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https://www.readbyqxmd.com/read/28637316/incorporating-comparative-genomics-into-the-design-test-learn-cycle-of-microbial-strain-engineering
#1
Maria Sardi, Audrey P Gasch
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals, and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling, and regulatory rewiring have proven to significantly advance industrial strain engineering...
June 16, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#2
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28636825/a-new-mixed-all-atom-coarse-grained-model-application-to-melittin-aggregation-in-aqueous-solution
#3
Mee Y Shelley, Myvizhi Esai Selvan, Jun Zhao, Volodymyr Babin, Chenyi Liao, Jianing Li, John Clarence Shelley
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG) for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636682/excited-state-characterization-of-carbonyl-containing-carotenoids-a-comparison-between-single-and-multireference-descriptions
#4
Riccardo Spezia, Stefan Knecht, Benedetta Mennucci
Carotenoids can play multiple roles in biological photoreceptors thanks to their rich photophysics. In the present work, we have investigated six of the most common carbonyl containing carotenoids: echinenone, canthaxanthin, astaxanthin, fucoxanthin, capsanthin and capsorubin. Their excitation properties are investigated by means of a hybrid density functional theory (DFT) and multireference configuration interaction (MRCI) approach to elucidate the role of the carbonyl group: the bright transition is of ππ* character, as expected, but the presence of a C[double bond, length as m-dash]O moiety reduces the energy of nπ* transitions which may become closer to the ππ* transition, in particular as the conjugation chain decreases...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636670/identification-of-novel-small-molecules-that-inhibit-stat3-dependent-transcription-and-function
#5
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/28636654/characterization-of-human-fcrl4-positive-b-cells
#6
Michel Jourdan, Nicolas Robert, Maïlys Cren, Coraline Thibaut, Christophe Duperray, Alboukadel Kassambara, Michel Cogné, Karin Tarte, Bernard Klein, Jérôme Moreaux
FCRL4 is an immunoregulatory receptor that belongs to the Fc receptor-like (FCRL) family. In healthy individuals, FCRL4 is specifically expressed by memory B cells (MBCs) localized in sub-epithelial regions of lymphoid tissues. Expansion of FCRL4+ B cells has been observed in blood and other tissues in various infectious and autoimmune disorders. Currently, the mechanisms involved in pathological FCRL4+ B cell generation are actively studied, but they remain elusive. As in vivo FCRL4+ cells are difficult to access and to isolate, here we developed a culture system to generate in vitro FCRL4+ B cells from purified MBCs upon stimulation with soluble CD40 ligand and/or CpG DNA to mimic T-cell dependent and/or T-cell independent activation, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28636542/niaoduqing-granules-relieve-chronic-kidney-disease-symptoms-by-decreasing-renal-fibrosis-and-anemia
#7
Xu Wang, Suyun Yu, Qi Jia, Lichuan Chen, Jinqiu Zhong, Yanhong Pan, Peiliang Shen, Yin Shen, Siliang Wang, Zhonghong Wei, Yuzhu Cao, Yin Lu
NiaoDuQing (NDQ) granules, a traditional Chinese medicine, has been clinically used in China for over fourteen years to treat chronic kidney disease (CKD). To elucidate the mechanisms underlying the therapeutic benefits of NDQ, we designed an approach incorporating chemoinformatics, bioinformatics, network biology methods, and cellular and molecular biology experiments. A total of 182 active compounds were identified in NDQ granules, and 397 putative targets associated with different diseases were derived through ADME modelling and target prediction tools...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28636461/genice-a-novel-framework-for-gene-network-inference-by-clustering-exhaustive-search-and-multivariate-analysis
#8
Ricardo de Souza Jacomini, David Correa Martins-Jr, Felipe Leno da Silva, Anna Helena Reali Costa
Gene network (GN) inference from temporal gene expression data is a crucial and challenging problem in systems biology. Expression data sets usually consist of dozens of temporal samples, while networks consist of thousands of genes, thus rendering many inference methods unfeasible in practice. To improve the scalability of GN inference methods, we propose a novel framework called GeNICE, based on probabilistic GNs; the main novelty is the introduction of a clustering procedure to group genes with related expression profiles and to provide an approximate solution with reduced computational complexity...
June 21, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28636366/oxygenation-via-c-h-c-c-bond-activation-with-molecular-oxygen
#9
Yu-Feng Liang, Ning Jiao
The selective oxidation of organic molecules is a fundamentally important component of modern synthetic chemistry. In the past decades, direct oxidative C-H and C-C bond functionalization has proved to be one of the most efficient and straightforward methods to synthesize complex products from simple and readily available starting materials. Among these oxidative processes, the use of molecular oxygen as a green and sustainable oxidant has attracted considerable attention because of its highly atom-economical, abundant, and environmentally friendly characteristics...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636358/transferable-atom-centered-potentials-for-the-correction-of-basis-set-incompleteness-errors-in-density-functional-theory
#10
Alberto Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of non-covalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis-set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28636349/water-dynamics-from-the-surface-to-the-interior-of-a-supramolecular-nanostructure
#11
Julia H Ortony, Baofu Qiao, Christina J Newcomb, Timothy J Keller, Liam C Palmer, Elad Deiss-Yehiely, Monica Olvera de la Cruz, Songi Han, Samuel I Stupp
Water within and surrounding the structure of a biological system adopts context-specific dynamics that mediate virtually all of the events involved in the inner workings of a cell. These events range from protein folding and molecular recognition to the formation of hierarchical structures. Water dynamics are mediated by the chemistry and geometry of interfaces where water and biomolecules meet. Here we investigate experimentally and computationally the translational dynamics of vicinal water molecules within the volume of a supramolecular peptide nanofiber measuring 6...
June 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28636327/maldi-ms-guided-liquid-microjunction-extraction-for-ce-esi-ms-analysis-of-single-pancreatic-islet-cells
#12
Troy J Comi, Monika A Makurath, Marina C Philip, Stanislav S Rubakhin, Jonathan V Sweedler
The ability to characterize chemical heterogeneity in biological structures is essential to understanding cellular level function in both healthy and diseased states, but these variations remain difficult to assess using a single analytical technique. While mass spectrometry (MS) provides sufficient sensitivity to measure many analytes from volume-limited samples, each type of mass spectrometric analysis uncovers only a portion of the complete chemical profile of a single cell. Matrix-assisted laser desorp-tion/ionization (MALDI) MS and capillary electrophoresis electrospray ionization (CE-ESI)-MS are complementary analytical platforms frequently utilized for single cell analysis...
June 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28636294/-selective-therapeutic-de-escalation-in-early-stage-breast-cancer
#13
Aikaterini Liapi, Apostolos Sarivalasis, Wendy Jeanneret Sozzi, Loïc Lelièvre, Khalil Zaman
The survival of patients with breast cancer has improved considerably thanks to adjuvant radiotherapy and systemic treatments. Due to the potential adverse events associated with these treatments, a de-escalation effort was undertaken concerning surgery and more recently the adjuvant treatments. Conservative breast surgery and the avoidance of axillary dissection were possible for the majority of the patients without detrimental effect on survival. New radiotherapy techniques and the consideration of cancer biology allowed to better protect the peripheral organs and even to avoid treatment in certain low-risk patients...
May 17, 2017: Revue Médicale Suisse
https://www.readbyqxmd.com/read/28636123/sem-imaging-of-the-stimulatory-response-of-raw264-7-cells-against-porphyromonas-gingivalis-using-a-simple-technique-employing-new-conductive-materials
#14
Chisato Takahashi, Yoshiki Umemura, Ayako Naka, Hiromitsu Yamamoto
In the medical biology, it is essential to understand not only biological morphology but also the interaction between biological materials and agents. To study these, electron microscopy (EM) is often utilized. However, sample preparation techniques for EM require a high level of skill and a considerable time. Here, we conducted EM using a simple technique employing a conductive liquid, BEL-1, and compared the results with another simple technique employing an ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4 ])...
June 21, 2017: Journal of Biomedical Materials Research. Part B, Applied Biomaterials
https://www.readbyqxmd.com/read/28635639/immune-checkpoints-as-a-target-for-colorectal-cancer-treatment
#15
REVIEW
Alessandro Passardi, Matteo Canale, Martina Valgiusti, Paola Ulivi
Anti-tumor immunity is a new line of research for the treatment of patients with solid tumors. In this field, negative regulators of the immune system called immune checkpoints play a key role in limiting antitumor immunologic responses. For this reason, immune checkpoint-inhibiting agents, such as those directed against cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed death-1 receptor (PD1) and its ligand PD-L1, have been developed as antitumor drugs, producing interesting results in preclinical and clinical studies...
June 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28635617/the-dosimetric-impact-of-gadolinium-based-contrast-media-in-gbm-brain-patient-plans-for-a-mri-linac
#16
Syed Bilal Ahmad, Moti Raj Paudel, Arman Sarfehnia, Anthony Kim, Geordi Pang, Mark Ruschin, Arjun Sahgal, Brian M Keller
Dosimetric effects of gadolinium based contrast media (Gadovist) were evaluated for the Elekta MRI Linear accelerator (MRL) using the research version of Monaco treatment planning system (TPS). In order to represent a gadolinium uptake it was manually assigned to a phantom as well as to the Gross Tumour Volume (GTV) of 6 Glioblastoma Multiforme (GBM) patients. A preliminary estimate of dose enhancement, due to gadolinium, was performed using the phantom irradiated with a single beam. More complicated assessment was performed for the GBM patients using a 7 field IMRT technique...
June 21, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28635591/camoptimus-a-tool-for-exploiting-complex-adaptive-evolution-to-optimize-experiments-and-processes-in-biotechnology
#17
Ayca Cankorur-Cetinkaya, Joao M L Dias, Jana Kludas, Nigel K H Slater, Juho Rousu, Stephen G Oliver, Duygu Dikicioglu
Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners...
June 21, 2017: Microbiology
https://www.readbyqxmd.com/read/28635589/regulation-of-escherichia-coli-pathogenesis-by-alternative-sigma-factor-n
#18
James T Riordan, Avishek Mitra
σ(N) (also σ(54)) is an alternative sigma factor subunit of the RNA polymerase complex that regulates the expression of genes from many different ontological groups. It is broadly conserved in the Eubacteria with major roles in nitrogen metabolism, membrane biogenesis, and motility. σ(N) is encoded as the first gene of a five-gene operon including rpoN (σ(N)), ptsN, hpf, rapZ, and npr that has been genetically retained among species of Escherichia, Shigella, and Salmonella. In an increasing number of bacteria, σ(N) has been implicated in the control of genes essential to pathogenic behavior, including those involved in adherence, secretion, immune subversion, biofilm formation, toxin production, and resistance to both antimicrobials and biological stressors...
June 2017: EcoSal Plus
https://www.readbyqxmd.com/read/28635409/confronting-infertility-in-iranian-clients-a-grounded-theory
#19
Mitra Zandi, Eesa Mohammadi, Zohreh Vanaki, Marziyeh Shiva, Narges Bagheri Lankarani, Faezeh Zarei
The present study examined how infertile Iranian clients confront infertility. Research on infertility has confirmed the significance of a socio-cultural context in the formation of responses to infertility. This study used the grounded theory approach to explore the experiences of infertile individuals presenting at the Royan Institute in Iran from October 2013 to September 2014. Clients with infertility of at least two years in duration were recruited using purposive sampling followed by theoretical sampling...
February 10, 2017: Human Fertility: Journal of the British Fertility Society
https://www.readbyqxmd.com/read/28635367/in-vivo-and-in-vitro-depolymerizations-of-intracellular-medium-chain-length-poly-3-hydroxyalkanoates-produced-by-pseudomonas-putida-bet001
#20
Siti Nor Syairah Anis, Mohamad Suffian Mohamad Annuar, Khanom Simarani
In vivo and in vitro depolymerizations of intracellular medium-chain-length poly-3-hydroxyalkanoates (mcl-PHA) in Pseudomonas putida Bet001 grown on lauric acid was studied. Both processes were studied under optimum conditions for mcl-PHA depolymerization viz. 0.2 M Tris-HCl buffer, pH 9, ionic strength (I) = 0.2 M at 30 °C. For in vitro depolymerization studies, cell-free system was obtained from lysing bacterial cells suspension by ultrasonication at optimum conditions (frequency 37 kHz, 30% of power output, <25 (°)C for 120 minutes)...
June 21, 2017: Preparative Biochemistry & Biotechnology
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