scholarly journals A novel decatenation assay for DNA topoisomerases using a singly-linked catenated substrate

BioTechniques ◽  
2020 ◽  
Vol 69 (5) ◽  
pp. 356-362
Author(s):  
Nidda F Waraich ◽  
Shruti Jain ◽  
Sean D Colloms ◽  
William Marshall Stark ◽  
Nicolas P Burton ◽  
...  
Keyword(s):  
High Sensitivity ◽  
Enzyme Digestion ◽  
Restriction Enzyme Digestion ◽  
Kinetoplast Dna ◽  
Dna Topoisomerases ◽  
In Vitro Drug Screening ◽  
Drug Inhibition ◽  
Dna Substrate

Decatenation is a crucial in vivo reaction of DNA topoisomerases in DNA replication and is frequently used in in vitro drug screening. Usually this reaction is monitored using kinetoplast DNA as a substrate, although this assay has several limitations. Here we have engineered a substrate for Tn 3 resolvase that generates a singly-linked catenane that can readily be purified from the DNA substrate after restriction enzyme digestion and centrifugation. We show that this catenated substrate can be used with high sensitivity in topoisomerase assays and drug-inhibition assays.

scholarly journals Biological nanoscale fluorescent probes: From structure and performance to bioimaging

2020 ◽  
Vol 39 (1) ◽  
pp. 209-221
Author(s):  
Jiafeng Wan ◽  
Xiaoyuan Zhang ◽  
Kai Zhang ◽  
Zhiqiang Su
Keyword(s):  
Fluorescent Probes ◽  
Organic Dyes ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
High Sensitivity ◽  
Biological Imaging ◽  
Fluorescent Materials ◽  
And Performance

Abstract In recent years, nanomaterials have attracted lots of attention from researchers due to their unique properties. Nanometer fluorescent materials, such as organic dyes, semiconductor quantum dots (QDs), metal nano-clusters (MNCs), carbon dots (CDs), etc., are widely used in biological imaging due to their high sensitivity, short response time, and excellent accuracy. Nanometer fluorescent probes can not only perform in vitro imaging of organisms but also achieve in vivo imaging. This provides medical staff with great convenience in cancer treatment. Combined with contemporary medical methods, faster and more effective treatment of cancer is achievable. This article explains the response mechanism of three-nanometer fluorescent probes: the principle of induced electron transfer (PET), the principle of fluorescence resonance energy transfer (FRET), and the principle of intramolecular charge transfer (ICT), showing the semiconductor QDs, precious MNCs, and CDs. The excellent performance of the three kinds of nano fluorescent materials in biological imaging is highlighted, and the application of these three kinds of nano fluorescent probes in targeted biological imaging is also introduced. Nanometer fluorescent materials will show their significance in the field of biomedicine.

scholarly journals Bacteriophage-derived CHAP domain protein, P128, kills Staphylococcus cells by cleaving interpeptide cross-bridge of peptidoglycan

Microbiology ◽  
2014 ◽  
Vol 160 (10) ◽  
pp. 2157-2169 ◽  
Author(s):  
Sudarson Sundarrajan ◽  
Junjappa Raghupatil ◽  
Aradhana Vipra ◽  
Nagalakshmi Narasimhaswamy ◽  
Sanjeev Saravanan ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Mechanism Of Action ◽  
Catalytic Domain ◽  
Antibiotic Sensitivity ◽  
High Sensitivity ◽  
Common Mechanism ◽  
Cross Bridge ◽  
Sensitivity Pattern

P128 is an anti-staphylococcal protein consisting of the Staphylococcus aureus phage-K-derived tail-associated muralytic enzyme (TAME) catalytic domain (Lys16) fused with the cell-wall-binding SH3b domain of lysostaphin. In order to understand the mechanism of action and emergence of resistance to P128, we isolated mutants of Staphylococcus spp., including meticillin-resistant Staphylococcus aureus (MRSA), resistant to P128. In addition to P128, the mutants also showed resistance to Lys16, the catalytic domain of P128. The mutants showed loss of fitness as shown by reduced rate of growth in vitro. One of the mutants tested was found to show reduced virulence in animal models of S. aureus septicaemia suggesting loss of fitness in vivo as well. Analysis of the antibiotic sensitivity pattern showed that the mutants derived from MRSA strains had become sensitive to meticillin and other β-lactams. Interestingly, the mutant cells were resistant to the lytic action of phage K, although the phage was able to adsorb to these cells. Sequencing of the femA gene of three P128-resistant mutants showed either a truncation or deletion in femA, suggesting that improper cross-bridge formation in S. aureus could be causing resistance to P128. Using glutathione S-transferase (GST) fusion peptides as substrates it was found that both P128 and Lys16 were capable of cleaving a pentaglycine sequence, suggesting that P128 might be killing S. aureus by cleaving the pentaglycine cross-bridge of peptidoglycan. Moreover, peptides corresponding to the reported cross-bridge of Staphylococcus haemolyticus (GGSGG, AGSGG), which were not cleaved by lysostaphin, were cleaved efficiently by P128. This was also reflected in high sensitivity of S. haemolyticus to P128. This showed that in spite of sharing a common mechanism of action with lysostaphin, P128 has unique properties, which allow it to act on certain lysostaphin-resistant Staphylococcus strains.

scholarly journals Transitional B cells are the target of negative selection in the B cell compartment.

1995 ◽  
Vol 181 (6) ◽  
pp. 2129-2140 ◽  
Author(s):  
R Carsetti ◽  
G Köhler ◽  
M C Lamers
Keyword(s):  
B Cells ◽  
Negative Selection ◽  
Tolerance Induction ◽  
High Sensitivity ◽  
Target Population ◽  
Fas Antigen ◽  
Transitional B Cells ◽  
Immature B Cells

B lymphocytes recognize antigen through membrane-bound antigen-receptors, membrane IgM and IgD (mIgM and mIgD). Binding to foreign antigens initiates a cascade of biochemical events that lead to activation and differentiation. In contrast, binding to self-antigens leads to death or to inactivation. It is commonly believed that the B cells acquire the ability to discriminate between self and nonself in the early phases of development. We report here that immature B cells, which have just emerged from the mIgMneg, B220pos pool, are not deleted upon binding of self-antigen. In vivo, developing B cells become sensitive to tolerance induction in a relatively late window of differentiation, when they are in transition from the immature (HSAbright, B220dull) to the mature (HSAdull, B220bright) stage. In the transitional B cells, early markers of differentiation such as Pgp1 (CD44) and ThB reach the highest level of expression, while the expression of CD23 and mIgD, late markers of differentiation, and expression of class II MHC, progressively increases. Most of the transitional B cells, but only few of the mature and of the immature B cells, express the fas antigen, while mature B cells, but not immature and transitional B cells, express bcl-2 protein. mIgM is present in low amounts in immature B cells, reaches the highest level of expression in transitional B cells and is down-regulated in mature resting B cells, where it is coexpressed with mIgD. The high expression of mIgM, the presence of the fas antigen and the absence of bcl-2 protein is compatible with the high sensitivity of transitional B cells to negative selection. In vitro, immature B cells die rapidly by apoptosis after cross-linking of mIgM. This result, combined with the resistance of immature B cells to elimination in vivo, suggests that early in development the stroma cell microenvironment modulates signals transduced through mIgM. The functional and phenotypic division of IgMpos bone marrow B cells in three compartments not only allows to define the target population of physiological processes like negative selection, but will also be a helpful tool for an accurate description of possible developmental blocks in mutant mice.

scholarly journals Intermediate step of cohesin’s ATPase cycle allows cohesin to entrap DNA

2018 ◽  
Vol 115 (39) ◽  
pp. 9732-9737 ◽  
Author(s):  
Gamze Ö. Çamdere ◽  
Kristian K. Carlborg ◽  
Douglas Koshland
Keyword(s):  
Atp Hydrolysis ◽  
Intermediate Step ◽  
Mutant Form ◽  
In Vitro Reconstitution ◽  
Chromatid Cohesion ◽  
The Family ◽  
Structural Maintenance Of Chromosomes ◽  
Dna Substrate

Cohesin is a four-subunit ATPase in the family of structural maintenance of chromosomes (SMC). Cohesin promotes sister chromatid cohesion, chromosome condensation, DNA repair, and transcription regulation. Cohesin performs these functions as a DNA tether and potentially a DNA-based motor. At least one of its DNA binding activities involves entrapment of DNA within a lumen formed by its subunits. This activity can be reconstituted in vitro by incubating cohesin with DNA, ATP, and cohesin loader. Previously we showed that a mutant form of cohesin (DE-cohesin) possesses the ability to bind and tether DNA in vivo. Using in vitro reconstitution assays, we show that DE-cohesin can form stable complexes with DNA without ATP hydrolysis. We show that wild-type cohesin with ADP aluminum fluoride (cohesinADP/AlFx) can also form stable cohesin–DNA complexes. These results suggest that an intermediate nucleotide state of cohesin, likely cohesinADP-Pi, is capable of initially dissociating one interface between cohesin subunits to allow DNA entry into a cohesin lumen and subsequently interacting with the bound DNA to stabilize DNA entrapment. We also show that cohesinADP/AlFx binding to DNA is enhanced by cohesin loader, suggesting a function for loader other than stimulating the ATPase. Finally, we show that loader remains stably bound to cohesinADP/AlFx after DNA entrapment, potentially revealing a function for loader in tethering the second DNA substrate. These results provide important clues on how SMC complexes like cohesin can function as both DNA tethers and motors.

Measurement of the Optical Properties of Muscle Tissue In Vivo

2000 ◽  
Author(s):  
P. L. Kopsombut ◽  
D. Willis ◽  
A. E. Schen ◽  
L. X. Xu ◽  
X. Xu
Keyword(s):  
Optical Properties ◽  
Transport Theory ◽  
Rapid Development ◽  
Ccd Camera ◽  
High Sensitivity ◽  
Biological Tissues ◽  
In Vivo Measurement ◽  
Living Tissues

Abstract Along with rapid development of diagnostic and therapeutic applications of lasers in medicine, optical properties of various biological tissues have been extensively studied [1]. Most of the studies were performed in vitro owing to the complexity involved in in vivo measurement. To date, it is well understood that living tissue is an absorbing and scattering heterogeneous medium because of its complex structures including blood network. The transport theory cannot be readily used due to the heterogeneity and the absence of the optical properties of living tissues [2]. In this research, we have developed a procedure for measuring the total attenuation coefficient (μ1) of the exteriorized rat 2-D spinotrapezius muscle in the wavelength ranged from 480–560 nm using the collimated light from a Nitrogen-pumped dye laser and a high-sensitivity CCD camera.

What can we Predict Before it's Implanted?

1985 ◽  
Vol 55 ◽  
Author(s):  
Donald F. Gibbons
Keyword(s):  
Biological Response ◽  
High Sensitivity ◽  
Biological Pathways ◽  
Surface Topology ◽  
Dystrophic Calcification ◽  
Vitro Assay ◽  
In Vivo Assays ◽  
Tissue Interface

ABSTRACTThe material factors which relate to the degradation and/or leaching of ions or molecules are described and the possible biological pathways which they may activate are described, i.e. cytotoxic, immune, tumor and nonspecific inflammatory response. Cytotoxicity is the only biological response which may be measured with high sensitivity by an in vitro assay prior to implantation. All other biological pathways require some degree of in vivo involvement. Three examples of biological response to material factors associated with devices which require evaluation by in vivo assays are discussed, namely: surface topology (texture), mechanically induced factors at the device/tissue interface caused by differences in compliance, and dystrophic calcification in connective tissue and vascular devices.

scholarly journals A fast response fluorescence probe specific for hypochlorous acid detection and its applications in bioimaging

2018 ◽  
Vol 16 (12) ◽  
pp. 2074-2082 ◽  
Author(s):  
Hongmin Jia ◽  
Shuhe Xia ◽  
Huan Feng ◽  
Qingtao Meng ◽  
Chengchen Duan ◽  
...  
Keyword(s):  
Hypochlorous Acid ◽  
Fluorescence Probe ◽  
High Sensitivity ◽  
Fast Response ◽  
Rapid Response

The features ofDNPH-NA, including its high sensitivity, selectivity, and reliability at physiological pH, together with a rapid response, enable its successful application in the detection of endogenous HOClin vitroandin vivo.

scholarly journals Label-Free Split Aptamer Sensor for Femtomolar Detection of Dopamine by Means of Flexible Organic Electrochemical Transistors

Materials ◽  
2020 ◽  
Vol 13 (11) ◽  
pp. 2577 ◽  
Author(s):  
Yuanying Liang ◽  
Ting Guo ◽  
Lei Zhou ◽  
Andreas Offenhäusser ◽  
Dirk Mayer
Keyword(s):  
Detection Limit ◽  
Electrochemical Sensors ◽  
Limit Of Detection ◽  
High Sensitivity ◽  
Label Free ◽  
Dopamine Detection ◽  
Electrochemical Transistor ◽  
Sensitivity And Selectivity

The detection of chemical messenger molecules, such as neurotransmitters in nervous systems, demands high sensitivity to measure small variations, selectivity to eliminate interferences from analogues, and compliant devices to be minimally invasive to soft tissue. Here, an organic electrochemical transistor (OECT) embedded in a flexible polyimide substrate is utilized as transducer to realize a highly sensitive dopamine aptasensor. A split aptamer is tethered to a gold gate electrode and the analyte binding can be detected optionally either via an amperometric or a potentiometric transducer principle. The amperometric sensor can detect dopamine with a limit of detection of 1 μM, while the novel flexible OECT-based biosensor exhibits an ultralow detection limit down to the concentration of 0.5 fM, which is lower than all previously reported electrochemical sensors for dopamine detection. The low detection limit can be attributed to the intrinsic amplification properties of OECTs. Furthermore, a significant response to dopamine inputs among interfering analogues hallmarks the selective detection capabilities of this sensor. The high sensitivity and selectivity, as well as the flexible properties of the OECT-based aptasensor, are promising features for their integration in neuronal probes for the in vitro or in vivo detection of neurochemical signals.

scholarly journals Cancer-Specific Biomarker hNQO1-Activatable Fluorescent Probe for Imaging Cancer Cells In Vitro and In Vivo

Cancers ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 470 ◽  
Author(s):  
Surendra Punganuru ◽  
Hanumantha Madala ◽  
Viswanath Arutla ◽  
Kalkunte Srivenugopal
Keyword(s):  
Cancer Cells ◽  
Fluorescent Probe ◽  
Stokes Shift ◽  
High Sensitivity ◽  
Cell Permeability ◽  
Quinone Oxidoreductase ◽  
Brain Tumor Cells ◽  
Sensitivity And Selectivity

Human NAD(P)H quinone oxidoreductase-1 (hNQO1) is an important cancer-related biomarker, which shows significant overexpression in malignant cells. Developing an effective method for detecting NQO1 activity with high sensitivity and selectivity in tumors holds a great potential for cancer diagnosis, treatment, and management. In the present study, we report a new dicyanoisophorone (DCP) based fluorescent probe (NQ-DCP) capable of monitoring hNQO1 activity in vitro and in vivo in both ratiometric and turn-on model. NQ-DCP was prepared by conjugating dicyanoisophorone fluoroprobe with hNQO1 activatable quinone propionic acid (QPA), which remain non-fluorescent until activation by tumor-specific hNQO1. NQ-DCP featured a large Stokes shift (145 nm), excellent biocompatibility, cell permeability, and selectivity towards hNQO1 allowed to differentiate cancer cells from healthy cells. We have successfully employed NQ-DCP to monitor non-invasive endogenous hNQO1 activity in brain tumor cells in vitro and in xenografted tumors developed in nude mice.

scholarly journals MCM7 promotes cancer progression through cyclin D1-dependent signaling and serves as a prognostic marker for patients with hepatocellular carcinoma

2017 ◽  
Vol 8 (2) ◽  
pp. e2603-e2603 ◽  
Author(s):  
Kai Qu ◽  
Zhixin Wang ◽  
Haining Fan ◽  
Juan Li ◽  
Jie Liu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Dna Replication ◽  
Cyclin D1 ◽  
Cancer Progression ◽  
Cellular Proliferation ◽  
High Sensitivity ◽  
Mapk Signaling ◽  
High Expression

Abstract DNA replication is a central procedure of cell proliferation, whereas aberrant DNA replication is indicated to be a driving force of oncogenesis. Minichromosome maintenance complex component 7 (MCM7) plays an essential role in initiating DNA replication. To investigate the potential oncogenic properties and prognostic value of MCM7 in hepatocellular carcinoma (HCC), we conducted immunohistochemistry staining of MCM7 in 153 HCC samples and found that MCM7 high expression level was associated with worse overall survival (OS) of HCC patients. Mechanistically, knockdown of MCM7 significantly inhibited cellular proliferation in vitro and HCC tumorigenicity in vivo. Cyclin D1 was proved to be regulated by MCM7–MAPK signaling pathway. Clinically, high expression of both MCM7 and cyclin D1 exhibited a relatively high sensitivity and specificity to predict worse outcome of HCC patients. Taken together, our results suggest that MCM7–cyclin D1 pathway may participate in cancer progression and serve as a biomarker for prognosis in HCC.

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