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https://www.readbyqxmd.com/read/28527179/making-time-conservation-of-biological-clocks-from-fungi-to-animals
#1
Jay C Dunlap, Jennifer J Loros
The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes...
May 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28526811/proteomic-analysis-of-cerebrospinal-fluid-from-children-with-central-nervous-system-tumors-identifies-candidate-proteins-relating-to-tumor-metastatic-spread
#2
Filippo Spreafico, Italia Bongarzone, Sara Pizzamiglio, Ruben Magni, Elena Taverna, Maida De Bortoli, Chiara M Ciniselli, Elena Barzanò, Veronica Biassoni, Alessandra Luchini, Lance A Liotta, Weidong Zhou, Michele Signore, Paolo Verderio, Maura Massimino
Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS)...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28526714/constans-imparts-dna-sequence-specificity-to-the-histone-fold-nf-yb-nf-yc-dimer
#3
Nerina Gnesutta, Roderick W Kumimoto, Swadhin Swain, Matteo Chiara, Chamindika Siriwardana, David Stephen Horner, Ben F Holt, Roberto Mantovani
NF-Y is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence-specificity. NF-YA shares a conserved domain with the CCT (CONSTANS, CONSTANS-LIKE, TOC1) proteins. We show that CONSTANS (CO/BBX1), a master flowering regulator, forms a trimer with Arabidopsis NF-YB2/NF-YC3 to efficiently bind the CORE element of the FT promoter. We term this complex NF-CO. Using saturation mutagenesis EMSAs and RNA-Seq profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site...
May 19, 2017: Plant Cell
https://www.readbyqxmd.com/read/28526069/xlf-mediated-nhej-activity-in-hepatocellular-carcinoma-therapy-resistance
#4
Sitian Yang, Xiao Qi Wang
BACKGROUND: DNA repair pathways are used by cancer cells to overcome many standard anticancer treatments, causing therapy resistance. Here, we investigated the role of XRCC4-like factor (XLF), a core member of the non-homologous end joining (NHEJ) repair pathway, in chemoresistance in hepatocellular carcinoma (HCC). METHODS: qRT-PCR analysis and western blotting were performed to detect expression levels of genes and proteins related to NHEJ. NHEJ repair capacity was assessed in vitro (cell-free) and in vivo by monitoring the activity of the NHEJ pathway...
May 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28525743/bromodomain-protein-brd4-is-a-transcriptional-repressor-of-autophagy-and-lysosomal-function
#5
Jun-Ichi Sakamaki, Simon Wilkinson, Marcel Hahn, Nilgun Tasdemir, Jim O'Prey, William Clark, Ann Hedley, Colin Nixon, Jaclyn S Long, Maria New, Tim Van Acker, Sharon A Tooze, Scott W Lowe, Ivan Dikic, Kevin M Ryan
Autophagy is a membrane-trafficking process that directs degradation of cytoplasmic material in lysosomes. The process promotes cellular fidelity, and while the core machinery of autophagy is known, the mechanisms that promote and sustain autophagy are less well defined. Here we report that the epigenetic reader BRD4 and the methyltransferase G9a repress a TFEB/TFE3/MITF-independent transcriptional program that promotes autophagy and lysosome biogenesis. We show that BRD4 knockdown induces autophagy in vitro and in vivo in response to some, but not all, situations...
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28525736/a-flick-of-the-tail-keeps-the-circadian-clock-in-line
#6
Rajesh Narasimamurthy, David M Virshup
Circadian clocks signal and adapt to an ever-changing world by juggling a panoply of transcriptional and post-translational modifications. In this issue of Molecular Cell, Gustafson et al. (2017) report an additional requirement for accurate timekeeping, a cis/trans conformational flicker in the transcriptional activation domain of the core clock protein BMAL1.
May 18, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28525579/modulation-of-cyclobutane-thymine-photodimer-formation-in-t11-tracts-in-rotationally-phased-nucleosome-core-particles-and-dna-minicircles
#7
Kesai Wang, John-Stephen A Taylor
Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggests that DNA bending causes the modulation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we have developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been rotationally phased with respect to the histone octamer by TG motifs...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525568/scenery-a-web-application-for-causal-network-reconstruction-from-cytometry-data
#8
Georgios Papoutsoglou, Giorgos Athineou, Vincenzo Lagani, Iordanis Xanthopoulos, Angelika Schmidt, Szabolcs Éliás, Jesper Tegnér, Ioannis Tsamardinos
Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525378/irf5-is-elevated-in-childhood-onset-sle-and-regulated-by-histone-acetyltransferase-and-histone-deacetylase-inhibitors
#9
Jin Shu, Ling Li, Lan-Bo Zhou, Jun Qian, Zhi-Dan Fan, Li-Li Zhuang, Lu-Lu Wang, Rui Jin, Hai-Guo Yu, Guo-Ping Zhou
Interferon regulatory factor 5 (IRF5) plays a critical role in the induction of type I interferon, proinflammatory cytokines and chemokines, and participates in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). However, the relationship between IRF5 and childhood-onset SLE remains elusive. In the present study, we demonstrated that levels of mRNA expression of IRF5, IFN-α, and Sp1 were significantly increased in childhood-onset SLE, as seen on quantitative real-time PCR, and the expression of Sp1 and IFN-α was positively correlated with IRF5...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28524357/double-caging-linker-for-and-type-fluorogenic-construction-of-protein-antibody-bioconjugates-and-in-situ-quantification
#10
Shiyong Liu, Guhuan Liu, Guohai Shi, Haoyue Sheng, Yanyan Jiang, Haojun Liang
We report on in situ fluorescent quantification of the conjugation efficiency between azide-terminated synthetic polymers/ imaging probes and thiol-functionalized antibodies/proteins/peptides, by utilizing a doubly caged profluorescent and heterodifunctional core molecule (C1) as the self-sorting bridging unit. Orthogonal dual 'click' coupling of C1 with azide- and thiol-functionalized precursors leads to highly fluorescent bioconjugates, whereas single click products of C1 remain essentially nonfluorescent...
May 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28523294/autophagy-in-aging-and-disease
#11
Mădălina Fîlfan, Raluca Elena Sandu, Alexandra Daniela Zăvăleanu, Andrei GreşiŢă, Daniela Gabriela Glăvan, Denissa Greta Olaru, Aurel Popa-Wagner
Autophagy is a catabolic degradation system used to destroy and recycle the unnecessary or damaged components of a cell. Autophagy is present at a basal level in all mammals and is regulated by some conditions, such as oxidative stress, starvation or hypoxia. In aged tissues, increased but also decreased expression of autophagy-specific proteins, Beclin 1, LC3, Atg5 and Atg7 has been reported. Likewise, it could be shown that the lifespan of yeast, nematodes and flies is prolonged by pharmacologically stimulated autophagy using exogenous administered spermidine...
2017: Romanian Journal of Morphology and Embryology, Revue Roumaine de Morphologie et Embryologie
https://www.readbyqxmd.com/read/28522430/the-drosophila-lin54-homolog-mip120-controls-two-aspects-of-oogenesis
#12
Mei-Hsin Cheng, Laura Andrejka, Paul J Vorster, Albert Hinman, Joseph S Lipsick
The conserved multi-protein MuvB core associates with the Myb oncoproteins and with the RB-E2F-DP tumor suppressor proteins in complexes that regulate cell proliferation, differentiation, and apoptosis. Drosophila Mip120, a homolog of LIN54, is a sequence-specific DNA-binding protein within the MuvB core. A mutant of Drosophila mip120 was previously shown to cause female and male sterility. We now show that Mip120 regulates two different aspects of oogenesis. First, in the absence of the Mip120 protein, egg chambers arrest during the transition from stage 7 to 8 with a failure of the normal program of chromosomal dynamics in the ovarian nurse cells...
May 18, 2017: Biology Open
https://www.readbyqxmd.com/read/28521775/genome-wide-association-study-of-subclinical-interstitial-lung-disease-in-mesa
#13
Ani Manichaikul, Xin-Qun Wang, Li Sun, Josée Dupuis, Alain C Borczuk, Jennifer N Nguyen, Ganesh Raghu, Eric A Hoffman, Suna Onengut-Gumuscu, Emily A Farber, Joel D Kaufman, Dan Rabinowitz, Karen D Hinckley Stukovsky, Steven M Kawut, Gary M Hunninghake, George R Washko, George T O'Connor, Stephen S Rich, R Graham Barr, David J Lederer
BACKGROUND: We conducted a genome-wide association study (GWAS) of subclinical interstitial lung disease (ILD), defined as high attenuation areas (HAA) on CT, in the population-based Multi-Ethnic Study of Atherosclerosis Study. METHODS: We measured the percentage of high attenuation areas (HAA) in the lung fields on cardiac CT scan defined as voxels with CT attenuation values between -600 and -250 HU. Genetic analyses were performed in MESA combined across race/ethnic groups: non-Hispanic White (n = 2,434), African American (n = 2,470), Hispanic (n = 2,065) and Chinese (n = 702), as well as stratified by race/ethnicity...
May 18, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28521419/expression-of-excision-repair-cross-complementation-group-1-and-class-iii-%C3%AE-tubulin-in-thymic-carcinoma
#14
Katsuhiro Okuda, Risa Oda, Ayumi Suzuki, Tsutomu Tatematsu, Hiroshi Haneda, Satoru Moriyama, Motoki Yano, Ryoichi Nakanishi
Thymic carcinoma is a rare mediastinum malignant tumor derived from thymic epithelial cells. With the exception of complete resection, an effective therapy has not been established to date for advanced or relapsed thymic carcinoma. The present study examined the protein expression of excision repair cross-complementation group 1 (ERCC1) and class III β-tubulin (TUBB3), which are consider to be indicators of the anticancer activity of platinum-based and taxane-based chemotherapy, respectively. The expression of ERCC1 and TUBB3 proteins was examined in 40 thymic carcinoma patients who underwent either surgical resection or core-needle biopsy...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28520987/proteosign-an-end-user-online-differential-proteomics-statistical-analysis-platform
#15
Georgios Efstathiou, Andreas N Antonakis, Georgios A Pavlopoulos, Theodosios Theodosiou, Peter Divanach, David C Trudgian, Benjamin Thomas, Nikolas Papanikolaou, Michalis Aivaliotis, Oreste Acuto, Ioannis Iliopoulos
Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment...
May 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28518128/an-in-vitro-caseum-binding-assay-that-predicts-drug-penetration-in-tuberculosis-lesions
#16
Jansy P Sarathy, Hsin-Pin Ho Liang, Danielle Weiner, Jacqueline Gonzales, Laura E Via, Véronique Dartois
The eradication of tuberculosis disease requires drug regimens that can penetrate the multiple layers of complex pulmonary lesions. Drug distribution in the caseous cores of cavities and lesions is especially crucial because they harbor subpopulations of drug-tolerant bacteria also commonly referred to as persisters. Existing methods for the measurement of drug penetration in tuberculosis lesions involve costly and time-consuming in vivo pharmacokinetic studies coupled to bioanalytical or imaging techniques...
May 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28516862/non-essential-mcm-related-proteins-mediate-a-response-to-dna-damage-in-the-archaeon-methanococcus-maripaludis
#17
Alison D Walters, James P J Chong
The single minichromosome maintenance (MCM) protein found in most archaea has been widely studied as a simplified model for the MCM complex that forms the catalytic core of the eukaryotic replicative helicase. Organisms of the order Methanococcales are unusual in possessing multiple MCM homologues. The Methanococcus maripaludis S2 genome encodes four MCM homologues, McmA-McmD. DNA helicase assays reveal that the unwinding activity of the three MCM-like proteins is highly variable despite sequence similarities and suggests additional motifs that influence MCM function are yet to be identified...
May 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28516782/exploring-site-specific-n-glycosylation-of-hek293-and-plant-produced-human-iga-isotypes
#18
Kathrin Göritzer, Daniel Maresch, Friedrich Altmann, Christian Obinger, Richard Strasser
The full potential of recombinant Immunoglobulin A as therapeutic antibody is not fully explored, owing to the fact that structure-function relationships of these extensively glycosylated proteins are not well understood. Here, monomeric IgA1, IgA2m(1) and IgA2m(2) variants of the anti-HER2 antibody (IgG1) trastuzumab were expressed in glyco-engineered Nicotiana benthamiana plants and in human HEK293-6E cells. All three IgA isotypes were purified and subjected to biophysical and biochemical characterization...
May 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28516122/two-electrode-voltage-clamp-recordings-in-xenopus-laevis-oocytes-reconstitution-of-abscisic-acid-activation-of-slac1-anion-channel-via-pyl9-aba-receptor
#19
Cun Wang, Jingbo Zhang, Julian I Schroeder
Two-Electrode Voltage-Clamp (TEVC) recording in Xenopus laevis oocytes provides a powerful method to investigate the functions and regulation of ion channel proteins. This approach provides a well-known tool to characterize ion channels or transporters expressed in Xenopus laevis oocytes. The plasma membrane of the oocyte is impaled by two microelectrodes, one for voltage sensing and the other one for current injection. Here we list a protocol that allows robust reconstitution of multi-component signaling pathways...
January 20, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28515296/hepatitis-c-virus-lipoviroparticles-hcv-lvp-assemble-in-the-endoplasmic-reticulum-er-and-bud-off-from-the-er-to-golgi-in-copii-vesicles
#20
Gulam H Syed, Mohsin Khan, Song Yang, Aleem Siddiqui
Hepatitis C virus (HCV) exists as a lipoprotein-virus hybrid lipoviroparticle (LVP). In vitro studies have demonstrated the importance of apolipoproteins in HCV secretion and infectivity leading to the notion that HCV co-opts the secretion of very-low density lipoprotein (VLDL) for its egress. However, our understanding of the mechanisms involved in virus particle assembly and egress, are still elusive. Biogenesis of VLDL particle occurs in the ER followed by subsequent lipidation in the ER and Golgi. Secretion of mature VLDL particles occurs through the Golgi secretory pathway...
May 17, 2017: Journal of Virology
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