scholarly journals Effects of the expression of random sequence clones on growth and transcriptome regulation in Escherichia coli

2021 ◽  
Author(s):  
Devika Bhave ◽  
Diethard Tautz
Keyword(s):  
De Novo ◽  
Random Sequence ◽  
Inducible Promoter ◽  
Comparative Genomic ◽  
General Stress Response ◽  
Positive Effects ◽  
Transcriptome Regulation ◽  
Genomic Analyses ◽  
Transcriptomic Changes ◽  
Candidate Clone

Comparative genomic analyses have provided evidence that new genetic functions can emerge out of random nucleotide sequences. Here, we apply a direct experimental approach to study the effects of plasmids harbouring random sequence inserts under the control of an inducible promoter. Based on data from previously described experiments dealing with the growth of clones within whole libraries, we extracted specific clones that had shown either negative or positive effects on relative cell growth. We analysed these individually with respect to growth characteristics and impact on the transcriptome. We find that candidate clones for negative peptides lead to growth arrest by eliciting a general stress response. Overexpression of positive clones, on the other hand, does not change the exponential growth rates of hosts, but they show a growth advantage over a neutral candidate clone when tested in direct competition experiments. Transcriptomic changes in positive clones are relatively moderate and specific to each clone. We conclude from our experiments that random sequence peptides are in-deed a suitable source for the de novo evolution of genetic functions.

Effects of the Expression of Random Sequence Clones on Growth and Transcriptome Regulation in Escherichia coli

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 53
Author(s):  
Devika Bhave ◽  
Diethard Tautz
Keyword(s):  
De Novo ◽  
Random Sequence ◽  
Inducible Promoter ◽  
Comparative Genomic ◽  
General Stress Response ◽  
Positive Effects ◽  
Transcriptome Regulation ◽  
Genomic Analyses ◽  
Transcriptomic Changes ◽  
The Impact

Comparative genomic analyses have provided evidence that new genetic functions can emerge out of random nucleotide sequences. Here, we apply a direct experimental approach to study the effects of plasmids harboring random sequence inserts under the control of an inducible promoter. Based on data from previously described experiments dealing with the growth of clones within whole libraries, we extracted specific clones that had shown either negative, neutral or positive effects on relative cell growth. We analyzed these individually with respect to growth characteristics and the impact on the transcriptome. We find that candidate clones for negative peptides lead to growth arrest by eliciting a general stress response. Overexpression of positive clones, on the other hand, does not change the exponential growth rates of hosts, and they show a growth advantage over a neutral clone when tested in direct competition experiments. Transcriptomic changes in positive clones are relatively moderate and specific to each clone. We conclude from our experiments that random sequence peptides are indeed a suitable source for the de novo evolution of genetic functions.

scholarly journals A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Fan Jiang ◽  
Yaoxin Jiang ◽  
Wenxuan Wang ◽  
Changyi Xiao ◽  
Ruiyi Lin ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Carcass Composition ◽  
Influenza Viruses ◽  
Comparative Genomic ◽  
Muscovy Duck ◽  
Cairina Moschata ◽  
Genomic Analyses ◽  
Chromosome Level

Abstract Background The Muscovy duck (Cairina moschata) is an economically important duck species, with favourable growth and carcass composition parameters in comparison to other ducks. However, limited genomic resources for Muscovy duck hinder our understanding of its evolution and genetic diversity. Results We combined linked-reads sequencing technology and reference-guided methods for de novo genome assembly. The final draft assembly was 1.12 Gbp with 29 autosomes, one sex chromosome and 4,583 unlocalized scaffolds with an N50 size of 77.35 Mb. Based on universal single-copy orthologues (BUSCO), the draft genome assembly completeness was estimated to be 93.30 %. Genome annotation identified 15,580 genes, with 15,537 (99.72 %) genes annotated in public databases. We conducted comparative genomic analyses and found that species-specific and rapidly expanding gene families (compared to other birds) in Muscovy duck are mainly involved in Calcium signaling, Adrenergic signaling in cardiomyocytes, and GnRH signaling pathways. In comparison to the common domestic duck (Anas platyrhynchos), we identified 104 genes exhibiting strong signals of adaptive evolution (Ka/Ks > 1). Most of these genes were associated with immune defence pathways (e.g. IFNAR1 and TLR5). This is indicative of the existence of differences in the immune responses between the two species. Additionally, we combined divergence and polymorphism data to demonstrate the “faster-Z effect” of chromosome evolution. Conclusions The chromosome-level genome assembly of Muscovy duck and comparative genomic analyses provide valuable resources for future molecular ecology studies, as well as the evolutionary arms race between the host and influenza viruses.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

Complete chloroplast genomes of Leptodermis scabrida complex: comparative genomic analyses and phylogenetic relationships

Gene ◽  
2021 ◽  
pp. 145715
Author(s):  
Ying Zhang ◽  
Zhengfeng Wang ◽  
Yanan Guo ◽  
Sheng Chen ◽  
Xianyi Xu ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Comparative Genomic ◽  
Chloroplast Genomes ◽  
Genomic Analyses

scholarly journals Minimal Effects, Maximum Panic: Social Media and Democracy in Latin America

2020 ◽  
Vol 6 (4) ◽  
pp. 205630512098445
Author(s):  
Eugenia Mitchelstein ◽  
Mora Matassi ◽  
Pablo J. Boczkowski
Keyword(s):  
Social Media ◽  
Latin America ◽  
Social Engagement ◽  
Hate Speech ◽  
De Novo ◽  
Electronic Government ◽  
Qualitative Assessment ◽  
Common Denominator ◽  
Negative Effects ◽  
Positive Effects

In face of public discourses about the negative effects that social media might have on democracy in Latin America, this article provides a qualitative assessment of existing scholarship about the uses, actors, and effects of platforms for democratic life. Our findings suggest that, first, campaigning, collective action, and electronic government are the main political uses of platforms. Second, politicians and office holders, social movements, news producers, and citizens are the main actors who utilize them for political purposes. Third, there are two main positive effects of these platforms for the democratic process—enabling social engagement and information diffusion—and two main negative ones—the presence of disinformation, and the spread of extremism and hate speech. A common denominator across positive and negative effects is that platforms appear to have minimal effects that amplify pre-existing patterns rather than create them de novo.

scholarly journals Genomic analyses unveil helmeted guinea fowl (Numida meleagris) domestication in West Africa

2021 ◽  
Author(s):  
Quan-Kuan Shen ◽  
Min-Sheng Peng ◽  
Adeniyi C Adeola ◽  
Ling Kui ◽  
Shengchang Duan ◽  
...  
Keyword(s):  
West Africa ◽  
De Novo ◽  
Guinea Fowl ◽  
Chromatin Interaction ◽  
De Novo Genome Assembly ◽  
Numida Meleagris ◽  
Whole Genomes ◽  
Genomic Analyses ◽  
Related Wild Species ◽  
Wild Progenitors

Abstract Domestication of the helmeted guinea fowl (HGF; Numida meleagris) in Africa remains elusive. Here we report a high-quality de novo genome assembly for domestic HGF generated by long and short-reads sequencing together with optical and chromatin interaction mapping. Using this assembly as the reference, we performed population genomic analyses for newly sequenced whole-genomes for 129 birds from Africa, Asia, and Europe, including domestic animals (n = 89), wild progenitors (n = 34), and their closely related wild species (n = 6). Our results reveal domestication of HGF in West Africa around 1,300-5,500 years ago. Scanning for selective signals characterized the functional genes in behavior and locomotion changes involved in domestication of HGF. The pleiotropy and linkage in genes affecting plumage color and fertility were revealed in the recent breeding of Italian domestic HGF. In addition to presenting a missing piece to the jigsaw puzzle of domestication in poultry, our study provides valuable genetic resources for researchers and breeders to improve production in this species.

Evidence from comparative genomic analyses indicating that Lactobacillus-mediated irritable bowel syndrome alleviation is mediated by the conjugated linoleic acid synthesis

2021 ◽  
Author(s):  
Yang Liu ◽  
Wei Xiao ◽  
Leilei Yu ◽  
Fengwei Tian ◽  
Gang Wang ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Linoleic Acid ◽  
Gut Microbiota ◽  
Acid Synthesis ◽  
Comparative Genomic ◽  
Low Grade ◽  
Genomic Analyses ◽  
Irritable Bowel ◽  
Low Grade Inflammation ◽  
Gut Microbiota Dysbiosis

Irritable bowel syndrome (IBS) is a chronic intestinal disorder accompanied by low-grade inflammation, visceral hypersensitivity, and gut microbiota dysbiosis. Several studies have indicated that Lactobacillus supplementation can help to alleviate...

scholarly journals Comparative genomic analyses of a virulent pseudorabies virus and a series of its in vitro passaged strains

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Chao Ye ◽  
Jiqiang Wu ◽  
Wu Tong ◽  
Tongling Shan ◽  
Xuefei Cheng ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Comparative Genomic ◽  
Genomic Analyses
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