scholarly journals DNA-loop extruding SMC complexes can traverse one another in vivo

2021 ◽  
Author(s):  
Xindan Wang ◽  
Hugo Brandão ◽  
Zhongqing Ren ◽  
Xheni Karaboja ◽  
Leonid Mirny
Keyword(s):  
Chromosome Conformation ◽  
Common Assumption ◽  
Dna Loop ◽  
Track System ◽  
Subtilis Chromosome ◽  
The Common ◽  
Living Organisms ◽  
Bacillus Subtilis Chromosome ◽  
Structural Maintenance Of Chromosomes

Abstract Chromosome organization by structural maintenance of chromosomes (SMC) complexes is vital to living organisms. SMC complexes were recently found to be motors that extrude DNA loops. However, it remains unclear what happens when multiple complexes encounter one another in vivo on the same DNA and how interactions help organize an active genome. We created a crash-course track system to study SMC complex encounters in vivo by engineering the Bacillus subtilis chromosome to have defined SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Via 3D polymer simulations and theory, we find that these patterns require SMC complexes to bypass each other in vivo, contrary to the common assumption that SMC complexes mutually block each other’s loop extrusion activity. We posit that the bypassing activity enables SMC complexes to spatially organize a functional and busy genome.

scholarly journals DNA-loop extruding SMC complexes can traverse one another in vivo

2020 ◽  
Author(s):  
Hugo B. Brandão ◽  
Zhongqing Ren ◽  
Xheni Karaboja ◽  
Leonid A. Mirny ◽  
Xindan Wang
Keyword(s):  
Spatial Organization ◽  
Quantitative Model ◽  
Chromosome Conformation ◽  
Common Assumption ◽  
Dna Loop ◽  
Track System ◽  
The Common ◽  
Set Up ◽  
Structural Maintenance Of Chromosomes

SummaryThe spatial organization of chromosomes by structural maintenance of chromosomes (SMC) complexes is vital to organisms from bacteria to humans 1,2. SMC complexes were recently found to be motors that extrude DNA loops 3–11. It remains unclear, however, what happens when multiple SMC complexes encounter one another in vivo on the same DNA, how encounters are resolved, or how interactions help organize an active genome 12. Here, we set up a “crash-course track” system to study what happens when SMC complexes encounter one another. Using the parS/ParB system, which loads SMC complexes in a targeted manner13–17, we engineered the Bacillus subtilis chromosome to have multiple SMC loading sites. Chromosome conformation capture (Hi-C) analyses of over 20 engineered strains show an amazing variety of never-before-seen chromosome folding patterns. Polymer simulations indicate these patterns require SMC complexes to traverse past each other in vivo, contrary to the common assumption that SMC complexes mutually block each other’s extrusion activity 18. Our quantitative model of bypassing predicted that increasing the numbers of SMCs on the chromosome could overwhelm the bypassing mechanism, create SMC traffic jams, and lead to major chromosome reorganization. We validated these predictions experimentally. We posit that SMC complexes traversing one another is part of a larger phenomenon of bypassing large steric barriers which enables these loop extruders to spatially organize a functional and busy genome.

Relaxation of DNA torsional tension in defined domains of bacterial chromosomes in vivo

1988 ◽  
Vol 34 (4) ◽  
pp. 522-525 ◽  
Author(s):  
Scott Winston ◽  
David E. Pettijohn
Keyword(s):  
Dna Analysis ◽  
Bacterial Cells ◽  
Chromosomal Dna ◽  
Dna Breaks ◽  
Long Wavelength ◽  
Subtilis Chromosome ◽  
Bacterial Chromosomes ◽  
The Difference ◽  
Bacillus Subtilis Chromosome

A procedure is described for selectively relaxing the DNA torsional tension in defined regions of the chromosome of living bacterial cells. Regions of the chromosomal DNA labelled with bromodeoxyuridine are selectively nicked by irradiation of the cells with long-wavelength ultraviolet light and then trimethylpsoralen residues are photobound to the chromosome in vivo. It is demonstrated that the rate of photobinding to the bromouridine-labelled parts of the chromosomes declines relative to the unlabelled parts of the same chromosomes as nicks are introduced into the former regions. The maximal difference in photobinding rates is that expected for the difference between relaxed and negatively supercoiled DNA. Analysis of the number of DNA breaks required for minimizing the photobinding rates permits a calculation of the number of domains of supercoiling per Bacillus subtilis chromosome.

scholarly journals A cautionary note: Toxicity of polyethylene glycol 200 injected intraperitoneally into mice

2019 ◽  
Vol 54 (4) ◽  
pp. 391-396
Author(s):  
Wilko Thiele ◽  
Lenka Kyjacova ◽  
Almut Köhler ◽  
Jonathan P Sleeman
Keyword(s):  
Polyethylene Glycol ◽  
Dimethyl Sulfoxide ◽  
Organic Solvents ◽  
Cautionary Note ◽  
Common Assumption ◽  
Regulatory Authorities ◽  
Polyethylene Glycol 200 ◽  
Hydrophobic Substances ◽  
The Common

The parenteral administration of hydrophobic substances in vivo requires the use of organic solvents to ensure sufficient solubility and avoid precipitation. Dimethyl sulfoxide is commonly used for this purpose. Based on the common assumption that polyethylene glycol (PEG) is non-toxic, our local regulatory authorities recently recommended the use of PEG instead. However, mice injected intraperitoneally (i.p.) with PEG 200 at a dose of 8 mL/kg (i.e. 9 g/kg) did not tolerate PEG 200 well, and half of the animals had to be euthanized. Our results demonstrate that although PEG 200 is generally considered to be harmless, it can be toxic when injected i.p. and is painful for the recipient mice. Nevertheless, it can be used as a solvent for repeated i.p. injections in mice at a dose of 2 mL/kg (i.e. 2.25 g/kg) without obvious signs of systemic toxicity.

scholarly journals Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites

2021 ◽  
Author(s):  
Frank B&uumlrmann ◽  
Louise F.H. Funke ◽  
Jason W. Chin ◽  
Jan L&oumlwe
Keyword(s):  
Escherichia Coli ◽  
Atomic Structure ◽  
Cross Linking ◽  
Genome Maintenance ◽  
Electron Cryomicroscopy ◽  
Double Helices ◽  
Dna Loop ◽  
Replication Terminus ◽  
Structural Maintenance Of Chromosomes

The ring-like structural maintenance of chromosomes (SMC) complex MukBEF folds the genome of Escherichia coli and related bacteria into large loops, presumably by active DNA loop extrusion. MukBEF activity within the replication terminus macrodomain is suppressed by the sequence specific unloader MatP. Here we present the complete atomic structure of MukBEF in complex with MatP and DNA as determined by electron cryomicroscopy (cryo-EM). The complex binds two distinct DNA double helices corresponding to the arms of a plectonemic loop. MatP-bound DNA threads through the MukBEF ring, while the second DNA is clamped by the kleisin MukF, MukE and the MukB ATPase heads. Combinatorial cysteine cross-linking confirms this topology of DNA loop entrapment in vivo. Our findings illuminate how a class of near-ubiquitous DNA organizers with important roles in genome maintenance interacts with the bacterial chromosome.

scholarly journals Facile in vivo Transfer of Mutations Between the Bacillus subtilis Chromosome and a Plasmid Harbouring Homologous DNA

Microbiology ◽  
1982 ◽  
Vol 128 (11) ◽  
pp. 2813-2816 ◽  
Author(s):  
K. F. Chak ◽  
H. De Lencastre ◽  
H-M. Liu ◽  
P. J. Piggot
Keyword(s):  
Bacillus Subtilis ◽  
Subtilis Chromosome ◽  
Bacillus Subtilis Chromosome

In vivo Experiments of Natural Products Protection of Antagonistic Effects of Lead on Iron

2018 ◽  
Vol 68 (12) ◽  
pp. 2747-2751
Author(s):  
Marioara Nicula ◽  
Nicolae Pacala ◽  
Lavinia Stef ◽  
Ioan Pet ◽  
Dorel Dronca ◽  
...  
Keyword(s):  
Aquatic Environment ◽  
Iron Homeostasis ◽  
Iron Concentration ◽  
Antagonistic Effect ◽  
Tissue Samples ◽  
Antagonistic Effects ◽  
In Vivo Experiments ◽  
Living Organisms ◽  
Toxic Potential

Living organisms take nutrients from the environment, and together with them, substances with toxic potential � such as heavy metals. Lead is one common metal pollutant especially in aquatic environment, from where the fish can be intoxicated very easily. Bioavailability, distribution, toxic action, synergistic and antagonistic effects are characteristics which can alter the fish health. Our experimental study followed the effects of lead overload in water on iron distribution, in different tissues sample Carassius gibelio Bloch fish. We performed the experiment in four different fish groups: control C; lead � Pb (administration of lead in water 0.075mg/mL of water, as Pb(NO3)2 x � H2O); lead (the same dose) and 2% of freeze-dry garlic incorporated into fishes� food � Pb+garlic; lead (the same dose) and 2% chlorella incorporated into fishes� food � Pb+chlorella, for 21 consecutive days. The iron concentration was analysed with AAS (Atomic Absorption Spectroscopy) from gills, muscle, skin (and scales), intestine, liver, heart, brain, ovary, testicles, and kidney. The obtained data presented a significantly decrease of iron content in all tested tissue samples that demonstrated, alteration of iron homeostasis, explained by a strong antagonistic effect of lead on iron. Our experiment showed that biologic active principles from garlic and chlorella act like natural protectors, and potentiate the iron deficiency even in the case of lead overload in aquatic environment, for fish.

Current Challenges in the Development of Vaccines and Drugs Against Emerging Vector-borne Diseases

2019 ◽  
Vol 26 (16) ◽  
pp. 2974-2986 ◽  
Author(s):  
Kwang-sun Kim
Keyword(s):  
New Host ◽  
In Vivo Models ◽  
Vector Borne Diseases ◽  
Novel Drugs ◽  
Huge Impact ◽  
Tick Borne Disease ◽  
Vector Borne ◽  
Living Organisms

Vectors are living organisms that transmit infectious diseases from an infected animal to humans or another animal. Biological vectors such as mosquitoes, ticks, and sand flies carry pathogens that multiply within their bodies prior to delivery to a new host. The increased prevalence of Vector-Borne Diseases (VBDs) such as Aedes-borne dengue, Chikungunya (CHIKV), Zika (ZIKV), malaria, Tick-Borne Disease (TBD), and scrub typhus has a huge impact on the health of both humans and livestock worldwide. In particular, zoonotic diseases transmitted by mosquitoes and ticks place a considerable burden on public health. Vaccines, drugs, and vector control methods have been developed to prevent and treat VBDs and have prevented millions of deaths. However, development of such strategies is falling behind the rapid emergence of VBDs. Therefore, a comprehensive approach to fighting VBDs must be considered immediately. In this review, I focus on the challenges posed by emerging outbreaks of VBDs and discuss available drugs and vaccines designed to overcome this burden. Research into promising drugs needs to be upgraded and fast-tracked, and novel drugs or vaccines being tested in in vitro and in vivo models need to be moved into human clinical trials. Active preventive tactics, as well as new and upgraded diagnostics, surveillance, treatments, and vaccination strategies, need to be monitored constantly if we are to manage VBDs of medical importance.

The Application of the Cold Atmospheric Plasma-Activated Solutions in Cancer Treatment

2018 ◽  
Vol 18 (6) ◽  
pp. 769-775 ◽  
Author(s):  
Dayun Yan ◽  
Jonathan H. Sherman ◽  
Michael Keidar
Keyword(s):  
Cancer Treatment ◽  
Atmospheric Plasma ◽  
Current Status ◽  
Cold Atmospheric Plasma ◽  
Anti Cancer ◽  
Long Time ◽  
Key Topics ◽  
The Common

Background: Over the past five years, the cold atmospheric plasma-activated solutions (PAS) have shown their promissing application in cancer treatment. Similar as the common direct cold plasma treatment, PAS shows a selective anti-cancer capacity in vitro and in vivo. However, different from the direct cold atmospheric plasma (CAP) treatment, PAS can be stored for a long time and can be used without dependence on a CAP device. The research on PAS is gradually becoming a hot topic in plasma medicine. Objectives: In this review, we gave a concise but comprehensive summary on key topics about PAS including the development, current status, as well as the main conclusions about the anti-cancer mechanism achieved in past years. The approaches to make strong and stable PAS are also summarized.

Student Perceptions of Community: A Different Perspective

NASPA Journal ◽  
1998 ◽  
Vol 35 (4) ◽  
Author(s):  
Jackie Clark ◽  
Joan Hirt
Keyword(s):  
Student Perceptions ◽  
Large Scale ◽  
Research University ◽  
Small Scale ◽  
Social Environments ◽  
Common Assumption ◽  
Small Communities ◽  
Public Research University ◽  
The Common ◽  
Using Data

The creation of small communities has been proposed as a way of enhancing the educational experience of students at large institutions. Using data from a survey of students living in large and small residences at a public research university, this study does not support the common assumption that small-scale social environments are more conducive to positive community life than large-scale social environments.

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