scholarly journals Large-scale annotation and evolution analysis of miRNA in insects

2021 ◽  
Author(s):  
Xingzhou Ma ◽  
Kang He ◽  
Zhenmin Shi ◽  
Meizhen Li ◽  
Fei Li ◽  
...  
Keyword(s):  
Gene Networks ◽  
Large Scale ◽  
Biological Evolution ◽  
Morphological Diversity ◽  
Scale Insects ◽  
Evolutionary Analysis ◽  
Mirna Genes ◽  
Arthropod Species ◽  
Homology Searching ◽  
Relationship Of

Abstract Insects are among the most diverse and successful groups of animals and exhibit great morphological diversity and complexity. The innovation of wings and metamorphosis are some examples of the fascinating biological evolution of insects. Most miRNAs contribute to canalization by conferring robustness to gene networks and thus increase the heritability of important phenotypes. Though previous studies have demonstrated how miRNAs regulate important phenotypes, little is still known about miRNA evolution in insects. Here, we used both small RNA-seq data and homology searching methods to annotate the miRNA repertoires of 152 arthropod species, including 135 insects and 17 non-insect arthropods. We identified 16,212 miRNA genes, and classified them into highly-conserved (62), insect-conserved (90) and lineage-specific (354) miRNA families. The phylogenetic relationship of miRNA binary presence/absence dynamics implies that homoplastic loss of conserved miRNA families tends to occur in far-related morphologically-simplified taxa, including scale insects (Coccoidea) and twisted-wing insects (Strepsiptera), leading to inconsistent phylogenetic tree reconstruction. The common ancestor of Insecta shares 62 conserved miRNA families, of which five were rapidly gained in the early winged-insects (Pterygota). We also detected extensive miRNA losses in Paraneoptera that are correlated with morphological reduction, and miRNA gains in early Endopterygota around the time holometabolous metamorphosis appeared. This was followed by abundant miRNA gains in Hymenoptera and Lepidoptera. In summary, we provide a comprehensive dataset and a detailed evolutionary analysis of miRNAs in insects. These data will be important for future studies on miRNA functions associated with insect morphological innovation and trait biodiversity.

scholarly journals Geo-Spatial Analysis of Population Density and Annual Income to Identify Large-Scale Socio-Demographic Disparities

2021 ◽  
Vol 10 (7) ◽  
pp. 432
Author(s):  
Nicolai Moos ◽  
Carsten Juergens ◽  
Andreas P. Redecker
Keyword(s):  
Population Density ◽  
Large Scale ◽  
Methodological Approach ◽  
Spatial Relationship ◽  
Postal Code ◽  
Annual Income ◽  
Choropleth Maps ◽  
Clustering Approach ◽  
Relationship Of ◽  
Insight Into

This paper describes a methodological approach that is able to analyse socio-demographic and -economic data in large-scale spatial detail. Based on the two variables, population density and annual income, one investigates the spatial relationship of these variables to identify locations of imbalance or disparities assisted by bivariate choropleth maps. The aim is to gain a deeper insight into spatial components of socioeconomic nexuses, such as the relationships between the two variables, especially for high-resolution spatial units. The used methodology is able to assist political decision-making, target group advertising in the field of geo-marketing and for the site searches of new shop locations, as well as further socioeconomic research and urban planning. The developed methodology was tested in a national case study in Germany and is easily transferrable to other countries with comparable datasets. The analysis was carried out utilising data about population density and average annual income linked to spatially referenced polygons of postal codes. These were disaggregated initially via a readapted three-class dasymetric mapping approach and allocated to large-scale city block polygons. Univariate and bivariate choropleth maps generated from the resulting datasets were then used to identify and compare spatial economic disparities for a study area in North Rhine-Westphalia (NRW), Germany. Subsequently, based on these variables, a multivariate clustering approach was conducted for a demonstration area in Dortmund. In the result, it was obvious that the spatially disaggregated data allow more detailed insight into spatial patterns of socioeconomic attributes than the coarser data related to postal code polygons.

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

scholarly journals Analysis of blood-based gene expression in idiopathic Parkinson disease

Neurology ◽  
2017 ◽  
Vol 89 (16) ◽  
pp. 1676-1683 ◽  
Author(s):  
Ron Shamir ◽  
Christine Klein ◽  
David Amar ◽  
Eva-Juliane Vollstedt ◽  
Michael Bonin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parkinson Disease ◽  
Gene Networks ◽  
Large Scale ◽  
Expression Profiles ◽  
Area Under The Curve ◽  
Gene Expression Profiles ◽  
Gene Signature ◽  
Gene Profiles ◽  
Independent Test

Objective:To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples).Methods:Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks.Results:A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E–6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E–4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1, ATP5A1, and VDAC3.Conclusions:We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers.

Sex differences in white adipose tissue expansion: emerging molecular mechanisms

2021 ◽  
Vol 135 (24) ◽  
pp. 2691-2708
Author(s):  
Simon T. Bond ◽  
Anna C. Calkin ◽  
Brian G. Drew
Keyword(s):  
Sex Differences ◽  
Sexual Dimorphism ◽  
Gene Networks ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Tissue Expansion ◽  
Economic Systems ◽  
Genomic Association ◽  
Males And Females

Abstract The escalating prevalence of individuals becoming overweight and obese is a rapidly rising global health problem, placing an enormous burden on health and economic systems worldwide. Whilst obesity has well described lifestyle drivers, there is also a significant and poorly understood component that is regulated by genetics. Furthermore, there is clear evidence for sexual dimorphism in obesity, where overall risk, degree, subtype and potential complications arising from obesity all differ between males and females. The molecular mechanisms that dictate these sex differences remain mostly uncharacterised. Many studies have demonstrated that this dimorphism is unable to be solely explained by changes in hormones and their nuclear receptors alone, and instead manifests from coordinated and highly regulated gene networks, both during development and throughout life. As we acquire more knowledge in this area from approaches such as large-scale genomic association studies, the more we appreciate the true complexity and heterogeneity of obesity. Nevertheless, over the past two decades, researchers have made enormous progress in this field, and some consistent and robust mechanisms continue to be established. In this review, we will discuss some of the proposed mechanisms underlying sexual dimorphism in obesity, and discuss some of the key regulators that influence this phenomenon.

scholarly journals The power of materialism among young adults: exploring the effects of values on impulsiveness and responsible financial behavior

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Andrea Lučić ◽  
Marija Uzelac ◽  
Andrea Previšić
Keyword(s):  
Young Adults ◽  
Large Scale ◽  
Brand Management ◽  
Mediating Effect ◽  
Financial Behavior ◽  
Purchase Decisions ◽  
Content Type ◽  
Financial Behaviour ◽  
Relationship Of ◽  
The Relationship

Purpose The purpose of this paper is to investigate the effects of values of materialism on cognitive and affective impulsiveness and responsible financial behavior among young adults. Design/methodology/approach A large-scale study (n = 483) was conducted on a sample of young adults 18 to 25 years of age in Croatia. Findings The research found that materialism has no direct effect on responsible financial behaviour (RFB), however, cognitive impulsiveness fully mediates the relationship of all three there three elements of materialism, centrality, success and happiness and RFB. Affective impulsiveness has no effect on the relationship. Furthermore, only materialism as centrality strongly and positively influences cognitive and affective impulsiveness. Practical implications Presented conclusions could be used by policymakers as guidelines for developing educational plans and curriculum to build financial capability and consumer protection among young adults and could be helpful for brand management activities targeting young people purchase decisions. Originality/value This paper’s ultimate purpose is to uncover the mechanism and the power of materialism on impulsiveness and responsible financial behavior. The paper’s originality is established by the focus on the investigation of materialism as an antecedent factor of impulsiveness and by questioning the nature of the relationship between materialism and responsible financial behavior through the mediating effect of impulsiveness.

scholarly journals Governance and Financial Difficulties of Conventional Banks

2019 ◽  
Vol 2 (2) ◽  
pp. 121-134
Author(s):  
La Ode Sumail
Keyword(s):  
Fixed Effects ◽  
Large Scale ◽  
Lagrange Multiplier Test ◽  
Fixed Effects Model ◽  
Insider Ownership ◽  
Financial Difficulties ◽  
Private Banks ◽  
Conventional Banks ◽  
Relationship Of ◽  
The Relationship

This study examines the connection between governance, financial performance, and financial difficulties of 27 conventional private banks during the pe3riod of 2015-2018. In order to meet the accuracy of the model in the regression analysis, the Lagrange Multiplier test was previously performed so that the Fixed Effects model was chosen. The relationship of insider ownership with ROA tends to be in the shape of inversed-U and the relationship between institutional ownership and ROA is significantly positive. The relationship between ROA and financial difficulties is significantly negative. Older or established large scale banks tend to have high ROA. This happens because the greater the assets, the healthier the cash flow of the bank, so that the potential for return of asset is quite high and financial difficulties tend to be low or avoidable.

scholarly journals miRmedon: confident detection of microRNA editing

2019 ◽  
Author(s):  
Amitai Mordechai ◽  
Alal Eran
Keyword(s):  
Cancer Progression ◽  
Large Scale ◽  
Complex Processes ◽  
Mirna Genes ◽  
Multiple Loci ◽  
Rnaseq Data ◽  
Error Distributions ◽  
Improved Performance ◽  
Mirna Editing ◽  
Small Rnaseq

SummarymicroRNA (miRNA), key regulators of gene expression, are prime targets for adenosine deaminase acting on RNA (ADAR) enzymes. Although ADAR-mediated A-to-I miRNA editing has been shown to be essential for orchestrating complex processes, including neurodevelopment and cancer progression, only a few human miRNA editing sites have been reported. Several computational approaches have been developed for the detection of miRNA editing in small RNAseq data, all based on the identification of systematic mismatches of ‘G’ at primary adenosine sites in known miRNA sequences. However, these methods have several limitations, including their ability to detect only one editing site per sequence (although editing of multiple sites per miRNA has been reproducibly validated), their focus on uniquely mapping reads (although 20% of human miRNA are transcribed from multiple loci), and their inability to detect editing in miRNA genes harboring genomic variants (although 73% of human miRNA loci include a reported SNP or indel). To overcome these limitations, we developed miRmedon, that leverages large scale human variation data, a combination of local and global alignments, and a comparison of the inferred editing and error distributions, for a confident detection of miRNA editing in small RNAseq data. We demonstrate its improved performance as compared to currently available methods and describe its advantages.Availability and implementationPython source code is available at https://github.com/Amitai88/[email protected]

Czech civil sector face-to-face with freelance activism

2016 ◽  
Vol 36 (11/12) ◽  
pp. 774-791
Author(s):  
Pavol Frič ◽  
Martin Vávra
Keyword(s):  
Large Scale ◽  
Civil Society Organizations ◽  
Political Consumerism ◽  
Data Set ◽  
Content Type ◽  
Individual Level ◽  
Face To Face ◽  
Online Activism ◽  
Civil Sector ◽  
Relationship Of

Purpose The purpose of this paper is to answer following question: what is the relationship between member activism performed through civil society organizations (CSOs) and individualized freelance activism (in form of online activism, everyday making, political consumerism or checkbook activism) independent of organizational framework? Is it a relationship of mutual competition or support? Design/methodology/approach Analysis is carried out on data from 2009 questionnaire-based survey on volunteering, representative for adult Czech population. The data set allowed the authors to relate member activism with freelance activism and in case of member activism distinguish the type of organization and the level of its professionalization. Findings Dominant pattern the authors identified in data is mutual support of both types of volunteering documented by significant overlap of these forms of public engagement. The most striking is the overlap for active members of new advocacy NGOs and the weakest for traditional clubs. Regression analysis shows that on an individual level “mixed activism” (compared with “pure freelance activism”) is linked with higher education and higher confidence in civic organizations. Originality/value The civil practice of individualized freelance activism was described and analysed by various authors as an activity of specific types of activist, but there has not yet been any research giving reflection on such a large scale of freelance activism types as in the analysis. The authors set them together in contrast to the member (collective, organized) form of civic activism and also took into account the influence of professionalization and type of CSOs.

CREATING KIN: NEW FAMILY ASSOCIATIONS AS WELFARE PROVIDERS IN LIBERALIZING JORDAN

2006 ◽  
Vol 38 (3) ◽  
pp. 349-368 ◽  
Author(s):  
Anne Marie Baylouny
Keyword(s):  
Large Scale ◽  
Family Relations ◽  
The State ◽  
National Politics ◽  
New Family ◽  
Traditional Elite ◽  
Family Associations ◽  
Relationship Of ◽  
Social Provisioning ◽  
The Relationship

In the decade and a half since economic liberalization began in Jordan, a little noticed but large-scale organizing trend has taken over the formal provision of social welfare, redefining the institutional conception of familial identity in the process. For over one third of the population, kin solidarities have been reorganized, formalized, and registered as nongovernmental organizations in an attempt to cope with the removal of basic social provisioning by the state. Although kinship clearly has been a major element in Jordan's history, the present phenomena alter traditional familial institutions, change kin lineages, and institutionalize the economic salience of family relations. In turn, the relationship of the populace to the state has changed, marginalizing previously regime-supporting groups and facilitating the implementation of economic neoliberalism without significant protest. Repackaged as charitable elements of civil society, these family associations are sanctioned and encouraged by the state and international community. Although they are not regime creations, family associations reinforce the Jordanian regime's efforts at political deliberalization. The new elites who head the organizations have been placated through indirect incorporation into the regime; they now wield significant economic power over fellow kin and have enhanced social status backed by the new group. Furthermore, the trend mainly consists of families without immediate ambitions of entering national politics. These are not the traditional elite families.

The Dawn of Civilization

2018 ◽  
pp. 234-263
Author(s):  
Kevin N. Laland
Keyword(s):  
Cultural Evolution ◽  
Slow Rate ◽  
Large Scale ◽  
Cultural Practices ◽  
Morphological Evolution ◽  
Biological Evolution ◽  
Genetic Evolution ◽  
The Third ◽  
The World ◽  
Adaptive Challenges

This chapter traces the evolution of human civilization from nomadic hunter-gatherer societies to the advent of agriculture and its large-scale impacts on the world. It describes this history in three ages of adaptive evolution. First, there was the age in which biological evolution dominated, in which we adapted to the circumstances of life in a manner no different from every other creature. Second came the age when gene–culture coevolution was in the ascendency. Through cultural activities, our ancestors set challenges to which they adapted biologically. In doing so, they released the brake that the relatively slow rate of independent environmental change imposes on other species. The results are higher rates of morphological evolution in humans compared to other mammals, with human genetic evolution reported as accelerating more than a hundredfold over the last 40,000 years. Now we live in the third age, where cultural evolution dominates. Cultural practices provide humanity with adaptive challenges, but these are then solved through further cultural activity, before biological evolution gets moving.

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