RESUMEN
Ubiquitin ligation is typically executed by hallmark E3 catalytic domains. Two such domains, 'cullin-RING' and 'RBR', are individually found in several hundred human E3 ligases, and collaborate with E2 enzymes to catalyze ubiquitylation. However, the vertebrate-specific CUL9 complex with RBX1 (also called ROC1), of interest due to its tumor suppressive interaction with TP53, uniquely encompasses both cullin-RING and RBR domains. Here, cryo-EM, biochemistry and cellular assays elucidate a 1.8-MDa hexameric human CUL9-RBX1 assembly. Within one dimeric subcomplex, an E2-bound RBR domain is activated by neddylation of its own cullin domain and positioning from the adjacent CUL9-RBX1 in trans. Our data show CUL9 as unique among RBX1-bound cullins in dependence on the metazoan-specific UBE2F neddylation enzyme, while the RBR domain protects it from deneddylation. Substrates are recruited to various upstream domains, while ubiquitylation relies on both CUL9's neddylated cullin and RBR domains achieving self-assembled and chimeric cullin-RING/RBR E3 ligase activity.
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Microscopía por Crioelectrón , Proteínas Cullin , Enzimas Ubiquitina-Conjugadoras , Ubiquitinación , Humanos , Proteínas Portadoras/metabolismo , Proteínas Portadoras/química , Proteínas Portadoras/genética , Proteínas Cullin/metabolismo , Proteínas Cullin/química , Células HEK293 , Modelos Moleculares , Proteína NEDD8/metabolismo , Proteína NEDD8/genética , Proteína NEDD8/química , Unión Proteica , Multimerización de Proteína , Enzimas Ubiquitina-Conjugadoras/metabolismo , Enzimas Ubiquitina-Conjugadoras/química , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitina-Proteína Ligasas/química , Ubiquitina-Proteína Ligasas/genéticaRESUMEN
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
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Ubiquitina-Proteína Ligasas , Ubiquitina , Humanos , Ubiquitina/química , Microscopía por Crioelectrón , Ubiquitina-Proteína Ligasas/metabolismo , Enzimas Ubiquitina-Conjugadoras/metabolismo , Ubiquitinas/metabolismo , UbiquitinaciónRESUMEN
Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.
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Saccharomyces cerevisiae , Enzimas Ubiquitina-Conjugadoras , Humanos , Enzimas Ubiquitina-Conjugadoras/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Fosforilación , Microscopía por Crioelectrón , Ubiquitina-Proteína Ligasas/metabolismo , UbiquitinaciónRESUMEN
BACKGROUND: Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. RESULTS: To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). CONCLUSIONS: Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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Proteínas de Drosophila , Infertilidad , Femenino , Animales , Drosophila , Drosophila melanogaster/genética , Histonas/genética , Ensamble y Desensamble de Cromatina/genética , Biología Computacional , Proteínas de Drosophila/genética , Factores de Transcripción/genética , Proteínas de Homeodominio/genética , Proteínas Serina-Treonina QuinasasRESUMEN
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Quirópteros , Animales , Filogenia , Quirópteros/genética , ADN Mitocondrial/genética , Evolución Biológica , CromosomasRESUMEN
Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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The efficient removal of organic refractory pollutants such as dyes and antibiotics in wastewater is crucial for protecting the environment and human health. In this work, a NiCo-layered double hydroxide (NiCo-LDH) with a uniform microspherical, hierarchical structure and a high surface area was successfully synthesized as an effective peroxymonosulfate (PMS) activator for the degradation of various organic dyes and antibiotics. The influence of various parameters on the catalytic activity of the NiCo-LDH was determined. Radical scavenger studies unveiled the major reactive oxygen species (ROSs) generated in the NiCo-LDH/PSM system to be 1O2, SO4â¢-, and O2â¢-. Ex-situ X-ray photoelectron spectroscopy (XPS) analysis uncovered the role of Co sites and oxygen vacancy as active sites and revealed the reversible redox properties of NiCo-LDH based on Co2+/Co3+ cycles. The activation mechanism and Rhodamine B (RhB) degradation pathways were experimentally studied and proposed. The NiCo-LDH is highly versatile, reusable and stable as shown by post-catalysis characterizations. This work shows the excellent catalysis performances and provides insights into the activation mechanism of PMS by NiCo-LDH for organic pollutant remediation.
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Hidróxidos , Peróxidos , Humanos , Peróxidos/química , Hidróxidos/química , ColorantesRESUMEN
Novel species of fungi described in this study include those from various countries as follows: Argentina, Neocamarosporium halophilum in leaf spots of Atriplex undulata. Australia, Aschersonia merianiae on scale insect (Coccoidea), Curvularia huamulaniae isolated from air, Hevansia mainiae on dead spider, Ophiocordyceps poecilometigena on Poecilometis sp. Bolivia, Lecanora menthoides on sandstone, in open semi-desert montane areas, Sticta monlueckiorum corticolous in a forest, Trichonectria epimegalosporae on apothecia of corticolous Megalospora sulphurata var. sulphurata, Trichonectria puncteliae on the thallus of Punctelia borreri. Brazil, Catenomargarita pseudocercosporicola (incl. Catenomargarita gen. nov.) hyperparasitic on Pseudocercospora fijiensis on leaves of Musa acuminata, Tulasnella restingae on protocorms and roots of Epidendrum fulgens. Bulgaria, Anthracoidea umbrosae on Carex spp. Croatia, Hymenoscyphus radicis from surface-sterilised, asymptomatic roots of Microthlaspi erraticum, Orbilia multiserpentina on wood of decorticated branches of Quercus pubescens. France, Calosporella punctatispora on dead corticated twigs of Aceropalus. French West Indies (Martinique), Eutypella lechatii on dead corticated palm stem. Germany, Arrhenia alcalinophila on loamy soil. Iceland, Cistella blauvikensis on dead grass (Poaceae). India, Fulvifomes maritimus on living Peltophorum pterocarpum, Fulvifomes natarajanii on dead wood of Prosopis juliflora, Fulvifomes subazonatus on trunk of Azadirachta indica, Macrolepiota bharadwajii on moist soil near the forest, Narcissea delicata on decaying elephant dung, Paramyrothecium indicum on living leaves of Hibiscus hispidissimus, Trichoglossum syamviswanathii on moist soil near the base of a bamboo plantation. Iran, Vacuiphoma astragalicola from stem canker of Astragalus sarcocolla. Malaysia, Neoeriomycopsis fissistigmae (incl. Neoeriomycopsidaceae fam. nov.) on leaf spots on flower Fissistigma sp. Namibia, Exophiala lichenicola lichenicolous on Acarospora cf. luederitzensis. Netherlands, Entoloma occultatum on soil, Extremus caricis on dead leaves of Carex sp., Inocybe pseudomytiliodora on loamy soil. Norway, Inocybe guldeniae on calcareous soil, Inocybe rupestroides on gravelly soil. Pakistan, Hymenagaricus brunneodiscus on soil. Philippines, Ophiocordyceps philippinensis parasitic on Asilus sp. Poland, Hawksworthiomyces ciconiae isolated from Ciconia ciconia nest, Plectosphaerella vigrensis from leaf spots on Impatiens noli-tangere, Xenoramularia epitaxicola from sooty mould community on Taxus baccata. Portugal, Inocybe dagamae on clay soil. Saudi Arabia, Diaporthe jazanensis on branches of Coffea arabica. South Africa, Alternaria moraeae on dead leaves of Moraea sp., Bonitomyces buffels-kloofinus (incl. Bonitomyces gen. nov.) on dead twigs of unknown tree, Constrictochalara koukolii on living leaves of Itea rhamnoides colonised by a Meliola sp., Cylindromonium lichenophilum on Parmelina tiliacea, Gamszarella buffelskloofina (incl. Gamszarella gen. nov.) on dead insect, Isthmosporiella africana (incl. Isthmosporiella gen. nov.) on dead twigs of unknown tree, Nothoeucasphaeria buffelskloofina (incl. Nothoeucasphaeria gen. nov.), on dead twigs of unknown tree, Nothomicrothyrium beaucarneae (incl. Nothomicrothyrium gen. nov.) on dead leaves of Beaucarnea stricta, Paramycosphaerella proteae on living leaves of Protea caffra, Querciphoma foliicola on leaf litter, Rachicladosporium conostomii on dead twigs of Conostomium natalense var. glabrum, Rhamphoriopsis synnematosa on dead twig of unknown tree, Waltergamsia mpumalanga on dead leaves of unknown tree. Spain, Amanita fulvogrisea on limestone soil, in mixed forest, Amanita herculis in open Quercus forest, Vuilleminia beltraniae on Cistus symphytifolius. Sweden, Pachyella pulchella on decaying wood on sand-silt riverbank. Thailand, Deniquelata cassiae on dead stem of Cassia fistula, Stomiopeltis thailandica on dead twigs of Magnolia champaca. Ukraine, Circinaria podoliana on natural limestone outcrops, Neonematogonum carpinicola (incl. Neonematogonum gen. nov.) on dead branches of Carpinus betulus. USA, Exophiala wilsonii water from cooling tower, Hygrophorus aesculeticola on soil in mixed forest, and Neocelosporium aereum from air in a house attic. Morphological and culture characteristics are supported by DNA barcodes. Citation: Crous PW, Costa MM, Kandemir H, et al. 2023. Fungal Planet description sheets: 1550-1613. Persoonia 51: 280-417. doi: 10.3767/persoonia.2023.51.08.
RESUMEN
Panax vietnamensis Ha et Grushv. is a precious medicinal species native to the tropical forests of Vietnam. Due to habitat loss and over-harvesting, this species is endangered in Vietnam. To conserve the species, we investigated genetic variability and population structure using nine microsatellites for 148 individuals from seven populations across the current distribution range of P. vietnamensis in Vietnam. We determined a moderate genetic diversity within populations (HO = 0.367, HE = 0.437) and relatively low population differentiation (the Weir and Cockerham index of 0.172 and the Hedrick index of 0.254) and showed significant differentiation (P < 0.05), which suggested fragmented habitats, over-utilization and over-harvesting of P. vietnamensis. Different clustering methods revealed that individuals were grouped into two major clusters, which were associated with gene flow across the geographical range of P. vietnamensis. This study also detected that ginseng populations can have undergone a recent bottleneck. We recommend measures in future P. vietnamensis conservation and breeding programs.
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Panax , Humanos , Panax/genética , Panax/química , Vietnam , Fitomejoramiento , Repeticiones de Microsatélite/genética , Pueblo Asiatico , Variación Genética/genéticaRESUMEN
BACKGROUND: Optimal drug dosing is important to ensure adequate response to treatment, prevent development of drug resistance and reduce drug toxicity. The aim of these clinical standards is to provide guidance on 'best practice´ for dosing and management of TB drugs.METHODS: A panel of 57 global experts in the fields of microbiology, pharmacology and TB care were identified; 51 participated in a Delphi process. A 5-point Likert scale was used to score draft standards. The final document represents the broad consensus and was approved by all participants.RESULTS: Six clinical standards were defined: Standard 1, defining the most appropriate initial dose for TB treatment; Standard 2, identifying patients who may be at risk of sub-optimal drug exposure; Standard 3, identifying patients at risk of developing drug-related toxicity and how best to manage this risk; Standard 4, identifying patients who can benefit from therapeutic drug monitoring (TDM); Standard 5, highlighting education and counselling that should be provided to people initiating TB treatment; and Standard 6, providing essential education for healthcare professionals. In addition, consensus research priorities were identified.CONCLUSION: This is the first consensus-based Clinical Standards for the dosing and management of TB drugs to guide clinicians and programme managers in planning and implementation of locally appropriate measures for optimal person-centred treatment to improve patient care.
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Antituberculosos , Monitoreo de Drogas , Tuberculosis , Humanos , Atención al Paciente , Estándares de Referencia , Tuberculosis/tratamiento farmacológico , Antituberculosos/administración & dosificaciónRESUMEN
We propose a theoretical model to elucidate intermolecular electrostatic interactions between a virus and a substrate. Our model treats the virus as a homogeneous particle having surface charge and the polymer fiber of the respirator as a charged plane. Electric potentials surrounding the virus and fiber are influenced by the surface charge distribution of the virus. We use Poisson-Boltzmann equations to calculate electric potentials. Then, Derjaguin's approximation and a linear superposition of the potential function are extended to determine the electrostatic force. In this work, we apply this model for coronavirus or SARS-CoV-2 case and numerical results quantitatively agree with prior simulation. We find that the influence of fiber's potential on the surface charge of the virus is important and is considered in interaction calculations to obtain better accuracy. The electrostatic interaction significantly decays with increasing separation distance, and this curve becomes steeper when adding more salt. Although the interaction force increases with heating, one can observe the repulsive-attractive transition when the environment is acidic.
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Background: Various studies have reported a decrease in emergency department admissions in correlation with major sporting events. However, these studies limit the investigation of selected variables to the 24-hour periods on game days. For our study, we assessed the impact of New Orleans Saints football team games on medical admissions on game days and also on post-game days. Methods: We collected Saints game results from the 2013-2014 to 2019-2020 season and admissions data from 3 local hospitals during the same 7-year period. We compared the average daily census of game days vs non-game days as our control group using a 2-sample t test with unequal variances. Results: The results demonstrate a statistically significant reduction in the average number of internal medicine admissions on game days (19.6%, P=0.0001). This reduction in admissions was not observed on post-game days (5.84%, P>0.05). On post-game days following a Saints victory, we found a statistically significant increase in the average number of admissions compared to when the team lost the previous day (18.2%, P=0.0105). Conclusion: To our knowledge, the relationship between a recurring major sporting event and inpatient internal medicine admissions has not been previously quantified. Our study of the impact of the New Orleans Saints football games on internal medicine admissions provides insights into the relationship between social sporting events and health outcomes in the city. While our results may not be directly generalizable to other locations-particularly those that are not in a National Football League team market-we showed that during a 7-year period, Saints football games correlated with a 19.6% decrease in internal medicine admissions on the day of the game. This finding suggests that Saints games may serve as a protective factor associated with decreased negative health outcomes among residents in the city.
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BACKGROUND: Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Allo-HSCT recipients with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated pipeline and de novo analysis on pooled routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal, and unexpected viruses. RESULTS: Median duration of intensive immunosuppression was 5.1 months (IQR 5.5). GvHD-related mortality rate was 36%. mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥ 3 distinct viruses were detected in 16/25 patients; Anelloviridae (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7 patients with fatal outcomes, viral sequences not assessed by routine investigations were identified with mNGS and confirmed by RT-PCR. These cases included Usutu virus (1), rubella virus (1 vaccine strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1). CONCLUSIONS: Clinically unrecognized viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid-refractory/dependent GvHD in consecutive samples. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations, or re-infection. Video abstract.
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Enfermedad Injerto contra Huésped/sangre , Enfermedad Injerto contra Huésped/virología , Secuenciación de Nucleótidos de Alto Rendimiento , Metagenómica , Esteroides , Adulto , Anciano , Humanos , Masculino , Persona de Mediana Edad , Estudios Prospectivos , Esteroides/efectos adversos , Esteroides/uso terapéutico , Adulto JovenRESUMEN
We theoretically investigate high-pressure effects on the atomic dynamics of metallic glasses. The theory predicts compression-induced rejuvenation and the resulting strain hardening that have been recently observed in metallic glasses. Structural relaxation under pressure is mainly governed by local cage dynamics. The external pressure restricts the dynamical constraints and slows down the atomic mobility. In addition, the compression induces a rejuvenated metastable state (local minimum) at a higher energy in the free-energy landscape. Thus, compressed metallic glasses can rejuvenate and the corresponding relaxation is reversible. This behavior leads to strain hardening in mechanical deformation experiments. Theoretical predictions agree well with experiments.
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Enfermedades Autoinmunes/psicología , Enfermedades Autoinmunes/terapia , Trastorno Obsesivo Compulsivo/psicología , Trastorno Obsesivo Compulsivo/terapia , Infecciones Estreptocócicas/psicología , Infecciones Estreptocócicas/terapia , Enfermedad Aguda , Antibacterianos/uso terapéutico , Enfermedades Autoinmunes/tratamiento farmacológico , Azitromicina/uso terapéutico , Terapia Conductista/métodos , Niño , Diagnóstico Diferencial , Humanos , Masculino , Trastorno Obsesivo Compulsivo/tratamiento farmacológico , Penicilinas/uso terapéutico , Infecciones Estreptocócicas/tratamiento farmacológicoRESUMEN
We theoretically investigate equilibrium behaviors and photothermal effects of a flexible plasmonic metamaterial composed of aramid nanofibers and gold nanoparticles. The fiber matrix is considered as an external field to reconfigure a nanoparticle assembly. We find that the heating process tunes particle-particle and fiber-particle interactions, which alter adsorption of nanoparticles on fiber surfaces or clustering in pore spaces. Thus, it is possible to control the nanoparticle self-assembly by laser illumination. Gold nanoparticles strongly absorb radiations and efficiently dissipate absorbed energy into heat. By solving the heat transfer equation associated with an effective medium approximation, we calculate the spatial temperature rise. Remarkably, our theoretical results quantitatively agree with prior experiments. This indicates that we can ignore plasmonic coupling effects induced by particle clustering. Effects of the laser spot size and intensity on the photothermal heating are also discussed.
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The photothermal energy conversion in hanging and floating polyaniline (PANi)-cotton fabrics is investigated using a model based on the heat diffusion equation. Perfect absorption and anti-reflection of wet hanging PANi-cotton fabrics cause quick transfer of total incident light into water confining nearly 100% of the sunlight. As a result, a hanging membrane is found to have more attractive properties than a floating above water fabric. We find, however, that the photothermal properties of a floating PANi-cotton membrane can greatly be enhanced by dispersing TiN nanoparticles in the water below the fabric. The calculated temperature gradients for TiN nanoparticle solutions show that the absorbed energy grows with increasing the nanoparticle density and that the photothermal process occurs mostly near the surface. The collective heating effects depend on the size and density of nanoparticles, which can further be used to modulate the photothermal process.
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Species identification lies at the heart of biodiversity studies that has in recent years favoured DNA-based approaches. Microbial Biological Resource Centres are a rich source for diverse and high-quality reference materials in microbiology, and yet the strains preserved in these biobanks have been exploited only on a limited scale to generate DNA barcodes. As part of a project funded in the Netherlands to barcode specimens of major national biobanks, sequences of two nuclear ribosomal genetic markers, the Internal Transcribed Spaces and 5.8S gene (ITS) and the D1/D2 domain of the 26S Large Subunit (LSU), were generated as DNA barcode data for ca. 100â000 fungal strains originally assigned to ca. 17â000 species in the CBS fungal biobank maintained at the Westerdijk Fungal Biodiversity Institute, Utrecht. Using more than 24â000 DNA barcode sequences of 12â000 ex-type and manually validated filamentous fungal strains of 7â300 accepted species, the optimal identity thresholds to discriminate filamentous fungal species were predicted as 99.6 % for ITS and 99.8 % for LSU. We showed that 17 % and 18 % of the species could not be discriminated by the ITS and LSU genetic markers, respectively. Among them, â¼8 % were indistinguishable using both genetic markers. ITS has been shown to outperform LSU in filamentous fungal species discrimination with a probability of correct identification of 82 % vs. 77.6 %, and a clustering quality value of 84 % vs. 77.7 %. At higher taxonomic classifications, LSU has been shown to have a better discriminatory power than ITS. With a clustering quality value of 80 %, LSU outperformed ITS in identifying filamentous fungi at the ordinal level. At the generic level, the clustering quality values produced by both genetic markers were low, indicating the necessity for taxonomic revisions at genus level and, likely, for applying more conserved genetic markers or even whole genomes. The taxonomic thresholds predicted for filamentous fungal identification at the genus, family, order and class levels were 94.3 %, 88.5 %, 81.2 % and 80.9 % based on ITS barcodes, and 98.2 %, 96.2 %, 94.7 % and 92.7 % based on LSU barcodes. The DNA barcodes used in this study have been deposited to GenBank and will also be publicly available at the Westerdijk Institute's website as reference sequences for fungal identification, marking an unprecedented data release event in global fungal barcoding efforts to date.