scholarly journals Adaptive ratchets and the evolution of molecular complexity

2021 ◽  
Author(s):  
Tom Röschinger ◽  
Roberto Morán Tovar ◽  
Simone Pompei ◽  
Michael Lässig
Keyword(s):  
Sequence Similarity ◽  
Dynamic Environment ◽  
Sequence Information ◽  
Code Length ◽  
Human Immune System ◽  
Recognition Sites ◽  
Molecular Complexity ◽  
Selection For ◽  
Static Target ◽  
Selection Of

Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or peptides binding a cognate recognition target of sufficient sequence similarity. Such sites are simple, ubiquitous modules of sequence information, cellular function, and evolution. Here we show that recognition sites, if coupled to a time-dependent target, can rapidly evolve to complex states with larger code length and smaller coding density than sites recognising a static target. The underlying fitness model contains selection for recognition, which depends on the sequence similarity between site and target, and a uniform cost per unit of code length. Site sequences are shown to evolve in a specific adaptive ratchet, which produces selection of different strength for code extensions and compressions. Ratchet evolution increases the adaptive width of evolved sites, accelerating the adaptation to moving targets and facilitating refinement and innovation of recognition functions. We apply these results to the recognition of fast-evolving antigens by the human immune system. Our analysis shows how molecular complexity can evolve as a collateral to selection for function in a dynamic environment.

Identifying Measurement Invariant Item Sets in Cross-Cultural Settings Using an Automated Item Selection Procedure

Methodology ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 177-188 ◽  
Author(s):  
Martin Schultze ◽  
Michael Eid
Keyword(s):  
Measurement Invariance ◽  
Optimal Solution ◽  
Selection Procedure ◽  
Cross Cultural ◽  
Item Selection ◽  
Ant System ◽  
Item Quality ◽  
Ant System Algorithm ◽  
Selection For ◽  
Selection Of

Abstract. In the construction of scales intended for the use in cross-cultural studies, the selection of items needs to be guided not only by traditional criteria of item quality, but has to take information about the measurement invariance of the scale into account. We present an approach to automated item selection which depicts the process as a combinatorial optimization problem and aims at finding a scale which fulfils predefined target criteria – such as measurement invariance across cultures. The search for an optimal solution is performed using an adaptation of the [Formula: see text] Ant System algorithm. The approach is illustrated using an application to item selection for a personality scale assuming measurement invariance across multiple countries.

ESTIMASI NILAI HERITABILITAS BOBOT IKAN MAS VARIETAS PUNTEN DALAM PROGRAM SELEKSI INDIVIDU

2016 ◽  
Vol 11 (3) ◽  
pp. 217
Author(s):  
Estu Nugroho ◽  
Budi Setyono ◽  
Mochammad Su’eb ◽  
Tri Heru Prihadi
Keyword(s):  
Body Weight ◽  
Selection Response ◽  
Base Population ◽  
Breeding Programs ◽  
Male And Female ◽  
Body Weight Trait ◽  
Population Selection ◽  
Selection For ◽  
Weight Trait ◽  
Selection Of

Program pemuliaan ikan mas varietas Punten dilakukan dengan seleksi individu terhadap karakter bobot ikan. Pembentukan populasi dasar untuk kegiatan seleksi dilakukan dengan memijahkan secara massal induk ikan mas yang terdiri atas 20 induk betina dan 21 induk jantan yang dikoleksi dari daerah Punten, Kepanjen (delapan betina dan enam jantan), Kediri (tujuh betina dan 12 jantan), Sragen (27 betina dan 10 jantan), dan Blitar (15 betina dan 11 jantan). Larva umur 10 hari dipelihara selama empat bulan. Selanjutnya dilakukan penjarangan sebesar 50% dan benih dipelihara selama 14 bulan untuk dilakukan seleksi dengan panduan hasil sampling 250 ekor individu setiap populasi. Seleksi terhadap calon induk dilakukan saat umur 18 bulan pada populasi jantan dan betina secara terpisah dengan memilih berdasarkan 10% bobot ikan yang terbaik. Calon induk yang terseleksi kemudian dipelihara hingga matang gonad, kemudian dipilih sebanyak 150 pasang dan dipijahkan secara massal. Didapatkan respons positif dari hasil seleksi berdasarkan bobot ikan, yaitu 49,89 g atau 3,66% (populasi ikan jantan) dan 168,47 g atau 11,43% (populasi ikan betina). Nilai heritabilitas untuk bobot ikan adalah 0,238 (jantan) dan 0,505 (betina).Punten carp breeding programs were carried out by individual selection for body weight trait. The base population for selection activities were conducted by mass breeding of parent consisted of 20 female and 21 male collected from area Punten, eight female and six male (Kepanjen), seven female and 12 male (Kediri), 27 female and 10 male (Sragen), 15 female and 11 male (Blitar). Larvae 10 days old reared for four moths. Then after spacing out 50% of total harvest, the offspring reared for 14 months for selection activity based on the sampling of 250 individual each population. Selection of broodstock candidates performed since 18 months age on male and female populations separately by selecting based on 10% of fish with best body weight. Candidates selected broodstocks were then maintained until mature. In oder to produce the next generation 150 pairs were sets and held for mass spawning. The results revealed that selection response were positive, 49.89 g (3.66%) for male and 168.47 (11.43%) for female. Heritability for body weight is 0.238 (male) and 0.505 (female).

Evaluation of Large-Sunflower Lines of Sunflower on Quantitative Morphological Traits

2020 ◽  
pp. 46-55
Keyword(s):  
Fertility Restoration ◽  
Morphological Characters ◽  
Direct Selection ◽  
Oilseed Crops ◽  
Turkish Origin ◽  
Self Pollination ◽  
Special Area ◽  
Pericarp Color ◽  
Selection For ◽  
Selection Of

Confectionery sunflower - a special area of use of sunflower, which requires the creation of marketable seeds quality features. One of the possible ways to create large-fruited sunflower is to create production hybrids and lines. Objective: to evaluate the created new large-fruited sunflower lines by a complex of morphological characters and determine the best lines for use as large-seeds hybrids as parent components or source material. In 2016-2019 years on the basis of the Institute of Oilseed Crops NAAS a study was conducted to assess the economic characteristics of large-fruited sunflower lines. We studied a collection of 27 lines of large-seeds sources. The lines were created by direct selection or crossing and sampling: Reyny of Argentinean origin, Zaporizhzhya confectionery variety, confectionery hybrid with striped pericarp color of Israeli origin, white seed of Turkish origin, synthetic population - donor of complex resistance. To study from the collection, lines were drawn that went through at least 7 generations with selection for seed size. Experience has shown that the shortest growing season for lines 174d and KP11 was 99 days, and the longest for lines I2K670 was 109 days. In the studied collection, the greatest mass of 1000 seeds has the KP11-146.47g line, which is the mother component and does not have branching. The second by weight of 1000 seeds (109 g) stood out line 168v, which also had branches and pollen fertility restoration genes and will be used as the paternal form. The third largest is also one basket line ZKN51-100. The collection included lines originating from the same combination, but with a different morphotype for the presence and absence of branching. So, based on the combination of KP11 x Zaporizhzhya Confectionery, three lines were obtained. A mass of 1000 seeds was observed in 98-86 g, with the branching line having the largest mass of 1000 seeds. The lines created with one combination VK678 x ZKN32: with a branch 168a had a mass of 1000 seeds 95g, and a line 168b - without a branch 109 g. Of the two lines obtained from the descendants of the combination KP11 x the striped hybrid both had branches, but the seeds were much smaller (weight of 1000 seeds 59 and 79 g). The collection also studied samples created on the basis of varieties and populations 160c, 174, 175b, the mass of 1000 seeds of which turned out to be more acceptable for large-fruited use from 83 to 99 g. Summing up the results of studying the collection of newly created lines, we can highlight the lines 162d, 168v, 175b, KP11 that are potentially promising for use in hybrids. The selections showed that large-fruited lines can be obtained from large-fruited varieties, self-pollination of large-fruited hybrids and crossing lines with hybrids and varieties. Self-pollination and selection of large-fruited lines in several generations does not provide the necessary variability for positive changes in selections. The result of the selection by weight of 1000 seeds in the offspring from crosses and from populations creates opportunities for new large-seeds sunflower.

IsoDetect: Detection of splice isoforms from third generation long reads based on short feature sequences

2020 ◽  
Vol 15 ◽  
Author(s):  
Hongdong Li ◽  
Wenjing Zhang ◽  
Yuwen Luo ◽  
Jianxin Wang
Keyword(s):  
Sequence Similarity ◽  
Detection Methods ◽  
Sequence Information ◽  
Third Generation ◽  
Sequencing Data ◽  
Splice Isoforms ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Feature Sequence ◽  
Generation Sequencing

Aims: Accurately detect isoforms from third generation sequencing data. Background: Transcriptome annotation is the basis for the analysis of gene expression and regulation. The transcriptome annotation of many organisms such as humans is far from incomplete, due partly to the challenge in the identification of isoforms that are produced from the same gene through alternative splicing. Third generation sequencing (TGS) reads provide unprecedented opportunity for detecting isoforms due to their long length that exceeds the length of most isoforms. One limitation of current TGS reads-based isoform detection methods is that they are exclusively based on sequence reads, without incorporating the sequence information of known isoforms. Objective: Develop an efficient method for isoform detection. Method: Based on annotated isoforms, we propose a splice isoform detection method called IsoDetect. First, the sequence at exon-exon junction is extracted from annotated isoforms as the “short feature sequence”, which is used to distinguish different splice isoforms. Second, we aligned these feature sequences to long reads and divided long reads into groups that contain the same set of feature sequences, thereby avoiding the pair-wise comparison among the large number of long reads. Third, clustering and consensus generation are carried out based on sequence similarity. For the long reads that do not contain any short feature sequence, clustering analysis based on sequence similarity is performed to identify isoforms. Result: Tested on two datasets from Calypte Anna and Zebra Finch, IsoDetect showed higher speed and compelling accuracy compared with four existing methods. Conclusion: IsoDetect is a promising method for isoform detection. Other: This paper was accepted by the CBC2019 conference.

scholarly journals Regulating the Regulators: Mechanisms of Substrate Selection of the O-GlcNAc Cycling Enzymes OGT and OGA

Glycobiology ◽  
2021 ◽  
Author(s):  
Hannah M Stephen ◽  
Trevor M Adams ◽  
Lance Wells
Keyword(s):  
Nutrient Sensing ◽  
Substrate Selection ◽  
Disease States ◽  
Dynamic Modification ◽  
Selection For ◽  
Outstanding Question ◽  
Glcnac Transferase ◽  
Future Work ◽  
Partner Proteins ◽  
Selection Of

Abstract Thousands of nuclear and cytosolic proteins are modified with a single β-N-acetylglucosamine on serine and threonine residues in mammals, a modification termed O-GlcNAc. This modification is essential for normal development and plays important roles in virtually all intracellular processes. Additionally, O-GlcNAc is involved in many disease states, including cancer, diabetes, and X-linked intellectual disability. Given the myriad of functions of the O-GlcNAc modification, it is therefore somewhat surprising that O-GlcNAc cycling is mediated by only two enzymes: the O-GlcNAc transferase (OGT), which adds O-GlcNAc, and the O-GlcNAcase (OGA), which removes it. A significant outstanding question in the O-GlcNAc field is how do only two enzymes mediate such an abundant and dynamic modification. In this review, we explore the current understanding of mechanisms for substrate selection for the O-GlcNAc cycling enzymes. These mechanisms include direct substrate interaction with specific domains of OGT or OGA, selection of interactors via partner proteins, posttranslational modification of OGT or OGA, nutrient sensing, and localization alteration. Altogether, current research paints a picture of an exquisitely regulated and complex system by which OGT and OGA select substrates. We also make recommendations for future work, toward the goal of identifying interaction mechanisms for specific substrates that may be able to be exploited for various research and medical treatment goals.

scholarly journals Selection of Tree Nut Allergen Peptide Markers: A Need for Improved Protein Sequence Databases

2019 ◽  
Vol 102 (5) ◽  
pp. 1263-1270 ◽  
Author(s):  
Weili Xiong ◽  
Melinda A McFarland ◽  
Cary Pirone ◽  
Christine H Parker
Keyword(s):  
Food Allergen ◽  
Protein Sequence ◽  
Sequence Information ◽  
Sequencing Data ◽  
Reference Tree ◽  
Candidate Peptide ◽  
Tree Nut ◽  
Allergen Detection ◽  
Sequence Databases ◽  
Selection Of

Abstract Background: To effectively safeguard the food-allergic population and support compliance with food-labeling regulations, the food industry and regulatory agencies require reliable methods for food allergen detection and quantification. MS-based detection of food allergens relies on the systematic identification of robust and selective target peptide markers. The selection of proteotypic peptide markers, however, relies on the availability of high-quality protein sequence information, a bottleneck for the analysis of many plant-based proteomes. Method: In this work, data were compiled for reference tree nut ingredients and evaluated using a parsimony-driven global proteomics workflow. Results: The utility of supplementing existing incomplete protein sequence databases with translated genomic sequencing data was evaluated for English walnut and provided enhanced selection of candidate peptide markers and differentiation between closely related species. Highlights: Future improvements of protein databases and release of genomics-derived sequences are expected to facilitate the development of robust and harmonized LC–tandem MS-based methods for food allergen detection.

Selection for rate and efficiency of lean gain in Hereford cattle 1. Selection pressure applied and direct responses

1990 ◽  
Vol 51 (1) ◽  
pp. 23-34 ◽  
Author(s):  
R. A. Mrode ◽  
C. Smith ◽  
R. Thompson
Keyword(s):  
Genetic Parameters ◽  
Control Line ◽  
Correlated Responses ◽  
Direct Response ◽  
Lean Growth ◽  
Hereford Cattle ◽  
Frozen Semen ◽  
Phenotypic Standard Deviation ◽  
Selection For ◽  
Selection Of

ABSTRACTSelection of bulls for rate and efficiency of lean gain was studied in a herd of Hereford cattle. There were two selection lines, one selected for lean growth rate (LGR) from birth to 400 days and the other for lean food conversion ratio (LFCR) from 200 to 400 days of age, for a period of 8 years. A control line bred by frozen semen from foundation bulls was also maintained. Generation interval was about 2·4 years and average male selection differentials, per generation were 1·2 and — 1·1 phenotypic standard deviation units for LGR and LFCR respectively.Genetic parameters and responses to selection were estimated from the deviation of the selected lines from a control line and by restricted maximum likelihood (REML) techniques on the same material. Realized heritabilities were 0·40 (s.e. 0·12) for LGR and 0·40 (s.e. 0·13) for LFCR using the control line. Corresponding estimates from REML were 0·42 (s.e. 0·10) and 0·37 (s.e. 0·14). The estimate of the genetic correlation between LGR and LFCR was about — 0·69 (s.e. 0·12) using REML.The estimates of direct annual genetic change using deviations from the control were 3·6 (s.e. 1·3) g/day for LGR and — 0·14 (s.e. 0·07) kg food per kg lean gain for LFCR. Corrsponding estimates from REML were similar but more precisely estimated. The correlated responses for LFCR in the LGR line was higher than the direct response for LFCR.

LINGUOCULTURAL POTENTIAL OF EUPHEMISMS-AMULETS

2021 ◽  
pp. 68-74
Author(s):  
SERGEY I. ROMANOV ◽  
Keyword(s):  
Target Selection ◽  
Cultural Factors ◽  
Point Of View ◽  
Negative Consequences ◽  
Cultural Community ◽  
Magical Power ◽  
Selection For ◽  
Cultural Code ◽  
Russian Linguistic ◽  
Selection Of

The article deals with a special type of euphemisms-amulets, that is, linguocultural units endowed with the function of protection. There are two types of euphemisms-amulets from the point of view of relevance: obsolete and current units. Obsolete euphemisms- amulets have targets that are not recognized as dangerous by the modern linguistic and cultural community. Current euphemisms-amulets, although not always consciously, are used by representatives of the modern Russian linguistic and cultural community to protect against something bad. The paper establishes that the use of the euphemism-amulet is based on the transla- tion of the target's representation into another cultural code. The work reveals that the euphemisms-amulets are directed not to mitigate an unwanted nomination but how to replace it. An undesirable nomination is endowed with negative magical properties, which is why the linguocultural community imposes a ban on its use. A protective cultural function is superim- posed on the euphemism. The main pragmatic explanation for the use of the euphemism- amulet is the speaker's desire not to predict an encounter with an unwanted object, which is based on belief in the magical power of the word. The factors that determine the linguocultural specificity of euphemisms-amulets are revealed. The first factor is target selection. For the Russian linguocultural community, such targets include a totemic animal, evil forces representing another world, death. The second factor is the selection of nominations for the euphemistic function, which is determined by culturally marked background knowledge, ideas, and typical practices. The communicative- pragmatic platform for the use of euphemisms-amulets is the belief in the magical power of the word, in the fact that the use of the forbidden word can lead to negative consequences (in particular, to cause the appearance of something dangerous, undesirable). The work proves that the identified cultural factors are universal, based on universal archetypes: one's own / another's, permission / prohibition, life / death. At the same time, the fact of the appearance of the euphemism-amulet, the choice of its internal form is determined by national and cultural factors.

Le fonti, i metodi e le narrazioni della storia della videoarte in Italia negli anni Settanta

2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Lisa Parola
Keyword(s):  
Comparative Study ◽  
Contemporary Art ◽  
Narrative Structure ◽  
Video Art ◽  
Wide Range ◽  
History Of ◽  
Selection For ◽  
The Many ◽  
Art And Architecture ◽  
Selection Of

This essay derives from the primary need to make order between direct and indirect sources available for the reconstruction of the history of video art in Italy in the seventies. In fact, during the researches for the Ph.D. thesis it became clear that in most cases it is difficult to define, in terms of facts, which of the different historiographies should be taken into consideration to deepen the study of video art in Italy. Beyond legitimate differences of perspectives and methods, historiographical narratives all share similar issues and narrative structure. The first intention of the essay is, therefore, to compare the different historiographic narratives on Italian video art of the seventies, verifying their genealogy, the sources used and the accuracy of the narrated facts. For the selection of the corpus, it was decided to analyze in particular monographic volumes dealing with the history of the origins of video art in Italy. The aim was, in fact, to get a wide range of types of "narrations", as in the case of contemporary art and architecture magazines, which are examined in the second part of the essay. After the selection, for an analytical and comparative study of the various historiography, the essay focuses only on the Terza Biennale Internazionale della Giovane Pittura. Gennaio ’70. Comportamenti, oggetti e mediazioni (Third International Biennial of Young Painting. January '70. Behaviors, Objects and Mediations, 1970, Bologna), the exhibition which - after Lucio Fontana's pioneering experiments - is said to be the first sign of the arrival of videotape in Italy (called at the time videorecording), curated by Renato Barilli, Tommaso Trini, Andrea Emiliani and Maurizio Calvesi. The narration given so far of this exhibition appeared more mythological than historical and could be compared structurally to that of the many numerous beginnings that historiographyies on international video art identify as ‘first’ and ‘generative’. In the first part of the essay the 'facts' related to Gennaio ’70, as narrated by historiography on video art, are compared. In the second part the survey is carried out through some of the direct sources identified during the research, with the aim of answering to questions raised by the comparison between historiographies. Concluding, it is important to underline that the tapes containing the videos transmitted have not been found and seem to have disappeared since the ending of the exhibition. Nevertheless, the deepening of the works and documentation transmitted during the exhibition is possible thanks to other types of sources which give us many valuable information regarding video techniques and practices at the beginning of 1970 in Italy.

Surgical treatment of bilateral temporal lobe pharmacoresistant epilepsy

2020 ◽  
pp. 60-82
Author(s):  
Igor Sergeevich Trifonov ◽  
Mikhail Vladimirovich Sinkin ◽  
Elena Vladimirovna Grigoryeva ◽  
Rashid Abdurakhmanovich Navruzov
Keyword(s):  
Surgical Treatment ◽  
Temporal Lobe ◽  
Clinical Picture ◽  
Clinical Manifestations ◽  
Epileptogenic Zone ◽  
Pharmacoresistant Epilepsy ◽  
Modern Methods ◽  
Selection For ◽  
Selection Of Patients ◽  
Selection Of

Surgical treatment of bilateral temporal lobe pharmacoresistant epilepsy is associated with some difficulties: particularly, the lack of stereotypical clinical picture in the same patient and controversial data on modern methods of diagnostics — all these statements make identifying epileptogenic zone more difficult and lack of clear criteria for the selection of patients for surgical treatment. In this review, issues of aetiology, pathogenesis, clinical manifestations and criteria for the selection for surgical treatment suggested by different authors are presented.

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