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Preprint REVIEW | doi:10.20944/preprints202209.0364.v1

Expression and Signaling Pathways of Nerve Growth Factor (NGF) And Pro-NGF in Breast Cancer: A Systematic Review

Francesco Bruno, Domenico Arcuri, Francesca Vozzo, Antonio Malvaso, Alberto Montesanto, Raffaele Maletta

Subject: Life Sciences, Molecular Biology Keywords: breast cancer; Nerve Growght Factor (NGF); TrkA; p75NTR; NGFR; pro-NGF; angiogenesis; invasion; metastasis; diagnosis; prognosis; treatment

Online: 23 September 2022 (09:18:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202209.0290.v1

Sulfatide Deficiency, An Early Alzheimer’s Lipidomic Signature, Causes Brain Ventricular Enlargement in the Absence of Classical Neuropathological Hallmarks

Lin Ding, Juan Pablo Palavicini, Meixia Pan, Shulan Qiu, Hu Wang, Qiang Shen, Jeffrey L. Dupree, Xianlin Han

Subject: Life Sciences, Molecular Biology Keywords: Sulfatide; cerebroside sulfotransferase; ventricular enlargement; Alzheimer’s disease; brain MRI; aquaporins

Online: 20 September 2022 (03:56:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202209.0260.v1

Diversity and Life-cycle Analysis of Pacific Ocean Zooplankton by Videomicroscopy and DNA Barcoding: Gastropods

Peter Bryant, Timothy Arehart

Subject: Life Sciences, Molecular Biology Keywords: Mollusks; gastropods; Zooplankton; Plankton; Pacific Ocean; larvae; DNA barcoding

Online: 19 September 2022 (04:57:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202209.0227.v1

Advances on Cellular Clonotypic Immunity in Amyotrophic Lateral Sclerosis

Giuseppe Schirò, Vincenzo Di Stefano, Filippo Brighina, Salvatore Iacono, Roberto Monastero, Carmela Rita Balistreri

Subject: Life Sciences, Molecular Biology Keywords: Amyotrophic lateral sclerosis (ALS); neurodegeneration; neuroinflammation; neuromuscular disease; autoimmunity; the clonotypic immune system

Online: 15 September 2022 (08:51:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202209.0091.v1

Sex Specific Differences in Response to Calorie Restriction in Skeletal Muscle of Young Rats

Margalida Torrens-Mas, Cayetano Navas-Enamorado, Devin Wahl, Andres Sanchez-Polo, Anna Picca, Jordi Oliver, Pilar Roca, Marta Gonzalez-Freire

Subject: Life Sciences, Molecular Biology Keywords: calorie restriction; aging; inflammation; autophagy; senescence.; skeletal muscle

Online: 6 September 2022 (11:01:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0527.v1

Structural Basis for the Binding of Allosteric Activators Leucine and ADP to Mammalian Glutamate Dehydrogenase

Vasily A. Aleshin, Victoria I. Bunik, Eduardo M. Bruch, Marco Bellinzoni

Subject: Life Sciences, Molecular Biology Keywords: Glutamate dehydrogenase; allosteric regulation; leucine; ADP; potassium; acetylation; thiamine triphosphate

Online: 31 August 2022 (02:39:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0482.v1

Identification and Characterisation of Nontuberculous Mycobacteria that may Impede the Diagnosis of Bovine Tuberculosis in African Buffaloes (Syncerus caffer), South Africa

Charlene Clarke, Tanya J. Kerr, Robin M. Warren, Léanie Kleynhans, Michele Ann Miller, Wynand Johan Goosen

Subject: Life Sciences, Molecular Biology Keywords: African buffaloes; bovine tuberculosis; cfp-10; esat-6; hsp65; nontuberculous mycobacteria; rpoB; Syncerus caffer

Online: 29 August 2022 (09:48:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0462.v1

Small Extracellular Vesicles from Hypoxic Triple-Negative Breast Cancer Cells induce Oxygen-dependent Cell Invasion

Bianca Cruz Pachane, Ana Carolina Caetano Nunes, Thais Regiani Cataldi, Kelli Cristina Micocci, Bianca Caruso Moreira, Carlos Alberto Labate, Heloisa Sobreiro Selistre-de-Araujo, Wanessa Fernanda Altei

Subject: Life Sciences, Molecular Biology Keywords: Hypoxia; Extracellular vesicles; Breast Cancer; Cell Invasion

Online: 26 August 2022 (14:08:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0413.v1

Alec C. Gleason, Ghanashyam Ghadge, Yoshifumi Sonobe, Raymond P. Roos

Subject: Life Sciences, Molecular Biology Keywords: translation initiation; canonical and noncanonical translation initiation codons; protein translation; oncogene; oncogenesis; tumorigenesis; cancer

Online: 24 August 2022 (05:30:03 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0343.v1

Structural Landscape and Deduced Functions of The Cardiac 14-3-3 Protein Interactome

Jia-Hua Qu, Kirill V. Tarasov, Khalid Chakir, Yelena S. Tarasova, Daniel R. Riordon, Edward G. Lakatta

Subject: Life Sciences, Molecular Biology Keywords: 14-3-3; interactome; protein-protein interaction; mitochondria; metabolism; protein quality control; homeostasis; left ventricule; network

Online: 18 August 2022 (10:54:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0323.v1

Ikaros Regulates microRNA Networks in Acute Lymphoblastic Leukemia

Sophie Kogut, Hana Paculova, Princess Rodriguez, Joseph Boyd, Alyssa Richman, Amrita Palaria, Hilde Schjerven, Seth Frietze

Subject: Life Sciences, Molecular Biology Keywords: miRNA; IKZF1; Acute Lymphoblastic Leukemia

Online: 17 August 2022 (11:29:02 CEST)

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Preprint REVIEW | doi:10.20944/preprints202208.0285.v1

The Present and Future of Clinical Management in Metastatic Breast Cancer

Pauline Lin, George Laliotis

Subject: Life Sciences, Molecular Biology Keywords: Breast; cancer; metastasis; oncology

Online: 16 August 2022 (09:52:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202208.0263.v1

Trans-Differentiation of Non-Stem Cells to Nerve Cells or Neural Stem Cells through MicroRNA Reprogramming

Amin Foroughi Nezhad, Sina Dehghan

Subject: Life Sciences, Molecular Biology Keywords: Neural stem cells; Reprogramming; Neurons; MicroRNA; Somatic cells; Trans-Differentiation; miRNA

Online: 15 August 2022 (12:00:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202208.0191.v1

Snakemake Workflows for Long-read Bacterial Genome Assembly and Evaluation

Peter Menzel

Subject: Life Sciences, Molecular Biology Keywords: bacterial genomics; de novo assembly; Oxford Nanopore Technologies; Snakemake

Online: 10 August 2022 (04:37:01 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0442.v1

Performance Comparison of a Duplex Implementation of the CDC EUA 2019-nCoV Assay with the Seegene Allplex-SARS-CoV-2 Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Swab Samples

Karen Marcela Jiménez, Dora Janeth Fonseca-Mendoza, Adrien Morel, Oscar Ortega-Recalde, Nora Contreras, Camilo Andres Velandia-Piedrahita, Adriana Steevens, Luisa Caldas, Juan Pablo Ribón, Martha Sanchez, Carlos Martín Restrepo, Rodrigo Cabrera

Subject: Life Sciences, Molecular Biology Keywords: COVID-19; molecular diagnostic; SARS-CoV-2; Real-time PCR

Online: 29 July 2022 (03:10:47 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0409.v1

MicroRNAs within Basal-Like Signature of Quadruple Negative Breast Cancer Impact Overall Survival in African Americans

Clayton Yates, Anusha Angajala, Aliyu Muhammad, Hughley Raymond, Shakir Md Ahmed, Saadia Haleema, Monira Haque, Honghe Wang, Rachel Martini, Balasubramanian Karanam, Andrea G. Kahn, Deepa Bedi, Melissa Davis, Ming Tan, Windy Dean-Colomb

Subject: Life Sciences, Molecular Biology Keywords: QNBC (Quadruple negative breast cancer); AR (Androgen receptor); AA (African American); CA (Caucasian); BC (Breast cancer)

Online: 27 July 2022 (04:07:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0127.v1

JmjC Family of Histone Demethylases form Nuclear Condensates

Marta Vicioso-Mantis, Samuel Aguirre, Marian A Martínez-Balbás

Subject: Life Sciences, Molecular Biology Keywords: Epigenetic regulation; Histone demthylases; JMJC; IDR; biomolecular condensates

Online: 7 July 2022 (12:59:29 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0125.v1

A Fish of Multiple Faces, which Show us Enigmatic and Incredible Phenomena in Nature: Biology and Cytogenetics of the Genus Carassius

Martin Knytl, Adrian Forsythe, Lukáš Kalous

Subject: Life Sciences, Molecular Biology Keywords: hybridization; sexuality; asexuality; biotype; species; sex determination; ploidy level; Carassius auratus complex

Online: 7 July 2022 (09:56:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0099.v1

The Bacterial ClpXP-ClpB Family is Enriched with RNA-Binding Protein Complexes

Georg Auburger, Jana Key, Suzana Gispert

Subject: Life Sciences, Molecular Biology Keywords: mass spectrometry; substrate-trapping assay; BioID; POLDIP2; LRPPRC; GRSF1; PNPT1; MTIF2; ataxia

Online: 6 July 2022 (15:26:30 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0030.v1

Meta-Analysis Identifies Novel Common Genes Differently Altered in Cross-Species Models of Rett Syndrome

Florencia Dagmar Haase, Rachna Singh, Brian Gloss, Patrick Tam, Wendy Gold

Subject: Life Sciences, Molecular Biology Keywords: Rett syndrome; WGCNA; MECP2

Online: 4 July 2022 (04:39:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0025.v1

First Molecular Identification of Bulinus africanus in Lake Malawi Implicated in Transmitting Schistosoma Parasites

Mohammad Alharbi, Cynthia Iravoga, Sekeleghe A. Kayuni1, E. James LaCourse, Peter Makaula, J. Russell Stothard

Subject: Life Sciences, Molecular Biology Keywords: Bulinus; Schistosoma haematobium; urogenital schistosomiasis

Online: 1 July 2022 (17:58:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202207.0024.v1

Kinases and Their Potential as Therapeutic Targets in Huntington’s Disease

Angel White, Anna McGlone, Rocio Gomez-Pastor

Subject: Life Sciences, Molecular Biology Keywords: post-translation modifications; CK2; Huntington’s Disease; Kinase Inhibition; HTT phosphorylation

Online: 1 July 2022 (17:47:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202207.0009.v1

Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks Under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis

Nilesh Kumar, Bharat Kumar Mishra, Jinbao Liu, Binoop Mohan, Karolina Marta Pajerowska-Mukhtar, M. Shahid Mukhtar

Subject: Life Sciences, Molecular Biology Keywords: co-expression network, water deprivation, drought, systems biology, network centrality, computational simulation, Arabidopsis, transcriptional regulation

Online: 1 July 2022 (08:15:36 CEST)

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Preprint REVIEW | doi:10.20944/preprints202206.0403.v1

Promising Strategies for Preserving Adult Endothelium Health and Reversing Its Dysfunction: From the Liquid Biopsy to New Omics Technologies and Non-invasive Circulating Biomarkers

Carmela Balistreri

Subject: Life Sciences, Molecular Biology Keywords: Endothelium; Endothelium dysfunction; Newer omics technologies; network medicine; biomarkers and therapeutic targets

Online: 29 June 2022 (09:48:20 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0385.v1

Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome

Tatiana A. Bessonova, Maria S. Fando, Olga S. Kostareva, Maria N. Tutukina, Olga N. Ozoline, Mikhail S. Gelfand, Alexey D. Nikulin, Svetlana V. Tishchenko

Subject: Life Sciences, Molecular Biology Keywords: UxuR; ExuR; Ashwell pathway; uxuAB; fliC; proteome; motility; biofilm formation

Online: 28 June 2022 (10:42:44 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0372.v1

Genotype-Phenotype Correlation and Functional Insights for Two Monoallelic Trex1 Missense Variants Affecting the Catalytic Core

Giulia Amico, Wayne O Hemphill, Mariasavina Severino, Claudio Moratti, Rosario Pascarella, Marta Bertamino, Flavia Napoli, Stefano Volpi, Francesca Rosamilia, Sara Signa, Fred W Perrino, Marialuisa Zedde, Isabella Ceccherini

Subject: Life Sciences, Molecular Biology Keywords: exonuclease; autoimmunity; mutation; trex1

Online: 28 June 2022 (04:08:17 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0310.v1

Characterization of Calpain and Caspase-6 Generated Glial Fibrillary Acidic Protein Breakdown Products Following Traumatic Brain Injury and Astroglial Cell Injury

Zhihui Yang, Rawad Daniel Arja, Tian Zhu, George Anis Sarkis, Robert Logan Patterson, Pammela Romo, Disa S. Rathore, Emily Jaalouk, Amanda Weissman, Aaron Tin-Chuk Wong, Zhiqun Zhang, Yuan Shi, Richard A. Yost, Ahmed Moghieb, Susan Abbatiello, Claudia S. Robertson, William E. Haskins, Firas Kobeissy, Kevin K. W. Wang

Subject: Life Sciences, Molecular Biology Keywords: astroglial injury; GFAP; calpain; caspase; biomarkers; traumatic brain injury

Online: 22 June 2022 (08:28:02 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0177.v1

Deuterium Content of the Organic Compounds in Food Has an Impact on Tumor Growth in Mice

Gábor Somlyai, Lajos I. Nagy, László G. Puskás, András Papp, Beáta Zs. Kovács, István Fórizs, György Czuppon, Ildikó Somlyai

Subject: Life Sciences, Molecular Biology Keywords: Deuterium-depleted water (DDW); deuterium-depleted organic compounds (DDOC); anticancer drug development; D/H ratio; production of metabolic water; ketogenic diet

Online: 13 June 2022 (09:49:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202206.0016.v1

Characterization of the Nuclear Proteome of Chlamydomonas in Response to Salt Stress

Larissa de Oliveira Magalhães, Fabio Nunes de Mello, Flavia Vischi Winck

Subject: Life Sciences, Molecular Biology Keywords: lipids; regulation; microalgae; transcription factors

Online: 1 June 2022 (11:09:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0364.v1

LRF Promotes Indirectly Advantageous Chromatin Conformation via BGLT3-lncRNA Expression and Switch from Fetal to Adult Hemoglobin

Vasiliki Chondrou, Athanasios-Nasir Shaukat, Georgios Psarias, Katerina Athanasopoulou, Evanthia Iliopoulou, Ariadne Damanaki, Constantinos Stathopoulos, Argyro Sgourou

Subject: Life Sciences, Molecular Biology Keywords: Hemoglobin switch; BGLT3-lncRNA expression; chromatin conformation; LRF/ZBTB7A overexpression

Online: 26 May 2022 (10:39:49 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0340.v1

Unlocking the Molecular and Biochemical Machinery of Insect Herbivore Resistance: the Key is a Perception of Herbivore-Associated Elicitors

Saiful Malook, Saiqa Maqbool, Muhammad Hafeez, Samantha Chandranath Karunarathna, Nakarin Suwannarach

Subject: Life Sciences, Molecular Biology Keywords: herbivore-associated elicitors; plant defense; secondary metabolites; signaling metabolites; pattern recognition receptors

Online: 25 May 2022 (03:53:53 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0318.v1

Reversal of CSF HIV-1 Escape During Treatment of HIV-Associated Cryptococcal Meningitis in Botswana

Nametso Kelentse, Sikhulile Moyo, Kesaobaka Molebatsi, Olorato Morerinyane, Shatho Bitsang, Ontlametse T. Bareng, Kwana Lechiile, Tshepo B. Leeme, David S. Lawrence, Ishmael Kasvosve, Rosemary Musonda, Mosepele Mosepele, Thomas S. Harrison, Joseph N. Jarvis, Simani Gaseitsiwe

Subject: Life Sciences, Molecular Biology Keywords: HIV; cryptococcal meningitis; HIV-1 viral load; cerebrospinal fluid (CSF) viral escape; Botswana

Online: 24 May 2022 (04:20:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0014.v2

SARS-CoV-2 infection and Diabetes: Pathophysiological Mechanism of Multi-System Organ Failure

Bipradas Roy, Sadia Afrin Runa

Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; Diabetes; Neurological dysfunction; Cardiovascular complications; Pulmonary dysfunction; Renal dysfunction; bone loss; Eye disease; Gastrointestinal complications

Online: 23 May 2022 (11:00:06 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0289.v1

The Reactive Species Interactome - Mitochondria Axis

Laurent Chatre

Subject: Life Sciences, Molecular Biology Keywords: mitochondria; reactive species; eustress; distress; bioenergetic; microbiota

Online: 23 May 2022 (09:41:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0224.v1

SIG-1451, A Novel, Non-Steroidal Anti-Inflammatory Compound, Attenuates Light-Induced Photoreceptor Degeneration by Inhibiting Microglial Activation

Yuki Kikuchi, Eriko Sugano, Shiori Yuki, Kitako Tabata, Yuka Endo, Yuya Takita, Reina Onoguchi, Taku Ozaki, Tomokazu Fukuda, Yoshihiro Takai, Takahiro Kurose, Koichi Tanaka, Yoichi Honma, Eduardo Perez, Maxwell Stock, Jose Fernandez, Masanori Tamura, Michael Voronkov, Jeffry B Stock, Hiroshi Tomita

Subject: Life Sciences, Molecular Biology Keywords: age-related macular degeneration; light-induced photoreceptor degeneration; anti-inflammatory drug; toll-like receptor 4

Online: 17 May 2022 (08:03:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0184.v1

Amyloid Precursor Protein, Alpha-, Beta- and Gamma-Secretases Expression in Penumbra Cells after Photothrombotic Stroke. Evaluation of the Neuroprotective Effect of Secretase Inhibitors

Svetlana Sharifulina, Valeria Guzenko, Alexandr Logvinov, Andrey Khaitin, Yuliya Kalyuzhnaya, Natalia Dobaeva, Yan Li, Lei Chen, Вin He, Svetlana Demyanenko

Subject: Life Sciences, Molecular Biology Keywords: amyloid precursor protein; photothrombotic stroke; ischemia; alpha-secretase; beta-secretase; gamma-secretase

Online: 13 May 2022 (08:39:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0166.v1

Antimicrobial Peptides (AMPs) In the Pathogenesis of Alzheimer’s Disease: Implications for Diagnosis and Treatment

Francesco Bruno, Antonio Malvaso, Sonia Canterini, Amalia Cecilia Bruni

Subject: Life Sciences, Molecular Biology Keywords: Antimicrobial Peptides (AMPs); Alzheimer’s Disease (AD); infectious hypothesis; beta-amyloid (Ab); lactoferrin; defensins; cystatins; thymosin β4; histatin 1; statherin

Online: 12 May 2022 (09:40:33 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0141.v1

Alterations of Mitochondrial Network by Cigarette and e-Cigarette Vaping

Manasa Kanithi, Sunil Junapudi, Syed Islamuddin Shah, Matta Reddy Alavala, Ghanim Ullah, Bojjibabu Chidipi

Subject: Life Sciences, Molecular Biology Keywords: Cigarette smoking; e-cigarette smoking; mitochondria; fusion; fission

Online: 10 May 2022 (12:54:42 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0117.v1

Transposable Elements in Human Diseases: Evolutionary and Therapeutic Perspectives

Kavi Shah, Ahmet C. Berkyurek

Subject: Life Sciences, Molecular Biology Keywords: Transposon; Cancer; Neurological Disease; Evolution; LINE; SINE; ERV

Online: 9 May 2022 (10:50:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0081.v1

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

Simara Larissa Fanalli, Bruna Pereira Martins Da Silva, Julia Dezen Gomes, Vivian Vezzoni De Almeida, Felipe André Oliveira Freitas, Gabriel Costa Monteiro Moreira, Bárbara Silva-Vignato, Juliana Afonso, James Reecy, James Koltes, Dawn Koltes, Luciana Correia de Almeida Regitano, Dorian J. Garrick, Julio Cesar de Carvalho Baileiro, Ariana Nascimento Meira, Luciana Freitas, Luiz Lehmann Coutinho, Heidge Fukumasu, Gerson Barreto Mourão, Severino Matias Alencar, Albino Luchiari Filho, Aline Silva Mello Cesar

Subject: Life Sciences, Molecular Biology Keywords: fatty acid; RNAseq; transcriptome; immune response; Huntington's disease; metabolism; hepatic tissue; Longissimus lomborum; biomedical model

Online: 6 May 2022 (13:58:59 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202205.0018.v2

First Identification in Italy of SARS-CoV-2 Omicron BA.4 Harboring KSF141_del: Genomic Comparison with Omicron Sub-Variants

Cinzia Peronace, Rossana Tallerico, Manuela Colosimo, Marco De Fazio, Federica Pasceri, Ilenia Talotta, Giuseppina Panduri, Letizia Pintomalli, Rosaria Oteri, Valeria Calantoni, Maria Teresa Fiorillo, Maria Cristina Caroleo, Rosita Curcio, Vincenza Dolce, Erika Cione, Pasquale Minchella

Subject: Life Sciences, Molecular Biology Keywords: SARS-CoV-2; Variant of Concern; BA.4; pandemic

Online: 6 May 2022 (11:55:20 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202205.0018.v1

First Identification of SARS-CoV-2 Omicron BA.4 Lineage in Italy: Genomic Comparison with Omicron Lineages

Cinzia Peronace, Rossana Tallerico, Manuela Colosimo, Marco De Fazio, Federica Pasceri, Ilenia Talotta, Giuseppina Panduri, Letizia Pintomalli, Rosaria Oteri, Valeria Calantoni, Maria Teresa Fiorillo, Maria Cristina Caroleo, Vincenza Dolce, Erika Cione, Pasquale Minchella

Subject: Life Sciences, Molecular Biology Keywords: SARS-CoV-2; Variant of Concern; BA.4; pandemic

Online: 4 May 2022 (16:06:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints202205.0014.v1

COVID-19 and Diabetes: Pathophysiological Mechanism of Multi-System Organ Failure

Bipradas Roy, Sadia Afrin Runa

Subject: Life Sciences, Molecular Biology Keywords: COVID-19; SARS-CoV-2; Diabetes; Neurological dysfunction; Cardiovascular complications; Pulmonary dysfunction; Renal dysfunction; bone loss; Eye disease; Gastrointestinal complications

Online: 4 May 2022 (14:17:42 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0008.v1

CRISPR/Cas9-directed Gene Trap Constitutes a Selection System for Corrected BCR/ABL Leukemic Cells in CML

Elena Vuelta, José Luis Ordoñez, David José Sanz, Sandra Ballesteros, Jesús María Hernández-Rivas, Lucía Méndez-Sánchez, Manuel Sánchez-Martín, Ignacio García-Tuñón

Subject: Life Sciences, Molecular Biology Keywords: Chronic Myeloid Leukaemia; BCR/ABL; CRISPR; Gene therapy; CRISPR-Trap.

Online: 4 May 2022 (12:30:11 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202205.0001.v1

A novel ALDH1A1 Inhibitor Blocks Platinum-Induced Senescence and Stemness in Ovarian Cancer

Vaishnavi Muralikrishnan, Fang Fang, Tyler C Given, Ram Podicheti, Mikhail Chtcherbinine, Shruthi Sriramkumar, Heather M O'Hagan, Thomas D. Hurley, Kenneth P. Nephew

Subject: Life Sciences, Molecular Biology Keywords: ovarian cancer; ALDH1A1; cancer stem cells; senescence; chemotherapy resistance

Online: 2 May 2022 (09:39:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0248.v1

Joint Transcriptome and Metabolome Analysis Prevails Biological Mechanisms Underlying the Prosurvival Fight in Heat Stressed Granulosa Cells

Abdul Sammad Sammad, Hanpeng Luo, Lirong Hu, Adnan Khan, Huabin Zhu, Yachun Wang

Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; integrated analysis; transcriptomics; metabolomics; differentially ex-pressed genes; metabolites; signaling pathways; metabolic pathways; cancer pathways

Online: 27 April 2022 (05:08:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0245.v1

ClpP-Deletion Causes Azoospermia, with Meiosis-I Delay and Insufficient Biosynthesis of Spermatid Factors, Due to Mitochondrial Dysfunction with Accumulation of Perrault Proteins ERAL1, PEO1, and HARS2

Suzana Gispert, Jana Key, Aneesha Kohli, Sylvia Torres-Odio, Gabriele Koepf, Shady Amr, Marina Reichlmeir, Patrick N. Harter, A. Phillip West, Christian Münch, Georg Auburger

Subject: Life Sciences, Molecular Biology Keywords: meiosis-I; zygotene-pachytene; homologous recombination; H3K9ac; acetyl-tubulin; Twinkle helicase; RMND1; tRNA /rRNA processing; cGAS-STING signaling

Online: 27 April 2022 (02:55:32 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202204.0208.v1

Evolutionary and Gene Expression Analyses Reveal New Insights into the Role of LSU Gene-Family in Plant Responses to Sulfate-Deficiency

Felipe Uribe, Carlos Henríquez-Valencia, Anita Arenas-M, Joaquín Medina, Elena A. Vidal, Javier Canales

Subject: Life Sciences, Molecular Biology Keywords: sulfate deficiency; Arabidopsis thaliana; Solanum lycopersicum; Triticum aestivum; LSU; response to low sulfur; abiotic stress; sulfur nutrition

Online: 22 April 2022 (03:32:19 CEST)

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Preprint HYPOTHESIS | doi:10.20944/preprints202204.0124.v1

Revisiting Epithelial Carcinogenesis

Luis Fernando Méndez-López

Subject: Life Sciences, Molecular Biology Keywords: Senescence; EMT; NF-κB; Inflammation; Epigenetics; Aging

Online: 13 April 2022 (10:22:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202204.0117.v1

Mechanisms of Cold Signaling in Wheat (Triticum aestivum L.)

Qiangbo Liu, Xiang Zhang, Ying Hua Su, Xian Sheng Zhang

Subject: Life Sciences, Molecular Biology Keywords: cold stress; wheat; hormonal; reactive oxygen species; epigenetic regulation

Online: 13 April 2022 (07:35:35 CEST)

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Preprint REVIEW | doi:10.20944/preprints202204.0055.v1

Activity-Dependent Induction of Younger Molecular, Cellular and Organism Phenotypes

Thomas Lissek

Subject: Life Sciences, Molecular Biology Keywords: cell; biology; aging; medicine; transcription; activity; neurons; brain; immune system; muscle

Online: 7 April 2022 (04:24:23 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202203.0251.v1

XAF1 Inactivation Increases Tumor Cell Resistance to Endoplasmic Reticulum Stress-Induced Apoptosis Through Stabilization of GRP78 and CHIP

Kyung-Woo Lee, Huira Hong, Ji-Sun Lim, Kyung-Phil Ko, Min-Goo Lee, Sung-Gil Chi

Subject: Life Sciences, Molecular Biology Keywords: ER stress; XAF1; GRP78; ZNF313; CHIP

Online: 17 March 2022 (10:59:09 CET)

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Preprint REVIEW | doi:10.20944/preprints202203.0170.v2

Entropy Perspectives of Molecular and Evolutionary Biology

Bartolomé Sabater

Subject: Life Sciences, Molecular Biology Keywords: cancer; DNA informational entropy; cell compartmentation; evolutionary Biology; lactate dehydrogenase (LDH); lactic acid; metabolism; thermodynamic entropy; Warburg effect

Online: 17 March 2022 (03:37:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0357.v1

Transcriptomics Reveals Granulosa Cell’s Coping through Redox, Inflammatory, Metabolic and Cytoskeleton Mechanisms under Acute Heat Stress

Abdul Sammad, Hanpeng Luo, Lirong Hu, Huabin Zhu, Yachun Wang

Subject: Life Sciences, Molecular Biology Keywords: granulosa cells; heat stress; apoptosis; oxidative stress; RNA-seq; transcriptomics; differentially expressed genes; signaling pathways

Online: 28 February 2022 (11:08:42 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0249.v1

Modulation in the Gene Expression Profile of Astrocytes and Monocytes by HIV-1 Nef Variants

Sushama Jadhav, Prajakta Makar, Vijay Nema

Subject: Life Sciences, Molecular Biology Keywords: HIV Nef; neurotoxicity; inflammatory cytokines; kynurenine metabolite

Online: 21 February 2022 (10:00:10 CET)

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HIV-1 Nef is a multifunctional protein with well-known lethal properties. HIV infects various cells from the brain compartment and expressed nef is responsible for developing neuropathogenic potential. HIV-infected glial cells express nefvirotoxinand stimulate the cascade of various pathways to activate uninfected cells to release neurotoxic elements damaging cells themselves. A lot of genetic variabilities of this protein have been reported from patients with HIV-associated neurocognitive disorders. To determine the neurotoxic potential of subtype-specific nef plasmids and nef plasmids of clinical samples with and without HAND were transfected in normal human astrocytes (NHA) and monocyte-derived macrophages (MDM) using nef-pCMV-HA plasmid constructs. Supernatants from subtype-specific Nef plasmids indicated the upregulation of proinflammatory cytokines. The induced expression might be due to the nef genetic variability or variations in the transfection efficiency and expression levels of nef.The mRNA expression of IL-6, IP-10, and TNF-α indicated upregulation of 5.0-fold in NHA and 3-fold in MDM with respect to empty vector control transfection. Further, the kynurenine metabolites were also assessed from culture supernatants of NHA and MDM indicating the upregulation of IDO and KYNU in NHA by 3.0-fold and 3.2-fold in MDM.The expression levels of nef and cytokines at the translational level were confirmed by western blotting and bio-plex Pro cytokine estimation assay respectively along with controls expressing green fluorescent protein (GFP).The oxidative stress was also found to be elevated as compared to control cells as determined by the estimation of nitric oxide from the culture supernatant to confirm the neurotoxic potential of HIV nef plasmids. The downregulation in the levels of cytokines, as well as kynurenine metabolites, was observed in culture supernatants after blocking the expression of nef using HIV nef siRNA. Phylogenetic analysis of Nef sequences indicated subtype C predominance except one sequence showing the partial sequence of HIV-1 subtype B sequence forming BC recombinantThe upregulation in the cytokine and pathway-specific metabolites might be linked with the neurotoxic potential of HIV-1 Nef leading to neuropathogenesis. In conclusion, the variation in the transfection efficiency, nef expression levels, and the genetic variability of Nef might be responsible for upregulating the expression levels of cytokines and kynurenine metabolites in astrocytes and MDM.

Preprint ARTICLE | doi:10.20944/preprints202202.0149.v1

Effect of Dietary Soybean Oil Inclusion on Liver-Related Transcription Factors in a Pig Model for Metabolic Diseases

Simara Larissa Fanalli, Bruna Pereira Martins da Silva, Julia Dezen Gomes, Fernanda Nery Ciconello, Vivian Vezzoni de Almeida, Felipe André Oliveira Freitas, Gabriel Costa Monteiro Moreira, Bárbara Silva-Vignato, Juliana Afonso, James Reecy, James Koltes, Dawn Koltes, Luciana Correia de Almeida Regitano, Julio Cesar de Carvalho Baileiro, Luciana Freitas, Luiz Lehmann Coutinho, Heidge Fukumasu, Severino Matias de Alencar, Albino Luchiari Filho, Aline Silva Mello Cesar

Subject: Life Sciences, Molecular Biology Keywords: immune response; fatty acid; lipid metabolism; RNA-Seq; transcriptome

Online: 10 February 2022 (10:57:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0103.v1

Integrated Analysis of microRNA-mRNA Network Predicts Potential Regulators of Atrial Fibrillation in Human

Rong Wang, Emre Bektik, Phraew Sakon, Xiaowei Wang, Shanying Huang, Xiangbin Meng, Mo Chen, Wenqiang Han, Jie Chen, Yanhong Wang, Jingquan Zhong

Subject: Life Sciences, Molecular Biology Keywords: heart disease; atrial fibrillation; atrial fibrosis; transcriptome; microRNA; RNA sequencing; syndecan-1; miR-302

Online: 7 February 2022 (19:01:55 CET)

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Preprint ARTICLE | doi:10.20944/preprints202202.0084.v1

Spatial and Functional Mapping of Spliceosome and Centrosome Proximity Revealed by Proteogenomics Profiling

Lorella Del Grosso, Luigi Cerulo, Andrea Remo, Brunella Franco, Johan Busselez, Massimo Pancione

Subject: Life Sciences, Molecular Biology Keywords: ribonucleoproteins; spliceosome; centrosome; CEP250

Online: 7 February 2022 (12:12:18 CET)

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Ribonucleoproteins (RNP) condensates often contain intrinsically disordered proteins (IDPs) able to confer an exceptional multifunctionality necessary for gene expression, a process that defines cell types and enables cellular adaptation in metazoans. Centosomes, the microtubule-organizing centers of animal cells, are particularly enriched in disordered proteins but the role of RNPs surrounding the centrosome and the ciliary basal body remains largely unknown. By refining and integrating the existing protein-protein interaction network, spatial proteomics and transcriptomic data, we here report the subcellular and genomic proximity between the spliceosome, a huge nuclear RNP complex that removes introns from a transcribed pre-mRNA, and centrosome/cilia components. We present a comprehensive map of pre-RNA processing factors and other RNA-binding proteins playing a role in the regulation of splicing but localized to the centrosome and cilia. Protein-protein interactions studies reveal that a large number of spliceosome components interact with both centrosome linker and centriolar satellites elements, necessary for cellular division and ciliogenesis. RNAseq data from mouse Embryonic Stem Cells (mESC) and human tissues revealed a co-transcriptional coordination program of splicing and centrosome-related genes with relevance to tissue-specific neurosensory disorders and cancer types. Additionally, we found that centrosome and spliceosome genes form linearly and spatially colocalized genomic loci (CEP250, RBBM39, DHX35, and CTNNBL1) conserved in human and mouse genome, then explaining similarities in co-modification and subcellular distribution. Our results suggest that centrosome and cilia constitute cytoplasmic sites for the exchange of molecular machinery with nucleus, storage of RNA splicing and spliceosome condensates previously unrecognized. These complexes in response to external signals, could play an integral part in ciliogenesis and nuclear division to establish and maintain cellular identity in metazoans.

Preprint ARTICLE | doi:10.20944/preprints202201.0425.v1

Function Overcomes Taxonomy for Organella Genes Triplet Composition

Michael Sadovsky, Maria Yu Senashova, Olga Mutovina, Anna A Molyavko, Viktoria D Fedotovskaya, Tatiana Shpagina, Yana Nedorez, Yulia Putintseva

Subject: Life Sciences, Molecular Biology Keywords: transposon; order; triplet frequency; tRNA; clustering; taxonomy; symmetry; photosystem

Online: 27 January 2022 (17:40:07 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0324.v1

Mitochondrial ROS Produced in Human Colon Carcinoma HCT116 Cells Reduces Cell Survival via Autophagy

Eunji Gwak, Dasol Kim, Hui-Yun Hwang, Ho Jeong Kwon

Subject: Life Sciences, Molecular Biology Keywords: UQCRB; mROS; Autophagy; Colorectal cancer; Lysosome

Online: 21 January 2022 (12:59:47 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0321.v1

Palmitate-triggered COX2/PGE2-Mediated Hyperinflammation In Dual-stressed Pdl Fibroblasts Is Mediated by Repressive H3K27 Trimethylation

Lisa Schuldt, Michael Reimann, Katrin von Brandenstein, Julia Steinmetz, Annika Döding, Ulrike Schulze-Späte, Collin Jacobs, Judit Symmank

Subject: Life Sciences, Molecular Biology Keywords: Periodontitis; Tooth movement; Obesity; Palmitic Acid; Histone Modification; Inflammation; COX2/PGE2; IL10

Online: 21 January 2022 (12:50:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0225.v1

Misdiagnosis of Bacterial Pathogens by the Diagnostic Centers: A Prospective Route for Antibiotic Resistance

Shanaz Fatema Bristy, Md Reaz Uddin, Bushra Ayat Meghla, Taslima Akter Tisha, Md. Aftab Uddin, Mohammad Tarequl Islam, Masayasu Mie, Eiry Kobatake, Mohib Ullah Khondoker, Md. Ahsanul Haq, Zinia Islam, Sharif Hossain, Nafisa Azmuda, Mohd. Raeed Jamiruddin, Mainul Haque, Nihad Adnan

Subject: Life Sciences, Molecular Biology Keywords: Misdiagnosis; Random Amplification of Polymorphic DNA; 16S rRNA Sequencing; Loop-Mediated Isothermal Amplification; Antibiotic Resistance

Online: 17 January 2022 (12:35:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202201.0141.v1

Modulation of DNA Damage Response by SAM and HD Domain Containing Deoxynucleoside Triphosphate Triphosphohydrolase (SAMHD1) Determines Prognosis and Treatment Efficacy in Different Solid Tumor Types

Eudald Felip, Lucia Gutierrez-Chamorro, Maica Gómez-Plaza, Edurne Garcia-Vidal, Margarita Romeo, Teresa Moran, Laura Layos, Laia Pérez-Roca, Eva Riveira-Muñoz, Bonaventura Clotet, Pedro Luis Fernandez, Ricard Mesía, Anna Martínez-Cardús, Ester Ballana, Mireia Margelí

Subject: Life Sciences, Molecular Biology Keywords: SAMHD1; NSCLC; breast cancer; ovarian cancer; solid tumors

Online: 11 January 2022 (13:05:00 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202201.0108.v1

Spermidine Binding to the Acetinobacter baumannii Efflux Protein AceI Observed by Near-UV Synchrotron Radiation Circular Dichroism Spectroscopy

Simon Patching

Subject: Life Sciences, Molecular Biology Keywords: Acinetobacter baumannii; antimicrobial resistance; circular dichroism spectroscopy; efflux protein; efflux pump; foodborne pathogen; hospital-acquired infection; polyamine

Online: 10 January 2022 (12:19:07 CET)

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Preprint REVIEW | doi:10.20944/preprints202201.0102.v1

Normal and Neoplastic Growth Suppression by The Extended Myc Network

Huabo Wang, Edward Prochownik

Subject: Life Sciences, Molecular Biology Keywords: ChREBP; L-Myc; Max; Mga; Mlx; Mnt; MondoA; Mxd; N-Myc; tumor suppressor

Online: 10 January 2022 (12:01:35 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0501.v1

Disparities in Lung Cancer: miRNA Isoform Characterization in Lung Adenocarcinoma

Rosario Distefano, Giovanni Nigita, Patricia Le, Giulia Romano, Mario Acunzo, Patrick Nana-Sinkam

Subject: Life Sciences, Molecular Biology Keywords: miRNA isoform; isomiR, miRNA editing; lung adenocarcinoma; race-disparities

Online: 31 December 2021 (10:41:04 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0290.v3

Epigenetic Modulation of Gremlin-1/NOTCH Pathway in Experimental Crescentic Immune-Mediated Glomerulonephritis

Lucia Tejedor-Santamaria, Jose Luis Morgado-Pascual, Laura Marquez-Exposito, Beatriz Suarez-Alvarez, Raul R. Rodrigues-Diez, Antonio Tejera-Muñoz, Vanessa Marchant, Sergio Mezzano, Carlos López-Larrea, Anna Sola, Gema Maria Fernandez-Juarez, Alberto Ortiz, Sandra Rayego-Mateos, Marta Ruiz-Ortega

Subject: Life Sciences, Molecular Biology Keywords: crescentic glomerulonephritis; BET proteins; NOTCH; GREMLIN; Chronic kidney disease; Bromodomain

Online: 23 December 2021 (14:40:45 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0290.v2

Epigenetic Modulation of Gremlin-1/NOTCH Pathway in Experimental Crescentic Immune-Mediated Glomerulonephritis

Lucia Tejedor-Santamaria, Jose Luis Morgado-Pascual, Laura Marquez-Exposito, Beatriz Suarez-Alvarez, Raul R. Rodrigues-Diez, Antonio Tejera-Muñoz, Vanessa Marchant, Sergio Mezzano, Carlos López-Larrea, Anna Sola, Gema Maria Fernandez-Juarez, Alberto Ortiz, Sandra Rayego-Mateos, Marta Ruiz-Ortega

Subject: Life Sciences, Molecular Biology Keywords: crescentic glomerulonephritis; BET proteins; NOTCH; GREMLIN; Chronic kidney disease; Bromodomain

Online: 20 December 2021 (15:48:29 CET)

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Preprint COMMUNICATION | doi:10.20944/preprints202112.0300.v1

Current and Future Methodology for Quantitation and Site-specific Mapping the Location of DNA Adducts

Gunnar Boysen, Intawat Nookaew

Subject: Life Sciences, Molecular Biology Keywords: DNA adducts; nanopore; Oxford Nanopore Technology; mass spectrometry; adductomics; exposome

Online: 20 December 2021 (09:53:53 CET)

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Preprint ARTICLE | doi:10.20944/preprints202112.0290.v1

Epigenetic Modulation of Gremlin-1/NOTCH Pathway in Experimental Crescentic Immune-Mediated Glomerulonephritis

Lucia Tejedor-Santamaria, Jose Luis Morgado-Pascual, Laura Marquez-Exposito, Beatriz Suarez-Alvarez, Raul R. Rodrigues-Diez, Antonio Tejera-Muñoz, Vanessa Marchant, Sergio Mezzano, Carlos López-Larrea, Anna Sola, Gema Maria Fernandez-Juarez, Alberto Ortiz, Sandra Rayego-Mateos, Marta Ruiz-Ortega

Subject: Life Sciences, Molecular Biology Keywords: crescentic glomerulonephritis; BET proteins; NOTCH; GREMLIN; Chronic kidney disease; Bromodomain

Online: 17 December 2021 (14:35:42 CET)

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Preprint REVIEW | doi:10.20944/preprints202111.0545.v1

Paving Therapeutic Avenues for FOXG1 Syndrome: Untangling Genotypes and Phenotypes from a Molecular Perspective

Ipek Akol, Fabian Gather, Tanja Vogel

Subject: Life Sciences, Molecular Biology Keywords: Rett syndrome; FOXG1; FOXG1 syndrome; Neurodevelopmental disorders; Disease modelling; hiPSCs; Brain development; Cerebral organoids

Online: 29 November 2021 (15:29:13 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0539.v1

Delineation of the Ancestral Tus-Dependent Replication Fork Trap

Casey Toft, Morgane Moreau, Jiri Perutka, Savitri Mandapati, Peter Enyeart, Alanna Sorenson, Andrew D. Ellington, Patrick Schaeffer

Subject: Life Sciences, Molecular Biology Keywords: Replication fork trap; Tus-Ter; dif; ChIP-Seq; GC-skew; Enterobacterales

Online: 29 November 2021 (12:52:31 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0381.v1

Inverse Boltzmann Iterative Multi-Scale Molecular Dynamics Study between Carbon Nanotubes and Amino Acids

Wanying Huang, Xinwen Ou, JunYan Luo

Subject: Life Sciences, Molecular Biology Keywords: Multi-scale molecular dynamics； IBI； CBNs

Online: 22 November 2021 (11:08:58 CET)

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Preprint REVIEW | doi:10.20944/preprints202111.0317.v1

Histone Modifications and Their Targeting in Lymphoid Malignancies

Miranda Fernández-Serrano, René Winkler, Juliana Carvalho Santos, Marguerite-Marie Le Pannérer, Marcus Buschbeck, Gaël Roué

Subject: Life Sciences, Molecular Biology Keywords: Non-Hodgkin lymphoma; Epigenetics; DNA methylation; HAT; HDAC; EZH2; bromodomain inhibitors; Drug combination; clinical testing

Online: 17 November 2021 (23:45:00 CET)

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Preprint REVIEW | doi:10.20944/preprints202111.0164.v1

Structure, Activity, and Function of SETMAR protein Lysine Methyltransferase

Michael Tellier

Subject: Life Sciences, Molecular Biology Keywords: SETMAR; Metnase; H3K36me2; Hsmar1; non-homologous end joining repair; NHEJ; transposase; transposable elements; histone; methyltransferase

Online: 9 November 2021 (11:30:21 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0107.v1

Dealing with the Ambiguity of Glycan Substructure Search

Vincenzo Daponte, Catherine Hayes, Julien Mariethoz, Frederique Lisacek

Subject: Life Sciences, Molecular Biology Keywords: Glycan structure; Knowledge representation; Pattern recognition; Ontology; Semantic web

Online: 5 November 2021 (08:34:05 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0082.v1

Heat Shock Factor 1 Directly Regulates Postsynaptic Scaffolding PSD-95 in Aging and Huntington’s Disease and Influences Striatal Synaptic Density

Nicole Zarate, Taylor A Intihar, Dahyun Yu, Jacob Sawyer, Wei Tsai, Maha Syed, Luke Carlson, Rocio Gomez-Pastor

Subject: Life Sciences, Molecular Biology Keywords: HSF1; PSD-95; aging; Huntington’s disease

Online: 3 November 2021 (14:08:46 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0066.v1

Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX With Its Interactors at the Nucleoid and RNA Granule

Jana Key, Sylvia Torres-Odio, Nina C. Bach, Suzana Gispert, Gabriele Koepf, Marina Reichlmeir, A. Phillip West, Holger Prokisch, Peter Freisinger, William G. Newman, Stavit Shalev, Stephan A. Sieber, Ilka Wittig, Georg Auburger

Subject: Life Sciences, Molecular Biology Keywords: Leukodystrophy; Ataxia; Parkinson’s disease; HARS2, LARS2; TWNK; ERAL1; ClpB

Online: 3 November 2021 (08:40:03 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0049.v1

C57BL/6 Background Attenuates mHTT Toxicity in the Striatum of YAC128 Mice

Michaela Kerstin Back, Johanna Kurzawa, Sonia Ruggieri, Jakob von Engelhardt

Subject: Life Sciences, Molecular Biology Keywords: Huntington’s disease; YAC128; HdhQ150; strain background; C57BL/6; synaptic pathology; extrasynaptic NMDAR

Online: 2 November 2021 (12:11:26 CET)

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Preprint ARTICLE | doi:10.20944/preprints202111.0013.v1

CRISPR/Cas9-Mediated Gene-Knockout of UPF3B Alters Expression of Cell Cycle and Neuron-Specific Genes

Pratap Chandra, Bhagyashree Deka, Sweta Kumari, Ayushi Rehman, Priyanka Yadav, Kusum K. Singh

Subject: Life Sciences, Molecular Biology Keywords: Nonsense-mediated mRNA Decay; UPF3B-knockout; RNA-Sequencing; Intellectual disability; Neuro-developmental disorders

Online: 1 November 2021 (12:17:15 CET)

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Preprint ARTICLE | doi:10.20944/preprints202110.0396.v1

Genetic Diversity of Cassava (Manihot esculenta Crantz) in Ecuador by Using SSR Markers

Nelly Paredes, Valeria Alulema, Luis Lima, Marten Sørensen, and Álvaro Monteros-Altamirano

Subject: Life Sciences, Molecular Biology Keywords: SSR; variability; ethnobotany

Online: 26 October 2021 (17:31:55 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0344.v1

gp120 Alters Its Conformation to Enhance Evasiveness and Infectivity

Joseph A. Ayariga, Logan Gildea, Ayodeji Ipimoroti, Qiana L. Matthews

Subject: Life Sciences, Molecular Biology Keywords: Glycoprotein; gp120; HIV-1; conformation; immunity

Online: 25 October 2021 (11:50:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202110.0211.v1

The Past, the Present, and the Future of the Size Exclusion Chromatography in Extracellular Vesicles Separation

Hussein Kaddour, Malik Tranquille, Chioma M. Okeoma

Subject: Life Sciences, Molecular Biology Keywords: Extracellular Vesicles (EVs); Exosomes; Size Exclusion Chromatography (SEC); gradient Size Exclusion Chromatography (gSEC); Ion Exchange Chromatography; Hybrid Chromatography

Online: 14 October 2021 (10:23:28 CEST)

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Working Paper REVIEW

EHMT2/G9a as an Epigenetic Target in Pediatric and Adult Brain Tumors

Barbara Kunzler Souza, Natalia Hogetop Freire, Mariane Jaeger, Caroline Brunetto de Farias, Algemir Lunardi Brunetto, André T. Brunetto, Rafael Roesler

Subject: Life Sciences, Molecular Biology Keywords: G9a; EHMT2; glioblastoma; medulloblastoma; epigenetics; brain tumor

Online: 8 October 2021 (10:57:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202110.0001.v1

Identification of Key Proteins in the Alternative Lengthening of Telomeres Associated Promyelocytic Leukemia Nuclear Bodies

Isaac Armendáriz-Castillo, Katherine Hidalgo-Fernández, Andy Pérez-Villa, Jennyfer García-Cárdenas, Andrés López-Cortés, Santiago Guerrero

Subject: Life Sciences, Molecular Biology Keywords: ALT; PML; Telomeres; Pan-Cancer; TCGA

Online: 1 October 2021 (08:18:18 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0454.v1

Comprehensive Analysis of CPA4 as a Poor Prognostic Biomarker Correlated with Immune Cells Infiltration in Bladder Cancer

Chengcheng Wei, Yuancheng Zhou, Qi Xiong, Ming Xiong, Zhaohui Chen

Subject: Life Sciences, Molecular Biology Keywords: CPA4; Bladder Urothelial Carcinoma; Immune cells; T cell exhaustion; checkpoint

Online: 27 September 2021 (16:02:31 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0401.v1

Relationships Between Mitochondrial Function, AMPK and TORC1 Signalling in Lymphoblasts with Premutation Alleles of the FMR1 Gene

Paul Fisher, Claire Y Allan, Oana Sanislav, Anna Atkinson, Kevin Ngoie, Bruce Kemp, Elsdon Storey, Danuta Loesch, Sarah J Annesley

Subject: Life Sciences, Molecular Biology Keywords: AMPK; TOR Complex I; mitochondria; FMR1; Fragile X-associated Tremor/Ataxia Syndrome (FXTAS); CGG trinucleotide repeat

Online: 23 September 2021 (11:10:47 CEST)

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The X-linked FMR1 gene contains a non-coding trinucleotide repeat in its 5’ region that in normal, healthy individuals contains 20-44 copies. Large expansions of this region (>200 copies) cause fragile X syndrome (FXS), but expansions of 55-199 copies (referred to as premutation alleles) predispose carriers to a neurodegenerative disease called fragile X-associated tremor/ataxia syndrome (FXTAS). The cytopathological mechanisms underlying FXTAS are poorly understood, but abnormalities in mitochondrial function are believed to play a role. We previously reported that lymphoblastoid cell lines (LCLs, or lymphoblasts) of premutation carriers have elevated mitochondrial respiratory activities. In the carriers, especially those not clinically affected with FXTAS, AMPK activity was shown to be elevated. In the FXTAS patients, however, it was negatively correlated with brain white matter lesions, suggesting a protective role in the molecular mechanisms. Here we report an enlarged and extended study of mitochondrial function and associated cellular stress-signalling pathways in lymphoblasts isolated from male and female premutation carriers, regardless of their clinical status, and healthy controls. The results confirmed the elevation of AMPK and mitochondrial respiratory activities and reduction of reactive O2 species (ROS) levels in premutation cells and revealed for the first time that TORC1 activities are reduced. Extensive correlation, multiple regression and Principal Components analysis revealed the best fitting statistical explanations of these changes in terms of the other variables measured. These suggested which variables might be the most “proximal” regulators of the others in the extensive network of known causal interactions amongst the measured parameters of mitochondrial function and cellular stress signalling. In the resulting model, the premutation alleles activate AMPK and inhibit both TORC1 and ROS production, the reduced TORC1 activity contributes to activation of AMPK activation and of nonmitochondrial metabolism, and the higher AMPK activity results in elevated catabolic metabolism, mitochondrial respiration and ATP steady state levels. In addition the results suggest a separate CGG repeat number-dependent elevation of TORC1 activity that is insufficient to overcome the inhibition of TORC1 in premutation cells, but may presage the previously reported activation of TORC1 in FXS cells.

Preprint REVIEW | doi:10.20944/preprints202109.0242.v1

The landscape of PDK1 in Breast Cancer

Na Wang, Jianjiang Fu, Zhihua Li, Ningni Jiang, Yanhong Chen, Juan Peng

Subject: Life Sciences, Molecular Biology Keywords: PDK1; breast cancer; survival; prognosis; targeted therapy

Online: 14 September 2021 (14:51:06 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0189.v1

Epigenetic Clock, Circadian Rhythms and Cell Aging

Ekaterina Samoilova, Vladimir Belopasov, Evgenia Ekusheva, Chao Zhang, Alexander Troitskiy, Vladimir Baklaushev

Subject: Life Sciences, Molecular Biology Keywords: circadian clock; epigenetic clock; aging; senescence; reprogramming; methylome; DNA methylation; CpG-islands; induced pluripotent stem cells

Online: 10 September 2021 (15:13:04 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints202109.0183.v1

CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin

Annelien Morlion, Eva Hulstaert, Jasper Anckaert, Celine Everaert, Jo Vandesompele, Pieter Mestdagh

Subject: Life Sciences, Molecular Biology Keywords: bioinformatics; circRNA

Online: 10 September 2021 (11:17:04 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0182.v1

Organoids: An Emerging Tool To Study Aging Signature Across Human Tissues. Modeling Aging With Patient-derived Organoids

Margalida Torrens-Mas, Catalina Perello-Reus, Cayetano Navas-Enamorado, Lesly Ibargüen, Andres Sanchez -Polo, Juan Jose Segura-Sampedro, Lluís Masmiquel, Carles Barcelo, Marta Gonzalez-Freire

Subject: Life Sciences, Molecular Biology Keywords: organoids; aging; precision medicine.

Online: 10 September 2021 (11:07:13 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0109.v1

Convergent Canonical Pathways in Autism Spectrum Disorder from Proteomic, Transcriptomic and DNA Methylation Data

Caitlyn Mahony, Colleen O'Ryan

Subject: Life Sciences, Molecular Biology Keywords: proteomics; transcriptomics; DNA methylation; mitochondria; metabolism; OXPHOS; ASD; neurogenesis; gliosis; neurodevelopment

Online: 6 September 2021 (17:14:37 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0073.v1

Mitochondrial Dysfunction: a Notable Contributor to the Progression of Alzheimer’s & Parkinson’s Disease

Abolaji Samson Olagunju, Abiola Adeyanju Alagbe, Titilayomi Ayomide Otenaike, Babatunde Oladayo Fabiyi, John Oluwafemi Teibo, Naeem Qusty, Safaa Qusti, Eida Mohammed Alshammari, Gaber El-Saber Batiha, Olabode Omotoso

Subject: Life Sciences, Molecular Biology Keywords: Mitochondrial dysfunction; Alzheimer's disease; Parkinson's disease; Neurodegeneration; Amyloid beta; Parkin

Online: 3 September 2021 (16:01:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints202109.0041.v1

Mechanisms of Connexin Mimetic Peptides

D. Ryan King, Meghan W. Sedovy, Xinyan Leng, Jianxiang Xue, Samy Lamouille, Michael Koval, Brant E. Isakson, Scott R. Johnstone

Subject: Life Sciences, Molecular Biology Keywords: connexin; gap junction; hemichannel; pannexin; peptide; cell signaling

Online: 2 September 2021 (13:38:54 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202109.0013.v1

Construction of a Novel Chimeric Dextransucrase Fused to the Carbohydrate-Binding Module CBM2a

Reinaldo Fraga Vidal, Roberto Carlos Aristicas Ribalta, Lisandra Teresa Martínez Valdés, Meinardo Lafargue Gámez, Amanda Montes Alvarez, Arianne Rubio Sánchez, Eric Dubreucq, Benoit Moreau

Subject: Life Sciences, Molecular Biology Keywords: dextransucrases; GH70; lactic acid bacteria; sucrose-active enzymes; carbohydrate binding module; glucansucrase; cellulose binding domain; Leuconostoc

Online: 1 September 2021 (12:12:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints202108.0335.v1

EHMT2/G9a as an Epigenetic Target in Pediatric and Adult Brain Tumors

Barbara Kunzler Souza, Natalia Hogetop Freire, Mariane Jaeger, Caroline Brunetto de Farias, Algemir Lunardi Brunetto, André T. Brunetto, Rafael Roesler

Subject: Life Sciences, Molecular Biology Keywords: G9a; EHMT2; glioblastoma; medulloblastoma; epigenetics; brain tumor

Online: 16 August 2021 (12:31:31 CEST)

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Preprint REVIEW | doi:10.20944/preprints202108.0283.v1

Recent Expeditious Growth of Type 1 Diabetes in the Gulf Arab Countries

Mohamed Jahromi, Mona Al Sheikh, Jaakko Tuomilehto

Subject: Life Sciences, Molecular Biology Keywords: Type 1 diabetes; human leukocyte antigen; Kuwait Type 1 Diabetes Study; Islet autoantibodies; Insulin; prediction

Online: 13 August 2021 (08:19:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints202108.0058.v1

Genetic and Epigenetic Variations of SARS-Cov-2 and Host Genes and Their Impact in Covid-19 Pandemic

Muhammed Elayadeth Meethal, Punnoth Poonkuzhi Naseef, Mohamed Saheer Kuruniyan, Mansoor C Abdulla, Shyju Ollakkod, Shahul Ebrahim, Godavarma Girish Varma

Subject: Life Sciences, Molecular Biology Keywords: SARS-CoV-2; COVID-19; Phylogenetic analysis; Next generation sequence analysis; Virus-Host interaction; Immunology; Antiviral agents; Vaccine; Virus diagnosis

Online: 2 August 2021 (16:17:24 CEST)

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Preprint REVIEW | doi:10.20944/preprints202106.0145.v1

Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs

Chao Zeng, Atsushi Takeda, Kotaro Sekine, Naoki Osato, Tsukasa Fukunaga, Michiaki Hamada

Subject: Life Sciences, Molecular Biology Keywords: Repetitive element; Transposable element; Non-coding RNA; ncRNA; Functional element; Bioinformatics

Online: 4 June 2021 (15:33:17 CEST)

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Preprint REVIEW | doi:10.20944/preprints202105.0513.v1

Cell Penetrating Peptides: Applications in Tumor Diagnosis and Therapeutics

Jeffrey William Stiltner, Kayla Anne McCandless, Maliha Zahid

Subject: Life Sciences, Molecular Biology Keywords: Cell penetrating peptides; protein transduction domains; tumor imaging; targeted therapies.

Online: 21 May 2021 (09:44:48 CEST)

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Since their identification over twenty-five years ago, the plethora of cell penetrating peptides (CPP) and their applications has skyrocketed. These 5 to 30 amino acid long peptides have the unique property of breaching the cell membrane barrier while carrying cargoes larger then themselves into cells in an intact, functional form. CPPs can be conjugated to fluorophores, activatable probes, radioisotopes or contrast agents for imaging tissues, such as tumors. There is no singular mechanism for translocation of CPPs into a cell, and therefore, many CPPs are taken up by a multitude of cell types, creating the challenge of tumor specific translocation and hindering clinical effectiveness. Varying strategies have been developed to combat this issue and enhance their diagnostic potential by derivatizing CPPs for better targeting by constructing specific cell activated forms. These methods are currently being used to image integrin expressing tumors, breast cancer cells, human histiocytic lymphoma and protease secreting fibrosarcoma cells, to name a few. Additionally, identifying safe, effective therapeutics for malignant tumors has long been an active area of research. CPPs can circumvent many of the complications found in treating cancer with conventional therapeutics by targeted delivery of drugs into tumors, thereby decreasing off-target side effects, a feat not achievable by currently employed conventional chemotherapeutics. Myriad types of chemotherapeutics such as tyrosine kinase inhibitors, anti-tumor antibodies and nanoparticles can be functionally attached to these peptides leading to the possibility of delivering established and novel cancer therapeutics directly to tumor tissue. While much research is needed to overcome potential issues with these peptides, they offer a significant advancement over current mechanisms to treat cancer. In this review, we present a brief overview of the research leading to identification of CPPs with a comprehensive state of the art review on the role of these novel peptides in both cancer diagnostics as well as therapeutics.

LIFE SCIENCES