The integration, proliferation, and expansion of functional categories

2015 ◽  
Author(s):  
Lisa deMena Travis
Keyword(s):  
Functional Categories

scholarly journals Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 304
Author(s):  
Yan Chen ◽  
Min Liu ◽  
Zhicheng Dong
Keyword(s):  
Enrichment Analysis ◽  
Close Correlation ◽  
Stress Conditions ◽  
Functional Categories ◽  
Molecular Pattern ◽  
Mrna Pool ◽  
Selective Translation ◽  
Stress Responsive Genes ◽  
Highly Correlated ◽  
Response To Water

The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in Arabidopsis. We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

scholarly journals Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species

2021 ◽  
Vol 13 (3) ◽  
Author(s):  
Xiuqin Zhong ◽  
Max Lundberg ◽  
Lars Råberg
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Immune Function ◽  
Sequence Divergence ◽  
Expression Divergence ◽  
Functional Categories ◽  
Coding Sequence ◽  
Immune Genes ◽  
Genes Encoding ◽  
Signal Transduction Proteins

Abstract Differences in immune function between species could be a result of interspecific divergence in coding sequence and/or expression of immune genes. Here, we investigate how the degree of divergence in coding sequence and expression differs between functional categories of immune genes, and if differences between categories occur independently of other factors (expression level, pleiotropy). To this end, we compared spleen transcriptomes of wild-caught yellow-necked mice and bank voles. Immune genes expressed in the spleen were divided into four categories depending on the function of the encoded protein: pattern recognition receptors (PRR); signal transduction proteins; transcription factors; and cyto- and chemokines and their receptors. Genes encoding PRR and cyto-/chemokines had higher sequence divergence than genes encoding signal transduction proteins and transcription factors, even when controlling for potentially confounding factors. Genes encoding PRR also had higher expression divergence than genes encoding signal transduction proteins and transcription factors. There was a positive correlation between expression divergence and coding sequence divergence, in particular for PRR genes. We propose that this is a result of that divergence in PRR coding sequence leads to divergence in PRR expression through positive feedback of PRR ligand binding on PRR expression. When controlling for sequence divergence, expression divergence of PRR genes did not differ from other categories. Taken together, the results indicate that coding sequence divergence of PRR genes is a major cause of differences in immune function between species.

scholarly journals A Variationist Study of Subject Pronoun Expression in Medellín, Colombia

Languages ◽  
2020 ◽  
Vol 6 (1) ◽  
pp. 5
Author(s):  
Rafael Orozco ◽  
Luz Marcela Hurtado
Keyword(s):  
Latin American ◽  
Random Effect ◽  
Routine Activities ◽  
Null Subjects ◽  
Functional Categories ◽  
Lexical Effect ◽  
Spanish Speaking ◽  
Baseline Knowledge ◽  
Subject Pronoun ◽  
Reflexive Verbs

This variationist study of subject pronoun expression (SPE) in Medellín, Colombia uses multivariate regressions to probe the effects of ten predictors on 4623 tokens from the Proyecto para el Estudio Sociolingüístico del Español de España y de América (PRESEEA) corpus. We implement analytical innovations by exploring transitivity and the lexical effect of the verb, which we analyze by testing infinitives and subject pronoun + verb collocations, respectively, as standalone, random-effect factors. Our results reveal the highest pronominal rate (28%) found in a mainland Spanish-speaking community. Additionally, we uncover that pronominal rates increase with age, a finding which appears to have cognitive implications. The internal conditioning contributes to pronombrista studies by showing the effects of discourse type and transitivity. Narratives and opinion statements favor overt subjects, but statements indicating routine activities favor null subjects. Whereas unergative verbs promote overt subjects, reflexive verbs favor null subjects. The lexical effect of the verb reveals opposing tendencies between verbs in the same category as well as within different collocations of the same verb, providing more definitive answers than the semantically guided approaches used for the last four decades and showing that verb groupings do not constitute functional categories with regard to SPE. Overall, this study contributes to expand our baseline knowledge of SPE in mainland Latin American communities and opens interesting research avenues.

scholarly journals Unveiling Putative Functions of Mucus Proteins and Their Tryptic Peptides in Seven Gastropod Species Using Comparative Proteomics and Machine Learning-Based Bioinformatics Predictions

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3475
Author(s):  
Viroj Tachapuripunya ◽  
Sittiruk Roytrakul ◽  
Pramote Chumnanpuen ◽  
Teerasak E-kobon
Keyword(s):  
Bioactive Peptides ◽  
Nearest Neighbor ◽  
Peptide Identification ◽  
Comparative Proteomics ◽  
Mass Spectrometric ◽  
Functional Categories ◽  
K Nearest Neighbor ◽  
Gastropod Species ◽  
Bioactive Properties ◽  
Sds Page

Gastropods are among the most diverse animals. Gastropod mucus contains several glycoproteins and peptides that vary by species and habitat. Some bioactive peptides from gastropod mucus were identified only in a few species. Therefore, using biochemical, mass spectrometric, and bioinformatics approaches, this study aimed to comprehensively identify putative bioactive peptides from the mucus proteomes of seven commonly found or commercially valuable gastropods. The mucus was collected in triplicate samples, and the proteins were separated by 1D-SDS-PAGE before tryptic digestion and peptide identification by nano LC-MS/MS. The mucus peptides were subsequently compared with R scripts. A total of 2818 different peptides constituting 1634 proteins from the mucus samples were identified, and 1218 of these peptides (43%) were core peptides found in the mucus of all examined species. Clustering and correspondence analyses of 1600 variable peptides showed unique mucous peptide patterns for each species. The high-throughput k-nearest neighbor and random forest-based prediction programs were developed with more than 95% averaged accuracy and could identify 11 functional categories of putative bioactive peptides and 268 peptides (9.5%) with at least five to seven bioactive properties. Antihypertensive, drug-delivering, and antiparasitic peptides were predominant. These peptides provide an understanding of gastropod mucus, and the putative bioactive peptides are expected to be experimentally validated for further medical, pharmaceutical, and cosmetic applications.

Divergent scaling of fine-root nitrogen and phosphorus in different root diameters, orders and functional categories: A meta-analysis

2021 ◽  
Vol 495 ◽  
pp. 119384
Author(s):  
Zhiqiang Wang ◽  
Heng Huang ◽  
Buqing Yao ◽  
Jianming Deng ◽  
Zeqing Ma ◽  
...  
Keyword(s):  
Fine Root ◽  
Meta Analysis ◽  
Functional Categories ◽  
Nitrogen And Phosphorus ◽  
Root Nitrogen

scholarly journals The Impact of COVID-19 on Pedestrian Flow Patterns in Urban POIs—An Example from Beijing

2021 ◽  
Vol 10 (7) ◽  
pp. 479
Author(s):  
Yihang Li ◽  
Liyan Xu
Keyword(s):  
Prevention And Control ◽  
Control Period ◽  
Flow Patterns ◽  
Control Measures ◽  
Pedestrian Flow ◽  
Prevention Measures ◽  
Government Control ◽  
Functional Categories ◽  
And Control ◽  
The Impact

The COVID-19 pandemic is a major challenge for society as a whole, and analyzing the impact of the spread of the epidemic and government control measures on the travel patterns of urban residents can provide powerful help for city managers to designate top-level epidemic prevention policies and specific epidemic prevention measures. This study investigates whether it is more appropriate to use groups of POIs with similar pedestrian flow patterns as the unit of study rather than functional categories of POIs. In this study, we analyzed the hour-by-hour pedestrian flow data of key locations in Beijing before, during, and after the strict epidemic prevention and control period, and we found that the pedestrian flow patterns differed greatly in different periods by using a composite clustering index; we interpreted the clustering results from two perspectives: groups of pedestrian flow patterns and functional categories. The results show that depending on the specific stage of epidemic prevention and control, the number of unique pedestrian flow patterns decreased from four before the epidemic to two during the strict control stage and then increased to six during the initial resumption of work. The restrictions on movement are correlated with most of the visitations, and the release of restrictions led to an increase in the variety of unique pedestrian flow patterns compared to that in the pre-restriction period, even though the overall number of visitations decreased, indicating that social restrictions led to differences in the flow patterns of POIs and increased social distance.

Lexically specific constructions in the acquisition of inflection in English

2003 ◽  
Vol 30 (1) ◽  
pp. 75-115 ◽  
Author(s):  
STEPHEN WILSON
Keyword(s):  
General Construction ◽  
Functional Categories ◽  
Grammatical Category ◽  
Closed Class ◽  
Lexical Items ◽  
Do So ◽  
Learning English

Children learning English often omit grammatical words and morphemes, but there is still much debate over exactly why and in what contexts they do so. This study investigates the acquisition of three elements which instantiate the grammatical category of ‘inflection’ – copula be, auxiliary be and 3sg present agreement – in longitudinal transcripts from five children, whose ages range from 1;6 to 3;5 in the corpora examined. The aim is to determine whether inflection emerges as a unitary category, as predicted by some recent generative accounts, or whether it develops in a more piecemeal fashion, consistent with constructivist accounts. It is found that for each child the relative pace of development of the three morphemes studied varies significantly, suggesting that these morphemes do not depend on a unitary underlying category. Furthermore, early on, be is often used primarily with particular closed-class subjects, suggesting that forms such as he's and that's are learned as lexically specific constructions. These findings are argued to support the idea that children learn ‘inflection’ (and by hypothesis, other functional categories) not by filling in pre-specified slots in an innate structure, but by learning some specific constructions involving particular lexical items, before going on to gradually abstract more general construction types.

Second language acquisition: Theoretical and experimental issues in contemporary research

1996 ◽  
Vol 19 (4) ◽  
pp. 677-714 ◽  
Author(s):  
Samuel David Epstein ◽  
Suzanne Flynn ◽  
Gita Martohardjono
Keyword(s):  
Second Language ◽  
Second Language Acquisition ◽  
Universal Grammar ◽  
Functional Categories ◽  
L2 Acquisition ◽  
Psycholinguistic Research ◽  
Explanatory Theory ◽  
Parameter Values ◽  
Theoretical Issues

AbstractTo what extent, if any, does Universal Grammar (UG) constrain second language (L2) acquisition? This is not only an empirical question, but one which is currently investigable. In this context, L2 acquisition is emerging as an important new domain of psycholinguistic research. Three logical possibilities have been articulated regarding the role of UG in L2 acquisition: The first is the “no access” hypothesis that claims that no aspect of UG is available to the L2 learner. The second is the “partial access” hypothesis that claims that only LI instantiated principles and LI instantiated parameter-values of UG are available to the learner. The third, called the “full access” hypothesis, asserts that UG in its entirety constrains L2 acquisition.In this paper we argue that there is no compelling evidence to support either of the first two hypotheses. Moreover, we provide evidence concerning functional categories in L2 acquisition consistent with the claim that UG is fully available to the L2 learner (see also Flynn 1987; Li 1993; Martohardjono 1992; Schwartz & Sprouse 1991; Thomas 1991; White 1989). In addition, we will attempt to clarify some of currently unclear theoretical issues that arise with respect to positing UG as an explanatory theory of L2 acquisition. We will also investigate in some detail certain crucial methodological questions involved in experimentally testing the role of UG in L2 acquisition and finally, we will present a set of experimental results of our own supporting the “Full Access” hypothesis.

Parameters or cues?

2004 ◽  
Vol 7 (1) ◽  
pp. 35-36 ◽  
Author(s):  
BRIAN MACWHINNEY
Keyword(s):  
Second Language ◽  
Second Language Acquisition ◽  
Language Acquisition ◽  
Hebbian Learning ◽  
Universal Grammar ◽  
Back Propagation ◽  
Parameter Setting ◽  
Functional Categories ◽  
The Core ◽  
Over Time

Truscott and Sharwood Smith (henceforth T&SS) attempt to show how second language acquisition can occur without any learning. In their APT model, change depends only on the tuning of innate principles through the normal course of processing of L2. There are some features of their model that I find attractive. Specifically, their acceptance of the concepts of competition and activation strength brings them in line with standard processing accounts like the Competition Model (Bates and MacWhinney, 1982; MacWhinney, 1987, in press). At the same time, their reliance on parameters as the core constructs guiding learning leaves this model squarely within the framework of Chomsky's theory of Principles and Parameters (P&P). As such, it stipulates that the specific functional categories of Universal Grammar serve as the fundamental guide to both first and second language acquisition. Like other accounts in the P&P framework, this model attempts to view second language acquisition as involving no real learning beyond the deductive process of parameter-setting based on the detection of certain triggers. The specific innovation of the APT model is that changes in activation strength during processing function as the trigger to the setting of parameters. Unlike other P&P models, APT does not set parameters in an absolute fashion, allowing their activation weight to change by the processing of new input over time. The use of the concept of activation in APT is far more restricted than its use in connectionist models that allow for Hebbian learning, self-organizing features maps, or back-propagation.

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