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https://www.readbyqxmd.com/read/28231445/principles-of-systems-biology-no-14
#1
(no author information available yet)
This month: sage advice from phage to their offspring; systematic analyses of protein quality control, mitochondrial respiration, and woody biomass; a continental-scale experiment; and engineered protein tools galore.
February 22, 2017: Cell Systems
https://www.readbyqxmd.com/read/28193863/modular-electron-transport-chains-from-eukaryotic-organelles-function-to-support-nitrogenase-activity
#2
Jianguo Yang, Xiaqing Xie, Mingxuan Yang, Ray Dixon, Yi-Ping Wang
A large number of genes are necessary for the biosynthesis and activity of the enzyme nitrogenase to carry out the process of biological nitrogen fixation (BNF), which requires large amounts of ATP and reducing power. The multiplicity of the genes involved, the oxygen sensitivity of nitrogenase, plus the demand for energy and reducing power, are thought to be major obstacles to engineering BNF into cereal crops. Genes required for nitrogen fixation can be considered as three functional modules encoding electron-transport components (ETCs), proteins required for metal cluster biosynthesis, and the "core" nitrogenase apoenzyme, respectively...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28188893/ultra-deep-next-generation-mitochondrial-genome-sequencing-reveals-widespread-heteroplasmy-in-chinese-hamster-ovary-cells
#3
Paul S Kelly, Colin Clarke, Alan Costello, Craig Monger, Justine Meiller, Heena Dhiman, Nicole Borth, Michael J Betenbaugh, Martin Clynes, Niall Barron
Recent sequencing of the Chinese hamster ovary (CHO) cell and Chinese hamster genomes has dramatically advanced our ability to understand the biology of these mammalian cell factories. In this study, we focus on the powerhouse of the CHO cell, the mitochondrion. Utilizing a high-resolution next generation sequencing approach we sequenced the Chinese hamster mitochondrial genome for the first time and surveyed the mutational landscape of CHO cell mitochondrial DNA (mtDNA). Depths of coverage ranging from ~3,319X to 8,056X enabled accurate identification of low frequency mutations (>1%) revealing that mtDNA heteroplasmy is widespread in CHO cells...
February 7, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28187683/proteomics-profiling-of-chimeric-truncated-tissue-plasminogen-activator-producing-chinese-hamster-ovary-cells-cultivated-in-a-chemically-defined-medium-supplemented-with-protein-hydrolysates
#4
Bahareh Azarian, Seyedeh Matin Sajedin, Amin Azimi, Mozhgan Raigani, Behrouz Vaziri, Fatemeh Davami
Background: Culture media enrichment through the addition of protein hydrolysates is beneficial for achieving higher protein expression. Methods: In this study, designing the optimum mixture of four soy and casein-derived hydrolysates was successfully performed by design of experiment and specific productivity increased in all predicted combinations. Protein profile of recombinant CHO (rCHO) cells producing tissue plasminogen activator in a serum-free medium (SFM) supplemented with designed hydrolysate additives was compared to that of rCHO cells cultivated in SFM...
11, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28187082/harnessing-the-power-of-genetic-engineering-for-patients-with-mitochondrial-eye-diseases
#5
Patrick Yu-Wai-Man
No abstract text is available yet for this article.
March 2017: Journal of Neuro-ophthalmology: the Official Journal of the North American Neuro-Ophthalmology Society
https://www.readbyqxmd.com/read/28186127/optogenetic-control-of-cellular-forces-and-mechanotransduction
#6
Léo Valon, Ariadna Marín-Llauradó, Thomas Wyatt, Guillaume Charras, Xavier Trepat
Contractile forces are the end effectors of cell migration, division, morphogenesis, wound healing and cancer invasion. Here we report optogenetic tools to upregulate and downregulate such forces with high spatiotemporal accuracy. The technology relies on controlling the subcellular activation of RhoA using the CRY2/CIBN light-gated dimerizer system. We fused the catalytic domain (DHPH domain) of the RhoA activator ARHGEF11 to CRY2-mCherry (optoGEF-RhoA) and engineered its binding partner CIBN to bind either to the plasma membrane or to the mitochondrial membrane...
February 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28183602/a-biological-method-for-in-situ-synthesis-of-hydroxyapatite-coated-magnetite-nanoparticles-using-enterobacter-aerogenes-characterization-and-acute-toxicity-assessments
#7
Elham Ahmadzadeh, Farid Talebnia Rowshan, Morteza Hosseini
Hydroxyapatite (HA)-coated magnetite nanoparticles (MNPs) are being widely investigated for various applications in medical engineering and wastewater treatment. In this work, the MNPs were thoroughly coated by bacterial synthesized HA nanoparticles during biomineralization process using Enterobacter aerogenes. The resulting bacterial-induced precipitate was then calcined at 600°C and investigated with respect to structural characteristics, particle size and magnetic strength by XRD, FT-IR, SEM, EDS, TEM and VSM analyses...
April 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28170191/metabolomic-profiling-of-pompe-disease-induced-pluripotent-stem-cell-derived-cardiomyocytes-reveals-that-oxidative-stress-is-associated-with-cardiac-and-skeletal-muscle-pathology
#8
Yohei Sato, Hiroshi Kobayashi, Takashi Higuchi, Yohta Shimada, Hiroyuki Ida, Toya Ohashi
Pompe disease (PD) is a lysosomal storage disease that is caused by a deficiency of the acid α-glucosidase, which results in glycogen accumulation in the lysosome. The major clinical symptoms of PD include skeletal muscle weakness, respiratory failure, and cardiac hypertrophy. Based on its severity and symptom onset, PD is classified into infantile and late-onset forms. Lysosomal accumulation of glycogen can promote many types of cellular dysfunction, such as autophagic dysfunction, endoplasmic reticulum stress, and abnormal calcium signaling within skeletal muscle...
January 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28132834/human-ipsc-derived-neural-progenitors-are-an-effective-drug-discovery-model-for-neurological-mtdna-disorders
#9
Carmen Lorenz, Pierre Lesimple, Raul Bukowiecki, Annika Zink, Gizem Inak, Barbara Mlody, Manvendra Singh, Marcus Semtner, Nancy Mah, Karine Auré, Megan Leong, Oleksandr Zabiegalov, Ekaterini-Maria Lyras, Vanessa Pfiffer, Beatrix Fauler, Jenny Eichhorst, Burkhard Wiesner, Norbert Huebner, Josef Priller, Thorsten Mielke, David Meierhofer, Zsuzsanna Izsvák, Jochen C Meier, Frédéric Bouillaud, James Adjaye, Markus Schuelke, Erich E Wanker, Anne Lombès, Alessandro Prigione
Mitochondrial DNA (mtDNA) mutations frequently cause neurological diseases. Modeling of these defects has been difficult because of the challenges associated with engineering mtDNA. We show here that neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (iPSCs) retain the parental mtDNA profile and exhibit a metabolic switch toward oxidative phosphorylation. NPCs derived in this way from patients carrying a deleterious homoplasmic mutation in the mitochondrial gene MT-ATP6 (m.9185T>C) showed defective ATP production and abnormally high mitochondrial membrane potential (MMP), plus altered calcium homeostasis, which represents a potential cause of neural impairment...
January 25, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28126659/molecular-engineering-of-a-mitochondrial-targeting-two-photon-in-and-near-infrared-out-fluorescent-probe-for-gaseous-signal-molecules-h2s-in-deep-tissue-bioimaging
#10
Liyi Zhou, Danqing Lu, Qianqian Wang, Sihua Liu, Qinlu Lin, Hongyan Sun
Hydrogen sulfide (H2S), one of the biologically important gaseous signal molecules, plays an essential role in diverse normal biochemical functions and pathological processes. Herein, an efficient two-photon in and near-infrared out mitochondria-targeting dye has been designed, synthesized and characterized. It is easily synthesized by the condensation reaction (C˭C) of 4-hydroxybenzaldehyde and 6-(diethylamino)-1,2,3,4-tetrahydroxanthylium (mitochondria-targeting), which possesses large two-photon action absorption cross-section ~160g and high fluorescence quantum yield ~0...
May 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28122942/comparative-analysis-of-mitochondrial-n-termini-from-mouse-human-and-yeast
#11
Sarah E Calvo, Olivier Julien, Karl R Clauser, Hongying Shen, Kimberli J Kamer, James A Wells, Vamsi K Mootha
The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by a N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that while presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved including a length of ~20-60aa, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-termini of mature proteins that follows the N-end rule from bacteria...
January 25, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28114303/mfn1-structures-reveal-nucleotide-triggered-dimerization-critical-for-mitochondrial-fusion
#12
Yu-Lu Cao, Shuxia Meng, Yang Chen, Jian-Xiong Feng, Dong-Dong Gu, Bing Yu, Yu-Jie Li, Jin-Yu Yang, Shuang Liao, David C Chan, Song Gao
Mitochondria are double-membraned organelles with variable shapes influenced by metabolic conditions, developmental stage, and environmental stimuli. Their dynamic morphology is a result of regulated and balanced fusion and fission processes. Fusion is crucial for the health and physiological functions of mitochondria, including complementation of damaged mitochondrial DNAs and the maintenance of membrane potential. Mitofusins are dynamin-related GTPases that are essential for mitochondrial fusion. They are embedded in the mitochondrial outer membrane and thought to fuse adjacent mitochondria via combined oligomerization and GTP hydrolysis...
February 16, 2017: Nature
https://www.readbyqxmd.com/read/28107625/gold-nanoshell-mediated-remote-myotube-activation
#13
Attilio Marino, Satoshi Arai, Yanyan Hou, Andrea Degl'Innocenti, Valentina Cappello, Barbara Mazzolai, Young-Tae Chang, Virgilio Mattoli, Madoka Suzuki, Gianni Ciofani
Mild heat stimulation of muscle cells within the physiological range represents an intriguing approach for the modulation of their functions. In this work, photothermal conversion was exploited to remotely stimulate striated muscle cells by using gold nanoshells (NS) in combination with near-infrared (NIR) radiation. Temperature increments of approximately 5°C were recorded by using an intracellular fluorescent molecular thermometer and were demonstrated to efficiently induce myotube contraction. The mechanism at the base of this phenomenon was thoroughly investigated and was observed to be a Ca2+-independent event directly involving actin-myosin interactions...
January 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28088541/secretory-pathway-optimization-of-cho-producer-cells-by-co-engineering-of-the-mitosrna-1978-target-genes-cers2-and-tbc1d20
#14
Lisa A Pieper, Michaela Strotbek, Till Wenger, Martin Gamer, Monilola A Olayioye, Angelika Hausser
Chinese Hamster Ovary (CHO) cells are the most commonly used host for the production of biopharmaceuticals. Although transcription and translation engineering strategies have been employed to generate high-producer cell clones, the secretory pathway still remains a bottleneck in cellular productivity. In this study we show that ectopic expression of a human mitochondrial genome-encoded small RNA (mitosRNA-1978) in an IgG expressing CHO cell line strongly improved specific productivity by functioning in a microRNA-like fashion...
January 11, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28054019/validation-data-supporting-the-characterization-of-novel-copper-complexes-as-anticancer-agents
#15
Ceyda Acilan, Buse Cevatemre, Zelal Adiguzel, Didem Karakas, Engin Ulukaya, Nádia Ribeiro, Isabel Correia, João Costa Pessoa
Three copper(II) complexes, Cu(Sal-Gly)(phen), Cu(Sal-Gly)pheamine, Cu(Sal-Gly)phepoxy were synthesized and characterized for their anticancer properties and mechanism of action (Acilan et al., in press) [1]. Here, we provide supporting data on colon cancer cell lines complementing our previous findings in cervix cells. This paper also contains a data table for the fold changes and p-values of all genes analyzed in this study via a custom RT-qPCR array. All compounds induced DNA damage (based on 8-oxo-guanidine, ɣH2AX staining in cells) and apoptosis (based on elevated DNA condensation/fragmentation, Annexin V staining, caspase 3/7 activity and mitochondrial membrane depolarization) in HCT-116 colon cancer cells...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/28038913/rlj-rgd3-induces-apoptosis-via-the-mitochondrial-dependent-pathway-and-inhibits-adhesion-migration-and-invasion-of-human-heya8-cells-via-fak-pathway
#16
Qi Jiang, Qingwei Li, Jianmei Han, Meng Gou, Yuanyuan Zheng, Bowen Li, Rong Xiao, Jihong Wang
Ovarian carcinoma is a tumor derived from ovary, which brings relatively higher mortality rate among the fatal gynecological cancers. Recently, lots of studies have concentrated on the anti-tumor effects of Arg-Gly-Asp (RGD) motif containing peptides due to their integrin binding properties. In order to meet the criterion of genetic engineering drugs, a recombinant RGD toxin protein (rLj-RGD3) without a His-tag was cloned from the buccal glands of Lampetra japonica in the present study. After endotoxin removal, the His-tag removed rLj-RGD3 was shown to inhibit the proliferation of HeyA8 cells...
December 27, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28025274/mitochondrial-phylogenomics-resolves-the-global-spread-of-higher-termites-ecosystem-engineers-of-the-tropics
#17
Thomas Bourguignon, Nathan Lo, Jan Šobotník, Simon Y W Ho, Naeem Iqbal, Eric Coissac, Maria Lee, Martin M Jendryka, David Sillam-Dussès, Barbora Křížková, Yves Roisin, Theodore A Evans
The higher termites (Termitidae) are keystone species and ecosystem engineers. They have exceptional biomass and play important roles in decomposition of dead plant matter, in soil manipulation, and as the primary food for many animals, especially in the tropics. Higher termites are most diverse in rainforests, with estimated origins in the late Eocene (∼54 Ma), postdating the breakup of Pangaea and Gondwana when most continents became separated. Since termites are poor fliers, their origin and spread across the globe requires alternative explanation...
December 25, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28011589/maternal-engineered-nanomaterial-exposure-disrupts-progeny-cardiac-function-and-bioenergetics
#18
Quincy A Hathaway, Cody E Nichols, Danielle L Shepherd, Phoebe A Stapleton, Sarah L Mclaughlin, Janelle C Stricker, Stephanie L Rellick, Mark V Pinti, Alaeddin B Abukabda, Caroll R McBride, Jinghai Yi, Seth M Stine, Timothy R Nurkiewicz, John M Hollander
Nanomaterial production is expanding as new industrial and consumer applications are introduced. Nevertheless, the impacts of exposure to these compounds are not fully realized. The current study was designed to determine whether gestational nano-TiO2 exposure impacts cardiac and metabolic function of developing progeny. Pregnant Sprague Dawley rats were exposed to nano-TiO2 aerosols (~10 mg/m(3), 130 - 150 nm count median aerodynamic diameter) for 7-8 non-consecutive days beginning at gestational day 5-6. Physiological and bioenergetic effects on heart function and cardiomyocytes across three time points: fetal (gestational day 20), neonatal (4-10 days), and young adult (6-12 weeks) were evaluated...
December 23, 2016: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/27994461/biofabrication-of-a-novel-biomolecule-assisted-reduced-graphene-oxide-an-excellent-biocompatible-nanomaterial
#19
Xi-Feng Zhang, Sangiliyandi Gurunathan
Graphene has been shown much interest, both in academics and industry due to its extraordinary physical, chemical, and biological proprieties. It shows great promises in biotechnological and biomedical applications as an antibacterial and anticancer agent, nanocarrier, sensor, etc. However, many studies demonstrated the toxicity of graphene in several cell lines, which is an obstacle to its use in biomedical applications. In this study, to improve the biocompatibility of graphene, we used nicotinamide (NAM) as a reducing and stabilizing agent to catalyze the reduction of graphene oxide (GO) to reduced graphene oxide (rGO)...
2016: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/27987887/alginate-and-gelatin-based-bioactive-photocross-linkable-hybrid-materials-for-bone-tissue-engineering
#20
Joanna Lewandowska-Łańcucka, Katarzyna Mystek, Arn Mignon, Sandra Van Vlierberghe, Anna Łatkiewicz, Maria Nowakowska
The paper presents the synthesis, the physico-chemical and the biological properties of novel hybrid materials prepared from photo-crosslinked gelatin/alginate-based hydrogels and silica particles exhibiting potential for the regeneration of bone tissue. Both alginate and gelatin were functionalized with methacrylate and methacrylamide moieties, respectively to render them photo-crosslinkable. Submicron silica particles of two sizes were dispersed within three types of polymeric sols including alginate, gelatin, and gelatin/alginate blends, which were subsequently photo-crosslinked...
February 10, 2017: Carbohydrate Polymers
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