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Chemical biology

Lance R English, Erin C Tilton, Benjamin J Ricard, Steven T Whitten
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions...
December 9, 2016: Proteins
Ebaa M El-Hossary, Cheng Cheng, Mostafa M Hamed, Ashraf Nageeb El-Sayed Hamed, Knut Ohlsen, Ute Hentschel, Usama Ramadan Abdelmohsen
Fungal diseases represent an increasing threat to human health worldwide which in some cases might be associated with substantial morbidity and mortality. However, only few antifungal drugs are currently available for the treatment of life-threatening fungal infections. Furthermore, plant diseases caused by fungal pathogens represent a worldwide economic problem for the agriculture industry. The marine environment continues to provide structurally diverse and biologically active secondary metabolites, several of which have inspired the development of new classes of therapeutic agents...
November 14, 2016: European Journal of Medicinal Chemistry
Nazmul Abedin Khan, Sung Hwa Jhung
Efficient removal and separation of chemicals from the environment has become a vital issue from a biological and environmental point of view. Currently, adsorptive removal/separation is one of the most promising approaches for cleaning purposes. Selective adsorption/removal of various sulfur- and nitrogen-containing compounds, olefins, and π-electron-rich gases via π-complex formation between an adsorbent and adsorbate molecules is very competitive. Porous metal-organic framework (MOF) materials are very promising in the adsorption/separation of various liquids and gases owing to their distinct characteristics...
November 27, 2016: Journal of Hazardous Materials
Abhishek Singharoy, Christophe Chipot, Mahmoud Moradi, Klaus Schulten
ATP synthase is the most prominent bioenergetic macromolecular motor in all life-forms, utilizing the proton gradient across the cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, the precise molecular mechanism whereby vacuolar (V-type) ATP synthase fulfills its biological function remains largely fragmentary. Recently, crystallographers provided the first high-resolution view of ATP activity in Enterococcus hirae V1-ATPase...
December 9, 2016: Journal of the American Chemical Society
Milena Stranska-Zachariasova, Isma Kurniatanty, Helena Gbelcova, Monika Jiru, Josep Rubert, Tjokorda Gde Tirta Nindhia, Cosimo Walter D'Acunto, Sony Heru Sumarsono, Marselina Irasonia Tan, Jana Hajslova, Tomas Ruml
The present study aims to focus on the bioprospecting of marine macroalgae of Turbinaria species, plenteous biomass of the world ocean. Three types of solvents, i.e. water, methanol:water (80:20, v/v) and hexane:isopropanol (50:50, v/v), were used for extraction. Both the biological activity, as well as the pattern of present chemicals were characterized. For the cell proliferation assay, the human embryonic kidney 293 cells, cervix / breast / pancreatic adenocarcinoma, and osteosarcoma cells were used. For the antioxidant activity determination, both intracellular assay with human embryonic kidney and cervix adenocarcinoma cells, as well as the biochemical DPPH test, were employed...
December 9, 2016: Chemistry & Biodiversity
Lei Wang, Akiko Ishida, Yasuyuki Hashidoko, Makoto Hashimoto
A novel strategy for the dehydrogenation of the NH-NH bond is disclosed using potassium tert-butoxide (tBuOK) in liquid ammonia (NH3 ) under air at room temperature. Its synthetic value is well demonstrated by the highly efficient synthesis of aromatic azo compounds (up to 100 % yield, 3 min), heterocyclic azo compounds, and dehydrazination of phenylhydrazine. The broad application of this strategy and its benefit to chemical biology is proved by a novel, convenient, one-pot synthesis of aliphatic diazirines, which are important photoreactive agents for photoaffinity labeling...
December 9, 2016: Angewandte Chemie
Zineb Djerrad, Abderrahmane Djouahri, Leila Kadik
The impact of growth stages during vegetative cycle (B0 -B5 ) on chemical composition and antioxidant activities of Pinus halepensis Mill. needles essential oils was investigated for the first time. GC and GC-MS analyses pointed to a quantitative variability of components; terpene hydrocarbons derivatives, represented by α-pinene (8.5-12.9%), myrcene (17.5-21.6%), p-cymene (7.9-11.9%) and (Z)-β-caryophyllene (17.3-21.2%) as major components, decreased from 88.9% at B0 growth stage to 66.9% at B5 growth stage, whereas oxygenated derivatives, represented by caryophyllene oxide (5...
December 9, 2016: Chemistry & Biodiversity
Vladimir A D'yakonov, Gulnara N Kadikova, Lilya U Dzhemileva, Guzel F Gazizullina, Ilfir R Ramazanov, Usein M Dzhemilev
A new, effective catalytic system based on Co(acac)2 has been developed for [6+2]-cycloaddition of terminal alkynes to 1,3,5,7-cyclooctatetraene to give substituted bicyclo[4.2.2]deca-2,4,7,9-tetraenes in high yields (68-85%). The electrophilic activation of double bonds in the bicyclic products with m-CPBA is an efficient method for the synthesis of substituted bicyclo[4.3.1]deca-2,4,8-triene-7,10-diols, which form the key structural moiety of numerous natural biologically active compounds. The structures of the obtained compounds were reliably proven by modern spectral methods and X-ray diffraction...
December 9, 2016: Journal of Organic Chemistry
Monika Gupta, K Parvathi, Soumyaditya Mula, Dilip K Maity, Alok K Ray
One cationic BODIPY chromophore was synthesized and its complexation behaviour with the macrocyclic host cucurbit[7]uril (CB[7]) was studied using different spectroscopy techniques such as UV-vis absorption, steady-state and time-resolved fluorescence, (1)H NMR as well as DFT based quantum calculations. The dye showed formation of a 1 : 1 dye-CB[7] complex with improvement in the fluorescence intensity. These new results of the formation of moderate association of aqueous BODIPYs with the nontoxic host CB[7] may lead to promising applications of the dye molecule as a sensitive and efficient off-on mode fluorescent probe in chemical and biological studies...
December 9, 2016: Photochemical & Photobiological Sciences
Madhumita Chakraborty, Siddhartha Roy
Selectively regulating genes is an important goal in Chemical Biology. We report the development of a peptide-based synthetic transcription factor which binds the targeted DNA sequence with high affinity and single base-pair discrimination capability. When delivered inside a tumor cell, it regulated targeted genes selectively and inhibited cell proliferation.
December 9, 2016: Chemical Communications: Chem Comm
Ruochen Fang, Huacheng Zhang, Liulin Yang, Huanting Wang, Ye Tian, Xi Zhang, Lei Jiang
Artificial nanochannels, inheriting smart gating functions of biological ion channels, promote the development of artificial functional nanofluidic devices for high-performance biosensing and electricity generation. However, gating states of the artificial nanochannels have been mainly realized through chemical modification of the channels with responsive molecules, and their gating states cannot be further regulated once the nanochannel is modified. In this work, we employed a new supramolecular layer-by-layer (LbL) self-assembly method to achieve reversible and adjustable multiple gating features in nanofluidic diodes...
December 9, 2016: Journal of the American Chemical Society
Yong Liang, Xin Jiang, Rong Yuan, Yang Zhou, Caixia Ji, Limin Yang, Haifeng Chen, Qiuquan Wang
Although we believe that the cell surface sialic acids (Sias) are playing an important role in cell-cell interactions and related tumor metastasis processes, acquisition of their quantitative information has yet been a challenge to date. Here, we reported the construction of a new analytical platform for Sias-specific imaging and quantification. We used N-Azidoacetyl-Mannosamine tetraacylated as a metabolic sugar substrate to bioassemble azido-Sias on the surface of cells via the metabolic pathway of Sias de novo synthesis...
December 9, 2016: Analytical Chemistry
Nicholas C Butzin, Philip Hochendoner, Curtis T Ogle, William H Mather
Internal chemical oscillators (chemical clocks) direct the behavior of numerous biological systems, and maintenance of a given period and phase between many such oscillators may be important for their proper function. However, both environmental variability and fundamental molecular noise can cause biochemical oscillators to lose coherence. One solution to maintaining coherence is entrainment, where an external signal provides a cue that resets the phase of oscillators. In this work, we study the entrainment of gene networks by a queueing interaction established by competition between proteins for a common proteolytic pathway...
December 9, 2016: ACS Synthetic Biology
Nika Galic, Volker Grimm, Valery Forbes
Freshwater ecosystems are exposed to many stressors, including toxic chemicals and global warming, which can impair, separately or in combination, important processes in organisms and hence higher levels of organization. Investigating combined effects of warming and toxicants has been a topic of little research, but neglecting their combined effects may seriously misguide management efforts. To explore how toxic chemicals and warming, alone and in combination, propagate across levels of biological organization, including a key ecosystem process, we developed an individual-based model (IBM) of a freshwater amphipod detritivore, Gammarus pseudolimnaeus, feeding on leaf litter...
December 9, 2016: Global Change Biology
Katie J Denby, Jeffrey Iwig, Claudine Bisson, Jodie Westwood, Matthew D Rolfe, Svetlana E Sedelnikova, Khadine Higgins, Michael J Maroney, Patrick J Baker, Peter T Chivers, Jeffrey Green
Most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. Therefore, biology has evolved systems to perceive and detoxify formaldehyde. The frmRA(B) operon that is present in many bacteria represents one such system. The FrmR protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (FrmA and FrmB, when the latter is present). The X-ray structure of the formaldehyde-treated Escherichia coli FrmR (EcFrmR) protein reveals the formation of methylene bridges that link adjacent Pro2 and Cys35 residues in the EcFrmR tetramer...
December 9, 2016: Scientific Reports
Ena Bolaina-Lorenzo, Cristina Martínez-Ramos, Manuel Monleón-Pradas, Wilberth Herrera-Kao, Juan V Cauich-Rodríguez, José M Cervantes-Uc
Electrospun polycaprolactone (PCL)/chitosan (CH) blend scaffolds with different CH weight ratios were prepared to study the effect of scaffold composition on its physicochemical and biological properties. Scanning electron microscopy showed bead-free homogeneous randomly arranged nanofibers whose average diameter decreased from 240 to 110 nm with increasing CH content. The infrared spectra of the PCL/CH blends were very similar to the neat PCL scaffold. Energy-dispersive x-ray spectroscopy analysis confirmed the presence of carbon, oxygen and nitrogen in the scaffolds, although fluorine-from chemicals used as solvent-was also detected...
December 9, 2016: Biomedical Materials
Tomáš Pluskal, Mitsuhiro Yanagida
Metabolomics is a modern field of chemical biology that strives to simultaneously quantify hundreds of cellular metabolites. Techniques for metabolomic analysis in Schizosaccharomyces pombe have only recently been developed. Here we introduce methods that provide a complete workflow for metabolomic analysis in S. pombe Based on available literature, we estimate the yeast metabolome to comprise on the order of several thousand different metabolites. We discuss the feasibility of extraction and detection of such a large number of metabolites, and the influences of various parameters on the results...
December 1, 2016: Cold Spring Harbor Protocols
Lin Zhou, Kun Wang, Zhenhua Wu, Haidao Dong, Hao Sun, Xuanhong Cheng, Hong Lian Zhang, Hongbo Zhou, Chunping Jia, Qinghui Jin, Hongju Mao, Jean-Luc Coll, Jianlong Zhao
Two-dimensional graphene devices are widely used for biomolecule detection. Nevertheless, the surface modification of graphene is critical to achieve the high sensitivity and specificity required for biological detection. Herein, native bovine serum albumin (BSA) in inorganic solution is denatured on the graphene surface by heating, leading to the formation of nanoscale BSA protein films adsorbed on the graphene substrate via π-stacking interactions. This technique yields a controllable, scalable, uniform, and high-coverage method for graphene biosensors...
December 6, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Mary E Marisa, Shiliang Zhou, Brent C Melot, Graham F Peaslee, James R Neilson
Hydroxyapatite is an inorganic mineral closely resembling the mineral phase in bone. However, as a biological mineral, it is highly disordered, and its composition and atomistic structure remain poorly understood. Here, synchrotron X-ray total scattering and pair distribution function analysis methods provide insight into the nature of atomistic disorder in a synthetic bone mineral analogue, chemically substituted hydroxyapatite. By varying the effective hydrolysis rate and/or carbonate concentration during growth of the mineral, compounds with varied degrees of paracrystallinity are prepared...
December 5, 2016: Inorganic Chemistry
Pawel Roman, Johannes B M Klok, João A B Sousa, Elias Broman, Mark Dopson, Erik Van Zessen, Martijn F M Bijmans, Dimitry Y Sorokin, Albert J H Janssen
After the first commercial applications of a new biological process for the removal of hydrogen sulfide (H2S) from low pressure biogas, the need arose to broaden the operating window to also enable the removal of organosulfur compounds from high pressure sour gases. In this study we have selected microorganisms from a full-scale biodesulfurization system that are capable of withstanding the presence of thiols. This full-scale unit has been in stable operation for more than 10 years. We investigated the microbial community by using high-throughput sequencing of 16S rRNA gene amplicons which showed that methanethiol gave a competitive advantage to bacteria belonging to the genera Thioalkalibacter (Halothiobacillaceae family) and Alkalilimnicola (Ectothiorhosdospiraceae family)...
December 6, 2016: Environmental Science & Technology
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