Unlocking genetic diversity for low-input systems in a changing climate through participatory characterization and GWAS of lentil landraces by Elisa Lorenzetti, Mercy Wairimu Macharia, Svenja Mager, Matteo Dell’Acqua, Stefano Carlesi, Paolo Bàrberi

“…Meanwhile, we genotyped the landrace collection with a DNA sequencing approach, obtaining 91,136 high quality single nucleotide polymorphisms (SNPs). …”
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Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M by Shuwen Hou, Yuesong Jiang, Feng Zhang, Tianfan Cheng, Dan Zhao, Jilong Yao, Ping Wen, Ping Wen, Lijian Jin, Shi Huang

“…However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.MethodsHere, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. …”
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Cecropin AD ameliorates pneumonia and intestinal injury in mice with mycoplasma pneumoniae by mediating gut microbiota by Bowen Li, Mingming Liu, Wenjing Du, Shuaidong Wang, Zekang Xu, Xiaoqian Zhang, Yang Zhang, Song Hua

“…Additionally, there was a notable upsurge in inflammatory factors within the affected tissues. 16 S rDNA sequencing revealed alterations in the colonic microbiota, including a decrease in the abundance of beneficial bacteria such as Corynebacterium_glutamicum and Candidatus_Saccharimonas, and an increase in the abundance of potential pathogens like Lachnospiraceae_NK4A136_group and Escherichia-Shigella. …”
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‘Two in One’ Cloning Vector Applied for Blunt-End and T-A Cloning with One-Step Digestion–Ligation and Screening of Positive Recombinants by Unaided Eyes by Xingli Zhang, Chong Teng, Kaidi Lyu, Shanhua Lyu, Yinglun Fan

“…To clone DNA sequences quickly and precisely into plasmids is essential for molecular biology studies. …”
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Molecular Sex Identification in the Hardy Rubber Tree (Eucommia ulmoides Oliver) via ddRAD Markers by Wencai Wang, Guoqian Yang, Xin Deng, Fengqing Shao, Yongquan Li, Wei Guo, Hong Liang, Xianzhi Zhang

“…In this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) was applied to screen sex-linked molecular markers for sex identification and investigation of the sex determination system in 20 male and female E. ulmoides individual plants, respectively. …”
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Establishment of performance parameters for the Qubit™ 1X dsDNA HS Assay for use in forensic genetics casework by Adele Lauren Kaleigh Naidoo, Donna-Lee Pamela Martin, Laura Jane Heathfield

“…The precision of the measurements (1.2–2.44 % CV), however, was deemed acceptable for our laboratory, as downstream DNA sequencing results surpassed quality thresholds. Additionally, precision between operators was poor. …”
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Temporal transcriptional profiling of host cells infected by a veterinary alphaherpesvirus using nanopore sequencing by Dóra Tombácz, Zoltán Maróti, Péter Oláh, Ákos Dörmő, Gábor Gulyás, Tibor Kalmár, Zsolt Csabai, Zsolt Boldogkői

“…Abstract In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. …”
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Sox6 and ALDH1A1 Truncation by Asparagine Endopeptidase Defines Selective Neuronal Vulnerability in Parkinson's Disease by Shuke Nie, Bowei Li, Mengmeng Wang, Zijun Chen, Jiayan Ren, Zixuan Li, Xinli Xu, Zhengjiang Qian, Zhongyun Xie, Jianxin Han, Zhentao Zhang, Zhaohui Zhang, Yingjie Zhu, Zuxin Chen, Xifei Yang, Keqiang Ye

“…Here, it is shown that Legumain, also known as asparagine endopeptidase (AEP), is activated in a subgroup of SRY‐box transcription factor 6 /Aldehyde dehydrogenase 1 family member A1, (Sox6+/ALDH1A1+) neurons in the ventral tier of the SNpc and cleaves Sox6 and ALDH1A1, leading to repression of Special AT‐rich sequence binding protein 1 (Satb1) that is a dimeric/tetrameric transcription factor specifically binding to AT‐rich DNA sequences, and toxic dopamine metabolite accumulation. …”
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Studies on banana for propagation, conservation and genome analysis by Susmita Shukla, Ritambhara Bhutani, Nibha Gupta, Shiv Kant Shukla, Taramla Raman, Mohamed A. El-Sheikh, Hosam O. Elansary, Ihab Mohamed Moussa

“…DNA barcoding using Internal Transcribed Spacer1 (ITS1) markers facilitated the molecular analysis and sequence alignment of these Musa species, which illustrated their genetic relationships. DNA sequences were submitted to the NCBI and received accession numbers. 15 days old suckers were initiated on Murashige and Skoog (MS) medium supplemented with various concentrations of phytohormones, adjuvants etc. …”
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A faunal inventory of methane seeps on the Pacific margin of Costa Rica by Charlotte A. Seid, Avery S. Hiley, Marina F. McCowin, José I. Carvajal, Harim Cha, Shane T. Ahyong, Oliver S. Ashford, Odalisca Breedy, Douglas J. Eernisse, Shana K. Goffredi, Michel E. Hendrickx, Kevin M. Kocot, Christopher L. Mah, Allison K. Miller, Nicolás Mongiardino Koch, Rich Mooi, Timothy D. O'Hara, Fredrik Pleijel, Josefin Stiller, Ekin Tilic, Paul Valentich-Scott, Anders Warén, Mary K. Wicksten, Nerida G. Wilson, Erik E. Cordes, Lisa A. Levin, Jorge Cortés, Greg W. Rouse

“…Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. …”
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Expression of Sclerostin in Osteoporotic Fracture Patients Is Associated with DNA Methylation in the CpG Island of the SOST Gene by Yanming Cao, Bin Wang, Ding Wang, Dongxiang Zhan, Caiyuan Mai, Peng Wang, Qiushi Wei, Yamei Liu, Haibin Wang, Wei He, Liangliang Xu

“…The genomic DNA of non-OPF (non-osteoporotic fracture bone tissues) and OPF (osteoporotic fracture bone tissues) were treated by bisulfite modification, and methylation status of CpG sites in the CpG island of SOST gene promoter was determined by DNA sequencing. Results. SOST gene expression in the non-OPF group was lower than that in OPF group. …”
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Screening of Indigenous Oxalate Degrading Lactic Acid Bacteria from Human Faeces and South Indian Fermented Foods: Assessment of Probiotic Potential by Sivasamy Gomathi, Ponnusamy Sasikumar, Kolandaswamy Anbazhagan, Sundaresan Sasikumar, Murugan Kavitha, M. S. Selvi, Govindan Sadasivam Selvam

“…These were identified as Lactobacillus fermentum and Lactobacillus salivarius using 16S rDNA sequencing. Three strains, Lactobacillus fermentum TY5, Lactobacillus fermentum AB1, and Lactobacillus salivarius AB11, exhibited good adhesion to HT-29 cells and strong antimicrobial activity. …”
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Genetic Diversity and Structure of a Critically Endangered Ornamental Species, <i>Rhododendron farinosum</i>, with Extremely Small Populations by Fengjuan Li, Linyuan Fan, Jingli Zhang, Wen Liu, Wei Li, Yongpeng Ma, Hong Ma

“…To unravel the reasons behind the endangerment of this species and provide guidance for the rational conservation of this species, this study obtained a large number of SNP loci by using double-digest restriction-site-associated DNA sequencing (ddRAD-seq) to evaluate the genetic diversity and genetic structure of <i>R. farinosum</i>, as well as to infer the population history of this species. …”
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Genetic coupling of enhancer activity and connectivity in gene expression control by Helen Ray-Jones, Chak Kei Sung, Lai Ting Chan, Alexander Haglund, Pavel Artemov, Monica Della Rosa, Luminita Ruje, Frances Burden, Roman Kreuzhuber, Anna Litovskikh, Eline Weyenbergh, Zoï Brusselaers, Vanessa Xue Hui Tan, Mattia Frontini, Chris Wallace, Valeriya Malysheva, Leonardo Bottolo, Elena Vigorito, Mikhail Spivakov

“…Abstract Gene enhancers often form long-range contacts with promoters, but it remains unclear if the activity of enhancers and their chromosomal contacts are mediated by the same DNA sequences and recruited factors. Here, we study the effects of expression quantitative trait loci (eQTLs) on enhancer activity and promoter contacts in primary monocytes isolated from 34 male individuals. …”
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Coupling of an Au@AgPt nanozyme array with an micrococcal nuclease-specific responsiveness strategy for colorimetric/SERS sensing of Staphylococcus aureus in patients with sepsis by Xueqin Huang, Yingqi Yang, Hanlin Zhou, Liping Hu, Annan Yang, Hua Jin, Biying Zheng, Jiang Pi, Jun Xu, Pinghua Sun, Huai-Hong Cai, Xujing Liang, Bin Pan, Junxia Zheng, Haibo Zhou

“…In the presence of S. aureus, the secreted MNase preferentially cut the nucleobase AT-rich regions of DNA sequences on magnetic beads (MBs) to release alkaline phosphatase (ALP), which subsequently mediated the oxTMB reduction for inducing the colorimetric/SERS signal fade away. …”
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Interactions of miR-34b/c and TP53 Polymorphisms on the Risk of Intracranial Aneurysm by Lijuan Li, Xiutian Sima, Peng Bai, Lushun Zhang, Hong Sun, Weibo Liang, Jianxing Liu, Lin Zhang, Linbo Gao

“…., miR-34b/c rs4938723 and TP53 Arg72-Pro) were genotyped by polymerase chain reaction-restriction fragment length polymorphism assay and DNA sequencing. We found that the CC genotype of miR-34b/c rs4938723 was significantly associated with a decreased risk of IA compared with the TT genotype. …”
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Catfishes from the North-Western Part of Lake Tanganyika: Contribution to a Reference Library of DNA Barcodes by Archimède Mushagalusa Mulega, Arthur F. Boom, Imane Rahmouni, Hocein Bazairi, Abdelaziz Benhoussa, Maarten P. M. Vanhove, Maarten Van Steenberge

“…We identified 11 species using morphology, compared DNA sequences with those available on GenBank, and employed Automatic Barcode Gap Discovery (ABGD) and phylogenetic approaches. …”
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Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencing by Navarro-Escalante, Lucio, Benavides, Pablo, Acevedo, Flor E.

“…Based on PCR screening and DNA sequencing of the wsp gene, Wolbachia infection was confirmed in almost 80% of samples, and represented by two different isolates or strains within the supergroup B. …”
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Liangxue Tongyu Prescription exerts neuroprotection by regulating the microbiota-gut-brain axis of rats with acute intracerebral hemorrhage by Yingying Sun, Dandan Zhou, Anlan Liu, Yu Zhou, Yang Zhao, Yuan Yuan, Weifeng Guo, Jianxiang Li

“…Additionally, 16S rDNA sequencing revealed that LTP mitigated dysbiosis of intestinal microbiota in AICH rats. …”
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Gut microbial composition associated with risk of premature aging in women with Yin-deficiency constitution by Yingying Zhai, Yingying Zhai, Jing Li, Jing Li, Yanqi Cao, Yanqi Cao, Yufei Li, Yufei Li, Xuejie Bao, Xuejie Bao, Jinfeng Liang, Jinfeng Liang, Qi Liu, Qi Liu, Yifan Xia, Ruoxi Yu

“…We integrated 16S rDNA sequencing with machine learning methods to reveal the association between gut microbiota and premature aging in YinDC women.ResultsWe found a significant difference in the composition of gut microbiota between the YinDC and the BC group. …”
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