scholarly journals Search for a new type of spatial organization of nucleic acids in human genome

2020 ◽  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Spatial Organization ◽  
New Type

scholarly journals Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Geneviève Bart ◽  
Daniel Fischer ◽  
Anatoliy Samoylenko ◽  
Artem Zhyvolozhnyi ◽  
Pavlo Stehantsev ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Body Fluids ◽  
Lower Percentage ◽  
Rna Seq ◽  
Protein Coding ◽  
Human Sweat ◽  
Dna And Rna ◽  
Ribonucleoprotein Complexes ◽  
Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

scholarly journals Nucleic Acids in Cancer Diagnosis and Therapy

Cancers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2597
Author(s):  
Taewan Kim
Keyword(s):  
Cancer Research ◽  
Nucleic Acids ◽  
Human Genome ◽  
Cancer Diagnosis ◽  
Diagnosis And Therapy ◽  
Cancer Diagnosis And Therapy

Cancer research has been focused on the coding genes occupying 1–2% of the human genome [...]

scholarly journals A short peptide that preferentially binds c-MYC G-quadruplex DNA

2020 ◽  
Vol 56 (63) ◽  
pp. 8940-8943 ◽  
Author(s):  
Aisling Minard ◽  
Danielle Morgan ◽  
Federica Raguseo ◽  
Anna Di Porzio ◽  
Denise Liano ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Promoter Region ◽  
Secondary Structures ◽  
Quadruplex Dna ◽  
Short Peptide ◽  
G Quadruplex

G-quadruplexes are nucleic-acids secondary structures that are highly abundant in the human genome. In this work,we identified a short-peptide that displays selectivity for the G-quadruplex formed in the promoter region of the oncogene c-MYC.

scholarly journals Unwinding and Rewinding: Double Faces of Helicase?

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Yuliang Wu
Keyword(s):  
Nucleic Acids ◽  
Biological Functions ◽  
Recq Helicase ◽  
Biochemical Activity ◽  
Double Stranded Dna ◽  
New Type ◽  
Regulation Mechanisms ◽  
Strand Annealing

Helicases are enzymes that use ATP-driven motor force to unwind double-stranded DNA or RNA. Recently, increasing evidence demonstrates that some helicases also possess rewinding activity—in other words, they can anneal two complementary single-stranded nucleic acids. All five members of the human RecQ helicase family, helicase PIF1, mitochondrial helicase TWINKLE, and helicase/nuclease Dna2 have been shown to possess strand-annealing activity. Moreover, two recently identified helicases—HARP and AH2 have only ATP-dependent rewinding activity. These findings not only enhance our understanding of helicase enzymes but also establish the presence of a new type of protein: annealing helicases. This paper discusses what is known about these helicases, focusing on their biochemical activity to zip and unzip double-stranded DNA and/or RNA, their possible regulation mechanisms, and biological functions.

Effect of Nanocrystallized Hydroxyapatite Coating on Bone Healing Evaluated by Synchrotron Radiation Diffraction

2015 ◽  
Vol 1088 ◽  
pp. 481-486
Author(s):  
Abdelilah Benmarouane ◽  
Helene Citterio ◽  
Pierre Millet ◽  
Thomas Buslaps ◽  
Alain Lodini ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Spatial Organization ◽  
High Energy ◽  
Bone Maturation ◽  
Bone Implant ◽  
Synchrotron Radiation Diffraction ◽  
Before And After ◽  
New Type ◽  
Non Destructive ◽  
Uncoated Titanium

The properties of the interface between biomaterials and the host tissue play an important role for the process of successful adaptation of implants. Extensive research has focused on shortening the time of osseointegration by modifying the surface in adding a coating such as hydroxyapatite (HAp). We have developed a new type of biocompatible nanohydroxyapatite (n-HAp) coatings, which are characterized before and after deposit on a Ti-6Al-4V substrate using neutron diffraction and scanning electron microscopy. Three months after the implantation in the sheep tibias, high-energy synchrotron radiation (ID15B, ESRF, Grenoble, France) diffraction studies of the cortical bone identify that the c-axes of HAp are preferentially oriented in the direction of the stresses that bone usually withstands. This non destructive analysis of the bone-implant interface proves that bone maturation is achieved successfully with this novel n-HAp coating and demonstrates that the mineralization is completed without spatial organization. None of these findings are obtained with uncoated titanium alloys. The presence of this n-HAp coating on Ti-6Al-4V substrate is decisive in obtaining this mature bone at the interface.

scholarly journals Dynamic regulation of DNA nanostructures by noncanonical nucleic acids

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Shiliang He ◽  
Zhilei Ge ◽  
Xiaolei Zuo ◽  
Chunhai Fan ◽  
Xiuhai Mao
Keyword(s):  
Nucleic Acids ◽  
Spatial Organization ◽  
Dna Nanostructures ◽  
Stimuli Responsive ◽  
Structural Morphology ◽  
Dynamic Regulation ◽  
Hierarchical Assembly ◽  
Dna Triplexes ◽  
Potential Applications ◽  
External Stimuli

AbstractDNA nanostructures are among the most fascinating self-assembled nanostructures in diverse areas of science and technology, because of their nanoscale precision in biomolecule and nanoparticle organization. The implementation of dynamic and spatial regulation in structural morphology and hierarchical assembly upon specific external stimuli will greatly expand their applications in biocomputation, clinical diagnosis, and cancer therapy. Recently, noncanonical nucleic acids, particularly DNA triplexes, i-motifs, and G-quadruplexes, have become powerful tools for biosensing and mechanical switching. Developments in incorporating stimuli-responsive noncanonical nucleic acids into DNA nanostructures provide a promising approach to regulating the spatial organization and hierarchical assembly of DNA nanostructures. In this review, we briefly introduce recent progress in constructing DNA nanostructures with dynamic regulation of the structural transformation and programmable assembly pathways at the nanometer scale by noncanonical nucleic acids and discuss their potential applications and challenges.

scholarly journals Algorithms of Processing Fluorescence Signals for Mass Parallel Sequencing of Nucleic Acids

2019 ◽  
Vol 18 (4) ◽  
pp. 1010-1036
Author(s):  
Vladimir Manoilov ◽  
Andrew Borodinov ◽  
Igor Zarutsky ◽  
Alexander Petrov ◽  
Vladimir Kurochkin
Keyword(s):  
Nucleic Acid ◽  
Genetic Analysis ◽  
Nucleic Acids ◽  
Human Genome ◽  
High Performance ◽  
Reaction Cell ◽  
Parallel Sequencing ◽  
Software Complex ◽  
Optical Channels ◽  
Long Time

Determination of the nucleotide sequence of DNA or RNA containing from several hundred to hundreds of millions of monomers units allows to obtain detailed information about the genome of humans, animals and plants. The deciphering of nucleic acids’ structure was learned quite a long time ago, but initially the decoding methods were low-performing, inefficient and expensive. Methods for decoding nucleotide nucleic acid sequences are usually called sequencing methods. Instruments designed to implement sequencing methods are called sequencers. Sequencing new generation (SNP), mass parallel sequencing are related terms that describe the technology of high-performance DNA sequencing in which the entire human genome can be sequenced within a day or two. The previous technology used to decipher the human genome required more than ten years to get final results. A hardware-software complex (HSC) is being developed to decipher the nucleic acid sequence (NA) of pathogenic microorganisms using the method of NGS in the Institute for Analytical Instrumentation of the Russian Academy of Sciences. The software included in the HSC plays an essential role in solving genome deciphering problems. The purpose of this article is to show the need to create algorithms for the software of the HSC for processing signals obtained in the process of genetic analysis when solving genome deciphering problems, and also to demonstrate the capabilities of these algorithms. The paper discusses the main problems of signal processing and methods for solving them, including: automatic and semi-automatic focusing, background correction, detection of cluster images, estimation of the coordinates of their positions, creation of templates of clusters of NA molecules on the surface of the reaction cell, correction of influence neighboring optical channels for intensities of signals and the assessment of the reliability of the results of genetic analysis

scholarly journals Classification and monomer-by-monomer annotation of suprachromosomal family 1 alpha satellite higher-order repeats in hg38 human genome assembly

2018 ◽  
Author(s):  
L. Uralsky ◽  
V.A. Shepelev ◽  
A.A. Alexandrov ◽  
Y.B. Yurov ◽  
E.I. Rogaev ◽  
...  
Keyword(s):  
Human Genome ◽  
Genome Assembly ◽  
Higher Order ◽  
Index Number ◽  
Alpha Satellite ◽  
Genomic Context ◽  
Low Copy Number ◽  
Human Genome Assembly ◽  
New Type ◽  
Analysis Platform

AbstractIn the latest hg38 human genome assembly, centromeric gaps has been filled in by alpha satellite (AS) reference models (RMs) which are statistical representations of homogeneous higher-order repeat (HOR) arrays that make up the bulk of the centromeric regions. We studied these models to compose an atlas of human HORs where each monomer of a HOR could be characterized and represented by a number of its polymorphic sequence variants. We further used these data and HMMER sequence analysis platform to annotate AS HORs in the assembly. This led to discovery and annotation of a new type of low copy number highly divergent HORs which were not represented by RMs. The annotation can be viewed as UCSC Genome Browser custom track (the HOR-track) and used together with our previous annotation of AS SFs in the same assembly where each AS monomer can be viewed in its genomic context together with its classification into one of the 5 major SFs (the SF-track). To catalog the diversity of AS HORs in the human genome we introduced a new naming system. Each HOR received a name which showed its SF, chromosomal location and index number. Here we present the first installment of the HOR-track covering only the 17 HORs that belong to SF1 which forms live functional centromeres in chromosomes 1, 3, 5, 6, 7, 10, 12, 16 and 19 and also a large number of minor dead HOR domains, both homogeneous (pseudo) and divergent (relic). The 4 newly discovered divergent SF1 HORs have provided the missing links in SF1 early evolution and substantiated its partition into 2 generations, archaic and modern, which we reported earlier. Additionally, we demonstrated that monomer-by-monomer HOR annotation was useful for mapping and quantification of various structural variants of AS HORs which would be important for studies of inter-individual polymorphism of AS including centromeric functional epialleles.

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