scholarly journals Principles of organelle membrane bridging established using cytosolic tether mimics

2020 ◽  
Author(s):  
Mohammad Arif Kamal ◽  
Josip Augustin Janeš ◽  
Long Li ◽  
Franck Thibaudau ◽  
Ana-Suncana Smith ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Relative Difference ◽  
Giant Unilamellar Vesicle ◽  
Supported Lipid Bilayer ◽  
Double Stranded Dna ◽  
Transmission Electron ◽  
Tremendous Progress ◽  
Sticky End ◽  
Organelle Membrane ◽  
Cellular Organelles

AbstractThe interactions between different intra-cellular organelles, including the endoplasmic reticulum, have recently been in focus thanks to the tremendous progress in imaging them using cryogenic transmission electron microscopy. However, they are still difficult to study in cellulo, and reconstituting these systems has been a standing challenge. Here we achieve this task using a giant unilamellar vesicle (GUV) and supported lipid bilayer (SLB) system. The tethers, which may reside in the cytosol when unbound, are mimicked by single (or double) stranded DNA sequences of two different lengths with ends that are self-sticky, and with terminal cholesterol moieties which insert into GUV or SLB membranes. The DNA-tethers, bound by their sticky-end, can exist in two possible states - either with both cholesterols in the same membrane or each cholesterol in a different membrane, the latter conformation leading to adhesion. Exchange of tether-molecules between the membranes occurs through the aqueous phase. By developing theoretical arguments that are supported in our experiments, we show that this possibility of exchange and the relative difference in the projected area between the two states drives the adhesion due to collective entropic considerations, rather than the usually considered enthalpy of binding. The establishment of this fundamentally different interaction between two membranes suggests that in physiological conditions, the regulation of contact formation inside cells may be very different from the case of the much studied ligand-receptor pairing on the external cell membrane.

Scanning Secondary Electron Microscopy of Myofibrils Using Transmission Techniques

1975 ◽  
Vol 33 ◽  
pp. 556-557
Author(s):  
M. K. Lamvik
Keyword(s):  
Electron Microscopy ◽  
Electron Microscope ◽  
Carbon Films ◽  
Photographic Recording ◽  
Transmission Electron ◽  
Thin Carbon ◽  
The Common ◽  
Scanning Electron ◽  
Better Than ◽  
Cellular Organelles

When observing small objects such as cellular organelles by scanning electron microscopy, it is often valuable to use the techniques of transmission electron microscopy. The common practice of mounting and coating for SEM may not always be necessary. These possibilities are illustrated using vertebrate skeletal muscle myofibrils.Micrographs for this study were made using a Hitachi HFS-2 scanning electron microscope, with photographic recording usually done at 60 seconds per frame. The instrument was operated at 25 kV, with a specimen chamber vacuum usually better than 10-7 torr. Myofibrils were obtained from rabbit back muscle using the method of Zak et al. To show the component filaments of this contractile organelle, the myofibrils were partially disrupted by agitation in a relaxing medium. A brief centrifugation was done to clear the solution of most of the undisrupted myofibrils before a drop was placed on the grid. Standard 3 mm transmission electron microscope grids covered with thin carbon films were used in this study.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

scholarly journals Isolation and characterization of bacteriophages from India, with lytic activity againstMycobacterium tuberculosis

2018 ◽  
Vol 64 (7) ◽  
pp. 483-491 ◽  
Author(s):  
Urmi Bajpai ◽  
Abhishek Kumar Mehta ◽  
Kandasamy Eniyan ◽  
Avni Sinha ◽  
Ankita Ray ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Sequence Similarity ◽  
Gc Content ◽  
Polymerase Chain Reaction Analysis ◽  
Open Reading Frames ◽  
Genome Maintenance ◽  
Isolation And Characterization ◽  
Virion Release ◽  
Double Stranded Dna ◽  
Transmission Electron

Bacteriophages are being considered as a promising natural resource for the development of alternative strategies against mycobacterial diseases, especially in the context of the wide-spread occurrence of drug resistance among the clinical isolates of Mycobacterium tuberculosis. However, there is not much information documented on mycobacteriophages from India. Here, we report the isolation of 17 mycobacteriophages using Mycobacterium smegmatis as the bacterial host, where 9 phages also lyse M. tuberculosis H37Rv. We present detailed analysis of one of these mycobacteriophages — PDRPv. Transmission electron microscopy and polymerase chain reaction analysis (of a conserved region within the TMP gene) show PDRPv to belong to the Siphoviridae family and B1 subcluster, respectively. The genome (69 110 bp) of PDRPv is circularly permuted double-stranded DNA with ∼66% GC content and has 106 open reading frames (ORFs). On the basis of sequence similarity and conserved domains, we have assigned function to 28 ORFs and have broadly categorized them into 6 groups that are related to replication and genome maintenance, DNA packaging, virion release, structural proteins, lysogeny-related genes and endolysins. The present study reports the occurrence of novel antimycobacterial phages in India and highlights their potential to contribute to our understanding of these phages and their gene products as potential antimicrobial agents.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization

1981 ◽  
Vol 1 (2) ◽  
pp. 136-143
Author(s):  
M Pellegrini ◽  
W E Timberlake ◽  
R B Goldberg
Keyword(s):  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Microscopic Analysis ◽  
Single Copy ◽  
Electron Microscopic ◽  
Sequence Organization ◽  
Double Stranded Dna ◽  
Copy Dna ◽  
Gene 32 ◽  
Single Copy Dna

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.

scholarly journals Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2

2020 ◽  
Vol 48 (7) ◽  
pp. 3869-3887 ◽  
Author(s):  
Linlin Hou ◽  
Yuanjie Wei ◽  
Yingying Lin ◽  
Xiwei Wang ◽  
Yiwei Lai ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Target Genes ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
High Mobility ◽  
Binding Motif ◽  
Dna And Rna ◽  
Somatic Cell Reprogramming ◽  
Double Stranded Dna

Abstract Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.

scholarly journals Heterogeneous nuclear ribonucleoprotein D0B is a sequence-specificDNA-binding protein

1999 ◽  
Vol 338 (2) ◽  
pp. 417-425 ◽  
Author(s):  
Mate TOLNAY ◽  
Lyudmila A. VERESHCHAGINA ◽  
George C. TSOKOS
Keyword(s):  
Dna Sequences ◽  
Rna Binding ◽  
Binding Protein ◽  
Double Helix ◽  
Physiological Role ◽  
Single Stranded Dna ◽  
Heterogeneous Nuclear Ribonucleoprotein ◽  
Double Stranded Dna ◽  
Nuclear Ribonucleoprotein

Complement receptor 2 (CR2) is important in the regulation of the B lymphocyte response; the regulation of its expression is therefore of central importance. We recently reported that a 42 kDa heterogeneous nuclear ribonucleoprotein (hnRNP) is involved in the transcriptional regulation of the human CR2 gene [Tolnay, Lambris and Tsokos (1997) J. Immunol. 159, 5492–5501]. We cloned the cDNA encoding this protein and found it to be identical with hnRNP D0B, a sequence-specific RNA-binding protein. By using a set of mutated oligonucleotides, we demonstrated that the recombinant hnRNP D0B displays sequence specificity for double-stranded oligonucleotide defined by the CR2 promoter. We conducted electrophoretic mobility-shift assays to estimate the apparent Kd of hnRNP D0B for the double-stranded DNA motif and found it to be 59 nM. Interestingly, hnRNP D0B displayed affinities of 28 and 18 nM for the sense and anti-sense strands of the CR2 promoter-defined oligonucleotide respectively. The significantly greater binding affinity of hnRNP D0B for single-stranded DNA than for double-stranded DNA suggests that the protein might melt the double helix. The intranuclear concentration of sequence-specific protein was estimated to be 250–400 nM, indicating that the protein binds to the CR2 promoter in vivo. Co-precipitation of a complex formed in vivo between hnRNP D0B and the TATA-binding protein demonstrates that hnRNP D0B interacts with the basal transcription apparatus. Our results suggest a new physiological role for hnRNP D0B that involves binding to double- and single-stranded DNA sequences in a specific manner and functioning as a transcription factor.

An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences

2020 ◽  
Vol 12 (37) ◽  
pp. 4541-4550
Author(s):  
Mehran Ahmadi ◽  
Fatemeh Ahour
Keyword(s):  
Graphene Oxide ◽  
Dna Sequences ◽  
Electrochemical Biosensor ◽  
Graphite Electrode ◽  
Direct Detection ◽  
Pencil Graphite Electrode ◽  
Label Free ◽  
Double Stranded Dna

A simple electrochemical biosensor using a GO modified PGE for label-free and direct detection of ds-DNA in plasmid samples without denaturation.

scholarly journals First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties

Nanomaterials ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 613 ◽  
Author(s):  
Liam E. Yourston ◽  
Alexander Y. Lushnikov ◽  
Oleg A. Shevchenko ◽  
Kirill A. Afonin ◽  
Alexey V. Krasnoslobodtsev
Keyword(s):  
Optical Properties ◽  
Dna Sequences ◽  
Silver Nanoclusters ◽  
Conformational Heterogeneity ◽  
Individual Element ◽  
Double Stranded Dna ◽  
Close Proximity ◽  
Template Design ◽  
Fluorescent Nanomaterials

Besides being a passive carrier of genetic information, DNA can also serve as an architecture template for the synthesis of novel fluorescent nanomaterials that are arranged in a highly organized network of functional entities such as fluorescent silver nanoclusters (AgNCs). Only a few atoms in size, the properties of AgNCs can be tuned using a variety of templating DNA sequences, overhangs, and neighboring duplex regions. In this study, we explore the properties of AgNCs manufactured on a short DNA sequence—an individual element designed for a construction of a larger DNA-based functional assembly. The effects of close proximity of the double-stranded DNA, the directionality of templating single-stranded sequence, and conformational heterogeneity of the template are presented. We observe differences between designs containing the same AgNC templating sequence—twelve consecutive cytosines, (dC)12. AgNCs synthesized on a single “basic” templating element, (dC)12, emit in “red”. The addition of double-stranded DNA core, required for the larger assemblies, changes optical properties of the silver nanoclusters by adding a new population of clusters emitting in “green”. A new population of “blue” emitting clusters forms only when ssDNA templating sequence is placed on the 5′ end of the double-stranded core. We also compare properties of silver nanoclusters, which were incorporated into a dimeric structure—a first step towards a larger assembly.

High-resolution structural analysis of eukaryotic ribosomal RNAs by scanning transmission electron microscopy

1984 ◽  
Vol 42 ◽  
pp. 688-689
Author(s):  
G.T. Oostergetel ◽  
J.F. Hainfeld ◽  
J.S. Wall ◽  
M. Boublik
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Scanning Transmission Electron Microscopy ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
Evolutionary Level ◽  
And Function ◽  
Similar Domain ◽  
Cellular Organelles

The structure and function of ribosomes, small cellular organelles involved in protein synthesis, are determined by both their macromolecular components - proteins and RNAs. The protein/RNA ratio depends on the evolutionary level of the organism. In eukaryotic ribosomes the protein/RNA ratio is ~ 1:1 (w/w). While the number and composition of ribosomal proteins varies from species to species, the number and composition of RNAs is highly conserved.We have chosen the 18S and 28S ribosomal RNA isolated from baby hamster kidney cells to study the structural role of eukaryotic RNAs on the ribosome. Similarity in the extent of secondary structure suggests that the eukaryotic RNAs have similar “domain” structure as their prokaryotic counterparts. This structure consists of segments of double stranded stems, single strands and loops. However, folding of these segments into a conformation contributing to the 3-D structure of the ribosome remains to be established.

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