Article
Virology
Fernanda L. S. G. Santos, Maria C. V. Invencao, Edilaine D. Araujo, Gerlane S. Barros, Marcus V. A. Batista
Summary: This study evaluated the effectiveness of three different PCR-based strategies for HPV detection and genotyping from cervical samples. The results showed that different primer design strategies influenced the sensitivity and specificity of detecting different HPV types. EntroA primers were able to detect HPV in more samples compared to MY09/MY11, while multiplex PCR had higher sensitivity despite targeting a limited number of HPV types.
JOURNAL OF MEDICAL VIROLOGY
(2021)
Article
Ecology
Brock T. Burgess, Robyn L. Irvine, Michael A. Russello
Summary: This study developed a genetic sequencing method using noninvasive samples, which can provide large amounts of high-quality genetic data for elusive and at-risk species. The method was successfully validated and can be used for invasive species management and other studies employing noninvasive genetic sampling.
ECOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Physical
Rupa Haldavnekar, Swarna Ganesh, Krishnan Venkatakrishnan, Bo Tan
Summary: Cancer diagnosis and determining tissue of origin are crucial for personalized medicine. Existing diagnostic techniques have limitations, but circulating tumor DNA (ctDNA) and cancer stem cell-ctDNA can overcome these challenges. Quantum superstructures offer ultra-sensitive detection of ctDNA and can effectively diagnose cancer.
Article
Multidisciplinary Sciences
Wentao Chen, Hao Luo, Lihong Zeng, Yuying Pan, Jonathan B. Parr, Yinbo Jiang, Clark H. Cunningham, Kelly L. Hawley, Justin D. Radolf, Wujian Ke, Jiangli Ou, Jianjiang Yang, Bin Yang, Heping Zheng
Summary: This study develops a PCR-LwCas13a assay for the diagnosis of syphilis, which achieves better sensitivity and specificity compared to traditional methods. It also demonstrates the potential of CRISPR-based approaches for improving syphilis diagnosis and surveillance.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Monia Ardhaoui, Emna Ennaifer, Anna Christina De Matos Salim, Flavio Marcom Gomez, Thalja Laasili, Med Samir Boubaker, Ikram Guizani
Summary: The study developed a sensitive HPV genotyping method based on nested PCR followed by NGS, which showed higher sensitivity and specificity compared to the traditional RLH method. The NGS assay detected more HPV types in clinical samples, including new HPV types not previously described in Tunisia.
Article
Oncology
Laura Costas, Irene Onieva, Beatriz Pelegrina, Fatima Marin, Alvaro Carmona, Marta Lopez-Querol, Jon Frias-Gomez, Paula Peremiquel-Trillas, Jose Manuel Martinez, Eduard Dorca, Joan Brunet, Marta Pineda, Jordi Ponce, Xavier Matias-Guiu, Silvia de Sanjose, Francesc Xavier Bosch, Laia Alemany, Sonia Paytubi
Summary: This study evaluated the use of urine samples for the detection and molecular classification of endometrial cancer. Mutations in DNA from urine supernatant samples were identified in 100% of endometrial cancer cases, while only one control showed variants at a low frequency. The results suggest that urine samples may offer a user-friendly and reliable tool for endometrial cancer detection and classification.
CLINICAL CANCER RESEARCH
(2023)
Article
Developmental Biology
Ji Yun Jang, Ting Liang, Myeong-Kyu Kim, Kyung Wook Kang, Bora Lee, Seok-Yong Choi
Summary: Genotyping involves analysis of PCR products using genomic DNA as template, and is used to validate mutant or transgenic organisms. We developed a rapid and noninvasive method for extracting PCR-ready gDNA from adult zebrafish by combining skin swabbing with proteinase K treatment.
Article
Biochemistry & Molecular Biology
Malcolm Hillebrand, George Kalosakas, Alan R. Bishop, Charalampos Skokos
Summary: Understanding the timescales of large bubbles in DNA is crucial for understanding its characteristics and biological function. In this study, a coarse-grained model was used to investigate the relaxation dynamics of large bubbles in homopolymer DNA. The results showed that relaxation times increased with bubble size and were two orders of magnitude longer in guanine-cytosine sequences compared to adenine-thymine sequences. These findings highlight the lasting impact of large bubbles on DNA dynamics, affecting the long-term evolution of the molecule.
Article
Biochemistry & Molecular Biology
Kara J. Andres, Suresh A. Sethi, David M. Lodge, Jose Andres
Summary: Advances in environmental DNA (eDNA) methodologies have shown the capability to detect intraspecific diversity in the nuclear genome, estimate allele frequencies, and assess genetic contributors in eDNA samples. Results from experimental and field trials indicate high correlation between eDNA-based allele frequencies and those from genotyped tissue samples, suggesting reliable amplification of nuclear markers from water samples. DNA mixture analyses successfully estimated the number of genetic contributors in eDNA samples and simulated mixtures, with the accuracy influenced by the filtering scheme of low-frequency alleles.
Article
Chemistry, Analytical
Zhou-Jie Liu, Liang-Yong Yang, Tai-Cheng Lu, Chen Huang, Yu-Qi Liang, Xiong-Wei Xu, Yan-Fang Xu, Meng-Meng Liu, Xin-Hua Lin, Jin-Yuan Chen
Summary: A ratiometric electrochemical DNA sensor was proposed for precise typing of wobble-type allele. By utilizing the traditionally recognized negative signal of wobble-base pair-mediated amplification as a positive one and employing a ratiometric readout mode, the detection accuracy of the wobble-type allele was improved.
ANALYTICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Wenman Wu, Xuanyou Zhou, Zhengwen Jiang, Dazhi Zhang, Feng Yu, Lanlan Zhang, Xuefeng Wang, Songchang Chen, Chenming Xu
Summary: This study demonstrates a cost-effective, less time consuming, and accurate method for noninvasive prenatal diagnosis (NIPD) of monogenic disorders.
Article
Biochemistry & Molecular Biology
Cornelis A. M. Wagemaker, Liesje Mommer, Eric J. W. Visser, Alexandra Weigelt, Thomas P. van Gurp, Maarten Postuma, Annemiek E. Smit-Tiekstra, Hans de Kroon
Summary: Plant interactions belowground are important and difficult to quantify accurately. The msGBS method presented in this study allows for high taxonomic resolution and parallel quantification of multiple species in root samples. Compared to qPCR, msGBS offers similar results with advantages in revealing hidden belowground interactions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Microbiology
Gregorio V. Linchangco, Brian Foley, Thomas Leitner
Summary: This study reconstructed 90 new HIV-1 subtype and CRF consensus sequences and compared them with worldwide HIV-1 genome sequences. The 2021 consensus sequences were found to be shorter than the 2002 sequences, but closer to the global genome sequences. The results suggest that the 2021 consensus sequences are likely good representations of the typical subtype/CRF genome nucleotide states.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biology
Vincent Pamugas Reyes, Justine Kipruto Kitony, Shunsaku Nishiuchi, Daigo Makihara, Kazuyuki Doi
Summary: Molecular markers are crucial in rice improvement, and genotyping-by-sequencing has enabled high-throughput sequencing and genotyping, making it more efficient and cost-effective for the utilization of rice genetic resources. Currently, genotyping-by-sequencing is being used in rice pre-breeding programs to discover beneficial genes and QTL, leading to advancements in rice cultivar improvement.
Article
Psychiatry
Beatriz Carvalho Henriques, Avery Buchner, Xiuying Hu, Yabing Wang, Vasyl Yavorskyy, Keanna Wallace, Rachael Dong, Kristina Martens, Michael S. Carr, Bahareh Behroozi Asl, Joshua Hague, Sudhakar Sivapalan, Wolfgang Maier, Mojca Z. Dernovsek, Neven Henigsberg, Joanna Hauser, Daniel Souery, Annamaria Cattaneo, Ole Mors, Marcella Rietschel, Gerald Pfeffer, Stacey Hume, Katherine J. Aitchison
Summary: This study aimed to cross-validate various technologies for genotyping CYP2D6 and CYP2C19, providing a wide range of assay options, automated haplotype translation, and workflow optimization to enhance feasibility for clinical implementation of these genetic profiles.
TRANSLATIONAL PSYCHIATRY
(2021)
Article
Anthropology
Joanna Malukiewicz, Crystal M. Hepp, Katerina Guschanski, Anne C. Stone
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2017)
Article
Zoology
Joanna Malukiewicz, Katerina Guschanski, Adriana D. Grativol, Maria Adelia B. Oliveira, Carlos R. Ruiz-Miranda, Anne C. Stone
AMERICAN JOURNAL OF PRIMATOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Katerina Guschanski, Maria Warnefors, Henrik Kaessmann
Article
Biodiversity Conservation
Katerina Guschanski, Linda Vigilant, Alastair McNeilage, Maryke Gray, Edwin Kagoda, Martha M. Robbins
BIOLOGICAL CONSERVATION
(2009)
Article
Biology
Justin Roy, Mimi Arandjelovic, Brenda J. Bradley, Katerina Guschanski, Colleen R. Stephens, Dan Bucknell, Henry Cirhuza, Chifundera Kusamba, Jean Claude Kyungu, Vince Smith, Martha M. Robbins, Linda Vigilant
Article
Evolutionary Biology
Olaf Thalmann, Daniel Wegmann, Marie Spitzner, Mimi Arandjelovic, Katerina Guschanski, Christoph Leuenberger, Richard A. Bergl, Linda Vigilant
BMC EVOLUTIONARY BIOLOGY
(2011)
Article
Biochemistry & Molecular Biology
Julien Meunier, Frederic Lemoine, Magali Soumillon, Angelica Liechti, Manuela Weier, Katerina Guschanski, Haiyang Hu, Philipp Khaitovich, Henrik Kaessmann
Article
Biochemistry & Molecular Biology
M. Arandjelovic, K. Guschanski, G. Schubert, T. R. Harris, O. Thalmann, H. Siedel, L. Vigilant
MOLECULAR ECOLOGY RESOURCES
(2009)
Article
Multidisciplinary Sciences
Susanna Sawyer, Johannes Krause, Katerina Guschanski, Vincent Savolainen, Svante Paeaebo
Article
Evolutionary Biology
Katerina Guschanski, Johannes Krause, Susanna Sawyer, Luis M. Valente, Sebastian Bailey, Knut Finstermeier, Richard Sabin, Emmanuel Gilissen, Gontran Sonet, Zoltan T. Nagy, Georges Lenglet, Frieder Mayer, Vincent Savolainen
SYSTEMATIC BIOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Tom van der Valk, David Diez-del-Molino, Tomas Marques-Bonet, Katerina Guschanski, Love Dalen
Article
Zoology
Martha M. Robbins, Moses Akantorana, Joseph Arinaitwe, Peter Kabano, Charles Kayijamahe, Maryke Gray, Katerina Guschanski, Jack Richardson, Justin Roy, Vastine Tindimwebwa, Linda Vigilant, Andrew M. Robbins
Article
Multidisciplinary Sciences
Amy Porter, Winnie Eckardt, Veronica Vecellio, Katerina Guschanski, Peter Philip Niehoff, Urbain Ngobobo-As-Ibungu, Radar Nishuli Pekeyake, Tara Stoinski, Damien Caillaud
Article
Biochemistry & Molecular Biology
Tom van der Valk, Catalina M. Gonda, Henri Silegowa, Sandra Almanza, Itzel Sifuentes-Romero, Terese B. Hart, John A. Hart, Kate M. Detwiler, Katerina Guschanski
MOLECULAR BIOLOGY AND EVOLUTION
(2020)