Article
Biochemistry & Molecular Biology
Erin E. Hahn, Marina R. Alexander, Alicia Grealy, Jiri Stiller, Donald M. Gardiner, Clare E. Holleley
Summary: This study successfully recovered complete mitochondrial genomes and up to 3x nuclear genome coverage from formalin-preserved tissues by refining sample processing methods and identifying specimen characteristics predictive of sequencing success. The overall specimen condition was found to be the strongest predictor of DNA yield, interacting with preservation conditions to accelerate DNA degradation.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Multidisciplinary Sciences
Danang Crysnanto, Alexander S. Leonard, Zih-Hua Fang, Hubert Pausch
Summary: This study builds a diverse pangenome from multiple cattle assemblies, revealing genetic differences between different breeds and capturing previously undetected genetic variations. By utilizing whole-genome sequencing and transcriptome data, the research uncovers genes and transcripts that were previously unseen in the traditional reference genome, opening up new avenues for genetic investigations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Nicolas Bejerman, Ralf G. Dietzgen, Humberto Debat
Summary: This study reports the discovery of 45 novel varicosavirus genomes in publicly available metatranscriptomic data, expanding our knowledge on varicosaviruses. These findings reveal the sequence diversity and genome architecture plasticity of varicosaviruses, and shed new light on the phylogenetic relationships and evolutionary landscape of this group of plant rhabdoviruses.
Review
Microbiology
Alican Topaloglu, Omer Esen, Burcu Turanli-Yildiz, Mevlut Arslan, Zeynep Petek Cakar
Summary: With increasing human population and the decline of fossil fuels, there has been a global shift towards alternative fuel sources. Ethanol has emerged as a primary alternative due to its low carbon emissions and ease of microbial production. Baker's yeast Saccharomyces cerevisiae has been the focus of research for enhanced ethanol production processes. Metabolic engineering and evolutionary engineering strategies have been employed to manipulate the ethanol metabolism genes and improve bioethanol production. This review highlights the current state of metabolic and evolutionary engineering in first- and second-generation S. cerevisiae bioethanol production processes.
Review
Biochemistry & Molecular Biology
Xuan Zhou, Zhenhua Liu
Summary: Plants produce diverse natural chemicals that play adaptive roles throughout their life cycles. However, the complexity and size of plant genomes hinder the exploration of metabolic diversity. Advances in genome sequencing and pan-genomic data analysis have revealed gene clusters associated with important agronomic traits in plants, leading to the discovery of plant metabolic diversification. The future of investigating metabolic diversity in plants lies in the pan-genomics era.
PLANT COMMUNICATIONS
(2022)
Review
Biotechnology & Applied Microbiology
Eduarde Rohner, Ran Yang, Kylie S. Foo, Alexander Goedel, Kenneth R. Chien
Summary: mRNA therapeutics face challenges, but with the help of solutions, they have the potential to become a widely applicable treatment modality for both rare and common diseases.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Chuan Zhou, Michelle M. Halstead, Amelie Bonnet-Garnier, Richard M. Schultz, Pablo J. Ross
Summary: Using CUT&Tag, researchers profiled histone modifications in bovine oocytes, embryos, and blastocysts to understand gene expression changes during preimplantation development. They found that broad bivalent domains mark developmental genes in oocytes, and repressive marks H3K9me3 and H3K27me3 are present before embryonic genome activation (EGA), suggesting a global transcription repression mechanism. Chromatin accessibility is established before activating marks H3K4me3 and H3K27ac during EGA. Transcription is required for the remodeling process, indicating the insufficiency of maternal products alone. H3K27me3 plays a major role in cellular potency restriction and blastocyst lineage determination.
Article
Multidisciplinary Sciences
Andreas Boes, Lin Chang, Carsten Langrock, Mengjie Yu, Mian Zhang, Qiang Lin, Martin Fejer, John Bowers, Arnan Mitchell
Summary: This article reviews the history of lithium niobate as an optical material, covering its various photonic platforms, engineering concepts, spectral coverage, and major applications, while also providing a glimpse into its future prospects.
Article
Multidisciplinary Sciences
Rotem Raz, Zvi Roth, Moran Gershoni
Summary: This study obtained and analyzed raw data from 262 whole-exome sequencing samples of Bos Taurus, and established a comprehensively annotated database of over 20 million short variants, some of which contribute to diseases and traits.
Editorial Material
Immunology
Raul Y. Sanchez-David, Pierre V. Maillard
Summary: The study highlights the significance of RNA interference in antiviral immunity in mammals and demonstrates the potential of designer peptides as a promising approach for antiviral therapy.
Article
Multidisciplinary Sciences
Simone Mozzachiodi, Kristoffer Krogerus, Brian Gibson, Alain Nicolas, Gianni Liti
Summary: The authors propose a non-GMO workflow to improve industrial yeast strains by inducing genome-wide recombination using the return-to-growth approach. This approach allows for the identification of clones with superior biotechnological traits, overcoming the sterility of domesticated industrial yeast strains.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Chalani Dilshani Perera, Muhammad Idrees, Abdul Majid Khan, Zaheer Haider, Safeer Ullah, Ji-Su Kang, Seo-Hyun Lee, Seon-Min Kang, Il-Keun Kong, Dmitry S. Bogolyubov
Summary: This study reveals the critical role of the PDGFR beta-NFYA axis in bovine embryonic genome activation and embryonic development. Inhibition of PDGFR beta leads to downregulation of NFYA, which affects the expression of critical EGA-related genes, bovine embryo development rate, and implantation potential.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Julia D. Sigwart, Robert Blasiak, Marcel Jaspars, Jean-Baptiste Jouffray, Deniz Tasdemir
Summary: The diverse life in the ocean is a rich source of inspiration for drug discovery, but the marine biodiscovery pipeline faces chronic underfunding, bottlenecks, and untapped potential. To broaden the biodiscovery pipeline and unlock the social and economic potential of the ocean genome, investments in fundamental research, equitable collaborations between academia and industry, opportunities for early-career researchers, data sharing, and conservation efforts are essential. Proper utilization of the treasures in the ocean can provide breakthroughs in human health, but efforts must be made to ensure the biodiscovery pipeline is not obstructed in favor of quick-fix solutions.
NATURAL PRODUCT REPORTS
(2021)
Article
Veterinary Sciences
Jennifer N. Kiser, Holly L. Neibergs
Summary: This study identified loci and heritability estimates associated with BCoV infection and BRD in dairy calves and feedlot cattle. Results suggest that selection breeding may help reduce susceptibility to BCoV infection and BRD in cattle.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Review
Energy & Fuels
Tholkappiyan Ramachandran, Siva Sankar Sana, Kulurumotlakatla Dasha Kumar, Yedluri Anil Kumar, H. H. Hegazy, Seong Cheol Kim
Summary: With the proliferation of new electronic and optoelectronic devices worldwide, the development of more reliable power sources with better energy densities and longer lifespans has become necessary. Supercapacitors have emerged as excellent energy storage technologies due to their high power, quick charging and discharging, and prolonged cyclic stability. However, the extremely low energy density of existing supercapacitors significantly limits their wide range of applications. Asymmetric supercapacitors (ASCs) built with two different electrode materials offer a wide operational voltage window, which considerably improves energy density. This critical analysis explores the materials and fabrication advancements in ASCs over the past few decades, as well as the current challenges and prospects for the future.
JOURNAL OF ENERGY STORAGE
(2023)
Article
Nutrition & Dietetics
Mary E. Kable, Elizabeth L. Chin, David Storms, Danielle G. Lemay, Charles B. Stephensen
Summary: This study investigated the relationship between diet patterns and gut microbial community composition in a diverse, healthy US adult cohort. Results showed significant correlations between diet dry weight, carbohydrates, fiber, and gut microbial diversity. Bifidobacterium and Lachnospira were found to be enriched in diets with specific nutrient profiles. The use of a tree structure annotated with grams of carbohydrates provided a robust method for comparing self-reported diet to gut microbial community composition.
JOURNAL OF NUTRITION
(2022)
Editorial Material
Multidisciplinary Sciences
ThankGod Echezona Ebenezer, Anne W. T. Muigai, Simplice Nouala, Bouabid Badaoui, Mark Blaxter, Alan G. Buddie, Erich D. Jarvis, Jonas Korlach, Josiah O. Kuja, Harris A. Lewin, Roksana Majewska, Ntanganedzeni Mapholi, Suresh Maslamoney, Michele Mbo'o-Tchouawou, Julian O. Osuji, Ole Seehausen, Oluwaseyi Shorinola, Christian Keambou Tiambo, Nicola Mulder, Cathrine Ziyomo, Appolinaire Djikeng
Article
Multidisciplinary Sciences
Marco Corbo, Joana Damas, Madeline G. Bursell, Harris A. Lewin
Summary: This study used high throughput chromatin conformation capture (Hi-C) to investigate the evolutionary stability of chromatin conformation at the chromosomal level in 11 species from three carnivore families. The results showed that chromatin conformation is conserved during carnivore evolution and can be accurately identified through Hi-C contact maps analysis. The study also discovered significant differences in chromatin conformation for the X chromosome and the red fox genome.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Nutrition & Dietetics
Juan J. Castillo, Garret Couture, Nikita P. Bacalzo, Ye Chen, Elizabeth L. Chin, Sarah E. Blecksmith, Yasmine Y. Bouzid, Yael Vainberg, Chad Masarweh, Qingwen Zhou, Jennifer T. Smilowitz, J. Bruce German, David A. Mills, Danielle G. Lemay, Carlito B. Lebrilla
Summary: The molecular complexity of carbohydrates consumed by humans has been oversimplified due to the lack of suitable analytical methods. This work presents a detailed catalogue of glycans in commonly consumed foods and establishes an open-access database. The Glycopedia can be used to formulate targeted diets that modulate the gut microbiome, opening possibilities for new preventative or therapeutic diets.
Article
Cell Biology
Ana C. Almeida, Joana Soares-de-Oliveira, Danica Drpic, Liam P. Cheeseman, Joana Damas, Harris A. Lewin, Denis M. Larkin, Paulo Aguiar, Antonio J. Pereira, Helder Maiato
Summary: Chromosome segregation in mammals relies on the maturation of K-fibers, and augmin plays a key role in this process. Our study reveals that augmin promotes turnover and poleward flux of kinetochore and interpolar microtubules and increases the frequency of microtubule growth through branched microtubule nucleation. These findings are important for understanding the self-organization and maturation of K-fibers in mammals.
Article
Biochemistry & Molecular Biology
Yang Zhou, Lv Yang, Xiaotao Han, Jiazheng Han, Yan Hu, Fan Li, Han Xia, Lingwei Peng, Clarissa Boschiero, Benjamin D. Rosen, Derek M. Bickhart, Shujun Zhang, Aizhen Guo, Curtis P. Van Tassell, Timothy P. L. Smith, Liguo Yang, George E. Liu
Summary: A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified novel sequence and structural variants, providing valuable insights into the diversity and evolutionary history of cattle.
Article
Plant Sciences
Noah Fahlgren, Muskan Kapoor, Galabina Yordanova, Irene Papatheodorou, Jamie Waese, Benjamin Cole, Peter Harrison, Doreen Ware, Timothy Tickle, Benedict Paten, Tony Burdett, Christine G. Elsik, Christopher K. Tuggle, Nicholas J. Provart
Summary: Building a data infrastructure for the Plant Cell Atlas using existing infrastructure and platforms will allow biologists and data scientists to gain new insights into plant biology. The development of the Human Cell Atlas and the Single Cell Expression Atlas by the European Bioinformatics Institute has laid the foundation for constructing the data infrastructure for the Plant Cell Atlas. The utilization of appropriate ontologies is crucial for describing plant single cell experiments.
Article
Multidisciplinary Sciences
M. Jennifer Woodward-Greene, Jason M. Kinser, Tad S. Sonstegard, Johann Soelkner, Iosif I. Vaisman, Curtis P. Van Tassell
Summary: Computer vision is a tool that can provide livestock producers with digital body measurements important for animal health and production. The scarcity of labeled training data sets poses a challenge in building these tools. To address this, the PreciseEdge image segmentation algorithm is introduced, which employs a standard image collection protocol and a semi-automated image labeling method for efficient and accurate body measurement extraction.
Article
Agriculture, Dairy & Animal Science
F. L. Guinan, G. R. Wiggans, H. D. Norman, J. W. Durr, J. B. Cole, C. P. Van Tassell, I. Misztal, D. Lourenco
Summary: Genomic selection accelerates genetic changes in populations by increasing accuracy and decreasing generation interval. The genetic gain and inbreeding levels of US dairy cattle breeds since the implementation of genomic evaluations in 2009 were examined. The Holstein and Jersey breeds have seen the most significant increase in genetic gain since then.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Badjibassa Akounda, Dominique Ouedraogo, Albert Soudre, Pamela A. Burger, Benjamin D. Rosen, Curtis P. Van Tassell, Johann Soelkner
Summary: This study explores the morphological differences between different goat populations in Burkina Faso using morphometric traits. The results show that there is no strict distinction between the two populations, indicating a close genetic relationship. Four groups were identified based on body size, representing the main breeds and their crosses. These different goat morphotypes are the result of farmers breeding practices. The study highlights the need for sustainable genetic improvement approaches for the use of these adapted local goat genetic resources.
Article
Microbiology
Laurynne C. Coates, Sierra D. Durham, David H. Storms, Andrew D. Magnuson, Diane L. Van Hekken, Benjamin M. Plumier, John W. Finley, Naomi K. Fukagawa, Peggy M. Tomasula, Danielle G. Lemay, Matthew J. Picklo, Daniela Barile, Kenneth F. Kalscheur, Mary E. Kable
Summary: Milk oligosaccharides (MOs) and fatty acids (MFAs) have prebiotic, antiadhesive, and antimicrobial effects. Their relationships with milk microbes and inflammation have been studied in humans, but not in cows. Studying the relationships among milk microbiota, MFAs, MOs, lactose, and somatic cell counts in cows can provide valuable insights for improving milk quality and reducing waste.
MICROBIOLOGY SPECTRUM
(2023)
Article
Multidisciplinary Sciences
Sierra D. Durham, Zhe Wei, Danielle G. Lemay, Matthew C. Lange, Daniela Barile
Summary: The carbohydrate fraction in mammalian milks contains various oligosaccharides with different structures and compositions. Human milk oligosaccharides (HMOs) have been studied extensively due to their biological roles. However, understanding milk oligosaccharides in other mammals is challenging due to inconsistent data reporting methods. This study created a comprehensive database, MilkOligoDB, which consists of 3193 entries of milk oligosaccharides from 77 different species across 113 publications.
SCIENTIFIC REPORTS
(2023)
Article
Mathematical & Computational Biology
Andrew Oliver, Matthew Kay, Danielle G. Lemay
Summary: Biologists are increasingly using machine learning models not only for prediction but also for explanation. The algorithm TaxaHFE is designed to collapse information-poor features into higher taxonomic levels, leading to a significant reduction in the number of features and improved model performance. Compared to other hierarchical feature engineering implementations, TaxaHFE introduces the unique ability to consider both categorical and continuous response variables, enhancing model interpretability.
BIOINFORMATICS ADVANCES
(2023)
Article
Nutrition & Dietetics
Laurynne C. Coates, David Storms, John W. Finley, Naomi K. Fukagawa, Danielle G. Lemay, Kenneth F. Kalscheur, Mary E. Kable
Summary: This study found that feeding lactating cows a more sustainable, low-starch and high-fiber diet is associated with changes in raw milk microbiota composition and somatic cell count. It has implications for udder health and milk spoilage.
CURRENT DEVELOPMENTS IN NUTRITION
(2022)
