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Chemistry
Role of Modulators in Controlling the Colloidal Stability and Polydispersity of the UiO-66 Metal-Organic Framework
May 16, 2017   ACS Applied Materials & Interfaces
Morris W, Wang S, Cho D, Auyeung E, Li P, Farha OK, Mirkin CA
Role of Modulators in Controlling the Colloidal Stability and Polydispersity of the UiO-66 Metal-Organic Framework
May 16, 2017
ACS Applied Materials & Interfaces
Nanoscale UiO-66 Zr6(OH)4O4(C8O4H4)6 has been synthesized with a series of carboxylic acid modulators, R-COOH (where R = H, CH3, CF3, and CHCl2). The phase purity and size of each MOF was confirmed by powder X-ray diffraction, BET surface area analysis, and scanning transmission electron microscopy (STEM). Size control of UiO-66 crystals from 20 nm to over 1 μm was achieved, and confirmed by STEM. The colloidal stability of each MOF was evaluated by dynamic light scattering and was found to be highly dependent on the modulator conditions utilized in the synthesis, with both lower pKa and higher acid concentration resulting in more stable structures. Furthermore, STEM was carried out on both colloidally stable samples and those that exhibited a large degree of aggregation, which allowed for visualization of the different degrees of dispersion of the samples. The use of modulators at higher concentrations and with lower pKas leads to the formation of more defects, as a consequence of terephthalic acid ligands being replaced by modulator molecules, thereby enhancing the colloidal stability of the UiO-66 nanoparticles. These findings could have a significant impact on nanoscale MOF material syntheses and applications, especially in the areas of catalysis and drug delivery.
BIRC6 mediates imatinib resistance independently of Mcl-1
May 18, 2017   PloS One
Okumu DO, East MP, Levine M, Herring LE, Zhang R, Gilbert TSK, Litchfield DW, Zhang Y, Graves LM
BIRC6 mediates imatinib resistance independently of Mcl-1
May 18, 2017
PloS One
Baculoviral IAP repeat containing 6 (BIRC6) is a member of the inhibitors of apoptosis proteins (IAPs), a family of functionally and structurally related proteins that inhibit apoptosis. BIRC6 has been implicated in drug resistance in several different human cancers, however mechanisms regulating BIRC6 have not been extensively explored. Our phosphoproteomic analysis of an imatinib-resistant chronic myelogenous leukemia (CML) cell line (MYL-R) identified increased amounts of a BIRC6 peptide phosphorylated at S480, S482, and S486 compared to imatinib-sensitive CML cells (MYL). Thus we investigated the role of BIRC6 in mediating imatinib resistance and compared it to the well-characterized anti-apoptotic protein, Mcl-1. Both BIRC6 and Mcl-1 were elevated in MYL-R compared to MYL cells. Lentiviral shRNA knockdown of BIRC6 in MYL-R cells increased imatinib-stimulated caspase activation and resulted in a ~20-25-fold increase in imatinib sensitivity, without affecting Mcl-1. Treating MYL-R cells with CDK9 inhibitors decreased BIRC6 mRNA, but not BIRC6 protein levels. By contrast, while CDK9 inhibitors reduced Mcl-1 mRNA and protein, they did not affect imatinib sensitivity. Since the Src family kinase Lyn is highly expressed and active in MYL-R cells, we tested the effects of Lyn inhibition on BIRC6 and Mcl-1. RNAi-mediated knockdown or inhibition of Lyn (dasatinib/ponatinib) reduced BIRC6 protein stability and increased caspase activation. Inhibition of Lyn also increased formation of an N-terminal BIRC6 fragment in parallel with reduced amount of the BIRC6 phosphopeptide, suggesting that Lyn may regulate BIRC6 phosphorylation and stability. In summary, our data show that BIRC6 stability is dependent on Lyn, and that BIRC6 mediates imatinib sensitivity independently of Mcl-1 or CDK9. Hence, BIRC6 may be a novel target for the treatment of drug-resistant CML where Mcl-1 or CDK9 inhibitors have failed.
Investigating the causal effect of smoking on hay fever and asthma: a Mendelian randomization meta-analysis in the CARTA consortium
May 23, 2017   Scientific Reports
Skaaby T, Taylor AE, Jacobsen RK, Paternoster L, Thuesen BH,   . . . . . .   , Romundstad PR, Skorpen F, Kaprio J, R Munafò M, Linneberg A
Investigating the causal effect of smoking on hay fever and asthma: a Mendelian randomization meta-analysis in the CARTA consortium
May 23, 2017
Scientific Reports
Observational studies on smoking and risk of hay fever and asthma have shown inconsistent results. However, observational studies may be biased by confounding and reverse causation. Mendelian randomization uses genetic variants as markers of exposures to examine causal effects. We examined the causal effect of smoking on hay fever and asthma by using the smoking-associated single nucleotide polymorphism (SNP) rs16969968/rs1051730. We included 231,020 participants from 22 population-based studies. Observational analyses showed that current vs never smokers had lower risk of hay fever (odds ratio (OR) = 0·68, 95% confidence interval (CI): 0·61, 0·76; P 
Sex-specific metabolic profiles of androgens and its main binding protein SHBG in a middle aged population without diabetes
May 23, 2017   Scientific Reports
Piontek U, Wallaschofski H, Kastenmüller G, Suhre K, Völzke H, Do KT, Artati A, Nauck M, Adamski J, Friedrich N, Pietzner M
Sex-specific metabolic profiles of androgens and its main binding protein SHBG in a middle aged population without diabetes
May 23, 2017
Scientific Reports
The role of androgens in metabolism with respect to sex-specific disease associations is poorly understood. Therefore, we aimed to provide molecular signatures in plasma and urine of androgen action in a sex-specific manner using state-of-the-art metabolomics techniques. Our study population consisted of 430 men and 343 women, aged 20-80 years, who were recruited for the cross-sectional population-based Study of Health in Pomerania (SHIP-TREND), Germany. We used linear regression models to identify associations between testosterone, androstenedione and dehydroepiandrosterone-sulfate (DHEAS) as well as sex hormone-binding globulin and plasma or urine metabolites measured by mass spectrometry. The analyses revealed major sex-specific differences in androgen-associated metabolites, particularly for levels of urate, lipids and metabolic surrogates of lifestyle factors, like cotinine or piperine. In women, in particular in the postmenopausal state, androgens showed a greater impact on the metabolome than in men (especially DHEAS and lipids were highly related in women). We observed a novel association of androstenedione on the metabolism of biogenic amines and only a small sex-overlap of associations within steroid metabolism. The present study yields new insights in the interaction between androgens and metabolism, especially about their implication in female metabolism.
Psychosine enhances the shedding of membrane microvesicles: Implications in demyelination in Krabbe's disease
May 22, 2017   PloS One
D'Auria L, Reiter C, Ward E, Moyano AL, Marshall MS, Nguyen D, Scesa G, Hauck Z, van Breemen R, Givogri MI, Bongarzone ER
Psychosine enhances the shedding of membrane microvesicles: Implications in demyelination in Krabbe's disease
May 22, 2017
PloS One
In prior studies, our laboratory showed that psychosine accumulates and disrupts lipid rafts in brain membranes of Krabbe's disease. A model of lipid raft disruption helped explaining psychosine's effects on several signaling pathways important for oligodendrocyte survival and differentiation but provided more limited insight in how this sphingolipid caused demyelination. Here, we have studied how this cationic inverted coned lipid affects the fluidity, stability and structure of myelin and plasma membranes. Using a combination of cutting-edge imaging techniques in non-myelinating (red blood cell), and myelinating (oligodendrocyte) cell models, we show that psychosine is sufficient to disrupt sphingomyelin-enriched domains, increases the rigidity of localized areas in the plasma membrane, and promotes the shedding of membranous microvesicles. The same physicochemical and structural changes were measured in myelin membranes purified from the mutant mouse Twitcher, a model for Krabbe's disease. Areas of higher rigidity were measured in Twitcher myelin and correlated with higher levels of psychosine and of myelin microvesiculation. These results expand our previous analyses and support, for the first time a pathogenic mechanism where psychosine's toxicity in Krabbe disease involves deregulation of cell signaling not only by disruption of membrane rafts, but also by direct local destabilization and fragmentation of the membrane through microvesiculation. This model of membrane disruption may be fundamental to introduce focal weak points in the myelin sheath, and consequent diffuse demyelination in this leukodystrophy, with possible commonality to other demyelinating disorders.
MiR-145 mediates zebrafish hepatic outgrowth through progranulin A signaling
May 22, 2017   PloS One
Li YW, Chiang KY, Li YH, Wu SY, Liu W, Lin CR, Wu JL
MiR-145 mediates zebrafish hepatic outgrowth through progranulin A signaling
May 22, 2017
PloS One
MicroRNAs (miRs) are mRNA-regulatory molecules that fine-tune gene expression and modulate both processes of development and tumorigenesis. Our previous studies identified progranulin A (GrnA) as a growth factor which induces zebrafish hepatic outgrowth through MET signaling. We also found that miR-145 is one of potential fine-tuning regulators of GrnA involved in embryonic hepatic outgrowth. The low level of miR-145 seen in hepatocarinogenesis has been shown to promote pathological liver growth. However, little is known about the regulatory mechanism of miR-145 in embryonic liver development. In this study, we demonstrate a significant decrease in miR-145 expression during hepatogenesis. We modulate miR-145 expression in zebrafish embryos by injection with a miR-145 mimic or a miR-145 hairpin inhibitor. Altered embryonic liver outgrowth is observed in response to miR-145 expression modulation. We also confirm a critical role of miR-145 in hepatic outgrowth by using whole-mount in situ hybridization. Loss of miR-145 expression in embryos results in hepatic cell proliferation, and vice versa. Furthermore, we demonstrate that GrnA is a target of miR-145 and GrnA-induced MET signaling is also regulated by miR-145 as determined by luciferase reporter assay and gene expression analysis, respectively. In addition, co-injection of GrnA mRNA with miR-145 mimic or MO-GrnA with miR-145 inhibitor restores the liver defects caused by dysregulation of miR-145 expression. In conclusion, our findings suggest an important role of miR-145 in regulating GrnA-dependent hepatic outgrowth in zebrafish embryonic development.
Livestock metabolomics and the livestock metabolome: A systematic review
May 22, 2017   PloS One
Goldansaz SA, Guo AC, Sajed T, Steele MA, Plastow GS, Wishart DS
Livestock metabolomics and the livestock metabolome: A systematic review
May 22, 2017
PloS One
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions. As a result, metabolomics has become an increasingly popular "omics" approach to assist with the robust phenotypic characterization of humans, crop plants and model organisms. Indeed, metabolomics is now routinely used in biomedical, nutritional and crop research. It is also being increasingly used in livestock research and livestock monitoring. The purpose of this systematic review is to quantitatively and objectively summarize the current status of livestock metabolomics and to identify emerging trends, preferred technologies and important gaps in the field. In conducting this review we also critically assessed the applications of livestock metabolomics in key areas such as animal health assessment, disease diagnosis, bioproduct characterization and biomarker discovery for highly desirable economic traits (i.e., feed efficiency, growth potential and milk production). A secondary goal of this critical review was to compile data on the known composition of the livestock metabolome (for 5 of the most common livestock species namely cattle, sheep, goats, horses and pigs). These data have been made available through an open access, comprehensive livestock metabolome database (LMDB, available at http://www.lmdb.ca). The LMDB should enable livestock researchers and producers to conduct more targeted metabolomic studies and to identify where further metabolome coverage is needed.
Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed
May 22, 2017   PloS One
Carlin DA, Hapig-Ward S, Chan BW, Damrau N, Riley M, Caster RW, Bethards B, Siegel JB
Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed
May 22, 2017
PloS One
Accurate modeling of enzyme activity and stability is an important goal of the protein engineering community. However, studies seeking to evaluate current progress are limited by small data sets of quantitative kinetic constants and thermal stability measurements. Here, we report quantitative measurements of soluble protein expression in E. coli, thermal stability, and Michaelis-Menten constants (kcat, KM, and kcat/KM) for 129 designed mutants of a glycoside hydrolase. Statistical analyses reveal that functional Tm is independent of kcat, KM, and kcat/KM in this system, illustrating that an individual mutation can modulate these functional parameters independently. In addition, this data set is used to evaluate computational predictions of protein stability using the established Rosetta and FoldX algorithms. Predictions for both are found to correlate only weakly with experimental measurements, suggesting improvements are needed in the underlying algorithms.
Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells
May 22, 2017   Nature Reviews. Genetics
Cuvier O, Fierz B
Dynamic chromatin technologies: from individual molecules to epigenomic regulation in cells
May 22, 2017
Nature Reviews. Genetics
The establishment and maintenance of chromatin states involves multiscale dynamic processes integrating transcription factor and multiprotein effector dynamics, cycles of chemical chromatin modifications, and chromatin structural organization. Recent developments in genomic technologies are emerging that are enabling a view beyond ensemble- and time-averaged properties and are revealing the importance of dynamic chromatin states for cell fate decisions, differentiation and reprogramming at the single-cell level. Concurrently, biochemical and single-molecule methodologies are providing key insights into the underlying molecular mechanisms. Combining results from defined in vitro and single-molecule studies with single-cell genomic approaches thus holds great promise for understanding chromatin-based transcriptional memory and cell fate. In this Review, we discuss recent developments in biochemical, single-molecule biophysical and single-cell genomic technologies and review how the findings from these approaches can be integrated to paint a comprehensive picture of dynamic chromatin states.
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
Yu M, 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.
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
May 18, 2017   Neuron
Shah S, Lubeck E, Zhou W, Cai L
seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus
May 18, 2017
Neuron
We recently applied multiplexed seqFISH to profile expressions of hundreds of genes at the single-cell level in situ (Shah et al., 2016) and provided a map of spatial heterogeneity within each subregion, reconciling previously contradictory descriptions of CA1 at lower spatial resolutions. The accompanying Matters Arising paper from Cembrowski and Spruston questions the spatial organization described for CA1 and raise concerns that the results were determined only by high expression, non-barcoded genes. In response, we show that the same robust spatial structure is observed when only lower average abundance genes measured by barcoded seqFISH are used. In fact, many genes with low average abundance are informative of cell states because they can be expressed strongly in specific subpopulation of cells. Our discussion highlights the importance of single-cell in situ analysis in resolving cellular and spatial heterogeneities otherwise lost in population-averaged measurements. This Matters Arising Response paper addresses the Cembrowski and Spruston (2017) Matters Arising paper, published concurrently in this issue of Neuron. Copyright © 2017 Elsevier Inc. All rights reserved.
Atypical Endocannabinoid Signaling Initiates a New Form of Memory-Related Plasticity at a Cortical Input to Hippocampus
May 18, 2017   Cerebral Cortex (New York, N.Y. : 1991)
Wang W, Jia Y, Pham DT, Palmer LC, Jung KM, Cox CD, Rumbaugh G, Piomelli D, Gall CM, Lynch G
Atypical Endocannabinoid Signaling Initiates a New Form of Memory-Related Plasticity at a Cortical Input to Hippocampus
May 18, 2017
Cerebral Cortex (New York, N.Y. : 1991)
Endocannabinoids (ECBs) depress transmitter release at sites throughout the brain. Here, we describe another form of ECB signaling that triggers a novel form of long-term potentiation (LTP) localized to the lateral perforant path (LPP) which conveys semantic information from cortex to hippocampus. Two cannabinoid CB1 receptor (CB1R) signaling cascades were identified in hippocampus. The first is pregnenolone sensitive, targets vesicular protein Munc18-1 and depresses transmitter release; this cascade is engaged by CB1Rs in Schaffer-Commissural afferents to CA1 but not in the LPP, and it does not contribute to LTP. The second cascade is pregnenolone insensitive and LPP specific; it entails co-operative CB1R/β1-integrin signaling to effect synaptic potentiation via stable enhancement of transmitter release. The latter cascade is engaged during LPP-dependent learning. These results link atypical ECB signaling to the encoding of a fundamental component of episodic memory and suggest a novel route whereby endogenous and exogenous cannabinoids affect cognition. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae
May 18, 2017   PloS One
Choi J, Rajagopal A, Xu YF, Rabinowitz JD, O'Shea EK
A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae
May 18, 2017
PloS One
Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Furthermore, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.
Enhanced Photoelectrochemical activity by autologous Cd/CdO/CdS heterojunction photoanode with high conductivity and separation efficiency
May 16, 2017   Chemistry (Weinheim An Der Bergstrasse, Germany)
Xie S, Zhang P, Zhang M, Liu P, Li W, Lu X, Cheng F, Tong Y
Enhanced Photoelectrochemical activity by autologous Cd/CdO/CdS heterojunction photoanode with high conductivity and separation efficiency
May 16, 2017
Chemistry (Weinheim An Der Bergstrasse, Germany)
The development of hydrogen from solar energy has attracted great attention due to the global demand for clean energy and environment. Herein, autologous Cd/CdO/CdS heterojunctions was prepared by carefully controlling process with the metallic Cd as the inner-layer and CdO as the interlayer. Further research revealed that the transportation and separation of photogenerated pairs were enhanced due to low resistance of Cd inner-layer and the type-II CdO/CdS heterojunction. As a result, the optimized Cd/CdO/CdS heterojunction photoanode showed outstanding and long-term photoelectrochemical activity for the water splitting, with the current density of 3.52 mA cm-2, or benchmark specific hydrogen production rate of 1.65 μmol cm-2 min-1 at -0.3 V vs. Ag/AgCl, by using the environmental pollutants of sulfide and sulfite as the sacrificial agents. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Transcriptomic analysis of salt stress responsive genes in Rhazya stricta
May 18, 2017   PloS One
Hajrah NH, Obaid AY, Atef A, Ramadan AM, Arasappan D,   . . . . . .   , Sabir JSM, Khiyami MA, Hall N, Bahieldin A, Jansen RK
Transcriptomic analysis of salt stress responsive genes in Rhazya stricta
May 18, 2017
PloS One
Rhazya stricta is an evergreen shrub that is widely distributed across Western and South Asia, and like many other members of the Apocynaceae produces monoterpene indole alkaloids that have anti-cancer properties. This species is adapted to very harsh desert conditions making it an excellent system for studying tolerance to high temperatures and salinity. RNA-Seq analysis was performed on R. stricta exposed to severe salt stress (500 mM NaCl) across four time intervals (0, 2, 12 and 24 h) to examine mechanisms of salt tolerance. A large number of transcripts including genes encoding tetrapyrroles and pentatricopeptide repeat (PPR) proteins were regulated only after 12 h of stress of seedlings grown in controlled greenhouse conditions. Mechanisms of salt tolerance in R. stricta may involve the upregulation of genes encoding chaperone protein Dnaj6, UDP-glucosyl transferase 85a2, protein transparent testa 12 and respiratory burst oxidase homolog protein b. Many of the highly-expressed genes act on protecting protein folding during salt stress and the production of flavonoids, key secondary metabolites in stress tolerance. Other regulated genes encode enzymes in the porphyrin and chlorophyll metabolic pathway with important roles during plant growth, photosynthesis, hormone signaling and abiotic responses. Heme biosynthesis in R. stricta leaves might add to the level of salt stress tolerance by maintaining appropriate levels of photosynthesis and normal plant growth as well as by the participation in reactive oxygen species (ROS) production under stress. We speculate that the high expression levels of PPR genes may be dependent on expression levels of their targeted editing genes. Although the results of PPR gene family indicated regulation of a large number of transcripts under salt stress, PPR actions were independent of the salt stress because their RNA editing patterns were unchanged.
DNA recognition by an RNA-guided bacterial Argonaute
May 18, 2017   PloS One
Doxzen KW, Doudna JA
DNA recognition by an RNA-guided bacterial Argonaute
May 18, 2017
PloS One
Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.
Identification of human short introns
May 18, 2017   PloS One
Abebrese EL, Ali SH, Arnold ZR, Andrews VM, Armstrong K,   . . . . . .   , Lee G, Luo Y, Mugayo D, Raza Z, Friend K
Identification of human short introns
May 18, 2017
PloS One
Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing-intron excision without the spliceosome-has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. We identify hundreds of short introns conserved among multiple human cell lines. These short introns are often alternatively spliced and are found in a variety of RNAs-both mRNAs and lncRNAs. Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. In many cases, splicing of these short introns from mRNAs is predicted to alter the reading frame and change protein output. Our findings imply that standard gene prediction models which often assume a lower limit for intron size fail to predict short introns effectively. We conclude that short introns are abundant in the human transcriptome, and short intron splicing represents an added layer to mRNA regulation.
Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling
May 18, 2017   Journal Of Proteome Research
Suarez-Diez M, Adam J, Adamski J, Chasapi SA, Luchinat C, Peters A, Prehn C, Santucci C, Spyridonidis A, Spyroulias GA, Tenori L, Wang-Sattler R, Saccenti E
Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling
May 18, 2017
Journal Of Proteome Research
Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA-MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids.
Abstracts of the 52nd Workshop for Pediatric Research : Frankfurt, Germany. 27-28 October 2016
May 18, 2017   Molecular And Cellular Pediatrics
van den Bruck R, Weil PP, Ziegenhals T, Schreiner P, Juranek S,   . . . . . .   , Nonnenmacher L, Langhans J, Schneele L, Trenkler N, Debatin KM
Abstracts of the 52nd Workshop for Pediatric Research : Frankfurt, Germany. 27-28 October 2016
May 18, 2017
Molecular And Cellular Pediatrics
van den Bruck R, Weil PP, Ziegenhals T, Schreiner P, Juranek S, Gödde D, Vogel S, Schuster F, Orth V, Dörner J, Pembaur D, Röper M, Störkel S, Zirngibl H, Wirth S, Jenke ACW, Postberg J, Boy N, Heringer J, Haege G, Glahn EM, Hoffmann GF, Garbade SF, Burgard P, Kölker S, Chao CM, Yahya F, Moiseenko A, Shrestha A, Ahmadvand N, Quantius J, Wilhelm J, El-Agha E, Zimmer KP, Bellusci S, Staufner C, Kölker S, Prokisch H, Hoffmann GF, Seeliger S, Müller M, Hippe A, Steinkraus H, Wauer R, Lachmann B, Hofmann SR, Hedrich CM, Zierk J, Arzideh F, Haeckel R, Rascher W, Rauh M, Metzler M, Thieme S, Bandoła J, Richter C, Ryser M, Jamal A, Ashton MP, von Bonin M, Kuhn M, Hedrich CM, Bonifacio E, Berner R, Brenner S, Hammersen J, Has C, Naumann-Bartsch N, Stachel D, Kiritsi D, Söder S, Tardieu M, Metzler M, Bruckner-Tuderman L, Schneider H, Bohne F, Langer D, Cencic R, Eggermann T, Zechner U, Pelletier J, Zepp F, Enklaar T, Prawitt D, Pech M, Weckmann M, Heinsen FA, Franke A, Happle C, Dittrich AM, Hansen G, Fuchs O, von Mutius E, Oliver BG, Kopp MV, Paret C, Russo A, Theruvath J, Keller B, El Malki K, Lehmann N, Wingerter A, Neu MA, Aslihan GA, Wagner W, Sommer C, Pietsch T, Seidmann L, Faber J, Schreiner F, Ackermann M, Michalik M, Rother E, Bilkei-Gorzo A, Racz I, Bindila L, Lutz B, Dötsch J, Zimmer A, Woelfle J, Fischer HS, Ullrich TL, Bührer C, Czernik C, Schmalisch G, Stein R, Hofmann SR, Hagenbuchner J, Kiechl-Kohlendorfer U, Obexer P, Ausserlechner MJ, Loges NT, Frommer AT, Wallmeier J, Omran H, Öner-Sieben S, Gimpfl M, Rozman J, Irmler M, Beckers J, De Angelis MH, Roscher A, Wolf E, Ensenauer R, Nemes K, Frühwald M, Hasselblatt M, Siebert R, Kordes U, Kool M, Wang H, Hardy H, Refai O, Barwick KES, Zimmerman HH, Weis J, Baple EL, Crosby AH, Cirak S, Hellmuth C, Uhl O, Standl M, Heinrich J, Thiering E, Koletzko B, Blümel L, Kerl K, Picard D, Frühwald MC, Liebau MC, Reifenberger G, Borkhardt A, Hasselblatt M, Remke M, Tews D, Wabitsch M, Fischer-Posovszky P, Westhoff MA, Nonnenmacher L, Langhans J, Schneele L, Trenkler N, Debatin KM
Isotopic evidence of multiple controls on atmospheric oxidants over climate transitions
May 17, 2017   Nature Add nature.com free-link Cancel
Geng L, Murray LT, Mickley LJ, Lin P, Fu Q, Schauer AJ, Alexander B
Isotopic evidence of multiple controls on atmospheric oxidants over climate transitions
May 17, 2017
Nature
The abundance of tropospheric oxidants, such as ozone (O3) and hydroxyl (OH) and peroxy radicals (HO2 + RO2), determines the lifetimes of reduced trace gases such as methane and the production of particulate matter important for climate and human health. The response of tropospheric oxidants to climate change is poorly constrained owing to large uncertainties in the degree to which processes that influence oxidants may change with climate and owing to a lack of palaeo-records with which to constrain levels of atmospheric oxidants during past climate transitions. At present, it is thought that temperature-dependent emissions of tropospheric O3 precursors and water vapour abundance determine the climate response of oxidants, resulting in lower tropospheric O3 in cold climates while HOx (= OH + HO2 + RO2) remains relatively buffered. Here we report observations of oxygen-17 excess of nitrate (a proxy for the relative abundance of atmospheric O3 and HOx) from a Greenland ice core over the most recent glacial-interglacial cycle and for two Dansgaard-Oeschger events. We find that tropospheric oxidants are sensitive to climate change with an increase in the O3/HOx ratio in cold climates, the opposite of current expectations. We hypothesize that the observed increase in O3/HOx in cold climates is driven by enhanced stratosphere-to-troposphere transport of O3, and that reactive halogen chemistry is also enhanced in cold climates. Reactive halogens influence the oxidative capacity of the troposphere directly as oxidants themselves and indirectly via their influence on O3 and HOx. The strength of stratosphere-to-troposphere transport is largely controlled by the Brewer-Dobson circulation, which may be enhanced in colder climates owing to a stronger meridional gradient of sea surface temperatures, with implications for the response of tropospheric oxidants and stratospheric thermal and mass balance. These two processes may represent important, yet relatively unexplored, climate feedback mechanisms during major climate transitions.
Structure of the full-length glucagon class B G-protein-coupled receptor
May 17, 2017   Nature Add nature.com free-link Cancel
Zhang H, Qiao A, Yang D, Yang L, Dai A,   . . . . . .   , Stevens RC, Zhao Q, Jiang H, Wang MW, Wu B
Structure of the full-length glucagon class B G-protein-coupled receptor
May 17, 2017
Nature
The human glucagon receptor, GCGR, belongs to the class B G-protein-coupled receptor family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both the extracellular domain and transmembrane domain in an inactive conformation. The two domains are connected by a 12-residue segment termed the stalk, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of the GCGR transmembrane domain. The first extracellular loop exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen-deuterium exchange, disulfide crosslinking and molecular dynamics studies suggest that the stalk and the first extracellular loop have critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding of the signalling mechanisms of class B G-protein-coupled receptors.
Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators
May 17, 2017   Nature Add nature.com free-link Cancel
Song G, Yang D, Wang Y, de Graaf C, Zhou Q,   . . . . . .   , Wu B, Hanson MA, Liu ZJ, Wang MW, Stevens RC
Human GLP-1 receptor transmembrane domain structure in complex with allosteric modulators
May 17, 2017
Nature
The glucagon-like peptide-1 receptor (GLP-1R) and the glucagon receptor (GCGR) are members of the secretin-like class B family of G-protein-coupled receptors (GPCRs) and have opposing physiological roles in insulin release and glucose homeostasis. The treatment of type 2 diabetes requires positive modulation of GLP-1R to inhibit glucagon secretion and stimulate insulin secretion in a glucose-dependent manner. Here we report crystal structures of the human GLP-1R transmembrane domain in complex with two different negative allosteric modulators, PF-06372222 and NNC0640, at 2.7 and 3.0 Å resolution, respectively. The structures reveal a common binding pocket for negative allosteric modulators, present in both GLP-1R and GCGR and located outside helices V-VII near the intracellular half of the receptor. The receptor is in an inactive conformation with compounds that restrict movement of the intracellular tip of helix VI, a movement that is generally associated with activation mechanisms in class A GPCRs. Molecular modelling and mutagenesis studies indicate that agonist positive allosteric modulators target the same general region, but in a distinct sub-pocket at the interface between helices V and VI, which may facilitate the formation of an intracellular binding site that enhances G-protein coupling.
Haematopoietic stem and progenitor cells from human pluripotent stem cells
May 17, 2017   Nature Add nature.com free-link Cancel
Sugimura R, Jha DK, Han A, Soria-Valles C, da Rocha EL,   . . . . . .   , Keller G, Engelman AN, Snapper SB, Doulatov S, Daley GQ
Haematopoietic stem and progenitor cells from human pluripotent stem cells
May 17, 2017
Nature
A variety of tissue lineages can be differentiated from pluripotent stem cells by mimicking embryonic development through stepwise exposure to morphogens, or by conversion of one differentiated cell type into another by enforced expression of master transcription factors. Here, to yield functional human haematopoietic stem cells, we perform morphogen-directed differentiation of human pluripotent stem cells into haemogenic endothelium followed by screening of 26 candidate haematopoietic stem-cell-specifying transcription factors for their capacity to promote multi-lineage haematopoietic engraftment in mouse hosts. We recover seven transcription factors (ERG, HOXA5, HOXA9, HOXA10, LCOR, RUNX1 and SPI1) that are sufficient to convert haemogenic endothelium into haematopoietic stem and progenitor cells that engraft myeloid, B and T cells in primary and secondary mouse recipients. Our combined approach of morphogen-driven differentiation and transcription-factor-mediated cell fate conversion produces haematopoietic stem and progenitor cells from pluripotent stem cells and holds promise for modelling haematopoietic disease in humanized mice and for therapeutic strategies in genetic blood disorders.
SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands
May 16, 2017   PloS One
Huber S, Casagrande F, Hug MN, Wang L, Heine P, Kummer L, Plückthun A, Hennig M
SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands
May 16, 2017
PloS One
The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands. In this report, surface plasmon resonance was used as primary method to screen 6369 compounds. Thereby 44 hits were identified and confirmed in competition as well as dose-response experiments. Furthermore, 4 out of 8 selected hits were validated using nuclear magnetic resonance spectroscopy as orthogonal biophysical method. Computational analysis of the compound structures, taking the known crystal structure of the endogenous peptide agonist into consideration, gave insight into the potential fragment-binding location and interactions and inspires chemistry efforts for further exploration of the fragments.
Tea and coffee consumption in relation to DNA methylation in four European cohorts
May 23, 2017   Human Molecular Genetics
Ek WE, Tobi EW, Ahsan M, Lampa E, Ponzi E,   . . . . . .   , Vineis P, Lind L, Flanagan JM, Johansson Å, Epigenome-Wide Association study Consortium
Tea and coffee consumption in relation to DNA methylation in four European cohorts
May 23, 2017
Human Molecular Genetics
Lifestyle factors, such as food choices and exposure to chemicals, can alter DNA methylation and lead to changes in gene activity. Two such exposures with pharmacologically active components are coffee and tea consumption. Both coffee and tea has been suggested to play an important role in modulating disease-risk in humans by suppressing tumour progression, decreasing inflammation and influencing estrogen metabolism. These mechanisms may be mediated by changes in DNA methylation.To investigate if DNA methylation in blood is associated with coffee and tea consumption we performed a genome-wide DNA methylation study for coffee and tea consumption in four European cohorts (N = 3,096). DNA methylation was measured from whole blood at 421,695 CpG sites distributed throughout the genome and analysed in men and women both separately and together in each cohort. Meta-analyses of the results and additional regional-level analyses were performed.After adjusting for multiple testing, the meta-analysis revealed that two individual CpG-sites, mapping to DNAJC16 and TTC17, were differentially methylated in relation to tea consumption in women. No individual sites were associated in men or in the sex-combined analysis for tea or coffee. The regional analysis revealed that 28 regions were differentially methylated in relation to tea consumption in women. These regions contained genes known to interact with estradiol metabolism and cancer. No significant regions were found in the sex-combined and male-only analysis for either tea or coffee consumption. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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