Single molecule mechanical manipulation for studying biological properties of proteins, DNA, and sugars

2013 ◽  
Vol 6 (3) ◽  
pp. 211-229 ◽  
Author(s):  
Zackary N. Scholl ◽  
Qing Li ◽  
Piotr E. Marszalek
Keyword(s):  
Single Molecule ◽  
Biological Properties ◽  
Mechanical Manipulation

scholarly journals A simple DNA handle attachment method for single molecule mechanical manipulation experiments

2016 ◽  
Vol 25 (8) ◽  
pp. 1535-1544 ◽  
Author(s):  
Duyoung Min ◽  
Mark A. Arbing ◽  
Robert E. Jefferson ◽  
James U. Bowie
Keyword(s):  
Single Molecule ◽  
Mechanical Manipulation

scholarly journals A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 570
Author(s):  
Shuangyang Wu ◽  
Shenghan Gao ◽  
Sen Wang ◽  
Jie Meng ◽  
Jacob Wickham ◽  
...  
Keyword(s):  
Single Molecule ◽  
Native Species ◽  
Reference Genome ◽  
Draft Genome ◽  
Morphological Characteristics ◽  
Bursaphelenchus Xylophilus ◽  
Biological Properties ◽  
Pinewood Nematode ◽  
Competitive Displacement ◽  
Bursaphelenchus Mucronatus

The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties—but had weaker pathogenicity to forests—was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the invasive B. xylophilus has been published, the absence of a reference genome of B. mucronatus still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of B. mucronatus, including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between B. xylophilus and B. mucronatus. However, the losing of orphan genes and species-specific orthologous genes in B. mucronatus may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in B. mucronatus may jointly contribute to its displacement by B. xylophilus. Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of B. mucronatus, especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases.

scholarly journals (+)-(E)-Chrysanthenyl Acetate: A Molecule with Interesting Biological Properties Contained in the Anthemis secundiramea (Asteraceae) Flowers

2020 ◽  
Vol 10 (19) ◽  
pp. 6808 ◽  
Author(s):  
Michela Di Napoli ◽  
Viviana Maresca ◽  
Mario Varcamonti ◽  
Maurizio Bruno ◽  
Natale Badalamenti ◽  
...  
Keyword(s):  
Antioxidant Activity ◽  
Single Molecule ◽  
Biofilm Formation ◽  
Mediterranean Basin ◽  
Antimicrobial Properties ◽  
Biological Properties ◽  
Perennial Herb ◽  
Gram Positive ◽  
The Mediterranean ◽  
The Mediterranean Basin

Anthemis secundiramea is a perennial herb native widespread throughout the Mediterranean basin. The oil obtained from the flowers of this plant has antimicrobial properties against gram-positive and -negative bacteria, and inhibits the biofilm formation. The extract of A. secundiramea also has antioxidant activity—increasing the activity of different enzymes (SOD, CAT, and GPx). Surprisingly, in the oil extracted from the flowers, there is a single molecule, called (+)-(E)-chrysanthenyl acetate: This makes the A. secundiramea flowers extract extremely interesting for future topical, cosmetic, and nutraceutical applications.

scholarly journals A Simple DNA Handle Attachment Method for Single Molecule Mechanical Manipulation Experiments

2017 ◽  
Vol 112 (3) ◽  
pp. 300a
Author(s):  
Duyoung Min ◽  
Mark A. Arbing ◽  
Robert E. Jefferson ◽  
James U. Bowie
Keyword(s):  
Single Molecule ◽  
Mechanical Manipulation

scholarly journals Studying heat shock proteins through single-molecule mechanical manipulation

2020 ◽  
Vol 25 (4) ◽  
pp. 615-628 ◽  
Author(s):  
Dhawal Choudhary ◽  
Laura Mediani ◽  
Serena Carra ◽  
Ciro Cecconi
Keyword(s):  
Heat Shock ◽  
Heat Shock Proteins ◽  
Single Molecule ◽  
Mechanical Manipulation ◽  
Shock Proteins

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

The method of replication affects metal film granularity and resolution

1989 ◽  
Vol 47 ◽  
pp. 708-709
Author(s):  
George C. Ruben
Keyword(s):  
Electron Beam ◽  
High Resolution ◽  
Film Thickness ◽  
Single Molecule ◽  
Metal Film ◽  
Vertical Surface ◽  
High Resolution Imaging ◽  
Controllable Factors ◽  
Resolution Imaging

Single molecule resolution in electron beam sensitive, uncoated, noncrystalline materials has been impossible except in thin Pt-C replicas ≤ 150Å) which are resistant to the electron beam destruction. Previously the granularity of metal film replicas limited their resolution to ≥ 20Å. This paper demonstrates that Pt-C film granularity and resolution are a function of the method of replication and other controllable factors. Low angle 20° rotary , 45° unidirectional and vertical 9.7±1 Å Pt-C films deposited on mica under the same conditions were compared in Fig. 1. Vertical replication had a 5A granularity (Fig. 1c), the highest resolution (table), and coated the whole surface. 45° replication had a 9Å granulartiy (Fig. 1b), a slightly poorer resolution (table) and did not coat the whole surface. 20° rotary replication was unsuitable for high resolution imaging with 20-25Å granularity (Fig. 1a) and resolution 2-3 times poorer (table). Resolution is defined here as the greatest distance for which the metal coat on two opposing faces just grow together, that is, two times the apparent film thickness on a single vertical surface.

Single molecule optical diffraction: A tool for understanding the structure of triple stranded left-hand helical cellulose

1989 ◽  
Vol 47 ◽  
pp. 1024-1025
Author(s):  
George C. Ruben ◽  
William Krakow
Keyword(s):  
Single Molecule ◽  
Helical Structure ◽  
Optical Diffraction ◽  
Maximum Diameter ◽  
Primary Cell Wall ◽  
Cellulose Synthesis ◽  
Left Hand ◽  
Left Handed ◽  
Freeze Dried ◽  
Diffraction Patterns

Tobacco primary cell wall and normal bacterial Acetobacter xylinum cellulose formation produced a 36.8±3Å triple-stranded left-hand helical microfibril in freeze-dried Pt-C replicas and in negatively stained preparations for TEM. As three submicrofibril strands exit the wall of Axylinum , they twist together to form a left-hand helical microfibril. This process is driven by the left-hand helical structure of the submicrofibril and by cellulose synthesis. That is, as the submicrofibril is elongating at the wall, it is also being left-hand twisted and twisted together with two other submicrofibrils. The submicrofibril appears to have the dimensions of a nine (l-4)-ß-D-glucan parallel chain crystalline unit whose long, 23Å, and short, 19Å, diagonals form major and minor left-handed axial surface ridges every 36Å.The computer generated optical diffraction of this model and its corresponding image have been compared. The submicrofibril model was used to construct a microfibril model. This model and corresponding microfibril images have also been optically diffracted and comparedIn this paper we compare two less complex microfibril models. The first model (Fig. 1a) is constructed with cylindrical submicrofibrils. The second model (Fig. 2a) is also constructed with three submicrofibrils but with a single 23 Å diagonal, projecting from a rounded cross section and left-hand helically twisted, with a 36Å repeat, similar to the original model (45°±10° crossover angle). The submicrofibrils cross the microfibril axis at roughly a 45°±10° angle, the same crossover angle observed in microflbril TEM images. These models were constructed so that the maximum diameter of the submicrofibrils was 23Å and the overall microfibril diameters were similar to Pt-C coated image diameters of ∼50Å and not the actual diameter of 36.5Å. The methods for computing optical diffraction patterns have been published before.

Membrane–cytoskeleton interactions in cholesterol-dependent domain formation

2015 ◽  
Vol 57 ◽  
pp. 177-187 ◽  
Author(s):  
Jennifer N. Byrum ◽  
William Rodgers
Keyword(s):  
Biological Properties ◽  
Membrane Rafts ◽  
Membrane Domains ◽  
Biological Functions ◽  
Membrane Cytoskeleton ◽  
Heterogeneous Structures ◽  
Integral Role ◽  
Model Cell ◽  
Actomyosin Cytoskeleton ◽  
Dependent Domain

Since the inception of the fluid mosaic model, cell membranes have come to be recognized as heterogeneous structures composed of discrete protein and lipid domains of various dimensions and biological functions. The structural and biological properties of membrane domains are represented by CDM (cholesterol-dependent membrane) domains, frequently referred to as membrane ‘rafts’. Biological functions attributed to CDMs include signal transduction. In T-cells, CDMs function in the regulation of the Src family kinase Lck (p56lck) by sequestering Lck from its activator CD45. Despite evidence of discrete CDM domains with specific functions, the mechanism by which they form and are maintained within a fluid and dynamic lipid bilayer is not completely understood. In the present chapter, we discuss recent advances showing that the actomyosin cytoskeleton has an integral role in the formation of CDM domains. Using Lck as a model, we also discuss recent findings regarding cytoskeleton-dependent CDM domain functions in protein regulation.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

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