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1.
Nature ; 612(7941): 714-719, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36477531

RESUMO

Molecular phylogenetics of microbial eukaryotes has reshaped the tree of life by establishing broad taxonomic divisions, termed supergroups, that supersede the traditional kingdoms of animals, fungi and plants, and encompass a much greater breadth of eukaryotic diversity1. The vast majority of newly discovered species fall into a small number of known supergroups. Recently, however, a handful of species with no clear relationship to other supergroups have been described2-4, raising questions about the nature and degree of undiscovered diversity, and exposing the limitations of strictly molecular-based exploration. Here we report ten previously undescribed strains of microbial predators isolated through culture that collectively form a diverse new supergroup of eukaryotes, termed Provora. The Provora supergroup is genetically, morphologically and behaviourally distinct from other eukaryotes, and comprises two divergent clades of predators-Nebulidia and Nibbleridia-that are superficially similar to each other, but differ fundamentally in ultrastructure, behaviour and gene content. These predators are globally distributed in marine and freshwater environments, but are numerically rare and have consequently been overlooked by molecular-diversity surveys. In the age of high-throughput analyses, investigation of eukaryotic diversity through culture remains indispensable for the discovery of rare but ecologically and evolutionarily important eukaryotes.


Assuntos
Eucariotos , Cadeia Alimentar , Microbiologia , Filogenia , Organismos Aquáticos/classificação , Organismos Aquáticos/genética , Organismos Aquáticos/ultraestrutura , Biodiversidade , Ecologia , Eucariotos/classificação , Eucariotos/genética , Eucariotos/ultraestrutura , Células Eucarióticas/classificação , Células Eucarióticas/metabolismo , Células Eucarióticas/ultraestrutura , Comportamento Predatório , Especificidade da Espécie
2.
Syst Biol ; 72(3): 505-515, 2023 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-35900180

RESUMO

The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the "Aphelida $+$ Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.].


Assuntos
Eucariotos , Microsporídios , Filogenia , Fungos/genética , Microsporídios/genética , Análise de Sequência de DNA/métodos
3.
J Eukaryot Microbiol ; 70(5): e12977, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37051778

RESUMO

The aphelids, intracellular parasitoids of algae, represent a large cluster of species sister to Fungi in molecular phylogenetic trees. Sharing a common ancestor with Fungi, they are very important in terms of evolution of these groups of Holomycota. Aphelid life cycle being superficially similar to that of Chytridiomycetes is understudied. We have found in the aphelids a new stage-big multiflagellar and amoeboid cells, formed from a plasmodium that has two sorts of nuclei after trophic stage fusion. The families of protein-coding genes involved in the vegetative cell fusion in Opisthokonta were also discussed.


Assuntos
Quitridiomicetos , Eucariotos , Animais , Filogenia , Fusão Celular , Fungos , Estágios do Ciclo de Vida
4.
Phys Chem Chem Phys ; 24(39): 24062-24075, 2022 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-36172859

RESUMO

We study the influence of media on the interaction of ultra-fine plasmonic nanoparticles (≤ 8 nm) with radiation. The important role of the surface layer of the nanoparticles, with properties that differ from the ones in the inner part, is established. Using an atomistic representation of the nanoparticle material and its interaction with light, we find a highly inhomogeneous distribution of the electric field inside and around the particles. It is predicted that with an increase in the refractive index of the ambient medium, the extension of the surface layer of atoms increases, something that also is accompanied by an enhanced red shift of the plasmon resonance band compared to large particles in which the influence of this layer and its relative volume is reduced. It is shown that the physical origin for the formation of a surface layer of atoms near the nanoparticle boundary is related to the anisotropy of the local environment of atoms in this layer which changes the conditions for the interaction of neighboring atoms with each other and with the incident radiation. It is shown that a growth of the refractive index of the ambient medium results in an increase in the local field in the dielectric cavity in which a plasmonic nanoparticle is embedded and which is accompanied by a growth of the amplitude of the plasmon resonance. We predict that in the ultra-fine regime the refractive index sensitivity shows a decreasing trend with respect to size which is opposite to that for larger particles. With the applied atomistic model this work demonstrates close relations between field distributions and properties of ultra-fine nanoparticles.

5.
Opt Express ; 29(22): 35792-35805, 2021 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-34809006

RESUMO

Coupled electrical-thermal-optical simulations of a high-power AlGaInP-based red light-emitting diode (LED) are reported and compared with detailed characterization data of the device available in literature. The simulations enabled identification of the most critical factors limiting the LED performance. Among them, the following ones are found to be of primary importance: (i) absorption of emitted photons in a p+-GaAs contact layer, limiting the light extraction efficiency; (ii) device self-heating producing thermally stimulated electron leakage into the p-side of the LED structure; and (iii) current crowding around small circular p-electrodes enhancing additionally the electron leakage. Possible room for efficiency improvement is estimated by modeling. Optimization of some structural units of the LED design is discussed as well as further directions of the simulation model improvements.

6.
J Eukaryot Microbiol ; 66(6): 892-898, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31034699

RESUMO

Fungi encompass, in addition to classically well-studied lineages, an ever-expanding diversity of poorly known lineages that include, among others, zoosporic chytrid-like parasites. According to recent phylogenetic analysis based on 18S + 28S rRNA concatenated genes two unusual chytrid-like fungi Amoeboradix gromovi and Sanchytrium tribonematis form a monophyletic group, the family Sanchytriaceae, which represents a new divergent taxon that remains incertae sedis within Fungi. Zoospores of Amoeboradix gromovi contain one of the longest kinetosomes known in eukaryotic cells, which are composed of microtubular singlets or doublets. However, the ultrastructure of S. tribonematis, the type species of the genus had not been yet studied. Here, we provide the results of TEM investigations of zoospores and sporangia from two strains of S. tribonematis. The two strains are endowed with unusual features. Like in A. gromovi, amoeboid zoospores of S. tribonematis contain a long kinetosome composed of microtubular singlets, and the two orthogonal centrioles in their sporangia have nine microtubular singlets with an internal ring. The morphological and ultrastructural features of S. tribonematis are now included in the improved taxonomic diagnosis for this species.


Assuntos
Fungos/classificação , Fungos/citologia , Fungos/ultraestrutura , Microscopia , Microscopia Eletrônica
7.
J Eukaryot Microbiol ; 66(6): 911-924, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31077482

RESUMO

The aphelids (phylum Aphelida) are phagotrophic parasitoids of algae and represent the most basal branch in superphylum Opisthosporidia, which contains the Microsporidia, Rozellosporidia and Aphelida. Being the closest group to traditional fungi, the aphelids should have ancestral features of both phyla. As in chytrids and other zoosporic fungi, the structure of zoospores is the most informative and important morphological feature for the phylogeny and taxonomy of aphelids. Though a general zoospore description exists for some aphelid species, their flagellar apparatus (kinetid) structure, which contains pivotal taxonomic and phylogenetic characters, has not been studied. Here we represent the kinetid structure in two genera, Aphelidium and Paraphelidium, and demonstrate independent reduction in the kinetid in each genus. The kinetid-mitochondrion connection found in Aphelidium and Paraphelidium is rare for opisthokonts in general, but present in the most basal branches of Fungi and Opisthosporidia. We suggest, therefore, that this connection represents an ancestral character for both these phyla.


Assuntos
Evolução Biológica , Fungos/ultraestrutura , Fungos/classificação , Microscopia Eletrônica de Transmissão
8.
J Eukaryot Microbiol ; 66(4): 582-591, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30460733

RESUMO

Molecular phylogenetic analysis of 18S rRNA gene sequences of nearly any species of Chytridiomycota has typically challenged traditional classification and triggered taxonomic revision. This has often led to the establishment of new taxa which, normally, appears well supported by zoospore ultrastructure, which provides diagnostic characters. To construct a meaningful and comprehensive classification of Chytridiomycota, the combination of molecular phylogenies and morphological studies of traditionally defined chytrid species is needed. In this work, we have studied morphological and ultrastructural features based on light and transmission electron microscopy as well as molecular phylogenetic analysis of a parasite (strain X-124 CCPP ZIN RAS) morphologically similar to Rhizophydium granulosporum living on the yellow-green alga Tribonema gayanum. Phylogenetic analysis of the 18S rRNA gene sequence of this strain supports that it represents a new genus and species affiliated to the recently established order Gromochytriales. The ultrastructure of X-124 confirms its phylogenetic position sister to Gromochytrium and serves as the basis for the description of the new genus and species Apiochytrium granulosporum. The 18S rRNA gene of A. granulosporum contains a S943 group I intron that carries a homing endonuclease pseudogene.


Assuntos
Quitridiomicetos/classificação , Quitridiomicetos/genética , Quitridiomicetos/ultraestrutura , Microscopia , Microscopia Eletrônica de Transmissão , Filogenia , RNA Fúngico/análise , RNA Ribossômico 18S/análise
9.
J Eukaryot Microbiol ; 66(1): 4-119, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30257078

RESUMO

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.


Assuntos
Biodiversidade , Eucariotos/classificação , Filogenia , Terminologia como Assunto
10.
J Eukaryot Microbiol ; 64(5): 573-578, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-27987526

RESUMO

Aphelids remain poorly known parasitoids of algae and have recently raised considerable interest due to their phylogenetic position at the base of Holomycota. Together with Cryptomycota (Rozellosporidia) and Microsporidia, they have been recently re-classified as the Opisthosporidia, which constitutes the sister group to the fungi within the Holomycota. Molecular environmental studies have revealed a huge diversity of aphelids, but only four genera have been described: Aphelidium, Amoeboaphelidium, Paraphelidium, and Pseudaphelidium. Here, we describe the life cycle of a new representative of Aphelida, Paraphelidium letcheri sp. nov., and provide the 18S rRNA gene sequence for this species. Molecular phylogenetic analysis indicates that P. letcheri is sister to Paraphelidium tribonemae and together they form a monophyletic cluster which is distantly related to both, Aphelidium, with flagellated zoospores, and Amoebaphelidium, with amoeboid zoospores.


Assuntos
Eucariotos/classificação , Eucariotos/fisiologia , Análise de Sequência de DNA/métodos , DNA Ribossômico/genética , Eucariotos/genética , Evolução Molecular , Estágios do Ciclo de Vida , Filogenia , RNA Ribossômico 18S/genética
11.
J Eukaryot Microbiol ; 64(2): 204-212, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27487286

RESUMO

Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as the Opisthosporidia, which constitute the sister group to the fungi within the Holomycota. Despite their huge diversity, as revealed by molecular environmental studies, and their phylogenetic interest, only three genera have been described (Aphelidium, Amoeboaphelidium, and Pseudaphelidium), from which 18S rRNA gene sequences exist only for Amoeboaphelidium and Aphelidium species. Here, we describe the life cycle and ultrastructure of a new representative of Aphelida, Paraphelidium tribonemae gen. et sp. nov., and provide the first 18S rRNA gene sequence obtained for this genus. Molecular phylogenetic analysis indicates that Paraphelidium is distantly related to both Aphelidium and Amoebaphelidium, highlighting the wide genetic diversity of aphelids. Paraphelidium tribonemae has amoeboflagellate zoospores containing a lipid-microbody complex, dictyosomes, and mitochondria with rhomboid cristae, which are also present in trophonts and plasmodia. The amoeboid trophont uses pseudopodia to feed from the host cytoplasm. Although genetically distinct, the genus Paraphelidium is morphologically indistinguishable from other aphelid genera and has zoospores able to produce lamellipodia with subfilopodia like those of Amoeboaphelidium.


Assuntos
Eucariotos/classificação , Eucariotos/genética , Eucariotos/ultraestrutura , Variação Genética , Filogenia , Amoeba/genética , Cistos/ultraestrutura , DNA de Protozoário/genética , DNA Ribossômico/genética , Ecologia , Eucariotos/fisiologia , Estágios do Ciclo de Vida , Microscopia Eletrônica de Transmissão , Organelas/ultraestrutura , Plasmodium/ultraestrutura , RNA Ribossômico 18S/genética , Análise de Sequência de DNA , Esporos/ultraestrutura
12.
Nanotechnology ; 28(27): 275201, 2017 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-28612754

RESUMO

We present a study of blue III-nitride light-emitting diodes (LEDs) with multiple quantum well (MQW) and quantum dot (QD) active regions (ARs), comparing experimental and theoretical results. The LED samples were grown by metalorganic vapor phase epitaxy, utilizing growth interruption in the hydrogen/nitrogen atmosphere and variable reactor pressure to control the AR microstructure. Realistic configuration of the QD AR implied in simulations was directly extracted from HRTEM characterization of the grown QD-based structures. Multi-scale 2D simulations of the carrier transport inside the multiple QD AR have revealed a non-trivial pathway for carrier injection into the dots. Electrons and holes are found to penetrate deep into the multi-layer AR through the gaps between individual QDs and get into the dots via their side edges rather than via top and bottom interfaces. This enables a more homogeneous carrier distribution among the dots situated in different layers than among the laterally uniform quantum well (QWs) in the MQW AR. As a result, a lower turn-on voltage is predicted for QD-based LEDs, as compared to MQW ones. Simulations did not show any remarkable difference in the efficiencies of the MQW and QD-based LEDs, if the same recombination coefficients are utilized, i.e. a similar crystal quality of both types of LED structures is assumed. Measurements of the current-voltage characteristics of LEDs with both kinds of the AR have shown their close similarity, in contrast to theoretical predictions. This implies the conventional assumption of laterally uniform QWs not to be likely an adequate approximation for the carrier transport in MQW LED structures. Optical characterization of MQW and QD-based LEDs has demonstrated that the later ones exhibit a higher efficiency, which could be attributed to better crystal quality of the grown QD-based structures. The difference in the crystal quality explains the recently observed correlation between the growth pressure of LED structures and their efficiency and should be taken into account while further comparing performances of MQW and QD-based LEDs. In contrast to experimental results, our simulations did not reveal any advantages of using QD-based ARs over the MQW ones, if the same recombination constants are assumed for both cases. This fact demonstrates importance of accounting for growth-dependent factors, like crystal quality, which may limit the device performance. Nevertheless, a more uniform carrier injection into multi-layer QD ARs predicted by modeling may serve as the basis for further improvement of LED efficiency by lowering carrier density in individual QDs and, hence, suppressing the Auger recombination losses.

13.
Nanotechnology ; 28(1): 015701, 2017 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-27897139

RESUMO

The impact of electromechanical coupling on optical properties of light-emitting diodes (LEDs) with InGaN/GaN quantum-dot (QD) active regions is studied by numerical simulations. The structure, i.e. the shape and the average In content of the QDs, has been directly derived from experimental data on out-of-plane strain distribution obtained from the geometric-phase analysis of a high-resolution transmission electron microscopy image of an LED structure grown by metalorganic vapor-phase epitaxy. Using continuum [Formula: see text] calculations, we have studied first the lateral and full electromechanical coupling between the QDs in the active region and its impact on the emission spectrum of a single QD located in the center of the region. Our simulations demonstrate the spectrum to be weakly affected by the coupling despite the strong common strain field induced in the QD active region. Then we analyzed the effect of vertical coupling between vertically stacked QDs as a function of the interdot distance. We have found that QCSE gives rise to a blue-shift of the overall emission spectrum when the interdot distance becomes small enough. Finally, we compared the theoretical spectrum obtained from simulation of the entire active region with an experimental electroluminescence (EL) spectrum. While the theoretical peak emission wavelength of the selected central QD corresponded well to that of the EL spectrum, the width of the latter one was determined by the scatter in the structures of various QDs located in the active region. Good agreement between the simulations and experiment achieved as a whole validates our model based on realistic structure of the QD active region and demonstrates advantages of the applied approach.

14.
J Org Chem ; 81(15): 6402-8, 2016 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-27384963

RESUMO

A novel route for synthesis of 2-acyl-1,1,3,3-tetracyanopropenides (ATCN) salts in high yields and excellent purities starting from readily available methyl ketones, malononitrile, bromine, and alkali metal acetates is reported. The starting aryl(heteroaryl) methyl ketones were oxidized to the corresponding α-ketoaldehydes by new a DMSO-NaBr-H2SO4 oxidation system in yields up to 90% within a short reaction time of 8-10 min. The subsequent stages of ATCN preparation are realized in aqueous media without use of any toxic solvents, in accordance with principle 5 of "green chemistry". Lithium, sodium, potassium, rubidium, and cesium 2-benzoyl-1,1,3,3-tetracyanopropenides were characterized by X-ray diffraction analysis. These salts show a good potential for synthesis of five- and six-membered heterocycles and may serve as potentially useful ligands in coordination and supramolecular chemistry.

15.
Gene ; 921: 148520, 2024 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-38702020

RESUMO

A phylogenetic analysis of transcription factors of the Sox-Tcf/Lef-Mata (STM) family of the HMG-B superfamily was carried out in order to clarify the evolutionary roots of the Wnt signaling pathway in unicellular organisms. The data set for analysis included protein sequences of metazoans, fungi, unicellular opisthokonts, apusomonads and amoebozoans. The topology of the phylogenetic tree suggests that STM-related proteins arose in the common ancestor of Opisthokonta and Amoebozoa, two of amoebozoan STM proteins are sister-related to opisthokont ones and the three known lineages of STM transcription factors (STM family in narrow sence) are found in Opisthokonta only. Of these, the holozoan Sox protein branch is the result of either the first or second branching, that originated in the common ancestor of Opisthokonta. The lineage containing Tcf/Lef proteins (holozoan) and the lineage containing Mata proteins (holomycotan) are sister. They derived either at the time of the Holozoa and Holomycota divergence or originate from two paralogs of the common ancestor of Opisthokonta, which arose after the separation of the Sox lineage. Interaction with Armadillo-like proteins may be an original feature of the STM protein family and existed in the unicellular ancestors of multicellular animals; a connection is possible between the presence of Mata-related proteins in Aphelidium protococcorum and specific genome feature of this species.


Assuntos
Evolução Molecular , Filogenia , Animais , Fungos/genética , Fungos/metabolismo , Proteínas HMGB/genética , Proteínas HMGB/metabolismo , Fatores de Transcrição SOX/genética , Fatores de Transcrição SOX/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , Via de Sinalização Wnt
16.
Eur J Protistol ; 93: 126053, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38350179

RESUMO

We identified two new parasite species of Chytridiomycota isolated during blooms of the dinoflagellate Alexandrium minutum in the coastal Mediterranean Sea. Light and electron microscopy together with molecular characterization of the nuclear 18S, ITS, and 28S rDNA regions led to their identification as two new species, Dinomyces gilberthii and Paradinomyces evelyniae, both belonging to the family Dinomycetaceae, order Rhizophydiales. Dinomyces gilberthii differs from the previously described D. arenysensis by the presence of discharge papillae and the development of a drop-shaped sporangium. Paradinomyces evelyniae differs from the previously described P. triforaminorum by the prominent lipid globule present in early sporangia and by the pointed end producing a rhizoid. The two chytrids differed in their geographical distribution. Dinomyces gilberthii was detected in several Mediterranean habitats, including harbours and beaches, and was particularly prevalent during summer dinoflagellate blooms. Its widespread occurrence in coastal ecosystems suggested a high level of adaptability to this environment. Paradinomyces evelyniae had a more restricted distribution in the coastal-marine environment, occurring in harbour sediments and only occasionally in the water column during winter and early spring. Paradinomyces evelyniae has previously been detected in the Baltic Sea, suggesting that its distribution encompasses contrasting coastal environments, although its presence is rare.


Assuntos
Quitridiomicetos , Dinoflagellida , Parasitos , Animais , Dinoflagellida/genética , Ecossistema , Quitridiomicetos/genética , Filogenia
17.
Nanomaterials (Basel) ; 13(8)2023 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-37110952

RESUMO

A possible solution for the realization of high-efficiency visible light-emitting diodes (LEDs) exploits InGaN-quantum-dot-based active regions. However, the role of local composition fluctuations inside the quantum dots and their effect of the device characteristics have not yet been examined in sufficient detail. Here, we present numerical simulations of a quantum-dot structure restored from an experimental high-resolution transmission electron microscopy image. A single InGaN island with the size of ten nanometers and nonuniform indium content distribution is analyzed. A number of two- and three-dimensional models of the quantum dot are derived from the experimental image by a special numerical algorithm, which enables electromechanical, continuum k→·p→, and empirical tight-binding calculations, including emission spectra prediction. Effectiveness of continuous and atomistic approaches are compared, and the impact of InGaN composition fluctuations on the ground-state electron and hole wave functions and quantum dot emission spectrum is analyzed in detail. Finally, comparison of the predicted spectrum with the experimental one is performed to assess the applicability of various simulation approaches.

18.
J Fungi (Basel) ; 9(10)2023 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-37888277

RESUMO

Aphelids are a holomycotan group, represented exclusively by parasitoids infecting algae. They form a sister lineage to Fungi in the phylogenetic tree and represent a key group for reconstruction of the evolution of Holomycota and for analysis of the origin of Fungi. The newly assembled genome of Aphelidium insullamus (Holomycota, Aphelida) with a total length of 18.9 Mb, 7820 protein-coding genes and a GC percentage of 52.05% was obtained by a hybrid assembly based on Oxford Nanopore long reads and Illumina paired reads. In order to trace the origin and the evolution of fungal osmotrophy and its presence or absence in Aphelida, we analyzed the set of main fungal transmembrane transporters, which are proteins of the Major Facilitator superfamily (MFS), in the predicted aphelid proteomes. This search has shown an absence of a specific fungal protein family Drug:H+ antiporters-2 (DAH-2) and specific fungal orthologs of the sugar porters (SP) family, and the presence of common opisthokont's orthologs of the SP family in four aphelid genomes. The repertoire of SP orthologs in aphelids turned out to be less diverse than in free-living opisthokonts, and one of the most limited among opisthokonts. We argue that aphelids do not show signs of similarity with fungi in terms of their osmotrophic abilities, despite the sister relationships of these groups. Moreover, the osmotrophic abilities of aphelids appear to be reduced in comparison with free-living unicellular opisthokonts. Therefore, we assume that the evolution of fungi-specific traits began after the separation of fungal and aphelid lineages, and there are no essential reasons to consider aphelids as a prototype of the fungal ancestor.

19.
BMC Microbiol ; 12: 271, 2012 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-23171165

RESUMO

BACKGROUND: Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities. RESULTS: Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches. CONCLUSIONS: Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.


Assuntos
Coanoflagelados/classificação , Coanoflagelados/ultraestrutura , Mitocôndrias/ultraestrutura , Água do Mar/parasitologia , Anaerobiose , Coanoflagelados/isolamento & purificação , Coanoflagelados/fisiologia , Análise por Conglomerados , DNA de Protozoário/química , DNA de Protozoário/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Genes de RNAr , Microscopia , Dados de Sequência Molecular , Filogenia , RNA de Protozoário/genética , RNA Ribossômico 18S/genética , RNA Ribossômico 28S/genética , Análise de Sequência de DNA
20.
Nanomaterials (Basel) ; 13(1)2022 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-36616095

RESUMO

The major issues confronting the performance of deep-UV (DUV) laser diodes (LDs) are reviewed along with the different approaches aimed at performance improvement. The impact of threading dislocations on the laser threshold current, limitations on heavy n- and p-doping in Al-rich AlGaN alloys, unavoidable electron leakage into the p-layers of (0001) LD structures, implementation of tunnel junctions, and non-uniform hole injection into multiple quantum wells in the active region are discussed. Special attention is paid to the current status of n- and p-type doping and threading dislocation density reduction, both being the factors largely determining the performance of DUV-LDs. It is shown that most of the above problems originate from intrinsic properties of the wide-bandgap AlGaN semiconductors, which emphasizes their fundamental role in the limitation of deep-UV LD performance. Among various remedies, novel promising technological and design approaches, such as high-temperature face-to-face annealing and distributed polarization doping, are discussed. Whenever possible, we provided a comparison between the growth capabilities of MOVPE and MBE techniques to fabricate DUV-LD structures.

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