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1.
Nature ; 618(7967): 992-999, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37316666

RESUMO

In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2-4. Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.


Assuntos
Archaea , Eucariotos , Filogenia , Archaea/classificação , Archaea/citologia , Archaea/genética , Eucariotos/classificação , Eucariotos/citologia , Eucariotos/genética , Células Eucarióticas/classificação , Células Eucarióticas/citologia , Células Procarióticas/classificação , Células Procarióticas/citologia , Conjuntos de Dados como Assunto , Duplicação Gênica , Evolução Molecular
2.
Genome Res ; 2024 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-39406503

RESUMO

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into the Atabeyarchaeum deiterrae-1 chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

3.
J Bacteriol ; 206(9): e0022824, 2024 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-39158294

RESUMO

Until recently, microbiologists have relied on cultures to understand the microbial world. As a result, model organisms have been the focus of research into understanding Bacteria and Archaea at a molecular level. Diversity surveys and metagenomic sequencing have revealed that these model species are often present in low abundance in the environment; instead, there are microbial taxa that are cosmopolitan in nature. Due to the numerical dominance of these microorganisms and the size of their habitats, these lineages comprise mind-boggling population sizes upward of 1028 cells on the planet. Many of these dominant groups have cultured representatives and have been shown to be involved in mediating key processes in nature. Given their importance and the increasing need to understand changes due to climate change, we propose that members of Nitrosophaerota (Nitrosopumilus maritimus), SAR11 (Pelagibacter ubique), Hadesarchaeia, Bathyarchaeia, and others become models in the future. Abundance should not be the only measure of a good model system; there are other organisms that are well suited to advance our understanding of ecology and evolution. For example, the most well-studied symbiotic bacteria, like Buchnera, Aliivibrio, and Rhizobium, should be models for understanding host-associations. Also, there are organisms that hold new insights into major transitions in the evolution of life on the planet like the Asgard Archaea (Heimdallarchaeia). Innovations in a variety of in situ techniques have enabled us to circumvent culturing when studying everything from genetics to physiology. Our deepest understanding of microbiology and its impact on the planet will come from studying these microbes in nature. Laboratory-based studies must be grounded in nature, not the other way around.


Assuntos
Archaea , Bactérias , Bactérias/genética , Bactérias/classificação , Archaea/genética , Archaea/classificação
4.
Int Wound J ; 21(4): e14817, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38567778

RESUMO

This Phase 1b study was designed to evaluate the safety and efficacy of pravibismane, a novel broad-spectrum topical anti-infective, in managing moderate or severe chronic diabetic foot ulcer (DFU) infections. This randomized, double-blind, placebo-controlled, multicenter study consisted of 39 individuals undergoing pravibismane treatment and 13 individuals in the placebo group. Assessment of safety parameters included clinical observations of tolerability and pharmacokinetics from whole blood samples. Pravibismane was well-tolerated and exhibited minimal systemic absorption, as confirmed by blood concentrations that were below the lower limit of quantitation (0.5 ng/mL) or in the low nanomolar range, which is orders of magnitude below the threshold of pharmacological relevance for pravibismane. Pravibismane treated subjects showed approximately 3-fold decrease in ulcer size compared to the placebo group (85% vs. 30%, p = 0.27). Furthermore, the incidence of ulcer-related lower limb amputations was approximately 6-fold lower (2.6%) in the pooled pravibismane group versus 15.4% in the placebo group (p = 0.15). There were no treatment emergent or serious adverse events related to study drug. The initial findings indicate that topical pravibismane was safe and potentially effective treatment for improving recovery from infected chronic ulcers by reducing ulcer size and facilitating wound healing in infected DFUs (ClinicalTrials.gov Identifier NCT02723539).


Assuntos
Anti-Infecciosos , Diabetes Mellitus , Pé Diabético , Humanos , Antibacterianos/efeitos adversos , Anti-Infecciosos/efeitos adversos , Pé Diabético/tratamento farmacológico , Método Duplo-Cego , Resultado do Tratamento , Úlcera/tratamento farmacológico
5.
Nature ; 541(7637): 353-358, 2017 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-28077874

RESUMO

The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.


Assuntos
Archaea/citologia , Archaea/genética , Eucariotos/citologia , Células Eucarióticas/citologia , Evolução Molecular , Genoma Arqueal/genética , Modelos Biológicos , Filogenia , Archaea/classificação , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Transporte Biológico/genética , Vesículas Revestidas pelo Complexo de Proteína do Envoltório/metabolismo , Eucariotos/classificação , Eucariotos/genética , Células Eucarióticas/classificação , Células Eucarióticas/metabolismo , Metagenômica
6.
Artigo em Inglês | MEDLINE | ID: mdl-36642322

RESUMO

The functional role of membrane-bound carbonic anhydrases (CAs) has been of keen interest in the past decade, and in particular, studies have linked CA in red muscle, heart, and eye to enhanced tissue oxygen extraction in bony fishes (teleosts). However, the number of purported membrane-bound CA isoforms in teleosts, combined with the imperfect system of CA isoform nomenclature, present roadblocks for ascribing physiological functions to particular CA isoforms across different teleost lineages. Here we developed an organizational framework for membrane-bound CAs in teleosts, providing the latest phylogenetic analysis of extant CA4 and CA4-like isoforms. Our data confirm that there are three distinct isoforms of CA4 (a, b, and c) that are conserved across major teleost lineages, with the exception of CA4c gene being lost in salmonids. Tissue distribution analyses suggest CA4a functions in oxygen delivery across teleost lineages, while CA4b may be specialized for renal acid-base balance and ion regulation. This work provides an important foundation for researchers to elucidate the functional significance of CA4 isoforms in fishes.


Assuntos
Anidrase Carbônica IV , Anidrases Carbônicas , Animais , Anidrase Carbônica IV/genética , Filogenia , Anidrases Carbônicas/genética , Isoformas de Proteínas/genética , Peixes/genética , Oxigênio
7.
Phonetica ; 80(1-2): 79-115, 2023 02 23.
Artigo em Inglês | MEDLINE | ID: mdl-37013664

RESUMO

Nonnative or second language (L2) perception of segmental sequences is often characterised by perceptual modification processes, which may "repair" a nonnative sequence that is phonotactically illegal in the listeners' native language (L1) by transforming the sequence into a sequence that is phonotactically legal in the L1. Often repairs involve the insertion of phonetic materials (epenthesis), but we focus, here, on the less-studied phenomenon of perceptual deletion of nonnative phonemes by testing L1 Mandarin listeners' perception of post-vocalic laterals in L2 English using the triangulating methods of a cross-language goodness rating task, an AXB task, and an AX task. The data were analysed in the framework of the Perceptual Assimilation Model (PAM/PAM-L2), and we further investigated the role of L2 vocabulary size on task performance. The experiments indicate that perceptual deletion occurs when the post-vocalic lateral overlaps with the nucleus vowel in terms of tongue backness specification. In addition, Mandarin listeners' discrimination performance in some contexts was significantly correlated with their English vocabulary size, indicating that continuous growth of vocabulary knowledge can drive perceptual learning of novel L2 segmental sequences and phonotactic structures.


Assuntos
Multilinguismo , Percepção da Fala , Humanos , Gestos , Idioma , Fonética , Vocabulário
8.
J Child Lang ; : 1-37, 2023 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-37493012

RESUMO

Many Aboriginal Australian communities are undergoing language shift from traditional Indigenous languages to contact varieties such as Kriol, an English-lexified Creole. Kriol is reportedly characterised by lexical items with highly variable phonological specifications, and variable implementation of voicing and manner contrasts in obstruents (Sandefur, 1986). A language, such as Kriol, characterised by this unusual degree of variability presents Kriol-acquiring children with a potentially difficult language-learning task, and one which challenges the prevalent theories of acquisition. To examine stop consonant acquisition in this unusual language environment, we present a study of Kriol stop and affricate production, followed by a mispronunciation detection study, with Kriol-speaking children (ages 4-7) from a Northern Territory community where Kriol is the lingua franca. In contrast to previous claims, the results suggest that Kriol-speaking children acquire a stable phonology and lexemes with canonical phonemic specifications, and that English experience would not appear to induce this stability.

9.
Environ Microbiol ; 22(5): 1764-1783, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-31775181

RESUMO

Microbial communities inhabit algae cell surfaces and produce a variety of compounds that can impact the fitness of the host. These interactions have been studied via culturing, single-gene diversity and metagenomic read survey methods that are limited by culturing biases and fragmented genetic characterizations. Higher-resolution frameworks are needed to resolve the physiological interactions within these algal-bacterial communities. Here, we infer the encoded metabolic capabilities of four uncultured bacterial genomes (reconstructed using metagenomic assembly and binning) associated with the marine dinoflagellates Gambierdiscus carolinianus and G. caribaeus. Phylogenetic analyses revealed that two of the genomes belong to the commonly algae-associated families Rhodobacteraceae and Flavobacteriaceae. The other two genomes belong to the Phycisphaeraceae and include the first algae-associated representative within the uncultured SM1A02 group. Analyses of all four genomes suggest these bacteria are facultative aerobes, with some capable of metabolizing phytoplanktonic organosulfur compounds including dimethylsulfoniopropionate and sulfated polysaccharides. These communities may biosynthesize compounds beneficial to both the algal host and other bacteria, including iron chelators, B vitamins, methionine, lycopene, squalene and polyketides. These findings have implications for marine carbon and nutrient cycling and provide a greater depth of understanding regarding the genetic potential for complex physiological interactions between microalgae and their associated bacteria.


Assuntos
Dinoflagellida/microbiologia , Flavobacteriaceae/genética , Genoma Bacteriano/genética , Microalgas/microbiologia , Rhodobacteraceae/genética , Fenômenos Bioquímicos , Metagenoma , Metagenômica , Microbiota/genética , Filogenia , Fitoplâncton/microbiologia
10.
Appl Environ Microbiol ; 85(15)2019 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-31126943

RESUMO

Metagenomics of marine sediments has uncovered a broad diversity of new uncultured taxa and provided insights into their metabolic capabilities. Here, we detected microbial lineages from a sediment core near the Jiulong methane reef of the northern South China Sea (at 1,100-m depth). Assembly and binning of the metagenomes resulted in 11 genomes (>85% complete) that represented nine distinct phyla, including candidate phyla TA06 and LCP-89, Lokiarchaeota, Heimdallarchaeota, and a newly described globally distributed phylum (B38). The genome of LCP-89 has pathways for nitrate, selenate, and sulfate reduction, suggesting that they may be involved in mediating these important processes. B38 are able to participate in the cycling of hydrogen and selenocompounds. Many of these uncultured microbes may also be capable of autotrophic CO2 fixation, as exemplified by identification of the Wood-Ljungdahl (W-L) pathway. Genes encoding carbohydrate degradation, W-L pathway, Rnf-dependent energy conservation, and Ni/Fe hydrogenases were detected in the transcriptomes of these novel members. Characterization of these new lineages provides insight to the undescribed branches in the tree of life.IMPORTANCE Sedimentary microorganisms in the South China Sea (SCS) remain largely unknown due to the complexity of sediment communities impacted by continent rifting and extension. Distinct geochemical environments may breed special microbial communities including microbes that are still enigmatic. Functional inference of their metabolisms and transcriptional activity provides insight in the ecological roles and substrate-based interactivity of these uncultured Archaea and Bacteria These microorganisms play different roles in utilizing inorganic carbon and scavenging diverse organic compounds involved in the deep-sea carbon cycle. The genomes recovered here contributed undescribed species to the tree of life and laid the foundation for future study on these novel phyla persisting in marginal sediments of the SCS.


Assuntos
Archaea/classificação , Bactérias/classificação , Ciclo do Carbono , Água do Mar/microbiologia , Archaea/metabolismo , Bactérias/metabolismo , China , Genoma Arqueal , Genoma Bacteriano , Metagenoma , Nutrientes/metabolismo , Taiwan
11.
Appl Environ Microbiol ; 85(19)2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31324636

RESUMO

Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (Vmax) decreased with increasing sediment depth, although Vmax expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km ) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (d-phenylalanine and l-ornithine) increased relative to enzymes that act on l-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.IMPORTANCE Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.


Assuntos
Estuários , Sedimentos Geológicos/química , Microbiota , Peptídeo Hidrolases/isolamento & purificação , Peptídeo Hidrolases/metabolismo , Carbono/química , Processos Heterotróficos , Cinética , Metagenoma , North Carolina , Compostos Orgânicos/química
12.
Int J Sports Med ; 40(1): 52-56, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30481828

RESUMO

We determined whether the incidence of injuries would increase with advancing age and whether the participation in cross-training would be related to a decreased rate of injuries and healthcare costs in Masters swimmers. A total of 499 swimmers (55±14 years of age) belonging to US Masters Swimming completed a comprehensive questionnaire that included questions regarding their medical history as well as their training history. In average, swimmers had been training for 13±12 years, and 35, 40, and 47% participated in running, cycling, and dryland resistance training, respectively. According to the logistic regression, prevalence of injuries increased significantly but modestly with advancing age (p<0.05). Linear regression analysis showed that for every 1 month increase in the length of injury, healthcare costs increased by 7.4% (p<0.05). Linear regression and logistic regression analyses determined that overall volume of swimming training was not related to age or incidence of injuries, respectively. Multinomial logistic regression analyses using age and sex as predictors demonstrated that the odds of reporting a swim-related injury were significantly lower for individuals who participated in any number of cross-training activities compared with those who do not cross-train (p<0.05). Regular participation in any cross-training modality was inversely related to age (p<0.05). We concluded that the diversification of the overall training program by incorporating cross-training may be an important strategy to reduce sport-specific injuries among Masters athletes.


Assuntos
Traumatismos em Atletas/epidemiologia , Condicionamento Físico Humano , Natação/lesões , Adulto , Idoso , Atletas , Traumatismos em Atletas/prevenção & controle , Feminino , Humanos , Incidência , Modelos Lineares , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Inquéritos e Questionários
13.
Phys Chem Chem Phys ; 20(38): 24979-24991, 2018 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-30239541

RESUMO

The Zn(ii)-(Imidazole(ate))n coordination motif occurs in numerous biochemical systems, including carbonic anhydrase and the matrix metalloproteinases (MMPs). Additionally, it has been used in synthetic materials, such as the zinc-based zeolitic imidazolate framework (ZIF) structures. Zinc centers in these systems typically act as Lewis acids that form complexes with small molecules, such as H2O, which is activated catalytically toward a number of important and useful hydrolysis reactions. The results reported herein from density functional theory (M05-2X) and ab initio (MP2 and CCSD(T)) calculations demonstrate that both the coordination number and the molecular geometry have a sizable impact on the binding strength, deprotonation energy, and acidity of the Zn(ii) coordinated water. Through a series of quantum mechanical calculations on [(ImH)nZn-OH2]2+ complexes (n = 1-5), both the solution-phase pKa and the gas-phase proton dissociation energy significantly increase as n increases. While this should not be too surprising, the Zn-OH2 bond dissociation energies and bond lengths don't necessarily undergo a concurrent decrease, and therefore would be of limited use as a prediction tool regarding Zn-OH2 acidity. In an effort to dissect the impacts of coordination number and molecular geometry on these thermodynamic parameters, we performed constrained geometry optimizations on the three- (n = 2) and four-coordinate (n = 3) complexes. These calculations surprisingly reveal a marked impact on the pKa and proton dissociation energy of the coordinated water, upon exclusive changes in the Zn(ii) coordination geometry, whether in the gas-phase or in aqueous solution. We discuss the relevance of these results to the catalytic peptide hydrolysis mechanism of the MMPs and possible implications for catalytic activity within or on the surfaces of ZIFs.

14.
Int J Sports Med ; 39(11): 835-839, 2018 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30130814

RESUMO

Age-related decreases in performance are thought to be driven by decreases in exercise training stimuli. We determined the influence of changes in training stimuli with advancing age on swimming performance using cross-sectional and longitudinal data analyses. Totals of 692 and 98 competitive swimmers belonging to the US Masters Swimming Association were analyzed in cross-sectional and longitudinal analyses. Swimming times increased with advancing age, and age was the strongest predictor of swimming performance, followed by training volume, in both the cross-sectional and longitudinal analyses. In the cross-sectional data analyses, an increase in training volume by 10 km/month, was associated with improved performance by 0.69 s regardless of age. In the longitudinal analyses, training volume was not a significant predictor for younger swimmers. In middle-aged swimmers, however, increases in training volume resulted in faster swimming times, and its effect was more pronounced in older swimmers. We concluded that there was a graded positive relationship between yearly increases in training volume and improved swimming performance, and that such effects were greater with advancing age.


Assuntos
Envelhecimento/fisiologia , Desempenho Atlético/fisiologia , Comportamento Competitivo/fisiologia , Condicionamento Físico Humano/métodos , Natação/fisiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos Transversais , Feminino , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Adulto Jovem
16.
Environ Microbiol ; 18(4): 1200-11, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26626228

RESUMO

Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.


Assuntos
Archaea , Metabolismo dos Carboidratos/genética , Carbono/metabolismo , Sedimentos Geológicos/microbiologia , Acetilcoenzima A/metabolismo , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Carboidratos , DNA Arqueal/genética , Estuários , Genômica , Filogenia , RNA Ribossômico 16S/genética , Microbiologia do Solo , Microbiologia da Água
17.
J Acoust Soc Am ; 140(4): 2794, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27794291

RESUMO

Substantial research has established that place of articulation of stop consonants (labial, alveolar, velar) are reliably differentiated using a number of acoustic measures such as closure duration, voice onset time (VOT), and spectral measures such as centre of gravity and the relative energy distribution in the mid-to-high spectral range of the burst. It is unclear, however, whether such measurable acoustic differences are present in multiple place of articulation contrasts among coronal stops. This article presents evidence from the highly endangered indigenous Australian language Wubuy, which maintains a 4-way coronal stop place contrast series in all word positions. The authors examine the temporal and burst characteristics of / t̪ t ʈ/ in three prosodic positions (utterance-initial, word-initial but phrase medial, and word-medial). The results indicate that VOT, closure duration, and the spectral quality of the burst may indeed differentiate multiple coronal place contrasts, in most positions, although measures that distinguish the apical contrast in absolute initial position remain elusive. The authors also examine measures (spectrum kurtosis, spectral tilt) previously used in other studies of multiple coronals in Australian languages. These results suggest that the authors' measures perform at least as well as those previously applied to multiple coronals in other Australian languages.

18.
Environ Microbiol ; 16(1): 60-71, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23826624

RESUMO

Particulate membrane-associated hydrocarbon monooxygenases (pHMOs) are critical components of the aerobic degradation pathway for low molecular weight hydrocarbons, including the potent greenhouse gas methane. Here, we analysed pHMO gene diversity in metagenomes and metatranscriptomes of hydrocarbon-rich hydrothermal plumes in the Guaymas Basin (GB) and nearby background waters in the deep Gulf of California. Seven distinct phylogenetic groups of pHMO were present and transcriptionally active in both plume and background waters, including several that are undetectable with currently available polymerase chain reaction (PCR) primers. The seven groups of pHMOs included those related to a putative ethane oxidizing Methylococcaceae-like group, a group of the SAR324 Deltaproteobacteria, three deep-sea clades (Deep sea-1/symbiont-like, Deep sea-2/PS-80 and Deep sea-3/OPU3) within gammaproteobacterial methanotrophs, one clade related to Group Z and one unknown group. Differential abundance of pHMO gene transcripts in plume and background suggests niche differentiation between groups. Corresponding 16S rRNA genes reflected similar phylogenetic and transcriptomic abundance trends. The novelty of transcriptionally active pHMOs we recovered from a hydrocarbon-rich hydrothermal plume suggests there are significant gaps in our knowledge of the diversity and function of these enzymes in the environment.


Assuntos
Proteínas de Bactérias/genética , Deltaproteobacteria/enzimologia , Hidrocarbonetos/metabolismo , Metagenoma , Metano/metabolismo , Methylococcaceae/enzimologia , Oxigenases de Função Mista/genética , Água do Mar/microbiologia , Proteínas de Bactérias/metabolismo , California , Deltaproteobacteria/classificação , Deltaproteobacteria/genética , Deltaproteobacteria/metabolismo , Methylococcaceae/classificação , Methylococcaceae/genética , Methylococcaceae/metabolismo , Oxigenases de Função Mista/metabolismo , Dados de Sequência Molecular , Filogenia , RNA Ribossômico 16S/genética , Transcriptoma
19.
mBio ; 15(10): e0034724, 2024 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-39207169

RESUMO

DPANN archaea have characteristically small cells and unique genomes that were long overlooked in diversity surveys. Their reduced genomes often lack essential metabolic pathways, requiring symbiotic relationships with other archaeal and bacterial hosts for survival. Yet a long-standing question remains, what is the advantage of maintaining ultrasmall cells. A recent study by Zhang et al. examined genomes of DPANN archaea from marine oxygen deficient zones (ODZs) (I. H. Zhang, B. Borer, R. Zhao, S. Wilbert, et al., mBio 15:e02918-23, 2024, https://doi.org/10.1128/mbio.02918-23). Surprisingly, these genomes contain a broad array of metabolic pathways including genes predicted to be involved in nitrous oxide (N2O) reduction. However, N2O levels are likely too low in ODZs to make this metabolically feasible. Modeling co-localization of DPANN archaea (N2O consumers) with other larger cells (N2O producers) demonstrates that N2O uptake rates can be optimized by maximizing the producer-to-consumer size ratio and proximity of consumer cells to producers. This may explain why such a diversity of archaea maintain extremely small cell sizes.


Assuntos
Archaea , Genoma Arqueal , Simbiose , Archaea/metabolismo , Archaea/genética , Archaea/classificação , Redes e Vias Metabólicas/genética , Óxido Nitroso/metabolismo
20.
AJPM Focus ; 3(3): 100202, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38596163

RESUMO

Introduction: The novel COVID-19 disease detected in 2019 widely affected individuals' social movements, likely disrupting the ability to participate in leisure-related physical activity. Because of this, participation in sedentary behavior is thought to have increased. The purpose of this study was to determine how the COVID-19 pandemic affected U.S. young adult physical activity and sedentary behavior. Methods: A total of 333 U.S. young adults (aged between 18 and 30 years) completed an online, comprehensive questionnaire during the early parts of COVID-19. Wilcoxon signed-rank tests were used to determine the change in time spent in physical activity and sedentary behavior during COVID-19 compared with that before COVID-19. Results: There was a significant decrease in physical activity minutes (p<0.0001) and a significant increase in sedentary behavior (p<0.005) during COVID-19 compared with that before COVID-19. Significant differences were found by stratifying the data by sex and relationship status. Although both males and females reduced their physical activity, only males significantly increased their time in sedentary behavior during COVID-19 compared with that before COVID-19 (p<0.05). Furthermore, married young adults significantly reduced their physical activity during COVID-19 (p<0.001), whereas single individuals did not. Single young adults saw significant increases in sedentary behavior during COVID-19 (p<0.005), whereas married individuals did not exhibit any change in sedentary behavior. Conclusions: Stay-at-home orders enforced in the U.S. during the summer of 2020 led to increases in sedentary behavior and decreases in physical activity, particularly among males and single young adults. Future studies should determine whether these behavior changes persist.

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