A computer system for the analysis of molecular evolution modes of protein-encoding genes (SAMEM): The relationship between molecular evolution and phenotypic traits

ABSTRACT Many small nucleolar RNAs (snoRNAs) are encoded within introns of protein-encoding genes and are released by processing of their host pre-mRNA. We have investigated the mechanism of processing of the yeast U18 snoRNA, which is found in the intron of the gene coding for translational elongation factor EF-1β. We have focused our analysis on the relationship between splicing of the EF-1β pre-mRNA and production of the mature snoRNA. Mutations inhibiting splicing of the EF-1β pre-mRNA have been shown to produce normal U18 snoRNA levels together with the accumulation of intermediates deriving from the pre-mRNA, thus indicating that the precursor is an efficient processing substrate. Inhibition of 5′→3′ exonucleases obtained by insertion of G cassettes or by the use of a rat1-1 xrn1Δ mutant strain does not impair U18 release. In the Exo− strain, 3′ cutoff products, diagnostic of an endonuclease-mediated processing pathway, were detected. Our data indicate that biosynthesis of the yeast U18 snoRNA relies on two different pathways, depending on both exonucleolytic and endonucleolytic activities: a major processing pathway based on conversion of the debranched intron and a minor one acting by endonucleolytic cleavage of the pre-mRNA.

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HUBUNGAN GAYA BELAJAR SISWA TERHADAP ASPEK PENGETAHUAN SISWA PADA MATA PELAJARAN SISTEM KOMPUTER DI SMK IT RAHMATAN KARIMAH BENGKULU TENGAH

Computer and Informatics Education Review ◽

10.33258/cier.1012020.1065.13-20 ◽

2020 ◽

Vol 1 (01) ◽

pp. 13-20

Author(s):

Dian Saputra

Keyword(s):

Learning Styles ◽

Computer System ◽

Learning Style ◽

Descriptive Analysis ◽

Visual Learning ◽

Auditory Learning ◽

Analysis Techniques ◽

Post Test ◽

The Subject ◽

The Relationship

This study aims to find out the relationship between learning style and students’ knowledge aspect on Computer System Subject at SMK IT Rahmatan Karimah of Central Bengkulu, the type of research is quantitative and the subject of research is grade X in SMK IT Rahmatan Karimah of Central Bengkulu. Data collection techniques using observation, Questionnaire and documentation. Data analysis techniques used were Descriptive Analysis, and inferential Statistical Analysis. The results of visual learning style post-test were 11 people with a mean of 76.36, an auditory learning style of 8 people at a mean of 62.14, a kinesthetic learning style of 3 people at a mean of 50.33, apart from that (r x y = 2.35) and the magnitude of r is reflected in the table (r table = 0.4132). Then rxy > r table ie = 2.35> 0.4132. In other words, Ho is rejected and Ha is accepted. It has a significant relationship between the learning styles of students and students’ knowledge aspect on Computer System Subject of grade X TKJ in SMK IT Rahmatan Karimah of Central Bengkulu

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Accountability in Computer Systems

The Oxford Handbook of Ethics of AI ◽

10.1093/oxfordhb/9780190067397.013.10 ◽

2020 ◽

pp. 179-196

Author(s):

Joshua A. Kroll

Keyword(s):

Computer System ◽

Computer Systems ◽

The Relationship

This chapter addresses the relationship between AI systems and the concept of accountability. To understand accountability in the context of AI systems, one must begin by examining the various ways the term is used and the variety of concepts to which it is meant to refer. Accountability is often associated with transparency, the principle that systems and processes should be accessible to those affected through an understanding of their structure or function. For a computer system, this often means disclosure about the system’s existence, nature, and scope; scrutiny of its underlying data and reasoning approaches; and connection of the operative rules implemented by the system to the governing norms of its context. Transparency is a useful tool in the governance of computer systems, but only insofar as it serves accountability. There are other mechanisms available for building computer systems that support accountability of their creators and operators. Ultimately, accountability requires establishing answerability relationships that serve the interests of those affected by AI systems.

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Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽

10.1186/s12864-021-07605-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qi Wu ◽

Yiming Luo ◽

Xiaoyong Wu ◽

Xue Bai ◽

Xueling Ye ◽

...

Keyword(s):

Expression Profiles ◽

Functional Characterization ◽

Chenopodium Quinoa ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Rna Seq ◽

Short Day ◽

Homologous Genes ◽

The Relationship ◽

Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

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Understanding the Overdispersed Molecular Clock

Genetics ◽

10.1093/genetics/154.3.1403 ◽

2000 ◽

Vol 154 (3) ◽

pp. 1403-1417 ◽

Cited By ~ 1

Author(s):

David J Cutler

Keyword(s):

Molecular Evolution ◽

Molecular Clock ◽

Time Scale ◽

Population Parameter ◽

Deleterious Mutations ◽

Slow Time ◽

Slow Time Scale ◽

Key Population ◽

Protein Encoding ◽

Rates Of Molecular Evolution

Abstract Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.

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What’s all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry

RSC Chemical Biology ◽

10.1039/d1cb00083g ◽

2021 ◽

Author(s):

Blase Matthew LeBlanc ◽

Rosamaria Yvette Moreno ◽

Edwin Escobar ◽

Mukesh Kumar Venkat Ramani ◽

Jennifer S Brodbelt ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Phosphorylation State ◽

Terminal Domain ◽

Carboxy Terminal Domain ◽

Protein Encoding ◽

Small Nuclear Rnas ◽

Rnap Ii ◽

Carboxy Terminal ◽

Encoding Genes

RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and...

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Autotransporter Protein-Encoding Genes of Diarrheagenic Escherichia coli Are Found in both Typical and Atypical Enteropathogenic E. coli Strains

Applied and Environmental Microbiology ◽

10.1128/aem.02635-12 ◽

2012 ◽

Vol 79 (1) ◽

pp. 411-414 ◽

Cited By ~ 21

Author(s):

Afonso G. Abreu ◽

Vanessa Bueris ◽

Tatiane M. Porangaba ◽

Marcelo P. Sircili ◽

Fernando Navarro-Garcia ◽

...

Keyword(s):

Escherichia Coli ◽

Content Type ◽

E Coli ◽

Diarrheagenic Escherichia Coli ◽

Virulence Markers ◽

Protein Encoding ◽

Encoding Genes ◽

Specific Virulence

ABSTRACTAutotransporter (AT) protein-encoding genes of diarrheagenicEscherichia coli(DEC) pathotypes (cah,eatA,ehaABCDJ,espC,espI,espP,pet,pic,sat, andtibA) were detected in typical and atypical enteropathogenicE. coli(EPEC) in frequencies between 0.8% and 39.3%. Although these ATs have been described in particular DEC pathotypes, their presence in EPEC indicates that they should not be considered specific virulence markers.

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Phenotyping plants: genes, phenes and machines

Functional Plant Biology ◽

10.1071/fpv39n11_in ◽

2012 ◽

Vol 39 (11) ◽

pp. 813 ◽

Cited By ~ 66

Author(s):

Roland Pieruschka ◽

Hendrik Poorter

Keyword(s):

Structural Information ◽

Plant Phenotyping ◽

Phenotypic Traits ◽

Special Issue ◽

Non Invasive ◽

The Core ◽

The Relationship ◽

Non Destructive ◽

Major Progress ◽

Meaningful Data

No matter how fascinating the discoveries in the field of molecular biology are, in the end it is the phenotype that matters. In this paper we pay attention to various aspects of plant phenotyping. The challenges to unravel the relationship between genotype and phenotype are discussed, as well as the case where ‘plants do not have a phenotype’. More emphasis has to be placed on automation to match the increased output in the molecular sciences with analysis of relevant traits under laboratory, greenhouse and field conditions. Currently, non-destructive measurements with cameras are becoming widely used to assess plant structural properties, but a wider range of non-invasive approaches and evaluation tools has to be developed to combine physiologically meaningful data with structural information of plants. Another field requiring major progress is the handling and processing of data. A better e-infrastructure will enable easier establishment of links between phenotypic traits and genetic data. In the final part of this paper we briefly introduce the range of contributions that form the core of a special issue of this journal on plant phenotyping.

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