scholarly journals A different point of view of plant-bacterial interactions: RNA-Seq analysis of a PGP bacterial endophyte colonizing rapeseed plants

2020 ◽  
Author(s):  
Zaki Saati-Santamaría ◽  
Daniel Morais ◽  
Vojtěch Tláskal ◽  
Oldřich Benada ◽  
Olga Kofroňová ◽  
...  
Keyword(s):  
Point Of View ◽  
Rna Seq ◽  
Bacterial Interactions ◽  
Bacterial Endophyte

scholarly journals Uncovering the Complexity of Transcriptomes with RNA-Seq

2010 ◽  
Vol 2010 ◽  
pp. 1-19 ◽  
Author(s):  
Valerio Costa ◽  
Claudia Angelini ◽  
Italia De Feis ◽  
Alfredo Ciccodicola
Keyword(s):  
Massively Parallel Sequencing ◽  
Point Of View ◽  
Rna Seq ◽  
Specific Expression ◽  
Allele Specific ◽  
Data Files ◽  
Sequencing Platforms ◽  
New Applications ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

In recent years, the introduction of massively parallel sequencing platforms for Next Generation Sequencing (NGS) protocols, able to simultaneously sequence hundred thousand DNA fragments, dramatically changed the landscape of the genetics studies. RNA-Seq for transcriptome studies, Chip-Seq for DNA-proteins interaction, CNV-Seq for large genome nucleotide variations are only some of the intriguing new applications supported by these innovative platforms. Among them RNA-Seq is perhaps the most complex NGS application. Expression levels of specific genes, differential splicing, allele-specific expression of transcripts can be accurately determined by RNA-Seq experiments to address many biological-related issues. All these attributes are not readily achievable from previously widespread hybridization-based or tag sequence-based approaches. However, the unprecedented level of sensitivity and the large amount of available data produced by NGS platforms provide clear advantages as well as new challenges and issues. This technology brings the great power to make several new biological observations and discoveries, it also requires a considerable effort in the development of new bioinformatics tools to deal with these massive data files. The paper aims to give a survey of the RNA-Seq methodology, particularly focusing on the challenges that this application presents both from a biological and a bioinformatics point of view.

scholarly journals Using pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs

2018 ◽  
Author(s):  
Xiaofeng Xu ◽  
Haishuo Ji ◽  
Zhi Cheng ◽  
Xiufeng Jin ◽  
Xue Yao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Steady State ◽  
Small Rnas ◽  
Gene Expression Regulation ◽  
Regulation Of Gene Expression ◽  
Cost Effective ◽  
Rna Degradation ◽  
Point Of View ◽  
Rna Seq ◽  
Dsrna Cleavage

AbstractIn this study, we used pan RNA-seq analysis to reveal the ubiquitous existence of 5’ end and 3’ end small RNAs. 5’ and 3’ sRNAs alone can be used to annotate mitochondrial with 1-bp resolution and nuclear non-coding genes and identify new steady-state RNAs, which are usually from functional genes. Using 5’, 3’ and intronic sRNAs, we revealed that the enzymatic dsRNA cleavage and RNAi could involve in the RNA degradation and gene expression regulation of U1 snRNA in human. The further study of 5’, 3’ and intronic sRNAs help rediscover double-stranded RNA (dsRNA) cleavage, RNA interference (RNAi) and the regulation of gene expression, which challenges the classical theories. In this study, we provided a simple and cost effective way for the annotation of mitochondrial and nuclear non-coding genes and the identification of new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). We also provided a different point of view for cancer and virus, based on the new discoveries of dsRNA cleavage, RNAi and the regulation of gene expression.

scholarly journals Transcriptome Analysis of Gene Expression in Dermacoccus abyssi HZAU 226 under Lysozyme Stress

2020 ◽  
Vol 8 (5) ◽  
pp. 707
Author(s):  
Xinshuai Zhang ◽  
Yao Ruan ◽  
Wukang Liu ◽  
Qian Chen ◽  
Lihong Gu ◽  
...  
Keyword(s):  
Bactericidal Effect ◽  
Luria Bertani ◽  
Point Of View ◽  
Antimicrobial Protein ◽  
Rna Seq ◽  
Tolerance Mechanism ◽  
Glutathione Biosynthesis ◽  
Peptidoglycan Biosynthesis ◽  
New Perspective ◽  
Bacterial Peptidoglycan

Lysozyme acts as a kind of cationic antimicrobial protein and effectively hydrolyzes bacterial peptidoglycan to have a bactericidal effect, which also plays an important role in protecting eggs from microbial contamination. Dermacoccus abyssi HZAU 226, a Gram-positive bacterium isolated from spoiled eggs, has egg white and lysozyme tolerance, but its survival mechanism is unknown, especially from a transcriptomics point of view. In this study, the high lysozyme tolerance of D. abyssi HZAU 226 was characterized by three independent experiments, and then the Illumina RNA-seq was used to compare the transcriptional profiles of this strain in Luria–Bertani (LB) medium with and without 5 mg/mL lysozyme to identify differentially expressed genes (DEGs); 1024 DEGs were identified by expression analysis, including 544 up-regulated genes and 480 down-regulated genes in response to lysozyme treatment. The functional annotation analysis results of DEGs showed that these genes were mainly involved in glutathione biosynthesis and metabolism, ion transport, energy metabolism pathways, and peptidoglycan biosynthesis. This study is the first report of bacterial-related lysozyme RNA-seq, and our results help in understanding the lysozyme-tolerance mechanism of bacteria from a new perspective and provide transcriptome resources for subsequent research in related fields.

scholarly journals Interpretation of differential gene expression results of RNA-seq data: review and integration

2018 ◽  
Vol 20 (6) ◽  
pp. 2044-2054 ◽  
Author(s):  
Adam McDermaid ◽  
Brandon Monier ◽  
Jing Zhao ◽  
Bingqiang Liu ◽  
Qin Ma
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Point Of View ◽  
Data Sets ◽  
Bioconductor Package ◽  
Rna Seq ◽  
Real World Data ◽  
Vitis Riparia ◽  
Differential Gene ◽  
Functional Point

Abstract Differential gene expression (DGE) analysis is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes across two or more conditions and is widely used in many applications of RNA-seq data analysis. Interpretation of the DGE results can be nonintuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we reviewed DGE results analysis from a functional point of view for various visualizations. We also provide an R/Bioconductor package, Visualization of Differential Gene Expression Results using R, which generates information-rich visualizations for the interpretation of DGE results from three widely used tools, Cuffdiff, DESeq2 and edgeR. The implemented functions are also tested on five real-world data sets, consisting of one human, one Malus domestica and three Vitis riparia data sets.

The Geosciences Applied to Lunar Exploration

1962 ◽  
Vol 14 ◽  
pp. 169-257 ◽  
Author(s):  
J. Green
Keyword(s):  
Lunar Surface ◽  
Probable Mechanism ◽  
Point Of View ◽  
Lunar Exploration ◽  
Geological Model ◽  
Apply Geophysics ◽  
Surface Features ◽  
The Impact

The term geo-sciences has been used here to include the disciplines geology, geophysics and geochemistry. However, in order to apply geophysics and geochemistry effectively one must begin with a geological model. Therefore, the science of geology should be used as the basis for lunar exploration. From an astronomical point of view, a lunar terrain heavily impacted with meteors appears the more reasonable; although from a geological standpoint, volcanism seems the more probable mechanism. A surface liberally marked with volcanic features has been advocated by such geologists as Bülow, Dana, Suess, von Wolff, Shaler, Spurr, and Kuno. In this paper, both the impact and volcanic hypotheses are considered in the application of the geo-sciences to manned lunar exploration. However, more emphasis is placed on the volcanic, or more correctly the defluidization, hypothesis to account for lunar surface features.

How a sheperd guides a sheep herd?

1984 ◽  
Vol 75 ◽  
pp. 331-337
Author(s):  
Richard Greenberg
Keyword(s):  
Point Of View ◽  
Single Ring ◽  
Damping Effects ◽  
Ring Particle

ABSTRACTThe mechanism by which a shepherd satellite exerts a confining torque on a ring is considered from the point of view of a single ring particle. It is still not clear how one might most meaningfully include damping effects and other collisional processes into this type of approach to the problem.

The growth of mica polytypes as studied by conventional and high-resolution TEM

1983 ◽  
Vol 41 ◽  
pp. 174-177
Author(s):  
A. Baronnet ◽  
M. Amouric
Keyword(s):  
Water Pressure ◽  
Point Of View ◽  
Temperature Fields ◽  
Natural Occurrence ◽  
Growth Mechanisms ◽  
Long Period ◽  
High Resolution Tem ◽  
Layer Stacking ◽  
Experimental Works ◽  
Potential Use

The origin of mica polytypes has long been a challenging problem for crystal- lographers, mineralogists and petrologists. From the petrological point of view, interest in this field arose from the potential use of layer stacking data to furnish further informations about equilibrium and/or kinetic conditions prevailing during the crystallization of the widespread mica-bearing rocks. From the compilation of previous experimental works dealing with the occurrence domains of the various mica "polymorphs" (1Mr, 1M, 2M1, 2M2 and 3T) within water-pressure vs temperature fields, it became clear that most of these modifications should be considered as metastable for a fixed mica species. Furthermore, the natural occurrence of long-period (or complex) polytypes could not be accounted for by phase considerations. This highlighted the need of a more detailed kinetic approach of the problem and, in particular, of the role growth mechanisms of basal faces could play in this crystallographic phenomenon.

Radiation Damage in Ceramics

1982 ◽  
Vol 40 ◽  
pp. 600-603
Author(s):  
T. E. Mitchell ◽  
M. R. Pascucci ◽  
R. A. Youngman
Keyword(s):  
Radiation Damage ◽  
Outer Space ◽  
Point Of View ◽  
Nuclear Waste Storage ◽  
Waste Storage ◽  
Storage Media ◽  
Transmission Electron ◽  
Fundamental Point ◽  
Small Defect ◽  
Present Understanding

1. Introduction. Studies of radiation damage in ceramics are of interest not only from a fundamental point of view but also because it is important to understand the behavior of ceramics in various practical radiation enyironments- fission and fusion reactors, nuclear waste storage media, ion-implantation devices, outer space, etc. A great deal of work has been done on the spectroscopy of point defects and small defect clusters in ceramics, but relatively little has been performed on defect agglomeration using transmission electron microscopy (TEM) in the same kind of detail that has been so successful in metals. This article will assess our present understanding of radiation damage in ceramics with illustrations using results obtained from the authors' work.

Structural aspects of osmoregulation in porphyra

1978 ◽  
Vol 36 (2) ◽  
pp. 412-413
Author(s):  
C. Wiencke ◽  
A. Lauchli
Keyword(s):  
Culture Medium ◽  
Point Of View ◽  
Chemical Fixation ◽  
Cellular Organization ◽  
Osmotic Adaptation ◽  
Osmotic Balance ◽  
Activity Of Enzymes ◽  
Osmotic Agents ◽  
Vacuolar System ◽  
Structural Aspects

Osmoregulatory mechanisms in algae were investigated mainly from a physiological point of view (KAUSS 1977, HELLEBUST 1976). In Porphyra two osmotic agents, i. e. floridoside/isofloridoside (KAUSS 1968) and certain ions, such as K+ and Na+(EPPLEY et al. 1960) are considered for osmotic balance. Accumulations of ions (particularly Na+) in the cytoplasm during osmotic adaptation is improbable, because the activity of enzymes is generally inhibited by high ionic concentrations (FLOWERS et al. 1977).The cellular organization of Porphyra was studied with special emphasis on the development of the vacuolar system under different hyperosmotic conditions. Porphyra was cultivated at various strengths of the culture medium ASP 12 (PROVASOLI 1961) ranging from normal to 6 times concentrated (6x) culture medium. Por electron microscopy freeze fracturing was used (specimens fixed in 2% glutaraldehyde and incubated in 30% glycerol, preparation in a BALZERS BA 360 M apparatus), because chemical fixation gave poor results.

Elucidation of block boundaries as the dissolution channels in hydrated cement

1978 ◽  
Vol 36 (1) ◽  
pp. 484-485
Author(s):  
N.V. Belov ◽  
U.I. Papiashwili ◽  
B.E. Yudovich
Keyword(s):  
Liquid Phase ◽  
Grain Boundaries ◽  
Benzoyl Peroxide ◽  
Phase Contrast ◽  
Active Role ◽  
Point Of View ◽  
Hardened Cement ◽  
Hydrated Cement ◽  
Hardened Cement Paste

It has been almost universally adopted that dissolution of solids proceeds with development of uniform, continuous frontiers of reaction.However this point of view is doubtful / 1 /. E.g. we have proved the active role of the block (grain) boundaries in the main phases of cement, these boundaries being the areas of hydrate phases' nucleation / 2 /. It has brought to the supposition that the dissolution frontier of cement particles in water is discrete. It seems also probable that the dissolution proceeds through the channels, which serve both for the liquid phase movement and for the drainage of the incongruant solution products. These channels can be appeared along the block boundaries.In order to demonsrate it, we have offered the method of phase-contrast impregnation of the hardened cement paste with the solution of methyl metacrylahe and benzoyl peroxide. The viscosity of this solution is equal to that of water.

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