Article added to library!
x
Pubchase is a service of protocols.io - free, open access, crowdsourced protocols repository. Explore protocols.
Sign in
Reset password
or connect with
Facebook
By signing in you are agreeing to our
Terms Of Service and Privacy Policy
Biochemistry
Caution Does Not Preclude Predictive and Testable Models of Cytoplasmic Incompatibility: A Reply to Shropshire et al.
Apr 17, 2019   Trends In Genetics : TIG
Beckmann JF, Bonneau M, Chen H, Hochstrasser M, Poinsot D, Merçot H, Weill M, Sicard M, Charlat S
Definitions and guidelines for research on antibiotic persistence.
Apr 13, 2019   Nature Reviews. Microbiology
Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B,   . . . . . .   , Storz G, Tan MW, Tenson T, Van Melderen L, Zinkernagel A
Definitions and guidelines for research on antibiotic persistence.
Apr 13, 2019
Nature Reviews. Microbiology
Increasing concerns about the rising rates of antibiotic therapy failure and advances in single-cell analyses have inspired a surge of research into antibiotic persistence. Bacterial persister cells represent a subpopulation of cells that can survive intensive antibiotic treatment without being resistant. Several approaches have emerged to define and measure persistence, and it is now time to agree on the basic definition of persistence and its relation to the other mechanisms by which bacteria survive exposure to bactericidal antibiotic treatments, such as antibiotic resistance, heteroresistance or tolerance. In this Consensus Statement, we provide definitions of persistence phenomena, distinguish between triggered and spontaneous persistence and provide a guide to measuring persistence. Antibiotic persistence is not only an interesting example of non-genetic single-cell heterogeneity, it may also have a role in the failure of antibiotic treatments. Therefore, it is our hope that the guidelines outlined in this article will pave the way for better characterization of antibiotic persistence and for understanding its relevance to clinical outcomes.
Living in future ocean acidification, physiological adaptive responses of the immune system of sea urchins resident at a CO2 vent system.
Apr 17, 2019   The Science Of The Total Environment
Migliaccio O, Pinsino A, Maffioli E, Smith AM, Agnisola C, Matranga V, Nonnis S, Tedeschi G, Byrne M, Gambi MC, Palumbo A
Living in future ocean acidification, physiological adaptive responses of the immune system of sea urchins resident at a CO2 vent system.
Apr 17, 2019
The Science Of The Total Environment
The effects of ocean acidification, a major anthropogenic impact on marine life, have been mainly investigated in laboratory/mesocosm experiments. We used the CO2 vents at Ischia as a natural laboratory to study the long-term effects of ocean acidification on the sea urchin Paracentrotus lividus population resident in low-pH (7.8 ± 0.2) compared to that at two control sites (pH 8.02 ± 0.00; 8.02 ± 0.01). The novelty of the present study is the analysis of the sea urchin immune cells, the sentinels of environmental stress responses, by a wide-ranging approach, including cell morphology, biochemistry and proteomics. Immune cell proteomics showed that 311 proteins were differentially expressed in urchins across sites with a general shift towards antioxidant processes in the vent urchins. The vent urchin immune cells showed higher levels of total antioxidant capacity, up-regulation of phagosome and microsomal proteins, enzymes of ammonium metabolism, amino-acid degradation, and modulation of carbon metabolism proteins. Lipid-hydroperoxides and nitric oxide levels were not different in urchins from the different sites. No differences in the coelomic fluid pH, immune cell composition, animal respiration, nitrogen excretion and skeletal mineralogy were observed. Our results reveal the phenotypic plasticity of the immune system of sea urchins adapted to life at vent site, under conditions commensurate with near-future ocean acidification projections.
Effect of plasma processing and storage on microparticle abundance, nitric oxide scavenging, and vasoactivity.
Apr 13, 2019   Transfusion
Rogers SC, Moynihan FT, McDonough R, Timm DD, Hovmand-Warner E, Frazier E, Thomas KA, Spinella PC, Doctor A
Effect of plasma processing and storage on microparticle abundance, nitric oxide scavenging, and vasoactivity.
Apr 13, 2019
Transfusion
BACKGROUND: We set out to define the impact of collection, processing, and storage on plasma product microparticle (MP) abundance, potential for nitric oxide (NO) scavenging, and vasoactivity. STUDY DESIGN AND METHODS: Three currently US licensed products were tested: liquid plasma (LP), fresh frozen plasma (FFP), and solvent detergent plasma (SDP), along with a product under development, spray-dried solvent detergent plasma (SD-SDP) with/without beads. Vasoactivity was assessed in vitro using rabbit aortic vascular rings; MP abundance was determined by flow cytometry; and NO scavenging capacity/rate was determined using a biochemical NO consumption assay. All samples were analyzed unprocessed and following centrifugation at two speeds (2,500× g to remove platelets, and 25,000× g to remove microparticles). RESULTS: Significant differences in vasoactivity were observed, with SD-SDP minus beads demonstrating the greatest constriction and FFP the lowest constriction response. All products exhibited the same total NO scavenging capacity; however, significant differences were observed in the maximal rate of scavenging, with SD-SDP minus beads and FFP reacting fastest and SDP the slowest. Across all products, platelet and microparticle depletion had no effect on vasoactivity or NO scavenging (total or rate). Microparticles (RBC derived) were found only in FFP and LP, with relative abundance (LP > FFP). Additionally, storage had no effect on total or RBC-derived MP abundance, NO scavenging, or vasoactivity. CONCLUSION: Although vasoactivity differed between plasma products, we did not find similar differences in either total or RBC-derived MP abundance or NO scavenging capacity/rate.
The role of cell adhesion in hematopoiesis and leukemogenesis.
Apr 13, 2019   Journal Of Cellular Physiology
Heath JL, Cohn GM, Zaidi SK, Stein GS
The role of cell adhesion in hematopoiesis and leukemogenesis.
Apr 13, 2019
Journal Of Cellular Physiology
The cells of the bone marrow microenvironment are emerging as important contributors and regulators of normal hematopoiesis. This microenvironment is perturbed during leukemogenesis, and evidence points toward a bidirectional communication between leukemia cells and the normal cells of the bone marrow, mediated by direct cell-cell contact as well as soluble factors. These interactions are increasingly appreciated to play a role in leukemogenesis and possibly in resistance to chemotherapy. In fact, several compounds that specifically target the bone marrow microenvironment, including inhibitors of cell adhesion, are being tested as adjuncts to leukemia therapy.
Osteocytic connexin 43 channels affect fracture healing.
Apr 16, 2019   Journal Of Cellular Physiology
Chen Y, Chen M, Xue T, Li G, Wang D, Shang P, Jiang JX, Xu H
Osteocytic connexin 43 channels affect fracture healing.
Apr 16, 2019
Journal Of Cellular Physiology
The cross-talk between cells is very critical for moving forward fracture healing in an orderly manner. Connexin (Cx) 43-formed gap junctions and hemichannels mediate the communication between adjacent cells and cells and extracellular environment. Loss of Cx43 in osteoblasts/osteocytes results in delayed fracture healing. For investigating the role of two channels in osteocytes in bone repair, two transgenic mouse models with Cx43 dominant negative mutants driven by a 10 kb-DMP1 promoter were generated: R76W (gap junctions are blocked, whereas hemichannels are promoted) and Δ130-136 (both gap junctions and hemichannels are blocked). R76W mice (promotion of hemichannels) showed a significant increase of new bone formation, whereas delayed osteoclastogenesis and healing was observed in Δ130-136 (impairment of gap junctions), but not in R76W mice (hemichannel promotion may recover the delay). These results suggest that gap junctions and hemichannels play some similar and cooperative roles in bone repair.
Intracellular Antimicrobial Peptides Targeting the Protein Synthesis Machinery.
Apr 13, 2019   Advances In Experimental Medicine And Biology
Graf M, Wilson DN
Intracellular Antimicrobial Peptides Targeting the Protein Synthesis Machinery.
Apr 13, 2019
Advances In Experimental Medicine And Biology
While antimicrobial peptides (AMPs) are well-known for their disruptive effects on bacterial membranes, the mechanism of many intracellular AMPs is still being elucidated. In the recent years, it has been demonstrated that the subclass of proline-rich AMPs (PrAMPs) can pass through the bacterial membrane and kill bacteria by inhibiting protein synthesis. PrAMPs are a product of the innate immune system and are secreted in response to bacterial infection. So far PrAMPs have been identified in many arthropods, such as beetles, wasps, and flies, as well as some mammals, such as sheep, cows, and goats. PrAMPs show high potency against Gram-negative bacteria, while exhibiting low toxicity in eukaryotes, suggesting that they may represent a promising avenue for the development of future antimicrobial agents to combat the increase of multidrug-resistant bacterial pathogens. Structural and biochemical data have revealed the PrAMP binding sites on the ribosome as well as insight into their mechanisms of action. While the binding site of all so far investigated PrAMPs is situated within nascent polypeptide exit tunnel, the mechanism of action is distinct between class I and II PrAMPs. Specifically, class I PrAMPs, such as Bac7, Onc112, pyrrhocoricin, and metalnikowin, block the delivery of aa-tRNA by EF-Tu to the ribosomal A-site, whereas the class II PrAMPs, such as apidaecin 1b and Api137, act during translation termination and inhibit protein synthesis by trapping of release factors on the 70S ribosome following hydrolysis of the nascent polypeptide chain.
The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.
Apr 13, 2019   Methods In Molecular Biology (Clifton, N.J.)
Stewart PA, Kuenzi BM, Mehta S, Kumar P, Johnson JE, Jagtap P, Griffin TJ, Haura EB
The Galaxy Platform for Reproducible Affinity Proteomic Mass Spectrometry Data Analysis.
Apr 13, 2019
Methods In Molecular Biology (Clifton, N.J.)
Affinity proteomics (AP-MS) is growing in importance for characterizing protein-protein interactions (PPIs) in the form of protein complexes and signaling networks. The AP-MS approach necessitates several different software tools, integrated into reproducible and accessible workflows. However, if the scientist (e.g., a bench biologist) lacks a computational background, then managing large AP-MS datasets can be challenging, manually formatting AP-MS data for input into analysis software can be error-prone, and data visualization involving dozens of variables can be laborious. One solution to address these issues is Galaxy, an open source and web-based platform for developing and deploying user-friendly computational pipelines or workflows. Here, we describe a Galaxy-based platform enabling AP-MS analysis. This platform enables researchers with no prior computational experience to begin with data from a mass spectrometer (e.g., peaklists in mzML format) and perform peak processing, database searching, assignment of interaction confidence scores, and data visualization with a few clicks of a mouse. We provide sample data and a sample workflow with step-by-step instructions to quickly acquaint users with the process.
Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond.
Apr 13, 2019   Methods In Molecular Biology (Clifton, N.J.)
Lund PJ, Kori Y, Zhao X, Sidoli S, Yuan ZF, Garcia BA
Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond.
Apr 13, 2019
Methods In Molecular Biology (Clifton, N.J.)
Lysine acetylation is an important posttranslational modification (PTM) that regulates the function of proteins by affecting their localization, stability, binding, and enzymatic activity. Aberrant acetylation patterns have been observed in numerous diseases, most notably cancer, which has spurred the development of potential therapeutics that target acetylation pathways. Mass spectrometry (MS) has become the most adopted tool not only for the qualitative identification of acetylation sites but also for their large-scale quantification. By using heavy isotope labeling in cell culture combined with MS, it is now possible to accurately quantify newly synthesized acetyl groups and other PTMs, allowing differentiation between dynamically regulated and steady-state modifications. Here, we describe MS-based protocols to identify acetylation sites and quantify acetylation rates on both proteins in general and in the special case of histones. In the experimental approach for the former, 13C-glucose and D3-acetate are used to metabolically label protein acetylation in cells with stable isotopes, thus allowing isotope incorporation to be tracked over time. After protein extraction and digestion, acetylated peptides are enriched via immunoprecipitation and then analyzed by MS. For histones, a similar metabolic labeling approach is performed, followed by acid extraction, derivatization with propionic anhydride, and trypsin digestion prior to MS analysis. The procedures presented may be adapted to investigate acetylation dynamics in a broad range of experimental contexts, including different cell types and stimulation conditions.
Next Generation Proteomics for Clinical Biomarker Detection Using SWATH-MS.
Apr 13, 2019   Methods In Molecular Biology (Clifton, N.J.)
Lin Q, Tan HT, Chung MCM
Next Generation Proteomics for Clinical Biomarker Detection Using SWATH-MS.
Apr 13, 2019
Methods In Molecular Biology (Clifton, N.J.)
The technology of "sequential windowed acquisition of all theoretical fragment ion spectra," known as SWATH-MS, is rapidly gaining popularity as a next generation proteomics technology for comprehensive proteome quantitation. In this chapter, we describe the use of SWATH-MS as a label-free quantitative technique in a proteomics study to identify novel serological biomarker for colorectal cancer. We compared the secreted glycoprotein profiles (glyco-secretomes) enriched from the colon adenocarcinoma cell line HCT-116 and its metastatic derivative, E1, and observed that laminin β-1 (LAMB1) was oversecreted in E1 cells. This novel oversecretion of LAMB1 was validated in colorectal cancer patient serum samples, and ROC analyses showed that LAMB1 performed better than carcinoembryonic antigen (CEA) as a clinical diagnostic biomarker for colorectal cancer. We focus here on the sample preparation methodology and data processing workflow for SWATH-MS studies.
The deubiquitinase OTUD5 regulates Ku80 stability and non-homologous end joining.
Apr 13, 2019   Cellular And Molecular Life Sciences : CMLS
Li F, Sun Q, Liu K, Han H, Lin N, Cheng Z, Cai Y, Tian F, Mao Z, Tong T, Zhao W
The deubiquitinase OTUD5 regulates Ku80 stability and non-homologous end joining.
Apr 13, 2019
Cellular And Molecular Life Sciences : CMLS
The ability of cells to repair DNA double-strand breaks (DSBs) is important for maintaining genome stability and eliminating oncogenic DNA lesions. Two distinct and complementary pathways, non-homologous end joining (NHEJ) and homologous recombination (HR), are employed by mammalian cells to repair DNA DSBs. Each pathway is tightly controlled in response to increased DSBs. The Ku heterodimer has been shown to play a regulatory role in NHEJ repair. Ku80 ubiquitination contributes to the selection of a DSB repair pathway by causing the removal of Ku heterodimers from DSB sites. However, whether Ku80 deubiquitination also plays a role in regulating DSB repair is unknown. To address this question, we performed a comprehensive study of the deubiquitinase specific for Ku80, and our study showed that the deubiquitinase OTUD5 serves as an important regulator of NHEJ repair by increasing the stability of Ku80. Further studies revealed that OTUD5 depletion impaired NHEJ repair, and hence reduced overall DSB repair. Furthermore, OTUD5-depleted cells displayed excess end resection; as a result, HR repair was facilitated by OTUD5 depletion during the S/G2 phase. In summary, our study demonstrates that OTUD5 is a specific deubiquitinase for Ku80 and establishes OTUD5 as an important and positive regulator of NHEJ repair.
Contrasting paternal and maternal genetic histories of Thai and Lao populations.
Apr 13, 2019   Molecular Biology And Evolution
Kutanan W, Kampuansai J, Srikummool M, Brunelli A, Ghirotto S, Arias L, Macholdt E, Hübner A, Schröder R, Stoneking M
Contrasting paternal and maternal genetic histories of Thai and Lao populations.
Apr 13, 2019
Molecular Biology And Evolution
The human demographic history of Mainland Southeast Asia (MSEA) has not been well-studied; in particular there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males, and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major MSEA families: Austroasiatic (AA), Tai-Kadai (TK) and Sino-Tibetan (ST). Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* (O-M95*) and O2a* (O-M324*)) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyse complete mtDNA genome sequences published previously from the same groups, and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of post-marital residence pattern on genetic diversity in patrilocal vs. matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 kya), with two later major male-specific expansions during the Neolithic period (∼4-5 kya) and the Bronze/Iron Age (∼2.0-2.5 kya). These two later expansions are characteristic of the modern AA and TK groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion and cultural diffusion) of major Thai groups and find different results from mtDNA simulations, supporting contrasting male and female genetic histories.
Nongenetic optical neuromodulation with silicon-based materials.
Apr 13, 2019   Nature Protocols Add nature.com free-link Cancel
Jiang Y, Parameswaran R, Li X, Carvalho-de-Souza JL, Gao X, Meng L, Bezanilla F, Shepherd GMG, Tian B
Nongenetic optical neuromodulation with silicon-based materials.
Apr 13, 2019
Nature Protocols
Optically controlled nongenetic neuromodulation represents a promising approach for the fundamental study of neural circuits and the clinical treatment of neurological disorders. Among the existing material candidates that can transduce light energy into biologically relevant cues, silicon (Si) is particularly advantageous due to its highly tunable electrical and optical properties, ease of fabrication into multiple forms, ability to absorb a broad spectrum of light, and biocompatibility. This protocol describes a rational design principle for Si-based structures, general procedures for material synthesis and device fabrication, a universal method for evaluating material photoresponses, detailed illustrations of all instrumentation used, and demonstrations of optically controlled nongenetic modulation of cellular calcium dynamics, neuronal excitability, neurotransmitter release from mouse brain slices, and brain activity in the mouse brain in vivo using the aforementioned Si materials. The entire procedure takes ~4-8 d in the hands of an experienced graduate student, depending on the specific biological targets. We anticipate that our approach can also be adapted in the future to study other systems, such as cardiovascular tissues and microbial communities.
Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7.
Apr 13, 2019   Biophysical Journal
De Bruyn P, Hadži S, Vandervelde A, Konijnenberg A, Prolič-Kalinšek M, Sterckx YG, Sobott F, Lah J, Van Melderen L, Loris R
Thermodynamic Stability of the Transcription Regulator PaaR2 from Escherichia coli O157:H7.
Apr 13, 2019
Biophysical Journal
PaaR2 is a putative transcription regulator encoded by a three-component parDE-like toxin-antitoxin module from Escherichia coli O157:H7. Although this module's toxin, antitoxin, and toxin-antitoxin complex have been more thoroughly investigated, little remains known about its transcription regulator PaaR2. Using a wide range of biophysical techniques (circular dichroism spectroscopy, size-exclusion chromatography-multiangle laser light scattering, dynamic light scattering, small-angle x-ray scattering, and native mass spectrometry), we demonstrate that PaaR2 mainly consists of α-helices and displays a concentration-dependent octameric build-up in solution and that this octamer contains a global shape that is significantly nonspherical. Thermal unfolding of PaaR2 is reversible and displays several transitions, suggesting a complex unfolding mechanism. The unfolding data obtained from spectroscopic and calorimetric methods were combined into a unifying thermodynamic model, which suggests a five-state unfolding trajectory. Furthermore, the model allows the calculation of a stability phase diagram, which shows that, under physiological conditions, PaaR2 mainly exists as a dimer that can swiftly oligomerize into an octamer depending on local protein concentrations. These findings, based on a thorough biophysical and thermodynamic analysis of PaaR2, may provide important insights into biological function such as DNA binding and transcriptional regulation.
Early impairments in the retina of rats fed with high fructose/high fat diet are associated with glucose metabolism deregulation but not dyslipidaemia.
Apr 13, 2019   Scientific Reports
Vidal E, Lalarme E, Maire MA, Febvret V, Grégoire S, Gambert S, Acar N, Bretillon L
Early impairments in the retina of rats fed with high fructose/high fat diet are associated with glucose metabolism deregulation but not dyslipidaemia.
Apr 13, 2019
Scientific Reports
Way of life changes such as high consumption of processed foods rich in fat and sugar and sedentary lifestyle are associated with the increasing prevalence of metabolic syndrome (MetS) that affects about 35% in the American population. MetS is the main risk factor for diabetes mellitus, which is associated with vascular changes in the retina. However, the early consequences of MetS in the retina are not well described. We therefore aimed at characterizing the early effects of a high fructose and high fat diet (HFHF) on the function and structure of the rat retina, and evaluate the associations with metabolic changes. Brown Norway rats of 6 weeks of age were fed for 8 days, 5 weeks or 13 weeks with HFHF diet, or a standard chow. After only 4 weeks of this diet, rats exhibited a reduction in cone photoreceptor sensitivity to light. Moreover, we observed that MetS significantly exacerbated laser-induced choroidal neovascularization by 72% and 67% 2 weeks and 3 weeks post laser treatment, respectively. These retinal abnormalities were associated with deregulation of glucose metabolism but not lipid metabolism. These data showed retinal modifications in HFHF-induced MetS in the rat, at very early stage of the disease.
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.
Apr 13, 2019   Scientific Reports
Mitkowski P, Jagielska E, Nowak E, Bujnicki JM, Stefaniak F, Niedziałek D, Bochtler M, Sabała I
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain.
Apr 13, 2019
Scientific Reports
Staphylococcus simulans lysostaphin cleaves pentaglycine cross-bridges between stem peptides in the peptidoglycan of susceptible staphylococci, including S. aureus. This enzyme consists of an N-terminal catalytic domain and a cell wall binding domain (SH3b), which anchors the protein to peptidoglycan. Although structures of SH3bs from lysostaphin are available, the binding modes of peptidoglycan to these domains are still unclear. We have solved the crystal structure of the lysostaphin SH3b domain in complex with a pentaglycine peptide representing the peptidoglycan cross-bridge. The structure identifies a groove between β1 and β2 strands as the pentaglycine binding site. The structure suggests that pentaglycine specificity of the SH3b arises partially directly by steric exclusion of Cβ atoms in the ligand and partially indirectly due to the selection of main chain conformations that are easily accessible for glycine, but not other amino acid residues. We have revealed further interactions of SH3b with the stem peptides with the support of bioinformatics tools. Based on the structural data we have attempted engineering of the domain specificity and have investigated the relevance of the introduced substitutions on the domain binding and specificity, also in the contexts of the mature lysostaphin and of its bacteriolytic activity.
Development of a Synthetic 3-ketosteroid Δ1-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells.
Apr 13, 2019   Scientific Reports
D'Arcy BM, Swingle MR, Schambeau L, Pannell L, Prakash A, Honkanen RE
Development of a Synthetic 3-ketosteroid Δ1-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells.
Apr 13, 2019
Scientific Reports
Cholesterol is an essential component of membranes, which is acquired by cells via receptor-mediated endocytosis of lipoproteins or via de novo synthesis. In specialized cells, anabolic enzymes metabolize cholesterol, generating steroid hormones or bile acids. However, surplus cholesterol cannot be catabolized due to the lack of enzymes capable of degrading the cholestane ring. The inability to degrade cholesterol becomes evident in the development and progression of cardiovascular disease, where the accumulation of cholesterol/cholesteryl-esters in macrophages can elicit a maladaptive immune response leading to the development and progression of atherosclerosis. The discovery of cholesterol catabolic pathways in Actinomycetes led us to the hypothesis that if enzymes enabling cholesterol catabolism could be genetically engineered and introduced into human cells, the atherosclerotic process may be prevented or reversed. Comparison of bacterial enzymes that degrade cholesterol to obtain carbon and generate energy with the action of human enzymes revealed that humans lack a 3-ketosteroid Δ1-dehydrogenase (Δ1-KstD), which catalyzes the C-1 and C-2 desaturation of ring A. Here we describe the construction, heterologous expression, and actions of a synthetic humanized Δ1-KstD expressed in Hep3B and U-937 cells, providing proof that one of three key enzymes required for cholesterol ring opening can be functionally expressed in human cells.
Changes in the Canine Plasma Lipidome after Short- and Long-Term Excess Glucocorticoid Exposure.
Apr 13, 2019   Scientific Reports
Sieber-Ruckstuhl NS, Burla B, Spoerel S, Schmid F, Venzin C, Cazenave-Gassiot A, Bendt AK, Torta F, Wenk MR, Boretti FS
Changes in the Canine Plasma Lipidome after Short- and Long-Term Excess Glucocorticoid Exposure.
Apr 13, 2019
Scientific Reports
Glucocorticoids (GCs) are critical regulators of metabolic control in mammals and their aberrant function has been linked to several pathologies. GCs are widely used in human and veterinary clinical practice as potent anti-inflammatory and immune suppressive agents. Dyslipidaemia is a frequently observed consequence of GC treatment, typified by increased lipolysis, lipid mobilization, liponeogenesis, and adipogenesis. Dogs with excess GC show hyperlipidaemia, hypertension, and a higher risk of developing type 2 diabetes mellitus, but the risk of developing atherosclerotic lesions is low as compared to humans. This study aimed to examine alterations in the canine plasma lipidome in a model of experimentally induced short-term and long-term GC excess. Both treatments led to significant plasma lipidome alterations, which were more pronounced after long-term excess steroid exposure. In particular, monohexosylceramides, phosphatidylinositols, ether phosphatidylcholines, acyl phosphatidylcholines, triacylglycerols and sphingosine 1-phosphates showed significant changes. The present study highlights the hitherto unknown effects of GCs on lipid metabolism, which will be important in the further elucidation of the role and function of GCs as drugs and in metabolic and cardiovascular diseases.
Altered steady state and activity-dependent de novo protein expression in fragile X syndrome.
Apr 17, 2019   Nature Communications
Bowling H, Bhattacharya A, Zhang G, Alam D, Lebowitz JZ,   . . . . . .   , Sharp K, Kirshenbaum K, Berry-Kravis E, Neubert TA, Klann E
Altered steady state and activity-dependent de novo protein expression in fragile X syndrome.
Apr 17, 2019
Nature Communications
Whether fragile X mental retardation protein (FMRP) target mRNAs and neuronal activity contributing to elevated basal neuronal protein synthesis in fragile X syndrome (FXS) is unclear. Our proteomic experiments reveal that the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation, but the proteins expressed differ under these conditions. Several altered proteins, including Hexokinase 1 and Ras, also are expressed in the blood of FXS model mice and pharmacological treatments previously reported to ameliorate phenotypes modify their abundance in blood. In addition, plasma levels of Hexokinase 1 and Ras differ between FXS patients and healthy volunteers. Our data suggest that brain-based de novo proteomics in FXS model mice can be used to find altered expression of proteins in blood that could serve as disease-state biomarkers in individuals with FXS.
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis.
Apr 16, 2019   Nature Communications
Yan W, Chen D, Schumacher J, Durantini D, Engelhorn J, Chen M, Carles CC, Kaufmann K
Dynamic control of enhancer activity drives stage-specific gene expression during flower morphogenesis.
Apr 16, 2019
Nature Communications
Enhancers are critical for developmental stage-specific gene expression, but their dynamic regulation in plants remains poorly understood. Here we compare genome-wide localization of H3K27ac, chromatin accessibility and transcriptomic changes during flower development in Arabidopsis. H3K27ac prevalently marks promoter-proximal regions, suggesting that H3K27ac is not a hallmark for enhancers in Arabidopsis. We provide computational and experimental evidence to confirm that distal DNase І hypersensitive sites are predictive of enhancers. The predicted enhancers are highly stage-specific across flower development, significantly associated with SNPs for flowering-related phenotypes, and conserved across crucifer species. Through the integration of genome-wide transcription factor (TF) binding datasets, we find that floral master regulators and stage-specific TFs are largely enriched at developmentally dynamic enhancers. Finally, we show that enhancer clusters and intronic enhancers significantly associate with stage-specific gene regulation by floral master TFs. Our study provides insights into the functional flexibility of enhancers during plant development, as well as hints to annotate plant enhancers.
Modulation of asymmetric cell division as a mechanism to boost CD8+ T cell memory.
Apr 13, 2019   Science Immunology
Borsa M, Barnstorf I, Baumann NS, Pallmer K, Yermanos A, Gräbnitz F, Barandun N, Hausmann A, Sandu I, Barral Y, Oxenius A
Modulation of asymmetric cell division as a mechanism to boost CD8+ T cell memory.
Apr 13, 2019
Science Immunology
Asymmetric partitioning of fate determinants is a mechanism that contributes to T cell differentiation. However, it remains unclear whether the ability of T cells to divide asymmetrically is influenced by their differentiation state, as well as whether enforcing asymmetric cell division (ACD) rates would have an impact on T cell differentiation and memory formation. Using the murine LCMV infection model, we established a correlation between cell stemness and the ability of CD8+ T cells to undergo ACD. Transient mTOR inhibition was proven to increase ACD rates in naïve and memory cells and to install this ability in exhausted CD8+ T cells. Functionally, enforced ACD correlated with increased memory potential, leading to more efficient recall response and viral control upon acute or chronic LCMV infection. Moreover, transient mTOR inhibition also increased ACD rates in human CD8+ T cells. Transcriptional profiling revealed that progenies emerging from enforced ACD exhibited more pronounced early memory signatures, which functionally endowed these cells with better survival in the absence of antigen exposure and more robust homing to secondary lymphoid organs, providing critical access to survival niches. Our data provide important insights into how ACD can improve long-term survival and function of T cells and open new perspectives for vaccination and adoptive T cell transfer therapies.
Regulation of death receptor signaling by the autophagy protein TP53INP2.
Apr 13, 2019   The EMBO Journal
Ivanova S, Polajnar M, Narbona-Perez AJ, Hernandez-Alvarez MI, Frager P, Slobodnyuk K, Plana N, Nebreda AR, Palacin M, Gomis RR, Behrends C, Zorzano A
Regulation of death receptor signaling by the autophagy protein TP53INP2.
Apr 13, 2019
The EMBO Journal
TP53INP2 positively regulates autophagy by binding to Atg8 proteins. Here, we uncover a novel role of TP53INP2 in death-receptor signaling. TP53INP2 sensitizes cells to apoptosis induced by death receptor ligands. In keeping with this, TP53INP2 deficiency in cultured cells or mouse livers protects against death receptor-induced apoptosis. TP53INP2 binds caspase-8 and the ubiquitin ligase TRAF6, thereby promoting the ubiquitination and activation of caspase-8 by TRAF6. We have defined a TRAF6-interacting motif (TIM) and a ubiquitin-interacting motif in TP53INP2, enabling it to function as a scaffold bridging already ubiquitinated caspase-8 to TRAF6 for further polyubiquitination of caspase-8. Mutations of key TIM residues in TP53INP2 abrogate its interaction with TRAF6 and caspase-8, and subsequently reduce levels of death receptor-induced apoptosis. A screen of cancer cell lines showed that those with higher protein levels of TP53INP2 are more prone to TRAIL-induced apoptosis, making TP53INP2 a potential predictive marker of cancer cell responsiveness to TRAIL treatment. These findings uncover a novel mechanism for the regulation of caspase-8 ubiquitination and reveal TP53INP2 as an important regulator of the death receptor pathway.
Proteomics derived biomarker panel improves diagnostic precision to classify endometrioid and high-grade serous ovarian carcinoma.
Apr 13, 2019   Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
Postovit LM, Dieters-Castator DZ, Rambau PF, Kelemen LE, Siegers GM, Lajoie GA, Köbel M
Proteomics derived biomarker panel improves diagnostic precision to classify endometrioid and high-grade serous ovarian carcinoma.
Apr 13, 2019
Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research
PURPOSE: Ovarian carcinomas are a group of distinct diseases classified by histotypes. As histotype-specific treatment evolves, accurate classification will become critical for optimal precision medicine approaches. EXPERIMENTAL DESIGN: To uncover differences between the two most common histotypes - high-grade serous (HGSC) and endometrioid carcinoma (EC) - we performed label-free quantitative proteomics on freshly frozen tumour tissues (HGSC, n=10; EC, n=10). Eight candidate protein biomarkers specific to EC were validated by immunohistochemistry using tissue microarrays representing 361 cases of either EC or HGSC. RESULTS: Over 500 proteins were differentially expressed (p
Overexpression of PIMREG promotes breast cancer aggressiveness via constitutive activation of NF-κB signaling.
Apr 13, 2019   EBioMedicine
Jiang L, Ren L, Zhang X, Chen H, Chen X,   . . . . . .   , Huang H, Huang D, Yang J, Liang Y, Li J
Overexpression of PIMREG promotes breast cancer aggressiveness via constitutive activation of NF-κB signaling.
Apr 13, 2019
EBioMedicine
BACKGROUND: It is well-established that activation of nuclear factor-kappa B (NF-κB) signaling plays important roles in cancer development and progression. However, the underlying mechanism by which the NF-κB pathway is constitutively activated in cancer remains largely unclear. The present study aimed to investigate the effect of PICALM interacting mitotic regulator (PIMREG) on sustaining NF-κB activation in breast cancer. METHODS: The underlying mechanisms in which PIMREG-mediated NF-κB constitutive activation were determined via immunoprecipitation, EMSA and luciferase reporter assays. The expression of PIMREG was examined by quantitative PCR and western blotting analyses and immunohistochemical assay. The effect of PIMREG on aggressiveness of breast cancer cell was measured using MTT, soft agar clonogenic assay, wound healing and transwell matrix penetration assays in vitro and a Xenografted tumor model in vivo. FINDINGS: PIMREG competitively interacted with the REL homology domain (RHD) of NF-κB with IκBα, and sustained NF-κB activation by promotion of nuclear accumulation and transcriptional activity of NF-κB via disrupting the NF-κB/IκBα negative feedback loop. PIMREG overexpression significantly enhanced NF-κB transactivity and promoted the breast cancer aggressiveness. The expression of PIMREG was markedly upregulated in breast cancer and positively correlated with clinical characteristics of patients with breast cancer, including the clinical stage, tumor-node-metastasis classification and poorer survival. INTERPRETATION: PIMREG promotes breast cancer aggressiveness via disrupting the NF-κB/IκBα negative feedback loop, which suggests that PIMREG might be a valuable prognostic factor and potential target for diagnosis and therapy of metastatic breast cancer. FUND: The science foundation of China, Guangdong Province, Guangzhou Education System, and the Science and Technology Program of Guangzhou.
A patient with homozygous nonsense variants in two Leigh syndrome disease genes: Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant.
Apr 13, 2019   Human Mutation
Lake NJ, Formosa LE, Stroud DA, Ryan MT, Calvo SE, Mootha VK, Morar B, Procopis PG, Christodoulou J, Compton AG, Thorburn DR
A patient with homozygous nonsense variants in two Leigh syndrome disease genes: Distinguishing a dual diagnosis from a hypomorphic protein-truncating variant.
Apr 13, 2019
Human Mutation
Leigh syndrome is a mitochondrial disease caused by pathogenic variants in over 85 genes. Whole exome sequencing of a patient with Leigh-like syndrome identified homozygous protein-truncating variants in two genes associated with Leigh syndrome; a reported pathogenic variant in PDHX (NP_003468.2:p.(Arg446*)), and an uncharacterized variant in complex I (CI) assembly factor TIMMDC1 (NP_057673.2:p.(Arg225*)). The TIMMDC1 variant was predicted to truncate 61 amino acids at the C-terminus and functional studies demonstrated a hypomorphic impact of the variant on CI assembly. However, the mutant protein could still rescue CI assembly in TIMMDC1 knockout cells and the patient's clinical phenotype was not clearly distinct from that of other patients with the same PDHX defect. Our data suggest that the hypomorphic effect of the TIMMDC1 protein-truncating variant does not constitute a dual diagnosis in this individual. We recommend cautious assessment of variants in the C-terminus of TIMMDC1 and emphasize the need to consider the caveats detailed within the American College of Medical Genetics and Genomics (ACMG) criteria when assessing variants.

The link you entered does not seem to be valid

Please make sure the link points to nature.com contains a valid shared_access_token

Downloading PDF to your library...

Uploading PDF...

PDF uploading

Delete tag: