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 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.

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.

Income Diversification and Bank Efficiency in Vietnam

2017 ◽  
pp. 52-67
Author(s):  
Sang Nguyen Minh
Keyword(s):  
Regression Model ◽  
Commercial Banks ◽  
Banking System ◽  
Operational Efficiency ◽  
Commercial Banking ◽  
Tobit Regression ◽  
Income Diversification ◽  
Positive Effects ◽  
Study Results ◽  
The Impact

This study uses the DEA (Data Envelopment Analysis) method to estimate the technical efficiency index of 34 Vietnamese commercial banks in the period 2007-2015, and then it analyzes the impact of income diversification on the operational efficiency of Vietnamese commercial banks through a censored regression model - the Tobit regression model. Research results indicate that income diversification has positive effects on the operational efficiency of Vietnamese commercial banks in the research period. Based on study results, in this research some recommendations forpolicy are given to enhance the operational efficiency of Vietnam’s commercial banking system.

Impact of Digitalization on Service Work in Knowledge-Intensive Business Services: An Empirical Study in Tax Consultancies

2019 ◽  
Vol 3 (4) ◽  
pp. 209-222
Author(s):  
Philipp K. Görs ◽  
Henning Hummert ◽  
Anne Traum ◽  
Friedemann W. Nerdinger
Keyword(s):  
Work Engagement ◽  
Service Work ◽  
Psychological Consequences ◽  
Business Services ◽  
Knowledge Intensive Business Services ◽  
Positive Effects ◽  
Knowledge Intensive ◽  
The Impact ◽  
Positive Effect ◽  
Special Case

Digitalization is a megatrend, but there is relatively little knowledge about its consequences for service work in general and specifically in knowledge-intensive business services (KIBS). We studied the impact of digitalization on psychological consequences for employees in tax consultancies as a special case of KIBS. We compare two tax consulting jobs with very different job demands, those of tax consultants (TCs) and assistant tax consultants (ATCs). The results show that the extent of digitalization at the workplace level for ATCs correlates significantly positively with their job satisfaction. For TCs, the same variable correlates positively with their work engagement. These positive effects of digitalization are mediated in the case of ATCs by the impact on important job characteristics. In the case of TCs, which already have very good working conditions, the impact is mediated by the positive effect on self-efficacy. Theoretical and practical consequences of these results are discussed.

HOW CLIMATE CHANGE CAN INFLUENCE THE AGRICULTURE IN UKRAINE: A REVIEW

2020 ◽  
Author(s):  
N. Maidanovych ◽  
Keyword(s):  
Climate Change ◽  
Crop Yields ◽  
Soil Surface ◽  
Winter Period ◽  
Negative Consequences ◽  
Resource Saving ◽  
Impact Of Climate Change ◽  
Positive Effects ◽  
Average Annual Temperature ◽  
The Impact

The purpose of this work is to review and analyze the main results of modern research on the impact of climate change on the agro-sphere of Ukraine. Results. Analysis of research has shown that the effects of climate change on the agro-sphere are already being felt today and will continue in the future. The observed climate changes in recent decades have already significantly affected the shift in the northern direction of all agro-climatic zones of Europe, including Ukraine. From the point of view of productivity of the agro-sphere of Ukraine, climate change will have both positive and negative consequences. The positives include: improving the conditions of formation and reducing the harvesting time of crop yields; the possibility of effective introduction of late varieties (hybrids), which require more thermal resources; improving the conditions for overwintering crops; increase the efficiency of fertilizer application. Model estimates of the impact of climate change on wheat yields in Ukraine mainly indicate the positive effects of global warming on yields in the medium term, but with an increase in the average annual temperature by 2 ° C above normal, grain yields are expected to decrease. The negative consequences of the impact of climate change on the agrosphere include: increased drought during the growing season; acceleration of humus decomposition in soils; deterioration of soil moisture in the southern regions; deterioration of grain quality and failure to ensure full vernalization of grain; increase in the number of pests, the spread of pathogens of plants and weeds due to favorable conditions for their overwintering; increase in wind and water erosion of the soil caused by an increase in droughts and extreme rainfall; increasing risks of freezing of winter crops due to lack of stable snow cover. Conclusions. Resource-saving agricultural technologies are of particular importance in the context of climate change. They include technologies such as no-till, strip-till, ridge-till, which make it possible to partially store and accumulate mulch on the soil surface, reduce the speed of the surface layer of air and contribute to better preservation of moisture accumulated during the autumn-winter period. And in determining the most effective ways and mechanisms to reduce weather risks for Ukrainian farmers, it is necessary to take into account the world practice of climate-smart technologies.

INFLUENCE OF GREENHOUSE SHADING AND DIFFERENT NUTRIENT MANAGEMENT PRACTICES ON ALLEVIATING HEAT STRESS, IMPROVING PLANT NUTRIENTS STATUS, FLOWERING GROWTH AND YIELD OF TOMATO

2020 ◽  
Vol 51 (4) ◽  
pp. 1001-1014
Author(s):  
Sulaiman & Sadiq
Keyword(s):  
Heat Stress ◽  
Management Practices ◽  
Nutrient Management ◽  
Block Design ◽  
Nutrient Status ◽  
Growth And Yield ◽  
Reproductive Growth ◽  
Positive Effects ◽  
Nutrition Programs ◽  
The Impact

The experiment was conducted in a greenhouse during 2017 and 2018 growing seasons to evaluate the impact of the shading and various nutrition programs on mitigating heat stress, reducing the use of chemical minerals, improving the reproductive growth and yield of tomato plant. Split-plot within Randomized Complete Block Design (RCBD) with three replications was conducted in this study. Shading factor was allocated in the main plots and the nutrition programs distributed randomly in the subplots. Results indicate that shading resulted in the decrease of daytime temperature by 5.7˚C as an average for both seasons; thus a significant increasing was found in leaf contents of macro nutrients (Nitrogen, Phosphorous, and Potassium), and micro nutrients (Iron, Zinc and Boron), except the Iron content in 2018 growing season. Furthermore, shading improved significantly the reproductive growth and tomato yield. Among the plant nutrition programs, the integrated nutrient management (INM) including the application of organic substances, bio inoculum of AMF and 50% of the recommended dose of chemical fertilizers; lead to the enhancement of nutrients content, reproductive characteristics and plant yield. Generally, combination of both shading and INM showed positive effects on plants nutrient status and persisting balance on tomato flowering growth and fruits yield.

The Impact of Ultraviolet Radiation on Barrier Function in Human Skin: Molecular Mechanisms and Topical Therapeutics

2019 ◽  
Vol 25 (40) ◽  
pp. 5503-5511 ◽  
Author(s):  
Abdulaziz Alhasaniah ◽  
Michael J. Sherratt ◽  
Catherine A. O'Neill
Keyword(s):  
Ultraviolet Radiation ◽  
Barrier Function ◽  
Molecular Mechanisms ◽  
Transepidermal Water Loss ◽  
Protective Effects ◽  
Barrier Dysfunction ◽  
Epidermal Barrier ◽  
Positive Effects ◽  
Terrestrial Mammals ◽  
The Impact

A competent epidermal barrier is crucial for terrestrial mammals. This barrier must keep in water and prevent entry of noxious stimuli. Most importantly, the epidermis must also be a barrier to ultraviolet radiation (UVR) from the sunlight. Currently, the effects of ultraviolet radiation on epidermal barrier function are poorly understood. However, studies in mice and more limited work in humans suggest that the epidermal barrier becomes more permeable, as measured by increased transepidermal water loss, in response UVR, at doses sufficiently high to induce erythema. The mechanisms may include disturbance in the organisation of lipids in the stratum corneum (the outermost layer of the epidermis) and reduction in tight junction function in the granular layer (the first living layer of the skin). By contrast, suberythemal doses of UVR appear to have positive effects on epidermal barrier function. Topical sunscreens have direct and indirect protective effects on the barrier through their ability to block UV and also due to their moisturising or occlusive effects, which trap water in the skin, respectively. Some topical agents such as specific botanical extracts have been shown to prevent the loss of water associated with high doses of UVR. In this review, we discuss the current literature and suggest that the biology of UVR-induced barrier dysfunction, and the use of topical products to protect the barrier, are areas worthy of further investigation.

AML1/RUNX1 mutations in 470 adult patients with de novo acute myeloid leukemia: prognostic implication and interaction with other gene alterations

Blood ◽  
2009 ◽  
Vol 114 (26) ◽  
pp. 5352-5361 ◽  
Author(s):  
Jih-Luh Tang ◽  
Hsin-An Hou ◽  
Chien-Yuan Chen ◽  
Chieh-Yu Liu ◽  
Wen-Chien Chou ◽  
...  
Keyword(s):  
Overall Survival ◽  
Acute Myeloid Leukemia ◽  
Myeloid Leukemia ◽  
De Novo ◽  
Remission Rate ◽  
Adult Patients ◽  
Poor Prognostic Factor ◽  
The Impact ◽  
Runx1 Mutation ◽  
Acute Myeloid

AbstractSomatic mutation of the AML1/RUNX1(RUNX1) gene is seen in acute myeloid leukemia (AML) M0 subtype and in AML transformed from myelodysplastic syndrome, but the impact of this gene mutation on survival in AML patients remains unclear. In this study, we sought to determine the clinical implications of RUNX1 mutations in 470 adult patients with de novo non-M3 AML. Sixty-three distinct RUNX1 mutations were identified in 62 persons (13.2%); 32 were in N-terminal and 31, C-terminal. The RUNX1 mutation was closely associated with male sex, older age, lower lactic dehydrogenase value, French-American-British M0/M1 subtypes, and expression of HLA-DR and CD34, but inversely correlated with CD33, CD15, CD19, and CD56 expression. Furthermore, the mutation was positively associated with MLL/PTD but negatively associated with CEBPA and NPM1 mutations. AML patients with RUNX1 mutations had a significantly lower complete remission rate and shorter disease-free and overall survival than those without the mutation. Multivariate analysis demonstrated that RUNX1 mutation was an independent poor prognostic factor for overall survival. Sequential analysis in 133 patients revealed that none acquired novel RUNX1 mutations during clinical courses. Our findings provide evidence that RUNX1 mutations are associated with distinct biologic and clinical characteristics and poor prognosis in patients with de novo AML.

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.

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