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Biochemistry
The receptor for advanced glycation endproducts mediates podocyte heparanase expression through NF-κB signaling pathway
May 07, 2017   Molecular And Cellular Endocrinology
An X, Zhang L, Yao Q, Li L, Wang B, Zhang J, He M, Zhang J
The receptor for advanced glycation endproducts mediates podocyte heparanase expression through NF-κB signaling pathway
May 07, 2017
Molecular And Cellular Endocrinology
Heparanase degrades heparan sulfate in glomerular basement membrane (GBM) and plays an important role in diabetic nephropathy (DN). However, its regulating mechanisms remain to be deciphered. Our present study showed that the major advanced glycation endproducts (AGEs), CML-BSA, significantly increased heparanase expression in cultured podocytes and the effect was blocked by the receptor for advanced glycation endproducts (RAGE) knockdown, antibody and antagonist. In addition, NF-κB p65 phosphorylation was elevated and the increased heparanase expression and secretion upon CML-BSA could be attenuated by NF-κB inhibitor PDTC. Mechanistically, CML-BSA activated heparanase promoter through p65 directly binding to its promoter. Furthermore, the in vivo study showed that serum and renal cortex AGEs levels, glomerular p65 phosphorylation and heparanase expression were significantly increased in DN mice. Taken together, our data suggest that AGEs and RAGE interaction increases podocyte heparanase expression by activating NF-κB signal pathway, which is involved in GBM damages of DN. Copyright © 2017. Published by Elsevier B.V.
Cancer progression by reprogrammed BCAA metabolism in myeloid leukaemia
May 17, 2017   Nature Add nature.com free-link Cancel
Hattori A, Tsunoda M, Konuma T, Kobayashi M, Nagy T, Glushka J, Tayyari F, McSkimming D, Kannan N, Tojo A, Edison AS, Ito T
Cancer progression by reprogrammed BCAA metabolism in myeloid leukaemia
May 17, 2017
Nature
Reprogrammed cellular metabolism is a common characteristic observed in various cancers. However, whether metabolic changes directly regulate cancer development and progression remains poorly understood. Here we show that BCAT1, a cytosolic aminotransferase for branched-chain amino acids (BCAAs), is aberrantly activated and functionally required for chronic myeloid leukaemia (CML) in humans and in mouse models of CML. BCAT1 is upregulated during progression of CML and promotes BCAA production in leukaemia cells by aminating the branched-chain keto acids. Blocking BCAT1 gene expression or enzymatic activity induces cellular differentiation and impairs the propagation of blast crisis CML both in vitro and in vivo. Stable-isotope tracer experiments combined with nuclear magnetic resonance-based metabolic analysis demonstrate the intracellular production of BCAAs by BCAT1. Direct supplementation with BCAAs ameliorates the defects caused by BCAT1 knockdown, indicating that BCAT1 exerts its oncogenic function through BCAA production in blast crisis CML cells. Importantly, BCAT1 expression not only is activated in human blast crisis CML and de novo acute myeloid leukaemia, but also predicts disease outcome in patients. As an upstream regulator of BCAT1 expression, we identified Musashi2 (MSI2), an oncogenic RNA binding protein that is required for blast crisis CML. MSI2 is physically associated with the BCAT1 transcript and positively regulates its protein expression in leukaemia. Taken together, this work reveals that altered BCAA metabolism activated through the MSI2-BCAT1 axis drives cancer progression in myeloid leukaemia.
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
May 19, 2017   Cell
Nora EP, Goloborodko A, Valton AL, Gibcus JH, Uebersohn A, Abdennur N, Dekker J, Mirny LA, Bruneau BG
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
May 19, 2017
Cell
The molecular mechanisms underlying folding of mammalian chromosomes remain poorly understood. The transcription factor CTCF is a candidate regulator of chromosomal structure. Using the auxin-inducible degron system in mouse embryonic stem cells, we show that CTCF is absolutely and dose-dependently required for looping between CTCF target sites and insulation of topologically associating domains (TADs). Restoring CTCF reinstates proper architecture on altered chromosomes, indicating a powerful instructive function for CTCF in chromatin folding. CTCF remains essential for TAD organization in non-dividing cells. Surprisingly, active and inactive genome compartments remain properly segregated upon CTCF depletion, revealing that compartmentalization of mammalian chromosomes emerges independently of proper insulation of TADs. Furthermore, our data support that CTCF mediates transcriptional insulator function through enhancer blocking but not as a direct barrier to heterochromatin spreading. Beyond defining the functions of CTCF in chromosome folding, these results provide new fundamental insights into the rules governing mammalian genome organization. Copyright © 2017 Elsevier Inc. All rights reserved.
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses
May 19, 2017   Cell
Wec AZ, Herbert AS, Murin CD, Nyakatura EK, Abelson DM,   . . . . . .   , Walker LM, Ward AB, Dye JM, Chandran K, Bornholdt ZA
Antibodies from a Human Survivor Define Sites of Vulnerability for Broad Protection against Ebolaviruses
May 19, 2017
Cell
Experimental monoclonal antibody (mAb) therapies have shown promise for treatment of lethal Ebola virus (EBOV) infections, but their species-specific recognition of the viral glycoprotein (GP) has limited their use against other divergent ebolaviruses associated with human disease. Here, we mined the human immune response to natural EBOV infection and identified mAbs with exceptionally potent pan-ebolavirus neutralizing activity and protective efficacy against three virulent ebolaviruses. These mAbs recognize an inter-protomer epitope in the GP fusion loop, a critical and conserved element of the viral membrane fusion machinery, and neutralize viral entry by targeting a proteolytically primed, fusion-competent GP intermediate (GPCL) generated in host cell endosomes. Only a few somatic hypermutations are required for broad antiviral activity, and germline-approximating variants display enhanced GPCL recognition, suggesting that such antibodies could be elicited more efficiently with suitably optimized GP immunogens. Our findings inform the development of both broadly effective immunotherapeutics and vaccines against filoviruses. Copyright © 2017 Elsevier Inc. All rights reserved.
The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
May 19, 2017   Cell
Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, Conrad NK
The U6 snRNA m6A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
May 19, 2017
Cell
Maintenance of proper levels of the methyl donor S-adenosylmethionine (SAM) is critical for a wide variety of biological processes. We demonstrate that the N6-adenosine methyltransferase METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Upon SAM depletion by methionine starvation, cells induce MAT2A expression by enhanced splicing of a retained intron. Induction requires METTL16 and its methylation substrate, a vertebrate conserved hairpin (hp1) in the MAT2A 3' UTR. Increasing METTL16 occupancy on the MAT2A 3' UTR is sufficient to induce efficient splicing. We propose that, under SAM-limiting conditions, METTL16 occupancy on hp1 increases due to inefficient enzymatic turnover, which promotes MAT2A splicing. We further show that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA). These observations suggest that the conserved U6 snRNA methyltransferase evolved an additional function in vertebrates to regulate SAM homeostasis. Copyright © 2017 Elsevier Inc. All rights reserved.
Targeting FBW7 as a strategy to overcome resistance to targeted therapy in non-small cell lung cancer
May 19, 2017   Cancer Research
Ye M, Zhang Y, Zhang X, Zhang JB, Jing P, Cao L, Li N, Li X, Yao L, Zhang J, Zhang J
Targeting FBW7 as a strategy to overcome resistance to targeted therapy in non-small cell lung cancer
May 19, 2017
Cancer Research
Inhibition of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) signaling is highly effective in a subgroup of non-small cell lung cancer (NSCLC) patients with distinct clinicopathological features. However, resistance to EGFR and ALK inhibitors inevitably occurs, and the molecular mechanism underlying resistance is not fully understood. In this study, we report a PI3K/Akt- and MEK/Erk-independent resistance mechanism by which loss of the E3 ubiquitin ligase F-box and WD repeat domain containing 7 (FBW7α) leads to targeted therapy resistance via stabilization of anti-apoptotic protein MCL-1. Using a panel of in vitro and in vivo studies, we showed that the regulatory machinery responsible for MCL-1 protein degradation was a step-wise event involving phosphorylation and nucleus translocation. Erk cooperated with GSKβ to phosphorylate MCL-1 Ser159 residue, which enabled MCL-1 to translocate into the nucleus and bind FBW7. Defects in this sequence impaired MCL-1 degradation and cell apoptosis, recapitulating phenotypes observed in FBW7 deficiency. Downregulation of FBW7 was found in EGFR inhibitor-resistant human NSCLC specimens and correlated with increased MCL-1 protein expression. Reactivation of FBW7 sensitized resistant cells to targeted therapy and facilitated MCL-1 degradation. Overall, our study provides proof-of-principle insight into a PI3K/Akt- and MEK/Erk-independent resistant model and suggests that targeting FBW7 can overcome resistance to targeted therapy. Copyright ©2017, American Association for Cancer Research.
Super-resolution microscopy with DNA-PAINT
May 18, 2017   Nature Protocols Add nature.com free-link Cancel
Schnitzbauer J, Strauss MT, Schlichthaerle T, Schueder F, Jungmann R
Super-resolution microscopy with DNA-PAINT
May 18, 2017
Nature Protocols
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy. Using the programmability and specificity of DNA molecules as imaging and labeling probes allows researchers to decouple blinking from dye photophysics, alleviating limitations of current super-resolution techniques, making them compatible with virtually any single-molecule-compatible dye. Recent developments in DNA-PAINT have enabled spectrally unlimited multiplexing, precise molecule counting and ultra-high, molecular-scale (sub-5-nm) spatial resolution, reaching ∼1-nm localization precision. DNA-PAINT can be applied to a multitude of in vitro and cellular applications by linking docking strands to antibodies. Here, we present a protocol for the key aspects of the DNA-PAINT framework for both novice and expert users. This protocol describes the creation of DNA origami test samples, in situ sample preparation, multiplexed data acquisition, data simulation, super-resolution image reconstruction and post-processing such as drift correction, molecule counting (qPAINT) and particle averaging. Moreover, we provide an integrated software package, named Picasso, for the computational steps involved. The protocol is designed to be modular, so that individual components can be chosen and implemented per requirements of a specific application. The procedure can be completed in 1-2 d.
Molecular mechanism of Gαi activation by non-GPCR proteins with a Gα-Binding and Activating motif
May 18, 2017   Nature Communications
de Opakua AI, Parag-Sharma K, DiGiacomo V, Merino N, Leyme A,   . . . . . .   , Ramachandran S, Baillie GS, Cerione RA, Blanco FJ, Garcia-Marcos M
Molecular mechanism of Gαi activation by non-GPCR proteins with a Gα-Binding and Activating motif
May 18, 2017
Nature Communications
Heterotrimeric G proteins are quintessential signalling switches activated by nucleotide exchange on Gα. Although activation is predominantly carried out by G-protein-coupled receptors (GPCRs), non-receptor guanine-nucleotide exchange factors (GEFs) have emerged as critical signalling molecules and therapeutic targets. Here we characterize the molecular mechanism of G-protein activation by a family of non-receptor GEFs containing a Gα-binding and -activating (GBA) motif. We combine NMR spectroscopy, computational modelling and biochemistry to map changes in Gα caused by binding of GBA proteins with residue-level resolution. We find that the GBA motif binds to the SwitchII/α3 cleft of Gα and induces changes in the G-1/P-loop and G-2 boxes (involved in phosphate binding), but not in the G-4/G-5 boxes (guanine binding). Our findings reveal that G-protein-binding and activation mechanisms are fundamentally different between GBA proteins and GPCRs, and that GEF-mediated perturbation of nucleotide phosphate binding is sufficient for Gα activation.
Prognostic significance of TCF21 mRNA expression in patients with lung adenocarcinoma
May 18, 2017   Scientific Reports
Xiao J, Liu A, Lu X, Chen X, Li W, He S, He B, Chen Q
Prognostic significance of TCF21 mRNA expression in patients with lung adenocarcinoma
May 18, 2017
Scientific Reports
Several prognostic indicators have shown inconsistencies in patients of different genders with lung adenocarcinoma, indicating that these variations may be due to the different genetic background of males and females with lung adenocarcinoma. In this study, we first used the Gene-Cloud of Biotechnology Information (GCBI) bioinformatics platform to identify differentially expressed genes (DEGs) that eliminated gender differences between lung adenocarcinoma and normal lung tissues. Then, we screened out that transcription factor 21 (TCF21) is a hub gene among these DEGs by creating a gene co-expression network on the GCBI platform. Furthermore, we used the comprehensive survival analysis platforms Kaplan-Meier plotter and PrognoScan to assess the prognostic value of TCF21 expression in lung adenocarcinoma patients. Finally, we concluded that decreased mRNA expression of TCF21 is a predictor for poor prognosis in patients with lung adenocarcinoma.
Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method
May 08, 2017   Journal Of Chemical Theory And Computation
Yuan D, Li Y, Ni Z, Pulay P, Li W, Li S
Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method
May 08, 2017
Journal Of Chemical Theory And Computation
The generalized energy-based fragmentation (GEBF) method has been applied to investigate relative energies of large water clusters (H2O)n (n = 32, 64) with the coupled-cluster singles and doubles with noniterative triple excitations (CCSD(T)) and second-order Møller-Plesset perturbation theory (MP2) at the complete basis set (CBS) limit. Here large water clusters are chosen to be representative structures sampled from molecular dynamics (MD) simulations of liquid water. Our calculations show that the GEBF method is capable of providing highly accurate relative energies for these water clusters in a cost-effective way. We demonstrate that the relative energies from GEBF-MP2/CBS are in excellent agreement with those from GEBF-CCSD(T)/CBS for these water clusters. With the GEBF-CCSD(T)/CBS relative energies as the benchmark results, we have assessed the performance of several theoretical methods widely used for ab initio MD simulations of liquids and aqueous solutions. These methods include density functional theory (DFT) with a number of different functionals, MP2, and density functional tight-binding (the third generation, DFTB3 in short). We find that MP2/aug-cc-pVDZ and several DFT methods (such as LC-ωPBE-D3 and ωB97XD) with the aug-cc-pVTZ basis set can provide satisfactory descriptions for these water clusters. Some widely used functionals (such as B3LYP, PBE0) and DFTB3 are not accurate enough for describing the relative energies of large water clusters. Although the basis set dependence of DFT is less than that of ab initio electron correlation methods, we recommend the combination of a few best functionals and large basis sets (at least aug-cc-pVTZ) in theoretical studies on water clusters or aqueous solutions.
Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes
May 17, 2017   Nature Add nature.com free-link Cancel
Liu Y, Liu J, Du S, Shan C, Nie K, Zhang R, Li XF, Zhang R, Wang T, Qin CF, Wang P, Shi PY, Cheng G
Evolutionary enhancement of Zika virus infectivity in Aedes aegypti mosquitoes
May 17, 2017
Nature
Zika virus (ZIKV) remained obscure until the recent explosive outbreaks in French Polynesia (2013-2014) and South America (2015-2016). Phylogenetic studies have shown that ZIKV has evolved into African and Asian lineages. The Asian lineage of ZIKV was responsible for the recent epidemics in the Americas. However, the underlying mechanisms through which ZIKV rapidly and explosively spread from Asia to the Americas are unclear. Non-structural protein 1 (NS1) facilitates flavivirus acquisition by mosquitoes from an infected mammalian host and subsequently enhances viral prevalence in mosquitoes. Here we show that NS1 antigenaemia determines ZIKV infectivity in its mosquito vector Aedes aegypti, which acquires ZIKV via a blood meal. Clinical isolates from the most recent outbreak in the Americas were much more infectious in mosquitoes than the FSS13025 strain, which was isolated in Cambodia in 2010. Further analyses showed that these epidemic strains have higher NS1 antigenaemia than the FSS13025 strain because of an alanine-to-valine amino acid substitution at residue 188 in NS1. ZIKV infectivity was enhanced by this amino acid substitution in the ZIKV FSS13025 strain in mosquitoes that acquired ZIKV from a viraemic C57BL/6 mouse deficient in type I and II interferon (IFN) receptors (AG6 mouse). Our results reveal that ZIKV evolved to acquire a spontaneous mutation in its NS1 protein, resulting in increased NS1 antigenaemia. Enhancement of NS1 antigenaemia in infected hosts promotes ZIKV infectivity and prevalence in mosquitoes, which could have facilitated transmission during recent ZIKV epidemics.
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
May 17, 2017   Nature Reviews. Molecular Cell Biology
Clapier CR, Iwasa J, Cairns BR, Peterson CL
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
May 17, 2017
Nature Reviews. Molecular Cell Biology
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells
May 15, 2017   Nature Biotechnology Add nature.com free-link Cancel
Gornalusse GG, Hirata RK, Funk SE, Riolobos L, Lopes VS, Manske G, Prunkard D, Colunga AG, Hanafi LA, Clegg DO, Turtle C, Russell DW
HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells
May 15, 2017
Nature Biotechnology
Polymorphisms in the human leukocyte antigen (HLA) class I genes can cause the rejection of pluripotent stem cell (PSC)-derived products in allogeneic recipients. Disruption of the Beta-2 Microglobulin (B2M) gene eliminates surface expression of all class I molecules, but leaves the cells vulnerable to lysis by natural killer (NK) cells. Here we show that this 'missing-self' response can be prevented by forced expression of minimally polymorphic HLA-E molecules. We use adeno-associated virus (AAV)-mediated gene editing to knock in HLA-E genes at the B2M locus in human PSCs in a manner that confers inducible, regulated, surface expression of HLA-E single-chain dimers (fused to B2M) or trimers (fused to B2M and a peptide antigen), without surface expression of HLA-A, B or C. These HLA-engineered PSCs and their differentiated derivatives are not recognized as allogeneic by CD8+ T cells, do not bind anti-HLA antibodies and are resistant to NK-mediated lysis. Our approach provides a potential source of universal donor cells for applications where the differentiated derivatives lack HLA class II expression.
Metabolic Phenotypes of Response to Vaccination in Humans
May 15, 2017   Cell
Li S, Sullivan NL, Rouphael N, Yu T, Banton S,   . . . . . .   , Mulligan MJ, Nakaya HI, Levin M, Ahmed R, Pulendran B
Metabolic Phenotypes of Response to Vaccination in Humans
May 15, 2017
Cell
Herpes zoster (shingles) causes significant morbidity in immune compromised hosts and older adults. Whereas a vaccine is available for prevention of shingles, its efficacy declines with age. To help to understand the mechanisms driving vaccinal responses, we constructed a multiscale, multifactorial response network (MMRN) of immunity in healthy young and older adults immunized with the live attenuated shingles vaccine Zostavax. Vaccination induces robust antigen-specific antibody, plasmablasts, and CD4+ T cells yet limited CD8+ T cell and antiviral responses. The MMRN reveals striking associations between orthogonal datasets, such as transcriptomic and metabolomics signatures, cell populations, and cytokine levels, and identifies immune and metabolic correlates of vaccine immunity. Networks associated with inositol phosphate, glycerophospholipids, and sterol metabolism are tightly coupled with immunity. Critically, the sterol regulatory binding protein 1 and its targets are key integrators of antibody and T follicular cell responses. Our approach is broadly applicable to study human immunity and can help to identify predictors of efficacy as well as mechanisms controlling immunity to vaccination. Copyright © 2017 Elsevier Inc. All rights reserved.
Restoration of p53 using the novel MDM2-p53 antagonist APG115 suppresses dedifferentiated papillary thyroid cancer cells
May 12, 2017   Oncotarget
Chen H, Luo D, Zhang L, Lin X, Luo Q,   . . . . . .   , Zhang H, Liu S, Qiu M, Yang D, Jiang N
Restoration of p53 using the novel MDM2-p53 antagonist APG115 suppresses dedifferentiated papillary thyroid cancer cells
May 12, 2017
Oncotarget
Dedifferentiated papillary thyroid cancer (DePTC) is characterized by aggressive growth, recurrence, distant metastasis, and resistance to radioactive iodine (RAI) therapy. DePTC is also accompanied by poor prognosis and high early-mortality. Nevertheless, most DePTC cells show intact p53 downstream functionality. In cells with wild-type p53, the murine double minute2 (MDM2) protein interacts with p53 and abrogates its activity. Inhibition of the MDM2-p53 interaction restores p53 activity and leads to cell cycle arrest and apoptosis. Restoring p53 function by inhibiting its interaction with p53 suppressors such as MDM2 is thus a promising therapeutic strategy for the treatment of DePTC. The novel MDM2-p53 interaction antagonist APG115 is an analogue of SAR405838, and is being tested in a phase I clinical trial. In this study, we evaluated the efficacy of APG115 as a single-agent to treat DePTC. APG115 diminished the viability of p53 wild-type DePTC cells and induced cell cycle arrest and apoptosis. In a human xenograft mouse model, APG115 elicited robust tumor regression and cell apoptosis. These data demonstrate that further research is warranted to determine whether APG115 can be used to effectively treat DePTC patients.
A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo
May 12, 2017   Cell Reports
Yang YP, Ma H, Starchenko A, Huh WJ, Li W, Hickman FE, Zhang Q, Franklin JL, Mortlock DP, Fuhrmann S, Carter BD, Ihrie RA, Coffey RJ
A Chimeric Egfr Protein Reporter Mouse Reveals Egfr Localization and Trafficking In Vivo
May 12, 2017
Cell Reports
EGF receptor (EGFR) is a critical signaling node throughout life. However, it has not been possible to directly visualize endogenous Egfr in mice. Using CRISPR/Cas9 genome editing, we appended a fluorescent reporter to the C terminus of the Egfr. Homozygous reporter mice appear normal and EGFR signaling is intact in vitro and in vivo. We detect distinct patterns of Egfr expression in progenitor and differentiated compartments in embryonic and adult mice. Systemic delivery of EGF or amphiregulin results in markedly different patterns of Egfr internalization and trafficking in hepatocytes. In the normal intestine, Egfr localizes to the crypt rather than villus compartment, expression is higher in adjacent epithelium than in intestinal tumors, and following colonic injury expression appears in distinct cell populations in the stroma. This reporter, under control of its endogenous regulatory elements, enables in vivo monitoring of the dynamics of Egfr localization and trafficking in normal and disease states. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Discovering and linking public omics data sets using the Omics Discovery Index
May 09, 2017   Nature Biotechnology Add nature.com free-link Cancel
Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM,   . . . . . .   , Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H
Facile fabrication of 3D porous hybrid sphere by co-immobilization of multi-enzyme directly from cell lysates as an efficient and recyclable biocatalyst for asymmetric reduction with coenzyme regeneration in situ
May 20, 2017   International Journal Of Biological Macromolecules
MinganYu , Liu D, Sun L, Li J, Chen Q, Pan L, Shang J, Zhang S, Li W
Facile fabrication of 3D porous hybrid sphere by co-immobilization of multi-enzyme directly from cell lysates as an efficient and recyclable biocatalyst for asymmetric reduction with coenzyme regeneration in situ
May 20, 2017
International Journal Of Biological Macromolecules
Ni2+-agarose bead-wrapped multi-enzyme/inorganic hybrid sphere composed of the immobilized enzymes as organic component and NaH2PO4 and NaCl as inorganic component was developed by co-immobilizing extracellular His-tagged 3-quinuclidinone reductases and glucose dehydrogenase without pre-purification. The resulting biocatalysts has 3D porous architectures as confirmed by SEM and FESEM, and it enabled the continuous biotransformation of 3-quinuclidone to (R)-3-quinuclidinol with cofactor regeneration in situ. The 3D porous biocatalysts were formed via three steps: First, immobilization of the His-tagged enzymes directly from the cell lysates supernatant. Next, formation of enzyme aggregates, ribbons and gels. Finally, the enzymes, the formed aggregates/ribbons/gels and salt were incorporated to the foam and then covered the Ni2+-agarose bead. The technique made the immobilization of these enzymes effective such that specific enzyme loading of 60.8mg/g support and enzyme loading efficiency of 92.3% were achieved. As a direct consequence, the biocatalyst catalyzed the conversion of 3-quinuclidinone (204g/L) to (R)-3-quinuclidinol in 100% yield and 100% ee at 4.5h, and the recyclability of the biocatalyst was excellent, retaining>95% conversion yield and 100% ee even after the fifteenth runs. Overall, our strategy is demonstrated to be a promising method for developing efficient and robust biocatalyst for asymmetric synthesis. Copyright © 2017 Elsevier B.V. All rights reserved.
CaMKII Autophosphorylation Is Necessary for Optimal Integration of Ca2+ Signals during LTP Induction, but Not Maintenance
May 18, 2017   Neuron
Chang JY, Parra-Bueno P, Laviv T, Szatmari EM, Lee SR, Yasuda R
CaMKII Autophosphorylation Is Necessary for Optimal Integration of Ca2+ Signals during LTP Induction, but Not Maintenance
May 18, 2017
Neuron
CaMKII plays a critical role in decoding calcium (Ca2+) signals to initiate long-lasting synaptic plasticity. However, the properties of CaMKII that mediate Ca2+ signals in spines remain elusive. Here, we measured CaMKII activity in spines using fast-framing two-photon fluorescence lifetime imaging. Following each pulse during repetitive Ca2+ elevations, CaMKII activity increased in a stepwise manner. Thr286 phosphorylation slows the decay of CaMKII and thus lowers the frequency required to induce spine plasticity by several fold. In the absence of Thr286 phosphorylation, increasing the stimulation frequency results in high peak mutant CaMKIIT286A activity that is sufficient for inducing plasticity. Our findings demonstrate that Thr286 phosphorylation plays an important role in induction of LTP by integrating Ca2+ signals, and it greatly promotes, but is dispensable for, the activation of CaMKII and LTP. Copyright © 2017 Elsevier Inc. All rights reserved.
PGBD5 promotes site-specific oncogenic mutations in human tumors
May 15, 2017   Nature Genetics Add nature.com free-link Cancel
Henssen AG, Koche R, Zhuang J, Jiang E, Reed C,   . . . . . .   , Jackson SP, Torrents D, Weng Z, Armstrong SA, Kentsis A
PGBD5 promotes site-specific oncogenic mutations in human tumors
May 15, 2017
Nature Genetics
Genomic rearrangements are a hallmark of human cancers. Here, we identify the piggyBac transposable element derived 5 (PGBD5) gene as encoding an active DNA transposase expressed in the majority of childhood solid tumors, including lethal rhabdoid tumors. Using assembly-based whole-genome DNA sequencing, we found previously undefined genomic rearrangements in human rhabdoid tumors. These rearrangements involved PGBD5-specific signal (PSS) sequences at their breakpoints and recurrently inactivated tumor-suppressor genes. PGBD5 was physically associated with genomic PSS sequences that were also sufficient to mediate PGBD5-induced DNA rearrangements in rhabdoid tumor cells. Ectopic expression of PGBD5 in primary immortalized human cells was sufficient to promote cell transformation in vivo. This activity required specific catalytic residues in the PGBD5 transposase domain as well as end-joining DNA repair and induced structural rearrangements with PSS breakpoints. These results define PGBD5 as an oncogenic mutator and provide a plausible mechanism for site-specific DNA rearrangements in childhood and adult solid tumors.
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
May 08, 2017   Nature Genetics Add nature.com free-link Cancel
Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O,   . . . . . .   , Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J
Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
May 08, 2017
Nature Genetics
Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.
A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568
May 19, 2017   Science (New York, N.Y.)
Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun MA, Wolf G, Baker M, Chien HC, Lai KN, Cheng X, Shen CJ, Macfarlan TS
A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568
May 19, 2017
Science (New York, N.Y.)
Insulin-like growth factor 2 (IGF2) is the major fetal growth hormone in mammals. We identify zinc finger protein 568 (ZFP568), a member of the rapidly evolving Kruppel-associated box-zinc finger protein (KRAB-ZFP) family linked primarily to silencing of endogenous retroelements, as a direct repressor of a placental-specific Igf2 transcript (designated Igf2-P0) in mice. Loss of Zfp568, which causes gastrulation failure, or mutation of the ZFP568-binding site at the Igf2-P0 promoter causes inappropriate Igf2-P0 activation. Deletion of Igf2 can completely rescue Zfp568 gastrulation phenotypes through late gestation. Our data highlight the exquisite selectivity with which members of the KRAB-ZFP family repress their targets and identify an additional layer of transcriptional control of a key growth factor regulating fetal and placental development. Copyright © 2017, American Association for the Advancement of Science.
Resistance to malaria through structural variation of red blood cell invasion receptors
May 19, 2017   Science (New York, N.Y.)
Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS,   . . . . . .   , Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP, Malaria Genomic Epidemiology Network
Resistance to malaria through structural variation of red blood cell invasion receptors
May 19, 2017
Science (New York, N.Y.)
The malaria parasite Plasmodium falciparum invades human red blood cells via interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.
Mechanism of transmembrane signaling by sensor histidine kinases
May 19, 2017   Science (New York, N.Y.)
Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A,   . . . . . .   , Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V
Mechanism of transmembrane signaling by sensor histidine kinases
May 19, 2017
Science (New York, N.Y.)
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases (HKs), parts of two-component signaling systems (TCS). The structural mechanisms of transmembrane signaling by these sensors are poorly understood. We present here crystal structures of the periplasmic sensor domain, the TM domain and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor HK NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces significant rearrangements and piston-like shifts of TM helices. The HAMP domain protomers undergo lever-like motions and convert the piston-like motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCS. Copyright © 2017, American Association for the Advancement of Science.
Local amplifiers of IL-4Rα-mediated macrophage activation promote repair in lung and liver
May 12, 2017   Science (New York, N.Y.)
Minutti CM, Jackson-Jones LH, García-Fojeda B, Knipper JA, Sutherland TE,   . . . . . .   , Stamme C, Chroneos ZC, Zaiss DM, Casals C, Allen JE
Local amplifiers of IL-4Rα-mediated macrophage activation promote repair in lung and liver
May 12, 2017
Science (New York, N.Y.)
The type 2 immune response controls helminth infection and maintains tissue homeostasis but can lead to allergy and fibrosis if not adequately regulated. We have discovered local tissue-specific amplifiers of type-2 mediated-macrophage activation. In the lung, surfactant protein A (SP-A) enhanced IL-4-dependent macrophage proliferation and activation, accelerating parasite clearance and reducing pulmonary injury following infection with a lung-migrating helminth. In the peritoneal cavity and liver, C1q enhancement of type 2 macrophage activation was required for liver repair following bacterial infection, but resulted in fibrosis following peritoneal dialysis. IL-4 drives production of these structurally related defense collagens, SP-A and C1q, and the expression of their receptor, myosin 18A. These findings reveal the existence within different tissues of an amplification system needed for local type 2 responses. Copyright © 2017, American Association for the Advancement of Science.

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