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Thouvenin O, Keiser L, Cantaut-Belarif Y, Carbo-Tano M, Verweij F, Jurisch-Yaksi N, Bardet PL, van Niel G, Gallaire F, Wyart C. Origin and role of the cerebrospinal fluid bidirectional flow in the central canal. eLife 2020; 9:e47699. [PMID: 31916933 PMCID: PMC6989091 DOI: 10.7554/elife.47699] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Circulation of the cerebrospinal fluid (CSF) contributes to body axis formation and brain development. Here, we investigated the unexplained origins of the CSF flow bidirectionality in the central canal of the spinal cord of 30 hpf zebrafish embryos and its impact on development. Experiments combined with modeling and simulations demonstrate that the CSF flow is generated locally by caudally-polarized motile cilia along the ventral wall of the central canal. The closed geometry of the canal imposes the average flow rate to be null, explaining the reported bidirectionality. We also demonstrate that at this early stage, motile cilia ensure the proper formation of the central canal. Furthermore, we demonstrate that the bidirectional flow accelerates the transport of particles in the CSF via a coupled convective-diffusive transport process. Our study demonstrates that cilia activity combined with muscle contractions sustain the long-range transport of extracellular lipidic particles, enabling embryonic growth.
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7277
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Younes SHH, Tieves F, Lan D, Wang Y, Süss P, Brundiek H, Wever R, Hollmann F. Chemoenzymatic Halocyclization of γ,δ-Unsaturated Carboxylic Acids and Alcohols. CHEMSUSCHEM 2020; 13:97-101. [PMID: 31588652 PMCID: PMC6973245 DOI: 10.1002/cssc.201902240] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/04/2019] [Indexed: 06/10/2023]
Abstract
A chemoenzymatic method for the halocyclization of unsaturated alcohols and acids by using the robust V-dependent chloroperoxidase from Curvularia inaequalis (CiVCPO) as catalyst has been developed for the in situ generation of hypohalites. A broad range of halolactones and cyclic haloethers are formed with excellent performance of the biocatalyst.
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Gross-Vered M, Trzebanski S, Shemer A, Bernshtein B, Curato C, Stelzer G, Salame TM, David E, Boura-Halfon S, Chappell-Maor L, Leshkowitz D, Jung S. Defining murine monocyte differentiation into colonic and ileal macrophages. eLife 2020; 9:e49998. [PMID: 31916932 PMCID: PMC6952180 DOI: 10.7554/elife.49998] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 11/27/2019] [Indexed: 12/22/2022] Open
Abstract
Monocytes are circulating short-lived macrophage precursors that are recruited on demand from the blood to sites of inflammation and challenge. In steady state, classical monocytes give rise to vasculature-resident cells that patrol the luminal side of the endothelium. In addition, classical monocytes feed macrophage compartments of selected organs, including barrier tissues, such as the skin and intestine, as well as the heart. Monocyte differentiation under conditions of inflammation has been studied in considerable detail. In contrast, monocyte differentiation under non-inflammatory conditions remains less well understood. Here we took advantage of a combination of cell ablation and precursor engraftment to investigate the generation of gut macrophages from monocytes. Collectively, we identify factors associated with the gradual adaptation of monocytes to tissue residency. Moreover, comparison of monocyte differentiation into the colon and ileum-resident macrophages revealed the graduated acquisition of gut segment-specific gene expression signatures.
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7279
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Weiss T, Soroka T, Gorodisky L, Shushan S, Snitz K, Weissgross R, Furman-Haran E, Dhollander T, Sobel N. Human Olfaction without Apparent Olfactory Bulbs. Neuron 2020; 105:35-45.e5. [PMID: 31706696 PMCID: PMC6953431 DOI: 10.1016/j.neuron.2019.10.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/16/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022]
Abstract
The olfactory bulbs (OBs) are the first site of odor representation in the mammalian brain, and their unique ultrastructure is considered a necessary substrate for spatiotemporal coding of smell. Given this, we were struck by the serendipitous observation at MRI of two otherwise healthy young left-handed women, yet with no apparent OBs. Standardized tests revealed normal odor awareness, detection, discrimination, identification, and representation. Functional MRI of these women's brains revealed that odorant-induced activity in piriform cortex, the primary OB target, was similar in its extent to that of intact controls. Finally, review of a public brain-MRI database with 1,113 participants (606 women) also tested for olfactory performance, uncovered olfaction without anatomically defined OBs in ∼0.6% of women and ∼4.25% of left-handed women. Thus, humans can perform the basic facets of olfaction without canonical OBs, implying extreme plasticity in the functional neuroanatomy of this sensory system.
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7280
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Asadian M, Chan KV, Norouzi M, Grande S, Cools P, Morent R, De Geyter N. Fabrication and Plasma Modification of Nanofibrous Tissue Engineering Scaffolds. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E119. [PMID: 31936372 PMCID: PMC7023287 DOI: 10.3390/nano10010119] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/13/2019] [Accepted: 12/21/2019] [Indexed: 12/15/2022]
Abstract
This paper provides a comprehensive overview of nanofibrous structures for tissue engineering purposes and the role of non-thermal plasma technology (NTP) within this field. Special attention is first given to nanofiber fabrication strategies, including thermally-induced phase separation, molecular self-assembly, and electrospinning, highlighting their strengths, weaknesses, and potentials. The review then continues to discuss the biodegradable polyesters typically employed for nanofiber fabrication, while the primary focus lies on their applicability and limitations. From thereon, the reader is introduced to the concept of NTP and its application in plasma-assisted surface modification of nanofibrous scaffolds. The final part of the review discusses the available literature on NTP-modified nanofibers looking at the impact of plasma activation and polymerization treatments on nanofiber wettability, surface chemistry, cell adhesion/proliferation and protein grafting. As such, this review provides a complete introduction into NTP-modified nanofibers, while aiming to address the current unexplored potentials left within the field.
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7281
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Strepis N, Naranjo HD, Meier-Kolthoff J, Göker M, Shapiro N, Kyrpides N, Klenk HP, Schaap PJ, Stams AJM, Sousa DZ. Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species. BMC Genomics 2020; 21:24. [PMID: 31914924 PMCID: PMC6950789 DOI: 10.1186/s12864-019-6410-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 12/18/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The genus Trichococcus currently contains nine species: T. flocculiformis, T. pasteurii, T. palustris, T. collinsii, T. patagoniensis, T. ilyis, T. paludicola, T. alkaliphilus, and T. shcherbakoviae. In general, Trichococcus species can degrade a wide range of carbohydrates. However, only T. pasteurii and a non-characterized strain of Trichococcus, strain ES5, have the capacity of converting glycerol to mainly 1,3-propanediol. Comparative genomic analysis of Trichococcus species provides the opportunity to further explore the physiological potential and uncover novel properties of this genus. RESULTS In this study, a genotype-phenotype comparative analysis of Trichococcus strains was performed. The genome of Trichococcus strain ES5 was sequenced and included in the comparison with the other nine type strains. Genes encoding functions related to e.g. the utilization of different carbon sources (glycerol, arabinan and alginate), antibiotic resistance, tolerance to low temperature and osmoregulation could be identified in all the sequences analysed. T. pasteurii and Trichococcus strain ES5 contain a operon with genes encoding necessary enzymes for 1,3-PDO production from glycerol. All the analysed genomes comprise genes encoding for cold shock domains, but only five of the Trichococcus species can grow at 0 °C. Protein domains associated to osmoregulation mechanisms are encoded in the genomes of all Trichococcus species, except in T. palustris, which had a lower resistance to salinity than the other nine studied Trichococcus strains. CONCLUSIONS Genome analysis and comparison of ten Trichococcus strains allowed the identification of physiological traits related to substrate utilization and environmental stress resistance (e.g. to cold and salinity). Some substrates were used by single species, e.g. alginate by T. collinsii and arabinan by T. alkaliphilus. Strain ES5 may represent a subspecies of Trichococcus flocculiformis and contrary to the type strain (DSM 2094T), is able to grow on glycerol with the production of 1,3-propanediol.
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Wu C, Lien Y, Bondage D, Lin J, Pilhofer M, Shih Y, Chang JH, Lai E. Effector loading onto the VgrG carrier activates type VI secretion system assembly. EMBO Rep 2020; 21:e47961. [PMID: 31808291 PMCID: PMC6945064 DOI: 10.15252/embr.201947961] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023] Open
Abstract
The type VI secretion system (T6SS) is used by many bacteria to engage in social behavior and can affect the health of its host plant or animal. Because activities associated with T6SSs are often costly, T6SSs must be tightly regulated. However, our knowledge regarding how T6SS assembly and contraction are regulated remains limited. Using the plant pathogen Agrobacterium tumefaciens, we show that effectors are not just passengers but also impact on T6SS assembly. The A. tumefaciens strain C58 encodes one T6SS and two Tde DNase toxin effectors used as major weapons for interbacterial competition. Here, we demonstrate that loading of Tde effectors onto their cognate carriers, the VgrG spikes, is required for active T6SS secretion. The assembly of the TssBC contractile sheath occurs only in the presence of Tde effectors. The requirement of effector loading for efficient T6SS secretion was also validated in other A. tumefaciens strains. We propose that such a mechanism is used by bacteria as a strategy for efficacious T6SS firing and to ensure that effectors are loaded onto the T6SS prior to completing its assembly.
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Abstract
Herein, a visible-light photochemical approach for practical helicene functionalization at very mild reaction conditions is described. The photochemical reactions allow for the regiospecific and innate late-stage functionalization of helicenes and are easily executed either through the activation of C(sp2 )-Br bonds in helicenes using K2 CO3 as inorganic base or direct C(sp2 )-H helicene bond functionalization under oxidative photoredox reaction conditions. Overall, using these transformations six different functional groups are introduced to the helicene scaffold through C-C and four different C-heteroatom bond-forming reactions.
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Kentepozidou E, Aitken SJ, Feig C, Stefflova K, Ibarra-Soria X, Odom DT, Roller M, Flicek P. Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains. Genome Biol 2020; 21:5. [PMID: 31910870 PMCID: PMC6945661 DOI: 10.1186/s13059-019-1894-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/21/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS We carry out an experimental and computational study that exploits the natural genetic variation across five closely related species to assess how CTCF binding patterns stably fixed by evolution in each species contribute to the establishment and evolutionary dynamics of TAD boundaries. We perform CTCF ChIP-seq in multiple mouse species to create genome-wide binding profiles and associate them with TAD boundaries. Our analyses reveal that CTCF binding is maintained at TAD boundaries by a balance of selective constraints and dynamic evolutionary processes. Regardless of their conservation across species, CTCF binding sites at TAD boundaries are subject to stronger sequence and functional constraints compared to other CTCF sites. TAD boundaries frequently harbor dynamically evolving clusters containing both evolutionarily old and young CTCF sites as a result of the repeated acquisition of new species-specific sites close to conserved ones. The overwhelming majority of clustered CTCF sites colocalize with cohesin and are significantly closer to gene transcription start sites than nonclustered CTCF sites, suggesting that CTCF clusters particularly contribute to cohesin stabilization and transcriptional regulation. CONCLUSIONS Dynamic conservation of CTCF site clusters is an apparently important feature of CTCF binding evolution that is critical to the functional stability of a higher-order chromatin structure.
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Pedersini CA, Guàrdia-Olmos J, Montalà-Flaquer M, Cardobi N, Sanchez-Lopez J, Parisi G, Savazzi S, Marzi CA. Functional interactions in patients with hemianopia: A graph theory-based connectivity study of resting fMRI signal. PLoS One 2020; 15:e0226816. [PMID: 31905211 PMCID: PMC6944357 DOI: 10.1371/journal.pone.0226816] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
The assessment of task-independent functional connectivity (FC) after a lesion causing hemianopia remains an uncovered topic and represents a crucial point to better understand the neural basis of blindsight (i.e. unconscious visually triggered behavior) and visual awareness. In this light, we evaluated functional connectivity (FC) in 10 hemianopic patients and 10 healthy controls in a resting state paradigm. The main aim of this study is twofold: first of all we focused on the description and assessment of density and intensity of functional connectivity and network topology with and without a lesion affecting the visual pathway, and then we extracted and statistically compared network metrics, focusing on functional segregation, integration and specialization. Moreover, a study of 3-cycle triangles with prominent connectivity was conducted to analyze functional segregation calculated as the area of each triangle created connecting three neighboring nodes. To achieve these purposes we applied a graph theory-based approach, starting from Pearson correlation coefficients extracted from pairs of regions of interest. In these analyses we focused on the FC extracted by the whole brain as well as by four resting state networks: The Visual (VN), Salience (SN), Attention (AN) and Default Mode Network (DMN), to assess brain functional reorganization following the injury. The results showed a general decrease in density and intensity of functional connections, that leads to a less compact structure characterized by decrease in functional integration, segregation and in the number of interconnected hubs in both the Visual Network and the whole brain, despite an increase in long-range inter-modules connections (occipito-frontal connections). Indeed, the VN was the most affected network, characterized by a decrease in intra- and inter-network connections and by a less compact topology, with less interconnected nodes. Surprisingly, we observed a higher functional integration in the DMN and in the AN regardless of the lesion extent, that may indicate a functional reorganization of the brain following the injury, trying to compensate for the general reduced connectivity. Finally we observed an increase in functional specialization (lower between-network connectivity) and in inter-networks functional segregation, which is reflected in a less compact network topology, highly organized in functional clusters. These descriptive findings provide new insight on the spontaneous brain activity in hemianopic patients by showing an alteration in the intrinsic architecture of a large-scale brain system that goes beyond the impairment of a single RSN.
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Assiotis T. Determinantal Structures in Space-Inhomogeneous Dynamics on Interlacing Arrays. ANNALES HENRI POINCARE 2020; 21:909-940. [PMID: 32256187 PMCID: PMC7099887 DOI: 10.1007/s00023-019-00881-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 12/23/2019] [Indexed: 06/11/2023]
Abstract
We introduce a space-inhomogeneous generalization of the dynamics on interlacing arrays considered by Borodin and Ferrari (Commun Math Phys 325:603-684, 2014). We show that for a certain class of initial conditions the point process associated with the dynamics has determinantal correlation functions, and we calculate explicitly, in the form of a double contour integral, the correlation kernel for one of the most classical initial conditions, the densely packed. En route to proving this, we obtain some results of independent interest on non-intersecting general pure-birth chains, that generalize the Charlier process, the discrete analogue of Dyson's Brownian motion. Finally, these dynamics provide a coupling between the inhomogeneous versions of the TAZRP and PushTASEP particle systems which appear as projections on the left and right edges of the array, respectively.
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7287
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Haeger A, Alexander S, Vullings M, Kaiser FM, Veelken C, Flucke U, Koehl GE, Hirschberg M, Flentje M, Hoffman RM, Geissler EK, Kissler S, Friedl P. Collective cancer invasion forms an integrin-dependent radioresistant niche. J Exp Med 2020; 217:e20181184. [PMID: 31658985 PMCID: PMC7037234 DOI: 10.1084/jem.20181184] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 06/25/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022] Open
Abstract
Cancer fatalities result from metastatic dissemination and therapy resistance, both processes that depend on signals from the tumor microenvironment. To identify how invasion and resistance programs cooperate, we used intravital microscopy of orthotopic sarcoma and melanoma xenografts. We demonstrate that these tumors invade collectively and that, specifically, cells within the invasion zone acquire increased resistance to radiotherapy, rapidly normalize DNA damage, and preferentially survive. Using a candidate-based approach to identify effectors of invasion-associated resistance, we targeted β1 and αVβ3/β5 integrins, essential extracellular matrix receptors in mesenchymal tumors, which mediate cancer progression and resistance. Combining radiotherapy with β1 or αV integrin monotargeting in invading tumors led to relapse and metastasis in 40-60% of the cohort, in line with recently failed clinical trials individually targeting integrins. However, when combined, anti-β1/αV integrin dual targeting achieved relapse-free radiosensitization and prevented metastatic escape. Collectively, invading cancer cells thus withstand radiotherapy and DNA damage by β1/αVβ3/β5 integrin cross-talk, but efficient radiosensitization can be achieved by multiple integrin targeting.
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Celetti G, Paci G, Caria J, VanDelinder V, Bachand G, Lemke EA. The liquid state of FG-nucleoporins mimics permeability barrier properties of nuclear pore complexes. J Cell Biol 2020; 219:e201907157. [PMID: 31723007 PMCID: PMC7039189 DOI: 10.1083/jcb.201907157] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 09/21/2019] [Accepted: 10/09/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear pore complexes (NPCs) regulate all cargo traffic across the nuclear envelope. The transport conduit of NPCs is highly enriched in disordered phenylalanine/glycine-rich nucleoporins (FG-Nups), which form a permeability barrier of still elusive and highly debated molecular structure. Here we present a microfluidic device that triggered liquid-to-liquid phase separation of FG-Nups, which yielded droplets that showed typical properties of a liquid state. On the microfluidic chip, droplets were perfused with different transport-competent or -incompetent cargo complexes, and then the permeability barrier properties of the droplets were optically interrogated. We show that the liquid state mimics permeability barrier properties of the physiological nuclear transport pathway in intact NPCs in cells: that is, inert cargoes ranging from small proteins to large capsids were excluded from liquid FG-Nup droplets, but functional import complexes underwent facilitated import into droplets. Collectively, these data provide an experimental model of how NPCs can facilitate fast passage of cargoes across an order of magnitude in cargo size.
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7289
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Casanova A, Gomis-Berenguer A, Canizares A, Simon P, Calzada D, Ania CO. Carbon Black as Conductive Additive and Structural Director of Porous Carbon Gels. MATERIALS (BASEL, SWITZERLAND) 2020; 13:E217. [PMID: 31947941 PMCID: PMC6981367 DOI: 10.3390/ma13010217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 11/16/2022]
Abstract
This work investigates the impact of carbon black (CB) as a porogenic agent and conductive additive in the preparation of electrically conductive nanoporous carbon gels. For this, a series of materials were prepared by the polycondensation of resorcinol/formaldehyde mixtures in the presence of increasing amounts of carbon black. The conductivity of the carbon gel/CB composites increased considerably with the amount of CB, indicating a good dispersion of the additive within the carbon matrix. A percolation threshold of ca. 8 wt.% of conductive additive was found to achieve an adequate "point to point" conductive network. This value is higher than that reported for other additives, owing to the synthetic route chosen, as the additive was incorporated in the reactant's mixture (pre-synthesis) rather than in the formulation of the electrodes ink (post-synthesis). The CB strongly influenced the development of the porous architecture of the gels that exhibited a multimodal mesopore structure comprised of two distinct pore networks. The microporosity and the primary mesopore structure remained rather unchanged. On the contrary, a secondary network of mesopores was formed in the presence of the additive. Furthermore, the average mesopore size and the volume of the secondary network increased with the amount of CB.
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7290
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Murugadoss S, van den Brule S, Brassinne F, Sebaihi N, Mejia J, Lucas S, Petry J, Godderis L, Mast J, Lison D, Hoet PH. Is aggregated synthetic amorphous silica toxicologically relevant? Part Fibre Toxicol 2020; 17:1. [PMID: 31900181 PMCID: PMC6942297 DOI: 10.1186/s12989-019-0331-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/10/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The regulatory definition(s) of nanomaterials (NMs) frequently uses the term 'agglomerates and aggregates' (AA) despite the paucity of evidence that AA are significantly relevant from a nanotoxicological perspective. This knowledge gap greatly affects the safety assessment and regulation of NMs, such as synthetic amorphous silica (SAS). SAS is used in a large panel of industrial applications. They are primarily produced as nano-sized particles (1-100 nm in diameter) and considered safe as they form large aggregates (> 100 nm) during the production process. So far, it is indeed believed that large aggregates represent a weaker hazard compared to their nano counterpart. Thus, we assessed the impact of SAS aggregation on in vitro cytotoxicity/biological activity to address the toxicological relevance of aggregates of different sizes. RESULTS We used a precipitated SAS dispersed by different methods, generating 4 ad-hoc suspensions with different aggregate size distributions. Their effect on cell metabolic activity, cell viability, epithelial barrier integrity, total glutathione content and, IL-8 and IL-6 secretion were investigated after 24 h exposure in human bronchial epithelial (HBE), colon epithelial (Caco2) and monocytic cells (THP-1). We observed that the de-aggregated suspension (DE-AGGR), predominantly composed of nano-sized aggregates, induced stronger effects in all the cell lines than the aggregated suspension (AGGR). We then compared DE-AGGR with 2 suspensions fractionated from AGGR: the precipitated fraction (PREC) and the supernatant fraction (SuperN). Very large aggregates in PREC were found to be the least cytotoxic/biologically active compared to other suspensions. SuperN, which contains aggregates larger in size (> 100 nm) than in DE-AGGR but smaller than PREC, exhibited similar activity as DE-AGGR. CONCLUSION Overall, aggregation resulted in reduced toxicological activity of SAS. However, when comparing aggregates of different sizes, it appeared that aggregates > 100 nm were not necessarily less cytotoxic than their nano-sized counterparts. This study suggests that aggregates of SAS are toxicologically relevant for the definition of NMs.
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Vink JNA, Martens KJA, Vlot M, McKenzie RE, Almendros C, Estrada Bonilla B, Brocken DJW, Hohlbein J, Brouns SJJ. Direct Visualization of Native CRISPR Target Search in Live Bacteria Reveals Cascade DNA Surveillance Mechanism. Mol Cell 2020; 77:39-50.e10. [PMID: 31735642 DOI: 10.1016/j.molcel.2019.10.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 07/31/2019] [Accepted: 10/11/2019] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas systems encode RNA-guided surveillance complexes to find and cleave invading DNA elements. While it is thought that invaders are neutralized minutes after cell entry, the mechanism and kinetics of target search and its impact on CRISPR protection levels have remained unknown. Here, we visualize individual Cascade complexes in a native type I CRISPR-Cas system. We uncover an exponential relation between Cascade copy number and CRISPR interference levels, pointing to a time-driven arms race between invader replication and target search, in which 20 Cascade complexes provide 50% protection. Driven by PAM-interacting subunit Cas8e, Cascade spends half its search time rapidly probing DNA (∼30 ms) in the nucleoid. We further demonstrate that target DNA transcription and CRISPR arrays affect the integrity of Cascade and affect CRISPR interference. Our work establishes the mechanism of cellular DNA surveillance by Cascade that allows the timely detection of invading DNA in a crowded, DNA-packed environment.
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Shin D, Mukherjee R, Liu Y, Gonzalez A, Bonn F, Liu Y, Rogov VV, Heinz M, Stolz A, Hummer G, Dötsch V, Luo ZQ, Bhogaraju S, Dikic I. Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB. Mol Cell 2020; 77:164-179.e6. [PMID: 31732457 PMCID: PMC6941232 DOI: 10.1016/j.molcel.2019.10.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/07/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
Abstract
The family of bacterial SidE enzymes catalyzes non-canonical phosphoribosyl-linked (PR) serine ubiquitination and promotes infectivity of Legionella pneumophila. Here, we describe identification of two bacterial effectors that reverse PR ubiquitination and are thus named deubiquitinases for PR ubiquitination (DUPs; DupA and DupB). Structural analyses revealed that DupA and SidE ubiquitin ligases harbor a highly homologous catalytic phosphodiesterase (PDE) domain. However, unlike SidE ubiquitin ligases, DupA displays increased affinity to PR-ubiquitinated substrates, which allows DupA to cleave PR ubiquitin from substrates. Interfering with DupA-ubiquitin binding switches its activity toward SidE-type ligase. Given the high affinity of DupA to PR-ubiquitinated substrates, we exploited a catalytically inactive DupA mutant to trap and identify more than 180 PR-ubiquitinated host proteins in Legionella-infected cells. Proteins involved in endoplasmic reticulum (ER) fragmentation and membrane recruitment to Legionella-containing vacuoles (LCV) emerged as major SidE targets. The global map of PR-ubiquitinated substrates provides critical insights into host-pathogen interactions during Legionella infection.
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Erratum. Clin Infect Dis 2020; 70:359. [PMID: 31750890 PMCID: PMC7392166 DOI: 10.1093/cid/ciz1048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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7294
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Huang L, Zhu C, Yi L, Yue H, Kancherla R, Rueping M. Cascade Cross-Coupling of Dienes: Photoredox and Nickel Dual Catalysis. Angew Chem Int Ed Engl 2020; 59:457-464. [PMID: 31778289 PMCID: PMC6973272 DOI: 10.1002/anie.201911109] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Indexed: 12/12/2022]
Abstract
Chemical transformations based on cascade reactions have the potential to simplify the preparation of diverse and architecturally complex molecules dramatically. Herein, we disclose an unprecedented and efficient method for the cross-coupling of radical precursors, dienes, and electrophilic coupling partners via a photoredox- and nickel-enabled cascade cross-coupling process. The cascade reaction furnishes a diverse array of saturated carbo- and heterocyclic scaffolds, thus providing access to a quick gain in C-C bond saturation.
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7295
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Blueschke D, Savin I, Blueschke-Nikolaeva V. An Evolutionary Approach to Passive Learning in Optimal Control Problems. COMPUTATIONAL ECONOMICS 2020; 56:659-673. [PMID: 33268916 PMCID: PMC7674569 DOI: 10.1007/s10614-019-09961-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 11/16/2019] [Indexed: 06/12/2023]
Abstract
We consider the optimal control problem of a small nonlinear econometric model under parameter uncertainty and passive learning (open-loop feedback). Traditionally, this type of problems has been approached by applying linear-quadratic optimization algorithms. However, the literature demonstrated that those methods are very sensitive to the choice of random seeds frequently producing very large objective function values (outliers). Furthermore, to apply those established methods, the original nonlinear problem must be linearized first, which runs the risk of solving already a different problem. Following Savin and Blueschke (Comput Econ 48(2):317-338, 2016) in explicitly addressing parameter uncertainty with a large Monte Carlo experiment of possible parameter realizations and optimizing it with the Differential Evolution algorithm, we extend this approach to the case of passive learning. Our approach provides more robust results demonstrating greater benefit from learning, while at the same time does not require to modify the original nonlinear problem at hand. This result opens new avenues for application of heuristic optimization methods to learning strategies in optimal control research.
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7296
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Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes (Basel) 2020; 11:E50. [PMID: 31906474 PMCID: PMC7017230 DOI: 10.3390/genes11010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
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7297
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Yang S, Chen G, Ricciardulli AG, Zhang P, Zhang Z, Shi H, Ma J, Zhang J, Blom PWM, Feng X. Topochemical Synthesis of Two-Dimensional Transition-Metal Phosphides Using Phosphorene Templates. Angew Chem Int Ed Engl 2020; 59:465-470. [PMID: 31593361 PMCID: PMC6972539 DOI: 10.1002/anie.201911428] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Indexed: 11/18/2022]
Abstract
Transition-metal phosphides (TMPs) have emerged as a fascinating class of narrow-gap semiconductors and electrocatalysts. However, they are intrinsic nonlayered materials that cannot be delaminated into two-dimensional (2D) sheets. Here, we demonstrate a general bottom-up topochemical strategy to synthesize a series of 2D TMPs (e.g. Co2 P, Ni12 P5 , and Cox Fe2-x P) by using phosphorene sheets as the phosphorus precursors and 2D templates. Notably, 2D Co2 P is a p-type semiconductor, with a hole mobility of 20.8 cm2 V-1 s-1 at 300 K in field-effect transistors. It also behaves as a promising electrocatalyst for the oxygen evolution reaction (OER), thanks to the charge-transport modulation and improved surface exposure. In particular, iron-doped Co2 P (i.e. Co1.5 Fe0.5 P) delivers a low overpotential of only 278 mV at a current density of 10 mA cm-2 that outperforms the commercial Ir/C benchmark (304 mV).
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7298
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Heidemann J, Kölbel K, Konijnenberg A, Van Dyck J, Garcia-Alai M, Meijers R, Sobott F, Uetrecht C. Further insights from structural mass spectrometry into endocytosis adaptor protein assemblies. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 447:116240. [PMID: 33244295 PMCID: PMC7116418 DOI: 10.1016/j.ijms.2019.116240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
As a fundament in many biologically relevant processes, endocytosis in its different guises has been arousing interest for decades and still does so. This is true for the actual transport and its initiation alike. In clathrin-mediated endocytosis, a comparatively well understood endocytic pathway, a set of adaptor proteins bind specific lipids in the plasma membrane, subsequently assemble and thus form a crucial bridge from clathrin to actin for the ongoing process. These adaptor proteins are highly interesting themselves and the subject of this manuscript. Using many of the instruments that are available now in the mass spectrometry toolbox, we added some facets to the picture of how these minimal assemblies may look, how they form, and what influences the structure. Especially, lipids in the adaptor protein complexes result in reduced charging of a normal sized complex due to their specific binding position. The results further support our structural model of a double ring structure with interfacial lipids.
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7299
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Pinheiro de Castro ÉC, Demirtas R, Orteu A, Olsen CE, Motawie MS, Zikan Cardoso M, Zagrobelny M, Bak S. The dynamics of cyanide defences in the life cycle of an aposematic butterfly: Biosynthesis versus sequestration. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 116:103259. [PMID: 31698083 DOI: 10.1016/j.ibmb.2019.103259] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 06/10/2023]
Abstract
Heliconius butterflies are highly specialized in Passiflora plants, laying eggs and feeding as larvae only on them. Interestingly, both Heliconius butterflies and Passiflora plants contain cyanogenic glucosides (CNglcs). While feeding on specific Passiflora species, Heliconius melpomene larvae are able to sequester simple cyclopentenyl CNglcs, the most common CNglcs in this plant genus. Yet, aromatic, aliphatic, and modified CNglcs have been reported in Passiflora species and they were never tested for sequestration by heliconiine larvae. As other cyanogenic lepidopterans, H. melpomene also biosynthesize the aliphatic CNglcs linamarin and lotaustralin, and their toxicity does not rely exclusively on sequestration. Although the genes encoding the enzymes in the CNglc biosynthesis have not yet been biochemically characterized in butterflies, the cytochromes P450 CYP405A4, CYP405A5, CYP405A6 and CYP332A1 have been hypothesized to be involved in this pathway in H. melpomene. In this study, we determine how the CNglc composition and expression of the putative P450s involved in the biosynthesis of these compounds vary at different developmental stages of Heliconius butterflies. We also establish which kind of CNglcs H. melpomene larvae can sequester from Passiflora. By analysing the chemical composition of the haemolymph from larvae fed with different Passiflora diets, we show that H. melpomene is able to sequestered prunasin, an aromatic CNglcs, from P. platyloba. They are also able to sequester amygdalin, gynocardin, [C13/C14]linamarin and [C13/C14]lotaustralin painted on the plant leaves. The CNglc tetraphyllin B-sulphate from P. caerulea is not detected in the larval haemolymph, suggesting that such modified CNglcs cannot be sequestered by Heliconius. Although pupae and virgin adults contain dihydrogynocardin resulting from larval sequestration, this compound was metabolized during adulthood, and not used as nuptial gift or transferred to the offspring. Thus, we speculate that dihydrogynocardin is catabolized to recycle nitrogen and glucose, and/or to produce fitness signals during courtship. Mature adults have a higher concentration of CNglcs than any other developmental stages due to increased de novo biosynthesis of linamarin and lotaustralin. Accordingly, all CYP405As are expressed in adults, whereas larvae mostly express CYP405A4. Our results shed light on the importance of CNglcs for Heliconius biology and their coevolution with Passiflora.
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7300
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Fu C, Yao M, Chen X, Maulana LZ, Li X, Yang J, Imasato K, Zhu F, Li G, Auffermann G, Burkhardt U, Schnelle W, Zhou J, Zhu T, Zhao X, Shi M, Dressel M, Pronin AV, Snyder GJ, Felser C. Revealing the Intrinsic Electronic Structure of 3D Half-Heusler Thermoelectric Materials by Angle-Resolved Photoemission Spectroscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1902409. [PMID: 31921571 PMCID: PMC6947594 DOI: 10.1002/advs.201902409] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/02/2019] [Indexed: 05/28/2023]
Abstract
Accurate determination of the intrinsic electronic structure of thermoelectric materials is a prerequisite for utilizing an electronic band engineering strategy to improve their thermoelectric performance. Herein, with high-resolution angle-resolved photoemission spectroscopy (ARPES), the intrinsic electronic structure of the 3D half-Heusler thermoelectric material ZrNiSn is revealed. An unexpectedly large intrinsic bandgap is directly observed by ARPES and is further confirmed by electrical and optical measurements and first-principles calculations. Moreover, a large anisotropic conduction band with an anisotropic factor of 6 is identified by ARPES and attributed to be one of the most important reasons leading to the high thermoelectric performance of ZrNiSn. These successful findings rely on the grown high-quality single crystals, which have fewer Ni interstitial defects and negligible in-gap states on the electronic structure. This work demonstrates a realistic paradigm to investigate the electronic structure of 3D solid materials by using ARPES and provides new insights into the intrinsic electronic structure of the half-Heusler system benefiting further optimization of thermoelectric performance.
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