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Marcello Mancini, Paul Summers, Francesco Faita, Maurizia R Brunetto, Francesco Callea, Andrea De Nicola, Nicole Di Lascio, Fabio Farinati, Amalia Gastaldelli, Bruno Gridelli, Peppino Mirabelli, Emanuele Neri, Piero A Salvadori, Eleni Rebelos, Claudio Tiribelli, Luca Valenti, Marco Salvatore, Ferruccio Bonino
The rapidly growing field of functional, molecular and structural bio-imaging is providing an extraordinary new opportunity to overcome the limits of invasive liver biopsy and introduce a "digital biopsy" for in vivo study of liver pathophysiology. To foster the application of bio-imaging in clinical and translational research, there is a need to standardize the methods of both acquisition and the storage of the bio-images of the liver. It can be hoped that the combination of digital, liquid and histologic liver biopsies will provide an innovative synergistic tri-dimensional approach to identifying new aetiologies, diagnostic and prognostic biomarkers and therapeutic targets for the optimization of personalized therapy of liver diseases and liver cancer...
February 27, 2018: World Journal of Hepatology
Charlene Babra Waryah, Colette Moses, Mahira Arooj, Pilar Blancafort
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications...
2018: Methods in Molecular Biology
Yinfei Lu, Cornelius Louwrens Pieterse, Wesley Daniel Robertson, R J Dwayne Miller
We report the soft laser extraction and production of highly charged peptide and protein ions for mass spectrometry directly from bulk liquid water at atmospheric pressure and room temperature, using picosecond infrared laser ablation. Stable ion signal from singly charged small molecules, as well as highly charged biomolecular ions, from aqueous solutions at low laser pulse fluence (~0.3 J cm-2) is demonstrated. Sampling via single picosecond laser pulses is shown to extract less than 27 pL of volume from the sample, producing highly charged peptide and protein ions for mass spectrometry detection...
March 9, 2018: Analytical Chemistry
Deborah Traversi, Ilaria Gorrasi, Cristina Pignata, Raffaella Degan, Elisa Anedda, Giulia Carletto, Greta Vercellino, Stefania Fornasero, Antonino Bertino, Francesca Filippi, Maria Gullo, Giorgio Gilli
Anaerobic digestion is a consolidated biotechnology able to produce renewable energy from biomasses. In the European countries, quick growth of biogas production from different organic matrices including wastes has been observed. In relation to the characteristics and quantity of the anaerobic digestion of feedstock, there are different technologies, advantages and criticisms. An accurate occupational risk assessment and development of management tools for green jobs involved in the anaerobic digestion plants are due...
March 5, 2018: Environment International
Eniko Farkas, Andras Szekacs, Boglarka Kovacs, Marianna Olah, Robert Horvath, Inna Szekacs
Rapid and inexpensive biosensor technologies allowing real-time analysis of biomolecular and cellular events have become the basis of next-generation cell-based screening techniques. Our work opens up novel opportunities in the application of the high-throughput label-free Epic BenchTop optical biosensor in cell toxicity studies. The Epic technology records integrated cellular responses about changes in cell morphology and dynamic mass redistribution of cellular contents at the 100-150 nm layer above the sensor surface...
February 23, 2018: Journal of Hazardous Materials
Erik W Martin, Tanja Mittag
Liquid-liquid phase separation seems to play critical roles in the compartmentalization of cells through the formation of biomolecular condensates. Many proteins with low-complexity regions are found in these condensates, and they can undergo phase separation in vitro in response to changes in temperature, pH and ion concentration. Low-complexity regions are thus likely important players in mediating compartmentalization in response to stress. However, how the phase behavior is encoded in their amino acid composition and patterning is only poorly understood...
March 8, 2018: Biochemistry
Francis Mairet
Homeostasis is the capacity of living organisms to keep internal conditions regulated at a constant level, despite environmental fluctuations. Integral feedback control is known to play a key role in this behaviour. Here, I show that a feedback system involving transcriptional and post-translational regulations of the same executor protein acts as a proportional integral (PI) controller, leading to enhanced transient performances in comparison with a classical integral loop. Such a biomolecular controller-which I call a level and activity-PI controller (LA-PI)-is involved in the regulation of ammonium uptake by Escherichia coli through the transporter AmtB...
February 2018: Royal Society Open Science
M Gianneli, E Polo, H Lopez, V Castagnola, T Aastrup, K A Dawson
Nanomedicine, nanotargeting and nanotherapeutics have in the last few years faced several difficulties in translating the promising results obtained in vitro to an in vivo scenario. The origin of this discrepancy might be found in the lack of a detailed and realistic characterization of the biological surface of nanoparticles. Despite the capability to engineer nanomaterials with a great variety and a precise control of the surface functionalization, the targeting capability is lost when the nanoparticles are embedded in complex biological media, due to the formation of a biological layer (biomolecular corona)...
March 7, 2018: Nanoscale
Molinaro Francesco, Cobellis Giovanni, Cerchia Elisa, Ferrara Francesco, Tallarico Rosella, Sica Marina, Noviello Carmine, Martino Ascanio, Angotti Rossella, Messina Mario
Background: The varicocele is the most commonly diagnosed pre-pubertal andrological condition with an incidence of 10%-15% between adolescents. The aim of this study was to evaluate the efficacy of retroperitoneoscopic varicocelectomy (RV) in two Italian centres with particular attention to post-operative testicular volume and semen analysis after 18 years of life. Materials and Methods: From 1999 to 2010, 286 adolescents underwent retroperitoneoscopic left varicocelectomy...
April 2017: African Journal of Paediatric Surgery: AJPS
Ján Kozempel, Olga Mokhodoeva, Martin Vlk
This review summarizes recent progress and developments as well as the most important pitfalls in targeted alpha-particle therapy, covering single alpha-particle emitters as well as in vivo alpha-particle generators. It discusses the production of radionuclides like211 At,223 Ra,225 Ac/213 Bi, labelling and delivery employing various targeting vectors (small molecules, chelators for alpha-emitting nuclides and their biomolecular targets as well as nanocarriers), general radiopharmaceutical issues, preclinical studies, and clinical trials including the possibilities of therapy prognosis and follow-up imaging...
March 5, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Christopher Joseph Fennell, Neda Ghousifam, Jennifer M Haseleu, Heather Gappa-Fahlenkamp
We present an atomistic level computational investigation of the dynamics of a signaling protein, Monocyte Chemoattractant Protein-1 (MCP-1), that explores how simulation geometry and solution ionic strength affect the calculated diffusion coefficient. Using a simple extension of non-cubic finite size diffusion correction expressions, it is possible to calculate experimentally comparable diffusion coefficients that are fully consistent with those determined from cubic box simulations. Additionally, increasing the concentration of salt in the solvent environment leads to changes in protein dynamics that are not explainable through changes in solvent viscosity alone...
March 6, 2018: Journal of Physical Chemistry. B
Yi-Hsuan Lin, Julie D Forman-Kay, Hue Sun Chan
Liquid-liquid phase separation and related condensation processes of intrinsically disordered proteins (IDPs), proteins with intrinsically disordered regions and nucleic acids underpin various condensed-liquid droplets or gel-like assemblies in the cellular environment. Collectively referred to as condensates, these bodies provide spatial/temporal compartmentalization, often serving as hubs for regulated biomolecular interactions. Examples include certain extracellular materials, transcription complexes, and membraneless organelles such as germ and stress granules and the nucleolus...
March 6, 2018: Biochemistry
Anastasia Ioanna Skilitsi, Damianos Agathangelou, Ievgen Shulov, Jamie Conyard, Stefan Haacke, Yves Mély, Andrey Klymchenko, Jérémie Léonard
The excited state intramolecular proton transfer (ESIPT) of 3-hydroxyflavone derivatives results in a fluorescence spectrum composed of two emission bands, the relative intensity of which is strongly influenced by the interaction with the local environment. We use time-resolved fluorescence and ultrafast transient absorption spectroscopies to investigate the photophysics of 4'-methoxy-3-hydroxyflavone in different solvents characterized by various polarities and hydrogen (H) bonding capabilities. We evidence that in this compound, the ESIPT reaction rate varies by more than 3 orders of magnitude, depending on the H-bonding capability of its local environment...
March 6, 2018: Physical Chemistry Chemical Physics: PCCP
Sam Asami, Wolfgang Kallies, Johannes Günther, Maria Stavropoulou, Steffen Glaser, Michael Sattler
NMR spectroscopy at ultra-high magnetic fields requires improved radiofrequency (rf) pulses to cover the increased spectral bandwidth. We introduce optimized 90° pulse pairs as Ramsey-type cooperative (Ram-COOP) pulses for biomolecular NMR applications. The Ram-COOP element provides broadband excitation with enhanced sensitivity and reduced artifacts even at magnetic fields >1.0 GHz 1H Larmor frequency (23 T). A pair of 30 μs Ram-COOP pulses achieves an excitation bandwidth of 100 kHz with a maximum rf field of 20 kHz, more than three-fold improved compared to achievable excitation by rectangular pulses...
March 5, 2018: Angewandte Chemie
Andrea Bianco, Tullio Valente, Maria Luisa De Rimini, Giacomo Sica, Alfonso Fiorelli
Malignant pleural mesothelioma (MPM) is a tumour which, despite progress in diagnostic procedures and biomolecular research, has poor prognosis. Symptoms reflect extension of disease and include shortness of breath and chest pain. Unexplained pleural effusion and pleural pain in patients exposed to asbestos should raise the suspicion of MPM. MPM diagnosis requires imaging procedures X-ray and computed tomography (CT) scans; magnetic resonance imaging (MRI) better defines the extension of the tumor while PET scanning provides additional information on metabolic activity, metastases, and response to treatment...
January 2018: Journal of Thoracic Disease
Tirayut Vilaivan
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal...
2018: Beilstein Journal of Organic Chemistry
Jerome M Fox, Mengxia Zhao, Michael J Fink, Kyungtae Kang, George M Whitesides
Biomolecular recognition can be stubborn; changes in the structures of associating molecules, or the environments in which they associate, often yield compensating changes in enthalpies and entropies of binding and no net change in affinities. This phenomenon-termed enthalpy/entropy (H/S) compensation-hinders efforts in biomolecular design, and its incidence-often a surprise to experimentalists-makes interactions between biomolecules difficult to predict. Although characterizing H/S compensation requires experimental care, it is unquestionably a real phenomenon that has, from an engineering perspective, useful physical origins...
March 5, 2018: Annual Review of Biophysics
Maria Ejlersen, Niels Johan Christensen, Kasper K Sørensen, Knud J Jensen, Jesper Wengel, Chenguang Lou
Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes...
March 5, 2018: Bioconjugate Chemistry
Toshiyuki Takayanagi, Taiki Nakatomi
Many catalytic and biomolecular reactions containing transition metals involve changes in the electronic spin state. These processes are referred to as "spin-forbidden" reactions within nonrelativistic quantum mechanics framework. To understand detailed reaction mechanisms of spin-forbidden reactions, one must characterize reaction pathways on potential energy surfaces with different spin states and then identify crossing points. Here we propose a practical computational scheme, where only the lowest mixed-spin eigenstate obtained from the diagonalization of the spin-coupled Hamiltonian matrix is used in reaction path search calculations...
March 5, 2018: Journal of Computational Chemistry
Maristela P Rangel, Vanessa K de Sá, Tabatha Prieto, João Roberto M Martins, Eloísa R Olivieri, Dirce Carraro, Teresa Takagaki, Vera Luiza Capelozzi
Matrix proteoglycans (PGs) have shown promise as biomarker in malignancies. We employed agarose gel eletrophoresis, quantitative real- time reverse transcription-polymerase chain reaction and immunohistochemistry to evaluate the content of sulfated glicosaminoglycans (chondroitin sulfate and heparan sulfate) and expression of PG (biglycan, glypican, perlecan, syndecan e versican) in patient-matched normal and tumor tissues obtained from resected specimens of lung cancer. A significant increase of heparan sulfate (HS) and chondroitin sulfate (CS) concentrations was found in tumor tissue samples when compared to normal lung tissue samples...
March 3, 2018: Glycoconjugate Journal
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