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1.
Cell ; 184(11): 2927-2938.e11, 2021 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-34010620

RESUMO

Defining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, spike (S). Here, we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using coronavirus disease 2019 (COVID-19) convalescent plasma. Antibody binding was common in two regions, the fusion peptide and the linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.


Assuntos
Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/imunologia , COVID-19/imunologia , Epitopos/imunologia , SARS-CoV-2/imunologia , Glicoproteína da Espícula de Coronavírus/imunologia , Algoritmos , COVID-19/terapia , COVID-19/virologia , Linhagem Celular , Biblioteca Gênica , Humanos , Imunização Passiva , Mutação , Domínios Proteicos , SARS-CoV-2/genética , Software , Glicoproteína da Espícula de Coronavírus/química , Glicoproteína da Espícula de Coronavírus/genética , Soroterapia para COVID-19
2.
Cell ; 169(5): 905-917.e11, 2017 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-28525757

RESUMO

The physiological relevance of structures within mammalian mRNAs has been elusive, as these mRNAs are less folded in cells than in vitro and have predicted secondary structures no more stable than those of random sequences. Here, we investigate the possibility that mRNA structures facilitate the 3'-end processing of thousands of human mRNAs by juxtaposing poly(A) signals (PASs) and cleavage sites that are otherwise too far apart. We find that RNA structures are predicted to be more prevalent within these extended 3'-end regions than within PAS-upstream regions and indeed are substantially more folded within cells, as determined by intracellular probing. Analyses of thousands of ectopically expressed variants demonstrate that this folding both enhances processing and increases mRNA metabolic stability. Even folds with predicted stabilities resembling those of random sequences can enhance processing. Structure-controlled processing can also regulate neighboring gene expression. Thus, RNA structure has widespread roles in mammalian mRNA biogenesis and metabolism.


Assuntos
Poliadenilação , Processamento Pós-Transcricional do RNA , Estabilidade de RNA , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Sequência de Bases , Linhagem Celular , Humanos , Dobramento de RNA
3.
RNA ; 30(11): 1437-1450, 2024 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-39084880

RESUMO

The SARS-CoV-2 frameshifting element (FSE) has been intensely studied and explored as a therapeutic target for coronavirus diseases, including COVID-19. Besides the intriguing virology, this small RNA is known to adopt many length-dependent conformations, as verified by multiple experimental and computational approaches. However, the role these alternative conformations play in the frameshifting mechanism and how to quantify this structural abundance has been an ongoing challenge. Here, we show by DMS and dual-luciferase functional assays that previously predicted FSE mutants (using the RAG graph theory approach) suppress structural transitions and abolish frameshifting. Furthermore, correlated mutation analysis of DMS data by three programs (DREEM, DRACO, and DANCE-MaP) reveals important differences in their estimation of specific RNA conformations, suggesting caution in the interpretation of such complex conformational landscapes. Overall, the abolished frameshifting in three different mutants confirms that all alternative conformations play a role in the pathways of ribosomal transition.


Assuntos
Mudança da Fase de Leitura do Gene Ribossômico , Mutação , Conformação de Ácido Nucleico , RNA Viral , SARS-CoV-2 , SARS-CoV-2/genética , RNA Viral/genética , RNA Viral/química , Mudança da Fase de Leitura do Gene Ribossômico/genética , Humanos , COVID-19/virologia , COVID-19/genética
4.
Mol Cell ; 70(2): 274-286.e7, 2018 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-29628307

RESUMO

Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. Whereas the circuitry controlling the heat shock response is well understood, that controlling the E. coli cold shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases, and open reading frame (ORF)-wide mRNA secondary structure decreases. To identify the regulatory system controlling this process, we screened for players required for increased translation. We identified a two-member mRNA surveillance system that enables recovery of translation during acclimation: RNase R assures appropriate mRNA degradation and the Csps dynamically adjust mRNA secondary structure to globally modulate protein expression level. An autoregulatory switch in which Csps tune their own expression to cellular demand enables dynamic control of global translation. The universality of Csps in bacteria suggests broad utilization of this control mechanism.


Assuntos
Temperatura Baixa , Resposta ao Choque Frio , Escherichia coli/genética , RNA Bacteriano/genética , RNA Mensageiro/genética , Regiões 5' não Traduzidas , Proteínas e Peptídeos de Choque Frio/genética , Proteínas e Peptídeos de Choque Frio/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Exorribonucleases/genética , Exorribonucleases/metabolismo , Regulação Bacteriana da Expressão Gênica , Conformação de Ácido Nucleico , Biossíntese de Proteínas , Estabilidade de RNA , RNA Bacteriano/química , RNA Bacteriano/metabolismo , RNA Mensageiro/química , RNA Mensageiro/metabolismo , Relação Estrutura-Atividade
5.
Mol Cell ; 72(5): 849-861.e6, 2018 12 06.
Artigo em Inglês | MEDLINE | ID: mdl-30318446

RESUMO

Alternative polyadenylation generates numerous 3' mRNA isoforms that can vary in biological properties, such as stability and localization. We developed methods to obtain transcriptome-scale structural information and protein binding on individual 3' mRNA isoforms in vivo. Strikingly, near-identical mRNA isoforms can possess dramatically different structures throughout the 3' UTR. Analyses of identical mRNAs in different species or refolded in vitro indicate that structural differences in vivo are often due to trans-acting factors. The level of Pab1 binding to poly(A)-containing isoforms is surprisingly variable, and differences in Pab1 binding correlate with the extent of structural variation for closely spaced isoforms. A pattern encompassing single-strandedness near the 3' terminus, double-strandedness of the poly(A) tail, and low Pab1 binding is associated with mRNA stability. Thus, individual 3' mRNA isoforms can be remarkably different physical entities in vivo. Sequences responsible for isoform-specific structures, differential Pab1 binding, and mRNA stability are evolutionarily conserved, indicating biological function.


Assuntos
Regulação Fúngica da Expressão Gênica , Proteínas de Ligação a Poli(A)/genética , Isoformas de RNA/química , RNA Fúngico/química , RNA Mensageiro/química , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Sequência de Bases , Conformação de Ácido Nucleico , Proteínas de Ligação a Poli(A)/metabolismo , Poliadenilação , Ligação Proteica , Isoformas de RNA/genética , Isoformas de RNA/metabolismo , Estabilidade de RNA , RNA Fúngico/genética , RNA Fúngico/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Transcriptoma
6.
Cell Mol Life Sci ; 81(1): 223, 2024 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-38767677

RESUMO

Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.


Assuntos
Doença de Parkinson , Ubiquitina-Proteína Ligases , Humanos , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo , Doença de Parkinson/genética , Doença de Parkinson/patologia , Doença de Parkinson/metabolismo , Mitocôndrias/metabolismo , Mitocôndrias/genética , Mitocôndrias/patologia , Ubiquitinação/genética , Mitofagia/genética , Animais
7.
Nano Lett ; 24(34): 10554-10561, 2024 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-39151058

RESUMO

Low-dimensional metal halide perovskites have unique optical and electrical properties that render them attractive for the design of diluted magnetic semiconductors. However, the nature of dopant-exciton exchange interactions that result in spin-polarization of host-lattice charge carriers as a basis for spintronics remains unexplored. Here, we investigate Mn2+-doped CsPbCl3 nanocrystals using magnetic circular dichroism spectroscopy and show that Mn2+ dopants induce excitonic Zeeman splitting which is strongly dependent on the nature of the band-edge structure. We demonstrate that the largest splitting corresponds to exchange interactions involving the excited state at the M-point along the spin-orbit split-off conduction band edge. This splitting gives rise to an absorption-like C-term excitonic MCD signal, with the estimated effective g-factor (geff) of ca. 70. The results of this work help resolve the assignment of absorption transitions observed for metal halide perovskite nanocrystals and allow for a design of new diluted magnetic semiconductor materials for spintronics applications.

8.
Immunology ; 172(3): 451-468, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38544428

RESUMO

Glucagon-like peptide-1 receptor agonists (GLP-1RAs), which are drugs used for treating type 2 diabetes, have been reported to exert anti-inflammatory effects on inflammatory bowel disease (IBD), the mechanism of which remains elusive. Here, we report that GLP-1RAs ameliorate dextran sulfate sodium (DSS)-induced colitis in both wild-type and T/B-cell-deficient mice through modulating group 3 innate lymphoid cells (ILC3s), a subset of innate lymphoid cells that regulate intestinal immunity. GLP-1RAs promote IL-22 production by ILC3, and the protective effect of GLP-1RAs on DSS-induced colitis was abrogated in ILC3-deficient RORgtgfp/gfp mice. Furthermore, the treatment effect of GLP-RAs on colitis, as well as the generation of IL-22-producing ILC3s by GLP-RAs, is dependent on the gut microbiota. GLP-1RAs increase the abundance of Firmicutes and Proteobacteria in the gut, particularly beneficial bacteria such as Lactobacillus reuteri, and decrease the abundance of enteropathogenic Staphylococcus bacteria. The untargeted gas chromatography (GC)/liquid chromatography (LC)-mass spectrometry (MS) of faecal metabolites further revealed enrichment of N,N-dimethylsphingosine (DMS), an endogenous metabolite derived from sphingosine, in the GLP-1RA-treated group. Strikingly, DMS ameliorates colitis while promoting intestinal IL-22-producing ILC3s. Taken together, our findings show that GLP-1RAs exert a therapeutic effect on colitis possibly by regulating the microbiota-DMS-IL-22+ILC3 axis, highlighting the potential beneficial role of GLP-RAs in inflammatory intestinal disorders with diabetes complications.


Assuntos
Colite , Sulfato de Dextrana , Microbioma Gastrointestinal , Receptor do Peptídeo Semelhante ao Glucagon 1 , Imunidade Inata , Interleucina 22 , Linfócitos , Animais , Microbioma Gastrointestinal/imunologia , Microbioma Gastrointestinal/efeitos dos fármacos , Colite/imunologia , Colite/tratamento farmacológico , Colite/metabolismo , Colite/induzido quimicamente , Camundongos , Receptor do Peptídeo Semelhante ao Glucagon 1/agonistas , Receptor do Peptídeo Semelhante ao Glucagon 1/metabolismo , Imunidade Inata/efeitos dos fármacos , Linfócitos/imunologia , Linfócitos/metabolismo , Linfócitos/efeitos dos fármacos , Camundongos Endogâmicos C57BL , Modelos Animais de Doenças , Interleucinas/metabolismo , Camundongos Knockout , Colo/imunologia , Colo/microbiologia , Colo/efeitos dos fármacos , Colo/metabolismo , Colo/patologia , Liraglutida/farmacologia , Liraglutida/uso terapêutico , Agonistas do Receptor do Peptídeo 1 Semelhante ao Glucagon
9.
Annu Rev Genet ; 50: 235-266, 2016 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-27648642

RESUMO

Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.


Assuntos
Genômica/métodos , RNA/química , Bioquímica/métodos , Genoma , Conformação de Ácido Nucleico , Poliadenilação , Biossíntese de Proteínas , RNA/metabolismo , Processamento Pós-Transcricional do RNA , Splicing de RNA , Estabilidade de RNA , Spliceossomos/genética , Spliceossomos/metabolismo
10.
Mol Syst Biol ; 19(8): e11474, 2023 08 08.
Artigo em Inglês | MEDLINE | ID: mdl-37310135

RESUMO

The assessment of variant effect predictor (VEP) performance is fraught with biases introduced by benchmarking against clinical observations. In this study, building on our previous work, we use independently generated measurements of protein function from deep mutational scanning (DMS) experiments for 26 human proteins to benchmark 55 different VEPs, while introducing minimal data circularity. Many top-performing VEPs are unsupervised methods including EVE, DeepSequence and ESM-1v, a protein language model that ranked first overall. However, the strong performance of recent supervised VEPs, in particular VARITY, shows that developers are taking data circularity and bias issues seriously. We also assess the performance of DMS and unsupervised VEPs for discriminating between known pathogenic and putatively benign missense variants. Our findings are mixed, demonstrating that some DMS datasets perform exceptionally at variant classification, while others are poor. Notably, we observe a striking correlation between VEP agreement with DMS data and performance in identifying clinically relevant variants, strongly supporting the validity of our rankings and the utility of DMS for independent benchmarking.


Assuntos
Benchmarking , Mutação de Sentido Incorreto , Humanos , Mutação , Proteínas/genética
11.
Nanotechnology ; 35(17)2024 Feb 09.
Artigo em Inglês | MEDLINE | ID: mdl-38241719

RESUMO

Fe-doped SiGe bulk alloys are fabricated using non-equilibrium spark plasma sintering (SPS) and their structure and ferromagnetic and magneto-transport properties are investigated. X-ray diffraction and high-resolution transmission electron microscope measurements show that the obtained alloys are composed of SiGe polycrystals. Magnetization measurements reveal that the Fe-doped SiGe alloys exhibit ferromagnetism up to 259 K, and their Curie temperature increases with Fe doping concentration up to 8%. Moreover, transport measurements of the Fe-doped SiGe alloys show typical metal-insulator transition characteristics of doped semiconductors as well as anomalous Hall effect and intriguing positive-to-negative magnetoresistance, indicating that the obtained alloys are diluted magnetic semiconductors (DMSs). Our results provide insight into the SPS-prepared Fe-doped SiGe bulk alloys and may be useful for the design, fabrication, and application of group-IV DMSs.

12.
Environ Sci Technol ; 2024 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-38344765

RESUMO

Volatile sulfur compounds, such as dimethyl sulfide (DMS), carbonyl sulfide (OCS), and carbon disulfide (CS2), have significant implications for both atmospheric chemistry and climate change. Despite the crucial role of oceans in regulating their atmospheric budgets, our comprehension of their cycles in seawater remains insufficient. To address this gap, a field investigation was conducted in the western North Pacific to clarify the sources, sinks, and biogeochemical controls of these gases in two different marine environments, including relatively eutrophic Kuroshio-Oyashio extension (KOE) and oligotrophic North Pacific subtropical gyre. Our findings revealed higher concentrations of these gases in both seawater and the atmosphere in the KOE compared to the subtropical gyre. In the KOE, nutrient-rich upwelling stimulated rapid DMS biological production, while reduced seawater temperatures hindered the removal of OCS and CS2, leading to their accumulation. Furthermore, we have quantitatively evaluated the relative contribution of each pathway to the source and sink of DMS, OCS, and CS2 within the mixed layer and identified vertical exchange as a potential sink in most cases, transporting substantial amounts of these gases from the mixed layer to deeper waters. This research advances our understanding of sulfur gas source-sink dynamics in seawater, contributing to the assessment of their marine emissions and atmospheric budgets.

13.
Sensors (Basel) ; 24(9)2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38732887

RESUMO

The widespread adoption of Internet of Things (IoT) devices in home, industrial, and business environments has made available the deployment of innovative distributed measurement systems (DMS). This paper takes into account constrained hardware and a security-oriented virtual local area network (VLAN) approach that utilizes local message queuing telemetry transport (MQTT) brokers, transport layer security (TLS) tunnels for local sensor data, and secure socket layer (SSL) tunnels to transmit TLS-encrypted data to a cloud-based central broker. On the other hand, the recent literature has shown a correlated exponential increase in cyber attacks, mainly devoted to destroying critical infrastructure and creating hazards or retrieving sensitive data about individuals, industrial or business companies, and many other entities. Much progress has been made to develop security protocols and guarantee quality of service (QoS), but they are prone to reducing the network throughput. From a measurement science perspective, lower throughput can lead to a reduced frequency with which the phenomena can be observed, generating, again, misevaluation. This paper does not give a new approach to protect measurement data but tests the network performance of the typically used ones that can run on constrained hardware. This is a more general scenario typical for IoT-based DMS. The proposal takes into account a security-oriented VLAN approach for hardware-constrained solutions. Since it is a worst-case scenario, this permits the generalization of the achieved results. In particular, in the paper, all OpenSSL cipher suites are considered for compatibility with the Mosquitto server. The most used key metrics are evaluated for each cipher suite and QoS level, such as the total ratio, total runtime, average runtime, message time, average bandwidth, and total bandwidth. Numerical and experimental results confirm the proposal's effectiveness in foreseeing the minimum network throughput concerning the selected QoS and security. Operating systems yield diverse performance metric values based on various configurations. The primary objective is identifying algorithms to ensure suitable data transmission and encryption ratios. Another aim is to explore algorithms that ensure wider compatibility with existing infrastructures supporting MQTT technology, facilitating secure connections for geographically dispersed DMS IoT networks, particularly in challenging environments like suburban or rural areas. Additionally, leveraging open firmware on constrained devices compatible with various MQTT protocols enables the customization of the software components, a crucial necessity for DMS.

14.
J Environ Manage ; 362: 121320, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38843750

RESUMO

The efficient removal of volatile sulfur compounds (VSCs), such as dimethyl sulfide (DMS), dimethyl disulfide (DMDS) and dimethyl trisulfide (DMTS), is crucial due to their foul odor and corrosive potential in sewer systems. Biofilters (BFs) offer promise for VSCs removal, but face challenges related to pH control and changing conditions at full scale. Two BFs, operated under acidophilic conditions for 78 days, were evaluated for their performance at varying inlet concentrations and empty bed residence times (EBRTs). BF1, incorporating 4-6 mm marble limestone for pH control, outperformed BF2, which used NaHCO3 in the nutrient solution. BF1 displayed better resilience, maintained a stable pH of 4.6 ± 0.6, and achieved higher maximum elimination capacities (ECmax, 41 mg DMS m-3 h-1 (RE 38.3%), 146 mg DMDS m-3 h-1 (RE 83.1%), 47 mg DMTS m-3 h-1 (RE 93.1%)) at an EBRT of 56 s compared to BF2 (9 mg DMS m-3 h-1 (RE 7.1%), 9 mg DMDS m-3 h-1 (RE 4.8%) and 11 mg DMTS m-3 h-1 (RE 26.6%)). BF2 exhibited pH stratification and decreased performance after feeding interruptions. The biodegradability of VSCs followed the order DMTS > DMDS > DMS, and several microorganisms were identified contributing to VSCs degradation in BF1, including Bacillus (14%), Mycobacterium (11%), Acidiphilium (7%), and Acidobacterium (3%).


Assuntos
Dissulfetos , Filtração , Sulfetos , Sulfetos/química , Concentração de Íons de Hidrogênio
15.
Medicina (Kaunas) ; 60(4)2024 Apr 22.
Artigo em Inglês | MEDLINE | ID: mdl-38674324

RESUMO

Transarterial chemoembolization (TACE) has revolutionized the treatment landscape for malignant liver disease, offering localized therapy with reduced systemic toxicity. This manuscript delves into the use of degradable microspheres (DMS) in TACE, exploring its potential advantages and clinical applications. DMS-TACE emerges as a promising strategy, offering temporary vessel occlusion and optimized drug delivery. The manuscript reviews the existing literature on DMS-TACE, emphasizing its tolerability, toxicity, and efficacy. Notably, DMS-TACE demonstrates versatility in patient selection, being suitable for both intermediate and advanced stages. The unique properties of DMS provide advantages over traditional embolic agents. The manuscript discusses the DMS-TACE procedure, adverse events, and tumor response rates in HCC, ICC, and metastases.


Assuntos
Quimioembolização Terapêutica , Neoplasias Hepáticas , Microesferas , Humanos , Quimioembolização Terapêutica/métodos , Neoplasias Hepáticas/terapia , Carcinoma Hepatocelular/terapia
16.
Methods ; 204: 249-257, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35550176

RESUMO

DMS (dimethylsulfate) is a time-tested chemical probe for nucleic acid secondary structure that has recently re-emerged as a powerful tool to study RNA structure and structural changes, by coupling it to high throughput sequencing techniques. This variant, termed DMS-MaPseq, allows for mapping of all RNAs in a cell at the same time. However, if an RNA adopts different structures, for example during the assembly of an RNA-protein complex, or as part of its functional cycle, then DMS-MaPseq cannot differentiate between these structures, and an ensemble average will be produced. This is especially challenging for long-lived RNAs, such as ribosomes, whose steady-state abundance far exceeds that of any assembly intermediates, rendering those inaccessible to DMS-MaPseq on total RNAs. These challenges can be overcome by purification of assembly intermediates stalled at specific assembly steps (or steps in the functional cycle), via a combination of affinity tags and mutants stalled at defined steps, and subsequent DMS probing of these intermediates. Interpretation of the differences in DMS accessibility is facilitated by additional structural information, e.g. from cryo-EM experiments, available for many functional RNAs. While this approach is generally useful for studying RNA folding or conformational changes within RNA-protein complexes, it can be particularly valuable for studying the role(s) of DEAD-box proteins, as these tend to lead to larger conformational rearrangements, often resulting from the release of an RNA-binding protein from a bound RNA. Here we provide an adaptation of the DMS-MaPseq protocol to study RNA conformational transitions during ribosome assembly, which addresses the challenges arising from the presence of many assembly intermediates, all at concentrations far below that of mature ribosomes. While this protocol was developed for the yeast S. cerevisiae, we anticipate that it should be readily transferable to other model organisms for which affinity purification has been established.


Assuntos
RNA , Saccharomyces cerevisiae , RNA Helicases DEAD-box/metabolismo , Conformação de Ácido Nucleico , RNA/química , Ribossomos/genética , Ribossomos/metabolismo , Saccharomyces cerevisiae/metabolismo
17.
J Phycol ; 59(5): 963-979, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37464562

RESUMO

Phaeocystis antarctica forms extensive spring blooms in the Southern Ocean that coincide with high concentrations of dimethylsulfoniopropionate (DMSP), dimethylsulfoxide (DMSO), dimethylsulfide (DMS), and acrylate. We determined how concentrations of these compounds changed during the growth of axenic P. antarctica cultures exposed to light-limiting, sub-saturating, and saturating PAR irradiances. Cellular DMSP concentrations per liter cell volume (CV) ranged between 199 and 403 mmol · LCV -1 , with the highest concentrations observed under light-limiting PAR. Cellular acrylate concentrations did not change appreciably with a change in irradiance level or growth, ranging between 18 and 45 mmol · LCV -1 , constituting an estimated 0.2%-2.8% of cellular carbon. Both dissolved acrylate and DMSO increased substantially with irradiance during exponential growth on a per-cell basis, ranging from 0.91 to 3.15 and 0.24 to 1.39 fmol · cell-1 , respectively, indicating substantial export of these compounds into the dissolved phase. Average cellular DMSO:DMSP ratios increased 7.6-fold between exponential and stationary phases of batch growth, with a 3- to 13-fold increase in cellular DMSO likely formed from abiotic reactions of DMSP and DMS with reactive oxygen species (ROS). At mM levels, cellular DMSP and acrylate are proposed to serve as de facto antioxidants in P. antarctica not regulated by oxidative stress or changes in ROS. Instead, cellular DMSP concentrations are likely controlled by other physiological processes including an overflow mechanism to remove excess carbon via acrylate, DMS, and DMSO during times of unbalanced growth brought on by physical stress or nutrient limitation. Together, these compounds should aid P. antarctica in adapting to a range of PAR irradiances by maintaining cellular functions and reducing oxidative stress.


Assuntos
Haptófitas , Compostos de Sulfônio , Dimetil Sulfóxido , Espécies Reativas de Oxigênio , Acrilatos , Carbono
18.
Lasers Med Sci ; 38(1): 203, 2023 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-37668791

RESUMO

Previous research has demonstrated the beneficial effect brought by transcranial photobiomodulation (tPBM). The present study is a further investigation of pulsed transcranial light delivery, from the perspective of wavelength, operation mode, and pulse frequency. A total of 56 healthy young adults (28 males and 28 females) were included in this randomized, sham-controlled experimental study. The wavelength of tPBM was 660 nm and 850 nm, and under each wavelength, subjects were randomly assigned to one of the following four treatments: (1) sham control; (2) continuous-wave (CW) tPBM; (3) pulsed-wave (PW) tPBM (40 Hz); and (4) PW tPBM (100 Hz). The tPBM duration was 8 min and the mean power density was fixed at 250 mW/cm2. Karolinska Sleepiness Scale (KSS) questionnaire, psychomotor vigilance task (PVT), and delayed match-to-sample (DMS) task were completed by subjects before and after the intervention to test whether PW tPBM produced distinct beneficial effects with measures of sleepiness, attention, and memory. 32-channel electroencephalography (EEG) signals were obtained from subjects before, during and after receiving tPBM or sham intervention. Paired sample T test showed that the KSS score, the number of correct responses of PVT, and DMS rate correct score (RCS) of PW tPBM groups improved significantly after intervention (p < 0.05). With regard to EEG analysis, paired one-way repeated ANOVA test showed that during the intervention of PW tPBM, the average power within the Gamma band was higher than the baseline (p < 0.05). Our study presented that PW tPBM could generate better beneficial cognitive effects and change brain electrical activity under certain circumstances.


Assuntos
Eletroencefalografia , Sonolência , Feminino , Masculino , Adulto Jovem , Humanos , Raios gama , Nível de Saúde , Frequência Cardíaca
19.
J Environ Manage ; 331: 117242, 2023 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-36630800

RESUMO

In this study, numerical groundwater modelling software (GMS) was applied for a 2D transient state predictive (flow and contaminant fate and transport) conceptual model for heavy metal (Selenium in this research) contaminated groundwater, Imamzadeh-Jafar Aquifer, Kohgiluyeh and Boyer-Ahmad Province, Iran. The performances of permeable reactive barrier (PRB) in pollutant removal in the contaminated aquifers were studied by helping the MODFLOW-MT3DMS model. The spatiotemporal distribution of Selenium (Se) contaminant over the aquifer was illustrated using the calibrated flow and contaminant model. According to the findings, the downward movement of Se has resulted in an unsafe and undesirable water quality status in the Imamzadeh-Jafar aquifer, which is supported by field data. The sensitivity analysis of PRB layouts, geometric features, and reactant material characteristics was conducted in groundwater remediation. The numerical model results illustrated that the PRB thickness, ranging from 10 to 500 m, manifested the drop in Se concentration approximately from 40 to 46%. The results shed light on the hydraulic conductivity variations of reactant materials have effects less than 0.5% in Se removals. Furthermore, the decay rate variations in the ranges from 0.0001 to 0.01 d-1 could result in Se removal from 5 to 100%. According to studies, if the contaminant sources are prevented, in a) installation of PRB and b) not installation of PRB scenarios, the Imamzadeh-Jafar aquifer remediation will take 6 months and 84 months, respectively.


Assuntos
Água Subterrânea , Selênio , Poluentes Químicos da Água , Poluentes Químicos da Água/análise , Selênio/análise , Modelos Teóricos , Irã (Geográfico)
20.
Artigo em Inglês | MEDLINE | ID: mdl-37924417

RESUMO

Dimethyl sulfate (DMS) is a highly toxic chemical that appears innocuous and is commonly used as a methylating agent in industry. It can be readily absorbed leading to poisoning or death through the skin or mucous membranes of the respiratory tract in the process of production or transportation. Although there are some articles on treatment for DMS poisoning, reports of death resulting from acute fatal DMS poisoning are very rare. Here, we present a case of a 50-year-old Chinese man who died accidentally from DMS poisoning after he broke a plastic storage tank full of DMS during transportation. The patient complained of eye irritation. In addition, the corrosive damage could be seen in his corneas and skin. The autopsy revealed erosions and ulcers in the respiratory tract, as well as massive congestion, necrosis, edema, and pseudomembrane formation on the mucous layer of the trachea and main bronchi. Histopathological examination confirmed extensive pulmonary edema, multifocal hemorrhages, whole-cell swelling in the brain, as well as disintegration of the neuronal cell. We inferred that DMS poisoning caused the symptoms resulting from the production of methanol and sulfate through hydrolysis, including respiratory toxicity and neurotoxicity, and these symptoms had temporal continuity. Toxicological analysis revealed no DMS or methanol, but formic acid was detected in the brain, both qualitatively and quantitatively. In this report, we also present a retrospective study of 8 similar cases of DMS poisoning in literature in China, including some clinical data and autopsy information.

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