scholarly journals MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes

mSystems ◽  
2021 ◽  
Author(s):  
Jia Liu ◽  
Paul Villanueva ◽  
Jinlyung Choi ◽  
Santosh Gunturu ◽  
Yang Ouyang ◽  
...  
Keyword(s):  
High Throughput ◽  
Target Genes ◽  
Primer Design ◽  
Design Tool ◽  
Functional Gene ◽  
Functional Genes ◽  
Gene Characterization

Amplification-based gene characterization allows for sensitive and specific quantification of functional genes. There is often a large diversity of genes represented for functional gene groups, and multiple primers may be necessary to target associated genes.

scholarly journals MetaFunPrimer: primer design for targeting genes observed in metagenomes

2020 ◽  
Author(s):  
Jia Liu ◽  
Paul Villanueva ◽  
Jinlyung Choi ◽  
Santosh Gunturu ◽  
Yang Ouyang ◽  
...  
Keyword(s):  
High Throughput ◽  
Primer Design ◽  
Functional Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Design Tools ◽  
Ammonia Monooxygenase ◽  
Bioinformatic Pipeline ◽  
Subunit A ◽  
Gene Characterization ◽  
Qpcr Primer

ABSTRACTHigh throughput primer design is needed to simultaneously design primers for multiple genes of interest, such as a group of functional genes. We have developed MetaFunPrimer, a bioinformatic pipeline to design primer targets for genes of interests, with a prioritization based on ranking the presence of gene targets in references, such as metagenomes. MetaFunPrimer takes inputs of protein and nucleotide sequences for gene targets of interest accompanied by a set of reference metagenomes or genomes for determining genes of interest. Its output is a set of primers that may be used to amplify genes of interest. To demonstrate the usage and benefits of MetaFunPrimer, a total of 78 HT-qPCR primer pairs were designed to target observed ammonia monooxygenase subunit A (amoA) genes of ammonia-oxidizing bacteria (AOB) in 1,550 soil metagenomes. We demonstrate that these primers can significantly improve targeting of amoA-AOB genes in soil metagenomes compared to previously published primers.IMPORTANCEAmplification-based gene characterization allows for sensitive and specific quantification of functional genes. Often, there is a large diversity of genes represented for a function of interest, and multiple primers may be necessary to target associated genes. Current primer design tools are limited to designing primers for only a few genes of interest. MetaFunPrimer allows for high throughput primer design for functional genes of interest and also allows for ranking gene targets by their presence and abundance in environmental datasets. This tool enables high throughput qPCR approaches for characterizing functional genes.

scholarly journals MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

2016 ◽  
Vol 8 (1) ◽  
Author(s):  
Ram Vinay Pandey ◽  
Walter Pulverer ◽  
Rainer Kallmeyer ◽  
Gabriel Beikircher ◽  
Stephan Pabinger ◽  
...  
Keyword(s):  
Dna Methylation ◽  
High Throughput ◽  
Primer Design ◽  
Design Tool ◽  
Methylation Analysis ◽  
Assay Design ◽  
Dna Methylation Analysis

HTP-OligoDesigner: An Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis

2016 ◽  
Vol 23 (1) ◽  
pp. 27-29 ◽  
Author(s):  
Cesar M. Camilo ◽  
Gustavo M.A. Lima ◽  
Fernando V. Maluf ◽  
Rafael V.C. Guido ◽  
Igor Polikarpov
Keyword(s):  
Gene Cloning ◽  
High Throughput ◽  
Primer Design ◽  
Design Tool ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis

High Speed FPGA Based 128-bit Advance Encryption Standard (AES)

2021 ◽  
Vol 11 ◽  
Author(s):  
Ibrahem M. T. Hamidi ◽  
Farah S. H. Al-aassi
Keyword(s):  
High Throughput ◽  
Field Programmable Gate Array ◽  
High Speed ◽  
Design Tool ◽  
Advanced Encryption Standard ◽  
Clock Frequency ◽  
Advance Encryption Standard ◽  
Field Programmable ◽  
Internal Component ◽  
Gate Array

Aim: Achieve high throughput 128 bits FPGA based Advanced Encryption Standard. Background: Field Programmable Gate Array (FPGA) provides an efficient platform for design AES cryptography system. It provides the capability to control over each bit using HDL programming language such as VHDL and Verilog which results an output speed in Gbps rang. Objective: Use Field Programmable Gate Array (FPGA) to design high throughput 128 bits FPGA based Advanced Encryption Standard. Method: Pipelining technique has used to achieve maximum possible speed. The level of pipelining includes round pipelining and internal component pipelining where number of registers inserted in particular places to increase the output speed. The proposed design uses combinatorial logic to implement the byte substitution. The s-box implemented using composed field arithmetic with 7 stages of pipelining to reduce the combinatorial logic level. The presented model has implemented using VHDL in Xilinix ISETM 14.4 design tool. Result: The achieved results were 18.55 Gbps at a clock frequency of 144.96 MHz and area of 1568 Slices in Spartan3 xc3s1000 hardware. Conclusion: The results show that the proposed design reaches a high throughput with acceptable area usage compare with other designs in the literature.

scholarly journals Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions duringIn SituUranium Reduction

2012 ◽  
Vol 78 (8) ◽  
pp. 2966-2972 ◽  
Author(s):  
Yuting Liang ◽  
Joy D. Van Nostrand ◽  
Lucie A. N′Guessan ◽  
Aaron D. Peacock ◽  
Ye Deng ◽  
...  
Keyword(s):  
Functional Diversity ◽  
Field Experiments ◽  
Gene Diversity ◽  
Functional Gene ◽  
Redox Conditions ◽  
Functional Genes ◽  
Microbial Functional Diversity ◽  
Content Type ◽  
Microbial Functional Gene

ABSTRACTTo better understand the microbial functional diversity changes with subsurface redox conditions duringin situuranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance ofdsrABgenes (dissimilatory sulfite reductase genes) and methane generation-relatedmcrgenes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily fromGeobactersp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect thein situredox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation.

scholarly journals High-Throughput Approaches onto Uncover (Epi)Genomic Architecture of Type 2 Diabetes

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 374 ◽  
Author(s):  
Anna Dziewulska ◽  
Aneta Dobosz ◽  
Agnieszka Dobrzyn
Keyword(s):  
Type 2 Diabetes ◽  
Pancreatic Islets ◽  
High Throughput ◽  
Target Genes ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Genomic Landscape ◽  
A Genome ◽  
Next Generation Sequencing Ngs

Type 2 diabetes (T2D) is a complex disorder that is caused by a combination of genetic, epigenetic, and environmental factors. High-throughput approaches have opened a new avenue toward a better understanding of the molecular bases of T2D. A genome-wide association studies (GWASs) identified a group of the most common susceptibility genes for T2D (i.e., TCF7L2, PPARG, KCNJ1, HNF1A, PTPN1, and CDKAL1) and illuminated novel disease-causing pathways. Next-generation sequencing (NGS)-based techniques have shed light on rare-coding genetic variants that account for an appreciable fraction of T2D heritability (KCNQ1 and ADRA2A) and population risk of T2D (SLC16A11, TPCN2, PAM, and CCND2). Moreover, single-cell sequencing of human pancreatic islets identified gene signatures that are exclusive to α-cells (GCG, IRX2, and IGFBP2) and β-cells (INS, ADCYAP1, INS-IGF2, and MAFA). Ongoing epigenome-wide association studies (EWASs) have progressively defined links between epigenetic markers and the transcriptional activity of T2D target genes. Differentially methylated regions were found in TCF7L2, THADA, KCNQ1, TXNIP, SOCS3, SREBF1, and KLF14 loci that are related to T2D. Additionally, chromatin state maps in pancreatic islets were provided and several non-coding RNAs (ncRNA) that are key to T2D pathogenesis were identified (i.e., miR-375). The present review summarizes major progress that has been made in mapping the (epi)genomic landscape of T2D within the last few years.

A Comparison Analysis for Protein-Protein Interaction Network-Based Methods in Prioritizing Arabidopsis Functional Genes

2021 ◽  
Vol 16 ◽  
Author(s):  
Chun-Jing Si ◽  
Si-Min Deng ◽  
Yuan Quan ◽  
Hong-Yu Zhang
Keyword(s):  
Hybrid Model ◽  
Protein Interaction ◽  
High Throughput Sequencing ◽  
Functional Gene ◽  
Functional Genes ◽  
Systems Genetics ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Gene Enrichment ◽  
Comprehensive Score

Background: Connecting genes to phenotypes is still a great challenge in genetics. Research related to gene-phenotype associations has made remarkable progress recently due to high-throughput sequencing technology and genome-wide association study (GWAS). However, these genes, which are considered to be significantly associated with a target phenotype according to traditional GWAS, are less precise or subject to greater confounding. Objective: The present study is an attempt to prioritize functional genes for complex phenotypes employing protein-protein interaction (PPI) network-based systems genetics methods on available GWAS results. Method: In this paper, we calculated the functional gene enrichment ratios of the trait ontology of A. thaliana for three common systems genetics methods (i.e. GeneRank, K-shell and HotNet2). Then, comparison of gene enrichment ratios obtained by PPI network-based methods was performed. Finally, a hybrid model was proposed, integrating GeneRank, comprehensive score algorithm and HotNet diffusion-oriented subnetworks (HotNet2) to prioritize functional genes. Results: These PPI network-based systems genetics methods were indeed useful for prioritizing phenotype-associated genes. And functional gene enrichment ratios calculated from the top 20% of GeneRank-identified genes were higher than these ratios of K-shell and these ratios of HotNet2 for most phenotypes. However, the hybrid model can improve the efficiency of functional gene enrichment for A. thaliana (up to 40%). Conclusion: The present study provides a hybrid method integrating GeneRank, comprehensive score algorithm and HotNet2 to prioritize functional genes. The method will contribute to functional genomics in plants. The source data and codes are freely available at http://47.242.161.60/Plant/.

M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers

2020 ◽  
Author(s):  
Shuang Deng ◽  
Hongwan Zhang ◽  
Kaiyu Zhu ◽  
Xingyang Li ◽  
Ying Ye ◽  
...  
Keyword(s):  
High Throughput ◽  
Target Gene ◽  
Target Genes ◽  
Biological Processes ◽  
Public Repository ◽  
Reversible Process ◽  
Comprehensive Database ◽  
Dynamic Modification ◽  
Gene Database ◽  
User Friendly

Abstract N6-methyladenosine (m6A) is the most abundant posttranscriptional modification in mammalian mRNA molecules and has a crucial function in the regulation of many fundamental biological processes. The m6A modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Different WERs might have different functions, and even the same WER might function differently in different conditions, which are mostly due to different downstream genes being targeted by the WERs. Therefore, identification of the targets of WERs is particularly important for elucidating this dynamic modification. However, there is still no public repository to host the known targets of WERs. Therefore, we developed the m6A WER target gene database (m6A2Target) to provide a comprehensive resource of the targets of m6A WERs. M6A2Target provides a user-friendly interface to present WER targets in two different modules: ‘Validated Targets’, referred to as WER targets identified from low-throughput studies, and ‘Potential Targets’, including WER targets analyzed from high-throughput studies. Compared to other existing m6A-associated databases, m6A2Target is the first specific resource for m6A WER target genes. M6A2Target is freely accessible at http://m6a2target.canceromics.org.

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

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