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https://www.readbyqxmd.com/read/28637248/expression-and-comparison-of-codon-optimised-aspergillus-tubingensis-amylase-variants-in-saccharomyces-cerevisiae
#1
Rosemary A Cripwell, Shaunita H Rose, Willem H van Zyl
The expression of codon optimised genes is a popular genetic engineering approach for the production of industrially relevant proteins. This study investigates and compares the expression of codon optimised and codon adapted amylase variants. The Aspergillus tubingensis raw starch hydrolysing α-amylase (amyA) and glucoamylase (glaA) encoding genes were redesigned using synonymous codons and expressed in S. cerevisiae Y294. Codon optimisation to favour S. cerevisiae codon bias resulted in a decrease in extracellular enzyme activity of 72% (30...
June 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28637186/cpg-and-methylation-dependent-dna-binding-and-dynamics-of-the-methylcytosine-binding-domain-2-protein-at-the-single-molecule-level
#2
Hai Pan, Stephanie M Bilinovich, Parminder Kaur, Robert Riehn, Hong Wang, David C Williams
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2...
June 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28637183/nuclitrack-an-integrated-nuclei-tracking-application
#3
Sam Cooper, Alexis R Barr, Robert Glen, Chris Bakal
Summary: Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently-labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly...
June 20, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28637165/quantification-of-the-methane-concentration-using-anaerobic-oxidation-of-methane-coupled-to-extracellular-electron-transfer
#4
Yaohuan Gao, Hodon Ryu, Bruce E Rittmann, Abid Hussain, Hyung-Sool Lee
A biofilm anode acclimated with growth media containing acetate, then acetate+methane, and finally methane alone produced electrical current in a microbial electrochemical cell (MxC) fed with methane as the sole electron donor. Geobacter was the dominant genus for the bacterial domain (93%) in the biofilm anode, while methanogens (Methanocorpusculum labreanum and Methanosaeta concilii) accounted for 82% of the total archaeal clones in the biofilm. Fluorescence in situ hybridization (FISH) imaging clearly showed a biofilm of mixed bacteria and archaea, suggesting a syntrophic interaction between them for performing anaerobic oxidation of methane (AOM) in the biofilm anode...
June 13, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28637159/methane-production-and-fertilizing-value-of-organic-waste-organic-matter-characterization-for-a-better-prediction-of-valorization-pathways
#5
Julie Jimenez, Han Lei, Jean-Philippe Steyer, Sabine Houot, Dominique Patureau
Organic wastes are potential sources of both energy as well as crop production fertilizers. Correlations and models, involving organic matter characterization, have been previously described by several authors although there is still a lack in knowledge on the potential of simultaneous predictions of methane and organic fertilizer quality to optimize the wastes treatments. A methodology combining chemical accessibility and fluorescence spectroscopy was used to characterize 82 different organic wastes. Characterization data were compared with the biochemical methane potential (BMP), and with the biodegradable organic carbon obtained by soil incubation (C_bio)...
May 31, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28637094/acclimation-responses-to-high-light-by-guazuma-ulmifolia-lam-malvaceae-leaves-at-different-stages-of-development
#6
Anderson Kikuchi Calzavara, Juliana Silva Rocha, Geovana Lourenço, Karina Sanada, Cristiano Medri, Edmilson Bianchini, José Antonio Pimenta, Renata Stolf-Moreira, Halley Caixeta Oliveira
The recomposition of deforested environments requires the prior acclimation of seedlings to full sun in nurseries. Seedlings can overcome excessive light either through the acclimation of pre-existing fully expanded leaves or through the development of new leaves that are acclimated to the new light environment. Here, we compared the acclimation capacity of mature (MatL, fully expanded at the time of transfer) and newly expanded leaves (NewL, expanded after the light shift) of Guazuma ulmifolia Lam. (Malvaceae) seedlings to high light...
June 21, 2017: Plant Biology
https://www.readbyqxmd.com/read/28637019/clinicopathological-characteristics-of-ros1-and-ret-rearranged-nsclc-in-caucasian-patients-data-from-a-cohort-of-713-non-squamous-nsclc-lacking-kras-egfr-her2-braf-pik3ca-alk-alterations
#7
Frédéric Dugay, Francisco Llamas-Gutierrez, Marjory Gournay, Sarah Medane, François Mazet, Dan Christian Chiforeanu, Emmanuelle Becker, Régine Lamy, Hervé Léna, Nathalie Rioux-Leclercq, Marc-Antoine Belaud-Rotureau, Florian Cabillic
Targeted therapies have substantially changed the management of non-small cell lung cancer (NSCLC) patients with driver oncogenes. Given the high frequency, EGFR and ALK aberrations were the first to be detected and paved the way for tyrosine kinase inhibitor (TKI) treatments. Other kinases such as ROS1 and more recently RET have emerged as promising targets, and ROS1 and RET TKIs are already available for precision medicine.We screened a large cohort of 713 Caucasian non-squamous NSCLC patients lacking EGFR/KRAS/BRAF/HER2/PI3KCA/ALK aberrations for ROS1 and RET rearrangements using fluorescence in situ hybridization to determine the frequency and clinicopathological characteristics of ROS1- and RET-positive patients...
June 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636988/role-of-the-jak2-stat3-signaling-pathway-in-the-pathogenesis-of-type-2-diabetes-mellitus-with-macrovascular-complications
#8
Mengxue Yang, Mei Tian, Xuan Zhang, Jie Xu, Bo Yang, Jie Yu, Fengping Li, Ya Li, Sicheng Li, Xianwen Li
This study investigated the role of the JAK2/STAT3/SOCS pathway in type 2 diabetes mellitus (T2DM) and macrovascular complications (DV) (T2DM+DV) conditions. Human umbilical vein endothelial cells (HUVECs) were co-cultured with human monocytes (THP-1) and exposed to peripheral blood sera from 30 T2DM patients, 30 patients with T2DM+DV and 30 healthy controls; the groups were divided into the control, T2DM, DV, T2DM+AG490 and DV+AG490 groups. Chemotaxis of treated HUVECs toward THP-1 cells was assessed using Transwell migration...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636920/nanog-fluctuations-in-embryonic-stem-cells-highlight-the-problem-of-measurement-in-cell-biology
#9
Rosanna C G Smith, Patrick S Stumpf, Sonya J Ridden, Aaron Sim, Sarah Filippi, Heather A Harrington, Ben D MacArthur
A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, pluripotency. However, because temporal changes in intracellular protein abundances cannot be measured directly in live cells, fluctuations are typically assessed using genetically engineered reporter cell lines that produce a fluorescent signal as a proxy for protein expression...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636798/a-ccpe-based-xenon-biosensor-for-magnetic-resonance-imaging-of-claudin-expressing-cells
#10
Anna Piontek, Christopher Witte, Honor May Rose, Miriam Eichner, Jonas Protze, Gerd Krause, Jörg Piontek, Leif Schröder
The majority of malignant tumors originate from epithelial cells, and many of them are characterized by an overexpression of claudins (Cldns) and their mislocalization out of tight junctions. We utilized the C-terminal claudin-binding domain of Clostridium perfringens enterotoxin (cCPE), with its high affinity to specific members of the claudin family, as the targeting unit for a claudin-sensitive cancer biosensor. To overcome the poor sensitivity of conventional relaxivity-based magnetic resonance imaging (MRI) contrast agents, we utilized the superior sensitivity of xenon Hyper-CEST biosensors...
June 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28636776/facile-synthesis-and-chain-length-dependent-optical-and-structural-properties-of-diketopyrrolopyrrole-based-oligomers
#11
Satish Patil, Tushita Mukhopadhyay, Boregowda Puttaraju, Palas Roy, Jyotishman Dasgupta, Andreas Meyer
Here we report the synthesis, optical properties and solid-state packing of monodisperse oligomers of DPP up to five repeating units. Optical properties of DPP-oligomers in solution and solid state were investigated by a combination of steady-state, and transient spectroscopy. Transient absorption spectroscopy and time-correlated single photon counting (TCSPC) measurements show that the fluorescence lifetime decreases with increase in the oligomer size from monomer to trimer, thereby reaching saturation for pentameric DPP oligomer...
June 21, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28636670/identification-of-novel-small-molecules-that-inhibit-stat3-dependent-transcription-and-function
#12
Iryna Kolosenko, Yasmin Yu, Sander Busker, Matheus Dyczynski, Jianping Liu, Martin Haraldsson, Caroline Palm Apergi, Thomas Helleday, Katja Pokrovskaja Tamm, Brent D G Page, Dan Grander
Activation of Signal Transducer and Activator of Transcription 3 (STAT3) has been linked to several processes that are critical for oncogenic transformation, cancer progression, cancer cell proliferation, survival, drug resistance and metastasis. Inhibition of STAT3 signaling has shown a striking ability to inhibit cancer cell growth and therefore, STAT3 has become a promising target for anti-cancer drug development. The aim of this study was to identify novel inhibitors of STAT-dependent gene transcription...
2017: PloS One
https://www.readbyqxmd.com/read/28636641/development-of-a-range-of-fluorescent-reagentless-biosensors-for-atp-based-on-malonyl-coenzyme-a-synthetase
#13
Renée Vancraenenbroeck, Simone Kunzelmann, Martin R Webb
The range of ATP concentrations that can be measured with a fluorescent reagentless biosensor for ATP has been increased by modulating its affinity for this analyte. The ATP biosensor is an adduct of two tetramethylrhodamines with MatB from Rhodopseudomonas palustris. Mutations were introduced into the binding site to modify ATP binding affinity, while aiming to maintain the concomitant fluorescence signal. Using this signal, the effect of mutations in different parts of the binding site was measured. This mutational analysis revealed three variants in particular, each with a single mutation in the phosphate-binding loop, which had potentially beneficial changes in ATP binding properties but preserving a fluorescence change of ~3-fold on ATP binding...
2017: PloS One
https://www.readbyqxmd.com/read/28636640/targeted-nanodiamonds-for-identification-of-subcellular-protein-assemblies-in-mammalian-cells
#14
Michael P Lake, Louis-S Bouchard
Transmission electron microscopy (TEM) can be used to successfully determine the structures of proteins. However, such studies are typically done ex situ after extraction of the protein from the cellular environment. Here we describe an application for nanodiamonds as targeted intensity contrast labels in biological TEM, using the nuclear pore complex (NPC) as a model macroassembly. We demonstrate that delivery of antibody-conjugated nanodiamonds to live mammalian cells using maltotriose-conjugated polypropylenimine dendrimers results in efficient localization of nanodiamonds to the intended cellular target...
2017: PloS One
https://www.readbyqxmd.com/read/28636537/metabolic-pathway-for-the-universal-fluorescent-recognition-of-tumor-cells
#15
Ana Fernandez-Carrascal, Manuel Garcia-Algar, Moritz Nazarenus, Alicia Torres-Nuñez, Luca Guerrini, Neus Feliu, Wolfgang J Parak, Eduardo Garcia-Rico, Ramon A Alvarez-Puebla
Quantification of circulating tumor cells (CTCs) in blood samples from cancer patients is a non-invasive approach to monitoring the status of the disease. Most of the methods proposed in the recent years are phenomenological and rely on the use of antibodies labelled with fluorophores, magnetic particles, or immobilized on surfaces to capture the CTCs. Herein, we designed and optimized a method that employs a glucose analogue labelled with a fluorophore which takes advantage of the different metabolic pathways of cancer cells to discern them from normal ones...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636436/signal-on-fluorescent-sensor-based-on-n-cqds-for-the-detection-of-glutathione-in-human-serum-and-pharmaceutic-preparation
#16
Chengfei Zhao, Kangying Wang, Qihong Cai, Haijian Tu, Linghong Pan, Liumin Yu
Nitrogen-doped carbon quantum dots (N-CQDs) with citric acid and ethylenediamine as raw materials were synthesized by an efficient one-step strategy. The N-CQDs showed a special property that the fluorescence was quenched by Fe(3+). The quenched fluorescence of N-CQDs could be recovered by glutathione (GSH). Therefore, a "signal-on" fluorescent sensor was developed to detect GSH. The fluorescent sensor could favorably avoid the interference of ascorbic acid, dopamine, glucose, oxidized glutathione and other amino acids in the detecting process of GSH...
June 21, 2017: Preparative Biochemistry & Biotechnology
https://www.readbyqxmd.com/read/28636400/click-biotinylation-of-plga-template-for-biotin-receptor-oriented-delivery-of-doxorubicin-hydrochloride-in-4t1-cell-induced-breast-cancer
#17
Yuvraj Singh, K K Durga Rao Viswanadham, Arun Kumar Jajoriya, Jayagopal Meher, Kavit Raval, Swati Jaiswal, Jayant Dewangan, H K Bora, Srikanta Kumar Rath, Jawahar Lal, Durga Prasad Mishra, Manish Kumar Chourasia
PLGA was functionalized with PEG and biotin using click chemistry to generate a biotin receptor targeted copolymer (Biotinylated-PEG-PLGA) which in turn was used to fabricate ultrafine nanoparticles (BPNP) of doxorubicin hydrochloride (DOX) for effective delivery in 4T1 cell induced breast cancer. However adequate entrapment of a hydrophilic bioactive like DOX in a hydrophobic polymer system made of PLGA is not usually possible. We therefore modified a conventional W/O/W emulsion method by utilizing ammonium chloride in the external phase to constrain DOX in dissolved polymer phase by supressing its inherent aqueous solubility as per common ion effect...
June 21, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28636336/a-mg-cp-with-in-situ-encapsulated-photochromic-guest-as-sensitive-fluorescence-sensor-for-fe-3-cr-3-ions-and-nitro-explosives
#18
Zhao-Feng Wu, Liao-Kuo Gong, Xiao-Ying Huang
Here we report a fluorescent magnesium coordination polymer (Mg-CP), namely, [CH3-dpb]2[Mg3(1,4-NDC)4(μ-H2O)2(CH3OH)(H2O)]·1.5H2O (1, 1,4-H2NDC = 1,4-naphthalene dicarboxylic acid, dpb = 1,4-bis(pyrid-4-yl)benzene). Compound 1 possesses a three-dimensional (3D) host-guest structure constructed by the 1,4-NDC linkers bridging the linear trinuclear secondary building units of [Mg3(COO)8(μ-H2O)2]. The dpb molecules were in situ reacted with CH3OH resulting in photochromic cations of [CH3-dpb](+) that acted as guests located in the channels parallel to the b-axis...
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28636310/sensing-mechanisms-in-the-redox-regulated-2fe-2s-cluster-containing-bacterial-transcriptional-factor-soxr
#19
Kazuo Kobayashi
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636236/assessment-of-silibinin-as-a-potential-antifungal-agent-and-investigation-of-its-mechanism-of-action
#20
Dae Gyu Yun, Dong Gun Lee
Silibinin, which is derived from Silybum marianum (milk thistle), has used as a traditional remedy for liver or biliary disorders and known to have superior antioxidant activity. In addition, silibinin was recently reported to have antifungal effect related to fungal apoptosis against Candida albicans and the interest in the therapeutic effect is increasing. In this study, we found another mode of antifungal action of silibinin and its antibiofilm activity on C. albicans. To investigate influence on fungal plasma membrane, propidium iodide and bis-(1, 3-dibutylbarbituric acid) trimethineoxonol [DiBAC4 (3)] assay were primarily carried out...
June 21, 2017: IUBMB Life
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