scholarly journals How Important Are Structural Variants for Speciation?

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1084
Author(s):  
Linyi Zhang ◽  
Radka Reifová ◽  
Zuzana Halenková ◽  
Zachariah Gompert
Keyword(s):  
Reproductive Isolation ◽  
Statistical Methods ◽  
Genetic Basis ◽  
Structural Changes ◽  
Underlying Mechanism ◽  
Structural Variants ◽  
Research Directions ◽  
New Research ◽  
Empirical Approaches

Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribution of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation.

MATERIAL HANDLING MACHINES AND SYSTEMS – UMI-TWINN PROJECT CONTRIBUTION

2019 ◽  
Vol 12 (1) ◽  
pp. 7-20
Author(s):  
Péter Telek ◽  
Béla Illés ◽  
Christian Landschützer ◽  
Fabian Schenk ◽  
Flavien Massi
Keyword(s):  
Material Handling ◽  
Digital Data ◽  
Flow Process ◽  
Research Directions ◽  
Scientific Excellence ◽  
Research Activities ◽  
New Research ◽  
Eu Project ◽  
The University

Nowadays, the Industry 4.0 concept affects every area of the industrial, economic, social and personal sectors. The most significant changings are the automation and the digitalization. This is also true for the material handling processes, where the handling systems use more and more automated machines; planning, operation and optimization of different logistic processes are based on many digital data collected from the material flow process. However, new methods and devices require new solutions which define new research directions. In this paper we describe the state of the art of the material handling researches and draw the role of the UMi-TWINN partner institutes in these fields. As a result of this H2020 EU project, scientific excellence of the University of Miskolc can be increased and new research activities will be started.

scholarly journals The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190540 ◽  
Author(s):  
Henry L. North ◽  
Pierre Caminade ◽  
Dany Severac ◽  
Khalid Belkhir ◽  
Carole M. Smadja
Keyword(s):  
Mate Choice ◽  
Copy Number Variation ◽  
Reproductive Isolation ◽  
House Mouse ◽  
Copy Number ◽  
Structural Changes ◽  
Sexual Isolation ◽  
Number Variation ◽  
Tandem Duplications

Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These ‘Choosiness-associated’ CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110 , that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice—the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Analyzing the response to epidemics: concept of evidence-based Haddon matrix

2017 ◽  
Vol 7 (3) ◽  
pp. 266-283 ◽  
Author(s):  
Azrah Anparasan ◽  
Miguel Lejeune
Keyword(s):  
Physical Environment ◽  
Evidence Based ◽  
Research Directions ◽  
Content Type ◽  
Humanitarian Organizations ◽  
The Matrix ◽  
New Research ◽  
Future Work ◽  
Haddon Matrix

Purpose The purpose of this paper is to propose a novel evidence-based Haddon matrix that identifies intervention options for organizations and governments responding to an epidemic in a developing economy. Design/methodology/approach A literature review of articles published within a year of the cholera outbreak in Haiti. Two separate types of literature sources are used – academic and non-academic – to apprehend the value and role of interventions implemented and/or identified. Findings The Haddon matrix helps break down the challenges involved in the containment of an epidemic into smaller, manageable components. This research shows that the matrix enables visualization of past evidence, help dissect various informational sources, and increase collaboration across humanitarian organizations. It will also serve as a building block for academics to identify new research directions to respond to epidemic outbreaks. Research limitations/implications The analysis focuses on the cholera epidemic in Haiti. Future work will be directed to generalize the identified recommendations and insights to a broader context. Originality/value This paper presents an evidence-based Haddon matrix that infers recommendations and insights based on past evidence for each phase (pre-event, response, and post-event) and factor (agent, host, physical environment, and socio-cultural environment) of an epidemic and for various stakeholders (humanitarian organizations, governments, and academics). The matrix provides a structured framework to identify interventions and best practices to address challenges during an epidemic outbreak.

scholarly journals Genetic basis and molecular biology of cardiac arrhythmias in cardiomyopathies

2020 ◽  
Vol 116 (9) ◽  
pp. 1600-1619 ◽  
Author(s):  
Ali J Marian ◽  
Babken Asatryan ◽  
Xander H T Wehrens
Keyword(s):  
Molecular Biology ◽  
Cardiac Arrhythmias ◽  
Genetic Basis ◽  
Structural Changes ◽  
Causal Role ◽  
Ion Currents ◽  
Pathogenic Variants ◽  
Life Threatening ◽  
Shared Genetic

Abstract Cardiac arrhythmias are common, often the first, and sometimes the life-threatening manifestations of hereditary cardiomyopathies. Pathogenic variants in several genes known to cause hereditary cardiac arrhythmias have also been identified in the sporadic cases and small families with cardiomyopathies. These findings suggest a shared genetic aetiology of a subset of hereditary cardiomyopathies and cardiac arrhythmias. The concept of a shared genetic aetiology is in accord with the complex and exquisite interplays that exist between the ion currents and cardiac mechanical function. However, neither the causal role of cardiac arrhythmias genes in cardiomyopathies is well established nor the causal role of cardiomyopathy genes in arrhythmias. On the contrary, secondary changes in ion currents, such as post-translational modifications, are common and contributors to the pathogenesis of arrhythmias in cardiomyopathies through altering biophysical and functional properties of the ion channels. Moreover, structural changes, such as cardiac hypertrophy, dilatation, and fibrosis provide a pro-arrhythmic substrate in hereditary cardiomyopathies. Genetic basis and molecular biology of cardiac arrhythmias in hereditary cardiomyopathies are discussed.

scholarly journals Agricultural cooperatives in netchains

2016 ◽  
Vol 16 (1) ◽  
pp. 1-6 ◽  
Author(s):  
C. Iliopoulos ◽  
M.L. Cook ◽  
F. Chaddad
Keyword(s):  
Policy Implications ◽  
Agricultural Cooperatives ◽  
Scholarly Work ◽  
Special Issue ◽  
Research Papers ◽  
Research Themes ◽  
Multi Stakeholder ◽  
New Research ◽  
Empirical Approaches

This special issue of the Journal on Chain and Network Science on ‘Agricultural cooperatives in netchains’ includes new research on three research themes: (1) explanation of why are cooperatives particularly important in certain food netchains; (2) willingness of farmers to invest in their cooperative’s netchain; and (3) the role of ambidexterity in the emergence of multi-stakeholder cooperatives. The issue is organized into six papers; one editorial and five research papers. The findings reported in this issue inform scholarly work on agricultural cooperatives through multiple theoretical lenses and empirical approaches. They also have important managerial and public policy implications.

scholarly journals Open science and the academic profession

2021 ◽  
Vol 13 (2) ◽  
pp. 184-205
Author(s):  
Rosanna De Rosa ◽  
Biagio Aragona
Keyword(s):  
Subjective Experience ◽  
Open Science ◽  
Academic Profession ◽  
Epistemic Communities ◽  
Research Directions ◽  
New Science ◽  
Professional Transition ◽  
New Research

Open science is considered a new science paradigm to make research accessible, accountable, and effective. Open science is already changing the academic profession starting from micro-practices to professional relations with epistemic communities and stakeholders, with implications that we are not yet able to predict. The article delves first into literature and official documentation to unfold the discursive regimes which sustain the spread of open science. A specific focus is then devoted to the professional transition, highlighting the role of funding organizations in setting the new science environment and the subjective experience of academics. The article is completed by a case study in the field of Research Data Management where the misalignment among incumbent/changing processes can be more apparent. Finally, a research agenda that focuses on how academic micro-practices are affecting organizations and science structures is proposed. This article aims at beginning to plow the ground for new research directions to emerge.

scholarly journals Population genomic evidence of selection on structural variants in a natural hybrid zone

2022 ◽  
Author(s):  
Linyi Zhang ◽  
Samridhi Chaturvedi ◽  
Chris Nice ◽  
Lauren Lucas ◽  
Zachariah Gompert
Keyword(s):  
Reproductive Isolation ◽  
Hybrid Zone ◽  
Structural Variants ◽  
Hybrid Fitness ◽  
Genome Wide ◽  
Oxford Nanopore ◽  
Jackson Hole ◽  
Long Read ◽  
Genomic Regions

Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviating from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average then SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess introgression from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might contribute disproportionately to hybrid fitness and thus (partial) reproductive isolation.

scholarly journals Role of long noncoding RNA taurine‐upregulated gene 1 in cancers

2021 ◽  
Vol 27 (1) ◽  
Author(s):  
Miao Da ◽  
Jing Zhuang ◽  
Yani Zhou ◽  
Quan Qi ◽  
Shuwen Han
Keyword(s):  
Noncoding Rna ◽  
Cancer Cell Proliferation ◽  
Research Directions ◽  
Protein Coding ◽  
Clinical Biomarker ◽  
Non Coding Rnas ◽  
New Research ◽  
Taurine Upregulated Gene 1 ◽  
Competitive Endogenous Rna

AbstractLong non-coding RNAs (lncRNAs) are a group of non-protein coding RNAs with a length of more than 200 bp. The lncRNA taurine up-regulated gene 1 (TUG1) is abnormally expressed in many human malignant cancers, where it acts as a competitive endogenous RNA (ceRNA), regulating gene expression by specifically sponging its corresponding microRNAs. In the present review, we summarised the current understanding of the role of lncRNA TUG1 in cancer cell proliferation, metastasis, angiogenesis, chemotherapeutic drug resistance, radiosensitivity, cell regulation, and cell glycolysis, as well as highlighting its potential application as a clinical biomarker or therapeutic target for malignant cancer. This review provides the basis for new research directions for lncRNA TUG1 in cancer prevention, diagnosis, and treatment.

scholarly journals The role of thrombin in the development of complications after intracoronary stenting

2015 ◽  
Vol 14 (3) ◽  
pp. 4-13
Author(s):  
G. A. Berezovskaya ◽  
M. A. Karpenko ◽  
N. N. Petrishchev ◽  
A. N. Yakovlev
Keyword(s):  
Coronary Intervention ◽  
Original Data ◽  
Laboratory Evaluation ◽  
Personal View ◽  
Research Directions ◽  
Percutaneous Coronary ◽  
Intracoronary Stenting ◽  
New Research ◽  
Practical Recommendations

The purpose of this review is to increase the awareness of the experts about the multifaceted role of thrombin in the development of complications after percutaneous coronary intervention: restenosis and stent thrombosis. Here we present the analysis of clinical data obtained from 1990 to 2014, dealing with the study of basic mechanisms of thrombin action after angioplasty and coronary stenting, as well as the characteristics of the laboratory evaluation of thrombin generation and new antithrombotic drugs that block its activity. The article presents not only the original data, but also the personal view of the authors on the problem. The above information can be used in the learning process, as well as for the formation of new research directions and practical recommendations for physicians.

Play at Work: An Integrative Review and Agenda for Future Research

2017 ◽  
Vol 44 (1) ◽  
pp. 161-190 ◽  
Author(s):  
Claire Aislinn Petelczyc ◽  
Alessandra Capezio ◽  
Lu Wang ◽  
Simon Lloyd D. Restubog ◽  
Karl Aquino
Keyword(s):  
Work Outcomes ◽  
Future Research ◽  
Research Directions ◽  
Academic Literature ◽  
Current State ◽  
Theoretical Perspectives ◽  
Antecedents And Consequences ◽  
New Research ◽  
Core Features

Play has gained increasing interest among progressive-minded managers as an important driver of motivation and productivity in work contexts. Despite its popularity in contemporary organizations, there is little consensus in the academic literature about the role of play in the workplace. This review organizes and synthesizes the current state of knowledge of play at work in order to gain a more comprehensive understanding of what play at work is, when individuals engage in play at work, and the effects of workplace play on work outcomes. First, we review existing definitions of play and their limitations. We then introduce a recent conceptualization of play in adulthood that defines play based on three core features and discuss its relevance in the workplace. Second, we review theoretical perspectives on play and extant empirical research on the antecedents and consequences of play at work, organizing it according to three levels of analysis. Third, we propose a promising agenda for future research by focusing on a number of important issues that have emerged from our review of existing work. These issues are organized into two sections: refining and extending the current research on play, and generating novel ideas and new research directions on unexplored areas of inquiry. We believe this review makes important and timely contributions to the research on play at work by providing comprehensive analysis of the diverse and fragmented literature on play in the workplace.

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