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https://www.readbyqxmd.com/read/27933338/progress-in-research-and-application-of-hiv-1-tat-derived-cell-penetrating-peptide
#1
REVIEW
Le Zou, Qilin Peng, Ping Wang, Boting Zhou
Human immunodeficiency virus type I (HIV-1) transactivator of transcription (TAT) is encoded by HIV-1. It is a peptide rich in basic amino acids and belongs to the protein transduction domain family. It has been found that HIV-1 TAT and its core peptide segment TAT47-57 play an important role in promoting the cellular uptake of coupled bioactive macromolecules, such as peptides, proteins, oligonucleotides, and drug molecules. HIV-1 TAT can also significantly increase the soluble expression of extrinsic proteins...
December 8, 2016: Journal of Membrane Biology
https://www.readbyqxmd.com/read/27932305/scavenging-of-highly-reactive-gamma-ketoaldehydes-attenuates-cognitive-dysfunction-associated-with-epileptogenesis
#2
Jennifer N Pearson, Eric Warren, Li-Ping Liang, L Jackson Roberts, Manisha Patel
Cognitive dysfunction is a major comorbidity of the epilepsies; however, treatments targeting seizure-associated cognitive dysfunction, particularly deficits in learning and memory are not available. Isoketals and neuroketals, collectively known as gamma-ketoaldehydes are formed via the non-enzymatic, free radical catalyzed oxidation of arachidonic acid and docosahexaenoic acid, respectively. They are attractive candidates for oxidative protein damage and resultant cognitive dysfunction due to their formation within the plasma membrane and their high proclivity to form cytotoxic adducts on protein lysine residues...
December 5, 2016: Neurobiology of Disease
https://www.readbyqxmd.com/read/27931798/differential-expression-of-low-density-lipoprotein-receptor-related-protein-1-lrp-1-and-matrix-metalloproteinase-9-mmp-9-in-prostate-gland-from-normal-to-malignant-lesions
#3
Mónica B Gilardoni, María M Remedi, Mabel Oviedo, Tristán Dellavedova, Juan P Sarría, Laura Racca, Mariana Dominguez, Claudia G Pellizas, Ana C Donadio
BACKGROUND: Metalloproteinases (MMPs) are relevant modulators of inflammation, tumor microenvironment, cancer invasion and metastasis. They can be regulated by the Low density lipoprotein Receptor-related Protein 1 (LRP-1), a receptor reported to mediate the clearance of lipoproteins, extracellular matrix (ECM) macromolecules and proteinases. The aim of this study was to evaluate the expression of LRP-1, MMP-2 and MMP-9 across various grades of prostatic diseases as benign prostatic hyperplasia (BPH), BPH plus prostatitis (BPH+P), high grade prostatic intraepithelial neoplasia (HGPIN) and prostate cancer (PCa)...
November 24, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/27928782/a-method-for-decomposition-of-the-basic-reaction-of-biological-macromolecules-into-exponential-components
#4
Yu M Barabash, A K Lyamets
The structural and dynamical properties of biological macromolecules under non-equilibrium conditions determine the kinetics of their basic reaction to external stimuli. This kinetics is multiexponential in nature. This is due to the operation of various subsystems in the structure of macromolecules, as well as the effect of the basic reaction on the structure of macromolecules. The situation can be interpreted as a manifestation of the stationary states of macromolecules, which are represented by monoexponential components of the basic reaction (Monod-Wyman-Changeux model) Monod et al...
December 2016: Nanoscale Research Letters
https://www.readbyqxmd.com/read/27928571/diffusion-dynamics-of-latex-nanoparticles-coated-with-ssdna-across-a-single-nanopore
#5
Sébastien Balme, Mathilde Lepoitevin, Ludovic F Dumée, Mikhael Bechelany, Jean-Marc Janot
The fundamental understanding of the transport mechanisms of objects across a single nanopore is one key point to develop Coulter counters at the nanoscale for macromolecule or nanoparticle detection. In this area, nanoparticles have been less investigated than biomacromolecules such as DNA or proteins due to their self-aggregation in the presence of salts. In this work, the transport of modified latex nanoparticles across solid-state nanopores was investigated. To prevent their aggregation, their surface was modified with a low molecular weight single strand DNA coating...
December 8, 2016: Soft Matter
https://www.readbyqxmd.com/read/27927232/publication-of-nuclear-magnetic-resonance-experimental-data-with-semantic-web-technology-and-the-application-thereof-to-biomedical-research-of-proteins
#6
Masashi Yokochi, Naohiro Kobayashi, Eldon L Ulrich, Akira R Kinjo, Takeshi Iwata, Yannis E Ioannidis, Miron Livny, John L Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
BACKGROUND: The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. FINDINGS: To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data...
May 5, 2016: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/27925458/an-engineered-breast-cancer-model-on-a-chip-to-replicate-ecm-activation-in-vitro-during-tumor-progression
#7
Filomena Gioiella, Francesco Urciuolo, Giorgia Imparato, Virginia Brancato, Paolo A Netti
In this work, a new model of breast cancer is proposed featuring both epithelial and stromal tissues arranged on a microfluidic chip. The main task of the work is the in vitro replication of the stromal activation during tumor epithelial invasion. The activation of tumor stroma and its morphological/compositional changes play a key role in tumor progression. Despite emerging evidences, to date the activation of tumor stroma in vitro has not been achieved yet. The tumor-on-chip proposed in this work is built in order to replicate the features of its native counterpart: multicellularity (tumor epithelial cell and stromal cell); 3D engineered stroma compartment composed of cell-assembled extracellular matrix (ECM); reliable 3D tumor architecture...
December 2016: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/27924044/plamom-a-comprehensive-database-compiles-plant-mobile-macromolecules
#8
Daogang Guan, Bin Yan, Christoph Thieme, Jingmin Hua, Hailong Zhu, Kenneth R Boheler, Zhongying Zhao, Friedrich Kragler, Yiji Xia, Shoudong Zhang
In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets...
October 24, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27920897/impact-of-biopolymer-matrices-on-relaxometric-properties-of-contrast-agents
#9
Alfonso Maria Ponsiglione, Maria Russo, Paolo Antonio Netti, Enza Torino
Properties of water molecules at the interface between contrast agents (CAs) for magnetic resonance imaging and macromolecules could have a valuable impact on the effectiveness of metal chelates. Recent studies, indeed, demonstrated that polymer architectures could influence CAs' relaxivity by modifying the correlation times of the metal chelate. However, an understanding of the physico-chemical properties of polymer/CA systems is necessary to improve the efficiency of clinically used CAs, still exhibiting low relaxivity...
December 6, 2016: Interface Focus
https://www.readbyqxmd.com/read/27920202/the-translational-significance-of-the-neurovascular-unit-a-mini-review
#10
Heather L McConnell, Cymon N Kersch, Randall L Woltjer, Edward A Neuwelt
The mammalian brain is supplied with blood by specialized vasculature that is structurally and functionally distinct from that of the periphery. A defining feature of this vasculature is a physical blood-brain barrier (BBB). The BBB separates blood components from the brain microenvironment, regulating the entry and exit of ions, nutrients, macromolecules, and energy metabolites. Over the last two decades, physiological studies of cerebral blood flow dynamics have demonstrated that substantial intercellular communication occurs between cells of the vasculature and the neurons and glia that abut the vasculature...
December 5, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27919066/designed-proteins-induce-the-formation-of-nanocage-containing-extracellular-vesicles
#11
Jörg Votteler, Cassandra Ogohara, Sue Yi, Yang Hsia, Una Nattermann, David M Belnap, Neil P King, Wesley I Sundquist
Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids or proteins, but strategies for engineering hybrid biological materials are only beginning to emerge. Here we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27916801/macromolecular-interactions-control-structural-and-thermal-properties-of-regenerated-tri-component-blended-films
#12
Ashley Lewis, Joshua C Waters, John Stanton, Joseph Hess, David Salas-de la Cruz
With a growing need for sustainable resources research has become highly interested in investigating the structure and physical properties of biomaterials composed of natural macromolecules. In this study, we assessed the structural, morphological, and thermal properties of blended, regenerated films comprised of cellulose, lignin, and hemicellulose (xylan) using the ionic liquid 1-allyl-3-methylimidazolium chloride (AMIMCl). Attenuated total reflectance Fourier transform infrared (ATR-FTIR) analysis, scanning electron microscopy (SEM), atomic force microscopy (AFM), X-ray scattering, and thermogravimetric analysis (TGA) were used to qualitatively and quantitatively measure bonding interactions, morphology, and thermal stability of the regenerated films...
November 28, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27914066/computational-tools-for-allosteric-drug-discovery-site-identification-and-focus-library-design
#13
Wenkang Huang, Ruth Nussinov, Jian Zhang
Allostery is an intrinsic phenomenon of biological macromolecules involving regulation and/or signal transduction induced by a ligand binding to an allosteric site distinct from a molecule's active site. Allosteric drugs are currently receiving increased attention in drug discovery because drugs that target allosteric sites can provide important advantages over the corresponding orthosteric drugs including specific subtype selectivity within receptor families. Consequently, targeting allosteric sites, instead of orthosteric sites, can reduce drug-related side effects and toxicity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914060/a-protocol-for-the-design-of-protein-and-peptide-nanostructure-self-assemblies-exploiting-synthetic-amino-acids
#14
Nurit Haspel, Jie Zheng, Carlos Aleman, David Zanuy, Ruth Nussinov
In recent years there has been increasing interest in nanostructure design based on the self-assembly properties of proteins and polymers. Nanodesign requires the ability to predictably manipulate the properties of the self-assembly of autonomous building blocks, which can fold or aggregate into preferred conformational states. The design includes functional synthetic materials and biological macromolecules. Autonomous biological building blocks with available 3D structures provide an extremely rich and useful resource...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914048/geometric-potentials-for-computational-protein-sequence-design
#15
Jie Li, Patrice Koehl
Computational protein sequence design is the rational design based on computer simulation of new protein molecules to fold to target three-dimensional structures, with the ultimate goal of designing novel functions. It requires a good understanding of the thermodynamic equilibrium properties of the protein of interest. Here, we consider the contribution of the solvent to the stability of the protein. We describe implicit solvent models, focusing on approximations of their nonpolar components using geometric potentials...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913884/plasmid-pvax1-nh36-purification-by-membrane-and-bead-perfusion-chromatography
#16
Diana Ivonne Franco-Medrano, Patricia Guerrero-Germán, Rosa María Montesinos-Cisneros, Jaime Ortega-López, Armando Tejeda-Mansir
The demand for plasmid DNA (pDNA) has increased in response to the rapid advances in vaccines applications to prevent and treat infectious diseases caused by virus, bacteria or parasites, such as Leishmania species. The immunization protocols require large amounts of supercoiled plasmid DNA (sc-pDNA) challenging the development of efficient and profitable processes for capturing and purified pDNA molecules from large volumes of lysates. A typical bioprocess involves four steps: fermentation, primary recovery, intermediate recovery and final purification...
December 2, 2016: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/27913854/the-role-of-macromolecules-in-the-formation-of-kidney-stones
#17
REVIEW
Jeffrey D Rimer, Ann M Kolbach-Mandel, Michael D Ward, Jeffrey A Wesson
The formation of crystal aggregates, one of the critical processes in kidney stone pathogenesis, involves interactions between crystals (predominantly calcium oxalate monohydrate, COM) and urinary constituents (e.g., proteins), which serve as an adhesive "glue" between crystals in stones. To develop a better understanding of the protein-crystal interactions that lead to crystal aggregation, we have measured the effect of model proteins on bulk COM crystal properties as well as their adsorption on crystal surfaces using three synthetic polyanions: poly(aspartic acid) (polyD), poly(glutamic acid) (polyE), and poly(acrylic acid) (polyAA)...
December 2, 2016: Urolithiasis
https://www.readbyqxmd.com/read/27913418/a-novel-rhamnose-rich-hetero-exopolysaccharide-isolated-from-lactobacillus-paracasei-dg-activates-thp-1-human-monocytic-cells
#18
Silvia Balzaretti, Valentina Taverniti, Simone Guglielmetti, Walter Fiore, Mario Minuzzo, Hansel N Ngo, Judith B Ngere, Sohaib Sadiq, Paul N Humphreys, Andrew P Laws
: Lactobacillus paracasei DG is a bacterial strain with recognized probiotic properties and is used in commercial probiotic products. However, the mechanisms underlying its probiotic properties are mainly unknown. In this study, we tested the hypothesis that the capability of strain DG to interact with the host is, at least partly, associated with its ability to synthesize a surface-associated exopolysaccharide (EPS). Comparative genomics revealed the presence of putative EPS gene clusters in DG genome; accordingly, EPS was isolated from the surface of the bacterium...
December 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27913241/evaluation-of-highly-branched-cyclic-dextrin-in-inhalable-particles-of-combined-antibiotics-for-the-pulmonary-delivery-of-anti-tuberculosis-drugs
#19
Kazunori Kadota, Arisa Senda, Hideaki Tagishi, John Oluwasogo Ayorinde, Yuichi Tozuka
This work aims to identify a suitable formulation for the pulmonary delivery of combinations of inhalational drugs using highly branched cyclic dextrin (HBCD) macromolecules. We compared the effectiveness between powders prepared from HBCD with those prepared from five alternative excipients (lactose, maltose, sucrose, β-cyclodextrin and methyl β-cyclodextrin) in the pulmonary delivery of a single-dosage form of two anti-tuberculosis drugs (isoniazid and rifampicin). Fine particles of untreated active pharmaceutical ingredients (APIs) and combination products using excipients were prepared by spray drying...
November 29, 2016: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/27912165/biomarker-analysis-of-american-toad-anaxyrus-americanus-and-grey-tree-frog-hyla-versicolor-tadpoles-following-exposure-to-atrazine
#20
Marcía N Snyder, W Matthew Henderson, Donna A Glinski, S Thomas Purucker
The objective of the current study was to use a biomarker-based approach to investigate the influence of atrazine exposure on American toad (Anaxyrus americanus) and grey tree frog (Hyla versicolor) tadpoles. Atrazine is one of the most frequently detected herbicides in environmental matrices throughout the United States. In surface waters, it has been found at concentrations from 0.04-2859μg/L and thus presents a likely exposure scenario for non-target species such as amphibians. Studies have examined the effect of atrazine on the metamorphic parameters of amphibians, however, the data are often contradictory...
November 21, 2016: Aquatic Toxicology
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