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https://www.readbyqxmd.com/read/29224136/a-summary-of-the-biological-processes-disease-associated-changes-and-clinical-applications-of-dna-methylation
#1
Gitte Brinch Andersen, Jörg Tost
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224081/electrochemical-applications-in-metal-bioleaching
#2
Christoph Kurt Tanne, Axel Schippers
Biohydrometallurgy comprises the recovery of metals by biologically catalyzed metal dissolution from solids in an aqueous solution. The application of this kind of bioprocessing is described as "biomining," referring to either bioleaching or biooxidation of sulfide metal ores. Acidophilic iron- and sulfur-oxidizing microorganisms are the key to successful biomining. However, minerals such as primary copper sulfides are recalcitrant to dissolution, which is probably due to their semiconductivity or passivation effects, resulting in low reaction rates...
December 10, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/29224074/sampling-extraction-and-high-throughput-sequencing-methods-for-environmental-microbial-and-viral-communities
#3
Pedro J Torres, Scott T Kelley
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223890/gold-core-ceria-shell-based-redox-active-nanozyme-mimicking-the-biological-multienzyme-complex-phenomenon
#4
Stuti Bhagat, N V Srikanth Vallabani, Vaithiyalingam Shutthanandan, Mark Bowden, Ajay S Karakoti, Sanjay Singh
Catalytically active individual gold (Au) and cerium oxide (CeO2) nanoparticles (NPs) are well known to exhibit specific enzyme-like activities, such as natural catalase, oxidase, superoxide dismutase, and peroxidase enzymes. These activities have been maneuvered to design several biological applications such as immunoassays, glucose detection, radiation and free radical protection and tissue engineering. In biological systems, multienzyme complexes are involved in catalyzing important reactions of essential metabolic processes such as respiration, biomolecule synthesis, and photosynthesis...
December 7, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/29223848/foliar-spraying-of-salicylic-acid-induced-accumulation-of-phenolics-increased-radical-scavenging-activity-and-modified-the-composition-of-the-essential-oil-of-water-stressed-thymus-vulgaris-l
#5
Noha Khalil, Mostafa Fekry, Mokhtar Bishr, Soheir El-Zalabani, Osama Salama
Polyphenolic compounds are considered valuable secondary plant metabolites owing to the myriad of biological activities they exert. This study aimed to investigate the effect of applying various concentrations of the plant growth regulator, salicylic acid (SA), on Thymus vulgaris L. while subjecting the plant to decreasing amounts of irrigation water. The following parameters were monitored; total polyphenolic and flavonoid content, yield and composition of the essential oil, and antioxidant activity of the alcoholic extracts...
December 6, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29223730/characterization-of-a-new-decellularized-bovine-pericardial-biological-mesh-structural-and-mechanical-properties
#6
Alessandra Bielli, Roberta Bernardini, Dimitrios Varvaras, Piero Rossi, Giancarlo Di Blasi, Giuseppe Petrella, Oreste Claudio Buonomo, Maurizio Mattei, Augusto Orlandi
Implants made from naturally-derived biomaterials, also called biological meshes or biomeshes, typically derive from decellularized extracellular matrix of either animal or human tissue. Biomeshes have many biomedical applications such as ligament repair, bone and cartilage regeneration and soft tissue replacement. Bovine collagen is one of the most widely used and abundantly available xenogenic materials. In particular, bovine pericardium is widely used as extracellular matrix bioprosthetic tissue. The efficiency of a pericardial mesh to function as scaffold depends on the quality of the decellularization protocol used...
December 5, 2017: Journal of the Mechanical Behavior of Biomedical Materials
https://www.readbyqxmd.com/read/29223402/genetic-regulation-mechanism-of-the-yjdf-riboswitch
#7
Sha Gong, Yanli Wang, Zhen Wang, Yujie Wang, Wenbing Zhang
The yjdF riboswitch resides in potential 5' UTRs of homologues of protein-coding gene yjdF in Firmicutes. Unlike other 30 riboswitch classes previously validated, this riboswitch class, can sense and bind to a broad collection of azaaromatic ligands. Among these compounds, some do activate production of yjdF protein driven by the riboswitch, while others are out of riboswitch-mediated modulation possibly because of the toxicity at high ligand concentrations. By incorporating the structures with pseudoknots and ligand binding kinetics into the co-transcriptional folding theory, we theoretically studied the co-transcriptional folding behaviors of the yjdF riboswitch from Bacillus subtilis at different transcription conditions...
December 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29223071/bioactive-potential-of-silica-coatings-and-its-effect-on-the-adhesion-of-proteins-to-titanium-implants
#8
F Romero-Gavilan, N Araújo-Gomes, A M Sánchez-Pérez, I García-Arnáez, F Elortza, M Azkargorta, J J Martín de Llano, C Carda, M Gurruchaga, J Suay, I Goñi
There is an ever-increasing need to develop dental implants with ideal characteristics to achieve specific and desired biological response in the scope of improve the healing process post-implantation. Following that premise, enhancing and optimizing titanium implants through superficial treatments, like silica sol-gel hybrid coatings, are regarded as a route of future research in this area. These coatings change the physicochemical properties of the implant, ultimately affecting its biological characteristics...
December 6, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/29223005/the-emerging-role-of-systems-biology-for-engineering-protein-production-in-cho-cells
#9
REVIEW
Chih-Chung Kuo, Austin Wt Chiang, Isaac Shamie, Mojtaba Samoudi, Jahir M Gutierrez, Nathan E Lewis
To meet the ever-growing demand for effective, safe, and affordable protein therapeutics, decades of intense efforts have aimed to maximize the quantity and quality of recombinant proteins produced in CHO cells. Bioprocessing innovations and cell engineering efforts have improved product titer; however, uncharacterized cellular processes and gene regulatory mechanisms still hinder cell growth, specific productivity, and protein quality. Herein, we summarize recent advances in systems biology and data-driven approaches aiming to unravel how molecular pathways, cellular processes, and extrinsic factors (e...
December 6, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29222984/suicidal-behaviour-is-associated-with-decreased-esterified-cholesterol-in-plasma-and-membrane-fluidity-of-platelets
#10
Boby Mathew, Krishnamachari Srinivasan, Johnson Pradeep, Tinku Thomas, Amit Kumar Mandal
BACKGROUND: Altered cholesterol levels in body fluids and brain tissues have been shown to be associated with suicidal behaviour, violence and aggression. But the biological underpinnings of this association in the pathophysiology of suicide are not clear. Cholesterol plays a crucial role in maintaining the cellular membrane fluidity and alterations in cellular membrane fluidity may impair serotonergic neurotransmission in the central nervous system. METHODS: We measured plasma esterified cholesterol and platelet membrane fluidity using fluorescence anisotropy and estimated flow activation energy which is a measure of order of membrane lipid bilayer in patients with recent suicidal attempt and compared with age and gender matched controls...
December 2, 2017: Asian Journal of Psychiatry
https://www.readbyqxmd.com/read/29222925/quantification-of-photonic-localization-properties-of-targeted-nuclear-mass-density-variations-application-in-cancer-stage-detection
#11
Peeyush Sahay, Aditya Ganju, Huda M Almabadi, Hemendra M Ghimire, Murali M Yallapu, Omar Skalli, Meena Jaggi, Subhash C Chauhan, Prabhakar Pradhan
Light localization is a phenomenon which arises due to the interference effects of light waves inside a disordered optical medium. Quantification of degree light localization in optical media is widely used for characterizing degree of structural disorder in that media. Recently, this light localization approach was extended to analyze structural changes in biological cell like heterogeneous optical media, with potential application in cancer diagnostics. Confocal fluorescence microscopy was used to construct 'optical lattices', which represents 2D refractive index map corresponding to the spatial mass density distribution of a selected molecule inside the cell...
December 9, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/29222921/optimizing-rna-seq-studies-to-investigate-herbicide-resistance
#12
REVIEW
Darci A Giacomini, Todd Gaines, Roland Beffa, Patrick J Tranel
Transcriptomic profiling, specifically via RNA-seq, is becoming one of the more commonly used methods for investigating non-target site resistance (NTSR) to herbicides due to its high throughput capabilities and utility in organisms with little to no previous sequence information. A review of the weed science RNA-seq literature has revealed some basic principles behind generating quality data from these types of studies. First, studies that included more replicates per biotype and took steps to control for genetic background had significantly better control of false positives and, consequently, shorter lists of potential resistance genes to sift through...
December 9, 2017: Pest Management Science
https://www.readbyqxmd.com/read/29222769/neurotrophic-factors-an-overview
#13
Stephen D Skaper
The neurotrophins are a family of closely related proteins that were first identified as survival factors for sympathetic and sensory neurons and have since been shown to control a number of aspects of survival, development, and function of neurons in both the central and peripheral nervous systems. Limiting quantities of neurotrophins during development control the numbers of surviving neurons to ensure a match between neurons and the requirement for a suitable density of target innervation. Biological effects of each of the four mammalian neurotrophins are mediated through activation of one or more of the three members of the tropomyosin-related kinase (Trk) family of receptor tyrosine kinases (TrkA, TrkB, and TrkC)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222706/acute-toxicity-of-fresh-and-aged-residues-of-pesticides-to-the-parasitoid-tamarixia-radiata-and-to-the-hlb-bacteria-vector-diaphorina-citri
#14
V H Beloti, G R Alves, R A Moral, C G B Demétrio, P T Yamamoto
One method for controlling the Asian citrus psyllid (ACP) Diaphorina citri Kuwayama, the vector of the putative causal agent of Huanglongbing, uses the parasitoid Tamarixia radiata (Waterston). However, the general intensive use of insecticides has reduced the numbers of this parasitoid. This study evaluated the effect of the residual action of 24 insecticides on T. radiata and also determined the differential toxicity of insecticides to D. citri and T. radiata, using three bioassays. In the first, when adults of the parasitoid were exposed to residues of the 24 insecticides, ten were considered short-life (class 1), six slightly persistent (class 2), five moderately persistent (class 3), and three insecticides were considered persistent (class 4), under the IOBC/WPRS classification system...
December 8, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/29222611/kiwifruit-svp2-controls-developmental-and-drought-stress-pathways
#15
Rongmei Wu, Tianchi Wang, Ben A W Warren, Susan J Thomson, Andrew C Allan, Richard C Macknight, Erika Varkonyi-Gasic
Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy...
December 8, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/29222483/atlantic-deep-water-provenance-decoupled-from-atmospheric-co2-concentration-during-the-lukewarm-interglacials
#16
Jacob N W Howe, Alexander M Piotrowski
Ice core records show that atmospheric CO2 concentrations and Antarctic temperature were lower during the 'lukewarm interglacials' from 800 to 430 ka than the subsequent five interglacials. These different interglacial 'strengths' have been hypothesised to be controlled by Antarctic overturning circulation. How these variations in Antarctic overturning relate to Northern Atlantic overturning circulation, a major driver of Northern Hemisphere climate, is uncertain. Here we present a high-resolution record of authigenic neodymium isotopes-a water mass tracer that is independent of biological processes-and use it to reconstruct Atlantic overturning circulation during the last 800 kyr...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222306/therapy-of-primary-cns-lymphoma-role-of-intensity-radiation-and-novel-agents
#17
REVIEW
Andrés José María Ferreri
Primary central nervous system (CNS) lymphomas represent a subgroup of malignancies with specific characteristics, an aggressive course, and unsatisfactory outcome in contrast with other lymphomas comparable for tumor burden and histological type. Despite the high sensitivity to conventional chemotherapy and radiotherapy, remissions are frequently short lasting. Treatment efficacy is limited by several factors, including the biology and microenvironment of this malignancy and the "protective" effect of the blood-brain barrier, which limits the access of most drugs to the CNS...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29222070/regulation-of-trna-biogenesis-in-plants-and-its-link-to-plant-growth-and-response-to-pathogens
#18
REVIEW
Adriana Santos Soprano, Juliana Helena Costa Smetana, Celso Eduardo Benedetti
tRNA biology has fascinated scientists over the years. Besides their fundamental role in protein translation, new evidence indicates that tRNA-derived molecules also regulate gene expression and protein synthesis in all domains of life. In this review, we will highlight some of the recent findings linking tRNA transcription and modification with plant cell growth and response to pathogens. In fact, mutations in proteins directly involved in tRNA synthesis and modification most often lead to pleiotropic effects on plant growth and immunity...
December 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29221926/plasma-protein-profiling-of-patients-with-intraductal-papillary-mucinous-neoplasm-of-the-pancreas-as-potential-precursor-lesions-of-pancreatic-cancer
#19
Maria Ilies, Praveen Kumar Sappa, Cristina Adela Iuga, Felicia Loghin, Manuela Gesell Salazar, Frank Ulrich Weiss, Georg Beyer, Markus M Lerch, Uwe Völker, Julia Mayerle, Elke Hammer
Efforts for the early diagnosis of the pancreatic ductal adenocarcinoma (PDAC) have recently been driven to one of the precursor lesions, namely intraductal papillary mucinous neoplasm of the pancreas (IPMN). Only a few studies have focused on IPMN molecular biology and its overall progression to cancer. Therefore, IPMN lacks comprehensive characterization which makes its clinical management controversial. In this study, we characterized plasma proteins in the presence of IPMNs in comparison to healthy controls, chronic pancreatitis, and PDAC by a proteomics approach using data-independent acquisition based mass spectrometry...
December 5, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29221872/proposal-of-concentration-limits-for-determining-the-hazard-property-hp-14-for-waste-using-ecotoxicological-tests
#20
Pierre Hennebert
Different ecotoxicological test batteries and concentration limits have been proposed to assess the hazard property (HP) HP 14 'Ecotoxic' for waste in the European Union and its member states. In test batteries, if the concentration of waste in the culture/dilution medium producing 50% of inhibitory biological effect in one or more test(s) is below the concentration limit of the test, the waste is classified as hazardous. A summarized review of the test batteries proposed since 1998 is presented. The last proposed test battery uses seven aquatic and terrestrial species with standardized methods, but with options and uniform concentration limits of 10% of waste eluate or solid waste in the culture/dilution medium...
December 5, 2017: Waste Management
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