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Published: 7 July 2024
Last updated: 7 July 2024

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1

He, Christine, Ray Keren, Michael L. Whittaker, Ibrahim F. Farag, Jennifer A. Doudna, Jamie H. D. Cate, and Jillian F. Banfield. "Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems." Nature Microbiology 6, no. 3 (January 25, 2021): 354–65. http://dx.doi.org/10.1038/s41564-020-00840-5.

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AbstractCandidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.
2

Williams, Tom A., Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, and T. Martin Embley. "Integrative modeling of gene and genome evolution roots the archaeal tree of life." Proceedings of the National Academy of Sciences 114, no. 23 (May 22, 2017): E4602—E4611. http://dx.doi.org/10.1073/pnas.1618463114.

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A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
3

Reinhardt, Astrid, and David Eisenberg. "DPANN: Improved sequence to structure alignments following fold recognition." Proteins: Structure, Function, and Bioinformatics 56, no. 3 (April 28, 2004): 528–38. http://dx.doi.org/10.1002/prot.20144.

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4

Castelle, Cindy J., Christopher T. Brown, Karthik Anantharaman, Alexander J. Probst, Raven H. Huang, and Jillian F. Banfield. "Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations." Nature Reviews Microbiology 16, no. 10 (September 4, 2018): 629–45. http://dx.doi.org/10.1038/s41579-018-0076-2.

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5

Mathlouthi, Nour El Houda, Imen Belguith, Mariem Yengui, Hamadou Oumarou Hama, Jean-Christophe Lagier, Leila Ammar Keskes, Ghiles Grine, and Radhouane Gdoura. "The Archaeome’s Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures." Microorganisms 11, no. 11 (November 10, 2023): 2742. http://dx.doi.org/10.3390/microorganisms11112742.

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Background and Aims: Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea’s role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC. Methods: We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions. Results: Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype. Conclusions: The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea’s role in CRC dynamics.
6

Lipsewers, Yvonne A., Ellen C. Hopmans, Jaap S. Sinninghe Damsté, and Laura Villanueva. "Potential recycling of thaumarchaeotal lipids by DPANN Archaea in seasonally hypoxic surface marine sediments." Organic Geochemistry 119 (May 2018): 101–9. http://dx.doi.org/10.1016/j.orggeochem.2017.12.007.

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7

Makarova, Kira S., Yuri I. Wolf, and Eugene V. Koonin. "Towards functional characterization of archaeal genomic dark matter." Biochemical Society Transactions 47, no. 1 (February 1, 2019): 389–98. http://dx.doi.org/10.1042/bst20180560.

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Abstract A substantial fraction of archaeal genes, from ∼30% to as much as 80%, encode ‘hypothetical' proteins or genomic ‘dark matter'. Archaeal genomes typically contain a higher fraction of dark matter compared with bacterial genomes, primarily, because isolation and cultivation of most archaea in the laboratory, and accordingly, experimental characterization of archaeal genes, are difficult. In the present study, we present quantitative characteristics of the archaeal genomic dark matter and discuss comparative genomic approaches for functional prediction for ‘hypothetical' proteins. We propose a list of top priority candidates for experimental characterization with a broad distribution among archaea and those that are characteristic of poorly studied major archaeal groups such as Thaumarchaea, DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota) and Asgard.
8

Ortiz-Alvarez, Rudiger, and Emilio O. Casamayor. "High occurrence ofPacearchaeotaandWoesearchaeota(Archaea superphylum DPANN) in the surface waters of oligotrophic high-altitude lakes." Environmental Microbiology Reports 8, no. 2 (January 28, 2016): 210–17. http://dx.doi.org/10.1111/1758-2229.12370.

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9

Jaffe, Alexander L., Cindy J. Castelle, Christopher L. Dupont, and Jillian F. Banfield. "Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea." Molecular Biology and Evolution 36, no. 3 (December 13, 2018): 435–46. http://dx.doi.org/10.1093/molbev/msy234.

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10

Colombet, Jonathan, Maxime Fuster, Hermine Billard, and Télesphore Sime-Ngando. "Femtoplankton: What’s New?" Viruses 12, no. 8 (August 12, 2020): 881. http://dx.doi.org/10.3390/v12080881.

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Since the discovery of high abundances of virus-like particles in aquatic environment, emergence of new analytical methods in microscopy and molecular biology has allowed significant advances in the characterization of the femtoplankton, i.e., floating entities filterable on a 0.2 µm pore size filter. The successive evidences in the last decade (2010–2020) of high abundances of biomimetic mineral–organic particles, extracellular vesicles, CPR/DPANN (Candidate phyla radiation/Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaeota), and very recently of aster-like nanoparticles (ALNs), show that aquatic ecosystems form a huge reservoir of unidentified and overlooked femtoplankton entities. The purpose of this review is to highlight this unsuspected diversity. Herein, we focus on the origin, composition and the ecological potentials of organic femtoplankton entities. Particular emphasis is given to the most recently discovered ALNs. All the entities described are displayed in an evolutionary context along a continuum of complexity, from minerals to cell-like living entities.
11

Zhou, Lei, Zhichao Zhou, Yu-Wei Lu, Lei Ma, Yang Bai, Xiao-Xiao Li, Serge Maurice Mbadinga, et al. "The newly proposed TACK and DPANN archaea detected in the production waters from a high-temperature petroleum reservoir." International Biodeterioration & Biodegradation 143 (September 2019): 104729. http://dx.doi.org/10.1016/j.ibiod.2019.104729.

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12

Tang, Moran, Qian Chen, Haohui Zhong, Shufeng Liu, and Weiling Sun. "CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater." Water Research 251 (March 2024): 121137. http://dx.doi.org/10.1016/j.watres.2024.121137.

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13

Nauroth, Julie Marie, Mary Van Elswyk, Ying Liu, and Linda Arterburn. "Anti-inflammatory activity of algal oils containing Docosahexaenoic Acid (DHA) and omega-6 Docosapentaenoic Acid (DPAn-6) (101.5)." Journal of Immunology 178, no. 1_Supplement (April 1, 2007): S201. http://dx.doi.org/10.4049/jimmunol.178.supp.101.5.

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Abstract Background: Studies have shown anti-inflammatory activity associated with fish oil and ascribed this effect to the long-chain omega-3 fatty acids DHA and especially eicosapentaenoic acid (EPA). Objective: The purpose of this study was to examine the anti-inflammatory effects of DHA-rich algal oils which contain little or no EPA and determine the contribution of their individual constituent fatty acids, particularly DHA and DPAn-6. Results: The effects of feeding DHA-rich Martek DHA-T™ algal oil and DHA/DPAn-6-rich Martek DHA-S™ algal oil on rat carrageenan-induced hind paw edema was examined. The S-oil was more effective at reducing edema than the T-oil, suggesting that DPAn-6 has anti-inflammatory properties. We next tested the in vitro effects of the individual pure fatty acids on reducing LPS-stimulated IL-1β and TNF-α secretion by human peripheral blood mononuclear cells. The relative potency was DPAn-6 (most potent) &gt; DHA &gt; EPA. All three fatty acids were effective at reducing by &gt;50% neutrophil fMLP-mediated migration in vitro. Further in vivo analyses demonstrated that feeding pure DHA and EPA ethyl esters (EE) reduced paw edema and the combination of DHA/DPAn6-EE which mimics algal oil was more potent than the combination of DHA/EPA-EE which mimics fish oil. Conclusions: DHA, DPAn-6, and EPA have anti-inflammatory activity in vitro and in vivo. Algal S-oil containing the combination of DHA and DPAn-6 shows potential for use in anti-inflammatory applications.
14

Hamm, Joshua N., Susanne Erdmann, Emiley A. Eloe-Fadrosh, Allegra Angeloni, Ling Zhong, Christopher Brownlee, Timothy J. Williams, et al. "Unexpected host dependency of Antarctic Nanohaloarchaeota." Proceedings of the National Academy of Sciences 116, no. 29 (June 28, 2019): 14661–70. http://dx.doi.org/10.1073/pnas.1905179116.

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In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.
15

Reysenbach, Anna-Louise, Emily St. John, Jennifer Meneghin, Gilberto E. Flores, Mircea Podar, Nina Dombrowski, Anja Spang, et al. "Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities." Proceedings of the National Academy of Sciences 117, no. 51 (December 4, 2020): 32627–38. http://dx.doi.org/10.1073/pnas.2019021117.

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Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum “DPANN,” two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.
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Ullah, Numan, Naisu Yang, Zhongxia Guan, Kuilin Xiang, Yali Wang, Mohamed Diaby, Cai Chen, Bo Gao, and Chengyi Song. "Comparative Analysis and Phylogenetic Insights of Cas14-Homology Proteins in Bacteria and Archaea." Genes 14, no. 10 (October 6, 2023): 1911. http://dx.doi.org/10.3390/genes14101911.

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Type-V-F Cas12f proteins, also known as Cas14, have drawn significant interest within the diverse CRISPR-Cas nucleases due to their compact size. This study involves analyzing and comparing Cas14-homology proteins in prokaryotic genomes through mining, sequence comparisons, a phylogenetic analysis, and an array/repeat analysis. In our analysis, we identified and mined a total of 93 Cas14-homology proteins that ranged in size from 344 aa to 843 aa. The majority of the Cas14-homology proteins discovered in this analysis were found within the Firmicutes group, which contained 37 species, representing 42% of all the Cas14-homology proteins identified. In archaea, the DPANN group had the highest number of species containing Cas14-homology proteins, a total of three species. The phylogenetic analysis results demonstrate the division of Cas14-homology proteins into three clades: Cas14-A, Cas14-B, and Cas14-U. Extensive similarity was observed at the C-terminal end (CTD) through a domain comparison of the three clades, suggesting a potentially shared mechanism of action due to the presence of cutting domains in that region. Additionally, a sequence similarity analysis of all the identified Cas14 sequences indicated a low level of similarity (18%) between the protein variants. The analysis of repeats/arrays in the extended nucleotide sequences of the identified Cas14-homology proteins highlighted that 44 out of the total mined proteins possessed CRISPR-associated repeats, with 20 of them being specific to Cas14. Our study contributes to the increased understanding of Cas14 proteins across prokaryotic genomes. These homologous proteins have the potential for future applications in the mining and engineering of Cas14 proteins.
17

Bajgain, Pratima, Zuben E. Sauna, and Vijaya Simhadri. "Archaeal and bacteriophage derived Cas proteins demonstrate memory T cell response in humans." Journal of Immunology 210, no. 1_Supplement (May 1, 2023): 87.04. http://dx.doi.org/10.4049/jimmunol.210.supp.87.04.

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Abstract The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system is a powerful gene editing tool with clinical applications in the pipeline. In vivodelivery of Cas proteins could induce immune responses which would limit the utility of the technology. Previously, we and others have demonstrated pre-existing immunity to Cas9 proteins derived from Staphylococcus aureus(Sa) and Streptococcus pyogenes(Sp) in human populations. As these Cas proteins are of microbial origin this finding was not surprising. There are numerous naturally occurring alternatives to Cas9 and many of these are being leveraged for gene editing. Alternatives to Cas9 that have successfully been used in gene editing technologies include Cas12a (derived from Acidaminococcus sp), Cas14a (derived from DPANN, a super-phylum of archaea) and Casϕ (derived from a huge bacteriophage). It has been postulated that humans would not have pre-existing immunity to some of these Cas proteins. In the comparative study described here, we evaluated pre-existing antibodies and memory T-cell responses to Cas9, Cas12a, Cas14a and Casϕ from the same 18 healthy donors for all proteins. Pre-existing antibodies were identified using ELISA and memory T-cell responses were measured using the ELISpot assay. All four Cas proteins tested positive for both assays in at least some donors. It has been speculated that pre-existing immunity to Cas9 proteins is due to human exposure to the pathogenic bacteria they are derived from. Consequently, Cas14a and Casϕ should not be associated with pre-existing immunity. However, our results show that anti-Cas14a and anti-Casϕ antibodies were detected in ~50% of the study population and these donors also showed memory T-cell responses.
18

Besseling, Marc A., Ellen C. Hopmans, R. Christine Boschman, Jaap S. Sinninghe Damsté, and Laura Villanueva. "Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone." Biogeosciences 15, no. 13 (July 4, 2018): 4047–64. http://dx.doi.org/10.5194/bg-15-4047-2018.

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Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN (superphylum grouping Micrarchaeota, Diapherotrites, Aenigmarchaeota, Nanohaloarchaeota, Parvarchaeota, Nanoarchaeota, Pacearchaeota and Woesearchaeota). Members of the MCG were diverse, with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, -2 and -3 with dihexose IPL types, GDGT-0 with a cyclopentanetetraol molecule and hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.
19

Tzetlin, A. B., A. A. Klyukina, A. G. Elcheninov, P. A. Shcherbakova, L. A. Gavirova, A. I. Shestakov, E. V. Vortsepneva, A. E. Zhadan, and I. V. Kublanov. "THE STUDY OF MICROBIAL ASSOCIATIONS HELPS US UNDERSTAND THE LIFESTYLE OF <i>TEREBELLIDES</i> CF. <i>STROEMII</i> (ANNELIDA, TEREBELLIFORMIA, TRICHOBRANCHIDAE) IN THE WHITE SEA." Зоологический журнал 102, no. 12 (December 1, 2023): 1331–51. http://dx.doi.org/10.31857/s0044513423120127.

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Polychaete annelids are one of the main components of oceanic benthos, but little is known about their microbial symbionts. The purpose of this work is to study the microbiome associated with representatives of Terebellides cf. stroemii and to describe their lifestyle in the White Sea. To do this, the worms and their tubes were examined using light and electron microscopy, and the composition of the microbiome was studied by sequencing the hypervariable V4 regions of the 16S rRNA gene. The tubes of Terebellides cf. stroemii are shown to be loose and, most likely, temporary, whereas the worms dig actively into the ground, yet spending part of their time collecting food from the ground surface with the help of tentacles. Bacteria were found neither in integument cells nor in the intestinal epithelium. Phylogenetic and cluster analyses revealed significant differences in the taxonomic composition of the microbiomes of T. cf. stroemii worms from the soil microbiome and allowed us to determine specific components of the microbiomes of intestines and tentacles, whereas the microbiomes of bottom sediments and worm tubes appeared to be similar. The microbiomes of the tubes are dominated by Pseudomonadota, Desulfobacterota and Bacteroidota. While the intestines are home to Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteriota, Chloroflexota and Planctomycetota, this bacterial community is very different from the microbiomes both of the surrounding sediment and the tentacles. The microbiome of the tentacles of T. cf. stroemii differs significantly from that of the surrounding soil, tube and intestine, as it contains Pseudomonadota, Bacillota and Bacteroidota, in addition to a significant number of representatives of the archaeal superfilium DPANN observed in two samples. Modern technologies for studying microbiomes demonstrate the presence of specific communities of microorganisms associated with the study species, with a combination of morphological and molecular methods being promising for studying the microbiomes associated with marine annelids and their functional relationships with the animals.
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Cavalier-Smith, Thomas, and Ema E.-Yung Chao. "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)." Protoplasma 257, no. 3 (January 3, 2020): 621–753. http://dx.doi.org/10.1007/s00709-019-01442-7.

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AbstractPalaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many ‘rDNA-phyla’ belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including ‘Asgardia’) and Euryarchaeota sensu-lato (including ultrasimplified ‘DPANN’ whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
21

Pitman, Kent M. "dpANS Common Lisp." ACM SIGPLAN Lisp Pointers V, no. 3 (August 1992): 34–37. http://dx.doi.org/10.1145/147135.147249.

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22

Li, Xiaojun, Yide Ma, Zhaobin Wang, and Wenrui Yu. "Geometry-Invariant Texture Retrieval Using a Dual-Output Pulse-Coupled Neural Network." Neural Computation 24, no. 1 (January 2012): 194–216. http://dx.doi.org/10.1162/neco_a_00194.

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This letter proposes a novel dual-output pulse coupled neural network model (DPCNN). The new model is applied to obtain a more stable texture description in the face of the geometric transformation. Time series, which are computed from output binary images of DPCNN, are employed as translation-, rotation-, scale-, and distortion-invariant texture features. In the experiments, DPCNN has been well tested by using Brodatz's album and the VisTex database. Several existing models are compared with the proposed DPCNN model. The experimental results, based on different testing data sets for images with different translations, orientations, scales, and affine transformations, show that our proposed model outperforms existing models in geometry-invariant texture retrieval. Furthermore, the robustness of DPCNN to noisy data is examined in the experiments.
23

Ding, Gang, Da Lei, and Wei Yao. "Health Condition Prognostics of Complex Equipment Based on Discrete Input Process Neural Networks." Applied Mechanics and Materials 423-426 (September 2013): 2347–54. http://dx.doi.org/10.4028/www.scientific.net/amm.423-426.2347.

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Considering the problem of health condition prognostics of complex equipment, a discrete input process neural networks (DPNN) model based on process neural networks (PNN) is proposed in this paper. DPNN utilizes vector inputs together with convolution operator to gain the capability of time and spatial aggregation operation, which is implemented with continuous function inputs and integral operator by PNN. Different from PNN, DPNN can use discrete samples as inputs directly, thus can avoid precision loss during procedures of data fitting and function expanding required by PNN. The application of DPNN to health condition prognostics of complex equipment is described through the prediction of the future health state of the civil aircraft engines, where the short-term and long-term predictions of the health condition represented by the exhausted gas temperature time series are conducted. Moreover, the performance of DPNN is compared with common artificial neural networks (NN) and PNN. The results show that DPNN has satisfied performance for health condition prognostics of civil aircraft engines, and DPNN performs better than both NN and PNN, which prove that DPNN is suitable for health condition prognostics of complex equipment.
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Arterburn, Linda M., Bindi Dangi, Julie Nauroth, Mah Teymourlouei, and Marcus Obeng. "Oxylipins Derived from Docosapentaenoic Acid (DPAn-6) Possess Potent Anti-inflammatory Activity (101.4)." Journal of Immunology 178, no. 1_Supplement (April 1, 2007): S201. http://dx.doi.org/10.4049/jimmunol.178.supp.101.4.

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Abstract Background: The resolution of inflammation is an active process mediated by endogenous lipids formed by lipoxygenases and cyclo-oxygenases at the site of inflammation. Enzymatically oxygenated derivatives (oxylipins) of the omega-3 fatty acids DHA and EPA (resolvins) have potent resolution activity. Objectives: To determine if oxylipins are enzymatically synthesized from the omega-6 fatty acid DPAn-6 and whether these molecules possess pro-resolution, anti-inflammatory properties. Results: Two major metabolites, 17-hydroxy-DPAn-6 and 10,17-dihydroxy-DPAn-6, were formed from DPAn-6 following reaction with soybean 15-lipoxygenase. The identity of these metabolites was confirmed by LC/MS/MS, NMR, and UV analysis. 17-hydroxy-DPAn-6 was also formed following incubation of DPAn-6 with whole human blood. In a mouse air pouch model of acute inflammation, local administration of 100 ng (0.005 mg/kg) of either 17-hydroxy-DPAn-6 or 10,17-dihydroxy DPAn-6 resulted in 70–80% reduction in leukocyte trafficking, comparable to that observed following indomethacin (5 mg/kg ip) administration. The anti-inflammatory activity of both compounds was confirmed in a rat hind paw edema model of acute inflammation. Intravenous administration of 5 μg (~0.025 mg/ml) of either compound resulted in ~25% reduction in paw edema post carrageenan challenge. Both DPAn-6 oxylipins were also active in the hind paw model after oral administration. Conclusions: Oxylipins derived from DPAn-6 are natural compounds possessing potent anti-inflammatory activity. These compounds or analogs thereof are candidates for new drugs that act uniquely to resolve inflammation.
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LOU, XUYANG, and BAOTONG CUI. "GLOBAL EXPONENTIAL STABILITY CONDITIONS FOR DELAYED PARABOLIC NEURAL NETWORKS WITH VARIABLE COEFFICIENTS." International Journal of Bifurcation and Chaos 17, no. 12 (December 2007): 4409–15. http://dx.doi.org/10.1142/s0218127407020063.

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In this paper, we present a class of delayed parabolic neural networks (DPNN) with variable coefficients. Some sufficient conditions for the global exponential stability of the DPNN with variable coefficients are derived by a method based on delay differential inequality. The method, which does not make use of Lyapunov functionals, is simple and effective for the stability analysis of DPNN with variable coefficients.
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Reza, AHM Mohsinul, Sharmin Ferdewsi Rakhi, Xiaochen Zhu, Youhong Tang, and Jianguang Qin. "Visualising the Emerging Platform of Using Microalgae as a Sustainable Bio-Factory for Healthy Lipid Production through Biocompatible AIE Probes." Biosensors 12, no. 4 (March 31, 2022): 208. http://dx.doi.org/10.3390/bios12040208.

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Nowadays, a particular focus is using microalgae to get high-valued health beneficiary lipids. The precise localisation of the lipid droplets (LDs) and biochemical changes are crucial to portray the lipid production strategy in algae, but it requires an in vivo tool to rapidly visualise LD distribution. As a novel strategy, this study focuses on detecting lipid bioaccumulation in a green microalga, Chlamydomonas reinhardtii using the aggregation-induced emission (AIE) based probe, 2-DPAN (C24H18N2O). As the messenger molecule and stress biomarker, hydrogen peroxide (H2O2) activity was detected in lipid synthesis with the AIE probe, TPE-BO (C38H42B2O4). Distinctive LDs labelled with 2-DPAN have elucidated the lipid inducing conditions, where more health beneficiary α-linolenic acid has been produced. TPE-BO labelled H2O2 have clarified the involvement of H2O2 during lipid biogenesis. The co-staining procedure with traditional green BODIPY dye and red chlorophyll indicates that 2-DPAN is suitable for multicolour LD imaging. Compared with BODIPY, 2-DPAN was an efficient sample preparation technique without the washing procedure. Thus, 2-DPAN could improve traditional fluorescent probes currently used for lipid imaging. In addition, the rapid, wash-free, multicolour AIE-based in vivo probe in the study of LDs with 2-DPAN could advance the research of lipid production in microalgae.
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Hou, Xinyu, Lijian Sun, Ying Hu, Xianhui An, and Xueren Qian. "De-Doped Polyaniline as a Mediating Layer Promoting In-Situ Growth of Metal–Organic Frameworks on Cellulose Fiber and Enhancing Adsorptive-Photocatalytic Removal of Ciprofloxacin." Polymers 13, no. 19 (September 27, 2021): 3298. http://dx.doi.org/10.3390/polym13193298.

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New kinds of inorganic–organic hybrid porous materials, metal–organic frameworks (MOFs), have shown great application potential in various fields, but their powdery nature limits their application to a certain extent. As a green and renewable biomass material in nature, cellulose fiber (CelF) has the advantages of biodegradability, recyclability and easy processing, and can be used as an excellent flexible substrate for MOFs. However, the efficient deposition of MOFs on CelF is still a great challenge for the development of this new material. Herein, polyaniline (PANI) and de-doped PANI (DPANI) with rich functional groups as a mediating layer was proposed to promote the in-situ growth and immobilization of some MOFs on CelF. The PANI (especially DPANI) layer greatly promoted the deposition of the four MOFs, and more encouragingly, significantly promoted the in-situ growth and nanocrystallization of MIL-100(Fe). MIL-100(Fe)@DPANI@CelF was selected as an adsorbent-photocatalyst to be used for the adsorptive-photocatalytic removal of ciprofloxacin (CIP) in water. The removal efficiency of CIP by MIL-100(Fe)@DPANI@CelF reached 82.78%, and the removal capacity of CIP was as high as 105.96 mg g−1. The study found that DPANI had a synergistic effect on both the in-situ growth of MIL-100(Fe) on CelF and the adsorption-photocatalysis of CIP in water. The universal platform of PANI-mediated in-situ growth and immobilization of MOFs on CelF constructed in this study widens the road for the development of MOF@CelF composites.
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Zhang, Pei Yin, G. B. Yu, B. Dai, and Ying Jie Ao. "Improved Dynamic Process Neural Network and its Application." Key Engineering Materials 458 (December 2010): 143–48. http://dx.doi.org/10.4028/www.scientific.net/kem.458.143.

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The tourism demand is essential in terms of national economy and the improvement of people’ income. But it is difficult for traditional methods to predict the tendency of the tourism demand. In this paper, a time series prediction method based on dynamic process neural network (DPNN) is proposed to solve this problem. An improved particle swarm optimization (IPSO) is developed. By tuning the structure and improving the connection weights of PNN simultaneously, a partially connected DPNN can be obtained. The effectiveness of the proposed DPNN is proved by Henon system. Finally, the proposed DPNN is utilized to predict the tourism demand, and the test results indicate that the proposed model seems to perform well and appears suitable for using as a predictive maintenance tool.
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Astia, Hafizha, and Rita Damayanti. "Upaya Meningkatkan Pengetahuan Mengenai Bahaya Narkoba dan Pencegahannya pada Calon Duta Pelajar Anti Narkoba (DPAN)." Media Publikasi Promosi Kesehatan Indonesia (MPPKI) 6, no. 3 (March 3, 2023): 497–502. http://dx.doi.org/10.56338/mppki.v6i3.2938.

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Latar belakang: Kasus penyalahgunaan narkoba di Indonesia terus meningkat setiap tahunnya terutama pada remaja. Penyebarluasan informasi tentang bahaya penyalahgunaan dan peredaran narkoba merupakan salah satu cara yang dianggap strategis untuk memberantasnya. Duta Pelajar Anti Narkoba (DPAN) Sumatera Utara merupakan salah satu wadah yang dapat dijadikan sebagai pendekatan untuk melakukan sosialisasi kepada rekan sebaya mengenai bahaya dan pencegahan narkoba, untuk itu DPAN nantinya dituntut untuk memiliki keterampilan komunikasi serta pemahaman yang baik mengenai narkoba. Dalam upaya meningkatkan pengetahuan calon DPAN 2022 maka dilakukanlah intervensi berupa pemberian materi terkait narkoba dan pencegahannya Tujuan: Penelitian ini bertujuan untuk mengetahui pengaruh intervensi yang dilakukan dalam meningkatkan pengetahuan calon DPAN Sumatera Utara 2022 sebagai role model bagi rekan sebayanya. Metode: Penelitian ini menggunakan penelitian kuantitatif dengan metode pre-experimental menggunakan pre-posttest design. Hasil: Sebelum dilakukan intervensi didapatkan rerata sebesar 69,01 dan 79,4 setelah dilakukan intervensi. Artinya terdapat peningkatan rerata sebesar 10,39 Kesimpulan: Ada pengaruh intervensi yaitu pemberian materi terkait narkoba dan pencegahannya terhadap peningkatan pengetahuan calon DPAN 2022.
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Zhang, Xue-Guang. "A practicable estimation of opening angle of dust torus in Type-1.9 AGN with double-peaked broad Hα." Monthly Notices of the Royal Astronomical Society 519, no. 3 (January 9, 2023): 4461–66. http://dx.doi.org/10.1093/mnras/stad024.

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ABSTRACT In this manuscript, an independent method is proposed to estimate opening angle of dust torus in AGN, through unique properties of Type-1.9 AGN with double-peaked broad Hα (Type-1.9 DPAGN) coming from central accretion disc. Type-1.9 AGN without broad Hβ can be expected by the commonly accepted unified model of AGN, considering central BLRs seriously obscured by dust torus with its upper boundary in the line of sight. For the unique Type-1.9 DPAGN, accretion disc originations of double-peaked broad Hα can be applied to determine the inclination angle of the central accretion disc, which is well accepted as substitute of the half opening angle of the central dust torus. Then, among low redshift Type-1.9 DPAGN in SDSS, SDSS J1607+3319 at redshift 0.063 is collected, and the half opening angle of the central dust torus is determined to be around 46 ± 4°, after considering the disfavoured BBH system to explain the double-peaked broad Hα through long-term none variabilities and disfavoured local physical conditions to explain the disappearance of broad Hβ through virial BH mass properties. The results indicate that more detailed studying on dust torus of AGN can be appropriately done through Type-1.9 DPAGN in the near future.
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Li, Yong, Mark F. Seifert, Sun-Young Lim, Norman Salem, and Bruce A. Watkins. "Bone mineral content is positively correlated to n-3 fatty acids in the femur of growing rats." British Journal of Nutrition 104, no. 5 (April 27, 2010): 674–85. http://dx.doi.org/10.1017/s0007114510001133.

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The present study was conducted to determine whether provision of preformed dietary docosapentaenoic acid (DPAn-6) can replace DHA for normal long bone growth as assessed by dual-energy X-ray absorptiometry for mineral content (BMC). A newly modified artificial rearing method was employed to generate n-3 fatty acid-deficient rats. Except the dam-reared (DR; 3·1 % α-linolenic acid) group, newborn pups were separated from their mothers at age 2 d and given artificial rat milk containing linoleic acid (LA), or LA supplemented with 1 % DHA (22 : 6n-3; DHA), 1 % DPAn-6 (DPA), or 1 % DHA plus 0·4 % DPAn-6 (DHA/DPA). The rats were later weaned onto similar pelleted diets. At adulthood, the rats were euthanised and bones (femur, tibia, and lumbar vertebrae) collected for tissue fatty acid analysis and bone mineral density (BMD) determination. The analyses showed that long bones such as femur and tibia in DPAn-6-treated rats contained higher DPAn-6 content and generally had the lowest BMC and BMD values. Hence, DPAn-6 did not replace DHA for normal bone growth and maximal BMC in femur, indicating an indispensible role of DHA in bone health. In conclusion, DHA accumulates in the osteoblast-rich and nerve-abundant periosteum of femur; DHA but not EPA appears to be a vital constituent of marrow and periosteum of healthy modelling bone; and both DHA and total n-3 PUFA strongly correlate to BMC.
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Zhang, Jinya, Min Jiang, Jingyi Zhang, Mengchen Gu, and Ziping Cao. "Ultrasonic Through-Metal Communication Based on Deep-Learning-Assisted Echo Cancellation." Sensors 24, no. 7 (March 27, 2024): 2141. http://dx.doi.org/10.3390/s24072141.

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Ultrasound is extremely efficient for wireless signal transmission through metal barriers due to no limit of the Faraday shielding effect. Echoing in the ultrasonic channel is one of the most challenging obstacles to performing high-quality communication, which is generally coped with by using a channel equalizer or pre-distorting filter. In this study, a deep learning algorithm called a dual-path recurrent neural network (DPRNN) was investigated for echo cancellation in an ultrasonic through-metal communication system. The actual system was constructed based on the combination of software and hardware, consisting of a pair of ultrasonic transducers, an FPGA module, some lab-made circuits, etc. The approach of DPRNN echo cancellation was applied to signals with a different signal-to-noise ratio (SNR) at a 2 Mbps transmission rate, achieving higher than 20 dB SNR improvement for all situations. Furthermore, this approach was successfully used for image transmission through a 50 mm thick aluminum plate, exhibiting a 24.8 dB peak-signal-to-noise ratio (PSNR) and a about 95% structural similarity index measure (SSIM). Additionally, compared with three other echo cancellation methods—LMS, RLS and PNLMS—DPRNN has demonstrated higher efficiency. All those results firmly validate that the DPRNN algorithm is a powerful tool to conduct echo cancellation and enhance the performance of ultrasonic through-metal transmission.
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Wang, Zhaobin, Xiaoguang Sun, Zekun Yang, Yaonan Zhang, Ying Zhu, and Yide Ma. "Leaf Recognition Based on DPCNN and BOW." Neural Processing Letters 47, no. 1 (May 20, 2017): 99–115. http://dx.doi.org/10.1007/s11063-017-9635-1.

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Yeung, Jennifer, Reheman Adili, Adriana Yamaguchi, Cody J. Freedman, Angela Chen, Ryan Shami, Aditi Das, Theodore R. Holman, and Michael Holinstat. "Omega-6 DPA and its 12-lipoxygenase–oxidized lipids regulate platelet reactivity in a nongenomic PPARα-dependent manner." Blood Advances 4, no. 18 (September 18, 2020): 4522–37. http://dx.doi.org/10.1182/bloodadvances.2020002493.

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Abstract Arterial thrombosis is the underlying cause for a number of cardiovascular-related events. Although dietary supplementation that includes polyunsaturated fatty acids (PUFAs) has been proposed to elicit cardiovascular protection, a mechanism for antithrombotic protection has not been well established. The current study sought to investigate whether an omega-6 essential fatty acid, docosapentaenoic acid (DPAn-6), and its oxidized lipid metabolites (oxylipins) provide direct cardiovascular protection through inhibition of platelet reactivity. Human and mouse blood and isolated platelets were treated with DPAn-6 and its 12-lipoxygenase (12-LOX)–derived oxylipins, 11-hydroxy-docosapentaenoic acid and 14-hydroxy-docosapentaenoic acid, to assess their ability to inhibit platelet activation. Pharmacological and genetic approaches were used to elucidate a role for DPA and its oxylipins in preventing platelet activation. DPAn-6 was found to be significantly increased in platelets following fatty acid supplementation, and it potently inhibited platelet activation through its 12-LOX–derived oxylipins. The inhibitory effects were selectively reversed through inhibition of the nuclear receptor peroxisome proliferator activator receptor-α (PPARα). PPARα binding was confirmed using a PPARα transcription reporter assay, as well as PPARα−/− mice. These approaches confirmed that selectivity of platelet inhibition was due to effects of DPA oxylipins acting through PPARα. Mice administered DPAn-6 or its oxylipins exhibited reduced thrombus formation following vessel injury, which was prevented in PPARα−/− mice. Hence, the current study demonstrates that DPAn-6 and its oxylipins potently and effectively inhibit platelet activation and thrombosis following a vascular injury. Platelet function is regulated, in part, through an oxylipin-induced PPARα-dependent manner, suggesting that targeting PPARα may represent an alternative strategy to treat thrombotic-related diseases.
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Yu, Shuangmin, Fan Qin, and Gengchao Wang. "Improving the dielectric properties of poly(vinylidene fluoride) composites by using poly(vinyl pyrrolidone)-encapsulated polyaniline nanorods." Journal of Materials Chemistry C 4, no. 7 (2016): 1504–10. http://dx.doi.org/10.1039/c5tc04026d.

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A promising PVDF-based dielectric polymer nanocomposite based on easily dispersed and poly(vinyl pyrrolidone)-encapsulated polyaniline nanorods (dPANI@PVP) was fabricated and displayed a high dielectric constant and low dielectric loss.
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B, Marina, and A. Senthilrajan. "HFIPO-DPNN: A Framework for Predicting the Dropout of Physically Impaired Student from Education." International Journal of Information and Education Technology 13, no. 4 (2023): 696–703. http://dx.doi.org/10.18178/ijiet.2023.13.4.1855.

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Education plays a significant role in individuals’ development and the economic growth of developing countries like India. Dropout of students from their studies is the major concern for any order of education. Some models for predicting the dropout of students are developed with several factors. Many of them lacked consistency as they backed their studies with the academic performance of the students. Especially, for those students who suffered from physical impairment, the dropout depends on several external factors. Hence, this work proposes a novel HFIPO-DPNN to predict the student dropout rooted in the previous semester’s marks. The proposed model enclosed the hybrid firefly and improved particle swarm algorithm to optimize the feature selection that influences the dropout of hearing-impaired students. The optimized feature data are used to predict the dropout with the novel DPNN. The optimized data was split and used for training the DPNN. The testing data is used to evaluate the performance of the proposed framework. The attributes used for predicting the student dropout are Family Size, Subject, Medium of Instruction, and so on. The data must be collected from 250 physically impaired children belonging to ITI institute, Bangalore. The outcome of the proposed framework is evaluated on several metrics. The accuracy of the proposed model is about 99.02%. The HFIPO-DPNN framework can be enhanced for predicting the dropout for students with other disabilities. The optimization showed that factors influencing education other than familial factors are to be considered in the prediction of dropout.
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Huang, Weichun, Jiawei Nie, and Xiaohui Huang. "Text sentiment classification method based on DPCNN and BiLSTM." ITM Web of Conferences 45 (2022): 01040. http://dx.doi.org/10.1051/itmconf/20224501040.

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In recent years, deep learning network models have been widely used in the aspect of text emotion classification and have achieved remarkable achievements. The traditional TextCNN network can only extract local spatial features of sentences, while the improved DPCNN model has the ability to capture long-distance dependence of the text by deepening the network depth. At the same time, bi-LSTM model is characterized by learning temporal information of text. Therefore, this paper combines the two models, which can not only obtain the spatial local information of the text, but also further strengthen the ability to understand and learn the semantic association information of the text. Experimental results show that the classification effect of the model used in this paper is better than the single model.
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Yang, Lin, and Chen. "Using Deep Principal Components Analysis-Based Neural Networks for Fabric Pilling Classification." Electronics 8, no. 5 (April 28, 2019): 474. http://dx.doi.org/10.3390/electronics8050474.

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A manufacturer’s fabric first undergoes an abrasion test and manual visual inspection to grade the fabric prior to shipment to ensure that there are no defects present. Manual visual classification consumes a considerable amount of human resources. Furthermore, extended use of the eyes during visual inspection often causes occupational injuries, resulting in a decrease in the efficiency of the entire operation. In order to overcome and avoid such situations, this study proposed the use of deep principal components analysis-based neural networks (DPCANNs) for fabric pilling identification. In the proposed DPCANN, the characteristics of the hairball were automatically captured using deep principal components analysis (DPCA), and the hairball class was identified using the neural network and the support vector machine (SVM). The experimental results showed that the proposed DPCANN has an average accuracy of 99.7% at the hairball level, which is in line with the needs of the industry. The results also confirmed that the proposed hairball classification method is superior to other methods.
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Yu, Cheng-Hsuan, Pei-Yu Chiang, and Yi-Cheun Yeh. "Di(2-picolyl)amine-functionalized poly(ethylene glycol) hydrogels with tailorable metal–ligand coordination crosslinking." Polymer Chemistry 12, no. 45 (2021): 6626–39. http://dx.doi.org/10.1039/d1py01325d.

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Shahzad, Ahsan, Abid Mushtaq, Abdul Quddoos Sabeeh, Yazeed Yasin Ghadi, Zohaib Mushtaq, Saad Arif, Muhammad Zia ur Rehman, Muhammad Farrukh Qureshi, and Faisal Jamil. "Automated Uterine Fibroids Detection in Ultrasound Images Using Deep Convolutional Neural Networks." Healthcare 11, no. 10 (May 20, 2023): 1493. http://dx.doi.org/10.3390/healthcare11101493.

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Fibroids of the uterus are a common benign tumor affecting women of childbearing age. Uterine fibroids (UF) can be effectively treated with earlier identification and diagnosis. Its automated diagnosis from medical images is an area where deep learning (DL)-based algorithms have demonstrated promising results. In this research, we evaluated state-of-the-art DL architectures VGG16, ResNet50, InceptionV3, and our proposed innovative dual-path deep convolutional neural network (DPCNN) architecture for UF detection tasks. Using preprocessing methods including scaling, normalization, and data augmentation, an ultrasound image dataset from Kaggle is prepared for use. After the images are used to train and validate the DL models, the model performance is evaluated using different measures. When compared to existing DL models, our suggested DPCNN architecture achieved the highest accuracy of 99.8 percent. Findings show that pre-trained deep-learning model performance for UF diagnosis from medical images may significantly improve with the application of fine-tuning strategies. In particular, the InceptionV3 model achieved 90% accuracy, with the ResNet50 model achieving 89% accuracy. It should be noted that the VGG16 model was found to have a lower accuracy level of 85%. Our findings show that DL-based methods can be effectively utilized to facilitate automated UF detection from medical images. Further research in this area holds great potential and could lead to the creation of cutting-edge computer-aided diagnosis systems. To further advance the state-of-the-art in medical imaging analysis, the DL community is invited to investigate these lines of research. Although our proposed innovative DPCNN architecture performed best, fine-tuned versions of pre-trained models like InceptionV3 and ResNet50 also delivered strong results. This work lays the foundation for future studies and has the potential to enhance the precision and suitability with which UF is detected.
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Zhang, Jianhua, Yuxin Guan, Jiali Yang, Wenqiang Hua, Shuanglong Wang, Zhitian Ling, Hong Lian, et al. "Highly-efficient solution-processed green phosphorescent organic light-emitting diodes with reduced efficiency roll-off using ternary blend hosts." Journal of Materials Chemistry C 7, no. 36 (2019): 11109–17. http://dx.doi.org/10.1039/c9tc02701g.

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We have investigated the effect of various materials mCP DpAn-5BzAc poly(9-vinylcarbazole) and TCTA as the hosts on the performance of solution-processed green phosphorescent organic light-emitting diodes (PhOLEDs).
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Zhang, Yaonan, Jing Cui, Zhaobin Wang, Jianfang Kang, and Yufang Min. "Leaf Image Recognition Based on Bag of Features." Applied Sciences 10, no. 15 (July 28, 2020): 5177. http://dx.doi.org/10.3390/app10155177.

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Plants are ubiquitous in human life. Recognizing an unknown plant by its leaf image quickly is a very interesting and challenging research. With the development of image processing and pattern recognition, plant recognition based on image processing has become possible. Bag of features (BOF) is one of the most powerful models for classification, which has been used for many projects and studies. Dual-output pulse-coupled neural network (DPCNN) has shown a good ability for texture features in image processing such as image segmentation. In this paper, a method based on BOF and DPCNN (BOF_DP) is proposed for leaf classification. BOF_DP achieved satisfactory results in many leaf image datasets. As it is hard to get a satisfactory effect on the large dataset by a single feature, a method (BOF_SC) improved from bag of contour fragments is used for shape feature extraction. BOF_DP and LDA (linear discriminant analysis) algorithms are, respectively, employed for textual feature extraction and reducing the feature dimensionality. Finally, both features are used for classification by a linear support vector machine (SVM), and the proposed method obtained higher accuracy on several typical leaf datasets than existing methods.
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Vigneron, Adrien, Perrine Cruaud, Connie Lovejoy, and Warwick F. Vincent. "Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia." ISME Communications 2, no. 1 (January 20, 2022). http://dx.doi.org/10.1038/s43705-022-00088-6.

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AbstractDPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for “vampiristic” metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.
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Zhang, Irene H., Benedict Borer, Rui Zhao, Steven Wilbert, Dianne K. Newman, and Andrew R. Babbin. "Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential." mBio, February 21, 2024. http://dx.doi.org/10.1128/mbio.02918-23.

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ABSTRACT Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%–50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs. IMPORTANCE Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.
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Bernard, Charles, Romain Lannes, Yanyan Li, Éric Bapteste, and Philippe Lopez. "Rich Repertoire of Quorum Sensing Protein Coding Sequences in CPR and DPANN Associated with Interspecies and Interkingdom Communication." mSystems 5, no. 5 (October 13, 2020). http://dx.doi.org/10.1128/msystems.00414-20.

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ABSTRACT The bacterial candidate phyla radiation (CPR) and the archaeal DPANN superphylum are two novel lineages that have substantially expanded the tree of life due to their large phylogenetic diversity. Because of their ultrasmall size, reduced genome, and lack of core biosynthetic capabilities, most CPR and DPANN members are predicted to be sustained through their interactions with other species. How the few characterized CPR and DPANN symbionts achieve these critical interactions is, however, poorly understood. Here, we conducted an in silico analysis on 2,597 CPR/DPANN genomes to test whether these ultrasmall microorganisms might encode homologs of reference proteins involved in the synthesis and/or the detection of 26 different types of communication molecules (quorum sensing [QS] signals), since QS signals are well-known mediators of intra- and interorganismic relationships. We report the discovery of 5,693 variants of QS proteins distributed across 63 CPR and 6 DPANN phyla and associated with 14 distinct types of communication molecules, most of which were characterized as interspecies QS signals. IMPORTANCE The selection of predicted genes for interspecies communication within the CPR and DPANN genomes sheds some light onto the underlying mechanisms supporting their inferred symbiotic lifestyle. Also, considering the lack of core pathways such as the de novo synthesis of nucleotides or amino acids in the CPR and DPANN lineages, the persistence of these genes highlights how determinant social traits can be for the survival of some microorganisms. Finally, the considerable number of variants of QS proteins identified among the 69 CPR and DPANN phyla substantially expands our knowledge of prokaryotic communication across the tree of life and suggests that the multiplicity of “dialects” in the microbial world is probably larger than previously appreciated.
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Sakai, Hiroyuki D., Naswandi Nur, Shingo Kato, Masahiro Yuki, Michiru Shimizu, Takashi Itoh, Moriya Ohkuma, Antonius Suwanto, and Norio Kurosawa. "Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses." Proceedings of the National Academy of Sciences 119, no. 3 (January 12, 2022). http://dx.doi.org/10.1073/pnas.2115449119.

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Significance The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic symbiotic archaeon (ARM-1) from the DPANN superphylum was successfully cultivated and characterized. We determined its physiological, morphological, and genomic characteristics in detail and obtained experimental evidence of the symbiotic lifestyle of this archaeon. Notably, ARM-1 is a symbiotic archaeal strain that showed dependence on a range of host species in a laboratory culture. The results significantly contribute to the true understanding of the physiology and ecology of DPANN archaea.
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Castelle, Cindy J., Raphaël Méheust, Alexander L. Jaffe, Kiley Seitz, Xianzhe Gong, Brett J. Baker, and Jillian F. Banfield. "Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea." Frontiers in Microbiology 12 (June 1, 2021). http://dx.doi.org/10.3389/fmicb.2021.660052.

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DPANN are small-celled archaea that are generally predicted to be symbionts, and in some cases are known episymbionts of other archaea. As the monophyly of the DPANN remains uncertain, we hypothesized that proteome content could reveal relationships among DPANN lineages, constrain genetic overlap with bacteria, and illustrate how organisms with hybrid bacterial and archaeal protein sets might function. We tested this hypothesis using protein family content that was defined in part using 3,197 genomes including 569 newly reconstructed genomes. Protein family content clearly separates the final set of 390 DPANN genomes from other archaea, paralleling the separation of Candidate Phyla Radiation (CPR) bacteria from all other bacteria. This separation is partly driven by hypothetical proteins, some of which may be symbiosis-related. Pacearchaeota with the most limited predicted metabolic capacities have Form II/III and III-like Rubisco, suggesting metabolisms based on scavenged nucleotides. Intriguingly, the Pacearchaeota and Woesearchaeota with the smallest genomes also tend to encode large extracellular murein-like lytic transglycosylase domain proteins that may bind and degrade components of bacterial cell walls, indicating that some might be episymbionts of bacteria. The pathway for biosynthesis of bacterial isoprenoids is widespread in Woesearchaeota genomes and is encoded in proximity to genes involved in bacterial fatty acids synthesis. Surprisingly, in some DPANN genomes we identified a pathway for synthesis of queuosine, an unusual nucleotide in tRNAs of bacteria. Other bacterial systems are predicted to be involved in protein refolding. For example, many DPANN have the complete bacterial DnaK-DnaJ-GrpE system and many Woesearchaeota and Pacearchaeota possess bacterial group I chaperones. Thus, many DPANN appear to have mechanisms to ensure efficient protein folding of both archaeal and laterally acquired bacterial proteins.
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Kato, Shingo, Yuhei O. Tahara, Yuki Nishimura, Katsuyuki Uematsu, Takahiro Arai, Daisuke Nakane, Ayaka Ihara, et al. "Cell surface architecture of the cultivated DPANN archaeon Nanobdella aerobiophila." Journal of Bacteriology, January 30, 2024. http://dx.doi.org/10.1128/jb.00351-23.

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ABSTRACT The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1 T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1 T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1 T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1 T and MJ1HA were motile, but sole MJ1 T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila . IMPORTANCE DPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila , using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila , which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.
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Vázquez-Campos, Xabier, Andrew S. Kinsela, Mark W. Bligh, Timothy E. Payne, Marc R. Wilkins, and T. David Waite. "Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site." Frontiers in Microbiology 12 (October 18, 2021). http://dx.doi.org/10.3389/fmicb.2021.732575.

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During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and ‘Candidatus Methanoperedenaceae’ (ANME-2D). Within the undescribed DPANN, the newly proposed orders ‘Ca. Gugararchaeales’, ‘Ca. Burarchaeales’ and ‘Ca. Anstonellales’, constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the ‘Ca. Micrarchaeota’ phylum compared to most other DPANN. The analysis of new and extant ‘Ca. Methanoperedens spp.’ MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most ‘Ca. Methanoperedens’ also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and ‘Ca. Methanoperedens’, while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
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Gaisin, Vasil A., Marleen van Wolferen, Sonja-Verena Albers, and Martin Pilhofer. "Distinct life cycle stages of an ectosymbiotic DPANN archaeon." ISME Journal, May 1, 2024. http://dx.doi.org/10.1093/ismejo/wrae076.

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Abstract DPANN archaea are a diverse group of microorganisms that are thought to rely on an ectosymbiotic lifestyle; however, the cell biology of these cell–cell interactions remains largely unknown. We applied live-cell imaging and cryo-electron tomography to the DPANN archaeon Nanobdella aerobiophila and its host, revealing two distinct life cycle stages. Free cells possess archaella and are motile. Ectobiotic cells are intimately linked with the host through an elaborate attachment organelle. Our data suggest that free cells may actively seek a new host, while the ectobiotic state is adapted to mediate intricate interaction with the host.

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