Research note: Whole-genome sequencing revealed genomic diversity dynamics in duck conserved populations by Yu-Ze Yang, Zhong-Tao Yin, Xiao-Ran Lin, Chun-Ying Zhao, Fang-Xi Yang, Fei-Fan Chen, Zhuo-Cheng Hou

“…Each duck was sequenced at about 10X whole-genome coverage, while over 7.4 million single nucleotide polymorphisms (SNPs) in total were detected for genetic diversity analysis. …”
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Rule-Based Knowledge Acquisition Method for Promoter Prediction in Human and Drosophila Species by Wen-Lin Huang, Chun-Wei Tung, Chyn Liaw, Hui-Ling Huang, Shinn-Ying Ho

“…The top-ranked informative rules with high certainty grades reveal that the global sequence descriptor, the length of nucleotide A at the first position of the sequence, and two physicochemical properties, absorption maxima and molecular weight, are effective in distinguishing promoters from non-promoters in human and Drosophila species, respectively.…”
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CD40 Gene Polymorphisms Associated with Susceptibility and Coronary Artery Lesions of Kawasaki Disease in the Taiwanese Population by Ho-Chang Kuo, Mei-Chyn Chao, Yu-Wen Hsu, Ying-Chi Lin, Ying-Hsien Huang, Hong-Ren Yu, Ming-Feng Hou, Chi-Di Liang, Kuender D. Yang, Wei-Chiao Chang, Chih-Lu Wang

“…A total of 950 subjects (381 KD patients and 569 controls) were investigated to identify 2 tagging single-nucleotide polymorphisms (tSNPs) of CD40 (rs4810485 and rs1535045) by using the TaqMan allelic discrimination assay. …”
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CLONING OF GENES ENCODING TRANSMEMBRANE PROTEINS AND PROTEINS RESPONSIBLE FOR AFRICAN SWINE FEVER VIRUS VIRULENCE by Ali Mazloum, N. G. Zinyakov, A. S. Igolkin, N. N. Vlasova

“…Results of cloning X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate and analysis of their nucleotide sequences are presented. Obtained clones were added to the previously constructed clone library comprising clones of 8 genes of Krasnodar 06/12 isolate. …”
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Differential gene expression analysis of papillary thyroid carcinoma reveals important genes for lymph node metastasis by Wan Fahmi Wan Mohamad Nazarie, Azliana Mohamad Yusof, Francis Yew Fu Tieng, Nur Fadhlina Mohamad Pakarulrazy, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Nani Harlina Md Latar, Sazuita Saidin, Isa Mohamed Rose, Learn-Han Lee, Nurul-Syakima Ab Mutalib

“…The biological processes of genes expressed at higher levels in PTC LNM compared to PTC LNN were involved in cell communication, energy pathway, and metabolism, whereas ion transport, energy pathways, and regulation of nucleobase, nucleoside, nucleotide, and nucleic acid metabolisms, were downregulated. …”
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Polymorphisms of ATG5 Gene Are Associated with Autoimmune Thyroid Diseases, Especially Thyroid Eye Disease by Wen Wang, Zheng-yao Yu, Rong-hua Song, Shuang-tao He, Liang-feng Shi, Jin-an Zhang

“…Methods. rs6568431, rs548234, and rs6937876 were selected to investigate the correlation of single-nucleotide polymorphisms of ATG5 gene with AITDs. Their frequencies in 824 AITD patients, including 271 HT patients and 553 GD patients, and 764 healthy controls were tested using both ligase detection reaction and multiplex polymerase chain reaction. …”
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Identification and Characterization of a Novel Rat MAVS Variant Modulating NFκB Signaling by Ihsan Nalkiran, Hatice Sevim Nalkiran

“…In this study, we identified and characterized a novel rat MAVS variant (MAVS500) with a twenty-one-nucleotide deletion, resulting in a protein seven amino acids shorter than the wild-type (WT) rat MAVS. …”
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Inflammatory Bowel Disease: Progress Towards a Gene by David A van Heel, Jack Satsangi, Alisoun H Carey, Derek P Jewell

“…The goals of continuing research include narrowing the regions of linkages and analysis of candidate genes, and possibly the application of newly developed methods using single nucleotide polymorphisms. Advances in IBD genetics hold the potential to provide knowledge about the disease pathogenesis at the molecular level, with ensuing benefits for clinical practice.…”
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Phylogeny of Macrobrachium spp. (Decapoda, Pleocyemata) from Peru based on mitochondrial and nuclear data reveals a species complex comprising M. digueti (Bouvier, 1895) and M. tra... by Eliana Zelada-Mázmela, Lorenzo E. Reyes-Flores, Luis De Stefano-Beltrán

“…To investigate the systematics of Macrobrachium species from Peru, morphological identification and molecular data from nucleotide sequences of three genes were used: cytochrome c oxidase subunit I, 16S rRNA, and 28S rRNA. …”
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Uncovering the genetic basis of milk production traits in Mexican Holstein cattle based on individual markers and genomic windows. by José G Cortes-Hernández, Adriana García-Ruiz, Francisco Peñagaricano, Hugo H Montaldo, Felipe J Ruiz-López

“…The objective of this study was to evaluate the proportion of genetic variance explained by single nucleotide polymorphism markers, individually or clustered in 1, 2, and 5 Mb windows, for milk yield, fat yield, protein yield, fat content, protein content, and somatic cell score in Mexican Holstein cattle. …”
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From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis? by Kedra M. Ousmael, Ole K. Hansen

“…Abstract Premise Leveraging DNA markers, particularly single‐nucleotide polymorphisms (SNPs), in parentage analysis, sib‐ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. …”
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Blueprint for a high-performance biomaterial: full-length spider dragline silk genes. by Nadia A Ayoub, Jessica E Garb, Robin M Tinghitella, Matthew A Collin, Cheryl Y Hayashi

“…Patterns of variation among sequence repeats at the amino acid and nucleotide levels indicate that the interaction of selection, intergenic recombination, and intragenic recombination governs the evolution of these highly unusual, modular proteins. …”
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The role of transposable elements in the ecological morphogenesis under the influence of stress by R. N. Mustafin, E. K. Khusnutdinova

“…These genes contain nucleotide sequences that interact with non-coding RNAs processed from transposons transcripts, and therefore they are under the control of epigenetic regulatory networks involving transposons. …”
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Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of epithelial cancers. by Andrew Erickson, Sandy Figiel, Timothy Rajakumar, Srinivasa Rao, Wencheng Yin, Dimitrios Doultsinos, Anette Magnussen, Reema Singh, Ninu Poulose, Richard J Bryant, Olivier Cussenot, Freddie C Hamdy, Dan Woodcock, Ian G Mills, Alastair D Lamb

“…Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data. …”
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CLONING OF GENES ENCODING TRANSMEMBRANE PROTEINS AND PROTEINS RESPONSIBLE FOR AFRICAN SWINE FEVER VIRUS VIRULENCE by Ali Mazloum, N. G. Zinyakov, A. S. Igolkin, N. N. Vlasova

“…Results of cloning X69R, A179L, E248R, I215L and DP96R genes of ASF virus Krasnodar 07/17 isolate and analysis of their nucleotide sequences are presented. Obtained clones were added to the previously constructed clone library comprising clones of 8 genes of Krasnodar 06/12 isolate. …”
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From DNA to sustainability: the genomics approach in livestock production by Juan Carlos Gutiérrez-Añez

“…In this sense, genomic selection uses information from many genetic markers or single nucleotide polymorphisms (SNPs) in conjunction with measurements (phenotypes) of essential traits in livestock to improve selection accuracy, reduce the generation intervals, and increase genetic gains since the observation can be read and estimated with a DNA sequencing before the population express the character even before the animal is born. …”
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Mitochondrial genome of Cordyceps blackwelliae: organization, transcription, and evolutionary insights into Cordyceps by Yong-Jie Zhang, Xiang-Ping Fan, Jia-Ni Li, Shu Zhang

“…Mitochondrial phylogeny based on either nucleotide or amino acid sequences confirmed the taxonomic position of C. blackwelliae in Cordycipitaceae, clustering together with C. chanhua. …”
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Association between dietary components and gut microbiota: a Mendelian randomization study by CHEN Haimiao, MA Yan, LIU Mingqi, MA Shanshan, LI Jun, XU Laichao

“…Methods: Genome-wide association study (GWAS) data for dietary components were collected from the DietGen, while GWAS data for gut microbiota were collected from the MiBioGen. Single nucleotide polymorphism (SNP) loci associated with the four dietary components were used as instrumental variables, and 119 known gut microbiota genera were used as the outcomes. …”
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Estimation of Indole-3-Acetic Acid Production from New Molecularly Characterized Rhizobacterial Strains by Mohammed Ayad Harbawi, Najwa Ibrahim Khaleel Al-Barhawee

“… From different fields in Mosul city, we collected sixteen samples of soil surrounding the rhizosphere zone to isolate and characterize rhizobacterial species based on biochemical tests, 16S rRNA gene primer amplification using PCR and nucleotide sequence analysis, and similarity to global isolates in the gene bank. …”
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The extension of the largest generalized-eigenvalue based distance metric ) in arbitrary feature spaces to classify composite data points by Mosaab Daoud

“…We propose a new concept: the limiting dispersion map of the existing clusters in heterogeneous sets of biosequences embedded in linear and nonlinear feature spaces, which is based on the limiting distribution of nucleotide compositions estimated from real data sets. …”
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