Article
Genetics & Heredity
Kenta Shirasawa, Kazuhiro Sasaki, Hideki Hirakawa, Sachiko Isobe
Summary: Pea was chosen as the research material to study the laws of inheritance by Gregor Mendel. By determining the genome sequence of a pea line with yellow pods, researchers identified a genomic region controlling pod color, potentially accelerating pan-genome studies in pea and aiding in the identification of genes controlling traits studied by Mendel.
G3-GENES GENOMES GENETICS
(2021)
Article
Microbiology
Gina Faraci, Sung Yong Park, Tanzy M. T. Love, Michael P. Dube, Ha Youn Lee
Summary: HIV microdrop sequencing is a powerful tool for large-scale and high-precision HIV genomic surveillance. The study successfully identified individuals with recent infections and achieved high detection accuracies. Moreover, the analysis of chronic HIV infection confirmed the false recency rate and estimated the time since infection with high consistency.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Brianne Edwards, Eli D. Hornstein, Nathan J. Wilson, Heike Sederoff
Summary: This study developed a simple method using T-DNA-specific primers and high-throughput sequencing to identify transgene insertion sites in the T-1 generation of any crop transformed via Agrobacterium. The example using allohexaploid oil-seed plant Camelina sativa demonstrated the feasibility of determining insertion site location of two transgenes. This new methodology allows for early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
Article
Multidisciplinary Sciences
Shuhei Yasumoto, Toshiya Muranaka
Summary: Genome editing is a powerful breeding technique that introduces mutations into specific gene sequences in genomes. However, there is still no widely authorized method for detecting foreign genes in genome-edited crops.
SCIENTIFIC REPORTS
(2023)
Review
Biochemistry & Molecular Biology
Paula Arribas, Carmelo Andujar, Martin I. Bidartondo, Kristine Bohmann, Eric Coissac, Simon Creer, Jeremy R. deWaard, Vasco Elbrecht, Gentile F. Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel, Florian Leese, Vojtech Novotny, Fredrik Ronquist, Douglas W. Yu, Lucie Zinger, Thomas J. Creedy, Emmanouil Meramveliotakis, Victor Noguerales, Isaac Overcast, Helene Morlon, Alfried P. Vogler, Anna Papadopoulou, Brent C. Emerson
Summary: High-throughput sequencing technology is increasingly used for biodiversity characterization and monitoring, offering a deeper understanding of global biodiversity when applied across broad geographical scales. International collaborative efforts are needed to maximize the potential of HTS data for global integration and synthesis, particularly in establishing an effective Genomic Observatories network for terrestrial biodiversity integration.
Article
Ecology
Hideyuki Doi, Shunsuke Matsuoka, Shin-ichiro S. Matsuzaki, Mariko Nagano, Hirotoshi Sato, Hiroki Yamanaka, Saeko Matsuhashi, Satoshi Yamamoto, Toshifumi Minamoto, Hitoshi Araki, Kousuke Ikeda, Atsuko Kato, Kouichi Kumei, Nobutaka Maki, Takashi Mitsuzuka, Teruhiko Takahara, Kimihito Toki, Natsuki Ueda, Takeshi Watanabe, Kanji Yamazoe, Masaki Miya
Summary: Although eDNA metabarcoding is a valuable tool for biodiversity monitoring, the influence of organism traits and ecosystem characteristics on its performance remains unclear. To address this knowledge gap, we conducted a nationwide study on fish communities in 18 Japanese lakes. Our results indicate that certain organism traits, such as body size and habitat preference, as well as ecosystem size, can affect eDNA detection. These findings highlight the importance of considering species traits and ecosystem characteristics in broad-scale eDNA metabarcoding monitoring.
FRESHWATER BIOLOGY
(2023)
Article
Biochemical Research Methods
Maxime de Ronne, Gaetan Legare, Francois Belzile, Brian Boyle, Davoud Torkamaneh
Summary: 3D-GBS is an optimized GBS procedure that provides an ultra-high-throughput and ultra-low-cost genotyping solution for large-scale studies. It reduces the genotyping cost significantly and improves the efficiency of marker discovery.
Review
Biochemistry & Molecular Biology
Angela Bekesi, Eszter Holub, Hajnalka Laura Palinkas, Beata G. Vertessy
Summary: The appearance of uracil in DNA is a common genomic modification, with three different routes of formation, two of which do not require specific enzymes. Efficient uracil-DNA detection methods are crucial to understanding the potential roles of genomic uracil.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Poppy Sephton-Clark, Jennifer L. Tenor, Dena L. Toffaletti, Nancy Meyers, Charles Giamberardino, Sile F. Molloy, Julia R. Palmucci, Adrienne Chan, Tarsizio Chikaonda, Robert Heyderman, Mina Hosseinipour, Newton Kalata, Cecilia Kanyama, Christopher Kukacha, Duncan Lupiya, Henry C. Mwandumba, Thomas Harrison, Tihana Bicanic, John R. Perfect, Christina A. Cuomo
Summary: The genetic diversity of Cryptococcus neoformans is associated with clinically relevant phenotypes and animal model pathogenesis, shedding light on the survival mechanisms and pathways involved in yeast persistence.
Article
Biochemistry & Molecular Biology
Jesus Gonzalez-Bosquet, Nicholas D. D. Cardillo, Henry D. D. Reyes, Brian J. J. Smith, Kimberly K. K. Leslie, David P. P. Bender, Michael J. J. Goodheart, Eric J. J. Devor
Summary: Prediction models based on genomic variation can accurately discriminate high grade serous ovarian cancer from benign tissue. Further refining of these models has the potential to detect ovarian cancer in blood with cell free DNA, even in early stage.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Aparna Lajmi, Felix Glinka, Eyal Privman
Summary: Double-digest Restriction-site Associated DNA sequencing (ddRADseq) is commonly used for generating genomic data in evolutionary and ecological studies. However, designing a ddRADseq experiment can be challenging due to various factors. This study investigates the effects of enzyme choice and size selection on sequencing efficiency and develops a user-friendly webtool, ddgRADer, to aid in experimental design and improve sequencing efficiency.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
YunCan Liu, Man Ao, Ming Lu, Shubo Zheng, Fangbo Zhu, Yanye Ruan, Yixin Guan, Ao Zhang, Zhenhai Cui
Summary: This study reveals the influencing factors of husk tightness in maize in different environments, providing an authoritative reference method for molecular breeding of maize.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
Teng Jin-yan, Ye Shoo-pan, Gao Ning, Chen Zi-tao, Diao Shu-qi, Li Xiu-jin, Yuan Xiao-long, Zhang Hao, Li Jia-qi, Zhang Xi-quan, Zhang Zhe
Summary: This study extended the ssGBLUP model by incorporating genomic annotation information and whole-genome sequence (WGS) data, improving its predictive ability. Additionally, the impact of genotyping strategies in the reference population on ssGBLUP was investigated.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Multidisciplinary Sciences
Anubhab Khan, Kaushalkumar Patel, Harsh Shukla, Ashwin Viswanathan, Tom van der Valk, Udayan Borthakur, Parag Nigam, Arun Zachariah, Yadavendradev Jhala, Marty Kardos, Uma Ramakrishnan
Summary: Habitat fragmentation leads to small populations, increasing the risk of inbreeding depression. Small populations can reduce inbreeding depression by purging deleterious recessive alleles. The study on Indian tiger populations found differences in inbreeding levels and mutation load between small and large populations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Anna Scoppola, Simone Cardoni, Thomas Marcussen, Marco Cosimo Simeone
Summary: Viola sect. Melanium, also known as the pansy, is a morphologically well-defined allopolyploid group consisting of approximately 110 perennial and annual species in the northern hemisphere. Italy has four morphologically similar annual pansies belonging to the 'V. tricolor species complex', which are difficult to distinguish in the field and have resulted in uncertain records in field inventories and European herbaria. The lack of comprehensive intra- and interspecific comparative studies, appropriate genetic markers, and clear cytological descriptions have hindered the clear circumscription and phylogenetic inferences within this group. In this study, the researchers used DNA sequence variation of three plastid markers and High-Throughput Sequencing (HTS) to investigate species identity, genome organization, and evolution within the V tricolor species complex. The results revealed close relationships within this group, provided reliable molecular resolution for V. tricolor, and demonstrated the common ancestry of V. arvensis, V. kitaibeliana, and V. hymettia. The researchers also found evidence of significant geographic divergence within V. tricolor and V. arvensis, suggesting the presence of different eco-cytotypes within these species. The overall diversity patterns and the occurrence of multiple diverging 5S-IGS lineages are discussed in relation to the taxonomy and genomic evolution of Viola sect. Melanium.
Article
Oncology
Christina Raftopoulou, Fani-Marlen Roumelioti, Eleni Dragona, Stefanie Gimelli, Frederique Sloan-Bena, Vasilis Gorgoulis, Stylianos E. Antonarakis, Sarantis Gagos
Article
Biochemistry & Molecular Biology
Stylianos E. Antonarakis, Ales Holoubek, Melivoia Rapti, Jesse Rademaker, Jenny Meylan, Justyna Iwaszkiewicz, Vincent Zoete, Callum Wilson, Juliet Taylor, Muhammad Ansar, Christelle Borel, Olivier Menzel, Katerina Kuzelova, Federico A. Santoni
Summary: Knobloch syndrome, typically linked to the COL18A1 gene, can also be associated with the PAK2 gene. A study on a specific family revealed that KNO2 syndrome in the family is dominantly caused by a deleterious variant in the PAK2 gene.
HUMAN MOLECULAR GENETICS
(2022)
Article
Environmental Sciences
James M. Muthoka, Edward E. Salakpi, Edward Ouko, Zhuang-Fang Yi, Alexander S. Antonarakis, Pedram Rowhani
Summary: The study successfully detected Opuntia stricta in the ASAL of Kenya using Sentinel-2 multispectral sensors and ensemble machine learning classifiers, achieving high overall accuracies. The combination of topographic and vegetation indices improved classification accuracy.
Article
Green & Sustainable Science & Technology
Ushuki A. Amuyou, Yi Wang, Francis Bisong, Alexander S. Antonarakis
Summary: The rate of landcover change due to deforestation in tropical environments continues to rise, despite efforts such as the REDD+ policy to combat forest destruction. The study in Cross River State, Nigeria, found that financial payment and increased natural resources were perceived benefits of forest carbon protection. Household income was a key factor influencing support for forest carbon protection, with an increase in income attributed to a ban on logging.
Article
Immunology
Samuel Cordey, Florian Laubscher, Mary-Anne Hartley, Thomas Junier, Kristina Keitel, Mylene Docquier, Nicolas Guex, Christian Iseli, Gael Vieille, Philippe Le Mercier, Anne Gleizes, Josephine Samaka, Tarsis Mlaganile, Frank Kagoro, John Masimba, Zamzam Said, Hosiana Temba, Gasser H. Elbanna, Caroline Tapparel, Marie-Celine Zanella, Ioannis Xenarios, Jacques Fellay, Valerie D'Acremont, Laurent Kaiser
Summary: This study explored the blood virome of febrile children in sub-Saharan Africa, identifying common viruses causing human infection/disease in half of the patients. It also detected a number of viruses related to arthropod, vertebrate, or mammalian species that have not yet been known to cause human infection/disease, highlighting the need for further surveillance of emerging pathogens.
EMERGING MICROBES & INFECTIONS
(2021)
Biographical-Item
Genetics & Heredity
Stylianos E. Antonarakis
Summary: In the past 45 years, there has been a triumph in the discovery of genes and genetic variation causing Mendelian disorders, leading to the identification of thousands of monogenic phenotypes. The work can be divided into three phases with different laboratory strategies used for gene discovery related to diseases. However, more work is still needed to identify all high impact genomic variation contributing substantially to phenotypic variation.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2021)
Article
Genetics & Heredity
Charles Lee, Stylianos E. Antonarakis, Ada Hamosh, John Burn
Summary: HUGO was established in 1988 to integrate international genomic activity and accelerate knowledge diffusion from the human genome project. In 2020, HUGO merged with HGVS and HVP to gather human genomic variation worldwide, under a new Executive Board and seven focused committees to bring benefits of genome diversity knowledge to people globally.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2021)
Article
Biodiversity Conservation
Alexander S. Antonarakis, Stacy A. Bogan, Michael L. Goulden, Paul R. Moorcroft
Summary: Accurate descriptions of ecosystem composition using imaging spectrometry can significantly improve terrestrial biosphere model predictions of carbon, water, and energy fluxes. The study also found that the 2012-2015 Californian drought led to significant reductions in regional ecosystem productivity, with the most pronounced impact seen in high basal area mid-elevation forests.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ana Paula Machado, Tristan Cumer, Christian Iseli, Emmanuel Beaudoing, Anne-Lyse Ducrest, Melanie Dupasquier, Nicolas Guex, Klaus Dichmann, Rui Lourenco, John Lusby, Hans-Dieter Martens, Laure Prevost, David Ramsden, Alexandre Roulin, Jerome Goudet
Summary: Research suggests that barn owls colonized the British Isles directly from a white-colored refugium in the Iberian Peninsula after the last glaciation, rather than crossing over Doggerland as previously believed. They maintained their white color in the British Isles through low gene flow with the mainland, suggesting neutral processes rather than selection for the contrasting color. This unexpected colonization route may have implications for other species from the paleo community as well.
Article
Green & Sustainable Science & Technology
Alexander S. Antonarakis, Lucia Pacca, Andreas Antoniades
Summary: This study examines the impact of financial crises on deforestation rates globally, finding a reduction in deforestation during crisis periods. It also notes that financial crises have a larger effect on deforestation in low-income countries. The study emphasizes the need for governments to enhance sustainable forest management during crisis periods to maintain the benefits of reduced deforestation.
SUSTAINABILITY SCIENCE
(2022)
Article
Multidisciplinary Sciences
Anjali Kaushal, Julien Dorier, Bihan Wang, Giriram Mohana, Michael Taschner, Pascal Cousin, Patrice Waridel, Christian Iseli, Anastasiia Semenova, Simon Restrepo, Nicolas Guex, Erez Lieberman Aiden, Maria Cristina Gambetta
Summary: Boundaries in animal genomes play a crucial role in limiting regulatory cross-talk and guiding enhancers to target promoters. This study reveals that the formation and function of boundaries in flies are different from mammals. Unlike mammalian boundaries, most Drosophila boundaries form independently of CTCF and are recruited by Cp190. These boundaries are essential for early development and prevent regulatory cross-talk between specific gene loci, but are dispensable for long-range enhancer-promoter communication.
Article
Environmental Sciences
Ushuki A. Amuyou, Yi Wang, Bisong Francis Ebuta, Chima J. Iheaturu, Alexander S. Antonarakis
Summary: This study estimated the regional distribution of aboveground biomass (AGB) in the Cross River State, Nigeria, using Sentinel-2 imagery and random forest machine learning algorithm. The results showed that the AGB estimation using random forest yielded favorable results compared to previous products, and the biomass map could be used for REDD+ monitoring and reporting.
Article
Biochemistry & Molecular Biology
Nina Vesel, Christian Iseli, Nicolas Guex, Alexandre Lemopoulos, Melanie Blokesch
Summary: A. baumannii is a dangerous nosocomial pathogen that can rapidly acquire antibiotic resistance genes. This study investigates the role of epigenetic DNA modification in horizontal gene transfer, finding that diverse A. baumannii strains have different methylome patterns that influence DNA exchange.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Bernard Conrad, Christian Iseli, Magnus Pirovino, Jordi Villa-Freixa
Summary: All life forms on earth can be traced back to a common ancestor called LUCA through Darwinian evolution. These life forms share two important features - a metabolism for extracting and converting energy, and a genetic system for heredity. However, genome replication often leads to the emergence of genetic parasites. In this study, we propose a model that simulates the energetic and replicative conditions of LUCA-like organisms and their parasites, and investigate the problem-solving abilities of host-parasite pairs. Our findings suggest that a nested parasitism model involving three host-parasite pairs can achieve robust and stable homeostasis, forming a complete life cycle. This model, which includes competition and habitat restriction, efficiently captures, channels, and transforms energy, enabling dynamic host survival and adaptation.
Article
Development Studies
Bernardo Cantone, Alexander S. Antonarakis, Andreas Antoniades
Summary: The study shows that the global economic slowdown has exacerbated environmental issues, particularly in terms of biodiversity and fisheries. However, there have been improvements in some environmental indicators, indicating that economic stagnation alone cannot drive sustainable development.
SUSTAINABLE DEVELOPMENT
(2021)