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1.
Nat Chem Biol ; 2024 Oct 17.
Artigo em Inglês | MEDLINE | ID: mdl-39420228

RESUMO

The paenilamicins are a group of hybrid nonribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here we determine structures of paenilamicin PamB2-stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site transfer RNAs (tRNAs). In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms used by P. larvae. We further demonstrate that PamB2 interferes with the translocation of messenger RNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a class of context-specific translocation inhibitors.

2.
Virus Evol ; 10(1): veae080, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-39411152

RESUMO

Ross River virus (RRV) and Barmah Forest virus (BFV) are arthritogenic arthropod-borne viruses (arboviruses) that exhibit generalist host associations and share distributions in Australia and Papua New Guinea (PNG). Using stochastic mapping and discrete-trait phylogenetic analyses, we profiled the independent evolution of RRV and BFV signature mutations. Analysis of 186 RRV and 88 BFV genomes demonstrated their viral evolution trajectories have involved repeated selection of mutations, particularly in the nonstructural protein 1 (nsP1) and envelope 3 (E3) genes suggesting convergent evolution. Convergent mutations in the nsP1 genes of RRV (residues 248 and 441) and BFV (residues 297 and 447) may be involved with catalytic enzyme mechanisms and host membrane interactions during viral RNA replication and capping. Convergent E3 mutations (RRV site 59 and BFV site 57) may be associated with enzymatic furin activity and cleavage of E3 from protein precursors assisting viral maturation and infectivity. Given their requirement to replicate in disparate insect and vertebrate hosts, convergent evolution in RRV and BFV may represent a dynamic link between their requirement to selectively 'fine-tune' intracellular host interactions and viral replicative enzymatic processes. Despite evidence of evolutionary convergence, selection pressure analyses did not reveal any RRV or BFV amino acid sites under strong positive selection and only weak positive selection for nonstructural protein sites. These findings may indicate that their alphavirus ancestors were subject to positive selection events which predisposed ongoing pervasive convergent evolution, and this largely supports continued purifying selection in RRV and BFV populations during their replication in mosquito and vertebrate hosts.

3.
ACS Cent Sci ; 10(10): 1910-1919, 2024 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-39463842

RESUMO

Metalloenzymes can efficiently achieve the multielectron interconversion of carbon dioxide and carbon monoxide under mild conditions. Anaerobic carbon monoxide dehydrogenase (CODH) performs these reactions at the C cluster, a unique nickel-iron-sulfide cluster that features an apparent three-coordinate nickel site. How nature assembles the [NiFe3S4]-Feu cluster is not well understood. We use synthetic clusters to demonstrate that electron transfer can drive insertion of a Ni0 precursor into an [Fe4S4]3+ cluster to assemble higher nuclearity nickel-iron-sulfide clusters with the same complement of metal ions as the C cluster. Initial electron transfer results in a [1Ni-4Fe-4S] cluster in which a Ni1+ ion sits outside of the cluster. Modifying the Ni0 precursor results in the insertion of two nickel atoms into the cluster, concomitant with ejection of an iron to yield an unprecedented [2Ni-3Fe-4S] cluster possessing four three-coordinate metal sites. Both clusters are characterized using magnetometry, electron paramagnetic resonance (EPR), Mössbauer, and X-ray absorption spectroscopy and supported by DFT computations that are consistent with both clusters having nickel in the +1 oxidation state. These results demonstrate that Ni1+ is a viable oxidation state within iron-sulfur clusters and that redox-driven transformations can give rise to higher nuclearity clusters of relevance to the CODH C cluster.

4.
Chem Commun (Camb) ; 60(89): 13051-13054, 2024 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-39434625

RESUMO

The reversible insertion of carbon dioxide into the silicon-nitrogen bond of an N-heterocyclic iminosilane is reported. Solution-phase thermodynamic investigations indicate that this process is thermoneutral and reversible, whereas in the solid-phase CO2 can be stored for extended periods and is only released upon heating to 133 °C.

5.
J Infect ; 89(5): 106265, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39245152

RESUMO

OBJECTIVES: Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. METHODS: During routine US national surveillance (2009-2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. RESULTS: Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. CONCLUSIONS: National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. DATA AVAILABILITY: All sequence reads were uploaded and shared on NCBI's Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).


Assuntos
Infecções por Campylobacter , Campylobacter , Aprendizado de Máquina , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/microbiologia , Infecções por Campylobacter/veterinária , Animais , Estados Unidos/epidemiologia , Humanos , Campylobacter/genética , Campylobacter/classificação , Campylobacter/isolamento & purificação , Bovinos , Estudos Retrospectivos , Galinhas/microbiologia , Monitoramento Epidemiológico , Suínos , Aves Domésticas/microbiologia , Genoma Bacteriano
6.
Nucleic Acids Res ; 52(19): 12005-12020, 2024 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-39217469

RESUMO

The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.


Assuntos
Códon de Terminação , Terminação Traducional da Cadeia Peptídica , RNA de Transferência de Arginina , RNA de Transferência de Lisina , Ribossomos , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Ribossomos/metabolismo , RNA de Transferência de Arginina/metabolismo , RNA de Transferência de Arginina/genética , RNA de Transferência de Arginina/química , RNA de Transferência de Lisina/metabolismo , RNA de Transferência de Lisina/genética , RNA de Transferência de Lisina/química , Transportadores de Cassetes de Ligação de ATP/metabolismo , Transportadores de Cassetes de Ligação de ATP/genética , Microscopia Crioeletrônica , Fatores de Terminação de Peptídeos/metabolismo , Fatores de Terminação de Peptídeos/genética , Adenosina Trifosfatases/metabolismo , Adenosina Trifosfatases/genética , RNA Helicases
7.
J Am Chem Soc ; 146(30): 21034-21043, 2024 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-39023163

RESUMO

Acetyl coenzyme A synthase (ACS) catalyzes the formation and deconstruction of the key biological metabolite, acetyl coenzyme A (acetyl-CoA). The active site of ACS features a {NiNi} cluster bridged to a [Fe4S4]n+ cubane known as the A-cluster. The mechanism by which the A-cluster functions is debated, with few model complexes able to replicate the oxidation states, coordination features, or reactivity proposed in the catalytic cycle. In this work, we isolate the first bimetallic models of two hypothesized intermediates on the paramagnetic pathway of the ACS function. The heteroligated {Ni2+Ni1+} cluster, [K(12-crown-4)2][1], effectively replicates the coordination number and oxidation state of the proposed "Ared" state of the A-cluster. Addition of carbon monoxide to [1]- allows for isolation of a dinuclear {Ni2+Ni1+(CO)} complex, [K(12-crown-2)n][2] (n = 1-2), which bears similarity to the "ANiFeC" enzyme intermediate. Structural and electronic properties of each cluster are elucidated by X-ray diffraction, nuclear magnetic resonance, cyclic voltammetry, and UV/vis and electron paramagnetic resonance spectroscopies, which are supplemented by density functional theory (DFT) calculations. Calculations indicate that the pseudo-T-shaped geometry of the three-coordinate nickel in [1]- is more stable than the Y-conformation by 22 kcal mol-1, and that binding of CO to Ni1+ is barrierless and exergonic by 6 kcal mol-1. UV/vis absorption spectroscopy on [2]- in conjunction with time-dependent DFT calculations indicates that the square-planar nickel site is involved in electron transfer to the CO π*-orbital. Further, we demonstrate that [2]- promotes thioester synthesis in a reaction analogous to the production of acetyl coenzyme A by ACS.


Assuntos
Níquel , Níquel/química , Níquel/metabolismo , Acetato-CoA Ligase/química , Acetato-CoA Ligase/metabolismo , Modelos Moleculares , Complexos de Coordenação/química , Complexos de Coordenação/metabolismo , Oxirredução , Acetilcoenzima A/metabolismo , Acetilcoenzima A/química
8.
Neurosci Biobehav Rev ; 166: 105827, 2024 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-39074673

RESUMO

It is little appreciated not only how closely linked are the disciplines of neurology, psychiatry, and anthropology but even more so the degree to which they share a "common ancestry". This paper briefly reviews the definition and historical origins of each area of study to then begin to illustrate how their "genealogies" overlap. This illustration is by way of a sampling of the many key figures who contributed to the rise of not just neurology, psychiatry or anthropology but of all three disciplines. That is, a selective review is undertaken of paragons whose careers bridged medicine, neuropsychiatry, and anthropology. A sampling from among the dozens who have made major contributions to spanning these disciplines illuminates the significant extent of their co-mingled intellectual ancestry. This series is akin to a data table of necessarily concise biographical vignettes - past scholars with some or full medical training who also advanced both anthropology and neuropsychiatry as these disciplines grew into intellectual maturity. Each is, in a sense, a data point that bolsters the overarching thesis that the intellectual history of these disciplines have shared ancestry. Thus, even this preliminary and topical survey of a few past "exemplars" underscores the importance of this unique intellectual siblingship. Moreover, there is now a profusion of living scholars who add fulsomely to what might be deemed this 'trilateral marriage' of anthropology, psychiatry, and neurology. A compilation of more contemporary contributors is well worthy of a future review that expands from this first consideration. This initial work is meant to engender more robust scholarship that better elucidates and, thereby, enriches and enlivens further work while also uncovering new avenues of deeper insight, notably as to the "conceptual and heuristic progression" of evolutionary neurosciences with respect to the normative and pathologic.


Assuntos
Antropologia , Neurologia , Psiquiatria , Humanos , Antropologia/história , Antropologia/métodos , Antropologia/tendências , História do Século XVIII , História do Século XIX , História do Século XX , Neurologia/história , Neurologia/métodos , Neurologia/tendências , Psiquiatria/história , Psiquiatria/métodos , Psiquiatria/tendências , História do Século XVI , História do Século XVII
9.
bioRxiv ; 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38826346

RESUMO

The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.

10.
bioRxiv ; 2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38854126

RESUMO

The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.

11.
Front Oncol ; 14: 1356173, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38860001

RESUMO

Purpose: The primary aim of this study was to explore whether intravoxel incoherent motion (IVIM) can offer a contrast-agent-free alternative to dynamic contrast-enhanced (DCE)-MRI for measuring breast tumor perfusion. The secondary aim was to investigate the relationship between tissue diffusion measures from DWI and DCE-MRI measures of the tissue interstitial and extracellular volume fractions. Materials and methods: A total of 108 paired DWI and DCE-MRI scans were acquired at 1.5 T from 40 patients with primary breast cancer (median age: 44.5 years) before and during neoadjuvant chemotherapy (NACT). DWI parameters included apparent diffusion coefficient (ADC), tissue diffusion (Dt), pseudo-diffusion coefficient (Dp), perfused fraction (f), and the product f×Dp (microvascular blood flow). DCE-MRI parameters included blood flow (Fb), blood volume fraction (vb), interstitial volume fraction (ve) and extracellular volume fraction (vd). All were extracted from three tumor regions of interest (whole-tumor, ADC cold-spot, and DCE-MRI hot-spot) at three MRI visits: pre-treatment, after one, and three cycles of NACT. Spearman's rank correlation was used for assessing between-subject correlations (r), while repeated measures correlation was employed to assess within-subject correlations (rrm) across visits between DWI and DCE-MRI parameters in each region. Results: No statistically significant between-subject or within-subject correlation was found between the perfusion parameters estimated by IVIM and DCE-MRI (f versus vb and f×Dp versus Fb; P=0.07-0.81). Significant moderate positive between-subject and within-subject correlations were observed between ADC and ve (r=0.461, rrm=0.597) and between Dt and ve (r=0.405, rrm=0.514) as well as moderate positive within-subject correlations between ADC and vd and between Dt and vd (rrm=0.619 and 0.564, respectively) in the whole-tumor region. Conclusion: No correlations were observed between the perfusion parameters estimated by IVIM and DCE-MRI. This may be attributed to imprecise estimates of fxDp and vb, or an underlying difference in what IVIM and DCE-MRI measure. Care should be taken when interpreting the IVIM parameters (f and f×Dp) as surrogates for those measured using DCE-MRI. However, the moderate positive correlations found between ADC and Dt and the DCE-MRI parameters ve and vd confirms the expectation that as the interstitial and extracellular volume fractions increase, water diffusion increases.

12.
Int J Sports Physiol Perform ; 19(8): 765-772, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-38834184

RESUMO

PURPOSE: This study assessed the reliability and load-velocity profiles of 3 different landmine-punch-throw variations (seated without trunk rotation, seated with trunk rotation, and standing whole body) with different loads (20, 22.5, and 25.0 kg), all with the dominant hand and nondominant hand. METHODS: In a quasi-randomized order, 14 boxers (24.1 [4.3] y, 72.6 [10.1] kg) performed 3 repetitions of each variation with their dominant hand and their nondominant hand, with maximal effort and 3 minutes of interset rest. Peak velocity was measured via the GymAware Power Tool (Kinetic Performance Technologies). The interclass correlation coefficients and their 95% CIs were used to determine the intrasession reliability of each variation × load × hand combination. Additionally, a 2 (hand) × 3 (variation) repeated-measures analysis of variance assessed the load-velocity profile slope, and a 3 (variation) × 2 (hand) × 3 (load) repeated-measures analysis of variance assessed the peak velocity of each variation. RESULTS: Most variations were highly reliable (intraclass correlation coefficient > .91), with the nondominant hand being as reliable or more reliable than the dominant hand. Very strong linear relationships were observed for the group average for each variation (R2 ≥ .96). However, there was no variation × hand interaction for the slope, and there was no main effect for variation or hand. Additionally, there was no interaction for the peak velocity, but there were main effects for variation, hand, and load (P < .01). CONCLUSION: Each variation was reliable and can be used to create upper-body ballistic unilateral load-velocity profiles. However, as with other research on load-velocity profile, individual data allowed for more accurate profiling than group average data.


Assuntos
Mãos , Humanos , Reprodutibilidade dos Testes , Adulto Jovem , Mãos/fisiologia , Masculino , Fenômenos Biomecânicos , Adulto , Lateralidade Funcional/fisiologia , Rotação , Postura Sentada
13.
Int J Biol Macromol ; 273(Pt 2): 132951, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38848851

RESUMO

The current work focuses on developing nanocomposite films using taro starch and cellulose nanofibers extracted from the root's peel. Films were prepared using mixtures of starch, cellulose nanofibers (0 %, 5 %, 10 %, and 15 % w/w), glycerol, and water. Results showed that the addition of cellulose nanofibers increased film thickness, opacity, UV-light barrier capacity, and water swelling percentage. All films showed a typical B-type X-ray diffraction pattern characteristic of semicrystalline materials. FTIR analysis confirmed chemical interactions between the starch chains and the nanofibers, which probably interact through hydrogen bonds. Nanocomposite films exhibited increased tensile strength and reduced strain at break compared to control materials. Films with cellulose nanofibers showed an increase in Young's modulus compared to control ones, with no differences observed between films with cellulose nanofibers at 10 % and 15 %. Furthermore, films with cellulose nanofibers at 5 % and 10 % exhibited lower water vapor permeability than control samples, while those with cellulose nanofibers at 15 % showed an increase in this parameter compared to other materials. These results suggest that incorporating taro cellulose nanofibers is a promising alternative for obtaining taro starch nanocomposites films with improved properties.


Assuntos
Celulose , Nanocompostos , Nanofibras , Permeabilidade , Amido , Nanofibras/química , Nanocompostos/química , Celulose/química , Amido/química , Resistência à Tração , Vapor , Água/química , Difração de Raios X
14.
Dent Med Probl ; 61(3): 417-426, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38888224

RESUMO

Severe tooth wear is related to substantial loss of tooth structure, with dentin exposure and significant loss (≥1/3) of the clinical crown. The objective of this systematic review was to summarize and analyze the scientific evidence regarding the mechanical performance of computer-aided design/computer-aided manufacturing (CAD/CAM) composite resin and CAD/CAM lithium disilicate ceramic occlusal veneers, in terms of fatigue and fracture resistance, on severely worn posterior teeth. Currently, occlusal veneers are an alternative for treating worn posterior teeth. Although scientific evidence demonstrates the good performance of lithium disilicate occlusal veneers, there are less brittle materials with a modulus of elasticity more similar to dentin than ceramics, such as resin CAD/CAM blocks. Therefore, it is important to identify which type of material is best for restoring teeth with occlusal wear defects and which material can provide better clinical performance. This review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive search of the PubMed, Embase, Web of Science, Scopus, Cochrane, OpenGrey, Redalyc, DSpace, and Grey Literature Report databases was conducted and supplemented by a manual search, with no time or language limitations, until January 2022. We aimed to identify studies evaluating the fatigue and fracture resistance of CAD/CAM composite resin and ceramic occlusal veneers. The quality of the full-text articles was evaluated according to the modified Consolidated Standards of Reporting Trials (CONSORT) criteria for in vitro studies, and 400 articles were initially identified. After removing duplicates and applying the selection criteria, 6 studies were included in the review. The results demonstrated that the mechanical performance of CAD/CAM composite resin occlusal veneers is comparable to that of CAD/CAM lithium disilicate occlusal veneers in terms of fatigue and fracture resistance.


Assuntos
Cerâmica , Resinas Compostas , Desenho Assistido por Computador , Facetas Dentárias , Humanos , Porcelana Dentária , Falha de Restauração Dentária , Desgaste dos Dentes/etiologia , Desgaste dos Dentes/terapia
15.
PLoS Comput Biol ; 20(5): e1011200, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38709852

RESUMO

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and government entities led by the Centers for Disease Control and Prevention and the US COVID-19 Forecast Hub (https://covid19forecasthub.org). We evaluated approximately 9.7 million forecasts of weekly state-level COVID-19 cases for predictions 1-4 weeks into the future submitted by 24 teams from August 2020 to December 2021. We assessed coverage of central prediction intervals and weighted interval scores (WIS), adjusting for missing forecasts relative to a baseline forecast, and used a Gaussian generalized estimating equation (GEE) model to evaluate differences in skill across epidemic phases that were defined by the effective reproduction number. Overall, we found high variation in skill across individual models, with ensemble-based forecasts outperforming other approaches. Forecast skill relative to the baseline was generally higher for larger jurisdictions (e.g., states compared to counties). Over time, forecasts generally performed worst in periods of rapid changes in reported cases (either in increasing or decreasing epidemic phases) with 95% prediction interval coverage dropping below 50% during the growth phases of the winter 2020, Delta, and Omicron waves. Ideally, case forecasts could serve as a leading indicator of changes in transmission dynamics. However, while most COVID-19 case forecasts outperformed a naïve baseline model, even the most accurate case forecasts were unreliable in key phases. Further research could improve forecasts of leading indicators, like COVID-19 cases, by leveraging additional real-time data, addressing performance across phases, improving the characterization of forecast confidence, and ensuring that forecasts were coherent across spatial scales. In the meantime, it is critical for forecast users to appreciate current limitations and use a broad set of indicators to inform pandemic-related decision making.


Assuntos
COVID-19 , Previsões , Pandemias , SARS-CoV-2 , COVID-19/epidemiologia , COVID-19/transmissão , Humanos , Previsões/métodos , Estados Unidos/epidemiologia , Pandemias/estatística & dados numéricos , Biologia Computacional , Modelos Estatísticos
16.
Nucleic Acids Res ; 52(14): 8483-8499, 2024 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-38811035

RESUMO

Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.


Assuntos
Bacillus subtilis , Proteínas de Bactérias , Biossíntese de Proteínas , Ribossomos , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Ribossomos/metabolismo , Domínios Proteicos , Microscopia Crioeletrônica , Ligação Proteica , Proteínas de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/genética , Modelos Moleculares , Aminoacil-RNA de Transferência
17.
Dalton Trans ; 53(23): 9921-9932, 2024 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-38808633

RESUMO

Complexes featuring multiple metal centres are of growing interest regarding metal-metal cooperation and its tuneability. Here the synthesis and characterisation of heterobimetallic complexes of a 3d metal (4: Mn, 5: Co) and lanthanum supported by a (1,1,1-tris[(3-methoxysalicylideneamino)methyl]ethane) ligand is reported, as well as discussion of their electronic structure via electron paramagnetic resonance (EPR) spectroscopy, electrochemical experiments and computational studies. Competitive binding experiments of the ligand and various metal salts unequivocally demonstrate that in these heterobimetallic complexes the 3d metal (Mn, Co) selectively occupies the κ6-N3O3 binding site of the ligand, whilst La occupies the κ6-O6 metal binding site in line with their relative oxophilicities. EPR spectroscopy supported by density functional theory analysis indicates that the 3d metal is high spin in both cases (S = 5/2 (Mn), 3/2 (Co)). Cyclic voltammetry studies on the Mn/La and Co/La bimetallic complexes revealed a quasi-reversible Mn2+/3+ redox process and poorly-defined irreversible oxidation events respectively.

19.
Nat Commun ; 15(1): 3315, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38632311

RESUMO

This study investigates the humoral and cellular immune responses and health-related quality of life measures in individuals with mild to moderate long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24 months. LC participants show elevated nucleocapsid IgG levels at 3 months, and higher neutralizing capacity up to 8 months post-infection. Increased spike-specific and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells were observed at 3 and 8 months, but these differences do not persist at 24 months. Some LC participants had detectable IFN-γ and IFN-ß, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at the 24 month timepoint shows similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC and MC. No significant differences in exhaustion scores or antigen-specific T cell clones are observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24 months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count are associated with improvements in health-related quality of life.


Assuntos
COVID-19 , Síndrome de COVID-19 Pós-Aguda , Humanos , Linfócitos T CD8-Positivos , Qualidade de Vida , SARS-CoV-2 , Anticorpos Antivirais
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