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Structural biology

Chau Yee Ng, Hsi Yen, Hui-Yi Hsiao, Shih-Chi Su
Skin is the largest human organ, our protection against various environmental assaults and noxious agents. Accumulation of these stress events may lead to the formation of skin cancers, including both melanoma and non-melanoma skin cancers. Although modern targeted therapies have ameliorated the management of cutaneous malignancies, a safer, more affordable, and more effective strategy for chemoprevention and treatment is clearly needed for the improvement of skin cancer care. Phytochemicals are biologically active compounds derived from plants and herbal products...
March 22, 2018: International Journal of Molecular Sciences
Faezeh Kashanian, Mehran Habibi Rezaei, Ali Akbar Moosavi Movahedi, Alireza Bagherpour, Maryam Vatani
Due to the numerous biological applications of Magnetite [Fe3O4] nanoparticles (MNPs), it is essential to identify the influence of these nanoparticles on basic biological processes. Therefore, in this research, the effect of MNPs on the structure and activity of hen egg white lysozyme (HEWL) (EC as a model protein was examined using tryptophan intrinsic fluorescence, UV/Vis, and circular dichroism (CD) spectroscopy. Moreover, enzyme activities were analyzed by a turbidometric approach in the presence of MNPs at concentrations providing MNPs/HEWL ratios in the range of 0...
March 22, 2018: Biomedical Materials
Avneet Kaur, Sharad Wakode, Dharam Pal Pathak, Vidushi Sharma, Ashok K Shakya
BACKGROUND: Non-steroidal anti-inflammatory drugs are widely used for many years, but the chronic use of NSAID's leads to gastric side effects, ulceration and kidney problems. These side effects are due to non-selective inhibition of COX-2 along with COX-1. Therefore, it is imperative to develop novel and selective COX-2 inhibitors Objective: In this paper wehave synthesized a series of novel hybrids comprising of substituted-N-(3,4,5-trimethoxyphenyl)-benzo[d]oxazole derivatives and screened for the treatment of inflammation...
March 21, 2018: Medicinal Chemistry
Kfir Kuchuk, Uri Sivan
Hydration interaction shapes biomolecules and is a dominant inter-molecular force. Mapping the hydration patterns of biomolecules is therefore essential for understanding molecular processes in biology. Numerous studies have been devoted to this challenge but current methods cannot map the hydration of single biomolecules, let alone under physiological conditions. Here, we show that FM-AFM can fill this gap and generate 3D hydration maps of single DNA molecules under near-physiological conditions. Additionally, we present real space images of DNA in which the double helix is resolved with unprecedented resolution, clearly revealing individual phosphate groups along the DNA backbone...
March 22, 2018: Nano Letters
Matthaeus Schwarz-Schilling, Aurore Dupin, Fabio Chizzolini, Swati Krishnan, Sheref Mansy, Friedrich C Simmel
Molecular complexes composed of RNA molecules and proteins are promising multifunctional nanostructures for a wide variety of applications in biological cells or in artificial cellular systems. In this study, we systematically address some of the challenges associated with the expression and assembly of such hybrid structures using cell-free gene expression systems. As a model structure, we investigated a pRNA-derived RNA scaffold functionalized with four distinct aptamers, three of which bind to proteins - streptavidin and two fluorescent proteins - while one binds the small molecule dye malachite green (MG)...
March 22, 2018: Nano Letters
Martin Poot
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis...
2018: Methods in Molecular Biology
Yoshihiko Tsukamoto
The mouse retina has a layered structure that is composed of five classes of neurons supported by Müller glial and pigment epithelial cells. Recent studies have made progress in the classification of bipolar and ganglion cells, and also in the wiring of rod-driven signaling, color coding, and directional selectivity. Molecular biological techniques, such as genetic manipulation, transcriptomics, and fluorescence imaging, have contributed a lot to these advancements. The mouse retina has consistently been an important experimental system for both basic and clinical neurosciences...
2018: Methods in Molecular Biology
Estela G García-González, Bladimir Roque-Ramirez, Carlos Palma-Flores, J Manuel Hernández-Hernández
Epigenetic regulation is achieved at many levels by different factors such as tissue-specific transcription factors, members of the basal transcriptional apparatus, chromatin-binding proteins, and noncoding RNAs. Importantly, chromatin structure dictates the availability of a specific genomic locus for transcriptional activation as well as the efficiency with which transcription can occur. Chromatin immunoprecipitation (ChIP) is a method that allows elucidating gene regulation at the molecular level by assessing if chromatin modifications or proteins are present at a specific locus...
2018: Methods in Molecular Biology
Emma Langella, Martina Buonanno, Daniela Vullo, Nina Dathan, Marilisa Leone, Claudiu T Supuran, Giuseppina De Simone, Simona Maria Monti
Human carbonic anhydrase IX (hCA IX) is a tumour-associated enzyme present in a limited number of normal tissues, but overexpressed in several malignant human tumours. It is a transmembrane protein, where the extracellular region consists of a greatly investigated catalytic CA domain and a much less investigated proteoglycan-like (PG) domain. Considering its important role in tumour biology, here, we report for the first time the full characterization of the PG domain, providing insights into its structural and functional features...
March 21, 2018: Cellular and Molecular Life Sciences: CMLS
Muhammad Ehsan, Yang Du, Iago Molist, Alpay B Seven, Parameswaran Hariharan, Jonas S Mortensen, Lubna Ghani, Claus J Loland, Georgios Skiniotis, Lan Guan, Bernadette Byrne, Brian K Kobilka, Pil Seok Chae
Membrane proteins play critical roles in a variety of cellular processes. For a detailed molecular level understanding of their biological functions and roles in disease, it is necessary to extract them from the native membranes. While the amphipathic nature of these bio-macromolecules presents technical challenges, amphiphilic assistants such as detergents serve as useful tools for membrane protein structural and functional studies. Conventional detergents are limited in their ability to maintain the structural integrity of membrane proteins and thus it is essential to develop novel agents with enhanced properties...
March 22, 2018: Organic & Biomolecular Chemistry
Sean F Gilmore, Timothy S Carpenter, Helgi I Ingólfsson, Sandra K G Peters, Paul T Henderson, Craig D Blanchette, Nicholas O Fischer
Nanolipoprotein particles (NLPs) are reconstituted high-density lipoproteins, consisting of a phospholipid bilayer stabilized by an apolipoprotein scaffold protein. This class of nanoparticle has been a vital tool in the study of membrane proteins, and in recent years has been increasingly used for in vivo applications. Previous work demonstrated that the composition of the lipid bilayer component affects the stability of these particles in serum solutions. In the current study, NLPs assembled with phosphatidylcholine lipids featuring different acyl chain structures were systematically tested to understand the effect that lipid composition has on NLP stability in both neat serum and cell culture media supplemented with 10% serum by volume...
March 22, 2018: Nanoscale
Mohammad-Ali Abtahi, Alireza Zandi, Hassan Razmjoo, Sara Ghaffari, Seyed-Mojtaba Abtahi, Hamidreza Jahanbani-Ardakani, Zahra Kasaei, Samira Kasaei-Koupaei, Sepideh Sajjadi, Seyed-Ali Sonbolestan, Seyed-Hossein Abtahi
Purpose: Ameloblastoma is a non-encapsulated and slow-growing tumor with high recurrence rate. Orbital involvement by this neoplasm is an extremely rare entity. In this study, we present a systematic review on this situation along with clinical and paraclinical features of a case. Methods: An electronic search was conducted on major medical sources. Data of the cases in the literature in addition to our own case were extracted, summarized, and statistically analyzed...
March 2018: Journal of Current Ophthalmology
Ovidiu Palea, Michelle Granville, Robert E Jacobson
The clinical effectiveness of percutaneous and transforaminal endoscopic discectomy procedures has been evaluated by the system used or compared to open laminectomy or micro-discectomy but are not evaluated based on the location and characteristics of the abnormal disc. This review proposes that outcomes are primarily related to disc size, biomechanics, location, and associated segmental fibrotic and bone changes as well as the surgeon's skill in using various systems rather than the specific system used...
January 20, 2018: Curēus
Fathima Kamil, Julie H Rowe
The tumor microenvironment (TME) is defined as the structural and dynamic network of cellular and non-cellular interactions between malignant cells and the surrounding non-malignant matrix. Hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC) are two of the most challenging gastrointestinal malignancies. Despite clinical advancements in understanding tumor biology and growth of the chemotherapeutic industry, there have been no corresponding improvements in prognosis and overall survival of HCC and PDAC...
February 2018: Journal of Gastrointestinal Oncology
Ensaf M Al-Hujaily, Tanvir Khatlani, Zeyad Alehaideb, Rizwan Ali, Bader Almuzaini, Bahauddeen M Alrfaei, Jahangir Iqbal, Imadul Islam, Shuja Malik, Bader A Marwani, Salam Massadeh, Atef Nehdi, Barrak Alsomaie, Bader Debasi, Ibraheem Bushnak, Saeed Noibi, Syed Hussain, Wahid Abdul Wajid, Jean-Pierre Armand, Sheraz Gul, Julen Oyarzabal, Rana Rais, Chas Bountra, Ahmed Alaskar, Bander Al Knawy, Mohamed Boudjelal
The 'Therapeutics discovery: From bench to first in-human trials' conference, held at the King Abdullah International Medical Research Center (KAIMRC), Ministry of National Guard Health Affairs (MNGHA), Kingdom of Saudi Arabia (KSA) from October 10-12, 2017, provided a unique opportunity for experts worldwide to discuss advances in drug discovery and development, focusing on phase I clinical trials. It was the first event of its kind to be hosted at the new research center, which was constructed to boost drug discovery and development in the KSA in collaboration with institutions, such as the Academic Drug Discovery Consortium in the United States of America (USA), Structural Genomics Consortium of the University of Oxford in the United Kingdom (UK), and Institute of Materia Medica of the Chinese Academy of Medical Sciences in China...
March 2018: Biomedical Reports
Zahra Rostami, Sajad Jafari
Complex anatomical and physiological structure of an excitable tissue (e.g., cardiac tissue) in the body can represent different electrical activities through normal or abnormal behavior. Abnormalities of the excitable tissue coming from different biological reasons can lead to formation of some defects. Such defects can cause some successive waves that may end up to some additional reorganizing beating behaviors like spiral waves or target waves. In this study, formation of defects and the resulting emitted waves in an excitable tissue are investigated...
April 2018: Cognitive Neurodynamics
Aparajita Banerjee, Björn Hamberger
Catalyzing stereo- and regio-specific oxidation of inert hydrocarbon backbones, and a range of more exotic reactions inherently difficult in formal chemical synthesis, cytochromes P450 (P450s) offer outstanding potential for biotechnological engineering. Plants and their dazzling diversity of specialized metabolites have emerged as rich repository for functional P450s with the advances of deep transcriptomics and genome wide discovery. P450s are of outstanding interest for understanding chemical diversification throughout evolution, for gaining mechanistic insights through the study of their structure-function relationship, and for exploitation in Synthetic Biology...
2018: Phytochemistry Reviews: Proceedings of the Phytochemical Society of Europe
Ryan M Weatherwax, Nigel K Harris, Andrew E Kilding, Lance C Dalleck
Background: Even though cardiorespiratory fitness (CRF) training elicits numerous health benefits, not all individuals have positive training responses following a structured CRF intervention. It has been suggested that the technical error (TE), a combination of biological variability and measurement error, should be used to establish specific training responsiveness criteria to gain further insight on the effectiveness of the training program. To date, most training interventions use an absolute change or a TE from previous findings, which do not take into consideration the training site and equipment used to establish training outcomes or the specific cohort being evaluated...
2018: Open Access Journal of Sports Medicine
Ollie Yiru Yu, Irene Shuping Zhao, May Lei Mei, Edward Chin-Man Lo, Chun-Hung Chu
Mechanistic studies on demineralization-remineralization play a critical role in investigating caries pathogenicity, testing effects of new caries prevention methods, and developing new caries-preventing products. Simulating the cariogenic challenges in the mouth, various demineralization-remineralization models have been used for cariology research. This review aimed to provide an overview of the common mechanistic studies on demineralization-remineralization for cariology research in recent literature. Most mechanistic studies were in vitro studies ( n = 294, 84%) among the 350 cariology studies indexed in the Web of Science from 2014 to 2016...
June 18, 2017: Dent J (Basel)
David Thybert, Maša Roller, Fábio C P Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, Václav Janoušek, Wasiu Akanni, Bronwen Aken, Sarah Aldridge, Varshith Chakrapani, William Chow, Laura Clarke, Carla Cummins, Anthony Doran, Matthew Dunn, Leo Goodstadt, Kerstin Howe, Matthew Howell, Ambre-Aurore Josselin, Robert C Karn, Christina M Laukaitis, Lilue Jingtao, Fergal Martin, Matthieu Muffato, Stefanie Nachtweide, Michael A Quail, Cristina Sisu, Mario Stanke, Klara Stefflova, Cock Van Oosterhout, Frederic Veyrunes, Ben Ward, Fengtang Yang, Golbahar Yazdanifar, Amonida Zadissa, David J Adams, Alvis Brazma, Mark Gerstein, Benedict Paten, Son Pham, Thomas M Keane, Duncan T Odom, Paul Flicek
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae...
March 21, 2018: Genome Research
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