIDI to manage and combine both identifications and semiquantitative data related to multiple LC-MS/MS analyses. This paper describes how, through a user-friendly interface, hEIDI can be used to compile analyses and retrieve lists of nonredundant protein groups. Moreover, hEIDI allows direct comparison of series of analyses, on the basis of protein groups, while ensuring consistent protein inference and also computing spectral counts. hEIDI ensures that validated results are compliant with MIAPE guidelines as all information related to samples and results is stored in appropriate databases. Thanks to the database structure, validated results generated within hEIDI can be easily exported in the PRIDE XML format for subsequent publication. hEIDI can be downloaded from http://biodev.extra.cea.fr/docs/heidi .

Nuclear processes associated with plant immunity and pathogen susceptibility

PubMed Central

Motion, Graham B.; Amaro, Tiago M.M.M.; Kulagina, Natalja

2015-01-01

Plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. Plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. Genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. Similarly, functional genomics and the emergence of pathogen genomes have allowed reciprocal studies on the mechanisms governing pathogen virulence and host susceptibility, collectively allowing more comprehensive views on the processes that govern disease and resistance. Among others, the identification of secreted pathogen molecules (effectors) that modify immunity-associated processes has changed the plant–microbe interactions conceptual landscape. Effectors are now considered both important factors facilitating disease and novel probes, suited to study immunity in plants. In this review, we will describe the various mechanisms and processes that take place in the nucleus and help regulate immune responses in plants. Based on the premise that any process required for immunity could be targeted by pathogen effectors, we highlight and describe a number of functional assays that should help determine effector functions and their impact on immune-related processes. The identification of new effector functions that modify nuclear processes will help dissect nuclear signalling further and assist us in our bid to bolster immunity in crop plants. PMID:25846755

Nuclear processes associated with plant immunity and pathogen susceptibility.

PubMed

Motion, Graham B; Amaro, Tiago M M M; Kulagina, Natalja; Huitema, Edgar

2015-07-01

Plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. Plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. Genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. Similarly, functional genomics and the emergence of pathogen genomes have allowed reciprocal studies on the mechanisms governing pathogen virulence and host susceptibility, collectively allowing more comprehensive views on the processes that govern disease and resistance. Among others, the identification of secreted pathogen molecules (effectors) that modify immunity-associated processes has changed the plant-microbe interactions conceptual landscape. Effectors are now considered both important factors facilitating disease and novel probes, suited to study immunity in plants. In this review, we will describe the various mechanisms and processes that take place in the nucleus and help regulate immune responses in plants. Based on the premise that any process required for immunity could be targeted by pathogen effectors, we highlight and describe a number of functional assays that should help determine effector functions and their impact on immune-related processes. The identification of new effector functions that modify nuclear processes will help dissect nuclear signalling further and assist us in our bid to bolster immunity in crop plants. © The Author 2015. Published by Oxford University Press.

Molecular Barcoding of Aquatic Oligochaetes: Implications for Biomonitoring

PubMed Central

Vivien, Régis; Wyler, Sofia; Lafont, Michel; Pawlowski, Jan

2015-01-01

Aquatic oligochaetes are well recognized bioindicators of quality of sediments and water in watercourses and lakes. However, the difficult taxonomic determination based on morphological features compromises their more common use in eco-diagnostic analyses. To overcome this limitation, we investigated molecular barcodes as identification tool for broad range of taxa of aquatic oligochaetes. We report 185 COI and 52 ITS2 rDNA sequences for specimens collected in Switzerland and belonging to the families Naididae, Lumbriculidae, Enchytraeidae and Lumbricidae. Phylogenetic analyses allowed distinguishing 41 lineages separated by more than 10 % divergence in COI sequences. The lineage distinction was confirmed by Automatic Barcode Gap Discovery (ABGD) method and by ITS2 data. Our results showed that morphological identification underestimates the oligochaete diversity. Only 26 of the lineages could be assigned to morphospecies, of which seven were sequenced for the first time. Several cryptic species were detected within common morphospecies. Many juvenile specimens that could not be assigned morphologically have found their home after genetic analysis. Our study showed that COI barcodes performed very well as species identifiers in aquatic oligochaetes. Their easy amplification and good taxonomic resolution might help promoting aquatic oligochaetes as bioindicators for next generation environmental DNA biomonitoring of aquatic ecosystems. PMID:25856230

Ultraweak photon emission and proteomics analyses in soybean under abiotic stress.

PubMed

Komatsu, Setsuko; Kamal, Abu Hena Mostafa; Makino, Takahiro; Hossain, Zahed

2014-07-01

Biophotons are ultraweak photon emissions that are closely related to various biological activities and processes. In mammals, biophoton emissions originate from oxidative bursts in immunocytes during immunological responses. Biophotons emitted from plant organs provide novel information about the physiological state of plant under in vivo condition. In this review, the principles and recent advances in the measurement of biophoton emissions in plants are described. Furthermore, examples of biophoton emission and proteomics in soybean under abiotic stress are reviewed and discussed. Finally, this review suggests that the application of proteomics should provide a better interpretation of plant response to biophoton emission and allow the identification of genes that will allow the screening of crops able to produce maximal yields, even in stressful environments. Copyright © 2014 Elsevier B.V. All rights reserved.

Translational research in pediatrics III: bronchoalveolar lavage.

PubMed

Radhakrishnan, Dhenuka; Yamashita, Cory; Gillio-Meina, Carolina; Fraser, Douglas D

2014-07-01

The role of flexible bronchoscopy and bronchoalveolar lavage (BAL) for the care of children with airway and pulmonary diseases is well established, with collected BAL fluid most often used clinically for microbiologic pathogen identification and cellular analyses. More recently, powerful analytic research methods have been used to investigate BAL samples to better understand the pathophysiological basis of pediatric respiratory disease. Investigations have focused on the cellular components contained in BAL fluid, such as macrophages, lymphocytes, neutrophils, eosinophils, and mast cells, as well as the noncellular components such as serum molecules, inflammatory proteins, and surfactant. Molecular techniques are frequently used to investigate BAL fluid for the presence of infectious pathologies and for cellular gene expression. Recent advances in proteomics allow identification of multiple protein expression patterns linked to specific respiratory diseases, whereas newer analytic techniques allow for investigations on surfactant quantification and function. These translational research studies on BAL fluid have aided our understanding of pulmonary inflammation and the injury/repair responses in children. We review the ethics and practices for the execution of BAL in children for translational research purposes, with an emphasis on the optimal handling and processing of BAL samples. Copyright © 2014 by the American Academy of Pediatrics.

Serial analysis of gene expression (SAGE) in bovine trypanotolerance: preliminary results

PubMed Central

2003-01-01

In Africa, trypanosomosis is a tsetse-transmitted disease which represents the most important constraint to livestock production. Several indigenous West African taurine (Bos taurus) breeds, such as the Longhorn (N'Dama) cattle are well known to control trypanosome infections. This genetic ability named "trypanotolerance" results from various biological mechanisms under multigenic control. The methodologies used so far have not succeeded in identifying the complete pool of genes involved in trypanotolerance. New post genomic biotechnologies such as transcriptome analyses are efficient in characterising the pool of genes involved in the expression of specific biological functions. We used the serial analysis of gene expression (SAGE) technique to construct, from Peripheral Blood Mononuclear Cells of an N'Dama cow, 2 total mRNA transcript libraries, at day 0 of a Trypanosoma congolense experimental infection and at day 10 post-infection, corresponding to the peak of parasitaemia. Bioinformatic comparisons in the bovine genomic databases allowed the identification of 187 up- and down- regulated genes, EST and unknown functional genes. Identification of the genes involved in trypanotolerance will allow to set up specific microarray sets for further metabolic and pharmacological studies and to design field marker-assisted selection by introgression programmes. PMID:12927079

Serial analysis of gene expression (SAGE) in bovine trypanotolerance: preliminary results.

PubMed

Berthier, David; Quéré, Ronan; Thevenon, Sophie; Belemsaga, Désiré; Piquemal, David; Marti, Jacques; Maillard, Jean-Charles

2003-01-01

In Africa, trypanosomosis is a tsetse-transmitted disease which represents the most important constraint to livestock production. Several indigenous West African taurine Bos taurus) breeds, such as the Longhorn (N'Dama) cattle are well known to control trypanosome infections. This genetic ability named "trypanotolerance" results from various biological mechanisms under multigenic control. The methodologies used so far have not succeeded in identifying the complete pool of genes involved in trypanotolerance. New post genomic biotechnologies such as transcriptome analyses are efficient in characterising the pool of genes involved in the expression of specific biological functions. We used the serial analysis of gene expression (SAGE) technique to construct, from Peripheral Blood Mononuclear Cells of an N'Dama cow, 2 total mRNA transcript libraries, at day 0 of a Trypanosoma congolense experimental infection and at day 10 post-infection, corresponding to the peak of parasitaemia. Bioinformatic comparisons in the bovine genomic databases allowed the identification of 187 up- and down- regulated genes, EST and unknown functional genes. Identification of the genes involved in trypanotolerance will allow to set up specific microarray sets for further metabolic and pharmacological studies and to design field marker-assisted selection by introgression programmes.

RFID in the Apparel Retail Industry: A Case Study from Galeria Kaufhof

NASA Astrophysics Data System (ADS)

Al-Kassab, Jasser; Blome, Philipp; Wolfram, Gerd; Thiesse, Frédéric; Fleisch, Elgar

This contribution deals with the business valueof radio frequency identification (RFID) technology in the apparel retail industry. We present a case study of an RFID project at Galeria Kaufhof, a subsidiary of Metro Group and one of the largest department store chains in Europe. The trial shows that operational efficiency gains through the automation of logistical in-store processes, such as inventory counting or goods receipt, are possible. Moreover, RFID enables new customer applications on the sales floor, which allow for a redesign of the customer interface, and thus an improvement of the service processes and the service quality. In addition, the analyses of the gathered data on the sales floor help to close the "data void" between the goods receipt and the point of sales of the department store, thus offering the opportunity to directly observe and analyze physical in-store processes. The RFID data analyses allow for deriving valuable information for the department store management in the areas of inventory management, category management, store layout management, and department store processes.

Microfluidic DNA sample preparation method and device

DOEpatents

Krulevitch, Peter A.; Miles, Robin R.; Wang, Xiao-Bo; Mariella, Raymond P.; Gascoyne, Peter R. C.; Balch, Joseph W.

2002-01-01

Manipulation of DNA molecules in solution has become an essential aspect of genetic analyses used for biomedical assays, the identification of hazardous bacterial agents, and in decoding the human genome. Currently, most of the steps involved in preparing a DNA sample for analysis are performed manually and are time, labor, and equipment intensive. These steps include extraction of the DNA from spores or cells, separation of the DNA from other particles and molecules in the solution (e.g. dust, smoke, cell/spore debris, and proteins), and separation of the DNA itself into strands of specific lengths. Dielectrophoresis (DEP), a phenomenon whereby polarizable particles move in response to a gradient in electric field, can be used to manipulate and separate DNA in an automated fashion, considerably reducing the time and expense involved in DNA analyses, as well as allowing for the miniaturization of DNA analysis instruments. These applications include direct transport of DNA, trapping of DNA to allow for its separation from other particles or molecules in the solution, and the separation of DNA into strands of varying lengths.

Identification of large geomorphological anomalies based on 2D discrete wavelet transform

NASA Astrophysics Data System (ADS)

Doglioni, A.; Simeone, V.

2012-04-01

The identification and analysis based on quantitative evidences of large geomorphological anomalies is an important stage for the study of large landslides. Numerical geomorphic analyses represent an interesting approach to this kind of studies, allowing for a detailed and pretty accurate identification of hidden topographic anomalies that may be related to large landslides. Here a geomorphic numerical analyses of the Digital Terrain Model (DTM) is presented. The introduced approach is based on 2D discrete wavelet transform (Antoine et al., 2003; Bruun and Nilsen, 2003, Booth et al., 2009). The 2D wavelet decomposition of the DTM, and in particular the analysis of the detail coefficients of the wavelet transform can provide evidences of anomalies or singularities, i.e. discontinuities of the land surface. These discontinuities are not very evident from the DTM as it is, while 2D wavelet transform allows for grid-based analysis of DTM and for mapping the decomposition. In fact, the grid-based DTM can be assumed as a matrix, where a discrete wavelet transform (Daubechies, 1992) is performed columnwise and linewise, which basically represent horizontal and vertical directions. The outcomes of this analysis are low-frequency approximation coefficients and high-frequency detail coefficients. Detail coefficients are analyzed, since their variations are associated to discontinuities of the DTM. Detailed coefficients are estimated assuming to perform 2D wavelet transform both for the horizontal direction (east-west) and for the vertical direction (north-south). Detail coefficients are then mapped for both the cases, thus allowing to visualize and quantify potential anomalies of the land surface. Moreover, wavelet decomposition can be pushed to further levels, assuming a higher scale number of the transform. This may potentially return further interesting results, in terms of identification of the anomalies of land surface. In this kind of approach, the choice of a proper mother wavelet function is a tricky point, since it conditions the analysis and then their outcomes. Therefore multiple levels as well as multiple wavelet analyses are guessed. Here the introduced approach is applied to some interesting cases study of south Italy, in particular for the identification of large anomalies associated to large landslides at the transition between Apennine chain domain and the foredeep domain. In particular low Biferno valley and Fortore valley are here analyzed. Finally, the wavelet transforms are performed on multiple levels, thus trying to address the problem of which is the level extent for an accurate analysis fit to a specific problem. Antoine J.P., Carrette P., Murenzi R., and Piette B., (2003), Image analysis with two-dimensional continuous wavelet transform, Signal Processing, 31(3), pp. 241-272, doi:10.1016/0165-1684(93)90085-O. Booth A.M., Roering J.J., and Taylor Perron J., (2009), Automated landslide mapping using spectral analysis and high-resolution topographic data: Puget Sound lowlands, Washington, and Portland Hills, Oregon, Geomorphology, 109(3-4), pp. 132-147, doi:10.1016/j.geomorph.2009.02.027. Bruun B.T., and Nilsen S., (2003), Wavelet representation of large digital terrain models, Computers and Geoscience, 29(6), pp. 695-703, doi:10.1016/S0098-3004(03)00015-3. Daubechies, I. (1992), Ten lectures on wavelets, SIAM.

Analysis of Radiocarbon, Stable Isotopes and DNA in Teeth to Facilitate Identification of Unknown Decedents

PubMed Central

Alkass, Kanar; Saitoh, Hisako; Buchholz, Bruce A.; Bernard, Samuel; Holmlund, Gunilla; Senn, David R.; Spalding, Kirsty L.; Druid, Henrik

2013-01-01

The characterization of unidentified bodies or suspected human remains is a frequent and important task for forensic investigators. However, any identification method requires clues to the person’s identity to allow for comparisons with missing persons. If such clues are lacking, information about the year of birth, sex and geographic origin of the victim, is particularly helpful to aid in the identification casework and limit the search for possible matches. We present here results of stable isotope analysis of 13C and 18O, and bomb-pulse 14C analyses that can help in the casework. The 14C analysis of enamel provided information of the year of birth with an average absolute error of 1.8±1.3 years. We also found that analysis of enamel and root from the same tooth can be used to determine if the 14C values match the rising or falling part of the bomb-curve. Enamel laydown times can be used to estimate the date of birth of individuals, but here we show that this detour is unnecessary when using a large set of crude 14C data of tooth enamel as a reference. The levels of 13C in tooth enamel were higher in North America than in teeth from Europe and Asia, and Mexican teeth showed even higher levels than those from USA. DNA analysis was performed on 28 teeth, and provided individual-specific profiles in most cases and sex determination in all cases. In conclusion, these analyses can dramatically limit the number of possible matches and hence facilitate person identification work. PMID:23922751

Model identification methodology for fluid-based inerters

NASA Astrophysics Data System (ADS)

Liu, Xiaofu; Jiang, Jason Zheng; Titurus, Branislav; Harrison, Andrew

2018-06-01

Inerter is the mechanical dual of the capacitor via the force-current analogy. It has the property that the force across the terminals is proportional to their relative acceleration. Compared with flywheel-based inerters, fluid-based forms have advantages of improved durability, inherent damping and simplicity of design. In order to improve the understanding of the physical behaviour of this fluid-based device, especially caused by the hydraulic resistance and inertial effects in the external tube, this work proposes a comprehensive model identification methodology. Firstly, a modelling procedure is established, which allows the topological arrangement of the mechanical networks to be obtained by mapping the damping, inertance and stiffness effects directly to their respective hydraulic counterparts. Secondly, an experimental sequence is followed, which separates the identification of friction, stiffness and various damping effects. Furthermore, an experimental set-up is introduced, where two pressure gauges are used to accurately measure the pressure drop across the external tube. The theoretical models with improved confidence are obtained using the proposed methodology for a helical-tube fluid inerter prototype. The sources of remaining discrepancies are further analysed.

A Method for Identification and Analysis of Non-Overlapping Myeloid Immunophenotypes in Humans

PubMed Central

Gustafson, Michael P.; Lin, Yi; Maas, Mary L.; Van Keulen, Virginia P.; Johnston, Patrick B.; Peikert, Tobias; Gastineau, Dennis A.; Dietz, Allan B.

2015-01-01

The development of flow cytometric biomarkers in human studies and clinical trials has been slowed by inconsistent sample processing, use of cell surface markers, and reporting of immunophenotypes. Additionally, the function(s) of distinct cell types as biomarkers cannot be accurately defined without the proper identification of homogeneous populations. As such, we developed a method for the identification and analysis of human leukocyte populations by the use of eight 10-color flow cytometric protocols in combination with novel software analyses. This method utilizes un-manipulated biological sample preparation that allows for the direct quantitation of leukocytes and non-overlapping immunophenotypes. We specifically designed myeloid protocols that enable us to define distinct phenotypes that include mature monocytes, granulocytes, circulating dendritic cells, immature myeloid cells, and myeloid derived suppressor cells (MDSCs). We also identified CD123 as an additional distinguishing marker for the phenotypic characterization of immature LIN-CD33+HLA-DR- MDSCs. Our approach permits the comprehensive analysis of all peripheral blood leukocytes and yields data that is highly amenable for standardization across inter-laboratory comparisons for human studies. PMID:25799053

Automated coronal hole identification via multi-thermal intensity segmentation

NASA Astrophysics Data System (ADS)

Garton, Tadhg M.; Gallagher, Peter T.; Murray, Sophie A.

2018-01-01

Coronal holes (CH) are regions of open magnetic fields that appear as dark areas in the solar corona due to their low density and temperature compared to the surrounding quiet corona. To date, accurate identification and segmentation of CHs has been a difficult task due to their comparable intensity to local quiet Sun regions. Current segmentation methods typically rely on the use of single Extreme Ultra-Violet passband and magnetogram images to extract CH information. Here, the coronal hole identification via multi-thermal emission recognition algorithm (CHIMERA) is described, which analyses multi-thermal images from the atmospheric image assembly (AIA) onboard the solar dynamics observatory (SDO) to segment coronal hole boundaries by their intensity ratio across three passbands (171 Å, 193 Å, and 211 Å). The algorithm allows accurate extraction of CH boundaries and many of their properties, such as area, position, latitudinal and longitudinal width, and magnetic polarity of segmented CHs. From these properties, a clear linear relationship was identified between the duration of geomagnetic storms and coronal hole areas. CHIMERA can therefore form the basis of more accurate forecasting of the start and duration of geomagnetic storms.

On the identification of folium and orchil on illuminated manuscripts.

PubMed

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-15

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books. Copyright © 2016 Elsevier B.V. All rights reserved.

Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing

PubMed Central

2011-01-01

Background Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21-24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. Results We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analysed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. Conclusion We have discovered and analysed a large number of conserved and melon-specific sRNAs, including miRNAs and their potential target genes. This provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melon-virus interactions. PMID:21812964

Method optimization for proteomic analysis of soybean leaf: Improvements in identification of new and low-abundance proteins

PubMed Central

Mesquita, Rosilene Oliveira; de Almeida Soares, Eduardo; de Barros, Everaldo Gonçalves; Loureiro, Marcelo Ehlers

2012-01-01

The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes of TCA precipitated protein with acetone, using a final wash with 80% ethanol and using sonication to ressuspend the pellet increased the number of detected proteins as well the resolution of the 2-DE gels. Using this approach we have constructed a soybean protein map. The major group of identified proteins corresponded to genes of unknown function. The second and third most abundant groups of proteins were composed of photosynthesis and metabolism related genes. The resulting protocol improved protein solubility and gel resolution allowing the identification of 122 soybean leaf proteins, 72 of which were not detected in other published soybean leaf 2-DE gel datasets, including a transcription factor and several signaling proteins. PMID:22802721

Vital nodes identification in complex networks

NASA Astrophysics Data System (ADS)

Lü, Linyuan; Chen, Duanbing; Ren, Xiao-Long; Zhang, Qian-Ming; Zhang, Yi-Cheng; Zhou, Tao

2016-09-01

Real networks exhibit heterogeneous nature with nodes playing far different roles in structure and function. To identify vital nodes is thus very significant, allowing us to control the outbreak of epidemics, to conduct advertisements for e-commercial products, to predict popular scientific publications, and so on. The vital nodes identification attracts increasing attentions from both computer science and physical societies, with algorithms ranging from simply counting the immediate neighbors to complicated machine learning and message passing approaches. In this review, we clarify the concepts and metrics, classify the problems and methods, as well as review the important progresses and describe the state of the art. Furthermore, we provide extensive empirical analyses to compare well-known methods on disparate real networks, and highlight the future directions. In spite of the emphasis on physics-rooted approaches, the unification of the language and comparison with cross-domain methods would trigger interdisciplinary solutions in the near future.

Influenza A Virus Isolation, Culture and Identification

PubMed Central

Eisfeld, Amie J.; Neumann, Gabriele; Kawaoka, Yoshihiro

2017-01-01

SUMMARY Influenza A viruses (IAV) cause epidemics and pandemics that result in considerable financial burden and loss of human life. To manage annual IAV epidemics and prepare for future pandemics, improved understanding of how IAVs emerge, transmit, cause disease, and acquire pandemic potential is urgently needed. Fundamental techniques essential for procuring such knowledge are IAV isolation and culture from experimental and surveillance samples. Here, we present a detailed protocol for IAV sample collection and processing, amplification in chicken eggs and mammalian cells, and identification from samples containing unknown pathogens. This protocol is robust, and allows for generation of virus cultures that can be used for downstream analyses. Once experimental or surveillance samples are obtained, virus cultures can be generated and the presence of IAV can be verified in 3–5 days. Increased time-frames may be required for less experienced laboratory personnel, or when large numbers of samples will be processed. PMID:25321410

Cryptic diversity in Australian stick insects (Insecta; Phasmida) uncovered by the DNA barcoding approach.

PubMed

Velonà, A; Brock, P D; Hasenpusch, J; Mantovani, B

2015-05-18

The barcoding approach was applied to analyze 16 Australian morphospecies of the order Phasmida, with the aim to test if it could be suitable as a tool for phasmid species identification and if its discrimination power would allow uncovering of cryptic diversity. Both goals were reached. Eighty-two specimens representing twelve morphospecies (Sipyloidea sp. A, Candovia annulata, Candovia sp. A, Candovia sp. B, Candovia sp. C, Denhama austrocarinata, Xeroderus kirbii, Parapodacanthus hasenpuschorum, Tropidoderus childrenii, Cigarrophasma tessellatum, Acrophylla wuelfingi, Eurycantha calcarata) were correctly recovered as clades through the molecular approach, their sequences forming monophyletic and well-supported clusters. In four instances, Neighbor-Joining tree and barcoding gap analyses supported either a specific (Austrocarausius mercurius, Anchiale briareus) or a subspecific (Anchiale austrotessulata, Extatosoma tiaratum) level of divergence within the analyzed morphospecies. The lack of an appropriate database of homologous coxI sequences prevented more detailed identification of undescribed taxa.

Identification of the nucleophile catalytic residue of GH51 α-l-arabinofuranosidase from Pleurotus ostreatus

DOE PAGES

Amore, Antonella; Iadonisi, Alfonso; Vincent, Florence; ...

2015-12-21

In this paper, the recombinant α-l-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis in order to identify the catalytic nucleophile residue. Based on bioinformatics and homology modelling analyses, E449 was revealed to be the potential nucleophilic residue. Thus, the mutant E449G of PoAbf was recombinantly expressed in Pichia pastoris and its recombinant expression level and reactivity were investigated in comparison to the wild-type. The design of a suitable set of hydrolysis experiments in the presence or absence of alcoholic arabinosyl acceptors and/or formate salts allowed to unambiguously identify the residue E449 as the nucleophile residue involvedmore » in the retaining mechanism of this GH51 arabinofuranosidase. 1H NMR analysis was applied for the identification of the products and the assignement of their anomeric configuration.« less

The genetics of human obesity.

PubMed

Xia, Qianghua; Grant, Struan F A

2013-04-01

It has long been known that there is a genetic component to obesity, and that characterizing this underlying factor would likely offer the possibility of better intervention in the future. Monogenic obesity has proved to be relatively straightforward, with a combination of linkage analysis and mouse models facilitating the identification of multiple genes. In contrast, genome-wide association studies have successfully revealed a variety of genetic loci associated with the more common form of obesity, allowing for very strong consensus on the underlying genetic architecture of the phenotype for the first time. Although a number of significant findings have been made, it appears that very little of the apparent heritability of body mass index has actually been explained to date. New approaches for data analyses and advances in technology will be required to uncover the elusive missing heritability, and to aid in the identification of the key causative genetic underpinnings of obesity. © 2013 New York Academy of Sciences.

Leucocyte classification for leukaemia detection using image processing techniques.

PubMed

Putzu, Lorenzo; Caocci, Giovanni; Di Ruberto, Cecilia

2014-11-01

The counting and classification of blood cells allow for the evaluation and diagnosis of a vast number of diseases. The analysis of white blood cells (WBCs) allows for the detection of acute lymphoblastic leukaemia (ALL), a blood cancer that can be fatal if left untreated. Currently, the morphological analysis of blood cells is performed manually by skilled operators. However, this method has numerous drawbacks, such as slow analysis, non-standard accuracy, and dependences on the operator's skill. Few examples of automated systems that can analyse and classify blood cells have been reported in the literature, and most of these systems are only partially developed. This paper presents a complete and fully automated method for WBC identification and classification using microscopic images. In contrast to other approaches that identify the nuclei first, which are more prominent than other components, the proposed approach isolates the whole leucocyte and then separates the nucleus and cytoplasm. This approach is necessary to analyse each cell component in detail. From each cell component, different features, such as shape, colour and texture, are extracted using a new approach for background pixel removal. This feature set was used to train different classification models in order to determine which one is most suitable for the detection of leukaemia. Using our method, 245 of 267 total leucocytes were properly identified (92% accuracy) from 33 images taken with the same camera and under the same lighting conditions. Performing this evaluation using different classification models allowed us to establish that the support vector machine with a Gaussian radial basis kernel is the most suitable model for the identification of ALL, with an accuracy of 93% and a sensitivity of 98%. Furthermore, we evaluated the goodness of our new feature set, which displayed better performance with each evaluated classification model. The proposed method permits the analysis of blood cells automatically via image processing techniques, and it represents a medical tool to avoid the numerous drawbacks associated with manual observation. This process could also be used for counting, as it provides excellent performance and allows for early diagnostic suspicion, which can then be confirmed by a haematologist through specialised techniques. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali

PubMed Central

Diarra, Adama Zan; Almeras, Lionel; Berenger, Jean-Michel; Koné, Abdoulaye K.; Bocoum, Zakaria; Dabo, Abdoulaye; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

2017-01-01

Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks. A total of 1,333 ticks were collected from mammals in three distinct sites from Mali. Morphological identification allowed classification of ticks into 6 species including Amblyomma variegatum, Hyalomma truncatum, Hyalomma marginatum rufipes, Rhipicephalus (Boophilus) microplus, Rhipicephalus evertsi evertsi and Rhipicephalus sanguineus sl. Among those, 471 ticks were randomly selected for molecular and proteomic analyses. Tick legs submitted to MALDI-TOF MS revealed a concordant morpho/molecular identification of 99.6%. The inclusion in our MALDI-TOF MS arthropod database of MS reference spectra from ethanol-preserved tick leg specimens was required to obtain reliable identification. When tested by molecular tools, 76.6%, 37.6%, 20.8% and 1.1% of the specimens tested were positive for Rickettsia spp., Coxiella burnetii, Anaplasmataceae and Borrelia spp., respectively. These results support the fact that MALDI-TOF is a reliable tool for the identification of ticks conserved in alcohol and enhances knowledge about the diversity of tick species and pathogens transmitted by ticks circulating in Mali. PMID:28742123

Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali.

PubMed

Diarra, Adama Zan; Almeras, Lionel; Laroche, Maureen; Berenger, Jean-Michel; Koné, Abdoulaye K; Bocoum, Zakaria; Dabo, Abdoulaye; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

2017-07-01

Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks. A total of 1,333 ticks were collected from mammals in three distinct sites from Mali. Morphological identification allowed classification of ticks into 6 species including Amblyomma variegatum, Hyalomma truncatum, Hyalomma marginatum rufipes, Rhipicephalus (Boophilus) microplus, Rhipicephalus evertsi evertsi and Rhipicephalus sanguineus sl. Among those, 471 ticks were randomly selected for molecular and proteomic analyses. Tick legs submitted to MALDI-TOF MS revealed a concordant morpho/molecular identification of 99.6%. The inclusion in our MALDI-TOF MS arthropod database of MS reference spectra from ethanol-preserved tick leg specimens was required to obtain reliable identification. When tested by molecular tools, 76.6%, 37.6%, 20.8% and 1.1% of the specimens tested were positive for Rickettsia spp., Coxiella burnetii, Anaplasmataceae and Borrelia spp., respectively. These results support the fact that MALDI-TOF is a reliable tool for the identification of ticks conserved in alcohol and enhances knowledge about the diversity of tick species and pathogens transmitted by ticks circulating in Mali.

Geochemistry of minor elements in the Monterey Formation, California; seawater chemistry of deposition

USGS Publications Warehouse

Piper, D.Z.; Isaacs, C.M.

1995-01-01

Approximately 24 samples of the Monterey Formation, Southern California, have been analyzed for their major-element oxide and minor-element content. These analyses allow identification of a detrital fraction, composed of terrigenous quartz, clay minerals, and other Al silicate minerals, and a marine fraction, composed of biogenic silica, calcite, dolomite, organic matter, apatite, and minor amounts of pyrite. The minor-element contents in the marine fraction alone are interpreted to have required, at the time of deposition, a high level of primary productivity in the photic zone and denitrifying bacterial respiration in the bottom water.

Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins

NASA Astrophysics Data System (ADS)

Champeimont, Raphaël; Laine, Elodie; Hu, Shuang-Wei; Penin, Francois; Carbone, Alessandra

2016-05-01

A novel computational approach of coevolution analysis allowed us to reconstruct the protein-protein interaction network of the Hepatitis C Virus (HCV) at the residue resolution. For the first time, coevolution analysis of an entire viral genome was realized, based on a limited set of protein sequences with high sequence identity within genotypes. The identified coevolving residues constitute highly relevant predictions of protein-protein interactions for further experimental identification of HCV protein complexes. The method can be used to analyse other viral genomes and to predict the associated protein interaction networks.

A Parameter Identification Method for Helicopter Noise Source Identification and Physics-Based Semi-Empirical Modeling

NASA Technical Reports Server (NTRS)

Greenwood, Eric, II; Schmitz, Fredric H.

2010-01-01

A new physics-based parameter identification method for rotor harmonic noise sources is developed using an acoustic inverse simulation technique. This new method allows for the identification of individual rotor harmonic noise sources and allows them to be characterized in terms of their individual non-dimensional governing parameters. This new method is applied to both wind tunnel measurements and ground noise measurements of two-bladed rotors. The method is shown to match the parametric trends of main rotor Blade-Vortex Interaction (BVI) noise, allowing accurate estimates of BVI noise to be made for operating conditions based on a small number of measurements taken at different operating conditions.

Investigating the effect of nurse-team communication on nurse turnover: relationships among communication processes, identification, and intent to leave.

PubMed

Apker, Julie; Propp, Kathleen M; Ford, Wendy S Zabava

2009-03-01

Enhanced team communication may strengthen nurses' attachment to their organizations and teams and improve nurse retention. This study examines the relationships among nurse-team communication, identification (organizational and team), and intent to leave. Hospital nurses (N = 201) completed surveys measuring 3 nurse-team communication processes: promoting team synergy, ensuring quality decisions, and individualizing communication. Hierarchical regression analyses revealed that promoting team synergy was a significant predictor of intent to leave, whereas ensuring quality decisions and individualizing communication did not account for significant additional variance in intent to leave. Separate analyses showed that the relationship between promoting team synergy and intent to leave was partially mediated by team identification or by organizational identification. Further analyses were conducted on the 7 communication practices for promoting team synergy. Mentoring emerged as the only significant predictor of intent to leave; however, its relationship to intent to leave was fully mediated by organizational identification or partially mediated by team identification. Pragmatic suggestions are offered to improve nurse identification and reduce turnover.

Refining cost-effectiveness analyses using the net benefit approach and econometric methods: an example from a trial of anti-depressant treatment.

PubMed

Sabes-Figuera, Ramon; McCrone, Paul; Kendricks, Antony

2013-04-01

Economic evaluation analyses can be enhanced by employing regression methods, allowing for the identification of important sub-groups and to adjust for imperfect randomisation in clinical trials or to analyse non-randomised data. To explore the benefits of combining regression techniques and the standard Bayesian approach to refine cost-effectiveness analyses using data from randomised clinical trials. Data from a randomised trial of anti-depressant treatment were analysed and a regression model was used to explore the factors that have an impact on the net benefit (NB) statistic with the aim of using these findings to adjust the cost-effectiveness acceptability curves. Exploratory sub-samples' analyses were carried out to explore possible differences in cost-effectiveness. Results The analysis found that having suffered a previous similar depression is strongly correlated with a lower NB, independent of the outcome measure or follow-up point. In patients with previous similar depression, adding an selective serotonin reuptake inhibitors (SSRI) to supportive care for mild-to-moderate depression is probably cost-effective at the level used by the English National Institute for Health and Clinical Excellence to make recommendations. This analysis highlights the need for incorporation of econometric methods into cost-effectiveness analyses using the NB approach.

Use of MALDI-TOF Mass Spectrometry and a Custom Database to Characterize Bacteria Indigenous to a Unique Cave Environment (Kartchner Caverns, AZ, USA)

PubMed Central

Zhang, Lin; Vranckx, Katleen; Janssens, Koen; Sandrin, Todd R.

2015-01-01

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level. PMID:25590854

Use of MALDI-TOF mass spectrometry and a custom database to characterize bacteria indigenous to a unique cave environment (Kartchner Caverns, AZ, USA).

PubMed

Zhang, Lin; Vranckx, Katleen; Janssens, Koen; Sandrin, Todd R

2015-01-02

MALDI-TOF mass spectrometry has been shown to be a rapid and reliable tool for identification of bacteria at the genus and species, and in some cases, strain levels. Commercially available and open source software tools have been developed to facilitate identification; however, no universal/standardized data analysis pipeline has been described in the literature. Here, we provide a comprehensive and detailed demonstration of bacterial identification procedures using a MALDI-TOF mass spectrometer. Mass spectra were collected from 15 diverse bacteria isolated from Kartchner Caverns, AZ, USA, and identified by 16S rDNA sequencing. Databases were constructed in BioNumerics 7.1. Follow-up analyses of mass spectra were performed, including cluster analyses, peak matching, and statistical analyses. Identification was performed using blind-coded samples randomly selected from these 15 bacteria. Two identification methods are presented: similarity coefficient-based and biomarker-based methods. Results show that both identification methods can identify the bacteria to the species level.

Qualitative and quantitative determination of yohimbine in authentic yohimbe bark and in commercial aphrodisiacs by HPLC-UV-API/ MS methods.

PubMed

Zanolari, Boris; Ndjoko, Karine; Ioset, Jean-Robert; Marston, Andrew; Hostettmann, Kurt

2003-01-01

The development and validation of a rapid qualitative and quantitative method based on an HPLC-UV-MS technique with atmospheric pressure chemical ionisation and electrospray ionisation for the analysis of yohimbine in a number of commercial aphrodisiac products is reported. HPLC with multiple-stage mass spectrometry experiments allowed the identification of the target compound and increased the selectivity of complex analyses such as those involved with multi-botanical preparations. The precision and the robustness of the method were improved by the use of two internal standards: codeine for UV detection and deuterium-labelled yohimbine for MS detection. Twenty commercial aphrodisiac preparations were analysed and the amount of yohimbine measured and expressed as the maximal dose per day suggested on product labels ranged from 1.32 to 23.16 mg.

Proteomic profiling of mitochondria: what does it tell us about the ageing brain?

PubMed

Ingram, Thomas; Chakrabarti, Lisa

2016-12-13

Mitochondrial dysfunction is evident in numerous neurodegenerative and age-related disorders. It has also been linked to cellular ageing, however our current understanding of the mitochondrial changes that occur are unclear. Functional studies have made some progress reporting reduced respiration, dynamic structural modifications and loss of membrane potential, though there are conflicts within these findings. Proteomic analyses, together with functional studies, are required in order to profile the mitochondrial changes that occur with age and can contribute to unravelling the complexity of the ageing phenotype. The emergence of improved protein separation techniques, combined with mass spectrometry analyses has allowed the identification of age and cell-type specific mitochondrial changes in energy metabolism, antioxidants, fusion and fission machinery, chaperones, membrane proteins and biosynthesis pathways. Here, we identify and review recent data from the analyses of mitochondria from rodent brains. It is expected that knowledge gained from understanding age-related mitochondrial changes of the brain should lead to improved biomarkers of normal ageing and also age-related disease progression.

Characterisation and discrimination of various types of lac resin using gas chromatography mass spectrometry techniques with quaternary ammonium reagents.

PubMed

Sutherland, K; del Río, J C

2014-04-18

A variety of lac resin samples obtained from artists' suppliers, industrial manufacturers, and museum collections were analysed using gas chromatography mass spectrometry (GCMS) and reactive pyrolysis GCMS with quaternary ammonium reagents. These techniques allowed a detailed chemical characterisation of microgram-sized samples, based on the detection and identification of derivatives of the hydroxy aliphatic and cyclic (sesquiterpene) acids that compose the resin. Differences in composition could be related to the nature of the resin, e.g. wax-containing (unrefined), bleached, or aged samples. Furthermore, differences in the relative abundances of aliphatic hydroxyacids appear to be associated with the biological source of the resin. The diagnostic value of newly characterised lac components, including 8-hydroxyacids, is discussed here for the first time. Identification of derivatised components was aided by AMDIS deconvolution software, and discrimination of samples was enhanced by statistical evaluation of data using principal component analysis. The robustness of the analyses, together with the minimal sample size required, make these very powerful approaches for the characterisation of lac resin in museum objects. The value of such analyses for enhancing the understanding of museum collections is illustrated by two case studies of objects in the collection of the Philadelphia Museum of Art: a restorer's varnish on a painting by Luca Signorelli, and a pictorial inlay in an early nineteenth-century High Chest by George Dyer. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparison of alternative approaches for analysing multi-level RNA-seq data

PubMed Central

Mohorianu, Irina; Bretman, Amanda; Smith, Damian T.; Fowler, Emily K.; Dalmay, Tamas

2017-01-01

RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments. PMID:28792517

The Role of Ethnic and National Identifications in Perceived Discrimination for Asian Americans: Toward a Better Understanding of the Buffering Effect of Group Identifications on Psychological Distress

PubMed Central

Huynh, Que-Lam; Devos, Thierry; Goldberg, Robyn

2013-01-01

A robust relationship between perceived racial discrimination and psychological distress has been established. Yet, mixed evidence exists regarding the extent to which ethnic identification moderates this relationship, and scarce attention has been paid to the moderating role of national identification. We propose that the role of group identifications in the perceived discrimination–psychological distress relationship is best understood by simultaneously and interactively considering ethnic and national identifications. A sample of 259 Asian American students completed measures of perceived discrimination, group identifications (specific ethnic identification stated by respondents and national or “mainstream American” identification), and psychological distress (anxiety and depression symptoms). Regression analyses revealed a significant three-way interaction of perceived discrimination, ethnic identification, and national identification on psychological distress. Simple-slope analyses indicated that dual identification (strong ethnic and national identifications) was linked to a weaker relationship between perceived discrimination and psychological distress compared with other group identification configurations. These findings underscore the need to consider the interconnections between ethnic and national identifications to better understand the circumstances under which group identifications are likely to buffer individuals against the adverse effects of racial discrimination. PMID:25258674

Noninvasive molecular tracking of colonizing wolf (Canis lupus) packs in the western Italian Alps.

PubMed

Lucchini, V; Fabbri, E; Marucco, F; Ricci, S; Boitani, L; Randi, E

2002-05-01

We used noninvasive methods to obtain genetic and demographic data on the wolf packs (Canis lupus), which are now recolonizing the Alps, a century after their eradication. DNA samples, extracted from presumed wolf scats collected in the western Italian Alps (Piemonte), were genotyped to determine species and sex by sequencing parts of the mitochondrial DNA (mtDNA) control-region and ZFX/ZFY genes. Individual genotypes were identified by multilocus microsatellite analyses using a multiple tubes polymerase chain reaction (PCR). The performance of the laboratory protocols was affected by the age of samples. The quality of excremental DNA extracts was higher in samples freshly collected on snow in winter than in samples that were older or collected during summer. Preliminary mtDNA screening of all samples allowed species identification and was a good predictor of further PCR performances. Wolf, and not prey, DNA targets were preferentially amplified. Allelic dropout occurred more frequently than false alleles, but the probability of false homozygote determinations was always < 0.001. A panel of six to nine microsatellites would allow identification of individual wolf genotypes, also whether related, with a probability of identity of < 0.015. Genealogical relationships among individuals could be determined reliably if the number of candidate parents was 6-8, and most of them had been sampled and correctly genotyped. Genetic data indicate that colonizing Alpine wolves originate exclusively from the Italian source population and retain a high proportion of its genetic diversity. Spatial and temporal locations of individual genotypes, and kinship analyses, suggest that two distinct packs of closely related wolves, plus some unrelated individuals, ranged in the study areas. This is in agreement with field observations.

Species identification in forensic samples using the SPInDel approach: A GHEP-ISFG inter-laboratory collaborative exercise.

PubMed

Alves, Cíntia; Pereira, Rui; Prieto, Lourdes; Aler, Mercedes; Amaral, Cesar R L; Arévalo, Cristina; Berardi, Gabriela; Di Rocco, Florencia; Caputo, Mariela; Carmona, Cristian Hernandez; Catelli, Laura; Costa, Heloísa Afonso; Coufalova, Pavla; Furfuro, Sandra; García, Óscar; Gaviria, Anibal; Goios, Ana; Gómez, Juan José Builes; Hernández, Alexis; Hernández, Eva Del Carmen Betancor; Miranda, Luís; Parra, David; Pedrosa, Susana; Porto, Maria João Anjos; Rebelo, Maria de Lurdes; Spirito, Matteo; Torres, María Del Carmen Villalobos; Amorim, António; Pereira, Filipe

2017-05-01

DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis. The exercise was organized during 2014 by a Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG), created in 2013. The 24 participating laboratories from 10 countries were asked to identify the species in 11 DNA samples from previous GHEP-ISFG proficiency tests using a SPInDel primer mix and control samples of the 10 target species. A computer software was also provided to the participants to assist the analyses of the results. All samples were correctly identified by 22 of the 24 laboratories, including samples with low amounts of DNA (hair shafts) and mixtures of saliva and blood. Correct species identifications were obtained in 238 of the 241 (98.8%) reported SPInDel profiles. Two laboratories were responsible for the three cases of misclassifications. The SPInDel was efficient in the identification of species in mixtures considering that only a single laboratory failed to detect a mixture in one sample. This result suggests that SPInDel is a valid method for mixture analyses without the need for DNA sequencing, with the advantage of identifying more than one species in a single reaction. The low frequency of wrong (5.0%) and missing (2.1%) alleles did not interfere with the correct species identification, which demonstrated the advantage of using a method based on the analysis of multiple loci. Overall, the SPInDel method was easily implemented by laboratories using different genotyping platforms, the interpretation of results was straightforward and the SPInDel software was used without any problems. The results of this collaborative exercise indicate that the SPInDel method can be applied successfully in forensic casework investigations. Copyright © 2017 Elsevier B.V. All rights reserved.

DNA Barcoding of Malagasy Rosewoods: Towards a Molecular Identification of CITES-Listed Dalbergia Species.

PubMed

Hassold, Sonja; Lowry, Porter P; Bauert, Martin R; Razafintsalama, Annick; Ramamonjisoa, Lolona; Widmer, Alex

2016-01-01

Illegal selective logging of tropical timber is of increasing concern worldwide. Madagascar is a biodiversity hotspot and home to some of the world's most sought after tropical timber species. Malagasy rosewoods belong to the genus Dalbergia (Fabaceae), which is highly diverse and has a pantropical distribution, but these timber species are among the most threatened as a consequence of intensive illegal selective logging and deforestation. Reliable identification of Dalbergia species from Madagascar is important for law enforcement but is almost impossible without fertile plant material, which is often unavailable during forest inventories or when attempting to identify logged trees of cut wood. DNA barcoding has been promoted as a promising tool for species identification in such cases. In this study we tested whether DNA barcoding with partial sequences of three plastid markers (matK, rbcL and trnL (UAA)) can distinguish between Dalbergia from Madagascar and from other areas of its distributional range, and whether Malagasy species can be distinguished from one another. Phylogenetic analyses revealed that the Malagasy Dalbergia species studied form two monophyletic groups, each containing two subgroups, only one of which corresponds to a single species. We characterized diagnostic polymorphisms in the three DNA barcoding markers that allow rapid discrimination between Dalbergia from Madagascar and from other areas of its distribution range. Species identification success based on individual barcoding markers or combinations was poor, whereas subgroup identification success was much higher (up to 98%), revealing both the value and limitations of a DNA barcoding approach for the identification of closely related Malagasy rosewoods.

TOXICITY IDENTIFICATION EVALUATION (TIE) RESULTS FOR METAL CONTAMINATED SEDIMENTS

EPA Science Inventory

Identification of contaminants in sediment is necessary for sound management decisions on sediment disposal, remediation, determination of ecological risk, and source identification. We have been developing sediment toxicity identification evaluation (TIE) techniques that allow ...

Use of phylogenetic and phenotypic analyses to identify nonhemolytic streptococci isolated from bacteremic patients.

PubMed

Hoshino, Tomonori; Fujiwara, Taku; Kilian, Mogens

2005-12-01

The aim of this study was to evaluate molecular and phenotypic methods for the identification of nonhemolytic streptococci. A collection of 148 strains consisting of 115 clinical isolates from cases of infective endocarditis, septicemia, and meningitis and 33 reference strains, including type strains of all relevant Streptococcus species, were examined. Identification was performed by phylogenetic analysis of nucleotide sequences of four housekeeping genes, ddl, gdh, rpoB, and sodA; by PCR analysis of the glucosyltransferase (gtf) gene; and by conventional phenotypic characterization and identification using two commercial kits, Rapid ID 32 STREP and STREPTOGRAM and the associated databases. A phylogenetic tree based on concatenated sequences of the four housekeeping genes allowed unequivocal differentiation of recognized species and was used as the reference. Analysis of single gene sequences revealed deviation clustering in eight strains (5.4%) due to homologous recombination with other species. This was particularly evident in S. sanguinis and in members of the anginosus group of streptococci. The rate of correct identification of the strains by both commercial identification kits was below 50% but varied significantly between species. The most significant problems were observed with S. mitis and S. oralis and 11 Streptococcus species described since 1991. Our data indicate that identification based on multilocus sequence analysis is optimal. As a more practical alternative we recommend identification based on sodA sequences with reference to a comprehensive set of sequences that is available for downloading from our server. An analysis of the species distribution of 107 nonhemolytic streptococci from bacteremic patients showed a predominance of S. oralis and S. anginosus with various underlying infections.

Evaluation of diversity among common beans (Phaseolus vulgaris L.) from two centers of domestication using 'omics' technologies

PubMed Central

2010-01-01

Background Genetic diversity among wild accessions and cultivars of common bean (Phaseolus vulgaris L.) has been characterized using plant morphology, seed protein allozymes, random amplified polymorphic DNA, restriction fragment length polymorphisms, DNA sequence analysis, chloroplast DNA, and microsatellite markers. Yet, little is known about whether these traits, which distinguish among genetically distinct types of common bean, can be evaluated using omics technologies. Results Three 'omics' approaches: transcriptomics, proteomics, and metabolomics were used to qualitatively evaluate the diversity of common bean from two Centers of Domestication (COD). All three approaches were able to classify common bean according to their COD using unsupervised analyses; these findings are consistent with the hypothesis that differences exist in gene transcription, protein expression, and synthesis and metabolism of small molecules among common bean cultivars representative of different COD. Metabolomic analyses of multiple cultivars within two common bean gene pools revealed cultivar differences in small molecules that were of sufficient magnitude to allow identification of unique cultivar fingerprints. Conclusions Given the high-throughput and low cost of each of these 'omics' platforms, significant opportunities exist for their use in the rapid identification of traits of agronomic and nutritional importance as well as to characterize genetic diversity. PMID:21126341

Zymography Methods to Simultaneously Analyze Superoxide Dismutase and Catalase Activities: Novel Application for Yeast Species Identification.

PubMed

Gamero-Sandemetrio, Esther; Gómez-Pastor, Rocío; Matallana, Emilia

2017-01-01

We provide an optimized protocol for a double staining technique to analyze superoxide dismutase enzymatic isoforms Cu-Zn SOD (Sod1) and Mn-SOD (Sod2) and catalase in the same polyacrylamide gel. The use of NaCN, which specifically inhibits yeast Sod1 isoform, allows the analysis of Sod2 isoform while the use of H 2 O 2 allows the analysis of catalase. The identification of a different zymography profiling of SOD and catalase isoforms in different yeast species allowed us to propose this technique as a novel yeast identification and classification strategy.

Assessing Plausibility of Tentative Chemical Identifications from Suspect Screening Analyses via Chemical Function

EPA Science Inventory

Suspect screening (SSA) and non-targeted analysis (NTA) have become increasingly useful methods for identifying chemicals in indoor environments, which is where many chemical exposures occur. However, the tentative chemical identifications from these analyses must be confirmed. T...

Mapping the structure of the world economy.

PubMed

Lenzen, Manfred; Kanemoto, Keiichiro; Moran, Daniel; Geschke, Arne

2012-08-07

We have developed a new series of environmentally extended multi-region input-output (MRIO) tables with applications in carbon, water, and ecological footprinting, and Life-Cycle Assessment, as well as trend and key driver analyses. Such applications have recently been at the forefront of global policy debates, such as about assigning responsibility for emissions embodied in internationally traded products. The new time series was constructed using advanced parallelized supercomputing resources, and significantly advances the previous state of art because of four innovations. First, it is available as a continuous 20-year time series of MRIO tables. Second, it distinguishes 187 individual countries comprising more than 15,000 industry sectors, and hence offers unsurpassed detail. Third, it provides information just 1-3 years delayed therefore significantly improving timeliness. Fourth, it presents MRIO elements with accompanying standard deviations in order to allow users to understand the reliability of data. These advances will lead to material improvements in the capability of applications that rely on input-output tables. The timeliness of information means that analyses are more relevant to current policy questions. The continuity of the time series enables the robust identification of key trends and drivers of global environmental change. The high country and sector detail drastically improves the resolution of Life-Cycle Assessments. Finally, the availability of information on uncertainty allows policy-makers to quantitatively judge the level of confidence that can be placed in the results of analyses.

Achieving high confidence protein annotations in a sea of unknowns

NASA Astrophysics Data System (ADS)

Timmins-Schiffman, E.; May, D. H.; Noble, W. S.; Nunn, B. L.; Mikan, M.; Harvey, H. R.

2016-02-01

Increased sensitivity of mass spectrometry (MS) technology allows deep and broad insight into community functional analyses. Metaproteomics holds the promise to reveal functional responses of natural microbial communities, whereas metagenomics alone can only hint at potential functions. The complex datasets resulting from ocean MS have the potential to inform diverse realms of the biological, chemical, and physical ocean sciences, yet the extent of bacterial functional diversity and redundancy has not been fully explored. To take advantage of these impressive datasets, we need a clear bioinformatics pipeline for metaproteomics peptide identification and annotation with a database that can provide confident identifications. Researchers must consider whether it is sufficient to leverage the vast quantities of available ocean sequence data or if they must invest in site-specific metagenomic sequencing. We have sequenced, to our knowledge, the first western arctic metagenomes from the Bering Strait and the Chukchi Sea. We have addressed the long standing question: Is a metagenome required to accurately complete metaproteomics and assess the biological distribution of metabolic functions controlling nutrient acquisition in the ocean? Two different protein databases were constructed from 1) a site-specific metagenome and 2) subarctic/arctic groups available in NCBI's non-redundant database. Multiple proteomic search strategies were employed, against each individual database and against both databases combined, to determine the algorithm and approach that yielded the balance of high sensitivity and confident identification. Results yielded over 8200 confidently identified proteins. Our comparison of these results allows us to quantify the utility of investing resources in a metagenome versus using the constantly expanding and immediately available public databases for metaproteomic studies.

Identification of metal elements by time-resolved LIBS technique in sediments lake the “Cisne”

NASA Astrophysics Data System (ADS)

Pacheco, P.; Arregui, E.; Álvarez, J.; Rangel, N.; Sarmiento, R.

2017-01-01

Laser induced breakdown spectroscopy (LIBS), is a kind of spectral method of atomic emission that uses pulses of radiation high energy laser as excitation source. One of the advantages of technical LIBS lies in the possibility of analyse the substances in any State of aggregation, already is solid, liquid or gaseous, even in colloids as aerosols, gels and others. Another advantage over other conventional techniques is the simultaneous analysis of elements present in a sample of multielement. This work is made in the use of this technique for the identification of metal pollutants in the Swan Lake sediment samples, collected by drilling cores. Plasmas were generated by focusing the radiation of Nd: YAG laser with an energy per pulse 13mJ and 4ns duration, wavelength of 532nm. The spectra of radiation from the plasmas of sediment were recorded with an Echelle spectrograph type coupled to an ICCD camera. The delay times were between 0.5μs and 7μs, while the gate width was of 2μs. To ensure the homogeneity of the plasmas, the sediment sample was placed in a positioning system of linear and rotary adjustment of smooth step synchronized with the trigger of the laser pulse. The registration of the spectra of the sediment to different times of delay, allowed to identify the lines prominent of the different elements present in the sample. The analysis of the Spectra allowed the identification of some elements in the sample as if, Ca, Na, Mg, and Al through the measurement of wavelengths of the prominent peaks.

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis

PubMed Central

Padula, Matthew P.; Berry, Iain J.; O′Rourke, Matthew B.; Raymond, Benjamin B.A.; Santos, Jerran; Djordjevic, Steven P.

2017-01-01

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O′Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single ‘spots’ in a polyacrylamide gel, allowing the quantitation of changes in a proteoform′s abundance to ascertain changes in an organism′s phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the ‘Top-Down’. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O’Farrell’s paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism′s proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer. PMID:28387712

A Comprehensive Guide for Performing Sample Preparation and Top-Down Protein Analysis.

PubMed

Padula, Matthew P; Berry, Iain J; O Rourke, Matthew B; Raymond, Benjamin B A; Santos, Jerran; Djordjevic, Steven P

2017-04-07

Methodologies for the global analysis of proteins in a sample, or proteome analysis, have been available since 1975 when Patrick O'Farrell published the first paper describing two-dimensional gel electrophoresis (2D-PAGE). This technique allowed the resolution of single protein isoforms, or proteoforms, into single 'spots' in a polyacrylamide gel, allowing the quantitation of changes in a proteoform's abundance to ascertain changes in an organism's phenotype when conditions change. In pursuit of the comprehensive profiling of the proteome, significant advances in technology have made the identification and quantitation of intact proteoforms from complex mixtures of proteins more routine, allowing analysis of the proteome from the 'Top-Down'. However, the number of proteoforms detected by Top-Down methodologies such as 2D-PAGE or mass spectrometry has not significantly increased since O'Farrell's paper when compared to Bottom-Up, peptide-centric techniques. This article explores and explains the numerous methodologies and technologies available to analyse the proteome from the Top-Down with a strong emphasis on the necessity to analyse intact proteoforms as a better indicator of changes in biology and phenotype. We arrive at the conclusion that the complete and comprehensive profiling of an organism's proteome is still, at present, beyond our reach but the continuing evolution of protein fractionation techniques and mass spectrometry brings comprehensive Top-Down proteome profiling closer.

High-resolution melt and morphological analyses of mealybugs (Hemiptera: Pseudococcidae) from cacao: tools for the control of Cacao swollen shoot virus spread.

PubMed

Wetten, Andy; Campbell, Colin; Allainguillaume, Joël

2016-03-01

Mealybugs (Hemiptera: Coccoidea: Pseudococcidae) are key vectors of badnaviruses, including Cacao swollen shoot virus (CSSV), the most damaging virus affecting cacao (Theobroma cacao L.). The effectiveness of mealybugs as virus vectors is species dependent, and it is therefore vital that CSSV resistance breeding programmes in cacao incorporate accurate mealybug identification. In this work, the efficacy of a CO1-based DNA barcoding approach to species identification was evaluated by screening a range of mealybugs collected from cacao in seven countries. Morphologically similar adult females were characterised by scanning electron microscopy, and then, following DNA extraction, were screened with CO1 barcoding markers. A high degree of CO1 sequence homology was observed for all 11 individual haplotypes, including those accessions from distinct geographical regions. This has allowed the design of a high-resolution melt (HRM) assay capable of rapid identification of the commonly encountered mealybug pests of cacao. HRM analysis readily differentiated between mealybug pests of cacao that cannot necessarily be identified by conventional morphological analysis. This new approach, therefore, has potential to facilitate breeding for resistance to CSSV and other mealybug-transmitted diseases. © 2015 Society of Chemical Industry.

Development and validation of a multiplex real-time PCR method to simultaneously detect 47 targets for the identification of genetically modified organisms.

PubMed

Cottenet, Geoffrey; Blancpain, Carine; Sonnard, Véronique; Chuah, Poh Fong

2013-08-01

Considering the increase of the total cultivated land area dedicated to genetically modified organisms (GMO), the consumers' perception toward GMO and the need to comply with various local GMO legislations, efficient and accurate analytical methods are needed for their detection and identification. Considered as the gold standard for GMO analysis, the real-time polymerase chain reaction (RTi-PCR) technology was optimised to produce a high-throughput GMO screening method. Based on simultaneous 24 multiplex RTi-PCR running on a ready-to-use 384-well plate, this new procedure allows the detection and identification of 47 targets on seven samples in duplicate. To comply with GMO analytical quality requirements, a negative and a positive control were analysed in parallel. In addition, an internal positive control was also included in each reaction well for the detection of potential PCR inhibition. Tested on non-GM materials, on different GM events and on proficiency test samples, the method offered high specificity and sensitivity with an absolute limit of detection between 1 and 16 copies depending on the target. Easy to use, fast and cost efficient, this multiplex approach fits the purpose of GMO testing laboratories.

Identification of Arabidopsis mutants with altered freezing tolerance.

PubMed

Perea-Resa, Carlos; Salinas, Julio

2014-01-01

Low temperature is an important determinant in the configuration of natural plant communities and defines the range of distribution and growth of important crops. Some plants, including Arabidopsis, have evolved sophisticated adaptive mechanisms to tolerate low and freezing temperatures. Central to this adaptation is the process of cold acclimation. By means of this process, many plants from temperate regions are able to develop or increase their freezing tolerance in response to low, nonfreezing temperatures. The identification and characterization of factors involved in freezing tolerance are crucial to understand the molecular mechanisms underlying the cold acclimation response and have a potential interest to improve crop tolerance to freezing temperatures. Many genes implicated in cold acclimation have been identified in numerous plant species by using molecular approaches followed by reverse genetic analysis. Remarkably, however, direct genetic analyses have not been conveniently exploited in their capacity for identifying genes with pivotal roles in that adaptive response. In this chapter, we describe a protocol for evaluating the freezing tolerance of both non-acclimated and cold-acclimated Arabidopsis plants. This protocol allows the accurate and simple screening of mutant collections for the identification of novel factors involved in freezing tolerance and cold acclimation.

[Personality structure and subjective illness concepts of neurotically depressed patients. Qualitative comparison of 11 individual cases analyses of initial psychotherapy interviews].

PubMed

Frommer, J; Jüttemann-Lembke, A; Stratkötter, A; Tress, W

1995-07-01

Verbatim transcripts of 11 psychotherapeutic interviews with patients suffering from depressive neurosis were examined, focusing on subjective theories of illness, biography, and descriptions of the patient's own personality. The results of our qualitative content analysis allow reconstruction of some characteristic features of these patients, like over identification with social roles and norms (1), feeling of being dependent and injured by another person (2), problems of self-esteem (3), shyness (4), unfulfilled wishes to be loved and accepted (5). These findings are discussed in the context of psychopathological and psychoanalytic concepts of depression.

Benchmark studies of induced radioactivity produced in LHC materials, Part I: Specific activities.

PubMed

Brugger, M; Khater, H; Mayer, S; Prinz, A; Roesler, S; Ulrici, L; Vincke, H

2005-01-01

Samples of materials which will be used in the LHC machine for shielding and construction components were irradiated in the stray radiation field of the CERN-EU high-energy reference field facility. After irradiation, the specific activities induced in the various samples were analysed with a high-precision gamma spectrometer at various cooling times, allowing identification of isotopes with a wide range of half-lives. Furthermore, the irradiation experiment was simulated in detail with the FLUKA Monte Carlo code. A comparison of measured and calculated specific activities shows good agreement, supporting the use of FLUKA for estimating the level of induced activity in the LHC.

Evolution of infectious hematopoietic necrosis virus (IHNV), a fish rhabdovirus, in Europe over 20 years: implications for control.

PubMed

Enzmann, Peter-Joachim; Castric, Jeannette; Bovo, Giuseppe; Thiery, Richard; Fichtner, Dieter; Schütze, Heike; Wahli, Thomas

2010-02-24

The fish pathogenic rhabdovirus infectious hematopoietic necrosis virus (IHNV) causes substantial losses in European aquaculture. IHNV was first detected in Europe in 1987 and has since undergone considerable spread. Phylogenetic analyses of the full G-gene sequences of 73 isolates obtained from 4 countries in Europe (France, n = 18; Italy, 9; Switzerland, 4; Germany, 42) enable determination of the evolution of the virus in Europe since the first detection, and identification of characteristic changes within the G-genes of European strains. Further, the database allows us to analyse the pathways of distribution in Europe over time. The results suggest that in most of the recent cases, spread of IHNV was related to trade of infected fish. The data further demonstrate that knowledge of the sequence is required to determine the source of infections in farms.

Otolith patterns of rockfishes from the northeastern Pacific.

PubMed

Tuset, Victor M; Imondi, Ralph; Aguado, Guillermo; Otero-Ferrer, José L; Santschi, Linda; Lombarte, Antoni; Love, Milton

2015-04-01

Sagitta otolith shape was analysed in twenty sympatric rockfishes off the southern California coast (Northeastern Pacific). The variation in shape was quantified using canonical variate analysis based on fifth wavelet function decomposition of otolith contour. We selected wavelets because this representation allow the identifications of zones or single morphological points along the contour. The entire otoliths along with four subsections (anterior, ventral, posterodorsal, and anterodorsal) with morphological meaning were examined. Multivariate analyses (MANOVA) showed significant differences in the contours of whole otolith morphology and corresponding subsection among rockfishes. Four patterns were found: fusiform, oblong, and two types of elliptic. A redundancy analysis indicated that anterior and anterodorsal subsections contribute most to define the entire otolith shape. Complementarily, the eco-morphological study indicated that the depth distribution and strategies for capture prey were correlated to otolith shape, especially with the anterodorsal zone. © 2014 Wiley Periodicals, Inc.

Analyse d'un programme d'electromecanique en ses concepts et principes physiques: Methode et application

NASA Astrophysics Data System (ADS)

Gagnon, Richard; Besançon, Jacques; Jean, Pascale

1989-09-01

In many Western countries there is growing interest in the usefulness of scientific knowledge in vocational and technical training. Moreover, there is an increasing tendency in these countries to formulate objectives within teaching programmes, in order to come closer to the real tasks of the world of work. To determine what knowledge is required, a general method of analysing objective-based vocational training programmes was developed. This allows the identification of the minimum scientific and mathematical concepts and principles which are necessary to reach the learning objectives, and the establishment of their relative significance and the requisite level of detail. It has been used to determine the essential physical concepts of the industrial mechanics section (625 hours) of a programme on the electromechanics of automated systems. The results reveal the existence of 41 concepts needed for a total of 2,452.5 hours. A limited group of these is of particular importance.

A metagenomic framework for the study of airborne microbial communities.

PubMed

Yooseph, Shibu; Andrews-Pfannkoch, Cynthia; Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B; Fadrosh, Douglas; Glass, John; Adams, Mark D; Friedman, Robert; Venter, J Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.

A Metagenomic Framework for the Study of Airborne Microbial Communities

PubMed Central

Tenney, Aaron; McQuaid, Jeff; Williamson, Shannon; Thiagarajan, Mathangi; Brami, Daniel; Zeigler-Allen, Lisa; Hoffman, Jeff; Goll, Johannes B.; Fadrosh, Douglas; Glass, John; Adams, Mark D.; Friedman, Robert; Venter, J. Craig

2013-01-01

Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria. PMID:24349140

Requirements, techniques, and costs for contaminant removal from landfill gas.

PubMed

Kuhn, John N; Elwell, Anthony C; Elsayed, Nada H; Joseph, Babu

2017-05-01

Waste-to-energy projects are an increasingly prominent component of future energy portfolios. Landfill gas (LFG)-to-energy (LFGTE) projects are particularly important as they address greenhouse gas emissions. Contaminants in LFG may hamper these projects both from environmental and economic standpoints. The purpose of this review is to highlight key aspects (LFG composition ranges, LFG flowrates, and allowable tolerances for LFGTE technologies, performance and costs for contaminant removal by adsorption). Removal of key contaminants, H 2 S and siloxanes, by adsorption are surveyed in terms of adsorption capacities and regeneration abilities. Based on the open literature, costing analyses are tabulated and discussed. The findings indicate economics of contaminant removal depend heavily on the feed concentrations of contaminants, allowable tolerances for the LFGTE technology, and the current market for the product. Key trends, identification of challenges, and general purification guidelines for purifying LFG for energy projects are also discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

PubMed

Roosaare, Märt; Vaher, Mihkel; Kaplinski, Lauris; Möls, Märt; Andreson, Reidar; Lepamets, Maarja; Kõressaar, Triinu; Naaber, Paul; Kõljalg, Siiri; Remm, Maido

2017-01-01

Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. A tool named StrainSeeker was developed that constructs a list of specific k -mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k -mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II.

PubMed

Barrera, Gloria Patricia; Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth; Ghiringhelli, Pablo Daniel; Vargas, Germán

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification.

Identification of Diatraea spp. (Lepidoptera: Crambidae) based on cytochrome oxidase II

PubMed Central

Villamizar, Laura Fernanda; Espinel, Carlos; Quintero, Edgar Mauricio; Belaich, Mariano Nicolás; Toloza, Deisy Liseth

2017-01-01

Diatraea spp. (Lepidoptera: Crambidae) are a group of insects that are agriculture pests in many economically relevant crops such as sugarcane, sorghum, corn and rice. Recognized species for this genus respond differentially to natural enemies used in their biological control, emphasizing the importance of species in a regional approach. Currently, identification is based on the male genitalia. However, the availability of specimens collected from field and subjectivity based on the character recognition can seriously hamper species identification, and therefore result in inadequate pest management. To overcome this, individuals of Diatraea spp. preliminarily classified male genitalia and obtained from reared conditions and the field (both derived from natural populations occurring in Colombia) were analyzed using genitalic morphometry and molecular biology specifically using a fragment of the cytochrome oxidase subunit II (CO II) mitochondrial gene. Although morphometric analysis did not show any overriding results regarding genitalia morphology, the bioinformatics analyses of CO II sequences resulted in an adequate classification of the individuals within the recognized species. It also, revealed that the occurrence of clades associated with geographical distribution may be associated with cryptic species. The latter was also confirmed by a Single-Strand Conformation Polymorphism (SSCP) methodology evaluating the same fragment of CO II. This experimental approach allows properly recognizing each species and in consequence is proposed as an effective tool in Diatraea species identification. PMID:28873431

Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.

PubMed

Uchiyama, Ikuo

2017-01-01

Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a "My MBGD" mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.

Identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by righ-resolution melting analysis

PubMed Central

2017-01-01

The objective of this study was to standardize the high-resolution melting method for identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by amplification of 18S ribosomal DNA (rDNA) using a single primer pair. The analyses were performed on individual reactions (containing DNA from a single species of a protozoan), on duplex reactions (containing DNA from two species of protozoa in each reaction), and on a multiplex reaction (containing DNA of four parasites in a single reaction). The proposed method allowed us to identify and discriminate the four species by analyzing the derivative, normalized, and difference melting curves, with high reproducibility among and within the experiments, as demonstrated by low coefficients of variation (less than 2.2% and 2.0%, respectively). This is the first study where this method is used for discrimination of these four species of protozoa in a single reaction. PMID:28346485

Agronomic, chemical and genetic profiles of hot peppers (Capsicum annuum ssp.).

PubMed

De Masi, Luigi; Siviero, Pietro; Castaldo, Domenico; Cautela, Domenico; Esposito, Castrese; Laratta, Bruna

2007-08-01

A study on morphology, productive yield, main quality parameters and genetic variability of eight landraces of hot pepper (Capsicum annuum ssp.) from Southern Italy has been performed. Morphological characters of berries and productivity values were evaluated by agronomic analyses. Chemical and genetic investigations were performed by HPLC and random amplified polymorphic DNA (RAPD)-PCR, respectively. In particular, carotenoid and capsaicinoid (pungency) contents were considered as main quality parameters of hot pepper. For the eight selected samples, genetic similarity values were calculated from the generated RAPD fragments and a dendrogram of genetic similarity was constructed. All the eight landraces exhibited characteristic RAPD patterns that allowed their characterization. Agro-morphological and chemical determinations were found to be adequate for selection, but they resulted useful only for plants grown in the same environmental conditions. RAPD application may provide a more reliable way based on DNA identification. The results of our study led to the identification of three noteworthy populations, suitable for processing, which fitted into different clusters of the dendrogram.

The MicrOmega Investigation Onboard Hayabusa2

NASA Astrophysics Data System (ADS)

Bibring, J.-P.; Hamm, V.; Langevin, Y.; Pilorget, C.; Arondel, A.; Bouzit, M.; Chaigneau, M.; Crane, B.; Darié, A.; Evesque, C.; Hansotte, J.; Gardien, V.; Gonnod, L.; Leclech, J.-C.; Meslier, L.; Redon, T.; Tamiatto, C.; Tosti, S.; Thoores, N.

2017-07-01

MicrOmega is a near-IR hyperspectral microscope designed to characterize in situ the texture and composition of the surface materials of the Hayabusa2 target asteroid. MicrOmega is implemented within the MASCOT lander (Ho et al. in Space Sci. Rev., 2016, this issue, doi:10.1007/s11214-016-0251-6). The spectral range (0.99-3.65 μm) and the spectral sampling (20 cm^{-1}) of MicrOmega have been chosen to allow the identification of most potential constituent minerals, ices and organics, within each 25 μm pixel of the 3.2× 3.2 mm2 FOV. Such an unprecedented characterization will (1) enable the identification of most major and minor phases, including the potential organic phases, and ascribe their mineralogical context, as a critical set of clues to decipher the origin and evolution of this primitive body, and (2) provide the ground truth for the orbital measurements as well as a reference for the analyses later performed on returned samples.

Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration

PubMed Central

Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

2004-01-01

We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4°C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database (∼150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4°C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4°C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated. PMID:15345453

Performance analysis and prediction in triathlon.

PubMed

Ofoghi, Bahadorreza; Zeleznikow, John; Macmahon, Clare; Rehula, Jan; Dwyer, Dan B

2016-01-01

Performance in triathlon is dependent upon factors that include somatotype, physiological capacity, technical proficiency and race strategy. Given the multidisciplinary nature of triathlon and the interaction between each of the three race components, the identification of target split times that can be used to inform the design of training plans and race pacing strategies is a complex task. The present study uses machine learning techniques to analyse a large database of performances in Olympic distance triathlons (2008-2012). The analysis reveals patterns of performance in five components of triathlon (three race "legs" and two transitions) and the complex relationships between performance in each component and overall performance in a race. The results provide three perspectives on the relationship between performance in each component of triathlon and the final placing in a race. These perspectives allow the identification of target split times that are required to achieve a certain final place in a race and the opportunity to make evidence-based decisions about race tactics in order to optimise performance.

Identification of food and beverage spoilage yeasts from DNA sequence analyses

USDA-ARS?s Scientific Manuscript database

Detection, identification, and classification of yeasts has undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of th...

A visual identification key utilizing both gestalt and analytic approaches to identification of Carices present in North America (Plantae, Cyperaceae)

PubMed Central

2013-01-01

Abstract Images are a critical part of the identification process because they enable direct, immediate and relatively unmediated comparisons between a specimen being identified and one or more reference specimens. The Carices Interactive Visual Identification Key (CIVIK) is a novel tool for identification of North American Carex species, the largest vascular plant genus in North America, and two less numerous closely-related genera, Cymophyllus and Kobresia. CIVIK incorporates 1288 high-resolution tiled image sets that allow users to zoom in to view minute structures that are crucial at times for identification in these genera. Morphological data are derived from the earlier Carex Interactive Identification Key (CIIK) which in turn used data from the Flora of North America treatments. In this new iteration, images can be viewed in a grid or histogram format, allowing multiple representations of data. In both formats the images are fully zoomable. PMID:24723777

Consistency of the Performance and Nonperformance Methods in Gifted Identification

ERIC Educational Resources Information Center

Acar, Selcuk; Sen, Sedat; Cayirdag, Nur

2016-01-01

Current approaches to gifted identification suggest collecting multiple sources of evidence. Some gifted identification guidelines allow for the interchangeable use of "performance" and "nonperformance" identification methods. This multiple criteria approach lacks a strong overlap between the assessment tools; however,…

6-Iso-chlortetracycline or keto form of chlortetracycline? Need for clarification for relevant monitoring of chlortetracycline residues in food.

PubMed

Gaugain, Murielle; Gautier, Sophie; Bourcier, Sophie; Jacques, Anne-Marie; Laurentie, Michel; Abjean, Jean-Pierre; Hurtaud-Pessel, Dominique; Verdon, Eric

2015-01-01

Chlortetracycline (CTC) is a broad-spectrum antibiotic used in veterinary medicine for pulmonary or digestive infections and having a regulatory maximum residue limit (MRL) necessitating an official analytical control method. The purpose of this study was to clarify the identification of different forms of CTC observed in standard solution, in spiked muscle samples and in naturally incurred muscle samples of pigs analysed by LC-MS/MS and to demonstrate the in vivo formation of 6-iso-chlortetracycline and 4-epi-6-iso-CTC as a metabolite of CTC and 4-epi-CTC in muscle. The six following forms were identified, all being isobaric with a protonated molecule at m/z 479 (precursor ion): the keto-enol forms of CTC and the keto-enol forms of 4-epi-chlortetracycline (4-epi-CTC), 6-iso-chlortetracycline (6-iso-CTC) and 4-epi-6-iso-chlortetracycline (4-epi-6-iso-CTC). The 6-iso-CTC and 4-epi-6-iso-CTC were observed only in incurred pig samples so were identified for the first time as metabolites of CTC and 4-epi-CTC. Identification of the different forms was obtained by comparing incurred muscle samples with standard solutions and with spiked samples. Then the differences between the features of the chromatograms obtained by LC-TQ-MS and the fragmentation study of the different forms of CTC obtained by LC-Q-TOF-MS helped us to support this identification. The extraction steps and the LC-MS/MS conditions developed to analyse muscle tissue samples are described. This clarification concerning the rigorous identification of chromatographic peaks allowed us to evaluate the relevance of our monitoring method with regard to the regulations in place in the European Union and could be of help to laboratories involved in official control of antibiotic residues in food of animal origin. Additional results are also presented highlighting the transformation of the CTC when prepared in a mixture with other antibiotics.

Sliding Window Analyses for Optimal Selection of Mini-Barcodes, and Application to 454-Pyrosequencing for Specimen Identification from Degraded DNA

PubMed Central

Boyer, Stephane; Brown, Samuel D. J.; Collins, Rupert A.; Cruickshank, Robert H.; Lefort, Marie-Caroline; Malumbres-Olarte, Jagoba; Wratten, Stephen D.

2012-01-01

DNA barcoding remains a challenge when applied to diet analyses, ancient DNA studies, environmental DNA samples and, more generally, in any cases where DNA samples have not been adequately preserved. Because the size of the commonly used barcoding marker (COI) is over 600 base pairs (bp), amplification fails when the DNA molecule is degraded into smaller fragments. However, relevant information for specimen identification may not be evenly distributed along the barcoding region, and a shorter target can be sufficient for identification purposes. This study proposes a new, widely applicable, method to compare the performance of all potential ‘mini-barcodes’ for a given molecular marker and to objectively select the shortest and most informative one. Our method is based on a sliding window analysis implemented in the new R package SPIDER (Species IDentity and Evolution in R). This method is applicable to any taxon and any molecular marker. Here, it was tested on earthworm DNA that had been degraded through digestion by carnivorous landsnails. A 100 bp region of 16 S rDNA was selected as the shortest informative fragment (mini-barcode) required for accurate specimen identification. Corresponding primers were designed and used to amplify degraded earthworm (prey) DNA from 46 landsnail (predator) faeces using 454-pyrosequencing. This led to the detection of 18 earthworm species in the diet of the snail. We encourage molecular ecologists to use this method to objectively select the most informative region of the gene they aim to amplify from degraded DNA. The method and tools provided here, can be particularly useful (1) when dealing with degraded DNA for which only small fragments can be amplified, (2) for cases where no consensus has yet been reached on the appropriate barcode gene, or (3) to allow direct analysis of short reads derived from massively parallel sequencing without the need for bioinformatic consolidation. PMID:22666489

Modeling and Parameter Estimation of Spacecraft Fuel Slosh with Diaphragms Using Pendulum Analogs

NASA Technical Reports Server (NTRS)

Chatman, Yadira; Gangadharan, Sathya; Schlee, Keith; Ristow, James; Suderman, James; Walker, Charles; Hubert, Carl

2007-01-01

Prediction and control of liquid slosh in moving containers is an important consideration in the design of spacecraft and launch vehicle control systems. Even with modern computing systems, CFD type simulations are not fast enough to allow for large scale Monte Carlo analyses of spacecraft and launch vehicle dynamic behavior with slosh included. It is still desirable to use some type of simplified mechanical analog for the slosh to shorten computation time. Analytic determination of the slosh analog parameters has met with mixed success and is made even more difficult by the introduction of propellant management devices such as elastomeric diaphragms. By subjecting full-sized fuel tanks with actual flight fuel loads to motion similar to that experienced in flight and measuring the forces experienced by the tanks, these parameters can be determined experimentally. Currently, the identification of the model parameters is a laborious trial-and-error process in which the hand-derived equations of motion for the mechanical analog are evaluated and their results compared with the experimental results. This paper will describe efforts by the university component of a team comprised of NASA's Launch Services Program, Embry Riddle Aeronautical University, Southwest Research Institute and Hubert Astronautics to improve the accuracy and efficiency of modeling techniques used to predict these types of motions. Of particular interest is the effect of diaphragms and bladders on the slosh dynamics and how best to model these devices. The previous research was an effort to automate the process of slosh model parameter identification using a MATLAB/SimMechanics-based computer simulation. These results are the first step in applying the same computer estimation to a full-size tank and vehicle propulsion system. The introduction of diaphragms to this experimental set-up will aid in a better and more complete prediction of fuel slosh characteristics and behavior. Automating the parameter identification process will save time and thus allow earlier identification of potential vehicle performance problems.

Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples.

PubMed

Biondi, Enrico; Zamorano, Alan; Vega, Ernesto; Ardizzi, Stefano; Sitta, Davide; De Salvador, Flavio Roberto; Campos-Vargas, Reinaldo; Meneses, Claudio; Perez, Set; Bertaccini, Assunta; Fiore, Nicola

2018-05-01

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

Skin sensitizer identification by IL-8 secretion and CD86 expression on THP-1 cells.

PubMed

Parise, Carolina Bellini; Sá-Rocha, Vanessa Moura; Moraes, Jane Zveiter

2015-12-25

Substantial progress has been made in the development of alternative methods for skin sensitization in the last decade in several countries around the world. Brazil is experiencing an increasing concern about using animals for product development, since the publication of the Law 9605/1998, which prohibits the use of animals when an alternative method is available. In this way, an in vitro test to evaluate allergenic potential is a pressing need.This preliminary study started setting the use of myelomonocytic THP-1 cell line, according to the human cell line activation test (h-CLAT), already under validation process. We found that 48-h chemical exposure was necessary to identify 22 out of 23 sensitizers by the analyses of CD86 expression. In addition, the CD54 expression analyses presented a poor efficiency to discriminate sensitizers from non-sensitizers in our conditions. In view of these results, we looked for changes of pro-inflammatory interleukin profile. The IL-8 secretion analyses after 24-h chemical incubation seemed to be an alternative for CD54 expression assessing.Altogether, our findings showed that the combination of the analyses of CD86 expression and IL-8 secretion allowed predicting allergenicity.

Direct identification of pathogens from positive blood cultures using matrix-assisted laser desorption-ionization time-of-flight mass spectrometry.

PubMed

Rodríguez-Sánchez, B; Sánchez-Carrillo, C; Ruiz, A; Marín, M; Cercenado, E; Rodríguez-Créixems, M; Bouza, E

2014-07-01

In recent years, matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has proved a rapid and reliable method for the identification of bacteria and yeasts that have already been isolated. The objective of this study was to evaluate this technology as a routine method for the identification of microorganisms directly from blood culture bottles (BCBs), before isolation, in a large collection of samples. For this purpose, 1000 positive BCBs containing 1085 microorganisms have been analysed by conventional phenotypic methods and by MALDI-TOF MS. Discrepancies have been resolved using molecular methods: the amplification and sequencing of the 16S rRNA gene or the Superoxide Dismutase gene (sodA) for streptococcal isolates. MALDI-TOF predicted a species- or genus-level identification of 81.4% of the analysed microorganisms. The analysis by episode yielded a complete identification of 814 out of 1000 analysed episodes (81.4%). MALDI-TOF identification is available for clinicians within hours of a working shift, as oppose to 18 h later when conventional identification methods are performed. Moreover, although further improvement of sample preparation for polymicrobial BCBs is required, the identification of more than one pathogen in the same BCB provides a valuable indication of unexpected pathogens when their presence may remain undetected in Gram staining. Implementation of MALDI-TOF identification directly from the BCB provides a rapid and reliable identification of the causal pathogen within hours. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry I. Screening analysis.

PubMed

Badoud, F; Grata, E; Perrenoud, L; Avois, L; Saugy, M; Rudaz, S; Veuthey, J-L

2009-05-15

The general strategy to perform anti-doping analyses of urine samples starts with the screening for a wide range of compounds. This step should be fast, generic and able to detect any sample that may contain a prohibited substance while avoiding false negatives and reducing false positive results. The experiments presented in this work were based on ultra-high-pressure liquid chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry. Thanks to the high sensitivity of the method, urine samples could be diluted 2-fold prior to injection. One hundred and three forbidden substances from various classes (such as stimulants, diuretics, narcotics, anti-estrogens) were analysed on a C(18) reversed-phase column in two gradients of 9min (including two 3min equilibration periods) for positive and negative electrospray ionisation and detected in the MS full scan mode. The automatic identification of analytes was based on retention time and mass accuracy, with an automated tool for peak picking. The method was validated according to the International Standard for Laboratories described in the World Anti-Doping Code and was selective enough to comply with the World Anti-Doping Agency recommendations. In addition, the matrix effect on MS response was measured on all investigated analytes spiked in urine samples. The limits of detection ranged from 1 to 500ng/mL, allowing the identification of all tested compounds in urine. When a sample was reported positive during the screening, a fast additional pre-confirmatory step was performed to reduce the number of confirmatory analyses.

The Listeria monocytogenes strain 10403S BioCyc database

PubMed Central

Orsi, Renato H.; Bergholz, Teresa M.; Wiedmann, Martin; Boor, Kathryn J.

2015-01-01

Listeria monocytogenes is a food-borne pathogen of humans and other animals. The striking ability to survive several stresses usually used for food preservation makes L. monocytogenes one of the biggest concerns to the food industry, while the high mortality of listeriosis in specific groups of humans makes it a great concern for public health. Previous studies have shown that a regulatory network involving alternative sigma (σ) factors and transcription factors is pivotal to stress survival. However, few studies have evaluated at the metabolic networks controlled by these regulatory mechanisms. The L. monocytogenes BioCyc database uses the strain 10403S as a model. Computer-generated initial annotation for all genes also allowed for identification, annotation and display of predicted reactions and pathways carried out by a single cell. Further ongoing manual curation based on published data as well as database mining for selected genes allowed the more refined annotation of functions, which, in turn, allowed for annotation of new pathways and fine-tuning of previously defined pathways to more L. monocytogenes-specific pathways. Using RNA-Seq data, several transcription start sites and promoter regions were mapped to the 10403S genome and annotated within the database. Additionally, the identification of promoter regions and a comprehensive review of available literature allowed the annotation of several regulatory interactions involving σ factors and transcription factors. The L. monocytogenes 10403S BioCyc database is a new resource for researchers studying Listeria and related organisms. It allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database. Database URL: http://biocyc.org/organism-summary?object=10403S_RAST PMID:25819074

The Listeria monocytogenes strain 10403S BioCyc database.

PubMed

Orsi, Renato H; Bergholz, Teresa M; Wiedmann, Martin; Boor, Kathryn J

2015-01-01

Listeria monocytogenes is a food-borne pathogen of humans and other animals. The striking ability to survive several stresses usually used for food preservation makes L. monocytogenes one of the biggest concerns to the food industry, while the high mortality of listeriosis in specific groups of humans makes it a great concern for public health. Previous studies have shown that a regulatory network involving alternative sigma (σ) factors and transcription factors is pivotal to stress survival. However, few studies have evaluated at the metabolic networks controlled by these regulatory mechanisms. The L. monocytogenes BioCyc database uses the strain 10403S as a model. Computer-generated initial annotation for all genes also allowed for identification, annotation and display of predicted reactions and pathways carried out by a single cell. Further ongoing manual curation based on published data as well as database mining for selected genes allowed the more refined annotation of functions, which, in turn, allowed for annotation of new pathways and fine-tuning of previously defined pathways to more L. monocytogenes-specific pathways. Using RNA-Seq data, several transcription start sites and promoter regions were mapped to the 10403S genome and annotated within the database. Additionally, the identification of promoter regions and a comprehensive review of available literature allowed the annotation of several regulatory interactions involving σ factors and transcription factors. The L. monocytogenes 10403S BioCyc database is a new resource for researchers studying Listeria and related organisms. It allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database. © The Author(s) 2015. Published by Oxford University Press.

Use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry analyser in a diagnostic microbiology laboratory in a developing country.

PubMed

Bulane, Atang; Hoosen, Anwar

2017-01-01

Rapid and accurate identification of pathogens is of utmost importance for management of patients. Current identification relies on conventional phenotypic methods which are time consuming. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) is based on proteomic profiling and allows for rapid identification of pathogens. We compared MALDI-TOF MS against two commercial systems, MicroScan Walkaway and VITEK 2 MS. Over a three-month period from July 2013 to September 2013, a total of 227 bacteria and yeasts were collected from an academic microbiology laboratory ( N = 121; 87 Gram-negatives, seven Gram-positives, 27 yeasts) and other laboratories ( N = 106; 35 Gram-negatives, 34 Gram-positives, 37 yeasts). Sixty-five positive blood cultures were initially processed with Bruker Sepsityper kit for direct identification. From the 65 blood culture bottles, four grew more than one bacterial pathogen and MALDI-TOF MS identified only one isolate. The blood cultures yielded 21 Gram-negatives, 43 Gram-positives and one Candida . There were 21 Escherirchia coli isolates which were reported by the MALDI-TOF MS as E. coli / Shigella . Of the total 292 isolates, discrepant results were found for one bacterial and three yeast isolates. Discrepant results were resolved by testing with the API system with MALDI-TOF MS showing 100% correlation. The MALDI-TOF MS proved to be very useful for rapid and reliable identification of bacteria and yeasts directly from blood cultures and after culture of other specimens. The difference in time to identification was significant for all isolates. However, for positive blood cultures with minimal sample preparation time there was a massive difference in turn-around time with great appreciation by clinicians.

Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS

PubMed Central

Lafri, Ismail; Almeras, Lionel; Bitam, Idir; Caputo, Aurelia; Yssouf, Amina; Forestier, Claire-Lise; Izri, Arezki; Raoult, Didier; Parola, Philippe

2016-01-01

Background Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Methodology/Principal Findings Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M’sila where P. (Phlebotomus) papatasi was the only sand fly species detected. Conclusion The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF MS analyses opens up new ways in the management of phlebotomine sand fly-borne diseases. PMID:26771833

Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS.

PubMed

Lafri, Ismail; Almeras, Lionel; Bitam, Idir; Caputo, Aurelia; Yssouf, Amina; Forestier, Claire-Lise; Izri, Arezki; Raoult, Didier; Parola, Philippe

2016-01-01

Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M'sila where P. (Phlebotomus) papatasi was the only sand fly species detected. The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF MS analyses opens up new ways in the management of phlebotomine sand fly-borne diseases.

Microbe-ID: an open source toolbox for microbial genotyping and species identification.

PubMed

Tabima, Javier F; Everhart, Sydney E; Larsen, Meredith M; Weisberg, Alexandra J; Kamvar, Zhian N; Tancos, Matthew A; Smart, Christine D; Chang, Jeff H; Grünwald, Niklaus J

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.

Nitrogen-isotopes and multi-parameter sewage water test for identification of nitrate sources: Groundwater body Marchfeld East of Vienna

NASA Astrophysics Data System (ADS)

Kralik, Martin

2017-04-01

The application of nitrogen and oxygen isotopes in nitrate allows, under favourable circumstances, to identify potential sources such as precipitation, chemical fertilisers and manure or sewage water. Without any additional tracer, the source distinction of nitrate from manure or sewage water is still difficult. Even the application of boron isotopes can in some cases not avoid ambiguous interpretation. Therefore, the Environment Agency Austria developed a new multi parametrical indicator test to allow the identification and quantification of pollution by domestic sewage water. The test analyses 8 substances well known to occur in sewage water: Acesulfame and sucralose (two artificial, calorie-free sweeteners), benzotriazole and tolyltriazole (two industrial chemicals/corrosion inhibitors), metoprolol, sotalol, carbamazepine and the metabolite 10,11-Dihydro-10,11-dihydroxycarbamazepine (pharmaceuticals) [1]. These substances are polar and degradation in the aquatic system by microbiological processes is not documented. These 8 Substances do not occur naturally which make them ideal tracers. The test can detect wastewater in the analysed water sample down to 0.1 %. This ideal coupling of these analytic tests helps to identify the nitrogen sources in the groundwater body Marchfeld East of Vienna to a high confidence level. In addition, the results allow a reasonable quantification of nitrogen sources from different types of fertilizers as well as sewage water contributions close to villages and in wells recharged by bank filtration. Recent investigations of groundwater in selected wells in Marchfeld [2] indicated a clear nitrogen contribution by wastewater leakages (sewers or septic tanks) to the total nitrogen budget. However, this contribution is shrinking and the main source comes still from agricultural activities. [1] Humer, F.; Weiss, S.; Reinnicke, S.; Clara, M.; Grath, J.; Windhofer, G. (2013): Multi parametrical indicator test for urban wastewater influence. EGU General Assembly 2013, held 7-12 April, 2013 in Vienna, Austria, id. EGU2013-5332, EGU2013-5332. [2] Kralik, M.; Humer, F. & Grath, J. (2008): Pilotprojekt Grundwasseralter: Herkunftsanalyse von Nitrat mittels Stickstoff-, Sauerstoff-, Schwefel und Kohlenstoffisotopen. 57 S.2, Environment Agency Austria/Ministry of Agriculture, Forestry, Environment and Water Management, Vienna.

Intellicount: High-Throughput Quantification of Fluorescent Synaptic Protein Puncta by Machine Learning

PubMed Central

Fantuzzo, J. A.; Mirabella, V. R.; Zahn, J. D.

2017-01-01

Abstract Synapse formation analyses can be performed by imaging and quantifying fluorescent signals of synaptic markers. Traditionally, these analyses are done using simple or multiple thresholding and segmentation approaches or by labor-intensive manual analysis by a human observer. Here, we describe Intellicount, a high-throughput, fully-automated synapse quantification program which applies a novel machine learning (ML)-based image processing algorithm to systematically improve region of interest (ROI) identification over simple thresholding techniques. Through processing large datasets from both human and mouse neurons, we demonstrate that this approach allows image processing to proceed independently of carefully set thresholds, thus reducing the need for human intervention. As a result, this method can efficiently and accurately process large image datasets with minimal interaction by the experimenter, making it less prone to bias and less liable to human error. Furthermore, Intellicount is integrated into an intuitive graphical user interface (GUI) that provides a set of valuable features, including automated and multifunctional figure generation, routine statistical analyses, and the ability to run full datasets through nested folders, greatly expediting the data analysis process. PMID:29218324

Input-output identification of controlled discrete manufacturing systems

NASA Astrophysics Data System (ADS)

Estrada-Vargas, Ana Paula; López-Mellado, Ernesto; Lesage, Jean-Jacques

2014-03-01

The automated construction of discrete event models from observations of external system's behaviour is addressed. This problem, often referred to as system identification, allows obtaining models of ill-known (or even unknown) systems. In this article, an identification method for discrete event systems (DESs) controlled by a programmable logic controller is presented. The method allows processing a large quantity of observed long sequences of input/output signals generated by the controller and yields an interpreted Petri net model describing the closed-loop behaviour of the automated DESs. The proposed technique allows the identification of actual complex systems because it is sufficiently efficient and well adapted to cope with both the technological characteristics of industrial controllers and data collection requirements. Based on polynomial-time algorithms, the method is implemented as an efficient software tool which constructs and draws the model automatically; an overview of this tool is given through a case study dealing with an automated manufacturing system.

Modified filter-aided sample preparation (FASP) method increases peptide and protein identifications for shotgun proteomics.

PubMed

Ni, Mao-Wei; Wang, Lu; Chen, Wei; Mou, Han-Zhou; Zhou, Jie; Zheng, Zhi-Guo

2017-01-30

Mass spectrometry (MS)-based protein identification depends mainly on protein extraction and digestion. Although sodium dodecyl sulfate (SDS) can preclude enzymatic digestion and interfere with MS analysis, it is still the most widely used surfactant in these steps. To overcome these disadvantages, a SDS-compatible proteomic technique for SDS removal prior to MS-based analyses was developed, namely filter-aided sample preparation (FASP). Herein, based on the effectiveness of sodium deoxycholate and a detergent removal spin column, we developed a modified FASP (mFASP) method and compared its overall performance, total number of peptides and proteins identified for shotgun proteomic experiments with that of the FASP method. Identification of 4570 ± 392 and 9139 ± 317 peptides and description of 862 ± 46 and 1377 ± 33 protein groups with two or more peptides from the ovarian cancer cell line A2780 was accomplished by FASP and mFASP methods, respectively. The mFASP method (21.2 ± 0.2%) had higher average peptide to protein coverage than FASP method (13.2 ± 0.5%). More hydrophobic peptides were identified by mFASP than by FASP, as indicated by the GRAVY score distribution. The reported method enables reliable and efficient identification of proteins and peptides in whole-cell extracts containing SDS. The new approach allows for higher throughput (the simultaneous identification of more proteins), a more comprehensive investigation of proteins, and potentially the discovery of new biomarkers. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fast and accurate identification of clinically relevant Aspergillus species.

PubMed

Alanio, A; Beretti, J-L; Dauphin, B; Mellado, E; Quesne, G; Lacroix, C; Amara, A; Berche, P; Nassif, X; Bougnoux, M-E

2011-05-01

New Aspergillus species have recently been described with the use of multilocus sequencing in refractory cases of invasive aspergillosis. The classical phenotypic identification methods routinely used in clinical laboratories failed to identify them adequately. Some of these Aspergillus species have specific patterns of susceptibility to antifungal agents, and misidentification may lead to inappropriate therapy. We developed a matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS)-based strategy to adequately identify Aspergillus species to the species level. A database including the reference spectra of 28 clinically relevant species from seven Aspergillus sections (five common and 23 unusual species) was engineered. The profiles of young and mature colonies were analysed for each reference strain, and species-specific spectral fingerprints were identified. The performance of the database was then tested on 124 clinical and 16 environmental isolates previously characterized by partial sequencing of the β-tubulin and calmodulin genes. One hundred and thirty-eight isolates of 140 (98.6%) were correctly identified. Two atypical isolates could not be identified, but no isolate was misidentified (specificity: 100%). The database, including species-specific spectral fingerprints of young and mature colonies of the reference strains, allowed identification regardless of the maturity of the clinical isolate. These results indicate that MALDI-TOF MS is a powerful tool for rapid and accurate identification of both common and unusual species of Aspergillus. It can give better results than morphological identification in clinical laboratories. © 2010 The Authors. Clinical Microbiology and Infection © 2010 European Society of Clinical Microbiology and Infectious Diseases.

Diversity patterns, Leishmania DNA detection, and bloodmeal identification of Phlebotominae sand flies in villages in northern Colombia

PubMed Central

León, Cielo; Paz, Andrea; López, Marla; Molina, Gisell; Toro, Diana; Ortiz, Mario; Cordovez, Juan Manuel; Atencia, María Claudia; Aguilera, Germán; Tovar, Catalina

2018-01-01

Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections. The study was carried out in Colombia, in 13 municipalities of Cordoba department, implementing a methodology that could be further used for the evaluation of vector-borne diseases in villages or towns. Our sampling design included 24 houses randomly selected in each of 15 villages distributed in 13 municipalities, which were sampled in two seasons in 2015 and 2016. Sand flies were collected using CDC light traps placed in intra and peridomestic habitats. In addition to the morphological identification, molecular identification through DNA barcodes was also performed. A total of 19,743 sand flies were collected and 13,848 of them (10,268 females and 3,580 males) were used in molecular procedures. Circulation of two known parasite species–Leishmania infantum and Leishmania panamensis was confirmed. Blood source analyses showed that sand flies fed on humans, particularly in the case of the known L. infantum vector, P. evansi; further analyses are advised to evaluate the reservoirs involved in parasite transmission. Our sampling design allowed us to evaluate potential transmission cycles on a department scale, by defining suspected vector species, parasite species present in different municipalities and feeding habits. PMID:29320544

Diversity patterns, Leishmania DNA detection, and bloodmeal identification of Phlebotominae sand flies in villages in northern Colombia.

PubMed

González, Camila; León, Cielo; Paz, Andrea; López, Marla; Molina, Gisell; Toro, Diana; Ortiz, Mario; Cordovez, Juan Manuel; Atencia, María Claudia; Aguilera, Germán; Tovar, Catalina

2018-01-01

Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections. The study was carried out in Colombia, in 13 municipalities of Cordoba department, implementing a methodology that could be further used for the evaluation of vector-borne diseases in villages or towns. Our sampling design included 24 houses randomly selected in each of 15 villages distributed in 13 municipalities, which were sampled in two seasons in 2015 and 2016. Sand flies were collected using CDC light traps placed in intra and peridomestic habitats. In addition to the morphological identification, molecular identification through DNA barcodes was also performed. A total of 19,743 sand flies were collected and 13,848 of them (10,268 females and 3,580 males) were used in molecular procedures. Circulation of two known parasite species-Leishmania infantum and Leishmania panamensis was confirmed. Blood source analyses showed that sand flies fed on humans, particularly in the case of the known L. infantum vector, P. evansi; further analyses are advised to evaluate the reservoirs involved in parasite transmission. Our sampling design allowed us to evaluate potential transmission cycles on a department scale, by defining suspected vector species, parasite species present in different municipalities and feeding habits.

Mechanical Analog Approach to Parameter Estimation of Lateral Spacecraft Fuel Slosh

NASA Technical Reports Server (NTRS)

Chatman, Yadira; Gangadharan, Sathya; Schlee, Keith; Sudermann, James; Walker, Charles; Ristow, James; Hubert, Carl

2007-01-01

The nutation (wobble) of a spinning spacecraft in the presence of energy dissipation is a well-known problem in dynamics and is of particular concern for space missions. Even with modern computing systems, CFD type simulations are not fast enough to allow for large scale Monte Carlo analyses of spacecraft and launch vehicle dynamic behavior with slosh included. Simplified mechanical analogs for the slosh are preferred during the initial stages of design to reduce computational time and effort to evaluate the Nutation Time Constant (NTC). Analytic determination of the slosh analog parameters has met with mixed success and is made even more difficult by the introduction of propellant management devices such as elastomeric diaphragms. By subjecting full-sized fuel tanks with actual flight fuel loads to motion similar to that experienced in flight and measuring the forces experienced by the tanks, these parameters can be determined experimentally. Currently, the identification of the model parameters is a laborious trial-and-error process in which the hand-derived equations of motion for the mechanical analog are evaluated and their results compared with the experimental results. Of particular interest is the effect of diaphragms and bladders on the slosh dynamics and how best to model these devices. An experimental set-up is designed and built to include a diaphragm in the simulated spacecraft fuel tank subjected to lateral slosh. This research paper focuses on the parameter estimation of a SimMechanics model of the simulated spacecraft propellant tank with and without diaphragms using lateral fuel slosh experiments. Automating the parameter identification process will save time and thus allow earlier identification of potential vehicle problems.

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

PubMed Central

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

PubMed

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling

PubMed Central

Moreira, João Luiz S; Mota, Rodrigo M; Horta, Maria F; Teixeira, Santuza MR; Neumann, Elisabeth; Nicoli, Jacques R; Nunes, Álvaro C

2005-01-01

Background The accurate identification of Lactobacillus and other co-isolated bacteria during microbial ecological studies of ecosystems such as the human or animal intestinal tracts and food products is a hard task by phenotypic methods requiring additional tests such as protein and/or lipids profiling. Results Bacteria isolated in different probiotic prospecting studies, using de Man, Rogosa and Sharpe medium (MRS), were typed at species level by PCR amplification of 16S-23S rRNA intergenic spacers using universal primers that anneal within 16S and 23S genes, followed by restriction digestion analyses of PCR products. The set of enzymes chosen differentiates most species of Lactobacillus genus and also co-isolated bacteria such as Enterococcus, Streptococcus, Weissella, Staphylococcus, and Escherichia species. The in silico predictions of restriction patterns generated by the Lactobacillus shorter spacers digested with 11 restriction enzymes with 6 bp specificities allowed us to distinguish almost all isolates at the species level but not at the subspecies one. Simultaneous theoretical digestions of the three spacers (long, medium and short) with the same set of enzymes provided more complex patterns and allowed us to distinguish the species without purifying and cloning of PCR products. Conclusion Lactobacillus isolates and several other strains of bacteria co-isolated on MRS medium from gastrointestinal ecosystem and fermented food products could be identified using DNA fingerprints generated by restriction endonucleases. The methodology based on amplified ribosomal DNA restriction analysis (ARDRA) is easier, faster and more accurate than the current methodologies based on fermentation profiles, used in most laboratories for the purpose of identification of these bacteria in different prospecting studies. PMID:15788104

The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota

PubMed Central

Lagier, Jean-Christophe; Hugon, Perrine; Khelaifia, Saber; Fournier, Pierre-Edouard; La Scola, Bernard

2015-01-01

SUMMARY Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a “dark matter” of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the “great plate count anomaly,” which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire. PMID:25567229

DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

When teachers go the extra mile: foci of organisational identification as determinants of different forms of organisational citizenship behaviour among schoolteachers.

PubMed

Christ, Oliver; van Dick, Rolf; Wagner, Ulrich; Stellmacher, Jost

2003-09-01

Psychological variables should play an important role in determining teachers' involvement in behaviours not directly or formally forced by contracts. Organisational identification as proposed from the Social Identity Approach is examined as a possible determinant of organisational citizenship behaviour (OCB) among schoolteachers. The aim of the present study was to explore the relationships between different foci of organisational identification and different forms of OCB in schools. Data sets of altogether 447 German school teachers who filled in all relevant items in a cross-sectional questionnaire are used for analyses in the present study. Standardised questionnaires measuring organisational identification and OCB were administered. Exploratory and confirmatory factor analyses revealed the proposed foci of identification (i.e., career identification, team identification, and organisational identification), as well as different forms of OCB (i.e., OCB towards the own qualification, towards the team, and towards the organisation). Structural equation modelling supports the main hypothesis that foci of identification relate differentially to forms of OCB. The results emphasise the importance of organisational identification as a determinant of OCB in schools. Practical implications are discussed.

TRU Waste Management Program. Cost/schedule optimization analysis

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

Detamore, J.A.; Raudenbush, M.H.; Wolaver, R.W.

This Current Year Work Plan presents in detail a description of the activities to be performed by the Joint Integration Office Rockwell International (JIO/RI) during FY86. It breaks down the activities into two major work areas: Program Management and Program Analysis. Program Management is performed by the JIO/RI by providing technical planning and guidance for the development of advanced TRU waste management capabilities. This includes equipment/facility design, engineering, construction, and operations. These functions are integrated to allow transition from interim storage to final disposition. JIO/RI tasks include program requirements identification, long-range technical planning, budget development, program planning document preparation, taskmore » guidance development, task monitoring, task progress information gathering and reporting to DOE, interfacing with other agencies and DOE lead programs, integrating public involvement with program efforts, and preparation of reports for DOE detailing program status. Program Analysis is performed by the JIO/RI to support identification and assessment of alternatives, and development of long-term TRU waste program capabilities. These analyses include short-term analyses in response to DOE information requests, along with performing an RH Cost/Schedule Optimization report. Systems models will be developed, updated, and upgraded as needed to enhance JIO/RI's capability to evaluate the adequacy of program efforts in various fields. A TRU program data base will be maintained and updated to provide DOE with timely responses to inventory related questions.« less

FY 1986 current fiscal year work plan

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

Not Available

This Current Year Work Plan presents in detail a description of the activities to be performed by the Joint Integration Office/RI during FY86. It breaks down the activities into two major work areas: Program Management and Program Analysis. Program Management is performed by the JIO/RI by providing technical planning and guidance for the development of advanced TRU waste management capabilities. This includes equipment/facility design, engineering, construction, and operations. These functions are integrated to allow transition from interim storage to final disposition. JIO/RI tasks include program requirements identification, long-range technical planning, budget development, program planning document preparation, task guidance development, taskmore » monitoring, task progress information gathering and reporting to DOE, interfacing with other agencies and DOE lead programs, integrating public involvement with program efforts, and preparation of reports for DOE detailing program status. Program Analysis is performed by the JIO/RI to support identification and assessment of alternatives, and development of long-term TRU waste program capabilities. These analyses include short term analyses in response to DOE information requests, along with performing an RH Cost/Schedule Optimization report. System models will be developed, updated, and upgraded as needed to enhance JIO/RI's capability to evaluate the adequacy of program efforts in various fields. A TRU program data base will be maintained and updated to provide DOE with timely responses to inventory related questions.« less

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites.

PubMed

Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G

2016-01-01

Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

PubMed Central

Gutierrez-Heredia, Luis; Benzoni, Francesca; Murphy, Emma; Reynaud, Emmanuel G.

2016-01-01

Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis. PMID:26901845

Matrix-Assisted Laser Desorption Ionization (MALDI)-Time of Flight Mass Spectrometry- and MALDI Biotyper-Based Identification of Cultured Biphenyl-Metabolizing Bacteria from Contaminated Horseradish Rhizosphere Soil▿

PubMed Central

Uhlik, Ondrej; Strejcek, Michal; Junkova, Petra; Sanda, Miloslav; Hroudova, Miluse; Vlcek, Cestmir; Mackova, Martina; Macek, Tomas

2011-01-01

Bacteria that are able to utilize biphenyl as a sole source of carbon were extracted and isolated from polychlorinated biphenyl (PCB)-contaminated soil vegetated by horseradish. Isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The usage of MALDI Biotyper for the classification of isolates was evaluated and compared to 16S rRNA gene sequence analysis. A wide spectrum of bacteria was isolated, with Arthrobacter, Serratia, Rhodococcus, and Rhizobium being predominant. Arthrobacter isolates also represented the most diverse group. The use of MALDI Biotyper in many cases permitted the identification at the level of species, which was not achieved by 16S rRNA gene sequence analyses. However, some isolates had to be identified by 16S rRNA gene analyses if MALDI Biotyper-based identification was at the level of probable or not reliable identification, usually due to a lack of reference spectra included in the database. Overall, this study shows the possibility of using MALDI-TOF MS and MALDI Biotyper for the fast and relatively nonlaborious identification/classification of soil isolates. At the same time, it demonstrates the dominant role of employing 16S rRNA gene analyses for the identification of recently isolated strains that can later fill the gaps in the protein-based identification databases. PMID:21821747

New Coumarinyl Ethers in Daphne oleoides Schreb. Collected from Sardinia Island.

PubMed

Venditti, Alessandro; Sanna, Cinzia; Lorenzetti, Lorenzo M; Ballero, Mauro; Bianco, Armandodoriano

2017-06-01

The phytochemical analysis of the ethanolic extract obtained from D. oleoides collected from Sardinia Island allowed the isolation of several new constituents for the species (3, 8, and 9) together with two new coumarinyl ethers (1 and 2) besides the chemotaxonomic markers of the Daphne genus (4 - 7 and 10) which are also known to possess interesting biological activities. The structure of the new compounds were elucidated by extensive spectroscopic and spectrometric analyses. The identification of these compounds gives an experimental evidence of the variability in the secondary metabolites pattern owned by populations growing in restricted area in respect to populations not confined by geographical barrier. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Identification of technology options for reducing nitrogen pollution in cropping systems of Pujiang*

PubMed Central

Fang, Bin; Wang, Guang-huo; Van den berg, Marrit; Roetter, Reimund

2005-01-01

This work analyses the potential role of nitrogen pollution technology of crop systems of Pujiang, County in Eastern China’s Zhejiang Province, rice and vegetables are important cropping systems. We used a case study approach involving comparison of farmer practices and improved technologies. This approach allows assessing the impact of technology on pollution, is forward looking, and can yield information on the potential of on-the-shelf technology and provide opportunities for technology development. The approach particularly suits newly developed rice technologies with large potential of reducing nitrogen pollution and for future rice and vegetables technologies. The results showed that substantial reductions in nitrogen pollution are feasible for both types of crops. PMID:16187411

Identification of technology options for reducing nitrogen pollution in cropping systems of Pujiang.

PubMed

Fang, Bin; Wang, Guang-Huo; Van, Den Berg Marrit; Roetter, Reimund

2005-10-01

This work analyses the potential role of nitrogen pollution technology of crop systems of Pujiang, County in Eastern China's Zhejiang Province, rice and vegetables are important cropping systems. We used a case study approach involving comparison of farmer practices and improved technologies. This approach allows assessing the impact of technology on pollution, is forward looking, and can yield information on the potential of on-the-shelf technology and provide opportunities for technology development. The approach particularly suits newly developed rice technologies with large potential of reducing nitrogen pollution and for future rice and vegetables technologies. The results showed that substantial reductions in nitrogen pollution are feasible for both types of crops.

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses.

PubMed

Montenegro-Burke, J Rafael; Phommavongsay, Thiery; Aisporna, Aries E; Huan, Tao; Rinehart, Duane; Forsberg, Erica; Poole, Farris L; Thorgersen, Michael P; Adams, Michael W W; Krantz, Gregory; Fields, Matthew W; Northen, Trent R; Robbins, Paul D; Niedernhofer, Laura J; Lairson, Luke; Benton, H Paul; Siuzdak, Gary

2016-10-04

Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms. These mobile apps allow for the visualization and analysis of metabolic data throughout the entire analytical process. Specifically, XCMS Mobile and METLIN Mobile provide the capabilities for remote monitoring of data processing, real time notifications for the data processing, visualization and interactive analysis of processed data (e.g., cloud plots, principle component analysis, box-plots, extracted ion chromatograms, and hierarchical cluster analysis), and database searching for metabolite identification. These apps, available on Apple iOS and Google Android operating systems, allow for the migration of metabolomic research onto mobile devices for better accessibility beyond direct instrument operation. The utility of XCMS Mobile and METLIN Mobile functionalities was developed and is demonstrated here through the metabolomic LC-MS analyses of stem cells, colon cancer, aging, and bacterial metabolism.

Coprolites as a source of information on the genome and diet of the cave hyena

PubMed Central

Bon, Céline; Berthonaud, Véronique; Maksud, Frédéric; Labadie, Karine; Poulain, Julie; Artiguenave, François; Wincker, Patrick; Aury, Jean-Marc; Elalouf, Jean-Marc

2012-01-01

We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet. PMID:22456883

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses

PubMed Central

2016-01-01

Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms. These mobile apps allow for the visualization and analysis of metabolic data throughout the entire analytical process. Specifically, XCMS Mobile and METLIN Mobile provide the capabilities for remote monitoring of data processing, real time notifications for the data processing, visualization and interactive analysis of processed data (e.g., cloud plots, principle component analysis, box-plots, extracted ion chromatograms, and hierarchical cluster analysis), and database searching for metabolite identification. These apps, available on Apple iOS and Google Android operating systems, allow for the migration of metabolomic research onto mobile devices for better accessibility beyond direct instrument operation. The utility of XCMS Mobile and METLIN Mobile functionalities was developed and is demonstrated here through the metabolomic LC-MS analyses of stem cells, colon cancer, aging, and bacterial metabolism. PMID:27560777

Combined meta-genomics analyses unravel candidate genes for the grain dietary fiber content in bread wheat (Triticum aestivum L.).

PubMed

Quraishi, Umar Masood; Murat, Florent; Abrouk, Mickael; Pont, Caroline; Confolent, Carole; Oury, François Xavier; Ward, Jane; Boros, Danuta; Gebruers, Kurt; Delcour, Jan A; Courtin, Christophe M; Bedo, Zoltan; Saulnier, Luc; Guillon, Fabienne; Balzergue, Sandrine; Shewry, Peter R; Feuillet, Catherine; Charmet, Gilles; Salse, Jerome

2011-03-01

Grain dietary fiber content in wheat not only affects its end use and technological properties including milling, baking and animal feed but is also of great importance for health benefits. In this study, integration of association genetics (seven detected loci on chromosomes 1B, 3A, 3D, 5B, 6B, 7A, 7B) and meta-QTL (three consensus QTL on chromosomes 1B, 3D and 6B) analyses allowed the identification of seven chromosomal regions underlying grain dietary fiber content in bread wheat. Based either on a diversity panel or on bi-parental populations, we clearly demonstrate that this trait is mainly driven by a major locus located on chromosome 1B associated with a log of p value >13 and a LOD score >8, respectively. In parallel, we identified 73 genes differentially expressed during the grain development and between genotypes with contrasting grain fiber contents. Integration of quantitative genetics and transcriptomic data allowed us to propose a short list of candidate genes that are conserved in the rice, sorghum and Brachypodium chromosome regions orthologous to the seven wheat grain fiber content QTL and that can be considered as major candidate genes for future improvement of the grain dietary fiber content in bread wheat breeding programs.

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses

DOE PAGES

Montenegro-Burke, J. Rafael; Phommavongsay, Thiery; Aisporna, Aries E.; ...

2016-08-25

Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms. These mobile apps allow for the visualization and analysis of metabolic data throughout the entire analytical process.more » Specifically, XCMS Mobile and METLIN Mobile provide the capabilities for remote monitoring of data processing, real time notifications for the data processing, visualization and interactive analysis of processed data (e.g., cloud plots, principle component analysis, box-plots, extracted ion chromatograms, and hierarchical cluster analysis), and database searching for metabolite identification. These apps, available on Apple iOS and Google Android operating systems, allow for the migration of metabolomic research onto mobile devices for better accessibility beyond direct instrument operation. The utility of XCMS Mobile and METLIN Mobile functionalities was developed and is demonstrated here through the metabolomic LC-MS analyses of stem cells, colon cancer, aging, and bacterial metabolism.« less

Smartphone Analytics: Mobilizing the Lab into the Cloud for Omic-Scale Analyses

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

Montenegro-Burke, J. Rafael; Phommavongsay, Thiery; Aisporna, Aries E.

Active data screening is an integral part of many scientific activities, and mobile technologies have greatly facilitated this process by minimizing the reliance on large hardware instrumentation. In order to meet with the increasingly growing field of metabolomics and heavy workload of data processing, we designed the first remote metabolomic data screening platform for mobile devices. Two mobile applications (apps), XCMS Mobile and METLIN Mobile, facilitate access to XCMS and METLIN, which are the most important components in the computer-based XCMS Online platforms. These mobile apps allow for the visualization and analysis of metabolic data throughout the entire analytical process.more » Specifically, XCMS Mobile and METLIN Mobile provide the capabilities for remote monitoring of data processing, real time notifications for the data processing, visualization and interactive analysis of processed data (e.g., cloud plots, principle component analysis, box-plots, extracted ion chromatograms, and hierarchical cluster analysis), and database searching for metabolite identification. These apps, available on Apple iOS and Google Android operating systems, allow for the migration of metabolomic research onto mobile devices for better accessibility beyond direct instrument operation. The utility of XCMS Mobile and METLIN Mobile functionalities was developed and is demonstrated here through the metabolomic LC-MS analyses of stem cells, colon cancer, aging, and bacterial metabolism.« less

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing.

PubMed

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J; O'Donnell, Kerry; Geiser, David M; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education.

Global Cell Proteome Profiling, Phospho-signaling and Quantitative 
Proteomics for Identification of New Biomarkers in Acute Myeloid 
Leukemia Patients

PubMed Central

Aasebø, Elise; Forthun, Rakel B.; Berven, Frode; Selheim, Frode; Hernandez-Valladares, Maria

2016-01-01

The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low resolution mass spectrometers. However, most of the studies did not follow up, confirm or validate their candidates with more patient samples. Current proteomics methods, new high resolution and fast mass spectrometers allow the identification and quantification of several thousands of proteins obtained from few tens of μg of AML cell lysate. Enrichment methods for posttranslational modifications (PTM), such as phosphorylation, can isolate several thousands of site-specific phosphorylated peptides from AML patient samples, which subsequently can be quantified with high confidence in new mass spectrometers. While recent reports aiming to propose proteomic or phosphoproteomic biomarkers on the studied AML patient samples have taken advantage of the technological progress, the access to large cohorts of AML patients to sample from and the availability of appropriate control samples still remain challenging. PMID:26306748

Barcoding Fauna Bavarica: Myriapoda – a contribution to DNA sequence-based identifications of centipedes and millipedes (Chilopoda, Diplopoda)

PubMed Central

Spelda, Jörg; Reip, Hans S.; Oliveira–Biener, Ulla; Melzer, Roland R.

2011-01-01

Abstract We give a first account of our ongoing barcoding activities on Bavarian myriapods in the framework of the Barcoding Fauna Bavarica project and IBOL, the International Barcode of Life. Having analyzed 126 taxa (including 122 species) belonging to all major German chilopod and diplopod lineages, often using four or more specimens each, at the moment our species stock includes 82% of the diplopods and 65% of the chilopods found in Bavaria, southern Germany. The partial COI sequences allow correct identification of more than 95% of the current set of Bavarian species. Moreover, most of the myriapod orders and families appear as distinct clades in neighbour-joining trees, although the phylogenetic relationships between them are not always depicted correctly. We give examples of (1) high interspecific sequence variability among closely related species; (2) low interspecific variability in some chordeumatidan genera, indicating that recent speciations cannot be resolved with certainty using COI DNA barcodes; (3) high intraspecific variation in some genera, suggesting the existence of cryptic lineages; and (4) the possible polyphyly of some taxa, i.e. the chordeumatidan genus Ochogona. This shows that, in addition to species identification, our data may be useful in various ways in the context of species delimitations, taxonomic revisions and analyses of ongoing speciation processes. PMID:22303099

Genomic and Proteomic Characterization of Bacteriocin-Producing Leuconostoc mesenteroides Strains Isolated from Raw Camel Milk in Two Southwest Algerian Arid Zones

PubMed Central

Benmechernene, Zineb; Fernández-No, Inmaculada; Quintela-Baluja, Marcos; Kihal, Mebrouk; Calo-Mata, Pilar; Barros-Velázquez, Jorge

2014-01-01

Information on the microbiology of camel milk is very limited. In this work, the genetic characterization and proteomic identification of 13 putative producing bacteriocin Leuconostoc strains exhibiting antilisterial activity and isolated from camel milk were performed. DNA sequencing of the 13 selected strains revealed high homology among the 16S rRNA genes for all strains. In addition, 99% homology with Leuconostoc mesenteroides was observed when these sequences were analysed by the BLAST tool against other sequences from reference strains deposited in the Genbank. Furthermore, the isolates were characterized by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDITOF MS) which allowed for the identification of 2 mass peaks 6242 m/z and 5118 m/z that resulted to be specific to the species L. mesenteroides. Remarkably, the phyloproteomic tree provided more intraspecific information of L. mesenteroides than phylogenetic analysis. Accordingly, phyloproteomic analysis grouped L. mesenteroides strains into different subbranches, while all L. mesenteroides isolates were grouped in the same branch according to phylogenetic analysis. This study represents, to our knowledge, the first report on the use of MALDI-TOF MS on the identification of LAB isolated from camel milk. PMID:24809059

From Biography to Osteobiography: An Example of Anthropological Historical Identification of the Remains of St. Paul.

PubMed

Mihanović, Frane; Jerković, Ivan; Kružić, Ivana; Anđelinović, Šimun; Janković, Stipan; Bašić, Željana

2017-09-01

In the identification process of historical figures, and especially in cases of Saint's bodies or mummified remains, any method that includes physical encroachment or sampling is often not allowed. In these cases, one of the few remaining possibilities is the application of nondestructive radiographical and anthropological methods. However, although there have been a few attempts of such analyses, no systematic standard methodology has been developed until now. In this study, we developed a methodological approach that was used to test the authenticity of the alleged body of Saint Paul the Confessor. Upon imaging the remains on MSCT and post-processing, the images were analyzed by an interdisciplinary team to explore the contents beneath the binding media (e.g., the remains) and to obtain osetobiographical data for comparison with historical biological data. Obtained results: ancestry, sex, age, occupation, and social status were consistent with historical data. Although the methodological approach proved to be appropriate in this case, due to the discrepancy in the amount of data, identity could not be fully confirmed. Nonetheless, the hypothesis that the remains do not belong to St. Paul was rejected, whilst positive identification receives support. Anat Rec, 300:1535-1546, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Hemi-nested PCR and RFLP methodologies for identifying blood meals of the Chagas disease vector, Triatoma infestans.

PubMed

Roellig, Dawn M; Gomez-Puerta, Luis A; Mead, Daniel G; Pinto, Jesus; Ancca-Juarez, Jenny; Calderon, Maritza; Bern, Caryn; Gilman, Robert H; Cama, Vitaliano A

2013-01-01

Trypanosoma cruzi, the etiologic agent of Chagas disease, is transmitted by hematophagous reduviid bugs within the subfamily Triatominae. These vectors take blood meals from a wide range of hosts, and their feeding behaviors have been used to investigate the ecology and epidemiology of T. cruzi. In this study we describe two PCR-based methodologies that amplify a fragment of the 16S mitochondrial rDNA, aimed to improve the identification of blood meal sources for Triatoma infestans: a.--Sequence analyses of two heminested PCRs that allow the identification of mammalian and avian species, and b.--restriction fragment length polymorphism (RFLP) analysis from the mammalian PCR to identify and differentiate multi-host blood meals. Findings from both methodologies indicate that host DNA could be detected and the host species identified in samples from laboratory reared and field collected triatomines. The implications of this study are two-fold. First, these methods can be used in areas where the fauna diversity and feeding behavior of the triatomines are unknown. Secondly, the RFLP method led to the identification of multi-host DNA from T. infestans gut contents, enhancing the information provided by this assay. These tools are important contributions for ecological and epidemiological studies of vector-borne diseases.

Proteomics meets blood banking: identification of protein targets for the improvement of platelet quality.

PubMed

Schubert, Peter; Devine, Dana V

2010-01-03

Proteomics has brought new perspectives to the fields of hematology and transfusion medicine in the last decade. The steady improvement of proteomic technology is propelling novel discoveries of molecular mechanisms by studying protein expression, post-translational modifications and protein interactions. This review article focuses on the application of proteomics to the identification of molecular mechanisms leading to the deterioration of blood platelets during storage - a critical aspect in the provision of platelet transfusion products. Several proteomic approaches have been employed to analyse changes in the platelet protein profile during storage and the obtained data now need to be translated into platelet biochemistry in order to connect the results to platelet function. Targeted biochemical applications then allow the identification of points for intervention in signal transduction pathways. Once validated and placed in a transfusion context, these data will provide further understanding of the underlying molecular mechanisms leading to platelet storage lesion. Future aspects of proteomics in blood banking will aim to make use of protein markers identified for platelet storage lesion development to monitor proteome changes when alterations such as the use of additive solutions or pathogen reduction strategies are put in place in order to improve platelet quality for patients. (c) 2009 Elsevier B.V. All rights reserved.

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

PubMed Central

Park, Bongsoo; Park, Jongsun; Cheong, Kyeong-Chae; Choi, Jaeyoung; Jung, Kyongyong; Kim, Donghan; Lee, Yong-Hwan; Ward, Todd J.; O'Donnell, Kerry; Geiser, David M.; Kang, Seogchan

2011-01-01

The fungal genus Fusarium includes many plant and/or animal pathogenic species and produces diverse toxins. Although accurate species identification is critical for managing such threats, it is difficult to identify Fusarium morphologically. Fortunately, extensive molecular phylogenetic studies, founded on well-preserved culture collections, have established a robust foundation for Fusarium classification. Genomes of four Fusarium species have been published with more being currently sequenced. The Cyber infrastructure for Fusarium (CiF; http://www.fusariumdb.org/) was built to support archiving and utilization of rapidly increasing data and knowledge and consists of Fusarium-ID, Fusarium Comparative Genomics Platform (FCGP) and Fusarium Community Platform (FCP). The Fusarium-ID archives phylogenetic marker sequences from most known species along with information associated with characterized isolates and supports strain identification and phylogenetic analyses. The FCGP currently archives five genomes from four species. Besides supporting genome browsing and analysis, the FCGP presents computed characteristics of multiple gene families and functional groups. The Cart/Favorite function allows users to collect sequences from Fusarium-ID and the FCGP and analyze them later using multiple tools without requiring repeated copying-and-pasting of sequences. The FCP is designed to serve as an online community forum for sharing and preserving accumulated experience and knowledge to support future research and education. PMID:21087991

Impact of sequencing depth and read length on single cell RNA sequencing data of T cells.

PubMed

Rizzetto, Simone; Eltahla, Auda A; Lin, Peijie; Bull, Rowena; Lloyd, Andrew R; Ho, Joshua W K; Venturi, Vanessa; Luciani, Fabio

2017-10-06

Single cell RNA sequencing (scRNA-seq) provides great potential in measuring the gene expression profiles of heterogeneous cell populations. In immunology, scRNA-seq allowed the characterisation of transcript sequence diversity of functionally relevant T cell subsets, and the identification of the full length T cell receptor (TCRαβ), which defines the specificity against cognate antigens. Several factors, e.g. RNA library capture, cell quality, and sequencing output affect the quality of scRNA-seq data. We studied the effects of read length and sequencing depth on the quality of gene expression profiles, cell type identification, and TCRαβ reconstruction, utilising 1,305 single cells from 8 publically available scRNA-seq datasets, and simulation-based analyses. Gene expression was characterised by an increased number of unique genes identified with short read lengths (<50 bp), but these featured higher technical variability compared to profiles from longer reads. Successful TCRαβ reconstruction was achieved for 6 datasets (81% - 100%) with at least 0.25 millions (PE) reads of length >50 bp, while it failed for datasets with <30 bp reads. Sufficient read length and sequencing depth can control technical noise to enable accurate identification of TCRαβ and gene expression profiles from scRNA-seq data of T cells.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

PubMed Central

Jones, Andrew R.; Siepen, Jennifer A.; Hubbard, Simon J.; Paton, Norman W.

2010-01-01

Tandem mass spectrometry, run in combination with liquid chromatography (LC-MS/MS), can generate large numbers of peptide and protein identifications, for which a variety of database search engines are available. Distinguishing correct identifications from false positives is far from trivial because all data sets are noisy, and tend to be too large for manual inspection, therefore probabilistic methods must be employed to balance the trade-off between sensitivity and specificity. Decoy databases are becoming widely used to place statistical confidence in results sets, allowing the false discovery rate (FDR) to be estimated. It has previously been demonstrated that different MS search engines produce different peptide identification sets, and as such, employing more than one search engine could result in an increased number of peptides being identified. However, such efforts are hindered by the lack of a single scoring framework employed by all search engines. We have developed a search engine independent scoring framework based on FDR which allows peptide identifications from different search engines to be combined, called the FDRScore. We observe that peptide identifications made by three search engines are infrequently false positives, and identifications made by only a single search engine, even with a strong score from the source search engine, are significantly more likely to be false positives. We have developed a second score based on the FDR within peptide identifications grouped according to the set of search engines that have made the identification, called the combined FDRScore. We demonstrate by searching large publicly available data sets that the combined FDRScore can differentiate between between correct and incorrect peptide identifications with high accuracy, allowing on average 35% more peptide identifications to be made at a fixed FDR than using a single search engine. PMID:19253293

IDENTIFICATION OF TOXICANTS IN WHOLE MARINE SEDIMENTS: METHODS AND RESULTS

EPA Science Inventory

Identification of stressors in aquatic systems is critical to sound assessment and management of our nation's waterways. Information from stressor identification can be useful in designing effective sediment remediation methods, assessing options for sediment disposal, allowing m...

APPLYING TOXICITY IDENTIFICATION PROCEDURES TO FIELD COLLECTED SEDIMENTS

EPA Science Inventory

Identification of specific causes of sediment toxicity can allow for much more focused risk assessment and management decision making. We have been developing toxicity identification evaluation (TIE) methods for contaminated sediments and focusing on three toxicant groups (ammoni...

Identification of entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

This chapter provides essential assistance for the identification of the most important genera (and main species) of fungal pathogens affecting insects, mites, and spiders. The key allows identifications regardless of which major spore types might be present with the specimen. The phylogenetic affi...

Microbe-ID: an open source toolbox for microbial genotyping and species identification

PubMed Central

Tabima, Javier F.; Everhart, Sydney E.; Larsen, Meredith M.; Weisberg, Alexandra J.; Kamvar, Zhian N.; Tancos, Matthew A.; Smart, Christine D.; Chang, Jeff H.

2016-01-01

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. PMID:27602267

Should DNA sequence be incorporated with other taxonomical data for routine identifying of plant species?

PubMed

Suesatpanit, Tanakorn; Osathanunkul, Kitisak; Madesis, Panagiotis; Osathanunkul, Maslin

2017-08-31

A variety of plants in Acanthaceae have long been used in traditional Thai ailment and commercialised with significant economic value. Nowadays medicinal plants are sold in processed forms and thus morphological authentication is almost impossible. Full identification requires comparison of the specimen with some authoritative sources, such as a full and accurate description and verification of the species deposited in herbarium. Intake of wrong herbals can cause adverse effects. Identification of both raw materials and end products is therefore needed. Here, the potential of a DNA-based identification method, called Bar-HRM (DNA barcoding coupled with High Resolution Melting analysis), in raw material species identification is investigated. DNA barcode sequences from five regions (matK, rbcL, trnH-psbA spacer region, trnL and ITS2) of Acanthaceae species were retrieved for in silico analysis. Then the specific primer pairs were used in HRM assay to generate unique melting profiles for each plants species. The method allows identification of samples lacking necessary morphological parts. In silico analyses of all five selected regions suggested that ITS2 is the most suitable marker for Bar-HRM in this study. The HRM analysis on dried samples of 16 Acanthaceae medicinal species was then performed using primer pair derived from ITS2 region. 100% discrimination of the tested samples at both genus and species level was observed. However, two samples documented as Clinacanthus nutans and Clinacanthus siamensis were recognised as the same species from the HRM analysis. Further investigation reveals that C. siamensis is now accepted as C. nutans. The results here proved that Bar-HRM is a promising technique in species identification of the studied medicinal plants in Acanthaceae. In addition, molecular biological data is currently used in plant taxonomy and increasingly popular in recent years. Here, DNA barcode sequence data should be incorporated with morphological characters in the species identification.

IDENTIFICATION OF STRESSORS IN TOXIC SEDIMENTS: WHOLE SEDIMENT AND INSTITIAL WATER RESULTS

EPA Science Inventory

Identification of stressors in aquatic systems is critical to sound assessment and management of our nation's waterways. Information from stressor identification can be useful in designing effective sediment remediation methods, assessing options for sediment disposal, allowing m...

RESULTS OF APPLYING TOXICITY IDENTIFICATION PROCEDURES TO FIELD COLLECTED SEDIMENTS

EPA Science Inventory

Identification of specific causes of sediment toxicity can allow for much more focused risk assessment and management decision making. We have been developing toxicity identification evaluation TIE) methods for contaminated sediments and are focusing on three toxicant groups (amm...

Opening Perspectives from an Integrated Analysis: Language Attitudes, Place of Birth and Self-Identification

ERIC Educational Resources Information Center

Lapresta-Rey, Cecilio; Huguet-Canalís, Ángel; Janés-Carulla, Judit

2018-01-01

There is a theoretical and empirical tradition demonstrating the influence of the place of birth and self-identification in the shaping of language attitudes. But very few works analyse their joint effects. The main aim of this study is to analyse both the disaggregated and joint impact of these variables on the shaping of attitudes towards…

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2013 CFR

2013-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

50 CFR 622.60 - Adjustment of management measures.

Code of Federal Regulations, 2014 CFR

2014-10-01

... markings and identification, allowable biological catch (ABC) and ABC control rules, rebuilding plans, sale... harvested shrimp (maintaining shrimp in whole condition, use as bait), target effort and fishing mortality... identification, vessel markings and identification, ABC and ABC control rules, rebuilding plans, sale and...

A multilocus database for the identification of Aspergillus and Penicillium species

USDA-ARS?s Scientific Manuscript database

Identification of Aspergillus and Penicillium isolates using phenotypic methods is increasingly complex and difficult but genetic tools allow recognition and description of species formerly unrecognized or cryptic. We constructed a web-based taxonomic database using BIGSdb for the identification of ...

Quantification of fungal abundance on cultural heritage using real time PCR targeting the β-actin gene

PubMed Central

Ettenauer, Jörg; Piñar, Guadalupe; Tafer, Hakim; Sterflinger, Katja

2014-01-01

The traditional methodology used for the identification of microbes colonizing our cultural heritage was the application of cultivation methods and/or microscopy. This approach has many advantages, as living microorganisms may be obtained for physiological investigations. In addition, these techniques allow the quantitative and qualitative assessment of the investigated environment. Quantitative analyses are done by plate count and the determination of abundance by the colony forming unit (CFU). Nevertheless, these techniques have many drawbacks that lead to an underestimation of the cell numbers and do not provide a comprehensive overview of the composition of the inhabiting microbiota. In the last decades, several molecular techniques have been developed enabling many advantages over the cultivation approach. Mainly PCR-based, fingerprinting techniques allow a qualitative detection and identification of the microbiota. In this study, we developed a real time PCR method as a simple, rapid and reliable tool to detect and quantify fungal abundance using the β-actin gene, which is known to appear as a single-copy gene in fungi. To this end, five different indoor thermal insulation materials applied for historical buildings that were previously tested for their bio-susceptibility against various fungi were subjected to qPCR analyses. The obtained results were compared with those obtained from a previous study investigating the bio-susceptibility of the insulation materials using classical cultivation experiments. Both results correlated well, revealing that Perlite plaster was the most suitable insulation material, showing the lowest fungal CFU and qPCR values. In contrast, insulations made of wood showed to be not recommendable from the microbiological point of view. In addition, the potential of qPCR was tested in other materials of cultural heritage, as old parchments, showing to be a suitable method for measuring fungal abundance in these delicate materials. PMID:24904567

Three-year observations of halocarbons at the Nepal Climate Observatory at Pyramid (NCO-P, 5079 m a.s.l.) on the Himalayan range

NASA Astrophysics Data System (ADS)

Maione, M.; Giostra, U.; Arduini, J.; Furlani, F.; Bonasoni, P.; Cristofanelli, P.; Laj, P.; Vuillermoz, E.

2011-04-01

A monitoring programme for halogenated climate-altering gases has been established in the frame of the SHARE EV-K2-CNR project at the Nepal Climate Laboratory - Pyramid in the Himalayan range at the altitude of 5079 m a.s.l. The site is very well located to provide important insights on changes in atmospheric composition in a region that is of great significance for emissions of both anthropogenic and biogenic halogenated compounds. Measurements are performed since March 2006, with grab samples collected on a weekly basis. The first three years of data have been analysed. After the identification of the atmospheric background values for fourteen halocarbons, the frequency of occurrence of pollution events have been compared with the same kind of analysis for data collected at other global background stations. The analysis showed the fully halogenated species, whose production and consumption are regulated under the Montreal Protocol, show a significant occurrence of "above the baseline" values, as a consequence of their current use in the developing countries surrounding the region, meanwhile the hydrogenated gases, more recently introduced into the market, show less frequent spikes. Atmospheric concentration trends have been calculated as well, and they showed a fast increase, ranging from 5.7 to 12.6%, of all the hydrogenated species, and a clear decrease of methyl chloroform (-17.7%). The comparison with time series from other stations has also allowed to derive Meridional gradients, which are absent for long living well mixed species, while for the more reactive species, the gradient increases inversely with respect to their atmospheric lifetime. The effect of long range transport and of local events on the atmospheric composition at the station has been analysed as well, allowing the identification of relevant source regions the Northern half of the Indian sub-continent. Also, at finer spatial scales, a smaller, local contribution of forest fires from the Khumbu valley has been detected.

Next generation microbiological risk assessment-Potential of omics data for hazard characterisation.

PubMed

Haddad, Nabila; Johnson, Nick; Kathariou, Sophia; Métris, Aline; Phister, Trevor; Pielaat, Annemarie; Tassou, Chrysoula; Wells-Bennik, Marjon H J; Zwietering, Marcel H

2018-04-12

According to the World Health Organization estimates in 2015, 600 million people fall ill every year from contaminated food and 420,000 die. Microbial risk assessment (MRA) was developed as a tool to reduce and prevent risks presented by pathogens and/or their toxins. MRA is organized in four steps to analyse information and assist in both designing appropriate control options and implementation of regulatory decisions and programs. Among the four steps, hazard characterisation is performed to establish the probability and severity of a disease outcome, which is determined as function of the dose of toxin and/or pathogen ingested. This dose-response relationship is subject to both variability and uncertainty. The purpose of this review/opinion article is to discuss how Next Generation Omics can impact hazard characterisation and, more precisely, how it can improve our understanding of variability and limit the uncertainty in the dose-response relation. The expansion of omics tools (e.g. genomics, transcriptomics, proteomics and metabolomics) allows for a better understanding of pathogenicity mechanisms and virulence levels of bacterial strains. Detection and identification of virulence genes, comparative genomics, analyses of mRNA and protein levels and the development of biomarkers can help in building a mechanistic dose-response model to predict disease severity. In this respect, systems biology can help to identify critical system characteristics that confer virulence and explain variability between strains. Despite challenges in the integration of omics into risk assessment, some omics methods have already been used by regulatory agencies for hazard identification. Standardized methods, reproducibility and datasets obtained from realistic conditions remain a challenge, and are needed to improve accuracy of hazard characterisation. When these improvements are realized, they will allow the health authorities and government policy makers to prioritize hazards more accurately and thus refine surveillance programs with the collaboration of all stakeholders of the food chain. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Regularized quantile regression for SNP marker estimation of pig growth curves.

PubMed

Barroso, L M A; Nascimento, M; Nascimento, A C C; Silva, F F; Serão, N V L; Cruz, C D; Resende, M D V; Silva, F L; Azevedo, C F; Lopes, P S; Guimarães, S E F

2017-01-01

Genomic growth curves are generally defined only in terms of population mean; an alternative approach that has not yet been exploited in genomic analyses of growth curves is the Quantile Regression (QR). This methodology allows for the estimation of marker effects at different levels of the variable of interest. We aimed to propose and evaluate a regularized quantile regression for SNP marker effect estimation of pig growth curves, as well as to identify the chromosome regions of the most relevant markers and to estimate the genetic individual weight trajectory over time (genomic growth curve) under different quantiles (levels). The regularized quantile regression (RQR) enabled the discovery, at different levels of interest (quantiles), of the most relevant markers allowing for the identification of QTL regions. We found the same relevant markers simultaneously affecting different growth curve parameters (mature weight and maturity rate): two (ALGA0096701 and ALGA0029483) for RQR(0.2), one (ALGA0096701) for RQR(0.5), and one (ALGA0003761) for RQR(0.8). Three average genomic growth curves were obtained and the behavior was explained by the curve in quantile 0.2, which differed from the others. RQR allowed for the construction of genomic growth curves, which is the key to identifying and selecting the most desirable animals for breeding purposes. Furthermore, the proposed model enabled us to find, at different levels of interest (quantiles), the most relevant markers for each trait (growth curve parameter estimates) and their respective chromosomal positions (identification of new QTL regions for growth curves in pigs). These markers can be exploited under the context of marker assisted selection while aiming to change the shape of pig growth curves.

CrossQuery: a web tool for easy associative querying of transcriptome data.

PubMed

Wagner, Toni U; Fischer, Andreas; Thoma, Eva C; Schartl, Manfred

2011-01-01

Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.

Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture.

PubMed

Verroken, A; Defourny, L; Lechgar, L; Magnette, A; Delmée, M; Glupczynski, Y

2015-02-01

Speeding up the turn-around time of positive blood culture identifications is essential in order to optimize the treatment of septic patients. Several sample preparation techniques have been developed allowing direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of positive blood cultures. Yet, the hands-on time restrains their routine workflow. In this study, we evaluated an approach whereby MALDI-TOF MS identification without any additional steps was carried out on short subcultured colonies from positive blood bottles with the objective of allowing results reporting on the day of positivity detection. Over a 7-month period in 2012, positive blood cultures detected by 9 am with an automated system were inoculated onto a Columbia blood agar and processed after a 5-h incubation on a MALDI-TOF MicroFlex platform (Bruker Daltonik GmbH). Single-spotted colonies were covered with 1 μl formic acid and 1 μl matrix solution. The results were compared to the validated identification techniques. A total of 925 positive blood culture bottles (representing 470 bacteremic episodes) were included. Concordant identification was obtained in 727 (81.1 %) of the 896 monomicrobial blood cultures, with failure being mostly observed with anaerobes and yeasts. In 17 episodes of polymicrobic bacteremia, the identification of one of the two isolates was achieved in 24/29 (82.7 %) positive cultures. Routine implementation of MALDI-TOF MS identification on young positive blood subcultures provides correct results to the clinician in more than 80 % of the bacteremic episodes and allows access to identification results on the day of blood culture positivity detection, potentially accelerating the implementation of targeted clinical treatments.

Development of adolescents' peer crowd identification in relation to changes in problem behaviors.

PubMed

Doornwaard, Suzan M; Branje, Susan; Meeus, Wim H J; ter Bogt, Tom F M

2012-09-01

This 5-wave longitudinal study, which included 1,313 Dutch adolescents, examined the development of peer crowd identification in relation to changes in problem behaviors. Adolescents from 2 age cohorts annually reported their identification with 7 peer crowds and their levels of internalizing and externalizing problem behaviors. Univariate latent growth curve analyses revealed declines (i.e., "Hip Hoppers" and "Metal Heads") or declines followed by stabilization (i.e., "Nonconformists") in identification with nonconventional crowds and increases (i.e., "Elites" and "Brains") or declines followed by stabilization (i.e., "Normals" and "Jocks") in identification with conventional crowds. Multivariate latent growth curve analyses indicated that stronger and more persistent identifications with nonconventional crowds were generally associated with more problem behaviors throughout adolescence. In contrast, stronger and more persistent identifications with conventional crowds were generally associated with fewer problem behaviors throughout adolescence with the notable exception of Brains, who showed a mixed pattern. Though characterized by fewer externalizing problems, this group did report more anxiety problems. These findings and their implications are discussed. PsycINFO Database Record (c) 2012 APA, all rights reserved.

Mechanisms of atherosclerosis and cardiovascular disease in antiphospholipid syndrome and systemic lupus erythematosus. New therapeutic approaches.

PubMed

Lopez-Pedrera, Chary; Aguirre-Zamorano, M Ángeles; Pérez-Sánchez, Carlos

2017-08-22

Systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) are 2 highly related autoimmune-rheumatic diseases associated with an increased risk of developing cardiovascular (CV) diseases. Despite the great progresses made in understanding the pathological mechanisms leading to CV diseases in those pathologies, there is still the unmet need to improve long term prognosis. CV diseases in SLE and APS is thought to happen as the result of a complex interaction between traditional CV risk factors, immune deregulation and disease activity, including the synergic effect of cytokines, chemokines, adipokines, proteases, autoantibodies, adhesion receptors, oxidative stress and a plethora of intracellular signalling molecules. Genomic and epigenomic analyses have further allowed the identification of specific signatures explaining the proathero-thrombotic profiles of APS and SLE patients. This review examines the complex role of these heterogeneous factors, and analyses new therapeutic approaches under study to reduce the CV risk in these autoimmune disorders. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

What Information Does Your EHR Contain? Automatic Generation of a Clinical Metadata Warehouse (CMDW) to Support Identification and Data Access Within Distributed Clinical Research Networks.

PubMed

Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin

2017-01-01

Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.

A reverse genetics approach identifies novel mutants in light responses and anthocyanin metabolism in petunia.

PubMed

Berenschot, Amanda S; Quecini, Vera

2014-01-01

Flower color and plant architecture are important commercially valuable features for ornamental petunias (Petunia x hybrida Vilm.). Photoperception and light signaling are the major environmental factors controlling anthocyanin and chlorophyll biosynthesis and shade-avoidance responses in higher plants. The genetic regulators of these processes were investigated in petunia by in silico analyses and the sequence information was used to devise a reverse genetics approach to probe mutant populations. Petunia orthologs of photoreceptor, light-signaling components and anthocyanin metabolism genes were identified and investigated for functional conservation by phylogenetic and protein motif analyses. The expression profiles of photoreceptor gene families and of transcription factors regulating anthocyanin biosynthesis were obtained by bioinformatic tools. Two mutant populations, generated by an alkalyting agent and by gamma irradiation, were screened using a phenotype-independent, sequence-based method by high-throughput PCR-based assay. The strategy allowed the identification of novel mutant alleles for anthocyanin biosynthesis (CHALCONE SYNTHASE) and regulation (PH4), and for light signaling (CONSTANS) genes.

Structural characterization of humic-like substances with conventional and surface-enhanced spectroscopic techniques

NASA Astrophysics Data System (ADS)

Carletti, Paolo; Roldán, Maria Lorena; Francioso, Ornella; Nardi, Serenella; Sanchez-Cortes, Santiago

2010-10-01

Emission-excitation, synchronous fluorescence spectroscopy and surface-enhanced Raman scattering (SERS) combined with surface-enhanced fluorescence (SEF) were applied to aqueous solutions of a humic-like substance (HLS) extracted from earthworm faeces. All measurements were acquired in a wide range of pH (4-12) and analysed by the linear regression analysis. Diffuse Reflectance Infrared Fourier Transform (DRIFT) spectra were also acquired to assist in the structural characterization of this HLS. The emission and excitation spectra allowed the identification of two main fluorophores in the analysed sample. Moreover, a close correlation between fluorescence intensities of each fluorophore with pH variation was observed. SERS and SEF, in agreement with the fluorescence spectroscopy, showed that the HLS at low pH values exists in an aggregated and coiled molecular structure while it is dispersed and uncoiled at alkaline conditions. The obtained spectra also evidenced that different conditions modify the functional groups exposed to the surrounding aqueous environment.

[Use of the critical incident technique in the development of a measurement tool for satisfaction in psychiatry].

PubMed

Pourin, C; Daucourt, V; Barberger-Gateau, P

2001-06-01

Health care centers will have to set up a regular survey of their patients' satisfaction, in addition to the discharge questionnaire. Few instruments for measuring satisfaction are at present available. A working group associating 10 psychiatric hospitals in Aquitaine conducted a study on the specificity of this measure in psychiatry. To record the patient's perception on the stay in order to identify areas of satisfaction and dissatisfaction as perceived and reported by himself, using a qualitative approach. The critical incident technique was used in 3 volunteer hospitals, in patients hospitalised in psychiatric wards selected by their doctor. Interview using a semi-structured questionnaire were conducted by an investigator external to the departments. Data were analysed in a qualitative way. 32 interviews could be analysed, and 215 events were extracted. These events were classified in 12 themes. The events identified from these interviews have allowed identification of new areas of patient satisfaction, which could be used to build additional items centered on patients' preoccupations.

NMR, HS-SPME-GC/MS, and HPLC/MSn Analyses of Phytoconstituents and Aroma Profile of Rosmarinus eriocalyx.

PubMed

Bendif, Hamdi; Miara, Mohamed Djamel; Peron, Gregorio; Sut, Stefania; Dall'Acqua, Stefano; Flamini, Guido; Maggi, Filippo

2017-10-01

In this work, a comprehensive study on the chemical constituents of the aerial parts of Rosmarinus eriocalyx (Lamiaceae), an aromatic shrub traditionally consumed as a food and herbal remedy in Algeria, is presented. The aroma profile was analysed by headspace solid phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC/MS), whereas the crude extract constituents were analyzed by 1 H-NMR and by high performance liquid chromatography coupled with mass spectrometry (HPLC/MS n ). Thirty-nine volatile compounds, most of them being monoterpenes, have been identified, with camphor, camphene, and α-pinene as the most abundant constituents. 1 H-NMR analysis revealed the presence of phenolic compounds and betulinic acid while HPLC/MS n allowed the identification of glycosilated and aglyconic flavonoids as well as phenylpropanoid derivatives. Some of these constituents, namely as betulinic acid, rosmanol, and cirsimaritin were reported for the first time in R. eriocalyx. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Sediment heterogeneity and mobility in the morphodynamic modelling of gravel-bed braided rivers

NASA Astrophysics Data System (ADS)

Singh, Umesh; Crosato, Alessandra; Giri, Sanjay; Hicks, Murray

2017-06-01

The effects of sediment heterogeneity and sediment mobility on the morphology of braided rivers are still poorly studied, especially when the partial sediment mobility occurs. Nevertheless, increasing the bed sediment heterogeneity by coarse sediment supply is becoming a common practice in river restoration projects and habitat improvement all over the world. This research provides a step forward in the identification of the effects of sediment sorting on the evolution of sediment bars and braiding geometry of gravel-bed rivers. A two-dimensional morphodynamic model was used to simulate the long-term developments of a hypothetical braided system with discharge regime and morphodynamic parameters derived from the Waimakariri River, New Zealand. Several scenarios, differing in bed sediment heterogeneity and sediment mobility, were considered. The results agree with the tendencies already identified in linear analyses and experimental studies, showing that a larger sediment heterogeneity increases the braiding indes and reduces the bars length and height. The analyses allowed identifying the applicability limits of uniform sediment and variable discharge modelling approaches.

Infrared Multiphoton Dissociation for Quantitative Shotgun Proteomics

PubMed Central

Ledvina, Aaron R.; Lee, M. Violet; McAlister, Graeme C.; Westphall, Michael S.; Coon, Joshua J.

2012-01-01

We modified a dual-cell linear ion trap mass spectrometer to perform infrared multiphoton dissociation (IRMPD) in the low pressure trap of a dual-cell quadrupole linear ion trap (dual cell QLT) and perform large-scale IRMPD analyses of complex peptide mixtures. Upon optimization of activation parameters (precursor q-value, irradiation time, and photon flux), IRMPD subtly, but significantly outperforms resonant excitation CAD for peptides identified at a 1% false-discovery rate (FDR) from a yeast tryptic digest (95% confidence, p = 0.019). We further demonstrate that IRMPD is compatible with the analysis of isobaric-tagged peptides. Using fixed QLT RF amplitude allows for the consistent retention of reporter ions, but necessitates the use of variable IRMPD irradiation times, dependent upon precursor mass-to-charge (m/z). We show that IRMPD activation parameters can be tuned to allow for effective peptide identification and quantitation simultaneously. We thus conclude that IRMPD performed in a dual-cell ion trap is an effective option for the large-scale analysis of both unmodified and isobaric-tagged peptides. PMID:22480380

A mechanistic approach to studies of the possible digestion of retrograded starch by α-amylase revealed using a log of slope (LOS) plot

PubMed Central

Patel, Hamung; Day, Richard; Butterworth, Peter J.; Ellis, Peter R.

2014-01-01

The rate and extent of digestibility of starch were analysed using the logarithm of the slope (LOS) method. Digestibility curves with α-amylase were obtained for starches in their native, gelatinised and 24 h retrograded form. A LOS plot of the digestibility curves was then constructed, which allowed the rate constant (k) and the concentration of the product at the end of the reaction (C∞) to be calculated. It also allowed the identification of rapid and slow phases in starch digestion. Upon gelatinisation, both k and C∞ increased with dramatic changes notably in C∞; however after starch samples had been stored for 24 h at room temperature, k was not affected but C∞ decreased. This suggests that retrograded starch is virtually inert to amylase action. Both k and C∞ were strongly related to the increase in degree of order of the α-glucan chains, monitored by FTIR-ATR spectroscopy, in retrograded starch. PMID:25256473

In situ analysis of martian regolith with the SAM experiment during the first mars year of the MSL mission: Identification of organic molecules by gas chromatography from laboratory measurements

NASA Astrophysics Data System (ADS)

Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; François, P.; Coscia, D.; Bonnet, J. Y.; Teinturier, S.; Cabane, M.; Mahaffy, P. R.

2016-09-01

The Sample Analysis at Mars (SAM) instrument onboard the Curiosity rover, is specifically designed for in situ molecular and isotopic analyses of martian surface materials and atmosphere. It contributes to the Mars Science Laboratory (MSL) missions primary scientific goal to characterize the potential past, present or future habitability of Mars. In all of the analyses of solid samples delivered to SAM so far, chlorinated organic compounds have been detected above instrument background levels and identified by gas chromatography coupled to mass spectrometry (GC-MS) (Freissinet et al., 2015; Glavin et al., 2013). While some of these may originate from reactions between oxychlorines and terrestrial organic carbon present in the instrument background (Glavin et al., 2013), others have been demonstrated to originate from indigenous organic carbon present in samples (Freissinet et al., 2015). We present here laboratory calibrations that focused on the analyses performed with the MXT-CLP GC column (SAM GC-5 channel) used for nearly all of the GC-MS analyses of the martian soil samples carried out with SAM to date. Complementary to the mass spectrometric data, gas chromatography allows us to separate and identify the species analyzable in a nominal SAM-GC run time of about 21 min. To characterize the analytical capabilities of this channel within the SAM Flight Model (FM) operating conditions on Mars, and their implications on the detection of organic matter, it is required to perform laboratory experimental tests and calibrations on spare model components. This work assesses the SAM flight GC-5 column efficiency, confirms the identification of the molecules based on their retention time, and enables a better understanding of the behavior of the SAM injection trap (IT) and its release of organic molecules. This work will enable further optimization of the SAM-GC runs for additional samples to be analyzed during the MSL mission.

In Situ Analysis of Martian Regolith with the SAM Experiment During the First Mars Year of the MSL Mission: Identification of Organic Molecules by Gas Chromatography from Laboratory Measurements

NASA Technical Reports Server (NTRS)

Millan, M.; Szopa, C.; Buch, A.; Coll, P.; Glavin, D. P.; Freissinet, C.; Navarro-Gonzalez, R.; Francois, P.; Coscia, D.; Bonnet, J. Y.;

Application of Laser Induced Breakdown Spectroscopy to the identification of emeralds from different synthetic processes

NASA Astrophysics Data System (ADS)

Agrosì, G.; Tempesta, G.; Scandale, E.; Legnaioli, S.; Lorenzetti, G.; Pagnotta, S.; Palleschi, V.; Mangone, A.; Lezzerini, M.

2014-12-01

Laser Induced Breakdown Spectroscopy can provide a useful contribution in mineralogical field in which the quantitative chemical analyses (including the evaluation of light elements) can play a key role in the studies on the origin of the emeralds. In particular, the chemical analyses permit to determine those trace elements, known as fingerprints, that can be useful to study their provenance. This technique, not requiring sample preparation results particularly suitable for gemstones, that obviously must be studied in a non-destructive way. In this paper, the LIBS technique was applied to distinguish synthetic emeralds grown by Biron hydrothermal method from those grown by Chatham flux method. The analyses performed by collinear double-pulse LIBS give a signal enhancement useful for the quantitative chemical analyses while guaranteeing a minimal sample damage. In this way it was obtained a considerable improvement on the detection limit of the trace elements, whose determination is essential for determining the origin of emerald gemstone. The trace elements V, Cr, and Fe and their relative amounts allowed the correct attribution of the manufacturer. Two different methods for quantitative analyses were used for this study: the standard Calibration-Free LIBS (CF-LIBS) method and its recent evolution, the One Point Calibration LIBS (OPC-LIBS). This is the first approach to the evaluation of the emerald origin by means of the LIBS technique.

Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

PubMed Central

2013-01-01

Background Biomarker discovery datasets created using mass spectrum protein profiling of complex mixtures of proteins contain many peaks that represent the same protein with different charge states. Correlated variables such as these can confound the statistical analyses of proteomic data. Previously we developed an algorithm that clustered mass spectrum peaks that were biologically or technically correlated. Here we demonstrate an algorithm that clusters correlated technical aliases only. Results In this paper, we propose a preprocessing algorithm that can be used for grouping technical aliases in mass spectrometry protein profiling data. The stringency of the variance allowed for clustering is customizable, thereby affecting the number of peaks that are clustered. Subsequent analysis of the clusters, instead of individual peaks, helps reduce difficulties associated with technically-correlated data, and can aid more efficient biomarker identification. Conclusions This software can be used to pre-process and thereby decrease the complexity of protein profiling proteomics data, thus simplifying the subsequent analysis of biomarkers by decreasing the number of tests. The software is also a practical tool for identifying which features to investigate further by purification, identification and confirmation. PMID:24010718

In silico identification and characterization of the WRKY gene superfamily in pepper (Capsicum annuum L.).

PubMed

Cheng, Y; Yao, Z P; Ruan, M Y; Ye, Q J; Wang, R Q; Zhou, G Z; Luo, J

2016-09-23

The WRKY family is one of the most important transcription factor families in plants, involved in the regulation of a broad range of biological roles. The recent releases of whole-genome sequences of pepper (Capsicum annuum L.) allow us to perform a genome-wide identification and characterization of the WRKY family. In this study, 61 CaWRKY proteins were identified in the pepper genome. Based on protein structural and phylogenetic analyses, these proteins were classified into four main groups (I, II, III, and NG), and Group II was further divided into five subgroups (IIa to IIe). Chromosome mapping analysis indicated that CaWRKY genes are distributed across all 12 chromosomes, although the location of four CaWRKYs (CaWRKY58-CaWRKY61) could not be identified. Two pairs of CaWRKYs located on chromosome 01 appear to be tandem duplications. Furthermore, the phylogenetic tree showed a close evolutionary relationship of WRKYs in three species from Solanaceae. In conclusion, this comprehensive analysis of CaWRKYs will provide rich resources for further functional studies in pepper.

Development of a fractionation method for the detection and identification of oak ellagitannins in red wines.

PubMed

García-Estévez, Ignacio; Escribano-Bailón, M Teresa; Rivas-Gonzalo, Julián C; Alcalde-Eon, Cristina

2010-02-15

During maturation and ageing in oak barrels wines improve their organoleptic properties. Ellagitannins can be released from wood to the wine and be involved in oxidation reactions and seem to influence the astringency and colour properties of the wine. Nevertheless, the ellagitannins levels are lower than those of other wine constituents and, consequently, they are not easily detected. This study has developed a two-step fractionation method consisting of a solid phase extraction in C-18 Sep-Pak cartridges followed by size exclusion chromatography in hand-packed Sephadex LH-20 minicolumn for the detection of oak ellagitannins in different types of wines. An HPLC method has also been developed which allows the separation of compounds with the same m/z ratios, facilitating the ellagitannin identification by means of the mass spectrometric analyses. The main oak ellagitannins (grandinin, vescalagin, roburin E and castalagin) were isolated, detected separately and identified in a spiked wine and in three real ones, proving the usefulness of the fractionation method. Copyright 2009 Elsevier B.V. All rights reserved.

Molecular detection and identification of Rickettsiales pathogens in dog ticks from Costa Rica.

PubMed

Campos-Calderón, Liliana; Ábrego-Sánchez, Leyda; Solórzano-Morales, Antony; Alberti, Alberto; Tore, Gessica; Zobba, Rosanna; Jiménez-Rocha, Ana E; Dolz, Gaby

2016-10-01

Although vector-borne diseases are globally widespread with considerable impact on animal production and on public health, few reports document their presence in Central America. This study focuses on the detection and molecular identification of species belonging to selected bacterial genera (Ehrlichia, Anaplasma and Rickettsia) in ticks sampled from dogs in Costa Rica by targeting several genes: 16S rRNA/dsb genes for Ehrlichia; 16S rRNA/groEL genes for Anaplasma, and ompA/gltA/groEL genes for Rickettsia. PCR and sequence analyses provides evidences of Ehrlichia canis, Anaplasma platys, and Anaplasma phagocytophilum infection in Rhipicephalus sanguineus s.l ticks, and allow establishing the presence of Rickettsia monacensis in Ixodes boliviensis. Furthermore, the presence of recently discovered Mediterranean A. platys-like strains is reported for the first time in Central America. Results provide new background on geographical distribution of selected tick-transmitted bacterial pathogens in Costa Rica and on their molecular epidemiology, and are pivotal to the development of effective and reliable diagnostic tools in Central America. Copyright © 2016 Elsevier GmbH. All rights reserved.

Echinostoma caproni: identification of enolase in excretory/secretory products, molecular cloning, and functional expression.

PubMed

Marcilla, Antonio; Pérez-García, Ana; Espert, Ana; Bernal, Dolores; Muñoz-Antolí, Carla; Esteban, José Guillermo; Toledo, Rafael

2007-09-01

In order to investigate molecules that could be involved in host-trematode relationships, we have analysed the excretory/secretory products (ESP) of Echinostoma caproni following a proteomic approach. Actin, Gluthathione S-transferase (GST) and enolase have been identified in the ESP. Enolase, observed to be one of the most abundant proteins, was further characterized. The molecular cloning and in vitro expression in Escherichia coli of E. caproni enolase allowed us to determine that the protein contains 431 amino acids and a theoretical MW of 46272 Da. E. caproni enolase shows high homology to other trematode enolases. The recombinant protein binds specifically to human plasminogen in vitro, as observed for the native protein, confirming its properties as a host-interacting molecule.

[MALDI-TOF mass spectrometry in the investigation of large high-molecular biological compounds].

PubMed

Porubl'ova, L V; Rebriiev, A V; Hromovyĭ, T Iu; Minia, I I; Obolens'ka, M Iu

2009-01-01

MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry has become, in the recent years, a tool of choice for analyses of biological polymers. The wide mass range, high accuracy, informativity and sensitivity make it a superior method for analysis of all kinds of high-molecular biological compounds including proteins, nucleic acids and lipids. MALDI-TOF-MS is particularly suitable for the identification of proteins by mass fingerprint or microsequencing. Therefore it has become an important technique of proteomics. Furthermore, the method allows making a detailed analysis of post-translational protein modifications, protein-protein and protein-nucleic acid interactions. Recently, the method was also successfully applied to nucleic acid sequencing as well as screening for mutations.

Analysis of Volatile Fragrance and Flavor Compounds by Headspace Solid Phase Microextraction and GC-MS: An Undergraduate Instrumental Analysis Experiment

NASA Astrophysics Data System (ADS)

Galipo, Randolph C.; Canhoto, Alfredo J.; Walla, Michael D.; Morgan, Stephen L.

1999-02-01

A senior-level undergraduate laboratory experiment that demonstrates the use of solid-phase microextraction (SPME) and capillary gas chromatography-mass spectrometry (GC-MS) was developed for the identification of volatile compounds in consumer products. SPME minimizes sample preparation and concentrates volatile analytes in a solvent-free manner. Volatile flavor and fragrance compounds were extracted by SPME from the headspace of vials containing shampoos, chewing gums, and perfumes and analyzed by GC-MS. Headspace SPME was shown to be more sensitive than conventional headspace analysis of similar samples performed with an airtight syringe. Analysis times were less than 30 min, allowing multiple analyses to be performed in a typical laboratory class period.

Identification of Genes Potentially Regulated by Human Polynucleotide Phosphorylase (hPNPaseold-35) Using Melanoma as a Model

PubMed Central

Sokhi, Upneet K.; Bacolod, Manny D.; Dasgupta, Santanu; Emdad, Luni; Das, Swadesh K.; Dumur, Catherine I.; Miles, Michael F.; Sarkar, Devanand; Fisher, Paul B.

2013-01-01

Human Polynucleotide Phosphorylase (hPNPaseold-35 or PNPT1) is an evolutionarily conserved 3′→5′ exoribonuclease implicated in the regulation of numerous physiological processes including maintenance of mitochondrial homeostasis, mtRNA import and aging-associated inflammation. From an RNase perspective, little is known about the RNA or miRNA species it targets for degradation or whose expression it regulates; except for c-myc and miR-221. To further elucidate the functional implications of hPNPaseold-35 in cellular physiology, we knocked-down and overexpressed hPNPaseold-35 in human melanoma cells and performed gene expression analyses to identify differentially expressed transcripts. Ingenuity Pathway Analysis indicated that knockdown of hPNPaseold-35 resulted in significant gene expression changes associated with mitochondrial dysfunction and cholesterol biosynthesis; whereas overexpression of hPNPaseold-35 caused global changes in cell-cycle related functions. Additionally, comparative gene expression analyses between our hPNPaseold-35 knockdown and overexpression datasets allowed us to identify 77 potential “direct” and 61 potential “indirect” targets of hPNPaseold-35 which formed correlated networks enriched for cell-cycle and wound healing functional association, respectively. These results provide a comprehensive database of genes responsive to hPNPaseold-35 expression levels; along with the identification new potential candidate genes offering fresh insight into cellular pathways regulated by PNPT1 and which may be used in the future for possible therapeutic intervention in mitochondrial- or inflammation-associated disease phenotypes. PMID:24143183

Development of techniques for the analysis of isoflavones in soy foods and nutraceuticals.

PubMed

Dentith, Susan; Lockwood, Brian

2008-05-01

For over 20 years, soy isoflavones have been investigated for their ability to prevent a wide range of cancers and cardiovascular problems, and numerous other disease states. This research is underpinned by the ability of researchers to analyse isoflavones in various forms in a range of raw materials and biological fluids. This review summarizes the techniques recently used in their analysis. The speed of high performance liquid chromatography analysis has been improved, allowing analysis of more samples, and increasing the sensitivity of detection techniques allows quantification of isoflavones down to nanomoles per litre levels in biological fluids. The combination of high-performance liquid chromatography with immunoassay has allowed identification and estimation of low-level soy isoflavones. The use of soy isoflavone supplements has shown an increase in their circulating levels in plasma and urine, aiding investigation of their biological effects. The significance of the metabolite equol has spurned research into new areas, and recently the specific enantiomers have been studied. High-performance liquid chromatography, capillary electrophoresis and gas chromatography are widely used with a range of detection systems. Increasingly, immunoassay is being used because of its high sensitivity and low cost.

Conception d'un système de mesure automatisé pour la caractérisation expérimentale des moteurs piézo-électriquesAn automated test system for piezoelectric motors

NASA Astrophysics Data System (ADS)

Ferreira, A.

1996-04-01

This paper describes an automated test system for piezoelectric motors allowing the experimental characterization of its electromechanical behaviour. In the first part, an experimental method is given for evaluation of losses generated in the different mechanisms of conversion: electric energy into ultrasonic vibrating energy and ultrasonic vibrating energy into mechanical energy of revolving motion. In the second part, the present method is experimentally validated on a travelling-wave-type rotary motor (Shinsei USR-60). The free stator vibration is analysed by a laser vibrometer which gives a picture both of amplitude and of phase vibration. This result allows one to obtain an identification of vibrations modes and an evaluation of ultrasonic vibrating energy and electromechanical efficiency. To characterize the working of the complete motor, the no-load working mode is first considered. The measurement of its maximal mechanical characteristics (maximal no-load rotating speed, maximal driving torque) with respect to axial load allows the choice of optimum axial load. For this optimum value, the load working mode is, finally, investigated for the evaluation of load characteristics and conversion losses.

Texture and composition of the Rosa Marina beach sands (Adriatic coast, southern Italy): a sedimentological/ecological approach

NASA Astrophysics Data System (ADS)

Moretti, Massimo; Tropeano, Marcello; Loon, A. J. (Tom) van; Acquafredda, Pasquale; Baldacconi, Rossella; Festa, Vincenzo; Lisco, Stefania; Mastronuzzi, Giuseppe; Moretti, Vincenzo; Scotti, Rosa

2016-06-01

Beach sands from the Rosa Marina locality (Adriatic coast, southern Italy) were analysed mainly microscopically in order to trace the source areas of their lithoclastic and bioclastic components. The main cropping out sedimentary units were also studied with the objective to identify the potential source areas of lithoclasts. This allowed to establish how the various rock units contribute to the formation of beach sands. The analysis of the bioclastic components allows to estimate the actual role of organisms regarding the supply of this material to the beach. Identification of taxa that are present in the beach sands as shell fragments or other remains was carried out at the genus or family level. Ecological investigation of the same beach and the recognition of sub-environments (mainly distinguished on the basis of the nature of the substrate and of the water depth) was the key topic that allowed to establish the actual source areas of bioclasts in the Rosa Marina beach sands. The sedimentological analysis (including a physical study of the beach and the calculation of some statistical parameters concerning the grain-size curves) shows that the Rosa Marina beach is nowadays subject to erosion.

Identification of Particles in Parenteral Drug Raw Materials.

PubMed

Lee, Kathryn; Lankers, Markus; Valet, Oliver

2018-04-18

Particles in drug products are not good and are therefore regulated. These particles can come from the very beginning of the manufacturing process, from the raw materials. To prevent particles, it is important to understand what they are and where they come from so the raw material quality, processing, and shipping can be improved. Thus, it is important to correctly identify particles seen in raw materials. Raw materials need to be of a certain quality with respect to physical and chemical composition, and need to have no contaminants in the form of particles which could contaminate the product or indicate the raw materials are not pure enough to make a good quality product. Particles are often seen when handling raw materials due to color, size, or shape characteristics different from those in the raw materials. Particles may appear to the eye to be very different things than they actually are, so microscope, chemical, and elemental analyses are required for accuracy in proper identification. This paper shows how using three different spectroscopy tools correctly and together can be used to identify particles from extrinsic, intrinsic, and inherent particles. Sources of materials can be humans and the environment (extrinsic), from within the process (intrinsic), and part of the formulation (inherent). Microscope versions of Raman spectroscopy, laser-induced breakdown spectroscopy (LIBS), and IR spectroscopy are excellent tools for identifying particles because they are fast and accurate techniques needing minimal sample preparation that can provide chemical composition as well as images that can be used for identification. The micro analysis capabilities allow for easy analysis of different portions of samples so multiple components can be identified and sample preparation can be reduced. Using just one of these techniques may not be sufficient to give adequate identification results so that the source of contamination can be adequately identified. The complementarity of the techniques provides the advantage of identifying various chemical and molecular components, as well as elemental and image analyses. Correct interpretation of the results from these techniques is also very important. Copyright © 2018, Parenteral Drug Association.

Micro-computed tomography of false starts produced on bone by different hand-saws.

PubMed

Pelletti, Guido; Viel, Guido; Fais, Paolo; Viero, Alessia; Visentin, Sindi; Miotto, Diego; Montisci, Massimo; Cecchetto, Giovanni; Giraudo, Chiara

2017-05-01

The analysis of macro- and microscopic characteristics of saw marks on bones can provide useful information about the class of the tool utilized to produce the injury. The aim of the present study was to test micro-computed tomography (micro-CT) for the analysis of false starts experimentally produced on 32 human bone sections using 4 different hand-saws in order to verify the potential utility of micro-CT for distinguishing false starts produced by different saws and to correlate the morphology of the tool with that of the bone mark. Each sample was analysed through stereomicroscopy and micro-CT. Stereomicroscopic analysis allowed the identification of the false starts and the detection of the number of tool marks left by each saw. Micro-CT scans, through the integration of 3D renders and multiplanar reconstructions (MPR), allowed the identification of the shape of each false start correlating it to the injuring tool. Our results suggest that micro-CT could be a useful technique for assessing false starts produced by different classes of saws, providing accurate morphological profiles of the bone marks with all the advantages of high resolution 3D imaging (e.g., high accuracy, non-destructive analysis, preservation and documentation of evidence). However, further studies are necessary to integrate qualitative data with quantitative metrical analysis in order to further characterize the false start and the related injuring tool. Copyright © 2017 Elsevier B.V. All rights reserved.

A new system for parallel drug screening against multiple-resistant HIV mutants based on lentiviral self-inactivating (SIN) vectors and multi-colour analyses

PubMed Central

2013-01-01

Background Despite progress in the development of combined antiretroviral therapies (cART), HIV infection remains a significant challenge for human health. Current problems of cART include multi-drug-resistant virus variants, long-term toxicity and enormous treatment costs. Therefore, the identification of novel effective drugs is urgently needed. Methods We developed a straightforward screening approach for simultaneously evaluating the sensitivity of multiple HIV gag-pol mutants to antiviral drugs in one assay. Our technique is based on multi-colour lentiviral self-inactivating (SIN) LeGO vector technology. Results We demonstrated the successful use of this approach for screening compounds against up to four HIV gag-pol variants (wild-type and three mutants) simultaneously. Importantly, the technique was adapted to Biosafety Level 1 conditions by utilising ecotropic pseudotypes. This allowed upscaling to a large-scale screening protocol exploited by pharmaceutical companies in a successful proof-of-concept experiment. Conclusions The technology developed here facilitates fast screening for anti-HIV activity of individual agents from large compound libraries. Although drugs targeting gag-pol variants were used here, our approach permits screening compounds that target several different, key cellular and viral functions of the HIV life-cycle. The modular principle of the method also allows the easy exchange of various mutations in HIV sequences. In conclusion, the methodology presented here provides a valuable new approach for the identification of novel anti-HIV drugs. PMID:23286882

Non-invasive genetics outperforms morphological methods in faecal dietary analysis, revealing wild boar as a considerable conservation concern for ground-nesting birds.

PubMed

Oja, Ragne; Soe, Egle; Valdmann, Harri; Saarma, Urmas

2017-01-01

Capercaillie (Tetrao urogallus) and other grouse species represent conservation concerns across Europe due to their negative abundance trends. In addition to habitat deterioration, predation is considered a major factor contributing to population declines. While the role of generalist predators on grouse predation is relatively well known, the impact of the omnivorous wild boar has remained elusive. We hypothesize that wild boar is an important predator of ground-nesting birds, but has been neglected as a bird predator because traditional morphological methods underestimate the proportion of birds in wild boar diet. To distinguish between different mammalian predator species, as well as different grouse prey species, we developed a molecular method based on the analysis of mitochondrial DNA that allows accurate species identification. We collected 109 wild boar faeces at protected capercaillie leks and surrounding areas and analysed bird consumption using genetic methods and classical morphological examination. Genetic analysis revealed that the proportion of birds in wild boar faeces was significantly higher (17.3%; 4.5×) than indicated by morphological examination (3.8%). Moreover, the genetic method allowed considerably more precise taxonomic identification of consumed birds compared to morphological analysis. Our results demonstrate: (i) the value of using genetic approaches in faecal dietary analysis due to their higher sensitivity, and (ii) that wild boar is an important predator of ground-nesting birds, deserving serious consideration in conservation planning for capercaillie and other grouse.

Comparative genomic analysis of coffee-infecting Xylella fastidiosa strains isolated from Brazil.

PubMed

Barbosa, Deibs; Alencar, Valquíria Campos; Santos, Daiene Souza; de Freitas Oliveira, Ana Cláudia; de Souza, Alessandra A; Coletta-Filho, Helvecio D; de Oliveira, Regina Souza; Nunes, Luiz R

2015-05-01

Strains of Xylella fastidiosa constitute a complex group of bacteria that develop within the xylem of many plant hosts, causing diseases of significant economic importance, such as Pierce's disease in North American grapevines and citrus variegated chlorosis in Brazil. X. fastidiosa has also been obtained from other host plants, in direct correlation with the development of diseases, as in the case of coffee leaf scorch (CLS)--a disease with potential to cause severe economic losses to the Brazilian coffee industry. This paper describes a thorough genomic characterization of coffee-infecting X. fastidiosa strains, initially performed through a microarray-based approach, which demonstrated that CLS strains could be subdivided in two phylogenetically distinct subgroups. Whole-genomic sequencing of two of these bacteria (one from each subgroup) allowed identification of ORFs and horizontally transferred elements (HTEs) that were specific to CLS-related X. fastidiosa strains. Such analyses confirmed the size and importance of HTEs as major mediators of chromosomal evolution amongst these bacteria, and allowed identification of differences in gene content, after comparisons were made with previously sequenced X. fastidiosa strains, isolated from alternative hosts. Although direct experimentation still needs to be performed to elucidate the biological consequences associated with such differences, it was interesting to verify that CLS-related bacteria display variations in genes that produce toxins, as well as surface-related factors (such as fimbrial adhesins and LPS) that have been shown to be involved with recognition of specific host factors in different pathogenic bacteria. © 2015 The Authors.

Identification of Organic Colorants in Art Objects by Solution Spectrophotometry: Pigments.

ERIC Educational Resources Information Center

Billmeyer, Fred W., Jr.; And Others

1981-01-01

Describes solution spectrophotometry as a simple, rapid identification technique for organic paint pigments. Reports research which includes analytical schemes for the extraction and separation of organic pigments based on their solubilities, and the preparation of an extensive reference collection of spectral curves allowing their identification.…

78 FR 6222 - Importation of Avocados From Continental Spain

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-30

... avocados on the tree are not a host to Medfly. We would allow importation of other varieties of avocado if... identification of the fruit; Packinghouse requirements for safeguarding and identification of the fruit..., safeguarding, and identification that are described later in this document. Paragraph (a)(4) would state that...

Registry data for cross-country comparisons of migrants' healthcare utilization in the EU: a survey study of availability and content

PubMed Central

2009-01-01

Background Cross-national comparable data on migrants' use of healthcare services are important to address problems in access to healthcare; to identify high risk groups for prevention efforts; and to evaluate healthcare systems comparatively. Some of the main obstacles limiting analyses of health care utilization are lack of sufficient coverage and availability of reliable and valid healthcare data which includes information allowing for identification of migrants. The objective of this paper was to reveal which registry data on healthcare utilization were available in the EU countries in which migrants can be identified; and to determine to what extent data were comparable between the EU countries. Methods A questionnaire survey on availability of healthcare utilization registries in which migrants can be identified was carried out among all national statistic agencies and other relevant national health authorities in the 27 EU countries in 2008-9 as part of the Migrant and Ethnic Minority Health Observatory-project (MEHO). The information received was compared with information from a general survey on availability of survey and registry data on migrants conducted by Agency of Public Health, Lazio Region, Italy within the MEHO-project; thus, the information on registries was double-checked to assure accuracy and verification. Results Available registry data on healthcare utilization which allow for identification on migrants on a national/regional basis were only reported in 11 EU countries: Austria, Belgium, Denmark, Finland, Greece, Italy, Luxembourg, the Netherlands, Poland, Slovenia, and Sweden. Data on hospital care, including surgical procedures, were most frequently available whereas only few countries had data on care outside the hospital. Regarding identification of migrants, five countries reported having information on both citizenship and country of birth, one reported availability of information on country of birth, and five countries reported availability of information on citizenship. Conclusion Lack of registry data in 16 EU countries, shortage of data on healthcare utilization, and the diversity in the definition of migrant status hampers cross-national comparisons and calls for an urgent establishment of registries, expansion of the existing registry information, and adoption of a common, generally acceptable definition and identification method of migrants across the EU. PMID:19922657

System Identification of Mistuned Bladed Disks from Traveling Wave Response Measurements

NASA Technical Reports Server (NTRS)

Feiner, D. M.; Griffin, J. H.; Jones, K. W.; Kenyon, J. A.; Mehmed, O.; Kurkov, A. P.

2003-01-01

A new approach to modal analysis is presented. By applying this technique to bladed disk system identification methods, one can determine the mistuning in a rotor based on its response to a traveling wave excitation. This allows system identification to be performed under rotating conditions, and thus expands the applicability of existing mistuning identification techniques from integrally bladed rotors to conventional bladed disks.

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

PubMed

Yoshida, Catherine E; Kruczkiewicz, Peter; Laing, Chad R; Lingohr, Erika J; Gannon, Victor P J; Nash, John H E; Taboada, Eduardo N

2016-01-01

For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.

A 48 SNP set for grapevine cultivar identification

PubMed Central

2011-01-01

Background Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification. Results We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification. Conclusions We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable. PMID:22060012

Prevalence, identification by a DNA microarray-based assay of human and food isolates Listeria spp. from Tunisia.

PubMed

Hmaïed, F; Helel, S; Le Berre, V; François, J-M; Leclercq, A; Lecuit, M; Smaoui, H; Kechrid, A; Boudabous, A; Barkallah, I

2014-02-01

We aimed at evaluating the prevalence of Listeria species isolated from food samples and characterizing food and human cases isolates. Between 2005 and 2007, one hundred food samples collected in the markets of Tunis were analysed in our study. Five strains of Listeria monocytogenes responsible for human listeriosis isolated in hospital of Tunis were included. Multiplex PCR serogrouping and pulsed field gel electrophoresis (PFGE) applying the enzyme AscI and ApaI were used for the characterization of isolates of L. monocytogenes. We have developed a rapid microarray-based assay to a reliable discrimination of species within the Listeria genus. The prevalence of Listeria spp. in food samples was estimated at 14% by using classical biochemical identification. Two samples were assigned to L. monocytogenes and 12 to L. innocua. DNA microarray allowed unambiguous identification of Listeria species. Our results obtained by microarray-based assay were in accordance with the biochemical identification. The two food L. monocytogenes isolates were assigned to the PCR serogroup IIa (serovar 1/2a). Whereas human L. monocytogenes isolates were of PCR serogroup IVb, (serovars 4b). These isolates present a high similarity in PFGE. Food L. monocytogenes isolates were classified into two different pulsotypes. These pulsotypes were different from that of the five strains responsible for the human cases. We confirmed the presence of Listeria spp. in variety of food samples in Tunis. Increased food and clinical surveillance must be taken into consideration in Tunisia to identify putative infections sources. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Identification of resinous materials on 16th and 17th century reverse-glass objects by gas chromatography/mass spectrometry

NASA Astrophysics Data System (ADS)

Baumer, Ursula; Dietemann, Patrick; Koller, Johann

2009-07-01

Objects of hinterglasmalerei, reverse-glass paintings, are painted on the back side of glass panels. Obviously, the paint layers are applied in reverse order, starting with the uppermost layer. The finished hinterglas painting is viewed through the glass, thus revealing an impressive gloss and depth of colour. The binding media of two precious objects of hinterglasmalerei from the 16th and 17th century have been identified as almost exclusively resinous. Identification was performed by a special optimised analysis procedure, which is discussed in this paper: solvent extracts are analysed by gas chromatography/mass spectrometry, both with and without derivatisation or hydrolysis. In an additional step, oxalic acid is added to the methanol extracts prior to injection. This attenuates the peaks of the non-acidic compounds, whereas the acids elute with good resolution. The non-acidic compounds are emphasised after injection of the underivatised extracts. This approach minimises compositional changes caused by the sample preparation and derivatisation steps. Chromatograms of aged samples with a very complex composition are simplified, which allows a more reliable and straightforward identification of significant markers for various materials. The binding media of the hinterglas objects were thus shown to consist of mixtures of different natural resins, larch turpentine, heat-treated Pinaceae resin or mastic. Typical compounds of dragon's blood, a natural red resin, were also detectable in red glazes by the applied analysis routine. Identification of the binding media provides valuable information that can be used in the development of an adequate conservation treatment.

Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia

PubMed Central

Wang, Aisuo; Gopurenko, David; Wu, Hanwen; Lepschi, Brendan

2017-01-01

Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE—petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations. PMID:28399170

MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles

PubMed Central

2011-01-01

Background Improvements in the techniques for metabolomics analyses and growing interest in metabolomic approaches are resulting in the generation of increasing numbers of metabolomic profiles. Platforms are required for profile management, as a function of experimental design, and for metabolite identification, to facilitate the mining of the corresponding data. Various databases have been created, including organism-specific knowledgebases and analytical technique-specific spectral databases. However, there is currently no platform meeting the requirements for both profile management and metabolite identification for nuclear magnetic resonance (NMR) experiments. Description MeRy-B, the first platform for plant 1H-NMR metabolomic profiles, is designed (i) to provide a knowledgebase of curated plant profiles and metabolites obtained by NMR, together with the corresponding experimental and analytical metadata, (ii) for queries and visualization of the data, (iii) to discriminate between profiles with spectrum visualization tools and statistical analysis, (iv) to facilitate compound identification. It contains lists of plant metabolites and unknown compounds, with information about experimental conditions, the factors studied and metabolite concentrations for several plant species, compiled from more than one thousand annotated NMR profiles for various organs or tissues. Conclusion MeRy-B manages all the data generated by NMR-based plant metabolomics experiments, from description of the biological source to identification of the metabolites and determinations of their concentrations. It is the first database allowing the display and overlay of NMR metabolomic profiles selected through queries on data or metadata. MeRy-B is available from http://www.cbib.u-bordeaux2.fr/MERYB/index.php. PMID:21668943

Accelerating what works: using qualitative research methods in developing a change package for a learning collaborative.

PubMed

Sorensen, Asta V; Bernard, Shulamit L

2012-02-01

Learning (quality improvement) collaboratives are effective vehicles for driving coordinated organizational improvements. A central element of a learning collaborative is the change package-a catalogue of strategies, change concepts, and action steps that guide participants in their improvement efforts. Despite a vast literature describing learning collaboratives, little to no information is available on how the guiding strategies, change concepts, and action items are identified and developed to a replicable and actionable format that can be used to make measurable improvements within participating organizations. The process for developing the change package for the Health Resources and Services Administration's (HRSA) Patient Safety and Clinical Pharmacy Services Collaborative entailed environmental scan and identification of leading practices, case studies, interim debriefing meetings, data synthesis, and a technical expert panel meeting. Data synthesis involved end-of-day debriefings, systematic qualitative analyses, and the use of grounded theory and inductive data analysis techniques. This approach allowed systematic identification of innovative patient safety and clinical pharmacy practices that could be adopted in diverse environments. A case study approach enabled the research team to study practices in their natural environments. Use of grounded theory and inductive data analysis techniques enabled identification of strategies, change concepts, and actionable items that might not have been captured using different approaches. Use of systematic processes and qualitative methods in identification and translation of innovative practices can greatly accelerate the diffusion of innovations and practice improvements. This approach is effective whether or not an individual organization is part of a learning collaborative.

Evaluation of six candidate DNA barcode loci for identification of five important invasive grasses in eastern Australia.

PubMed

Wang, Aisuo; Gopurenko, David; Wu, Hanwen; Lepschi, Brendan

2017-01-01

Invasive grass weeds reduce farm productivity, threaten biodiversity, and increase weed control costs. Identification of invasive grasses from native grasses has generally relied on the morphological examination of grass floral material. DNA barcoding may provide an alternative means to identify co-occurring native and invasive grasses, particularly during early growth stages when floral characters are unavailable for analysis. However, there are no universal loci available for grass barcoding. We herein evaluated the utility of six candidate loci (atpF intron, matK, ndhK-ndhC, psbE-petL, ETS and ITS) for barcode identification of several economically important invasive grass species frequently found among native grasses in eastern Australia. We evaluated these loci in 66 specimens representing five invasive grass species (Chloris gayana, Eragrostis curvula, Hyparrhenia hirta, Nassella neesiana, Nassella trichotoma) and seven native grass species. Our results indicated that, while no single locus can be universally used as a DNA barcode for distinguishing the grass species examined in this study, two plastid loci (atpF and matK) showed good distinguishing power to separate most of the taxa examined, and could be used as a dual locus to distinguish several of the invasive from the native species. Low PCR success rates were evidenced among two nuclear loci (ETS and ITS), and few species were amplified at these loci, however ETS was able to genetically distinguish the two important invasive Nassella species. Multiple loci analyses also suggested that ETS played a crucial role in allowing identification of the two Nassella species in the multiple loci combinations.

Distributed acoustic cues for caller identity in macaque vocalization.

PubMed

Fukushima, Makoto; Doyle, Alex M; Mullarkey, Matthew P; Mishkin, Mortimer; Averbeck, Bruno B

2015-12-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured 'coo' call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral-temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call's fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized.

Distributed acoustic cues for caller identity in macaque vocalization

PubMed Central

Doyle, Alex M.; Mullarkey, Matthew P.; Mishkin, Mortimer; Averbeck, Bruno B.

2015-01-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured ‘coo’ call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral–temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call’s fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized. PMID:27019727

Obtaining big data of vegetation using artificial neural network

NASA Astrophysics Data System (ADS)

Ise, T.; Minagawa, M.; Onishi, M.

2017-12-01

To carry out predictive studies concerning ecosystems, obtaining appropriate datasets is one of the key factors. Recently, applications of neural network such as deep learning have successfully overcome difficulties in data acquisition and added large datasets for predictive science. For example, deep learning is very powerful in identifying and counting people, cars, etc. However, for vegetation science, deep learning has not been widely used. In general, differing from animals, plants have characteristics of modular growth. For example, numbers of leaves and stems which one individual plant typically possesses are not predetermined but change flexibly according to environmental conditions. This is clearly different from that the standard model of human face has predetermined numbers of parts, such as two eyes, one mouth, and so on. This characteristics of plants can make object identification difficult. In this study, a simple but effective technique was used to overcome the difficulty of visual identification of plants, and automated classification of plant types and quantitative analyses were become possible. For instance, when our method was applied to classify bryophytes, one of the most difficult plant types for computer vision due to their amorphous shapes, the performance of identification model was typically over 90% success. With this technology, it may be possible to obtain the big data of plant type, size, density etc. from satellite and/or drone imageries, in a quantitative manner. this will allow progress in predictive biogeosciences.

A hybrid LIBS-Raman system combined with chemometrics: an efficient tool for plastic identification and sorting.

PubMed

Shameem, K M Muhammed; Choudhari, Khoobaram S; Bankapur, Aseefhali; Kulkarni, Suresh D; Unnikrishnan, V K; George, Sajan D; Kartha, V B; Santhosh, C

2017-05-01

Classification of plastics is of great importance in the recycling industry as the littering of plastic wastes increases day by day as a result of its extensive use. In this paper, we demonstrate the efficacy of a combined laser-induced breakdown spectroscopy (LIBS)-Raman system for the rapid identification and classification of post-consumer plastics. The atomic information and molecular information of polyethylene terephthalate, polyethylene, polypropylene, and polystyrene were studied using plasma emission spectra and scattered signal obtained in the LIBS and Raman technique, respectively. The collected spectral features of the samples were analyzed using statistical tools (principal component analysis, Mahalanobis distance) to categorize the plastics. The analyses of the data clearly show that elemental information and molecular information obtained from these techniques are efficient for classification of plastics. In addition, the molecular information collected via Raman spectroscopy exhibits clearly distinct features for the transparent plastics (100% discrimination), whereas the LIBS technique shows better spectral feature differences for the colored samples. The study shows that the information obtained from these complementary techniques allows the complete classification of the plastic samples, irrespective of the color or additives. This work further throws some light on the fact that the potential limitations of any of these techniques for sample identification can be overcome by the complementarity of these two techniques. Graphical Abstract ᅟ.

Soft Biometrics; Human Identification Using Comparative Descriptions.

PubMed

Reid, Daniel A; Nixon, Mark S; Stevenage, Sarah V

2014-06-01

Soft biometrics are a new form of biometric identification which use physical or behavioral traits that can be naturally described by humans. Unlike other biometric approaches, this allows identification based solely on verbal descriptions, bridging the semantic gap between biometrics and human description. To permit soft biometric identification the description must be accurate, yet conventional human descriptions comprising of absolute labels and estimations are often unreliable. A novel method of obtaining human descriptions will be introduced which utilizes comparative categorical labels to describe differences between subjects. This innovative approach has been shown to address many problems associated with absolute categorical labels-most critically, the descriptions contain more objective information and have increased discriminatory capabilities. Relative measurements of the subjects' traits can be inferred from comparative human descriptions using the Elo rating system. The resulting soft biometric signatures have been demonstrated to be robust and allow accurate recognition of subjects. Relative measurements can also be obtained from other forms of human representation. This is demonstrated using a support vector machine to determine relative measurements from gait biometric signatures-allowing retrieval of subjects from video footage by using human comparisons, bridging the semantic gap.

General M13 phage display: M13 phage display in identification and characterization of protein-protein interactions.

PubMed

Hertveldt, Kirsten; Beliën, Tim; Volckaert, Guido

2009-01-01

In M13 phage display, proteins and peptides are exposed on one of the surface proteins of filamentous phage particles and become accessible to affinity enrichment against a bait of interest. We describe the construction of fragmented whole genome and gene fragment phage display libraries and interaction selection by panning. This strategy allows the identification and characterization of interacting proteins on a genomic scale by screening the fragmented "proteome" against protein baits. Gene fragment libraries allow a more in depth characterization of the protein-protein interaction site by identification of the protein region involved in the interaction.

Using population genetic analyses to understand seed dispersal patterns

NASA Astrophysics Data System (ADS)

Hamrick, J. L.; Trapnell, Dorset W.

2011-11-01

Neutral genetic markers have been employed in several ways to understand seed dispersal patterns in natural and human modified landscapes. Genetic differentiation among spatially separated populations, using biparentally and maternally inherited genetic markers, allows determination of the relative historical effectiveness of pollen and seed dispersal. Genetic relatedness among individuals, estimated as a function of spatial separation between pairs of individuals, has also been used to indirectly infer seed dispersal distances. Patterns of genetic relatedness among plants in recently colonized populations provide insights into the role of seed dispersal in population colonization and expansion. High genetic relatedness within expanding populations indicates original colonization by a few individuals and population expansion by the recruitment of the original colonists' progeny; low relatedness should occur if population growth results primarily from continuous seed immigration from multiple sources. Parentage analysis procedures can identify maternal parents of dispersed fruits, seeds, or seedlings providing detailed descriptions of contemporary seed dispersal patterns. With standard parent-pair analyses of seeds or seedlings, problems can arise in distinguishing the maternal parent. However, the use of maternal DNA from dispersed fruits or seed coats allows direct identification of maternal individuals and, as a consequence, the distance and patterns of seed dispersal and deposition. Application of combinations of these approaches provides additional insights into the role seed dispersal plays in the genetic connectivity between populations in natural and disturbed landscapes.

On-line hyphenation of centrifugal partition chromatography and high pressure liquid chromatography for the fractionation of flavonoids from Hippophaë rhamnoides L. berries.

PubMed

Michel, Thomas; Destandau, Emilie; Elfakir, Claire

2011-09-09

Centrifugal Partition Chromatography (CPC), a liquid-liquid preparative chromatography using two immiscible solvent systems, benefits from numerous advantages for the separation or purification of synthetic or natural products. This study presents the on-line hyphenation of CPC-Evaporative Light Scattering Detector (CPC-ELSD) with High Performance Liquid Chromatography-UV (HPLC-UV) for the fractionation of flavonols from a solvent-free microwave extract of sea buckthorn (Hippophaë rhamnoides L., Elaeagnaceae) berries. An Arizona G system was used for the fractionation of flavonoids by CPC and a fused core Halo C18 column allowed the on-line analyses of collected fractions by HPLC. The on-line CPC/HPLC procedure allowed the simultaneous fractionation step at preparative scale combined with the HPLC analyses which provide direct fingerprint of collected fractions. Thus the crude extract was simplified and immediate information on the composition of fractions could be obtained. Furthermore, this methodology reduced the time of post-fractionation steps and facilitated identification of main molecules by Mass Spectrometry (MS). Rutin, isorhamnetin-3-O-rutinoside, isorhamnetin-3-O-glucoside, quercetin-3-O-glucoside, isorhamnetin-rhamnoside, quercetin and isorhamnetin were identified. CPC-ELSD/HPLC-UV could be considered as a high-throughput technique for the guided fractionation of bioactive natural products from complex crude extracts. Copyright © 2011 Elsevier B.V. All rights reserved.

3-Hydroxyisobutyrate Dehydrogenase Is Involved in Both, Valine and Isoleucine Degradation in Arabidopsis thaliana.

PubMed

Schertl, Peter; Danne, Lennart; Braun, Hans-Peter

2017-09-01

In plants, amino acid catabolism is especially relevant in metabolic stress situations (e.g. limited carbohydrate availability during extended darkness). Under these conditions, amino acids are used as alternative substrates for respiration. Complete oxidation of the branched-chain amino acids (BCAAs) leucine, isoleucine (Ile), and valine (Val) in the mitochondria efficiently allows the formation of ATP by oxidative phosphorylation. However, the metabolic pathways for BCAA breakdown are largely unknown so far in plants. A systematic search for Arabidopsis ( Arabidopsis thaliana ) genes encoding proteins resembling enzymes involved in BCAA catabolism in animals, fungi, and bacteria as well as proteomic analyses of mitochondrial fractions from Arabidopsis allowed the identification of a putative 3-hydroxyisobutyrate dehydrogenase, AtHDH1 (At4g20930), involved in Val degradation. Systematic substrate screening analyses revealed that the protein uses 3-hydroxyisobutyrate but additionally 3-hydroxypropionate as substrates. This points to a role of the enzyme not only in Val but possibly also in Ile metabolism. At4g20930 knockdown plants were characterized to test this conclusion. Root toxicity assays revealed increased root growth inhibition of the mutants if cultivated in the presence of Val or Ile but not in the presence of leucine. We conclude that AtHDH1 has a dual role in BCAA metabolism in plants. © 2017 American Society of Plant Biologists. All Rights Reserved.

Improved orthologous databases to ease protozoan targets inference.

PubMed

Kotowski, Nelson; Jardim, Rodrigo; Dávila, Alberto M R

2015-09-29

Homology inference helps on identifying similarities, as well as differences among organisms, which provides a better insight on how closely related one might be to another. In addition, comparative genomics pipelines are widely adopted tools designed using different bioinformatics applications and algorithms. In this article, we propose a methodology to build improved orthologous databases with the potential to aid on protozoan target identification, one of the many tasks which benefit from comparative genomics tools. Our analyses are based on OrthoSearch, a comparative genomics pipeline originally designed to infer orthologs through protein-profile comparison, supported by an HMM, reciprocal best hits based approach. Our methodology allows OrthoSearch to confront two orthologous databases and to generate an improved new one. Such can be later used to infer potential protozoan targets through a similarity analysis against the human genome. The protein sequences of Cryptosporidium hominis, Entamoeba histolytica and Leishmania infantum genomes were comparatively analyzed against three orthologous databases: (i) EggNOG KOG, (ii) ProtozoaDB and (iii) Kegg Orthology (KO). That allowed us to create two new orthologous databases, "KO + EggNOG KOG" and "KO + EggNOG KOG + ProtozoaDB", with 16,938 and 27,701 orthologous groups, respectively. Such new orthologous databases were used for a regular OrthoSearch run. By confronting "KO + EggNOG KOG" and "KO + EggNOG KOG + ProtozoaDB" databases and protozoan species we were able to detect the following total of orthologous groups and coverage (relation between the inferred orthologous groups and the species total number of proteins): Cryptosporidium hominis: 1,821 (11 %) and 3,254 (12 %); Entamoeba histolytica: 2,245 (13 %) and 5,305 (19 %); Leishmania infantum: 2,702 (16 %) and 4,760 (17 %). Using our HMM-based methodology and the largest created orthologous database, it was possible to infer 13 orthologous groups which represent potential protozoan targets; these were found because of our distant homology approach. We also provide the number of species-specific, pair-to-pair and core groups from such analyses, depicted in Venn diagrams. The orthologous databases generated by our HMM-based methodology provide a broader dataset, with larger amounts of orthologous groups when compared to the original databases used as input. Those may be used for several homology inference analyses, annotation tasks and protozoan targets identification.

Job security and work performance in Chinese employees: The mediating role of organisational identification.

PubMed

Ma, Bing; Liu, Shanshi; Liu, Donglai; Wang, Hongchun

2016-04-01

This research focuses on investigating whether organisational identification mediates the effects of job security on in-role behaviour and extra-role behaviour and how these mediation mechanisms differ according to gender. Through analysing 212 supervisor-subordinate dyads from a Chinese air transportation group, the research indicated that organisational identification partially mediated the effect of job security on in-role behaviour and fully mediated the effect of job security on extra-role behaviour. A multi-group analysis also showed that there were significant differences between male and female employees in these relationships. In addition, moderated mediation analyses showed that gender moderated the indirect effects of job security on in-role behaviour and extra-role behaviour through organisational identification. Limitations and implications of these findings are discussed. © 2015 International Union of Psychological Science.

Software For Computer-Security Audits

NASA Technical Reports Server (NTRS)

Arndt, Kate; Lonsford, Emily

1994-01-01

Information relevant to potential breaches of security gathered efficiently. Automated Auditing Tools for VAX/VMS program includes following automated software tools performing noted tasks: Privileged ID Identification, program identifies users and their privileges to circumvent existing computer security measures; Critical File Protection, critical files not properly protected identified; Inactive ID Identification, identifications of users no longer in use found; Password Lifetime Review, maximum lifetimes of passwords of all identifications determined; and Password Length Review, minimum allowed length of passwords of all identifications determined. Written in DEC VAX DCL language.

41 CFR Appendix C to Chapter 301 - Standard Data Elements for Federal Travel [Traveler Identification

Code of Federal Regulations, 2013 CFR

2013-07-01

... for Federal Travel [Traveler Identification] C Appendix C to Chapter 301 Public Contracts and Property Management Federal Travel Regulation System TEMPORARY DUTY (TDY) TRAVEL ALLOWANCES Ch. 301, App. C Appendix C to Chapter 301—Standard Data Elements for Federal Travel [Traveler Identification] Group name Data...

Comparison of identification methods for oral asaccharolytic Eubacterium species.

PubMed

Wade, W G; Slayne, M A; Aldred, M J

1990-12-01

Thirty one strains of oral, asaccharolytic Eubacterium spp. and the type strains of E. brachy, E. nodatum and E. timidum were subjected to three identification techniques--protein-profile analysis, determination of metabolic end-products, and the API ATB32A identification kit. Five clusters were obtained from numerical analysis of protein profiles and excellent correlations were seen with the other two methods. Protein profiles alone allowed unequivocal identification.

Raman and Photoluminescence Spectroscopy in Mineral Identification

NASA Astrophysics Data System (ADS)

Kuehn, J. W.

2014-06-01

Raman spectroscopy is particularly useful for rapid identification of minerals and gemstones. Raman spectrometers also allow PL studies for authentication of samples and geological provenance, diamond type screening and detection of HPHT treatments.

Approach for the Development of a Framework for the Identification of Activities of Daily Living Using Sensors in Mobile Devices.

PubMed

Pires, Ivan Miguel; Garcia, Nuno M; Pombo, Nuno; Flórez-Revuelta, Francisco; Spinsante, Susanna

2018-02-21

Sensors available on mobile devices allow the automatic identification of Activities of Daily Living (ADL). This paper describes an approach for the creation of a framework for the identification of ADL, taking into account several concepts, including data acquisition, data processing, data fusion, and pattern recognition. These concepts can be mapped onto different modules of the framework. The proposed framework should perform the identification of ADL without Internet connection, performing these tasks locally on the mobile device, taking in account the hardware and software limitations of these devices. The main purpose of this paper is to present a new approach for the creation of a framework for the recognition of ADL, analyzing the allowed sensors available in the mobile devices, and the existing methods available in the literature.

Approach for the Development of a Framework for the Identification of Activities of Daily Living Using Sensors in Mobile Devices

PubMed Central

Pombo, Nuno

2018-01-01

Sensors available on mobile devices allow the automatic identification of Activities of Daily Living (ADL). This paper describes an approach for the creation of a framework for the identification of ADL, taking into account several concepts, including data acquisition, data processing, data fusion, and pattern recognition. These concepts can be mapped onto different modules of the framework. The proposed framework should perform the identification of ADL without Internet connection, performing these tasks locally on the mobile device, taking in account the hardware and software limitations of these devices. The main purpose of this paper is to present a new approach for the creation of a framework for the recognition of ADL, analyzing the allowed sensors available in the mobile devices, and the existing methods available in the literature. PMID:29466316

Advanced driver assistance system: Road sign identification using VIAPIX system and a correlation technique

NASA Astrophysics Data System (ADS)

Ouerhani, Y.; Alfalou, A.; Desthieux, M.; Brosseau, C.

2017-02-01

We present a three-step approach based on the commercial VIAPIX® module for road traffic sign recognition and identification. Firstly, detection in a scene of all objects having characteristics of traffic signs is performed. This is followed by a first-level recognition based on correlation which consists in making a comparison between each detected object with a set of reference images of a database. Finally, a second level of identification allows us to confirm or correct the previous identification. In this study, we perform a correlation-based analysis by combining and adapting the Vander Lugt correlator with the nonlinear joint transformation correlator (JTC). Of particular significance, this approach permits to make a reliable decision on road traffic sign identification. We further discuss a robust scheme allowing us to track a detected road traffic sign in a video sequence for the purpose of increasing the decision performance of our system. This approach can have broad practical applications in the maintenance and rehabilitation of transportation infrastructure, or for drive assistance.

Meta-analysis of aberrant lymphatic drainage in recurrent breast cancer.

PubMed

Ahmed, M; Baker, R; Rubio, I T

2016-11-01

Sentinel node biopsy (SNB) in recurrent breast cancer offers targeted axillary staging compared with axillary lymph node dissection (ALND) or no treatment. The evidence for lymphatic mapping in recurrent breast cancer is reviewed, focusing on aberrant drainage and its implications for patient management. A meta-analysis of studies evaluating lymphatic mapping in recurrent breast cancer was performed. Outcomes included sentinel node identification, aberrant lymphatic pathways and metastatic node rates in aberrant drainage and ipsilateral axilla. Pooled odds ratios (ORs) and 95 per cent confidence intervals (c.i.) were estimated using fixed-effect analyses, or random-effects analyses in the event of statistically significant heterogeneity. Seven studies reported data on lymphatic mapping in 1053 patients with recurrent breast cancer. The intraoperative sentinel node identification rate was 59·6 (95 per cent c.i. 56·7 to 62·6) per cent, and significantly greater when the original axillary surgery was SNB compared with ALND (OR 2·97, 95 per cent c.i. 1·66 to 5·32). The rate of aberrant lymphatic drainage identification was 25·7 (23·0 to 28·3) per cent, and significantly greater when the original axillary surgery was ALND (OR 0·27, 0·19 to 0·38). The metastatic sentinel node rate was 10·4 (8·6 to 12·3) per cent, and a significantly greater metastatic nodal burden was identified in the ipsilateral axilla (OR 6·31, 1·03 to 38·79). Lymphatic mapping is feasible in recurrent breast cancer. It avoids ALND in over 50 per cent of patients who have undergone SNB, and allows the 4 per cent of patients with metastatically involved aberrant nodes to receive targeted surgical and adjuvant therapies. © 2016 BJS Society Ltd Published by John Wiley & Sons Ltd.

Proteomic characterization of larval and adult developmental stages in Echinococcus granulosus reveals novel insight into host-parasite interactions.

PubMed

Cui, Shu-Jian; Xu, Lei-Lei; Zhang, Ting; Xu, Ming; Yao, Jun; Fang, Cai-Yun; Feng, Zheng; Yang, Peng-Yuan; Hu, Wei; Liu, Feng

2013-06-12

Cystic hydatid disease is an important zoonosis caused by Echinococcus granulosus infection. The expression profiles of its parasitic life stages and host-Echinococcus interactions remain to be elucidated. Here, we identified 157 adult and 1588 protoscolex proteins (1610 in all), including 1290 novel identifications. Paramyosins and an antigen B (AgB) were the dominant adult proteins. Dog proteins (30) identified in adults indicated diminished local inflammation caused by adult infection. The protoscolex expresses proteins that have been reported to be antigens in other parasites, such as 6-phosphofructokinase and calcineurin B. Pathway analyses suggested that E. granulosus uses both aerobic and anaerobic carbohydrate metabolisms to generate ATP. E. granulosus expresses proteins involved in synthesis and metabolism of lipids or steroids. At least 339 of 390 sheep proteins identified in protoscolex were novel identifications not seen in previous analyses. IgGs and lambda light chains were the most abundant antibody species. Sheep proteins were enriched for detoxification pathways, implying that host detoxification effects play a central role during host-parasite interactions. Our study provides valuable data on E. granulosus expression characteristics, allowing novel insights into the molecular mechanisms involved in host-parasite interactions. In this study, the Echinococcus granulosus adult worm proteome was analyzed for the first time. The protein identification of E. granulosus protoscoleces was extended dramatically. We also identified the most abundant host proteins co-purified with Echinococcus. The results provide useful information pertaining to the molecular mechanisms behind host-Echinococcus interaction and Echinococcus biology. This data also increases the potential for identifying vaccine candidates and new therapeutic targets, and may aid in the development of protein probes for selective and sensitive diagnosis of echinococcosis infection. In addition, the data collected here represents a valuable proteomic resource for subsequent genome annotation. Copyright © 2013 Elsevier B.V. All rights reserved.

Identifying low pH active and lactate-utilizing taxa within oral microbiome communities from healthy children using stable isotope probing techniques.

PubMed

McLean, Jeffrey S; Fansler, Sarah J; Majors, Paul D; McAteer, Kathleen; Allen, Lisa Z; Shirtliff, Mark E; Lux, Renate; Shi, Wenyuan

2012-01-01

Many human microbial infectious diseases including dental caries are polymicrobial in nature. How these complex multi-species communities evolve from a healthy to a diseased state is not well understood. Although many health- or disease-associated oral bacteria have been characterized in vitro, their physiology within the complex oral microbiome is difficult to determine with current approaches. In addition, about half of these species remain uncultivated to date with little known besides their 16S rRNA sequence. Lacking culture-based physiological analyses, the functional roles of uncultivated species will remain enigmatic despite their apparent disease correlation. To start addressing these knowledge gaps, we applied a combination of Magnetic Resonance Spectroscopy (MRS) with RNA and DNA based Stable Isotope Probing (SIP) to oral plaque communities from healthy children for in vitro temporal monitoring of metabolites and identification of metabolically active and inactive bacterial species. Supragingival plaque samples from caries-free children incubated with (13)C-substrates under imposed healthy (buffered, pH 7) and diseased states (pH 5.5 and pH 4.5) produced lactate as the dominant organic acid from glucose metabolism. Rapid lactate utilization upon glucose depletion was observed under pH 7 conditions. SIP analyses revealed a number of genera containing cultured and uncultivated taxa with metabolic capabilities at pH 5.5. The diversity of active species decreased significantly at pH 4.5 and was dominated by Lactobacillus and Propionibacterium species, both of which have been previously found within carious lesions from children. Our approach allowed for identification of species that metabolize carbohydrates under different pH conditions and supports the importance of Lactobacilli and Propionibacterium in the development of childhood caries. Identification of species within healthy subjects that are active at low pH can lead to a better understanding of oral caries onset and generate appropriate targets for preventative measures in the early stages.

Structure Identification Using the US EPA's CompTox Chemistry Dashboard (CompTox CoP)

EPA Science Inventory

Community of practice webinar presentation on the Identification of unknowns in non-targeted analyses (NTA) requires the integration of complementary data types to generate a confident consensus structure.

Genome-wide identification of aquaporin encoding genes in Brassica oleracea and their phylogenetic sequence comparison to Brassica crops and Arabidopsis

PubMed Central

Diehn, Till A.; Pommerrenig, Benjamin; Bernhardt, Nadine; Hartmann, Anja; Bienert, Gerd P.

2015-01-01

Aquaporins (AQPs) are essential channel proteins that regulate plant water homeostasis and the uptake and distribution of uncharged solutes such as metalloids, urea, ammonia, and carbon dioxide. Despite their importance as crop plants, little is known about AQP gene and protein function in cabbage (Brassica oleracea) and other Brassica species. The recent releases of the genome sequences of B. oleracea and Brassica rapa allow comparative genomic studies in these species to investigate the evolution and features of Brassica genes and proteins. In this study, we identified all AQP genes in B. oleracea by a genome-wide survey. In total, 67 genes of four plant AQP subfamilies were identified. Their full-length gene sequences and locations on chromosomes and scaffolds were manually curated. The identification of six additional full-length AQP sequences in the B. rapa genome added to the recently published AQP protein family of this species. A phylogenetic analysis of AQPs of Arabidopsis thaliana, B. oleracea, B. rapa allowed us to follow AQP evolution in closely related species and to systematically classify and (re-) name these isoforms. Thirty-three groups of AQP-orthologous genes were identified between B. oleracea and Arabidopsis and their expression was analyzed in different organs. The two selectivity filters, gene structure and coding sequences were highly conserved within each AQP subfamily while sequence variations in some introns and untranslated regions were frequent. These data suggest a similar substrate selectivity and function of Brassica AQPs compared to Arabidopsis orthologs. The comparative analyses of all AQP subfamilies in three Brassicaceae species give initial insights into AQP evolution in these taxa. Based on the genome-wide AQP identification in B. oleracea and the sequence analysis and reprocessing of Brassica AQP information, our dataset provides a sequence resource for further investigations of the physiological and molecular functions of Brassica crop AQPs. PMID:25904922

Connecting Self-Esteem and Achievement: Diversity in Academic Identification and Dis-Identification Patterns among Black College Students

ERIC Educational Resources Information Center

Hope, Elan C.; Chavous, Tabbye M.; Jagers, Robert J.; Sellers, Robert M.

2013-01-01

Using a person-oriented approach, we explored patterns of self-esteem and achievement among 324 Black college students across the freshman college year and identified four academic identification profiles. Multivariate analyses revealed profile differences in academic and psychological outcomes at beginning and end of freshman year (academic…

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-Rich DNA, and nuclear DNA analyses

USGS Publications Warehouse

Freeman, S.; Pham, M.; Rodriguez, R.J.

1993-01-01

Molecular genotyping of Colletotrichum species based on arbitrarily primed PCR, A + T-rich DNA, and nuclear DNA analyses. Experimental Mycology 17, 309-322. Isolates of Colletotrichum were grouped into 10 separate species based on arbitrarily primed PCR (ap-PCR), A + T-rich DNA (AT-DNA) and nuclear DNA banding patterns. In general, the grouping of Colletotrichum isolates by these molecular approaches corresponded to that done by classical taxonomic identification, however, some exceptions were observed. PCR amplification of genomic DNA using four different primers allowed for reliable differentiation between isolates of the 10 species. HaeIII digestion patterns of AT-DNA also distinguished between species of Colletotrichum by generating species-specific band patterns. In addition, hybridization of the repetitive DNA element (GcpR1) to genomic DNA identified a unique set of Pst 1-digested nuclear DNA fragments in each of the 10 species of Colletotrichum tested. Multiple isolates of C. acutatum, C. coccodes, C. fragariae, C. lindemuthianum, C. magna, C. orbiculare, C. graminicola from maize, and C. graminicola from sorghum showed 86-100% intraspecies similarity based on ap-PCR and AT-DNA analyses. Interspecies similarity determined by ap-PCR and AT-DNA analyses varied between 0 and 33%. Three distinct banding patterns were detected in isolates of C. gloeosporioides from strawberry. Similarly, three different banding patterns were observed among isolates of C. musae from diseased banana.

Using DNA barcoding to differentiate invasive Dreissena species (Mollusca, Bivalvia)

PubMed Central

Marescaux, Jonathan; Van Doninck, Karine

2013-01-01

Abstract The zebra mussel (Dreissena polymorpha) and the quagga mussel (Dreissena rostriformis bugensis) are considered as the most competitive invaders in freshwaters of Europe and North America. Although shell characteristics exist to differentiate both species, phenotypic plasticity in the genus Dreissena does not always allow a clear identification. Therefore, the need to find an accurate identification method is essential. DNA barcoding has been proven to be an adequate procedure to discriminate species. The cytochrome c oxidase subunit I mitochondrial gene (COI) is considered as the standard barcode for animals. We tested the use of this gene as an efficient DNA barcode and found that it allow rapid and accurate identification of adult Dreissena individuals. PMID:24453560

College Women's Feminist Identity: A Multidimensional Analysis with Implications for Coping with Sexism.

PubMed

Leaper, Campbell; Arias, Diana M

2011-04-01

This study examined components of women's feminist identity and possible relations to their reported coping responses to sexism. A sample of 169 undergraduate women (M = 19.4 y, SD = 1.2) from diverse ethnic backgrounds completed surveys assessing their experiences and gender-related views. The first set of analyses revealed that women's social gender identity, exposure to feminism, and gender-egalitarian attitudes independently contributed to feminist identification; moreover, non-stereotyping of feminists further predicted feminist self-identification. A second set of analyses tested the relative contribution of feminist identity components to women's cognitive appraisals of coping responses to sexual harassment. Seeking social support was predicted by self-identification as a feminist (for White European American women only). Confronting was predicted by social gender identity, non-stereotyping of feminists, and public identification as a feminist. Findings highlight possible components of women's feminist identity and their possible impact on coping responses to sexism.

Gait patterns for crime fighting: statistical evaluation

NASA Astrophysics Data System (ADS)

Sulovská, Kateřina; Bělašková, Silvie; Adámek, Milan

2013-10-01

The criminality is omnipresent during the human history. Modern technology brings novel opportunities for identification of a perpetrator. One of these opportunities is an analysis of video recordings, which may be taken during the crime itself or before/after the crime. The video analysis can be classed as identification analyses, respectively identification of a person via externals. The bipedal locomotion focuses on human movement on the basis of their anatomical-physiological features. Nowadays, the human gait is tested by many laboratories to learn whether the identification via bipedal locomotion is possible or not. The aim of our study is to use 2D components out of 3D data from the VICON Mocap system for deep statistical analyses. This paper introduces recent results of a fundamental study focused on various gait patterns during different conditions. The study contains data from 12 participants. Curves obtained from these measurements were sorted, averaged and statistically tested to estimate the stability and distinctiveness of this biometrics. Results show satisfactory distinctness of some chosen points, while some do not embody significant difference. However, results presented in this paper are of initial phase of further deeper and more exacting analyses of gait patterns under different conditions.

Spectroscopic analyses of Fe and water in clays: A Martian surface weathering study

NASA Technical Reports Server (NTRS)

Bishop, J. L.; Pieters, Carle M.; Edwards, J. O.; Coyne, L. M.; Chang, S.

1991-01-01

Martian surface morphology suggests the presence of liquid H2O on Mars in the past. Reflectance spectra of the Martian surface include features which correspond to the crystal field transitions of iron, as well as features supporting the presence of ice and minerals containing structural OH and surface water. Researchers initiated further spectroscopic studies of surface iron and water and structural OH in clays in order to determine what remotely obtained spectra can indicate about the presence of clays on Mars based on a clearer understanding of the factors influencing the spectral features. Current technology allows researchers to better correlate the low frequency fundamental stretching and bending vibrations of O-H bonds with the diagnostic near infrared overtone and combination bands used in mineral characterization and identification.

Investigating disparities in spatial accessibility to and characteristics of sport facilities: direction, strength, and spatial scale of associations with area income.

PubMed

Billaudeau, Nathalie; Oppert, Jean-Michel; Simon, Chantal; Charreire, Hélène; Casey, Romain; Salze, Paul; Badariotti, Dominique; Banos, Arnaud; Weber, Christiane; Chaix, Basile

2011-01-01

We conducted an environmental justice study of the spatial distribution of sport facilities, a major resource for physical activity, in the Paris Region in France. Comprehensive data of the French Census of Sport Facilities allowed us to investigate disparities not only in the spatial accessibility to facilities, but also in the characteristics of these facilities. We found that the associations between area income and the presence of facilities or favorable characteristics of these facilities varied from positive to negative depending on the facilities and on the characteristics examined. Sensitivity analyses defining area income in circular areas of different radii permitted a refined identification of areas underserved in sport facilities. Copyright © 2010 Elsevier Ltd. All rights reserved.

A laboratory information management system for DNA barcoding workflows.

PubMed

Vu, Thuy Duong; Eberhardt, Ursula; Szöke, Szániszló; Groenewald, Marizeth; Robert, Vincent

2012-07-01

This paper presents a laboratory information management system for DNA sequences (LIMS) created and based on the needs of a DNA barcoding project at the CBS-KNAW Fungal Biodiversity Centre (Utrecht, the Netherlands). DNA barcoding is a global initiative for species identification through simple DNA sequence markers. We aim at generating barcode data for all strains (or specimens) included in the collection (currently ca. 80 k). The LIMS has been developed to better manage large amounts of sequence data and to keep track of the whole experimental procedure. The system has allowed us to classify strains more efficiently as the quality of sequence data has improved, and as a result, up-to-date taxonomic names have been given to strains and more accurate correlation analyses have been carried out.

Synchrotron FTIR Imaging For The Identification Of Cell Types Within Human Tissues

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

Walsh, Michael J.; Pounder, F. Nell; Nasse, Michael J.

2010-02-03

The use of synchrotron Fourier Transform Infrared spectroscopy (S-FTIR) has been shown to be a very promising tool for biomedical research. S-FTIR spectroscopy allows for the fast acquisition of infrared (IR) spectra at a spatial resolution approaching the IR diffraction limit. The development of the Infrared Environmental Imaging (IRENI) beamline at the Synchrotron Radiation Center (SRC) at the University of Wisconsin-Madison has allowed for diffraction limited imaging measurements of cells in human prostate and breast tissues. This has allowed for the identification of cell types within tissues that would otherwise not have been resolvable using conventional FTIR sources.

Defining robustness protocols: a method to include and evaluate robustness in clinical plans

NASA Astrophysics Data System (ADS)

McGowan, S. E.; Albertini, F.; Thomas, S. J.; Lomax, A. J.

2015-04-01

We aim to define a site-specific robustness protocol to be used during the clinical plan evaluation process. Plan robustness of 16 skull base IMPT plans to systematic range and random set-up errors have been retrospectively and systematically analysed. This was determined by calculating the error-bar dose distribution (ebDD) for all the plans and by defining some metrics used to define protocols aiding the plan assessment. Additionally, an example of how to clinically use the defined robustness database is given whereby a plan with sub-optimal brainstem robustness was identified. The advantage of using different beam arrangements to improve the plan robustness was analysed. Using the ebDD it was found range errors had a smaller effect on dose distribution than the corresponding set-up error in a single fraction, and that organs at risk were most robust to the range errors, whereas the target was more robust to set-up errors. A database was created to aid planners in terms of plan robustness aims in these volumes. This resulted in the definition of site-specific robustness protocols. The use of robustness constraints allowed for the identification of a specific patient that may have benefited from a treatment of greater individuality. A new beam arrangement showed to be preferential when balancing conformality and robustness for this case. The ebDD and error-bar volume histogram proved effective in analysing plan robustness. The process of retrospective analysis could be used to establish site-specific robustness planning protocols in proton therapy. These protocols allow the planner to determine plans that, although delivering a dosimetrically adequate dose distribution, have resulted in sub-optimal robustness to these uncertainties. For these cases the use of different beam start conditions may improve the plan robustness to set-up and range uncertainties.

Forest Species Identification with High Spectral Resolution Data

NASA Technical Reports Server (NTRS)

Olson, C. E., Jr.; Zhu, Z.

1985-01-01

Data collected over the Sleeping Bear Sand Dunes Test Site and the Saginaw Forest Test Site (Michigan) with the JPL Airborne Imaging Spectrometer and the Collins' Airborne Spectroradiometer are being used for forest species identification. The linear discriminant function has provided higher identification accuracies than have principal components analyses. Highest identification accuracies are obtained in the 450 to 520 nm spectral region. Spectral bands near 1,300, 1,685 and 2,220 nm appear to be important, also.

Non-intrusive parameter identification procedure user's guide

NASA Technical Reports Server (NTRS)

Hanson, G. D.; Jewell, W. F.

1983-01-01

Written in standard FORTRAN, NAS is capable of identifying linear as well as nonlinear relations between input and output parameters; the only restriction is that the input/output relation be linear with respect to the unknown coefficients of the estimation equations. The output of the identification algorithm can be specified to be in either the time domain (i.e., the estimation equation coefficients) or in the frequency domain (i.e., a frequency response of the estimation equation). The frame length ("window") over which the identification procedure is to take place can be specified to be any portion of the input time history, thereby allowing the freedom to start and stop the identification procedure within a time history. There also is an option which allows a sliding window, which gives a moving average over the time history. The NAS software also includes the ability to identify several assumed solutions simultaneously for the same or different input data.

The impact of organizational support and leader-member exchange on the work-related behaviour of nursing professionals: the moderating effect of professional and organizational identification.

PubMed

Trybou, Jeroen; Gemmel, Paul; Pauwels, Yarrid; Henninck, Charlene; Clays, Els

2014-02-01

The aim of this study was to examine the relations between perceived organizational support, the quality of leader-member exchange, in-role and extra-role behaviour, professional identification and organizational identification among registered nurses and nurse assistants. Theoretically, employees will reciprocate received beneficial treatment with positive attitudes and behaviour. Recently, it has been shown that this principle may be more complex than originally anticipated. A quantitative, cross-sectional survey design was used. The quality of social exchange and identification was scored by the involved registered nurses and nurse assistants; in-role and extra-role behaviour was rated by the head nurse. The survey was administered to nurses and nurse assistants (n = 196) working in five Belgian nursing homes. Data were collected from February-March 2012. Pearson correlation analyses, t-test analyses and hierarchical regression were used to analyse the data. Our results showed no relationship between perceived organizational support and leader-member exchange and in-role behaviour. A positive relationship was found between perceived organizational support and extra-role behaviour and a trend towards significance between leader-member exchange and extra-role behaviour. Organizational and professional identification moderated the relationship between perceived organizational support and extra-role behaviour. Our study demonstrates the importance of social exchange to nurses and nurse assistants and therefore nursing administrators and leaders. When registered nurses and nurse assistants perceive high-quality social exchange, they are more likely to go the extra mile on behalf of the organization. Fostering social identification could enhance this. © 2013 John Wiley & Sons Ltd.

Following the Viterbi Path to Deduce Flagellar Actin-Interacting Proteins of Leishmania spp.: Report on Cofilins and Twinfilins

NASA Astrophysics Data System (ADS)

Pacheco, Ana Carolina L.; Araújo, Fabiana F.; Kamimura, Michel T.; Medeiros, Sarah R.; Viana, Daniel A.; Oliveira, Fátima de Cássia E.; Filho, Raimundo Araújo; Costa, Marcília P.; Oliveira, Diana M.

2007-11-01

For performing vital cellular processes, such as motility, eukaryotic cells rely on the actin cytoskeleton, whose structure and dynamics are tightly controlled by a large number of actin-interacting (AIP) or actin-related/regulating (ARP) proteins. Trypanosomatid protozoa, such as Leishmania, rely on their flagellum for motility and sensory reception, which are believed to allow parasite migration, adhesion, invasion and even persistence on mammalian host tissues to cause disease. Actin can determine cell stiffness and transmit force during mechanotransduction, cytokinesis, cell motility and other cellular shape changes, while the identification and analyses of AIPs can help to improve understanding of their mechanical properties on physiological architectures, such as the present case regarding Leishmania flagellar apparatus. This work conveniently apply bioinformatics tools in some refined pattern recognition techniques (such as hidden Markov models (HMMs) through the Viterbi algorithm/path) in order to improve the recognition of actin-binding/interacting activity through identification of AIPs in genomes, transcriptomes and proteomes of Leishmania species. We here report cofilin and twinfilin as putative components of the flagellar apparatus, a direct bioinformatics contribution in the secondary annotation of Leishmania and trypanosomatid genomes.

Stress Sensors and Signal Transducers in Cyanobacteria

PubMed Central

Los, Dmitry A.; Zorina, Anna; Sinetova, Maria; Kryazhov, Sergey; Mironov, Kirill; Zinchenko, Vladislav V.

2010-01-01

In living cells, the perception of environmental stress and the subsequent transduction of stress signals are primary events in the acclimation to changes in the environment. Some molecular sensors and transducers of environmental stress cannot be identified by traditional and conventional methods. Based on genomic information, a systematic approach has been applied to the solution of this problem in cyanobacteria, involving mutagenesis of potential sensors and signal transducers in combination with DNA microarray analyses for the genome-wide expression of genes. Forty-five genes for the histidine kinases (Hiks), 12 genes for serine-threonine protein kinases (Spks), 42 genes for response regulators (Rres), seven genes for RNA polymerase sigma factors, and nearly 70 genes for transcription factors have been successfully inactivated by targeted mutagenesis in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Screening of mutant libraries by genome-wide DNA microarray analysis under various stress and non-stress conditions has allowed identification of proteins that perceive and transduce signals of environmental stress. Here we summarize recent progress in the identification of sensory and regulatory systems, including Hiks, Rres, Spks, sigma factors, transcription factors, and the role of genomic DNA supercoiling in the regulation of the responses of cyanobacterial cells to various types of stress. PMID:22294932

Rapid identification of dairy lactic acid bacteria by M13-generated, RAPD-PCR fingerprint databases.

PubMed

Rossetti, Lia; Giraffa, Giorgio

2005-11-01

About a thousand lactic acid bacteria (LAB) isolated from dairy products, especially cheeses, were identified and typed by species-specific PCR and RAPD-PCR, respectively. RAPD-PCR profiles, which were obtained by using the M13 sequence as a primer, allowed us to implement a large database of different fingerprints, which were analysed by BioNumerics software. Cluster analysis of the combined RAPD-PCR fingerprinting profiles enabled us to implement a library, which is a collection of library units, which in turn is a selection of representative database entries. A library unit, in this case, can be considered to be a definable taxon. The strains belonged to 11 main RAPD-PCR fingerprinting library units identified as Lactobacillus casei/paracasei, Lactobacillus plantarum, Lactobacillus rhamnosus, Lactobacillus helveticus, Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus brevis, Enterococcus faecium, Enterococcus faecalis, Streptococcus thermophilus and Lactococcus lactis. The possibility to routinely identify newly typed, bacterial isolates by consulting the library of the software was valued. The proposed method could be suggested to refine previous strain identifications, eliminate redundancy and dispose of a technologically useful LAB strain collection. The same approach could also be applied to identify LAB strains isolated from other food ecosystems.

Identification of irradiated wheat by germination test, DNA comet assay and electron spin resonance

NASA Astrophysics Data System (ADS)

Barros, Adilson C.; Freund, Maria Teresa L.; Villavicencio, Ana Lúcia C. H.; Delincée, Henry; Arthur, Valter

2002-03-01

In several countries, there has been an increase in the use of radiation for food processing thus improving the quality and sanitary conditions, inhibiting pathogenic microorganisms, delaying the natural aging process and so extending product lifetime. The need to develop analytical methods to detect these irradiated products is also increasing. The goal of this research was to identify wheat irradiated using different radiation doses. Seeds were irradiated with a gamma 60Co source (Gammacell 220 GC) in the Centro de Energia Nuclear na Agricultura and the Instituto de Pesquisas Energéticas e Nucleares. Dose rate used were 1.6 and 5.8kGy/h. Applied doses were 0.0, 0.10, 0.25, 0.50, 0.75, 1.0, and 2.0kGy. After irradiation, seeds were analysed over a 6 month period. Three different detection methods were employed to determine how irradiation had modified the samples. Screening methods consisted of a germination test measuring the inhibition of shooting and rooting and analysis of DNA fragmentation. The method of electron spin resonance spectroscopy allowed a better dosimetric evaluation. These techniques make the identification of irradiated wheat with different doses possible.

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

PubMed

Sibout, Richard; Proost, Sebastian; Hansen, Bjoern Oest; Vaid, Neha; Giorgi, Federico M; Ho-Yue-Kuang, Severine; Legée, Frédéric; Cézart, Laurent; Bouchabké-Coussa, Oumaya; Soulhat, Camille; Provart, Nicholas; Pasha, Asher; Le Bris, Philippe; Roujol, David; Hofte, Herman; Jamet, Elisabeth; Lapierre, Catherine; Persson, Staffan; Mutwil, Marek

2017-08-01

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Analytical methods in sphingolipidomics: Quantitative and profiling approaches in food analysis.

PubMed

Canela, Núria; Herrero, Pol; Mariné, Sílvia; Nadal, Pedro; Ras, Maria Rosa; Rodríguez, Miguel Ángel; Arola, Lluís

2016-01-08

In recent years, sphingolipidomics has emerged as an interesting omic science that encompasses the study of the full sphingolipidome characterization, content, structure and activity in cells, tissues or organisms. Like other omics, it has the potential to impact biomarker discovery, drug development and systems biology knowledge. Concretely, dietary food sphingolipids have gained considerable importance due to their extensively reported bioactivity. Because of the complexity of this lipid family and their diversity among foods, powerful analytical methodologies are needed for their study. The analytical tools developed in the past have been improved with the enormous advances made in recent years in mass spectrometry (MS) and chromatography, which allow the convenient and sensitive identification and quantitation of sphingolipid classes and form the basis of current sphingolipidomics methodologies. In addition, novel hyphenated nuclear magnetic resonance (NMR) strategies, new ionization strategies, and MS imaging are outlined as promising technologies to shape the future of sphingolipid analyses. This review traces the analytical methods of sphingolipidomics in food analysis concerning sample extraction, chromatographic separation, the identification and quantification of sphingolipids by MS and their structural elucidation by NMR. Copyright © 2015 Elsevier B.V. All rights reserved.

An apparent Acanthamoeba genotype is the product of a chimeric 18S rDNA artifact.

PubMed

Corsaro, Daniele; Venditti, Danielle

2018-02-01

Free-living amoebae of the genus Acanthamoeba are potentially pathogenic protozoa widespread in the environment. The detection/diagnosis as well as environmental survey strategies is mainly based on the identification of the 18S rDNA sequences of the strains that allow the recovery of various distinct genotypes/subgenotypes. The accurate recording of such data is important to better know the environmental distribution of distinct genotypes and how they may be preferentially associated with disease. Recently, a putative new acanthamoebal genotype T99 was introduced, which comprises only environmental clones apparently with some anomalous features. Here, we analyze these sequences through partial treeing and BLAST analyses and find that they are actually chimeras. Our results show that the putative T99 genotype is very likely formed by chimeric sequences including a middle fragment from acanthamoebae of genotype T13, while the 5'- and 3'-end fragments came from a nematode and a cercozoan, respectively. Molecular phylogenies of Acanthamoeba including T99 are consequently erroneous as genotype T99 does not exist in nature. Careful identification of Acanthamoeba genotypes is therefore critical for both phylogenetic and diagnostic applications.

Bearing faults identification and resonant band demodulation based on wavelet de-noising methods and envelope analysis

NASA Astrophysics Data System (ADS)

Abdelrhman, Ahmed M.; Sei Kien, Yong; Salman Leong, M.; Meng Hee, Lim; Al-Obaidi, Salah M. Ali

2017-07-01

The vibration signals produced by rotating machinery contain useful information for condition monitoring and fault diagnosis. Fault severities assessment is a challenging task. Wavelet Transform (WT) as a multivariate analysis tool is able to compromise between the time and frequency information in the signals and served as a de-noising method. The CWT scaling function gives different resolutions to the discretely signals such as very fine resolution at lower scale but coarser resolution at a higher scale. However, the computational cost increased as it needs to produce different signal resolutions. DWT has better low computation cost as the dilation function allowed the signals to be decomposed through a tree of low and high pass filters and no further analysing the high-frequency components. In this paper, a method for bearing faults identification is presented by combing Continuous Wavelet Transform (CWT) and Discrete Wavelet Transform (DWT) with envelope analysis for bearing fault diagnosis. The experimental data was sampled by Case Western Reserve University. The analysis result showed that the proposed method is effective in bearing faults detection, identify the exact fault’s location and severity assessment especially for the inner race and outer race faults.

Differentiation and classification of phytoplasmas in the pigeon pea witches'-broom group (16SrIX): an update based on multiple gene sequence analysis.

PubMed

Lee, I-M; Bottner-Parker, K D; Zhao, Y; Bertaccini, A; Davis, R E

2012-09-01

The pigeon pea witches'-broom phytoplasma group (16SrIX) comprises diverse strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses of the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)-rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these lineages cannot be readily differentiated based on analysis of 16S rRNA gene sequences alone. The relative genetic distances among these closely related lineages were better assessed by including more variable genes [e.g. ribosomal protein (rp) and secY genes]. The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A coding system is proposed to designate each distinct rp and secY subgroup in the 16SrIX group.

Droplet microfluidic technology for single-cell high-throughput screening.

PubMed

Brouzes, Eric; Medkova, Martina; Savenelli, Neal; Marran, Dave; Twardowski, Mariusz; Hutchison, J Brian; Rothberg, Jonathan M; Link, Darren R; Perrimon, Norbert; Samuels, Michael L

2009-08-25

We present a droplet-based microfluidic technology that enables high-throughput screening of single mammalian cells. This integrated platform allows for the encapsulation of single cells and reagents in independent aqueous microdroplets (1 pL to 10 nL volumes) dispersed in an immiscible carrier oil and enables the digital manipulation of these reactors at a very high-throughput. Here, we validate a full droplet screening workflow by conducting a droplet-based cytotoxicity screen. To perform this screen, we first developed a droplet viability assay that permits the quantitative scoring of cell viability and growth within intact droplets. Next, we demonstrated the high viability of encapsulated human monocytic U937 cells over a period of 4 days. Finally, we developed an optically-coded droplet library enabling the identification of the droplets composition during the assay read-out. Using the integrated droplet technology, we screened a drug library for its cytotoxic effect against U937 cells. Taken together our droplet microfluidic platform is modular, robust, uses no moving parts, and has a wide range of potential applications including high-throughput single-cell analyses, combinatorial screening, and facilitating small sample analyses.

Microbial diversity on commercial eggs as affected by the production system. A first approach using PGM.

PubMed

Neira, Carmen; Laca, Amanda; Laca, Adriana; Díaz, Mario

2017-12-04

A novel DNA-based technique (PGM) has been employed for first time to analyse commercial eggs with the advantage of allowing an exhaustive identification of the microbiota present. Eggs from two different production systems, i.e. a free range system and a cage system, were analysed. Twenty-one and twenty-two phyla were identified on the surface of cage system and free range system eggs, respectively. In both cases, Firmicutes was the dominant phylum (representing around 50% of total phyla), being found families frequently reported to be present in the intestinal microbiota of chickens or hens, such as Clostridiaceae, Ruminococcaceae and Lachnospiraceae. Additionally, other phyla and families not previously described in association with eggshells could also be identified in this work. Most of the potential pathogenic genera associated with eggs (Salmonella, Clostridium, Helicobacter, Pseudomonas and Staphylococcus) showed higher incidence in eggs coming from cage systems than in eggs coming from free range systems, although the abundance of these genera were very low in both cases (<5% of total bacteria). Copyright © 2017 Elsevier B.V. All rights reserved.

The use of a non-invasive tool for capture-recapture studies on a seahorse Hippocampus guttulatus population.

PubMed

Correia, M; Palma, J; Koldewey, H; Andrade, J P

2014-04-01

In this study, the spot pattern in Hippocampus guttulatus was analysed using a computer programme algorithm that allowed individual comparison. This methodology was first tested in a controlled environment using 51 adult and 55 juvenile H. guttulatus. Positive matches were obtained in 86·3 and 83·6% of the adults and juveniles, respectively. In a second experiment, monthly surveys were carried out in five selected locations in the Ria Formosa Lagoon, south Portugal, over the course of a year and a total of 980 photographs were analysed. Photographed H. guttulatus were re-sighted one to nine times during the course of the survey period with an overall re-sight record of over 30%. Photo-identification was therefore shown to be a useful tool for non-invasive mark-recapture studies that can be successfully used to survey the population abundance of H. guttulatus aged 6 months or older in consecutive years. This could be of great value when considering the assessment of H. guttulatus populations and understanding changes over time. © 2014 The Fisheries Society of the British Isles.

Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

PubMed Central

Trentmann, Oliver; Haferkamp, Ilka

2013-01-01

Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

Element analysis: a wavelet-based method for analysing time-localized events in noisy time series.

PubMed

Lilly, Jonathan M

2017-04-01

A method is derived for the quantitative analysis of signals that are composed of superpositions of isolated, time-localized 'events'. Here, these events are taken to be well represented as rescaled and phase-rotated versions of generalized Morse wavelets, a broad family of continuous analytic functions. Analysing a signal composed of replicates of such a function using another Morse wavelet allows one to directly estimate the properties of events from the values of the wavelet transform at its own maxima. The distribution of events in general power-law noise is determined in order to establish significance based on an expected false detection rate. Finally, an expression for an event's 'region of influence' within the wavelet transform permits the formation of a criterion for rejecting spurious maxima due to numerical artefacts or other unsuitable events. Signals can then be reconstructed based on a small number of isolated points on the time/scale plane. This method, termed element analysis , is applied to the identification of long-lived eddy structures in ocean currents as observed by along-track measurements of sea surface elevation from satellite altimetry.

The identification of Oligo-Miocene mammalian palaeocommunities from the Riversleigh World Heritage Area, Australia and an appraisal of palaeoecological techniques

PubMed Central

Black, Karen H.; Archer, Michael; Hand, Suzanne J.

2017-01-01

Fourteen of the best sampled Oligo-Miocene local faunas from the Riversleigh World Heritage Area, north-western Queensland, Australia are analysed using classification and ordination techniques to identify potential mammalian palaeocommunities and palaeocommunity types. Abundance data for these faunas are used, for the first time, in conjunction with presence/absence data. An early Miocene Faunal Zone B and two middle Miocene Faunal Zone C palaeocommunities are recognised, as well as one palaeocommunity type. Change in palaeocommunity structure, between the early Miocene and middle Miocene, may be the result of significant climate change during the Miocene Carbon Isotope Excursion. The complexes of local faunas identified will allow researchers to use novel palaeocommunities in future analyses of Riversleigh’s fossil faunas. The utility of some palaeoecological multivariate indices and techniques is examined. The Dice index is found to outperform other binary similarity/distance coefficients, while the UPGMA algorithm is more useful than neighbour joining. Evidence is equivocal for the usefulness of presence/absence data compared to abundance. PMID:28674663

The speciation of the proteome

PubMed Central

Jungblut, Peter R; Holzhütter, Hermann G; Apweiler, Rolf; Schlüter, Hartmut

2008-01-01

Introduction In proteomics a paradox situation developed in the last years. At one side it is basic knowledge that proteins are post-translationally modified and occur in different isoforms. At the other side the protein expression concept disclaims post-translational modifications by connecting protein names directly with function. Discussion Optimal proteome coverage is today reached by bottom-up liquid chromatography/mass spectrometry. But quantification at the peptide level in shotgun or bottom-up approaches by liquid chromatography and mass spectrometry is completely ignoring that a special peptide may exist in an unmodified form and in several-fold modified forms. The acceptance of the protein species concept is a basic prerequisite for meaningful quantitative analyses in functional proteomics. In discovery approaches only top-down analyses, separating the protein species before digestion, identification and quantification by two-dimensional gel electrophoresis or protein liquid chromatography, allow the correlation between changes of a biological situation and function. Conclusion To obtain biological relevant information kinetics and systems biology have to be performed at the protein species level, which is the major challenge in proteomics today. PMID:18638390

Application of ¹H NMR for the characterisation and authentication of ''Tonda Gentile Trilobata" hazelnuts from Piedmont (Italy).

PubMed

Caligiani, Augusta; Coisson, Jean Daniel; Travaglia, Fabiano; Acquotti, Domenico; Palla, Gerardo; Palla, Luigi; Arlorio, Marco

2014-04-01

The Italian hazelnut (Corylus avellana L.) cultivar "Tonda Gentile Trilobata" (TGT) is covered by protected geographical indication "Nocciola Piemonte" and is well-known as the best-suited hazelnut for the industrial transformation into roasted kernel. The hazelnut cultivar identification is primarily based on morphological characteristics, so there is the need for more objective analytical methods for high quality hazelnut authentication. This study reports the (1)H NMR fingerprinting of raw and roasted hazelnut, with the aim of obtaining hazelnut classification based on their spectroscopic pattern. (1)H NMR analyses were carried out on polar extracts of TGT and other cultivars: the data were analysed with multivariate statistical methods. Results showed that (1)H NMR combined with chemometrics is useful to characterise the hazelnuts as a function of the cultivars, both on raw and roasted form. The classification models allowed identifying molecular markers useful to distinguish TGT from other types, among these trigonelline, amino acids and an unidentified orto-disubstituted aromatic compound. Copyright © 2013 Elsevier Ltd. All rights reserved.

Identification of a Functional Connectome for Long-Term Fear Memory in Mice

PubMed Central

Wheeler, Anne L.; Teixeira, Cátia M.; Wang, Afra H.; Xiong, Xuejian; Kovacevic, Natasa; Lerch, Jason P.; McIntosh, Anthony R.; Parkinson, John; Frankland, Paul W.

2013-01-01

Long-term memories are thought to depend upon the coordinated activation of a broad network of cortical and subcortical brain regions. However, the distributed nature of this representation has made it challenging to define the neural elements of the memory trace, and lesion and electrophysiological approaches provide only a narrow window into what is appreciated a much more global network. Here we used a global mapping approach to identify networks of brain regions activated following recall of long-term fear memories in mice. Analysis of Fos expression across 84 brain regions allowed us to identify regions that were co-active following memory recall. These analyses revealed that the functional organization of long-term fear memories depends on memory age and is altered in mutant mice that exhibit premature forgetting. Most importantly, these analyses indicate that long-term memory recall engages a network that has a distinct thalamic-hippocampal-cortical signature. This network is concurrently integrated and segregated and therefore has small-world properties, and contains hub-like regions in the prefrontal cortex and thalamus that may play privileged roles in memory expression. PMID:23300432

Five new species of entomopathogenic fungi from the Amazon and evolution of neotropical Ophiocordyceps.

PubMed

Sanjuan, Tatiana I; Franco-Molano, Ana E; Kepler, Ryan M; Spatafora, Joseph W; Tabima, Javier; Vasco-Palacios, Aída M; Restrepo, Silvia

2015-10-01

The neotropical biogeographic zone is a 'hot spot' of global biodiversity, especially for insects. Fungal pathogens of insects appear to track this diversity. However, the integration of this unique component of fungal diversity into molecular phylogenetic analyses remains sparse. The entomopathogenic fungal genus Ophiocordyceps is species rich in this region with the first descriptions dating to the early nineteenth century. In this study, material from various ecosystems throughout Colombia and Ecuador was examined. Molecular phylogenetic analyses of five nuclear loci including SSU, LSU, TEF, RPB1, and RPB2 were conducted alongside a morphological evaluation. Thirty-five specimens were examined representing fifteen different species of Ophiocordyceps, and five new species, Ophiocordyceps blattarioides, Ophiocordyceps tiputini, Ophiocordyceps araracuarensis, Ophiocordyceps fulgoromorphila, and Ophiocordyceps evansii, were described. An accurate identification of the host allowed us to conclude that host identity and host habitat are positively correlated with phylogenetic species of Ophiocordyceps and are probably strong drivers for speciation of neotropical entomopathogenic fungi. Copyright © 2015 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Functional Proteomic Analysis of Human NucleolusD⃞

PubMed Central

Scherl, Alexander; Couté, Yohann; Déon, Catherine; Callé, Aleth; Kindbeiter, Karine; Sanchez, Jean-Charles; Greco, Anna; Hochstrasser, Denis; Diaz, Jean-Jacques

2002-01-01

The notion of a “plurifunctional” nucleolus is now well established. However, molecular mechanisms underlying the biological processes occurring within this nuclear domain remain only partially understood. As a first step in elucidating these mechanisms we have carried out a proteomic analysis to draw up a list of proteins present within nucleoli of HeLa cells. This analysis allowed the identification of 213 different nucleolar proteins. This catalog complements that of the 271 proteins obtained recently by others, giving a total of ∼350 different nucleolar proteins. Functional classification of these proteins allowed outlining several biological processes taking place within nucleoli. Bioinformatic analyses permitted the assignment of hypothetical functions for 43 proteins for which no functional information is available. Notably, a role in ribosome biogenesis was proposed for 31 proteins. More generally, this functional classification reinforces the plurifunctional nature of nucleoli and provides convincing evidence that nucleoli may play a central role in the control of gene expression. Finally, this analysis supports the recent demonstration of a coupling of transcription and translation in higher eukaryotes. PMID:12429849

Acquisition and processing of data for isotope-ratio-monitoring mass spectrometry

NASA Technical Reports Server (NTRS)

Ricci, M. P.; Merritt, D. A.; Freeman, K. H.; Hayes, J. M.

1994-01-01

Methods are described for continuous monitoring of signals required for precise analyses of 13C, 18O, and 15N in gas streams containing varying quantities of CO2 and N2. The quantitative resolution (i.e. maximum performance in the absence of random errors) of these methods is adequate for determination of isotope ratios with an uncertainty of one part in 10(5); the precision actually obtained is often better than one part in 10(4). This report describes data-processing operations including definition of beginning and ending points of chromatographic peaks and quantitation of background levels, allowance for effects of chromatographic separation of isotopically substituted species, integration of signals related to specific masses, correction for effects of mass discrimination, recognition of drifts in mass spectrometer performance, and calculation of isotopic delta values. Characteristics of a system allowing off-line revision of parameters used in data reduction are described and an algorithm for identification of background levels in complex chromatograms is outlined. Effects of imperfect chromatographic resolution are demonstrated and discussed and an approach to deconvolution of signals from coeluting substances described.

Non-targeted metabolomic approach reveals urinary metabolites linked to steroid biosynthesis pathway after ingestion of citrus juice.

PubMed

Medina, S; Ferreres, F; García-Viguera, C; Horcajada, M N; Orduna, J; Savirón, M; Zurek, G; Martínez-Sanz, J M; Gil, J I; Gil-Izquierdo, A

2013-01-15

Citrus juice intake has been highlighted because of its health-promoting effects. LC-MS based metabolomics approaches are applied to obtain a better knowledge on changes in the concentration of metabolites due to its dietary intake and allow a better understanding of involved metabolic pathways. Eight volunteers daily consumed 400 mL of juice for four consecutive days and urine samples were collected before intake and 24h after each citrus juice intake. Urine samples were analysed by nanoHPLC-q-TOF, followed by principal component analysis (PCA) and Student's t-test (p<0.05). PCA showed a separation between two groups (before and after citrus juice consumption). This approach allowed the identification of four endocrine compounds (tetrahydroaldosterone-3-glucuronide, cortolone-3-glucuronide, testosterone-glucuronide and 17-hydroxyprogesterone), which belonged to the steroid biosynthesis pathway as significant metabolites upregulated by citrus juice intake. Additionally, these results confirmed the importance of using the non-targeted metabolomics technique to identify new endogenous metabolites, up- or down-regulated as a consequence of food intake. Copyright © 2012 Elsevier Ltd. All rights reserved.

Smart drugs: green shuttle or real drug?

PubMed

Cornara, L; Borghesi, B; Canali, C; Andrenacci, M; Basso, M; Federici, S; Labra, M

2013-11-01

We have combined morphological, molecular, and chemical techniques in order to identify the plant and chemical composition of some last-generation smart drugs, present on the market under the following names: Jungle Mistic Incense, B-52, Blendz, and Kratom 10x. Micromorphological analyses of botanical fragments allowed identification of epidermal cells, stomata, trichomes, starch, crystals, and pollen. DNA barcoding was carried out by the plastidial gene rbcL and the spacer trnH-psbA as universal markers. The combination of morphological and molecular data revealed a mixture of plants from different families, including aromatic species, viz., Lamiaceae and Turneraceae. GC-MS and LC-MS analyses on ethanol or methanol extracts showed the presence of synthetic cannabinoids, including JWH-250 in Jungle, JWH-122 in B-52, and JWH-073 and JWH-018 in Blendz. In Kratom 10x, only the indole alkaloid mitragynine was detected. All the identified synthetic cannabinoids, apart from mitragynine, are under the restriction of law in Italy (TU 309/90). Synthetic cannabinoid crystals were also identified by scanning electron microscopy and energy dispersive X-ray spectroscopy, which also detected other foreign organic chemicals, probably preservatives or antimycotics. In Kratom only leaf fragments from Mitragyna speciosa, containing the alkaloid mitragynine, were found. In the remaining products, aromatic plant species have mainly the role of hiding synthetic cannabinoids, thus acting as a "green shuttle" rather than as real drugs. Such a multidisciplinary approach is proposed as a method for the identification of herbal blends of uncertain composition, which are widely marketed in "headshops" and on the Internet, and represent a serious hazard to public health.

Multiple-approaches to the identification and quantification of cytochromes P450 in human liver tissue by mass spectrometry

PubMed Central

Seibert, Cathrin; Davidson, Brian R.; Fuller, Barry J.; Patterson, Laurence H.; Griffiths, William J.; Wang, Yuqin

2009-01-01

Here we report the identification and approximate quantification of cytochrome P450 (CYP) proteins in human liver microsomes as determined by nano-LC-MS/MS with application of the exponentially modified protein abundance index (emPAI) algorithm during database searching. Protocols based on 1D-gel protein separation and 2D-LC peptide separation gave comparable results. In total 18 CYP isoforms were unambiguously identified based on unique peptide matches. Further, we have determined the absolute quantity of two CYP enzymes (2E1 and 1A2) in human liver microsomes using stable-isotope dilution mass spectrometry, where microsomal proteins were separated by 1D-gel electrophoresis, digested with trypsin in the presence of either a CYP2E1- or 1A2-specific stable-isotope labelled tryptic peptide and analysed by LC-MS/MS. Using multiple reaction monitoring (MRM) for the isotope-labelled tryptic peptides and their natural unlabelled analogues quantification could be performed over the range of 0.1 – 1.5 pmol on column. Liver microsomes from four individuals were analysed for CYP2E1 giving values of 88 - 200 pmol/mg microsomal protein. The CYP1A2 content of microsomes from a further three individuals ranged from 165 – 263 pmol/mg microsomal protein. Although, in this proof-of-concept study for CYP quantification, the two CYP-isoforms were quantified from different samples, there are no practical reasons to prevent multiplexing the method to allow the quantification of multiple CYP-isoforms in a single sample. PMID:19714871

Odontogenic keratocysts in the Basal Cell Nevus (Gorlin-Goltz) Syndrome associated with paresthesia of the lower jaw: Case report, retrospective analysis of a representative Czech cohort and recommendations for the early diagnosis.

PubMed

Hubacek, Milan; Kripnerova, Tereza; Nemcikova, Michaela; Krepelová, Anna; Puchmajerova, Alena; Malikova, Marcela; Havlovicová, Markéta; Cadova, Jana; Kodet, Roman; Macek, Milan; Dostalova, Tatjana

2016-09-01

Identification of early presenting signs of the Basal Cell Nevus (BCNS; synonyme Gorlin-Goltz) syndrome, which is associated with a principal triad of multiple basal cell nevi, jaw odontogenic keratocysts, and skeletal anomalies, in stomatological and neurological practices. Proposal of multidisciplinary diagnostic algorithm comprising other medical specialists, including pathology, imaging, laboratory and molecular analyses based on the study outcomes. Case report of a male patient reporting paresthesia of their lower jaw, with right facial asymmetry (maxilla and mandible) and radiological detection of large osteolytic lesions in both jaws, including a retrospective analysis of a representative Czech cohort with BCNS from within the last decade. Clinical, imaging and laboratory analyses were carried out at a national tertiary centre. A multidisciplinary clinical approach followed by surgical management lead to the identification of odontogenic cysts, which were substantiated by histological examination. DNA sequencing of the PTCH1 gene detected a c.2929dupT resulting in p. Tyr977Leufs*16 pathogenic variant. This finding confirmed the clinical and laboraoty diagnosis of BCNS. Parental DNA analysis showed that this causal genetic defect arose de novo. Surgical management and orthodontic therapy were successful. Analysis of the reported case and retrospective data analysis provided evidence that paresthesia of the lower jaw should be considered as one of the early presenting signs of this rare disorder in stomatological and neurological practice. Obtained results allowed us to formulate recommendations for diagnostic practice in stomatology and neurology.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed.

PubMed

Martínez-Montes, Ángel M; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M; Fernández, Ana I

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0-3 Mb, for body weight, on SSC2, 3-9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.

Characterisation and confirmation of rare beta-thalassaemia mutations in the Malay, Chinese and Indian ethnic groups in Malaysia.

PubMed

Tan, Jin Ai Mary Anne; Chin, Pui See; Wong, Yean Ching; Tan, Kim Lian; Chan, Lee Lee; George, Elizabeth

2006-10-01

In Malaysia, about 4.5% of the Malay and Chinese populations are heterozygous carriers of beta-thalassaemia. The initial identification of rare beta-globin gene mutations by genomic sequencing will allow the development of simpler and cost-effective PCR-based techniques to complement the existing amplification refractory mutation system (ARMS) and gap-PCR used for the identification of beta-thalassaemia mutations. DNA from 173 beta-thalassaemia carriers and five beta-thalassaemia major patients from the Malay, Chinese and Indian ethnic groups were first analysed by ARMS and gap-PCR. Ninety-five per cent (174/183) of the 183 beta-globin genes studied were characterised using these two techiques. The remaining nine uncharacterised beta-globin genes (4.9%) were analysed using genomic sequencing of a 904 bp amplified PCR product consisting of the promoter region, exon 1, intervening sequence (IVS) 1, exon 2 and the 5' IVS2 regions of the beta-globin gene. The rare beta-globin mutations detected in the Chinese patients were CD27/28 (+C) and CD43 (GAG-TAG), and -88 (C-T) in an Indian patient. Beta-globin mutations at CD16 (-C), IVS1-1 (G-A), IVS2-1 (G-A), -86 (C-G) and Haemoglobin South Florida (CD1, GTG-ATG) were confirmed in the Malay patients. The seven rare beta-globin mutations and a rare haemoglobin variant confirmed in this study have been described in other populations but have not been previously described in Malaysian beta-thalassemia patients.

Identification of nitrate long term trends in Loire-Brittany river district (France) in connection with hydrogeological contexts, agricultural practices and water table level variations

NASA Astrophysics Data System (ADS)

Lopez, B.; Baran, N.; Bourgine, B.; Ratheau, D.

2009-04-01

The European Union (EU) has adopted directives requiring that Member States take measures to reach a "good" chemical status of water resources by the year 2015 (Water Framework Directive: WFD). Alongside, the Nitrates Directives (91/676/EEC) aims at controlling nitrogen pollution and requires Member States to identify groundwaters that contain more than 50 mg NO3 L-1 or could exceed this limit if preventive measures are not taken. In order to achieve these environmental objectives in the Loire-Brittany river basin, or to justify the non achievement of these objectives, a large dataset of nitrate concentrations (117.056 raw data distributed on 7.341 time-series) and water table level time-series (1.371.655 data distributed on 511 piezometers) is analysed from 1945 to 2007. The 156.700 sq km Loire-Brittany river basin shows various hydrogeological contexts, ranging from sedimentary aquifers to basement ones, with a few volcanic-rock aquifers. The knowledge of the evolution of agricultural practices is important in such a study and, even if this information is not locally available, agricultural practices have globally changed since the 1991 Nitrates Directives. The detailed dataset available for the Loire-Brittany basin aquifers is used to evaluate tools and to propose efficient methodologies for identifying and quantifying past and current trends in nitrate concentrations. Therefore, the challenge of this study is to propose a global and integrated approach which allows nitrate trend identifications for the whole Loire-Brittany river basin. The temporal piezometric behaviour of each aquifer is defined using geostatistical analyse of water table level time-series. This method requires the calculation of an experimental temporal variogram that can be fitted with a theoretical model valid for a large time range. Identification of contrasted behaviours (short term, annual or pluriannual water table fluctuations) allows a systematic classification of the Loire-Brittany superficial aquifers. The nitrate dataset shows too many irregularities to employ traditional time-series approaches such as linear regression trend tests. The non-parametric Mann-Kendall (MK) test is a robust statistical trend detection test that does not require verification of the normality of the dataset (Aguilar et al, 2007). Moreover, this test seems appropriate since it is less sensitive to missing or outlier data than a simple linear regression test. As the MK test can only detect monotonic trends, and as already done by Stuart et al., (2007) and Broers and Van der Grift (2004), the trend analyses are decennially partitioned in order to identify possible trend reversals for the studied period for each observation point. The trend identification is then spatialized by the use of the Kendall Regional (KR) test on homogenous zones characterized by their geology, their agricultural practices and their piezometric behaviour. The KR test, previously used by Frans and Helsel (2005) in the Columbia Basin Ground Water context, is quite similar to the MK test and consists of the creation of virtual regional boreholes using networks of boreholes located in the homogenous zones. This test allows the identification of regional monotonic trends, even in the zones where nitrate time-series are too small to detect significant trend per observation point. The MK test results show significant upward trends in nitrate concentrations in the Loire-Brittany superficial aquifers when the test is computed on the 1945-2007 period. However, the decennial MK test shows different behaviours at smaller time scale. Some zones are characterized by a constant and significant increase in nitrate concentrations since 1945 (North-East of Brittany, North of Beauce) whereas others show a trend reversal (South of Brittany, Callovo-Oxfordian marls between Le Mans and Alençon, under covered Jurassic limestone around Poitiers). Furthermore, some rare zones show an increase in nitrate concentrations that follow a significant downward trend period (Orléans). In the nineties, a transition period may have occurred with a higher proportion of upward than downward trends (82 % against 7 % respectively) for the 1980-1990 period and a lower proportion of upward than downward trends for the 2000-2007 period (37 % against 51 % respectively). Combined with the analyse of the current groundwater nitrate concentrations, the KR test reveals zones where trends in nitrate concentrations have been significantly raising with high nitrate current mean values (> 50 mg NO3 L-1). On the other hand, some zones show a significant regional downward trend since 1995 and low current nitrate concentrations (< 20 mg NO3 L-1). Causes of trend reversals cannot be determined by the MK and KR statistical trend analyses, but the cross analyse of nitrate and water table level time-series gives a hint of a positive correlation between these two variables. Evolution of nitrate concentrations in superficial aquifers may thus depend on a combined effect of changes in both agricultural practices and evolution of water table levels linked with climatic context. References Aguilar J.B., Orban P., Dassargues A., Brouyère S., (2007) - Identification of groundwater quality trends in a chalk aquifer threatened by intensive agriculture in Belgium. Hydrogeology journal 15: 1615-1627. Broers H.P., van der Grift B., (2004) - Regional monitoring of temporal changes in groundwater quality. Journal of hydrology 296: 192-220. Frans L.M., Helsel D.R. (2005) - Evaluating regional trends in ground water nitrate concentrations of the Columbia Basin Ground Water management Area, Washington. U.S. Geological Survey Scientific Investigations Report 2005-5078, 7p. Stuart M.E., Chilton P.J., Kiniiburgh D.G., Cooper D.M., (2007) - Screening for long-term trends in groundwater nitrate monitoring data. Quaterly Journal of Engineering Geology and Hydrogeology, 40: 361-376. Funding The study was funded by the Loire-Brittany River Basin Agency and from proper BRGM funds.

High-resolution proteomic profiling of spider venom: expanding the toxin diversity of Phoneutria nigriventer venom.

PubMed

Liberato, Tarcísio; Troncone, Lanfranco Ranieri Paolo; Yamashiro, Edson T; Serrano, Solange M T; Zelanis, André

2016-03-01

Here we present a proteomic characterization of Phoneutria nigriventer venom. A shotgun proteomic approach allowed the identification, for the first time, of O-glycosyl hydrolases (chitinases) in P. nigriventer venom. The electrophoretic profiles under nonreducing and reducing conditions, and protein identification by mass spectrometry, indicated the presence of oligomeric toxin structures in the venom. Complementary proteomic approaches allowed for a qualitative and semi-quantitative profiling of P. nigriventer venom complexity, expanding its known venom proteome diversity.

Galaxy triplets in Sloan Digital Sky Survey Data Release 7 - I. Catalogue

NASA Astrophysics Data System (ADS)

O'Mill, Ana Laura; Duplancic, Fernanda; García Lambas, Diego; Valotto, Carlos; Sodré, Laerte

2012-04-01

We present a new catalogue of galaxy triplets derived from the Sloan Digital Sky Survey (SDSS) Data Release 7. The identification of systems was performed considering galaxies brighter than Mr=-20.5 and imposing constraints over the projected distances, radial velocity differences of neighbouring galaxies and isolation. To improve the identification of triplets, we employed a data pixelization scheme, which allows us to handle large amounts of data as in the SDSS photometric survey. Using spectroscopic and photometric data in the redshift range 0.01 ≤z≤ 0.40, we obtain 5901 triplet candidates. We have used a mock catalogue to analyse the completeness and contamination of our methods. The results show a high level of completeness (˜80 per cent) and low contamination (˜5 per cent). By using photometric and spectroscopic data, we have also addressed the effects of fibre collisions in the spectroscopic sample. We have defined an isolation criterion considering the distance of the triplet brightest galaxy to the closest neighbour cluster, to describe a global environment, as well as the galaxies within a fixed aperture, around the triplet brightest galaxy, to measure the local environment. The final catalogue comprises 1092 isolated triplets of galaxies in the redshift range 0.01 ≤z≤ 0.40. Our results show that photometric redshifts provide very useful information, allowing us to complete the sample of nearby systems whose detection is affected by fibre collisions, as well as extending the detection of triplets to large distances, where spectroscopic redshifts are not available.

Excretory/secretory products in the Echinococcus granulosus metacestode: is the intermediate host complacent with infection caused by the larval form of the parasite?

PubMed

Santos, Guilherme B Dos; Monteiro, Karina M; da Silva, Edileuza Danieli; Battistella, Maria Eduarda; Ferreira, Henrique B; Zaha, Arnaldo

2016-12-01

The genus Echinococcus consists of parasites that have a life cycle with two mammalian hosts. Their larval stage, called the hydatid cyst, develops predominantly in the liver and lungs of intermediate hosts. The hydatid cyst is the causative agent of cystic hydatid disease and the species Echinococcus granulosus, G1 haplotype, is responsible for the vast majority of cases in humans, cattle and sheep. Protein characterization in hydatid cysts is essential for better understanding of the host-parasite relationship and the fertility process of Echinococcus. The aims of this work were the identification and quantitative comparison of proteins found in hydatid fluid from fertile and infertile cysts from E. granulosus, in order to highlight possible mechanisms involved in cyst fertility or infertility. Hydatid fluid samples containing proteins from both E. granulosus and Bos taurus were analysed by LC-MS/MS. Our proteomic analysis of fertile and infertile cysts allowed identification of a total of 498 proteins, of which 153 proteins were exclusively identified in the fertile cyst, 271 in the infertile cyst, and 74 in both. Functional in silico analysis allowed us to highlight some important aspects: (i) clues about the possible existence of an "arms race" involving parasite and host responses in fertile and infertile cysts; (ii) a number of proteins in hydatid fluid without functional annotation or with possible alternative functions; (iii) the presence of extracellular vesicles such as exosomes, which was confirmed by transmission electron microscopy. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Metabolomic Fingerprinting of Romaneschi Globe Artichokes by NMR Spectroscopy and Multivariate Data Analysis.

PubMed

de Falco, Bruna; Incerti, Guido; Pepe, Rosa; Amato, Mariana; Lanzotti, Virginia

2016-09-01

Globe artichoke (Cynara cardunculus L. var. scolymus L. Fiori) and cardoon (Cynara cardunculus L. var. altilis DC) are sources of nutraceuticals and bioactive compounds. To apply a NMR metabolomic fingerprinting approach to Cynara cardunculus heads to obtain simultaneous identification and quantitation of the major classes of organic compounds. The edible part of 14 Globe artichoke populations, belonging to the Romaneschi varietal group, were extracted to obtain apolar and polar organic extracts. The analysis was also extended to one species of cultivated cardoon for comparison. The (1) H-NMR of the extracts allowed simultaneous identification of the bioactive metabolites whose quantitation have been obtained by spectral integration followed by principal component analysis (PCA). Apolar organic extracts were mainly based on highly unsaturated long chain lipids. Polar organic extracts contained organic acids, amino acids, sugars (mainly inulin), caffeoyl derivatives (mainly cynarin), flavonoids, and terpenes. The level of nutraceuticals was found to be highest in the Italian landraces Bianco di Pertosa zia E and Natalina while cardoon showed the lowest content of all metabolites thus confirming the genetic distance between artichokes and cardoon. Metabolomic approach coupling NMR spectroscopy with multivariate data analysis allowed for a detailed metabolite profile of artichoke and cardoon varieties to be obtained. Relevant differences in the relative content of the metabolites were observed for the species analysed. This work is the first application of (1) H-NMR with multivariate statistics to provide a metabolomic fingerprinting of Cynara scolymus. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Evolutionary genomics of miniature inverted-repeat transposable elements (MITEs) in Brassica.

PubMed

Nouroz, Faisal; Noreen, Shumaila; Heslop-Harrison, J S

2015-12-01

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in most eukaryotic genomes. We aimed to characterize various MITEs families in Brassica in terms of their presence, sequence characteristics and evolutionary activity. Dot plot analyses involving comparison of homoeologous bacterial artificial chromosome (BAC) sequences allowed identification of 15 novel families of mobile MITEs. Of which, 5 were Stowaway-like with TA Target Site Duplications (TSDs), 4 Tourist-like with TAA/TTA TSDs, 5 Mutator-like with 9-10 bp TSDs and 1 novel MITE (BoXMITE1) flanked by 3 bp TSDs. Our data suggested that there are about 30,000 MITE-related sequences in Brassica rapa and B. oleracea genomes. In situ hybridization showed one abundant family was dispersed in the A-genome, while another was located near 45S rDNA sites. PCR analysis using primers flanking sequences of MITE elements detected MITE insertion polymorphisms between and within the three Brassica (AA, BB, CC) genomes, with many insertions being specific to single genomes and others showing evidence of more recent evolutionary insertions. Our BAC sequence comparison strategy enables identification of evolutionarily active MITEs with no prior knowledge of MITE sequences. The details of MITE families reported in Brassica enable their identification, characterization and annotation. Insertion polymorphisms of MITEs and their transposition activity indicated important mechanism of genome evolution and diversification. MITE families derived from known Mariner, Harbinger and Mutator DNA transposons were discovered, as well as some novel structures. The identification of Brassica MITEs will have broad applications in Brassica genomics, breeding, hybridization and phylogeny through their use as DNA markers.

Molecular identification of Nocardia species using the sodA gene: Identificación molecular de especies de Nocardia utilizando el gen sodA.

PubMed

Sánchez-Herrera, K; Sandoval, H; Mouniee, D; Ramírez-Durán, N; Bergeron, E; Boiron, P; Sánchez-Saucedo, N; Rodríguez-Nava, V

2017-09-01

Currently for bacterial identification and classification the rrs gene encoding 16S rRNA is used as a reference method for the analysis of strains of the genus Nocardia. However, it does not have enough polymorphism to differentiate them at the species level. This fact makes it necessary to search for molecular targets that can provide better identification. The sod A gene (encoding the enzyme superoxide dismutase) has had good results in identifying species of other Actinomycetes. In this study the sod A gene is proposed for the identification and differentiation at the species level of the genus Nocardia. We used 41 type species of various collections; a 386 bp fragment of the sod A gene was amplified and sequenced, and a phylogenetic analysis was performed comparing the genes rrs (1171 bp), hsp 65 (401 bp), sec A1 (494 bp), gyr B (1195 bp) and rpo B (401 bp). The sequences were aligned using the Clustal X program. Evolutionary trees according to the neighbour-joining method were created with the programs Phylo_win and MEGA 6. The specific variability of the sod A genus of the genus Nocardia was analysed. A high phylogenetic resolution, significant genetic variability, and specificity and reliability were observed for the differentiation of the isolates at the species level. The polymorphism observed in the sod A gene sequence contains variable regions that allow the discrimination of closely related Nocardia species. The clear specificity, despite its small size, proves to be of great advantage for use in taxonomic studies and clinical diagnosis of the genus Nocardia.

Molecular Species Delimitation in the Racomitrium canescens Complex (Grimmiaceae) and Implications for DNA Barcoding of Species Complexes in Mosses

PubMed Central

Stech, Michael; Veldman, Sarina; Larraín, Juan; Muñoz, Jesús; Quandt, Dietmar; Hassel, Kristian; Kruijer, Hans

2013-01-01

In bryophytes a morphological species concept is still most commonly employed, but delimitation of closely related species based on morphological characters is often difficult. Here we test morphological species circumscriptions in a species complex of the moss genus Racomitrium, the R. canescens complex, based on variable DNA sequence markers from the plastid (rps4-trnT-trnL region) and nuclear (nrITS) genomes. The extensive morphological variability within the complex has led to different opinions about the number of species and intraspecific taxa to be distinguished. Molecular phylogenetic reconstructions allowed to clearly distinguish all eight currently recognised species of the complex plus a ninth species that was inferred to belong to the complex in earlier molecular analyses. The taxonomic significance of intraspecific sequence variation is discussed. The present molecular data do not support the division of the R. canescens complex into two groups of species (subsections or sections). Most morphological characters, albeit being in part difficult to apply, are reliable for species identification in the R. canescens complex. However, misidentification of collections that were morphologically intermediate between species questioned the suitability of leaf shape as diagnostic character. Four partitions of the molecular markers (rps4-trnT, trnT-trnL, ITS1, ITS2) that could potentially be used for molecular species identification (DNA barcoding) performed almost equally well concerning amplification and sequencing success. Of these, ITS1 provided the highest species discrimination capacity and should be considered as a DNA barcoding marker for mosses, especially in complexes of closely related species. Molecular species identification should be complemented by redefining morphological characters, to develop a set of easy-to-use molecular and non-molecular identification tools for improving biodiversity assessments and ecological research including mosses. PMID:23341927

Disentangling diatom species complexes: does morphometry suffice?

PubMed Central

Borrego-Ramos, María; Olenici, Adriana

2017-01-01

Accurate taxonomic resolution in light microscopy analyses of microalgae is essential to achieve high quality, comparable results in both floristic analyses and biomonitoring studies. A number of closely related diatom taxa have been detected to date co-occurring within benthic diatom assemblages, sharing many morphological, morphometrical and ecological characteristics. In this contribution, we analysed the hypothesis that, where a large sample size (number of individuals) is available, common morphometrical parameters (valve length, width and stria density) are sufficient to achieve a correct identification to the species level. We focused on some common diatom taxa belonging to the genus Gomphonema. More than 400 valves and frustules were photographed in valve view and measured using Fiji software. Several statistical tools (mixture and discriminant analysis, k-means clustering, classification trees, etc.) were explored to test whether mere morphometry, independently of other valve features, leads to correct identifications, when compared to identifications made by experts. In view of the results obtained, morphometry-based determination in diatom taxonomy is discouraged. PMID:29250472

Affordability of alcohol as a key driver of alcohol demand in New Zealand: a co-integration analysis.

PubMed

Wall, Martin; Casswell, Sally

2013-01-01

To investigate whether affordability of alcohol is an important determinant of alcohol consumption along with price. This will inform effective tax policy to influence consumption. Co-integration analysis was used to analyse relationship between real price, affordability and consumption. Changes in retail availability of wine in 1990 and beer in 1999 were also included in the models. The econometric approach taken allows identification of short- and long-term responses. Separate analyses were performed for wine, beer, spirits and ready-to-drinks (spirits based pre-mixed drinks). New Zealand 1988-2011. Quarterly data on price and alcohol available for consumption for wine, beer, spirits and ready-to-drinks. Price data were analysed as: real price (own price of alcohol relative to the price of other goods) and affordability (average earnings relative to own price). There was strong evidence for co-integration between wine and beer consumption and affordability. There was weaker evidence for co-integration between consumption and real price. The affordability of alcohol is more important than real price in determining consumption of alcohol. This suggests that affordability needs to be considered by policy makers when determining tax and pricing policies to reduce alcohol-related harm. © 2012 The Authors, Addiction © 2012 Society for the Study of Addiction.

Using Cluster Analysis to Compartmentalize a Large Managed Wetland Based on Physical, Biological, and Climatic Geospatial Attributes.

PubMed

Hahus, Ian; Migliaccio, Kati; Douglas-Mankin, Kyle; Klarenberg, Geraldine; Muñoz-Carpena, Rafael

2018-04-27

Hierarchical and partitional cluster analyses were used to compartmentalize Water Conservation Area 1, a managed wetland within the Arthur R. Marshall Loxahatchee National Wildlife Refuge in southeast Florida, USA, based on physical, biological, and climatic geospatial attributes. Single, complete, average, and Ward's linkages were tested during the hierarchical cluster analyses, with average linkage providing the best results. In general, the partitional method, partitioning around medoids, found clusters that were more evenly sized and more spatially aggregated than those resulting from the hierarchical analyses. However, hierarchical analysis appeared to be better suited to identify outlier regions that were significantly different from other areas. The clusters identified by geospatial attributes were similar to clusters developed for the interior marsh in a separate study using water quality attributes, suggesting that similar factors have influenced variations in both the set of physical, biological, and climatic attributes selected in this study and water quality parameters. However, geospatial data allowed further subdivision of several interior marsh clusters identified from the water quality data, potentially indicating zones with important differences in function. Identification of these zones can be useful to managers and modelers by informing the distribution of monitoring equipment and personnel as well as delineating regions that may respond similarly to future changes in management or climate.

Venom Gland Transcriptomic and Proteomic Analyses of the Enigmatic Scorpion Superstitionia donensis (Scorpiones: Superstitioniidae), with Insights on the Evolution of Its Venom Components.

PubMed

Santibáñez-López, Carlos E; Cid-Uribe, Jimena I; Batista, Cesar V F; Ortiz, Ernesto; Possani, Lourival D

2016-12-09

Venom gland transcriptomic and proteomic analyses have improved our knowledge on the diversity of the heterogeneous components present in scorpion venoms. However, most of these studies have focused on species from the family Buthidae. To gain insights into the molecular diversity of the venom components of scorpions belonging to the family Superstitioniidae, one of the neglected scorpion families, we performed a transcriptomic and proteomic analyses for the species Superstitionia donensis . The total mRNA extracted from the venom glands of two specimens was subjected to massive sequencing by the Illumina protocol, and a total of 219,073 transcripts were generated. We annotated 135 transcripts putatively coding for peptides with identity to known venom components available from different protein databases. Fresh venom collected by electrostimulation was analyzed by LC-MS/MS allowing the identification of 26 distinct components with sequences matching counterparts from the transcriptomic analysis. In addition, the phylogenetic affinities of the found putative calcins, scorpines, La1-like peptides and potassium channel κ toxins were analyzed. The first three components are often reported as ubiquitous in the venom of different families of scorpions. Our results suggest that, at least calcins and scorpines, could be used as molecular markers in phylogenetic studies of scorpion venoms.

Venom Gland Transcriptomic and Proteomic Analyses of the Enigmatic Scorpion Superstitionia donensis (Scorpiones: Superstitioniidae), with Insights on the Evolution of Its Venom Components

PubMed Central

Santibáñez-López, Carlos E.; Cid-Uribe, Jimena I.; Batista, Cesar V. F.; Ortiz, Ernesto; Possani, Lourival D.

2016-01-01

Venom gland transcriptomic and proteomic analyses have improved our knowledge on the diversity of the heterogeneous components present in scorpion venoms. However, most of these studies have focused on species from the family Buthidae. To gain insights into the molecular diversity of the venom components of scorpions belonging to the family Superstitioniidae, one of the neglected scorpion families, we performed a transcriptomic and proteomic analyses for the species Superstitionia donensis. The total mRNA extracted from the venom glands of two specimens was subjected to massive sequencing by the Illumina protocol, and a total of 219,073 transcripts were generated. We annotated 135 transcripts putatively coding for peptides with identity to known venom components available from different protein databases. Fresh venom collected by electrostimulation was analyzed by LC-MS/MS allowing the identification of 26 distinct components with sequences matching counterparts from the transcriptomic analysis. In addition, the phylogenetic affinities of the found putative calcins, scorpines, La1-like peptides and potassium channel κ toxins were analyzed. The first three components are often reported as ubiquitous in the venom of different families of scorpions. Our results suggest that, at least calcins and scorpines, could be used as molecular markers in phylogenetic studies of scorpion venoms. PMID:27941686

How effective are geometric morphometric techniques for assessing functional shape variation? An example from the great ape temporomandibular joint.

PubMed

Terhune, Claire E

2013-08-01

Functional shape analyses have long relied on the use of shape ratios to test biomechanical hypotheses. This method is powerful because of the ease with which results are interpreted, but these techniques fall short in quantifying complex morphologies that may not have a strong biomechanical foundation but may still be functionally informative. In contrast, geometric morphometric methods are continually being adopted for quantifying complex shapes, but they tend to prove inadequate in functional analyses because they have little foundation in an explicit biomechanical framework. The goal of this study was to evaluate the intersection of these two methods using the great ape temporomandibular joint as a case study. Three-dimensional coordinates of glenoid fossa and mandibular condyle shape were collected using a Microscribe digitizer. Linear distances extracted from these landmarks were analyzed using a series of one-way ANOVAs; further, the landmark configurations were analyzed using geometric morphometric techniques. Results suggest that the two methods are broadly similar, although the geometric morphometric data allow for the identification of shape differences among taxa that were not immediately apparent in the univariate analyses. Furthermore, this study suggests several new approaches for translating these shape data into a biomechanical context by adjusting the data using a biomechanically relevant variable. Copyright © 2013 Wiley Periodicals, Inc.

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities.

PubMed

Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

2015-05-01

Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single 'omes'. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure-function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. © 2015 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Infrared remote sensing of hazardous vapours: surveillance of public areas during the FIFA Football World Cup 2006

NASA Astrophysics Data System (ADS)

Harig, Roland; Matz, Gerhard; Rusch, Peter; Gerhard, Hans-Hennig; Gerhard, Jörn-Hinnrich; Schlabs, Volker

2007-04-01

The German ministry of the interior, represented by the civil defence agency BBK, established analytical task forces for the analysis of released chemicals in the case of fires, chemical accidents, terrorist attacks, or war. One of the first assignments of the task forces was the provision of analytical services during the football world cup 2006. One part of the equipment of these emergency response forces is a remote sensing system that allows identification and visualisation of hazardous clouds from long distances, the scanning infrared gas imaging system SIGIS 2. The system is based on an interferometer with a single detector element in combination with a telescope and a synchronised scanning mirror. The system allows 360° surveillance. The system is equipped with a video camera and the results of the analyses of the spectra are displayed by an overlay of a false colour image on the video image. This allows a simple evaluation of the position and the size of a cloud. The system was deployed for surveillance of stadiums and public viewing areas, where large crowds watched the games. Although no intentional or accidental releases of hazardous gases occurred in the stadiums and in the public viewing areas, the systems identified and located various foreign gases in the air.

Human identification based on cranial computed tomography scan — a case report

PubMed Central

Silva, RF; Botelho, TL; Prado, FB; Kawagushi, JT; Daruge Júnior, E; Bérzin, F

2011-01-01

Today, there is increasing use of CT scanning on a clinical basis, aiding in the diagnosis of diseases or injuries. This exam also provides important information that allows identification of individuals. This paper reports the use of a CT scan on the skull, taken when the victim was alive, for the positive identification of a victim of a traffic accident in which the fingerprint analysis was impossible. The authors emphasize that the CT scan is a tool primarily used in clinical diagnosis and may contribute significantly to forensic purpose, allowing the exploration of virtual corpses before the classic autopsy. The use of CT scans might increase the quantity and quality of information involved in the death of the person examined. PMID:21493883

Single-particle aerosol mass spectrometry for the detection and identification of chemical warfare agent simulants.

PubMed

Martin, Audrey N; Farquar, George R; Frank, Matthias; Gard, Eric E; Fergenson, David P

2007-08-15

Single-particle aerosol mass spectrometry (SPAMS) was used for the real-time detection of liquid nerve agent simulants. A total of 1000 dual-polarity time-of-flight mass spectra were obtained for micrometer-sized single particles each of dimethyl methyl phosphonate, diethyl ethyl phosphonate, diethyl phosphoramidate, and diethyl phthalate using laser fluences between 0.58 and 7.83 nJ/microm2, and mass spectral variation with laser fluence was studied. The mass spectra obtained allowed identification of single particles of the chemical warfare agent (CWA) simulants at each laser fluence used although lower laser fluences allowed more facile identification. SPAMS is presented as a promising real-time detection system for the presence of CWAs.

Comparisons of protein profiles of beech bark disease resistant and susceptible American beech (Fagus grandifolia)

PubMed Central

2013-01-01

Background Beech bark disease is an insect-fungus complex that damages and often kills American beech trees and has major ecological and economic impacts on forests of the northeastern United States and southeastern Canadian forests. The disease begins when exotic beech scale insects feed on the bark of trees, and is followed by infection of damaged bark tissues by one of the Neonectria species of fungi. Proteomic analysis was conducted of beech bark proteins from diseased trees and healthy trees in areas heavily infested with beech bark disease. All of the diseased trees had signs of Neonectria infection such as cankers or fruiting bodies. In previous tests reported elsewhere, all of the diseased trees were demonstrated to be susceptible to the scale insect and all of the healthy trees were demonstrated to be resistant to the scale insect. Sixteen trees were sampled from eight geographically isolated stands, the sample consisting of 10 healthy (scale-resistant) and 6 diseased/infested (scale-susceptible) trees. Results Proteins were extracted from each tree and analysed in triplicate by isoelectric focusing followed by denaturing gel electrophoresis. Gels were stained and protein spots identified and intensity quantified, then a statistical model was fit to identify significant differences between trees. A subset of BBD differential proteins were analysed by mass spectrometry and matched to known protein sequences for identification. Identified proteins had homology to stress, insect, and pathogen related proteins in other plant systems. Protein spots significantly different in diseased and healthy trees having no stand or disease-by-stand interaction effects were identified. Conclusions Further study of these proteins should help to understand processes critical to resistance to beech bark disease and to develop biomarkers for use in tree breeding programs and for the selection of resistant trees prior to or in early stages of BBD development in stands. Early identification of resistant trees (prior to the full disease development in an area) will allow forest management through the removal of susceptible trees and their root-sprouts prior to the onset of disease, allowing management and mitigation of costs, economic impact, and impacts on ecological systems and services. PMID:23317283

Mars Sample Return: The Next Step Required to Revolutionize Knowledge of Martian Geological and Climatological History

NASA Technical Reports Server (NTRS)

Mittlefehldt, D. W.

2012-01-01

The capability of scientific instrumentation flown on planetary orbiters and landers has made great advances since the signature Viking mission of the seventies. At some point, however, the science return from orbital remote sensing, and even in situ measurements, becomes incremental, rather than revolutionary. This is primarily caused by the low spatial resolution of such measurements, even for landed instrumentation, the incomplete mineralogical record derived from such measurements, the inability to do the detailed textural, mineralogical and compositional characterization needed to demonstrate equilibrium or reaction paths, and the lack of chronological characterization. For the foreseeable future, flight instruments will suffer from this limitation. In order to make the next revolutionary breakthrough in understanding the early geological and climatological history of Mars, samples must be available for interrogation using the full panoply of laboratory-housed analytical instrumentation. Laboratory studies of samples allow for determination of parageneses of rocks through microscopic identification of mineral assemblages, evaluation of equilibrium through electron microbeam analyses of mineral compositions and structures, determination of formation temperatures through secondary ion or thermal ionization mass spectrometry (SIMS or TIMS) analyses of stable isotope compositions. Such details are poorly constrained by orbital data (e.g. phyllosilicate formation at Mawrth Vallis), and incompletely described by in situ measurements (e.g. genesis of Burns formation sediments at Meridiani Planum). Laboratory studies can determine formation, metamorphism and/or alteration ages of samples through SIMS or TIMS of radiogenic isotope systems; a capability well-beyond flight instrumentation. Ideally, sample return should be from a location first scouted by landers such that fairly mature hypotheses have been formulated that can be tested. However, samples from clastic sediments derived from an extensive region of Mars can provide important, detailed understanding of early martian geological and climatological history. Interrogating clastic "sediments" from the Earth, Moon and asteroids has allowed discovery of new crustal units, identification of now-vanished crust, and determination of the geological history of extensive, remote regions. Returned sample of martian fluvial and/or aeolian sediments, for example from Gale crater, could be "read like a book" in terrestrial laboratories to provide truly revolutionary new insights into early martian geological and climatological evolution.

The Hemiptera (Insecta) of Canada: Constructing a Reference Library of DNA Barcodes

PubMed Central

Gwiazdowski, Rodger A.; Foottit, Robert G.; Maw, H. Eric L.; Hebert, Paul D. N.

2015-01-01

DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided. PMID:25923328

Matrix Assisted Laser Desorption Ionization Mass Fingerprinting for Identification of Acacia Gum in Microsamples from Works of Art.

PubMed

Granzotto, Clara; Sutherland, Ken

2017-03-07

This paper reports an improved method for the identification of Acacia gum in cultural heritage samples using matrix assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) after enzymatic digestion of the polysaccharide component. The analytical strategy was optimized using a reference Acacia gum (gum arabic, sp. A. senegal) and provided an unambiguous MS profile of the gum, characterized by specific and recognized oligosaccharides, from as little as 0.1 μg of material. The enhanced experimental approach with reduced detection limit was successfully applied to the analysis of naturally aged (∼80 year) gum arabic samples, pure and mixed with lead white pigment, and allowed the detection of gum arabic in samples from a late painting (1949/1954) by Georges Braque in the collection of the Art Institute of Chicago. This first application of the technique to characterize microsamples from a painting, in conjunction with analyses by gas chromatography/mass spectrometry (GC/MS), provided important insights into Braque's unusual mixed paint media that are also helpful to inform appropriate conservation treatments for his works. The robustness of the analytical strategy due to the reproducibility of the gum MS profile, even in the presence of other organic and inorganic components, together with the minimal sample size required, demonstrate the value of this new MALDI-TOF MS method as an analytical tool for the identification of gum arabic in microsamples from museum artifacts.

Vital area identification for U.S. Nuclear Regulatory Commission nuclear power reactor licensees and new reactor applicants.

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

Whitehead, Donnie Wayne; Varnado, G. Bruce

2008-09-01

U.S. Nuclear Regulatory Commission nuclear power plant licensees and new reactor applicants are required to provide protection of their plants against radiological sabotage, including the placement of vital equipment in vital areas. This document describes a systematic process for the identification of the minimum set of areas that must be designated as vital areas in order to ensure that all radiological sabotage scenarios are prevented. Vital area identification involves the use of logic models to systematically identify all of the malicious acts or combinations of malicious acts that could lead to radiological sabotage. The models available in the plant probabilisticmore » risk assessment and other safety analyses provide a great deal of the information and basic model structure needed for the sabotage logic model. Once the sabotage logic model is developed, the events (or malicious acts) in the model are replaced with the areas in which the events can be accomplished. This sabotage area logic model is then analyzed to identify the target sets (combinations of areas the adversary must visit to cause radiological sabotage) and the candidate vital area sets (combinations of areas that must be protected against adversary access to prevent radiological sabotage). Any one of the candidate vital area sets can be selected for protection. Appropriate selection criteria will allow the licensee or new reactor applicant to minimize the impacts of vital area protection measures on plant safety, cost, operations, or other factors of concern.« less

Application of multiplex PCR approaches for shark molecular identification: feasibility and applications for fisheries management and conservation in the Eastern Tropical Pacific.

PubMed

Caballero, S; Cardeñosa, D; Soler, G; Hyde, J

2012-03-01

Here we describe the application of new and existing multiplex PCR methodologies for shark species molecular identification. Four multiplex systems (group ID, thresher sharks, hammerhead sharks and miscellaneous shark) were employed with primers previously described and some designed in this study, which allow for species identification after running PCR products through an agarose gel. This system was implemented for samples (bodies and fins) collected from unidentified sharks landed in the port of Buenaventura and from confiscated tissues obtained from illegal fishing around the Malpelo Island Marine Protected Area, Pacific Coast of Colombia. This method has allowed reliable identification, to date, of 407 samples to the genus and/or species levels, most of them (380) identified as the pelagic thresher shark (Alopias pelagicus). Another seven samples were identified as scalloped hammerhead sharks (Sphyrna lewini). This is an easy-to-implement and reliable identification method that could even be used locally to monitor shark captures in the main fishing ports of developed and developing countries. © 2011 Blackwell Publishing Ltd.

Optimizing use of the structural chemical analyser (variable pressure FESEM-EDX Raman spectroscopy) on micro-size complex historical paintings characterization.

PubMed

Guerra, I; Cardell, C

2015-10-01

The novel Structural Chemical Analyser (hyphenated Raman spectroscopy and scanning electron microscopy equipped with an X-ray detector) is gaining popularity since it allows 3-D morphological studies and elemental, molecular, structural and electronic analyses of a single complex micro-sized sample without transfer between instruments. However, its full potential remains unexploited in painting heritage where simultaneous identification of inorganic and organic materials in paintings is critically yet unresolved. Despite benefits and drawbacks shown in literature, new challenges have to be faced analysing multifaceted paint specimens. SEM-Structural Chemical Analyser systems differ since they are fabricated ad hoc by request. As configuration influences the procedure to optimize analyses, likewise analytical protocols have to be designed ad hoc. This paper deals with the optimization of the analytical procedure of a Variable Pressure Field Emission scanning electron microscopy equipped with an X-ray detector Raman spectroscopy system to analyse historical paint samples. We address essential parameters, technical challenges and limitations raised from analysing paint stratigraphies, archaeological samples and loose pigments. We show that accurate data interpretation requires comprehensive knowledge of factors affecting Raman spectra. We tackled: (i) the in-FESEM-Raman spectroscopy analytical sequence, (ii) correlations between FESEM and Structural Chemical Analyser/laser analytical position, (iii) Raman signal intensity under different VP-FESEM vacuum modes, (iv) carbon deposition on samples under FESEM low-vacuum mode, (v) crystal nature and morphology, (vi) depth of focus and (vii) surface-enhanced Raman scattering effect. We recommend careful planning of analysis strategies prior to research which, although time consuming, guarantees reliable results. The ultimate goal of this paper is to help to guide future users of a FESEM-Structural Chemical Analyser system in order to increase applications. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

TIES: EVERYTHING YOU WANTED TO KNOW BUT WERE AFRAID TO ASK

EPA Science Inventory

Identification of stressors in aquatic systems is critical to sound assessment and management of our nation's waterways. Information from stressor identification can be useful in designing effective sediment remediation methods, assessing options for sediment disposal, allowing m...

Identification and Characterization of Soluble Factors Involved in Delayed Effects of Low Dose Radiation. Final report

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

Baulch, Janet

2013-09-11

This is a 'glue grant' that was part of a DOE Low Dose project entitled 'Identification and Characterization of Soluble Factors Involved in Delayed Effects of Low Dose Radiation'. This collaborative program has involved Drs. David L. Springer from Pacific Northwest National Laboratory (PNNL), John H. Miller from Washington State University, Tri-cities (WSU) and William F. Morgan then from the University of Maryland, Baltimore (UMB). In July 2008, Dr. Morgan moved to PNNL and Dr. Janet E. Baulch became PI for this project at University of Maryland. In November of 2008, a one year extension with no new funds wasmore » requested to complete the proteomic analyses. The project stemmed from studies in the Morgan laboratory demonstrating that genomically unstable cells secret a soluble factor or factors into the culture medium, that cause cytogenetic aberrations and apoptosis in normal parental GM10115 cells. The purpose of this project was to identify the death inducing effect (DIE) factor or factors, estimate their relative abundance, identify the cell signaling pathways involved and finally recapitulate DIE in normal cells by exogenous manipulation of putative DIE factors in culture medium. As reported in detail in the previous progress report, analysis of culture medium from the parental cell line, and stable and unstable clones demonstrated inconsistent proteomic profiles as relate to candidate DIE factors. While the proposed proteomic analyses did not provide information that would allow DIE factors to be identified, the analyses provided another important set of observations. Proteomic analysis suggested that proteins associated with the cellular response to oxidative stress and mitochondrial function were elevated in the medium from unstable clones in a manner consistent with mitochondrial dysfunction. These findings correlate with previous studies of these clones that demonstrated functional differences between the mitochondria of stable and unstable clones. These mitochondrial abnormalities in the unstable clones contributes to oxidative stress.« less

Combining ANOVA-PCA with POCHEMON to analyse micro-organism development in a polymicrobial environment.

PubMed

Geurts, Brigitte P; Neerincx, Anne H; Bertrand, Samuel; Leemans, Manja A A P; Postma, Geert J; Wolfender, Jean-Luc; Cristescu, Simona M; Buydens, Lutgarde M C; Jansen, Jeroen J

2017-04-22

Revealing the biochemistry associated to micro-organismal interspecies interactions is highly relevant for many purposes. Each pathogen has a characteristic metabolic fingerprint that allows identification based on their unique multivariate biochemistry. When pathogen species come into mutual contact, their co-culture will display a chemistry that may be attributed both to mixing of the characteristic chemistries of the mono-cultures and to competition between the pathogens. Therefore, investigating pathogen development in a polymicrobial environment requires dedicated chemometric methods to untangle and focus upon these sources of variation. The multivariate data analysis method Projected Orthogonalised Chemical Encounter Monitoring (POCHEMON) is dedicated to highlight metabolites characteristic for the interaction of two micro-organisms in co-culture. However, this approach is currently limited to a single time-point, while development of polymicrobial interactions may be highly dynamic. A well-known multivariate implementation of Analysis of Variance (ANOVA) uses Principal Component Analysis (ANOVA-PCA). This allows the overall dynamics to be separated from the pathogen-specific chemistry to analyse the contributions of both aspects separately. For this reason, we propose to integrate ANOVA-PCA with the POCHEMON approach to disentangle the pathogen dynamics and the specific biochemistry in interspecies interactions. Two complementary case studies show great potential for both liquid and gas chromatography - mass spectrometry to reveal novel information on chemistry specific to interspecies interaction during pathogen development. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Tracing the first steps of American sturgeon pioneers in Europe

USGS Publications Warehouse

Ludwig, A.; Arndt, U.; Lippold, S.; Benecke, N.; Debus, L.; King, T.L.; Matsumura, S.

2008-01-01

Background. A Baltic population of Atlantic sturgeon was founded ???1,200 years ago by migrants from North America, but after centuries of persistence, the population was extirpated in the 1960s, mainly as a result of over-harvest and habitat alterations. As there are four genetically distinct groups of Atlantic sturgeon inhabiting North American rivers today, we investigated the genetic provenance of the historic Baltic population by ancient DNA analyses using mitochondrial and nuclear markers. Results. The phylogeographic signal obtained from multilocus microsatellite DNA genotypes and mitochondrial DNA control region haplotypes, when compared to existing baseline datasets from extant populations, allowed for the identification of the region-of-origin of the North American Atlantic sturgeon founders. Moreover, statistical and simulation analyses of the multilocus genotypes allowed for the calculation of the effective number of individuals that originally founded the European population of Atlantic sturgeon. Our findings suggest that the Baltic population of A. oxyrinchus descended from a relatively small number of founders originating from the northern extent of the species' range in North America. Conclusion. These results demonstrate that the most northerly distributed North American A. oxyrinchus colonized the Baltic Sea ???1,200 years ago, suggesting that Canadian specimens should be the primary source of broodstock used for restoration in Baltic rivers. This study illustrates the great potential of patterns obtained from ancient DNA to identify population-of-origin to investigate historic genotype structure of extinct populations. ?? 2008 Ludwig et al; licensee BioMed Central Ltd.

Flow cytometric analysis of microbial contamination in food industry technological lines--initial study.

PubMed

Józwa, Wojciech; Czaczyk, Katarzyna

2012-04-02

Flow cytometry constitutes an alternative for traditional methods of microorganisms identification and analysis, including methods requiring cultivation step. It enables the detection of pathogens and other microorganisms contaminants without the need to culture microbial cells meaning that the sample (water, waste or food e.g. milk, wine, beer) may be analysed directly. This leads to a significant reduction of time required for analysis allowing monitoring of production processes and immediate reaction in case of contamination or any disruption occurs. Apart from the analysis of raw materials or products on different stages of manufacturing process, the flow cytometry seems to constitute an ideal tool for the assessment of microbial contamination on the surface of technological lines. In the present work samples comprising smears from 3 different surfaces of technological lines from fruit and vegetable processing company from Greater Poland were analysed directly with flow cytometer. The measured parameters were forward and side scatter of laser light signals allowing the estimation of microbial cell contents in each sample. Flow cytometric analysis of the surface of food industry production lines enable the preliminary evaluation of microbial contamination within few minutes from the moment of sample arrival without the need of sample pretreatment. The presented method of fl ow cytometric initial evaluation of microbial state of food industry technological lines demonstrated its potential for developing a robust, routine method for the rapid and labor-saving detection of microbial contamination in food industry.

Eyewitness Identification Reform: Data, Theory, and Due Process.

PubMed

Clark, Steven E

2012-05-01

Some commentators view my analyses (Clark, 2012, this issue) as an important step forward in assessing the costs and benefits of eyewitness identification reform. Others suggest that the trade-off between correct identifications lost and false identifications avoided is well-known; that the expected utility model is misspecified; and that the loss of correct identifications due to the use of reformed eyewitness identification procedures is irrelevant to policy decisions, as those correct identifications are the illegitimate product of suggestion and lucky guesses. Contrary to these criticisms, the loss of correct identifications has not been adequately considered in theoretical or policy matters, criticisms regarding the various utilities do not substantively change the nature of the trade-off, and the dismissal of lost correct identifications is based not on data but on an outdated theory of recognition memory. © The Author(s) 2012.

Direct analysis in real time--high resolution mass spectrometry as a valuable tool for the pharmaceutical drug development.

PubMed

Srbek, Jan; Klejdus, Bořivoj; Douša, Michal; Břicháč, Jiří; Stasiak, Pawel; Reitmajer, Josef; Nováková, Lucie

2014-12-01

In this study, direct analysis in real time-mass spectrometry (DART-MS) was assessed for the analysis of various pharmaceutical formulations with intention to summarize possible applications for the routine pharmaceutical development. As DART is an ambient ionization technique, it allows direct analysis of pharmaceutical samples in solid or liquid form without complex sample preparation, which is often the most time-consuming part of the analytical method. This makes the technique suitable for many application fields, including pharmaceutical drug development. DART mass spectra of more than twenty selected tablets and other common pharmaceutical formulations, i.e. injection solutions, ointments and suppositories developed in the pharmaceutical industry during several recent years are presented. Moreover, as thin-layer chromatography (TLC) is still very popular for the monitoring of the reactions in the synthetic chemistry, several substances were analyzed directly from the TLC plates to demonstrate the simplicity of the technique. Pure substance solutions were spotted onto a TLC plate and then analyzed with DART without separation. This was the first DART-MS study of pharmaceutical dosage forms using DART-Orbitrap combination. The duration of sample analysis by the DART-MS technique lasted several seconds, allowing enough time to collect sufficient number of data points for compound identification. The experimental setup provided excellent mass accuracy and high resolution of the mass spectra which allowed unambiguous identification of the compounds of interest. Finally, DART mass spectrometry was also used for the monitoring of the selected impurity distribution in the atorvastatin tablets. These measurements demonstrated DART to be robust ionization technique, which provided easy-to-interpret mass spectra for the broad range of compounds. DART has high-throughput potential for various types of pharmaceutical analyses and therefore eliminates the time for sample cleanup and chromatographic separation. Copyright © 2014 Elsevier B.V. All rights reserved.

Reanalysis of Korean War Anthropological Records to Support the Resolution of Cold Cases.

PubMed

Wilson, Emily K

2017-09-01

Re-investigation of previously unidentified remains from the Korean War has yielded 55 new identifications, each with corresponding records of prior anthropological analyses. This study compares biological assessments for age at death, stature, and ancestry across (i) anthropological analyses from the 1950s, (ii) recent anthropological analyses of those same sets of remains, and (iii) the reported antemortem biological information for the identified individual. A comparison of long bone measurements from both the 1950s and during reanalysis is also presented. These comparisons demonstrate commonalities and continuing patterns of errors that are useful in refining both research on Korean War cold case records and forensic anthropological analyses performed using methods developed from the 1950s identifications. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Filtrates and Residues: Chlorophyll Separation and Spectral Identification.

ERIC Educational Resources Information Center

Diehl-Jones, Susan M.

1984-01-01

Describes an experiment in which students become familiar with the organic chemistry extraction process, perform analyses by thin layer and column chromatography, and use the absorption spectrum (obtained from a spectrophotometer) for identification. List of materials needed and procedures used are provided. (JN)

20180318 - Using the US EPA's CompTox Chemistry Dashboard for structure identification and non-targeted analyses (ACS Spring)

EPA Science Inventory

The CompTox Chemistry Dashboard provides access to data for ~760,000 chemicals. High quality curated data and rich metadata facilitates mass spec analysis. “MS-Ready” processed data enables structure identification.

IFPTarget: A Customized Virtual Target Identification Method Based on Protein-Ligand Interaction Fingerprinting Analyses.

PubMed

Li, Guo-Bo; Yu, Zhu-Jun; Liu, Sha; Huang, Lu-Yi; Yang, Ling-Ling; Lohans, Christopher T; Yang, Sheng-Yong

2017-07-24

Small-molecule target identification is an important and challenging task for chemical biology and drug discovery. Structure-based virtual target identification has been widely used, which infers and prioritizes potential protein targets for the molecule of interest (MOI) principally via a scoring function. However, current "universal" scoring functions may not always accurately identify targets to which the MOI binds from the retrieved target database, in part due to a lack of consideration of the important binding features for an individual target. Here, we present IFPTarget, a customized virtual target identification method, which uses an interaction fingerprinting (IFP) method for target-specific interaction analyses and a comprehensive index (Cvalue) for target ranking. Evaluation results indicate that the IFP method enables substantially improved binding pose prediction, and Cvalue has an excellent performance in target ranking for the test set. When applied to screen against our established target library that contains 11,863 protein structures covering 2842 unique targets, IFPTarget could retrieve known targets within the top-ranked list and identified new potential targets for chemically diverse drugs. IFPTarget prediction led to the identification of the metallo-β-lactamase VIM-2 as a target for quercetin as validated by enzymatic inhibition assays. This study provides a new in silico target identification tool and will aid future efforts to develop new target-customized methods for target identification.

Mediation, identification, and plausibility: an illustration using children's mental health services.

PubMed

Foster, E Michael

2014-10-01

Analyses of mediation are important for understanding the effects of mental health services and treatments. The most common approach is to add potential mediators as regressors and to estimate the direct and indirect effects of the treatment of interest. This practice makes the strong assumption that the mediator itself does not suffer from unobserved confounding--that it is as if randomly assigned. In many instances, this assumption seems rather implausible. The objective of this article is to describe the identification problem that represents the fundamental challenge of causal inference. It outlines how mediation complicates identification and considers several identification strategies. The goal of this article is not to propose a new method for handling mediation or to identify a best method for doing so. The latter, in fact, is impossible. The contribution of the article is to illustrate how one can think about possible approaches to mediation in the context of a specific empirical study. Using data from a large evaluation of a demonstration project in children's mental health services (n = 763), the article illustrates identification strategies. That demonstration improved service delivery in several ways but primarily by offering services "intermediate" between inpatient and outpatient. These analyses focus on the impact of these intermediate services on 6-month improvement in a behavior checklist commonly used to measure psychopathology and competence among children and youths. The results highlight how different identification strategies produce different answers to key questions. These alternative findings have to be assessed in light of substantive knowledge of the program involved. The analyses generally support the notion that children and youths treated at the demonstration site who received intermediate services benefited from them. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Integrative taxonomy of anisakid nematodes in stranded cetaceans from Brazilian waters: an update on parasite's hosts and geographical records.

PubMed

Di Azevedo, Maria Isabel N; Carvalho, Vitor L; Iñiguez, Alena M

2017-11-01

Anisakidae are represented mainly by species of Anisakis Dujardin, 1845, Pseudoterranova Krabbe, 1878, and Contracaecum Railliet and Henry, 1913. Integrative taxonomy, based on morphological and genetic approaches, can provide a precise identification of species, increasing the knowledge of their systematics, biology, and evolution. In this study, integrative taxonomy was applied in order to identify, at generic and/or specific taxonomic level, 245 anisakids from 63 cetaceans of 12 different species, which stranded in the Brazilian coast. Parasites from nine hosts were preserved by freezing and, from 54 hosts, were fixed in 70% ethanol (n = 43) or alcohol-formalin-acetic (n = 11) for a period varying from 6 to 19 years. The morphological analysis allowed the identification of 171 specimens at genus level: 120 as Anisakis sp. clade I, 47 as Anisakis sp. clade II, and four as Pseudoterranova sp. From those 15, specimens were identified at species level, seven as Anisakis typica, seven as Anisakis paggiae and one as Anisakis brevispiculata. Moreover, 74 specimens were identified as belonging to Anisakidae family. The genetic analysis based on cox2 gene allowed the identification/confirmation of Anisakis typica (n = 33), Anisakis paggiae (n = 1), and for the first time in the Brazilian coast, Anisakis brevispiculata (n = 4) and Anisakis ziphidarum (n = 1). Additionally, a probably new Anisakis species, genetically close to A. paggiae, is reported infecting a dwarf sperm whale. The results clearly indicated that the preservation of nematodes influenced significantly on the level of taxonomic definition, in both morphological and, mainly, genetic analyses. Pseudoterranova sp. was identified for the first time in the spinner dolphin, Stenella longirostris. The detection of nine A. paggiae specimens, in three Kogia breviceps animals, substantiates the austral occurrence of this species. The identification of A. brevispiculata in Kogia sima and K. breviceps confirms Kogiidae whales as their most common hosts. Anisakis typica was corroborated as a generalist species, the most widely distributed in the Brazilian coast, infecting a broad variety of Delphinidae and Kogiidae, with two new geographical records in Stenella frontalis and Lagenodelphis hosei. The study showed a new scenery of parasite diversity of marine anisakids, updating the Anisakis species distribution.

Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates.

PubMed

da Cunha, Keith C; Riat, Arnaud; Normand, Anne-Cecile; Bosshard, Philipp P; de Almeida, Margarete T G; Piarroux, Renaud; Schrenzel, Jacques; Fontao, Lionel

2018-05-15

Dermatophytes cause human infections limited to keratinized tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/ testing a panel of mass spectrum produced with strains genotypically identified and, 2/ comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The verbal facilitation effect: re-reading person descriptions as a system variable to improve identification performance.

PubMed

Sporer, Siegfried L; Kaminski, Kristina S; Davids, Maike C; McQuiston, Dawn

2016-11-01

When witnesses report a crime, police usually ask for a description of the perpetrator. Several studies suggested that verbalising faces leads to a detriment in identification performance (verbal overshadowing effect [VOE]) but the effect has been difficult to replicate. Here, we sought to reverse the VOE by inducing context reinstatement as a system variable through re-reading one's own description before an identification task. Participants (N = 208) watched a video film and were then dismissed (control group), only described the perpetrator, or described and later re-read their own descriptions before identification in either target-present or target-absent lineups after a 2-day or a 5-week delay. Identification accuracy was significantly higher after re-reading (85.0%) than in the no description control group (62.5%) irrespective of target presence. Data were internally replicated using a second target and corroborated by several small meta-analyses. Identification accuracy was related to description quality. Moreover, there was a tendency towards a verbal facilitation effect (VFE) rather than a VOE. Receiver operating characteristic (ROC) curve analyses confirm that our findings are not due to a shift in response bias but truly reflect improvement of recognition performance. Differences in the ecological validity of study paradigms are discussed.

Reducing time to identification of aerobic bacteria and fastidious micro-organisms in positive blood cultures.

PubMed

Intra, J; Sala, M R; Falbo, R; Cappellini, F; Brambilla, P

2016-12-01

Rapid and early identification of micro-organisms in blood has a key role in the diagnosis of a febrile patient, in particular, in guiding the clinician to define the correct antibiotic therapy. This study presents a simple and very fast method with high performances for identifying bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) after only 4 h of incubation. We used early bacterial growth on PolyViteX chocolate agar plates inoculated with five drops of blood-broth medium deposited in the same point and spread with a sterile loop, followed by a direct transfer procedure on MALDI-TOF MS target slides without additional modification. Ninety-nine percentage of aerobic bacteria were correctly identified from 600 monomicrobial-positive blood cultures. This procedure allowed obtaining the correct identification of fastidious pathogens, such as Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae that need complex nutritional and environmental requirements in order to grow. Compared to the traditional pathogen identification from blood cultures that takes over 24 h, the reliability of results, rapid performance and suitability of this protocol allowed a more rapid administration of optimal antimicrobial treatment in the patients. Bloodstream infections are serious conditions with a high mortality and morbidity rate. Rapid identification of pathogens and appropriate antimicrobial therapy have a key role for successful patient outcome. In this work, we developed a rapid, simplified, accurate, and efficient method, reaching 99 % identification of aerobic bacteria from monomicrobial-positive blood cultures by using early growth on enriched medium, direct transfer to target plate without additional procedures, matrix-assisted laser desorption ionization-time of flight mass spectrometry and SARAMIS database. The application of this protocol allows to anticipate appropriate antibiotic therapy. © 2016 The Society for Applied Microbiology.

A Comparison of three chromatographic retention time prediction models (ACS 2017 Fall meeting 2 of 3)

EPA Science Inventory

High resolution mass spectrometry (HRMS) data has revolutionized the identification of environmental contaminants through non-targeted analyses (NTA). However, data processing and chemical identification and prioritization remain challenging due to the vast number of unknowns ob...

Visual Recognition Software for Binary Classification and its Application to Pollen Identification

NASA Astrophysics Data System (ADS)

Punyasena, S. W.; Tcheng, D. K.; Nayak, A.

2014-12-01

An underappreciated source of uncertainty in paleoecology is the uncertainty of palynological identifications. The confidence of any given identification is not regularly reported in published results, so cannot be incorporated into subsequent meta-analyses. Automated identifications systems potentially provide a means of objectively measuring the confidence of a given count or single identification, as well as a mechanism for increasing sample sizes and throughput. We developed the software ARLO (Automated Recognition with Layered Optimization) to tackle difficult visual classification problems such as pollen identification. ARLO applies pattern recognition and machine learning to the analysis of pollen images. The features that the system discovers are not the traditional features of pollen morphology. Instead, general purpose image features, such as pixel lines and grids of different dimensions, size, spacing, and resolution, are used. ARLO adapts to a given problem by searching for the most effective combination of feature representation and learning strategy. We present a two phase approach which uses our machine learning process to first segment pollen grains from the background and then classify pollen pixels and report species ratios. We conducted two separate experiments that utilized two distinct sets of algorithms and optimization procedures. The first analysis focused on reconstructing black and white spruce pollen ratios, training and testing our classification model at the slide level. This allowed us to directly compare our automated counts and expert counts to slides of known spruce ratios. Our second analysis focused on maximizing classification accuracy at the individual pollen grain level. Instead of predicting ratios of given slides, we predicted the species represented in a given image window. The resulting analysis was more scalable, as we were able to adapt the most efficient parts of the methodology from our first analysis. ARLO was able to distinguish between the pollen of black and white spruce with an accuracy of ~83.61%. This compared favorably to human expert performance. At the writing of this abstract, we are also experimenting with experimenting with the analysis of higher diversity samples, including modern tropical pollen material collected from ground pollen traps.

Bayesian operational modal analysis with asynchronous data, Part II: Posterior uncertainty

NASA Astrophysics Data System (ADS)

Zhu, Yi-Chen; Au, Siu-Kui

2018-01-01

A Bayesian modal identification method has been proposed in the companion paper that allows the most probable values of modal parameters to be determined using asynchronous ambient vibration data. This paper investigates the identification uncertainty of modal parameters in terms of their posterior covariance matrix. Computational issues are addressed. Analytical expressions are derived to allow the posterior covariance matrix to be evaluated accurately and efficiently. Synthetic, laboratory and field data examples are presented to verify the consistency, investigate potential modelling error and demonstrate practical applications.

Size and species diversity of zooplankton communities in fluctuating Mediterranean salt marshes

NASA Astrophysics Data System (ADS)

Brucet, Sandra; Boix, Dani; López-Flores, Rocío; Badosa, Anna; Quintana, Xavier D.

2006-04-01

Differences in size and species diversity were analysed in a zooplankton community of a Mediterranean salt marsh (Empordà wetlands, NE Iberian Peninsula), where the dominance of a single species was frequent. In the permanent salt marsh, species diversity and size diversity had similar patterns along zooplankton succession. In the temporary salt marsh species diversity was high after flooding and diminished once water inputs ceased. As species diversity declined size diversity increased. Eventually, one species of calanoid dominated the zooplankton community. The high size diversity in situations of calanoid dominance was possibly due to the co-occurrence of different developmental stages, each of which have different diets. Size diversity would thus indicate trophic niche segregation among different sizes. The combined use of species and size diversity values allows the identification of the successional phases.

The High-Throughput Analyses Era: Are We Ready for the Data Struggle?

PubMed

D'Argenio, Valeria

2018-03-02

Recent and rapid technological advances in molecular sciences have dramatically increased the ability to carry out high-throughput studies characterized by big data production. This, in turn, led to the consequent negative effect of highlighting the presence of a gap between data yield and their analysis. Indeed, big data management is becoming an increasingly important aspect of many fields of molecular research including the study of human diseases. Now, the challenge is to identify, within the huge amount of data obtained, that which is of clinical relevance. In this context, issues related to data interpretation, sharing and storage need to be assessed and standardized. Once this is achieved, the integration of data from different -omic approaches will improve the diagnosis, monitoring and therapy of diseases by allowing the identification of novel, potentially actionably biomarkers in view of personalized medicine.

Time Series Expression Analyses Using RNA-seq: A Statistical Approach

PubMed Central

Oh, Sunghee; Song, Seongho; Grabowski, Gregory; Zhao, Hongyu; Noonan, James P.

2013-01-01

RNA-seq is becoming the de facto standard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis. PMID:23586021

Experimental design and statistical methods for improved hit detection in high-throughput screening.

PubMed

Malo, Nathalie; Hanley, James A; Carlile, Graeme; Liu, Jing; Pelletier, Jerry; Thomas, David; Nadon, Robert

2010-09-01

Identification of active compounds in high-throughput screening (HTS) contexts can be substantially improved by applying classical experimental design and statistical inference principles to all phases of HTS studies. The authors present both experimental and simulated data to illustrate how true-positive rates can be maximized without increasing false-positive rates by the following analytical process. First, the use of robust data preprocessing methods reduces unwanted variation by removing row, column, and plate biases. Second, replicate measurements allow estimation of the magnitude of the remaining random error and the use of formal statistical models to benchmark putative hits relative to what is expected by chance. Receiver Operating Characteristic (ROC) analyses revealed superior power for data preprocessed by a trimmed-mean polish method combined with the RVM t-test, particularly for small- to moderate-sized biological hits.

An analysis of Milwaukee county land use

NASA Technical Reports Server (NTRS)

Todd, W. J.; Mausel, P. E.

1973-01-01

The identification and classification of urban and suburban phenomena through analysis of remotely-acquired sensor data can provide information of great potential value to many regional analysts. Such classifications, particularly those using spectral data obtained from satellites such as the first Earth Resources Technology Satellite (ERTS-1) orbited by NASA, allow rapid frequent and accurate general land use inventories that are of value in many types of spatial analyses. In this study, Milwaukee County, Wisconsin was classified into several broad land use categories on the basis of computer analysis of four bands of ERTS spectral data (ERTS Frame Number E1017-16093). Categories identified were: (1) road-central business district, (2) grass (green vegetation), (3) suburban, (4) wooded suburb, (5) heavy industry, (6) inner city, and (7) water. Overall, 90 percent accuracy was attained in classification of these urban land use categories.

A novel approach for the quantitation of carbohydrates in mash, wort, and beer with RP-HPLC using 1-naphthylamine for precolumn derivatization.

PubMed

Rakete, Stefan; Glomb, Marcus A

2013-04-24

A novel universal method for the determination of reducing mono-, di-, and oligosaccharides in complex matrices on RP-HPLC using 1-naphthylamine for precolumn derivatization with sodium cyanoborhydride was established to study changes in the carbohydrate profile during beer brewing. Fluorescence and mass spectrometric detection enabled very sensitive analyses of beer-relevant carbohydrates. Mass spectrometry additionally allowed the identification of the molecular weight and thereby the degree of polymerization of unknown carbohydrates. Thus, carbohydrates with up to 16 glucose units were detected. Comparison demonstrated that the novel method was superior to fluorophore-assisted carbohydrate electrophoresis (FACE). The results proved the HPLC method clearly to be more powerful in regard to sensitivity and resolution. Analogous to FACE, this method was designated fluorophore-assisted carbohydrate HPLC (FAC-HPLC).

Time series expression analyses using RNA-seq: a statistical approach.

PubMed

Oh, Sunghee; Song, Seongho; Grabowski, Gregory; Zhao, Hongyu; Noonan, James P

2013-01-01

RNA-seq is becoming the de facto standard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis.

Airborne mapping of chemical plumes in the aftermath of Hurricanes Katrina and Rita

NASA Astrophysics Data System (ADS)

Lewis, Paul E.; Thomas, Mark J.; Kroutil, Robert T.; Combs, Roger; Cummings, Alan S.; Miller, Dave; Curry, Tim; Shen, Sylvia S.

2006-05-01

Infrared airborne spectral measurements were collected over the Gulf Coast area during the aftermath of Hurricanes Katrina and Rita. These measurements allowed surveillance for potentially hazardous chemical vapor releases from industrial facilities caused by storm damage. Data was collected with a mid-longwave infrared multispectral imager and a hyperspectral Fourier transform infrared spectrometer operating in a low altitude aircraft. Signal processing allowed detection and identification of targeted spectral signatures in the presence of interferents, atmospheric contributions, and thermal clutter. Results confirmed the presence of a number of chemical vapors. All detection results were immediately passed along to emergency first responders on the ground. The chemical identification, location, and vapor species concentration information were used by the emergency response ground teams for identification of critical plume releases and subsequent mitigation.

First identification of O,S-diethyl Thiocarbonate in Indian Cress absolute and odor evaluation of its synthesized homologues by GC-sniffing.

PubMed

Breme, Katharina; Guillamon, Nadine; Fernandez, Xavier; Tournayre, Pascal; Brevard, Hugues; Joulain, Daniel; Berdagué, Jean Louis; Meierhenrich, Uwe J

2009-03-25

Indian cress (Tropaeolum majus L.) absolute was studied by GC-olfactometry (VIDEO-Sniff method) in order to identify odor-active aroma compounds. Because of its fruity-sulfury odor note, a compound that has never been identified in plant extracts before stood out: O,S-diethyl thiocarbonate, present at 0.1% (percentage of the total GC/FID area) in the extract. GCxGC-TOFMS allowed for a clean mass spectrum to be obtained, and isolation by preparative GC followed by NMR studies allowed its identification. Here, we report on the first detection of O,S-diethyl thiocarbonate in Indian cress absolute by GC-olfactometry/VIDEO-Sniff and on its isolation and identification. The synthesis and odor evaluation of its homologues are presented.

Nuclear DNA markers for identification of Beluga and Sterlet sturgeons and their interspecific Bester hybrid.

PubMed

Havelka, Miloš; Fujimoto, Takafumi; Hagihara, Seishi; Adachi, Shinji; Arai, Katsutoshi

2017-05-10

Sturgeons (Acipenseriformes) are among the most endangered species in the world due to fragmentation and destruction of their natural habitats and to overexploitation, mainly for highly priced caviar. This has led to the development of sturgeon culture, originally for reintroduction, but more recently for caviar production. In both cases, accurate species identification is essential. We report a new tool for accurate identification of Huso huso and Acipenser ruthenus based on nuclear DNA markers. We employed ddRAD sequencing to identify species-specific nucleotide variants, which served as specific binding sites for diagnostic primers. The primers allowed identification of Huso huso and Acipenser ruthenus as well as their discrimination from A. baerii, A. schrenckii, A. gueldenstaedtii, A. stellatus, A. persicus, A. mikadoi, A. transmontanus, and H. dauricus and identification of A. ruthenus and H. huso hybrids with these species, except hybrid between A. ruthenus and A. stellatus. The species-specific primers also allowed identification of bester (H. huso × A. ruthenus), the most commercially exploited sturgeon hybrid. The tool, based on simple PCR and gel electrophoresis, is rapid, inexpensive, and reproducible. It will contribute to conservation of remaining wild populations of A. ruthenus and H. huso, as well as to traceability of their products.

Differences in a ribosomal DNA sequence of Strongylus species allows identification of single eggs.

PubMed

Campbell, A J; Gasser, R B; Chilton, N B

1995-03-01

In the current study, molecular techniques were evaluated for the species identification of individual strongyle eggs. Adult worms of Strongylus edentatus, S. equinus and S. vulgaris were collected at necropsy from horses from Australia and the U.S.A. Genomic DNA was isolated and a ribosomal transcribed spacer (ITS-2) amplified and sequenced using polymerase chain reaction (PCR) techniques. The length of the ITS-2 sequence of S. edentatus, S. equinus and S. vulgaris ranged between 217 and 235 nucleotides. Extensive sequence analysis demonstrated a low degree (0-0.9%) of intraspecific variation in the ITS-2 for the Strongylus species examined, whereas the levels of interspecific differences (13-29%) were significantly greater. Interspecific differences in the ITS-2 sequences allowed unequivocal species identification of single worms and eggs using PCR-linked restriction fragment length polymorphism. These results demonstrate the potential of the ribosomal spacers as genetic markers for species identification of single strongyle eggs from horse faeces.

On the identifiability of inertia parameters of planar Multi-Body Space Systems

NASA Astrophysics Data System (ADS)

Nabavi-Chashmi, Seyed Yaser; Malaek, Seyed Mohammad-Bagher

2018-04-01

This work describes a new formulation to study the identifiability characteristics of Serially Linked Multi-body Space Systems (SLMBSS). The process exploits the so called "Lagrange Formulation" to develop a linear form of Equations of Motion w.r.t the system Inertia Parameters (IPs). Having developed a specific form of regressor matrix, we aim to expedite the identification process. The new approach allows analytical as well as numerical identification and identifiability analysis for different SLMBSSs' configurations. Moreover, the explicit forms of SLMBSSs identifiable parameters are derived by analyzing the identifiability characteristics of the robot. We further show that any SLMBSS designed with Variable Configurations Joint allows all IPs to be identifiable through comparing two successive identification outcomes. This feature paves the way to design new class of SLMBSS for which accurate identification of all IPs is at hand. Different case studies reveal that proposed formulation provides fast and accurate results, as required by the space applications. Further studies might be necessary for cases where planar-body assumption becomes inaccurate.

MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review).

PubMed

Kriegsmann, Jörg; Kriegsmann, Mark; Casadonte, Rita

2015-03-01

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.

Environmental life cycle assessment of methanol and electricity co-production system based on coal gasification technology.

PubMed

Śliwińska, Anna; Burchart-Korol, Dorota; Smoliński, Adam

2017-01-01

This paper presents a life cycle assessment (LCA) of greenhouse gas emissions generated through methanol and electricity co-production system based on coal gasification technology. The analysis focuses on polygeneration technologies from which two products are produced, and thus, issues related to an allocation procedure for LCA are addressed in this paper. In the LCA, two methods were used: a 'system expansion' method based on two approaches, the 'avoided burdens approach' and 'direct system enlargement' methods and an 'allocation' method involving proportional partitioning based on physical relationships in a technological process. Cause-effect relationships in the analysed production process were identified, allowing for the identification of allocation factors. The 'system expansion' method involved expanding the analysis to include five additional variants of electricity production technologies in Poland (alternative technologies). This method revealed environmental consequences of implementation for the analysed technologies. It was found that the LCA of polygeneration technologies based on the 'system expansion' method generated a more complete source of information on environmental consequences than the 'allocation' method. The analysis shows that alternative technologies chosen for generating LCA results are crucial. Life cycle assessment was performed for the analysed, reference and variant alternative technologies. Comparative analysis was performed between the analysed technologies of methanol and electricity co-production from coal gasification as well as a reference technology of methanol production from the natural gas reforming process. Copyright © 2016 Elsevier B.V. All rights reserved.

New results on finite-time parameter identification and synchronization of uncertain complex dynamical networks with perturbation

NASA Astrophysics Data System (ADS)

Zhao, Hui; Zheng, Mingwen; Li, Shudong; Wang, Weiping

2018-03-01

Some existing papers focused on finite-time parameter identification and synchronization, but provided incomplete theoretical analyses. Such works incorporated conflicting constraints for parameter identification, therefore, the practical significance could not be fully demonstrated. To overcome such limitations, the underlying paper presents new results of parameter identification and synchronization for uncertain complex dynamical networks with impulsive effect and stochastic perturbation based on finite-time stability theory. Novel results of parameter identification and synchronization control criteria are obtained in a finite time by utilizing Lyapunov function and linear matrix inequality respectively. Finally, numerical examples are presented to illustrate the effectiveness of our theoretical results.

49 CFR Appendix D to Part 236 - Independent Review of Verification and Validation

Code of Federal Regulations, 2010 CFR

2010-10-01

... standards. (f) The reviewer shall analyze all Fault Tree Analyses (FTA), Failure Mode and Effects... for each product vulnerability cited by the reviewer; (4) Identification of any documentation or... not properly followed; (6) Identification of the software verification and validation procedures, as...

Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Pole-zero form fractional model identification in frequency domain

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

Mansouri, R.; Djamah, T.; Djennoune, S.

2009-03-05

This paper deals with system identification in the frequency domain using non integer order models given in the pole-zero form. The usual identification techniques cannot be used in this case because of the non integer orders of differentiation which makes the problem strongly nonlinear. A general identification method based on Levenberg-Marquardt algorithm is developed and allows to estimate the (2n+2m+1) parameters of the model. Its application to identify the ''skin effect'' of a squirrel cage induction machine modeling is then presented.

Laser scanning cytometry as a tool for biomarker validation

NASA Astrophysics Data System (ADS)

Mittag, Anja; Füldner, Christiane; Lehmann, Jörg; Tarnok, Attila

2013-03-01

Biomarkers are essential for diagnosis, prognosis, and therapy. As diverse is the range of diseases the broad is the range of biomarkers and the material used for analysis. Whereas body fluids can be relatively easily obtained and analyzed, the investigation of tissue is in most cases more complicated. The same applies for the screening and the evaluation of new biomarkers and the estimation of the binding of biomarkers found in animal models which need to be transferred into applications in humans. The latter in particular is difficult if it recognizes proteins or cells in tissue. A better way to find suitable cellular biomarkers for immunoscintigraphy or PET analyses may be therefore the in situ analysis of the cells in the respective tissue. In this study we present a method for biomarker validation using Laser Scanning Cytometry which allows the emulation of future in vivo analysis. The biomarker validation is exemplarily shown for rheumatoid arthritis (RA) on synovial membrane. Cryosections were scanned and analyzed by phantom contouring. Adequate statistical methods allowed the identification of suitable markers and combinations. The fluorescence analysis of the phantoms allowed the discrimination between synovial membrane of RA patients and non-RA control sections by using median fluorescence intensity and the "affected area". As intensity and area are relevant parameters of in vivo imaging (e.g. PET scan) too, the presented method allows emulation of a probable outcome of in vivo imaging, i.e. the binding of the target protein and hence, the validation of the potential of the respective biomarker.

Determination of new retention indices for quick identification of essential oils compounds.

PubMed

Hérent, Marie-France; De Bie, Véronique; Tilquin, Bernard

2007-02-19

The classical methods of chromatographic identification of compounds were based on calculation of retention indices by using different stationary phases. The aim of the work was to differentiate essential oils extracted from different plant species by identification of some of their major compounds. The method of identification was based on the calculation of new retention indices of essential oils compounds fractionated on a polar chromatographic column with temperature programming system. Similar chromatograms have been obtained on the same column for one plant family with two different temperature gradients allowing the rapid identification of essential oils of different species, sub-species or chemotypes of Citrus, Mentha and Thymus.

[Impact of interactivity on identification with characters in fiction].

PubMed

Soto-Sanfiel, María T; Aymerich-Franch, Laura; Ribes Guàrdia, Francesc Xavier

2010-11-01

The effect of interactivity on identification with characters in audiovisual fiction was observed. 310 participants were asked to watch a film in one of these two conditions: 1) interactive (they selected the plot), and 2) non-interactive (they consumed the fiction in a conventional way). After watching the movie, they completed a questionnaire with the EDI scale of identification and empathy with characters, created by Igartua and Paez. The capacity to intervene in the configuration of the plot (interactivity) affected identification with characters. The results provide data about the psychology of media and interactivity in communication and allow us to understand the processes of empathy and identification with characters.

Systematics of Cladophora spp. (Chlorophyta) from North Carolina, USA, based upon morphology and DNA sequence data with a description of Cladophora subtilissima sp. nov.

PubMed

Taylor, Robin L; Bailey, Jeffrey Craig; Freshwater, David Wilson

2017-06-01

Identification of Cladophora species is challenging due to conservation of gross morphology, few discrete autapomorphies, and environmental influences on morphology. Twelve species of marine Cladophora were reported from North Carolina waters. Cladophora specimens were collected from inshore and offshore marine waters for DNA sequence and morphological analyses. The nuclear-encoded rRNA internal transcribed spacer regions (ITS) were sequenced for 105 specimens and used in molecular assisted identification. The ITS1 and ITS2 region was highly variable, and sequences were sorted into ITS Sets of Alignable Sequences (SASs). Sequencing of short hyper-variable ITS1 sections from Cladophora type specimens was used to positively identify species represented by SASs when the types were made available. Secondary structures for the ITS1 locus were also predicted for each specimen and compared to predicted structures from Cladophora sequences available in GenBank. Nine ITS SASs were identified and representative specimens chosen for phylogenetic analyses of 18S and 28S rRNA gene sequences to reveal relationships with other Cladophora species. Phylogenetic analyses indicated that marine Cladophorales were polyphyletic and separated into two clades, the Cladophora clade and the "Siphonocladales" clade. Morphological analyses were performed to assess the consistency of character states within species, and complement the DNA sequence analyses. These analyses revealed intra- and interspecific character state variation, and that combined molecular and morphological analyses were required for the identification of species. One new report, Cladophora dotyana, and one new species Cladophora subtilissima sp. nov., were revealed, and increased the biodiversity of North Carolina marine Cladophora to 14 species. © 2017 Phycological Society of America.

[Molecular biology in clinical cancer research: the example of digestive cancers].

PubMed

Lièvre, A; Laurent-Puig, P

2005-06-01

Cancer is a DNA disease characterized by uncontrolled cell proliferation due to the accumulation of genetic alterations. Recent progress in molecular biology allowed the identification of markers potentially usefull for patients management through the identification of these genetic alterations and a best understanding of chemotherapy molecular targets. Several examples in digestive oncology underline the relevance of molecular biology in clinical research. If almost all colorectal cancers (CRC) correspond to the same histopathological type (adenocarcinoma), molecular biology allowed the identification of two different molecular mechanisms of colorectal carcinogenesis: chromosomal instability characterized by recurrent allelic losses on chromosomes 17, 5, 18, 8 and 22 that contribute to the inactivation of tumor suppressor genes, and genetic instability characterized by the instability of microsatellite loci due to an alteration of DNA mismatch repair leading to the accumulation of mutations in genes involved in the control of cell cycle and apoptosis. These data are potentially interesting for the management of CRC patients. Indeed, microsatellite instability seems not only to be a good prognostic factor but also a molecular factor that can predict response to adjuvant 5-fluorouracil based chemotherapy. Therapeutic clinical trials taking into account these molecular parameters are still going on. DNA microarray-based gene expression profiling technology that allows the simultaneous analysis of thousand of tumor genes represents also an interesting approach in oncology with the recent identification of a "genetic signature" as a risk factor of tumor recurrence in stage II CRC, a setting in which the benefit of adjuvant chemotherapy remains on debate. At last, a best understanding of chemotherapy molecular targets allowed the identification of genetic markers that can predict the response and/or the toxicity of anti-cancer drugs used in gastrointestinal cancers, which could be helpful in the future to propose for each patient a personalized treatment. Mutations that can predict the response of new target therapies such as the inhibitors of the c-KIT tyrosine kinase activity in gastrointestinal stromal tumors have also been found and will allow the selection of patients who can have benefit from these new therapeutic drugs.

Visual communication interface for severe physically disabled patients

NASA Astrophysics Data System (ADS)

Savino, M. J.; Fernández, E. A.

2007-11-01

During the last years several interfaces have been developed to allow communication to those patients suffering serious physical disabilities. In this work, a computer based communication interface is presented. It was designed to allow communication to those patients that cannot use neither their hands nor their voice but they can do it through their eyes. The system monitors the eyes movements by means of a webcam. Then, by means of an Artificial Neural Network, the system allows the identification of specified position on the screen through the identification of the eyes positions. This way the user can control a virtual keyboard on a screen that allows him to write and browse the system and enables him to send e-mails, SMS, activate video/music programs and control environmental devices. A patient was simulated to evaluate the versatility of the system. Its operation was satisfactory and it allowed the evaluation of the system potential. The development of this system requires low cost elements that are easily found in the market.

Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm

USDA-ARS?s Scientific Manuscript database

Coffee is one of the most widely consumed beverages that represent a multibillion dollar global industry. Accurate identification of coffee cultivars is essential for efficient management, exchange and use of coffee genetic resources. So far a universal platform that can allow data comparison across...

COMPARATIVE IN VITRO CARDIAC TOXICITY OF PRIMARY COMBUSTION PARTICLES: IDENTIFICATION OF CAUSAL CONSTITUENTS AND MECHANISMS OF INJURY

EPA Science Inventory

Identification of causal particle characteristics and mechanisms of injury would allow linkage of particulate air pollution adverse health effects to sources. Research has examined the direct cardiovascular effects of air pollution particle constituents since previous studies dem...

Searching for the elusive gift: advances in talent identification in sport.

PubMed

Mann, David L; Dehghansai, Nima; Baker, Joseph

2017-08-01

The incentives for sport organizations to identify talented athletes from a young age continue to grow, yet effective talent identification remains a challenging task. This opinion paper examines recent advances in talent identification, focusing in particular on the emergence of new approaches that may offer promise to identify talent (e.g., small-sided games, genetic testing, and advanced statistical analyses). We appraise new multi-disciplinary and large-scale population studies of talent identification, provide a consideration of the most recent psychological predictors of performance, examine the emergence of new approaches that strive to diminish biases in talent identification, and look at the rise in interest in talent identification in Paralympic sport. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Medicinal Plants Recommended by the World Health Organization: DNA Barcode Identification Associated with Chemical Analyses Guarantees Their Quality

PubMed Central

Palhares, Rafael Melo; Gonçalves Drummond, Marcela; dos Santos Alves Figueiredo Brasil, Bruno; Pereira Cosenza, Gustavo; das Graças Lins Brandão, Maria; Oliveira, Guilherme

2015-01-01

Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO), the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions) revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines. PMID:25978064

Comparison of System Identification Techniques for the Hydraulic Manipulator Test Bed (HMTB)

NASA Technical Reports Server (NTRS)

Morris, A. Terry

1996-01-01

In this thesis linear, dynamic, multivariable state-space models for three joints of the ground-based Hydraulic Manipulator Test Bed (HMTB) are identified. HMTB, housed at the NASA Langley Research Center, is a ground-based version of the Dexterous Orbital Servicing System (DOSS), a representative space station manipulator. The dynamic models of the HMTB manipulator will first be estimated by applying nonparametric identification methods to determine each joint's response characteristics using various input excitations. These excitations include sum of sinusoids, pseudorandom binary sequences (PRBS), bipolar ramping pulses, and chirp input signals. Next, two different parametric system identification techniques will be applied to identify the best dynamical description of the joints. The manipulator is localized about a representative space station orbital replacement unit (ORU) task allowing the use of linear system identification methods. Comparisons, observations, and results of both parametric system identification techniques are discussed. The thesis concludes by proposing a model reference control system to aid in astronaut ground tests. This approach would allow the identified models to mimic on-orbit dynamic characteristics of the actual flight manipulator thus providing astronauts with realistic on-orbit responses to perform space station tasks in a ground-based environment.

20180318 - Structure identification by Mass Spectrometry Non-Targeted Analysis using the US EPA’s CompTox Chemistry Dashboard (ACS Spring)

EPA Science Inventory

Identification of unknowns in mass spectrometry based non-targeted analyses (NTA) requires the integration of complementary pieces of data to arrive at a confident, consensus structure. Researchers use chemical reference databases, spectral matching, fragment prediction tools, r...

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae).

PubMed

von Beeren, Christoph; Maruyama, Munetoshi; Kronauer, Daniel J C

2016-01-01

Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks.

Community Sampling and Integrative Taxonomy Reveal New Species and Host Specificity in the Army Ant-Associated Beetle Genus Tetradonia (Coleoptera, Staphylinidae, Aleocharinae)

PubMed Central

von Beeren, Christoph; Maruyama, Munetoshi; Kronauer, Daniel J. C.

2016-01-01

Army ant colonies host a diverse community of arthropod symbionts. Among the best-studied symbiont communities are those of Neotropical army ants of the genus Eciton. It is clear, however, that even in these comparatively well studied systems, a large proportion of symbiont biodiversity remains unknown. Even more striking is our lack of knowledge regarding the nature and specificity of these host-symbiont interactions. Here we surveyed the diversity and host specificity of rove beetles of the genus Tetradonia Wasmann, 1894 (Staphylinidae: Aleocharinae). Systematic community sampling of 58 colonies of the six local Eciton species at La Selva Biological Station, Costa Rica, combined with an integrative taxonomic approach, allowed us to uncover species diversity, host specificity, and co-occurrence patterns of symbionts in unprecedented detail. We used an integrative taxonomic approach combining morphological and genetic analyses, to delineate species boundaries. Mitochondrial DNA barcodes were analyzed for 362 Tetradonia specimens, and additional nuclear markers for a subset of 88 specimens. All analyses supported the presence of five Tetradonia species, including two species new to science. Host specificity is highly variable across species, ranging from generalists such as T. laticeps, which parasitizes all six local Eciton species, to specialists such as T. lizonae, which primarily parasitizes a single species, E. hamatum. Here we provide a dichotomous key along with diagnostic molecular characters for identification of Tetradonia species at La Selva Biological Station. By reliably assessing biodiversity and providing tools for species identification, we hope to set the baseline for future studies of the ecological and evolutionary dynamics in these species-rich host-symbiont networks. PMID:27829037

New natural products isolated from Metarhizium robertsii ARSEF 23 by chemical screening and identification of the gene cluster through engineered biosynthesis in Aspergillus nidulans A1145.

PubMed

Kato, Hiroki; Tsunematsu, Yuta; Yamamoto, Tsuyoshi; Namiki, Takuya; Kishimoto, Shinji; Noguchi, Hiroshi; Watanabe, Kenji

2016-07-01

To rapidly identify novel natural products and their associated biosynthetic genes from underutilized and genetically difficult-to-manipulate microbes, we developed a method that uses (1) chemical screening to isolate novel microbial secondary metabolites, (2) bioinformatic analyses to identify a potential biosynthetic gene cluster and (3) heterologous expression of the genes in a convenient host to confirm the identity of the gene cluster and the proposed biosynthetic mechanism. The chemical screen was achieved by searching known natural product databases with data from liquid chromatographic and high-resolution mass spectrometric analyses collected on the extract from a target microbe culture. Using this method, we were able to isolate two new meroterpenes, subglutinols C (1) and D (2), from an entomopathogenic filamentous fungus Metarhizium robertsii ARSEF 23. Bioinformatics analysis of the genome allowed us to identify a gene cluster likely to be responsible for the formation of subglutinols. Heterologous expression of three genes from the gene cluster encoding a polyketide synthase, a prenyltransferase and a geranylgeranyl pyrophosphate synthase in Aspergillus nidulans A1145 afforded an α-pyrone-fused uncyclized diterpene, the expected intermediate of the subglutinol biosynthesis, thereby confirming the gene cluster to be responsible for the subglutinol biosynthesis. These results indicate the usefulness of our methodology in isolating new natural products and identifying their associated biosynthetic gene cluster from microbes that are not amenable to genetic manipulation. Our method should facilitate the natural product discovery efforts by expediting the identification of new secondary metabolites and their associated biosynthetic genes from a wider source of microbes.

In vitro characterization of potential CYP- and UGT-derived metabolites of the psychoactive drug 25B-NBOMe using LC-high resolution MS.

PubMed

Boumrah, Yacine; Humbert, Luc; Phanithavong, Melodie; Khimeche, Kamel; Dahmani, Abdallah; Allorge, Delphine

2016-02-01

One of the main challenges posed by the emergence of new psychoactive substances is their identification in human biological samples. Trying to detect the parent drug could lead to false-negative results when the delay between consumption and sampling has been too long. The identification of their metabolites could then improve their detection window in biological matrices. Oxidative metabolism by cytochromes P450 and glucuronidation are two major detoxification pathways in humans. In order to characterize possible CYP- and UGT-dependent metabolites of the 2-(4-bromo-2,5-dimethoxy-phenyl)-N-[(2-methoxyphenyl)methyl]ethanamine (25B-NBOMe), a synthetic psychoactive drug, analyses of human liver microsome (HLM) incubates were performed using an ultra-high performance liquid chromatography system coupled with a quadrupole-time of flight mass spectrometry detector (UHPLC-Q-TOF/MS). On-line analyses were performed using a Waters OASIS HLB column (30 x 2.1 mm, 20 µm) for the automatic sample loading and a Waters ACQUITY HSS C18 column (150 x 2 mm, 1.8 µm) for the chromatographic separation. Twenty-one metabolites, consisting of 12 CYP-derived and 9 UGT-derived metabolites, were identified. O-Desmethyl metabolites were the most abundant compounds after the phase I process, which appears to be in accordance with data from previously published NBOMe-intoxication case reports. Although other important metabolic transformations, such as sulfation, acetylation, methylation or glutathione conjugation, were not studied and artefactual metabolites might have been produced during the HLM incubation process, the record of all the metabolite MS spectra in our library should enable us to characterize relevant metabolites of 25B-NBOMe and allow us to detect 25B-MBOMe users. Copyright © 2015 John Wiley & Sons, Ltd.

Phylogeny of Comatulidae (Echinodermata: Crinoidea: Comatulida): a new classification and an assessment of morphological characters for crinoid taxonomy.

PubMed

Summers, Mindi M; Messing, Charles G; Rouse, Greg W

2014-11-01

Comatulidae Fleming, 1828 (previously, and incorrectly, Comasteridae A.H. Clark, 1908a), is a group of feather star crinoids currently divided into four accepted subfamilies, 21 genera and approximately 95 nominal species. Comatulidae is the most commonly-encountered and species-rich crinoid group on shallow tropical coral reefs, particularly in the Indo-western Pacific region (IWP). We conducted a molecular phylogenetic analysis of the group with concatenated data from up to seven genes for 43 nominal species spanning 17 genera and all subfamilies. Basal nodes returned low support, but maximum likelihood, maximum parsimony, and Bayesian analyses were largely congruent, permitting an evaluation of current taxonomy and analysis of morphological character transformations. Two of the four current subfamilies were paraphyletic, whereas 15 of the 17 included genera returned as monophyletic. We provide a new classification with two subfamilies, Comatulinae and Comatellinae n. subfamily Summers, Messing, & Rouse, the former containing five tribes. We revised membership of analyzed genera to make them all clades and erected Anneissia n. gen. Summers, Messing, & Rouse. Transformation analyses for morphological features generally used in feather star classification (e.g., ray branching patterns, articulations) and those specifically for Comatulidae (e.g., comb pinnule form, mouth placement) were labile with considerable homoplasy. These traditional characters, in combination, allow for generic diagnoses, but in most cases we did not recover apomorphies for subfamilies, tribes, and genera. New morphological characters that will be informative for crinoid taxonomy and identification are still needed. DNA sequence data currently provides the most reliable method of identification to the species-level for many taxa of Comatulidae. Copyright © 2014 Elsevier Inc. All rights reserved.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

PubMed Central

Martínez-Montes, Ángel M.; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M.

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed. PMID:29522525

Characterization of Botrytis cinerea isolates collected on pepper in Southern Turkey by using molecular markers, fungicide resistance genes and virulence assay.

PubMed

Polat, İlknur; Baysal, Ömür; Mercati, Francesco; Gümrükcü, Emine; Sülü, Görkem; Kitapcı, Aytül; Araniti, Fabrizio; Carimi, Francesco

2018-06-01

Botrytis cinerea is a polyphagous fungal pathogen causing gray mold disease. Moreover, it is one of the most destructive infections of small fruit crops such as pepper (Capsicum annnum L.). C. sativum is a species belonging to the Solanaceae family and Turkey is one of the main producers in the World. In the present work, aiming to obtain information useful for pest management, fifty B. cinerea isolates collected from Turkey and a reference isolate (B05.10) were characterized using molecular markers and fungicide resistance genes. Morphological and molecular (ITS1-ITS4) identification of B. cinerea isolates, the degree of virulence and mating types were determined. Since one or several allelic mutations in the histidine kinase (Bos1) and β-tubulin genes generally confer the resistance to fungicides, the sequences of these target genes were investigated in the selected isolates, which allowed the identification of two different haplotypes. Mating types were also determined by PCR assays using primer specific for MAT1-1 alpha gene (MAT1-1-1) and MAT1-2 HMG (MAT1-2-1) of B. cinerea. Twenty-two out of 50 isolates (44%) were MAT1-2, while 38% were MAT1-1. Interestingly, out of whole studied samples, 9 isolates (18%) were heterokaryotic or mixed colonies. In addition, cluster and population structure analyses identified five main groups and two genetic pools, respectively, underlining a good level of variability in the analysed panel. The results highlighted the presence of remarkable genetic diversity in B. cinerea isolates collected in a crucial economical area for pepper cultivation in Turkey and the data will be beneficial in view of future gray mold disease management. Copyright © 2018 Elsevier B.V. All rights reserved.

MALDI-TOF-mass spectrometry applications in clinical microbiology.

PubMed

Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

2010-11-01

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Analysis of the load selection on the error of source characteristics identification for an engine exhaust system

NASA Astrophysics Data System (ADS)

Zheng, Sifa; Liu, Haitao; Dan, Jiabi; Lian, Xiaomin

2015-05-01

Linear time-invariant assumption for the determination of acoustic source characteristics, the source strength and the source impedance in the frequency domain has been proved reasonable in the design of an exhaust system. Different methods have been proposed to its identification and the multi-load method is widely used for its convenience by varying the load number and impedance. Theoretical error analysis has rarely been referred to and previous results have shown an overdetermined set of open pipes can reduce the identification error. This paper contributes a theoretical error analysis for the load selection. The relationships between the error in the identification of source characteristics and the load selection were analysed. A general linear time-invariant model was built based on the four-load method. To analyse the error of the source impedance, an error estimation function was proposed. The dispersion of the source pressure was obtained by an inverse calculation as an indicator to detect the accuracy of the results. It was found that for a certain load length, the load resistance at the frequency points of one-quarter wavelength of odd multiples results in peaks and in the maximum error for source impedance identification. Therefore, the load impedance of frequency range within the one-quarter wavelength of odd multiples should not be used for source impedance identification. If the selected loads have more similar resistance values (i.e., the same order of magnitude), the identification error of the source impedance could be effectively reduced.

Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification.

PubMed

Masellis, Chiara; Khanal, Neelam; Kamrath, Michael Z; Clemmer, David E; Rizzo, Thomas R

2017-10-01

The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.

Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders.

PubMed

Codina-Solà, Marta; Rodríguez-Santiago, Benjamín; Homs, Aïda; Santoyo, Javier; Rigau, Maria; Aznar-Laín, Gemma; Del Campo, Miguel; Gener, Blanca; Gabau, Elisabeth; Botella, María Pilar; Gutiérrez-Arumí, Armand; Antiñolo, Guillermo; Pérez-Jurado, Luis Alberto; Cuscó, Ivon

2015-01-01

Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.

The German Chronic Kidney Disease (GCKD) study: design and methods.

PubMed

Eckardt, Kai-Uwe; Bärthlein, Barbara; Baid-Agrawal, Seema; Beck, Andreas; Busch, Martin; Eitner, Frank; Ekici, Arif B; Floege, Jürgen; Gefeller, Olaf; Haller, Hermann; Hilge, Robert; Hilgers, Karl F; Kielstein, Jan T; Krane, Vera; Köttgen, Anna; Kronenberg, Florian; Oefner, Peter; Prokosch, Hans-Ulrich; Reis, André; Schmid, Matthias; Schaeffner, Elke; Schultheiss, Ulla T; Seuchter, Susanne A; Sitter, Thomas; Sommerer, Claudia; Walz, Gerd; Wanner, Christoph; Wolf, Gunter; Zeier, Martin; Titze, Stephanie

2012-04-01

Chronic kidney disease (CKD) is increasingly recognized as a global health problem. The conditions leading to CKD, the health impact of CKD and the prognosis differ markedly between affected individuals. In particular, renal failure and cardiovascular mortality are competing risks for CKD patients. Opportunities for targeted intervention are very limited so far and require an improved understanding of the natural course of CKD, of the risk factors associated with various clinical end points and co-morbidities as well as of the underlying pathogenic mechanisms. The German Chronic Kidney Disease (GCKD) study is a prospective observational national cohort study. It aims to enrol a total of 5000 patients with CKD of various aetiologies, who are under nephrological care, and to follow them for up to 10 years. At the time of enrolment, male and female patients have an estimated glomerular filtration rate (eGFR) of 30-60 mL/min×1.73 m2 or overt proteinuria in the presence of an eGFR>60 mL/min×1.73 m2. Standardized collection of biomaterials, including DNA, serum, plasma and urine will allow identification and validation of biomarkers associated with CKD, CKD progression and related complications using hypothesis-driven and hypothesis-free approaches. Patient recruitment and follow-up is organized through a network of academic nephrology centres collaborating with practising nephrologists throughout the country. The GCKD study will establish one of the largest cohorts to date of CKD patients not requiring renal replacement therapy. Similarities in its design with other observational CKD studies, including cohorts that have already been established in the USA and Japan, will allow comparative and joint analyses to identify important ethnic and geographic differences and to enhance opportunities for identification of relevant risk factors and markers.

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

PubMed

Teo, Audrey S M; Verzotto, Davide; Yao, Fei; Nagarajan, Niranjan; Hillmer, Axel M

2015-01-01

Next-generation sequencing (NGS) technologies have changed our understanding of the variability of the human genome. However, the identification of genome structural variations based on NGS approaches with read lengths of 35-300 bases remains a challenge. Single-molecule optical mapping technologies allow the analysis of DNA molecules of up to 2 Mb and as such are suitable for the identification of large-scale genome structural variations, and for de novo genome assemblies when combined with short-read NGS data. Here we present optical mapping data for two human genomes: the HapMap cell line GM12878 and the colorectal cancer cell line HCT116. High molecular weight DNA was obtained by embedding GM12878 and HCT116 cells, respectively, in agarose plugs, followed by DNA extraction under mild conditions. Genomic DNA was digested with KpnI and 310,000 and 296,000 DNA molecules (≥ 150 kb and 10 restriction fragments), respectively, were analyzed per cell line using the Argus optical mapping system. Maps were aligned to the human reference by OPTIMA, a new glocal alignment method. Genome coverage of 6.8× and 5.7× was obtained, respectively; 2.9× and 1.7× more than the coverage obtained with previously available software. Optical mapping allows the resolution of large-scale structural variations of the genome, and the scaffold extension of NGS-based de novo assemblies. OPTIMA is an efficient new alignment method; our optical mapping data provide a resource for genome structure analyses of the human HapMap reference cell line GM12878, and the colorectal cancer cell line HCT116.

Looking at flood trends with different eyes: the value of a fuzzy flood classification scheme

NASA Astrophysics Data System (ADS)

Sikorska, A. E.; Viviroli, D.; Brunner, M. I.; Seibert, J.

2016-12-01

Natural floods can be governed by several processes such as heavy rainfall or intense snow- or glacier-melt. These processes result in different flood characteristics in terms of flood shape and magnitude. Pooling floods of different types might therefore impair the analyses of flood frequencies and trends. Thus, the categorization of flood events into different flood type classes and the determination of their respective frequencies is essential for a better understanding and for the prediction of floods. In reality however most flood events are caused by a mix of processes and a unique determination of a flood type per event often becomes difficult. This study proposes an innovative method for a more reliable categorization of floods according to similarities in flood drivers. The categorization of floods into subgroups relies on a fuzzy decision tree. While the classical (crisp) decision tree allows for the identification of only one flood type per event, the fuzzy approach enables the detection of mixed types. Hence, events are represented as a spectrum of six possible flood types, while a degree of acceptance attributed to each of them specifies the importance of each type during the event formation. Considered types are flash, short rainfall, long rainfall, snow-melt, rainfall-on-snow, and, in high altitude watersheds, also glacier-melt floods. The fuzzy concept also enables uncertainty present in the identification of flood processes and in the method to be incorporated into the flood categorization process. We demonstrate, for a set of nine Swiss watersheds and 30 years of observations, that this new concept provides more reliable flood estimates than the classical approach as it allows for a more dedicated flood prevention technique adapted to a specific flood type.

Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization.

PubMed

Wiese, Heike; Kuhlmann, Katja; Wiese, Sebastian; Stoepel, Nadine S; Pawlas, Magdalena; Meyer, Helmut E; Stephan, Christian; Eisenacher, Martin; Drepper, Friedel; Warscheid, Bettina

2014-02-07

Over the past years, phosphoproteomics has advanced to a prime tool in signaling research. Since then, an enormous amount of information about in vivo protein phosphorylation events has been collected providing a treasure trove for gaining a better understanding of the molecular processes involved in cell signaling. Yet, we still face the problem of how to achieve correct modification site localization. Here we use alternative fragmentation and different bioinformatics approaches for the identification and confident localization of phosphorylation sites. Phosphopeptide-enriched fractions were analyzed by multistage activation, collision-induced dissociation and electron transfer dissociation (ETD), yielding complementary phosphopeptide identifications. We further found that MASCOT, OMSSA and Andromeda each identified a distinct set of phosphopeptides allowing the number of site assignments to be increased. The postsearch engine SLoMo provided confident phosphorylation site localization, whereas different versions of PTM-Score integrated in MaxQuant differed in performance. Based on high-resolution ETD and higher collisional dissociation (HCD) data sets from a large synthetic peptide and phosphopeptide reference library reported by Marx et al. [Nat. Biotechnol. 2013, 31 (6), 557-564], we show that an Andromeda/PTM-Score probability of 1 is required to provide an false localization rate (FLR) of 1% for HCD data, while 0.55 is sufficient for high-resolution ETD spectra. Additional analyses of HCD data demonstrated that for phosphotyrosine peptides and phosphopeptides containing two potential phosphorylation sites, PTM-Score probability cutoff values of <1 can be applied to ensure an FLR of 1%. Proper adjustment of localization probability cutoffs allowed us to significantly increase the number of confident sites with an FLR of <1%.Our findings underscore the need for the systematic assessment of FLRs for different score values to report confident modification site localization.

Epithelial ovarian cancer: the molecular genetics of epithelial ovarian cancer.

PubMed

Krzystyniak, J; Ceppi, L; Dizon, D S; Birrer, M J

2016-04-01

Epithelial ovarian cancer (EOC) remains one of the leading causes of cancer-related deaths among women worldwide, despite gains in diagnostics and treatments made over the last three decades. Existing markers of ovarian cancer possess very limited clinical relevance highlighting the emerging need for identification of novel prognostic biomarkers as well as better predictive factors that might allow the stratification of patients who could benefit from a more targeted approach. A summary of molecular genetics of EOC. Large-scale high-throughput genomic technologies appear to be powerful tools for investigations into the genetic abnormalities in ovarian tumors, including studies on dysregulated genes and aberrantly activated signaling pathways. Such technologies can complement well-established clinical histopathology analysis and tumor grading and will hope to result in better, more tailored treatments in the future. Genomic signatures obtained by gene expression profiling of EOC may be able to predict survival outcomes and other important clinical outcomes, such as the success of surgical treatment. Finally, genomic analyses may allow for the identification of novel predictive biomarkers for purposes of treatment planning. These data combined suggest a pathway to progress in the treatment of advanced ovarian cancer and the promise of fulfilling the objective of providing personalized medicine to women with ovarian cancer. The understanding of basic molecular events in the tumorigenesis and chemoresistance of EOC together with discovery of potential biomarkers may be greatly enhanced through large-scale genomic studies. In order to maximize the impact of these technologies, however, extensive validation studies are required. © The Author 2016. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

In situ identification, pairing, and classification of meteorites from Antarctica through magnetic susceptibility measurements

NASA Astrophysics Data System (ADS)

Folco, Luigi; Rochette, Pierre; Gattacceca, JéRôMe; Perchiazzi, Natale

2006-03-01

We report on the effectiveness of using magnetic measurements in the search for meteorites on the Antarctic ice sheet, which is thus far the Earth's most productive terrain. Magnetic susceptibility measurements carried out with a pocket meter (SM30) during the 2003/04 PNRA meteorite collection expedition to northern Victoria Land (Antarctica) proved to be a rapid, sensitive, non-destructive means for the in situ identification, pairing, and classification of meteorites. In blue ice fields characterized by the presence of moraines and glacial drifts (e.g., Miller Butte, Roberts Butte, and Frontier Mountain), magnetic susceptibility measurements allowed discrimination of meteorites from abundant terrestrial stones that look like meteorites thanks to the relatively high magnetic susceptibility of the former with respect to terrestrial rocks. Comparative measurements helped identify 16 paired fragments found at Johannessen Nunataks, thereby reducing unnecessary duplication of laboratory analyses and statistical bias. Following classifications schemes developed by us in this and previous works, magnetic susceptibility measurements also helped classify stony meteorites directly in the field, thereby providing a means for selecting samples with higher research priority. A magnetic gradiometer capable of detecting perturbations in the Earth's magnetic field induced by the presence of meteorites was an efficient tool for locating meteorites buried in snow along the downwind margin of the Frontier Mountain blue ice field. Based on these results, we believe that magnetic sensors should constitute an additional payload for robotic search for meteorites on the Antarctic ice sheet and, by extension, on the surface of Mars where meteorite accumulations are predicted by theoretical works. Lastly, magnetic susceptibility data was successfully used to crosscheck the later petrographic classification of the 123 recovered meteorites, allowing the detection of misclassified or peculiar specimens.

Doping control analysis of 46 polar drugs in horse plasma and urine using a 'dilute-and-shoot' ultra high performance liquid chromatography-high resolution mass spectrometry approach.

PubMed

Kwok, Wai Him; Choi, Timmy L S; Kwok, Karen Y; Chan, George H M; Wong, Jenny K Y; Wan, Terence S M

2016-06-17

The high sensitivity of ultra high performance liquid chromatography coupled with high resolution mass spectrometry (UHPLC-HRMS) allows the identification of many prohibited substances without pre-concentration, leading to the development of simple and fast 'dilute-and-shoot' methods for doping control for human and equine sports. While the detection of polar drugs in plasma and urine is difficult using liquid-liquid or solid-phase extraction as these substances are poorly extracted, the 'dilute-and-shoot' approach is plausible. This paper describes a 'dilute-and-shoot' UHPLC-HRMS screening method to detect 46 polar drugs in equine urine and plasma, including some angiotensin-converting enzyme (ACE) inhibitors, sympathomimetics, anti-epileptics, hemostatics, the new doping agent 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR), as well as two threshold substances, namely dimethyl sulfoxide and theobromine. For plasma, the sample (200μL) was protein precipitated using trichloroacetic acid, and the resulting supernatant was diluted using Buffer A with an overall dilution factor of 3. For urine, the sample (20μL) was simply diluted 50-fold with Buffer A. The diluted plasma or urine sample was then analysed using a UHPLC-HRMS system in full-scan ESI mode. The assay was validated for qualitative identification purpose. This straightforward and reliable approach carried out in combination with other screening procedures has increased the efficiency of doping control analysis in the laboratory. Moreover, since the UHPLC-HRMS data were acquired in full-scan mode, the method could theoretically accommodate an unlimited number of existing and new doping agents, and would allow a retrospectively search for drugs that have not been targeted at the time of analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Identification and Functional Analysis of Healing Regulators in Drosophila

PubMed Central

Álvarez-Fernández, Carmen; Tamirisa, Srividya; Prada, Federico; Chernomoretz, Ariel; Podhajcer, Osvaldo; Blanco, Enrique; Martín-Blanco, Enrique

2015-01-01

Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the overall steps in wound healing, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process. However, they do allow the less understood aspects of the healing response to be explored, e.g., which signal(s) are responsible for initiating tissue remodeling? How is sealing of the epithelia achieved? Or, what inhibitory cues cancel the healing machinery upon completion? Answering these and other questions first requires the identification and functional analysis of wound specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method that is healing-permissive and that allows live imaging and biochemical analysis of cultured imaginal discs. We performed comparative genome-wide profiling between Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. Sets of potential wound-specific genes were subsequently identified. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in healing assays. This non-saturated analysis defines a relevant set of genes whose changes in expression level are functionally significant for proper tissue repair. Amongst these we identified the TCP1 chaperonin complex as a key regulator of the actin cytoskeleton essential for the wound healing response. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound healing response. PMID:25647511

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

PubMed Central

Nasheri, Neda; Petronella, Nicholas; Pagotto, Franco

2016-01-01

SUMMARY The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques. PMID:27559074

Metabolic Profiling and Identification of Shikonins in Root Periderm of Two Invasive Echium spp. Weeds in Australia.

PubMed

Skoneczny, Dominik; Weston, Paul A; Zhu, Xiaocheng; Gurr, Geoff M; Callaway, Ragan M; Barrow, Russel A; Weston, Leslie A

2017-02-21

Metabolic profiling can be successfully implemented to analyse a living system's response to environmental conditions by providing critical information on an organism's physiological state at a particular point in time and allowing for both quantitative and qualitative assessment of a specific subset(s) of key metabolites. Shikonins are highly reactive chemicals that affect various cell signalling pathways and possess antifungal, antibacterial and allelopathic activity. Based on previous bioassay results, bioactive shikonins, are likely to play important roles in the regulation of rhizosphere interactions with neighbouring plants, microbes and herbivores. An effective platform allowing for rapid identification and accurate profiling of numerous structurally similar, difficult-to-separate bioactive isohexenylnaphthazarins (shikonins) was developed using UHPLC Q-TOF MS. Root periderm tissues of the invasive Australian weeds Echium plantagineum and its congener E. vulgare were extracted overnight in ethanol for shikonin profiling. Shikonin production was evaluated at seedling, rosette and flowering stages. Five populations of each species were compared for qualitative and quantitative differences in shikonin formation. Each species showed little populational variation in qualitative shikonin production; however, shikonin was considerably low in one population of E. plantagineum from Western New South Wales . Seedlings of all populations produced the bioactive metabolite acetylshikonin and production was upregulated over time. Mature plants of both species produced significantly higher total levels of shikonins and isovalerylshikonin > dimethylacrylshikonin > shikonin > acetylshikonin in mature E. plantagineum . Although qualitative metabolic profiles in both Echium spp. were nearly identical, shikonin abundance in mature plant periderm was approximately 2.5 times higher in perennial E. vulgare extracts in comparison to those of the annual E. plantagineum. These findings contribute to our understanding of the biosynthesis of shikonins in roots of two related invasive plants and their expression in relation to plant phenological stage.

Functional expression of dental plaque microbiota.

PubMed

Peterson, Scott N; Meissner, Tobias; Su, Andrew I; Snesrud, Erik; Ong, Ana C; Schork, Nicholas J; Bretz, Walter A

2014-01-01

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.

Functional expression of dental plaque microbiota

PubMed Central

Peterson, Scott N.; Meissner, Tobias; Su, Andrew I.; Snesrud, Erik; Ong, Ana C.; Schork, Nicholas J.; Bretz, Walter A.

2014-01-01

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota. PMID:25177549

Resolution and Assignment of Differential Ion Mobility Spectra of Sarcosine and Isomers.

PubMed

Berthias, Francis; Maatoug, Belkis; Glish, Gary L; Moussa, Fathi; Maitre, Philippe

2018-04-01

Due to their central role in biochemical processes, fast separation and identification of amino acids (AA) is of importance in many areas of the biomedical field including the diagnosis and monitoring of inborn errors of metabolism and biomarker discovery. Due to the large number of AA together with their isomers and isobars, common methods of AA analysis are tedious and time-consuming because they include a chromatographic separation step requiring pre- or post-column derivatization. Here, we propose a rapid method of separation and identification of sarcosine, a biomarker candidate of prostate cancer, from isomers using differential ion mobility spectrometry (DIMS) interfaced with a tandem mass spectrometer (MS/MS) instrument. Baseline separation of protonated sarcosine from α- and β-alanine isomers can be easily achieved. Identification of DIMS peak is performed using an isomer-specific activation mode where DIMS- and mass-selected ions are irradiated at selected wavenumbers allowing for the specific fragmentation via an infrared multiple photon dissociation (IRMPD) process. Two orthogonal methods to MS/MS are thus added, where the MS/MS(IRMPD) is nothing but an isomer-specific multiple reaction monitoring (MRM) method. The identification relies on the comparison of DIMS-MS/MS(IRMPD) chromatograms recorded at different wavenumbers. Based on the comparison of IR spectra of the three isomers, it is shown that specific depletion of the two protonated α- and β-alanine can be achieved, thus allowing for clear identification of the sarcosine peak. It is also demonstrated that DIMS-MS/MS(IRMPD) spectra in the carboxylic C=O stretching region allow for the resolution of overlapping DIMS peaks. Graphical Abstract ᅟ.

Behavioral Assessment Instruments, Techniques, and Procedures: Summary and Annotated Bibliography.

ERIC Educational Resources Information Center

Shorkey, Clayton T.; Williams, Harry

This annotated bibliography cites 223 articles related to behavioral assessment reported in 18 professional journals between January 1960 and Spring 1976. A summary and a reference grouping of the articles are included to allow for identification of articles related to (1) electromechanical devices used in identification, measurement, and storage…

Seeing Stems Everywhere: Position-Independent Identification of Stem Morphemes

ERIC Educational Resources Information Center

Crepaldi, Davide; Rastle, Kathleen; Davis, Colin J.; Lupker, Stephen J.

2013-01-01

There is broad consensus that printed complex words are identified on the basis of their constituent morphemes. This fact raises the issue of how the word identification system codes for morpheme position, hence allowing it to distinguish between words like "overhang" and "hangover", and to recognize that "preheat" is…

National Plant Diagnostic Network, Taxonomic training videos: Introduction to AphID

USDA-ARS?s Scientific Manuscript database

Training is a critical part of aphid (Hemiptera: Aphididae) identification. This video provides visual instruction on the use of the expert system, AphID, for aphid examination and identification. The video demonstrates the use of different training modules that allow the user to gain familiarity wi...

Comparing metagenomic and morphological periphyton assemblage data to major environmental gradients: A pilot study from the National Rivers and Stream Assessment

EPA Science Inventory

Biomonitoring has historically utilized morphological identifications to assess biological assemblages, but in recent years, new methods have been developed that allow for faster and more complete identification of biological assemblages by DNA metabarcoding. Unlike morphologica...

50 CFR 648.75 - Cage identification.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Atlantic Surf Clam and Ocean Quahog Fisheries § 648.75 Cage identification. Link to an amendment published.... Before offloading, all cages that contain surfclams or ocean quahogs must be tagged with tags acquired...) Observers. (i) The Regional Administrator may allow the shucking of surfclams or ocean quahogs at sea if he...

Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing.

PubMed

O'Flaherty, Brigid M; Li, Yan; Tao, Ying; Paden, Clinton R; Queen, Krista; Zhang, Jing; Dinwiddie, Darrell L; Gross, Stephen M; Schroth, Gary P; Tong, Suxiang

2018-06-01

Next generation sequencing (NGS) technologies have revolutionized the genomics field and are becoming more commonplace for identification of human infectious diseases. However, due to the low abundance of viral nucleic acids (NAs) in relation to host, viral identification using direct NGS technologies often lacks sufficient sensitivity. Here, we describe an approach based on two complementary enrichment strategies that significantly improves the sensitivity of NGS-based virus identification. To start, we developed two sets of DNA probes to enrich virus NAs associated with respiratory diseases. The first set of probes spans the genomes, allowing for identification of known viruses and full genome sequencing, while the second set targets regions conserved among viral families or genera, providing the ability to detect both known and potentially novel members of those virus groups. Efficiency of enrichment was assessed by NGS testing reference virus and clinical samples with known infection. We show significant improvement in viral identification using enriched NGS compared to unenriched NGS. Without enrichment, we observed an average of 0.3% targeted viral reads per sample. However, after enrichment, 50%-99% of the reads per sample were the targeted viral reads for both the reference isolates and clinical specimens using both probe sets. Importantly, dramatic improvements on genome coverage were also observed following virus-specific probe enrichment. The methods described here provide improved sensitivity for virus identification by NGS, allowing for a more comprehensive analysis of disease etiology. © 2018 O'Flaherty et al.; Published by Cold Spring Harbor Laboratory Press.

Patient identification error among prostate needle core biopsy specimens--are we ready for a DNA time-out?

PubMed

Suba, Eric J; Pfeifer, John D; Raab, Stephen S

2007-10-01

Patient identification errors in surgical pathology often involve switches of prostate or breast needle core biopsy specimens among patients. We assessed strategies for decreasing the occurrence of these uncommon and yet potentially catastrophic events. Root cause analyses were performed following 3 cases of patient identification error involving prostate needle core biopsy specimens. Patient identification errors in surgical pathology result from slips and lapses of automatic human action that may occur at numerous steps during pre-laboratory, laboratory and post-laboratory work flow processes. Patient identification errors among prostate needle biopsies may be difficult to entirely prevent through the optimization of work flow processes. A DNA time-out, whereby DNA polymorphic microsatellite analysis is used to confirm patient identification before radiation therapy or radical surgery, may eliminate patient identification errors among needle biopsies.

Gene-expression signatures can distinguish gastric cancer grades and stages.

PubMed

Cui, Juan; Li, Fan; Wang, Guoqing; Fang, Xuedong; Puett, J David; Xu, Ying

2011-03-18

Microarray gene-expression data of 54 paired gastric cancer and adjacent noncancerous gastric tissues were analyzed, with the aim to establish gene signatures for cancer grades (well-, moderately-, poorly- or un-differentiated) and stages (I, II, III and IV), which have been determined by pathologists. Our statistical analysis led to the identification of a number of gene combinations whose expression patterns serve well as signatures of different grades and different stages of gastric cancer. A 19-gene signature was found to have discerning power between high- and low-grade gastric cancers in general, with overall classification accuracy at 79.6%. An expanded 198-gene panel allows the stratification of cancers into four grades and control, giving rise to an overall classification agreement of 74.2% between each grade designated by the pathologists and our prediction. Two signatures for cancer staging, consisting of 10 genes and 9 genes, respectively, provide high classification accuracies at 90.0% and 84.0%, among early-, advanced-stage cancer and control. Functional and pathway analyses on these signature genes reveal the significant relevance of the derived signatures to cancer grades and progression. To the best of our knowledge, this represents the first study on identification of genes whose expression patterns can serve as markers for cancer grades and stages.

On-line resources for bacterial micro-evolution studies using MLVA or CRISPR typing.

PubMed

Grissa, Ibtissem; Bouchon, Patrick; Pourcel, Christine; Vergnaud, Gilles

2008-04-01

The control of bacterial pathogens requires the development of tools allowing the precise identification of strains at the subspecies level. It is now widely accepted that these tools will need to be DNA-based assays (in contrast to identification at the species level, where biochemical based assays are still widely used, even though very powerful 16S DNA sequence databases exist). Typing assays need to be cheap and amenable to the designing of international databases. The success of such subspecies typing tools will eventually be measured by the size of the associated reference databases accessible over the internet. Three methods have shown some potential in this direction, the so-called spoligotyping assay (Mycobacterium tuberculosis, 40,000 entries database), Multiple Loci Sequence Typing (MLST; up to a few thousands entries for the more than 20 bacterial species), and more recently Multiple Loci VNTR Analysis (MLVA; up to a few hundred entries, assays available for more than 20 pathogens). In the present report we will review the current status of the tools and resources we have developed along the past seven years to help in the setting-up or the use of MLVA assays or lately for analysing Clustered Regularly Interspaced Short Palindromic Repeats called CRISPRs which are the basis for spoligotyping assays.

EgoNet: identification of human disease ego-network modules

PubMed Central

2014-01-01

Background Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks. Results We present EgoNet, a novel method based on egocentric network-analysis techniques, to exhaustively search and prioritize disease subnetworks and gene markers from a large-scale biological network. When applied to a triple-negative breast cancer (TNBC) microarray dataset, the top selected modules contain both known gene markers in TNBC and novel candidates, such as RAD51 and DOK1, which play a central role in their respective ego-networks by connecting many differentially expressed genes. Conclusions Our results suggest that EgoNet, which is based on the ego network concept, allows the identification of novel biomarkers and provides a deeper understanding of their roles in complex diseases. PMID:24773628

The Rhynie Chert, Scotland, and the Search for Life on Mars

NASA Astrophysics Data System (ADS)

Preston, Louisa J.; Genge, Matthew J.

2010-06-01

Knowledge of ancient terrestrial hydrothermal systems-how they preserve biological information and how this information can be detected-is important in unraveling the history of life on Earth and, perhaps, that of extinct life on Mars. The Rhynie Chert in Scotland was originally deposited as siliceous sinter from Early Devonian hot springs and contains exceptionally well-preserved fossils of some of the earliest plants and animals to colonize the land. The aim of this study was to identify biomolecules within the samples through Fourier transform infrared (FTIR) spectroscopy and aid current techniques in identification of ancient hot spring deposits and their biological components on Mars. Floral and faunal fossils within the Rhynie Chert are commonly known; but new, FTIR spectroscopic analyses of these fossils has allowed for identification of biomolecules such as aliphatic hydrocarbons and OH molecules that are potentially derived from the fossilized biota and their environment. Gas chromatograph-mass spectrometer (GCMS) data were used to identify n-alkanes; however, this alone cannot be related to the samples' biota. Silicified microfossils are more resistant to weathering or dissolution, which renders them more readily preservable over time. This is of particular interest in astropaleontological research, considering the similarities in the early evolution of Mars and Earth.

FDRAnalysis: a tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines.

PubMed

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R; Hubbard, Simon J

2011-04-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the postprocessing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server and a downloadable application that makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline also provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download.

FDRAnalysis: A tool for the integrated analysis of tandem mass spectrometry identification results from multiple search engines

PubMed Central

Wedge, David C; Krishna, Ritesh; Blackhurst, Paul; Siepen, Jennifer A; Jones, Andrew R.; Hubbard, Simon J.

2013-01-01

Confident identification of peptides via tandem mass spectrometry underpins modern high-throughput proteomics. This has motivated considerable recent interest in the post-processing of search engine results to increase confidence and calculate robust statistical measures, for example through the use of decoy databases to calculate false discovery rates (FDR). FDR-based analyses allow for multiple testing and can assign a single confidence value for both sets and individual peptide spectrum matches (PSMs). We recently developed an algorithm for combining the results from multiple search engines, integrating FDRs for sets of PSMs made by different search engine combinations. Here we describe a web-server, and a downloadable application, which makes this routinely available to the proteomics community. The web server offers a range of outputs including informative graphics to assess the confidence of the PSMs and any potential biases. The underlying pipeline provides a basic protein inference step, integrating PSMs into protein ambiguity groups where peptides can be matched to more than one protein. Importantly, we have also implemented full support for the mzIdentML data standard, recently released by the Proteomics Standards Initiative, providing users with the ability to convert native formats to mzIdentML files, which are available to download. PMID:21222473

Proteomic Screening of Antigenic Proteins from the Hard Tick, Haemaphysalis longicornis (Acari: Ixodidae)

PubMed Central

Kim, Young-Ha; slam, Mohammad Saiful; You, Myung-Jo

2015-01-01

Proteomic tools allow large-scale, high-throughput analyses for the detection, identification, and functional investigation of proteome. For detection of antigens from Haemaphysalis longicornis, 1-dimensional electrophoresis (1-DE) quantitative immunoblotting technique combined with 2-dimensional electrophoresis (2-DE) immunoblotting was used for whole body proteins from unfed and partially fed female ticks. Reactivity bands and 2-DE immunoblotting were performed following 2-DE electrophoresis to identify protein spots. The proteome of the partially fed female had a larger number of lower molecular weight proteins than that of the unfed female tick. The total number of detected spots was 818 for unfed and 670 for partially fed female ticks. The 2-DE immunoblotting identified 10 antigenic spots from unfed females and 8 antigenic spots from partially fed females. Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF) of relevant spots identified calreticulin, putative secreted WC salivary protein, and a conserved hypothetical protein from the National Center for Biotechnology Information and Swiss Prot protein sequence databases. These findings indicate that most of the whole body components of these ticks are non-immunogenic. The data reported here will provide guidance in the identification of antigenic proteins to prevent infestation and diseases transmitted by H. longicornis. PMID:25748713

The Rhynie Chert, Scotland, and the search for life on Mars.

PubMed

Preston, Louisa J; Genge, Matthew J

2010-06-01

Knowledge of ancient terrestrial hydrothermal systems-how they preserve biological information and how this information can be detected-is important in unraveling the history of life on Earth and, perhaps, that of extinct life on Mars. The Rhynie Chert in Scotland was originally deposited as siliceous sinter from Early Devonian hot springs and contains exceptionally well-preserved fossils of some of the earliest plants and animals to colonize the land. The aim of this study was to identify biomolecules within the samples through Fourier transform infrared (FTIR) spectroscopy and aid current techniques in identification of ancient hot spring deposits and their biological components on Mars. Floral and faunal fossils within the Rhynie Chert are commonly known; but new, FTIR spectroscopic analyses of these fossils has allowed for identification of biomolecules such as aliphatic hydrocarbons and OH molecules that are potentially derived from the fossilized biota and their environment. Gas chromatograph-mass spectrometer (GCMS) data were used to identify n-alkanes; however, this alone cannot be related to the samples' biota. Silicified microfossils are more resistant to weathering or dissolution, which renders them more readily preservable over time. This is of particular interest in astropaleontological research, considering the similarities in the early evolution of Mars and Earth.

Virtuous colours for Mary. Identification of lapis lazuli, smalt and cochineal in the Andean colonial image of Our Lady of Copacabana (Bolivia).

PubMed

Tomasini, Eugenia P; Marte, Fernando; Careaga, Valeria P; Landa, Carlos Rúa; Siracusano, Gabriela; Maier, Marta S

2016-12-13

The image of Our Lady of Copacabana, a gilded polychrome sculpture carved in maguey wood in 1583, is one of the most important devotions in the Americas. In former research, we have identified the use of gypsum, Armenian bole, cerussite and atacamite in its polychromy. In this study, a red sample taken from the Virgin's tunic and a blue sample extracted from the cloak have been analysed with the aim to identify both pigments and offer insights into the painting technique. Analysis by micro-Raman spectroscopy complemented with scanning electron microscopy-energy dispersive spectroscopy and high-performance liquid chromatography allowed the identification of carmine lake in the red sample. Analysis by micro-Raman spectroscopy of the surface of the blue sample and its cross section showed the presence of smalt-the blue-glass pigment-over a cerussite layer, bathed by a very thin ultramarine layer-from a probable native origin-following a pictorial tradition that would last even until the eighteenth century. This is the first time that lapis lazuli has been scientifically identified in a Spanish American colonial painted layer.This article is part of the themed issue 'Raman spectroscopy in art and archaeology'. © 2016 The Author(s).

Virtuous colours for Mary. Identification of lapis lazuli, smalt and cochineal in the Andean colonial image of Our Lady of Copacabana (Bolivia)

PubMed Central

Tomasini, Eugenia P.; Marte, Fernando; Careaga, Valeria P.; Landa, Carlos Rúa; Siracusano, Gabriela

2016-01-01

The image of Our Lady of Copacabana, a gilded polychrome sculpture carved in maguey wood in 1583, is one of the most important devotions in the Americas. In former research, we have identified the use of gypsum, Armenian bole, cerussite and atacamite in its polychromy. In this study, a red sample taken from the Virgin's tunic and a blue sample extracted from the cloak have been analysed with the aim to identify both pigments and offer insights into the painting technique. Analysis by micro-Raman spectroscopy complemented with scanning electron microscopy–energy dispersive spectroscopy and high-performance liquid chromatography allowed the identification of carmine lake in the red sample. Analysis by micro-Raman spectroscopy of the surface of the blue sample and its cross section showed the presence of smalt—the blue-glass pigment—over a cerussite layer, bathed by a very thin ultramarine layer—from a probable native origin—following a pictorial tradition that would last even until the eighteenth century. This is the first time that lapis lazuli has been scientifically identified in a Spanish American colonial painted layer. This article is part of the themed issue ‘Raman spectroscopy in art and archaeology’. PMID:27799431

Wing morphometrics as a possible tool for the diagnosis of the Ceratitis fasciventris, C. anonae, C. rosa complex (Diptera, Tephritidae).

PubMed

Van Cann, Joannes; Virgilio, Massimiliano; Jordaens, Kurt; De Meyer, Marc

2015-01-01

Previous attempts to resolve the Ceratitis FAR complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa, Diptera, Tephritidae) showed contrasting results and revealed the occurrence of five microsatellite genotypic clusters (A, F1, F2, R1, R2). In this paper we explore the potential of wing morphometrics for the diagnosis of FAR morphospecies and genotypic clusters. We considered a set of 227 specimens previously morphologically identified and genotyped at 16 microsatellite loci. Seventeen wing landmarks and 6 wing band areas were used for morphometric analyses. Permutational multivariate analysis of variance detected significant differences both across morphospecies and genotypic clusters (for both males and females). Unconstrained and constrained ordinations did not properly resolve groups corresponding to morphospecies or genotypic clusters. However, posterior group membership probabilities (PGMPs) of the Discriminant Analysis of Principal Components (DAPC) allowed the consistent identification of a relevant proportion of specimens (but with performances differing across morphospecies and genotypic clusters). This study suggests that wing morphometrics and PGMPs might represent a possible tool for the diagnosis of species within the FAR complex. Here, we propose a tentative diagnostic method and provide a first reference library of morphometric measures that might be used for the identification of additional and unidentified FAR specimens.

Virtuous colours for Mary. Identification of lapis lazuli, smalt and cochineal in the Andean colonial image of Our Lady of Copacabana (Bolivia)

NASA Astrophysics Data System (ADS)

Tomasini, Eugenia P.; Marte, Fernando; Careaga, Valeria P.; Landa, Carlos Rúa; Siracusano, Gabriela; Maier, Marta S.

2016-12-01

The image of Our Lady of Copacabana, a gilded polychrome sculpture carved in maguey wood in 1583, is one of the most important devotions in the Americas. In former research, we have identified the use of gypsum, Armenian bole, cerussite and atacamite in its polychromy. In this study, a red sample taken from the Virgin's tunic and a blue sample extracted from the cloak have been analysed with the aim to identify both pigments and offer insights into the painting technique. Analysis by micro-Raman spectroscopy complemented with scanning electron microscopy-energy dispersive spectroscopy and high-performance liquid chromatography allowed the identification of carmine lake in the red sample. Analysis by micro-Raman spectroscopy of the surface of the blue sample and its cross section showed the presence of smalt-the blue-glass pigment-over a cerussite layer, bathed by a very thin ultramarine layer-from a probable native origin-following a pictorial tradition that would last even until the eighteenth century. This is the first time that lapis lazuli has been scientifically identified in a Spanish American colonial painted layer. This article is part of the themed issue "Raman spectroscopy in art and archaeology".

Identification of resources and skills developed by partners of patients with advanced colon cancer: a qualitative study.

PubMed

Meunier-Beillard, N; Ponthier, N; Lepage, C; Gagnaire, A; Gheringuelli, F; Bengrine, L; Boudrant, A; Rambach, L; Quipourt, V; Devilliers, H; Lejeune, Catherine

2018-06-05

Family caregivers play an important role in caring for patients with advanced cancer. To become competent, individuals must draw on and mobilise an adequate combination of resources. Our goal was to identify the skills developed by caregivers of patients with advanced cancer and the associated resources mobilised. We chose to do it with partners of patients with colon cancer. The study used a cross-sectional qualitative design based on 20 individual interviews and a focus group. Partners were recruited from patients treated in three hospitals of France. Semi-structured interviews were conducted until data saturation was achieved. Each interview was transcribed verbatim, and thematic analyses were performed to extract significant themes and subthemes. Results from the individual and focus group interviews showed that the skills implemented by the partners (in domains of social relationships and health, domestic, organisational, emotional and well-being dimensions) were singular constructs, dependant on if resources (personal, external and schemes) may have been missing and insufficient. In addition, partners may have had these resources but not mobilised them. The identification of the skills and associated resources could allow healthcare professionals better identifying and understanding of the difficulties met by partners in taking care of patients. This could enable them to offer appropriate support to help the caregivers in their accompaniment.

Validation of a screening method for the simultaneous identification of fat-soluble and water-soluble vitamins (A, E, B1, B2 and B6) in an aqueous micellar medium of hexadecyltrimethylammonium chloride.

PubMed

León-Ruiz, V; Vera, S; San Andrés, M P

2005-04-01

Simultaneous determination of the fat-soluble vitamins A and E and the water-soluble vitamins B1, B2 and B6 has been carried using a screening method from fluorescence contour graphs. These graphs show different colour zones in relation to the fluorescence intensity measured for the pair of excitation/emission wavelengths. The identification of the corresponding excitation/emission wavelength zones allows the detection of different vitamins in an aqueous medium regardless of the fat or water solubility of each vitamin, owing to the presence of a surfactant which forms micelles in water at the used concentration (over the critical micelle concentration). The micelles dissolve very water insoluble compounds, such as fat-soluble vitamins, inside the aggregates. This approach avoids the use of organic solvents in determining these vitamins and offers the possibility of analysing fat- and water-soluble vitamins simultaneously. The method has been validated in terms of detection limit, cut-off limit, sensitivity, number of false positives, number of false negatives and uncertainty range. The detection limit is about microg L(-1). The screening method was applied to different samples such as pharmaceuticals, juices and isotonic drinks.

Multi parametrical indicator test for urban wastewater influence

NASA Astrophysics Data System (ADS)

Humer, Franko; Weiss, Stefan; Reinnicke, Sandra; Clara, Manfred; Grath, Johannes; Windhofer, Georg

2013-04-01

Austria's drinking water is abstracted from groundwater. While 50 % of the Austrian population are supplied with spring water, the other 50 % get their drinking water from groundwater supplies, in part from enormous quaternary valley and basin deposits, subjected to intensive use by population, industry, agriculture and traffic/transport. Due to protected areas around drinking water wells and springs, there is no treatment necessary in most cases. Water bodies, however, can be affected by different pathways from natural, industrial and urban sources. Identification of anthropogenic sources is paramount for taking appropriate measures to safeguard the quality of drinking water supply. Common parameters like boron are widely used as tracers indicating anthropogenic impacts (e.g. wastewater contamination of groundwater systems). Unfortunately application of these conventional indicators is often limited due to high dilution. Another application where common parameters have their limits is the identification and quantification of the diffuse nitrogen input to water by the stable isotopes of nitrogen and oxygen in nitrate. Without any additional tracers the source distinction of nitrate from manure or waste water is still difficult. Even the application of boron isotopes can in some cases not avoid ambiguous interpretation. Therefore the Umweltbundesamt (Environment Agency Austria) developed a multi parametrical indicator test which shall allow for identification and quantification of anthropogenic pollutions. The test aims at analysing eight target substances which are well known to occur in wastewater: Acesulfame and sucralose (two artificial, calorie-free sweeteners), benzotriazole and tolyltriazole (two industrial chemicals/corrosion inhibitors), metoprolol, sotalol, carbamazepine and the metabolite 10,11-Dihydro-10,11-dihydroxycarbamazepin (pharmaceuticals). These substances are polar and degradation in the aquatic system by microbiological processes is not suspected. Moreover, they do not occur naturally which make them to ideal tracer substances. Analysis is performed by ultra-performance liquid chromatography with mass selective detection (UPLC-MSMS). Samples are enriched by solid phase extraction before. The test is able to indicate an 0.1 % entry of municipal wastewater into the analysed water. Results of application in practise and advantages of the urban wastewater indicator test are discussed.

Changes in circulating microRNA levels can be identified as early as day 8 of pregnancy in cattle.

PubMed

Ioannidis, Jason; Donadeu, F Xavier

2017-01-01

Poor reproductive performance remains a major issue in the dairy industry, with low conception rates having a significant impact on milk production through extended calving intervals. A major limiting factor is the lack of reliable methods for early pregnancy diagnosis. Identification of animals within a herd that fail to conceive within 3 weeks after insemination would allow early re-insemination and shorten calving intervals. In a previous study, we found an increase in plasma miR-26a levels in Day 16-pregnant relative to non-pregnant heifers, however changes in miRNA levels that early during pregnancy were very small which likely prevented the identification of robust biomarkers. In this study, we extended our analyses to a wider interval during pregnancy (Days 8 to 60, n = 11 heifers) with the rationale that this may facilitate the identification of additional early pregnancy miRNA biomarkers. Using small RNA sequencing we identified a total of 77 miRNAs that were differentially expressed on Day 60 relative to Day 0 of pregnancy. We selected 14 miRNAs for validation by RT-qPCR and confirmed significant differences in the expression of let-7f, let-7c, miR-30c, miR-101, miR-26a, miR-205 and miR-143 between Days 0 and 60. RT-qPCR profiling throughout Days 0, 8, 16 and 60 of pregnancy showed a distinct increase in circulating levels of miR-26a (3.1-fold, P = 0.046) as early as Day 8 of pregnancy. In summary, in contrast to earlier stages of pregnancy (≤ Day 24), marked differences in the levels of multiple miRNAs can be detected in circulation by Day 60 in cattle. Retrospective analyses showed miR-26a levels to be increased in circulation as early as Day 8, sooner than previously reported in any species, suggesting a biological role for this miRNA in the very early events of pregnancy.

SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

PubMed

Kel, Ivan; Chang, Zisong; Galluccio, Nadia; Romeo, Margherita; Beretta, Stefano; Diomede, Luisa; Mezzelani, Alessandra; Milanesi, Luciano; Dieterich, Christoph; Merelli, Ivan

2016-10-18

The interpretation of genome-wide association study is difficult, as it is hard to understand how polymorphisms can affect gene regulation, in particular for trans-regulatory elements located far from their controlling gene. Using RNA or protein expression data as phenotypes, it is possible to correlate their variations with specific genotypes. This technique is usually referred to as expression Quantitative Trait Loci (eQTLs) analysis and only few packages exist for the integration of genotype patterns and expression profiles. In particular, tools are needed for the analysis of next-generation sequencing (NGS) data on a genome-wide scale, which is essential to identify eQTLs able to control a large number of genes (hotspots). Here we present SPIRE (Software for Polymorphism Identification Regulating Expression), a generic, modular and functionally highly flexible pipeline for eQTL processing. SPIRE integrates different univariate and multivariate approaches for eQTL analysis, paying particular attention to the scalability of the procedure in order to support cis- as well as trans-mapping, thus allowing the identification of hotspots in NGS data. In particular, we demonstrated how SPIRE can handle big association study datasets, reproducing published results and improving the identification of trans-eQTLs. Furthermore, we employed the pipeline to analyse novel data concerning the genotypes of two different C. elegans strains (N2 and Hawaii) and related miRNA expression data, obtained using RNA-Seq. A miRNA regulatory hotspot was identified in chromosome 1, overlapping the transcription factor grh-1, known to be involved in the early phases of embryonic development of C. elegans. In a follow-up qPCR experiment we were able to verify most of the predicted eQTLs, as well as to show, for a novel miRNA, a significant difference in the sequences of the two analysed strains of C. elegans. SPIRE is publicly available as open source software at , together with some example data, a readme file, supplementary material and a short tutorial.

Classification of coordination polygons and polyhedra according to their mode of self-assembly.

PubMed

Swiegers, G F; Malefetse, T J

2001-09-03

This work extends techniques for the controlled formation of synthetic molecular containers by metal-mediated self-assembly. A new classification system based on the self-assembly of such species is proposed. The system: 1) allows a systematic identification of suitable acceptor-donor combinations, 2) widens the variety of design possibilities available, 3) allows a ready comparison of the self-assembly of different compounds, 4) reveals useful commonalities between different compounds, 5) aids in the development of novel architectures, and 6) permits identification of systems capable of being switched back-and-forth between architectures.

30 CFR 251.1 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., identification of lithologic and fossil content, core analyses, laboratory analyses of physical and chemical..., often in the form of schematic cross sections, 3-dimensional representations, and maps, developed by.... Interpreted geophysical information means knowledge, often in the form of seismic cross sections, 3...

Methods to increase reproducibility in differential gene expression via meta-analysis

PubMed Central

Sweeney, Timothy E.; Haynes, Winston A.; Vallania, Francesco; Ioannidis, John P.; Khatri, Purvesh

2017-01-01

Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size. PMID:27634930

Identifying Homelessness among Veterans Using VA Administrative Data: Opportunities to Expand Detection Criteria.

PubMed

Peterson, Rachel; Gundlapalli, Adi V; Metraux, Stephen; Carter, Marjorie E; Palmer, Miland; Redd, Andrew; Samore, Matthew H; Fargo, Jamison D

2015-01-01

Researchers at the U.S. Department of Veterans Affairs (VA) have used administrative criteria to identify homelessness among U.S. Veterans. Our objective was to explore the use of these codes in VA health care facilities. We examined VA health records (2002-2012) of Veterans recently separated from the military and identified as homeless using VA conventional identification criteria (ICD-9-CM code V60.0, VA specific codes for homeless services), plus closely allied V60 codes indicating housing instability. Logistic regression analyses examined differences between Veterans who received these codes. Health care services and co-morbidities were analyzed in the 90 days post-identification of homelessness. VA conventional criteria identified 21,021 homeless Veterans from Operations Enduring Freedom, Iraqi Freedom, and New Dawn (rate 2.5%). Adding allied V60 codes increased that to 31,260 (rate 3.3%). While certain demographic differences were noted, Veterans identified as homeless using conventional or allied codes were similar with regards to utilization of homeless, mental health, and substance abuse services, as well as co-morbidities. Differences were noted in the pattern of usage of homelessness-related diagnostic codes in VA facilities nation-wide. Creating an official VA case definition for homelessness, which would include additional ICD-9-CM and other administrative codes for VA homeless services, would likely allow improved identification of homeless and at-risk Veterans. This also presents an opportunity for encouraging uniformity in applying these codes in VA facilities nationwide as well as in other large health care organizations.

Molecular identification of nematode larvae different from those of the Trichinella genus detected by muscle digestion.

PubMed

Marucci, Gianluca; Interisano, Maria; La Rosa, Giuseppe; Pozio, Edoardo

2013-05-20

Although larvae of the genus Trichinella are the most common parasite species detected in vertebrate muscles using artificial digestion, nematode larvae belonging to other genera are sometimes detected and incorrectly identified as Trichinella. However, it is often very difficult to identify these larvae at the species, genus or family level using microscopy because of the absence of specific morphological characters or cuticle damage, and the only means of identification is PCR and sequencing of specific molecular markers (12S mtDNA; COI; 18S rDNA; and ITS1). From 2008 to 2011, 18 nematode isolates not belonging to the genus Trichinella were collected from different host species. Eleven of these isolates were successfully identified at the species, genus or superfamily level: larvae from two common kestrels, three hooded crows, a hen harrier and a domestic pig were identified as Toxocara cati; larvae from a badger were identified as Toxocara canis; larvae from a domestic pig were identified as a free-living nematode of the genus Panagrolaimus; larvae from a wild boar were identified as belonging to the Metastrongylus genus; and larvae from a rough-legged buzzard were identified as belonging to the superfamily Filarioidea. The recovery of nematodes belonging to genera other than Trichinella during routine meat inspection suggests that the persons performing the analyses need to be informed of the possibility of false positives and that a molecular-based identification system that allows for a rapid and reliable response must be adopted (i.e., a DNA barcoding-like system). Copyright © 2013 Elsevier B.V. All rights reserved.

Analysis, Characterization, and Loci of the tuf Genes in Lactobacillus and Bifidobacterium Species and Their Direct Application for Species Identification

PubMed Central

Ventura, Marco; Canchaya, Carlos; Meylan, Valèrie; Klaenhammer, Todd R.; Zink, Ralf

2003-01-01

We analyzed the tuf gene, encoding elongation factor Tu, from 33 strains representing 17 Lactobacillus species and 8 Bifidobacterium species. The tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. We demonstrated that the synonymous substitution affecting this gene renders elongation factor Tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. In fact, the phylogeny generated by these tuf sequences is consistent with that derived from 16S rRNA analysis. The investigation of a multiple alignment of tuf sequences revealed regions conserved among strains belonging to the same species but distinct from those of other species. PCR primers complementary to these regions allowed species-specific identification of closely related species, such as Lactobacillus casei group members. These tuf gene-based assays developed in this study provide an alternative to present methods for the identification for lactic acid bacterial species. Since a variable number of tuf genes have been described for bacteria, the presence of multiple genes was examined. Southern analysis revealed one tuf gene in the genomes of lactobacilli and bifidobacteria, but the tuf gene was arranged differently in the genomes of these two taxa. Our results revealed that the tuf gene in bifidobacteria is flanked by the same gene constellation as the str operon, as originally reported for Escherichia coli. In contrast, bioinformatic and transcriptional analyses of the DNA region flanking the tuf gene in four Lactobacillus species indicated the same four-gene unit and suggested a novel tuf operon specific for the genus Lactobacillus. PMID:14602655

Cloning and Identification of Recombinant Argonaute-Bound Small RNAs Using Next-Generation Sequencing.

PubMed

Gangras, Pooja; Dayeh, Daniel M; Mabin, Justin W; Nakanishi, Kotaro; Singh, Guramrit

2018-01-01

Argonaute proteins (AGOs) are loaded with small RNAs as guides to recognize target mRNAs. Since the target specificity heavily depends on the base complementarity between two strands, it is important to identify small guide and long target RNAs bound to AGOs. For this purpose, next-generation sequencing (NGS) technologies have extended our appreciation truly to the nucleotide level. However, the identification of RNAs via NGS from scarce RNA samples remains a challenge. Further, most commercial and published methods are compatible with either small RNAs or long RNAs, but are not equally applicable to both. Therefore, a single method that yields quantitative, bias-free NGS libraries to identify small and long RNAs from low levels of input will be of wide interest. Here, we introduce such a procedure that is based on several modifications of two published protocols and allows robust, sensitive, and reproducible cloning and sequencing of small amounts of RNAs of variable lengths. The method was applied to the identification of small RNAs bound to a purified eukaryotic AGO. Following ligation of a DNA adapter to RNA 3'-end, the key feature of this method is to use the adapter for priming reverse transcription (RT) wherein biotinylated deoxyribonucleotides specifically incorporated into the extended complementary DNA. Such RT products are enriched on streptavidin beads, circularized while immobilized on beads and directly used for PCR amplification. We provide a stepwise guide to generate RNA-Seq libraries, their purification, quantification, validation, and preparation for next-generation sequencing. We also provide basic steps in post-NGS data analyses using Galaxy, an open-source, web-based platform.

In Silico Identification of Candidate Genes for Fertility Restoration in Cytoplasmic Male Sterile Perennial Ryegrass (Lolium perenne L.)

PubMed Central

Sykes, Timothy; Yates, Steven; Nagy, Istvan; Asp, Torben; Small, Ian

2017-01-01

Perennial ryegrass (Lolium perenne L.) is widely used for forage production in both permanent and temporary grassland systems. To increase yields in perennial ryegrass, recent breeding efforts have been focused on strategies to more efficiently exploit heterosis by hybrid breeding. Cytoplasmic male sterility (CMS) is a widely applied mechanism to control pollination for commercial hybrid seed production and although CMS systems have been identified in perennial ryegrass, they are yet to be fully characterized. Here, we present a bioinformatics pipeline for efficient identification of candidate restorer of fertility (Rf) genes for CMS. From a high-quality draft of the perennial ryegrass genome, 373 pentatricopeptide repeat (PPR) genes were identified and classified, further identifying 25 restorer of fertility-like PPR (RFL) genes through a combination of DNA sequence clustering and comparison to known Rf genes. This extensive gene family was targeted as the majority of Rf genes in higher plants are RFL genes. These RFL genes were further investigated by phylogenetic analyses, identifying three groups of perennial ryegrass RFLs. These three groups likely represent genomic regions of active RFL generation and identify the probable location of perennial ryegrass PPR-Rf genes. This pipeline allows for the identification of candidate PPR-Rf genes from genomic sequence data and can be used in any plant species. Functional markers for PPR-Rf genes will facilitate map-based cloning of Rf genes and enable the use of CMS as an efficient tool to control pollination for hybrid crop production. PMID:26951780

Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.

PubMed

Staats, Charley Christian; Junges, Angela; Guedes, Rafael Lucas Muniz; Thompson, Claudia Elizabeth; de Morais, Guilherme Loss; Boldo, Juliano Tomazzoni; de Almeida, Luiz Gonzaga Paula; Andreis, Fábio Carrer; Gerber, Alexandra Lehmkuhl; Sbaraini, Nicolau; da Paixão, Rana Louise de Andrade; Broetto, Leonardo; Landell, Melissa; Santi, Lucélia; Beys-da-Silva, Walter Orlando; Silveira, Carolina Pereira; Serrano, Thaiane Rispoli; de Oliveira, Eder Silva; Kmetzsch, Lívia; Vainstein, Marilene Henning; de Vasconcelos, Ana Tereza Ribeiro; Schrank, Augusto

2014-09-29

Metarhizium anisopliae is an entomopathogenic fungus used in the biological control of some agricultural insect pests, and efforts are underway to use this fungus in the control of insect-borne human diseases. A large repertoire of proteins must be secreted by M. anisopliae to cope with the various available nutrients as this fungus switches through different lifestyles, i.e., from a saprophytic, to an infectious, to a plant endophytic stage. To further evaluate the predicted secretome of M. anisopliae, we employed genomic and transcriptomic analyses, coupled with phylogenomic analysis, focusing on the identification and characterization of secreted proteins. We determined the M. anisopliae E6 genome sequence and compared this sequence to other entomopathogenic fungi genomes. A robust pipeline was generated to evaluate the predicted secretomes of M. anisopliae and 15 other filamentous fungi, leading to the identification of a core of secreted proteins. Transcriptomic analysis using the tick Rhipicephalus microplus cuticle as an infection model during two periods of infection (48 and 144 h) allowed the identification of several differentially expressed genes. This analysis concluded that a large proportion of the predicted secretome coding genes contained altered transcript levels in the conditions analyzed in this study. In addition, some specific secreted proteins from Metarhizium have an evolutionary history similar to orthologs found in Beauveria/Cordyceps. This similarity suggests that a set of secreted proteins has evolved to participate in entomopathogenicity. The data presented represents an important step to the characterization of the role of secreted proteins in the virulence and pathogenicity of M. anisopliae.

Identification of phenanthrene derivatives in Aerides rosea (Orchidaceae) using the combined systems HPLC-ESI-HRMS/MS and HPLC-DAD-MS-SPE-UV-NMR.

PubMed

Cakova, Veronika; Urbain, Aurélie; Antheaume, Cyril; Rimlinger, Nicole; Wehrung, Patrick; Bonté, Frédéric; Lobstein, Annelise

2015-01-01

In our continued efforts to contribute to the general knowledge on the chemical diversity of orchids, we have decided to focus our investigations on the Aeridinae subtribe. Following our previous phytochemical study of Vanda coerulea, which has led to the identification of phenanthrene derivatives, a closely related species, Aerides rosea Lodd. ex Lindl. & Paxton, was chosen for investigation. To identify new secondary metabolites, and to avoid isolation of those already known, by means of the combined systems HPLC-DAD(diode-array detector) with high-resolution tandem mass spectrometry (HRMS/MS) and HPLC-DAD-MS-SPE(solid-phase extraction)-UV-NMR. A dereplication strategy was developed using a HPLC-DAD-HRMS/MS targeted method and applied to fractions from A. rosea stem extract. Characterisation of unknown minor compounds was then performed using the combined HPLC-DAD-MS-SPE-UV-NMR system. The dereplication method allowed the characterisation of four compounds (gigantol, imbricatin, methoxycoelonin and coelonin), previously isolated from Vanda coerulea stem extract. The analyses of two fractions permitted the identification of five additional minor constituents including one phenanthropyran, two phenanthrene and two dihydrophenanthrene derivatives. The full set of NMR data of each compound was obtained from microgram quantities. Nine secondary metabolites were characterised in A. rosea stems, utilising HPLC systems combined with high-resolution analytical systems. Two of them are newly described phenanthrene derivatives: aerosanthrene (5-methoxyphenanthrene-2,3,7-triol) and aerosin (3-methoxy-9,10-dihydro-2,5,7-phenanthrenetriol). Copyright © 2014 John Wiley & Sons, Ltd.

Neuroanatomical Predictors of Functional Outcome in Individuals at Ultra-High Risk for Psychosis

PubMed Central

Lin, Ashleigh; Yung, Alison R.; Koutsouleris, Nikolaos; Nelson, Barnaby; Cropley, Vanessa L.; Velakoulis, Dennis; McGorry, Patrick D.; Pantelis, Christos; Wood, Stephen J.

2017-01-01

Abstract Most individuals at ultra-high risk (UHR) for psychosis do not transition to frank illness. Nevertheless, many have poor clinical outcomes and impaired psychosocial functioning. This study used voxel-based morphometry to investigate if baseline grey and white matter brain densities at identification as UHR were associated with functional outcome at medium- to long-term follow-up. Participants were help-seeking UHR individuals (n = 109, 54M:55F) who underwent magnetic resonance imaging at baseline; functional outcome was assessed an average of 9.2 years later. Primary analysis showed that lower baseline grey matter density, but not white matter density, in bilateral frontal and limbic areas, and left cerebellar declive were associated with poorer functional outcome (Social and Occupational Functioning Assessment Scale [SOFAS]). These findings were independent of transition to psychosis or persistence of the at-risk mental state. Similar regions were significantly associated with lower self-reported levels of social functioning and increased negative symptoms at follow-up. Exploratory analyses showed that lower baseline grey matter densities in middle and inferior frontal gyri were significantly associated with decline in Global Assessment of Functioning (GAF) score over follow-up. There was no association between baseline grey matter density and IQ or positive symptoms at follow-up. The current findings provide novel evidence that those with the poorest functional outcomes have the lowest grey matter densities at identification as UHR, regardless of transition status or persistence of the at-risk mental state. Replication and validation of these findings may allow for early identification of poor functional outcome and targeted interventions. PMID:27369472

Identifying Homelessness among Veterans Using VA Administrative Data: Opportunities to Expand Detection Criteria

PubMed Central

Peterson, Rachel; Gundlapalli, Adi V.; Metraux, Stephen; Carter, Marjorie E.; Palmer, Miland; Redd, Andrew; Samore, Matthew H.; Fargo, Jamison D.

2015-01-01

Researchers at the U.S. Department of Veterans Affairs (VA) have used administrative criteria to identify homelessness among U.S. Veterans. Our objective was to explore the use of these codes in VA health care facilities. We examined VA health records (2002-2012) of Veterans recently separated from the military and identified as homeless using VA conventional identification criteria (ICD-9-CM code V60.0, VA specific codes for homeless services), plus closely allied V60 codes indicating housing instability. Logistic regression analyses examined differences between Veterans who received these codes. Health care services and co-morbidities were analyzed in the 90 days post-identification of homelessness. VA conventional criteria identified 21,021 homeless Veterans from Operations Enduring Freedom, Iraqi Freedom, and New Dawn (rate 2.5%). Adding allied V60 codes increased that to 31,260 (rate 3.3%). While certain demographic differences were noted, Veterans identified as homeless using conventional or allied codes were similar with regards to utilization of homeless, mental health, and substance abuse services, as well as co-morbidities. Differences were noted in the pattern of usage of homelessness-related diagnostic codes in VA facilities nation-wide. Creating an official VA case definition for homelessness, which would include additional ICD-9-CM and other administrative codes for VA homeless services, would likely allow improved identification of homeless and at-risk Veterans. This also presents an opportunity for encouraging uniformity in applying these codes in VA facilities nationwide as well as in other large health care organizations. PMID:26172386

Laying the groundwork for NEON's continental-scale ecological research

NASA Astrophysics Data System (ADS)

Dethloff, G.; Denslow, M.

2013-12-01

The National Ecological Observatory Network (NEON) is designed to examine a suite of ecological issues. Field-collected data from 96 terrestrial and aquatic sites across the U.S. will be combined with remotely sensed data and existing continental-scale data sets. Field collections will include a range of physical and biological types, including soil, sediment, surface water, groundwater, precipitation, plants, animals, insects, and microbes as well as biological sub-samples such as leaf material, blood and tissue samples, and DNA extracts. Initial data analyses and identifications of approximately 175,000 samples per year will occur at numerous external laboratories when all sites are fully staffed in 2017. Additionally, NEON will archive biotic and abiotic specimens at collections facilities where they will be curated and available for additional analyses by the scientific community. The number of archived specimens is currently estimated to exceed 130,000 per year by 2017. We will detail how NEON is addressing the complexities and challenges around this set of analyses and specimens and how the resulting high-quality data can impact ecological understanding. The raw data returned from external laboratories that is quality checked and served by NEON will be the foundation for many NEON data products. For example, sequence-quality nucleic acids extracted from surface waters, benthic biofilms, and soil samples will be building blocks for data products on microbial diversity. The raw sequence data will also be available for uses such as evolutionary investigations, and the extracts will be archived so others can acquire them for additional research. Currently, NEON is establishing contracts for the analysis and archiving of field-collected samples through 2017. During this period, NEON will gather information on the progress and success of this large-scale effort in order to determine the most effective course to pursue with external facilities. Two areas that NEON already knows to evaluate are the need for geographic expertise in taxonomic identifications and the capacity necessary to handle the volume of samples. NEON is also addressing challenges associated with external entities and the logistics of sample movement, data formatting, data ingestion, and reporting. For example, NEON is considering tools, such as web APIs, which could allow efficient transfer of data from external facilities. Having a standard format in place for that data will be critical to transfer success and quality assessment. NEON is also working on the implementation of quality control measures for diverse analytical and taxonomic processes across laboratories, and is developing an external audit process. Additionally, given NEON's open access approach, the Network is focused on selecting a sample identification protocol that aids in tracking samples with more involved analytical needs and also allows maximum utility for the scientific community. Given the complex nature and breadth of the project, NEON will be developing novel sample management systems as well as metadata schemas. These efforts insure integrity and quality from field to external facility to archive for each sample taken, providing high-quality data now and confidence in future research stemming from raw data generated by NEON and its collection specimens.

Characterization and identification of microorganisms by FT-IR microspectrometry

NASA Astrophysics Data System (ADS)

Ngo-Thi, N. A.; Kirschner, C.; Naumann, D.

2003-12-01

We report on a novel FT-IR approach for microbial characterization/identification based on a light microscope coupled to an infrared spectrometer which offers the possibility to acquire IR-spectra of microcolonies containing only few hundred cells. Microcolony samples suitable for FT-IR microspectroscopic measurements were obtained by a replica technique with a stamping device that transfers spatially accurate cells of microcolonies growing on solid culture plates to a special, IR-transparent or reflecting stamping plate. High quality spectra could be recorded either by applying the transmission/absorbance or the reflectance/absorbance mode of the infrared microscope. Signal to noise ratios higher than 1000 were obtained for microcolonies as small as 40 μm in diameter. Reproducibility levels were established that allowed species and strain identification. The differentiation and classification capacity of the FT-IR microscopic technique was tested for different selected microorganisms. Cluster and factor analysis methods were used to evaluate the complex spectral data. Excellent discrimination between bacteria and yeasts, and at the same time Gram-negative and Gram-positive bacterial strains was obtained. Twenty-two selected strains of different species within the genus Staphylococcus were repetitively measured and could be grouped into correct species cluster. Moreover, the results indicated that the method allows also identifications at the subspecies level. Additionally, the new approach allowed spectral mapping analysis of single colonies which provided spatially resolved characterization of growth heterogeneity within complex microbial populations such as colonies.

Combination of cytochrome b heteroduplex-assay and sequencing for identification of triatomine blood meals.

PubMed

Buitrago, Rosio; Depickère, Stéphanie; Bosseno, Marie-France; Patzi, Edda Siñani; Waleckx, Etienne; Salas, Renata; Aliaga, Claudia; Brenière, Simone Frédérique

2012-01-01

The identification of blood meals in vectors contributes greatly to the understanding of interactions between vectors, microorganisms and hosts. The aim of the current work was to complement the validation of cytochrome b (Cytb) heteroduplex assay (HDA) previously described, and to add the sequencing of the Cytb gene of some samples for the identification of blood meals in triatomines. Experimental feedings of reared triatomines helped to clarify the sensitivity of the HDA. Moreover, the sequencing coupled with the HDA, allowed the assessment of the technique's taxonomic level of discrimination. The primers used to produce DNA fragments of Cytb genes for HDA had a very high sensitivity for vertebrate DNAs, rather similar for mammals, birds and reptiles. However, the formation of heteroduplex depended on blood meal's quality rather than its quantity; a correlation was observed between blood meals' color and the positivity of HDA. HDA electrophoresis profiles were reproducible, and allowed the discrimination of blood origins at the species level. However, in some cases, intraspecific variability of Cytb gene generated different HDA profiles. The HDA based on comparison of electrophoresis profiles is a very useful tool for screening large samples to determine blood origins; the subsequent sequencing of PCR products of Cytb corresponding to different HDA profiles allowed the identification of species whatever the biotope in which the vectors were captured. Copyright © 2011. Published by Elsevier B.V.

Susceptibility to Heat-Related Fluid and Electrolyte Imbalance Emergency Department Visits in Atlanta, Georgia, USA.

PubMed

Heidari, Leila; Winquist, Andrea; Klein, Mitchel; O'Lenick, Cassandra; Grundstein, Andrew; Ebelt Sarnat, Stefanie

2016-10-02

Identification of populations susceptible to heat effects is critical for targeted prevention and more accurate risk assessment. Fluid and electrolyte imbalance (FEI) may provide an objective indicator of heat morbidity. Data on daily ambient temperature and FEI emergency department (ED) visits were collected in Atlanta, Georgia, USA during 1993-2012. Associations of warm-season same-day temperatures and FEI ED visits were estimated using Poisson generalized linear models. Analyses explored associations between FEI ED visits and various temperature metrics (maximum, minimum, average, and diurnal change in ambient temperature, apparent temperature, and heat index) modeled using linear, quadratic, and cubic terms to allow for non-linear associations. Effect modification by potential determinants of heat susceptibility (sex; race; comorbid congestive heart failure, kidney disease, and diabetes; and neighborhood poverty and education levels) was assessed via stratification. Higher warm-season ambient temperature was significantly associated with FEI ED visits, regardless of temperature metric used. Stratified analyses suggested heat-related risks for all populations, but particularly for males. This work highlights the utility of FEI as an indicator of heat morbidity, the health threat posed by warm-season temperatures, and the importance of considering susceptible populations in heat-health research.

Genetic structure of lake whitefish (Coregonus clupeaformis) in Lake Michigan

USGS Publications Warehouse

VanDeHey, J.A.; Sloss, Brian L.; Peeters, Paul J.; Sutton, T.M.

2009-01-01

Genetic relationships among lake whitefish (Coregonus clupeaformis) spawning aggregates in Lake Michigan were assessed and used to predict a stock or management unit (MU) model for the resource. We hypothesized that distinct spawning aggregates represented potential MUs and that differences at molecular markers underlie population differentiation. Genetic stock identification using 11 microsatellite loci indicated the presence of six genetic MUs. Resolved MUs corresponded to geographically proximate spawning aggregates clustering into genetic groups. Within MUs, analyses suggested that all but one delineated MU was a stable grouping (i.e., no between-population differences), with the exception being the Hog Island - Traverse Bay grouping. Elk Rapids was the most genetically divergent population within Lake Michigan. However, low F st values suggested that moderate to high levels of gene flow occur or have occurred in the past between MUs. Significant tests of isolation by distance and low pairwise Fst values potentially led to conflicting results between traditional analyses and a Bayesian approach. This data set could provide baseline data from which a comprehensive mixed-stock analysis could be performed, allowing for more efficient and effective management of this economically and socially important resource.

Susceptibility to Heat-Related Fluid and Electrolyte Imbalance Emergency Department Visits in Atlanta, Georgia, USA

PubMed Central

Heidari, Leila; Winquist, Andrea; Klein, Mitchel; O’Lenick, Cassandra; Grundstein, Andrew; Ebelt Sarnat, Stefanie

2016-01-01

Identification of populations susceptible to heat effects is critical for targeted prevention and more accurate risk assessment. Fluid and electrolyte imbalance (FEI) may provide an objective indicator of heat morbidity. Data on daily ambient temperature and FEI emergency department (ED) visits were collected in Atlanta, Georgia, USA during 1993–2012. Associations of warm-season same-day temperatures and FEI ED visits were estimated using Poisson generalized linear models. Analyses explored associations between FEI ED visits and various temperature metrics (maximum, minimum, average, and diurnal change in ambient temperature, apparent temperature, and heat index) modeled using linear, quadratic, and cubic terms to allow for non-linear associations. Effect modification by potential determinants of heat susceptibility (sex; race; comorbid congestive heart failure, kidney disease, and diabetes; and neighborhood poverty and education levels) was assessed via stratification. Higher warm-season ambient temperature was significantly associated with FEI ED visits, regardless of temperature metric used. Stratified analyses suggested heat-related risks for all populations, but particularly for males. This work highlights the utility of FEI as an indicator of heat morbidity, the health threat posed by warm-season temperatures, and the importance of considering susceptible populations in heat-health research. PMID:27706089

Life cycle assessment for optimising the level of separated collection in integrated MSW management systems.

PubMed

Rigamonti, L; Grosso, M; Giugliano, M

2009-02-01

This life cycle assessment study analyses material and energy recovery within integrated municipal solid waste (MSW) management systems, and, in particular, the recovery of the source-separated materials (packaging and organic waste) and the energy recovery from the residual waste. The recovery of materials and energy are analysed together, with the final aim to evaluate possible optimum levels of source-separated collection that lead to the most favourable energetic and environmental results; this method allows identification of an optimum configuration of the MSW management system. The results show that the optimum level of source-separated collection is about 60%, when all the materials are recovered with high efficiency; it decreases to about 50%, when the 60% level is reached as a result of a very high recovery efficiency for organic fractions at the expense of the packaging materials, or when this implies an appreciable reduction of the quality of collected materials. The optimum MSW management system is thus characterized by source-separated collection levels as included in the above indicated range, with subsequent recycling of the separated materials and energy recovery of the residual waste in a large-scale incinerator operating in combined heat and power mode.

Element analysis: a wavelet-based method for analysing time-localized events in noisy time series

PubMed Central

2017-01-01

A method is derived for the quantitative analysis of signals that are composed of superpositions of isolated, time-localized ‘events’. Here, these events are taken to be well represented as rescaled and phase-rotated versions of generalized Morse wavelets, a broad family of continuous analytic functions. Analysing a signal composed of replicates of such a function using another Morse wavelet allows one to directly estimate the properties of events from the values of the wavelet transform at its own maxima. The distribution of events in general power-law noise is determined in order to establish significance based on an expected false detection rate. Finally, an expression for an event’s ‘region of influence’ within the wavelet transform permits the formation of a criterion for rejecting spurious maxima due to numerical artefacts or other unsuitable events. Signals can then be reconstructed based on a small number of isolated points on the time/scale plane. This method, termed element analysis, is applied to the identification of long-lived eddy structures in ocean currents as observed by along-track measurements of sea surface elevation from satellite altimetry. PMID:28484325

Integrative and conjugative elements and their hosts: composition, distribution and organization

PubMed Central

Touchon, Marie; Rocha, Eduardo P. C.

2017-01-01

Abstract Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses revealed that ICEs are structured in functional modules. Integrases and conjugation systems have different evolutionary histories, even if the gene repertoires of ICEs can be grouped in function of conjugation types. Our characterization of the composition and organization of ICEs paves the way for future functional and evolutionary analyses of their cargo genes, composed of a majority of unknown function genes. PMID:28911112

Genetic markers for antioxidant capacity in a reef-building coral.

PubMed

Jin, Young K; Lundgren, Petra; Lutz, Adrian; Raina, Jean-Baptiste; Howells, Emily J; Paley, Allison S; Willis, Bette L; van Oppen, Madeleine J H

2016-05-01

The current lack of understanding of the genetic basis underlying environmental stress tolerance in reef-building corals impairs the development of new management approaches to confronting the global demise of coral reefs. On the Great Barrier Reef (GBR), an approximately 51% decline in coral cover occurred over the period 1985-2012. We conducted a gene-by-environment association analysis across 12° latitude on the GBR, as well as both in situ and laboratory genotype-by-phenotype association analyses. These analyses allowed us to identify alleles at two genetic loci that account for differences in environmental stress tolerance and antioxidant capacity in the common coral Acropora millepora. The effect size for antioxidant capacity was considerable and biologically relevant (32.5 and 14.6% for the two loci). Antioxidant capacity is a critical component of stress tolerance because a multitude of environmental stressors cause increased cellular levels of reactive oxygen species. Our findings provide the first step toward the development of novel coral reef management approaches, such as spatial mapping of stress tolerance for use in marine protected area design, identification of stress-tolerant colonies for assisted migration, and marker-assisted selective breeding to create more tolerant genotypes for restoration of denuded reefs.

Anatomy of Subterranean Organs of Medicinally Used Cardueae and Related Species and its Value for Discrimination

PubMed Central

Fritz, Elisabeth; Saukel, Johannes

2011-01-01

Numerous species of the Asteraceae, the composites, are famous for their use in both traditional and conventional medicine. Reliable anatomical descriptions of these plants and of possible adulterations provide a basis for fast identification and cheap purity controls of respective medicinal drugs by means of light microscopy. Nevertheless, detailed comparative studies on root and rhizome anatomy of valuable as well as related inconsiderable composite plants are largely missing yet. The presented study aims to narrow this gap by performing anatomical analyses of roots and rhizomes of 16 species belonging to the tribe Cardueae, of formerly and currently used drugs as well as their near relatives as potential adulterations (Carlina acaulis L., Carlina vulgaris L., Arctium lappa L., Arctium tomentosum Mill., Carduus defloratus L., Carduus personata (L.) Jacq, Cirsium arvense (L.) Scop., Cirsium vulgare (Savi) Ten., Cirsium erisithales (Jacq.) Scop., Onopordum acanthium L., Silybum marianum (L.) Gaertn., Rhaponticum scariosum Lam., Centaurea jacea L., Centaurea scabiosa L., Centaurea cyanus L., Cnicus benedictus L.). A detailed verbal and graphical survey of the analysed anatomical features is provided. Several characters were finally extracted which allow for discrimination of the examined species and may be effectively used for drug quality controls. PMID:21617780

An analytical approach to the forensic identification of different classes of new psychoactive substances (NPSs) in seized materials.

PubMed

Strano Rossi, Sabina; Odoardi, Sara; Gregori, Adolfo; Peluso, Giuseppe; Ripani, Luigi; Ortar, Giorgio; Serpelloni, Giovanni; Romolo, Francesco Saverio

2014-09-15

New psychoactive substances (NPSs) are rapidly spreading worldwide, and forensic laboratories are often requested to identify new substances for which no reference standards or analytical data are available. This article describes an analytical approach that was adopted in Italy by a few collaborative centres of the Italian Early Warning System for Drugs, which has contributed many alerts for the identification of different classes of NPSs in the last 24 months. Seized crystals and powders were initially analysed via single quadrupole gas chromatography/mass spectrometry (GC/MS), followed by liquid chromatography/high-resolution mass spectrometry (LC/HRMS) in the positive electrospray ionisation (ESI) mode at 100,000 full width at half maximum resolution (FWHM) without fragmentation to elucidate the elemental compositions of unknown molecules. Different fragmentation voltages during LC/HRMS were applied to study the accurate masses of the obtained characteristic fragments. Nuclear magnetic resonance (NMR) analyses were performed to identify specific isomers when necessary. Some interesting examples of unknown NPSs from seizures later identified in our laboratories are reported, with special focus on those cases where analytical standards were not available during analyses. These cases include cathinones, such as 3-methylmethcathinone (3-MMC), methylone, bk-MBDB (butylone), 4-methylethcathinone (4-MEC), flephedrone, methylenedioxypyrovalerone (MDPV) and pentedrone, methoxetamine, apinaca or AKB48, benzydamine, meta-chlorophenylpiperazine (m-CPP), 5-MeO-N,N-dialkyl tryptamines, such as 5-MeO-DALT and 5-MeOMIPT, benzofurans, such as 6-APB and 4-APB, and diphenidine (identified for the first time in Europe). The identification of NPSs in confiscated materials was successfully achieved via GC/MS coupled with LC/HRMS and, in a few cases, NMR analyses. The availability of GC/MS libraries is of great assistance in the identification of new drugs. Alternatively, the study of characteristic molecule fragments combined with the determination of their accurate masses can be a useful approach to identify unknown samples not previously analysed. Copyright © 2014 John Wiley & Sons, Ltd.

Surface, Water and Air Biocharacterization - A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft Environment

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Cruz, Patricia; Buttner, Mark P.

2009-01-01

A Comprehensive Characterization of Microorganisms and Allergens in Spacecraft (SWAB) will use advanced molecular techniques to comprehensively evaluate microbes on board the space station, including pathogens (organisms that may cause disease). It also will track changes in the microbial community as spacecraft visit the station and new station modules are added. This study will allow an assessment of the risk of microbes to the crew and the spacecraft. Research Summary: Previous microbial analysis of spacecraft only identify microorganisms that will grow in culture, omitting greater than 90% of all microorganisms including pathogens such as Legionella (the bacterium which causes Legionnaires' disease) and Cryptosporidium (a parasite common in contaminated water) The incidence of potent allergens, such as dust mites, has never been systematically studied in spacecraft environments and microbial toxins have not been previously monitored. This study will use modern molecular techniques to identify microorganisms and allergens. Direct sampling of the ISS allows identification of the microbial communities present, and determination of whether these change or mutate over time. SWAB complements the nominal ISS environmental monitoring by providing a comparison of analyses from current media-based and advanced molecular-based technologies.

First diagnosis of septic arthritis in a dinosaur

NASA Astrophysics Data System (ADS)

Anné, Jennifer; Hedrick, Brandon P.; Schein, Jason P.

2016-08-01

Identification and interpretation of pathologies in the fossil record allows for unique insights into the life histories of extinct organisms. However, the rarity of such finds limits not only the sample size for palaeopathologic studies, but also the types of analyses that may be performed. In this study, we present the first occurrence of a palaeopathology in a vertebrate from the Mesozoic of the East Coast of North America (Appalachia), a pathologic ulna and radius of an indeterminate hadrosaur from the Navesink Formation (New Jersey). X-ray microtomography allowed for both detailed and more accurate diagnosis of the pathologic condition as well as virtual conservation of the specimen. Based on extant archosaurian comparisons, the hadrosaur was diagnosed with severe septic arthritis affecting the proximal ulna and radius. Diagnosis was based on erosion of the joint and highly reactive periosteal bone growth and fusion of the elements. To the best of our knowledge, this is the first recorded account of septic arthritis in dinosaurs. The severity of the pathology suggests the animal suffered with this condition for some time before death. Unfortunately, only the ulna and radius were found. Thus, the extent to which the condition spread to other parts of the body is unknown.

First diagnosis of septic arthritis in a dinosaur.

PubMed

Anné, Jennifer; Hedrick, Brandon P; Schein, Jason P

2016-08-01

Identification and interpretation of pathologies in the fossil record allows for unique insights into the life histories of extinct organisms. However, the rarity of such finds limits not only the sample size for palaeopathologic studies, but also the types of analyses that may be performed. In this study, we present the first occurrence of a palaeopathology in a vertebrate from the Mesozoic of the East Coast of North America (Appalachia), a pathologic ulna and radius of an indeterminate hadrosaur from the Navesink Formation (New Jersey). X-ray microtomography allowed for both detailed and more accurate diagnosis of the pathologic condition as well as virtual conservation of the specimen. Based on extant archosaurian comparisons, the hadrosaur was diagnosed with severe septic arthritis affecting the proximal ulna and radius. Diagnosis was based on erosion of the joint and highly reactive periosteal bone growth and fusion of the elements. To the best of our knowledge, this is the first recorded account of septic arthritis in dinosaurs. The severity of the pathology suggests the animal suffered with this condition for some time before death. Unfortunately, only the ulna and radius were found. Thus, the extent to which the condition spread to other parts of the body is unknown.

Metal nanoinks as chemically stable surface enhanced scattering (SERS) probes for the analysis of blue BIC ballpoint pens.

PubMed

Alyami, A; Saviello, D; McAuliffe, M A P; Mirabile, A; Lewis, L; Iacopino, D

2017-06-07

Metal nanoinks constituted by Ag nanoparticles and Au nanorods were employed as probes for the Surface Enhanced Raman Scattering (SERS) analysis of a blue BIC ballpoint pen. The dye components of the pen ink were first separated by thin layer chromatography (TLC) and subsequently analysed by SERS at illumination wavelengths of 514 nm and 785 nm. Compared to normal Raman conditions, enhanced spectra were obtained for all separated spots, allowing easy identification of phthalocyanine Blue 38 and triarylene crystal violet in the ink mixture. A combination of effects such as molecular resonance, electromagnetic and chemical effects were the contributing factors to the generation of spectra enhanced compared to normal Raman conditions. Enhancement factors (EFs) between 5 × 10 3 and 3 × 10 6 were obtained, depending on the combination of SERS probes and laser illumination used. In contrast to previous conflicting reports, the metal nanoinks were chemically stable, allowing the collection of reproducible spectra for days after deposition on TLC plates. In addition and in advance to previously reported SERS probes, no need for additional aggregating agents or correction of electrostatic charge was necessary to induce the generation of enhanced SERS spectra.

First-time observation of Mastro Giorgio masterpieces by means of non-destructive techniques

NASA Astrophysics Data System (ADS)

Padeletti, G.; Ingo, G. M.; Bouquillon, A.; Pages-Camagna, S.; Aucouturier, M.; Roehrs, S.; Fermo, P.

2006-06-01

For the first time some excellent pieces belonging to the majolica production of the great master Giorgio Andreoli from Gubbio (Central Italy) have been characterized from a chemical and structural point of view with the aim to identify the composition of both pigments and lustres. A series of particle-induced X-ray emission (PIXE), Rutherford backscattering spectrometry (RBS) and Raman analyses have been performed on some plates coming from Museo del Palazzo dei Consoli (Gubbio) and several French museums (Louvre, Musée National de la Céramique, Musée National de la Renaissance) lustred by Giorgio Andreoli and decorated by famous majolica painters such as Francesco Xanto Avelli. The three techniques are complementary and useful in the investigation of art objects since they are non-destructive. Furthermore, the low detection limits allow the identification of all elements and compounds present, and RBS allows concentration profiling, too. It is worth noticing that the examined objects are characterized by the presence of both gold and ruby-red lustres, a peculiarity of Mastro Giorgio’s technique. The measurements by PIXE and RBS have been carried out on the AGLAE accelerator at C2RMF, Louvre Palace.

Exploiting external reflection FTIR spectroscopy for the in-situ identification of pigments and binders in illuminated manuscripts. Brochantite and posnjakite as a case study

NASA Astrophysics Data System (ADS)

Zaffino, Chiara; Guglielmi, Vittoria; Faraone, Silvio; Vinaccia, Alessandro; Bruni, Silvia

2015-02-01

In the present work, the use of portable instrumentation allowing in-situ reflection FTIR analyses is exploited to identify the coloring matters of northern-Italian illuminations dating to the XVI century. In order to build a database of spectra, reference paint samples were prepared spreading the pigments on parchment with two different binders, i.e. gum arabic and egg white, used in antiquity. Pigments for the database were chosen considering their use in the Middle Ages and in the Renaissance and their response in the mid- and near-IR region. The reflection FTIR spectra obtained resulted to be dominated by the specular reflection component, allowing the use of the Kramers-Kronig transform to convert them to the more conventional absorbance FTIR spectra. Several pigments could thus be identified in ancient illuminations, even if some green details showed a spectral pattern different with respect to the most common commercial green pigments of the database. Therefore, in addition, basic copper sulfates brochantite and posnjakite were synthesized and characterized. In three green details, posnjakite was identified, both as a pure compound and together with malachite.

Exploiting external reflection FTIR spectroscopy for the in-situ identification of pigments and binders in illuminated manuscripts. Brochantite and posnjakite as a case study.

PubMed

Zaffino, Chiara; Guglielmi, Vittoria; Faraone, Silvio; Vinaccia, Alessandro; Bruni, Silvia

2015-02-05

In the present work, the use of portable instrumentation allowing in-situ reflection FTIR analyses is exploited to identify the coloring matters of northern-Italian illuminations dating to the XVI century. In order to build a database of spectra, reference paint samples were prepared spreading the pigments on parchment with two different binders, i.e. gum arabic and egg white, used in antiquity. Pigments for the database were chosen considering their use in the Middle Ages and in the Renaissance and their response in the mid- and near-IR region. The reflection FTIR spectra obtained resulted to be dominated by the specular reflection component, allowing the use of the Kramers-Kronig transform to convert them to the more conventional absorbance FTIR spectra. Several pigments could thus be identified in ancient illuminations, even if some green details showed a spectral pattern different with respect to the most common commercial green pigments of the database. Therefore, in addition, basic copper sulfates brochantite and posnjakite were synthesized and characterized. In three green details, posnjakite was identified, both as a pure compound and together with malachite. Copyright © 2014 Elsevier B.V. All rights reserved.

Phenotypic and genetic characterization of Paecilomyces lilacinus strains with biocontrol activity against root-knot nematodes.

PubMed

Gunasekera, T S; Holland, R J; Gillings, M R; Briscoe, D A; Neethling, D C; Williams, K L; Nevalainen, K M

2000-09-01

Efficient selection of fungi for biological control of nematodes requires a series of screening assays. Assessment of genetic diversity in the candidate species maximizes the variety of the isolates tested and permits the assignment of a particular genotype with high nematophagous potential using a rapid novel assay. Molecular analyses also facilitate separation between isolates, allowing the identification of proprietary strains and trace biocontrol strains in the environment. The resistance of propagules to UV radiation is an important factor in the survival of a biocontrol agent. We have analyzed 15 strains of the nematophagous fungus Paecilomyces lilacinus using these principles. Arbitrarily primed DNA and allozyme assays were applied to place the isolates into genetic clusters, and demonstrated that some genetically related P. lilacinus strains exhibit widespread geographic distributions. When exposed to UV radiation, some weakly nematophagous strains were generally more susceptible than effective isolates. A microtitre tray-based assay used to screen the pathogenic activity of each isolate to Meloidogyne javanica egg masses revealed that the nematophagous ability varied between 37%-100%. However, there was no clear relationship between nematophagous ability and genetic clusters. Molecular characterizations revealed sufficient diversity to allow tracking of strains released into the environment.

Development of a new screening method for the detection of antibiotic residues in muscle tissues using liquid chromatography and high resolution mass spectrometry with a LC-LTQ-Orbitrap instrument.

PubMed

Hurtaud-Pessel, D; Jagadeshwar-Reddy, T; Verdon, E

2011-10-01

A liquid chromatography-high resolution mass spectrometry (LC-HRMS) method was developed for screening meat for a wide range of antibiotics used in veterinary medicine. Full-scan mode under high resolution mass spectral conditions using an LTQ-Orbitrap mass spectrometer with resolving power 60,000 full width at half maximum (FWHM) was applied for analysis of the samples. Samples were prepared using two extraction protocols prior to LC-HRMS analysis. The scope of the method focuses on screening the following main families of antibacterial veterinary drugs: penicillins, cephalosporins, sulfonamides, macrolides, tetracyclines, aminoglucosides and quinolones. Compounds were successfully identified in spiked samples from their accurate mass and LC retention times from the acquired full-scan chromatogram. Automated data processing using ToxId software allowed rapid treatment of the data. Analyses of muscle tissues from real samples collected from antibiotic-treated animals was carried out using the above methodology and antibiotic residues were identified unambiguously. Further analysis of the data for real samples allowed the identification of the targeted antibiotic residues but also non-targeted compounds, such as some of their metabolites.

In-vitro bacterial identification using fluorescence spectroscopy with an optical fiber system

NASA Astrophysics Data System (ADS)

Spector, Brian C.; Werkhaven, Jay A.; Smith, Dana; Reinisch, Lou

2000-05-01

Acute otitis media (AOM) remains a source of significant morbidity in children. With the emergence of antibiotic resistant strains of bacteria, tympanocentesis has become an important method of bacterial identification in the setting of treatment failures. Previous studies described a prototype system for the non-invasive fluorescence identification of bacteria in vitro. We demonstrate the addition of an optical fiber to allow for the identification of a specimen distant to the spectrofluorometer. Emission spectra from three bacteria, Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus were successfully obtained in vitro. This represents a necessary step prior to the study of in vivo identification of bacteria in AOM using fluorescence spectroscopy.

Environmental durability diagnostic for printed identification codes of polymer insulation for distribution pipelines

NASA Astrophysics Data System (ADS)

Zhuravleva, G. N.; Nagornova, I. V.; Kondratov, A. P.; Bablyuk, E. B.; Varepo, L. G.

2017-08-01

A research and modelling of weatherability and environmental durability of multilayer polymer insulation of both cable and pipelines with printed barcodes or color identification information were performed. It was proved that interlayer printing of identification codes in distribution pipelines insulation coatings provides high marking stability to light and atmospheric condensation. This allows to carry out their distant damage control. However, microbiological fouling of upper polymer layer hampers the distant damage pipelines identification. The color difference values and density changes of PE and PVC printed insolation due to weather and biological factors were defined.

Relationships between digital signal processing and control and estimation theory

NASA Technical Reports Server (NTRS)

Willsky, A. S.

1978-01-01

Research areas associated with digital signal processing and control and estimation theory are identified. Particular attention is given to image processing, system identification problems (parameter identification, linear prediction, least squares, Kalman filtering), stability analyses (the use of the Liapunov theory, frequency domain criteria, passivity), and multiparameter systems, distributed processes, and random fields.

Structure identification for Non-Targeted Analytical Chemistry using the US EPA’s CompTox Chemistry Dashboard (ACS 2017 Fall meeting 3 of 3)

EPA Science Inventory

Identification of unknowns in non-targeted analyses (NTA) requires the integration of complementary data types to generate a confident consensus structure. Researchers use a variety of data and tools (e.g., chemical reference databases, spectral matching, fragment prediction too...

Identification and Expression Analyses of Poly[I:C]-stimulated Genes in Channel Catfish (Ictalurus punctatus)

USDA-ARS?s Scientific Manuscript database

Channel catfish (Ictalurus punctatus) have proven to be an excellent model with which to study immune responses in lower vertebrates. Identification of antiviral antibodies and cytotoxic cells, as well as both type I and II interferon (IFN), demonstrate that catfish likely mount a vigorous anti-vir...

Effect of Pollination Timing on the Rate of Apomictic Reproduction Revealed by RAPD Markers in Paspalum notatum

PubMed Central

ESPINOZA, F.; PESSINO, S. C.; QUARÍN, C. L.; VALLE, E. M.

2002-01-01

Progeny tests employing molecular markers allow the identification of individuals originated by sexual means among the offspring of a facultative apomict. The objective of this work was to evaluate the effect of the pollination timing on the proportion of sexually formed individuals in progenies of a facultative apomictic Paspalum notatum genotype. Progeny families of approx. 30 plants each were generated at five different pollination times: 1–3 d pre‐anthesis; at anthesis; and 2, 4 and 6 d post‐anthesis. Cytoembryological analyses indicated that approx. 17 % of the ovules carried a meiotic cytologically reduced embryo sac in florets formed simultaneously with those used for crosses. The parental plants and the five F1 families were analysed using RAPD molecular markers. Ninety‐five oligonucleotides were assayed on the progenitors in order to search for male‐specific bands. Eight primers presenting clear polymorphic bands were selected for use in the progeny tests. The proportion of sexually produced progeny reached 3·4 % before anthesis and 20 % at anthesis, while pollination after anthesis generated only maternal plants. A second progeny of 97 plants obtained from pollination at anthesis produced 16 off‐type plants (16·5 %), of which only one was a BIII hybrid (2n + n). Our results indicate that pollination at anthesis allows the greatest potential for sexuality to be expressed in this facultative apomictic genotype. When pollination is delayed as soon as 2 d after anthesis, only the aposporous sacs develop endosperm through pseudogamy to set seed. PMID:12099347

Longitudinal MRI assessment: the identification of relevant features in the development of Posterior Fossa Syndrome in children

NASA Astrophysics Data System (ADS)

Spiteri, M.; Lewis, E.; Windridge, D.; Avula, S.

2015-03-01

Up to 25% of children who undergo brain tumour resection surgery in the posterior fossa develop posterior fossa syndrome (PFS). This syndrome is characterised by mutism and disturbance in speech. Our hypothesis is that there is a correlation between PFS and the occurrence of hypertrophic olivary degeneration (HOD) in lobes within the posterior fossa, known as the inferior olivary nuclei (ION). HOD is exhibited as an increase in size and intensity of the ION on an MR image. Intra-operative MRI (IoMRI) is used during surgical procedures at the Alder Hey Children's Hospital, Liver- pool, England, in the treatment of Posterior Fossa tumours and allows visualisation of the brain during surgery. The final MR scan on the IoMRI allows early assessment of the ION immediately after the surgical procedure. The longitudinal MRI data of 28 patients was analysed in a collaborative study with Alder Hey Children's Hospital, in order to identify the most relevant imaging features that relate to the development of PFS, specifically related to HOD. A semi-automated segmentation process was carried out to delineate the ION on each MRI. Feature selection techniques were used to identify the most relevant features amongst the MRI data, demographics and clinical data provided by the hospital. A support vector machine (SVM) was used to analyse the discriminative ability of the selected features. The results indicate the presence of HOD as the most efficient feature that correlates with the development of PFS, followed by the change in intensity and size of the ION and whether HOD occurred bilaterally or unilaterally.

Comparison between non-invasive methods used on paintings by Goya and his contemporaries: hyperspectral imaging vs. point-by-point spectroscopic analysis.

PubMed

Daniel, Floréal; Mounier, Aurélie; Pérez-Arantegui, Josefina; Pardos, Carlos; Prieto-Taboada, Nagore; Fdez-Ortiz de Vallejuelo, Silvia; Castro, Kepa

2017-06-01

The development of non-invasive techniques for the characterization of pigments is crucial in order to preserve the integrity of the artwork. In this sense, the usefulness of hyperspectral imaging was demonstrated. It allows pigment characterization of the whole painting. However, it also sometimes requires the complementation of other point-by-point techniques. In the present article, the advantages of hyperspectral imaging over point-by-point spectroscopic analysis were evaluated. For that purpose, three paintings were analysed by hyperspectral imaging, handheld X-ray fluorescence and handheld Raman spectroscopy in order to determine the best non-invasive technique for pigment identifications. Thanks to this work, the main pigments used in Aragonese artworks, and especially in Goya's paintings, were identified and mapped by imaging reflection spectroscopy. All the analysed pigments corresponded to those used at the time of Goya. Regarding the techniques used, the information obtained by the hyperspectral imaging and point-by-point analysis has been, in general, different and complementary. Given this fact, selecting only one technique is not recommended, and the present work demonstrates the usefulness of the combination of all the techniques used as the best non-invasive methodology for the pigments' characterization. Moreover, the proposed methodology is a relatively quick procedure that allows a larger number of Goya's paintings in the museum to be surveyed, increasing the possibility of obtaining significant results and providing a chance for extensive comparisons, which are relevant from the point of view of art history issues.

Organizational health and quality of life: survey among ambulance nurses in prehospital emergency care.

PubMed

Sili, A; Fida, Roberta; Vellone, E; Gianlorenzi, Alessandra; Alvaro, Rosaria

2011-01-01

The workplace plays a central role in causing stress and different kinds of syndromes and diseases. More generally, organizational procedures and practices could have an impact on nurses' quality of life. Although several studies have investigated this link, none of them considered nurses working in prehospital emergency care. To investigate the role of organizational health factors that affect the quality of life and psychosomatic complaints of ambulance nurses. Our sample included 411 ambulance nurses. Workers were administered two questionnaires to assess organizational health and quality of life. Descriptive and correlational analyses were used to test our assumptions. Several organizational health dimensions provided an explanation for the complaints reported by nurses working in prehospital emergency care in terms of quality of life and psychosomatic disorders. The results allowed identification of possible interventions focusing on specific duties and organizational aspects that would improve the quality of nurses' health.

Genome-wide association study identifies multiple loci influencing human serum metabolite levels

PubMed Central

Kettunen, Johannes; Tukiainen, Taru; Sarin, Antti-Pekka; Ortega-Alonso, Alfredo; Tikkanen, Emmi; Lyytikäinen, Leo-Pekka; Kangas, Antti J; Soininen, Pasi; Würtz, Peter; Silander, Kaisa; Dick, Danielle M; Rose, Richard J; Savolainen, Markku J; Viikari, Jorma; Kähönen, Mika; Lehtimäki, Terho; Pietiläinen, Kirsi H; Inouye, Michael; McCarthy, Mark I; Jula, Antti; Eriksson, Johan; Raitakari, Olli T; Salomaa, Veikko; Kaprio, Jaakko; Järvelin, Marjo-Riitta; Peltonen, Leena; Perola, Markus; Freimer, Nelson B; Ala-Korpela, Mika; Palotie, Aarno; Ripatti, Samuli

2013-01-01

Nuclear magnetic resonance assays allow for measurement of a wide range of metabolic phenotypes. We report here the results of a GWAS on 8,330 Finnish individuals genotyped and imputed at 7.7 million SNPs for a range of 216 serum metabolic phenotypes assessed by NMR of serum samples. We identified significant associations (P < 2.31 × 10−10) at 31 loci, including 11 for which there have not been previous reports of associations to a metabolic trait or disorder. Analyses of Finnish twin pairs suggested that the metabolic measures reported here show higher heritability than comparable conventional metabolic phenotypes. In accordance with our expectations, SNPs at the 31 loci associated with individual metabolites account for a greater proportion of the genetic component of trait variance (up to 40%) than is typically observed for conventional serum metabolic phenotypes. The identification of such associations may provide substantial insight into cardiometabolic disorders. PMID:22286219

Identification and Analysis of Critical Gaps in Nuclear Fuel Cycle Codes Required by the SINEMA Program

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

Adrian Miron; Joshua Valentine; John Christenson

2009-10-01

The current state of the art in nuclear fuel cycle (NFC) modeling is an eclectic mixture of codes with various levels of applicability, flexibility, and availability. In support of the advanced fuel cycle systems analyses, especially those by the Advanced Fuel Cycle Initiative (AFCI), Unviery of Cincinnati in collaboration with Idaho State University carried out a detailed review of the existing codes describing various aspects of the nuclear fuel cycle and identified the research and development needs required for a comprehensive model of the global nuclear energy infrastructure and the associated nuclear fuel cycles. Relevant information obtained on the NFCmore » codes was compiled into a relational database that allows easy access to various codes' properties. Additionally, the research analyzed the gaps in the NFC computer codes with respect to their potential integration into programs that perform comprehensive NFC analysis.« less

Stigma Management Trajectories in Youth with Perinatally Acquired HIV and Their Families: A Qualitative Perspective.

PubMed

Proulx-Boucher, Karène; Fernet, Mylène; Blais, Martin; Lapointe, Normand; Samson, Johanne; Lévy, Joseph J; Otis, Joanne; Morin, Guylaine; Thériault, Jocelyne; Trottier, Germain

2017-09-01

This study explores how family, secrecy and silence contribute to the adoption of stigma management strategies among youth with perinatally acquired HIV (PAHIV). A qualitative method was used. Eighteen youths with PAHIV aged 13-22 years old took part in a semi-structured interview. An exploratory content analysis was performed. Analyses of interviews allowed identification of two HIV stigma management trajectories, both sensitive to the family context: [1] a consolidation of family ties, which contributes to solidarity in stigma management; and [2] a weakening or dissolution of family ties, which contributes to solitary stigma management strategy. Family conditions that support the children in their efforts to develop active stigma management strategies are described. Children likely to experience weakening or dissolution family ties must build strong bonds in the clinical environment and maintain these into adulthood so as to afford them the support they need.

Isolation of plasmodesmata from Arabidopsis suspension culture cells.

PubMed

Grison, Magali S; Fernandez-Calvino, Lourdes; Mongrand, Sébastien; Bayer, Emmanuelle M F

2015-01-01

Due to their position firmly anchored within the plant cell wall, plasmodesmata (PD) are notoriously difficult to isolate from plant tissue. Yet, getting access to isolated PD represents the most straightforward strategy for the identification of their molecular components. Proteomic and lipidomic analyses of such PD fractions have provided and will continue to provide critical information on the functional and structural elements that define these membranous nano-pores. Here, we describe a two-step simple purification procedure that allows isolation of pure PD-derived membranes from Arabidopsis suspension cells. The first step of this procedure consists in isolating cell wall fragments containing intact PD while free of contamination from other cellular compartments. The second step relies on an enzymatic degradation of the wall matrix and the subsequent release of "free" PD. Isolated PD membranes provide a suitable starting material for the analysis of PD-associated proteins and lipids.

Identification of pyrogallol as an antiproliferative compound present in extracts from the medicinal plant Emblica officinalis: effects on in vitro cell growth of human tumor cell lines.

PubMed

Khan, Mahmud Tareq Hassan; Lampronti, Ilaria; Martello, Dino; Bianchi, Nicoletta; Jabbar, Shaila; Choudhuri, Mohammad Shahabuddin Kabir; Datta, Bidduyt Kanti; Gambari, Roberto

2002-07-01

In this study we compared the in vitro antiproliferative activity of extracts from medicinal plants toward human tumor cell lines, including human erythromyeloid K562, B-lymphoid Raji, T-lymphoid Jurkat, erythroleukemic HEL cell lines. Extracts from Emblica officinalis were the most active in inhibiting in vitro cell proliferation, after comparison to those from Terminalia arjuna, Aphanamixis polystachya, Oroxylum indicum, Cuscuta reflexa, Aegle marmelos, Saraca asoka, Rumex maritimus, Lagerstroemia speciosa, Red Sandalwood. Emblica officinalis extracts have been studied previously, due to their hepatoprotective, antioxidant, antifungal, antimicrobial and anti-inflammatory medicinal activities. Gas chromatography/mass spectrometry analyses allowed to identify pyrogallol as the common compound present both in unfractionated and n-butanol fraction of Emblica officinalis extracts. Antiproliferative effects of pyrogallol were therefore determined on human tumor cell lines thus identifying pyrogallol as an active component of Emblica officinalis extracts.

Photometric anomalies in the Apollo landing sites as seen from the Lunar Reconnaissance Orbiter

NASA Astrophysics Data System (ADS)

Kaydash, Vadym; Shkuratov, Yuriy; Korokhin, Viktor; Videen, Gorden

2011-01-01

Phase-ratio imagery is a new tool of qualitative photometric analyses of the upper layer of the lunar regolith, which allows the identification of natural surface structure anomalies and artificially altered regolith. We apply phase-ratio imagery to analyze the Apollo-14, -15, and -17 landing sites. This reveals photometric anomalies of ˜170 × 120 m size that are characterized by lower values of the phase-function steepness, indicating a smoothing of the surface microstructure caused by the engine jets of the landing modules. Other photometric anomalies characterized by higher phase-function slopes are the result of regolith loosening by astronaut boots and the wheels of the Modular Equipment Transporter and the Lunar Roving Vehicle. We also provide a possible explanation for the high brightness of the wheel tracks seen in on-surface images acquired at very large phase angles.

Charting organellar importomes by quantitative mass spectrometry

PubMed Central

Peikert, Christian D.; Mani, Jan; Morgenstern, Marcel; Käser, Sandro; Knapp, Bettina; Wenger, Christoph; Harsman, Anke; Oeljeklaus, Silke; Schneider, André; Warscheid, Bettina

2017-01-01

Protein import into organelles is essential for all eukaryotes and facilitated by multi-protein translocation machineries. Analysing whether a protein is transported into an organelle is largely restricted to single constituents. This renders knowledge about imported proteins incomplete, limiting our understanding of organellar biogenesis and function. Here we introduce a method that enables charting an organelle's importome. The approach relies on inducible RNAi-mediated knockdown of an essential subunit of a translocase to impair import and quantitative mass spectrometry. To highlight its potential, we established the mitochondrial importome of Trypanosoma brucei, comprising 1,120 proteins including 331 new candidates. Furthermore, the method allows for the identification of proteins with dual or multiple locations and the substrates of distinct protein import pathways. We demonstrate the specificity and versatility of this ImportOmics method by targeting import factors in mitochondria and glycosomes, which demonstrates its potential for globally studying protein import and inventories of organelles. PMID:28485388

Everlasting Dark Printing on Alumina by Laser

NASA Astrophysics Data System (ADS)

Penide, J.; Quintero, F.; Arias-González, F.; Fernández, A.; del Val, J.; Comesaña, R.; Riveiro, A.; Lusquiños, F.; Pou, J.

Marks or prints are needed in almost every material, mainly for decorative or identification purposes. Despite alumina is widely employed in many different industries, the need of printing directly on its surface is still a complex problem. In this sense, lasers have largely demonstrated their high capacities to mark almost every material including ceramics, but performing dark permanent marks on alumina is still an open challenge. In this work we present the results of a comprehensive experimental analysis on the process of marking alumina by laser. Four different laser sources were used in this study: a fiber laser (1075 nm) and three diode pumped Nd:YVO4 lasers emitting at near-infrared (1064 nm), visible (532 nm) and ultraviolet (355 nm) wavelengths, respectively. The results obtained with the four lasers were compared and physical processes involved were explained in detail. Colorimetric analyses allowed to identify the optimal parameters and conditions to produce everlasting and high contrast marks on alumina.

A new karyotype for Rhipidomys (Rodentia, Cricetidae) from Southeastern Brazil

PubMed Central

de Carvalho, Ana Heloisa; Lopes, Maria Olímpia Garcia; Svartman, Marta

2012-01-01

Abstract In this work we present a new karyotype for Rhipidomys Tschudi, 1845 (Cricetidae, Rodentia) from Brazil. Our chromosome analyses included GTG- and CBG-banding patterns, the localization of the nucleolus organizer regions after silver staining (Ag-NORs) and fluorescence in situ hybridization (FISH) with a telomere probe. The new karyotype is composed of 44 chromosomes and has a fundamental number (number of autosomal arms) of 48. Most Rhipidomys species already karyotyped presented similar complements with 2n=44, but their fundamental numbers varied from FN=46 to 80, a variation that has been mainly attributed to pericentric inversions. The comparison of this new karyotype to those of other Rhipidomys already reported allowed us to conclude that it is a distinctive chromosome complement, which can be of great use as a tool for the very complicated taxonomic identification in this genus. PMID:24260664

Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges

PubMed Central

Bruder, Katherine; Malki, Kema; Cooper, Alexandria; Sible, Emily; Shapiro, Jason W.; Watkins, Siobhan C.; Putonti, Catherine

2016-01-01

Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations. PMID:27375355