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https://www.readbyqxmd.com/read/28441545/targeted-mass-spectrometry-an-emerging-powerful-approach-to-unblock-the-bottleneck-in-phosphoproteomics
#1
REVIEW
Nerea Osinalde, Kerman Aloria, Miren J Omaetxebarria, Irina Kratchmarova
Following the rapid expansion of the proteomics field, the investigation of post translational modifications (PTM) has become extremely popular changing our perspective of how proteins constantly fine tune cellular functions. Reversible protein phosphorylation plays a pivotal role in virtually all biological processes in the cell and it is one the most characterized PTM up to date. During the last decade, the development of phosphoprotein/phosphopeptide enrichment strategies and mass spectrometry (MS) technology has revolutionized the field of phosphoproteomics discovering thousands of new site-specific phosphorylations and unveiling unprecedented evidence about their modulation under distinct cellular conditions...
April 17, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28441530/aubergine-controls-germline-stem-cell-self-renewal-and-progeny-differentiation-via-distinct-mechanisms
#2
Xing Ma, Xiujuan Zhu, Yingying Han, Benjamin Story, Trieu Do, Xiaoqing Song, Su Wang, Ying Zhang, Marco Blanchette, Madelaine Gogol, Kate Hall, Allison Peak, Perera Anoja, Ting Xie
Piwi family protein Aubergine (Aub) maintains genome integrity in late germ cells of the Drosophila ovary through Piwi-associated RNA-mediated repression of transposon activities. Although it is highly expressed in germline stem cells (GSCs) and early progeny, it remains unclear whether it plays any roles in early GSC lineage development. Here we report that Aub promotes GSC self-renewal and GSC progeny differentiation. RNA-iCLIP results show that Aub binds the mRNAs encoding self-renewal and differentiation factors in cultured GSCs...
April 24, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28441382/hedgehog-signalling-pathway-orchestrates-angiogenesis-in-triple-negative-breast-cancers
#3
Concetta Di Mauro, Roberta Rosa, Valentina D'Amato, Paola Ciciola, Alberto Servetto, Roberta Marciano, Roberta Clara Orsini, Luigi Formisano, Sandro De Falco, Valeria Cicatiello, Maurizio Di Bonito, Monica Cantile, Francesca Collina, Angela Chambery, Bianca Maria Veneziani, Sabino De Placido, Roberto Bianco
BACKGROUND: Several evidences suggest a marked angiogenic dependency in triple-negative breast cancer (TNBC) tumorigenesis and a potential sensitivity to anti-angiogenic agents. Herein, the putative role of Hedgehog (Hh) pathway in regulating TNBC-dependent angiogenesis was investigated. METHODS: Expression and regulation of the Hh pathway transcription factor glioma-associated oncogene homolog1 protein (GLI1) were studied on the endothelial compartment and on TNBC-initiated angiogenesis...
April 25, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28440894/chromatin-sumoylation-in-heat-stress-to-protect-pause-and-organise-sumo-stress-response-on-chromatin
#4
REVIEW
Einari A Niskanen, Jorma J Palvimo
Post-translational modifications, e.g. SUMO modifications (SUMOylation), provide a mechanism for swiftly changing a protein's activity. Various stress conditions trigger a SUMO stress response (SSR) - a stress-induced rapid change in the conjugation of SUMO to multiple proteins, which predominantly targets nuclear proteins. The SSR has been postulated to protect stressed cells by preserving the functionality of crucial proteins. However, it is unclear how it exerts its protective functions. Interestingly, heat stress (HS) increases SUMOylation of proteins at active promoters and enhancers...
April 25, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28440496/pu-1-serves-a-critical-role-in-the-innate-defense-against-aspergillus%C3%A2-fumigatus-via-dendritic-cell-associated-c-type-lectin-receptor-1-and-toll-like-receptors-2-and-4-in-thp-1-derived-macrophages
#5
Chenyang Liu, Min Wang, Wenkui Sun, Feng Cai, Shen Geng, Xin Su, Yi Shi
Aspergillus fumigatus (A. fumigatus) is one of the most common fungal pathogens of invasive pulmonary aspergillosis (IPA), which may be life threatening in immunocompromised individuals. The dendritic cell-associated C-type lectin receptor (Dectin-1), toll‑like receptor (TLR)-2 and TLR-4 are major pattern recognition receptors in alveolar macrophages that recognize A. fumigatus components. The PU.1 transcription factor is known to be important for the transcriptional control of these three receptors in mature macrophages...
April 24, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28439834/an-assessment-of-the-next-generation-of-animal-mirna-target-prediction-algorithms
#6
Thomas Bradley, Simon Moxon
The advent of genome-wide next-generation sequencing technologies has revolutionized the genomic and transcriptomic fields. New technologies also present an opportunity for greater discovery and understanding of post-transcriptional processes, in particular, translational inhibition of transcripts by miRBP (microRNA-RNA binding protein) complexes. Not only have novel methodologies been developed for the direct sequencing of RBP-bound RNA, but a new class of miRNA (microRNA) target prediction algorithms trained on this data has emerged...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439831/predicting-functional-microrna-mrna-interactions
#7
Zixing Wang, Yin Liu
MicroRNAs (miRNAs) are small RNA molecules that play key regulatory roles in general biological processes and disease pathogenesis. These small RNA molecules interact with their target mRNAs to induce mRNA degradation and/or inhibit the translation of mRNAs into proteins. Therefore, identifying miRNA targets is an essential step to fully understand the regulatory effects of miRNAs. Here, we describe a regularized regression approach that integrates the sequence information with the miRNA and mRNA expression profiles for detecting miRNA targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439830/peptide-based-isolation-of-argonaute-protein-complexes-using-ago-app
#8
Judith Hauptmann, Gunter Meister
Argonaute (Ago) proteins bind small RNAs such as microRNAs (miRNAs) or short interfering RNAs (siRNAs), which guide them to distinct mRNAs for post-transcriptional gene silencing. Mammalian miRNA-guided gene silencing pathways mainly lead to translational repression and mRNA destabilization. To facilitate these processes, Ago proteins bind members of the GW protein family, which form central interaction platforms for the recruitment of downstream effector proteins. GW proteins use tryptophane residues (W) to bind to the surface of Ago proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439740/synthetic-cold-inducible-promoter-enhances-recombinant-protein-accumulation-during-agrobacterium-mediated-transient-expression-in-nicotiana-excelsior-at-chilling-temperatures
#9
I M Gerasymenko, Y V Sheludko
OBJECTIVES: To exploit cold-inducible biochemical processes beneficial for foreign mRNA transcription, translation and storage, as well as protein product stability, during Agrobacterium-mediated transient expression. RESULTS: The efficiency of three different 5'-regulatory sequences to achieve transient expression of the GFP-based reporter gene under chilling conditions (6-8 °C since the 3rd day post inoculation) was compared. We studied the upstream sequences of a cold-inducible Arabidopsis thaliana cor15a gene, the core element of 35S CaMV promoter fused to the TMV omega 5'-UTR, and the synthetic promoter including the 35S core sequence and two binding sites for cold-inducible CBF transcription factors (P_DRE::35S)...
April 24, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28439717/negligible-effect-of-enos-palmitoylation-on-fatty-acid-regulation-of-contraction-in-ventricular-myocytes-from-healthy-and-hypertensive-rats
#10
Chun Li Jin, Yu Na Wu, Ji Hyun Jang, Zai Hao Zhao, Goo Taeg Oh, Sung Joon Kim, Yin Hua Zhang
S-palmitoylation is an important post-translational modification that affects the translocation and the activity of target proteins in a variety of cell types including cardiomyocytes. Since endothelial nitric oxide synthase (eNOS) is known to be palmitoylated and the activity of eNOS is essential in fatty acid-dependent β-oxidation in muscle, we aimed to test whether palmitoylation of eNOS is involved in palmitic acid (PA) regulation of left ventricular (LV) myocyte contraction from healthy (sham) and hypertensive (HTN) rats...
April 25, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28439563/mechanism-of-vps4-hexamer-function-revealed-by-cryo-em
#11
Min Su, Emily Z Guo, Xinqiang Ding, Yan Li, Jeffrey T Tarrasch, Charles L Brooks, Zhaohui Xu, Georgios Skiniotis
Vps4 is a member of AAA(+) ATPase (adenosine triphosphatase associated with diverse cellular activities) that operates as an oligomer to disassemble ESCRT-III (endosomal sorting complex required for transport III) filaments, thereby catalyzing the final step in multiple ESCRT-dependent membrane remodeling events. We used electron cryo-microscopy to visualize oligomers of a hydrolysis-deficient Vps4 (vacuolar protein sorting-associated protein 4) mutant in the presence of adenosine 5'-triphosphate (ATP). We show that Vps4 subunits assemble into an asymmetric hexameric ring following an approximate helical path that sequentially stacks substrate-binding loops along the central pore...
April 2017: Science Advances
https://www.readbyqxmd.com/read/28439276/transcriptome-comparison-reveals-the-adaptive-evolution-of-two-contrasting-ecotypes-of-zn-cd-hyperaccumulator-sedum-alfredii-hance
#12
Qianying Yang, M J I Shohag, Ying Feng, Zhenli He, Xiaoe Yang
Hyperaccumulating ecotype (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii Hance belong to the same species but exhibit contrasting characteristics regarding hyperaccumulation and hypertolerance to cadmium and zinc. The Illumina Hiseq 2500 platform was employed to sequence HE and NHE to study the genetic evolution of this contrasting trait. Greater than 90 million clean reads were obtained and 118,479/228,051 unigenes of HE/NHE were annotated based on seven existing databases. We identified 149,668/319,830 single nucleotide polymorphisms (SNPs) and 12,691/14,428 simple sequence repeats (SSRs) of HE/NHE...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439079/translation-but-not-transfection-limits-clinically-relevant-exogenous-mrna-based-induction-of-alpha-4-integrin-expression-on-human-mesenchymal-stem-cells
#13
Adam Nowakowski, Anna Andrzejewska, Johannes Boltze, Franziska Nitzsche, Li-Li Cui, Jukka Jolkkonen, Piotr Walczak, Barbara Lukomska, Miroslaw Janowski
Mesenchymal stem cells (MSCs) represent promising resource of cells for regenerative medicine in neurological disorders. However, efficient and minimally invasive methods of MSCs delivery to the brain still have to be developed. Intra-arterial route is very promising, but MSCs are missing machinery for diapedesis through blood-brain barrier. Thus, here we have tested a mRNA-based method to induce transient expression of ITGA4, an adhesion molecule actively involved in cell extravasation. We observed that transfection with an ITGA4-mRNA construct bearing a conventional cap analogue (7-methylguanosine) failed to produce ITGA4 protein, but exogenous ITGA4-mRNA was detected in transfected MSCs...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439035/the-regulation-function-and-detection-of-protein-acetylation-in-bacteria
#14
Valerie J Carabetta, Ileana M Cristea
N(ε)-lysine acetylation is now recognized as an abundant post-translational modification (PTM) that influences many essential biological pathways. Advancements in mass spectrometry-based proteomics have led to the discovery that bacteria contain hundreds of acetylated proteins, contrary to the prior notion of rare acetylation events in bacteria. Although the mechanisms that regulate protein acetylation are still not fully defined, it is understood that this modification is finely-tuned via both enzymatic and non-enzymatic mechanisms...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28439016/astrocytes-locally-translate-transcripts-in-their-peripheral-processes
#15
Kristina Sakers, Allison M Lake, Rohan Khazanchi, Rebecca Ouwenga, Michael J Vasek, Adish Dani, Joseph D Dougherty
Local translation in neuronal processes is key to the alteration of synaptic strength necessary for long-term potentiation, learning, and memory. Here, we present evidence that regulated de novo protein synthesis occurs within distal, perisynaptic astrocyte processes. Astrocyte ribosomal proteins are found adjacent to synapses in vivo, and immunofluorescent detection of peptide elongation in acute slices demonstrates robust translation in distal processes. We have also developed a biochemical approach to define candidate transcripts that are locally translated in astrocyte processes...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28438983/light-dependent-expression-of-a-na-h-exchanger-3-like-transporter-in-the-ctenidium-of-the-giant-clam-tridacna-squamosa-can-be-related-to-increased-h-excretion-during-light-enhanced-calcification
#16
Kum C Hiong, Anh H Cao-Pham, Celine Y L Choo, Mel V Boo, Wai P Wong, Shit F Chew, Yuen K Ip
Na(+)/H(+) exchangers (NHEs) regulate intracellular pH and ionic balance by mediating H(+) efflux in exchange for Na(+) uptake in a 1:1 stoichiometry. This study aimed to obtain from the ctenidium of the giant clam Tridacna squamosa (TS) the complete cDNA sequence of a NHE3-like transporter (TSNHE3), and to determine the effect of light exposure on its mRNA expression level and protein abundance therein. The coding sequence of TSNHE3 comprised 2886 bp, encoding 961 amino acids with an estimated molecular mass of 105...
April 2017: Physiological Reports
https://www.readbyqxmd.com/read/28438781/transporter-mediated-disposition-clinical-pharmacokinetics-and-cholestatic-potential-of-glyburide-and-its-primary-active-metabolites
#17
Rui Li, Yi-An Bi, Anna Vildhede, Renato J Scialis, Sumathy Mathialagan, Xin Yang, Lisa D Marroquin, Jian Lin, Manthena V S Varma
Glyburide is widely used for the treatment of type 2 diabetes mellitus. We studied the mechanisms involved in the disposition of glyburide and its pharmacologically active hydroxy metabolites, M1 and M2b; and evaluated their clinical pharmacokinetics and the potential role in glyburide-induced cholestasis employing physiologically based pharmacokinetic (PBPK) modeling. Transport studies of parent and metabolites in human hepatocytes and transfected cell systems imply hepatic uptake mediated by organic anion transporting polypeptides...
April 24, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/28438689/non-coding-rna-in-hepatocellular-carcinoma-mechanisms-biomarkers-and-therapeutic-targets
#18
REVIEW
Marcel Klingenberg, Akiko Matsuda, Sven Diederichs, Tushar Patel
The majority of the human genome is not translated into proteins but can be transcribed into RNA. Even though the resulting non-coding RNAs (ncRNAs) do not encode for proteins, they contribute to diseases such as cancer. Here, we review examples of the functions of ncRNAs in liver cancer and their potential use for the detection of liver cancer as well as for the treatment of liver cancer.
April 21, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28438633/structural-insights-into-the-interaction-of-coronavirus-papain-like-proteases-and-interferon-stimulated-gene-product-15-from-different-species
#19
Courtney M Daczkowski, John V Dzimianski, Jozlyn R Clasman, Octavia Goodwin, Andrew D Mesecar, Scott D Pegan
Severe Acute and Middle East Respiratory syndrome coronaviruses (SARS-CoV and MERS-CoV) encode multifunctional papain-like proteases (PLPs) that have the ability to process the viral polyprotein to facilitate RNA replication as well as antagonize the host innate-immune response. The latter function involves reversing post-translational modification of cellular proteins conjugated with either ubiquitin (Ub) or Ub-like interferon stimulated gene product 15 (ISG15). Ubiquitin is known to be highly conserved among eukaryotes but surprisingly ISG15 is highly divergent among animals...
April 21, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28438511/nitric-oxide-inhibits-the-mitochondrial-carnitine-acylcarnitine-carrier-through-reversible-s-nitrosylation-of-cysteine-136
#20
Annamaria Tonazzi, Nicola Giangregorio, Lara Console, Annalisa De Palma, Cesare Indiveri
S-nitrosylation of the mitochondrial Carnitine/Acylcarnitine transporter (CACT) has been investigated on the native and the recombinant proteins reconstituted in proteoliposomes, and on intact mitochondria. The widely-used NO-releasing compound, GSNO, strongly inhibited the antiport measured in proteoliposomes reconstituted with the native CACT from rat liver mitochondria or the recombinant rat CACT over-expressed in E. coli. Inhibition was reversed by the reducing agent dithioerithritol, indicating a reaction mechanism based on nitrosylation of Cys residues of the CACT...
April 21, 2017: Biochimica et Biophysica Acta
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