Article
Microbiology
Andrew N. Miller, Jason Karakehian, Daniel B. Raudabaugh
Summary: Fungaria is an important resource for genetic data, especially for type specimens. However, ancient specimens often have fragmented and contaminated DNA, making sequencing difficult. This study successfully extracted and sequenced DNA from recent and ancient specimens, generating correct sequences for five samples. The results contribute to ongoing systematic studies.
Article
Biochemistry & Molecular Biology
Le Zhang, Yi-Wei Huang, Jia-Lin Huang, Ji-Dong Ya, Meng-Qing Zhe, Chun-Xia Zeng, Zhi-Rong Zhang, Shi-Bao Zhang, De-Zhu Li, Hong-Tao Li, Jun-Bo Yang
Summary: In this study, DNA barcoding was conducted for species identification of Cymbidium using plastomes. A comprehensive DNA barcode reference library for Cymbidium species identification was established. The plastome showed improved species identification rates compared to standard DNA barcodes, but still had limitations. Nuclear genome data were also explored for species identification and showed potential as next-generation nuclear barcodes.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Medical Laboratory Technology
Bennett Oh Vic Shum, Carel Jacobus Pretorius, Letitia Min Fen Sng, Ilya Henner, Paulette Barahona, Emre Basar, Jim McGill, Urs Wilgen, Anna Zournazi, Lilian Downie, Natalie Taylor, Liam Cheney, Sylvania Wu, Natalie Angela Twine, Denis Carolin Bauer, Gerald Francis Watts, Akash Navilebasappa, Kishore Rajagopal Kumar, Jacobus Petrus Johannes Ungerer, Glenn Bennett
Summary: The study found that newborn screening can be expanded using targeted gene sequencing (TGS), which is a feasible and cost-effective method. The TGS assay had a high sensitivity (>99%) and specificity (100%) with a turnaround time of 7 to 10 days and a maximum batch size of 1536 samples. This approach can increase the number of conditions screened and improve the effectiveness of newborn screening programs.
CLINICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Kang Huang, Wenkai Li, Bing Yang, Dan Wang, Shujun He, Yujia Shen, Jincuo Ao, Yuhang Li, Yunxia Cui, Yuchen Kong, Wei Li, Nianlong Li, Derek W. Dunn, Baoguo Li
Summary: Polyploid plants are important for studying evolution, molecular ecology, and agriculture. However, their unique genetic inheritance requires specific software for population genetic analysis.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Environmental Sciences
Yawen Mu, Chao Song, Jianghua Yang, Yong Zhang, Xiaowei Zhang
Summary: This study used DNA barcoding to identify species and assess biodiversity of fish in Tai Lake. High-throughput sequencing greatly improved the capture rate of barcode sequences of fish, and barcode gap analysis successfully delineated species in all specimens. The results are expected to provide new insights into fish diversity conservation in Tai Lake.
Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Review
Pharmacology & Pharmacy
Xiangjun Ji, Baitang Ning, Jinghua Liu, Ruth Roberts, Larry Lesko, Weida Tong, Zhichao Liu, Tieliu Shi
Summary: Pharmacogenomics plays essential roles in optimizing drug responses and avoiding adverse events. Population-specific therapeutic interventions and genotyping can improve clinical outcomes, highlighting the importance of precision medicine strategies. Challenges and regulatory efforts still exist in advancing this field further.
DRUG DISCOVERY TODAY
(2021)
Article
Urology & Nephrology
Jose Lazaro-Guevara, Julio Fierro-Morales, A. Hunter Wright, River Gunville, Christopher Simeone, Scott G. Frodsham, Melissa H. Pezzolesi, Courtney A. Zaffino, Laith Al-Rabadi, Nirupama Ramkumar, Marcus G. Pezzolesi
Summary: This study investigated the genetic basis of nondiabetic kidney disease (NDKD) and diabetic kidney disease (DKD) through targeted NGS, finding rare diagnostic variants consistent with clinical diagnoses in 19% of NDKD patients and in 22% of DKD patients. Additionally, genetic variants suggestive of NDKD were detected in 3% of diabetic patients. These findings suggest that rare variants in kidney disease-related genes may contribute to the pathogenesis of DKD and NDKD in patients with diabetes.
AMERICAN JOURNAL OF NEPHROLOGY
(2021)
Article
Ecology
Marie V. Brasseur, Jonas J. Astrin, Matthias F. Geiger, Christoph Mayer
Summary: Researchers developed MitoGeneExtractor, an innovative tool that extracts mitochondrial protein coding genes from next-generation sequencing datasets. It uses multiple sequence alignments to accurately and quickly extract these genes. In a case study with bird genomic datasets, MitoGeneExtractor showed higher sensitivity and faster speed compared to existing methods.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Oncology
Min Ruan, Lipeng Liu, Benquan Qi, Xiaoyan Chen, Lixian Chang, Aoli Zhang, Fang Liu, Shuchun Wang, Xiaoming Liu, Xiaojuan Chen, Li Zhang, Ye Guo, Yao Zou, Yingchi Zhang, Yumei Chen, LiXia Liu, Shanbo Cao, Feng Lou, Chengcheng Wang, Xiaofan Zhu
Summary: This study validates the diagnostic role of circulating tumor DNA in pediatric AML based on next-generation sequencing, showing that ctDNA can mirror genomic information from bone marrow and detect mutations exclusively. Monitoring ctDNA with NGS-based assays provides valuable information for precision treatment in pediatric AML.
FRONTIERS IN ONCOLOGY
(2021)
Article
Clinical Neurology
Jakub Scaber, Alexander G. Thompson, Lucy Farrimond, Emily Feneberg, Malcolm Proudfoot, Lynn Ossher, Martin R. Turner, Kevin Talbot
Summary: This study demonstrates that expanding genetic testing to all patients diagnosed with ALS can enhance recruitment potential for clinical trials, but also has significant resource implications for genetic counseling.
EUROPEAN JOURNAL OF NEUROLOGY
(2023)
Article
Ecology
Kristoffer Sahlin, Marisa C. W. Lim, Stefan Prost
Summary: NGSpeciesID is a program that generates highly accurate consensus sequences from long-read amplicon sequencing technologies by clustering reads and employing polishing strategies, improving quality while reducing preprocessing and software installation, enabling rapid processing of a large number of samples with similar consensus accuracy to current pipelines.
ECOLOGY AND EVOLUTION
(2021)
Article
Physiology
Agnes Bloch-Zupan, Tristan Rey, Alexandra Jimenez-Armijo, Marzena Kawczynski, Naji Kharouf, Muriel de La Dure-Molla, Emmanuelle Noirrit, Magali Hernandez, Clara Joseph-Beaudin, Serena Lopez, Corinne Tardieu, Beatrice Thivichon-Prince, Tatjana Dostalova, Milan Macek Jr, Mustapha El Alloussi, Leila Qebibo, Supawich Morkmued, Patimaporn Pungchanchaikul, Blanca Urzua Orellana, Marie-Cecile Maniere, Benedicte Gerard, Isaac Maximiliano Bugueno, Virginie Laugel-Haushalter
Summary: In this study, next-generation sequencing was used to analyze a cohort of Amelogenesis imperfecta (AI) patients, revealing more than 70 genes associated with AI. The findings showed that 73% of the cases were non-syndromic AI and 27% were syndromic AI. The genetic diagnosis provided important insights for the diagnosis and treatment of AI. This study demonstrated the potential of next-generation sequencing in AI research and provided new insights into the classification and treatment of AI.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Agronomy
Ivan Drahun, Kiana F. Wiebe, Cody W. Koloski, Willem G. van Herk, Bryan J. Cassone
Summary: This study investigated the population genetic structure of Hypnoidus bicolor wireworms and click beetles from the Canadian Prairies, revealing two genetically distinct clades that may be part of a species complex. Clade A was predominant and increased in prevalence towards the east, while clade B showed two mitochondrial DNA groups with uneven gene flow. Both clades exhibited low levels of regional genetic structuring, with clade A undergoing population and range expansions possibly linked to intensive agriculture practices in the prairies.
PEST MANAGEMENT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Raphael Rodriguez, Yamuna Krishnan
Summary: This article reviews the historical development of next-generation sequencing chemistry, highlighting the significant impact of the underlying chemical principles on biology.
NATURE BIOTECHNOLOGY
(2023)
Article
Biology
Hicham Mhamdi, Emmanuelle Stoetzel, Oussama Bouarakia, Hassan Aouraghe, Mohamed Souhir
Summary: The Guenfouda cave in eastern Morocco has revealed a diverse collection of macro- and microvertebrate fauna and a significant lithic industry dating back to various cultures. Through the study of teeth morphology and biometric data, two species of Gerbillus were identified for the first time, with one species being new to the North African fossil record. The taphonomic study suggests that a medium-sized nocturnal predator was responsible for the accumulation of small mammals in the cave. The paleoecological reconstruction indicates a semi-open steppic landscape with patches of wooded areas and water ponds, characteristic of the region both in the past and present.
HISTORICAL BIOLOGY
(2023)
Article
Geography, Physical
Jose Maria Pozo, Angela Trentacoste, Ariadna Nieto-Espinet, Silvia Guimaraes, Silvia Valenzuela-Lamas
Summary: Log Size Indexes (LSI) have been used in zooarchaeological studies since 1950 to increase the amount of data. However, there are unpublished standards for calculating log ratios, and the diversity of data recording practices makes the calculation of indexes tedious. The 'zoolog' R package solves these issues by allowing users to calculate thousands of log-ratios quickly and choose between different public references, increasing repeatability and comparability of results.
QUATERNARY INTERNATIONAL
(2023)
Article
Geography, Physical
Abel Moclan, Angel C. Dominguez-Garcia, Emmanuelle Stoetzel, Thomas Cucchi, Paloma Sevilla, Cesar Laplana
Summary: Taxonomic identification of fossils based on morphology is a key step in palaeontological studies. Machine Learning techniques have been shown to be powerful statistical approaches for analyzing quantitative morphometric data. In this study, Machine Learning algorithms were applied to two-dimensional geometric morphometric data of Mus spp. molars, demonstrating their effectiveness in taxonomic identification.
QUATERNARY SCIENCE REVIEWS
(2023)
Article
Geochemistry & Geophysics
Christiane Denys, Denne N. Reed, Yannicke Dauphin
Summary: Recent taphonomic studies have revealed that predators, such as owls, are responsible for the accumulation of small mammal fossils and their feeding activities lead to bone loss, breakage, and surface modifications. However, the specific physiological and chemical alterations induced by predators on bones remain poorly understood. To address this, an experimental study was conducted to simulate digestion by owls, where fresh rodent long bones were subjected to various solutions mimicking the effects of predator digestion. The results showed that acid action alone did not replicate the modifications observed in bones recovered from owl pellets, while enzymatic activity (such as trypsin and trypsin + lipase) produced similar modifications. These findings contribute to enhancing our understanding of early diagenetic modifications in small mammal bones caused by digestion, thereby improving our ability to identify nocturnal predators in fossil accumulations.
Article
Genetics & Heredity
Daniel Gaspar, Ana Usie, Celia Leao, Silvia Guimaraes, Ana Elisabete Pires, Claudino Matos, Antonio Marcos Ramos, Catarina Ginja
Summary: As global warming becomes more complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are becoming important. This study sequenced the genomes of Portuguese native sheep breeds to analyze their genomic diversity and population structure. The results provide insights into the potential of genomic data for guiding conservation efforts and identifying breed markers.
FRONTIERS IN GENETICS
(2023)
Editorial Material
Geosciences, Multidisciplinary
Emmanuelle Stoetzel, Janine Ochoa, Juan Rofes
Article
Zoology
Ahmad Mahmoudi, Ehsan Mostafavi, Ali Mohammadi, Tahmineh Jalali, Christiane Denys, Violaine Nicolas, Jean-Pierre Hugot, Aude Lalis, Mostafa Salehi-Vaziri
Summary: This study is the first attempt to detect orthohantavirus infections in rodents in Iran, identifying Tula orthohantavirus for the first time in the country. The findings suggest the need for further data collection to better understand the potential reservoirs, ecology, and epidemiological cycle of the virus in Iran.
Article
Geography, Physical
Emmanuelle Stoetzel, Helder Gomes Rodrigues, Raphael Cornette
Summary: The study utilizes geometric morphometric and dental microwear analyses to investigate the morphology and diet of modern and fossil species of the Arvicanthis genus. The geometric morphometric analysis successfully distinguishes the extant and fossil Arvicanthis species, and identifies probable geographical variations within the A. niloticus group. Microwear analyses reveal diet differences in various modern populations of A. niloticus and paleodiet inferences in the A. arambourgi fossil species. This research lays the groundwork for a comprehensive revision of Arvicanthis fossil remains from Quaternary deposits in northern Africa and enhances our understanding of the morphological variability of this genus in Africa.
QUATERNARY RESEARCH
(2023)
Article
Zoology
Florian Laurence, Violaine Nicolas, Halamoussa Joelle Ayoro, Annemarie Ohler
Summary: Species of Hylarana are common in the Oriental region, but their geographical distribution is poorly known. This study compiled data from various sources to create distribution maps for four Hylarana species. Climatic data was used to create Species Distribution Models and discrepancies between observed distribution and suitable climatic niches were discussed.
Article
Biology
Pierre Linchamps, Emmanuelle Stoetzel, Raphael Cornette, Christiane Denys, Raphael Hanon, Nompumelelo Maringa, Thalassa Matthews, Christine Steininger
Summary: This study provides the first taxonomic, taphonomic and palaeoecological description of the micromammal material from the 1.4 Ma assemblage of Cooper's D. The dominant rodent genera in this assemblage, Mystromys and Otomys, suggest an open landscape with grassland and savanna vegetation during the Early Pleistocene, supporting previous indications of a shift in African climate and vegetation towards more open habitats.
HISTORICAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Catarina Ginja, Silvia Guimaraes, Rute R. da Fonseca, Rita Rasteiro, Ricardo Rodriguez-Varela, Luciana G. Simoes, Cindy Sarmento, Maria Carme Belarte, Nabil Kallala, Joan Ramon Torres, Joan Sanmarti, Ana Margarida Arruda, Cleia Detry, Simon Davis, Jose Matos, Anders Gotherstrom, Ana Elisabete Pires, Silvia Valenzuela-Lamas
Summary: This article investigates the genetic makeup of domestic cattle from the Iron Age in the Eastern Maghreb, specifically Althiburos, Tunisia. The maternal lineages of these cattle can be traced back to the R and African-T1 haplogroups, suggesting hybridization with local aurochs. However, it is also possible that these cattle were independently domesticated in North Africa due to their shared ancestry with pre-domestic Moroccan aurochs and present-day African taurine cattle.
Article
Ecology
Joelle Halamoussa Ayoro, Violaine Nicolas, Gabriel Hoinsoude Segniagbeto, Emmanuel Midibahaye Hema, Annemarie Ohler, Gustave Boureima Kabre
Summary: Climate change can impact biodiversity by altering species habitats. This study focuses on the future distribution patterns of two amphibian species, Hyperolius nitidulus and Ptychadena bibroni, in the West African savannahs. The findings suggest that climate change could result in the loss of suitable habitats for H. nitidulus and the emergence of new habitats for P. bibroni.
AFRICAN JOURNAL OF ECOLOGY
(2023)
Article
Ecology
Malahat Dianat, Adam Konecny, Leonid A. Lavrenchenko, Julian C. Kerbis Peterhans, Terrence C. Demos, Violaine Nicolas, David Ortiz, Josef Bryja
Summary: This study reveals that Eastern Afromontane Crocidura shrews originated in the Ethiopian Highlands and colonized other areas through a dispersal event. The Ethiopian Highlands were found to be the cradle of diversity for this group of mammals.
JOURNAL OF BIOGEOGRAPHY
(2023)
Article
Ecology
E. Andrew Bennett, Oguzhan Parasayan, Sandrine Prat, Stephane Pean, Laurent Crepin, Alexandr Yanevich, Thierry Grange, Eva-Maria Geigl
Summary: The study of two Early Upper Palaeolithic genomes of humans that lived 36,000-37,000 years ago in Crimea reveals the dynamics of migration and admixture in the European population after 40,000 years ago.
NATURE ECOLOGY & EVOLUTION
(2023)