scholarly journals Genomics Insights: Inter-Laboratory Variability in Array-Based RNA Quantification Methods

2013 ◽  
Vol 6 ◽  
pp. GEI.S11909
Author(s):  
Victoria Y. Wong ◽  
Manuel X. Duval
Keyword(s):  
Large Fraction ◽  
State Level ◽  
Measurement Procedure ◽  
Subsequent Treatment ◽  
Biological Information ◽  
Dna Arrays ◽  
Ribonucleic Acids ◽  
Rna Molecules ◽  
Wide Range ◽  
The Stability

Ribonucleic acids (RNA) are hypothesized to have preceded their derivatives, deoxyribonucleic acids (DNA), as the molecular media of genetic information when life emerged on earth. Molecular biologists are accustomed to the dramatic effects a subtle variation in the ribose moiety composition between RNA and DNA can have on the stability of these molecules. While DNA is very stable after extraction from biological samples and subsequent treatment, RNA is notoriously labile. The short half-life property, inherent to RNA, benefits cells that do not need to express their entire repertoire of proteins. The cellular machinery turns off the production of a given protein by shutting down the transcription of its cognate coding gene and by either actively degrading the remaining mRNA or allowing it to decay on its own. The steady-state level of each mRNA in a given cell varies continuously and is specified by changing kinetics of synthesis and degradation. Because it is technically possible to simultaneously measure thousands of nucleic acid molecules, these quantities have been studied by the life sciences community to investigate a range of biological problems. Since the RNA abundance can change according to a wide range of perturbations, this makes it the molecule of choice for exploring biological systems; its instability, on the other hand, could be an underestimated source of technical variability. We found that a large fraction of the RNA abundance originally present in the biological system prior to extraction was masked by the RNA labeling and measurement procedure. The method used to extract RNA molecules from cells and to label them prior to hybridization operations on DNA arrays affects the original distribution of RNA. Only if RNA measurements are performed according to the same procedure can biological information be inferred from the assay read out.

scholarly journals NEAT1 and Paraspeckles in Cancer Development and Chemoresistance

2020 ◽  
Vol 6 (4) ◽  
pp. 43
Author(s):  
Gabriel Pisani ◽  
Byron Baron
Keyword(s):  
Cancer Progression ◽  
Drug Targets ◽  
Cellular Biology ◽  
Diverse Range ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Wide Range ◽  
Protein Research ◽  
The Stability ◽  
Abundant Transcript

Non-coding RNA were previously thought to be biologically useless molecules arising from simple transcriptional noise. These are now known to be an integral part of cellular biology and pathology. The wide range of RNA molecules have a diverse range of structures, functions, and mechanisms of action. However, structural long non-coding RNAs (lncRNAs) are a particular class of ncRNA that are proving themselves more and more important in cellular biology, as the exact structures that such RNAs form and stabilise become more understood. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a specific structural RNA emerging as a critical component in the progress and development of cancer. NEAT1 forms part of multiple biological pathways, acting through a diverse group of mechanisms. The most important of these is the formation of the paraspeckle, through which it can influence the stability of a tumour to develop resistance to drugs. This review will thus cover the range of effects by which NEAT1 interacts with cancer progression in order to describe the various roles of NEAT1 in chemoresistance, as well as to identify drug targets that protein research alone could not provide.

scholarly journals Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA

2019 ◽  
Vol 5 (2) ◽  
pp. 38 ◽  
Author(s):  
Yelyzaveta Shlyakhtina ◽  
Katherine L. Moran ◽  
Maximiliano M. Portal
Keyword(s):  
Cell Fate ◽  
Mammalian Cells ◽  
High Throughput Sequencing ◽  
General Pattern ◽  
Nuclear Architecture ◽  
Biological Information ◽  
Current Evidence ◽  
Rna Molecules ◽  
Sequencing Technologies ◽  
Wide Range

During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.

scholarly journals Key institutional actors of European security: Current state and challenges

2020 ◽  
Vol 2 (2) ◽  
pp. 37-49
Author(s):  
Boris Tučić
Keyword(s):  
International Relations ◽  
State Level ◽  
European Security ◽  
Security Challenges ◽  
Wide Range ◽  
The Face ◽  
Security Actor ◽  
The Stability ◽  
Institutional Actors ◽  
The Eu

This paper addresses the adaptability and ability of three institutional actors of European securitythe EU, the NATO, and the OSCE - to properly respond to security challenges facing Europe, especially those existing at the non-state level. The position, status, nature and functions, and the relations within and between the key institutional actors of European security are considered within the study of international relations. Weaknesses in their operation have been identified, which are of a structural nature, but also a consequence of the international environment. In the EU, it is possible to identify a wide range of security policies, different developments and efficiencies. As a "civil force", the EU addresses security challenges using civil, political and economic instruments, focusing on the stability of its immediate environment. However, in order to play the role of a global security actor, the EU must build an autonomous security identity, which is, for now, an unsolvable problem. The NATO continues to be the personification of hard, military power in the face of security challenges, which does not sufficiently guarantee its security, and often means breaching the security of other countries. The OSCE, like NATO, is a relic of the past and its basic quality is diplomatic inclusiveness. It is an organization of "displaced" political power, without the necessary authority. The weaknesses of these three institutional actors, as well as the complexity of international relations, require a far higher level of political, functional and operational adaptability in order to understand and address the existing security challenges.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

Evaluation of the accuracy indicators in determination of the coating thickness by crater grinding method

2020 ◽  
Vol 86 (7) ◽  
pp. 39-44
Author(s):  
K. V. Gogolinsky ◽  
A. E. Ivkin ◽  
V. V. Alekhnovich ◽  
A. Yu. Vasiliev ◽  
A. E. Tyurnina ◽  
...  
Keyword(s):  
Coating Thickness ◽  
Functional Dependence ◽  
Measurement Procedure ◽  
Metrological Certification ◽  
Measuring Instruments ◽  
Properties Of Coatings ◽  
Special Equipment ◽  
Grinding Method ◽  
Accuracy Of Measurements ◽  
Wide Range

Thickness is one of the key indicators characterizing the quality and functional properties of coatings. Various indirect methods (electromagnetic, radiation, optical) most often used in practice to measure thickness are based on the functional dependence of a particular physical parameter of the system «base – coating» on the coating thickness. The sensitivity of these procedures to the certain properties of coatings imposes the main restriction to the accuracy of measurements. Therefore, the development and implementation of the approaches based on direct measurements of geometric parameters of the coating appears expedient. These methods often belong to the class of «destructive» and, in addition to measuring instruments, require the use of special equipment. To ensure the uniformity of measurements in the laboratory or technological control, these methods are isolated as a separate procedure (method) and must undergo metrological certification in accordance with GOST R 8.563–2009. We present implementation, metrological certification and practical application of the method for measuring thickness of coatings by crater-grinding method. The principles of technical implementation of test equipment, measurement procedure and calculation formulas are described. The results of evaluating the accuracy indicators of the proposed procedure by calculation and experimental methods are presented. In both cases, the relative error did not exceed 6%. The applicability of the developed technique is shown for a wide range of coating materials (from soft metals to superhard ceramics) of different thickness (with from units to hundreds of micrometers). Apart from the goals of process control and outgoing inspection, the method can be recommended as a reference measurement procedure for calibration of measures and adjusting samples for various types of thickness gauges.

Safety assessment of biological raw materials in the system of medicines quality assurance

2020 ◽  
pp. 63-72
Author(s):  
Yu. Olefir ◽  
E. Sakanyan ◽  
I. Osipova ◽  
V. Dobrynin ◽  
M. Smirnova ◽  
...  
Keyword(s):  
Raw Materials ◽  
State Level ◽  
The State ◽  
Spongiform Encephalopathy ◽  
Safety Standards ◽  
Wide Range ◽  
The Russian Federation ◽  
Key Aspects ◽  
First Time ◽  
Medicines Quality

The entry of a wide range of biotechnological products into the pharmaceutical market calls for rein-forcement of the quality, efficacy and safety standards at the state level. The following general monographs have been elaborated for the first time to be included into the State Pharmacopoeia of the Russian Federation, XIV edition: "Viral safety" and "Reduction of the risk of transmitting animal spongiform encephalopathy via medicinal products". These general monographs were elaborated taking into account the requirements of foreign pharmacopoeias and the WHO recommendations. The present paper summarises the key aspects of the monographs.

Assessment of Water Footprint in Selected Crops: A State Level Appraisal

2017 ◽  
Vol 1 (1) ◽  
pp. 11-25
Author(s):  
Mohammad Suhail
Keyword(s):  
Water Use ◽  
Water Footprint ◽  
Large Fraction ◽  
State Level ◽  
Soil Survey ◽  
National Bureau ◽  
Blue Water ◽  
Total Water Consumption ◽  
Balanced Approach ◽  
Green Component

Every commodity or goods has intake of water i.e. either in processing or furnished stage. Thus, the present study propensities macro-level (states-level) water footprint (WFP) assessment of selected eight crops namely, Wheat, Barley, Maize, Millets, Rice, Sorghum, Soybeans and Tea. The aim of present research is to assess water use in selected crops at field level. In addition, the spatial evaluation at state level also considered as one of the significant objective to understand regional disparity and/or similarly. Methodology and approach of assessment was adopted from Water Footprint Assessment Manual (2011). Data was collected from state Agricultural Directorate, National Bureau of Soil Survey and landuse, published reports and online database such as FAOSTAT, WMO, WFN, and agriculture census. Results show that green component of WFP contributes large fraction as about 72 percent, while blue and grey component amounted of about 19 and 9 percent of the total water consumption, respectively. Moreover, spatial variability of blue, green and grey among the states assimilated by soil regime and climate barriers. Supply of blue water is high where the region imparted to semi-arid or arid land. Consequently, a balanced approach between green and blue water use has been recommended in the present study to address increasing water demand in the future.

Insights into Potent Therapeutical Antileukemic Agent L-glutaminase Enzyme Under Solid-state Fermentation: A Review

2020 ◽  
Vol 21 (3) ◽  
pp. 211-220 ◽  
Author(s):  
Chandrasai Potla Durthi ◽  
Madhuri Pola ◽  
Satish Babu Rajulapati ◽  
Anand Kishore Kola
Keyword(s):  
Solid State ◽  
Solid State Fermentation ◽  
Food Industry ◽  
Energy Requirement ◽  
Production Studies ◽  
Wide Range ◽  
Hybridoma Technology ◽  
Bacteria And Fungi ◽  
The Stability ◽  
Glutaminase Activity

Aim & objective: To review the applications and production studies of reported antileukemic drug L-glutaminase under Solid-state Fermentation (SSF). Overview: An amidohydrolase that gained economic importance because of its wide range of applications in the pharmaceutical industry, as well as the food industry, is L-glutaminase. The medical applications utilized it as an anti-tumor agent as well as an antiretroviral agent. L-glutaminase is employed in the food industry as an acrylamide degradation agent, as a flavor enhancer and for the synthesis of theanine. Another application includes its use in hybridoma technology as a biosensing agent. Because of its diverse applications, scientists are now focusing on enhancing the production and optimization of L-glutaminase from various sources by both Solid-state Fermentation (SSF) and submerged fermentation studies. Of both types of fermentation processes, SSF has gained importance because of its minimal cost and energy requirement. L-glutaminase can be produced by SSF from both bacteria and fungi. Single-factor studies, as well as multi-level optimization studies, were employed to enhance L-glutaminase production. It was concluded that L-glutaminase activity achieved by SSF was 1690 U/g using wheat bran and Bengal gram husk by applying feed-forward artificial neural network and genetic algorithm. The highest L-glutaminase activity achieved under SSF was 3300 U/gds from Bacillus sp., by mixture design. Purification and kinetics studies were also reported to find the molecular weight as well as the stability of L-glutaminase. Conclusion: The current review is focused on the production of L-glutaminase by SSF from both bacteria and fungi. It was concluded from reported literature that optimization studies enhanced L-glutaminase production. Researchers have also confirmed antileukemic and anti-tumor properties of the purified L-glutaminase on various cell lines.

scholarly journals Polymer-Drug Conjugates as Nanotheranostic Agents

2021 ◽  
Vol 2 (1) ◽  
pp. 63-81
Author(s):  
Sajana Manandhar ◽  
Erica Sjöholm ◽  
Johan Bobacka ◽  
Jessica M. Rosenholm ◽  
Kuldeep K. Bansal
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Treatment Options ◽  
The Body ◽  
Drug Conjugates ◽  
Imaging Characteristics ◽  
Wide Range ◽  
Systemic Side Effects ◽  
Theranostic Agents ◽  
The Stability

Since the last decade, the polymer-drug conjugate (PDC) approach has emerged as one of the most promising drug-delivery technologies owing to several benefits like circumventing premature drug release, offering controlled and targeted drug delivery, improving the stability, safety, and kinetics of conjugated drugs, and so forth. In recent years, PDC technology has advanced with the objective to further enhance the treatment outcomes by integrating nanotechnology and multifunctional characteristics into these systems. One such development is the ability of PDCs to act as theranostic agents, permitting simultaneous diagnosis and treatment options. Theranostic nanocarriers offer the opportunity to track the distribution of PDCs within the body and help to localize the diseased site. This characteristic is of particular interest, especially among those therapeutic approaches where external stimuli are supposed to be applied for abrupt drug release at the target site for localized delivery to avoid systemic side effects (e.g., Visudyne®). Thus, with the help of this review article, we are presenting the most recent updates in the domain of PDCs as nanotheranostic agents. Different methodologies utilized to design PDCs along with imaging characteristics and their applicability in a wide range of diseases, have been summarized in this article.

scholarly journals No-z Model for Magnetic Fields of Different Astrophysical Objects and Stability of the Solutions

Data ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Evgeny Mikhailov ◽  
Daniela Boneva ◽  
Maria Pashentseva
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Large Scale ◽  
Point Of View ◽  
Accretion Discs ◽  
Wide Range ◽  
Astrophysical Objects ◽  
Alpha Effect ◽  
The Stability ◽  
The Magnetic Field

A wide range of astrophysical objects, such as the Sun, galaxies, stars, planets, accretion discs etc., have large-scale magnetic fields. Their generation is often based on the dynamo mechanism, which is connected with joint action of the alpha-effect and differential rotation. They compete with the turbulent diffusion. If the dynamo is intensive enough, the magnetic field grows, else it decays. The magnetic field evolution is described by Steenbeck—Krause—Raedler equations, which are quite difficult to be solved. So, for different objects, specific two-dimensional models are used. As for thin discs (this shape corresponds to galaxies and accretion discs), usually, no-z approximation is used. Some of the partial derivatives are changed by the algebraic expressions, and the solenoidality condition is taken into account as well. The field generation is restricted by the equipartition value and saturates if the field becomes comparable with it. From the point of view of mathematical physics, they can be characterized as stable points of the equations. The field can come to these values monotonously or have oscillations. It depends on the type of the stability of these points, whether it is a node or focus. Here, we study the stability of such points and give examples for astrophysical applications.

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