Article
Multidisciplinary Sciences
Thomas Badet, Simone Fouche, Fanny E. Hartmann, Marcello Zala, Daniel Croll
Summary: This study analyzed a global set of telomere-to-telomere genome assemblies of a fungal pathogen of wheat to establish a nucleotide-level map of structural variation, demonstrating the causality between specific genomic features and chromosomal rearrangements. The use of machine learning to train a model on structural variation events revealed that base composition and gene density are major determinants of structural variation, with retrotransposons explaining most of the inversion, indel, and duplication events. The model trained on species-wide structural variation accurately predicted the position of over 74% of newly generated variants, highlighting the predictive power of specific sequence features in inducing chromosomal rearrangements.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Vincent A. Laufer, Thomas W. Glover, Thomas E. Wilson
Summary: This article discusses the impact of chromosomal structural variation (SV) on human health and disease, as well as the technical limitations of previous genomic assays. Recent advances in genomic technology enable accurate identification and localization of SVs, raising new research questions. The article also explores the assembly process of the human genome and evaluates the strengths and limitations of new SV technologies.
MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH
(2023)
Article
Genetics & Heredity
Ning Li, Qiang He, Juan Wang, Baike Wang, Jiantao Zhao, Shaoyong Huang, Tao Yang, Yaping Tang, Shengbao Yang, Patiguli Aisimutuola, Ruiqiang Xu, Jiahui Hu, Chunping Jia, Kai Ma, Zhiqiang Li, Fangling Jiang, Jie Gao, Haiyan Lan, Yongfeng Zhou, Xinyan Zhang, Sanwen Huang, Zhangjun Fei, Huan Wang, Hongbo Li, Qinghui Yu
Summary: Researchers constructed a tomato super-pangenome using chromosome-scale genomes of nine wild species and two cultivated accessions, revealing the genomic diversity and structural variation across wild and cultivated tomatoes.
Article
Evolutionary Biology
Kira E. Delmore, Benjamin M. Van Doren, Kristian Ullrich, Teja Curk, Henk P. van der Jeugd, Miriam Liedvogel
Summary: This study investigates structural variants (SVs) in Eurasian blackcap and finds that SVs have important evolutionary implications in natural populations, especially in relation to seasonal migration. It also identifies specific SVs associated with different migratory strategies and traits, highlighting the genetic basis of migration.
Article
Virology
Kaixin Diao, Guohui Li, Xueqin Sun, Hao Yi, Shiying Zhang, Wei Xiao
Summary: Salt mines are a unique hypersaline environment where the study on viruses is limited. However, understanding viruses in hypersaline environments is crucial for understanding microbial communities, energy flow, and host functions. A phage called YPHTV-1, infecting Halomonas titanicae, was isolated from a salt mine in China. It belongs to the siphovirus family and has a burst size of 69 PFUs cell(-1).
Review
Urology & Nephrology
Pranav S. Garimella, Clea du Toit, Nhu Ngoc Le, Sandosh Padmanabhan
Summary: Blood pressure is regulated by a complex neurohumoral system. The study of blood pressure genomics has provided valuable insights into the complex causation of hypertension. It has allowed for risk stratification, precision medicine, and the identification of opportunities for drug repurposing.
KIDNEY INTERNATIONAL
(2023)
Article
Computer Science, Hardware & Architecture
Ben Mildenhall, Pratul P. Srinivasan, Matthew Tancik, Jonathan T. Barron, Ravi Ramamoorthi, Ren Ng
Summary: This method achieves state-of-the-art results for synthesizing novel views of complex scenes by optimizing an underlying continuous volumetric scene function using a sparse set of input views. The algorithm represents a scene using a fully connected deep network and synthesizes views by querying 5D coordinates and using volume rendering techniques.
COMMUNICATIONS OF THE ACM
(2022)
Article
Microbiology
Lin-qian Fan, Xiao-yun Hu, Yi-yue Chen, Xiang-lei Peng, Yuan-hui Fu, Yan-peng Zheng, Jie-mei Yu, Jin-sheng He
Summary: Variants of SARS-CoV-2, such as the B.1.617 lineage, have been circulating globally since the start of the COVID-19 pandemic. This study analyzed genomic and spike sequences of B.1.617, identifying widespread single nucleotide polymorphisms and high frequency mutations, mostly in structural proteins. Haplotype network analysis showed continuous evolution of daughter haplotypes from the ancestor haplotype of B.1.617.2. Structural analysis indicated that new amino acid changes in B.1.617 reshaped viral bonding network.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
History & Philosophy Of Science
Michela Massimi
Summary: This paper sheds new light on the notion of perspectival knowledge proposed by Kant, introducing a novel concept of knowledge towards a vantage point in addition to the traditional knowledge from a vantage point. The origin and rationale of this new perspectival knowledge are traced back to Kant's transcendental illusion. The paper concludes by discussing the legacy of Kant's perspectival knowledge for contemporary debates on disagreement and the role of metaphysics in scientific knowledge.
Article
Biochemical Research Methods
Casey B. Bernhards, Alvin T. Liem, Kimberly L. Berk, Pierce A. Roth, Henry S. Gibbons, Matthew W. Lux
Summary: As genome editing becomes more accessible in various prokaryotic organisms, it is crucial to identify suitable insertion sites in the genome. This study presents a method to identify potentially neutral insertion sites in prokaryotes, along with software and experimental validation in Escherichia coli.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Chemistry, Analytical
Paolo Contardo, Paolo Sernani, Selene Tomassini, Nicola Falcionelli, Milena Martarelli, Paolo Castellini, Aldo Franco Dragoni
Summary: Although face recognition technology is widely used in industrial applications, there are still challenges in verifying and identifying faces from different poses. This study presents the Face Recognition from Mugshots Database (FRMDB), which includes mugshots and surveillance videos taken from various angles. The results indicate that using multiple mugshots, including the frontal picture and right profile, has an impact on the accuracy of face recognition in surveillance videos.
Article
Biochemical Research Methods
Swarnendu Tripathi, Nikita R. Dsouza, Raul Urrutia, Michael T. Zimmermann
Summary: This study evaluated missense variants from seven RAS genes and characterized hotspot variants using sequence- and 3D structure-based scores. New insights into the mechanistic inferences of both hot-spot and non-hotspot variants were reported. The study also demonstrated a lack of correlation between 3D scores and DNA sequence-based scores commonly used in Clinical Genetics.
Review
Biochemistry & Molecular Biology
Chin-Kai Chuang, Wei-Ming Lin
Summary: Cas9-sgRNA is a key tool for genome editing, with its simplicity, unique RNA-guided DNA recognition activity, and independent nuclease activities. Different variants of Cas9, in combination with sgRNA, can achieve various effects on target site breakage. Additionally, engineered enzyme activities can be introduced using Cas9 derivatives, and methods for transient expression and biosafety have been developed to address off-target effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Ecology
S. J. Robbins, W. Song, J. P. Engelberts, B. Glasl, B. M. Slaby, J. Boyd, E. Marangon, E. S. Botte, P. Laffy, T. Thomas, N. S. Webster
Summary: Sponges harbor diverse symbiotic microbes that can degrade organic matter in coral reef ecosystems. These symbionts contain functional compositions that can degrade coral reef organic matter, and many sponge-enriched genes are laterally transferred between microbial taxa.
