scholarly journals Large-scale identification of small noncoding RNA with strand-specific deep sequencing and characterization of a novel virulence-related sRNA in Brucella melitensis

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Zhijun Zhong ◽  
Xiaoyang Xu ◽  
Xinran Li ◽  
Shiwei Liu ◽  
Shuangshuang Lei ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Noncoding Rna ◽  
Large Scale ◽  
Brucella Melitensis ◽  
Small Noncoding Rna

scholarly journals Investigation of themiR16-1(C>T) + 7 Substitution in Seven Different Types of Cancer from Three Ethnic Groups

2009 ◽  
Vol 2009 ◽  
pp. 1-4 ◽  
Author(s):  
Hulya Yazici ◽  
Jennifer Zipprich ◽  
Tao Peng ◽  
Elif Z. Akisik ◽  
Hulya Tigli ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Ethnic Groups ◽  
Noncoding Rna ◽  
Large Scale ◽  
Prognostic Indicator ◽  
Genomic Region ◽  
Lymphocytic Leukemia ◽  
Aberrant Expression ◽  
Small Noncoding Rna ◽  
Different Types

Background. MicroRNAs are a type of small noncoding RNA molecules that have been shown to control gene expression in eukaryotes. Aberrant expression and alteration of miRNAs may be responsible for human diseases including cancer. AnmiR16-1(C>T)  + 7 gene mutation has been previously found in familial chronic lymphocytic leukemia patients, one of which reported a family history of breast cancer.miR16-1regulates the expression ofbcl-2, which is important in retinoblastoma, and is located in a genomic region that is frequently lost in nasopharyngeal and hepatocellular carcinomas (HCCs). Therefore,miR16-1may be potentially important in the etiology of several solid tumors. To understand the power of themiR16-1(C>T)  + 7 mutation as a prognostic and diagnostic risk factor, we investigated the mutation in patients with seven different types of cancer including 188 with breast, 102 with ovarian, and 22 nasopharyngeal carcinomas, 96 HCC, 872 chronic myeloid leukemia (CML), 39 chronic lymphocytic leukemia (CLL), and 46 retinoblastoma cases from three different ethnic groups and of hereditary and sporadic etiology.Methods.5′Nuclease TaqMan SNP genotyping assay was used to detect the miR16-1 geneC>Tsubstitution.Results. The miR16-1 (C>T)  + 7 substitution was not detected in any of the groups studied.Conclusions. Considering the large scale of our study, the representation of different ethnicities and levels of hereditary risk, we conclude that themiR-16-1(C>T)  + 7 mutation is not a good diagnostic or prognostic indicator of risk for the cancers tested.

scholarly journals Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants

2021 ◽  
Vol 22 (20) ◽  
pp. 11205
Author(s):  
Ziwei Li ◽  
Peng Tian ◽  
Tengbo Huang ◽  
Jianzi Huang
Keyword(s):  
Noncoding Rna ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Theoretical Study ◽  
Functional Characterization ◽  
Molecular Networks ◽  
Plant Responses ◽  
Crop Breeding ◽  
Target Module

Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.

scholarly journals The small noncoding RNA sr8384 determines solvent synthesis and cell growth in industrial solventogenic clostridia

2019 ◽  
Author(s):  
Yunpeng Yang ◽  
Nannan Lang ◽  
Huan Zhang ◽  
Lu Zhang ◽  
Changsheng Chai ◽  
...  
Keyword(s):  
Cell Growth ◽  
Clostridium Acetobutylicum ◽  
Noncoding Rna ◽  
Large Scale ◽  
Target Genes ◽  
Biological Processes ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Solventogenic Clostridia

ABSTRACTSmall noncoding RNAs (sncRNAs) are crucial regulatory molecules in organisms and are well known not only for their roles in the control of diverse essential biological processes but also for their value in genetic modification. However, to date, in gram-positive anaerobic solventogenic clostridia (which are a group of important industrial bacteria with exceptional substrate and product diversity), sncRNAs remain minimally explored, leading to a lack of detailed understanding regarding these important molecules and their use as targets for genetic improvement. Here, we performed large-scale phenotypic screens of a transposon-mediated mutant library ofClostridium acetobutylicum, a typical solventogenic clostridial species, and discovered a novel sncRNA (sr8384) that functions as a determinant positive regulator of growth and solvent synthesis. Comparative transcriptomic data combined with genetic and biochemical analyses revealed that sr8384 acts as a pleiotropic regulator and controls multiple targets that are associated with crucial biological processes, through direct or indirect interactions. Notably, modulation of the expression level of either sr8384 or its core target genes significantly increased the growth rate, solvent titer and productivity of the cells, indicating the importance of sr8384-mediated regulatory network inC. acetobutylicum. Furthermore, a homolog of sr8384 was discovered and proven to be functional in another importantClostridiumspecies,C. beijerinckii, suggesting the potential broad role of this sncRNA in clostridia. Our work showcases a previously unknown potent and complex role of sncRNAs in clostridia, providing new opportunities for understanding and engineering these anaerobes, including pathogenicClostridiumspecies.IMPORTANCEThe discovery of sncRNAs as new resources for functional studies and strain modifications are promising strategies in microorganisms. However, these crucial regulatory molecules have hardly been explored in industrially important solventogenic clostridia. Here, we identified sr8384 as a novel determinant sncRNA controlling cellular performance of solventogenicClostridium acetobutylicumand performed detailed functional analysis, which is the most in-depth study of sncRNAs in clostridia to date. We reveal the pleiotropic function of sr8384 and its multiple direct and indirect crucial targets, which represents a valuable source for understanding and optimizing this anaerobe. Of note, manipulation of these targets leads to improved cell growth and solvent synthesis. Our findings provide a new perspective for future studies on regulatory sncRNAs in clostridia.

scholarly journals A cancer-associated RNA polymerase III identity drives robust transcription and expression of SNAR-A noncoding RNA

2021 ◽  
Author(s):  
Kevin Van Bortle ◽  
David P. Marciano ◽  
Qing Liu ◽  
Andrew M. Lipchik ◽  
Sanjay Gollapudi ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Noncoding Rna ◽  
Large Scale ◽  
Immune Cell ◽  
Rna Polymerase Iii ◽  
Specific Class ◽  
Proliferating Cells ◽  
Small Noncoding Rna ◽  
Polymerase Iii ◽  
Pol Iii

ABSTRACTDysregulation of the RNA polymerase III (Pol III) transcription program, which synthesizes tRNA and other classes of small noncoding RNA critical for cell growth and proliferation, is associated with cancer and human disease. Previous studies have identified two distinct Pol III isoforms defined by the incorporation of either subunit POLR3G (RPC7α) during early development, or POLR3GL (RPC7β) in specialized tissues. Though POLR3G is re-established in cancer and immortalized cell lines, the contributions of these isoforms to transcription potential and transcription dysregulation in cancer remain poorly defined. Using an integrated Pol III genomic profiling approach in combination with in vitro differentiation and subunit disruption experiments, we discover that loss of subunit POLR3G is accompanied by a restricted repertoire of genes transcribed by Pol III. In particular, we observe that a specific class of small noncoding RNA, SNAR-A, is exquisitely sensitive to the availability of subunit POLR3G in proliferating cells. Taken further, large-scale analysis of Pol III subunit expression and downstream chromatin features identifies concomitant loss of POLR3G and SNAR-A activity across a multitude of differentiated primary immune cell lineages, and conversely, coordinate re-establishment of POLR3G expression and SNAR-A features in a variety of human cancers. These results altogether argue against strict redundancy models for subunits POLR3G and POLR3GL, and instead support a model in which Pol III identity itself functions as an important transcriptional regulatory mechanism. Upregulation of POLR3G, which is driven by MYC, identifies a subgroup of patients with unfavorable survival outcomes in specific cancers, further implicating the POLR3G-enhanced transcription repertoire as a potential disease factor.

scholarly journals Molecular Characterization of Brucella abortus Chromosome II Recombination

2003 ◽  
Vol 185 (20) ◽  
pp. 6130-6136 ◽  
Author(s):  
Georgios Tsoktouridis ◽  
Christian A. Merz ◽  
Simon P. Manning ◽  
Renée Giovagnoli-Kurtz ◽  
Leanne E. Williams ◽  
...  
Keyword(s):  
Brucella Abortus ◽  
Large Scale ◽  
Brucella Melitensis ◽  
Subtractive Hybridization ◽  
Open Reading Frames ◽  
Suppressive Subtractive Hybridization ◽  
Recombination Mechanism ◽  
Chromosome Ii ◽  
Reading Frames

ABSTRACT Large-scale genomic rearrangements including inversions, deletions, and duplications are significant in bacterial evolution. The recently completed Brucella melitensis 16M and Brucella suis 1330 genomes have facilitated the investigation of such events in the Brucella spp. Suppressive subtractive hybridization (SSH) was employed in identifying genomic differences between B. melitensis 16M and Brucella abortus 2308. Analysis of 45 SSH clones revealed several deletions on chromosomes of B. abortus and B. melitensis that encoded proteins of various metabolic pathways. A 640-kb inversion on chromosome II of B. abortus has been reported previously (S. Michaux Charachon, G. Bourg, E. Jumas Bilak, P. Guigue Talet, A. Allardet Servent, D. O'Callaghan, and M. Ramuz, J. Bacteriol. 179:3244-3249, 1997) and is further described in this study. One end of the inverted region is located on a deleted TATGC site between open reading frames BMEII0292 and BMEII0293. The other end inserted at a GTGTC site of the cyclic-di-GMP phosphodiesterase A (PDEA) gene (BMEII1009), dividing PDEA into two unequal DNA segments of 160 and 977 bp. As a consequence of inversion, the 160-bp segment that encodes the N-terminal region of PDEA was relocated at the opposite end of the inverted chromosomal region. The splitting of the PDEA gene most likely inactivated the function of this enzyme. A recombination mechanism responsible for this inversion is proposed.

scholarly journals Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

PLoS Genetics ◽  
2008 ◽  
Vol 4 (8) ◽  
pp. e1000163 ◽  
Author(s):  
Alexandra Sittka ◽  
Sacha Lucchini ◽  
Kai Papenfort ◽  
Cynthia M. Sharma ◽  
Katarzyna Rolle ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Noncoding Rna ◽  
Transcriptional Regulator ◽  
Sequencing Analysis ◽  
Small Noncoding Rna ◽  
Mrna Targets ◽  
Deep Sequencing Analysis

Some applications of electron beam microanalysis techniques in VLSI process evaluation

1983 ◽  
Vol 41 ◽  
pp. 160-161
Author(s):  
Simon Thomas
Keyword(s):  
Integrated Circuits ◽  
Process Evaluation ◽  
Large Scale ◽  
Technology Development ◽  
Analytical Techniques ◽  
Successful Implementation ◽  
Analysis Of Failures ◽  
Characterization Of Materials ◽  
Circuits Vlsi

Trends in the technology development of very large scale integrated circuits (VLSI) have been in the direction of higher density of components with smaller dimensions. The scaling down of device dimensions has been not only laterally but also in depth. Such efforts in miniaturization bring with them new developments in materials and processing. Successful implementation of these efforts is, to a large extent, dependent on the proper understanding of the material properties, process technologies and reliability issues, through adequate analytical studies. The analytical instrumentation technology has, fortunately, kept pace with the basic requirements of devices with lateral dimensions in the micron/ submicron range and depths of the order of nonometers. Often, newer analytical techniques have emerged or the more conventional techniques have been adapted to meet the more stringent requirements. As such, a variety of analytical techniques are available today to aid an analyst in the efforts of VLSI process evaluation. Generally such analytical efforts are divided into the characterization of materials, evaluation of processing steps and the analysis of failures.

Characterization of seawater reverse osmosis fouled membranes from large scale commercial desalination plant

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Reverse Osmosis ◽  
Large Scale ◽  
Retention Rate ◽  
Local Level ◽  
Microscopic Analysis ◽  
Transmembrane Pressure ◽  
Hydraulic Permeability ◽  
Seawater Reverse Osmosis ◽  
A Chain

The objective of this work is to study the ageing state of a used reverse osmosis (RO) membrane taken in Algeria from the Benisaf Water Company seawater desalination unit. The study consists of an autopsy procedure used to perform a chain of analyses on a membrane sheet. Wear of the membrane is characterized by a degradation of its performance due to a significant increase in hydraulic permeability (25%) and pressure drop as well as a decrease in salt retention (10% to 30%). In most cases the effects of ageing are little or poorly known at the local level and global measurements such as (flux, transmembrane pressure, permeate flow, retention rate, etc.) do not allow characterization. Therefore, a used RO (reverse osmosis) membrane was selected at the site to perform the membrane autopsy tests. These tests make it possible to analyze and identify the cause as well as to understand the links between performance degradation observed at the macroscopic scale and at the scale at which ageing takes place. External and internal visual observations allow seeing the state of degradation. Microscopic analysis of the used membranes surface shows the importance of fouling. In addition, quantification and identification analyses determine a high fouling rate in the used membrane whose foulants is of inorganic and organic nature. Moreover, the analyses proved the presence of a biofilm composed of protein.

Characterization of Interconnect Defects Using Scanning Thermal Conductivity Microscopy

2004 ◽  
Author(s):  
H.W. Ho ◽  
J.C.H. Phang ◽  
A. Altes ◽  
L.J. Balk
Keyword(s):  
Thermal Conductivity ◽  
Integrated Circuits ◽  
Large Scale

Abstract In this paper, scanning thermal conductivity microscopy is used to characterize interconnect defects due to electromigration. Similar features are observed both in the temperature and thermal conductivity micrographs. The key advantage of the thermal conductivity mode is that specimen bias is not required. This is an important advantage for the characterization of defects in large scale integrated circuits. The thermal conductivity micrographs of extrusion, exposed and subsurface voids are presented and compared with the corresponding topography and temperature micrographs.

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