Academic literature on the topic 'HTS sequencing'
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Journal articles on the topic "HTS sequencing"
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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 (November 20, 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, Mª Alma Bracho, Julia Hillung, Neris García-González, and Fernando González-Candelas. "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 (June 17, 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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Aronesty, Erik. "Comparison of Sequencing Utility Programs." Open Bioinformatics Journal 7, no. 1 (January 31, 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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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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Malapi-Wight, Martha, Bishwo Adhikari, Jing Zhou, Leticia Hendrickson, Clarissa J. Maroon-Lango, Clint McFarland, Joseph A. Foster, and Oscar P. Hurtado-Gonzales. "HTS-Based Diagnostics of Sugarcane Viruses: Seasonal Variation and Its Implications for Accurate Detection." Viruses 13, no. 8 (August 17, 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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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 (July 26, 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.
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Bester, Rachelle, Glynnis Cook, and Hans J. Maree. "Citrus Tristeza Virus Genotype Detection Using High-Throughput Sequencing." Viruses 13, no. 2 (January 23, 2021): 168. http://dx.doi.org/10.3390/v13020168.
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The application of high-throughput sequencing (HTS) has successfully been used for virus discovery to resolve disease etiology in many agricultural crops. The greatest advantage of HTS is that it can provide a complete viral status of a plant, including information on mixed infections of viral species or virus variants. This provides insight into the virus population structure, ecology, or evolution and can be used to differentiate among virus variants that may contribute differently toward disease etiology. In this study, the use of HTS for citrus tristeza virus (CTV) genotype detection was evaluated. A bioinformatic pipeline for CTV genotype detection was constructed and evaluated using simulated and real data sets to determine the parameters to discriminate between false positive read mappings and true genotype-specific genome coverage. A 50% genome coverage cut-off was identified for non-target read mappings. HTS with the associated bioinformatic pipeline was validated and proposed as a CTV genotyping assay.
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Kunej, Urban, Aida Dervishi, Valérie Laucou, Jernej Jakše, and Nataša Štajner. "The Potential of HTS Approaches for Accurate Genotyping in Grapevine (Vitis vinifera L.)." Genes 11, no. 8 (August 10, 2020): 917. http://dx.doi.org/10.3390/genes11080917.
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The main challenge associated with genotyping based on conventional length polymorphisms is the cross-laboratory standardization of allele sizes. This step requires the inclusion of standards and manual sizing to avoid false results. Capillary electrophoresis (CE) approaches limit the information to the length polymorphism and do not allow the determination of a complete marker sequence. As an alternative, high-throughput sequencing (HTS) offers complete information regarding marker sequences and their flanking regions. In this work, we investigated the suitability of a semi-quantitative sequencing approach for microsatellite genotyping using Illumina paired-end technology. Twelve microsatellite loci that are well established for grapevine CE typing were analysed on 96 grapevine samples from six different countries. We redesigned primers to the length of the amplicon for short sequencing (~100 bp). The primer pair was flanked with a 10 bp overhang for the introduction of barcodes on both sides of the amplicon to enable high multiplexing. The highest data peaks were determined as simple sequence repeat (SSR) alleles and compared with the CE dataset based on 12 reference samples. The comparison showed that HTS SSR genotyping can successfully replace the CE system in further experiments. We believe that, with next-generation sequencing, genotyping can be improved in terms of its speed, accuracy, and price.
Dissertations / Theses on the topic "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.Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Institute for Glycomics
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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.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 VHBChronic 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.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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博士國立交通大學
生物科技系所
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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.
Books on the topic "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.
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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.
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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.
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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.
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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
Book chapters on the topic "HTS sequencing"
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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, 1–12. Cham: 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, 385–91. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-31350-4_16.
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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, 59–77. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-69411-1_3.
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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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Garg, Vanika, and Rajeev K. Varshney. "Analysis of Small RNA Sequencing Data in Plants." In Plant Bioinformatics, 497–509. New York, NY: 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, 337–52. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-22997-8_16.
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Meier, Michael, and Megan J. Wilson. "Using RNA-Seq for Transcriptome Profiling of Botrylloides sp. Regeneration." In Methods in Molecular Biology, 599–615. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_32.
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AbstractThe decrease in sequencing costs and technology improvements has led to the adoption of RNA-sequencing to profile transcriptomes from further non-traditional regeneration model organisms such as the colonial ascidian Botrylloides leachii. The relatively unbiased way in which transcripts are identified and quantified makes this technique suitable to detect large-scale changes in expression, and the identification of novel transcripts and isoforms. Of particular interest to many researchers is the discovery of differentially expressed transcripts across different treatment conditions or stages of regeneration. This protocol describes a workflow starting from processing raw sequencing reads, mapping reads, assembly of transcripts, and measuring their abundance, creating lists of differentially expressed genes and their biological interpretation using gene ontologies. All programs used in this protocol are open-source software tools and freely available.
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Nundy, Samiran, Atul Kakar, and Zulfiqar A. Bhutta. "Ethics in Genetic Research." In How to Practice Academic Medicine and Publish from Developing Countries?, 455–65. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-5248-6_48.
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AbstractThe reader must be wondering about the need for this chapter in a book on pursuing academic medicine in developing countries, as the authors did when asked to write it. The foremost reason is that informing readers about ethics in a predominantly unethical world is not out of place. It is a reminder of the inherent good in man. Secondly, genetics, which was considered a luxury in developing countries has in recent years assumed importance in clinical practice. The completion of the project on the sequencing of the human genome also provided the impetus for the development of faster and cheaper sequencing technology, which came to be known as the next generation sequencing (NGS). To illustrate, the Human Genome Project (HGP) took 13 years to complete at a cost of US $2.7 billion (US contribution). It involved the sequencing of 3 billion base pairs. The same could be carried out in a few days for US 1500 in 2016 [1]. Indeed Hennekam and Bieseker (2012) have called NGS as ‘the most powerful diagnostic tool developed in medicine since the roentgenogram. Its value and utility in clinical medicine will be enormous’ [2]. Numerous perplexing disorders were unravelled by NGS, and in many patients it resulted in life-saving therapy, ushering in the era of precision medicine. Medical therapy, from a position of ‘one size, fits all’ changed to “the right size for each patient.
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Fernandez, Cassandria Tay, Jacob Marsh, Mônica Furaste Danilevicz, Clémentine Mercé, and David Edwards. "Application of pangenomics for wheat molecular breeding." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 236–46. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0013.
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Abstract This chapter discusses the application of pangenomics for molecular breeding of wheat. Pangenomes can be used by both researchers and breeders alike to develop elite wheat cultivars through the discovery and integration of genetic variations associated with agronomically beneficial traits. By providing a reference that accommodates for variation in individuals, variants whose presence and/or absence control abiotic stress resistance and yield can be identified. This tool has only become more informative as more wheat varieties are sequenced, new sequencing approaches such as long-read sequencing and genome mapping are utilized, and tools for pangenomic analysis are developed. With pangenomics, variable genes from wild wheat relatives and related species can be used to optimize wheat molecular breeding and develop improved varieties tailored for the changing global environment.
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Plessier, Flora, Sandrine Schmutz, Sophie Novault, and Heather Marlow. "Single-Cell Transcriptomic Analysis in the Regenerating Cnidarian Nematostella vectensis." In Methods in Molecular Biology, 565–81. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_30.
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AbstractCnidarians have historically served as excellent laboratory models for regenerative development given their capacity to regrow large portions of the adult organism. This capacity is notably absent or poorly developed in the powerful genetic laboratory models Drosophila, C. elegans, and mouse. Increasingly, development of genetic and genomic resources and the application of next-generation sequencing-based techniques in cnidarian systems has further expanded the potential of cnidarian regenerative models. Here, we present a workflow for the characterization of the regenerative response in the sea anemone Nematostella vectensis utilizing fluorescence-activated cell sorting and a plate-based single-cell RNA-sequencing pipeline. This approach can characterize the transcriptional response during regeneration in distinct populations of cells, thus providing a quantitative view of a whole organism process at cellular resolution.
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Sareen, Sindhu, Pawan Saini, Charan Singh, Pradeep Kumar, and Sonia Sheoran. "Genomics and molecular physiology for improvement of drought tolerance in wheat." In Molecular breeding in wheat, maize and sorghum: strategies for improving abiotic stress tolerance and yield, 51–81. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789245431.0004.
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Abstract This chapter discusses the complexity of drought tolerance in wheat focusing the morphological, biochemical, physiological and molecular responses. The breeding approaches, such as traditional and genomics-assisted strategies, for drought tolerance in wheat are described. Future perspectives are also mentioned. Before wheat genome sequencing, it was very difficult to dissect drought tolerance genomic regions because of large genome size and repetitive sequences. But with the availability of sequencing approaches, a large number of genomic resources has become available which extend the scope of utilization of advanced genomics approaches such as GWAM and GS, MutMap+, etc. A new genome editing approach, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPRassociated protein 9 (Cas9) system, can also be utilized for enhancement of drought tolerance in wheat. Therefore, integration of genomic approaches with precise phenotyping is the need of the hour for improving drought tolerance in wheat.
Conference papers on the topic "HTS sequencing"
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"Sequencing and iterative assembly of Ixiolirion tataricum plastome from total DNA using 2nd and 3rd generation HTS platforms." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/plantgen2019-131.
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O'Rourke, Dennis, Jorge F. Sanchez-Garcia, P. Alexander Rolfe, Alice Huang, Danyi Wang, Juergen Scheuenpflug, and Zheng Feng. "Abstract 2016: Comparison of HTG-edge targeted RNA sequencing platform with whole transcriptome RNA sequencing for clinical biomarker studies." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-2016.
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Sormaz, Dusan N. "Agent-Based Process Sequencing Using Search Algorithms." In ASME 2006 International Manufacturing Science and Engineering Conference. ASMEDC, 2006. http://dx.doi.org/10.1115/msec2006-21071.
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Process sequencing represents one of very important tasks in the process planning. The order of tasks and the use of resources are determined by sequencing, and therefore the decision carries the burden of finally optimizing the whole process plan of the part. This paper proposes a flexible, agent-based framework for process sequencing which allows for realtime selection of the sequencing algorithm, dependent on the stage of the product development. The framework has been developed around a tool called space searcher which provides for application of space search algorithms in various domain. Space searcher receives a sequencing agent which provides the sequencing algorithm and executes a space search in order to generate context-specific optimal process sequence. Several process sequencing algorithms (and corresponding agents for space searcher) are described in detail. The application of those algorithms is illustrated on few examples.
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Jiang, Zhaoliang, and Zhi Li. "Mixed-Model Assembly Line Sequencing Optimization Based on Workstation Overload Analysis." In ASME 2013 International Manufacturing Science and Engineering Conference collocated with the 41st North American Manufacturing Research Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/msec2013-1182.
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Reasonable task sequencing will be benefit for both productivity and industry energy saving. Mixed-model products assembly sequencing of mass customization manufacturing systems significantly affects material requirements, order delivery time, and manufacturing cost. A new approach for products sequencing of mixed model assembly line (MMAL) according to workstations overload analysis based on historical production data is proposed to obtain the optimized assembly sequence with the objectives of minimizing consumption waviness of each material, assembly line setup cost, and order delivery time. It will be efficient to cut down the assembly line blockage time, improve the assembly productivity, and save industry energy. A multi-objective optimization algorithm based on particle swarm is developed. An industrial case study has been performed in order to demonstrate the practicality and effectiveness of the proposed approach.
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Zhang, T., G. Wilkowski, D. Rudland, F. Brust, H. S. Mehta, D. V. Sommerville, and Y. Chen. "Weld-Overlay Analyses: An Investigation of the Effect of Weld Sequencing." In ASME 2008 Pressure Vessels and Piping Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/pvp2008-61560.
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The weld overlay process has been developed and applied to repair of nuclear reactor pipe girth welds for many years in BWR plants. The objectives of such repairs were to induce compressive axial residual stresses on the pipe inside surface, as well as increase the pipe thickness with a weld material that is not susceptible to stress-corrosion cracking. Hence, understanding the residual stress distribution is important to evaluate the reliability of pipe joints with weld overlay repairs. In this paper, a six-inch diameter Schedule 120 stainless steel pipe with an overlay thickness of 7.87 mm (0.31 inch) was picked as a validation case. Weld sequencing effects were thoroughly studied. The residual stresses were calculated by using thermal elasto-plastic finite-element analysis (FEA). After comparing results using different weld sequences, it was found that the calculated weld residual stresses on ID surface were very sensitive to weld sequencing in FE analyses as well as internal cooling rate. The influence of the weld sequencing was relatively secondary to the pipe distortion. An optimum (producing compressive residual stress on the ID surface) weld sequencing was obtained and applied to a 711.2 mm (28-inch) diameter pipe-to-elbow girth weld with an overlay thickness of 24.9 mm (0.98 inch) and a pipe thickness of 29.5 mm (1.16 inch).
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Sormaz, Dusan N., and Behrokh Khoshnevis. "Intelligent Process Planning Implemented As an Integrated Module of CIM." In ASME 1997 Design Engineering Technical Conferences. American Society of Mechanical Engineers, 1997. http://dx.doi.org/10.1115/detc97/dfm-4326.
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Abstract In this paper we describe an architecture of a new integrative process planning system as a part of computer integrated manufacturing research system. The process planning procedure is comprised of three phases: feature completion, process selection and process sequencing. We applied a knowledge-based approach to feature completion and process selection, and the space search algorithm for process sequencing. Description of these phases is provided and underlying knowledge representation explained. Integration between the process planning, on the one side, and CAD and scheduling, on the other, is discussed. System implementation has been described and several examples of the system execution are shown.
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Gribchenko, E. S. "The study of transcriptomes of symbiotic tissue of pea using the third-generation sequencing technology Oxford Nanopore." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.093.
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The transcriptome profiles the cv. Frisson mycorrhizal roots and inoculated nitrogen-fixing nodules were investigated using the Oxford Nanopore sequencing technology. A database of gene isoforms and their expression has been created.
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Foglino, Francesco, Christiano Coletto Christakou, Ricardo Luna Gutierrez, and Matteo Leonetti. "Curriculum Learning for Cumulative Return Maximization." In Twenty-Eighth International Joint Conference on Artificial Intelligence {IJCAI-19}. California: International Joint Conferences on Artificial Intelligence Organization, 2019. http://dx.doi.org/10.24963/ijcai.2019/320.
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Curriculum learning has been successfully used in reinforcement learning to accelerate the learning process, through knowledge transfer between tasks of increasing complexity. Critical tasks, in which suboptimal exploratory actions must be minimized, can benefit from curriculum learning, and its ability to shape exploration through transfer. We propose a task sequencing algorithm maximizing the cumulative return, that is, the return obtained by the agent across all the learning episodes. By maximizing the cumulative return, the agent not only aims at achieving high rewards as fast as possible, but also at doing so while limiting suboptimal actions. We experimentally compare our task sequencing algorithm to several popular metaheuristic algorithms for combinatorial optimization, and show that it achieves significantly better performance on the problem of cumulative return maximization. Furthermore, we validate our algorithm on a critical task, optimizing a home controller for a micro energy grid.
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Blomquist, Thomas, Erin L. Crawford, and James C. Willey. "Abstract 4150: Quantitative sequencing following PCR-driven library preparation with internal standard mixtures has improved analytical performance and lower cost." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-4150.
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Lingam, Rakesh, C. L. Harikrishnan, I. V. M. Kishan, and N. Venkata Reddy. "Importance of Feature Sequencing in Incremental Forming." In ASME 2015 International Manufacturing Science and Engineering Conference. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/msec2015-9471.
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Incremental Sheet Forming (ISF) is a flexible forming process suitable for low volume production of sheet metal components. Single Point Incremental Forming (SPIF), which has only one tool forming the geometry, is the simplest variant of incremental forming. Bending of sheet between the component opening and the fixed boundary is unavoidable in SPIF due to the absence of support/backup. Double Sided Incremental Forming (DSIF) has two tools which can be used interchangeably for forming and providing local support. The accuracy of parts formed using DSIF is superior to those formed using SPIF as the unwanted bending is substantially reduced by providing local support. In addition DSIF is capable of forming components with features on both sides of the initial plane of sheet and convex and concave features without additional setup. In ISF, as the deformation progresses, the intended geometry slowly develops, this increases the stiffness of the sheet. While forming multiple features, the forming sequence greatly affects the way stiffness builds-up, which further affects the geometry of formed components. In the present work, an experimental investigation is carried out to demonstrate the affect of forming sequence on the geometries and accuracy of formed component. Results presented show that the feature sequencing greatly affects the geometry and accuracy of formed components.
Reports on the topic "HTS sequencing"
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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, 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.
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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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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, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.
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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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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, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.
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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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Holland, Jeremy. Oxfam Bangladesh Economic Justice and Resilience Pillar: Integrated impact evaluation report. Oxfam GB, November 2022. http://dx.doi.org/10.21201/2022.9813.
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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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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, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.
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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.), September 2021. http://dx.doi.org/10.21079/11681/41867.
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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, February 2022. http://dx.doi.org/10.18235/0003982.
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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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Bacharach, Eran, and Sagar Goyal. Generation of Avian Pneumovirus Modified Clones for the Development of Attenuated Vaccines. United States Department of Agriculture, November 2008. http://dx.doi.org/10.32747/2008.7696541.bard.
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Abstract (one page maximum, single spaced), include: List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project: The main goal described in our original proposal has been the development of a molecular infectious clone of the avian metapneumovirus subtype B (aMPV-B) and the modification of this clone to create mutated viruses for the development of attenuated vaccines. The Achievements and Appendix/Part I sections of this report describes the accomplishments in creating such a molecular clone. These sections also contain the results of a longitudinal study that we made in Israel, demonstrating the infiltration of field strains of aMPV into vaccinated flocks and emphasizing the need for the development of better vaccines. We also describe our unexpected findings regarding the ability of aMPV to establish persistent infection in cell cultures. Although this direction of research was not described in the original proposal we feel that it is highly important for the understanding of aMPV pathogenesis. For example, this direction has provided us with evidence showing that aMPV replication can augment influenza replication. Moreover, we observed that viruses that were produced from chronically-infected cells show reduced ciliostasis. Accordingly, we carried vaccination trials using such viruses. In the original grant proposal we also offered that the American lab will clone and express immunomodulators in the context of an aMPV -based replicon that the Israeli lab has generated. However, as we reported in our annual reports, further analysis of this replicon by the Israeli lab has revealed that the level of expression achieved by this vehicle is relatively poor; thus, the American lab has focused on sequencing the genomes of different aMPV-C isolates that differ in their virulence (including vaccine strains). Achievements and Appendix/Part II sections of this report include the summary of this effort. Background to the topic: The aMPVs belong to the paramyxoviridae family and cause mild to severe respiratory tract diseases mainly in turkeys and also in chickens. Four aMPV subgroups, A, B, C and D, have been characterized; in Israel aMPV-A and B are the common subtypes while in the USA type C is the prevalent one. Although vaccine strains do exist for aMPVs, they do not always provide full protection against virulent strains and the vaccines themselves may induce disease to some extent. Improved vaccines against aMPV are needed, to achieve better protection of the poultry industry against this pathogen. Major conclusions, solutions, achievements: We isolated aMPV-B from a diseased flock and accomplished the sequencing and cloning of its full-genome. In addition, we cloned the four genes encoding the viral replicase. These should serve as the platform for generation of modified aMPV-Bs from molecular clones. We also identified aMPVs that are attenuated in respect to their ciliostatic activity and accordingly showed the potential of such viruses as vaccine strains. For aMPV-C, the different mutations scattered along the genome of different isolates with varied virulence have been determined. Implications, both scientific and agricultural: The newly identified pattern of mutations in attenuated strains will allow better understanding of the pathogenicity of aMPV and the generation of aMPV molecular clones, together with isolation of strains with attenuated ciliostatic activity should generate improved vaccine strains Abstract (one page maximum, single spaced), include: List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project: The main goal described in our original proposal has been the development of a molecular infectious clone of the avian metapneumovirus subtype B (aMPV-B) and the modification of this clone to create mutated viruses for the development of attenuated vaccines. The Achievements and Appendix/Part I sections of this report describes the accomplishments in creating such a molecular clone. These sections also contain the results of a longitudinal study that we made in Israel, demonstrating the infiltration of field strains of aMPV into vaccinated flocks and emphasizing the need for the development of better vaccines. We also describe our unexpected findings regarding the ability of aMPV to establish persistent infection in cell cultures. Although this direction of research was not described in the original proposal we feel that it is highly important for the understanding of aMPV pathogenesis. For example, this direction has provided us with evidence showing that aMPV replication can augment influenza replication. Moreover, we observed that viruses that were produced from chronically-infected cells show reduced ciliostasis. Accordingly, we carried vaccination trials using such viruses. In the original grant proposal we also offered that the American lab will clone and express immunomodulators in the context of an aMPV -based replicon that the Israeli lab has generated. However, as we reported in our annual reports, further analysis of this replicon by the Israeli lab has revealed that the level of expression achieved by this vehicle is relatively poor; thus, the American lab has focused on sequencing the genomes of different aMPV-C isolates that differ in their virulence (including vaccine strains). Achievements and Appendix/Part II sections of this report include the summary of this effort. Background to the topic: The aMPVs belong to the paramyxoviridae family and cause mild to severe respiratory tract diseases mainly in turkeys and also in chickens. Four aMPV subgroups, A, B, C and D, have been characterized; in Israel aMPV-A and B are the common subtypes while in the USA type C is the prevalent one. Although vaccine strains do exist for aMPVs, they do not always provide full protection against virulent strains and the vaccines themselves may induce disease to some extent. Improved vaccines against aMPV are needed, to achieve better protection of the poultry industry against this pathogen. Major conclusions, solutions, achievements: We isolated aMPV-B from a diseased flock and accomplished the sequencing and cloning of its full-genome. In addition, we cloned the four genes encoding the viral replicase. These should serve as the platform for generation of modified aMPV-Bs from molecular clones. We also identified aMPVs that are attenuated in respect to their ciliostatic activity and accordingly showed the potential of such viruses as vaccine strains. For aMPV-C, the different mutations scattered along the genome of different isolates with varied virulence have been determined. Implications, both scientific and agricultural: The newly identified pattern of mutations in attenuated strains will allow better understanding of the pathogenicity of aMPV and the generation of aMPV molecular clones, together with isolation of strains with attenuated ciliostatic activity should generate improved vaccine strains.
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Bloch, Guy, Gene E. Robinson, and Mark Band. Functional genomics of reproduction and division of labor in a key non-Apis pollinator. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699867.bard.
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i. List the original objectives, as defined in the approved proposal, and any revisions made at the beginning or during the course of project. Our objectives were: 1) develop state-of-the-art functional genomics tools for B. terrestris. These resources will be then used to: 2) characterize genes and molecular pathways that are associated with reproduction, 3) characterize genes and molecular pathways associated with specialization in foraging or nursing activities, and 4) determine the extent to which juvenile hormone (JH) is involved in the regulation of reproduction and division of labor. 5) Use RNA interference to down regulate genes associated with reproductive physiology, division of labor, or both. A decrease in the cost of RNA sequencing enabled us to further use the BARD support to extend our research to three additional related projects: A) The regulation of body size which is crucial for understanding both reproduction (castedetermination) and (size based) division of labor in bumblebees. B) Analyze RNA editing in our RNA sequencing data which improves the molecular understanding of the systems we study. C) The influence of JH on the fat body in addition to the brain on which we focused in our proposal. The fat body is a key tissue regulating insect reproduction and health. ii. Background to the topic. Bees are by far the most important pollinators in agricultural and natural ecosystems. The recent collapse of honey bee populations, together with declines in wild bee (including bumble bee) populations, puts their vital pollination services under severe threat. A promising strategy for circumventing this risk is the domestication and mass-rearing of non-Apis bees. This approach has been successfully implemented for several bumble bees including Bombusterrestris in Israel, and B. impatiens in the US, which are mass-reared in captivity. In spite of their critical economic and environmental value, little is known about the physiology and molecular biology of bumble bees. In this collaborative project we developed functional genomics tools for the bumble bee B. terrestris and use these tools for a first thorough study on the physiology and molecular biology of reproduction, dominance, and division of labor in a bumble bee. iii. Major conclusions, solutions. The valuable molecular data of this project together with the functional tools and molecular information generated in this BARD funded project significantly advanced the understanding of bumblebee biology which is essential for maintaining their vital pollination services for US and Israel agriculture.
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Bacharach, Eran, W. Ian Lipkin, and Avigdor Eldar. Identification of the etiological agent of tilapia disease in the Lake of Galillee. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7597932.bard.
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Background to the topic. Tilapines serve as the second most important group of farmed fish worldwide. Massive mortality of wild and cultured tilapia has been observed recently in Israel but the pathogen of this disease has not been identified. We proposed to identify the agent responsible for disease. Major conclusions, solutions, achievements. We characterized the lesions in diseased fish and found that the brain was one of the affected organs. We found conditions to isolate from brains of diseased fish the etiological agent of the tilapia disease and to propagate it in cell culture. This led to the identification of the pathogen as a novel RNA virus, which we named Tilapia Lake Virus (TiLV). Electron microscopy of TiLV revealed virion-like particles and ether/chloroform-sensitivity assays demonstrated that TiLV is enveloped. Low passage TiLV, injected intra-peritoneally to tilapia, induced a disease with over 80% mortality. Cohabitation of healthy with diseased fish demonstrated that the disease is contagious, and that mortalities occur within few days. Fish surviving initial mortality were immune to further TiLV infections, suggesting the mounting of protective immune response. Screening cDNA libraries and high throughput sequencing determined the sequence of TiLV genome. This demonstrated that TiLV is indeed a novel virus and allowed the design of a PCRbased diagnostic test. Implications, both scientific and agricultural. The characterization of a novel, emerging RNA virus that imposes major threat to the tilapia industry, enables the specific identification of the virus in tilapines. This allows prompt screening and surveillance of TiLV, epidemiological studies, and disease containment. This also potentially opens the way for the development of vaccines against TiLV.