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Working Paper BRIEF REPORT

Identification of Novel Missense Mutations in a Large Number of Recent SARS-CoV-2 Genome Sequences

Hugh Y. Cai, Kimberly K. Cai, Julang Li

Subject: Biology And Life Sciences, Virology Keywords: COVI-19; SARS-CoV-2; virus; mutation; polymorphism; genome sequence

Online: 21 May 2020 (04:09:53 CEST)

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Background: SARS-CoV-2 infection has spread to over 200 countries since it was first reported in December of 2019. Significant country-specific variations in infection and mortality rate have been noted. Although country-specific differences in public health response have had a large impact on infection rate control, it is currently unclear as to whether evolution of the virus itself has also contributed to variations in infection and mortality rate. Previous studies on SARS-CoV-2 mutations were based on the analysis of ~ 160 SARS-CoV-2 sequences available until mid-February 2020.^{2, 3, 4, 5} By mid-April, > 550 SARS-CoV-2 sequences had been deposited in GenBank, and over 8,200 in the GISAID database. Methods: We performed a sequence analysis on 474 SARS-CoV-2 genomes submitted to GenBank up to April 11, 2020 by multiple alignment using Map to a Reference Assembly and Variants/SNP identification. The results were verified on a larger scale, 8,126 hCoV-19 (SARS-CoV-2) sequences from GISAID database. Results: We identified 5 recently emerged mutations in many isolates (up to 40%). Our analysis highlights 5 frequent new mutations that have emerged since late February 2020. These mutations are: one each missense (non-synonymous) mutation in orf1ab (C1059T), orf3 (G25563T) and orf8 (C27964T), one in 5’UTR (C241T), one in a non-coding region (G29553A). The final mutation (G29553A) was found to be almost exclusive to the US isolates. The first 3 mutations are non-synonymous, leading to amino acid substitutions in the viral protein sequence. Except for C241T, all the novel mutations identified are absent in the isolates from Italy and Spain in the SARS-CoV-2 genomes deposited in GenBank and GISAID by April 13, 2020. Conclusion: The results of current study indicate that new mutations are emerging as COVID-19 pandemic are spreading to different countries and that geography specific mutants may exist. The findings of current study lay the foundation for further investigation into the impact of SARS-CoV-2 mutations on disease incidence, severity, and host immune response. In addition, it may also provide insights into vaccine development and serological response detection for the virus.

Preprint REVIEW | doi:10.20944/preprints202004.0359.v1

Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

M. Nazmul Hoque, Abed Chaudhury, Md. Abdul Mannan Akanda, M. Anwar Hossain, Md Tofazzal Islam

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: SARS-CoV-2; genetic diversity; genome evolution; diagnostics; therapeutics; vaccines

Online: 20 April 2020 (02:33:15 CEST)

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Preprint REVIEW | doi:10.20944/preprints201911.0076.v3

Exploring Mammalian Genome within Phase-Separated Nuclear Bodies: Experimental Methods and Implications for Gene Expression

Annick Lesne, Marie-Odile Baudement, Cosette Rebouissou, Thierry Forné

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: phase separation; nuclear bodies; self-assembly; genome organization; gene expression

Online: 11 December 2019 (11:17:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0378.v1

Characterization of Gene Families Encoding Beta-Lactamases of Gram-Negative Rods Isolated from Ready-to-Eat Vegetables in Mexico City

Rosalino Vázquez-López, Sandra Solano-Gálvez, Bertha Aliacia León-Chávez, María del Rocío Thompson-Bonilla, Tayde Guerrero-González, Eduardo Gómez-Conde, Daniel Martínez-Fong, Juan-Antonio González-Barrios

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: enterobacteriaceae; antibiotics; beta-lactamases; beta-lactam resistome; whole genome sequencing

Online: 19 September 2018 (09:47:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0337.v1

Reference Echovirus 7 and 19 Genomes from Nigeria

Temitope O. C. Faleye, Moses Olubusuyi Adewumi, Johnson Adekunle Adeniji

Subject: Biology And Life Sciences, Virology Keywords: Echovirus 7; Echovirus 19; Nigeria; Enterovirus Species B; Complete Genome

Online: 18 September 2018 (09:39:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0106.v1

Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions

Kyoung Su Choi, Keum Seon Jeong, Young-Ho Ha, Kyung Choi

Subject: Biology And Life Sciences, Plant Sciences Keywords: Clematis; chloroplast genome; rearrangement; inversion; IR expansion; synonymous substitution rate

Online: 9 April 2018 (10:34:28 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.1714.v1

Technology of Controlled Film Flow Granulation of Materials

Ivan Kazachkov

Subject: Physical Sciences, Applied Physics Keywords: film flow; controlled disintegration; drops and granules; high cooling rate; amorphous; three new phenomena; wide range of granules

Online: 28 March 2024 (09:34:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints201807.0380.v1

A Flexible Wireless Sensor Network based on Ultra-Wide Band Technology for Ground Instability Monitoring

Lorenzo Mucchi, Sara Jayousi, Alessio Martinelli, Stefano Caputo, Emanuele Intrieri, Giovanni Gigli, Teresa Gracchi, Francesco Mugnai, Massimiliano Favalli, Alessandro Fornaciai, Luca Nannipieri

Subject: Engineering, Electrical And Electronic Engineering Keywords: Ultra-Wide Band; wireless sensor networks; monitoring; warning system; ground instability; landslide; Time Of Flight, Two-way ranging.

Online: 20 July 2018 (11:56:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202403.0215.v1

Plant Immunity against Tobamoviruses

Yule Liu, Xiyin Zheng

Subject: Biology And Life Sciences, Virology Keywords: Plant immunity; Tobamovirus; RNA silencing; RNA decay; NLR; Phytohormone; Genome editing

Online: 5 March 2024 (06:30:52 CET)

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Preprint REVIEW | doi:10.20944/preprints202311.0461.v1

Ten Quick Tips for Accurate Reconstruction of Prokaryotic and Eukaryotic Genome-Scale Metabolic Models

Gabriela Canto-Encalada, Jenna Armstrong, Carlos Focil-Espinosa4, Ademikanra Adekunle-Fiyin, Ila Peeler, William R. Gebbie, Julio Nunez-Garcia, Alexis Saldivar, Diego Martinez, Cristal Zuniga

Subject: Biology And Life Sciences, Other Keywords: Genome-scale metabolic model reconstruction; manual curation; quick tips; systems biology

Online: 7 November 2023 (14:59:34 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202309.2156.v1

Evolutionary, Non-Mutational Cancers Cannot Be Considered Atavistic

Vladimir Niculescu, Eugenia R. Niculescu

Subject: Medicine And Pharmacology, Oncology And Oncogenics Keywords: stem cells; DNA-damage; precancerous cell state; repair; genome reprograming; carcinogenesids

Online: 30 September 2023 (07:58:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.1481.v1

Identification and Characterization of ten Escherichia coli Strains encoding Novel Shiga Toxin 2 Subtypes, Stx2n as well as Stx2j, Stx2m, and Stx2o, in the United States

Rebecca L Lindsey, Arjun Prasad, Michael Feldgarden, Narjol Gonzalez-Escalona, Curtis Kapsak, William Klimke, Angela Melton-Celsa, Peyton Smith, Alexandre Souvorov, Jenny Truong, Flemming Scheutz

Subject: Biology And Life Sciences, Other Keywords: Shiga Toxin-Producing Escherichia coli; Shiga toxin subtype; Stx2n; Genome Sequence

Online: 21 September 2023 (11:26:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints202309.1000.v1

Recent Advancements in Genome-Targeting Nucleic Acids and Their Potential for Therapeutic Applications

Yu Mikame, Asako Yamayoshi

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: oligonucleotide therapeutic; triplex-forming oligonucleotide; peptide nucleic acid; antigene; genome editing

Online: 14 September 2023 (11:37:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0457.v1

Genetic Predisposition to Differentiated Thyroid Cancer among Polish Population

Martyna Borowczyk, Mateusz Sypniewski, Joanna Szyda, Małgorzata Braszka, Katarzyna Ziemnicka, Marek Ruchała, Michalina Oszywa, Zbignie J. Król, Paula Dobosz

Subject: Medicine And Pharmacology, Endocrinology And Metabolism Keywords: thyroid cancer; whole-genome sequencing; non-medullary thyroid cancer; germline; genetics

Online: 7 September 2023 (03:46:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1167.v1

Phylogenetic, Sequencing, and Mutations Analysis of the SARS-CoV-2 Omicron (BA.1) and Sub-variants (BA.1.1, BA.2) during the Fifth Wave of the Pandemic in the Iraqi Kurdistan Region

Sherzad Majeed Taher, Jassim Mohammed Abdo, Muayad Aghali Merza

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: COVID-19; SARS-COV-2; Omicron Variants; Phylogenetic tree; Genome Sequence

Online: 16 August 2023 (07:47:50 CEST)

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Preprint REVIEW | doi:10.20944/preprints202307.1324.v2

Kimura’s Theory of Non-adaptive Radiation and Peto’s Paradox: A Missing Link?

John Herrick

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: karyotype diversity; genome stability; species richness; species eveneness; non-adaptive radiation

Online: 31 July 2023 (10:51:13 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.1081.v1

"Exploring the Potential Role of Ribosomal Proteins to Enhance Potato Resili-ence in the Face of Changing Climatic Conditions"

Eliana Valencia-Lozano, Lisset Herrera-Isidrón, Jorge Abraham Flores-López, Osiel Salvador Recoder-Meléndez, Braulio Uribe-López, Aarón Barraza, José Luis Cabrera-Ponce

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ribosome biogenesis; Potato; Carbon metabolism; Genome edition; CRISPR/Cas; Microtuberization; Potato

Online: 15 June 2023 (05:50:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202202.0166.v1

Characterization of Bifidobacterium asteroides Isolates

Alessandra Pino, Bachir Benkaddour, Rosanna Inturri, Pietro Amico, Susanna Vaccaro, Nunziatina Russo, Amanda Vaccalluzzo, Gianluigi Agolino, Cinzia Caggia, Cinzia L. Randazzo

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: microbiological characterization; safety; VanZ; isolation; vancomycin resistant gene; genome; bee; honey

Online: 11 February 2022 (21:17:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0467.v1

Genome-guided Discovery of the First Myxobacterial Biarylitide Myxarylin Reveals Distinct C–N Biaryl Crosslinking in RiPP Biosynthesis

Joachim J. Hug, Nicolas A. Frank, Christine Walt, Petra Šenica, Fabian Panter, Rolf Müller

Subject: Chemistry And Materials Science, Organic Chemistry Keywords: myxobacteria; secondary metabolites; biarylitide; natural product discovery; RiPPs; genome mining; myxarylin

Online: 25 November 2021 (10:42:39 CET)

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Working Paper CONCEPT PAPER

Hypothesis: AT Homopolymer Strings in Salmonella enterica subspecies I Contribute to Speciation and Serovar Diversity

Jean Guard, Adam R Rivers, Justin N Vaughn, Michael J Rothrock, Jr, Adelumola Oladeinde, Devendra H Shah

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Salmonella enterica; food safety; genome; theory; single nucleotide polymorphisms; recombination; serotype

Online: 31 August 2021 (12:47:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202107.0182.v1

CRISPR Cas9 Tip of an Iceberg: It’s Potential in Genome Editing and Many More

Jalal Ahmad, Nayyer Siddique

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: CRISPR-Cas9; Genome editing; plant editing; bacterial immune system; genetic disease

Online: 8 July 2021 (09:50:22 CEST)

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Preprint DATA DESCRIPTOR | doi:10.20944/preprints202106.0368.v1

Mash Sketched Reference Dataset for Genome-Based Taxonomy and Comparative Genomics

Ayixon Sánchez-Reyes, Maikel Gilberto Fernández-López

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Microbial Mash database, Mash distance, Genome containment, Type material, Microbial taxonomy

Online: 14 June 2021 (14:54:32 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202105.0520.v1

Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets

Felix Bröcker

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome evolution; ribozymes; RNA ligase; early Earth; autocatalytic sets; RNA world

Online: 21 May 2021 (10:16:35 CEST)

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Preprint SHORT NOTE | doi:10.20944/preprints202006.0225.v1

CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation

Joshua Singer, Robert Gifford, Matthew Cotten, David Robertson

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2; web application; virus genome; lineage assignment; amino acids

Online: 18 June 2020 (06:24:20 CEST)

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Preprint REVIEW | doi:10.20944/preprints201906.0106.v2

Cheating in the Viral World

Asher Leeks, Stuart A. West, Melanie Ghoul

Subject: Biology And Life Sciences, Virology Keywords: virus evolution; cheat; cooperation; social evolution; defective interfering genome; satellite virus

Online: 22 April 2020 (06:02:05 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0069.v1

Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains

Raz Avni, Leah Oren, Gai Shabtai, Siwar Assili, Curtis Pozniak, Iago Hale, Roi Ben-David, Zvi Peleg, Assaf Distelfeld

Subject: Biology And Life Sciences, Plant Sciences Keywords: Wheat, emmer; domestication; genome assembly; QTL, meta-QTL; grain weight; GRF4

Online: 2 November 2018 (15:16:48 CET)

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Preprint REVIEW | doi:10.20944/preprints201809.0440.v1

The Protecting Role of Dormant Origins in Response to Replicative Stress

Lilas Courtot, Jean-Sébastien Hoffmann, Valérie Bergoglio

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Dormant origins; replicative stress; replication timing; DNA damage; genome instability; cancer

Online: 21 September 2018 (16:00:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201703.0139.v1

The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species

Inkyu Park, Wook-Jin Kim, Sang-Min Yeo, Goya Choi, Young-Min Kang, Renzhe Piao, Byeong-Cheol Moon

Subject: Biology And Life Sciences, Plant Sciences Keywords: Fritillaria ussuriensis, Fritillaria cirrhosa, Chloroplast genome, Comparative analysis, Highly divergent region

Online: 17 March 2017 (16:30:34 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0410.v2

Development of Self-generated and LPWA-based Crop Growth Environment Monitoring and Bigdata Analysis System

Yeon-Jae Oh

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Smart Farm, Field Crop Growth Environment Monitoring, Bigdata analysis, Low Power Wide Area(LPWA), One Machine to Machine(oneM2M),

Online: 12 December 2023 (08:18:52 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1781.v1

Community Exercise Program Participation and Mental Well-Being in the U.S. Texas-Mexico Border Region

Belinda M Reininger, Alma G. Ochoa Del-Toro, Lisa A Mitchell-Bennett, Michael Machiorlatti, Candace A Robledo, Amanda C Davé, Rebecca N Lozoya

Subject: Public Health And Healthcare, Public Health And Health Services Keywords: US-Mexico border health; community-wide campaign; physical exercise; mental health; public health; Latino community health; health behavior promotion

Online: 27 September 2023 (05:19:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202301.0048.v1

Educational Multi-agent PLM System for Threaded Connections

Volodymyr Kopei, Oleh Onysko, Cristian Barz, Predrag Dašić, Vitalii Panchuk

Subject: Engineering, Mechanical Engineering Keywords: threaded connection; life cycle; information system; PLM; multi-agent; actor model; isomorphism; system-wide regularities; systematic approach; open-source

Online: 4 January 2023 (02:54:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202401.2015.v1

Wide-Field Choroidal Thickness Analysis after Half-fluence Photodynamic Therapy in Pachychoroid Neovasculopathy

Yosuke Fukuda, Shoji Notomi, Satomi Shiose, Yusuke Maehara, Kohei Kiyohara, Sawako Hashimoto, Kumiko Kano, Keijiro Ishikawa, Toshio Hisatomi, Koh-Hei Sonoda

Subject: Medicine And Pharmacology, Ophthalmology Keywords: age-related macular degeneration; pachychoroid neovasculopathy; photodynamic therapy; anti-vascular endothelial growth factor therapy; ultra-wide-field optical coherent tomography

Online: 29 January 2024 (13:01:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0191.v1

SMITS: Research on Smart Mobility Intelligent Traffic Signal System based on Distributed Deep Reinforcement Learning

Yeon-Jae Oh

Subject: Computer Science And Mathematics, Computer Science Keywords: Smart Mobility Intelligent Traffic Service, Intelligent Transportation System, Real-time Traffic Situation, Deep Reinforcement Learning (DRL), Optimal Network-wide Policy

Online: 4 October 2023 (11:16:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.0810.v1

Differences in Central and Peripheral Choroidal Thickness Among the Subtypes of Age-Related Macular Degeneration

Yosuke Fukuda, Shoji Notomi, Satomi Shiose, Kumiko Kano, Sawako Hashimoto, Kohta Fujiwara, Masato Akiyama, Keijiro Ishikawa, Toshio Hisatomi, Koh-Hei Sonoda

Subject: Medicine And Pharmacology, Ophthalmology Keywords: age-related macular degeneration; pachychoroid spectrum disease; polypoidal choroidal vasculopathy; pachychoroid neovasculopathy; ultra-wide-field swept-source optical coherent tomography

Online: 10 August 2023 (05:34:57 CEST)

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Preprint REVIEW | doi:10.20944/preprints201812.0267.v1

Epigenetic Factors in Late-Onset Alzheimer’s Disease: MTHFR and CTH Gene Polymorphisms, Metabolic Trans-sulfuration and Methylation Pathways, and B Vitamins

Gustavo C. Román, Oscar Mancera-Páez, Camilo Bernal

Subject: Medicine And Pharmacology, Neuroscience And Neurology Keywords: Alzheimer’s disease; CTH gene; DNA methylation; epigenetics; epigenome-wide association study; methylome; MTHFR gene; nutrition; S-adenosylmethionine; vitamin B complex

Online: 24 December 2018 (04:48:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202404.0184.v1

Carbohydrate Hydrolytic Activity, Antibiotic Resistance and Stress Tolerance of Lacticaseibacillus paracasei BCRC-16100 and Lacticaseibacillus paracasei ZFM54 for Probiotics Using Genomic and Biochemical Approaches

Peter James Icalia Gann, Jimmbeth Zenila P. Fabia, Althea Gay B. Pagurayan, Ma. Joy Theresa Agcaoili, Ryan James J. Pascual, Suerte M. Baranda, Arc Josam J. Racho, Marvielyn P. Olivar, Jayson F. Cariaga, Alvin Domingo, Dionisio S. Bucao, Shirley C. Agrupis

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: probiotics; nutrient digestion; antibiotic resistance; antibacterial activity; whole genome sequence

Online: 2 April 2024 (10:16:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.0535.v1

Unveiling the Probiotic Potential of Streptococcus thermophilus MCC0200: Insights from In-vitro Studies corroborated with Genome Analysis

Neelam Kapse, Vaidehi Pisu, Tanisha Dhakephalkar, Prajakta Margale, Deepa Shetty, Shilpa Wagh, Sumit Dagar, Prashant Dhakephalkar

Subject: Biology And Life Sciences, Life Sciences Keywords: Streptococcus thermophilus; gastrointestinal transit; adhesion; health-promoting; Anti-hypercholesterolemic activity; GRAS; genome

Online: 7 December 2023 (13:58:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202311.0685.v1

Chemical Composition and Genome Pattern as a Means of Identifying the Origin of Preserved Wild Garlic (Allium ursinum L.) in Poland

Emilia Bernaś, Jacek Słupski, Piotr Gębczyński, Katarína Ražná, Jana Žiarovská

Subject: Biology And Life Sciences, Food Science And Technology Keywords: wild garlic; freezing; air-drying; freeze-drying; genome pattern; polyphenol; antioxidant activity

Online: 10 November 2023 (07:15:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.0558.v1

Construction and Characterization of an F1DH Population and High-Density Genetic Map for Ornamental Kale Breeding

Ning Guo, Fan Liu, Shuo Han, Mei Zong, Guixiang Wang, Mengmeng Duan

Subject: Biology And Life Sciences, Horticulture Keywords: Ornamental kale, F1DH population, Whole-genome resequencing, High-density genetic linkage map

Online: 11 October 2023 (07:55:29 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202308.1259.v1

Growing in saltwater: biotechnological potential of novel Methylotuvimicrobium- and Methylomarinum-like methanotrophic bacteria

Ekaterina N. Tikhonova, Ruslan Z. Suleimanov, Igor Y. Oshkin, Aleksey A. Konopkin, Diana V. Fedoruk, Nikolai V. Pimenov, Svetlana N. Dedysh

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: methanotrophic bacteria; Methylomonarinum; Methylotuvimicrobium; single-cell protein; growth in seawater; genome analysis.

Online: 17 August 2023 (08:01:07 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202307.0601.v1

Virological and Clinical Outcomes in Adults Treated with Ribavirin Aerosol for COVID-19 Pneumonia

Emanuela Messina, Giulia Morsica, Sabrina Bagaglio, Laura Galli, Riccardo Lolatto, Michela Sampaolo, Maxime Barakat, Robert J Israel, Antonella Castagna, Nicola Clementi

Subject: Medicine And Pharmacology, Clinical Medicine Keywords: COVID-19; pneumonia; ribavirin aerosol; treatment; outcome; viral load; whole genome sequencing

Online: 10 July 2023 (10:16:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0404.v1

Isolation, Identification, and Whole Genome Analysis of Chicken Infectious Anemia Virus in an Outbreak of Disease in Adult Layer Hens

Yueyan Zeng, Hui Zhang, Huanrong Zhang

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: Chicken infectious anemia virus; isolation and identification; pathogenicity; whole genome; bioinformatics analysis

Online: 6 June 2023 (08:05:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202305.0622.v1

Whitefly Transmitted Begomovirus Infection in Plant and Host Response: A Review

Dew Biswas, Arunava Mandal

Subject: Biology And Life Sciences, Plant Sciences Keywords: Begomovirus; Whitefly; Viral genome; Viral transmission; Host-vector-pathogen interaction; Host defense

Online: 9 May 2023 (09:15:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202305.0462.v1

Evolutionary Adaptation of Genes Involved in Galactose Derivatives Metabolism in Oil-Tea Specialized Andrena Species

Gonghua Lin, Bo He, Kai Jiang, Tianjuan Su, Fang Zhao, Zuhao Huang

Subject: Biology And Life Sciences, Insect Science Keywords: Andrena camellia; genome; RNASeq; molecular evolution; gene expression; galactose derivatives; NAGA-like

Online: 8 May 2023 (08:08:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202211.0228.v1

Genomic Diversity and Chromosomal Rearrangements in Neisseria Gonorrhoeae and Neisseria Meningitidis

Boris Shaskolskiy, Dmitry Kravtsov, Ilya Kandinov, Ekaterina Dementieva, Dmitry Gryadunov

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Neisseria gonorrhoeae; Neisseria meningitidis; whole genome sequencing; chromosomal rearrange-ments; mobile elements

Online: 14 November 2022 (02:11:22 CET)

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Preprint REVIEW | doi:10.20944/preprints202207.0404.v1

Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses

Mohd Fadhli Hamdan, Chou Khai Soong Karlson, Ee Yang Teoh, Su-Ee Lau, Boon Chin Tan

Subject: Biology And Life Sciences, Plant Sciences Keywords: Abiotic stress; biotic stress; biotechnology; climate change; CRISPR; crop improvement; genome editing

Online: 26 July 2022 (10:44:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0375.v1

Vemurafenib Inhibits Enterovirus A71 Genome Replication and Virus Assembly

Bodan Hu, Kenn Ka-Heng Chik, Jasper Fuk-Woo Chan, Jian-Piao Cai, Jessica Oi-Ling Tsang, Zijiao Zou, Kaiming Tang, Lilong Jia, Cuiting Luo, Feifei Yin, Zi-Wei Ye, Hin Chu, Man-Lung Yeung, Shuofeng Yuan

Subject: Biology And Life Sciences, Virology Keywords: Enterovirus; vemurafenib; RAF; MAPK signaling pathway; genome replication; virus assembly; VP0 cleavage

Online: 25 July 2022 (12:25:13 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202112.0270.v1

Molecular Characterization of Circulating DENV-2 During Outbreak in Northern Senegal, Rosso 2018

Idrissa Dieng, Mignane Ndiaye, Marie Henriette Ndione, Safietou Sankhe, Moussa Moïse Diagne, Samba Niang Sagne, Aboubacry Gaye, Aliou Barry, Gamou Fall, Amadou Alpha Sall, Cheikh Loucoubar, Oumar Faye, Ousmane Faye

Subject: Biology And Life Sciences, Virology Keywords: Dengue; Dengue virus; cosmopolitan genotype; Senegal; Mauritania; Molecular characterization; Full genome sequencing

Online: 16 December 2021 (12:06:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0287.v1

Identification and Comparison of Colletotrichum Secreted Effector Candidates Reveal Two Independent Lineages Pathogenic to Soybean

Thaís Regina Boufleur, Nelson Sidnei Massola Júnior, Ísis Tikami, Serenella Ana Sukno, Michael Ronald Thon, Riccardo Baroncelli

Subject: Biology And Life Sciences, Plant Sciences Keywords: anthracnose; genome sequencing; pathogenicity factors; Colletotrichum truncatum; Colletotrichum orchidearum; Glomerella; Glycine max

Online: 20 October 2021 (10:11:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202108.0312.v1

Characterization of Komagataeibacter Isolate Reveals New Prospects on Waste Stream Valorization for Bacterial Cellulose Production

Pietro Cannazza, Antti Rissanen, Dieval Guizelini, Pauli Losoi, Essi Sarlin, Diego Romano, Ville Santala, Rahul Mangayil

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Komagataeibacter rhaeticus; Bacterial cellulose; Crude glycerol; Minimal medium; Whole-genome analysis; Acetate

Online: 16 August 2021 (08:32:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202107.0020.v1

Molecular Biology and Pathological Process of an Infectious Bronchitis Virus With Enteric Tropism in Commercial Broilers

Ana Paula da Silva, Ruediger Hauck, Sabrina R.C. Nociti, Colin Kern, H.L. Shivaprasad, Huaijun Zhou, Rodrigo A. Gallardo

Subject: Biology And Life Sciences, Anatomy And Physiology Keywords: IBV; infectious bronchitis; variants; whole-genome sequencing, enteric tropism; runting-stunting syndrome

Online: 1 July 2021 (11:25:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202105.0333.v1

Functional Validation of cas9/guideRNA Constructs for Site-directed Mutagenesis of Triticale ABA8’OH1 loci

Krzysztof Michalski, Christian Hertig, Dariusz Mańkowski, Jochen Kumlehn, Janusz Zimny, Anna M. Linkiewicz

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: genome editing; CRISPR; protoplast; , targeted mutagenesis; TREX2; construct validation; transi-ent expression

Online: 14 May 2021 (13:44:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202012.0473.v1

TEfinder: A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data

Vista Sohrab, Cristina López-Díaz, Antonio Di Pietro, Li-Jun Ma, Dilay Hazal Ayhan

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: transposable elements; mobile element insertion events; next generation sequencing (NGS); genome evolution

Online: 18 December 2020 (14:53:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints202009.0559.v1

Whole Genome Sequence Analysis of Porcine Astroviruses Reveals Novel Genetically Diverse Genotypes Circulating in East African Smallholder Pig Farms

Joshua O. Amimo, Eunice M. Machuka, Edward O. Abworo, Anastasia N. Vlasova, Roger Pelle

Subject: Biology And Life Sciences, Virology Keywords: porcine astroviruses; linear antigenic epitopes; recombination; glycosylation; whole genome sequences; East Africa

Online: 24 September 2020 (03:26:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0285.v1

Sequence Analysis of Egyptian Foot-And-Mouth Disease Virus Field and Vaccine Strains: Intertypic Recombination and Evidence for Accidental Release of Virulent Virus

Sahar Abd El Rahman, Bernd Hoffmann, Reham Karam, Mohamed El-Beskawy, Mohammed F. Hamed, Leonie F. Forth, Dirk Höper, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: FMDV; Egypt; full-genome sequencing; interserotypic recombination; vaccine composition analysis; frozen evolution

Online: 12 August 2020 (11:56:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202007.0144.v1

Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic

Alessia Lai, Annalisa Bergna, Sara Caucci, Nicola Clementi, Ilaria Vicenti, Filippo Dragoni, Anna Maria Cattelan, Stefano Menzo, Angelo Pan, Annapaola Callegaro, Adriano Tagliabracci, Arnaldo Caruso, Francesca Caccuri, Silvia Ronchiadin, Claudia Balotta, Maurizio Zazzi, Emanuela Vaccher, Massimo Clementi, Massimo Galli, Gianguglielmo Zehender

Subject: Biology And Life Sciences, Virology Keywords: phylodynamic analyses; SARS-CoV2 circulation in Italy; molecular tracing; Whole Genome Sequencing

Online: 8 July 2020 (11:00:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0181.v1

Comparative Plastomics of Ashwagandha (Withania, Solanaceae) and Identification of Mutational Hotspots for Barcoding Medicinal Plants

Furrukh Mehmood, Abdullah ., Zartasha Ubaid, Yiming Bao, Peter Poczai, Bushra Mirza

Subject: Biology And Life Sciences, Plant Sciences Keywords: Ashwagandha; Chloroplast Genome; InDels; Medicinal plants; Mutational hotspots; Phylogenomics; Solanaceae; Substitutions; Withania

Online: 11 March 2020 (10:21:56 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0354.v1

Whole-Genome Sequencing of Lactobacillus Helveticus D75 and D76 Confirms Safety and Probiotic Potential

Vyacheslav Toropov, Elena Demyanova, Olga Shalaeva, Stanislav Sitkin, Timur Vakhitov

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Lactobacillus helveticus; probiotics; whole genome sequencing; PacBio; probiotic genes; bacteriocins; gene expression

Online: 26 December 2019 (10:56:44 CET)

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Preprint ARTICLE | doi:10.20944/preprints201911.0353.v1

Unbiased High-Resolution Composition Analysis of an Inactivated Polyvalent Foot-and-Mouth Disease Vaccine

Leonie Forth, Dirk Höper, Martin Beer, Michael Eschbaumer

Subject: Biology And Life Sciences, Virology Keywords: inactivated vaccine; vaccine matching; composition; deep sequencing; degraded RNA; FMDV; whole genome

Online: 28 November 2019 (04:03:46 CET)

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Preprint REVIEW | doi:10.20944/preprints201911.0300.v1

Next Generation Biological Control: The Need for Integrating Genetics and Evolution

Kelley Leung, Erica Ras, Kim Ferguson, Simone Ariëns, Dirk Babendreier, Piter Bijma, Kostas Bourtzis, Jacques Brodeur, Margreet Bruins, Alejandra Centurión, Sophie Chattington, Milena Chinchilla-Ramírez, Marcel Dicke, Nina Fatouros, Joel González Cabrera, Thomas Groot, Tim Haye, Markus Knapp, Panagioata Koskinioti, Sophie Le Hesran, Manolis Lirakis, Angeliki Paspati, Meritxell Pérez-Hedo, Wouter Plouvier, Christian Schlötterer, Judith Stahl, Andra Thiel, Alberto Urbaneja, Louis van de Zande, Eveline Verhulst, Louise Vet, Sander Visser, John Werren, Shuwen Xia, Bas Zwaan, Sara Magalhães, Leo Beukeboom, Bart Pannebakker

Subject: Biology And Life Sciences, Insect Science Keywords: artificial selection; biological control; genetics; genome assembly; genomics; insect breeding; microbiome; modelling

Online: 24 November 2019 (17:10:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints201910.0156.v1

Complete Genomic Sequence of Noni mosaic virus (NoMV), a Novel Potyvirus Associated with a Mosaic Disease in Morinda citrifolia L.

Nai-Tong Yu, Zhi-Ying Cai, Zhongguo Xiong, Yan Yang, Zhi-Xin Liu

Subject: Biology And Life Sciences, Virology Keywords: noni mosaic virus; potyvirus; complete genome; morinda citrifolia l; illumina transcriptomic sequencing

Online: 14 October 2019 (09:29:57 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0154.v1

Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways

Aayushi Srivastava, Abhishek Kumar, Sara Giangiobbe, Elena Bonora, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: papillary thyroid cancer; germline mutations; whole genome sequencing; predisposition markers; pathway analysis

Online: 13 October 2019 (17:07:34 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0147.v1

Whole Genome Alignment Based Development of Molecular Marker for Detecting Leptosphaeria maculans and Leptosphaeria biglobosa, the Causal Agent of Blackleg Disease in Brassicas

Mostari Jahan Ferdous, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Jong-In Park, Hee-Jeong Jung, Hoy-Taek Kim, Ill-Sup Nou

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: blackleg; brassica; diagnosis; effector; genome alignment; leptosphaeria biglobosa; leptosphaeria maculans; marker; PCR

Online: 13 October 2019 (16:08:55 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201811.0297.v1

Development of a Transformation Method for Metschnikowia borealis and Other CUG-Serine Yeasts

Zachary Gordon, Maximillian P. M. Soltysiak, Christopher Leichthammer, Jasmine A. Therrien, Rebecca S. Meaney, Carolyn Lauzon, Matthew Adams, Dong Kyung Lee, Preetam Janakirama, Marc-Andre Lachance, Bogumil J. Karas

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: genome engineering; synthetic biology; yeasts; Metschnikowia; genetic tools; DNA delivery; CUG-Ser

Online: 13 November 2018 (05:17:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints201810.0638.v1

Whole Chloroplast Genome Characterization and Comparison of Two Sympatric Species in Genus Hippophae (Elaeagnaceae)

Luoyun Wang, Jing Wang, Caiyun He, Jianguo Zhang, Yanfei Zeng

Subject: Biology And Life Sciences, Plant Sciences Keywords: Chloroplast genome; H. gyantsensis; H. rhamnoides subsp. yunnanensis; Ka/ks; Optimal codons

Online: 26 October 2018 (15:40:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201809.0169.v1

“Out of the Can”: A Draft Genome Assembly, Liver Transcriptome and Nutrigenomics of the European Sardine, Sardina pilchardus

André M. Machado, Ole K. Tørresen, Naoki Kabeya, Alvarina Couto, Bent Petersen, Mónica Felício, Paula F. Campos, Elza Fonseca, Narcisa Bandarra, Mónica Lopes-Marques, Renato Ferraz, Raquel Ruivo, Miguel M. Fonseca, Sissel Jentoft, Óscar Monroig, Rute Da Fonseca, L. Filipe C. Castro

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: European sardine; draft genome; teleosts; comparative genomics; long chain polyunsaturated fatty acids

Online: 10 September 2018 (12:37:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0206.v1

Genome Characterization of a Novel Binary Toxin-Positive Strain of Clostridium difficile and Comparison with the Epidemic 027 and 078 Strains

Zhong Peng, Sidi Liu, Xiujuan Meng, Wan Liang, Biao Tang, Yuanguo Wang, Juping Duan, Chenchao Fu, Bin Wu, Anhua Wu, Chunhui Li

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Clostridium difficile; ST201; binary toxin-positive; whole genome sequencing; comparative genomic analysis

Online: 30 May 2017 (06:15:11 CEST)

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A novel binary toxin-positive non-027, non-078 Clostridium difficile strain designated LC693 whose sequence type was ST201 was isolated from the fecal sample of a patient with severe diarrhea in China. To understand the pathogenesis basis of C. difficile ST201, this recently recovered isolate LC693 was then chosen for whole genome sequencing. The project finally generated an estimated genome size of approximately 4.07 Mbp. The genome sequence was then analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. Genome size of the three ST201 strains ranged from 4.07 Mb~4.16 Mb, with an average GC content between 28.5%~28.9%. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance, suggesting that they may have a strong antibiotic resistance. The ST201 strains contained a typical clade 3 specific PaLoc with a Tn6218 element inserted, and those genes harbored on their PaLoc that participated in the toxin expression and regulation were highly homologues to the epidemic 027 and 078 strains, with the exception of tcdC. A truncated TcdC was found in the ST201 strains, which is suggestive to have a contribution to the toxin production of the ST201 strains. In addition, the ST201 strains contained intact binary toxin coding and regulation genes, which is also proposed to contribute to the virulence. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for the C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The identification of those genes also contributes to the pathogenesis of the ST201 strain. To our knowledge, this is the first study that the genome sequence of C. difficile ST201 was discussed in detail, and the present study would have a contribution to understanding the pathogenesis basis of C. difficile ST201.

Preprint ARTICLE | doi:10.20944/preprints202403.0244.v1

The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa

Nelson Nazzicari, Nicolo Franguelli, Barbara Ferrari, Luciano Pecetti, Paolo Annicchiarico

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: legumes; alfalfa; genomic selection; SNP calling pipeline; autotetraploidy; polyploidy; genome parametrization; SNP subsetting

Online: 5 March 2024 (10:25:28 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0701.v1

Increasing the Activity of the High-Fidelity SpyCas9 Form in Yeast by Directed Mutagenesis of the PAM Interacting Domain

Artem I Davletshin, Anna A Matveeva, Stanislav S Bachurin, Dmitry S Karpov, David G Garbuz

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Saccharomyces cerevisiae; genome editing; site-directed mutagenesis; CRISPR/Cas9; high-fidelity Cas9 forms

Online: 12 December 2023 (07:43:14 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202311.0774.v1

Syncytial Nets vs. Chemical Signaling: Emerging Properties of Alternative Integrative Systems

Leonid Moroz

Subject: Biology And Life Sciences, Neuroscience And Neurology Keywords: Ctenophora; Porifera; Placozoa; Cnidaria; nervous system evolution; neurotransmission; synapses; animal origins; genome; behavior

Online: 13 November 2023 (10:27:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints202309.1057.v1

An Outbreak of Vancomycin-Resistant Enterococci in a City Hospital Intensive Care Unit: Molecular Characterization of Resistance

Feray Ferda Şenol, Elif Seren Tanrıverdi, Zulal Aşçı Toraman, Barış Otlu

Subject: Medicine And Pharmacology, Medicine And Pharmacology Keywords: vancomycin-resistant enterococcus faecium; hospital epidemic; whole genome analysis; infection prevention and control

Online: 15 September 2023 (11:41:52 CEST)

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Vancomisin resistant enterococcus(VRE), is a resistant microorganism which colonizates and causes infections in hospitalized patients. It was aimed to show the spread of vancomycin-resistant Enterococcus (fVREfm) step-by-step in all intensive care units, which started with the growth of vancomycin-resistant Enterococcus faecium (VREfm) on 02.12.2021 in the blood culture of a patient hospitalized in the anesthesia intensive care unit of our hospital and was found to have reached epidemic size in the surveys. Rectal swab samples were taken from all patients hospitalized in intensive care units, VRE colonization was determined and the VanA and VanB resistance genes associated with vancomycin resistance of VREfm isolates were determined by PCR method, and clonal association analysis was performed by Arbitrarily Primed-PCR (AP-PCR) and Pulsed-Field Gel Electrophoresis. In our study, VRE was detected in 61 of 2601 rectal swab samples. 54 (85.52%) of the VRE isolates were Enterococcus faecium, 3 (4.91%) was Enterococcus faecalis, 3 (4.91%) was Enterococcus gallinorum, 1 (1.63%) was Enterococcus casseliflavus. It was determined that all of the 54 VREfm isolates, which were the most detected among all VRE isolates, carried the vanA gene. In the clonal association analysis of the isolates by AP-PCR and PFGE methods, it was found that they had 12 different genotypes, 48 of them were included in any cluster, the clustering rate was 88.8%, and the largest cluster was genotype 1 cluster with 36 isolates. Of the 54 patients with VREfm isolated recently, 18.51 percent of the clinical samples were isolated before the survey, and 9.24% were isolated after the survey. It was determined that 100% of VREfm isolates were resistant to ampicillin, levofloxacin, ciprofloxacin, high-level gentamicin, trimethoprim-sulfamethoxazole, teicoplanin, 7.4% to tigecycline and 1.85% to linezolid. In our study, in the clonal association analysis performed by isolating VREfm in rectal swab samples, it was found that 88.8% of the samples were indistinguishably similar and the increase in the number of VREfm infections after the index case in our hospital was associated with the epidemic. VREfm infections cause long term hospitalization, costs and also deaths, which shows the seriousness of the event, and the importance of the combination of epidemiological and molecular analysis in epidemic research.

Preprint ARTICLE | doi:10.20944/preprints202308.0658.v1

Validation and cross-species transferability of SSR markers developed from whole genome sequence (WGS) of Mungbean (Vigna radiata L. Wilczek) and their application of population genetics in Vigna species

Pawan Saini, Tejinderjit Singh Bains, Asmita Sirari, Inderjit Singh Yadav, Kamalpreet Singh Mandahal, Sayeed Abdul Hamid Patel, Javed Akhatar, Navkiran Ludhar, Pooja Saini, Sharon Nagpal, Aditya Pratap

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: Mungbean, Vigna, Whole genome sequence, SSR markers, Principal co-ordinate analysis, Genetic diversity

Online: 8 August 2023 (11:23:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.0010.v1

CoVigator – a Knowledge Base for Navigating SARS-CoV-2 Genomic Variants

Thomas Bukur, Pablo Riesgo-Ferreiro, Patrick Sorn, Ranganath Gudimella, Johannes Hausmann, Thomas Rösler, Martin Löwer, Barbara Schrörs, Ugur Sahin

Subject: Computer Science And Mathematics, Mathematical And Computational Biology Keywords: SARS-CoV-2; dashboard; genomic variants; software; pipeline; virus genome assemblies; knowledge base

Online: 1 June 2023 (03:16:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202212.0582.v1

COVID-19: The Ethno-Geographic Perspective of Differential Immunity

Usman Abdullah, Ned Saleh, Peter Shaw, Nasir Jalal

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: COVID-19; copy number variation (CNV); virome; microbiome; endoretroviral genome (ERV); geographic disparity

Online: 30 December 2022 (10:00:27 CET)

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Preprint ARTICLE | doi:10.20944/preprints202212.0232.v1

Retracing Phylogenetic, Host and Geographic Origins of Coronaviruses with Coloured Genomic Bootstrap Barcodes: SARS-CoV and SARS-CoV-2 as Case Studies

Alexandre Hassanin, Opale Rambaud

Subject: Biology And Life Sciences, Virology Keywords: coronavirus; genome; recombination; COVID-19; reservoir host; secondary host; phylogenetic support; tree reconstruction

Online: 13 December 2022 (07:44:48 CET)

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Preprint REVIEW | doi:10.20944/preprints202211.0169.v1

Resistance and Tolerance to Viroid Infection

Takashi Naoi, Shifang Li, Teruo Sano

Subject: Biology And Life Sciences, Virology Keywords: viroid; resistance; tolerance; RNA silencing; plant hormone; spray-induced gene silencing; genome editing

Online: 9 November 2022 (03:10:00 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202206.0409.v1

Evolutionary Honing in and Mutational Replacement: How Long-Term Directed Mutational Responses to Specific Environmental Pressures Are Possible

Adi Livnat, Daniel Melamed

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Non random mutation; interaction-based evolution; hemoglobin S; directed mutation; parallelism; genome organization

Online: 29 June 2022 (14:56:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0051.v1

Genetic Knockouts Indicate That the ABCC2 Gene in the Bollworm Helicoverpa Zea Is Not a Major Receptor for the Cry1Ac Insecticidal Protein.

Omaththage P. Perera, Nathan S LIttle, Heba Abdelgaffar, Juan Luis Jurat-Fuentes, Gadi V. P. Reddy

Subject: Biology And Life Sciences, Insect Science Keywords: Helicoverpa zea; Bollworm; CRISPR; Cry1A; Bt Toxin; Genome Editing; Knockout; Functional Genomics; Resistance

Online: 3 September 2021 (08:19:44 CEST)

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Preprint REVIEW | doi:10.20944/preprints202104.0244.v1

Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus

Alina Renz, Andreas Dräger

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Staphylococcus aureus; MRSA; genome-scale metabolic models; model-driven discovery; strain-specific models

Online: 8 April 2021 (14:25:31 CEST)

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Working Paper REVIEW

Discoveries and Biological Implications of Mammalian 45S rDNA Variants and Non-Structural rRNAs

Yih-Horng Shiao

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: Ribosomal DNA; ribosomal RNA; mammalian genome; intra- and inter-individual variations; development; diseases.

Online: 26 February 2021 (11:35:55 CET)

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Preprint REVIEW | doi:10.20944/preprints202003.0351.v1

Genome Editing: An Emerging Tool for Plant Breeders

Anand Kumar, Karansher Sandhu

Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: Conventional method; Clustered Regularly Interspaced Short Palindromic Sequence; Genome editing; RNA Interference; TALEN

Online: 23 March 2020 (10:23:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints201904.0085.v2

Meta-Analysis of Cancer Triploidy: Whole-Genome Rearrangements in Male Human Tumours Are Characterised by XXY Karyotypes

Ninel M. Vainshelbaum, Pawel Zayakin, Regina Kleina, Alessandro Giuliani, Jekaterina Erenpreisa

Subject: Biology And Life Sciences, Cell And Developmental Biology Keywords: cancer near-triploidy; male tumours; karyotype meta-analysis; XXY; whole genome rearrangements; digyny

Online: 14 July 2019 (09:25:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201902.0035.v1

Characterization of a Bbotybirnavirus Conferring Hypovirulence in the Pear Stem Wart Disease Phytopathogenic Fungus Botryosphaeria dothidea

Lifeng Zhai, Mengmeng Yang, Meixing Zhang, Ni Hong, Guoping Wang

Subject: Biology And Life Sciences, Virology Keywords: Botryosphaeria dothidea botybirnavirus 1; Hypovirulence; Botybirnavirus; Genome; Botryosphaeria dothidea; double-stranded RNA virus

Online: 4 February 2019 (13:44:22 CET)

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Preprint REVIEW | doi:10.20944/preprints201812.0156.v1

The Report of Marine Life Genomic Research

Guangyi Fan, Jianwei Chen, Tao Jin, Chengcheng Shi, Xiao Du, He Zhang, Yaolei Zhang, Hanbo Li, Ting Luo, Pengxu Yan, Guang Liu, Xiangqun Chi, Xiaoxuan Tan, Liangwei Li, Guilin Liu, Xiaochuan Liu, Shijie Hao, Kai Han, Xiaoyun Huang, Shuai Sun, Jing Zhou, Mengjun Yu, Lingfeng Meng, Yue Chang, Rui Zhang, Kaiqiang Liu, Mengqi Zhang, Yong Zhao, Chang Li, Jiao Guo, Xinyu Guo, Jiahao Wang, Meiqi Lv, Haoyang Gao, Yujie Liu, Yue Song, Shengjun Wang, Yang Deng, Binjie Ouyang, Jinzhong Lin, Yingjia Yu, lynn Fink, Xianwei Yang, Xun Xu, Xin Liu

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Marine microorganisms, marine fungi, algae, marine plants, marine invertebrates, marine vertebrates, genome, metagenome

Online: 12 December 2018 (15:44:09 CET)

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Preprint REVIEW | doi:10.20944/preprints201808.0089.v1

Molecular and Genetic Bases of Fruit Firmness Variation in Blueberry—A Review

Francesco Cappai, Juliana Benevenuto, Luis Felipe V. Ferrao, Patricio Munoz

Subject: Biology And Life Sciences, Agricultural Science And Agronomy Keywords: firmness; Vaccinium; ripening; cell wall; crispy; quantitative genetics; breeding; molecular markers; genome editing

Online: 5 August 2018 (10:11:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202403.1713.v1

All Screen Printed and Flexible Silicon Carbide NTC Thermistors for Temperature Sensing Applications

Arjun Wadhwa, Jaime Benavides Guerrero, Mathieu Gratuze, Martin Bolduc, Sylvain G Cloutier

Subject: Engineering, Electrical And Electronic Engineering Keywords: Temperature Sensing; Negative Temperature Coefficient (NTC); Printed Electronics; Printed Temperature Sensors; Thermistors; Silicon Carbide; Wide Band-gap Semiconductor; Screen Printing; Silver ink

Online: 28 March 2024 (15:35:55 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202311.0250.v1

Beyond Deep Learning—Space, Time, and Emergence

Ge Wang, Feng-Lei Fan

Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Artificial neural network; deep network; wide network; intra-layer links; Hopfield network; diffusion model; representation engineering; emergent properties; AI agents; netware engineering

Online: 3 November 2023 (11:44:39 CET)

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Preprint ARTICLE | doi:10.20944/preprints202405.0054.v1

Neuronal Ceroid Lipofuscinosis in a Mixed Breed Dog with a Splice Site Variant in CLN6

Tendai Mhlanga-Mutangadura, Garrett Bullock, Sofia Cerda-Gonzalez, Martin L Katz

Subject: Animal Science, Veterinary Science And Zoology, Biology And Life Sciences Keywords: neurodegeneration; lysosomal storage; mitochondrial subunit c protein; lipofusciin; fluorescence; whole genome sequencing; electron microscopy

Online: 1 May 2024 (08:15:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1298.v1

Machine Intelligence with Associative Memory and Event-Driven Transaction History

Rao Mikkilineni, W. Patrick Kelly

Subject: Artificial Intelligence And Machine Learning, Computer Science And Mathematics Keywords: Machine Intelligence; Associative Memory; Event-Driven Transaction History; Self-Regulation; Digital Genome; Autopoiesis; Cognition

Online: 19 April 2024 (14:57:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202404.1209.v1

Genetic Characterization and Population Structure of Drug Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing

Leonardo Souza Esteves, Lia Lima Gomes, Daniela Brites, Fátima Cristina Onofre Fandinho, Marcela Bhering, Márcia Aparecida da Silva Pereira, Emilyn Costa Conceição Sharma, Richard Salvato, Bianca Porphirio da Costa, Reginalda Ferreira de Melo Medeiros, Paulo Cesar de Souza Caldas, Paulo Redner, Margareth Pretti Dalcolmo, Vegard Eldholm, Sebastien Gagneux, Maria Lucia Rossetti, Afrânio Lineu Kritski, Philip Noel Suffys

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Mycobacterium tuberculosis; Drug Resistance; Whole Genome Sequencing; Genetic Diversity; Brazil; Novel Mutations

Online: 18 April 2024 (07:51:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202312.0929.v1

Comparative Genomic Analysis of Colletotrichum lini Strains with Different Virulence on Flax

Ekaterina M. Dvorianinova, Elizaveta A. Sigova, Timur D. Mollaev, Tatiana A. Rozhmina, Ludmila P. Kudryavtseva, Roman O. Novakovskiy, Anastasia A. Turba, Daiana A. Zhernova, Elena V. Borkhert, Elena N. Pushkova, Nataliya V. Melnikova, Alexey A. Dmitriev

Subject: Biology And Life Sciences, Ecology, Evolution, Behavior And Systematics Keywords: Colletotrichum lini; anthracnose; flax pathogen; virulence; Nanopore sequencing; de novo genome assembly

Online: 13 December 2023 (05:07:10 CET)

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Preprint ARTICLE | doi:10.20944/preprints202312.0628.v1

A Knockout of the IFITM3 Gene Increases the Sensitivity of WI-38 VA13 Cells to the Influenza a Virus

Natalya Eshchenko, Mariia Sergeeva, Evgenii Zhuravlev, Kira Kudria, Elena Goncharova, Andrey Komissarov, Grigory Stepanov

Subject: Biology And Life Sciences, Virology Keywords: IFITM; Influenza A virus; Human cells; WI-38; Genome editing; CRISPR/Cas9; RNA-seq

Online: 8 December 2023 (12:42:54 CET)

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Preprint ARTICLE | doi:10.20944/preprints202310.1454.v1

Whole Genome Sequencing Uncovers the Genetic Determinants of Colistin Resistance in Multi-Drug Resistant Klebsiella pneumoniae Isolated from Patients Admitted in the ICU of a Tertiary Care Hospital in Kampala, Uganda

Maximilian A. K. Magulye, Reuben S. Maghembe, Simon Sekyanzi, Beatrice Achan, Savannah Mwesigwa, Eric Katagirya

Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Klebsiella pneumoniae, whole genome sequences (WGS), antimicrobial resistance (AMR), multidrug resistance (MDR), colistin resistance

Online: 23 October 2023 (13:26:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202309.0727.v1

Differential Large and Small Terminase Subunit Assembly Mediate Bacteriophage P22 Genome Packaging

Julia Elise Cabral, Yanfei Qiu, Abert J.R. Heck, Reginald McNulty

Subject: Biology And Life Sciences, Virology Keywords: Salmonella virus; viral genome-packaging motor; small terminase; large terminase; Bacteriophage P22; electron microscopy

Online: 12 September 2023 (04:43:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202306.2105.v1

Whole-Genome Sequencing-Based Screening of Methicillin Resistant Staphylococcus aureus in Patients and Healthcare Workers in Public Hospitals in Benin

Carine Laurence Yehouenou, Bert Bogaerts, Kevin Vanneste, Sigrid C.J. De Keersmaecker, Nancy H.C. Roosens, Arsène A. Kpangon, Dissou Affolabi, Anne Simon, Francis Moise Dossou, Olivia Dalleur

Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Methicillin-resistant Staphylococcus aureus; healthcare workers; whole genome sequencing; low-or middle-income countries

Online: 29 June 2023 (12:46:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202303.0270.v1

Genomic Analysis of Infectious Bursal Disease Virus in Nigeria: Identification of Unique Mutations of Yet Unknown Biological Functions in Both Segments A and B

Ijeoma Nwagbo, Adelaide Milani, Annalisa Salviato, Gianpiero Zamperin, Lanre Sulaiman, Nanven Maurice, Clement Meseko, Alice Fusaro, Ismaila Shittu

Subject: Biology And Life Sciences, Animal Science, Veterinary Science And Zoology Keywords: genome sequence; infectious bursal disease virus; Nigeria; phylogenetic analysis; poultry; segments A and B

Online: 15 March 2023 (07:49:33 CET)

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Preprint REVIEW | doi:10.20944/preprints202211.0430.v1

Attenuation and Degeneration of SARS-CoV-2 Despite of Adaptive Evolution

Yingguang Liu

Subject: Biology And Life Sciences, Virology Keywords: SARS-CoV-2, evolution, immune evasion, codon usage, attenuation, genome degradation, degeneration, COVID-19

Online: 23 November 2022 (03:29:58 CET)

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Preprint ARTICLE | doi:10.20944/preprints202211.0059.v1

Genomic Epidemiology of SARS-Cov-2 in Western Burkina Faso, West Africa

Yacouba Sawadogo, Lokman Galal, Essia Belarbi, Arsène Zongo, Grit Schubert, Fabian Leendertz, Abdoulie Kanteh, Abdul Karim Sesay, Annette Erhart, Anne-Laure Bañuls, Zekiba Tarnagda, Sylvain Godreuil, Halidou Tinto, Abdoul-Salam Ouedraogo

Subject: Biology And Life Sciences, Virology Keywords: COVID-19; SARS-CoV-2; Whole Genome Sequencing; Genomic epidemiology; West Africa, Burkina Faso

Online: 2 November 2022 (11:14:27 CET)

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Preprint REVIEW | doi:10.20944/preprints202210.0313.v1

The Complex World of Emaraviruses – Challenges, Insights and Prospects

Marius Rehanek, David G. Karlin, Martina Bandte, Rim Al Kubrusli, Shaheen Nourinejhad Zarghani, Thierry Candresse, Carmen Büttner, Susanne Von Bargen

Subject: Biology And Life Sciences, Virology Keywords: diagnosis; distribution; emaraviruses; forest trees; Fimoviridae; genome organization; phylogenetic relations; protein domains; symptomatology; transmission

Online: 20 October 2022 (14:09:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202103.0717.v1

Role of the Non-Canonical RNAi Pathway in the Antifungal Resistance and Virulence of Mucorales

José Tomás Cánovas-Márquez, María Isabel Navarro-Mendoza, Carlos Pérez-Arques, Carlos Lax, Ghizlane Tahiri, José Antonio Pérez-Ruiz1, Damaris Lorenzo-Gutiérrez, Silvia Calo, Sergio López-García, Eusebio Navarro, Francisco Esteban Nicolás, Victoriano Garre, Laura Murcia-Flores

Subject: Biology And Life Sciences, Biochemistry And Molecular Biology Keywords: virulence; antifungal resistance; non-canonical RNAi; epimutant; R3B2; RdRP; transposon; genome stability; Mucorales; mucormycosis.

Online: 30 March 2021 (09:37:39 CEST)

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