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1.
Cell ; 177(2): 339-351.e13, 2019 04 04.
Artigo em Inglês | MEDLINE | ID: mdl-30879786

RESUMO

Pre-mRNA splicing is executed by the spliceosome. Structural characterization of the catalytically activated complex (B∗) is pivotal for understanding the branching reaction. In this study, we assembled the B∗ complexes on two different pre-mRNAs from Saccharomyces cerevisiae and determined the cryo-EM structures of four distinct B∗ complexes at overall resolutions of 2.9-3.8 Å. The duplex between U2 small nuclear RNA (snRNA) and the branch point sequence (BPS) is discretely away from the 5'-splice site (5'SS) in the three B∗ complexes that are devoid of the step I splicing factors Yju2 and Cwc25. Recruitment of Yju2 into the active site brings the U2/BPS duplex into the vicinity of 5'SS, with the BPS nucleophile positioned 4 Å away from the catalytic metal M2. This analysis reveals the functional mechanism of Yju2 and Cwc25 in branching. These structures on different pre-mRNAs reveal substrate-specific conformations of the spliceosome in a major functional state.


Assuntos
Spliceossomos/fisiologia , Spliceossomos/ultraestrutura , Domínio Catalítico/fisiologia , Microscopia Crioeletrônica/métodos , Éxons , Íntrons , Proteínas Nucleares/metabolismo , Precursores de RNA/metabolismo , Sítios de Splice de RNA/genética , Splicing de RNA/fisiologia , Fatores de Processamento de RNA/metabolismo , RNA Nuclear Pequeno/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Spliceossomos/metabolismo
2.
Cell ; 169(5): 918-929.e14, 2017 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-28502770

RESUMO

Mechanistic understanding of pre-mRNA splicing requires detailed structural information on various states of the spliceosome. Here we report the cryo electron microscopy (cryo-EM) structure of the human spliceosome just before exon ligation (the C∗ complex) at an average resolution of 3.76 Å. The splicing factor Prp17 stabilizes the active site conformation. The step II factor Slu7 adopts an extended conformation, binds Prp8 and Cwc22, and is poised for selection of the 3'-splice site. Remarkably, the intron lariat traverses through a positively charged central channel of RBM22; this unusual organization suggests mechanisms of intron recruitment, confinement, and release. The protein PRKRIP1 forms a 100-Å α helix linking the distant U2 snRNP to the catalytic center. A 35-residue fragment of the ATPase/helicase Prp22 latches onto Prp8, and the quaternary exon junction complex (EJC) recognizes upstream 5'-exon sequences and associates with Cwc22 and the GTPase Snu114. These structural features reveal important mechanistic insights into exon ligation.


Assuntos
Precursores de RNA/metabolismo , Spliceossomos/química , Spliceossomos/ultraestrutura , Sequência de Bases , Microscopia Crioeletrônica , RNA Helicases DEAD-box/metabolismo , Éxons , Humanos , Íntrons , Modelos Moleculares , Splicing de RNA , Fatores de Processamento de RNA/metabolismo , Proteínas de Ligação a RNA/metabolismo , Saccharomyces cerevisiae/química , Spliceossomos/metabolismo
3.
Mol Cell ; 80(1): 127-139.e6, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-33007253

RESUMO

Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the Bact to C transition. Structural comparisons with human Bact, C∗, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.


Assuntos
Fatores de Processamento de RNA/química , Fatores de Processamento de RNA/metabolismo , Spliceossomos/metabolismo , Animais , Catálise , Células HeLa , Humanos , Íntrons/genética , Modelos Moleculares , Complexos Multiproteicos/metabolismo , Complexos Multiproteicos/ultraestrutura , Ligação Proteica , Estabilidade Proteica , RNA/química , RNA/metabolismo , Ribonucleoproteínas/metabolismo , Saccharomyces cerevisiae/metabolismo , Especificidade da Espécie , Fatores de Tempo
4.
Proc Natl Acad Sci U S A ; 121(25): e2400546121, 2024 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-38857407

RESUMO

Reduction of carbon dioxide (CO2) by renewable electricity to produce multicarbon chemicals, such as ethylene (C2H4), continues to be a challenge because of insufficient Faradaic efficiency, low production rates, and complex mechanistic pathways. Here, we report that the rate-determining steps (RDS) on common copper (Cu) surfaces diverge in CO2 electroreduction, leading to distinct catalytic performances. Through a combination of experimental and computational studies, we reveal that C─C bond-making is the RDS on Cu(100), whereas the protonation of *CO with adsorbed water becomes rate-limiting on Cu(111) with a higher energy barrier. On an oxide-derived Cu(100)-dominant Cu catalyst, we reach a high C2H4 Faradaic efficiency of 72%, partial current density of 359 mA cm-2, and long-term stability exceeding 100 h at 500 mA cm-2, greatly outperforming its Cu(111)-rich counterpart. We further demonstrate constant C2H4 selectivity of >60% over 70 h in a membrane electrode assembly electrolyzer with a full-cell energy efficiency of 23.4%.

5.
Brief Bioinform ; 25(2)2024 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-38385881

RESUMO

Gene expression during brain development or abnormal development is a biological process that is highly dynamic in spatio and temporal. Previous studies have mainly focused on individual brain regions or a certain developmental stage. Our motivation is to address this gap by incorporating spatio-temporal information to gain a more complete understanding of brain development or abnormal brain development, such as Alzheimer's disease (AD), and to identify potential determinants of response. In this study, we propose a novel two-step framework based on spatial-temporal information weighting and multi-step decision trees. This framework can effectively exploit the spatial similarity and temporal dependence between different stages and different brain regions, and facilitate differential gene analysis in brain regions with high heterogeneity. We focus on two datasets: the AD dataset, which includes gene expression data from early, middle and late stages, and the brain development dataset, spanning fetal development to adulthood. Our findings highlight the advantages of the proposed framework in discovering gene classes and elucidating their impact on brain development and AD progression across diverse brain regions and stages. These findings align with existing studies and provide insights into the processes of normal and abnormal brain development.


Assuntos
Doença de Alzheimer , Encéfalo , Humanos , Doença de Alzheimer/genética , Expressão Gênica , Árvores de Decisões
6.
Development ; 149(21)2022 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-36205075

RESUMO

Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work has demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a previously unreported function of FGF8. By combining transgenic mouse models, quantitative imaging assays and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPC condensation at the UB. Chemokinetic effects have also been described for other FGFs and may be generally important for the formation of mesenchymal condensates.


Assuntos
Rim , Néfrons , Camundongos , Animais , Néfrons/metabolismo , Rim/metabolismo , Organogênese , Fatores de Crescimento de Fibroblastos/metabolismo , Células-Tronco/metabolismo , Camundongos Transgênicos , Fator 8 de Crescimento de Fibroblasto/genética , Fator 8 de Crescimento de Fibroblasto/metabolismo
7.
Cell Mol Life Sci ; 81(1): 354, 2024 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-39158743

RESUMO

Mature neurons have stable dendritic architecture, which is essential for the nervous system to operate correctly. The ability to undergo structural plasticity, required to support adaptive processes like memory formation, is still present in mature neurons. It is unclear what molecular and cellular processes control this delicate balance between dendritic structural plasticity and stabilization. Failures in the preservation of optimal dendrite structure due to atrophy or maladaptive plasticity result in abnormal connectivity and are associated with various neurological diseases. Vascular endothelial growth factor D (VEGFD) is critical for the maintenance of mature dendritic trees. Here, we describe how VEGFD affects the neuronal cytoskeleton and demonstrate that VEGFD exerts its effects on dendrite stabilization by influencing the actin cortex and reducing microtubule dynamics. Further, we found that during synaptic activity-induced structural plasticity VEGFD is downregulated. Our findings revealed that VEGFD, acting on its cognate receptor VEGFR3, opposes structural changes by negatively regulating dendrite growth in cultured hippocampal neurons and in vivo in the adult mouse hippocampus with consequences on memory formation. A phosphoproteomic screening identified several regulatory proteins of the cytoskeleton modulated by VEGFD. Among the actin cortex-associated proteins, we found that VEGFD induces dephosphorylation of ezrin at tyrosine 478 via activation of the striatal-enriched protein tyrosine phosphatase (STEP). Activity-triggered structural plasticity of dendrites was impaired by expression of a phospho-deficient mutant ezrin in vitro and in vivo. Thus, VEGFD governs the equilibrium between stabilization and plasticity of dendrites by acting as a molecular brake of structural remodeling.


Assuntos
Dendritos , Hipocampo , Plasticidade Neuronal , Transdução de Sinais , Animais , Dendritos/metabolismo , Camundongos , Hipocampo/metabolismo , Hipocampo/citologia , Camundongos Endogâmicos C57BL , Células Cultivadas , Citoesqueleto/metabolismo , Masculino , Neurônios/metabolismo , Neurônios/citologia , Actinas/metabolismo , Fosforilação , Microtúbulos/metabolismo
8.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-35074919

RESUMO

ATP-binding cassette (ABC) transporters are ubiquitous molecular pumps that transport a broad range of substrates across biological membranes. Although the structure and function of ABC transporters has been studied extensively, our understanding of their energetics and dynamics remains limited. Here, we present studies of the peptidase-containing ABC transporter 1 (PCAT1), a polypeptide processing and secretion ABC transporter that functions via the classic alternating access mechanism. PCAT1 is a homodimer containing two peptidase (PEP) domains, two transmembrane domains, and two nucleotide-binding domains (NBDs). Using cryo-electron microscopy, we analyzed the structures of wild-type PCAT1 under conditions that either prevent or permit ATP hydrolysis and observed two completely different conformational distributions. In the presence of ATP but absence of Mg2+, PCAT1 adopts an NBD-dimerized, outward-facing conformation. The two PEP domains are dissociated from the transporter core, preventing uncoupled substrate cleavage. The addition of Mg2+ to promote ATP hydrolysis shifts the majority of the particles into NBD-separated, inward-facing conformations. Under this ATP turnover condition, only a small fraction of PCAT1 adopts the NBD-dimerized conformation. These data give rise to two mechanistic conclusions: 1) the ATP-bound, NBD-dimerized conformation is the lowest energy state, and 2) the rate-limiting step in the PCAT1 transport cycle is the formation of the NBD dimer. The thermodynamic conclusion is likely a general property shared by many ABC transporters. The kinetic bottleneck, however, varies from transporter to transporter.


Assuntos
Transportadores de Cassetes de Ligação de ATP/química , Modelos Moleculares , Conformação Proteica , Transportadores de Cassetes de Ligação de ATP/genética , Transportadores de Cassetes de Ligação de ATP/metabolismo , Trifosfato de Adenosina/química , Trifosfato de Adenosina/metabolismo , Microscopia Crioeletrônica , Mutação , Ligação Proteica
9.
Proc Natl Acad Sci U S A ; 119(40): e2210203119, 2022 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-36161916

RESUMO

Hard carbon is regarded as the most promising anode material for sodium-ion (Na-ion) batteries, owing to its advantages of high abundance, low cost, and low operating potential. However, the rate capability and cycle life span of hard carbon anodes are far from satisfactory, severely hindering its industrial applications. Here, we demonstrate that the desolvation process defines the Na-ion diffusion kinetics and the formation of a solid electrolyte interface (SEI). The 3A zeolite molecular sieve film on the hard carbon is proposed to develop a step-by-step desolvation pathway that effectively reduces the high activation energy of the direct desolvation process. Moreover, step-by-step desolvation yields a thin and inorganic-dominated SEI with a lower activation energy for Na+ transport. As a result, it contributes to greatly improved power density and cycling stability for both ester and ether electrolytes. When the above insights are applied, the hard carbon anode achieves the longest life span and minimum capacity fading rate at all evaluated current densities. Moreover, with the increase in current densities, an improved plateau capacity ratio is observed. This step-by-step desolvation strategy comprehensively enhances various properties of hard carbon anodes, which provides the possibility of building practical Na-ion batteries with high power density, high energy density, and durability.

10.
Proc Natl Acad Sci U S A ; 119(2)2022 01 11.
Artigo em Inglês | MEDLINE | ID: mdl-34987099

RESUMO

The Earth's inner core started forming when molten iron cooled below the melting point. However, the nucleation mechanism, which is a necessary step of crystallization, has not been well understood. Recent studies have found that it requires an unrealistic degree of undercooling to nucleate the stable, hexagonal, close-packed (hcp) phase of iron that is unlikely to be reached under core conditions and age. This contradiction is referred to as the inner core nucleation paradox. Using a persistent embryo method and molecular dynamics simulations, we demonstrate that the metastable, body-centered, cubic (bcc) phase of iron has a much higher nucleation rate than does the hcp phase under inner core conditions. Thus, the bcc nucleation is likely to be the first step of inner core formation, instead of direct nucleation of the hcp phase. This mechanism reduces the required undercooling of iron nucleation, which provides a key factor in solving the inner core nucleation paradox. The two-step nucleation scenario of the inner core also opens an avenue for understanding the structure and anisotropy of the present inner core.

11.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-35042821

RESUMO

The adenosine triphosphate (ATP) analog ATPγS often greatly slows or prevents enzymatic ATP hydrolysis. The eukaryotic CMG (Cdc45, Mcm2 to 7, GINS) replicative helicase is presumed unable to hydrolyze ATPγS and thus unable to perform DNA unwinding, as documented for certain other helicases. Consequently, ATPγS is often used to "preload" CMG onto forked DNA substrates without unwinding before adding ATP to initiate helicase activity. We find here that CMG does hydrolyze ATPγS and couples it to DNA unwinding. Indeed, the rate of unwinding of a 20- and 30-mer duplex fork of different sequences by CMG is only reduced 1- to 1.5-fold using ATPγS compared with ATP. These findings imply that a conformational change is the rate-limiting step during CMG unwinding, not hydrolysis. Instead of using ATPγS for loading CMG onto DNA, we demonstrate here that nonhydrolyzable adenylyl-imidodiphosphate (AMP-PNP) can be used to preload CMG onto a forked DNA substrate without unwinding.


Assuntos
Trifosfato de Adenosina/análogos & derivados , DNA Helicases/metabolismo , Complexos Multiproteicos/metabolismo , Trifosfato de Adenosina/química , Trifosfato de Adenosina/metabolismo , Proteínas de Ciclo Celular/metabolismo , DNA/química , DNA Helicases/genética , Replicação do DNA , Proteínas de Ligação a DNA/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
12.
Proc Natl Acad Sci U S A ; 119(10): e2115955119, 2022 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-35238661

RESUMO

SignificanceStep-bunching instability (SBI) is one of the interfacial instabilities driven by self-organization of elementary step flow associated with crystal-growth dynamics, which has been observed in diverse crystalline materials. However, despite theoretical suggestions of its presence, no direct observations of SBI for simple melt growth have been achieved so far. Here, with the aid of a type of optical microscope and its combination with a two-beam interferometer, we realized quantitative in situ observations of the spatiotemporal dynamics of the SBI. This enables us to examine the origin of the SBI at the level of the step-step interaction. We also found that the SBI spontaneously induces a highly stable spiral growth mode, governing the late stage of the growth process.

13.
Nano Lett ; 24(30): 9253-9261, 2024 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-39037287

RESUMO

Ingenious microstructure construction and appropriate composition selection are effective strategies for achieving enhanced performance of photothermal materials. Herein, a broccoli-like hierarchical nickel black@graphene (Ni@Gr) membrane for solar-driven desalination was prepared by a one-step electrochemical method, which was carried out simultaneously with the electrochemical exfoliation of graphene and the co-deposition of Ni@Gr material. The bionic hierarchical structure and the chemical composition of the Ni@Gr membrane increased the sunlight absorption (90.36%) by the light-trapping effect and the introduction of graphene. The Ni@Gr membrane achieved high evaporation rates of 2.05 and 1.16 kg m-2 h-1 under simulated (1 sun) and outdoor sunlight conditions, respectively. The superhydrophilicity and the hierarchical structure of the Ni@Gr membrane jointly reduced the evaporation enthalpy (1343.6 kJ/kg), which was beneficial to break the theoretical limit of the evaporation rate (1.47 kg m-2 h-1). This work encourages the application of bionic metal-carbon composite photothermal materials in solar water evaporation.

14.
Nano Lett ; 24(1): 82-88, 2024 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-38109843

RESUMO

The ferroelectric semiconductor α-SnTe has been regarded as a topological crystalline insulator, and the dispersion of its surface states has been intensively measured with angle-resolved photoemission spectroscopy (ARPES) over the past decade. However, much less attention has been given to the impact of the ferroelectric transition on its electronic structure, and in particular on its bulk states. Here, we investigate the low-energy electronic structure of α-SnTe with ARPES and follow the evolution of the bulk-state Rashba splitting as a function of temperature, across its ferroelectric critical temperature of about Tc ≈ 110 K. Unexpectedly, we observe a persistent band splitting up to room temperature, which is consistent with an order-disorder contribution of local dipoles to the phase transition that requires the presence of fluctuating dipoles above Tc. We conclude that no topological surface state can occur under these conditions at the (111) surface of SnTe, at odds with recent literature.

15.
Nano Lett ; 24(13): 3866-3873, 2024 Apr 03.
Artigo em Inglês | MEDLINE | ID: mdl-38442405

RESUMO

The low wear resistance of macroscale graphene coatings does not match the ultrahigh mechanical strength and chemical inertness of the graphene layer itself; however, the wear mechanism responsible for this issue at low mechanical stress is still unclear. Here, we demonstrate that the susceptibility of the graphene monolayer to wear at its atomic step edges is governed by the mechanochemistry of frictional interfaces. The mechanochemical reactions activated by chemically active SiO2 microspheres result in atomic attrition rather than mechanical damage such as surface fracture and folding by chemically inert diamond tools. Correspondingly, the threshold contact stress for graphene edge wear decreases more than 30 times to the MPa level, and mechanochemical wear can be described well with the mechanically assisted Arrhenius-type kinetic model, i.e., exponential dependence of the removal rate on the contact stress. These findings provide a strategy for improving the antiwear of graphene-based materials by reducing the mechanochemical interactions at tribological interfaces.

16.
Nano Lett ; 24(18): 5556-5561, 2024 May 08.
Artigo em Inglês | MEDLINE | ID: mdl-38668651

RESUMO

We report step edge-induced localized defects suppressing subsequent antiphase boundary formation in the bulk structure of a trilayer oxide heterostructure. The heterostructure encompasses a layer of La0.66Sr0.34MnO3 sandwiched between a superconducting La1.84Sr0.16CuO4 bottom layer and an insulating La2CuO4 top layer. The combination of a minor a-axis mismatch (0.11 Å) and a pronounced c-axis mismatch (2.73 Å) at the step edges leads to the emergence of localized defects exclusively forming at the step edge. Employing atomically resolved electron energy-loss spectroscopy maps, we discern the electronic state of those structures in the second La0.66Sr0.34MnO3 unit cell near the step edge. In particular, a reduction in the pre-edge region of the O-K edge indicates the formation of oxygen vacancies induced by the strained step edge. This study underscores our capability to control defects at the nanoscale.

17.
Diabetologia ; 67(6): 1009-1022, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38502241

RESUMO

AIMS/HYPOTHESIS: Adults with type 1 diabetes should perform daily physical activity to help maintain health and fitness, but the influence of daily step counts on continuous glucose monitoring (CGM) metrics are unclear. This analysis used the Type 1 Diabetes Exercise Initiative (T1DEXI) dataset to investigate the effect of daily step count on CGM-based metrics. METHODS: In a 4 week free-living observational study of adults with type 1 diabetes, with available CGM and step count data, we categorised participants into three groups-below (<7000), meeting (7000-10,000) or exceeding (>10,000) the daily step count goal-to determine if step count category influenced CGM metrics, including per cent time in range (TIR: 3.9-10.0 mmol/l), time below range (TBR: <3.9 mmol/l) and time above range (TAR: >10.0 mmol/l). RESULTS: A total of 464 adults with type 1 diabetes (mean±SD age 37±14 years; HbA1c 48.8±8.1 mmol/mol [6.6±0.7%]; 73% female; 45% hybrid closed-loop system, 38% standard insulin pump, 17% multiple daily insulin injections) were included in the study. Between-participant analyses showed that individuals who exceeded the mean daily step count goal over the 4 week period had a similar TIR (75±14%) to those meeting (74±14%) or below (75±16%) the step count goal (p>0.05). In the within-participant comparisons, TIR was higher on days when the step count goal was exceeded or met (both 75±15%) than on days below the step count goal (73±16%; both p<0.001). The TBR was also higher when individuals exceeded the step count goals (3.1%±3.2%) than on days when they met or were below step count goals (difference in means -0.3% [p=0.006] and -0.4% [p=0.001], respectively). The total daily insulin dose was lower on days when step count goals were exceeded (0.52±0.18 U/kg; p<0.001) or were met (0.53±0.18 U/kg; p<0.001) than on days when step counts were below the current recommendation (0.55±0.18 U/kg). Step count had a larger effect on CGM-based metrics in participants with a baseline HbA1c ≥53 mmol/mol (≥7.0%). CONCLUSIONS/INTERPRETATION: Our results suggest that, compared with days with low step counts, days with higher step counts are associated with slight increases in both TIR and TBR, along with small reductions in total daily insulin requirements, in adults living with type 1 diabetes. DATA AVAILABILITY: The data that support the findings reported here are available on the Vivli Platform (ID: T1-DEXI; https://doi.org/10.25934/PR00008428 ).


Assuntos
Automonitorização da Glicemia , Glicemia , Diabetes Mellitus Tipo 1 , Exercício Físico , Humanos , Diabetes Mellitus Tipo 1/sangue , Diabetes Mellitus Tipo 1/terapia , Diabetes Mellitus Tipo 1/tratamento farmacológico , Adulto , Feminino , Masculino , Automonitorização da Glicemia/métodos , Glicemia/metabolismo , Glicemia/análise , Pessoa de Meia-Idade , Exercício Físico/fisiologia , Hemoglobinas Glicadas/metabolismo , Hemoglobinas Glicadas/análise , Insulina/uso terapêutico , Insulina/administração & dosagem , Estudos de Coortes , Monitoramento Contínuo da Glicose
18.
J Biol Chem ; 299(7): 104841, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37209823

RESUMO

Cytochrome P450 (P450, CYP) family 51 enzymes catalyze the 14α-demethylation of sterols, leading to critical products used for membranes and the production of steroids, as well as signaling molecules. In mammals, P450 51 catalyzes the 3-step, 6-electron oxidation of lanosterol to form (4ß,5α)-4,4-dimethyl-cholestra-8,14,24-trien-3-ol (FF-MAS). P450 51A1 can also use 24,25-dihydrolanosterol (a natural substrate in the Kandutsch-Russell cholesterol pathway). 24,25-Dihydrolanosterol and the corresponding P450 51A1 reaction intermediates, the 14α-alcohol and -aldehyde derivatives of dihydrolanosterol, were synthesized to study the kinetic processivity of the overall 14α-demethylation reaction of human P450 51A1. A combination of steady-state kinetic parameters, steady-state binding constants, dissociation rates of P450-sterol complexes, and kinetic modeling of the time course of oxidation of a P450-dihydrolanosterol complex showed that the overall reaction is highly processive, with koff rates of P450 51A1-dihydrolanosterol and the 14α-alcohol and 14α-aldehyde complexes being 1 to 2 orders of magnitude less than the forward rates of competing oxidations. epi-Dihydrolanosterol (the 3α-hydroxy analog) was as efficient as the common 3ß-hydroxy isomer in the binding and formation of dihydro FF-MAS. The common lanosterol contaminant dihydroagnosterol was found to be a substrate of human P450 51A1, with roughly one-half the activity of dihydrolanosterol. Steady-state experiments with 14α-methyl deuterated dihydrolanosterol showed no kinetic isotope effect, indicating that C-14α C-H bond breaking is not rate-limiting in any of the individual steps. The high processivity of this reaction generates higher efficiency and also renders the reaction less sensitive to inhibitors.


Assuntos
Sistema Enzimático do Citocromo P-450 , Desmetilação , Lanosterol , Humanos , Catálise , Sistema Enzimático do Citocromo P-450/metabolismo , Cinética , Lanosterol/química , Lanosterol/metabolismo , Oxirredução
19.
BMC Genomics ; 25(1): 93, 2024 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-38254039

RESUMO

BACKGROUNDING: Stayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life. RESULTS: The top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant. CONCLUSION: Our results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.


Assuntos
Estudo de Associação Genômica Ampla , Genômica , Feminino , Animais , Bovinos/genética , Fenótipo , Probabilidade , Reprodução/genética
20.
BMC Genomics ; 25(1): 9, 2024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38166623

RESUMO

BACKGROUND: Planting tested forest reproductive material is crucial to ensure the increased resilience of intensively managed productive stands for timber and wood product markets under climate change scenarios. Single-step Genomic Best Linear Unbiased Prediction (ssGBLUP) analysis is a cost-effective option for using genomic tools to enhance the accuracy of predicted breeding values and genetic parameter estimation in forest tree species. Here, we tested the efficiency of ssGBLUP in a tropical multipurpose tree species, Cordia africana, by partial population genotyping. A total of 8070 trees from three breeding seedling orchards (BSOs) were phenotyped for height. We genotyped 6.1% of the phenotyped individuals with 4373 single nucleotide polymorphisms. The results of ssGBLUP were compared with pedigree-based best linear unbiased prediction (ABLUP) and genomic best linear unbiased prediction (GBLUP), based on genetic parameters, theoretical accuracy of breeding values, selection candidate ranking, genetic gain, and predictive accuracy and prediction bias. RESULTS: Genotyping a subset of the study population provided insights into the level of relatedness in BSOs, allowing better genetic management. Due to the inbreeding detected within the genotyped provenances, we estimated genetic parameters both with and without accounting for inbreeding. The ssGBLUP model showed improved performance in terms of additive genetic variance and theoretical breeding value accuracy. Similarly, ssGBLUP showed improved predictive accuracy and lower bias than the pedigree-based relationship matrix (ABLUP). CONCLUSIONS: This study of C. africana, a species in decline due to deforestation and selective logging, revealed inbreeding depression. The provenance exhibiting the highest level of inbreeding had the poorest overall performance. The use of different relationship matrices and accounting for inbreeding did not substantially affect the ranking of candidate individuals. This is the first study of this approach in a tropical multipurpose tree species, and the analysed BSOs represent the primary effort to breed C. africana.


Assuntos
Cordia , Árvores , Humanos , Árvores/genética , Melhoramento Vegetal , Genoma , Genômica/métodos , Genótipo , Fenótipo , Modelos Genéticos
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