scholarly journals Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors

2015 ◽  
Author(s):  
Núria Radó-Trilla ◽  
Krisztina Arató ◽  
Cinta Pegueroles ◽  
Alicia Raya ◽  
Susana de la Luna ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Amino Acid ◽  
Driving Forces ◽  
Gene Families ◽  
Low Complexity ◽  
Individual Gene ◽  
Genome Duplications ◽  
The Individual ◽  
Tf Gene

The high regulatory complexity of vertebrates has been related to two closely spaced whole genome duplications (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental transcription factors (TFs) were retained in multiple copies and subsequently specialized in diverse functions, whereas others reverted to their singleton state. TFs are known to be generally rich in amino acid repeats or low-complexity regions (LCRs), such as polyalanine or polyglutamine runs, which can evolve rapidly and potentially influence the transcriptional activity of the protein. Here we test the hypothesis that LCRs have played a major role in the diversification of TF gene duplicates. We find that nearly half of the TF gene families (107 out of 237) originated during the 2R-WGD contain LCRs, compared to only a small percentage of the non-duplicated TF genes used as a control (15 out of 115). At the individual gene level, we observe that twice as many duplicated TFs have gained LCRs as non-duplicated TFs. In addition, duplicated TFs preferentially accumulate certain LCR types, the most prominent of which are alanine repeats. We experimentally test the role of alanine-rich LCRs in two different TF gene families, PHOX2A/PHOX2B and LHX2/LHX9. In both cases, the presence of the alanine-rich LCR in one of the copies (PHOX2B and LHX2) significantly increases the capacity of the TF to activate transcription. Taken together, the results provide strong evidence that LCRs are important driving forces of evolutionary change in duplicated genes.

scholarly journals The Role of Reticulate Evolution in Creating Innovation and Complexity

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kristen S. Swithers ◽  
Shannon M. Soucy ◽  
J. Peter Gogarten
Keyword(s):  
Metabolic Pathways ◽  
Driving Forces ◽  
Reticulate Evolution ◽  
Neutral Evolution ◽  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
New Host ◽  
Whole Genome Duplications ◽  
Genome Duplications

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.

scholarly journals Emigration intentions of youth: theoretical foundations of the study and categorical diversity (a review of international studies)

2021 ◽  
Vol 10 (3) ◽  
pp. 57-67
Author(s):  
N.V. Murashcenkova
Keyword(s):  
Driving Forces ◽  
Empirical Studies ◽  
Psychological Research ◽  
International Studies ◽  
Special Role ◽  
Research Strategies ◽  
Main Research ◽  
Current Trends ◽  
The Individual

The article deals with the overview of modern international studies of emigration intentions of youth. The special role of psychological research in this scientific field is substantiated. The article reviews the procedural models of voluntary emigration. The paper analyses the significance of the social context and the role of the “migration culture” by shaping the emigration activity of the individual. The article describes the categorical variety of youth emigration intentions in international studies. The article analyses the main research strategies, measurement methods and current trends by conducting such psychological research. It is promising to compare the analyzed results of international studies with those of national scientists in the area under consideration. The data presented in the article can be useful in organizing and conducting socio-psychological empirical studies aimed at identifying the driving forces behind the emigration activity of young people in Russia and other countries.

Financial planning for retirement: the role of income

2019 ◽  
Vol 37 (6) ◽  
pp. 1419-1440
Author(s):  
Milagros Vivel-Búa ◽  
Lucía Rey-Ares ◽  
Rubén Lado-Sestayo ◽  
Sara Fernández-López
Keyword(s):  
Driving Forces ◽  
Pension Plans ◽  
Retirement Savings ◽  
Content Type ◽  
Working Lives ◽  
Future Income ◽  
Wealth Inequalities ◽  
The Individual ◽  
The Impact

PurposeThe purpose of this paper is to study the driving forces of both the decision to participate in individual pension plans and the amount of money allocated to such plans. Moreover, this paper evaluates the potential role that income plays, which has not previously been considered in depth in the financial literature.Design/methodology/approachBased on a sample of the Spanish population over the period 2008–2015, this paper estimates probit and tobit models, using 165,791 observations. The driving forces of private retirement savings comprise demographic, financial and socio-economic characteristics.FindingsThis paper confirms the impact of socio-demographic and economic variables on participation and monetary contributions to pension plans. It also confirms that income plays a non-negligible role. Moreover, empirical evidence reveals that the effect of gender is related to the income stratum to which the individual belongs.Originality/valueRetirement planning plays a key role in retirees’ future income and several countries have emphasised the importance of private individual savings to supplement the minimum provided by public pension schemes. The previous literature has concluded that those who plan their retirement end their working lives with three times the wealth of non-planners. Consequently, analysis of whether people are saving enough for their retirement can contribute to avoiding future wealth inequalities among retirees. Spain is one of the countries with the greatest inequality in income distribution, so this issue is of even greater interest.

scholarly journals Perturbations of Ribosomal Protein Expression Reveal Overlapping Gene Networks between Drosophila Minutes and Human Cancer

2020 ◽  
Author(s):  
Jai A Denton ◽  
Mariana Velasque ◽  
Floyd A Reed
Keyword(s):  
Ribosomal Proteins ◽  
Gene Networks ◽  
Ribosome Biogenesis ◽  
Human Cancer ◽  
Whole Body ◽  
Individual Gene ◽  
Gene Level ◽  
The Individual ◽  
Time Specific

AbstractRibosomal proteins (RPs) are critical to all cellular operations through their key roles in ribosome biogenesis and translation, as well as their extra-ribosomal functions. Although highly tissue- and time-specific in expression, little is known about the macro-level roles of RPs in shaping transcriptomes. A wealth of RP mutants exist, including the Drosophila melanogaster Minutes, with RP encoding genes that vary from greatly under-expressed to greatly over-expressed. Leveraging a subset of these mutants and using whole-body RNA sequencing, we identified the RP macro transcriptome and then sought to compare it with transcriptomes of pathologies associated with failures of ribosomal function. Gene-based analysis revealed highly variable transcriptomes of RP mutations with little overlap in genes that were differentially expressed. In contrast, weighted gene co-expression network analysis (WGCNA) revealed a highly conserved pattern across all RP mutants studied. When we compared network changes in RP mutants, we observed similarities to transcriptome alterations in human cancer, and thus confirming the oncogenic role of RPs. Therefore, what may appear stochastic at the individual gene level, forms clearly predictable patterns when viewed as a whole.

scholarly journals MENTAL DEVELOPMENT: PROBLEMS OF PERIODIZATION IN THE VIEWS OF FOREIGN AND DOMESTIC THEORISTS

2021 ◽  
pp. 30-37
Author(s):  
Korokhod Ya.D.
Keyword(s):  
Human Development ◽  
Psychosocial Development ◽  
Driving Forces ◽  
Mental Development ◽  
Internal Factors ◽  
Analysis And Synthesis ◽  
Psychological Knowledge ◽  
Definition Of ◽  
The Individual

Purpose of the article is the analysis of the conceptual positions of the representatives of psychological science within the concept of “mental development” and definition of the periodization of mental development in the views of domestic and foreign representatives. Research methods. Analysis and synthesis, systematization of scientific sources, comparison and generalization.Results. It is determined that mental development covers various fields of human existence, including such as: psychophysiological, cognitive and psychosocial ones. It is characterized by features that are expressed in irreversibility, direction and regularity.It is considered the S. Hall's theory of recapitulation, which is based on the biogenetic law in the article. Taking into account the contribution of S. Hall to the development of psychological knowledge, E. Hutchison lays the extraction of food by man as a criterion in the basis of mental development. It is determined the role of ethical and moral ideas in the views of L. Kohlberg and the connection with the periodization of human development.It was taken into account the role of psychological orientations of a human in his life and their role at each stage of mental development of the individual through the theory of psychosocial development of E. Erickson. It is determined the place of intelligence in human development and its connection with the development of the human psyche in the views of J. Piaget. It is characterized the views of S. Khudoyan views in the periodization of human development, where in his research he relied on the functional significance of biological, social and psychological neoformations.Conclusions. According to the results of theoretical analysis, it is established that a mental development is influenced by both external and internal factors, or biological and social. Periodization of its development was devised by scientists and theorists in accordance with the driving forces, which in their opinion were decisive. It was identified the areas according to which theories of periodization of mental development were devised: biogenetic, sociogenetic and mixed.Key words: psyche, mental development, subjective and objective factors, age, crisis periods. Мета. Метою статті є аналіз концептуальних положень представників психологічної науки в рамках поняття «психічний розвиток» та визначення проблематики періодизації психічного розвитку в поглядах вітчизняних та зарубіжних представників. Методи. Аналіз та синтез, систематизація наукових джерел, порівняння та узагальнення.Результати. Визначено, що психічний розвиток охоплює собою різні сфери людського буття, вклю-чаючи психофізіологічну, когнітивну та психосоціальну сфери. Для нього характерні особливості, які виражаються в незворотності, спрямованості та закономірності.У статті розглянуто теорію рекапітуляцій С. Холла, в основі якої лежить біогенетичний закон. Беручи до уваги вклад С. Холла в розвиток психологічного знання, Е. Гетчисон в основу психічного розвитку закладає добування їжі людиною як критерій. Визначено роль етичних та моральних уявлень у поглядах Л. Колберга та зв’язок із періодизацією розвитку людини. Проаналізовано наявність кризових періодів у періодизації психологічного розвитку особистості в поглядах Л. Виготського та В. Слободчикова.Було взято до уваги роль психологічних орієнтирів людини в її житті та їх роль на кожному етапі психічного розвитку особистості через теорію психосоціального розвитку Е. Еріксона. Визначено місце інтелекту в розвитку особистості та зв’язок його з розвитком психіки в поглядах Ж. Піаже. Охарактеризовано погляди С. Худояна в періодизації розвитку людини, де у своїх дослідженнях він спирався на функціональне значення біологічних, соціальних та психологічних новоутворень.Висновки. За результатами теоретичного аналізу встановлено, що психічний розвиток зазнає впливу як зовнішніх, так і внутрішніх чинників, або ж біологічних і соціальних. Періодизація психічного розвитку розроблялась науковцями та теоретиками відповідно до рушійних сил, які, на їхню думку, були визначальними. Були виділені напрями, згідно з якими розроблялись теорії періодизації психічного розвитку: біогенетичний, соціогенетичний та змішаний. Подальші перспективи дослідження будуть розширювати ґрунтовність вивчення означеної проблеми.Ключові слова: психіка, психічний розвиток, суб’єктивні та об’єктивні чинники, вік, кризові періоди.

scholarly journals Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1α,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Developing Zebrafish

2012 ◽  
Vol 26 (9) ◽  
pp. 1630-1642 ◽  
Author(s):  
Theodore A. Craig ◽  
Yuji Zhang ◽  
Melissa S. McNulty ◽  
Sumit Middha ◽  
Hemamalini Ketha ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Fatty Acid ◽  
Amino Acid ◽  
Xenobiotic Metabolism ◽  
Peptide Hormones ◽  
Differentially Expressed ◽  
Dihydroxyvitamin D3 ◽  
Vitamin D Receptors ◽  
Whole Transcriptome

Abstract The biological role of vitamin D receptors (VDR), which are abundantly expressed in developing zebrafish (Danio rerio) as early as 48 h after fertilization, and before the development of a mineralized skeleton and mature intestine and kidney, is unknown. We probed the role of VDR in developing zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3)].We observed significant changes in RNAs of transcription factors, leptin, peptide hormones, and RNAs encoding proteins of fatty acid, amino acid, xenobiotic metabolism, receptor-activator of NFκB ligand (RANKL), and calcitonin-like ligand receptor pathways. Early highly restricted, and subsequent massive changes in more than 10% of expressed cellular RNA were observed. At days post fertilization (dpf) 2 [24 h 1α,25(OH)2D3-treatment], only four RNAs were differentially expressed (hormone vs. vehicle). On dpf 4 (72 h treatment), 77 RNAs; on dpf 6 (120 h treatment) 1039 RNAs; and on dpf 7 (144 h treatment), 2407 RNAs were differentially expressed in response to 1α,25(OH)2D3. Fewer RNAs (n = 481) were altered in dpf 7 larvae treated for 24 h with 1α,25(OH)2D3vs. those treated with hormone for 144 h. At dpf 7, in 1α,25(OH)2D3-treated larvae, pharyngeal cartilage was larger and mineralization was greater. Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL, and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1α,25(OH)2D3 functions in vivo in developing eukaryotes.

scholarly journals PRAT Proteins Operate in Organellar Protein Import and Export in Arabidopsis thaliana

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 958
Author(s):  
Claudia Rossig ◽  
John Gray ◽  
Oscar Valdes ◽  
Armin Springer ◽  
Sachin Rustgi ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Leaf Senescence ◽  
Reverse Genetics ◽  
Protein Import ◽  
Gene Families ◽  
Trigger Factor ◽  
Transporter Family ◽  
Unique System

Chloroplasts need to import preproteins and amino acids from the cytosol during their light-induced differentiation. Similarly, chloroplasts have to export organic matter including proteins and amino acids during leaf senescence. Members of the PRAT (preprotein and amino acid transporter) family are candidate transporters for both processes. Here, we defined the role of two small PRAT gene families, At4g26670 and At5g55510 (HP20 subfamily) versus At3g49560 and At5g24650 (HP30 subfamily) during greening of etiolated plants and during leaf senescence. Using a combination of reverse genetics, protein biochemistry and physiological tools, evidence was obtained for a role of chloroplast HP20, HP30 and HP30-2 in protein, but not amino acid, import into chloroplasts. HP20, HP30 and HP30-2 form larger complexes involved in the uptake of transit sequence-less cytosolic precursors. In addition, we identified a fraction of HP30-2 in mitochondria where it served a similar function as found for chloroplasts and operated in the uptake of transit sequence-less cytosolic precursor proteins. By contrast, HP22 was found to act in the export of proteins from chloroplasts during leaf senescence, and thus its role is entirely different from that of its orthologue, HP20. HP22 is part of a unique protein complex in the envelope of senescing chloroplasts that comprises at least 11 proteins and contains with HP65b (At5g55220) a protein that is related to the bacterial trigger factor chaperone. An ortholog of HP65b exists in the cyanobacterium Synechocystis and has previously been implicated in protein secretion. Whereas plants depleted of either HP22 or HP65b or even both were increasingly delayed in leaf senescence and retained much longer stromal chloroplast constituents than wild-type plants, HP22 overexpressors showed premature leaf senescence that was associated with accelerated losses of stromal chloroplast proteins. Together, our results identify the PRAT protein family as a unique system for importing and exporting proteins from chloroplasts.

scholarly journals Low complexity regions in the proteins of prokaryotes perform important functional roles and are highly conserved

2019 ◽  
Vol 47 (19) ◽  
pp. 9998-10009 ◽  
Author(s):  
Chrysa Ntountoumi ◽  
Panayotis Vlastaridis ◽  
Dimitris Mossialos ◽  
Constantinos Stathopoulos ◽  
Ioannis Iliopoulos ◽  
...  
Keyword(s):  
Amino Acid ◽  
Metal Ions ◽  
Acid Content ◽  
Amino Acid Content ◽  
Low Complexity ◽  
High Throughput Analysis ◽  
Functional Roles ◽  
Eukaryotic Proteins ◽  
Widespread Belief

Abstract We provide the first high-throughput analysis of the properties and functional role of Low Complexity Regions (LCRs) in more than 1500 prokaryotic and phage proteomes. We observe that, contrary to a widespread belief based on older and sparse data, LCRs actually have a significant, persistent and highly conserved presence and role in many and diverse prokaryotes. Their specific amino acid content is linked to proteins with certain molecular functions, such as the binding of RNA, DNA, metal-ions and polysaccharides. In addition, LCRs have been repeatedly identified in very ancient, and usually highly expressed proteins of the translation machinery. At last, based on the amino acid content enriched in certain categories, we have developed a neural network web server to identify LCRs and accurately predict whether they can bind nucleic acids, metal-ions or are involved in chaperone functions. An evaluation of the tool showed that it is highly accurate for eukaryotic proteins as well.

scholarly journals The Mutual Reciprocity of Education, Non-Formal Cultural Education and Social Capital

2016 ◽  
Vol 13 (2) ◽  
pp. 35-43
Author(s):  
Edīte Igaune ◽  
Ilze Liepa-Balode ◽  
Agnese Hermane
Keyword(s):  
Social Capital ◽  
Formal Education ◽  
Driving Forces ◽  
Social Role ◽  
Evaluation Model ◽  
Clear Understanding ◽  
Structured Interviews ◽  
Cultural Education ◽  
The Individual

Abstract Human knowledge and creative potential has become one of the most important driving forces of humanity progress. In the context of the twenty-first century, in order to create a high-quality culture environment, it requires a paradigm shift in education - the transition to education, which stimulates the imagination, intuition, emotions and creative ideas and develops critical thinking. Non-formal education and the skills and knowledge gained in it is still in evaluation and recognition phase in Latvia. It is still developing; therefore, it is important to create a clear understanding of the importance and social role of non-formal cultural education. The paper aims to explore the role of non-formal cultural education in strengthening social capital as well as to identify what social capital indicators can be attributed to non-formal cultural education programmes. The topicality of the study is determined by the fact that non-formal cultural education and social capital in the context of Latvia are little explored areas, as well as there is lack of research on mutual reciprocity. The study uses qualitative research methodology. Research analyses non-formal cultural education programmes of 10 subordinated institutions of Latvian Ministry of Culture (museums, theatres, concert institutions and opera) and on the basis of 19 in-depth and semi-structured interviews. Study contains new, theoretically based evaluation model of social capital and characterizes of indicators in the context of non-formal education. The study confirms that there is a mutual reciprocity between social capital and non-formal cultural education programmes, and these programmes have a positive and supportive role in strengthening both the individual and collective social capital.

scholarly journals Quantifying the regulatory role of individual transcription factors in Escherichia coli

2021 ◽  
Author(s):  
Sunil Guharajan ◽  
Shivani Chhabra ◽  
Vinuselvi Parisutham ◽  
Robert C Brewster
Keyword(s):  
Transcription Factors ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Target Genes ◽  
Regulatory Role ◽  
E Coli ◽  
Regulatory Dna Sequences ◽  
The Individual ◽  
Regulatory Dna

Transcription factors (TFs) modulate gene expression by binding to regulatory DNA sequences surrounding target genes. To isolate the fundamental regulatory interactions of E. coli TFs, we measure regulation of TFs acting on synthetic target genes that are designed to isolate the individual TF regulatory effect. This data is interpreted through a thermodynamic model that decouples the role of TF copy number and TF binding affinity from the interactions of the TF on RNA polymerase through two distinct mechanisms: (de)stabilization of the polymerase and (de)acceleration of transcription initiation. We find the contribution of each mechanism towards the observed regulation depends on TF identity and binding location; for the set of TFs studied here, regulation immediately downstream of the promoter is not sensitive to TF identity, however these same TFs regulate through distinct mechanisms at an upstream binding site. Furthermore, depending on binding location, these two mechanisms of regulation can act coherently, to reinforce the observed regulatory role (activation or repression), or incoherently, where the TF regulates two distinct steps with opposing effect.

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