scholarly journals Directed evolution of split APEX peroxidase

2018 ◽  
Author(s):  
Yisu Han ◽  
Jeffrey D. Martell ◽  
Tess C. Branon ◽  
Daniela Boassa ◽  
David M. Shechner ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Amino Acid ◽  
Directed Evolution ◽  
Noncoding Rna ◽  
Yeast Display ◽  
Rna Motifs ◽  
Contact Sites ◽  
Terminal Fragment ◽  
Wide Range ◽  
Fragment Libraries

AbstractAPEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications, from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). Twenty rounds of FACS-based selections from yeast-displayed fragment libraries, using three different yeast display configurations, produced a 200-amino acid N-terminal fragment (with 9 mutations relative to APEX2) called “AP” and a 50-amino acid C-terminal fragment called “EX”. AP and EX fragments were each inactive on their own but reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within telomerase noncoding RNA, and at mitochondria-endoplasmic reticulum contact sites.

scholarly journals The LisH Domain-Containing N-Terminal Fragment is Important for the Localization, Dimerization, and Stability of Katnal2 in Tetrahymena

Cells ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 292
Author(s):  
Ewa Joachimiak ◽  
Ewa Waclawek ◽  
Michal Niziolek ◽  
Anna Osinka ◽  
Hanna Fabczak ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Catalytic Domain ◽  
Tetrahymena Thermophila ◽  
Basal Bodies ◽  
Amino Acid Sequence Homology ◽  
Terminal Fragment ◽  
Wide Range ◽  
Microtubular Structures

Katanin-like 2 protein (Katnal2) orthologs have a tripartite domain organization. Two highly conserved regions, an N-terminal LisH (Lis-homology) domain and a C-terminal AAA catalytic domain, are separated by a less conserved linker. The AAA domain of Katnal2 shares the highest amino acid sequence homology with the AAA domain of the canonical katanin p60. Katnal2 orthologs are present in a wide range of eukaryotes, from protists to humans. In the ciliate Tetrahymena thermophila, a Katnal2 ortholog, Kat2, co-localizes with the microtubular structures, including basal bodies and ciliary outer doublets, and this co-localization is sensitive to levels of microtubule glutamylation. The functional analysis of Kat2 domains suggests that an N-terminal fragment containing a LisH domain plays a role in the subcellular localization, dimerization, and stability of Kat2.

Effect of RI-331, a new antifungal antibiotic, on the ultrastructure of Candida albicans

1990 ◽  
Vol 48 (3) ◽  
pp. 632-633
Author(s):  
Yayoi Nishiyama ◽  
Yukiyo Asagi ◽  
Tamio Hiratani ◽  
Maki Yamaguchi ◽  
Hideyo Yamaguchi ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Candida Albicans ◽  
Amino Acid ◽  
Antifungal Agent ◽  
Intact Cells ◽  
Antifungal Antibiotic ◽  
Transmission Electron ◽  
Wide Range ◽  
Medical Importance

An amino acid antibiotic RI-331, (S)-2-amino-5-hydroxy-4-oxopentanoic acid, produced by a Streptomyces sp., is a novel antifungal agent active against a wide range of yeasts of medical importance including Candida albicans. This antibiotic was found out as one of those natural compounds which preferentially inhibited regeneration of C.albicans protoplasts to intact cells during our screening works. In the present study, the effect of RI-331 on C.albicans growing cells and protoplasts prepared therefrom were investigated morphologically by transmission electron microscopy.

Recent Applications of High Resolution Electron Microscopy to Crystalline Arrays of Virus Particles

1978 ◽  
Vol 36 (3) ◽  
pp. 470-482 ◽  
Author(s):  
R.W. Horne
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
Analytical Techniques ◽  
Staining Technique ◽  
High Resolution Electron Microscopy ◽  
Optical Diffraction ◽  
Full Potential ◽  
Virus Particles ◽  
Resolution Electron ◽  
Wide Range

The technique of surrounding virus particles with a neutralised electron dense stain was described at the Fourth International Congress on Electron Microscopy, Berlin 1958 (see Home & Brenner, 1960, p. 625). For many years the negative staining technique in one form or another, has been applied to a wide range of biological materials. However, the full potential of the method has only recently been explored following the development and applications of optical diffraction and computer image analytical techniques to electron micrographs (cf. De Hosier & Klug, 1968; Markham 1968; Crowther et al., 1970; Home & Markham, 1973; Klug & Berger, 1974; Crowther & Klug, 1975). These image processing procedures have allowed a more precise and quantitative approach to be made concerning the interpretation, measurement and reconstruction of repeating features in certain biological systems.

Microwaves: Application in Electron Microscopy

1990 ◽  
Vol 48 (3) ◽  
pp. 140-141
Author(s):  
Anthony S-Y Leong ◽  
David W Gove
Keyword(s):  
Electron Microscopy ◽  
Light Microscopy ◽  
Chemical Reactions ◽  
Electromagnetic Waves ◽  
Tissue Fixation ◽  
Primary Method ◽  
Dipolar Molecules ◽  
Wide Range ◽  
Time Required ◽  
Cryostat Sections

Microwaves (MW) are electromagnetic waves which are commonly generated at a frequency of 2.45 GHz. When dipolar molecules such as water, the polar side chains of proteins and other molecules with an uneven distribution of electrical charge are exposed to such non-ionizing radiation, they oscillate through 180° at a rate of 2,450 million cycles/s. This rapid kinetic movement results in accelerated chemical reactions and produces instantaneous heat. MWs have recently been applied to a wide range of procedures for light microscopy. MWs generated by domestic ovens have been used as a primary method of tissue fixation, it has been applied to the various stages of tissue processing as well as to a wide variety of staining procedures. This use of MWs has not only resulted in drastic reductions in the time required for tissue fixation, processing and staining, but have also produced better cytologic images in cryostat sections, and more importantly, have resulted in better preservation of cellular antigens.

Recent Progress and Plans in Computer-Controlled High Resolution Electron Microscopy

1990 ◽  
Vol 48 (1) ◽  
pp. 154-155
Author(s):  
W.J. de Ruijter ◽  
Peter Rez ◽  
David J. Smith
Keyword(s):  
Electron Microscopy ◽  
Digital Processing ◽  
High Resolution Electron Microscopy ◽  
Objective Lens ◽  
Linear Filter ◽  
Contrast Transfer Function ◽  
Image Displacement ◽  
Spatially Resolved ◽  
Wide Range ◽  
On Line

Digital computers are becoming widely recognized as standard accessories for electron microscopy. Due to instrumental innovations the emphasis in digital processing is shifting from off-line manipulation of electron micrographs to on-line image acquisition, analysis and microscope control. An on-line computer leads to better utilization of the instrument and, moreover, the flexibility of software control creates the possibility of a wide range of novel experiments, for example, based on temporal and spatially resolved acquisition of images or microdiffraction patterns. The instrumental resolution in electron microscopy is often restricted by a combination of specimen movement, radiation damage and improper microscope adjustment (where the settings of focus, objective lens stigmatism and especially beam alignment are most critical). We are investigating the possibility of proper microscope alignment based on computer induced tilt of the electron beam. Image details corresponding to specimen spacings larger than ∼20Å are produced mainly through amplitude contrast; an analysis based on geometric optics indicates that beam tilt causes a simple image displacement. Higher resolution detail is characterized by wave propagation through the optical system of the microscope and we find that beam tilt results in a dispersive image displacement, i.e. the displacement varies with spacing. This approach is valid for weak phase objects (such as amorphous thin films), where transfer is simply described by a linear filter (phase contrast transfer function) and for crystalline materials, where imaging is described in terms of dynamical scattering and non-linear imaging theory. In both cases beam tilt introduces image artefacts.

Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using in silico Method

2012 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Mohd Fakharul Zaman Raja Yahya ◽  
Hasidah Mohd Sidek
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Nuclear Export ◽  
Nuclear Export Signal ◽  
Plasmodium Species ◽  
Mitogen Activated Protein Kinase ◽  
Multiple Sequence ◽  
Wide Range ◽  
Mitogen Activated Protein ◽  
Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range of hosts including humans and rodents. There are two copies of mitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise of presented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series of publicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localized and contain both a nuclear localization signal (NLS) and a Leucine-rich nuclear export signal (NES). The activation motifs of TDY and TSH were found to be fully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection of a multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising of different amino acids present in MAPKJ and MAPK2 respectively, with respect to rodent and human Plasmodia. It is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs. 

Comparative Study on Mitogen Activated Protein Kinase of Plasmodium Species by Using In silico Method

2012 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Mohd Fakharul Zaman Raja Yahya ◽  
Hasidah Mohd Sidek
Keyword(s):  
Amino Acid ◽  
In Silico ◽  
Nuclear Export ◽  
Nuclear Export Signal ◽  
Plasmodium Species ◽  
Mitogen Activated Protein Kinase ◽  
Multiple Sequence ◽  
Bioinformatic Tools ◽  
Wide Range ◽  
Human Plasmodium

Malaria parasites, Plasmodium can infect a wide range ofhosts including humans and rodents. There are two copies ofmitogen activated protein kinases (MAPKs) in Plasmodium, namely MAPK1 and MAPK2. The MAPKs have been studied extensively in the human Plasmodium, P. falciparum. However, the MAPKs from other Plasmodium species have not been characterized and it is therefore the premise ofpresented study to characterize the MAPKs from other Plasmodium species-P. vivax, P. knowlesi, P. berghei, P. chabaudi and P.yoelli using a series ofpublicly available bioinformatic tools. In silico data indicates that all Plasmodium MAPKs are nuclear-localizedandcontain both a nuclear localization signal (NLS) anda Leucine-rich nuclear export signal (NES). The activation motifs ofTDYand TSH werefound to befully conserved in Plasmodium MAPK1 and MAPK2, respectively. The detailed manual inspection ofa multiple sequence alignment (MSA) construct revealed a total of 17 amino acid stack patterns comprising ofdifferent amino acids present in MAPK1 and MAPK2 respectively, with respect to rodent and human Plasmodia. 1t is proposed that these amino acid stack patterns may be useful in explaining the disparity between rodent and human Plasmodium MAPKs.

Application of the Innovative and Non-Invasive Technique, Molecular Music Therapy (MMT), Bio-Frequency Therapy, for the Treatment of a Wide Range of Disorders and Pathologies, with Consequent Verification of Molecular Parameters by Using Bi-Digital O-Ring Test (BDORT)

2020 ◽  
Vol 44 (3) ◽  
pp. 177-189
Author(s):  
Momir Dunjic ◽  
Stefano Turini ◽  
Dejan Krstic ◽  
Katarina Dunjic ◽  
Marija Dunjic ◽  
...  
Keyword(s):  
Amino Acid ◽  
Music Therapy ◽  
Amino Acid Sequences ◽  
Sirtuin 1 ◽  
Ring Test ◽  
Invasive Technique ◽  
Specific Gene ◽  
Radiofrequency Therapy ◽  
Wide Range ◽  
Clinical Pictures

Radiofrequency therapy is an unconventional method, already applied for some time, with numerous results in numerous clinical pictures. Our group has developed a software, later called SONGENPROT-SOLARIS, capable of directly converting nucleotide sequences (DNA and/or RNA) and amino acid sequences (polypeptides and proteins) into musical sequences, based on mathematic matrices, designed by the French physicist and musician Joel Sternheimer, which allows to associate a musical note with a nucleotide or an amino acid. Innovation in our software is that, in the algorithm that defines it, a variant is directly implemented that allows the reproduction of sounds, phase-shifted by 30 Hz, between one ear and another reproducing the phenomenon of Binaural Tones, capable of induce a specific brain activity and also the release of particles called solitons. Thanks to this software we have developed a technique called MMT (Molecular Music Therapy) and currently, we are in the phase of applying the technique on a cohort of 91 patients, with a high spectrum of clinical pictures, examining the same, using the technique Bi-Digital-ORing-Test (BDORT), before and after treatment with MMT. Aim of project is to stimulate the expression of a specific gene (the same genetic sequence that the patient listens to, translated into music), only through the use of sound sequences. We have concentrated our attention on three main molecules: Sirtuin-1, Telomers and TP-53. The results obtained with BDORT, after treatment with MMT, showed a significant increase in the values of the three molecules, on all the examined patients, demonstrating the operative efficacy of the technique and the its applicability to numerous diseases. In order to confirm the data obtained by BDORT, we propose, with the help of an accredited laboratory, to perform epigenetic tests on the three parameters listed above, paving the way to understanding how frequencies can influence gene expression.

Positive and negative contractile effects of neuropeptide Y on ventricular cardiomyocytes

1991 ◽  
Vol 261 (6) ◽  
pp. H1727-H1733 ◽  
Author(s):  
B. C. Millar ◽  
T. Weis ◽  
H. M. Piper ◽  
M. Weber ◽  
U. Borchard ◽  
...  
Keyword(s):  
Amino Acid ◽  
Neuropeptide Y ◽  
Pertussis Toxin ◽  
Contractile Response ◽  
Contractile Responses ◽  
Contractile Effect ◽  
Terminal Fragment ◽  
Ventricular Cardiomyocytes ◽  
K Current

The potency of neuropeptide Y (NPY) to cause negative and positive contractile responses in rat ventricular cardiomyocytes was investigated. In these cells, NPY was found to activate the transient outward K+ current (Ito) and the slow inward Ca2+ current (Isi). As reported before (H. M. Piper, B. C. Millar, and J. R. McDermott, Naunyn Schmiedeberg's Arch. Pharmacol. 340: 333-337, 1989), NPY attenuated the increase in the contractile response induced by isoprenaline (10(-7) M). This effect of NPY could be abolished by 1) the presence of the inhibitor of Ito, 4-aminopyridine (4-AP, 0.5 mM); 2) pretreatment of the cells with pertussis toxin (1 microgram/ml for 6 h); and 3) the presence of the 19-amino acid COOH-terminal fragment of NPY, NPY-(18-36) (10(-6) M). In the absence of isoprenaline, but in the presence of 4-AP, NPY exerted a stimulatory effect on the cardiomyocytes. This effect could be abolished 1) by using the inhibitor of the Isi, verapamil (10(-8) M), but not 2) by pretreatment with pertussis toxin, nor 3) by coincubation with NPY-(18-36). The results indicate that in the rat the antiadrenergic negative contractile effect of NPY results from its action on the Ito. Blockade of this current by 4-AP unmasks a positive contractile effect of NPY that is related to activation of the Isi.

Cholinium-amino acid based ionic liquids: a new method of synthesis and physico-chemical characterization

2015 ◽  
Vol 17 (32) ◽  
pp. 20687-20698 ◽  
Author(s):  
Serena De Santis ◽  
Giancarlo Masci ◽  
Francesco Casciotta ◽  
Ruggero Caminiti ◽  
Eleonora Scarpellini ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Amino Acid ◽  
Room Temperature ◽  
Chemical Characterization ◽  
New Method ◽  
Room Temperature Ionic Liquids ◽  
Synthetic Method ◽  
Chemical Structures ◽  
Physico Chemical ◽  
Wide Range

Fourteen cholinium-amino acid based room temperature ionic liquids were prepared using a cleaner synthetic method. Chemicophysical properties were well correlated with the wide range of amino acid chemical structures.

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