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https://www.readbyqxmd.com/read/28107776/activity-based-probes-for-the-multicatalytic-proteasome
#1
REVIEW
David S Hewings, John A Flygare, Ingrid E Wertz, Matthew Bogyo
Proteasomes are multisubunit protease complexes responsible for degrading most intracellular proteins. In addition to removing damaged proteins, they regulate many important cellular processes through the controlled degradation of transcription factors, cell cycle regulators and enzymes. Eukaryotic proteasomes have three catalytic subunits, β1, β2 and β5, that each have different substrate specificities. Additionally, although we know that diverse cell types express proteasome variants with distinct activity and specificity profiles, the functions of these different pools of proteasomes are not fully understood...
January 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28107648/parp-1-controls-the-adipogenic-transcriptional-program-by-parylating-c-ebp%C3%AE-and-modulating-its-transcriptional-activity
#2
Xin Luo, Keun Woo Ryu, Dae-Seok Kim, Tulip Nandu, Carlos J Medina, Rebecca Gupte, Bryan A Gibson, Raymond E Soccio, Yonghao Yu, Rana K Gupta, W Lee Kraus
Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification of proteins mediated by PARP family members, such as PARP-1. Although PARylation has been studied extensively, few examples of definitive biological roles for site-specific PARylation have been reported. Here we show that C/EBPβ, a key pro-adipogenic transcription factor, is PARylated by PARP-1 on three amino acids in a conserved regulatory domain. PARylation at these sites inhibits C/EBPβ's DNA binding and transcriptional activities and attenuates adipogenesis in various genetic and cell-based models...
January 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28107482/a-circulating-microrna-signature-predicts-age-based-development-of-lymphoma
#3
Afshin Beheshti, Charles Vanderburg, J Tyson McDonald, Charusheila Ramkumar, Tatenda Kadungure, Hong Zhang, Ronald B Gartenhaus, Andrew M Evens
Extensive epidemiological data have demonstrated an exponential rise in the incidence of non-Hodgkin lymphoma (NHL) that is associated with increasing age. The molecular etiology of this remains largely unknown, which impacts the effectiveness of treatment for patients. We proposed that age-dependent circulating microRNA (miRNA) signatures in the host influence diffuse large B cell lymphoma (DLBCL) development. Our objective was to examine tumor development in an age-based DLBCL system using an inventive systems biology approach...
2017: PloS One
https://www.readbyqxmd.com/read/28107448/potential-of-endophytic-fungi-isolated-from-cotton-roots-for-biological-control-against-verticillium-wilt-disease
#4
Yuan Yuan, Hongjie Feng, Lingfei Wang, Zhifang Li, Yongqiang Shi, LiHong Zhao, Zili Feng, Heqin Zhu
Verticillium wilt is a soil-borne disease, and severely limits the development of cotton production. To investigate the role of endophytic fungi on Verticillium wilt, CEF-818 (Penicillium simplicissimum), CEF-714 (Leptosphaeria sp.), CEF-642 (Talaromyces flavus.) and CEF-193 (Acremonium sp.) isolated from cotton roots were used to assess their effects against cotton wilt disease caused by a defoliating V. dahliae strain Vd080. In the greenhouse, all treatments significantly reduced disease incidence and disease index, with the control efficacy ranging from 26% (CEF-642) to 67% (CEF-818) at 25 days (d) after inoculation...
2017: PloS One
https://www.readbyqxmd.com/read/28107365/parenclitic-network-analysis-of-methylation-data-for-cancer-identification
#5
Alexander Karsakov, Thomas Bartlett, Artem Ryblov, Iosif Meyerov, Mikhail Ivanchenko, Alexey Zaikin
We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of cancers and represented as parenclictic networks, wherein nodes correspond to genes, and edges are weighted according to pairwise variation from control group subjects. We demonstrate that for the 10 types of cancer under study, it is possible to obtain a high performance of binary classification between cancer-positive and negative samples based on network measures...
2017: PloS One
https://www.readbyqxmd.com/read/28106846/competition-between-methanogens-and-acetogens-in-biocathodes-a-comparison-between-potentiostatic-and-galvanostatic-control
#6
Sam D Molenaar, Pradip Saha, Annemerel R Mol, Tom H J A Sleutels, Annemiek Ter Heijne, Cees J N Buisman
Microbial electrosynthesis is a useful form of technology for the renewable production of organic commodities from biologically catalyzed reduction of CO₂. However, for the technology to become applicable, process selectivity, stability and efficiency need strong improvement. Here we report on the effect of different electrochemical control modes (potentiostatic/galvanostatic) on both the start-up characteristics and steady-state performance of biocathodes using a non-enriched mixed-culture inoculum. Based on our results, it seems that kinetic differences exist between the two dominant functional microbial groups (i...
January 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28106481/mir-320a-effectively-suppresses-lung-adenocarcinoma-cell-proliferation-and-metastasis-by-regulating-stat3-signals
#7
Qing Lv, Jin-Xia Hu, You-Jie Li, Ning Xie, Dan-Dan Song, Wei Zhao, Yun-Fei Yan, Bao-Sheng Li, Ping-Yu Wang, Shu-Yang Xie
MicroRNAs play important roles in tumorigenesis of various types of cancers. MiR-320a can inhibits cell proliferation of some cancers, but the biological roles of miR-320a in lung cancer need to be further studied. Here, we investigated the roles of miR-320a in suppressing the proliferation of lung adenocarcinoma cells. MiR-320a treatment was found to effectively suppresse LTEP-a-2 and A549 cell proliferation, and induce more apoptotic cells induced by irradiation compared with control treatment. Our results also showed that miR-320a, as a novel miRNA, directly regulated signal transducer and activator of transcription 3 (STAT3) and its signals, such as Bcl-2, Bax, and Caspase 3...
January 20, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28106357/possession-use-and-transfer-of-select-agents-and-toxins-biennial-review-of-the-list-of-select-agents-and-toxins-and-enhanced-biosafety-requirements-final-rule
#8
(no author information available yet)
In accordance with the Public Health Security and Bioterrorism Preparedness and Response Act of 2002 (the Bioterrorism Response Act), the Centers for Disease Control and Prevention (CDC) in the Department of Health and Human Services (HHS) has reviewed the list of biological agents and toxins that have the potential to pose a severe threat to public health and safety. Following the review, HHS has decided: Not to finalize the proposed changes to the list of select agents and toxins at this time; to finalize provisions to address toxin permissible limits and the inactivation of select agents; to finalize specific provisions to the section of the regulations addressing biosafety; and to clarify regulatory language concerning security, training, incident response, and records...
19, 2017: Federal Register
https://www.readbyqxmd.com/read/28106294/balancing-between-aging-and-cancer-molecular-genetics-meets-traditional-chinese-medicine
#9
Jing Liu, Lei Peng, Wenhui Huang, Zhiming Li, Jun Pan, Lei Sang, Siqian Lu, Jihong Zhang, Wanyi Li, Ying Luo
The biological consequences of cellular senescence and immortalization in aging and cancer are in conflict. Organisms have developed common cellular signaling pathways and surveillance mechanisms to control the processing of aging against tumorigenesis. The imbalance of any signals involved in this process may result in either premature aging or tumorigenesis and reduce the life span of the organism. In contrast, the balance between aging and tumorigenesis at a higher level (homeostatic-balance) may benefit the organism with tumor-free longevity...
January 20, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28106194/connectivity-pattern-modifies-excited-state-relaxation-dynamics-of-fluorophore-photoswitch-molecular-dyads
#10
F Schweighöfer, J Moreno, S Bobone, S Chiantia, A Herrmann, S Hecht, J Wachtveitl
In order to modulate the emission of BODIPY fluorophores, they were connected to a diarylethene (DAE) photoswitch via phenylene-ethynylene linkers of different lengths and orientations. The latter allowed for modulation of the electronic coupling in the prepared four BODIPY-DAE dyads, which were compared also to appropriate BODIPY and DAE model compounds by steady state as well as time-resolved spectroscopies. In their open isomers, all dyads show comparable luminescence behavior indicative of an unperturbed BODIPY fluorophore...
January 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28106081/shigatoxin-encoding-bacteriophage-%C3%AF-24b-modulates-bacterial-metabolism-to-raise-antimicrobial-tolerance
#11
G S Holt, J K Lodge, A J McCarthy, A K Graham, G Young, S H Bridge, A K Brown, M Veses-Garcia, C V Lanyon, A Sails, H E Allison, D L Smith
How temperate bacteriophages play a role in microbial infection and disease progression is not fully understood. They do this in part by carrying genes that promote positive evolutionary selection for the lysogen. Using Biolog phenotype microarrays and comparative metabolite profiling we demonstrate the impact of the well-characterised Shiga toxin-prophage ϕ24B on its Escherichia coli host MC1061. As a lysogen, the prophage alters the bacterial physiology by increasing the rates of respiration and cell proliferation...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106003/large-scale-self-assembly-of-uniform-submicron-silver-sulfide-material-driven-by-precise-pressure-control
#12
Juanjuan Qi, Ke Chen, Shuhao Zhang, Yun Yang, Lin Guo, Shihe Yang
The controllable self-assembly of nanosized building blocks into larger specific structures can provide an efficient method of synthesizing novel materials with excellent properties. The self-assembly of nanocrystals (NCs) by assisted means is becoming an extremely active area of research, because it provides a method of producing large-scale advanced functional materials with potential applications in the areas of energy, electronics, optics, and biologics. In this study, we applied an efficient strategy, namely, the use of ���pressure control��� to the assembly of silver sulfide (Ag2S) nanospheres (NSs) with a diameter of approximately 33 nm into large-scale, uniform Ag2S sub-microspheres (SMs) with a size of about 0...
January 20, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28105966/a-novel-approach-for-pathway-analysis-of-gwas-data-highlights-role-of-bmp-signaling-and-muscle-cell-differentiation-in-colorectal-cancer-susceptibility
#13
Aniket Mishra, Stuart MacGregor
Genome-wide association studies (GWAS) have revolutionized the field of gene mapping. As the GWAS field matures, it is becoming clear that for many complex traits, a proportion of the missing heritability is attributable to common variants of individually small effect. Detecting these small effects individually can be difficult, and statistical power would be increased if relevant variants could be grouped together for testing. Here, we propose a VEGAS2Pathway approach that aggregates association strength of individual markers into pre-specified biological pathways...
February 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28105938/the-influence-of-pro-longevity-gene-gclc-overexpression-on-the-age-dependent-changes-in-drosophila-transcriptome-and-biological-functions
#14
Alexey Moskalev, Mikhail Shaposhnikov, Ekaterina Proshkina, Alexey Belyi, Alexander Fedintsev, Svetlana Zhikrivetskaya, Zulfiya Guvatova, Asiya Sadritdinova, Anastasia Snezhkina, George Krasnov, Anna Kudryavtseva
BACKGROUND: Transcriptional changes that contribute to the organism's longevity and prevent the age-dependent decline of biological functions are not well understood. Here, we overexpressed pro-longevity gene encoding glutamate-cysteine ligase catalytic subunit (Gclc) and analyzed age-dependent changes in transcriptome that associated with the longevity, stress resistance, locomotor activity, circadian rhythmicity, and fertility. RESULTS: Here we reproduced the life extension effect of neuronal overexpression of the Gclc gene and investigated its influence on the age-depended dynamics of transcriptome and biological functions such as fecundity, spontaneous locomotor activity and circadian rhythmicity, as well as on the resistance to oxidative, proteotoxic and osmotic stresses...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105929/a-compendium-of-human-genes-regulating-feeding-behavior-and-body-weight-its-functional-characterization-and-identification-of-gwas-genes-involved-in-brain-specific-ppi-network
#15
Elena V Ignatieva, Dmitry A Afonnikov, Olga V Saik, Evgeny I Rogaev, Nikolay A Kolchanov
BACKGROUND: Obesity is heritable. It predisposes to many diseases. The objectives of this study were to create a compendium of genes relevant to feeding behavior (FB) and/or body weight (BW) regulation; to construct and to analyze networks formed by associations between genes/proteins; and to identify the most significant genes, biological processes/pathways, and tissues/organs involved in BW regulation. RESULTS: The compendium of genes controlling FB or BW includes 578 human genes...
December 22, 2016: BMC Genetics
https://www.readbyqxmd.com/read/28105728/invention-of-stimulus-responsive-peptide-bond-cleaving-residue-spr-and-its-application-to-chemical-biology-tools
#16
Akira Shigenaga, Jun Yamamoto, Taiki Kohiki, Tsubasa Inokuma, Akira Otaka
Elucidation of biological functions of peptides and proteins is essential for understanding peptide/protein-related biological events and developing drugs. Caged peptides and proteins that release a parent active peptide/protein by photo-irradiation have successfully been employed to elucidate the functions. Whereas the usual caged peptide/protein enables conversion of an inactive form to an active form (OFF-to-ON conversion) by photo-induced deprotection, photo-triggered main chain cleavage is reported to be applicable to ON-to-OFF conversion...
January 19, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28105684/bacterial-microcompartment-directed-polyphosphate-kinase-promotes-stable-polyphosphate-accumulation-in-e-coli
#17
Mingzhi Liang, Stefanie Frank, Heinrich Lünsdorf, Martin J Warren, Michael B Prentice
Processes for the biological removal of phosphate from wastewater rely on temporary manipulation of bacterial polyphosphate levels by phased environmental stimuli. In E. coli polyphosphate levels are controlled via the polyphosphate-synthesizing enzyme polyphosphate kinase (PPK1) and exopolyphosphatases (PPX and GPPA), and are temporarily enhanced by PPK1 overexpression and reduced by PPX overexpression. We hypothesised that partitioning PPK1 from cytoplasmic exopolyphosphatases would increase and stabilise E...
January 20, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28105603/resuscitation-fluid-composition-affects-hepatic-inflammation-in-a-murine-model-of-early-sepsis
#18
Amanda L Patrick, Peter M Grin, Nicole Kraus, Michelle Gold, Matthew Berardocco, Patricia C Liaw, Alison E Fox-Robichaud
BACKGROUND: Fluid resuscitation is a crucial therapy for sepsis, and the use of balanced fluids and/or isotonic albumin may improve patient survival. We have previously demonstrated that resuscitation with normal saline results in increased hepatic leukocyte recruitment in a murine model of sepsis. Given that clinical formulations of albumin are in saline, our objectives were to develop a novel balanced electrolyte solution specifically for sepsis and to determine if supplementing this solution with albumin would improve the inflammatory response in sepsis...
December 2017: Intensive Care Medicine Experimental
https://www.readbyqxmd.com/read/28105572/proteome-wide-identification-of-iron-binding-proteins-of-xanthomonas-translucens-pv-undulosa-focus-on-secretory-virulent-proteins
#19
Ankita Sharma, Dixit Sharma, Shailender Kumar Verma
Xanthomonas translucens pv. undulosa (Xtu) causes Bacterial Leaf Streak disease in the staple food crops such as wheat and barley. The survival strategies of pathogen and host are determined by the complex interactions occurring between the host plants and the pathogenic microbes. Iron binding proteins are important in the plant-microbe interactions as they are indulged in enzyme catalysis, virulence, metabolic and transport activities. In the presented study, we have identified that ~9.8% of Xtu proteome possess iron binding sequence motifs...
January 19, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28105473/recent-applications-of-the-combination-of-mesoporous-silica-nanoparticles-with-nucleic-acids-development-of-bioresponsive-devices-carriers-and-sensors
#20
REVIEW
Rafael R Castillo, Alejandro Baeza, María Vallet-Regí
The discovery and control of the biological roles mediated by nucleic acids have turned them into a powerful tool for the development of advanced biotechnological materials. Such is the importance of these gene-keeping biomacromolecules that even nanomaterials have succumbed to the claimed benefits of DNA and RNA. Currently, there could be found in the literature a practically intractable number of examples reporting the use of combination of nanoparticles with nucleic acids, so boundaries are demanded. Following this premise, this review will only cover the most recent and powerful strategies developed to exploit the possibilities of nucleic acids as biotechnological materials when in combination with mesoporous silica nanoparticles...
January 20, 2017: Biomaterials Science
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