Regulation Of Genetic Information Research Articles

Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations.

RNA plays critical roles in the transmission and regulation of genetic information and is increasingly used in biomedical and biotechnological applications. Functional RNAs contain extended double-stranded regions, and the structure of double-stranded RNA (dsRNA) has been revealed at high resolution. However, the dependence of the properties of the RNA double helix on environmental effects, notably temperature, is still poorly understood. Here, we use single-molecule magnetic tweezer measurements to determine the dependence of the dsRNA twist on temperature. We find that dsRNA unwinds with increasing temperature, even more than DNA, with ΔTwRNA = -14.4 ± 0.7°/(°C·kbp), compared to ΔTwDNA = -11.0 ± 1.2°/(°C·kbp). All-atom molecular dynamics (MD) simulations using a range of nucleic acid force fields, ion parameters, and water models correctly predict that dsRNA unwinds with rising temperature but significantly underestimate the magnitude of the effect. These MD data, together with additional MD simulations involving DNA and DNA-RNA hybrid duplexes, reveal a linear correlation between the twist temperature decrease and the helical rise, in line with DNA but at variance with RNA experimental data. We speculate that this discrepancy might be caused by some unknown bias in the RNA force fields tested or by as yet undiscovered transient alternative structures in the RNA duplex. Our results provide a baseline to model more complex RNA assemblies and to test and develop new parametrizations for RNA simulations. They may also inspire physical models of the temperature-dependent dsRNA structure.

Crosstalk between Tumor-Associated Macrophages and MicroRNAs: A Key Role in Tumor Microenvironment.

As an in-depth understanding of immunotherapy continues to grow, current anticancer therapy research is increasingly focused on the tumor microenvironment (TME). MicroRNAs (miRNAs) play crucial roles in the regulation of genetic information and expression and mediate interactions between tumor cells and components in the TME, such as tumor-associated macrophages (macrophages). Macrophages are abundant in the TME, and their different polarization directions can promote or inhibit tumor growth and progression. By regulating biological behaviors, such as macrophage recruitment, infiltration, and polarization, miRNAs can affect various molecular pathways to regulate tumor progression and treatment response. In this review, we discuss in detail the effects of macrophages on tumors and the multifaceted effects of miRNAs on macrophages. We also discuss the potential clinical applications and prospects of targeted therapy based on miRNAs, novel clinical biomarkers, and drug delivery systems.

Complete Mapping of DNA‐Protein Interactions at the Single‐Molecule Level

DNA–protein interaction plays an essential role in the storage, expression, and regulation of genetic information. A 1D/3D facilitated diffusion mechanism has been proposed to explain the extraordinarily rapid rate of DNA‐binding protein (DBP) searching for cognate sequence along DNA and further studied by single‐molecule experiments. However, direct observation of the detailed chronological protein searching image is still a formidable challenge. Here, for the first time, a single‐molecule electrical monitoring technique is utilized to realize label‐free detection of the DBP–DNA interaction process based on high‐gain silicon nanowire field‐effect transistors (SiNW FETs). The whole binding process of WRKY domain and DNA has been visualized with high sensitivity and single‐base resolution. Impressively, the swinging of hydrogen bonds between amino acid residues and bases in DNA induce the dynamic collective motion of DBP–DNA. This in situ, label‐free electrical detection platform provides a practical experimental methodology for dynamic studies of various biomolecules.

Modern Approaches to Treatment of Abacterial Prostatitis and Benign Prostate Hyperplasia Using a Prostate Extract of Bulls

The formation of the inflammatory process in the prostatic tissue in most cases occurs with minimal clinical manifestations, and their clinical and diagnostic verification often does not reflect the actual state of the problem. This requires a search for clinical solutions in order to minimize the formation of inflammatory processes and the regulation of trophic functions in the compromised tissues of the prostate gland. The use of conservative therapy in people with chronic prostatitis and benign prostatic hyperplasia is considered the leading preventive and therapeutic method, therefore, the search for new and improvement of existing pharmacological drugs is an urgent issue. The action of specific amino acid molecules of the mediator link of the bioregulation system – cytomedines, is due to the regulatory capabilities of low molecular weight peptides, which are multifunctional, capable of inducing the release of other regulatory substances and the formation of the so-called. «Peptide cascade» in a certain place in a short time. Their final effect is not enhanced by excessive intake, is not dose-dependent and is expressed by a complete systemic effect on general physiological processes (apoptosis, proliferation, various types of metabolism, regulation of genetic information). Vitaprost is an extract of the prostate gland of bulls, lyophilized from an aqueous solution, among the organ peptides it stands out with high clinical efficacy and the absence of side reactions. Its main clinical effects are considered: anti-inflammatory (the ability to reduce edema and leukocyte infiltration in the tissues of the prostate gland), vascular (able to improve the processes of microcirculation and platelet-vascular homeostasis), trophic (a positive effect on spermatogenesis in the form of an increase in the functional activity of spermatozoa and the qualitative characteristics of sperm) , immunoregulatory (stimulates the activity of the humoral link of immunity and some factors of the body’s resistance), antimicrobial (stimulates the antimicrobial activity of neutrophils), neurotrophic (effect on the muscle tone of the urinary bladder and rectum). The use of prostatilen, as an organotropic polypeptide with high tissue specificity, is a justified pharmacological model for the treatment of infectious-inflammatory and congestive conditions in the structures of the prostate-vesicular complex in men of various ages. The positive effect of prostatilen is due to a series of complementary pathogenetic mechanisms, which include anti-inflammatory, immunotropic, trophic and neurovascular effects on the above structures. The clinical effect of the rectal form of prostatilen, demonstrated in cases of a combination of chronic prostatitis with benign prostatic hyperplasia and confirmed by a series of long-term studies, makes it possible to use it both in mono- and in combination therapy of these conditions, taking into account the individual conditions of the course of the disease.

Recent Advances in the Application of CRISPR/Cas9 Gene Editing System in Poultry Species.

CRISPR/Cas9 system genome editing is revolutionizing genetics research in a wide spectrum of animal models in the genetic era. Among these animals, is the poultry species. CRISPR technology is the newest and most advanced gene-editing tool that allows researchers to modify and alter gene functions for transcriptional regulation, gene targeting, epigenetic modification, gene therapy, and drug delivery in the animal genome. The applicability of the CRISPR/Cas9 system in gene editing and modification of genomes in the avian species is still emerging. Up to date, substantial progress in using CRISPR/Cas9 technology has been made in only two poultry species (chicken and quail), with chicken taking the lead. There have been major recent advances in the modification of the avian genome through their germ cell lineages. In the poultry industry, breeders and producers can utilize CRISPR-mediated approaches to enhance the many required genetic variations towards the poultry population that are absent in a given poultry flock. Thus, CRISPR allows the benefit of accessing genetic characteristics that cannot otherwise be used for poultry production. Therefore CRISPR/Cas9 becomes a very powerful and robust tool for editing genes that allow for the introduction or regulation of genetic information in poultry genomes. However, the CRISPR/Cas9 technology has several limitations that need to be addressed to enhance its use in the poultry industry. This review evaluates and provides a summary of recent advances in applying CRISPR/Cas9 gene editing technology in poultry research and explores its potential use in advancing poultry breeding and production with a major focus on chicken and quail. This could aid future advancements in the use of CRISPR technology to improve poultry production.

International Legal Regulation of Preimplantation Genetic Diagnostics (PGD) and Trends in the Development of Russian Legislation in the Field of Assisted Reproductive Technologies

The article analyzes key instruments of international legal regulation of preimplantation genetic diagnostics (PGD) procedure. The authors substantiate the conclusion that the requirements and principles formulated in these instruments can be successfully used for the development and improvement of the national legal framework aimed at regulating the PGA. The main directions of such use are defined. First, it is necessary to consider the existence of genetic predisposition to a particular disease or chromosomal disorder (the medical purpose) and provide a qualified consultation of a genetic scientist concerning the mechanism and consequences of diagnostics. Secondly, the legal regulation of genetic information obtained through the PGA requires an independent normative framework: determining the framework the law-maker must be guided by the fact that any intervention in the human genome aimed at modifying it may be carried out only for preventive, diagnostic or therapeutic purposes. In this regard, it is important to prohibit the PGA for social purposes (selection of embryo according to specific characteristics, establishment of compatibility between a donor and a recipient, looking beyond the prohibition to choose the embryo gender that is currently imposed under Russian legislation). Third, a separate regulatory framework is needed to resolve the problem of informing the patient about the results of examination: in addition to the right to be informed of the results of examination, it is also necessary to recognize the individual’s «right not to know,» particularly relevant to predictive genetic research.

Insights into the non-covalent interaction between modified nucleobases and graphene nanoflake from first-principles

The four new modified nucleobases (NBs), 5-mC, 5-hmC, 5-fC and 5-caC, besides the regular adenine, thymine, cytosine, guanine and uracil, are important in expression and regulation of genetic information. These four new major NBs are all derived from base cytosine by adding various functional groups, and their identification from the regular ones are much desired currently. However, the four new major NBs interacted with graphene on its surface have not been well considered, though a number of studies of regular NBs adsorbed on low-dimensional carbon materials are available to identify different NBs. This work reveals the interaction between the four new major NBs and graphene nanoflake substrate by using first-principle calculations based on density functional theory. The structure, energy and non-covalent interaction of the graphene/NBs complex are calculated and explored in details. The energy decomposition analysis, reduced density gradient, charge transfer and projected density of states are also performed to investigate the nature of the interaction between NBs and graphene nanoflake. Electrostatic and orbital interaction are found to be important to stabilize the interaction between NBs and graphene nanoflake, though orbital interaction is less significant. It is very noticed that the proportion of dispersion interaction could be more than half of the sum attractive contributions. Thus, dispersion interaction is the most dominating factor in stabilizing graphene/NBs complexes. The results of reduced density gradient further confirm that the interaction between the graphene nanoflake and NBs is mainly the van der Waals type. Besides, much attention is paid to the interaction differences between the four new major NBs and the pristine cytosine, and the impact of the introduced functional groups of the four new major NBs on the structure, energy and interaction is also discussed.

Challenges and Opportunities in DNA-based Asymmetric Catalysis.

The biological importance of nucleic acids for the storage, expression and regulation of genetic information is now well understood. By taming the chemical synthesis of these biomolecules, chemists have been able to engineer new architectures based on the ability of DNA and RNA to fold into secondary or even more complex tertiary structures with applications in medicinal chemistry, diagnostics or even material sciences. Exploiting the fascinating helical structure of DNA and RNA to develop new chiral bio-hybrid catalysts capable of promoting highly stereoselective transformations under mild and eco-compatible conditions is also an emerging area of research. In this short review, we report our recent results in the field of DNA-based asymmetric catalysis as well as the challenges and promising perspectives that lie in front of us.

Summary and prospect of medicinal plant active substances in regulation of p65 nuclear translocation

As the most important nuclear transcription factors in the cells, NF-κB is involved in many intracellular signaling pathways and transcription and regulation of genetic information. The signal transduction pathways mainly include the activation of IκB kinase, degradation of IκB protein and the nuclear translocation of p65. p65 trans-nuclear binding with DNA is the key for NF-κB to play a role. Abnormal activation of NF-κB is a major factor in the induction of oxidative stress, inflammation, cancer and so on. Therefore, maintaining the balance of NF-κB activity and regulating the nuclear translocation of p65 have great significance for further research on related subjects. In this paper, the regulation effects of the main active substances of medicinal plants (such as polyphenols, saponins, and alkaloids) on p65 nuclear translocation and the upstream pathway of NF-κB were discussed, expecting to provide reference for the development of natural active substances for functional food.

Standardized collection of MNase-seq experiments enables unbiased dataset comparisons

BackgroundThe organization of eukaryotic DNA into chromatin has a strong influence on the accessibility and regulation of genetic information. The locations and occupancies of a principle component of chromatin, nucleosomes, are typically assayed through use of enzymatic digestion with micrococcal nuclease (MNase). MNase is an endo-exo nuclease that preferentially digests naked DNA and the DNA in linkers between nucleosomes, thus enriching for nucleosome-associated DNA. To determine nucleosome organization genome-wide, DNA remaining from MNase digestion is sequenced using high-throughput sequencing technologies (MNase-seq). Unfortunately, the results of MNase-seq can vary dramatically due to technical differences and this confounds comparisons between MNase-seq experiments, such as examining condition-dependent chromatin organizations.ResultsIn this study we use MNase digestion simulations to demonstrate how MNase-seq signals can vary for different nucleosome configuration when experiments are performed with different extents of MNase digestion. Signal variation in these simulations reveals an important DNA sampling bias that results from a neighborhood effect of MNase digestion techniques. The presence of this neighborhood effect ultimately confounds comparisons between different MNase-seq experiments. To address this issue we present a standardized chromatin preparation which controls for technical variance between MNase-based chromatin preparations and enables the collection of similarly sampled (matched) chromatin populations. Standardized preparation of chromatin includes a normalization step for DNA input into MNase digestions and close matching of the extent of digestion between each chromatin preparation using gel densitometry analysis. The protocol also includes directions for successful pairing with multiplex sequencing reactions.ConclusionsWe validated our method by comparing the experiment-to-experiment variation between biological replicates of chromatin preparations from S. cerevisiae. Results from our matched preparation consistently produced MNase-seq datasets that were more closely correlated than other unstandardized approaches. Additionally, we validated the ability of our approach at enabling accurate downstream comparisons of chromatin structures, by comparing the specificity of detecting Tup1-dependent chromatin remodeling events in comparisons between matched and un-matched wild-type and tup1Δ MNase-seq datasets. Our matched MNase-seq datasets demonstrated a significant reduction in non-specific (technical) differences between experiments and were able to maximize the detection of biologically-relevant (Tup1-dependent) changes in chromatin structure.

Abstract 157: Variability of microRNA measurements in breast ductal carcinomas

Abstract MicroRNAs (miRNAs) are a newly identified class of molecules involved in the post transcriptional regulation of genetic information. Multiple approaches have been developed to measure miRNAs including the measurement of miRNAs in paraffin embedded tissue. There have been few reported studies of the reproducibility of miRNA measurements, especially in paraffin embedded tissues, and how such measurements might vary due to tissue heterogeneity and/or analytical variability. We used microdissected paraffin embedded samples of ductal carcinoma of the breast enriched to a tumor nuclear cellularity of at least 80% to determine the reproducibility of analysis of miRNAs extracted from paraffin sections. From each of 3 microdissected paraffin embedded tissues, six 10μ paraffin sections were cut and combined as one specimen and the following six 10μ sections were combined as a second specimen from the same case. While the sections were adjacent, this would incorporate variation due to tissue heterogeneity over 0.12mm of the specimen that was analyzed. All six specimens were blinded and 1500 miRNAs including miRNAs from mice, rats and plants as controls were analyzed by High Throughput Genomics (HTG) considering each of these 6 specimens as an independent specimen. Even with tissue heterogeneity, the correlations of the values of miRNA of the three pairs of specimens were 0.96, 0.90 and 0.83; the 12 correlations between specimens of different cases did not excel 0.9 and only 2 exceeded 0.8. Results of combining alternative paraffin sections into 2 specimens from these same cases and laser capture microdissection specimens are pending to separate differences due to variation in tissue from analytical variables. Of note, the 22 most upregulated miRNAs (X20 to X30 basal levels) in these breast ductal carcinomas include the following: Let 7b, Let 7f, 1225-3P, 1228, 1237, 1280, 1281, 1308, 16, 1826, 191, 200c, 23a, 27a, 574-5p, 638, 663b, 720, 768-3P, 768-5P, 886-5P, and 92a. These studies are continuing and laser capture microdissection results will be incorporated in the study. Supported in part by the Breast SPORE at UAB (CA089019-09) and a grant from the Susan G Komen foundation (BCTR0600484). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 157. doi:10.1158/1538-7445.AM2011-157

Regulating Genetic Information in Germany and Israel: Towards a Policy Network Comparative Analysis

This article explores genetic information and database policy-making in Germany and Israel using policy network analysis. The article demonstrates that the policy network model could be a useful heuristic device for analyzing the complex relationships between government and non-governmental actors involved in formulating regulations within the context of a fast-changing area such as that of genetic information testing and databases. The comparative analysis of Israeli and German regulation of genetic information has shown that issue networks have been conducive to statutory regulation in genetic information policy domains such as privacy protection and non-discrimination. Thus, this article raises the need to widen the scope of statutory legislation of genetic information to include benefit-sharing guidelines to justify the voluntary participation of individuals and communities, without which genetic information databases could not exist.

Toward a Legal-Ethical Framework for Regulating Human Genetic Information in Vulnerable Populations: An Issue of Justice

AbstractThe main purpose of this work is to discuss the legal, psycho-social and ethical issues posed when handling genetic information in genomic research within developing countries. Following the method of “reflective equilibrium”(Rawls-Daniels) and from an interdisciplinary approach, I shall go through: (1) current normative laws concerning its regulation, advantages and limitations; (2) the psychosocial impact of genetics on health issues; and (3) the ethical grounds that should be taken into account in establishing the normative framework for the regulation of genetic information. In general terms, my opinion is that the ethical grounds of the normative framework regarding research with human beings cannot be formal or based exclusively on the law (e. g. “bureaucratisation of informed consent”). My suggestions is that a critical notion of real autonomy and material wellbeing of the moral person (following Doyal- Sen-Van Parijs) should be applied to justify the distributive principles implied in any research on human beings, in particular in genomic research (benefit sharing.)

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

The assumption that RNA can be readily classified into either protein-coding or non-protein–coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein–coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as protein-coding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted.

Trapped water molecules are essential to structural dynamics and function of a ribozyme

Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular dynamics simulation and single molecule fluorescence spectroscopy approaches, we find that a ribozyme from a subviral plant pathogen exhibits a coupled hydrogen bonding network that communicates dynamic structural rearrangements throughout the catalytic core in response to site-specific chemical modification. Trapped long-residency water molecules are critical for this network and only occasionally exchange with bulk solvent as they pass through a breathing interdomain base stack. These highly structured water molecules line up in a string that may potentially also be involved in specific base catalysis. Our observations suggest important, still underappreciated roles for specifically bound water molecules in the structural dynamics and function of noncoding RNAs.