Cell-free assays reveal that the HIV-1 capsid protects reverse transcripts from cGAS immune sensing. by Tiana M Scott, Lydia M Arnold, Jordan A Powers, Delaney A McCann, Ana B Rowe, Devin E Christensen, Miguel J Pereira, Wen Zhou, Rachel M Torrez, Janet H Iwasa, Philip J Kranzusch, Wesley I Sundquist, Jarrod S Johnson

“…However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. …”
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The tetracycline resistome is shaped by selection for specific resistance mechanisms by each antibiotic generation by Kevin S. Blake, Yao-Peng Xue, Vincent J. Gillespie, Skye R. S. Fishbein, Niraj H. Tolia, Timothy A. Wencewicz, Gautam Dantas

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Short tandem repeats delineate gene bodies across eukaryotes by William B. Reinar, Anders K. Krabberød, Vilde O. Lalun, Melinka A. Butenko, Kjetill S. Jakobsen

“…We report that all surveyed genomes have gene-proximal shifts in motif repetitiveness. …”
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Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts by Infanta Eden M., Umashankar Vetrivel

“…An important observation while evaluating the mapping approach is that when the adapter trimmed reads are first mapped to the pathogen genome, more reads align to the pathogen genome than the unmapped reads derived from the traditional host-first mapping approach. …”
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Bacterial community assembly of specific pathogen-free neonatal mice by Elizabeth A. Kennedy, James S. Weagley, Andrew H. Kim, Avan Antia, Anna L. DeVeaux, Megan T. Baldridge

“…Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species. …”
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Relationships between the menstrual cycle and neuropsychiatric and physical symptoms in females with Tourette syndrome by Daisy T. Noriega-Makarskyy, Evan Realbuto, Ariadne Kaylor, Lisa Osiecki, Angela Essa, Dongmei Yu, Dongmei Yu, Cornelia Illmann, Carol A. Mathews, Carol A. Mathews, Carol A. Mathews, Jeremiah M. Scharf, Jeremiah M. Scharf, Jeremiah M. Scharf, Jeremiah M. Scharf, Jeremiah M. Scharf

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Unraveling the metabolic landscape of Exophiala spinifera strain FM: Model reconstruction, insights into biodesulfurization and beyond. by Hamta Babaei Naeij, Zahra Etemadifar, John Kilbane, Mohammad Hossein Karimi-Jafari, Sepideh Mofidifar

“…In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. …”
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Tracking the genetic diversity of SARS-CoV-2 variants in Nicaragua throughout the COVID-19 pandemic by Gerald Vásquez Alemán, Cristhiam Cerpas, Jose G. Juarez, Hanny Moreira, Sonia Arguello, Josefina Coloma, Eva Harris, Aubree Gordon, Shannon N. Bennett, Ángel Balmaseda

“…This study characterizes the genomic diversity of SARS-CoV-2 in Nicaragua from March 2020 through December 2022, utilizing 1064 genomes obtained via next-generation sequencing. …”
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Museomics of Carabus giant ground beetles shows an Oligocene origin and in situ alpine diversification by Pauli, Marie T., Gauthier, Jérémy, Labédan, Marjorie, Blanc, Mickael, Bilat, Julia, Toussaint, Emmanuel F. A.

“…New approaches in this field allow the sequencing of hundreds to thousands of loci from across the genome using historical DNA. HyRAD-X, a recently introduced capture method using bench-top designed probes, has proved very efficient for recovering genomic-scale datasets using natural history collection specimens. …”
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Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells by John D. Blair, Austin Hartman, Fides Zenk, Philipp Wahle, Giovanna Brancati, Carol Dalgarno, Barbara Treutlein, Rahul Satija

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PIN2-mediated self-organizing transient auxin flow contributes to auxin maxima at the tip of Arabidopsis cotyledons by Patricio Pérez-Henríquez, Shingo Nagawa, Zhongchi Liu, Xue Pan, Marta Michniewicz, Wenxin Tang, Carolyn Rasmussen, Xinping Cui, Jaimie Van Norman, Lucia Strader, Zhenbiao Yang

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Insights into the origin, hybridisation and adaptation of Candida metapsilosis hybrid pathogens. by Valentina Del Olmo, Álvaro Redondo-Río, Alicia Benavente García, Savitree Limtong, Ester Saus, Toni Gabaldón

“…However, little is known about the genomic implications of hybridisation nor its impact on pathogenicity-related traits. …”
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Metabolic redundancy and specialisation of novel sulfide-oxidizing Sulfurimonas and Sulfurovum along the brine-seawater interface of the Kebrit Deep by Rayyan Alamoudi, Alan Barozzi, Grégoire Michoud, Marc W. Van Goethem, Charlene Odobel, Yue Chen, Ramona Marasco, Daniele Daffonchio

“…Fifty-four Campylobacterota MAGs were assembled and dereplicated into three distinct groups, with the highest-quality genome retained as representative. These genomes represent novel sulfide-oxidizing species within the Sulfurimonas and Sulfurovum genera, which differ from those found in mildly saline deep-sea sulfidic pools. …”
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The enigma of cancer polyploidy as deciphered by evolutionary cancer cell biology (ECCB) by Vladimir F. Niculescu, Eugenia R. Niculescu

“…The cells lose their stemness and differentiation potential but persist in proliferation as low-grade polyploids (4n) through defective symmetric cell division (DSCD). Genomic integrity can be restored through homotypic cell and nuclear fusion, resulting in the formation of high-grade polyploids known as multinucleated genome repair syncytia, or by inductive hyperpolyploidization of more than 64n, as observed in single-celled polyploid giant cancer cells. …”
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Geo-behavioural predictors of diagnosed hypertension in Igbo Ora Area, Oyo State, Nigeria by Olalekan J. Taiwo, Joshua O. Akinyemi, Ayodeji Adebayo, Oluwafemi A. Popoola, Rufus O. Akinyemi, Onoja M. Akpa, Paul Olowoyo, Akinkunmi P. Okekunle, Ezinne O. Uvere, Omotolani Titilayo Ajala, Chukwuemeka Nwimo, Olayinka J. Adebajo, Adewale E. Ayodele, Ayodeji Salami, Oyedunni S. Arulogun, Olanrewaju Olaniyan, Richard W. Walker, Carolyn Jenkins, Bruce Ovbiagele, Mayowa Owolabi

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Evolution of SARS-CoV-2 in white-tailed deer in Pennsylvania 2021-2024. by Andrew D Marques, Matthew Hogenauer, Natalie Bauer, Michelle Gibison, Beatrice DeMarco, Scott Sherrill-Mix, Carter Merenstein, Ronald G Collman, Roderick B Gagne, Frederic D Bushman

“…From the 165 SARS-CoV-2 positive WTD, we recovered 25 whole genome sequences and an additional 17 spike-targeted amplicon sequences. …”
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Shiga Toxin-Producing Escherichia coli: Detection, Differentiation, and Implications for Food Safety by William J. Zaragoza, Max Teplitski, Clifton K. Fagerquist

“… Shiga toxin is a protein found within the genome of a type of virus called a bacteriophage. …”
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Shiga Toxin-Producing Escherichia coli: Detection, Differentiation, and Implications for Food Safety by William J. Zaragoza, Max Teplitski, Clifton K. Fagerquist

“… Shiga toxin is a protein found within the genome of a type of virus called a bacteriophage. …”
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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues by Rebollo, Rita, Gerenton, Pierre, Cumunel, Eric, Mary, Arnaud, Sabot, François, Burlet, Nelly, Gillet, Benjamin, Hughes, Sandrine, S. Oliveira, Daniel, Goubert, Clément, Fablet, Marie, Vieira, Cristina, Lacroix, Vincent

“…However, assigning short reads to their correct genomic location, and genomic feature is not trivial. …”
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Charcot-Marie-Tooth disease: A case report initially manifested by bilateral vocal cord paralysis by Seyed Hossein Mirlohi, Sanaz Tajfirooz, Mitra Rouhi

“…Diagnosis was confirmed through whole genome sequencing, revealing mutations in genes associated with the disorder.…”
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