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1.
Plant Physiol ; 2024 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-39140314

RESUMO

Castor (Ricinus communis L.) is an importance crop cultivated for its oil and economic value. Seed size is a crucial factor that determines crop yield. Gaining insight into the molecular regulatory processes of seed development is essential for the genetic enhancement and molecular breeding of castor. Here, we successfully fine-mapped a major QTL related to seed size, qSS3, to a 180 kb interval on chromosome 03 using F2 populations (DL01×WH11). A 17.6-kb structural variation (SV) was detected through genomic comparison between DL01 and WH11. Analysis of haplotypes showed that the existence of the complete 17.6 kb structural variant may lead to the small seed characteristic in castor. In addition, we found that qSS3 contains the microRNA396b (miR396b) sequence, which is situated within the 17.6 kb SV. The results of our experiment offer additional evidence that miR396-Growth Regulating Factor 4 (GRF4) controls seed size by impacting the growth and multiplication of seed coat and endosperm cells. Furthermore, we found that RcGRF4 activates the expression of YUCCA6 (YUC6), facilitating the production of IAA in seeds and thereby impacting the growth of castor seeds. Our research has discovered a crucial functional module that controls seed size, offering a fresh understanding of the mechanism underlying seed size regulation in castor.

2.
Mol Ecol ; : e17356, 2024 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-38634782

RESUMO

DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome-wide association analysis with high-quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate-related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change.

3.
Environ Sci Technol ; 2024 Apr 26.
Artigo em Inglês | MEDLINE | ID: mdl-38668375

RESUMO

Pharmaceutically active compounds are an important category of emerging pollutants, and their biological transformation processes in the environment are crucial for understanding and evaluating the migration, transformation, and environmental fate of emerging pollutants. The cytochrome P450 105 enzyme family has been proven to play an important role in the degradation of exogenous environmental pollutants. However, its thermostability and catalytic activity still need to be improved to better adapt to complex environmental conditions. This work elucidates the key mechanisms and important residues of the degradation reaction through multiple computational strategies, establishes a mutation library, and obtains 21 single-point mutation designs. Experimental verification showed that 16 single mutants had enhanced thermostability, with the R89F and L197Y mutants showing the highest increases in thermostability at 135 and 119% relative to the wild-type enzyme, respectively. Additionally, as a result of the higher specific activity of D390Q, it was selected for combination mutagenesis, ultimately resulting in three combination mutants (R89F/L197Y, R89F/D390Q, and R89F/L197Y/D390Q) with enhanced thermostability and catalytic activity. This study provides a modification approach for constructing efficient enzyme variants through semirational design and can contribute to the development of control technologies for emerging pollutants.

4.
J Environ Manage ; 357: 120730, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38574705

RESUMO

Volatile organic compounds (VOCs) significantly contribute to ozone pollution formation, and many VOCs are known to be harmful to human health. Plastic has become an indispensable material in various industries and daily use scenarios, yet the VOC emissions and associated health risks in the plastic manufacturing industry have received limited attention. In this study, we conducted sampling in three typical plastic manufacturing factories to analyze the emission characteristics of VOCs, ozone formation potential (OFP), and health risks for workers. Isopropanol was detected at relatively high concentrations in all three factories, with concentrations in organized emissions reaching 322.3 µg/m3, 344.8 µg/m3, and 22.6 µg/m3, respectively. Alkanes are the most emitted category of VOCs in plastic factories. However, alkenes and oxygenated volatile organic compounds (OVOCs) exhibit higher OFP. In organized emissions of different types of VOCs in the three factories, alkenes and OVOCs contributed 22.8%, 67%, and 37.8% to the OFP, respectively, highlighting the necessity of controlling them. The hazard index (HI) for all three factories was less than 1, indicating a low non-carcinogenic toxic risk; however, there is still a possibility of non-cancerous health risks in two of the factories, and a potential lifetime cancer risk in all of the three factories. For workers with job tenures exceeding 5 years, there may be potential health risks, hence wearing masks with protective capabilities is necessary. This study provides evidence for reducing VOC emissions and improving management measures to ensure the health protection of workers in the plastic manufacturing industry.


Assuntos
Poluentes Atmosféricos , Ozônio , Compostos Orgânicos Voláteis , Humanos , Poluentes Atmosféricos/análise , Compostos Orgânicos Voláteis/análise , Monitoramento Ambiental , Medição de Risco , Indústria Manufatureira , Alcenos , China
5.
Natl Sci Rev ; 11(3): nwae008, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38390365

RESUMO

Over recent decades, advancements in complementary metal-oxide-semiconductor integrated circuits (ICs) have mainly relied on structural innovations in transistors. From planar transistors to the fin field-effect transistor (FinFET) and gate-all-around FET (GAAFET), more gate electrodes have been added to three-dimensional (3D) channels with enhanced control and carrier conductance to provide higher electrostatic integrity and higher operating currents within the same device footprint. Beyond the 1-nm node, Moore's law scaling is no longer expected to be applicable to geometrical shrinkage. Vertical transistor stacking, e.g. in complementary FETs (CFET), 3D stack (3DS) FETs and vertical-channel transistors (VFET), for enhanced density and variable circuit or system design represents a revolutionary scaling approach for sustained IC development. Herein, innovative works on specific structures, key process breakthroughs, shrinking cell sizes and design methodologies for transistor structure research and development are reviewed. Perspectives on future innovations in advanced transistors with new channel materials and operating theories are also discussed.

6.
Int J Gen Med ; 17: 1405-1417, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38617053

RESUMO

Aim: A high percentage of the elderly suffer from knee osteoarthritis (KOA), which imposes a certain economic burden on them and on society as a whole. The purpose of this study is to examine the risk of KOA and to develop a KOA nomogram model that can timely intervene in this disease to decrease patient psychological burdens. Methods: Data was collected from patients with KOA and without KOA at our hospital from February 2021 to February 2023. Initially, a comparison was conducted between the variables, identifying statistical differences between the two groups. Subsequently, the risk of KOA was evaluated using the Least Absolute Shrinkage and Selection Operator method and multivariate logistic regression to determine the most effective predictive index and develop a prediction model. The examination of the disease risk prediction model in KOA includes the corresponding nomogram, which encompasses various potential predictors. The assessment of disease risk entails the application of various metrics, including the consistency index (C index), the area under the curve (AUC) of the receiver operating characteristic curve, the calibration chart, the GiViTi calibration band, and the model for predicting KOA. Furthermore, the potential clinical significance of the model is explored through decision curve analysis (DCA) and clinical influence curve analysis. Results: The study included a total of 582 patients, consisting of 392 patients with KOA and 190 patients without KOA. The nomogram utilized age, haematocrit, platelet count, apolipoprotein a1, potassium, magnesium, hydroxybutyrate dehydrogenase, creatine kinase, and estimated glomerular filtration rate as predictors. The C index, AUC, calibration plot, Giviti calibration band, DCA and clinical influence KOA indicated the ability of nomogram model to differentiate KOA. Conclusion: Using nomogram based on disease risk, high-risk KOA can be identified directly without imaging.

7.
Chemosphere ; 358: 142238, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38705413

RESUMO

Predicting the metabolic activation mechanism and potential hazardous metabolites of environmental endocrine-disruptors is a challenging and significant task in risk assessment. Here the metabolic activation mechanism of benzophenone-3 catalyzed by P450 1A1 was investigated by using Molecular Dynamics, Quantum Mechanics/Molecular Mechanics and Density Functional Theory approaches. Two elementary reactions involved in the metabolic activation of BP-3 with P450 1A1: electrophilic addition and hydrogen abstraction reactions were both discussed. Further conversion reactions of epoxidation products, ketone products and the formaldehyde formation reaction were investigated in the non-enzymatic environment based on previous experimental reports. Binding affinities analysis of benzophenone-3 and its metabolites to sex hormone binding globulin indirectly demonstrates that they all exhibit endocrine-disrupting property. Toxic analysis shows that the eco-toxicity and bioaccumulation values of the benzophenone-3 metabolites are much lower than those of benzophenone-3. However, the metabolites are found to have skin-sensitization effects. The present study provides a deep insight into the biotransformation process of benzophenone-3 catalyzed by P450 1A1 and alerts us to pay attention to the adverse effects of benzophenone-3 and its metabolites in human livers.


Assuntos
Benzofenonas , Citocromo P-450 CYP1A1 , Disruptores Endócrinos , Benzofenonas/metabolismo , Disruptores Endócrinos/metabolismo , Citocromo P-450 CYP1A1/metabolismo , Teoria Quântica , Humanos , Simulação de Dinâmica Molecular , Catálise , Biotransformação
8.
J Hazard Mater ; 477: 135414, 2024 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-39102770

RESUMO

Polyethylene terephthalate (PET) is a widely used material in our daily life, particularly in areas such as packaging, fibers, and engineering plastics. However, PET waste can accumulate in the environment and pose a great threat to our ecosystem. Recently enzymatic conversion has emerged as an efficient and green strategy to address the PET crisis. Here, using a theoretical approach combining molecular dynamics simulation and quantum mechanics/molecular mechanics calculations, the depolymerization mechanism of the thermophilic cutinase BhrPETase was fully deciphered. Surprisingly, unlike the previously studied cutinase LCCICCG, our results indicate that the first step, catalytic triad assisted nucleophilic attack, is the rate-determining step. The corresponding Boltzmann weighted average energy barrier is 18.2 kcal/mol. Through extensive comparison between BhrPETase and LCCICCG, we evidence that key features like charge CHis@N1 and angle APET@C1-Ser@O1-His@H1 significantly impact the depolymerization efficiency of BhrPETase. Non-covalent bond interaction and distortion/interaction analysis inform new insights on enzyme engineer and may aid the recycling of enzymatic PET waste. This study will aid the advancement of the plastic bio-recycling economy and promote resource conservation and reuse.

9.
Sci Total Environ ; 949: 174877, 2024 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-39047816

RESUMO

The bimolecular reactions between Criegee intermediates (CIs) and atmospheric trace species have been extensively investigated, with a particular focus on the reaction with water, while the catalytic role of atmospheric organic compounds in hydration reactions was often neglected. In this study, we employed quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations to investigate the catalytic effects of atmospheric organic amines, organic acids, and alcohols on the hydration reactions of CIs in the gas phase and at the gas-liquid interface. The catalytic reactions were found to follow a cyclic catalytic structure and a stepwise reaction mechanism. Gas-phase studies revealed that organic acids exhibited stronger catalytic effects compared to amines and alcohols, and the catalytic efficiency of amines and alcohols was similar to those of single water molecule. In addition, the catalytic reaction barriers of organic acids and alcohols were positively correlated with their gas-phase acidity (R2 = 0.94 to 0.97). A negative correlation was observed between the catalytic reaction barrier of amines and their gas-phase basicity (R2 = 0.84 to 0.90) and proton affinity (R2 = 0.84 to 0.92). At the gas-liquid interface, organic acids promoted the formation of hydroxyethyl hydroperoxide (HEHP, CH3CH(OH)(OOH)), organic acid ions, and H3O+, whereas the catalytic hydration of CIs by organic amines resulted in the formation of CH3CH(OH)OO and amine ions. Both HEHP and CH3CH(OH)OO can be further decomposed to form OH and HO2, or participate in new particles formation as precursors. This study complements the research gap on the reaction of CIs with water, providing valuable insights into the atmospheric sources of HEHP and HOx as well as the formation of secondary organic aerosols (SOAs).

10.
J Hazard Mater ; 474: 134797, 2024 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-38865921

RESUMO

Poly(butylene adipate-co-terephthalate) (PBAT) is widely utilized in the production of food packaging and mulch films. Its extensive application has contributed significantly to global solid waste, posing numerous environmental challenges. Recently, enzymatic recycling has emerged as a promising eco-friendly solution for the management of plastic waste. Here, we systematically investigate the depolymerization mechanism of PBAT catalyzed by cutinase TfCutSI with molecular docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations. Although the binding affinities for acid ester and terephthalic acid ester bonds are similar, a regioselective depolymerization mechanism and a "chain-length" effect on regioselectivity were proposed and evidenced. The regioselectivity is highly associated with specific structural parameters, namely Substrate@O4-Met@H7 and Substrate@C1-Ser@O1 distances. Notably, the binding mode of BTa captured by X-ray crystallography does not facilitate subsequent depolymerization. Instead, a previously unanticipated binding mode, predicted through computational analysis, is confirmed to play a crucial role in BTa depolymerization. This finding proves the critical role of computational modelling in refining experimental results. Furthermore, our results revealed that both the hydrogen bond network and enzyme's intrinsic electric field are instrumental in the formation of the final product. In summary, these novel molecular insights into the PBAT depolymerization mechanism offer a fundamental basis for enzyme engineering to enhance industrial plastic recycling.


Assuntos
Simulação de Acoplamento Molecular , Poliésteres , Polimerização , Poliésteres/química , Poliésteres/metabolismo , Simulação de Dinâmica Molecular , Ácidos Ftálicos/química , Ácidos Ftálicos/metabolismo , Estereoisomerismo , Hidrolases de Éster Carboxílico
11.
Int J Biol Macromol ; 263(Pt 2): 130282, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38423901

RESUMO

Aiming at green and friendly environmental protection, polyvinyl alcohol/sodium alginate/chitosan (PSCS) double network hydrogel was successfully prepared through diffusing the high molecular weight chitosan into PVA/sodium alginate (PS) hydrogel without any other toxic reagents. The polyanion hydrogels could be significantly enhanced by immersing the polyanion hydrogel in high molecular weight chitosan solution without requiring specific structure. The PSCS hydrogel had a compact and rough surface structure with the smaller porosities and larger crystallization degree compared with polyvinyl alcohol/sodium alginate hydrogels and polyvinyl alcohol/sodium alginate/Ca2+ (PSCa) hydrogels. The PSCS hydrogel possessed excellent hydrolysis resistance, the significant pH-sensitive and salt-sensitive swelling. In addition, the flexibility, Young's modulus and mechanical properties of PSCS hydrogel can be adjusted through the changing the content of sodium alginate. Moreover, PS, PSCa and PSCS had electric conductivity, and PSCS showed twice the conductivity compared to PS hydrogel. Based on differences of swelling ratio, a PSCS bilayer hydrogel was designed and showed excellent pH-driven deformation ability. The PSCS hydrogel is expected to expand the application of hydrogels in conditions involving stimulus response, and might serve as a promising intelligent actuators or soft robots.


Assuntos
Quitosana , Polieletrólitos , Quitosana/química , Álcool de Polivinil/química , Hidrogéis/química , Alginatos/química , Concentração de Íons de Hidrogênio , Condutividade Elétrica
12.
Sci Total Environ ; 916: 170009, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38220017

RESUMO

Numerous studies have linked ozone (O3) production to its precursors and fine particulate matter (PM2.5), while the complex interaction effects of PM2.5 and volatile organic compounds (VOCs) on O3 remain poorly understood. A systematic approach based on an interpretable machine learning (ML) model was utilized to evaluate the primary driving factors that impact O3 and to elucidate how changes in PM2.5, VOCs from different sources, NOx, and meteorological conditions either promote or inhibit O3 formation through their individual and synergistic effects in a tropical coastal city, Haikou, from 2019 to 2020. The results suggest that under low PM2.5 levels, alongside the linear O3-PM2.5 relationship observed, O3 formation is suppressed by PM2.5 with higher proportions of traffic-derived aerosol. Vehicle VOC emissions contributed maximally to O3 formation at midday, despite the lowest concentration. VOCs from fossil fuel combustion and industry emissions, which have opposing effects on O3, act as inhibitors and promoters by inducing diverse photochemical regimes. As PM2.5 pollution escalates, the impact of these VOCs reverses, becoming more pronounced in shaping O3 variation. Sensitivity analysis reveals that the O3 formation regime is VOC-limited, and effective regional O3 mitigation requires prioritizing substantial VOC reductions to offset enhanced VOC sensitivity induced by the co-reduction in PM2.5, with a focus on industrial and vehicular emissions, and subsequently, fossil fuel combustion once PM2.5 is effectively controlled. This study underscores the potential of the SHAP-based ML approach to decode the intricate O3-NOx-VOCs-PM2.5 interplay, considering both meteorological and atmospheric compositional variations.

13.
Sci Total Environ ; 917: 170487, 2024 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38296079

RESUMO

Oxygenated organic molecules (OOMs) are recognized as important precursors for new particle formation (NPF) in the urban atmosphere. The paper theoretically studied the formation of OOMs by styrene oxidation processes initiated by OH radicals, focusing on the OOMs nucleation mechanism. The results found that in the presence of an H2SO4 molecule, lowly oxygenated organic molecules containing a benzene ring (LOMBs) can form stable clusters and grow to the scale of a critical nucleus through pi-pi stacking and OH hydrogen bonding. In addition, LOMBs are more readily generated in a styrene-oxidized system in the presence/absence of NOx than highly oxygenated organic molecules (HOMs). The reaction of OH radicals with other aromatics containing a branched chain on the benzene ring produces LOMBs to varying degrees, with pi-pi stacking playing an essential role. This result suggests that, in the presence of H2SO4 molecules, LOMBs may play a more significant role in promoting nucleation than HOMs. Our findings serve as a pivotal foundation for future investigations into the oxidation and nucleation processes of diverse aromatics in urban environments.

14.
Sci Total Environ ; 918: 170767, 2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38331293

RESUMO

Rapid prediction of the removal efficiency and energy consumption of organic contaminants under various operating conditions is crucial for advanced oxidation processes (AOPs) in industrial application. In this study, 1H-Benzotriazole (BTZ, CAS: 95-14-7) is selected as a model micropollutant, a validated incorporated Computational Fluid Dynamics (CFD) model is employed to comprehensively investigate the impacts of initial concentrations of H2O2, BTZ and dissolved organic carbon (DOC) (i.e., [DOC]0, [BTZ]0 and [DOC]0), as well as the effective UV lamp power P and volumetric flow rate Qv. Generally, the operation performance depends on [DOC]0 and [BTZ]0 in similar trends, but with quantitatively different ways. The increase in [H2O2]0 and P/Qv can promote •OH generation, leading to the elimination of BTZ. It is worth noting that P/Qv is found to be linearly correlated with the removal order of BTZ (ROBTZ) under specific conditions. Based on this finding, the degradation of other potential organic contaminants with a wide range of rate constants by UV/H2O2 is further investigated. A model for predicting energy consumption for target removal rates of organic pollutants is established from massive simulation data for the first time. Additionally, a handy Matlab app is first developed for convenient application in water treatment. This work proposes a new operable solution for fast predicting operation performance and energy consumption for the removal of organic contaminants in industrial applications of advanced oxidation processes.

15.
Biosensors (Basel) ; 14(3)2024 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-38534249

RESUMO

Silicon nanowire field effect (SiNW-FET) biosensors have been successfully used in the detection of nucleic acids, proteins and other molecules owing to their advantages of ultra-high sensitivity, high specificity, and label-free and immediate response. However, the presence of the Debye shielding effect in semiconductor devices severely reduces their detection sensitivity. In this paper, a three-dimensional stacked silicon nanosheet FET (3D-SiNS-FET) biosensor was studied for the high-sensitivity detection of nucleic acids. Based on the mainstream Gate-All-Around (GAA) fenestration process, a three-dimensional stacked structure with an 8 nm cavity spacing was designed and prepared, allowing modification of probe molecules within the stacked cavities. Furthermore, the advantage of the three-dimensional space can realize the upper and lower complementary detection, which can overcome the Debye shielding effect and realize high-sensitivity Point of Care Testing (POCT) at high ionic strength. The experimental results show that the minimum detection limit for 12-base DNA (4 nM) at 1 × PBS is less than 10 zM, and at a high concentration of 1 µM DNA, the sensitivity of the 3D-SiNS-FET is approximately 10 times higher than that of the planar devices. This indicates that our device provides distinct advantages for detection, showing promise for future biosensor applications in clinical settings.


Assuntos
Técnicas Biossensoriais , Nanofios , Ácidos Nucleicos , Silício/química , Transistores Eletrônicos , DNA , Técnicas Biossensoriais/métodos , Nanofios/química
16.
iScience ; 27(3): 109053, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38361623

RESUMO

The optimization of the CRISPR-Cas9 system for enhancing editing efficiency holds significant value in scientific research. In this study, we optimized single guide RNA and Cas9 promoters of the CRISPR-Cas9 vector and established an efficient protoplast isolation and transient transformation system in Eustoma grandiflorum, and we successfully applied the modified CRISPR-Cas9 system to detect editing efficiency of the EgPDS gene. The activity of the EgU6-2 promoter in E. grandiflorum protoplasts was approximately three times higher than that of the GmU6 promoter. This promoter, along with the EgUBQ10 promoter, was applied in the CRISPR-Cas9 cassette, the modified CRISPR-Cas9 vectors that pEgU6-2::sgRNA-2/pEgUBQ10::Cas9-2 editing efficiency was 37.7%, which was 30.3% higher than that of the control, and the types of mutation are base substitutions, small fragment deletions and insertions. Finally we obtained an efficient gene editing vector for E. grandiflorum. This project provides an important technical platform for the study of gene function in E. grandiflorum.

17.
ACS Appl Mater Interfaces ; 16(22): 28896-28904, 2024 Jun 05.
Artigo em Inglês | MEDLINE | ID: mdl-38770712

RESUMO

Herein, we present a novel ultrasensitive graphene field-effect transistor (GFET) biosensor based on lithium niobate (LiNbO3) ferroelectric substrate for the application of breast cancer marker detection. The electrical properties of graphene are varied under the electrostatic field, which is generated through the spontaneous polarization of the ferroelectric substrate. It is demonstrated that the properties of interface between graphene and solution are also altered due to the interaction between the electrostatic field and ions. Compared with the graphene field-effect biosensor based on the conventional Si/SiO2 gate structure, our biosensor achieves a higher sensitivity to 64.7 mV/decade and shows a limit of detection down to 1.7 fM (equivalent to 12 fg·mL-1) on the detection of microRNA21 (a breast cancer marker). This innovative design combining GFETs with ferroelectric substrates holds great promise for developing an ultrahigh-sensitivity biosensing platform based on graphene that enables rapid and early disease diagnosis.


Assuntos
Biomarcadores Tumorais , Técnicas Biossensoriais , Neoplasias da Mama , Grafite , MicroRNAs , Nióbio , Óxidos , Grafite/química , Técnicas Biossensoriais/métodos , Técnicas Biossensoriais/instrumentação , Humanos , Nióbio/química , Neoplasias da Mama/diagnóstico , Óxidos/química , MicroRNAs/análise , Biomarcadores Tumorais/análise , Feminino , Limite de Detecção , Transistores Eletrônicos
18.
Nat Commun ; 15(1): 5644, 2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-38969648

RESUMO

Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement ( > 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples.


Assuntos
Elementos de DNA Transponíveis , Drosophila melanogaster , Genoma de Inseto , Mutação , Wolbachia , Animais , Drosophila melanogaster/genética , Elementos de DNA Transponíveis/genética , Wolbachia/genética , Genoma de Inseto/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de DNA/métodos , Genômica/métodos , Conversão Gênica
19.
Sci Total Environ ; 948: 174452, 2024 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-38964396

RESUMO

Airborne trace elements (TEs) present in atmospheric fine particulate matter (PM2.5) exert notable threats to human health and ecosystems. To explore the impact of meteorological conditions on shaping the pollution characteristics of TEs and the associated health risks, we quantified the variations in pollution characteristics and health risks of TEs due to meteorological impacts using weather normalization and health risk assessment models, and analyzed the source-specific contributions and potential sources of primary TEs affecting health risks using source apportionment approaches at four sites in Shandong Province from September to December 2021. Our results indicated that TEs experience dual effects from meteorological conditions, with a tendency towards higher TE concentrations and related health risks during polluted period, while the opposite occurred during clean period. The total non-carcinogenic and carcinogenic risks of TEs during polluted period increased approximately by factors of 0.53-1.74 and 0.44-1.92, respectively. Selenium (Se), manganese (Mn), and lead (Pb) were found to be the most meteorologically influenced TEs, while chromium (Cr) and manganese (Mn) were identified as the dominant TEs posing health risks. Enhanced emissions of multiple sources for Cr and Mn were found during polluted period. Depending on specific wind speeds, industrialized and urbanized centers, as well as nearby road dusts, could be key sources for TEs. This study suggested that attentions should be paid to not only the TEs from primary emissions but also the meteorology impact on TEs especially during pollution episodes to reduce health risks in the future.


Assuntos
Poluentes Atmosféricos , Poluição do Ar , Monitoramento Ambiental , Aprendizado de Máquina , Material Particulado , Oligoelementos , Poluentes Atmosféricos/análise , Material Particulado/análise , Poluição do Ar/estatística & dados numéricos , Oligoelementos/análise , China , Medição de Risco
20.
Plant Sci ; 346: 112181, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38969141

RESUMO

White birch (Betula platyphylla Suk.) is an important pioneer tree which plays a critical role in maintaining ecosystem stability and forest regeneration. The growth of birch is dramatically inhibited by salt stress, especially the root inhibition. Salt Overly Sensitive 1 (SOS1) is the only extensively characterized Na+ efflux transporter in multiple plant species. The salt-hypersensitive mutant, sos1, display significant inhibition of root growth by NaCl. However, the role of SOS1 in birch responses to salt stress remains unclear. Here, we characterized a putative Na+/H+ antiporter BpSOS1 in birch and generated the loss-of-function mutants of the birch BpSOS1 by CRISPR/Cas9 approach. The bpsos1 mutant exhibit exceptional increased salt sensitivity which links to excessive Na+ accumulation in root, stem and old leaves. We observed a dramatic reduction of K+ contents in leaves of the bpsos1 mutant plants under salt stress. Furthermore, the Na+/K+ ratio of roots and leaves is significant higher in the bpsos1 mutants than the wild-type plants under salt stress. The ability of Na+ efflux in the root meristem zone is found to be impaired which might result the imbalance of Na+ and K+ in the bpsos1 mutants. Our findings indicate that the Na+/H+ exchanger BpSOS1 plays a critical role in birch salt tolerance by maintaining Na+ homeostasis and provide evidence for molecular breeding to improve salt tolerance in birch and other trees.


Assuntos
Betula , Tolerância ao Sal , Trocadores de Sódio-Hidrogênio , Tolerância ao Sal/genética , Betula/genética , Betula/fisiologia , Betula/metabolismo , Trocadores de Sódio-Hidrogênio/metabolismo , Trocadores de Sódio-Hidrogênio/genética , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética , Raízes de Plantas/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/fisiologia , Raízes de Plantas/crescimento & desenvolvimento , Estresse Salino/genética , Sódio/metabolismo
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