Article
Multidisciplinary Sciences
Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P. Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy P. L. Smith, Benjamin D. Rosen, Hubert Pausch
Summary: This study demonstrates the consistency of structural variant-based pangenomes regardless of sequence platform, assembler, or coverage using bovine haplotype-resolved assemblies. The study also reveals numerous structural variants overlapping with coding sequences that have the potential to affect phenotype.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Sadie L. Hennig, Bret R. McNabb, Josephine F. Trott, Alison L. Van Eenennaam, James D. Murray
Summary: A long intergenic non-coding RNA (lincRNA#1) is highly expressed in the horn bud region of polled bovine fetuses, but its absence alone does not result in a hornless phenotype.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher N. Balakrishnan, Dave Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce Robertson, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sovi, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Ivo Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio Mello, Samantha R. Friedrich, Peter Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H. S. Kraus, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Marques-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Haussler, Stephen J. O'Brien, Jonas Korlach, Harris A. Lewin, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis
Summary: The Vertebrate Genome Project and the international Genome 10K consortium have collaborated to generate high-quality genome assemblies for 16 species representing six major vertebrate lineages, leading to new biological discoveries. Long-read sequencing technologies are essential for maximizing genome quality, and addressing complex repeats and haplotype heterozygosity are crucial for reducing assembly errors and improving completeness of reference genomes. The lessons learned from this project have paved the way for the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all known vertebrate species.
Article
Biochemical Research Methods
Vincenzo Bonnici, Rosalba Giugno
Summary: PANPROVA is a benchmark tool that simulates prokaryotic pangenomic evolution by evolving the complete genomic sequence of an ancestral isolate. It enables operation in the pre-assembly phase and includes evolutionary features such as gene set variations, sequence variations, and horizontal acquisition from a pool of external genomes.
Article
Multidisciplinary Sciences
Feng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P. P. Kowalski, Edward M. M. Golenberg
Summary: This study constructed 49 transcriptome assemblies of Phragmites australis and selected the optimal assembly for functional annotation and downstream analyses. The transcriptome assembly provided a valuable resource for future studies on the invasive mechanism of non-native P. australis subspecies and identified genes related to herbicide and salinity resistance.
Review
Chemistry, Multidisciplinary
Zhiyu Liu, Jiaqi Guo, Yuchen Qiao, Bing Xu
Summary: This article reviews the use of enzyme-instructed self-assembly (EISA) to generate intracellular peptide assemblies for novel cancer nanomedicines and cell morphogenesis. EISA is a versatile and cell-compatible approach that can locally generate nondiffusive peptide assemblies with exceptional cell selectivity. The article discusses the concept, simplicity, and uniqueness of EISA, as well as highlights representative examples of EISA-formed intracellular peptide assemblies targeting subcellular organelles for potential cancer therapeutics. It also explores the transcytosis of peptide assemblies for controlling cell morphogenesis, providing a brief outlook of enzyme-instructed intracellular peptide assemblies.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Mechanics
Hendrik Reese, Siew-Wan Ohl, Claus-Dieter Ohl
Summary: A cavitation bubble exerts shear stresses on nearby structures during its expansion and collapse. Experimental and numerical simulations show good agreement in terms of bubble dynamics and displacement motions on an elastic surface. The study also finds that fracture may initiate from within the elastic material rather than from the surface.
Article
Multidisciplinary Sciences
Minghao Qu, Xiangrong Fan, Chenlu Hao, Yi Zheng, Sumin Guo, Sen Wang, Wei Li, Yanqin Xu, Lei Gao, Yuanyuan Chen
Summary: Water chestnut (Trapa L.) genome assemblies for cultivated large-seed species Trapa bicornis and wild small-seed relative Trapa incisa were generated using PacBio HiFi long reads and Hi-C technology. The assemblies had contig sizes of 479.90 Mb and 463.97 Mb, N50 values of 13.52 Mb and 13.77 Mb, and repeat contents of 62.88% and 62.49%, respectively. A total of 33,306 and 33,315 protein-coding genes were predicted in T. bicornis and T. incisa assemblies, respectively. Structural variants affecting over 11 thousand genes were detected between the two genomes. Phylogenetic analysis revealed a divergence of the Trapa lineage from the Sonneratia lineage approximately 23 million years ago. These assemblies serve as valuable resources for future research on the evolution, function, and breeding of water chestnut.
Article
Biochemistry & Molecular Biology
Dmitri S. Pavlichin, HoJoon Lee, Stephanie U. Greer, Susan M. Grimes, Tsachy Weissman, Hanlee P. Ji
Summary: K-mers are short DNA sequences used for genome sequence analysis. The computational requirements for analyzing K-mer information on a large scale can be enormous. KmerKeys addresses this challenge by developing a new indexing data structure and providing fast query speeds and cloud computation capabilities.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Tsung-Yu Lu, Mark J. P. Chaisson
Summary: Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They are difficult to analyze by short-read sequencing in disease studies. The authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph, which will help elucidate the contribution of VNTRs to diversity and disease.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
David R. Porubsky, Mitchell T. Vollger, William N. Harvey, Allison Rozanski, Peter Ebert, Glenn Hickey, Patrick D. Hasenfeld, Ashley Sanders, Catherine O. Stober, Jan Korbel, Benedict E. Paten, Tobias Marschall, Evan Eichler
Summary: There has been significant progress in phased genome assembly by combining long-read data with parental information or linked-read data. However, the typical phased genome assembly still has over 140 gaps. A detailed analysis of 182 haploid assemblies reveals that the majority of assembly gaps cluster near large and identical repeats, resulting in disrupted protein-coding genes. Misorientations and alignment discontinuities are also identified, highlighting the need for algorithmic development and pangenome representation.
Article
Multidisciplinary Sciences
Elena Zavala, Zenobia Jacobs, Benjamin Vernot, Michael Shunkov, Maxim B. Kozlikin, Anatoly P. Derevianko, Elena Essel, Cesare de Fillipo, Sarah Nagel, Julia Richter, Frederic Romagne, Anna Schmidt, Bo Li, Kieran O'Gorman, Viviane Slon, Janet Kelso, Svante Paabo, Richard G. Roberts, Matthias Meyer
Summary: Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals. The cave yielded hominin remains from different groups, indicating it was a contact zone between Neanderthals and Denisovans. The study reveals that Denisovans and Neanderthals repeatedly occupied the site, with modern human DNA appearing in the sediments at least 45,000 years ago.
Review
Biology
Kerstin Howe, William Chow, Joanna Collins, Sarah Pelan, Damon-Lee Pointon, Ying Sims, James Torrance, Alan Tracey, Jonathan Wood
Summary: Genome sequence assemblies are crucial for understanding biology, but achieving error-free assemblies remains a challenge. Assembly evaluation and curation play a key role in reducing errors and improving assembly quality. Insights gained from curation can lead to significant improvements in genome assembly.
Article
Genetics & Heredity
Samuel O'Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stephane Delmas, Fabien Dutreux, Teo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer
Summary: A reference assembly panel (ScRAP) of 142 strains was generated to study the genetic diversity of Saccharomyces cerevisiae. The study revealed the presence of structural variants in these genomes, which can impact gene expression and genome evolution.
Article
Biochemical Research Methods
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Summary: Motivation: A fast and efficient tool called FastRemap is introduced for remapping reads between genome assemblies. It provides a 7.82x speedup (6.47x on average) and consumes as low as 61.7% of peak memory compared to the state-of-the-art tool CrossMap.
Review
Multidisciplinary Sciences
John R. Bracht, Victoria J. Vieira-Potter, Roberta De Souza Santos, Orhan K. Oz, Biff F. Palmer, Deborah J. Clegg
ANNALS OF THE NEW YORK ACADEMY OF SCIENCES
(2020)
Article
Cell Biology
Alyssa D. Cordero, Evan C. Callihan, Rana Said, Yasir Alowais, Emily S. Paffhausen, John R. Bracht
Article
Immunology
Raud Razzaghi, Shreya Agarwal, Nikita Kotlov, Olga Plotnikova, Krystle Nomie, Da Wei Huang, George W. Wright, Grace A. Smith, Moyi Li, Katsuyoshi Takata, Maryam Yamadi, Chen Yao, John J. O'Shea, James D. Phelan, Stefania Pittaluga, David W. Scott, Jagan R. Muppidi
Summary: The study indicates that Fas serves as an intrinsic regulator in GC B cells and plays a crucial role in maintaining GC homeostasis. Mutations in FAS are associated with poor prognosis, enrichment of Tfh cells, and deficiencies in HVEM and PD-L1 in GC-derived DLBCL.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Thomas M. Asrat, Whirang Cho, Favian A. Liu, Sarah M. Shapiro, John R. Bracht, Alexander G. Zestos
Summary: The study demonstrates the subsecond codetection of nucleobases in DNA and RNA samples from the nematode using fast-scan cyclic voltammetry. FSCV shows higher sensitivity and peak oxidative currents when detecting shorter oligonucleotides and single-stranded DNA samples. Single-stranded DNA nucleobases are not hydrogen-bonded and can freely adsorb onto the electrode surface, enabling successful simultaneous determination of nucleobases even in complex biological samples.
Article
Evolutionary Biology
Kathryn C. Asalone, Ajuni K. Takkar, Colin J. Saldanha, John R. Bracht
Summary: The study introduces a new transcriptomic method for identifying GRC sequences in songbirds, successfully identifying 733 contigs as high confidence GRC sequences. By using comparative coverage analysis, two new GRC genes and 16 previously unplaced genes were identified.
GENOME BIOLOGY AND EVOLUTION
(2021)
Editorial Material
Biochemistry & Molecular Biology
Monessha Jayabalan, Madeline E. Caballero, Alyssa D. Cordero, Brandyn M. White, Kathryn C. Asalone, Madison M. Moore, Esohe G. Irabor, Shari E. Watkins, Kathryn B. Walters-Conte, Alexandra Taraboletti, Matthew R. Hartings, Brenda Y. Chow, Bushra A. Saeed, Kathryn A. Bracht, John R. Bracht
Summary: Diversity within STEM disciplines is low, especially in smaller institutions which have more diverse student populations but limited resources. Leveraging the unique advantages of smaller schools can help advance underrepresented scholars along STEM pathways.
Article
Biochemistry & Molecular Biology
Kara Ryan, Ryan Greenway, Jake Landers, Lenin Arias-Rodriguez, Michael Tobler, Joanna L. Kelley
Summary: Hydrogen sulfide is a toxic gas that disrupts biological processes, yet fish in the Poecilia mexicana species complex have evolved sulfide tolerance multiple times. This study investigates whether the repeated evolution of tolerance is due to similar genomic changes, finding evidence of both convergence and divergence in gene variation associated with sulfide processes and toxicity.