Article
Chemistry, Multidisciplinary
Huimin Wang, Jiaoli Wang, Ruiting Liu, Zhenxiang Liu, Kemin Wang, Jin Huang
Summary: This article introduces a new isothermal nucleic acid amplification technique, which can achieve miRNA amplification detection through reasonable probe design, avoiding the increase in cost and operation steps caused by temperature changes or the addition of additional reagents.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Yoshiya Kikukawa, Ryoji Kawazoe, Ryo Miyahara, Takato Sakurada, Yusuke Nagata, Shigeki Sasaki, Yosuke Taniguchi
Summary: In this study, a method for detecting the presence of 8-oxo-2'-deoxyguanosine in DNA was developed, and the signal was successfully amplified. This has important implications for elucidating the pathogenesis of various diseases.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Christina N. Giramma, McKenna B. DeFoer, Jue D. Wang
Summary: Primase plays a crucial role in DNA replication by synthesizing RNA primers, and its activity in bacteria can be regulated by (p)ppGpp. The presence of (p)ppGpp in Bacillus subtilis inhibits DNA replication, particularly primer extension, to ensure genome stability under environmental stress. High levels of (p)ppGpp, combined with low GTP concentration, effectively suppress primase activity in B. subtilis.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biophysics
Fengge Song, Yangdao Wei, Peng Wang, Xiaolin Ge, Chaoyang Li, Aimin Wang, Zhiqing Yang, Yi Wan, Jinghong Li
Summary: The study developed a universal nucleic acid magneto-DNA nanoparticle system using CRISPR-Cas14a, which can detect six different bacteria strains at 1 cfu/mL or 1 aM sensitivity. It offers fast, accurate, cost-effective, and sensitive diagnostic tools for environments with limited resources.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Biochemistry & Molecular Biology
Balaji Sundararaman, Alisa O. Vershinina, Samantha Hershauer, Joshua D. Kapp, Shelby Dunn, Beth Shapiro, Richard E. Green
Summary: Hybridization capture approaches are cost-effective for targeted high-throughput sequencing analysis in low-content, fragmented DNA samples. This study introduces a DNA bait synthesis method called CNER, which combines rolling-circle amplification and restriction digestion to generate discrete hybridization probes. The CNER method is successfully applied to capture and sequence a panel of ancient horse DNA libraries, outperforming a commercially available approach in terms of target coverage and depth.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Kevin S. Kuchinski, Kara D. Loos, Danae M. Suchan, Jennifer N. Russell, Ashton N. Sies, Charles Kumakamba, Francisca Muyembe, Placide Mbala Kingebeni, Ipos Ngay Lukusa, Frida N'Kawa, Joseph Atibu Losoma, Maria Makuwa, Amethyst Gillis, Matthew LeBreton, James A. Ayukekbong, Nicole A. Lerminiaux, Corina Monagin, Damien O. Joly, Karen Saylors, Nathan D. Wolfe, Edward M. Rubin, Jean J. Muyembe Tamfum, Natalie A. Prystajecky, David J. McIver, Christian E. Lange, Andrew D. S. Cameron
Summary: This study evaluated the feasibility of using hybridization probe capture technique to recover more extensive genomic information from specimens. The results showed that probe capture achieved more genome sequence compared to standard amplicon sequencing protocols, and identified new coronaviruses. The study suggests that probe capture can be effectively used alongside other sequencing technologies for high-throughput discovery and surveillance of coronaviruses.
Article
Biochemistry & Molecular Biology
Ezgi Ogutcen, Camille Christe, Kanae Nishii, Nicolas Salamin, Michael Moller, Mathieu Perret
Summary: Gesneriaceae, a pantropical plant family with diverse growth forms and floral morphology, has had its systematics improved with the development of a specific gene capture kit targeting 830 single-copy loci. This allowed for the resolution of phylogenetic relationships within the family, providing high support for major lineages and high resolution within recent radiations. This molecular resource opens new perspectives for studying Gesneriaceae phylogeny at different taxonomical levels and understanding the factors underlying the diversification of this plant group.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jelena Misic, Dusanka Milenkovic, Ali Al-Behadili, Xie Xie, Min Jiang, Shan Jiang, Roberta Filograna, Camilla Koolmeister, Stefan J. Siira, Louise Jenninger, Aleksandra Filipovska, Anders R. Clausen, Leonardo Caporali, Maria Lucia Valentino, Chiara La Morgia, Valerio Carelli, Thomas J. Nicholls, Anna Wredenberg, Maria Falkenberg, Nils-Goran Larsson
Summary: RNase H1 plays an essential role in mammalian mitochondria, particularly in the processing of RNA primers and regulation of mtDNA replication. Loss of RNase H1 leads to impaired mtDNA replication and depletion, as well as the formation of abnormal mtDNA molecules.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Virology
Jeffrey J. DeStefano, Frederic Iseni, Nicolas Tarbouriech
Summary: A modified SELEX protocol was used to select primer-template sequences with enhanced affinity to a specific virus polymerase. The selected sequence showed a several-fold greater binding ability compared to controls. The results suggest that other polymerases may also have sequence preferences that could be exploited in different protocols.
Article
Medicine, Legal
Dan Wen, Jian Shi, Ying Liu, Wei He, Weifeng Qu, Chudong Wang, Hao Xing, Yaoyuan Cao, Jienan Li, Lagabaiyila Zha
Summary: Forensic DNA phenotyping using methylation analysis identified smoking-related genetic loci in the Chinese population, with locus cg05575921 showing the best predictive ability. A stepwise multinomial logistic regression model based on two significant CpG loci was recommended for predicting smoking status.
FORENSIC SCIENCE INTERNATIONAL
(2022)
Article
Dentistry, Oral Surgery & Medicine
A. P. Meethil, S. Saraswat, P. P. Chaudhary, S. M. Dabdoub, P. S. Kumar
Summary: The study tracked the origins of microbiota in aerosols generated during dental procedures and found that most of the microbiota came from the dental irrigant, while saliva contributed minimally. The results indicate that dental treatment does not increase the risk of SARS-CoV-2 transmission in asymptomatic patients when infection control measures are used.
JOURNAL OF DENTAL RESEARCH
(2021)
Article
Plant Sciences
Heather R. Kates, Joshua R. Doby, Carol M. Siniscalchi, Raphael LaFrance, Douglas E. Soltis, Pamela S. Soltis, Robert P. Guralnick, Ryan A. Folk
Summary: Phylogenetic datasets are commonly generated using short-read sequencing technologies, which are now compatible with degraded DNA often extracted from herbarium specimens. Studies have shown that sample characteristics such as taxonomic group, source herbarium, greenness, and age are strong predictors of DNA yield and sequencing success. Surprisingly, older specimens perform slightly better in capture-based protocols, with DNA yield itself not being a strong predictor of sequencing success.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biology
Shilpa Padmanaban, Valerie M. Tesmer, Jayakrishnan Nandakumar
Summary: This study demonstrates that the three-way interaction among TEN-(IFD-TRAP)-TPP1 is critical for telomerase recruitment to telomeres and processive telomere repeat addition. Additionally, the study reveals the importance of TERT motif 3N and TEN domain loop 99FGF101 in telomerase action. Furthermore, the study identifies the role of TPP1 TEL patch loop residue F172 in the human-mouse species specificity of the telomerase-TPP1 interaction.
LIFE SCIENCE ALLIANCE
(2023)
Article
Biochemistry & Molecular Biology
Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Ganesh N. Pandian, Hiroshi Sugiyama
Summary: This study constructed a class of compounds that can selectively alkylate mutant mitochondrial DNA, with the potential to treat mitochondrial diseases. These compounds have programmability and can be used to target pathogenic mutations associated with mitochondrial diseases in future studies.
CELL CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Renzo J. M. Riemens, Gunter Kenis, Jennifer Nolz, Sonia C. Susano C. Chaves, Diane Duroux, Ehsan Pishva, Diego Mastroeni, Kristel Van Steen, Thomas Haaf, Daniel L. A. van den Hove
Summary: A novel approach combining LCM and LDBSP is developed to quantify and analyze the DNA methylation patterns of individual genes in neuronal cells. The method proves to be efficient and accurate, providing further validity to this approach in neuroepigenomic studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)