scholarly journals Cost-effective, high-throughput, single-haplotype iterative mapping and sequencing for complex genomic structures

2017 ◽  
Author(s):  
Daniel W. Bellott ◽  
Ting-Jan Cho ◽  
Jennifer F. Hughes ◽  
Helen Skaletsky ◽  
David C. Page
Keyword(s):  
High Throughput ◽  
Cost Effective ◽  
Reference Sequence ◽  
Sequencing Technologies ◽  
A Genome ◽  
Time Required ◽  
Genomic Regions ◽  
The Cost ◽  
Genome Center ◽  
Library Preparation Protocol

AbstractReference sequence of structurally complex regions can only be obtained through highly accurate clone-based approaches. We and others have successfully employed Single-Haplotype Iterative Mapping and Sequencing (SHIMS 1.0) to assemble structurally complex regions across the sex chromosomes of several vertebrate species and in targeted improvements to the reference sequences of human autosomes. However, SHIMS 1.0 was expensive and time consuming, requiring the resources that only a genome center could command. Here we introduce SHIMS 2.0, an improved SHIMS protocol to allow even a small laboratory to generate high-quality reference sequence from complex genomic regions. Using a streamlined and parallelized library preparation protocol, and taking advantage of high-throughput, inexpensive, short-read sequencing technologies, a small group can sequence and assemble hundreds of clones in a week. Relative to SHIMS 1.0, SHIMS 2.0 reduces the cost and time required by two orders of magnitude, while preserving high sequencing accuracy.

An International Campaign for Agricultural and Livestock Genomics (CALG)

2002 ◽  
Vol 06 (24) ◽  
pp. 958-965
Author(s):  
Jun Yu ◽  
Jian Wang ◽  
Huanming Yang
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Model Organisms ◽  
Environmental Biology ◽  
Cdna Sequences ◽  
Governmental Agencies ◽  
Technology Innovations ◽  
A Genome ◽  
Starting Point ◽  
The Cost

A coordinated international effort to sequence agricultural and livestock genomes has come to its time. While human genome and genomes of many model organisms (related to human health and basic biological interests) have been sequenced or plugged in the sequencing pipelines, agronomically important crop and livestock genomes have not been given high enough priority. Although we are facing many challenges in policy-making, grant funding, regional task emphasis, research community consensus and technology innovations, many initiatives are being announced and formulated based on the cost-effective and large-scale sequencing procedure, known as whole genome shotgun (WGS) sequencing that produces draft sequences covering a genome from 95 percent to 99 percent. Identified genes from such draft sequences, coupled with other resources, such as molecular markers, large-insert clones and cDNA sequences, provide ample information and tools to further our knowledge in agricultural and environmental biology in the genome era that just comes to its accelerated period. If the campaign succeeds, molecular biologists, geneticists and field biologists from all countries, rich or poor, would be brought to the same starting point and expect another astronomical increase of basic genomic information, ready to convert effectively into knowledge that will ultimately change our lives and environment into a greater and better future. We call upon national and international governmental agencies and organizations as well as research foundations to support this unprecedented movement.

scholarly journals Complete biosynthetic pathways of ascofuranone and ascochlorin inAcremonium egyptiacum

2019 ◽  
Vol 116 (17) ◽  
pp. 8269-8274 ◽  
Author(s):  
Yasuko Araki ◽  
Takayoshi Awakawa ◽  
Motomichi Matsuzaki ◽  
Rihe Cho ◽  
Yudai Matsuda ◽  
...  
Keyword(s):  
Differential Expression Analysis ◽  
Cost Effective ◽  
Drug Candidate ◽  
P450 Monooxygenase ◽  
Genome Wide ◽  
Common Precursor ◽  
A Genome ◽  
Membrane Bound ◽  
The Cost

Ascofuranone (AF) and ascochlorin (AC) are meroterpenoids produced by various filamentous fungi, includingAcremonium egyptiacum(synonym:Acremonium sclerotigenum), and exhibit diverse physiological activities. In particular, AF is a promising drug candidate against African trypanosomiasis and a potential anticancer lead compound. These compounds are supposedly biosynthesized through farnesylation of orsellinic acid, but the details have not been established. In this study, we present all of the reactions and responsible genes for AF and AC biosyntheses inA. egyptiacum, identified by heterologous expression, in vitro reconstruction, and gene deletion experiments with the aid of a genome-wide differential expression analysis. Both pathways share the common precursor, ilicicolin A epoxide, which is processed by the membrane-bound terpene cyclase (TPC) AscF in AC biosynthesis. AF biosynthesis branches from the precursor by hydroxylation at C-16 by the P450 monooxygenase AscH, followed by cyclization by a membrane-bound TPC AscI. All genes required for AC biosynthesis (ascABCDEFG) and a transcriptional factor (ascR) form a functional gene cluster, whereas those involved in the late steps of AF biosynthesis (ascHIJ) are present in another distantly located cluster. AF is therefore a rare example of fungal secondary metabolites requiring multilocus biosynthetic clusters, which are likely to be controlled by the single regulator, AscR. Finally, we achieved the selective production of AF inA. egyptiacumby genetically blocking the AC biosynthetic pathway; further manipulation of the strain will lead to the cost-effective mass production required for the clinical use of AF.

scholarly journals Use of Targeted Amplicon Sequencing in Peanut to Generate Allele Information on Allotetraploid Sub-Genomes

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1220
Author(s):  
Roshan Kulkarni ◽  
Ratan Chopra ◽  
Jennifer Chagoya ◽  
Charles E. Simpson ◽  
Michael R. Baring ◽  
...  
Keyword(s):  
Cost Effective ◽  
Amplicon Sequencing ◽  
Routine Practice ◽  
Specific Information ◽  
Illumina Hiseq ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Cost Effective Approach ◽  
A Genome ◽  
The Cost

The use of molecular markers in plant breeding has become a routine practice, but the cost per accession can be a hindrance to the routine use of Quantitative Trait Loci (QTL) identification in breeding programs. In this study, we demonstrate the use of targeted re-sequencing as a proof of concept of a cost-effective approach to retrieve highly informative allele information, as well as develop a bioinformatics strategy to capture the genome-specific information of a polyploid species. SNPs were identified from alignment of raw transcriptome reads (2 × 50 bp) to a synthetic tetraploid genome using BWA followed by a GATK pipeline. Regions containing high polymorphic SNPs in both A genome and B genomes were selected as targets for the resequencing study. Targets were amplified using multiplex PCR followed by sequencing on an Illumina HiSeq. Eighty-one percent of the SNP calls in diploids and 68% of the SNP calls in tetraploids were confirmed. These results were also confirmed by KASP validation. Based on this study, we find that targeted resequencing technologies have potential for obtaining maximum allele information in allopolyploids at reduced cost.

scholarly journals Cost-Effective and High-Throughput Plasmonic Interference Coupled Nanostructures by Using Quasi-Uniform Anodic Aluminum Oxide

Coatings ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 420 ◽  
Author(s):  
Bae ◽  
Yu ◽  
Jung ◽  
Lee ◽  
Choi
Keyword(s):  
Aluminum Oxide ◽  
High Throughput ◽  
Anodic Aluminum Oxide ◽  
Noble Metals ◽  
Cost Effective ◽  
Plasmonic Nanostructures ◽  
Large Area ◽  
Plasmonic Material ◽  
Anodic Aluminum ◽  
The Cost

Large-area and uniform plasmonic nanostructures have often been fabricated by simply evaporating noble metals such as gold and silver on a variety of nanotemplates such as nanopores, nanotubes, and nanorods. However, some highly uniform nanotemplates are limited to be utilized by long, complex, and expensive fabrication. Here, we introduce a cost-effective and high-throughput fabrication method for plasmonic interference coupled nanostructures based on quasi-uniform anodic aluminum oxide (QU-AAO) nanotemplates. Industrial aluminum, with a purity of 99.5%, and copper were used as a base template and a plasmonic material, respectively. The combination of these modifications saves more than 18 h of fabrication time and reduces the cost of fabrication 30-fold. From optical reflectance data, we found that QU-AAO based plasmonic nanostructures exhibit similar optical behaviors to highly ordered (HO) AAO-based nanostructures. By adjusting the thickness of the AAO layer and its pore size, we could easily control the optical properties of the nanostructures. Thus, we expect that QU-AAO might be effectively utilized for commercial plasmonic applications.

Inspection Manpower Planning for X & S Control Charts

2012 ◽  
Vol 488-489 ◽  
pp. 1624-1630
Author(s):  
Wen An Yang ◽  
Wen He Liao ◽  
Yu Guo
Keyword(s):  
Control Charts ◽  
Cost Effective ◽  
Manpower Planning ◽  
Sampling Interval ◽  
Optimal Number ◽  
Optimization Strategy ◽  
Effective Manner ◽  
Time Required ◽  
The Cost ◽  
And Control

A method of determining the optimal number of inspectors and/or working time required on a specific SPC activity is presented in the study. The issue of inspection manpower planning is handled as a constrained optimization problem. The optimization strategy is not only to minimize the avoidable surplus quality loss due to failure of detecting the out-of-control states but to determine the cost of inspection manpower from the perspective of deploying an appropriate amount of inspection manpower in a cost-effective manner, and meanwhile the values of sample size, sampling interval and control limits of control charts are also determined. The result obtained indicates that the total cost (or loss) can be substantially reduced if implementing control charts was equipped with adequate inspection manpower.

scholarly journals Improved contiguity of the threespine stickleback genome using long-read sequencing

2020 ◽  
Author(s):  
Shivangi Nath ◽  
Daniel E. Shaw ◽  
Michael A. White
Keyword(s):  
Gasterosteus Aculeatus ◽  
Genetic Model ◽  
Threespine Stickleback ◽  
Model Species ◽  
Long Distance ◽  
Sequencing Technologies ◽  
A Genome ◽  
Long Read ◽  
The Cost ◽  
Stickleback Genome

AbstractWhile the cost and time for assembling a genome have drastically reduced, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long sequencing reads to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we were able to fill over 76% of the gaps in the genome, improving contiguity over five-fold. Our approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.

scholarly journals Calibrating seed-based alignment heuristics with Sesame

2019 ◽  
Author(s):  
Guillaume J. Filion ◽  
Ruggero Cortini ◽  
Eduard Zorita
Keyword(s):  
Reference Sequence ◽  
General Strategy ◽  
Mapping Algorithms ◽  
Analytic Combinatorics ◽  
Sequencing Technologies ◽  
A Genome ◽  
Reasonable Cost ◽  
Empirical Performance ◽  
Correct Location ◽  
Theoretical Results

AbstractThe increasing throughput of DNA sequencing technologies creates a need for faster algorithms. The fate of most reads is to be mapped to a reference sequence, typically a genome. Modern mappers rely on heuristics to gain speed at a reasonable cost for accuracy. In the seeding heuristic, short matches between the reads and the genome are used to narrow the search to a set of candidate locations. Several seeding variants used in modern mappers show good empirical performance but they are difficult to calibrate or to optimize for lack of theoretical results. Here we develop a theory to estimate the probability that the correct location of a read is filtered out during seeding, resulting in mapping errors. We describe the properties of simple exact seeds, skip-seeds and MEM seeds (Maximal Exact Match seeds). The main innovation of this work is to use concepts from analytic combinatorics to represent reads as abstract sequences, and to specify their generative function to estimate the probabilities of interest. We provide several algorithms, which combined together give a workable solution for the problem of calibrating seeding heuristics for short reads. We also provide a C implementation of these algorithms in a library called Sesame. These results can improve current mapping algorithms and lay the foundation of a general strategy to tackle sequence alignment problems. The Sesame library is open source and available for download at https://github.com/gui11aume/sesame.

The Influence of Dose Frequency and Agent Toxicity on the Cost of Parenteral Antibiotic Therapy

1982 ◽  
Vol 16 (12) ◽  
pp. 935-938 ◽  
Author(s):  
Robert P. Rapp ◽  
Catherine L. Bannon ◽  
Brack A. Bivins
Keyword(s):  
Combination Therapy ◽  
Antibiotic Therapy ◽  
First Generation ◽  
Single Agent ◽  
Cost Effective ◽  
Generation Cephalosporin ◽  
Dose Frequency ◽  
Surgery Patient ◽  
Time Required ◽  
The Cost

The influence of the number of daily doses on the overall cost of antibiotic therapy is examined in a general surgery patient population. Patients receiving a single first-generation cephalosporin are compared with patients receiving two or three antibiotics (including an aminoglycoside) in terms of (1) the cost of the drug and the supplies, (2) time required for nursing and pharmacy personnel to prepare and administer the doses, and (3) the influence of agent toxicity (renal function) on physician-ordered laboratory tests. On the whole, combination therapy including an aminoglycoside was four times as expensive as single-agent (first-generation cephalosporin) therapy. If future studies demonstrate that single-agent antibiotic therapy is as effective as traditional combination therapy for specific infectious diseases, the influence of the number of daily doses of drug and agent toxicity may support the cost-effective use of the newer agents.

Development of an Economic and Efficient Installation Vessel for Tidal Stream Energy Converter Arrays

2013 ◽  
Author(s):  
Rachel Nicholls-Lee ◽  
Simon Hindley ◽  
Richard Parkinson
Keyword(s):  
Oil And Gas ◽  
Cost Effective ◽  
Concept Design ◽  
Market Place ◽  
Operations And Maintenance ◽  
Tidal Turbine ◽  
Tidal Stream ◽  
Tidal Stream Energy ◽  
Time Required ◽  
The Cost

In order for tidal stream technology to develop into a viable and cost effective energy solution, the overall cost of tidal array installation, operations and maintenance must be driven down. The key issues which drive the cost are the time required to conduct operations and susceptibility to weather risk coupled with the expense of marine assets. Current vessels have limited operational windows due to weather and tidal constraints, which result in considerable cumulative costs due to high charges for such vessels. The marine renewable industry is currently reliant on vessels of opportunity from the offshore oil and gas sector; which, while sufficient for single device demonstration deployments, are not viable for array installations. De-coupling the tidal sector from this market place offers the opportunity to reduce the volatility of vessel day rates. This paper presents the concept design of an efficient and economic, fit for purpose installation vessel for tidal stream energy converters. The vessel has good dynamic positioning capabilities for operation in strong tidal currents thus broadening the operational window. The environmental impact of the vessel is reduced when compared to existing vessels. A key criterion throughout the design process is minimizing the cost of the vessel to tidal turbine site developers.

scholarly journals SALTS – SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite

2021 ◽  
Author(s):  
Mohan V Kasukurthi ◽  
Dominika Houserova ◽  
Yulong Huang ◽  
Addison A. Barchie ◽  
Justin T. Roberts ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Protein Coding ◽  
Web Based ◽  
Functional Roles ◽  
Sequencing Technologies ◽  
Active Research ◽  
The Cost ◽  
Analysis Platform ◽  
Transcriptional Output

ABSTRACTThe widespread utilization of high-throughput sequencing technologies has unequivocally demonstrated that eukaryotic transcriptomes consist primarily (>98%) of non-coding RNA (ncRNA) transcripts significantly more diverse than their protein-coding counterparts.ncRNAs are typically divided into two categories based on their length. (1) ncRNAs less than 200 nucleotides (nt) long are referred as small non-coding RNAs (sncRNAs) and include microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), transfer ribonucleic RNAs (tRNAs), etc., and the majority of these are thought to function primarily in controlling gene expression. That said, the full repertoire of sncRNAs remains fairly poorly defined as evidenced by two entirely new classes of sncRNAs only recently being reported, i.e., snoRNA-derived RNAs (sdRNAs) and tRNA-derived fragments (tRFs). (2) ncRNAs longer than 200 nt long are known as long ncRNAs (lncRNAs). lncRNAs represent the 2nd largest transcriptional output of the cell (behind only ribosomal RNAs), and although functional roles for several lncRNAs have been reported, most lncRNAs remain largely uncharacterized due to a lack of predictive tools aimed at guiding functional characterizations.Importantly, whereas the cost of high-throughput transcriptome sequencing is now feasible for most active research programs, tools necessary for the interpretation of these sequencings typically require significant computational expertise and resources markedly hindering widespread utilization of these datasets. In light of this, we have developed a powerful new ncRNA transcriptomics suite, SALTS, which is highly accurate, markedly efficient, and extremely user-friendly. SALTS stands for SURFR (sncRNA) And LAGOOn (lncRNA) Transcriptomics Suite and offers platforms for comprehensive sncRNA and lncRNA profiling and discovery, ncRNA functional prediction, and the identification of significant differential expressions among datasets. Notably, SALTS is accessed through an intuitive Web-based interface, can be used to analyze either user-generated, standard next-generation sequencing (NGS) output file uploads (e.g., FASTQ) or existing NCBI Sequence Read Archive (SRA) data, and requires absolutely no dataset pre-processing or knowledge of library adapters/oligonucleotides.SALTS constitutes the first publically available, Web-based, comprehensive ncRNA transcriptomic NGS analysis platform designed specifically for users with no computational background, providing a much needed, powerful new resource capable of enabling more widespread ncRNA transcriptomic analyses. The SALTS WebServer is freely available online at http://salts.soc.southalabama.edu.

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