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1.
J Food Prot ; 87(6): 100275, 2024 Apr 10.
Artigo em Inglês | MEDLINE | ID: mdl-38609013

RESUMO

Leafy green vegetables are a major source of foodborne illnesses. Nevertheless, few studies have attempted to estimate attribution and burden of illness estimates for leafy greens. This study combines results from three outbreak-based attribution models with illness incidence and economic cost models to develop comprehensive pathogen-specific burden estimates for leafy greens and their subcategories in the United States. We find that up to 9.18% (90% CI: 5.81%-15.18%) of foodborne illnesses linked to identified pathogens are attributed to leafy greens. Including 'Unknown' illnesses not linked to specific pathogens, leafy greens account for as many as 2,307,558 (90% CI: 1,077,815-4,075,642) illnesses annually in the United States. The economic cost of these illnesses is estimated to be up to $5.278 billion (90% CI: $3.230-$8.221 billion) annually. Excluding the pathogens with small outbreak sizes, Norovirus, Shiga toxin-producingEscherichia coli (both non-O157 and O157:H7), Campylobacter spp., and nontyphoidal Salmonella, are associated with the highest number of illnesses and greatest costs from leafy greens. While lettuce (romaine, iceberg, "other lettuce") takes 60.8% of leafy green outbreaks, it accounts for up to 75.7% of leafy green foodborne illnesses and 70% of costs. Finally, we highlighted that 19.8% of Shiga toxin-producingEscherichia coli O157:H7 illnesses are associated with romaine among all food commodities, resulting in 12,496 estimated illnesses and $324.64 million annually in the United States.

2.
Front Microbiol ; 15: 1356478, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38633704

RESUMO

Background: Observational studies and some experimental investigations have indicated that gut microbiota are closely associated with the incidence and progression of chronic renal failure. However, the causal relationship between gut microbiota and chronic renal failure remains unclear. The present study employs a two-sample Mendelian randomization approach to infer the causal relationship between gut microbiota and chronic renal failure at the genetic level. This research aims to determine whether there is a causal effect of gut microbiota on the risk of chronic renal failure, aiming to provide new evidence to support targeted gut therapy for the treatment of chronic renal failure. Methods: Employing genome-wide association study (GWAS) data from the public MiBioGen and IEU OpenGWAS platform, a two-sample Mendelian randomization analysis was conducted. The causal relationship between gut microbiota and chronic renal failure was inferred using five different methods: Inverse Variance Weighted, MR-Egger, Weighted Median, Simple Mode, and Weighted Mode. The study incorporated sensitivity analyses that encompassed evaluations for pleiotropy and heterogeneity. Subsequently, the results of the Mendelian randomization analysis underwent a stringent correction for multiple testing, employing the False Discovery Rate method to enhance the validity of our findings. Results: According to the results from the Inverse Variance Weighted method, seven bacterial genera show a significant association with the outcome variable chronic renal failure. Of these, Ruminococcus (gauvreauii group) (OR = 0.82, 95% CI = 0.71-0.94, p = 0.004) may act as a protective factor against chronic renal failure, while the genera Escherichia-Shigella (OR = 1.22, 95% CI = 1.08-1.38, p = 0.001), Lactococcus (OR = 1.1, 95% CI = 1.02-1.19, p = 0.013), Odoribacter (OR = 1.23, 95% CI = 1.03-1.49, p = 0.026), Enterorhabdus (OR = 1.14, 95% CI = 1.00-1.29, p = 0.047), Eubacterium (eligens group) (OR = 1.18, 95% CI = 1.02-1.37, p = 0.024), and Howardella (OR = 1.18, 95% CI = 1.09-1.28, p < 0.001) may be risk factors for chronic renal failure. However, after correction for multiple comparisons using False Discovery Rate, only the associations with Escherichia-Shigella and Howardella remain significant, indicating that the other genera have suggestive associations. Sensitivity analyses did not reveal any pleiotropy or heterogeneity. Conclusion: Our two-sample Mendelian randomization study suggests that the genera Escherichia-Shigella and Howardella are risk factors for chronic renal failure, and they may serve as potential targets for future therapeutic interventions. However, the exact mechanisms of action are not yet clear, necessitating further research to elucidate their precise roles fully.

3.
Clin Exp Nephrol ; 2024 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-38643287

RESUMO

OBJECTIVE: Cardiovascular disease (CVD) represents the primary cause of mortality in patients afflicted with end-stage renal disease and undergoing peritoneal dialysis (PD) treatment. Galectin-3 (Gal-3), a molecule known to exhibit a correlation with CVD mortality garners considerable interest. The objective of this study was to explore the potential association between serum Gal-3 levels and other CVD risk factors among PD patients. METHODS: In this cross-sectional study, a total of 114 PD patients with a minimum of 3 months of PD treatment were enrolled. Serum Gal-3 levels were quantified using an enzyme-linked immunosorbent assay. The data of patients with Gal-3 levels higher and lower than 26.744 pg/ml were compared using Mann-Whitney U tests or t tests. Pearson's correlation or Spearman's correlation analysis and multivariate regression were used to assess the associations between the known risk factors for CVD and Gal-3. RESULTS: In comparison to the inter-group baseline data, the low Gal-3 group exhibited a higher glomerular filtration rate (GFR). Gal-3 levels correlate positively with PD duration, B-type natriuretic peptide (BNP), growth differentiation factor 15 (GDF-15), interventricular septal thickness in diastolic (IVST), and left ventricular mass index (LVMI). Conversely, Gal-3 exhibited a negative correlation with albumin levels. Multivariate linear regression analysis demonstrated a positive correlation between Gal-3 levels and BNP, GDF-15, PD duration, IVST and LVMI. Gal-3 levels were negatively correlated with albumin levels. CONCLUSIONS: Gal-3 was strongly associated with BNP, GDF-15, IVST and LVMI in patients undergoing PD treatment. Prospective studies should be carried out to determine whether Gal-3 can be a promising biomarker in predicting increased risk of adverse cardiovascular events in PD patients.

4.
Nat Commun ; 15(1): 2164, 2024 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-38461306

RESUMO

RNA splicing shapes the gene regulatory programs that underlie various physiological and disease processes. Here, we present the SCASL (single-cell clustering based on alternative splicing landscapes) method for interrogating the heterogeneity of RNA splicing with single-cell RNA-seq data. SCASL resolves the issue of biased and sparse data coverage on single-cell RNA splicing and provides a new scheme for classifications of cell identities. With previously published datasets as examples, SCASL identifies new cell clusters indicating potentially precancerous and early-tumor stages in triple-negative breast cancer, illustrates cell lineages of embryonic liver development, and provides fine clusters of highly heterogeneous tumor-associated CD4 and CD8 T cells with functional and physiological relevance. Most of these findings are not readily available via conventional cell clustering based on single-cell gene expression data. Our study shows the potential of SCASL in revealing the intrinsic RNA splicing heterogeneity and generating biological insights into the dynamic and functional cell landscapes in complex tissues.


Assuntos
Neoplasias , Splicing de RNA , Humanos , Splicing de RNA/genética , Processamento Alternativo/genética , Análise de Sequência de RNA/métodos
5.
Wiley Interdiscip Rev RNA ; 15(2): e1839, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38527900

RESUMO

Spatially resolved transcriptomics has been dramatically transforming biological and medical research in various fields. It enables transcriptome profiling at single-cell, multi-cellular, or sub-cellular resolution, while retaining the information of geometric localizations of cells in complex tissues. The coupling of cell spatial information and its molecular characteristics generates a novel multi-modal high-throughput data source, which poses new challenges for the development of analytical methods for data-mining. Spatial transcriptomic data are often highly complex, noisy, and biased, presenting a series of difficulties, many unresolved, for data analysis and generation of biological insights. In addition, to keep pace with the ever-evolving spatial transcriptomic experimental technologies, the existing analytical theories and tools need to be updated and reformed accordingly. In this review, we provide an overview and discussion of the current computational approaches for mining of spatial transcriptomics data. Future directions and perspectives of methodology design are proposed to stimulate further discussions and advances in new analytical models and algorithms. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Computational Analyses of RNA RNA Export and Localization > RNA Localization.


Assuntos
Pesquisa Biomédica , Perfilação da Expressão Gênica , Transcriptoma , Algoritmos , RNA
6.
Chemistry ; 30(18): e202303741, 2024 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-38206884

RESUMO

Compared with Li+, Na+ with a smaller stokes radius has faster de-solvation kinetics. An electrolyte with ultralow sodium salt (0.3 M NaPF6) is used to reduce the cell cost. However, the organic-dominated interface, mainly derived from decomposed solvents (SSIP solvation structure), is defective for the long cycling performance of sodium ion batteries. In this work, the simple application of dual additives, including sodium difluoro(oxalato)borate (NaDFOB) and tris(trimethylsilyl)borate (TMSB), is demonstrated to improve the cycling performance of the hard carbon/NaNi1/3Fe1/3Mn1/3O2 cell by constructing interface films on the anode and cathode. A significant improvement on cycling stability has been achieved by incorporating dual additives of NaDFOB and TMSB. Particularly, the capacity retention increased from 17 % (baseline) to 79 % (w/w, 2.0 wt % NaDFOB) and 83 % (w/w, 2.0 wt % NaDFOB and 1.0 wt % TMSB) after 200 cycles at room temperature. Insight into the mechanism of improved interfacial properties between electrodes and electrolyte in ultralow concentration electrolyte has been investigated through a combination of theoretical computation and experimental techniques.

7.
Chemistry ; 30(10): e202302768, 2024 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-38171767

RESUMO

Fe2 O3 with high theoretical capacity (1007 mA h g-1 ) and low cost is a potential anode material for lithium-ion batteries (LIBs), but its practical application is restricted by its low electrical conductivity and large volume changes during lithiation/delithiation. To solve these problems, Fe2 O3 @Ti3 C2 Tx composites were synthesized by a mussel-like modification method, which relies on the self-polymerization of dopamine under mild conditions. During polymerization, the electronegative group (-OH) on dopamine can easily coordinate with Fe3+ ions as well as form hydrogen bonds with the -OH terminal group on the surface of Ti3 C2 Tx , which induces a uniform distribution of Fe2 O3 on the Ti3 C2 Tx surface and mitigates self-accumulation of MXene nanosheets. In addition, the polydopamine-derived carbon layer protects Ti3 C2 Tx from oxidation during the hydrothermal process, which can further improve the electrical conductivity of the composites and buffer the volume expansion and particle agglomeration of Fe2 O3 . As a result, Fe2 O3 @Ti3 C2 Tx anodes exhibit ~100 % capacity retention with almost no capacity loss at 0.5 A g-1 after 250 cycles, and a stable capacity of 430 mA h g-1 at 2 A g-1 after 500 cycles. The unique structural design of this work provides new ideas for the development of MXene-based composites in energy storage applications.

8.
Plant J ; 118(1): 42-57, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38112614

RESUMO

Drought stress caused by global warming has resulted in significant tree mortality, driving the evolution of water conservation strategies in trees. Although phytohormones have been implicated in morphological adaptations to water deficits, the molecular mechanisms underlying these processes in woody plants remain unclear. Here, we report that overexpression of PtoMYB142 in Populus tomentosa results in a dwarfism phenotype with reduced leaf cell size, vessel lumen area, and vessel density in the stem xylem, leading to significantly enhanced drought resistance. We found that PtoMYB142 modulates gibberellin catabolism in response to drought stress by binding directly to the promoter of PtoGA2ox4, a GA2-oxidase gene induced under drought stress. Conversely, knockout of PtoMYB142 by the CRISPR/Cas9 system reduced drought resistance. Our results show that the reduced leaf size and vessel area, as well as the increased vessel density, improve leaf relative water content and stem water potential under drought stress. Furthermore, exogenous GA3 application rescued GA-deficient phenotypes in PtoMYB142-overexpressing plants and reversed their drought resistance. By suppressing the expression of PtoGA2ox4, the manifestation of GA-deficient characteristics, as well as the conferred resistance to drought in PtoMYB142-overexpressing poplars, was impeded. Our study provides insights into the molecular mechanisms underlying tree drought resistance, potentially offering novel transgenic strategies to enhance tree resistance to drought.


Assuntos
Resistência à Seca , Populus , Giberelinas/metabolismo , Populus/metabolismo , Fatores de Transcrição/metabolismo , Regulação da Expressão Gênica de Plantas , Água/metabolismo , Secas , Plantas Geneticamente Modificadas/genética
9.
Cell ; 186(15): 3245-3260.e23, 2023 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-37369203

RESUMO

Terrestrial organisms developed circadian rhythms for adaptation to Earth's quasi-24-h rotation. Achieving precise rhythms requires diurnal oscillation of fundamental biological processes, such as rhythmic shifts in the cellular translational landscape; however, regulatory mechanisms underlying rhythmic translation remain elusive. Here, we identified mammalian ATXN2 and ATXN2L as cooperating master regulators of rhythmic translation, through oscillating phase separation in the suprachiasmatic nucleus along circadian cycles. The spatiotemporal oscillating condensates facilitate sequential initiation of multiple cycling processes, from mRNA processing to protein translation, for selective genes including core clock genes. Depleting ATXN2 or 2L induces opposite alterations to the circadian period, whereas the absence of both disrupts translational activation cycles and weakens circadian rhythmicity in mice. Such cellular defect can be rescued by wild type, but not phase-separation-defective ATXN2. Together, we revealed that oscillating translation is regulated by spatiotemporal condensation of two master regulators to achieve precise circadian rhythm in mammals.


Assuntos
Relógios Circadianos , Camundongos , Animais , Relógios Circadianos/genética , Ritmo Circadiano/fisiologia , Núcleo Supraquiasmático/metabolismo , Processamento de Proteína Pós-Traducional , Mamíferos
10.
Nat Commun ; 14(1): 553, 2023 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-36725859

RESUMO

The quickly accumulating ribosome profiling data is an insightful resource for studying the critical details of translation regulation under various biological contexts. Rocaglamide A (RocA), an antitumor heterotricyclic natural compound, has been shown to inhibit translation initiation of a large group of mRNA species by clamping eIF4A onto poly-purine motifs in the 5' UTRs. However, reanalysis of previous ribosome profiling datasets reveals an unexpected shift of the ribosome occupancy pattern, upon RocA treatment in various types of cells, during early translation elongation for a specific group of mRNA transcripts without poly-purine motifs over-represented in their 5' UTRs. Such perturbation of translation elongation dynamics can be attributed to the blockage of translating ribosomes due to the binding of eIF4A to the poly-purine sequence in coding regions. In summary, our study presents the complete dual modes of RocA in blocking translation initiation and elongation, which underlie the potent antitumor effect of RocA.


Assuntos
Biossíntese de Proteínas , Perfil de Ribossomos , Regiões 5' não Traduzidas , RNA Mensageiro/metabolismo
11.
J Mater Chem B ; 11(10): 2145-2156, 2023 03 08.
Artigo em Inglês | MEDLINE | ID: mdl-36776022

RESUMO

Nitric oxide (NO) is reported to be elevated in osteoarthritis (OA) both in vitro and in vivo and may be adopted to develop fluorescent probes for detecting the progression of OA. Here we report a nitric oxide responsive aggregation induced emission (AIE) probe TPE-2NHCOCH2CH2-(PEG)24-NH-Diacerein, which is derived from tetraphenylethene (TPE) modified with the hydrophilic group long poly(ethylene glycol) chain and an anti-inflammatory drug diacerein. o-Phenylenediamine within its structure can react with NO to form benzotriazole and emit fluorescence. The results show that the NO-responsive AIE probe can smartly monitor the progression of OA with the change of fluorescence intensity in vitro and in vivo. This study may provide a new development direction for early OA monitoring in clinics.


Assuntos
Óxido Nítrico , Polietilenoglicóis , Corantes Fluorescentes/química , Antraquinonas
12.
ACS Appl Mater Interfaces ; 14(45): 50710-50717, 2022 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-36341571

RESUMO

All-solid-state Li metal batteries (ASSLBs) are currently regarded as one of the most promising next-generation energy storage technologies because of their great potential in realizing both high energy density and safety. However, the development of high performance ASSLBs is still restricted by the large interfacial resistance and Li dendrite propagation within solid electrolytes. Herein, a simple and efficient interfacial modification strategy is proposed to improve the interfacial contact between Li and Li6.4La3Zr1.4Ta0.6O12 (LLZTO) by introducing a uniform and thin Li2Se buffer layer. The Li2Se buffer layer formed by an in situ conversion reaction can not only enhance the wettability of lithium metal toward LLZTO electrolyte but also facilitate uniform lithium plating/stripping. As a result, the interfacial resistance of Li/LLZTO decreased from 270.5 to 5.1 Ω cm2, and the lithium symmetric cell can cycle stably for 350 h at a current density of 0.5 mA cm-2. Meanwhile, the Li|LLZTO-Li2Se|LiNi0.8Co0.1Mn0.1O2 full cells exhibit a high initial capacity of 162.3 mAh g-1 and good cycling stability with a capacity retention of 84.3% after 100 cycles at 0.2 C. These results prove the effectiveness of this modification method and provide new design strategies for the development of high performance ASSLBs.

13.
Genome Biol ; 23(1): 169, 2022 08 04.
Artigo em Inglês | MEDLINE | ID: mdl-35927743

RESUMO

BACKGROUND: Adenosine-to-inosine (A-to-I) editing is an important RNA posttranscriptional process related to a multitude of cellular and molecular activities. However, systematic characterizations of whether and how the events of RNA editing are associated with the binding preferences of RNA sequences to RNA-binding proteins (RBPs) are still lacking. RESULTS: With the RNA-seq and RBP eCLIP-seq datasets from the ENCODE project, we quantitatively survey the binding preferences of 150 RBPs to RNA editing events, followed by experimental validations. Such analyses of the RBP-associated RNA editing at nucleotide resolution and genome-wide scale shed light on the involvement of RBPs specifically in RNA editing-related processes, such as RNA splicing, RNA secondary structures, RNA decay, and other posttranscriptional processes. CONCLUSIONS: These results highlight the relevance of RNA editing in the functions of many RBPs and therefore serve as a resource for further characterization of the functional associations between various RNA editing events and RBPs.


Assuntos
Edição de RNA , Proteínas de Ligação a RNA , Genoma , RNA/metabolismo , Splicing de RNA , Proteínas de Ligação a RNA/metabolismo
14.
Nat Cell Biol ; 24(6): 968-980, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35697785

RESUMO

In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocytes or embryos per stage. Ribo-lite can also accommodate single oocytes. Combining PAIso-seq to interrogate poly(A) tail lengths, we found a global switch of translatome that closely parallels changes of poly(A) tails upon meiotic resumption. Translation activation correlates with polyadenylation and is supported by polyadenylation signal proximal cytoplasmic polyadenylation elements (papCPEs) in 3' untranslated regions. By contrast, translation repression parallels global de-adenylation. The latter includes transcripts containing no CPEs or non-papCPEs, which encode many transcription regulators that are preferentially re-activated before zygotic genome activation. CCR4-NOT, the major de-adenylation complex, and its key adaptor protein BTG4 regulate translation downregulation often independent of RNA decay. BTG4 is not essential for global de-adenylation but is required for selective gene de-adenylation and production of very short-tailed transcripts. In sum, our data reveal intimate interplays among translation, RNA stability and poly(A) tail length regulation underlying mammalian OET.


Assuntos
Desenvolvimento Embrionário , Oócitos , Regiões 3' não Traduzidas/genética , Animais , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/genética , Regulação da Expressão Gênica no Desenvolvimento , Mamíferos/genética , Mamíferos/metabolismo , Camundongos , Oócitos/metabolismo , Poliadenilação , Biossíntese de Proteínas , RNA Mensageiro/genética
15.
ACS Appl Mater Interfaces ; 14(25): 28706-28715, 2022 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-35695736

RESUMO

Evaluating the structural and electronic-state characteristics of long-range disordered amorphous iridium (Ir)-based oxides is still unsatisfying. Compared with the benchmark IrO2, the higher oxygen evolution reaction (OER) performance brought by IrOxOHy was normally considered to be associated with the pristine IrIII-containing species. However, such a conclusion conflicts with the opinion that high-valence metals can create excellent OER activity. To resolve such contradictions, we synthesized a pure amorphous Lu1.25IrOxOHy (Lu = lutetium) catalyst in this work. In combination with the comprehensive electrochemical evaluation in alkaline and acidic media, ex situ Ir L3-edge and O K-edge X-ray absorption spectroscopy and theoretical calculations revealed that the ultrahigh OER performance of reconstructed IrOx/Lu1.25IrOxOHy in acidic media was identified to be driven by the more d-hole-containing electronic state of IrV created by cationic vacancies. The pristine properties of IrIII-containing Lu1.25IrOxOHy conversely inhibit the OER activity in alkaline media. Additionally, the high edge-shared [IrOx]-[IrOx] motif proportion structure in amorphous Lu1.25IrOxOHy achieves a stable OER process, which exhibits a high S-number stability index similar to IrO2. We demonstrate that the key factor of the edge-shared [IrOx]-[IrOx] motif with cationic vacancies in IrVOxOHy could rationally reveal the source for most of the high-performance Ir-based materials.

16.
Genome Biol ; 23(1): 124, 2022 06 03.
Artigo em Inglês | MEDLINE | ID: mdl-35659722

RESUMO

Based on a deep generative model of variational graph autoencoder (VGAE), we develop a new method, DeepLinc (deep learning framework for Landscapes of Interacting Cells), for the de novo reconstruction of cell interaction networks from single-cell spatial transcriptomic data. DeepLinc demonstrates high efficiency in learning from imperfect and incomplete spatial transcriptome data, filtering false interactions, and imputing missing distal and proximal interactions. The latent representations learned by DeepLinc are also used for inferring the signature genes contributing to the cell interaction landscapes, and for reclustering the cells based on the spatially coded cell heterogeneity in complex tissues at single-cell resolution.


Assuntos
Comunicação Celular , Transcriptoma
17.
Tree Physiol ; 42(10): 2133-2147, 2022 10 07.
Artigo em Inglês | MEDLINE | ID: mdl-35640137

RESUMO

Drought is one of the main environmental factors that limit plant development and growth. Accordingly, plants have evolved strategies to prevent water loss under drought stress, such as stomatal closure, maintenance of root water uptake, enhancement of stem water transport, and synthesis and deposition of cuticular wax. However, the molecular evidence of cuticular wax biosynthesis regulation in response to drought is limited in woody plants. Here, we identified an MYB transcription factor, Populus tomentosa Carr. MYB transcription factor (PtoMYB142), in response to drought stress from P. tomentosa. Over-expression of PtoMYB142 (PtoMYB142-OE) resulted in increased wax accumulation in poplar leaves, and significantly enhanced drought resistance. We found that the expression of wax biosynthesis genes CER4 and 3-ketoacyl CoA synthase (KCS) were markedly induced under drought stress, and significantly up-regulated in PtoMYB142-OE lines. Biochemical analysis confirmed that PtoMYB142 could directly bind to the promoter of CER4 and KCS6, and regulate their expression in P. tomentosa. Taken together, this study reveals that PtoMYB142 regulates cuticular wax biosynthesis to adapt to water-deficient conditions.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Populus , Aldeído Oxirredutases/genética , Aldeído Oxirredutases/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Coenzima A/genética , Coenzima A/metabolismo , Secas , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Populus/genética , Populus/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Água/metabolismo , Ceras
18.
J Vis Exp ; (180)2022 02 18.
Artigo em Inglês | MEDLINE | ID: mdl-35253791

RESUMO

Identification of open reading frames (ORFs), especially those encoding small peptides and being actively translated under specific physiological contexts, is critical for comprehensive annotations of context-dependent translatomes. Ribosome profiling, a technique for detecting the binding locations and densities of translating ribosomes on RNA, offers an avenue to rapidly discover where translation is occurring at the genome-wide scale. However, it is not a trivial task in bioinformatics to efficiently and comprehensively identify the translating ORFs for ribosome profiling. Described here is an easy-to-use package, named RiboCode, designed to search for actively translating ORFs of any size from distorted and ambiguous signals in ribosome profiling data. Taking our previously published dataset as an example, this article provides step-by-step instructions for the entire RiboCode pipeline, from preprocessing of the raw data to interpretation of the final output result files. Furthermore, for evaluating the translation rates of the annotated ORFs, procedures for visualization and quantification of ribosome densities on each ORF are also described in detail. In summary, the present article is a useful and timely instruction for the research fields related to translation, small ORFs, and peptides.


Assuntos
Biossíntese de Proteínas , Ribossomos , Biologia Computacional/métodos , Fases de Leitura Aberta , Ribossomos/genética , Ribossomos/metabolismo , Análise de Sequência de RNA/métodos
19.
ACS Appl Mater Interfaces ; 13(46): 55700-55711, 2021 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-34752083

RESUMO

Currently, lithium-ion batteries (LIBs) are assembled with polar electrolytes; thus, resulting SEI layers are dominated with organics. Herein, a low-polarity electrolyte is formulated with a low-polarity solvent (tetraethyl silicate, TEOS) and a non-polar inert shielding co-solvent (cyclohexane, CYH); solvation behaviors of lithium salt are investigated. The use of such a low-polarity solvent is found to improve the fraction of anions in the solvation sheath of Li+, and the presence of the non-polar co-solvent further shields the reductive decomposition of the solvent on the anode. The resulting SEI layer is relatively rich in LiF and has a 3D cross-linked Si-O network as a skeleton from the decomposition of TEOS molecules, which is more robust to tolerate the damage from the volume expansion of silicon. A Si-nanoparticle-based anode in such a low-polarity electrolyte delivers a capacity as high as 1491 mAh g-1 after 200 cycles, outperforming those in the commercial polar electrolytes.

20.
Water Res ; 206: 117775, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34706320

RESUMO

Metrafenone (MF), as a new type of benzophenone fungicide, has been widely used in agriculture and is persistent in the environment. Understanding its photochemical fate is essential for the comprehensive evaluation of its ecological risk. In the present work, we reported a detailed study on the photochemical transformation of MF in aqueous solution under irradiation (at λ > 290 nm using a high pressure mercury lamp). MF was relatively photo-reactive showing a low polychromatic quantum yield of photolysis (1.06 × 10-4, 20 µM) counterbalanced by a significant light absorption above 290 nm. A series of photoproducts were identified by high resolution mass spectrometry (HR-MS) analysis, and three different pathways, including oxidation of the methyl group, debromination and replacement of bromine by hydroxyl group were proposed. Among them, debromination was identified as the dominating process that could be achieved via homolytic C-Br bond cleavage from singlet and triplet MF, as confirmed by laser flash photolysis (LFP) experiments and density functional theory (DFT) calculations. Toxicity assessment revealed that photochemical degradation reduced the ecotoxicity of MF efficiently. Nitrate ions and humic acid promoted the MF photolysis, while bicarbonate exhibited no effect. Results obtained in this work would increase our understanding on the environmental fate of MF in sunlit surface waters.


Assuntos
Fungicidas Industriais , Poluentes Químicos da Água , Benzofenonas , Bromo , Carbono , Cinética , Fotólise , Poluentes Químicos da Água/análise
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