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1.
Cell ; 186(5): 987-998.e15, 2023 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-36764290

RESUMO

RADAR is a two-protein bacterial defense system that was reported to defend against phage by "editing" messenger RNA. Here, we determine cryo-EM structures of the RADAR defense complex, revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites. RdrA and RdrB join to form a giant assembly up to 10 MDa, with RdrA docked as a funnel over the RdrB active site. Surprisingly, our structures reveal an RdrB active site that targets mononucleotides. We show that RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication. Our results define ATP mononucleotide deamination as a determinant of RADAR immunity and reveal supramolecular assembly of a nucleotide-modifying machine as a mechanism of anti-phage defense.


Assuntos
Bacteriófagos , Bacteriófagos/metabolismo , Microscopia Crioeletrônica/métodos , ATPases Associadas a Diversas Atividades Celulares , Trifosfato de Adenosina , Adenosina Desaminase/metabolismo
2.
Cell ; 184(12): 3109-3124.e22, 2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34004145

RESUMO

Glycans modify lipids and proteins to mediate inter- and intramolecular interactions across all domains of life. RNA is not thought to be a major target of glycosylation. Here, we challenge this view with evidence that mammals use RNA as a third scaffold for glycosylation. Using a battery of chemical and biochemical approaches, we found that conserved small noncoding RNAs bear sialylated glycans. These "glycoRNAs" were present in multiple cell types and mammalian species, in cultured cells, and in vivo. GlycoRNA assembly depends on canonical N-glycan biosynthetic machinery and results in structures enriched in sialic acid and fucose. Analysis of living cells revealed that the majority of glycoRNAs were present on the cell surface and can interact with anti-dsRNA antibodies and members of the Siglec receptor family. Collectively, these findings suggest the existence of a direct interface between RNA biology and glycobiology, and an expanded role for RNA in extracellular biology.


Assuntos
Membrana Celular/metabolismo , Polissacarídeos/metabolismo , RNA/metabolismo , Animais , Anticorpos/metabolismo , Sequência de Bases , Vias Biossintéticas , Linhagem Celular , Sobrevivência Celular , Humanos , Espectrometria de Massas , Ácido N-Acetilneuramínico/metabolismo , Poliadenilação , Polissacarídeos/química , RNA/química , RNA/genética , RNA não Traduzido/metabolismo , Lectinas Semelhantes a Imunoglobulina de Ligação ao Ácido Siálico/metabolismo , Coloração e Rotulagem
3.
Nature ; 628(8008): 657-663, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38509367

RESUMO

In response to pathogen infection, gasdermin (GSDM) proteins form membrane pores that induce a host cell death process called pyroptosis1-3. Studies of human and mouse GSDM pores have revealed the functions and architectures of assemblies comprising 24 to 33 protomers4-9, but the mechanism and evolutionary origin of membrane targeting and GSDM pore formation remain unknown. Here we determine a structure of a bacterial GSDM (bGSDM) pore and define a conserved mechanism of pore assembly. Engineering a panel of bGSDMs for site-specific proteolytic activation, we demonstrate that diverse bGSDMs form distinct pore sizes that range from smaller mammalian-like assemblies to exceptionally large pores containing more than 50 protomers. We determine a cryo-electron microscopy structure of a Vitiosangium bGSDM in an active 'slinky'-like oligomeric conformation and analyse bGSDM pores in a native lipid environment to create an atomic-level model of a full 52-mer bGSDM pore. Combining our structural analysis with molecular dynamics simulations and cellular assays, our results support a stepwise model of GSDM pore assembly and suggest that a covalently bound palmitoyl can leave a hydrophobic sheath and insert into the membrane before formation of the membrane-spanning ß-strand regions. These results reveal the diversity of GSDM pores found in nature and explain the function of an ancient post-translational modification in enabling programmed host cell death.


Assuntos
Gasderminas , Myxococcales , Microscopia Crioeletrônica , Gasderminas/química , Gasderminas/metabolismo , Gasderminas/ultraestrutura , Interações Hidrofóbicas e Hidrofílicas , Lipídeos de Membrana/química , Lipídeos de Membrana/metabolismo , Simulação de Dinâmica Molecular , Myxococcales/química , Myxococcales/citologia , Myxococcales/ultraestrutura , Estrutura Quaternária de Proteína , Subunidades Proteicas/química , Subunidades Proteicas/metabolismo , Proteólise , Piroptose
4.
Nature ; 625(7994): 360-365, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37992757

RESUMO

Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation1-5. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes1,6,7, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA-GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.


Assuntos
Bactérias , Proteínas de Bactérias , Bacteriófagos , Evasão da Resposta Imune , Multimerização Proteica , Bactérias/genética , Bactérias/imunologia , Bactérias/metabolismo , Bactérias/virologia , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/ultraestrutura , Bacteriófagos/genética , Bacteriófagos/imunologia , Bacteriófagos/metabolismo , Microscopia Crioeletrônica , Cristalografia por Raios X , Desoxirribonucleases/química , Desoxirribonucleases/metabolismo , Desoxirribonucleases/ultraestrutura , DNA Viral/química , DNA Viral/metabolismo , DNA Viral/ultraestrutura
5.
Nature ; 573(7775): 605-608, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31534220

RESUMO

Translation initiation determines both the quantity and identity of the protein that is encoded in an mRNA by establishing the reading frame for protein synthesis. In eukaryotic cells, numerous translation initiation factors prepare ribosomes for polypeptide synthesis; however, the underlying dynamics of this process remain unclear1,2. A central question is how eukaryotic ribosomes transition from translation initiation to elongation. Here we use in vitro single-molecule fluorescence microscopy approaches in a purified yeast Saccharomyces cerevisiae translation system to monitor directly, in real time, the pathways of late translation initiation and the transition to elongation. This transition was slower in our eukaryotic system than that reported for Escherichia coli3-5. The slow entry to elongation was defined by a long residence time of eukaryotic initiation factor 5B (eIF5B) on the 80S ribosome after the joining of individual ribosomal subunits-a process that is catalysed by this universally conserved initiation factor. Inhibition of the GTPase activity of eIF5B after the joining of ribosomal subunits prevented the dissociation of eIF5B from the 80S complex, thereby preventing elongation. Our findings illustrate how the dissociation of eIF5B serves as a kinetic checkpoint for the transition from initiation to elongation, and how its release may be governed by a change in the conformation of the ribosome complex that triggers GTP hydrolysis.


Assuntos
Fatores de Iniciação em Eucariotos/metabolismo , Elongação Traducional da Cadeia Peptídica/genética , Ribossomos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Ativação Enzimática , Fatores de Iniciação em Eucariotos/química , Fatores de Iniciação em Eucariotos/genética , Microscopia de Fluorescência , Ligação Proteica , Conformação Proteica , Ribossomos/química , Saccharomyces cerevisiae , Proteínas de Saccharomyces cerevisiae/genética
6.
Sex Transm Dis ; 51(1): 81-83, 2024 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-38100818

RESUMO

ABSTRACT: Syphilis has long been considered the "great masquerader," notorious for its varying presentations and ability to affect most organ systems in the body. We report the case of a 41-year-old immunocompetent man who presented to ophthalmology with rapidly progressive visual complaints from bilateral panuveitis and concomitant verrucous facial lesions initially disregarded by the patient as acne. Serum testing for syphilis was positive, and he was admitted for 14 days of intravenous (IV) penicillin with multiservice care from dermatology, ophthalmology, and infectious disease. We present photographic documentation showing his stepwise resolution of his facial and retinal involvement with penicillin treatment course. This case is unusual in the concomitant presentation of ocular and facial syphilitic findings in an immunocompetent patient and highlights the need to include syphilis in the differential for unusual appearances.


Assuntos
Antibacterianos , Penicilinas , Doenças Retinianas , Dermatopatias Bacterianas , Sífilis , Adulto , Humanos , Masculino , Penicilinas/uso terapêutico , Sífilis/diagnóstico , Sífilis/tratamento farmacológico , Sífilis/complicações , Face , Doenças Retinianas/tratamento farmacológico , Doenças Retinianas/etiologia , Doenças Retinianas/microbiologia , Dermatopatias Bacterianas/tratamento farmacológico , Dermatopatias Bacterianas/etiologia , Dermatopatias Bacterianas/microbiologia , Antibacterianos/uso terapêutico
7.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33479166

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta-CoV that recently emerged as a human pathogen and is the causative agent of the COVID-19 pandemic. A molecular framework of how the virus manipulates host cellular machinery to facilitate infection remains unclear. Here, we focus on SARS-CoV-2 NSP1, which is proposed to be a virulence factor that inhibits protein synthesis by directly binding the human ribosome. We demonstrate biochemically that NSP1 inhibits translation of model human and SARS-CoV-2 messenger RNAs (mRNAs). NSP1 specifically binds to the small (40S) ribosomal subunit, which is required for translation inhibition. Using single-molecule fluorescence assays to monitor NSP1-40S subunit binding in real time, we determine that eukaryotic translation initiation factors (eIFs) allosterically modulate the interaction of NSP1 with ribosomal preinitiation complexes in the absence of mRNA. We further elucidate that NSP1 competes with RNA segments downstream of the start codon to bind the 40S subunit and that the protein is unable to associate rapidly with 80S ribosomes assembled on an mRNA. Collectively, our findings support a model where NSP1 proteins from viruses in at least two subgenera of beta-CoVs associate with the open head conformation of the 40S subunit to inhibit an early step of translation, by preventing accommodation of mRNA within the entry channel.


Assuntos
COVID-19/genética , COVID-19/metabolismo , COVID-19/virologia , RNA Mensageiro/metabolismo , Ribossomos/metabolismo , SARS-CoV-2/metabolismo , Proteínas não Estruturais Virais/metabolismo , Fatores de Iniciação em Eucariotos/metabolismo , Humanos , Pandemias , Iniciação Traducional da Cadeia Peptídica/genética , Biossíntese de Proteínas , Processamento de Proteína Pós-Traducional , RNA Mensageiro/genética , RNA Viral/genética , Proteínas Ribossômicas/genética , Proteínas Ribossômicas/metabolismo , Subunidades Ribossômicas Menores de Eucariotos/metabolismo , Ribossomos/genética , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade , Proteínas não Estruturais Virais/genética
8.
Anal Chem ; 95(7): 3712-3719, 2023 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-36749928

RESUMO

In tandem mass spectrometry (MS2)-based multiplexed quantitative proteomics, the complement reporter ion approaches (TMTc and TMTproC) were developed to eliminate the ratio-compression problem of conventional MS2-level approaches. Resolving all high m/z complement reporter ions (∼6.32 mDa-spaced) requires mass resolution and scan speeds above the performance levels of OrbitrapTM instruments. Therefore, complement reporter ion quantification with TMT/TMTpro reagents is currently limited to 5 out of 11 (TMT) or 9 out of 18 (TMTpro) channels (∼1 Da spaced). We first demonstrate that a FusionTM LumosTM Orbitrap can resolve 6.32 mDa-spaced complement reporter ions with standard acquisition modes extended with 3 s transients. We then implemented a super-resolution mass spectrometry approach using the least-squares fitting (LSF) method for processing Orbitrap transients to achieve shotgun proteomics-compatible scan rates. The LSF performance resolves the 6.32 mDa doublets for all TMTproC channels in the standard mass range with transients as short as ∼108 ms (Orbitrap resolution setting of 50,000 at m/z 200). However, we observe a slight decrease in measurement precision compared to 1 Da spacing with the 108 ms transients. With 256 ms transients (resolution of 120,000 at m/z 200), coefficients of variation are essentially indistinguishable from 1 Da samples. We thus demonstrate the feasibility of highly multiplexed, accurate, and precise shotgun proteomics at the MS2 level.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Proteômica/métodos , Espectrometria de Massas em Tandem/métodos , Íons , Indicadores e Reagentes
9.
J Chem Phys ; 159(15)2023 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-37861122

RESUMO

An Achille's heel of lower-rung density-functional approximations is that the highest-occupied-molecular-orbital energy levels of anions, known to be stable or metastable in nature, are often found to be positive in the worst case or above the lowest-unoccupied-molecular-orbital levels on neighboring complexes that are not expected to accept charge. A trianionic example, [Cr(C2O4)3]3-, is of interest for constraining models linking Cr isotope ratios in rock samples to oxygen levels in Earth's atmosphere over geological timescales. Here we describe how crowd sourcing can be used to carry out self-consistent Fermi-Löwdin-Orbital-Self-Interaction corrected calculations (FLOSIC) on this trianion in solution. The calculations give a physically correct description of the electronic structure of the trianion and water. In contrast, uncorrected local density approximation (LDA) calculations result in approximately half of the anion charge being transferred to the water bath due to the effects of self-interaction error. Use of group-theory and the intrinsic sparsity of the theory enables calculations roughly 125 times faster than our initial implementation in the large N limit reached here. By integrating charge density densities and Coulomb potentials over regions of space and analyzing core-level shifts of the Cr and O atoms as a function of position and functional, we unambiguously show that FLOSIC, relative to LDA, reverses incorrect solute-solvent charge transfer in the trianion-water complex. In comparison to other functionals investigated herein, including Hartree-Fock and the local density approximation, the FLOSIC Cr 1s eigenvalues provide the best agreement with experimental core ionization energies.

10.
BMC Genomics ; 23(1): 688, 2022 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-36199042

RESUMO

BACKGROUND: MicroRNAs (miRNAs) are important post-transcriptional regulators involved in the control of a range of processes, including symbiotic interactions in plants. MiRNA involvement in arbuscular mycorrhizae (AM) symbiosis has been mainly studied in model species, and our study is the first to analyze global miRNA expression in the roots of AM colonized switchgrass (Panicum virgatum), an emerging biofuel feedstock. AM symbiosis helps plants gain mineral nutrition from the soil and may enhance switchgrass biomass production on marginal lands. Our goals were to identify miRNAs and their corresponding target genes that are controlling AM symbiosis in switchgrass. RESULTS: Through genome-wide analysis of next-generation miRNA sequencing reads generated from switchgrass roots, we identified 122 mature miRNAs, including 28 novel miRNAs. By comparing miRNA expression profiles of AM-inoculated and control switchgrass roots, we identified 15 AM-responsive miRNAs across lowland accession "Alamo", upland accession "Dacotah", and two upland/lowland F1 hybrids. We used degradome sequencing to identify target genes of the AM-responsive miRNAs revealing targets of miRNAs residing on both K and N subgenomes. Notably, genes involved in copper ion binding were targeted by downregulated miRNAs, while upregulated miRNAs mainly targeted GRAS family transcription factors. CONCLUSION: Through miRNA analysis and degradome sequencing, we revealed that both upland and lowland switchgrass genotypes as well as upland-lowland hybrids respond to AM by altering miRNA expression. We demonstrated complex GRAS transcription factor regulation by the miR171 family, with some miR171 family members being AM responsive while others remained static. Copper miRNA downregulation was common amongst the genotypes tested and we identified superoxide dismutases and laccases as targets, suggesting that these Cu-miRNAs are likely involved in ROS detoxification and lignin deposition, respectively. Other prominent targets of the Cu miRNAs were blue copper proteins. Overall, the potential effect of AM colonization on lignin deposition pathways in this biofuel crop highlights the importance of considering AM and miRNA in future biofuel crop development strategies.


Assuntos
MicroRNAs , Micorrizas , Panicum , Biocombustíveis , Cobre , Lignina , MicroRNAs/genética , MicroRNAs/metabolismo , Micorrizas/metabolismo , Panicum/metabolismo , Espécies Reativas de Oxigênio , Solo , Superóxidos , Fatores de Transcrição
11.
Nucleic Acids Res ; 48(13): 7279-7297, 2020 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-32463448

RESUMO

In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.


Assuntos
Mutação com Perda de Função , Fenótipo , Proteínas Ribossômicas/genética , Linhagem Celular Tumoral , Células HEK293 , Humanos , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Proteostase , Receptores de Quinase C Ativada/genética , Receptores de Quinase C Ativada/metabolismo , Proteínas Ribossômicas/metabolismo , Ribossomos/genética , Ribossomos/metabolismo
12.
Surg Innov ; 29(3): 353-359, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-33517863

RESUMO

Purpose. See-through head-mounted displays (HMDs) can be used to view fluoroscopic imaging during orthopedic surgical procedures. The goals of this study were to determine whether HMDs reduce procedure time, number of fluoroscopic images required, or number of head turns by the surgeon compared with standard monitors. Methods. Sixteen orthopedic surgery residents each performed fluoroscopy-guided drilling of 8 holes for placement of tibial nail distal interlocking screws in an anatomical model, with 4 holes drilled while using HMD and 4 holes drilled while using a standard monitor. Procedure time, number of fluoroscopic images needed, and number of head turns by the resident during the procedure were compared between the 2 modalities. Statistical significance was set at P < .05. Results. Mean (SD) procedure time did not differ significantly between attempts using the standard monitor (55 [37] seconds) vs the HMD (56 [31] seconds) (P = .73). Neither did mean number of fluoroscopic images differ significantly between attempts using the standard monitor vs the HMD (9 [5] images for each) (P = .84). Residents turned their heads significantly more times when using the standard monitor (9 [5] times) vs the HMD (1 [2] times) (P < .001). Conclusions. Head-mounted displays lessened the need for residents to turn their heads away from the surgical field while drilling holes for tibial nail distal interlocking screws in an anatomical model; however, there was no difference in terms of procedure time or number of fluoroscopic images needed using the HMD compared with the standard monitor.


Assuntos
Procedimentos Ortopédicos , Fluoroscopia , Monitorização Fisiológica
13.
Molecules ; 27(18)2022 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-36144677

RESUMO

Polyacrylamide hydrogels formed by free radical polymerisation were formed by entrapping anthracene and 4-amino-1,8-naphthalimide fluorescent logic gates based on photoinduced electron transfer (PET) and/or internal charge transfer (ICT). The non-covalent immobilisation of the molecules in the hydrogels resulted in semi-solid YES, NOT, and AND logic gates. Two molecular AND gates, examples of Pourbaix sensors, were tested in acidic aqueous methanol with ammonium persulfate, a strong oxidant, and displayed greater fluorescence quantum yields than previously reported. The logic hydrogels were exposed to aqueous solutions with chemical inputs, and the fluorescence output response was viewed under 365 nm UV light. All of the molecular logic gates diffuse out of the hydrogels to some extent when placed in solution, particularly those with secondary basic amines. The study exemplifies an effort of taking molecular logic gates from homogeneous solutions into the realm of solid-solution environments. We demonstrate the use of Pourbaix sensors as pE-pH indicators for monitoring oxidative and acidic conditions, notably for excess ammonium persulfate, a reagent used in the polymerisation of SDS-polyacrylamide gels.


Assuntos
Corantes , Metanol , Resinas Acrílicas , Aminas , Sulfato de Amônio , Antracenos , Hidrogéis/química , Oxidantes
14.
J Proteome Res ; 20(6): 3043-3052, 2021 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-33929851

RESUMO

Multiplexed proteomics is a powerful tool to assay cell states in health and disease, but accurate quantification of relative protein changes is impaired by interference from co-isolated peptides. Interference can be reduced by using MS3-based quantification, but this reduces sensitivity and requires specialized instrumentation. An alternative approach is quantification by complementary ions, the balancer group-peptide conjugates, which allows accurate and precise multiplexed quantification at the MS2 level and is compatible with most proteomics instruments. However, complementary ions of the popular TMT-tag form inefficiently and multiplexing is limited to five channels. Here, we evaluate and optimize complementary ion quantification for the recently released TMTpro-tag, which increases complementary ion plexing capacity to eight channels (TMTproC). Furthermore, the beneficial fragmentation properties of TMTpro increase sensitivity for TMTproC, resulting in ∼65% more proteins quantified compared to TMTpro-MS3 and ∼18% more when compared to real-time-search TMTpro-MS3 (RTS-SPS-MS3). TMTproC quantification is more accurate than TMTpro-MS2 and even superior to RTS-SPS-MS3. We provide the software for quantifying TMTproC data as an executable that is compatible with the MaxQuant analysis pipeline. Thus, TMTproC advances multiplexed proteomics data quality and widens access to accurate multiplexed proteomics beyond laboratories with MS3-capable instrumentation.


Assuntos
Peptídeos , Proteômica , Íons , Software
15.
Physiology (Bethesda) ; 35(1): 69-78, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31799907

RESUMO

Ovarian hormones are associated with risk for binge eating in women. Recent animal and human studies suggest that food-related reward processing may be one set of neurobiological factors that contribute to these relationships, but additional studies are needed to confirm and extend findings.


Assuntos
Ingestão de Alimentos/fisiologia , Comportamento Alimentar/fisiologia , Hormônios/metabolismo , Recompensa , Animais , Transtorno da Compulsão Alimentar/fisiopatologia , Feminino , Humanos
16.
RNA ; 25(7): 881-895, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31023766

RESUMO

Receptor for activated C kinase 1 (RACK1) is a eukaryote-specific ribosomal protein (RP) implicated in diverse biological functions. To engineer ribosomes for specific fluorescent labeling, we selected RACK1 as a target given its location on the small ribosomal subunit and other properties. However, prior results suggested that RACK1 has roles both on and off the ribosome, and such an exchange might be related to its various cellular functions and hinder our ability to use RACK1 as a stable fluorescent tag for the ribosome. In addition, the kinetics of spontaneous exchange of RACK1 or any RP from a mature ribosome in vitro remain unclear. To address these issues, we engineered fluorescently labeled human ribosomes via RACK1, and applied bulk and single-molecule biochemical analyses to track RACK1 on and off the human ribosome. Our results demonstrate that, despite its cellular nonessentiality from yeast to humans, RACK1 readily reassociates with the ribosome, displays limited conformational dynamics, and remains stably bound to the ribosome for hours in vitro. This work sheds insight into the biochemical basis of RPs exchange on and off a mature ribosome and provides tools for single-molecule analysis of human translation.


Assuntos
Proteínas de Neoplasias/metabolismo , Biossíntese de Proteínas , Receptores de Quinase C Ativada/metabolismo , Proteínas Ribossômicas/metabolismo , Ribossomos/metabolismo , Saccharomyces cerevisiae/metabolismo , Células HeLa , Humanos , Proteínas de Neoplasias/química , Proteínas de Neoplasias/genética , Ligação Proteica , Receptores de Quinase C Ativada/química , Receptores de Quinase C Ativada/genética , Proteínas Ribossômicas/genética , Saccharomyces cerevisiae/genética
17.
Theor Appl Genet ; 134(7): 1957-1975, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33760937

RESUMO

KEY MESSAGE: Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F2 mapping populations were developed by crossing two different F1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.


Assuntos
Ecótipo , Panicum/genética , Folhas de Planta/química , Locos de Características Quantitativas , Ceras/química , Mapeamento Cromossômico , Perfilação da Expressão Gênica , Ligação Genética , Panicum/química , Fenótipo , Polimorfismo de Nucleotídeo Único , Tetraploidia , Transcriptoma
18.
Can J Respir Ther ; 57: 60-67, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34164573

RESUMO

INTRODUCTION/BACKGROUND: Point-of-care testing (POCT) platforms support patient-centered approaches to health care delivery and may improve patient care. We evaluated implementation of a POCT platform at a large, acute care hospital in the Midwestern United States. METHODS: We used lactate testing as part of a sepsis bundle protocol to evaluate compliance and mortality outcomes. Respiratory team members were surveyed to assess perception of efficiency, ease of use, timely patient care, and overall engagement with the POCT system. Annualized cost per test of a benchtop analyzer and a POCT platform were compared across 3 years for each platform. RESULTS: Lactate testing volume increased from 61% to 91%, which was associated with improved sepsis bundle protocol compliance. Employees reported high levels of engagement, improvements in efficiency and time savings, and better patient care with POCT. Average cost per test was $10.02 for the benchtop system and $6.21 for the POCT platform. POCT saved our institution $88,476 annually in labor costs. DISCUSSION: Combined with a robust training program emphasizing the use of lactate testing in the context of the overall clinical picture, POCT enabled adherence to the sepsis bundle protocol and may have contributed to lower mortality. Additionally, the COVID-19 pandemic has provided us with unanticipated benefits of using POCT; it has enhanced our ability to deal with stringent infectious disease protocols, saving time and minimizing patient and staff exposure. CONCLUSIONS: Implementation of a POCT platform was associated with improved compliance to our sepsis protocol, reduced sepsis mortality, high employee engagement, and cost savings.

19.
Environ Sci Technol ; 54(7): 3823-3830, 2020 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-32162913

RESUMO

Biomass burning (BB) emits organic gases that, with chemical aging, can form secondary organic aerosol (SOA) in both the gas and aqueous phases. One class of biomass-burning emissions, phenols, are of interest because they react rapidly in the aqueous phase to efficiently form SOA, which might affect climate and human health. However, while measurements exist for the air-water partitioning constants of some simple phenols, Henry's law constants (KH) are unknown for more complex BB phenols. In this work, we use a custom-built apparatus to measure KH for a suite of biomass-burning phenols that span a wide range of air-water partitioning coefficients. Comparing our measurements to predicted values from EPI Suite shows that this model consistently overestimates KH unless a suitable measured phenol KH value is included to adjust the calculations. In addition, we determine the effect of five salts on phenol partitioning by measuring the Setschenow coefficients (KS). Across the eight phenols we examined, values of KS depend primarily on salt identity and descend in the order (NH4)2SO4 > NaCl > NH4Cl ≥ KNO3 > NH4NO3. Lastly, we use our KH and KS results to discuss the aqueous processing of biomass-burning phenols in cloud/fog water versus aerosol liquid water.


Assuntos
Fenóis , Água , Aerossóis , Biomassa , Humanos , Salinidade , Temperatura
20.
Nucleic Acids Res ; 46(2): e8, 2018 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-29136179

RESUMO

Human translation initiation relies on the combined activities of numerous ribosome-associated eukaryotic initiation factors (eIFs). The largest factor, eIF3, is an ∼800 kDa multiprotein complex that orchestrates a network of interactions with the small 40S ribosomal subunit, other eIFs, and mRNA, while participating in nearly every step of initiation. How these interactions take place during the time course of translation initiation remains unclear. Here, we describe a method for the expression and affinity purification of a fluorescently-tagged eIF3 from human cells. The tagged eIF3 dodecamer is structurally intact, functions in cell-based assays, and interacts with the HCV IRES mRNA and the 40S-IRES complex in vitro. By tracking the binding of single eIF3 molecules to the HCV IRES RNA with a zero-mode waveguides-based instrument, we show that eIF3 samples both wild-type IRES and an IRES that lacks the eIF3-binding region, and that the high-affinity eIF3-IRES interaction is largely determined by slow dissociation kinetics. The application of single-molecule methods to more complex systems involving eIF3 may unveil dynamics underlying mRNA selection and ribosome loading during human translation initiation.


Assuntos
Fator de Iniciação 3 em Eucariotos/metabolismo , Corantes Fluorescentes/química , Imagem Individual de Molécula/métodos , Análise Espectral/métodos , Fator de Iniciação 3 em Eucariotos/química , Fator de Iniciação 3 em Eucariotos/genética , Hepacivirus/genética , Humanos , Sítios Internos de Entrada Ribossomal/genética , Biossíntese de Proteínas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Viral/genética , RNA Viral/metabolismo , Reprodutibilidade dos Testes , Subunidades Ribossômicas Menores de Eucariotos/genética , Subunidades Ribossômicas Menores de Eucariotos/metabolismo
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