TranSuite: a software suite for accurate translation and characterization of transcripts

AbstractPRESENILIN 2 (PSEN2) is one of the genes mutated in early onset familial Alzheimer’s disease (EOfAD). PSEN2 shares significant amino acid sequence identity with another EOfAD-related gene PRESENILIN 1 (PSEN1), and partial functional redundancy is seen between these two genes. However, the complete range of functions of PSEN1 and PSEN2 is not yet understood. In this study, we performed targeted mutagenesis of the zebrafish psen2 gene to generate a premature termination codon close downstream of the translation start with the intention of creating a null mutation. Homozygotes for this mutation, psen2S4Ter, are viable and fertile, and adults do not show any gross pigmentation defects, arguing against significant loss of γ-secretase activity. Also, assessment of the numbers of Dorsal Longitudinal Ascending (DoLA) interneurons that are responsive to psen2 but not psen1 activity during embryogenesis did not reveal decreased psen2 function. Transcripts containing the S4Ter mutation show no evidence of destabilization by nonsense-mediated decay. Forced expression in zebrafish embryos of fusions of psen2S4Ter 5’ mRNA sequences with sequence encoding enhanced green fluorescent protein (EGFP) indicated that the psen2S4Ter mutation permits utilization of cryptic, novel downstream translation start codons. These likely initiate translation of N-terminally truncated Psen2 proteins that obey the “reading frame preservation rule” of PRESENILIN EOfAD mutations. Transcriptome analysis of entire brains from a 6-month-old family of wild type, heterozygous and homozygous psen2S4Ter female siblings revealed profoundly dominant effects on gene expression likely indicating changes in ribosomal, mitochondrial, and anion transport functions.

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Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

Viruses ◽

10.3390/v13040646 ◽

2021 ◽

Vol 13 (4) ◽

pp. 646

Author(s):

Jingyuan Liu ◽

Elizabeth Carino ◽

Sayanta Bera ◽

Feng Gao ◽

Jared P. May ◽

...

Keyword(s):

Genome Mapping ◽

Structural Features ◽

Full Length ◽

Nonsense Mediated Decay ◽

Reading Frame ◽

Road Map ◽

Shape Structure ◽

New Type ◽

Subviral Rna

We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a −1 ribosomal frameshift event, are 2.7–4.6 kb in length, and are related to umbraviruses, unlike similar RNA replicons that are related to tombusviruses. Three classes of ulaRNAs are proposed, with citrus yellow vein associated virus (CYVaV) placed in Class 2. With the exception of CYVaV, Class 2 and Class 3 ulaRNAs encode an additional open reading frame (ORF) with movement protein-like motifs made possible by additional sequences just past the RdRp termination codon. The full-length secondary structure of CYVaV was determined using Selective 2’ Hydroxyl Acylation analyzed by Primer Extension (SHAPE) structure probing and phylogenic comparisons, which was used as a template for determining the putative structures of the other Class 2 ulaRNAs, revealing a number of distinctive structural features. The ribosome recoding sites of nearly all ulaRNAs, which differ significantly from those of umbraviruses, may exist in two conformations and are highly efficient. The 3′ regions of Class 2 and Class 3 ulaRNAs have structural elements similar to those of nearly all umbraviruses, and all Class 2 ulaRNAs have a unique, conserved 3′ cap-independent translation enhancer. CYVaV replicates independently in protoplasts, demonstrating that the reported sequence is full-length. Additionally, CYVaV contains a sequence in its 3′ UTR that confers protection to nonsense mediated decay (NMD), thus likely obviating the need for umbravirus ORF3, a known suppressor of NMD. This initial characterization lays down a road map for future investigations into these novel virus-like RNAs.

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MOD5 translation initiation sites determine N6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA.

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2382 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2382-2390 ◽

Cited By ~ 57

Author(s):

E C Gillman ◽

L B Slusher ◽

N C Martin ◽

A K Hopper

Keyword(s):

Trna Modification ◽

Cellular Compartment ◽

Reading Frame ◽

Transcription Start Sites ◽

Amino Terminal ◽

Translation Start ◽

Long Form ◽

Cellular Compartments ◽

Selection Of

MOD5 is one of several genes that code for enzymes found in mitochondria and another cellular compartment. Like other such genes, it contains two in-frame ATGs that could be used to produce two proteins, differing from each other by an amino-terminal extension. Certain other genes produce heterogeneous mRNAs with some 5' ends falling upstream of the longest open reading frame and some 5' ends falling between the first and second ATGs. In these cases, selection of transcription start sites appears to play a significant role in translation start site selection. MOD5, in contrast, produces mRNAs with 5' ends that all fall upstream of both ATGs. To determine how MOD5 encodes isozymes that are located in different cellular compartments and to determine whether they differ in structure, we constructed MOD5 and MOD5-COXIV fusions with mutations of the first, second, or both ATGs. The effect of these alterations on protein production, tRNA modification, and cellular location was assessed. Both the first and second ATGs are used to produce MOD5 protein in vivo, but only the long form of the protein is imported into mitochondria. Thus, the first 11 amino acids present on the amino-terminal extended protein are necessary for mitochondrial import. Surprisingly, this extension does not promote complete import of the long form of the protein, but rather a functional pool of the extended protein remains in the cytoplasm. The amino-terminal extension is also unusual because it is probably not proteolytically removed upon import and therefore does not constitute part of a mitochondrial presequence.

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MOD5 translation initiation sites determine N6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA

Molecular and Cellular Biology ◽

10.1128/mcb.11.5.2382-2390.1991 ◽

1991 ◽

Vol 11 (5) ◽

pp. 2382-2390

Author(s):

E C Gillman ◽

L B Slusher ◽

N C Martin ◽

A K Hopper

Keyword(s):

Trna Modification ◽

Cellular Compartment ◽

Reading Frame ◽

Transcription Start Sites ◽

Amino Terminal ◽

Translation Start ◽

Long Form ◽

Cellular Compartments ◽

Selection Of

MOD5 is one of several genes that code for enzymes found in mitochondria and another cellular compartment. Like other such genes, it contains two in-frame ATGs that could be used to produce two proteins, differing from each other by an amino-terminal extension. Certain other genes produce heterogeneous mRNAs with some 5' ends falling upstream of the longest open reading frame and some 5' ends falling between the first and second ATGs. In these cases, selection of transcription start sites appears to play a significant role in translation start site selection. MOD5, in contrast, produces mRNAs with 5' ends that all fall upstream of both ATGs. To determine how MOD5 encodes isozymes that are located in different cellular compartments and to determine whether they differ in structure, we constructed MOD5 and MOD5-COXIV fusions with mutations of the first, second, or both ATGs. The effect of these alterations on protein production, tRNA modification, and cellular location was assessed. Both the first and second ATGs are used to produce MOD5 protein in vivo, but only the long form of the protein is imported into mitochondria. Thus, the first 11 amino acids present on the amino-terminal extended protein are necessary for mitochondrial import. Surprisingly, this extension does not promote complete import of the long form of the protein, but rather a functional pool of the extended protein remains in the cytoplasm. The amino-terminal extension is also unusual because it is probably not proteolytically removed upon import and therefore does not constitute part of a mitochondrial presequence.

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Applications of Transmission Electron Microscopy in the Characterization of Metal Machinability

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100101967 ◽

1968 ◽

Vol 26 ◽

pp. 442-443 ◽

Cited By ~ 1

Author(s):

L.E. Murr ◽

A.B. Draper

Keyword(s):

Electron Microscopy ◽

State Physics ◽

Test Material ◽

Milling Machine ◽

Rotary Table ◽

Solid State Physics ◽

Materials Properties ◽

Transmission Electron ◽

Selection Of

The industrial characterization of the machinability of metals and alloys has always been a very arbitrarily defined property, subject to the selection of various reference or test materials; and the adoption of rather naive and misleading interpretations and standards. However, it seems reasonable to assume that with the present state of knowledge of materials properties, and the current theories of solid state physics, more basic guidelines for machinability characterization might be established on the basis of the residual machined microstructures. This approach was originally pursued by Draper; and our presentation here will simply reflect an exposition and extension of this research.The technique consists initially in the production of machined chips of a desired test material on a horizontal milling machine with the workpiece (specimen) mounted on a rotary table vice. A single cut of a specified depth is taken from the workpiece (0.25 in. wide) each at a new tool location.

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Caracterização da Peneira Média em Clones de Coffea canephora

REVISTA FIMCA ◽

10.37157/fimca.v5i2.58 ◽

2018 ◽

Vol 5 (2) ◽

pp. 28-31

Author(s):

Darlan Darlan Sanches Barbosa Alves ◽

Victor Mouzinho Spinelli ◽

Marcos Santana Moraes ◽

Carolina Augusto De Souza ◽

Rodrigo da Silva Ribeiro ◽

...

Keyword(s):

Genetic Improvement ◽

Block Design ◽

Coffea Canephora ◽

Coffee Production ◽

Randomized Block Design ◽

Significant Difference ◽

The Mean ◽

Four Blocks ◽

Selection Of

Introdução: O estado de Rondônia se destaca como tradicional produtor de café, sendo o segundo maior produtor brasileiro de C. canephora. No melhoramento genético de C. canephora, a seleção de plantas de elevada peneira média está associada à bebida de qualidade superior. Objetivos: O objetivo desse estudo foi avaliar a variabilidade genética de clones de C. canephora para o tamanho dos grãos, mensurado a partir da avaliação da peneira média (PM). Materiais e Métodos: Para isso, foi conduzido ao longo de dois anos agrícolas experimento no campo experimental da Embrapa no município de Ouro Preto do Oeste-RO, para a avaliação da peneira média de 130 genótipos (clones) com características das variedades botânicas Conilon, Robusta e híbridos intervarietais. O delineamento experimental utilizado foi de blocos ao acaso, com quatro repetições de quatro plantas por parcela. Resultados: Não houve resultados significativos para a interação clones X anos, indicando uma maior consistência no comportamento das plantas ao longo do tempo. Porém foram observadas diferenças significativas para o tamanho dos grãos entre os genótipos avaliados, possibilitando selecionar genótipos superiores. Conclusão: Os genótipos agruparam-se em cinco classes de acordo com o teste de média, subsidiando a caracterização de um gradiente de variabilidade da característica avaliada ABSTRACTIntroduction: Coffea canephora accounts for approximately 35% of the world's coffee production. The state of Rondônia stands out as a traditional coffee producer, being the second largest Brazilian producer of C. canephora. In the classical genetic improvement of C. anephora, the selection of plants of high average sieve is associated with a drink of superior quality. Objectives: The objective of this udy was to evaluate the genetic variability of Coffea canephora clones for the agronomic medium sieve (PM). Materials and Methods: The experiment was conducted in the experimental field of Embrapa, municipality of OuroPreto do Oeste-RO, located at coordinates 10º44'53 "S and 62º12'57". One hundred thirty genotypes (clones) of botanical characteristics Conilon, Robusta and intervarietal hybrids were evaluated in the agricultural years 2013-2014 and 2014-2015. The experimental design was a randomized block design with four blocks and four plants per plot, spacing 3.5 x 1.5 meters between plants. Results: Significant difference was found for the grain size. According to the F test, at 5% probability, the genotypes were grouped into five classes according to the mean test. Conclusion: The results obtained subsidized the characterization of a variability gradient of the evaluated trait.

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Elaboration and Characterization of the Properties of Refractory Cr Base Alloys

Advances in Science and Technology ◽

10.4028/www.scientific.net/ast.72.46 ◽

2010 ◽

Vol 72 ◽

pp. 46-52 ◽

Cited By ~ 1

Author(s):

Laurent Royer ◽

Stéphane Mathieu ◽

Christophe Liebaut ◽

Pierre Steinmetz

Keyword(s):

Mechanical Properties ◽

Melting Point ◽

Molten Glass ◽

Energy Production ◽

Creep Properties ◽

Refractory Alloys ◽

Industrial Use ◽

Kinetics Of ◽

Selection Of

For energy production and also for the glass industry, finding new refractory alloys which could permit to increase the process temperatures to 1200°C or more is a permanent challenge. Chromium base alloys can be good candidates, considering the melting point of Cr itself, and also its low corrosion rate in molten glass. Two families of alloys have been studied for this purpose, Cr-Mo-W and Cr-Ta-X alloys (X= Mo, Si..). A finer selection of compositions has been done, to optimize their chemical and mechanical properties. Kinetics of HT oxidation by air, of corrosion by molten glass and also creep properties of several alloys have been measured up to 1250°C. The results obtained with the best alloys (Cr-Ta base) give positive indications as regards the possibility of their industrial use.

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Organelle Genetics in Plants

International Journal of Molecular Sciences ◽

10.3390/ijms22042104 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2104

Author(s):

Pedro Robles ◽

Víctor Quesada

Keyword(s):

Rna Editing ◽

Posttranscriptional Regulation ◽

Genome Engineering ◽

Plant Mitochondria ◽

Plastid Dna ◽

Chloroplast Genomes ◽

Wide Range ◽

Organelle Genetics ◽

Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

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Selection of lactose-adapted cells in vinca minor and Dantura innoxia cultures; location and characterization of β-galactosidase and lactase activities

Plant Science ◽

10.1016/0168-9452(88)90058-1 ◽

1988 ◽

Vol 54 (1) ◽

pp. 83-91 ◽

Cited By ~ 4

Author(s):

O.C. Elavummoottil ◽

S. Duret ◽

A. Vannereau ◽

L. Cosson ◽

J.C. Mestre

Keyword(s):

Vinca Minor ◽

Selection Of

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Preclinical Testing of Radiopharmaceuticals for the Detection and Characterization of Osteomyelitis: Experiences from a Porcine Model

Molecules ◽

10.3390/molecules26144221 ◽

2021 ◽

Vol 26 (14) ◽

pp. 4221

Author(s):

Aage Kristian Olsen Alstrup ◽

Svend Borup Jensen ◽

Ole Lerberg Nielsen ◽

Lars Jødal ◽

Pia Afzelius

Keyword(s):

Animal Model ◽

Animal Models ◽

Porcine Model ◽

Animal Experiments ◽

Radioactive Tracers ◽

The Individual ◽

Selection Of

The development of new and better radioactive tracers capable of detecting and characterizing osteomyelitis is an ongoing process, mainly because available tracers lack selectivity towards osteomyelitis. An integrated part of developing new tracers is the performance of in vivo tests using appropriate animal models. The available animal models for osteomyelitis are also far from ideal. Therefore, developing improved animal osteomyelitis models is as important as developing new radioactive tracers. We recently published a review on radioactive tracers. In this review, we only present and discuss osteomyelitis models. Three ethical aspects (3R) are essential when exposing experimental animals to infections. Thus, we should perform experiments in vitro rather than in vivo (Replacement), use as few animals as possible (Reduction), and impose as little pain on the animal as possible (Refinement). The gain for humans should by far exceed the disadvantages for the individual experimental animal. To this end, the translational value of animal experiments is crucial. We therefore need a robust and well-characterized animal model to evaluate new osteomyelitis tracers to be sure that unpredicted variation in the animal model does not lead to a misinterpretation of the tracer behavior. In this review, we focus on how the development of radioactive tracers relies heavily on the selection of a reliable animal model, and we base the discussions on our own experience with a porcine model.

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