Synthesis of glycosyl derivatives as dopamine prodrugs: interaction with glucose carrier GLUT-1Electronic supplementary information (ESI) available: experimental details for the preparation of all derivatives and biological assays. See http://www.rsc.org/suppdata/ob/b2/b212066f/

2003 ◽  
Vol 1 (5) ◽  
pp. 767-771 ◽  
Author(s):  
Caridad Fernández ◽  
Ofelia Nieto ◽  
José Angel Fontenla ◽  
Emilia Rivas ◽  
María L. de Ceballos ◽  
...  
Keyword(s):  
Supplementary Information ◽  
Biological Assays ◽  
Glucose Carrier

Structural similarity of ribosomes from E. coli and A. salina

1978 ◽  
Vol 36 (2) ◽  
pp. 242-243
Author(s):  
M. Boublik ◽  
R.M. Wydro ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Ribosomal Proteins ◽  
Direct Evidence ◽  
Structural Similarity ◽  
Carbon Support ◽  
Artemia Salina ◽  
Uranyl Acetate ◽  
Biological Assays ◽  
E Coli ◽  
And Function ◽  
Fine Carbon

Ribosomes are ribonucleoprotein particles necessary for processing the genetic information of mRNA into proteins. Analogy in composition and function of ribosomes from diverse species, established by biochemical and biological assays, implies their structural similarity. Direct evidence obtained by electron microscopy seems to be of increasing relevance in understanding the structure of ribosomes and the mechanism of their role in protein synthesis.The extent of the structural homology between prokaryotic and eukaryotic ribosomes has been studied on ribosomes of Escherichia coli (E.c.) and Artemia salina (A.s.). Despite the established differences in size and in the amount and proportion of ribosomal proteins and RNAs both types of ribosomes show an overall similarity. The monosomes (stained with 0.5% aqueous uranyl acetate and deposited on a fine carbon support) appear in the electron micrographs as round particles with a diameter of approximately 225Å for the 70S E.c. (Fig. 1) and 260Å for the 80S A.s. monosome (Fig. 2).

Anacyclamide D8P, a prenylated cyanobactin from a Sphaerospermopsis sp. cyanobacterium

2017 ◽  
Author(s):  
Joana Martins ◽  
Niina Leikoski ◽  
Matti Wahlsten ◽  
Joana Azevedo ◽  
Jorge Antunes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cyclic Peptides ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Tyrosine Residue ◽  
Biosynthetic Gene ◽  
Post Translational Modification ◽  
Biological Assays ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Cyanobactins are a family of linear and cyclic peptides produced through the post-translational modification of short precursor peptides. Anacyclamides are macrocyclic cyanobactins with a highly diverse sequence that are common in the genus <i>Anabaena</i>. A mass spectrometry-based screening of potential cyanobactin producers led to the discovery of a new prenylated member of this family of compounds, anacyclamide D8P (<b>1</b>), from <i>Sphaerospermopsis</i> sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (<i>acy</i>) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in <i>Escherichia</i> <i>coli</i> established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of <b>1</b> using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound <b>1</b> was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium <i>Halomonas aquamarina</i> CECT 5000.<br>

Model for Classification of ChEMBL Dataset of Anti-breast cancer Compounds According to Multiple Pharmacological Parameters, Biological Assays, and Receptors

2015 ◽  
Vol 13 (999) ◽  
pp. 1-1
Author(s):  
Francisco J. Prado-Prado ◽  
Angel G. Arguello-Chan ◽  
Coraima I. Estrada-Domínguez ◽  
Alejandra Aguirre-Crespo ◽  
Francisco J. Aguirre-Crespo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Biological Assays

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals MODER2: first-order Markov modeling and discovery of monomeric and dimeric binding motifs

2020 ◽  
Vol 36 (9) ◽  
pp. 2690-2696
Author(s):  
Jarkko Toivonen ◽  
Pratyush K Das ◽  
Jussi Taipale ◽  
Esko Ukkonen
Keyword(s):  
Markov Models ◽  
Expectation Maximization Algorithm ◽  
Software Tool ◽  
Specific Weight ◽  
Training Data ◽  
Supplementary Information ◽  
Markov Modeling ◽  
Binding Motifs ◽  
The Difference ◽  
Probability Matrices

Abstract Motivation Position-specific probability matrices (PPMs, also called position-specific weight matrices) have been the dominating model for transcription factor (TF)-binding motifs in DNA. There is, however, increasing recent evidence of better performance of higher order models such as Markov models of order one, also called adjacent dinucleotide matrices (ADMs). ADMs can model dependencies between adjacent nucleotides, unlike PPMs. A modeling technique and software tool that would estimate such models simultaneously both for monomers and their dimers have been missing. Results We present an ADM-based mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algorithm MODER2 for learning such models from training data and seeds. The model is a mixture that includes monomers and dimers, built from the monomers, with a description of the dimeric structure (spacing, orientation). The technique is modular, meaning that the co-operative effect of dimerization is made explicit by evaluating the difference between expected and observed models. The model is validated using HT-SELEX and generated datasets, and by comparing to some earlier PPM and ADM techniques. The ADM models explain data slightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (bHLH, bZIP, ETS and Homeodomain), the ADM mixture models by MODER2 being the best on average. Availability and implementation Software implementation is available from https://github.com/jttoivon/moder2. Supplementary information Supplementary data are available at Bioinformatics online.

Triticum aestivum Assay - A Useful Tool for Environmental Monitoring and Toxicity Assessment

2019 ◽  
Vol 47 (4) ◽  
pp. 1005-1018
Author(s):  
Alexandra JITĂREANU ◽  
Ioana-Cezara CABA ◽  
Adriana TRIFAN ◽  
Silvica PĂDUREANU ◽  
Luminița AGOROAEI
Keyword(s):  
Triticum Aestivum ◽  
Higher Plants ◽  
Low Cost ◽  
Environmental Pollutants ◽  
Rapid Test ◽  
Toxicity Assessment ◽  
Pollution Monitoring ◽  
Present Review ◽  
Digital Object Identifier ◽  
Biological Assays

The present review summarizes the literature data regarding the application of Triticum aestivum assay as an alternative method for toxicity assessment of environmental pollutants or potential therapeutic agents. Plant bioassays present several advantages among other biological assays (simplicity, low cost, rapid test activation, a wide array of assessment endpoints). They present a good correlation with animal and human cells models, and are a reliable tool for genotoxicity assessment. Furthermore, in the context of toxicology guidelines that promote the substitution of assays using animal models with other bioassays, genotoxicity assays using higher plants models have gained in popularity. The present review focuses on three major aspects regarding Triticum aestivum assay - its utility in environmental pollution monitoring, its application in genotoxicity assessment studies, and its application in phytotoxicity evaluation of nanomaterials.   ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 4, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

scholarly journals Returning to dialysis after kidney allograft failure: the experience of the Italian Registry of Paediatric Chronic Dialysis

2021 ◽  
Author(s):  
Edoardo La Porta ◽  
Ester Conversano ◽  
Daniela Zugna ◽  
Roberta Camilla ◽  
Raffaella Labbadia ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
Chronic Dialysis ◽  
Supplementary Information ◽  
Dialysis Modality ◽  
Specific Population ◽  
Kidney Allograft ◽  
Allograft Failure ◽  
Younger Age ◽  
Complicated Course ◽  
Significant Mortality

Abstract Background The need for dialysis after kidney allograft failure (DAGF) is among the top five reasons for dialysis initiation, making this an important topic in clinical nephrology. However, data are scarce on dialysis choice after transplantation and clinical outcomes for DAGF in children. Methods Patients receiving chronic dialysis < 18 years were recorded from January 1991 to January 2019 by the Italian Registry of Pediatric Chronic Dialysis (IRPCD). We investigated factors influencing choice of dialysis modality, patient outcome in terms of mortality, switching dialysis modality, and kidney transplantation. Results Among 118 patients receiving DAGF, 41 (35%) were treated with peritoneal dialysis (PD), and 77 (65%) with haemodialysis (HD). Significant predictors for treatment with PD were younger age at dialysis start (OR 0.85 per year increase [95%CI 0.72–1.00]) and PD use before kidney transplantation (OR 8.20 [95%CI 1.82–37.01]). Patients entering DAGF in more recent eras (OR 0.87 per year increase [95%CI 0.80–0.94]) and with more than one dialysis modality before kidney transplantation (OR 0.56 for being treated with PD [0.12–2.59]) were more likely to be initiated on HD. As compared to patients on HD, those treated with PD exhibited increased but non-significant mortality risk (HR 2.15 [95%CI 0.54–8.6]; p = 0.28) and higher prevalence of dialysis-related complications during DAGF (p = 0.002) Conclusions Patients entering DAGF in more recent years are more likely to be initiated on HD. In this specific population of children, use of PD seems associated with a more complicated course. Graphical abstract A higher resolution version of the Graphical abstract is available as Supplementary information

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