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Biological Chemistry

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https://www.readbyqxmd.com/read/27932801/dna-encoded-chemistry-enabling-the-deeper-sampling-of-chemical-space
#1
Robert A Goodnow, Christoph E Dumelin, Anthony D Keefe
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces...
December 9, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27930868/laser-surface-pattering-of-titanium-for-improving-the-biological-performance-of-dental-implants
#2
Christoph Zwahr, Denise Günther, Tina Brinkmann, Nikolai Gulow, Steffen Oswald, Marzellus Grosse Holthaus, Andrés Fabián Lasagni
Direct laser interference patterning (DLIP) is used to produce periodic line-like patterns on titanium surfaces. An Nd:YAG laser operating at 532 nm wavelength with a pulse duration of 8 ns is used for the laser patterning process. The generated periodic patterns with spatial periods of 5, 10, and 20 µm are produced with energy densities between 0.44 and 2.6 J cm(-)(2) with a single laser pulse. With variation of energy density, different shapes of the arising topography are observed due to the development of the solidification front of the molten material at the maxima positions...
December 8, 2016: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/27929431/internet-databases-of-the-properties-enzymatic-reactions-and-metabolism-of-small-molecules-search-options-and-applications-in-food-science
#3
REVIEW
Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak, Justyna Bucholska, Piotr Starowicz, Emilia Czyrko
Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of secondary analyses of large datasets. Information can be retrieved from databases by searching for the compound name or structure, annotating with the help of chemical codes or drawn using molecule editing software...
December 6, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27925666/enriching-s-4-u-rna-using-methane-thiosulfonate-mts-chemistry
#4
Erin E Duffy, Matthew D Simon
Metabolic labeling of cellular RNA is a useful approach to study RNA biology. 4-Thiouridine (s(4) U) is a convenient nucleoside for metabolic labeling because it is cell permeable and is incorporated into newly transcribed RNA, and the sulfur moiety provides a handle for biochemical purification. However, a critical step in the purification of s(4) U-RNA is the efficiency of the chemistry used to enrich s(4) U-RNA. Here, we present a protocol for s(4) U-RNA enrichment that includes efficient and reversible covalent chemistry to biotinylate s(4) U-RNA using the activated disulfide methane thiosulfonate conjugated to biotin (MTS-biotin), followed by enrichment on streptavidin beads...
December 7, 2016: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/27924725/anticancer-drug-targets-of-salvia-phytometabolites-chemistry-biology-and-omics
#5
Da-Cheng Hao, Guang-Bo Ge, Pei-Gen Xiao
Salvia displays diverse anticancer properties, which are attributable to their diterpene and phenolic contents. There is no comprehensive review on the anticancer diversity and molecular targets of Salvia components. We investigate the diversity and molecular targets of Salvia phytometabolites responsible for the prevention and treatment of cancer and sarcoma. Traditional therapeutic knowledge suggests that Salvia species can be used to develop anticancer drugs. Lots of concerns have been raised for tanshinone (Tan) IIA and cryptotanshinone...
December 7, 2016: Current Drug Targets
https://www.readbyqxmd.com/read/27924587/qualitative-and-quantitative-proteome-analysis-of-oral-fluids-in-health-and-periodontal-disease-by-mass-spectrometry
#6
Erdjan Salih
The significance of protein identification and characterization by classical protein chemistry approaches is clearly highlighted by our detailed understanding of the biological systems assembled over a time period of almost a century. The advent of state-of-the-art mass spectrometry (MS) with sensitivity, speed, and global protein analysis capacity without individual protein purification has transformed the classical protein chemistry with premise to accelerate discovery. These combined with the ability of the oral fluids such as whole saliva (WS) and gingival crevicular fluid (GCF) to reflect both systemic and locally derived proteins have generated significant interest to characterize these fluids more extensively by MS technology...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924007/bridging-of-double-stranded-breaks-by-the-nonhomologous-end-joining-ligation-complex-is-modulated-by-dna-end-chemistry
#7
Dylan A Reid, Michael P Conlin, Yandong Yin, Howard H Chang, Go Watanabe, Michael R Lieber, Dale A Ramsden, Eli Rothenberg
The nonhomologous end-joining (NHEJ) pathway is the primary repair pathway for DNA double strand breaks (DSBs) in humans. Repair is mediated by a core complex of NHEJ factors that includes a ligase (DNA Ligase IV; L4) that relies on juxtaposition of 3' hydroxyl and 5' phosphate termini of the strand breaks for catalysis. However, chromosome breaks arising from biological sources often have different end chemistries, and how these different end chemistries impact the way in which the core complex directs the necessary transitions from end pairing to ligation is not known...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27920947/the-daniel-k-inouye-college-of-pharmacy-scripts-poha-berry-physalis-peruviana-with-potential-anti-inflammatory-and-cancer-prevention-activities
#8
Leng Chee Chang, Mayuramas Sang-Ngern, John M Pezzuto, Carolyn Ma
The Daniel K. Inouye College of Pharmacy, during a historic event in Spring 2016, graduated the first two students in the Pacific region to earn a PhD in pharmaceutical sciences at the University of Hawai'i at Hilo. The college offers PhD programs in these five disciplines: Cancer Biology, Medicinal Chemistry, Pharmaceutics, Pharmacognosy, and Pharmacology. One of the Pharmacognosy dissertations focused on plant-derived natural products with potential anti-inflammatory and cancer chemopreventive activities...
November 2016: Hawai'i Journal of Medicine & Public Health: a Journal of Asia Pacific Medicine & Public Health
https://www.readbyqxmd.com/read/27917709/synthesis-of-some-steroidal-derivatives-with-side-chain-of-20-and-22-hydrazone-aromatic-heterocycles-and-their-antiproliferative-acitivity
#9
Chunfang Gan, Liang Liu, Jianguo Cui, Zhiping Liu, Haixin Shi, Qifu Lin, Haibing Sheng, Chunhui Yang, Yanmin Huang
BACKGROUND: The modification of steroidal structure is commonly used to change the biological activity of steroids in medicinal chemistry. Some steroids containing heterocycles exhibit distinct cytotoxicity against various cancer cell lines and have been gotten wide attention over the years by medicinal chemists for drug discovery. METHODS: Using pregnenolone and stigmasterol as starting materials, via different chemical reaction, two series of heterosteroids with side chain of 20- and 22-hydrazone aromatic cycles or heterocycles in their structures were synthesized and characterized by IR, NMR and HRMS...
December 5, 2016: Medicinal Chemistry
https://www.readbyqxmd.com/read/27917399/retinoids-and-retinal-diseases
#10
Philip D Kiser, Krzysztof Palczewski
Recent progress in molecular understanding of the retinoid cycle in mammalian retina stems from painstaking biochemical reconstitution studies supported by natural or engineered animal models with known genetic lesions and studies of humans with specific genetic blinding diseases. Structural and membrane biology have been used to detect critical retinal enzymes and proteins and their substrates and ligands, placing them in a cellular context. These studies have been supplemented by analytical chemistry methods that have identified small molecules by their spectral characteristics, often in conjunction with the evaluation of models of animal retinal disease...
October 2016: Annual Review of Vision Science
https://www.readbyqxmd.com/read/27915982/molecular-cellular-and-pharmaceutical-aspects-of-bone-grafting-materials-and-membranes-during-maxillary-sinus-lift-procedures-part-2-detailed-characteristics-of-the-materials
#11
Giovanna Iezzi, Adriano Piatelli, Alessandra Giuliani, Carlo Mangano, Antonio Barone, Licia Manzon, Marco Degidi, Antonio Scarano, Antonella Filippone, Vittoria Perrotti
Various grafts or combination of bone substitute materials have been used in sinus lift procedures. Currently, ongoing developments in several disciplines, from molecular biology and chemistry to computer science and engineering, have contributed to the understanding of biological processes leading to bone healing after the use of bone substitute materials (BSBs) and therefore of the behavior of BSBs. The understanding of the properties of each graft enables individual treatment concepts and therefore allows shift from a simple replacement material to the modern concept of an individually created composite biomaterial...
December 1, 2016: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/27915023/anisotropic-noble-metal-nanoparticles-synthesis-surface-functionalization-and-applications-in-biosensing-bioimaging-drug-delivery-and-theranostics
#12
REVIEW
Gokul Paramasivam, Namitharan Kayambu, Arul Maximus Rabel, Ashok K Sundramoorthy, Anandhakumar Sundaramurthy
Anisotropic nanoparticles have fascinated scientists and engineering communities for over a century because of their unique physical and chemical properties. In recent years, continuous advances in design and fabrication of anisotropic nanoparticles have opened new avenues for application in various areas of biology, chemistry and physics. Anisotropic nanoparticles have the plasmon absorption in the visible as well as near-infrared (NIR) region, which enable them to be used for crucial applications such as biological imaging, medical diagnostics and therapy ("theranostics")...
November 30, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#13
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27913023/in-stream-metabolism-and-atmospheric-carbon-sequestration-in-a-groundwater-fed-karst-stream
#14
Junbing Pu, Jianhong Li, Mitra B Khadka, Jonathan B Martin, Tao Zhang, Shi Yu, Daoxian Yuan
Atmospheric carbon sequestered in karst systems through dissolution of carbonate minerals is considered to have no net effect on long-term regional and global carbon budgets because precipitation of dissolved carbonate minerals emits CO2 back to the atmosphere. Even though recent studies have implied that rapid kinetics of carbonate dissolution coupled with the aquatic photosynthetic uptake of dissolve inorganic carbon (DIC) could facilitate a stable atmospheric C sink in karst rivers and streams, little is known about the magnitudes and long-term stability of this C sink...
November 29, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27911778/enhanced-stochastic-fluctuations-to-measure-steep-adhesive-energy-landscapes
#15
Ahmad Haider, Daniel Potter, Todd A Sulchek
Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions...
November 23, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910820/4d-bioprinting-the-next-generation-technology-for-biofabrication-enabled-by-stimuli-responsive-materials
#16
Yi-Chen Li, Yu Shrike Zhang, Ali Akpek, Su Ryon Shin, Ali Khademhosseini
Four-dimensional (4D) bioprinting, encompassing a wide range of disciplines including bioengineering, materials science, chemistry, and computer sciences, is emerging as the next-generation biofabrication technology. By utilizing stimuli-responsive materials and advanced three-dimensional (3D) bioprinting strategies, 4D bioprinting aims to create dynamic 3D patterned biological structures that can transform their shapes or behavior under various stimuli. In this review, we highlight the potential use of various stimuli-responsive materials for 4D printing and their extension into biofabrication...
December 2, 2016: Biofabrication
https://www.readbyqxmd.com/read/27910408/universal-handheld-micropipette
#17
Justin Beroz, A John Hart
The handheld micropipette is the most ubiquitous instrument for precision handling of microliter-milliliter liquid volumes, which is an essential capability in biology and chemistry laboratories. The range of one pipette is typically adjustable up to 10-fold its minimum volume, requiring the use and maintenance of multiple pipettes for liquid handling across larger ranges. Here we propose a design for a single handheld pipette adjustable from 0.1 μl to 1000 μl (i.e., 10(4)-fold) which spans the range of an entire suite of current commercial pipettes...
November 2016: Review of Scientific Instruments
https://www.readbyqxmd.com/read/27909941/degradation-and-half-life-of-dna-present-in-biomass-from-a-genetically-modified-organism-during-land-application
#18
Mathew C Halter, James A Zahn
White biotechnology has made a positive impact on the chemical industry by providing safer, more efficient chemical manufacturing processes that have reduced the use of toxic chemicals, harsh reaction conditions, and expensive metal catalysts, which has improved alignment with the principles of Green Chemistry. The genetically-modified (GM) biocatalysts that are utilized in these processes are typically separated from high-value products and then recycled, or eliminated. Elimination routes include disposal in sanitary landfills, incineration, use as a fuel, animal feed, or reuse as an agricultural soil amendment or other value-added products...
December 1, 2016: Journal of Industrial Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27909024/toward-high-school-biology-helping-middle-school-students-understand-chemical-reactions-and-conservation-of-mass-in-nonliving-and-living-systems
#19
Cari F Herrmann-Abell, Mary Koppal, Jo Ellen Roseman
Modern biology has become increasingly molecular in nature, requiring students to understand basic chemical concepts. Studies show, however, that many students fail to grasp ideas about atom rearrangement and conservation during chemical reactions or the application of these ideas to biological systems. To help provide students with a better foundation, we used research-based design principles and collaborated in the development of a curricular intervention that applies chemistry ideas to living and nonliving contexts...
2016: CBE Life Sciences Education
https://www.readbyqxmd.com/read/27909020/the-design-and-transformation-of-biofundamentals-a-nonsurvey-introductory-evolutionary-and-molecular-biology-course
#20
Michael W Klymkowsky, Jeremy D Rentsch, Emina Begovic, Melanie M Cooper
Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master...
2016: CBE Life Sciences Education
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