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https://www.readbyqxmd.com/read/28092828/a-flexible-microbial-co-culture-platform-for-simultaneous-utilization-of-methane-and-carbon-dioxide-from-gas-feedstocks
#1
Eric A Hill, William B Chrisler, Alex S Beliaev, Hans C Bernstein
A new co-cultivation technology is presented that converts greenhouse gasses, CH4 and CO2, into microbial biomass. The methanotrophic bacterium, Methylomicrobium alcaliphilum 20z, was coupled to a cyanobacterium, Synechococcus PCC 7002 via oxygenic photosynthesis. The system exhibited robust growth on diverse gas mixtures ranging from biogas to those representative of a natural gas feedstock. A continuous processes was developed on a synthetic natural gas feed that achieved steady-state by imposing coupled light and O2 limitations on the cyanobacterium and methanotroph, respectively...
January 3, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28092825/non-invasive-techniques-for-revealing-the-palette-of-the-romantic-painter-francesco-hayez
#2
Laura Rampazzi, Valentina Brunello, Cristina Corti, Elena Lissoni
This paper describes the first systematic analysis of the palette of Francesco Hayez, one of the most outstanding artists of European Romanticism, whose painting technique has never been extensively investigated despite the plethora of artistic studies. He lived in a particular moment in the history of painting, as in the first half of the 19th century many synthetic pigments were available, also in tin tubes, but traditional materials were still used. Sixteen paintings on canvas and on panels, created between 1823 and 1868, were analyzed in situ through non-invasive techniques (infrared reflectography and infrared reflection spectroscopy)...
January 5, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28092764/common-deregulated-gene-expression-profiles-and-morphological-changes-in-developing-zebrafish-larvae-exposed-to-environmental-relevant-high-to-low-concentrations-of-glucocorticoids
#3
Qiyu Chen, Caixia Li, Zhiyuan Gong, Eric Chun Yong Chan, Shane A Snyder, Siew Hong Lam
Synthetic glucocorticoids have been detected in environmental waters and their biological potency have raised concerns of their impact on aquatic vertebrates especially fish. In this study, developing zebrafish larvae exposed to representative glucocorticoids (dexamethasone, prednisolone and triamcinolone) at 50 pM to 50 nM from 3 h post-fertilisation to 5 days post-fertilisation were investigated. Microarray analysis identified 1255, 1531, and 2380 gene probes, which correspondingly mapped to 660, 882 and 1238 human/rodent homologs, as deregulated by dexamethasone, prednisolone and triamcinolone, respectively...
January 6, 2017: Chemosphere
https://www.readbyqxmd.com/read/28092722/synthetic-and-natural-peroxisome-proliferator-activated-receptor-ppar-agonists-as-candidates-for-the-therapy-of-the-metabolic-syndrome
#4
Chek Kun Tan, Yan Zhuang, Walter Wahli
Introduction Peroxisome proliferator-activated receptors (PPARs) are the molecular targets of hypolipidemic and insulin-sensitizing drugs and implicated in a multitude of processes that fine-tune the functions of all organs in vertebrates. As transcription factors they sense endogenous and exogenous lipid signaling molecules and convert these signals into intricate gene responses that impact health and disease. The PPARs act as modulators of cellular, organ, and systemic processes, such as lipid and carbohydrate metabolism, making them valuable for understanding body homeostasis influenced by nutrition and exercise...
January 16, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28092680/utilizing-somatic-mutation-data-from-numerous-studies-for-cancer-research-proof-of-concept-and-applications
#5
D Amar, S Izraeli, R Shamir
Large cancer projects measure somatic mutations in thousands of samples, gradually assembling a catalog of recurring mutations in cancer. Many methods analyze these data jointly with auxiliary information with the aim of identifying subtype-specific results. Here, we show that somatic gene mutations alone can reliably and specifically predict cancer subtypes. Interpretation of the classifiers provides useful insights for several biomedical applications. We analyze the COSMIC database, which collects somatic mutations from The Cancer Genome Atlas (TCGA) as well as from many smaller scale studies...
January 16, 2017: Oncogene
https://www.readbyqxmd.com/read/28092657/lipid-production-in-yarrowia-lipolytica-is-maximized-by-engineering-cytosolic-redox-metabolism
#6
Kangjian Qiao, Thomas M Wasylenko, Kang Zhou, Peng Xu, Gregory Stephanopoulos
Microbial factories have been engineered to produce lipids from carbohydrate feedstocks for production of biofuels and oleochemicals. However, even the best yields obtained to date are insufficient for commercial lipid production. To maximize the capture of electrons generated from substrate catabolism and thus increase substrate-to-product yields, we engineered 13 strains of Yarrowia lipolytica with synthetic pathways converting glycolytic NADH into the lipid biosynthetic precursors NADPH or acetyl-CoA. A quantitative model was established and identified the yield of the lipid pathway as a crucial determinant of overall process yield...
January 16, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28092587/learning-domain-invariant-subspace-using-domain-features-and-independence-maximization
#7
Ke Yan, Lu Kou, David Zhang
Domain adaptation algorithms are useful when the distributions of the training and the test data are different. In this paper, we focus on the problem of instrumental variation and time-varying drift in the field of sensors and measurement, which can be viewed as discrete and continuous distributional change in the feature space. We propose maximum independence domain adaptation (MIDA) and semi-supervised MIDA to address this problem. Domain features are first defined to describe the background information of a sample, such as the device label and acquisition time...
January 16, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28092560/diffeomorphic-multi-frame-non-rigid-registration-of-cell-nuclei-in-2d-and-3d-live-cell-images
#8
Marco Tektonidis, Karl Rohr
To gain a better understanding of cellular and molecular processes it is important to quantitatively analyze the motion of subcellular particles in live cell microscopy image sequences. Since generally the subcellular particles move and cell nuclei move as well as deform, it is important to decouple the movement of particles from that of the cell nuclei using nonrigid registration methods. We have developed a diffeomorphic multi-frame approach for non-rigid registration of cell nuclei in 2D and 3D live cell fluorescence microscopy images...
January 16, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28092520/robust-matrix-factorization-by-majorization-minimization
#9
Zhouchen Lin, Chen Xu, Hongbin Zha
L1-norm based low rank matrix factorization in the presence of missing data and outliers remains a hot topic in computer vision. Due to non-convexity and non-smoothness, all the existing methods either lack scalability or robustness, or have no theoretical guarantee on convergence. In this paper, we apply the Majorization Minimization technique to solve this problem. At each iteration, we upper bound the original function with a strongly convex surrogate. By minimizing the surrogate and updating the iterates accordingly, the objective function has sufficient decrease, which is stronger than just being non-increasing that other methods could offer...
January 11, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28092514/a-multivariate-approach-for-patient-specific-eeg-seizure-detection-using-empirical-wavelet-transform
#10
Abhijit Bhattacharyya, Ram Bilas Pachori
OBJECTIVE: This paper investigates the multivariate oscillatory nature of electroencephalogram (EEG) signals in adaptive frequency scales for epileptic seizure detection. METHODS: The empirical wavelet transform (EWT) has been explored for the multivariate signals in order to determine the joint instantaneous amplitudes and frequencies in signal adaptive frequency scales. The proposed multivariate extension of EWT has been studied on multivariate multi-component synthetic signal, as well as on multivariate EEG signals of CHB-MIT scalp EEG database...
January 9, 2017: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28092500/a-model-of-a-synthetic-biological-communication-interface-between-mammalian-cells-and-mechatronic-systems
#11
Keith C Heyde, Warren C Ruder
The creation of communication interfaces between abiotic and biotic systems represents a significant research challenge. In this work, we design and model a system linking the biochemical signaling pathways of mammalian cells to the actions of a mobile robotic prosthesis. We envision this system as a robotic platform carrying an optically monitored bioreactor that harbors mammalian cells. The cellular, optical signal is captured by an onboard fluorescent microscope and converted into an electronic signal. We first present a design for the overall cell-robot system, with a specific focus on the design of the synthetic gene networks needed for the system...
December 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28092486/use-of-polyclonal-monoclonal-antibody-therapies-in-transplantation
#12
Melissa Y Yeung, Steven Gabardi, Mohamed H Sayegh
For over thirty years, antibody (mAb)-based therapies have been a standard component of transplant immunosuppression, and yet much remains to be learned in order for us to truly harness their therapeutic capabilities. Current mAbs used in transplant directly target and destroy graft-destructive immune cells, interrupt cytokine and costimulation-dependent T and B cell activation, and prevent down-stream complement activation. Areas covered: This review summarizes our current approaches to using antibody-based therapies to prevent and treat allograft rejection...
January 16, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/28092474/novel-histone-deacetylase-6-hdac6-selective-inhibitors-a-patent-evaluation-wo2014181137
#13
Claudia A Simões-Pires, Philippe Bertrand, Muriel Cuendet
The invention described in this patent (WO2014181137) is related to hydroxamic acid derivatives with inhibitory activity towards histone deacetylases (HDACs), their synthetic process and pharmaceutical formulations, as well as a method for treating patients suffering from a list of selected tumoral, inflammatory, cardiac and chronic disorders. HDACs are known to deacetylate histones and other proteins, which makes HDAC inhibitors able to affect cell survival, cell signaling, transport, and gene expression. Those effects have been associated to the therapeutic success of HDAC inhibitors...
January 16, 2017: Expert Opinion on Therapeutic Patents
https://www.readbyqxmd.com/read/28092425/chemical-composition-of-the-essential-oil-of-nigeria-grown-hoslundia-opposita-vahl-lamiaceae-dried-leaves-and-its-bioactivity-against-cowpea-seed-bruchid
#14
Samuel Adelani Babarinde, Olufemi Olutoyin Richard Pitan, Ganiyu Olatunji Olatunde, Michael Oluwole Ajala
Due to several ecological and human hazards of synthetic pesticides in postharvest crop protection, there is the need to search for eco-friendly alternatives. In this study, chemical composition and insecticidal activities of essential oil (EO) obtained from Hoslundia opposita dried leaves were evaluated against cowpea seed bruchid. Eight constituents, predominated by oxygenated monoterpenes (78.86%), were identified using GC-MS. The constituents were 1,8-cineole (1; 61.15%), followed by α-terpineol (2; 16...
January 16, 2017: Chemistry & Biodiversity
https://www.readbyqxmd.com/read/28092361/designed-cell-consortia-as-fragrance-programmable-analog-to-digital-converters
#15
Marius Müller, Simon Ausländer, Andrea Spinnler, David Ausländer, Julian Sikorski, Marc Folcher, Martin Fussenegger
Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28092019/urb597-and-the-cannabinoid-win55-212-2-reduce-behavioral-and-neurochemical-deficits-induced-by-mptp-in-mice-possible-role-of-redox-modulation-and-nmda-receptors
#16
Angel Escamilla-Ramírez, Esperanza García, Guadalupe Palencia-Hernández, Ana Laura Colín-González, Sonia Galván-Arzate, Isaac Túnez, Julio Sotelo, Abel Santamaría
Several physiological events in the brain are regulated by the endocannabinoid system (ECS). While synthetic cannabinoid receptor (CBr) agonists such as WIN55,212-2 act directly on CBr, agents like URB597, a fatty acid amide hydrolase (FAAH) inhibitor, induce a more "physiological" activation of CBr by increasing the endogenous levels of the endocannabinoid anandamide (AEA). Herein, we compared the pre- and post-treatment efficacy of URB597 and WIN55,212-2 on different endpoints evaluated in the toxic model produced by the mitochondrial toxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) in mice...
January 14, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28091753/vtst-mt-studies-of-the-catalytic-mechanism-of-c-h-activation-by-transition-metal-complexes-with-cu2-%C3%AE-o2-fe2-%C3%AE-o2-and-fe-iv-o-cores-based-on-dft-potential-energy-surfaces
#17
REVIEW
Yongho Kim, Binh Khanh Mai, Sumin Park
High-valent Cu and Fe species, which are generated from dioxygen activation in metalloenzymes, carry out the functionalization of strong C-H bonds. Understanding the atomic details of the catalytic mechanism has long been one of the main objectives of bioinorganic chemistry. Large H/D kinetic isotope effects (KIEs) were observed in the C-H activation by high-valent non-heme Cu or Fe complexes in enzymes and their synthetic models. The H/D KIE depends significantly on the transition state properties, such as structure, energies, frequencies, and shape of the potential energy surface, when the tunneling effect is large...
January 16, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28091672/a-rapid-way-to-discover-nonstandard-macrocyclic-peptide-modulators-of-drug-targets
#18
Toby Passioura, Hiroaki Suga
Studies of the fundamental nature of RNA catalysis and the potential mechanism of a shift from the "RNA world" to proteinaceous life lead us to identify a set of ribozymes (flexizymes) capable of promiscuous tRNA acylation. Whilst theoretically and mechanistically interesting in their own right, flexizymes have turned out to have immense practical value for the simple synthesis of tRNAs acylated with unusual amino acids, which in turn can be used for the ribosomal synthesis of peptides containing non-canonical residues...
January 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28091658/insights-into-the-formation-of-inorganic-heterocycles-via-cyclocondensation-of-primary-amines-with-group-15-and-16-halides
#19
Tristram Chivers, Risto S Laitinen
Cyclocondensation is a major preparative route for the generation of inorganic heterocycles especially in the case of ring systems involving a Group 15 or 16 element linked to nitrogen. This Perspective will consider recent experimental and computational studies involving the reactions of primary amines (or their synthetic equivalents) with pnictogen and chalcogen halides. The major focus will be a discussion of the identity and role of acyclic intermediates in the reaction pathways to ring formation, as well as the nature of the heterocycles so formed...
January 16, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28091601/massively-parallel-digital-transcriptional-profiling-of-single-cells
#20
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu, Mark T Gregory, Joe Shuga, Luz Montesclaros, Jason G Underwood, Donald A Masquelier, Stefanie Y Nishimura, Michael Schnall-Levin, Paul W Wyatt, Christopher M Hindson, Rajiv Bharadwaj, Alexander Wong, Kevin D Ness, Lan W Beppu, H Joachim Deeg, Christopher McFarland, Keith R Loeb, William J Valente, Nolan G Ericson, Emily A Stevens, Jerald P Radich, Tarjei S Mikkelsen, Benjamin J Hindson, Jason H Bielas
Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs...
January 16, 2017: Nature Communications
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