Littérature scientifique sur le sujet « HTS sequencing »
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Articles de revues sur le sujet "HTS sequencing"
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Vuorio, Kristiina, Anita Mäki, Pauliina Salmi, Sanni Aalto, Marja Tiirola, and Marko Järvinen. "Consistency between high throughput sequencing and microscopy-based morphological characterization of phytoplankton communities." ARPHA Conference Abstracts 4 (March 4, 2021): e64972. https://doi.org/10.3897/aca.4.e64972.
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Thus far, the phytoplankton community composition analyses, used e.g. monitoring and assessment of the ecological status of water bodies, are based on time-consuming and expertise-demanding light microscopy analyses. Currently, DNA-based molecular tools are being developed to replace microscopy-based analyses. Although most of the DNA is expected to be found in living cells, long-lasting DNA in damaged cells or soluble extracellular or relic DNA can make up a large proportion of the total DNA in water samples. DNA-based phytoplankton analysis has been shown to be affected by the huge variation in the copy number of the rRNA gene between phytoplankton species (Mäki et al. 2017). On the contrary, RNA is present only in living organisms and reflects active protein synthesis. Therefore, RNA-based methods can provide a more reliable estimate of community composition.The large copy number variation of ribosomal genes and the absence of universal primers for simultaneous amplification of cyanobacterial and eukaryotic phytoplankton genes hinder the application of DNA-based molecular methods. We applied a directional random-primed high throughput sequencing (HTS) approach (Mäki and Tiirola 2018) to analyse 16S and 18S rRNA community structures of 83 boreal lakes in Finland, Northern Europe. With the method it was possible to simultaneously amplify all groups of aquatic microorganisms in addition to cyanobacteria and eukaryotic phytoplankton.A comparison between microscopy and HTS showed that the relative phylum (Fig. 0) and class level abundances of eukaryotic phytoplankton and order level abundances of cyanobacteria were consistent between the methods, despite that the HTS method overestimated the relative abundance of cyanobacteria. However, correspondence was low at genus and species level, mainly due to the lack of reference library sequences. HTS revealed more genera and was able to differentiate cryptic genera lacking morphological characteristics, but microscopy revealed a longer list of species (Vuorio et al. 2020).The RNA-based method applied showed potential, but it is not yet able to replace microscopy, mainly due to the lack of full length 16S and 18S sequences in the reference libraries. The main advantage of the method is that it is not limited to phytoplankton, but can be applied to simultaneous investigation of the total composition of microbes, including all bacteria, protists, ciliates, rotifers and zooplankton.
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Komarova, Natalia, Daria Barkova, and Alexander Kuznetsov. "Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology." International Journal of Molecular Sciences 21, no. 22 (2020): 8774. http://dx.doi.org/10.3390/ijms21228774.
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Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX.
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Pérez-Losada, Marcos, Miguel Arenas, Juan Carlos Galán, et al. "High-throughput sequencing (HTS) for the analysis of viral populations." Infection, Genetics and Evolution 80 (June 2020): 104208. http://dx.doi.org/10.1016/j.meegid.2020.104208.
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He, Xuejun, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, and Ning Yang. "Application Progress of High-Throughput Sequencing in Ocular Diseases." Journal of Clinical Medicine 11, no. 12 (2022): 3485. http://dx.doi.org/10.3390/jcm11123485.
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Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS has not only identified several normal ocular surface microorganisms but has also discovered many pathogenic bacteria, fungi, parasites, and viruses associated with eye diseases, including rare pathogens that were previously difficult to identify. At present, HTS can directly sequence RNA, which will promote research on the occurrence, development, and underlying mechanism of eye diseases. Although HTS has certain limitations, including low effectiveness, contamination, and high cost, it is still superior to traditional diagnostic methods for its efficient and comprehensive diagnosis of ocular diseases. This review summarizes the progress of the application of HTS in ocular diseases, intending to explore the pathogenesis of eye diseases and improve their diagnosis.
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GIZA, ALEKSANDRA, EWELINA IWAN, ARKADIUSZ BOMBA, and DARIUSZ WASYL. "Basics of high throughput sequencing Summary." Medycyna Weterynaryjna 77, no. 11 (2025): 6589–2025. http://dx.doi.org/10.21521/mw.6594.
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Sequencing can provide genomic characterisation of a specific organism, as well as of a whole environmental or clinical sample. High Throughput Sequencing (HTS) makes it possible to generate an enormous amount of genomic data at gradually decreasing costs and almost in real-time. HTS is used, among others, in medicine, veterinary medicine, microbiology, virology and epidemiology. The paper presents practical aspects of the HTS technology. It describes generations of sequencing, which vary in throughput, read length, accuracy and costs ̶ and thus are used for different applications. The stages of HTS, as well as their purposes and pitfalls, are presented: extraction of the genetic material, library preparation, sequencing and data processing. For success of the whole process, all stages need to follow strict quality control measurements. Choosing the right sequencing platform, proper sample and library preparation procedures, as well as adequate bioinformatic tools are crucial for high quality results.
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Aronesty, Erik. "Comparison of Sequencing Utility Programs." Open Bioinformatics Journal 7, no. 1 (2013): 1–8. http://dx.doi.org/10.2174/1875036201307010001.
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High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly. Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and effectiveness.
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Pu, Dan, and Pengfeng Xiao. "A real-time decoding sequencing technology—new possibility for high throughput sequencing." RSC Advances 7, no. 64 (2017): 40141–51. http://dx.doi.org/10.1039/c7ra06202h.
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Malapi-Wight, Martha, Bishwo Adhikari, Jing Zhou, et al. "HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection." Viruses 13, no. 8 (2021): 1627. http://dx.doi.org/10.3390/v13081627.
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Rapid global germplasm trade has increased concern about the spread of plant pathogens and pests across borders that could become established, affecting agriculture and environment systems. Viral pathogens are of particular concern due to their difficulty to control once established. A comprehensive diagnostic platform that accurately detects both known and unknown virus species, as well as unreported variants, is playing a pivotal role across plant germplasm quarantine programs. Here we propose the addition of high-throughput sequencing (HTS) from total RNA to the routine quarantine diagnostic workflow of sugarcane viruses. We evaluated the impact of sequencing depth needed for the HTS-based identification of seven regulated sugarcane RNA/DNA viruses across two different growing seasons (spring and fall). Our HTS analysis revealed that viral normalized read counts (RPKM) was up to 23-times higher in spring than in the fall season for six out of the seven viruses. Random read subsampling analyses suggested that the minimum number of reads required for reliable detection of RNA viruses was 0.5 million, with a viral genome coverage of at least 92%. Using an HTS-based total RNA metagenomics approach, we identified all targeted viruses independent of the time of the year, highlighting that higher sequencing depth is needed for the identification of DNA viruses.
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Ma, Hailun, Trent J. Bosma, and Arifa S. Khan. "Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X+ Genome Contains a 3.7 kb Internal Duplication." Viruses 15, no. 10 (2023): 1998. http://dx.doi.org/10.3390/v15101998.
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We previously reported a novel rhabdovirus produced from the Spodoptera frugiperda Sf9 cell line, designated as Sf-rhabdovirus X+ since it contained a unique accessory gene X. The Sf-rhabdovirus X+ genome sequence was generated using Sanger sequencing and short-read high-throughput sequencing (HTS). In this study, we have used long-read HTS technologies, PacBio’s single-molecule real-time sequencing and Oxford’s Nanopore RNA direct sequencing, to analyze the parent Sf9 cell line transcriptome and the virus RNA produced from an X+ cell clone, respectively. A unique 3.7 kb duplication was identified in the L gene between nucleotide position 8523 and 8524, preceded by a GA dinucleotide insertion. This duplication contained a partial G gene, the complete X gene, and a partial L gene, which extended from nucleotide positions 4767–8523 in the X+ virus. Thus, the X+ genome length is 17,361 nucleotides, and we have re-designated the virus as Sf-rhabdovirus X+3.7. The 3.7 kb duplication was found in all Sf9 cell clones producing the X+ variant virus. Furthermore, the Sf-rhabdovirus X+3.7 genome was stable at passage 30, which was the highest passage tested. These results highlight the importance of combining short-read and long-read technologies for accurately sequencing virus genomes using HTS.
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Bester, Rachelle, Chanel Steyn, Johannes H. J. Breytenbach, Rochelle de Bruyn, Glynnis Cook, and Hans J. Maree. "Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids." Plants 11, no. 15 (2022): 1939. http://dx.doi.org/10.3390/plants11151939.
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The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of the HTS assay was compared to routinely used RT-PCR assays in a time course experiment, to compensate for natural pathogen accumulation in plants over time. The HTS pipeline applied in this study produced reproducible and comparable results to standard RT-PCR assays for the detection of CTV and three viroid species in citrus. Even though the limit of detection of HTS can be influenced by pathogen concentration, sample processing method and sequencing depth, detection with HTS was found to be either equivalent or more sensitive than RT-PCR in this study.
Thèses sur le sujet "HTS sequencing"
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Solayman, Md. "High-Throughput Sequencing Based Probing of Protein/RNA Structures and Functions." Thesis, Griffith University, 2022. http://hdl.handle.net/10072/416290.
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The rapid advancement in sequencing chemistry, sequencing technologies, and bioinformatics has significantly increased the sequencing automation and lowered the cost. The applications of high-throughput sequencing (HTS) technologies are expanding from research laboratories to diagnostic clinics on a regular basis. Moreover, diverse methods used in epigenetics, proteomics, structure probing of macromolecules (DNA, RNA, and proteins) have been developed based on the HTS technology. This thesis describes the development of two novel techniques, high-throughput split-protein profiling (HiTS) and RNA solvent accessibility probing method (RL-Seq), broadening the applications of HTS technologies for probing protein/RNA structures and functions.
Chapter 1 of the thesis provides an overview of the history of HTS technologies, available platforms, ongoing development in this field, and their diverse applications, particularly in the area of proteomics and RNA structure probing.
In Chapter 2, we introduced the HiTS method that allowed fast identification of self- and assisted complementary positions of three antibiotic-resistant proteins (fosfomycin, fosA3; erythromycin, ermB; and chloramphenicol, catI resistant-proteins). The finding of suitable split sites in proteins is important because they are used as reporters in protein complementary assay (PCA) for studying protein-protein interactions in different organisms. However, only a small number of split-protein systems have been identified so far owing to manual, labourintensive optimization of the candidate genes. The proposed HiTS method employs transposon mutagenesis, conditional interaction of split fragments by rapamycin-regulated FRB-FKBP protein pairs, and deep sequencing for fast identification of self- and assisted complementary fragments, which are subsequently confirmed by low-throughput testing.
In Chapter 3, we further applied the HiTS method on T7 RNA polymerase (T7 RNAP), a bacteriophage RNA polymerase, considering its importance in synthetic biology in addition to the PCA. We found that the newly developed HiTS method could also be applicable to T7 RNAP for locating suitable split sites for self-complementing variants. Several selfcomplementing variants were found and one with a stronger signal than the wild type one.
In Chapter 4, in preparation of applying HTS technology to probe RNA solvent accessibility, we reviewed the available experimental and computational techniques for RNA solvent accessibility studies and identified existing research gaps. Current experimental approaches for studying RNA solvent accessibility include hydroxyl radical probing (HRF-Seq), light activated structural examination of RNA (LASER), and its modified versions (LASER-Seq, LASER-Map, and icLASER). The reactivity readouts of these methods are based on either the reverse transcriptase stop (RT-stop) at cleavage points or mutational profiling at adduct formation sites. These approaches rely on reverse transcriptase enzymes and random primers, which suffer from non-specific drop-off to create short truncated sequences, which successively lead to false-positive signals at probe-reactive sites.
In Chapter 5, we proposed the RL-Seq (RtcB Ligation-Seq) method to overcome the abovementioned limitations of the existing approaches. The method is illustrated by measuring the solvent accessibility of Escherichia coli complete ribosomal complexes at the single-nucleotide resolution. In this method, unique properties of RtcB ligase were used to identify the probing sites by ligating a pre-defined 5′-OH end containing linker with the hydroxyl radicals cleavage generated 3′-P ends. The application of this method to ribosomal RNAs (23S, 16S, and 5S rRNAs) confirmed its ability to estimate solvent accessibility with high sensitivity (required low sequencing depth) and accuracy (strong correlation to structure-derived values). In addition, the pre-defined linker employed in this method allowed using of a fixed primer in reverse transcription reaction and significantly minimized the biases during subsequent PCR amplification.
In Chapter 6, we discussed the future prospects of these HTS technology-based methods developed in this thesis.<br>Thesis (PhD Doctorate)<br>Doctor of Philosophy (PhD)<br>Institute for Glycomics<br>Full Text
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AGOSTINETTO, GIULIA. "Data-driven approaches for biodiversity exploration via DNA metabarcoding data analysis." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/365346.
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Gli approcci metagenomici hanno cambiato il modo di studiare la biologia e la biodiversità in diversi campi. In particolare, il progresso tecnologico ci consente di determinare la composizione tassonomica dei campioni e di studiare la biodiversità in ambienti molto diversi. Al giorno d'oggi, il DNA metabarcoding è una procedura standard, applicata in un'ampia gamma di settori, dalla salute umana all'ecologia, alle applicazioni industriali.
Negli ultimi anni, il DNA metabarcoding applicato al 16S rRNA è stato ampiamente utilizzato per studiare la comunità batterica, portando ad analisi di routine che hanno creato enormi quantità di dati, consentendo ai ricercatori di sviluppare strategie data-driven per rispondere a domande biologiche complesse. Inoltre, il DNA metabarcoding può essere utilizzato anche per studiare Piante, Animali o Funghi, grazie allo sviluppo di diversi marcatori molecolari.
In entrambi i casi, considerando l'enorme quantità di dati prodotti dai ricercatori e disponibili nelle banche dati, una prospettiva di ‘data mining’ nella gestione e nell'esplorazione dei dati di DNA metabarcoding potrebbe essere utile per identificare nuovi pattern ed estrarre maggiori informazioni dai dati.
Nella mia tesi di dottorato, mi sono focalizzata su una prospettiva incentrata sui dati di DNA metabarcoding, toccando quattro punti principali che possono potenziare e migliorare le strategie attuali: i) considerare le informazioni molecolari ottenute dal sequenziamento high-throughput del DNA (HTS) e disponibili in archivi pubblici, ii ) migliorare la fase di assegnazione della tassonomia, iii) studiare nuovi metodi per la ricostruzione di pattern di biodiversità e iv) utilizzare dati già prodotti come risorsa preziosa per la ricerca.
Questi quattro punti possono migliorare a diversi livelli le potenzialità delle applicazioni di tecniche fondate sul DNA metabarcoding, aprendo la strada a procedure di standardizzazione per marcatori meno diffusi e all'integrazione di nuove strategie di data mining e riutilizzo di dati di DNA metabarcoding.<br>Metagenomic approaches have changed the way to study biology and biodiversity in several fields. In particular, technology advancement enables us to determine taxa composition and to study complex biodiversity patterns in very different environments. Nowadays, DNA metabarcoding is a standard procedure, applied on a wide range of fields, from human health to ecology, to industry applications.
In the last few years, 16S rRNA metabarcoding was widely used to study the bacterial community, leading to routine analysis which created huge amounts of data, bringing researchers to develop data mining strategies in order to answer complex biological questions. On the other hand, DNA metabarcoding can be applied also to study Plants, Animals or Fungi, as very different molecular markers have been identified.
In both cases, considering the huge amount of data produced by researchers and available in repositories, a data-driven perspective in managing and exploring DNA metabarcoding data could be useful to collect hidden information and potentially determine undiscovered aspects.
In this PhD dissertation, I focused the attention on a data-centered perspective of DNA metabarcoding data, touching four main points that can enhance and ameliorate the current strategies: i) consider the molecular information obtained from high-throughput DNA sequencing (HTS) and available in public repositories, ii) enhance taxonomy assignment step, iii) investigate new methods for pattern reconstruction and iv) use data as a valuable resource for research.
These four steps can enhance at different levels the potentials of DNA metabarcoding applications, paving the way for standardization procedures for uncommon markers and the integration of new data mining and data reuse strategies of metabarcoding data.
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Snyder, Matthew Robert. "Environmental DNA Detection and Population Genetic Patterns of Native and Invasive Great Lakes Fishes." University of Toledo / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1564680483342507.
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Horton, Dean J. "Using molecular techniques to investigate soil invertebrate communities in temperate forests." Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1448799316.
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Eschlimann, Marine. "Influence de la variabilité des protéines d’enveloppe du virus de l’hépatite B sur l’évolution de l’infection évaluée par la persistance de l’antigène HBs." Thesis, Université de Lorraine, 2017. http://www.theses.fr/2017LORR0133/document.
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L’hépatite B chronique touche environ 257 millions de personnes dans le monde. La perte de l’antigène HBs (AgHBs), marqueur de guérison fonctionnelle, n’est que très rarement observée, même sous traitement antiviral (3-16 %). Les protéines d’enveloppe du virus de l’hépatite B (VHB), formant l’AgHBs, sont très variables et cruciales pour le pouvoir infectieux du virus de l’hépatite B (VHB) et la physiopathologie. Nous avons émis l’hypothèse que cette variabilité pourrait expliquer, au moins partiellement, l’évolution de l’infection par le VHB, évaluée par la clairance de l’AgHBs, chez des patients traités ou non par analogues nucléos(t)idiques anti-VHB. Chez 29 patients infectés par différents génotypes du VHB (A, C et D), présentant différents profils cliniques (infection aigüe ou chronique, co-infection VHB/VIH) et thérapeutiques, une très grande variabilité des protéines d’enveloppe du VHB a été mise en évidence. Chez ces patients, la persistance de l’AgHBs était corrélée avec la présence de mutations et délétions localisées dans des régions des protéines d’enveloppe virale jouant un rôle important dans la reconnaissance du virus par le système immunitaire. Ces résultats renforcent l’hypothèse que l’étude des protéines d’enveloppe du VHB pourrait mettre en évidence des signatures moléculaires influençant le fitness du VHB et par conséquent l’évolution clinique de la maladie liée à l’infection par le VHB<br>Chronic hepatitis B affects about 257 million people worldwide. The loss of HBS antigen (HBsAg), a marker of the functional cure, is very rarely observed, even on anti-HBV treatment (3-16%). The hepatitis B virus (HBV) envelope proteins (HBsAg) are highly variable and crucial for the viral infectivity and pathogeny. We hypothesized that the HBV variability in the envelope proteins could explain, at least partially, the evolution of HBV infection, evaluated by HBsAg clearance, in patients treated or not by anti-HBV nucleos(t)idic analogues. For 29 patients infected with different HBV genotypes (A, C and D), presenting different clinical profiles (acute or chronic infection, HBV/HIV co-infection) and therapies, a very high variability of HBV envelope proteins was observed. In these patients, the persistence of HBsAg was correlated with the presence of mutations and deletions located in areas that play a key role in the viral recognition by the immune system. These results reinforce the hypothesis that the study of HBV envelope proteins could highlight molecular signatures influencing HBV fitness which would subsequently modify the clinical evolution of HBV-related disease
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Young, Jennifer M. "Application of DNA metabarcoding and high-throughput sequencing for enhanced forensic soil DNA analysis." Thesis, 2014. http://hdl.handle.net/2440/91437.
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The complex and variable soil matrix can support a wide range of biota that can provide information about local vegetation, soil conditions (e.g. soil acidity) and habitat type. As the combination of microbes, plants and animals within a soil is often specific to a given site, identification of the soil biota can narrow the likely source of a soil sample. DNA fingerprinting analysis of soil microbes has been used as forensic evidence in court to establish a link between a suspect and a site, victim or object. However, previous genetic analyses have relied on patterns of fragment length variation produced by amplification of unidentified taxa in the soil extract, particularly bacteria. In contrast, the development of advanced DNA sequencing technologies now provides the ability to generate a detailed picture of soil communities and the taxa present, allowing for improved discrimination between samples. This thesis examines the use of DNA metabarcoding combined with high-throughput sequencing (HTS) technology to distinguish between soils from different locations in a forensic context. Specifically, I review the DNA extraction protocols available for soils and recommend best practice for successful analysis (Chapter 2). Following this, I examine the reproducibility and discriminatory power of four different genetic markers for forensic soil discrimination using HTS (Chapter 3). Non-bacterial
DNA, particularly fungi, were found to be the most promising target for soil discrimination and additionally showed consistent PCR amplification and low contamination risk. It is known that DNA extraction protocols can introduce discrepancies in soil community profiles, and the optimal sample size for an accurate and representative survey of soil diversity has been debated. Therefore I used various soil types to test the robustness of modified DNA extraction protocols (Chapter 4) and trace, or limited, amounts of soil (Chapter 5). I make recommendations about the optimal DNA extraction method and sample size given soil properties such as clay content, soil pH and texture. To assess the application of this method in forensic casework, I then designed a mock case scenario. DNA profiles of six soil samples recovered from a suspect’s belongings were compared to those collected from seven reference sites around Adelaide, South Australia. This study demonstrated that the soil from the suspect’s belongings had eukaryote diversity more similar to those collected from the crime scene than to any other sample collected at random. This suggested the presence of the suspect at the crime scene. This result was compared to that from a soil analysis method currently accepted in court. In this case example, both methods successfully established a link between the suspect’s belongings and the crime scene; however, DNA analysis improved resolution between reference locations. This thesis demonstrates the first practical application of DNA metabarcoding and high-throughput sequencing (HTS) to forensic soil analysis. I show that this approach is consistently able to distinguish between soil samples taken from different localities, and consequently may be employed as an additional line of evidence or investigation in forensic casework.<br>Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2014
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Lin, Wei-Chih, and 林威志. "Development of Pilot-Scale Chemical-Biological H2S Elimination Systems and Characterization of Genome and Transcriptome of Acidithiobacillus ferrooxidans Mutant W3 by Next Generation Sequencing." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/33913990273447439232.
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博士<br>國立交通大學<br>生物科技系所<br>102<br>The acidophilic and autotrophic Acidithiobacillus ferrooxidans oxidizes ferrous iron into ferric iron to obtain the electrons and reducing power. The ferric iron was used to be an oxidant for H2S elimination and A. ferrooxidans was immobilized in the bioreactor for the ferric iron regeneration. This combined and renewable system was applied for the biogas purification in this study. The former “carrier-based” reactors are unadvisable as H2S elimination system because they are prone to sulfur blockage problems under heavy loading operations. Therefore, the “scrubbing-style” reactor was designed for robust biogas purification under pilot-scale long-term operation. In the type I “scrubbing-style” system of laboratory scale study, various H2S inlet flow rates and spray pressures were used to evaluate the H2S removal efficiency (RE) in the chemical reactor. The high H2S RE (> 90%) demonstrated that this scrubbing-style system performed well under heavy loading (~ 1,300 g-S m-3 h-1) without severe sulfur blockage. In the scaled-up application, the type I system using A. ferrooxidans CP9 was operated for consecutive 356 days for biogas purification, including shock loading and shutdown tests. The system achieved an average RE of 94.8% with an elimination capacity (EC) value of 64 g-S m-3 h-1 under EBRT 216 s. In addition, the system recovered quickly in the shock loading and shutdown tests without permanent damage; however, the solid sulfur still caused blockage after the long-term operation. In the type II “scrubbing-style” system, the design of the connection between the chemical absorbers and the storage tank was improved to elevate the removal efficiency and quickly remove the sulfur solid. In laboratory scale study, the effects of droplet size and column size on the optimal H2S removal were characterized. In the scaled-up application, the type II system using the high growth rate strain W3 was operated for 500 consecutive days for biogas purification. The optimal conditions were an average RE of 90% with an EC of 302 g-S m-3 h-1 under EBRT 73 s. In the power generation test with 30 kW biogas generation, the maximum power output was 27.6 kW and the maximum thermal efficiency was 26.4% at a biogas supply rate of 220 litter per minute (LPM) using 70% CH4. The W3 strain in the type II system showed approximately 100% higher maximum iron oxidation rate than the CP9 in the type I system. Furthermore, only 34% EBRT was required for the type II system to deal with the 5 folds H2S loading higher than the type I system.
To further characterize the differences between A. ferrooxidans CH9 and W3, their genome and transcriptome were subjected to next-generation sequencing (NGS) analysis. The results show 88.4% of the sequenced genomes (2829 of 3309 genes) from CP9 and W3 were assembled by mapping to the reference ATCC 23270 genome. Moreover, 288 mutated paired bases were located on the 79 coding sequences (CDS), whereas 22 paired bases were located on the non-coding region of the W3 genome. The gene ontology (GO term) analysis showed similar hit term distributions for both mutant genes and total genes, which indicates that the mutation rate in each specific class is size-related and randomly mutated. In the NGS transcriptomic analysis, the total qualified paired-end sequencing reads from six samples mapped to the reference genome ranged from 80.3% to 81.9%. Also, this study is the first time to apply NGS in the differential expressed gene analysis of a different energy source for A. ferrooxidans. Collection of sulfur metabolism–related genes from the NGS data provided new evidence of candidate genes that encode key enzymes involved in unidentified pathways. For example, the sreABCD protein encoded in the sre operon was highly expressed under sulfur-growth conditions (fold change (FC) = 2–4), which was considered responsible for reducing sulfur into sulfide. Moreover, cysJ and cysI are highly expressed under iron-growth conditions (FC = 8). Thus, these genes encode proteins that catalyze the reduction of sulfite into sulfide and could involve in the only pathway for sulfide production under such conditions. Furthermore, 10 genes were found in the mutant W3 with differentially expressed under four various conditions. In particular, glcF was highly expressed (FC = 2.7) during the lag phase rather than in the log phase of the mutant W3; however, this gene was minimally expressed during both the lag phase and the log in the CP9 strain. The fold change was also examined by quantitative polymerase chain reaction (qPCR) and shows the evidence that glcF in W3 was highly expressed (FC = 6.1) in the lag phase than in the log phase. The glycolate oxidase encoded by the glc operon could catalyze the conversion of glycolate into innocuous glyoxylate in A. ferrooxidans carbon metabolism. Therefore, highly efficient detoxification could be account for the 8.5 folds higher growth rate during the lag phase of the mutant W3 than that of the CP9.
Livres sur le sujet "HTS sequencing"
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Newman, Abraham L. Sequencing, Layering, and Feedbacks in Global Regulation. Edited by Orfeo Fioretos, Tulia G. Falleti, and Adam Sheingate. Oxford University Press, 2016. http://dx.doi.org/10.1093/oxfordhb/9780199662814.013.38.
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From banking standards to data privacy, regulation has entered the lexicon of international affairs. Unlike trade or currencies, however, there are few formal treaty-based international organizations resolving disputes or setting the rules for the world. Instead, global regulation is frequently shaped by informal networks of regulators or at times by the extraterritorial extension of domestic law by large markets. Drawing on work from historical institutionalism, this chapter argues that the global politics of regulation is in important respects the product of domestic and international institutions interacting over time and across space. In developing three mechanisms—relative sequencing, cross-national layering, and transnational feedbacks —the chapter argues that historical institutionalism helps address lacunae in extant approaches to global regulation.
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Bantekas, Ilias. Sequencing Peace and Justice in Post-Conflict Africa. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198810568.003.0005.
Texte intégralRésumé :
This chapter discusses the extent to which there is any conflict or harm in the ICC Prosecutor’s involvement in cases undergoing mediation by the international community, most of which are currently in Africa. The ICC Prosecutor’s discretion, as per the Court’s Statute, to hold a prosecution in abeyance in anticipation of the outcomes of mediating efforts which aim at ending a conflict is at best ambivalent. Recent practice suggests that stakeholders engaged in ending long-running African conflicts prefer the Prosecutor to decline to exercise jurisdiction in order to encourage the parties to reach some agreement. For obvious reasons, discussions on such matters are often held confidentially and not in the context of official debates. The African experience with the peace–justice nexus shows that the peace-versus-justice debate has not been resolved in favour of any camp.
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Sadleir, Lynette G., Jozef Gecz, and Ingrid E. Scheffer. Epilepsies That Occur Predominantly in Girls. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199937837.003.0041.
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Availability of DNA sequencing has led to an increase in the number of children being identified with mutations in specific genes in specific epilepsy phenotypes. The presence of mutations that cause epilepsy only in females is one of the discoveries revealed in the sequencing era. Mutations in PCDH19 and CDKL5 are distinctive and identifiable forms of female-only epilepsy, and clinicians should consider PCDH19 in normal girls presenting with clusters of afebrile or febrile seizures in the first 3 years of life, and CDKL5 in girls or boys presenting with severe developmental delay within the first 6 months of life followed by intractable seizures including spasms within the first 2 years.
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Walsh, Richard A. Siblings with Instability. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190607555.003.0015.
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Over the past 5 years, there has been a shift in the approach to searching for a genetic diagnosis in familial ataxic syndromes. Whereas in the past, a limited but expensive search through a selection of commercially available genes using Sanger sequencing was performed, there is now widespread availability of gene panels utilizing next-generation sequencing techniques. This is an efficient and powerful approach that may achieve a diagnosis in more than 30% of patients with a familial ataxia that remain undiagnosed. However, accurate phenotyping remains critical to allow interpretation of sequence variants of uncertain significance, to identify biomarkers that may be useful to monitor future therapies, and to assist with the identification of underlying pathophysiology.
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Purcell, Shaun M. Genetic Methodologies and Applications. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0001.
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Mental illness is highly heritable, yet it has been difficult historically to identify the specific genes that comprise that risk. This difficulty resides in the fact that the genetic risk for all common mental disorders is polygenic, with perhaps hundreds of genetic variations, each of small effect, contributing to the overall risk. Despite these challenges, the field has made dramatic advances over the past decade in beginning to understand the genetic basis of mental illness. This chapter provides an overview of the experimental approaches used, beginning with epidemiology and population genetics to define the heritability of an illness, to classic studies of large families and linkage disequilibrium analysis, to genome-wide investigations including genome-wide association studies (GWAS), exome sequencing, and whole genome sequencing. Increasingly, these genetic advances are being understood within the biological context of disease pathophysiology.
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Maher, Christopher J., and Elaine R. Mardis. Genomic Landscape of Cancer. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780190238667.003.0004.
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The study of cancer genomics has advanced rapidly during the last decade due to the development of next generation or massively parallel technology for DNA sequencing. The resulting knowledge is transforming the understanding of both inherited (germline) genetic susceptibility and the somatic changes in tumor tissue that drive abnormal growth and progression. The somatic alterations in tumor tissue vary depending on the type of cancer and its characteristic “genomic landscape.” New technologies have increased the speed and lowered the cost of DNA sequencing and have enabled high-volume characterization of RNA, DNA methylation, DNA-protein complexes, DNA conformation, and a host of other factors that, when altered, can contribute to the development and/or progression of the cancer. Technologic advances have greatly expanded research on somatic changes in tumor tissue, revealing both the singularity of individual cancer genomes and the commonality of genetic alterations that drive cancer in different tissues.
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Munro, Carol A., and Duncan Wilson. Fungal genomics and transcriptomics. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0006.
Texte intégralRésumé :
The advent of whole-genome sequencing has resulted in a range of platforms for large-scale analysis of the DNA (genomics), RNA (transcriptomics), protein (proteomics), and metabolite (metabolomics) content of cells. These inclusive ‘omics’ approaches have allowed for unparalleled insights into fungal biology. In this chapter we will discuss how genomics and transcriptomics have been used to broaden our understanding of the biology of human pathogenic fungi and their interactions with their hosts.
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Ingles, Jodie, Charlotte Burns, and Laura Yeates. Genetic counselling. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198784906.003.0145.
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Cardiac genetic counselling is an emerging but important subspecialty. The qualifications of cardiac genetic counsellors depend on the country of practice, but at a minimum they are Master’s-level trained health professionals with expertise in genetics, and are integral members of the multidisciplinary inherited cardiovascular disease clinic. Though the framework is diverse in different countries, key roles include investigation and confirmation of family history details, discussion of inheritance risks and facilitation of cardiac genetic testing, communication with at-risk relatives, and increasingly, curation of genetic test results. The use of next-generation sequencing technologies has seen a recent shift in the uptake of genetic testing, due to greater availability and lowered costs. As these gene tests become more comprehensive, including large panels of genes and even whole exome or whole genome sequencing, the need for cardiac genetic counsellors to provide informed consent, appropriate pre- and post-test genetic counselling, and ongoing curation of the variants identified is evident. Finally, given the improved understanding of the psychological implications of living with a cardiovascular genetic disease, cardiac genetic counsellors are integral in delivering psychosocial care and identifying patients requiring intervention with a clinical psychologist.
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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.
Texte intégralRésumé :
The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
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Halliday, Catriona L., and Sarah E. Kidd. Cryptococcus species. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0012.
Texte intégralRésumé :
Cryptococcus neoformans and Cryptococcus gattii are the principal pathogenic species within the genus Cryptococcus and the causative agents of cryptococcosis. Although rare, the incidence of infection due to other Cryptococcus species previously regarded as saprophytes, has increased over the last 40 years. Irrespective of the infecting species, infections are acquired following inhalation from the environment, causing localised or disseminated disease. The severity of disease is dependent on the organism’s virulence factors and the host’s immune response, and the clinical manifestations are indistinguishable. Accurate identification of the pathogenic species relies on rDNA sequencing
Chapitres de livres sur le sujet "HTS sequencing"
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Quadros, Ayane F. F., and Francisco Murilo Zerbini. "High-throughput Sequencing (HTS)-Based Diagnosis of Geminiviruses." In Methods in Molecular Biology. Springer US, 2025. https://doi.org/10.1007/978-1-0716-4454-6_15.
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Lavín Trueba, José Luis, and Ana M. Aransay. "The High-Throughput Sequencing Technologies Triple-W Discussion: Why Use HTS, What Is the Optimal HTS Method to Use, and Which Data Analysis Workflow to Follow." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_1.
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O’Sullivan, Christopher, and Jonathan Trow. "Submitting Data to a Public Repository, the Final Step of a Successful HTS Experiment." In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_16.
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Bester, Rachelle, and Hans J. Maree. "Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids." In Methods in Molecular Biology. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3515-5_14.
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Arumugam, Ramitha, Prithivan Ravichandran, Swee Keong Yeap, et al. "Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST." In Metagenomic Data Analysis. Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3072-3_8.
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Sterflinger, Katja, and Guadalupe Piñar. "Molecular-Based Techniques for the Study of Microbial Communities in Artworks." In Microorganisms in the Deterioration and Preservation of Cultural Heritage. Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69411-1_3.
Texte intégralRésumé :
AbstractThanks to the revolutionary invention of the polymerase chain reaction and the sequencing of DNA and RNA by means of “Sanger sequencing” in the 1970th and 1980th, it became possible to detect microorganisms in art and cultural assets that do not grow on culture media or that are non-viable. The following generation of sequencing systems (next generation sequencing, NGS) already allowed the detection of microbial communities on objects without the intermediate step of cloning, but still most of the NGS technologies used for the study of microbial communities in objects of art rely on “target sequencing” linked to the selectivity of the primers used for amplification. Today, with the third generation of sequencing technology, whole genome and metagenome sequencing is possible, allowing the detection of taxonomic units of all domains and kingdoms as well as functional genes in the produced metagenome. Currently, Nanopore sequencing technology is a good, affordable, and simple way to characterize microbial communities, especially in the field of Heritage Science. It also has the advantage that a bioinformatic analysis can be performed automatically. In addition to genomics and metagenomics, other “-omics” techniques such as transcriptomics, proteomics, and metabolomics have a great potential for the study of processes in art and cultural heritage, but are still in their infancy as far as their application in this field is concerned.
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Zhao, Yuanzhe, Jie Zhang, Zepeng Sun, Zheqi Cao, Liqun Xu, and Jian Li. "Scheme Design and Challenges of DNA Sequencing Terminal Equipment Based on Solid-State Nanopore Sequencing." In Lecture Notes in Mechanical Engineering. Springer Nature Singapore, 2025. https://doi.org/10.1007/978-981-97-7887-4_13.
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Abstract Nanopore sequencing has become the primary technology for modern DNA sequencing. Solid nanopores are favored for their cost-effectiveness, stability, and scalability, particularly for portable applications. This paper presents a new design for a portable solid-state nanopore sequencing device based on the Linux platform. It employs a cutting-edge biological sequencing chip with a nanopore channel to capture through-hole data. Electrical signals from the chip are processed to create DNA sequence data files. The Linux-based Raspbian OS serves as the control terminal, facilitating seamless communication between components. Data is then transmitted to a cloud platform via a 5G unit for further analysis. This study integrates software and hardware for instrument validation.
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Garg, Vanika, and Rajeev K. Varshney. "Analysis of Small RNA Sequencing Data in Plants." In Plant Bioinformatics. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2067-0_26.
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AbstractOver the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies.
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Lau, Dawn Yan Lam, Jose Roberto Aguirre Sánchez, Craig Baker-Austin, and Jaime Martinez-Urtaza. "What Whole Genome Sequencing Has Told Us About Pathogenic Vibrios." In Advances in Experimental Medicine and Biology. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-22997-8_16.
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Clear, Rachel, Eric Dumonteil, and Claudia Herrera. "Decoding Chagas Disease: What Next-Generation Sequencing Has Taught Us." In Recent Advances in Parasitomics. Springer Nature Switzerland, 2025. https://doi.org/10.1007/978-3-031-70591-5_3.
Texte intégralActes de conférences sur le sujet "HTS sequencing"
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Shi, Wei, Paul Evans, Gabrielle Scheffer, and Casey Hubert. "Novel Application of Nitrate as H2S Control Strategy in Permian Basin Produced Water Storage Ponds." In CONFERENCE 2023. AMPP, 2023. https://doi.org/10.5006/c2023-18968.
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Abstract Produced water (PW) ponds are important facilities for supporting hydraulic fracturing in the Permian Basin. The control of H2S in these facilities is critical to safe and reliable frac and production operations. Effective microbial control strategies are required to mitigate sulfate-reducing bacteria (SRB) activity and fouling of production facilities with iron sulfide. Next generation sequencing (NGS) DNA analyses of Delaware Basin produced water (PW) samples highlighted a bacterial consortium dominated by putative halophilic fermentative and sulfate-reducing bacteria such as Halanaerobium spp. and Desulfohalobium spp. Anaerobic biodegradation of hydrocarbons can generate metabolites which serve as electron donors to support SRB activity. The novel application of calcium nitrate to produced water storage ponds for SRB control was piloted in Delaware Basin. DNA analysis demonstrated the impact of nitrate on the microbial consortium in the treated pond. Putative nitrate-reducing bacteria became dominant, with a greatly reduced abundance of SRB. Produced water bacterial growth experiments demonstrated the controls of redox potential and salinity on bacterial nitrate reduction, to aid in interpretation of the field data. The pilot was effective in preventing biogenic sulfidogenesis and has been adopted as a long-term mitigation strategy in PW storage ponds.
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Farschon, Christopher, Michael Hewins, and Charles Moran. "Repainting Bridges During Rehabilitation Projects: Sequencing Options." In Paint and Coatings Expo (PACE) 2006. SSPC, 2006. https://doi.org/10.5006/s2006-00025.
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Abstract Major bridge rehabilitation projects may include painting of the steel superstructure in addition to deck replacement, expansion joint improvements, bearing replacement, etc. This paper will review the scheduling of the coatings work during a bridge rehabilitation project and how the order of coatings work affects the project schedule, cost, and quality. Constructing and then painting a complex steel structure is no easy task. Designers and constructors face numerous challenges throughout the process, not the least of these is how to protect the steel from corrosion during the life of the structure. For many years through today painting a mild steel bridge is the desired corrosion control method. When steel bridges are new, contractors typically have the choice to use pre-painted components, to field paint the structure, or to do a combination of both. When an existing bridge is being rehabilitated the decisions related to painting the new components are similar, but what is often overlooked is the decision about when to re-paint the large amounts of existing steel. Common sense tells us to paint something when we want it to be “finished,” especially something that has to be assembled at a construction site such as a bridge. It is likely that paint on pre-finished components may be damaged during construction. So why would the designer of a steel bridge rehabilitation project specify that portions of the painting process be performed before or during other construction activities? In certain cases a cleaned and prime painted bridge can significantly benefit other construction work and result in a more efficient overall project. This article will outline the scope and sequencing of a steel bridge rehabilitation project, review the painting of four relevant projects, and list issues related to combining re-painting with other steel bridge rehabilitation tasks.
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Manna, Kathleen, Joseph Moore, Kenneth Wunch, et al. "Relative Performance of Various 16S iTag Amplicon Sequencing Primer Pairs in Profiling Microbial Communities Relevant to Oil & Gas Operations." In CORROSION 2019. NACE International, 2019. https://doi.org/10.5006/c2019-13442.
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Abstract The oil and gas industry's efforts to characterize microbial communities in oilfield process fluids has shed increasing light on the influence of bacteria and archaea on hydrocarbon production. Notably, topside or downhole water contamination by microorganisms such as sulfate-reducing bacteria, acid-producing bacteria, and/or other halophiles can negatively impact asset integrity and reduce the quality and quantity of produced hydrocarbons. Molecular microbiology methods have contributed to our understanding of these complex processes by providing unprecedented resolution of resident microbial communities. However, a lack of methodological consistency among industry and academic laboratories studying microbiological processes in oilfield systems has precluded the industry's ability to discern broad cause-and-effect trends or compare results across laboratories. For example, there exists no standard primer set for 16S rRNA gene amplicon sequencing agreed upon by the oil and gas community. Recently, a partnership between industrial and academic laboratories was initiated to perform a comprehensive microbial audit of multiple unconventional upstream operations. Over the course of the audit, samples were systematically taken during drilling, throughout completions, and periodically over the first year of production. Produced water samples were submitted for whole-genome metagenomics sequencing and assembly with near-complete genomes for input microbes and reservoir-colonizing microbes subsequently resolved. The intention of creating this genome-resolved metagenomics dataset was to remove the PCR bias of any given 16S rRNA gene amplification primer set, allowing for comparisons of the performance of common primer pairs. This, along with corroborating in silico evaluations, led to the conclusion that many of the primer pairs commonly used for 16S rRNA sequencing of environmental/energy samples provide accurate and comparable profiles of microbial communities associated with oil and gas operations. The choice of the optimal primer pair to use at a specific site depends on the metadata associated with that location. This optimized approach allows for comprehensive characterization of the microbial communities present in oilfield process fluids and facilitates the choice of the most effective microbial control solution.
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Almahamedh, Hussain H., Charles Williamson, John R. Spear, Brajendra Mishra, and David L. Olson. "Identification of Microorganisms and Their Effects on Corrosion of Carbon Steels Pipelines." In CORROSION 2011. NACE International, 2011. https://doi.org/10.5006/c2011-11231.
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Abstract Microbial influenced corrosion on different grades of carbon steel coupons used in pipelines were investigated in this study. Microbes were isolated and cultivated from oil well produced water samples, and immersion tests were conducted with these waters, microbes and coupons. Bacteria were identified with 16S rRNA gene sequencing. Sequencing analyses revealed the existence of different kinds of bacteria including iron, manganese, and sulfate-reducing bacteria. Corrosion products were characterized by X-ray diffraction (XRD), and scanning electron microscopy (SEM) coupled with energy dispersive spectroscopy (EDS) to characterize biofilm formation and pitting corrosion with resultant pit depth and morphology evaluated. XRD identified the presence of FeS, FeO(OH), and Fe3O4 in the corrosion products. In this investigation, the API X70 pipeline steel coupons experienced more severe MIC than API X52. The vulnerability of X70 to MIC suggests a causation role of metal microstructures. The microstructure analyses show that the smaller grain size steel has a higher susceptibility to MIC. This characterization of MIC in an oil-water environment offers specific information on the types of microbes that cause MIC, and this information may be used for future comprehensive analytical tests for establishing MIC mechanisms.
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Wallrath, Roderich, Edwin Zondervan, and Meik B. Franke. "Integration of MILP and Discrete-Event Simulation for Flowshop Scheduling Using Benders Decomposition." In The 35th European Symposium on Computer Aided Process Engineering. PSE Press, 2025. https://doi.org/10.69997/sct.180841.
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Real-world flowshop problems which are very common in the chemical industry are often difficult to solve in a reasonable time with allocation, sequencing, and lot-sizing decisions. Although great progress has been made in the last 20 years regarding MILP model formulations and solution algorithms, realistically-sized flowshop problems with resource and buffer constraints are still difficult to solve. On the other hand, discrete-event simulation (DES) allows for very detailed modelling of process plants, but lacking of optimization capabilities. Simulation Optimization (SO) combines the high-detail DES with mathematical optimization. We show that is possible to integrate MILP and DES using Benders decomposition. We explain the Benders-DES (BDES) approach with a small motivation example with makespan minimization objective and apply it to a real-world case study of a formulation plant with seven formulation and filling lines with sequencing, allocation, and lot-sizing decisions. We show that the BDES approach performs comparably to the original monolithic-sequential MILP-DES approach. However, the key advantage of this method is the ability to leverage MILP optimization power without requiring a detailed model description.
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Geissler, Brett, Carrie Keller-Schultz, and Vic Keasler. "Don’t Just Blame the SRBs and APBs for MIC." In CORROSION 2015. NACE International, 2015. https://doi.org/10.5006/c2015-06083.
Texte intégralRésumé :
Abstract Microbiologically influenced corrosion has historically been attributed to the activity of sulfate reducing and acid producing bacteria. Recent advances in DNA isolation and sequencing have led to the realization that these two classes of bacteria often represent only a small portion of the corrosive microbial population present in the oil and gas environment. Numerous different genera from multiple other classes of bacteria and archaea have been found to be associated with failures and are now recognized as contributors to the MIC process. The presence of these microbes, while not frequently identified through standard oil and gas industry culturing techniques, is now readily discernable through the use of Next-generation DNA sequencing platforms. This work builds on a paper from CORROSION 2014 that introduced a database with speciation results from over 4000 oilfield samples. However, the current paper discusses analyses that were performed on this database, which has grown to over 6000 samples, to discern the global distribution and relative incidence of several classes of these newly recognized contributors to MIC; bacteria and archaea capable of iron reduction and oxidation, sulfur/sulfide oxidation, as well as methanogenesis. This new understanding of the MIC-related oilfield microbial population will allow us to design better monitoring and treatment strategies that do not simply focus on sulfate reducers and acid producers.
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Demeter, Marc, Shawna Johnston, Kim Dockens, and Raymond J. Turner. "Molecular MIC Diagnoses from ATP Field Test: Streamlined Workflow from Field to 16S rRNA Gene Metagenomics Results." In CORROSION 2017. NACE International, 2017. https://doi.org/10.5006/c2017-09420.
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Abstract Microbiologically influenced corrosion (MIC) describes the negative impacts of microbial growth within various industries. While culture based growth tests are the traditional means of assessing MIC, they are not accurate. New culture-independent assays have been developed; one of which is the adenosine triphosphate (ATP) assay. This field assay allows for indirect enumeration of microorganisms; however, it does not divulge which microorganisms are present. Molecular methods such as 16S metagenomics (16S rRNA gene sequencing and data interpretation) are often used for characterizing the microbial populations; however, it has not been widely adopted due to prohibitive costs and complex workflows that are not feasible in the field. Microbial communities are highly sensitive to changes in their environment, and change in composition as a result of sample storage, transport, and handling, ultimately diminishing the quality of the knowledge gained from sequencing the community. Recently, the presence of microbial DNA in physical elements (filter and filtrate) of the ATP assay were found, suggesting the ATP assay itself may be used to acquire DNA for metagenomic analyses in the field. The ability to bundle the ATP MIC diagnostic assay with DNA acquisition for metagenomics would reduce the cost and labor intensity of DNA extraction, and alleviate complex sample storage and handling logistics that together may substantially improve resultant molecular assay accuracy and accessibility to the industry.
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De Paula, Renato, Cruz St Peter, Ian Alex Richardson, et al. "DNA Sequencing of Oilfield Samples: Impact of Protocol Choices on the Microbiological Conclusions." In CORROSION 2018. NACE International, 2018. https://doi.org/10.5006/c2018-11662.
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Abstract In the last decade, molecular microbiology techniques have significantly expanded the understanding of the resident microflora in hydrocarbon reservoirs and production systems. These methods have been steadily accepted by the industry and are widely viewed as accurate, comprehensive and highly valuable tools that augment or may eventually replace conventional methods. The resulting information has helped operators and service companies to develop better monitoring programs, assess risks and tailor mitigation strategies to control undesired microbial activities in wells, flowlines and separation facilities. Nonetheless, many molecular procedures cannot be performed onsite and samples are typically sent offsite for specialized analyses. The lack of standard procedures hinders comparison of findings between laboratories. Operators currently use dissimilar sampling and preservation protocols, different methods for DNA extraction, separate sequencing platforms and varied approaches for the analyses of the resulting molecular data. In this study, we retrieved multiple samples from several wells in an onshore oilfield and submitted them for 16S rDNA taxonomic analysis in two different laboratories. The results showed significant differences between laboratories in the total abundance of organisms, their taxonomic composition and the presence/absence of certain diagnostic bacteria. Close examination of the protocols revealed that the sample preservation techniques and specific 16S rDNA gene primer sets likely had a significant impact on the resulting information. Collectively, this experience suggests that while molecular techniques are extremely powerful tools to analyze oilfield microbiology, the lack of consensus on an industry wide protocol may lead to discrepancies that could negatively impact the exploitation of these promising methods.
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Geissler, Brett, Alicia M. Jones, and Vic Keasler. "Prevalence and Distribution of Sulfide Generating Microbes in the Oil and Gas Industry." In CORROSION 2016. NACE International, 2016. https://doi.org/10.5006/c2016-07569.
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Abstract Hydrogen sulfide generation is one of the key detriments linked to microbial activity in the oil and gas industry and is the most likely cause of most microbiologically influenced corrosion. H2S is extremely corrosive to most metals and can significantly devalue produced fluids and gases as well as raise HS&E concerns for production facilities. Microbial sulfidogenesis has historically been linked to only a few types of sulfate reducing bacteria that are capable of growth in Modified Postgate’s B medium, but recent advances in microbial identification techniques have shown that the sulfide generating population in the industry is made up of over 190 different genera. Metabolic studies have shown that the vast majority of these microbes require thiosulfate, elemental sulfur, (bi) sulfite, and other sulfur compounds for energy production, and can therefore not be cultured using standard oilfield methods. This paper discusses the prevalence and distribution of the varied population of sulfide generating bacteria and archaea that have been identified by DNA sequencing from over 7000 samples obtained from numerous sites throughout hydrocarbon production facilities found all over the world.
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Le Borgne, S., J. Jan, J. M. Romero, and M. Amaya. "Impact of Molecular Biology Techniques on the Detection and Characterization of Microorganisms and Biofilms Involved in MIC." In CORROSION 2002. NACE International, 2002. https://doi.org/10.5006/c2002-02461.
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Abstract Recently, the application of molecular techniques has greatly improved our knowledge of microbial diversity and distribution in environmental samples. In this paper, we have reviewed the molecular biology techniques that can be used to study microorganisms and biofilms involved in the MIC phenomenon. These techniques include 16S ribosomal DNA (16S rDNA) gene based techniques. In particular, 16S rDNA sequencing, the construction of 16S rDNAs libraries, Fluorescence In Situ Hybridization (FISH), Denaturing Gradient Gel Electrophoresis (DGGE) and Random Amplification of Polymorphic DNA (RAPD) are techniques which can be used to identify and detect bacteria, as well as, to monitor bacteria organized in complex MIC biofilms. In addition to 16S rDNA, the RAPD technique can be applied to obtain probes for detecting bacteria involved in MIC, without any information concerning the bacteria of interest. These techniques can greatly improve our knowledge about MIC.
Rapports d'organisations sur le sujet "HTS sequencing"
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Lora, Eduardo. What Makes Reforms Likely?: Timing and Sequencing of Structural Reforms in Latin America. Inter-American Development Bank, 2000. http://dx.doi.org/10.18235/0011559.
Texte intégralRésumé :
The wave of structural reforms in Latin America and elsewhere has stimulated the development of a wide body of theoretical literature on the political economy of reform, i.e., the study of the political constraints that condition the timing, speed and sequencing of reforms. This paper tests some of the hypotheses associated with these theoretical models, using a set of structural reform indicators for approximately twenty Latin American countries for the period 1985-1995. Although there is strong support for some hypotheses, recent reforms in Latin America cannot be adequately explained without either better theories or better data.
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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7593397.bard.
Texte intégralRésumé :
Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.
Texte intégralRésumé :
Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.
Texte intégralRésumé :
Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically efficient, and environmentally sound means of controlling plant diseases, especially in small grain cereals. The systems selected for study in this proposal are barley (Hordeum vulgare ssp. vulgare, Hvv), its wild progenitor (Hordeum vulgare ssp. spontaneum, Hvs) and the powdery mildew (Blumeria graminis f. sp. hordei, Bgs) and leaf rust (Puccinia hordei, Ph) pathogens. We compiled a diverse panel of Hvs accessions (the Wild Barley Diversity Collection or WBDC; N = 314) from across its native range and evaluated it to 40 isolates of Bgs and 12 isolates of Ph. We obtained genomic DNA sequences enriched for Nucleotide Binding Site-Leucine Rich Repeat (NLR) type resistance genes for 203 WBDC accessions, plus cultivar Morex for which the first reference genome sequence of barley was based. We assembled the 250 bp Illumina sequencing reads into contigs using CLC assembly cell. From this effort, we successfully assembled the sequences of 201 WBDC accessions plus Morex and used NLR Parser to identify contigs containing NLR genes. AgRenSeq was then used to identify k-mers (short oligonucleotide sequences of length k) that were associated with resistance to each isolate of the two pathogens. This analysis was performed individually for all WBDC accessions and each individual pathogen race (9,898 host accession x pathogen race combinations). We visualized the results from these analyses in Manhattan plots and identified 311 and 144 peaks for powdery mildew and leaf rust resistance, respectively. The next step in the analysis was to identify the contigs associated with the peaks in the Manhattan plots. BLAST (Basic Local Alignment Search Tool) searches were employed to identify closely related contigs in other WBDC accessions or in Morex. We identified two candidate R genes that were only present in resistant WBDC accessions. One of these was present in seven WBDC lines and was associated with resistance to four leaf rust isolates. BLAST analysis of this gene revealed that it was Rph15, one of the most widely effective leaf rust resistance genes reported in Hordeum. This gene was cloned and functionally validated in association with our Australian colleagues (Cheng et al., 2021). We are currently in the process of cloning six of other resistance genes: four for powdery mildew and two for leaf rust. As the contigs do not contain much of the promoter sequences, we have employed a genome walking approach to identify 2,500 bp of promoter sequence. To speed up and simplify the cloning of resistance genes from the WBDC, the PI established the International Wild Barley Sequencing Consortium (IWBSC; https://iwbsc.umn.edu/) comprised of over 60 researchers from 14 different countries and raised over $150,000 through crowdfunding to pay for 10X depth sequence coverage. Genome-wide association study (GWAS) of whole genome sequencing (WGS) data identified extremely strong and clear signals of association for several resistance genes which will facilitate gene cloning in concert with a wild barley pan-genome currently under construction. The cloning of multiple resistance gene can facilitate the development of durably resistant cultivars by inserting, through transgenesis, cassettes of multiple resistance genes.
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Holland, Jeremy. Oxfam Bangladesh Economic Justice and Resilience Pillar: Integrated impact evaluation report. Oxfam GB, 2022. http://dx.doi.org/10.21201/2022.9813.
Texte intégralRésumé :
The Economic Justice and Resilience Pillar of the Oxfam Bangladesh Country Strategy 2016–19 was an ambitious and far-reaching portfolio of initiatives conducted across widely varying contexts and with a large cast of partners. This integrated evaluation report is the result of a rich study process that captured this ambitious complexity through a careful sequencing of mixed-method data collection and multi-stakeholder sense making and analysis. Despite the ambitious scope and challenging context, this report confirms that the Pillar has been highly successful and effective across several of its flagship projects. It reveals compelling evidence of economic empowerment of women and youth, emerging enterprises and value chains that create more highly skilled and capital-intensive opportunities for women producers, strengthened community-level climate resilience, and partnership strengthening at different levels. Find out more by reading the full report now.
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, 2003. http://dx.doi.org/10.32747/2003.7586470.bard.
Texte intégralRésumé :
Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, 2012. http://dx.doi.org/10.32747/2012.7597925.bard.
Texte intégralRésumé :
Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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Hicks, Julie, Laurin Yates, and Jackie Pettway. Mat Sinking Unit supply study : Mississippi River revetment. Engineer Research and Development Center (U.S.), 2021. http://dx.doi.org/10.21079/11681/41867.
Texte intégralRésumé :
The Mississippi Valley Division (MVD) has maintained the Mississippi River banks for over 80 years. The Mat Sinking Unit (MSU), built in 1946, was considered state-of-the-art at the time. This system is still in operation today and has placed over 1,000 miles of Articulated Concrete Mats along the Mississippi River from Head of Passes, LA, to Cairo, IL. A new MSU has been designed and is expected to be fully mission capable and operational by the 2023 season, which is expected to increase the productivity from 2,000 squares/day up to 8,000 squares/day with double shifts and optimal conditions. This MSU supply study identifies and optimizes the supply chain logistics for increased production rates from the mat fields to the MSU. The production rates investigated for this effort are 2,000 squares/day, 4,000 squares/day, and 6,000 squares/day. RiskyProject® software, which utilizes a Monte Carlo method to determine a range of durations, manpower, and supplies based on logical sequencing is used for this study. The study identifies several potential supply and demand issues with the increased daily production rates. Distance to casting fields, number of barges, and square availability are the major issues to supply increased placement rates identified by this study.
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, 2022. http://dx.doi.org/10.18235/0003982.
Texte intégralRésumé :
The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.
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Minz-Dub, A., G. J. Muehlbauer, E. Millet, and A. Sharon. ing and characterization of a novel leaf rust and stripe rust resistance gene from Sharon goatgrass. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134171.bard.
Texte intégralRésumé :
Each year, significant global wheat yield loss occurs due to diseases that affect yield quantity or quality. Breeding for resistance has been the best economic and environmentally safe approach to control wheat diseases, however many disease resistance (R) genes succumbed to the pathogens and are no longer effective. Hence, new sources of resistance are necessary to boost the wheat gene pool. The main source for such genes are species of wheat wild relatives in the secondary gene pool that contain an unexploited reservoir of novel R genes. Sharon goatgrass (Aegilops sharonensis Eig) is a wild diploid relative of wheat (genome SshS sh). It is native to the coastal plain of Israel, growing mostly on stabilized dunes, and is highly resistant to rust pathogens. Previously, we introgressed a leaf and stripe rust resistance locus from Ae. sharonensis into bread wheat using chromosome engineering (Millet et al., 2014). We mapped the alien region to the short arm of chromosome six using genotyping by sequencing, identified SNPs, and used them to generate diagnostic markers (Khazan et al., 2020).