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Preprint ARTICLE | doi:10.20944/preprints202003.0356.v1

Initial Review and Analysis of COVID-19 Host Genetics and Associated Phenotypes

Yosuke Tanigawa, Manuel Rivas

Subject: Life Sciences, Genetics Keywords: COVID-19; SARS-CoV-2; host genetics; genetics; polygenic risk score

Online: 24 March 2020 (08:36:20 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0258.v1

Asians and Other Races Express Similar Levels of and Share the Same Genetic Polymorphisms of the SARS-CoV-2 Cell-Entry Receptor

Ying Chen, Kejia Shan, Wenfeng Qian

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; cell-entry receptor; ACE2 expression; The Cancer Genome Atlas; susceptibility; demographic factors; race

Online: 18 February 2020 (06:40:01 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0258.v2

Asians Do Not Exhibit Elevated Expression or Unique Genetic Polymorphisms for ACE2, the Cell-Entry Receptor of SARS-CoV-2

Ying Chen, Kejia Shan, Wenfeng Qian

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; cell-entry receptor; ACE2; The Cancer Genome Atlas; susceptibility; demographic factors; polymorphism

Online: 25 February 2020 (06:30:17 CET)

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Preprint ARTICLE | doi:10.20944/preprints202003.0360.v1

Transcriptional Inhibition of Host Viral Entry Proteins as a Therapeutic Strategy for SARS-CoV-2

Xinchen Wang, Ryan Dhindsa, Gundula Povysil, Anthony Zoghbi, Joshua Motelow, Joseph Hostyk, David Goldstein

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; transcriptional inhibition; COVID-19; drug repurposing; TMPRSS2

Online: 24 March 2020 (14:26:57 CET)

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Preprint ARTICLE | doi:10.20944/preprints201809.0139.v1

Six Fractal Codes of Biological Life:perspectives in Exobiology, Cancers Basic Research and Artificial Intelligence Biomimetism Decisions Making

Jean Claude Perez

Subject: Life Sciences, Genetics Keywords: /

Online: 7 September 2018 (13:30:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202003.0360.v2

TMPRSS2 Transcriptional Inhibition as a Therapeutic Strategy for COVID-19

Xinchen Wang, Ryan Dhindsa, Gundula Povysil, Anthony Zoghbi, Joshua Motelow, Joseph Hostyk, Nicholas Nickols, Matthew Rettig, David B. Goldstein

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; transcriptional inhibition; COVID-19; drug repurposing; TMPRSS2

Online: 28 April 2020 (09:39:02 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202204.0196.v1

Omicron Sublineages Current Status in Ecuador

Andrés Carrazco-Montalvo, Andrés Herrera-Yela, Damaris Alarcón-Vallejo, Diana Gutiérrez-Pallo, Isaac Armendáriz-Castillo, Derly Andrade-Molina, Karen Muñoz-Mawyin, Juan Carlos Fernández-Cadena, Gabriel Morey-León, Paúl Cárdenas, Rubén Armas-Gonzalez, Leandro Patiño

Subject: Life Sciences, Genetics Keywords: COVID-19; Omicron; Sublineages; Ecuador

Online: 21 April 2022 (08:24:19 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0332.v2

Witnessing Evolution of SARS-CoV-2 through Comparative Phylogenomics: The Proximate Origin is Guangdong, not Wuhan

Özgül Doğan, Ertan Mahir Korkmaz, Mahir Budak, Battal Çıplak, Hasan Hüseyin Başıbüyük

Subject: Life Sciences, Genetics Keywords: coronavirus; substitution rate; positive selection; demographic dynamics

Online: 21 June 2020 (16:10:26 CEST)

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A new form of coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) is currently causing a pandemic. A six-month evolutionary history of SARS-CoV-2 is witnessed by characterising the total genome of 821 samples using comparative phylogenomic approaches. Our analyses produced striking inclusive results that may guide scientists/professionals for the past/future of pandemic. Phylogenetic and time estimation analyses suggest the proximate origin of pandemic strain as Guangdong and the origin time as first half of September 2019, not Wuhan and December 2019, respectively. The viral genome experienced a substitution rate similar to other RNA viruses, but it is particularly high in some of the peptides encoding sequences such as leader protein, E gene, orf8, orf10, nsp10, N gene, S gene and M gene and nsp4, while low in nsp11, orf7a, 3C-like proteinase, nsp9, nsp8 and endoRNase. Most strikingly, the divergence rate of amino acid sequences is high proportional to nucleotide divergence. Additionally, specific non-synonymous mutations in nsp3 and nsp6 evolved under positive selection. The exponential growth rate (r), doubling time (Td) and R₀ were estimated to be 47.43 per year, 5.39 days and 2.72, respectively. Comparison of synapomorphies distinguishing the SARS-CoV-2 and the candidate ancestor bat coronavirus indicates that mutation pattern in nsp3 and S gene enabled the new strain to invade human and become a pandemic strain. We arrive at the following main conclusions: (i) six months evolution of viral genome is nearly neutral, (ii) origin of pandemic is not Wuhan and predates formal reports, (iii) although viral population is ongoing an exponential growth, the doubling time is evolving towards shortening, and (iv) divergence rate of total genome is similar to other RNA viruses, but it is prominently high in some genes while low in some others and evolution in these genes should be closely monitored as their protein products intervening to pathogenicity, virulence and immune response.

Preprint ARTICLE | doi:10.20944/preprints201701.0127.v3

Evidence for Recent Polygenic Selection on Educational Attainment and Underlying Cognitive Abilities Inferred from GWAS Hits: A Monte Carlo Simulation Using Random SNPs

Davide Piffer

Subject: Life Sciences, Genetics Keywords: educational attainment; polygenes; polygenic selection; IQ; GWAS

Online: 23 May 2017 (17:08:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201706.0039.v1

Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from GWAS Hits: A Replication of Previous Findings Using Recent Data

Davide Piffer

Subject: Life Sciences, Genetics Keywords: educational attainment; polygenes; polygenic selection; IQ; GWAS

Online: 8 June 2017 (08:11:07 CEST)

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Preprint REVIEW | doi:10.20944/preprints201904.0149.v1

Durum Wheat (Triticum durum Desf.) Origin, Cultivation, and Potential Expansion in Sub-Saharan Africa

Amadou Tidiane Sall, Tiberio Chiari, Wasihun Legesse, Kemal Seid-Ahmed, Rodomiro Ortiz, Maarten Van Ginkel, Filippo Maria Bassi

Subject: Life Sciences, Genetics Keywords: Agro-industry; Ethiopia; oasis wheat; pasta wheat; Senegal River; value chain

Online: 12 April 2019 (11:04:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0397.v1

Genetic Uniformity of a Specific Region in SARS-CoV-2 Genome and In-Silico Target-Oriented Repurposing of N-Acetyl-D-Glucosamine

Omur Baysal, Ragip Soner Silme, Cagatay Karaaslan

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; Drug repurposing; N-acetyl-D-glucosamine; ORF1ab; Biodata mining; Protein modelling

Online: 24 May 2020 (18:49:41 CEST)

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Working Paper ARTICLE

SARS-CoV-2 Infection of Cats and Dogs?

Min Shen, Chao Liu, Run Xu, Zijing Ruan, Shiying Zhao, Huidong Zhang, Wen Wang, Xinhe Huang, Li Yang, Yong Tang, Tai Yang, Xu Jia

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; angiotensin-converting enzyme 2 (ACE2); animal reservoir; cross-species transmission; cats

Online: 8 April 2020 (04:43:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0127.v2

Can We Detect Polygenic Selection on Cognitive Ability Using GWAS Hits? Employing Random SNPs as a Null Model.

Davide Piffer

Subject: Life Sciences, Genetics Keywords: GWAS; educational attainment; polygenic selection

Online: 29 January 2017 (07:55:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints201806.0201.v1

The Critical Needs and Challenges for Genetic Architecture Studies in Africa

Alicia R. Martin, Solomon Teferra, Marlo Möller, Eileen G. Hoal, Mark J. Daly

Subject: Life Sciences, Genetics Keywords: genetic architecture; Africa; GWAS; health disparities

Online: 13 June 2018 (11:17:04 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201610.0054.v1

Functional and Regulatory Profiling of Energy Metabolism in Fission Yeast

Michal Malecki, Danny A. Bitton, Maria Rodriguez-Lopez, Charalampos Rallis, Noelia Garcia Cavalia, Graeme C. Smith, Jurg Bahler

Subject: Life Sciences, Genetics Keywords: energy metabolism; respiration; fermentation; auxotrophy; retrograde response

Online: 14 October 2016 (10:58:50 CEST)

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Background: The control of energy metabolism is fundamental for cell growth and function, and anomalies are implicated in complex diseases and ageing. It is important for cells to carefully tune metabolic pathways to optimize their function in response to different nutrient or physiological conditions. Metabolism in yeast cells can be easily manipulated by supplying different carbon sources: on glucose yeast rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration. Results: We screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth. The growth medium and auxotrophic mutants strongly influenced respiratory metabolism. Most genes uncovered in the mutant screens have not been implicated in respiration in budding yeast. We applied gene expression profiling approaches to compare steady-state fermentative and respiratory growth and to analyse the dynamic adaptation to respiratory growth. The transcript levels of most genes functioning in key energy metabolism pathways were coherently tuned, reflecting anticipated differences in metabolic flows between fermenting and respiring cells. We show that the acetyl-CoA synthase, rather than the citrate lyase, is essential for acetyl-CoA synthesis in fission yeast. We also investigated the transcriptional response to mitochondrial damage by genetic or chemical perturbations, defining a retrograde response that involves the concerted regulation of distinct groups of nuclear genes that may avert harm from mitochondrial malfunction. Conclusions: These systematic and targeted analyses provide a rich framework of the genetic and regulatory basis of fundamental metabolic states to guide future studies on energy metabolism in fission yeast and beyond. Our study pinpoints weaknesses of commonly used auxotroph mutants for investigating energy metabolism. As a model for cellular energy regulation, fission yeast provides an attractive and complementary system to budding yeast.

Preprint REVIEW | doi:10.20944/preprints201710.0065.v1

How to Clear HBV cccDNA: CRISPR/Cas9 Might Be Promising

Yan Qiu, Ying Liu, Wen Ren, Jing Ren

Subject: Life Sciences, Genetics Keywords: hepatitis B virus; chronic hepatitis B; cccDNA; CRISPR/Cas9; gene therapy

Online: 10 October 2017 (17:59:11 CEST)

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Working Paper REVIEW

DNA Based Methods in Intelligence - Moving Towards Metagenomics

Gabriella Mason-Buck, Alexandra Graf, Eran Elhaik, Jake Robinson, Ewelina Pospiech, Manuela Oliveira, Josef Moser, Patrick K. H. Lee, Dedan Githae, David Ballard, Yana Bromberg, Carlos S. Casimiro-Soriguer, Eliza Dhungel, Tae-Hyuk Ahn, Jolanta Kawulok, Carlos Loucera, Feargal Ryan, Alejandro R. Walker, Chengsheng Zhu, Christopher E. Mason, António Amorim, Denise Syndercombe Court, Wojciech Branicki, Pawel Labaj

Subject: Life Sciences, Genetics Keywords: forensic; metagenomics

Online: 12 February 2020 (12:21:43 CET)

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Preprint BRIEF REPORT | doi:10.20944/preprints202110.0080.v2

SARS-CoV-2 and MERS-CoV Share the Furin Site CGG-CGG Genetic Footprint

Antonio R. Romeu

Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; MERS-CoV; arginine dimer; polybasic furin cleavage site; aginine codon; Markov model; bioinformatics

Online: 14 October 2021 (13:08:25 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201801.0266.v2

Can Genetics Predict Sports Injury? The Association of the Genes GDF5, AMPD1, COL5A1 and IGF2 on Soccer Player Injury Occurrence

Kiah McCabe, Christopher Collins

Subject: Life Sciences, Genetics Keywords: genetics; injury; sport; soccer; DNA; inflammation; football

Online: 9 February 2018 (02:24:40 CET)

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Preprint ARTICLE | doi:10.20944/preprints201610.0021.v1

Zinc Finger and X-Linked Factor (ZFX) Binds to Human SET Transcript 2 Promoter and Transactivates SET Expression

Siliang Xu, Shi-Wen Jiang, Fengbiao Guo, Tristan Senkowski, Jinping Li, Haibin Chen, Alberto Romero, Yugui Cui, Jiayin Liu

Subject: Life Sciences, Genetics Keywords: SET; I2PP2A; ZFX; transcriptional regulation; gynecologic cancers

Online: 8 October 2016 (10:52:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201709.0007.v1

Chromosome pairing and recombination in male hybrids between two chromosome races of the common shrew (Sorex araneus L., Soricidae, Eulipotyphla)

Nadezhda M. Belonogova, Andrei V. Polyakov, Tatyana V. Karamysheva, Anna A. Torgasheva, Jeremy B. Searle, Pavel Borodin

Subject: Life Sciences, Genetics Keywords: common shrew; meiotic chromosomes; Sorex araneus; synaptonemal complex; hybrids; MLH1

Online: 1 September 2017 (22:49:10 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201609.0080.v1

Determination of Genetic Variations of Toll-like Receptor (TLR) 2, 4 and 6 with Next Generation Sequencing in Native Cattle Breeds of Anatolia and Holstein Friesian

Nuket Bilgen, Bengi Cinar Kul, Victoria Offord, Dirk Werling, Okan Ertugrul

Subject: Life Sciences, Genetics Keywords: Anatolian Black; East Anatolian Red; South Anatolian Red; Turkish Grey; Holstein Friesian; Innate immunity; Next Generation Sequencing; TLR2; TLR4; TLR6

Online: 23 September 2016 (05:44:43 CEST)

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Preprint REVIEW | doi:10.20944/preprints202002.0068.v1

Mechanisms of Change: Unraveling the Roles of Modularity and Pleiotropy in Diversification

James J. Lewis, Steven M. Van Belleghem

Subject: Life Sciences, Genetics Keywords: cis-regulatory element; developmental modularity; evolutionary modularity; Heliconius

Online: 5 February 2020 (14:02:51 CET)

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Preprint ARTICLE | doi:10.20944/preprints201907.0120.v1

Epigenetics Theoretical Limits of Synthetic Genomes: The Cases of Artificials Caulobacter (C. eth-2.0), Mycoplasma Mycoides (JCVI-Syn 1.0, JCVI-Syn 3.0 and JCVI_3A), E-coli and YEAST chr XII

Jean-claude Perez

Subject: Life Sciences, Genetics Keywords: Synthetic genomes, Epigenetics, Transposons, Biomathematics, Fibonacci numbers

Online: 8 July 2019 (12:53:15 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0332.v1

A Comprehensive Comparative Phylogenomics and Demographic Evolutionary History of the SARS-CoV-2

Özgül Doğan, Ertan Mahir Korkmaz, Mahir Budak, Battal Çıplak, Hasan Hüseyin Başıbüyük

Subject: Life Sciences, Genetics Keywords: coronavirus; origin; substitution rate; positive selection; demographic dynamics

Online: 21 May 2020 (03:27:52 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0284.v1

Proprietary Algorithms for Polygenic Risk: Protecting Scientific Innovation or Hiding the Lack of It?

A. Cecile J.W. Janssens

Subject: Life Sciences, Genetics Keywords: personal genomics, DNA, polygenic, risk, regulation, discrimination, calibration, prediction, transparency, autonomy

Online: 23 May 2019 (16:23:57 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0324.v1

Methods for De-novo Genome Assembly

Arash Bayat, Hasindu Gamaarachchi, Nandan P. Deshpande, Marc R. Wilkins, Sri Parameswaran

Subject: Life Sciences, Genetics Keywords: De-novo Genome Assembly; Short Read Genome Assembly; Long Read Genome Assembly; Hybrid Genome Assembly

Online: 28 June 2020 (08:56:09 CEST)

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Preprint BRIEF REPORT | doi:10.20944/preprints202004.0076.v1

The Expression and Polymorphism of Entry Machinery for COVID-19 in Human: Juxtaposing Population Groups, Gender, and Different Tissues

Behrooz Darbani

Subject: Life Sciences, Genetics Keywords: COVID-19; gender; host entry machinery; polymorphism

Online: 7 April 2020 (02:27:40 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201705.0022.v1

Epigenetic Regulation of A Heat-Activated Retrotransposon in Cruciferous Vegetables

Kosuke Nozawa, Yuki Kawagishi, Akira Kawabe, Mio Sato, Yukari Masuta, Atsushi Kato, Hidetaka Ito

Subject: Life Sciences, Genetics Keywords: heat stress; cruciferae; ONSEN; retrotransposon

Online: 2 May 2017 (04:58:58 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201701.0127.v1

Polygenic Selection, Polygenic Scores, Spatial Autocorrelation and Correlated Allele Frequencies. Can We Model Polygenic Selection on Intellectual Abilities?

Davide Piffer

Subject: Life Sciences, Genetics Keywords: GWAS; educational attainment; polygenic selection

Online: 27 January 2017 (03:55:50 CET)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints201708.0107.v1

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

Corinne Rancurel, Ludovic Legrand, Etienne GJ Danchin

Subject: Life Sciences, Genetics Keywords: horizontal gene transfer; alien index; lateral gene transfer

Online: 31 August 2017 (15:03:30 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints201808.0480.v1

Unexplained Allele-Calling Errors May Account for Apparent Denisovan-Neanderthal F1 Genome

David Curtis

Subject: Life Sciences, Genetics Keywords: Neanderthal; Denisova; genome; allele

Online: 29 August 2018 (04:50:36 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201707.0047.v1

Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L.) in Xinjiang, Northwest China

Chenglin Zhang, Jianbo Zhang, Yan Fan, Ming Sun, Wendan Wu, Wenda Zhao, Xiaopeng Yang, Linkai Huang, Yan Peng, Xiao Ma, Xinquan Zhang

Subject: Life Sciences, Genetics Keywords: Festuca ovina L.; AFLP, genetic diversity; genetic barriers; environmental factors

Online: 18 July 2017 (10:05:56 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0333.v1

Visiting Bitter Gourd (Momordica charantia) from a Breeding Perspective: A Review

Hari Kesh, Prashant Kaushik

Subject: Life Sciences, Genetics Keywords: bitter gourd; breeding; genetic diversity; genomics; heterosis; molecular breeding; mutation breeding

Online: 19 April 2020 (06:00:00 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201710.0050.v1

Impact of Genetic Polymorphism of Sulpha Transferase Genes (SULT1A) Genes on the Risk of Females with Breast Cancer in Jordan

Mona Bustami, Abdel-Ellah Al-Shudifat, Nagham Hussein, Mohannad Yacoub, Eiad Atwa, Israr Sabri, Rania Abu-Hamdah, Walid Abu-Rayyan, Tawfiq Arafat, Adnan Badran, Luay Abu-Qatouseh

Subject: Life Sciences, Genetics Keywords: polymorphism; risk for breast cancer; SULT1A allele

Online: 9 October 2017 (12:34:55 CEST)

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Preprint COMMUNICATION | doi:10.20944/preprints202007.0403.v1

Complete Quantum Information in the DNA Genetic Code

Michel Planat, Raymond Aschheim, Marcelo Amaral, Fang Fang, Klee Irwin

Subject: Life Sciences, Genetics Keywords: DNA genetic code; informationally complete characters; finite groups,; hyperelliptic curve

Online: 17 July 2020 (16:20:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0016.v1

Molecular Classification of Colorectal Cancer Using Gene Expression Profile of Tumor Samples

Mamoon Rashid, Ramesh K. Vishwakarma, Ahmad Deeb, Mohamed A. Hussein, Mohammad A. Aziz

Subject: Life Sciences, Genetics Keywords: colorectal cancer; gene expression; molecular classification; molecular subtyping

Online: 2 April 2018 (09:55:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints202006.0203.v1

SH-SY5Y-derived Neurons: A Neuronal Model System for Investigating TAU Sorting Mechanisms and Neuronal Subtype-specific TAU Vulnerability

Michael Bell, Hans Zempel

Subject: Life Sciences, Genetics Keywords: SH-SY5Y-derived neurons; TAU sorting; neuronal identity; tauopathy; Alzheimer’s disease

Online: 16 June 2020 (09:41:46 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201801.0266.v1

Can Genetics Predict Sports Injury? The Association of the Genes GDF5, AMPD1, COL5A1 and IGF2 on Soccer Player Injury Occurrence

Kiah McCabe, Christopher Collins

Subject: Life Sciences, Genetics Keywords: injury; soccer; genetics; ankle injuries; knee injuries; dna testing; genes

Online: 29 January 2018 (04:13:08 CET)

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Preprint REVIEW | doi:10.20944/preprints201906.0282.v1

Resistance Components and Interactions of Aphis glycines (Hemiptera: Aphididae) and Heterodera glycines (Tylenchida: Heteroderidae) in Soybean

Surendra Neupane, Jordan Purintun, Febina M Mathew, Adam J Varenhorst, Madhav P Nepal

Subject: Life Sciences, Genetics Keywords: effectors; QTLs; GWAS; resistance; soybean-soybean aphid-soybean cyst nematode interactions

Online: 27 June 2019 (06:24:29 CEST)

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Preprint REVIEW | doi:10.20944/preprints201810.0708.v1

Overview of Genomic Tools for Circular Visualization in next-Generation Genomic Sequencing Era

Alisha Parveen, Sukank Khurana, Abhishek Kumar

Subject: Life Sciences, Genetics Keywords: circular visualization; circos; genomics; next-generation sequencing

Online: 30 October 2018 (07:06:35 CET)

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Preprint HYPOTHESIS | doi:10.20944/preprints202012.0506.v3

The Principle of Continuous Biological Information Flow as the Fundamental Foundation for the Biological Sciences. Implications for Ageing Research

Xavi Marsellach

Subject: Life Sciences, Genetics Keywords: Ageing; Epigenetics

Online: 15 November 2021 (13:34:33 CET)

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Preprint ARTICLE | doi:10.20944/preprints201803.0257.v1

Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data

Katarzyna Ropka-Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Katarzyna Piórkowska, Grzegorz Żak, Artur Gurgul, Natalia Derebecka, Joanna Wesoły

Subject: Life Sciences, Genetics Keywords: RNA-seq; miRNA; pig; NGS; transcript analysis; muscle

Online: 30 March 2018 (06:02:33 CEST)

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Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content. The comparison was performed between whole gene expression and miRNA profiles of muscle tissue collected from two sire-line pig breeds (Piertain, Hampshire). The RNA-seq approach allowed the identification of 627 and 416 differentially expressed genes (DEGs) between pig groups differing in terms of loin weight between Pietrain and Hampshire breeds, respectively. The comparison of miRNA profiles showed differential expression of 57 microRNAs for Hampshire and 34 miRNAs for Pietrain pigs. Next, 43 genes and 18 miRNAs were selected as differentially expressed in both breeds and potentially related to muscle development. According to Gene Ontology analysis, identified DEGs and microRNAs were involved in the regulation of the cell cycle, fatty acid biosynthesis and regulation of the actin cytoskeleton. The most deregulated pathways dependent on muscle mass were the Hippo signalling pathway connected with the TGF-beta signalling pathway and controlling organ size via the regulation of ubiquitin-mediated proteolysis, cell proliferation and apoptosis. The identified target genes were also involved in pathways such as the FoxO signalling pathway, signalling pathways regulating pluripotency of stem cells and the PI3K-Akt signalling pathway. The obtained results indicate molecular mechanisms controlling porcine muscle growth and development. Identified genes (SOX2, SIRT1, KLF4, PAX6 and genes belonging to the transforming growth factor beta superfamily) could be considered candidate genes for determining muscle mass in pigs.

Working Paper HYPOTHESIS

Human Genetic Diversity Possibly Determines Human's Compliance to COVID-19

Yiqiang Zhao, Yunchun Gu, Yongji Liu, Sa Li, Yuzhan Wang, Lina Bu, Qi Liu, Hongyi Lv, Fang Wan, Lida Wu, Zemin Ning

Subject: Life Sciences, Genetics Keywords: COVID-19; severe symptoms; inactivation; genetic diversity

Online: 16 April 2020 (09:15:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0321.v1

Whole Genome Diversity, Population Structure and Linkage Disequilibrium Analysis of Chickpea (Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers

Somayeh Farahani, Mojdeh Maleki, Rahim Mehrabi, Homayoun Kanouni, Reza Talebi

Subject: Life Sciences, Genetics Keywords: chickpea; genetic diversity; linkage disequilibrium; DArTseq-SNP markers

Online: 29 April 2019 (07:56:52 CEST)

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Characterization of genetic diversity, population structure and linkage disequilibrium is prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes including advanced “Kabuli” breeding lines and Iranian landrace “Desi” chickpea genotypes were genotyped using DArTseq-Based SNP markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that covered by SNPs varied from 16236.36 kbp (LG8) to 67923.99 kbp (LG5), while LG4 showed higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6 and LG8 showed higher mean PIC value than average. Un-weighted Neighbor Joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and Discriminant Analysis of Principal Component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r²≥0.8, while 2961 pairs of markers showed complete LD (r²=1) and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggesting the presence of a high genetic diversity among studied chickpea genotypes. This study also demonstrated the efficiency of DArTseq-based SNP genotyping for large scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits such as seed yield, abiotic and biotic stresses and therefore can be efficiently used in breeding programs to improve chickpea.

Preprint ARTICLE | doi:10.20944/preprints201709.0007.v2

Chromosome Synapsis and Recombination in Male Hybrids Between Two Chromosome Races of the Common Shrew (Sorex araneus L., Soricidae, Eulipotyphla)

Nadezhda M. Belonogova, Andrei V. Polyakov, Tatyana V. Karamysheva, Anna A. Torgasheva, Jeremy B. Searle, Pavel Borodin

Subject: Life Sciences, Genetics Keywords: common shrew; meiotic chromosomes; Sorex araneus; synaptonemal complex; hybrids; MLH1

Online: 7 March 2018 (09:24:11 CET)

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Preprint ARTICLE | doi:10.20944/preprints201803.0145.v1

Structural and Functional Analysis of Transposable Elements Focusing on B Chromosomes of the Cichlid Fish Astatotilapia latifasciata

Rafael Coan, Cesar Martins

Subject: Life Sciences, Genetics Keywords: repetitive elements; RNA-Seq; genomics; evolution; cytogenetics; supernumerary elements; extra chromosomes

Online: 19 March 2018 (08:33:48 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0116.v1

Computational Approaches to Functionally Annotate Long Noncoding RNA (lncRNA)

Yashpal Ramakrishnaiah, Levin Kuhlmann, Sonika Tyagi

Subject: Life Sciences, Genetics Keywords: noncoding RNA; lncRNA; epigenomics; gene regulation; machine learning; bioinformatics

Online: 9 June 2020 (04:45:12 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201804.0131.v1

The Genetic Coding System and Unitary Matrices

Sergey Petoukhov

Subject: Life Sciences, Genetics Keywords: genetic code, alphabet, unitary matrix, dyadic shift, decomposition, spectral presentation, fractal, tensor product, quantum informatics

Online: 10 April 2018 (16:20:14 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202008.0718.v1

Clinically Relevant Germline Mutations in a Cohort of Young Women with Breast Cancer: A Comprehensive Analysis of Hereditary-Cancer Genes from Whole-Exome Sequencing

Liliana Gomez-Flores-Ramos, Micheal Dean, Kristine Jones, Mingyi Wang, Cynthia Villarreal-Garza, Rosa María Álvarez-Gómez, Talia Wegman-Ostrosky, Nancy Reynoso-Noverón, Verónica Fragoso-Ontiveros, Luisa Sánchez-Zamorano, Miguel Trujillo-Martínez, Lizbeth Grimaldo, Patricia Gallegos-Arreola, Patricia Ostrosky-Wegman, Alejandro Mohar-Betancourt

Subject: Life Sciences, Genetics Keywords: early-onset breast cancer; hereditary cancer; whole-exome sequencing; young women

Online: 31 August 2020 (09:46:26 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201806.0329.v1

Ethical, Legal and Social Implications of Susceptibility Genetic Testing for Late-Onset Neurodegenerative Diseases

Amaranta Manrique de Lara, Elisa Núñez-Acosta, Garbiñe Saruwatari-Zavala, Liliana Soto-Gómez, Miguel E. Rentería

Subject: Life Sciences, Genetics Keywords: Alzheimer’s disease; Parkinson’s disease; Genetic testing; bioethics

Online: 21 June 2018 (04:38:35 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201907.0051.v1

Identification of Biomarker Signatures and Candidate Drugs in Non-Small Cell Lung Cancer

Amina Rownaq, Md. Parvez Mosharaf, S. M. Shahinul Islam, Md. Nurul Haque Mollah

Subject: Life Sciences, Genetics Keywords: lung cancer; molecular signature; molecular pathway; differentially expressed genes; protein-protein interaction; reporter biomolecules and bioinformatics

Online: 3 July 2019 (08:54:37 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201908.0288.v1

Genomic and Transcriptomic Characterization of the New Human Glioblastoma Cell Line AHOL1

Wallax Augusto Silva Ferreira, Carolina Koury Nassar Amorim, Rommel Rodriguez Burbano, Rolando André Rios Villacis, Fabio Albuquerque Machi, Tiago da Silva Medina, Edivaldo Herculano Correa de Oliveira

Subject: Life Sciences, Genetics Keywords: array-comparative genomic; gliomas; Cell culture; Cancer genomics; Cancer Transcriptomics; brain tumors; cell line; glioblastoma

Online: 27 August 2019 (16:34:22 CEST)

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Preprint REVIEW | doi:10.20944/preprints201811.0571.v2

Revisiting Prostate Cancer in India: A Genomic View

Prameesha Perera, Ayam Gupta, Nidhi Shukla, Mamta Nehra, Mukesh Sharma, Sneha Mishra, Vikram Singh Chauhan, Maneesh Kumar Vijay, Suresh Kumar Jatawa, Archana Tiwari, Krishna Mohan Medicherla, Praveen Mathur, Devendra Sharma, Prashanth Suravajhala

Subject: Life Sciences, Genetics Keywords: prostate cancer; prostate-specific antigen; incidence; genomics; next generation sequencing

Online: 3 April 2019 (10:15:50 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201911.0292.v1

Generation of a Mouse Model Lacking the Non-Homologous End-Joining Factor Mri/Cyren

Sergio Castañeda-Zegarra, Camilla Huse, Øystein Røsand, Antonio Sarno, Mengtan Xing, Raquel Gago-Fuentes, Qindong Zhang, Amin Alirezaylavasani, Julia Werner, Ping Ji, Nina-Beate Liabakk, Wei Wang, Magnar Bjørås, Valentyn Oksenych

Subject: Life Sciences, Genetics Keywords: NHEJ; double-strand breaks; mouse model; lymphocyte; neurodevelopment

Online: 24 November 2019 (15:57:38 CET)

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Preprint ARTICLE | doi:10.20944/preprints201906.0295.v1

Loci Controlling Adaptation to Heat Stress Occurring at the Reproductive Stage in Durum Wheat

Khaoula El Hassouni, Bouchra Belkadi, Amadou Tidiane Sall, Abdelkarim Filali-Maltouf, Ayed Al-Abdallat, Miloudi Mikel Nachit, Filippo Maria Bassi

Subject: Life Sciences, Genetics Keywords: Heat stress; durum wheat; yield; tolerance; fertility; climate change; resilience

Online: 28 June 2019 (11:51:31 CEST)

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Preprint REVIEW | doi:10.20944/preprints201911.0085.v1

Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing

Charles F Rowlands, Diana Baralle, Jamie M Ellingford

Subject: Life Sciences, Genetics Keywords: mendelian disease; diagnostics; variant interpretation; variant prioritization; rna splicing; bioinformatics; machine learning; genomic medicine; effect prediction

Online: 8 November 2019 (04:07:16 CET)

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Preprint ARTICLE | doi:10.20944/preprints202002.0004.v1

Differing Perception of DNA Evidence and Intelligence Capabilities in Criminal Investigations

Nathan Scudder, Sally F. Kelty, Janie Busby Grant, Casey Montgomerie, Simon J. Walsh, James Robertson, Dennis McNevin

Subject: Life Sciences, Genetics Keywords: DNA; phenotyping; intelligence; interpretation

Online: 3 February 2020 (03:27:19 CET)

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Preprint REVIEW | doi:10.20944/preprints201804.0275.v3

Moderate the MAOA-L Allele Expression with CRISPR/Cas9 System

Martin L. Nelwan

Subject: Life Sciences, Genetics Keywords: advanced therapy; aggressive; antisocial; behavior; MAOA

Online: 14 May 2018 (10:46:26 CEST)

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Preprint REVIEW | doi:10.20944/preprints201906.0178.v1

Evaluation of the Genomic Basis for Alzheimer’s and Parkinson’s Diseases

Pratip Rana, Edian F. Franco, Yug Rao, Khajamoinuddin Syed, Debmalya Barh, Vasco Azevedo, Rommel T. J. Ramos, Preetam Ghosh

Subject: Life Sciences, Genetics Keywords: Alzheimer's disease; Parkinson's disease; genetics; gene regulatory network; miRNAs

Online: 18 June 2019 (13:07:49 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201812.0142.v2

Structural Connections between Long Genetic and Literary Texts

Sergey Petoukhov

Subject: Life Sciences, Genetics Keywords: DNA sequences, literary texts, probability, binary opposition, alphabet, tensor product, quantum informatics

Online: 18 February 2019 (17:22:56 CET)

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Preprint ARTICLE | doi:10.20944/preprints201808.0330.v1

Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

Francisco Prosdocimi, Sávio Torres de Farias

Subject: Life Sciences, Genetics Keywords: ancestry of orthogs, ancestry of gene families; gene genealogy; FUCA; LUCA; origins of life; gradualism; evolutionary biology

Online: 18 August 2018 (08:24:09 CEST)

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Preprint REVIEW | doi:10.20944/preprints201811.0018.v1

Methods of CRISPR/Cas9 Exon Skipping for Duchenne Muscular Dystrophy

Kenji Rowel Q. Lim, Chantal Yoon, Toshifumi Yokota

Subject: Life Sciences, Genetics Keywords: Duchenne muscular dystrophy (DMD); CRISPR/Cas9; exon skipping therapy; gene editing; human induced pluripotent stem cells (hiPSCs); immortalized patient muscle cells; mdx mice; humanized dystrophic mouse models; deltaE50-MD dog model

Online: 2 November 2018 (05:14:23 CET)

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Preprint ARTICLE | doi:10.20944/preprints202109.0458.v1

Phenotype from SAMD9 Mutation at 7p21.1 Appears Attenuated by Novel Compound Heterozygous Variants at RUNX2 and SALL1

E. Scott Sills, Samuel H Wood

Subject: Life Sciences, Genetics Keywords: SAMD9; RUNX2; SALL1; ovarian anatomy; renal structure

Online: 28 September 2021 (08:36:59 CEST)

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Preprint CASE REPORT | doi:10.20944/preprints202107.0661.v1

Missense Variation in TPP1 Gene causes Neuronal Ceroid Lipofuscinosis Type 2 in a Family from Jammu and Kashmir-India

Arshia Angural, Kalaiarasan Ponnusamy, Diksha Langeh, Mamta Kumari, Akshi Spolia, Ekta Rai, Ankush Sharma, Kamal Kishore Pandita, Swarkar Sharma

Subject: Life Sciences, Genetics Keywords: CLN2; epilepsy; Jammu and Kashmir; loss of ambulation; neuronal ceroid lipofuscinoses type 2; neuroregression; seizures; TPP1

Online: 29 July 2021 (14:01:16 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201803.0215.v1

Estimation of Genetic Parameters and Prediction of Genotypic Values in Common Beans Using Mixed Models

Jessica Delfini, Vania Moda Cirino, Claudete de Fátima Ruas, Paulo Mauricio Ruas, José dos Santos Neto, Leandro Simões Azeredo Gonçalves

Subject: Life Sciences, Genetics Keywords: Phaseolus vulgaris L.; REML/BLUP; genetic diversity

Online: 26 March 2018 (10:35:00 CEST)

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Preprint REVIEW | doi:10.20944/preprints201805.0160.v1

Unravelling the Roles Of susceptibility Loci for Autoimmune Diseases in the Post-GWAS Era

Jody Ye, Kathleen Gillespie, Santiago Rodriguez

Subject: Life Sciences, Genetics Keywords: complex loci; autoimmune diseases

Online: 10 May 2018 (08:18:44 CEST)

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Preprint REVIEW | doi:10.20944/preprints201806.0191.v1

Recent Developments in Using Drosophila as a Model for Human Genetic Disease

Christine Oriel, Paul Lasko

Subject: Life Sciences, Genetics Keywords: rare disease; functional genomics; genetic variant validation

Online: 12 June 2018 (12:36:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0093.v1

Genome-Wide Association Study for Resistance to the Meloidogyne javanica Causing Root-Knot Nematode in Soybean

Jean Carlos Alekcevetch, André Luiz de Lima Passianotto, Everton Geraldo Capote Ferreira, Adriana Brombini dos Santos, Danielle Cristina Gregório da Silva, Waldir Pereira Dias, François Belzile, Ricardo Vilela Abdelnoor, Francismar Corrêa Marcelino-Guimarães

Subject: Life Sciences, Genetics Keywords: mixed linear model; genotyping-by-sequencing; functional validation; RT-qPCR; resistance genes; GWAS

Online: 7 December 2019 (12:41:39 CET)

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Preprint REVIEW | doi:10.20944/preprints201902.0090.v1

Germline Missense Variants in BRCA1: New Trends and Challenges for Clinical Annotation

Volha Golubeva, Thales Nepomuceno, Alvaro Monteiro

Subject: Life Sciences, Genetics Keywords: BRCA1; variants of uncertain clinical significance; VUS; germline variants; hereditary breast and ovarian cancer; breast cancer; genetic testing, ovarian cancer; variant classification; clinical annotation

Online: 11 February 2019 (16:12:03 CET)

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Preprint REVIEW | doi:10.20944/preprints202109.0220.v1

Advanced in Rootstock Breeding of Nut Trees: Objectives and Strategies

Kourosh Vahdati, Saadat Sarikhani, Mohammad Mehdi Arab, Charles A. Leslie, Abhaya M. Dandekar, Neus Aletà, Beatriz Bielsa, Thomas M. Gradziel, Álvaro Montesinos, María José Rubio-Cabetas, Gina M. Sideli, Ümit Serdar, Burak Akyüz, Gabriele Loris Beccaro, Dario Donno, Mercè Rovira, Louise Ferguson, Mohammad Akbari, Abdollatif Sheikhi, Adriana F. Sestras, Salih Kafkas, AIBIBULA PAIZILA, Mahmoud Reza Roozban, Amandeep Kaur, Srijana Panta, Lu Zhang, Radu E. Sestras, Shawn Mehlenbacher

Subject: Life Sciences, Genetics Keywords: Almond; Persian walnut; Pistachio; Hazelnut; Pecan; Chestnut; grafting; graft compatibility

Online: 13 September 2021 (15:52:06 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0209.v1

Agronomic Practices, Genetic Diversity and Population Structure of Moringa oleifera (Lam.) in Nigeria

Jacob Popoola, David Igwe, Opeyemi Jegede, Victoria Iwu, Adegoke Adegbite, Conrad Omonhinmin

Subject: Life Sciences, Genetics Keywords: agronomic practices; agrobiodiversity; aflp; climate change; cluster analysis; genetic diversity; moringa oleifera; food and nutrition security

Online: 18 October 2019 (07:34:50 CEST)

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Evaluation of agronomic practices, genetic diversity and population structure of Moringa oleifera (Lam.) is crucial to its sustainable utilization to ensure food and nutritional security. Four agronomic practices of field preparation and soil analysis, regeneration, weeding and pruning, as well as harvesting, were adopted. Genetic diversity and population structure of 20 populations were evaluated using amplified fragment length polymorphism (AFLP) primer pairs (E-ACC/M-CAC and E-ACA/M-CAG). The effects of agronomic practices on leaf quantity production were evaluated using standard procedures. The physico-chemical and morphological data were analyzed using descriptive statistics, while genetic diversity, population structure, dendrogram reconstruction, and Principal Component Analysis (PCA) were analyzed from the AFLP genetic data. Significant effects (P ≤ 0.05) of agronomic practices on the quantity of leaf production were recorded across the accessions. The two primer pairs generated a total of 80 alleles with a mean major allele frequency of 0.0250. Gene diversity and polymorphic information content (PIC) values were high with a mean of 0.98 and 0.974, respectively. The Gst value of 0.0490 indicated that 5 % of the total genetic divergence was among the population while 95 % within the population. Dendrogram reconstruction with genetic distance ranging from 0.87 to 0.96 segregated the accessions into eleven clusters while PCA generated six cluster groups. Field preparation and physico-chemical soil properties, regeneration, weeding and pruning, and stand development, as well as harvesting, influenced the leaf yield and genetic diversity observed in this study. The genetic data revealed that some accessions were clustered along eco-geographical lines while others grouped disparately. Identified potential parent genotypes with valuable and desirable genetic traits can be exploited for commercial, breeding and conservation purposes to ensure sustainable utilization of the species in Nigeria.

Preprint ARTICLE | doi:10.20944/preprints201903.0064.v1

The Expression of RN7SL494P (7SL) Predicts Nodal Metastasis and Prognosis in Lung Adenocarcinoma

Xiao Zhu, Yongmei Huang, Hui Luo, Ying Xu

Subject: Life Sciences, Genetics Keywords: TCGA; lung adenocarcinoma; RN7SL494P; nodal metastasis; prognosis

Online: 5 March 2019 (12:27:55 CET)

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The metastasis of lung cancer can spread to the lymph nodes around the lungs. Metastasis, rather than the primary cancer, judges patients survival. Wherefore, a more detailed study on transcriptome of metastatic lung adenocarcinoma including primary carcinoma was carried out. LUAD RNA-seq data and the corresponding clinical information were available from The Cancer Genome Atlas (TCGA), which included 522 cases but only 515 cases have transcriptome data. Differential expression analyses between cases and controls, between primary cancer and metastasis subgroup, or between TNM stages, were respectively carried out using edgeR package. Then, the Kruskal-Wallis tests were used to verify the gradient changes of cancer metastasis or staging with the differential expression genes. The survival analyses were calculated using the Kaplan-Meier algorithm and log-rank test. The functional predictions for the differentially expressed genes were porformed with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (GO/KEGG). Single gene set enrichment analysis (single GSEA) was run to explore the biological pathways associated with the expressions of RN7SL494P gene based on the Molecular Signatures Database (MSigDB). 406 and 439 differentially expressed genes were identified respectively in lymph node metastasis or TNM stages. 112/296 intersection genes were associated with nodal metastasis and/or staging, among them only 25 genes were associated with the nodal metastasis, 13 genes were associated with the staging with gradient changes. Only one gene (RN7SL494P) was found to be associated with prognosis. But RN7SL494P was not found joining any biological functions or processes or cellular components with GO/KEGG analyses. Finally, single GSEA enrichment and pathway analyses showed that RN7SL494P might be involving in cancer development process and poor outcome in lung adenocarcinoma. These findings highlight the potential applications of RN7SL494P as a promising molecular predictor not only in nodal metastasis but prognosis evalution in lung adenocarcinoma patients.

Working Paper ARTICLE

Identifying Genetic Variants and Pathways Associated with Extreme Levels of Fetal Hemoglobin in Sickle Cell Disease in Tanzania

Siana Nkya, Liberata Mwita, Josephine Mgaya, Happiness Kumburu, Marco van Zwetselaar, Stephan Menzel, Gaston K. Mazandu, Raphael Z. Sangeda, Emile R. Chimusa, Julie Makani

Subject: Life Sciences, Genetics Keywords: Sickle cell disease; genetic disorder; fetal hemoglobin; hemoglobinopathy; Tanzania

Online: 20 September 2019 (11:47:39 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0374.v1

Preclinical Evidence of STAT3 Inhibitor, Pacritinib, Overcomes Temozolomide Resistance via Down-Regulating miR-21-enriched Exosomes from M2 Glioblastoma-Associated Macrophages

Hao-Yu Chuang, Yu-kai Su, Heng-Wei Liu, Chao-Hsuan Chen, Shao-Chih Chiu, Der-Yang Cho, Shinn-Zong Lin, Yueh-Sheng Chen, Chien-Min Lin

Subject: Life Sciences, Genetics Keywords: Keywords: Tumor microenvironment (TME), glioblastoma multiforme (GBM), GBM- associated macrophages (GAMs), exosomes, oncomiR-21, STAT3 inhibitor.

Online: 31 May 2019 (08:18:33 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201904.0011.v2

Nucleotide Epi-Chains and New Nucleotide Probability Rules in Long DNA Sequences

Sergey Petoukhov

Subject: Life Sciences, Genetics Keywords: DNA sequence; helix; nucleotide frequencies; DNA epi-chains; helical antennas; Fröhlich's theory; long-range coherence; epigenetics; quantum biology; binary representation

Online: 14 May 2019 (06:22:48 CEST)

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Preprint ARTICLE | doi:10.20944/preprints202005.0081.v1

Identification of Biomarkers and Enriched Pathways Involved in Lung Cancer

Nikita Singh, Mukesh Kumar, Atanu Bhattacharjee, Prashant Kumar Sonker, Agni Saroj

Subject: Life Sciences, Genetics Keywords: Lung cancer; biomarker; gene ontology; protein-protein interaction networks; survival analysis

Online: 5 May 2020 (12:28:25 CEST)

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Preprint REVIEW | doi:10.20944/preprints202201.0265.v1

CRISPR Therapeutics for Duchenne Muscular Dystrophy

Esra Erkut, Toshifumi Yokota

Subject: Life Sciences, Genetics Keywords: CRISPR; gene editing; Duchenne muscular dystrophy (DMD); exon skipping; NHEJ; dystrophin

Online: 18 January 2022 (17:30:37 CET)

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Preprint ARTICLE | doi:10.20944/preprints201912.0415.v1

Appraisal of Genetics and Heterosis of Important Traits in Chilli Pepper Cultivated under the Influence of Chilli Leaf Curl Virus Disease

Vijeth S, Sreelathakumary I, Rafeekher M, Prashant Kaushik

Subject: Life Sciences, Genetics Keywords: chilli pepper; ChiLCV; GCA; SCA; Line × Tester

Online: 31 December 2019 (16:11:30 CET)

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Preprint ARTICLE | doi:10.20944/preprints201905.0383.v2

A Huntington’s disease (HD) phenocopy leads to the identification of the HD toxin as polyalanine. The relationship between repeat length and age of onset can be reframed as a rate equation and the toxic polyalanine length is found to be about 30.6.

Eugen Tarnow

Subject: Life Sciences, Genetics Keywords: Huntington’s disease, CAG, kinetics, repeat expansions

Online: 8 August 2019 (13:11:08 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201905.0037.v1

Characterization and Antimicrobial Efficacy of Bovine Dermcidin, a Novel Antimicrobial Peptide Gene

Nevien Sabry, Tarek Moussa

Subject: Life Sciences, Genetics Keywords: Bos taurus; skin; bovine dermcidin; RT-PCR; antimicrobial activity

Online: 6 May 2019 (08:35:59 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201808.0493.v1

Novel Quantitative Trait Loci for Weed Competitive Ability Traits Using the Early Generation of Backcross Rice Populations

Niña Dimaano, Jauhar Ali, Mahender Anumalla, Pompe Cruz, Aurora Baltazar, Maria Diaz, Yun Long Pang, Bart Acero, Zhikang Li

Subject: Life Sciences, Genetics Keywords: Weed competitive ability; early seed germination and seedling vigor traits; quantitative trait loci (QTLs); single nucleotide polymorphism; direct seeded rice

Online: 29 August 2018 (10:46:02 CEST)

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Weed competitive ability (WCA) is a desirable key trait for the improvement of grain yield under direct-seeded rice (DSR) and the aerobic rice ecosystem. The present study targeted screening of 167 introgression lines (ILs) of a Green Super Rice (GSR) IR2-6 population derived from a cross between Weed Tolerant Rice 1 (WTR1) as the recipient parent and Y134 as the donor parent developed at IRRI for weed competitiveness in screen house conditions (SHC). The ILs were phenotyped for WCA traits such as early seed germination (ESG) and early seedling vigor (ESV) in Petri dishes and pot experiment conditions. The results of phenotypic variance revealed ESG-related traits, especially first germination count (1st GC) that positively correlated with second germination count (2nd GC), germination percentage (GP), total dry weight (TDW), total fresh weight (TFW), and vigor index (VI-1), whereas, in ESV, all the traits were positively correlated with each other except for three traits: root dry weight (RDW), 1st GC, and GP-2. The ESG and ESV traits are vital for weed competitiveness. A 6K SNP array was used to study the genetic association for the WCA traits. Forty-four QTLs for WCA traits were mapped on all chromosomes (except on chromosomes 4 and 8) through single marker analysis (SMA). Out of 44 QTLs, 29 were associated with ESG traits and 15 with ESV traits, with LOD scores of 2.93 to 8.03 and 2.93 to 5.04 and explained phenotypic variance ranging from 7.85% to 19.9% and from 7.85% to 13.2%, respectively. However, 31 QTLs were contributed by a negative additive allele from Y134, whereas a positive additive allele was contributed by WTR1 in 13 QTLs. Among them, two QTL hotspot regions were mapped on chromosome 11 (24.7-27.9 Mb) and chromosome 12 (14.8-17.4 Mb). The majority of the QTLs related to WCA traits were grouped into two QTL hotspots: QTL hotspot-I (qAFW11.1, qFC11.1, qFC11.2, qSC11.1, qGP-111.1, qGP-111.2, qTFGS11.1, qVI-111.1, and qVI-111.2) and QTL hotspot-II (qFC12.1, qFC12.2, qSC12.1, qFC12.2, qGP-112.1, qGP-112.2, qTFGS12.1, qTFGS12.2, qVI-112.1, qIV12.2, qFC12.1, and qGC12.2), and a few of them were co-localized on chromosomes 11 and 12. Further, we fine-tuned in the genomic regions of QTL hotspots and identified a total of 13 putative candidate genes on chromosomes 11 and 12 collectively. The present study is the first report on the genetic basis of WCA-related traits and the co-localized QTLs, which could be highly valuable in future breeding programs aiming to improve WCA in rice.

Preprint REVIEW | doi:10.20944/preprints202111.0170.v1

A Deep Dive into Genome Assemblies of Non-vertebrate Animals

Nadège Guiglielmoni, Ramón Rivera-Vicéns, Romain Koszul, Jean-François Flot

Subject: Life Sciences, Genetics Keywords: genome assembly; sequencing; non-vertebrate animals

Online: 9 November 2021 (13:25:39 CET)

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Preprint REVIEW | doi:10.20944/preprints201909.0222.v1

Elucidating Biological Roles of Novel Murine Genes in Hearing Impairment in Africa

Oluwafemi Oluwole, Abdoulaye Yalcouye, Edmond Wonkam, Noluthando Manyisa, Jack Morrice, Gaston Mazanda, Ambroise Wonkam

Subject: Life Sciences, Genetics Keywords: hearing impairment; novel murine genes; gene enrichment; africa

Online: 19 September 2019 (11:27:27 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201807.0113.v1

Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations

Jeffrey A. Thompson, Brock C. Christensen, Carmen J. Marsit

Subject: Life Sciences, Genetics Keywords: pan-cancer; bidirectional promoters; head-to-head genes

Online: 6 July 2018 (09:37:08 CEST)

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Preprint REVIEW | doi:10.20944/preprints202004.0394.v1

Population Genetic Considerations for Using Biobanks as International Resources in the Pandemic Era and Beyond

Hannah Carress, Daniel Lawson, Eran Elhaik

Subject: Life Sciences, Genetics Keywords: bioinformatics; population structure; population stratification bias; genomic medicine; biobanks

Online: 22 April 2020 (07:39:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201912.0368.v1

Mediator of DNA Damage Checkpoint Protein 1 Facilitates V(D)J Recombination in Cells Lacking DNA Repair Factor XLF

Carole Beck, Sergio Castañeda-Zegarra, Camilla Huse, Mengtan Xing, Valentyn Oksenych

Subject: Life Sciences, Genetics Keywords: V(D)J recombination; vAbl cells; B lymphocytes; mouse genetics; genetic interaction

Online: 29 December 2019 (04:36:17 CET)

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Preprint REVIEW | doi:10.20944/preprints202006.0016.v1

Revisiting and Enlisting Important QTLs Identified in Frech Bean (Phaseolus vulgaris L.): A Review

Sandeep Kaur Dhaliwal, Pooja Salaria, Prashant Kaushik

Subject: Life Sciences, Genetics Keywords: abiotic stress; biotic stress; biofortification; breeding; French bean; QTLs

Online: 3 June 2020 (09:43:01 CEST)

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Preprint REVIEW | doi:10.20944/preprints202008.0088.v1

Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses

Richard Dormatey, Chao Sun, Kazim Ali, Jeffrey A Coulter, Zhenzhen Bi, Jiangping Bai

Subject: Life Sciences, Genetics Keywords: Gene pyramiding; marker assisted selection; stress resistance; crop improvement

Online: 4 August 2020 (11:10:22 CEST)

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Preprint ARTICLE | doi:10.20944/preprints201910.0235.v1

Climate Change and Fading Genetic Resources of Parkia biglobosa (Jacq.) in Nigeria Based on SSR Markers

Jacob Popoola, James Agbolade, Abiodun Ajiboye, Omotolani Akinola, Francis Lewu, Joseph Kioko, Conrad Omonhinmin

Subject: Life Sciences, Genetics Keywords: African locust bean; climate change; cluster analysis; genetic intra-specific diversity; polymorphic information content; food and nutrition security

Online: 20 October 2019 (16:01:21 CEST)

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African locust bean (Parkia biglobosa (Jacq.) is a multi-purpose economic tree with genetic potentials in sub-Saharan Africa. Its cultivation and production is declining with increased aging and genetically threatened throughout its natural ranges. Research efforts are needed to change the present scenario to sustainable cultivation and utilization, hence this present study. This study was aimed at evaluating genetic diversity and geographical spread relationships of twenty landraces collected from different ecological zones of Nigeria using simple sequence repeat (SSR) markers. Ten SSR markers were screened and five primers (PbL02, PbL03, PbL04, PbL05 and PbL09) were selected based on clear amplification products and reproducible scorable bands. The SSR primers detected a total of 55 alleles ranged from 10 to 14 alleles with a mean of 11. The percentage polymorphisms were high and ranged from 68.75 % in PbL04 to 84.21 % in PbL05 with a mean of 74.16 %. The polymorphic information content (PIC) was in the range of 0.31 in PbL02 to 0.37 in PbL09. The genetic diversity and heterozygosity values ranged from 0.39 to 0.50 and 0.00 to 0.68 while the average genetic distance for all pair wise comparisons was 0.31.The first five Principal Component (PC) accounted for 70.20 % of the total variation out of which PC1 (31.50%) and PC2 (19.20%) extracted 49.70% molecular similarity. The dendrogram resulted in separation of the 19 landraces into three major clusters based on unweighted pair group method with arithmetic average. Cluster I comprised of five landraces: ABNo130 and BENo023; OYNo11, KANo125 and NiNo262 while cluster II had only one (BANo116). Cluster III was diverse comprising 13 landraces: ZANo188, KNNo162, KENo220, GMNo076 and EbNo260, ADNo64, EdNo164, KANo137, KENo217, KwNo270, NiNo241, OsNo206 and PLNo120. The homogeneity of alleles among the studied landraces suggested suspicion of loss of genetic intra-specific variation among the landraces of P. biglobosa which calls for concerted efforts toward better cultivation, conservation, management, utilization and genetic improvement of the species in Nigeria.

Preprint ARTICLE | doi:10.20944/preprints201812.0356.v1

A Robust Approach for Identification of Cancer Biomarkers and Candidate Drugs

Md. Shahjaman, Md. Rezanur Rahman, S. M. Shahinul Islam, Md. Nurul Haque Mollah

Subject: Life Sciences, Genetics Keywords: cancer biomarker; DEGs; FC; β-divergence method; β-weight function; paired SAM; robustness

Online: 29 December 2018 (06:45:39 CET)

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Background: Identification of cancer biomarkers that are differentially expressed (DE) under two biological conditions is an important task in many microarray studies. There exist several methods in the literature in this regards and most of these methods designed especially for unpaired samples, which does not satisfy the requirements of paired samples where the gene expressions are taken from the same patients before and after treatment. Furthermore, the traditional biomarker identification methods based on either p-values or fold change (FC) values. However, sometimes, p-value based results do not comply with FC based results due to the smaller variance of gene expressions. There are some methods that combine both p-values and FC values to solve this problem. But, these methods also show weak performance for small-sample case in presence of outlying expressions. To overcome this problem, in this paper an attempt is made to develop a hybrid robust SAM-FC approach by combining rank of FC values and rank of p-values based on SAM statistic using minimum β-divergence method, which is designed for paired samples. This method introduces a weight function known as β-weight function. This weight function produces larger weights corresponding to usual/normal expressions and smaller weights for unusual/outlying expressions. The β-weight function plays the significant role on the performance of the proposed method. Results: The proposed method uses β-weight function as a measure of outlier detection by setting β=0.2. We unify both classical and robust estimates using β-weight function such that maximum likelihood estimators (MLEs) are used in absence of outliers and minimum β-divergence estimators are used in presence of outliers to obtain reasonable p-values and FC values in the proposed method. We examined the performance of proposed method in a comparison of some popular methods (t-test, SAM, LIMMA, Wilcoxon, WAD, RP and FCROS) using both simulated and real gene expression profiles for both small-and large-sample cases. From the simulation and a real spike in data analysis results we observed that the proposed method outperforms other methods for small-sample case in presence of outliers and it keeps almost equal performance with other robust methods (Wilcoxon, RP and FCROS) otherwise. From a head-and-neck cancer (HNC) dataset the proposed method identified 2 genes (CYP3A4, NOVA1) that are significantly enriched in linoleic acid metabolism, drug metabolism, steroid hormone biosynthesis and metabolic pathways. The survival analysis through Kaplan-Meier curve revealed that combined effect of these 2 genes has prognostic capability and they might be promising biomarker of HNC. Moreover, we retrieved the 12 candidate drugs based on gene interaction from glad4u and drug bank databases. Conclusion The identified drugs showed statistical significance and critical role of the proteins indicate that these proteins might be therapeutic target in cancer. Thus, elucidating the associations between the drugs identified in the present study require further investigations.

Preprint ARTICLE | doi:10.20944/preprints201908.0284.v2

Hyperbolic Numbers in Modeling Genetic Phenomena

Sergey Petoukhov

Subject: Life Sciences, Genetics Keywords: hyperbolic numbers; matrix; eigenvectors; genetics; Fibonacci numbers; phyllotaxis; music harmony; DNA

Online: 19 September 2019 (11:21:42 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: Life Sciences, Genetics 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/preprints202001.0188.v1

Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast

Leticia Pollo-Oliveira, Roland Klassen, Nick Davis, Akif Ciftci, Jo Marie Bacusmo, Maria Marinelli, Michael S. DeMott, Thomas J. Begley, Peter C. Dedon, Raffael Schaffrath, Valérie de Crécy-Lagard

Subject: Life Sciences, Genetics Keywords: tRNA modification; protein aggregation

Online: 17 January 2020 (10:20:39 CET)

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Preprint REVIEW | doi:10.20944/preprints201804.0275.v2

Moderate the MAOA-L Allele Expression with CRISPR/Cas9 System

Martin L. Nelwan

Subject: Life Sciences, Genetics Keywords: advanced therapy; aggressive; antisocial; behavior; MAOA

Online: 4 May 2018 (09:45:11 CEST)

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Preprint TECHNICAL NOTE | doi:10.20944/preprints201901.0126.v1

Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

Frank M. You, Sylvie Cloutier

Subject: Life Sciences, Genetics Keywords: flax; association mapping; genome-wide association study (GWAS); simple sequence repeat (SSR); single nucleotide polymorphism (SNP); quantitative trait loci (QTL); chromosome-scale pseudomolecules

Online: 14 January 2019 (07:19:08 CET)

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Preprint ARTICLE | doi:10.20944/preprints201811.0066.v2

Low RNA Binding Strength of Human X Chromosome May Explain X Chromosome Inactivation

Ning Ji, Lifang Yan, Zhixue Song, Shufeng Liu, Shufeng Liu, Shuangshuang Yang, Hongyi Cao, Xiufang Wang, Zhanjun Lv

Subject: Life Sciences, Genetics Keywords: Alu; LINE-1 (L1); X-chromosome inactivation (XCI); repetitive sequences; RNA binding strength

Online: 8 November 2018 (11:10:53 CET)

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Two X chromosomes of female mammals randomly inactivate one of paternal or maternal X chromosome in early embryonic development and all the daughter cells produced from these cells retain the same feature of X chromosome inactivation, which is called X chromosome inactivation (XCI). Studying the mechanisms of XCI is important for understanding epigenetic that plays an important role in age-associated diseases. The previous studies have demonstrated that binding of RNAs and DNAs may play a role in activating gene expression. In this paper, our study aims to explore whether the mechanisms of XCI involve the RNA binding strength to X chromosome DNAs. The bioinformatics analyses based on big data were used to analyze the simulated binding strength of RNAs (RNA binding strength) to 23 chromosomes (including X chromosome and 22 human autosomes) and the characteristics of repetitive sequences in the X-inactivation centre. The results revealed that RNA binding strength of the long arm of the X chromosome that is almost entirely inactivated in XCI was significantly lower than that of all autosomes and the short arm of X chromosome, meanwhile the RNA binding strengths of inactivation regions in X chromosome were significantly lower than that of regions escaping from XCI. Different repetitive sequence clusters within the center of XCI presented a cross distribution characteristic. To further prove whether the repetitive sequences in human X chromosome involve in XCI, we cloned long interspersed element (LINE-1, L1) and short interspersed element (Alu) from human Xq13, the center of XCI, and constructed expression vectors carrying sense-antisense combination repetitive sequences (L1s or Alus). Effects of combined L1 or combined Alu sequences on expression of EGFP reporter gene were examined in stably transfected HeLa cells, which simulates the effects of repetitive sequences located on chromosomes. The results of experiments revealed transcribed L1 repetitive sequences activated EGFP reporter gene expression, so did the Alus. The experiment results suggested repetitive sequences activated genes by interaction of transcribed RNAs and DNAs. Since the binding of RNAs and DNAs can activate gene, so the low RNA binding strength of human X chromosome may be one of reasons of XCI. The cross distribution characteristics of different repetitive sequence clusters leading to a cascade of gene activation or gene inactivation may be the reason of transcriptional silencing one of the X chromosomes in female mammals.

Preprint ARTICLE | doi:10.20944/preprints201804.0311.v1

Gene Set Enrichment Analysis (GSEA) of Upregulated Genes in Cocaine Addiction Reveals miRNAs as Potential Therapeutic Agents

Ishtiaque Ahammad

Subject: Life Sciences, Genetics Keywords: GSEA; cocaine; addiction; enrichment analysis; bioinformatics; in silico research

Online: 24 April 2018 (08:46:31 CEST)

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Working Paper ARTICLE

Operationalising Forensic Genetic Genealogy in an Australian Context

Nathan Scudder, Runa Daniel, Jennifer Raymond, Alison Sears

Subject: Life Sciences, Genetics Keywords: forensic genetic genealogy; investigative genetic genealogy; DNA; forensic DNA

Online: 1 August 2020 (16:29:22 CEST)

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