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2.
Heliyon ; 10(4): e25984, 2024 Feb 29.
Artigo em Inglês | MEDLINE | ID: mdl-38390085

RESUMO

Various studies have investigated the presence of microplastics (MPs) in food and their potential hazardous impact on human health. The frequency of human exposure to MPs, particularly through the consumption of manufactured food and drinking water, is increasing. However, data regarding MP contamination in brine and brined cabbage used for the production of kimchi are limited. Here, we quantified MPs in brine process water during the production of brined cabbage. Pretreatment of the brine process water by performing a filtration step resulted in an MP-removal efficiency of 98.7-100%; 3671 ± 174 MP particles were observed in brining process water that was not filtered. A glass filter, STS filter, and Si Filter showed significant MP-removal efficiency, decreasing the number of MP particles in brining process water to 2,361, 2,775, and 3,490, respectively (p < 0.05). Our results provide data on how filtering of brine can effectively safeguard kimchi from MP contamination and e can be produced. However, to overcome the limitations of our laboratory-scale study, additional technologies should be used in the future for large-scale filtration processes.

3.
Dev Cell ; 59(2): 187-198.e7, 2024 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-38198888

RESUMO

Chromatin organization is essential for maintaining cell-fate trajectories and developmental programs. Here, we find that disruption of H3K36 methylation dramatically impairs normal epithelial differentiation and development, which promotes increased cellular plasticity and enrichment of alternative cell fates. Specifically, we observe a striking increase in the aberrant generation of excessive epithelial glandular tissues, including hypertrophic salivary, sebaceous, and meibomian glands, as well as enhanced squamous tumorigenesis. These phenotypic and gene expression manifestations are associated with loss of H3K36me2 and rewiring of repressive H3K27me3, changes we also observe in human patients with glandular hyperplasia. Collectively, these results have identified a critical role for H3K36 methylation in both in vivo epithelial cell-fate decisions and the prevention of squamous carcinogenesis and suggest that H3K36 methylation modulation may offer new avenues for the treatment of numerous common disorders driven by altered glandular function, which collectively affect large segments of the human population.


Assuntos
Carcinoma de Células Escamosas , Histonas , Humanos , Histonas/metabolismo , Plasticidade Celular , Metilação , Carcinogênese/genética , Carcinoma de Células Escamosas/genética
4.
Acad Radiol ; 31(4): 1239-1247, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-37914625

RESUMO

RATIONALE AND OBJECTIVES: To assess patient preferences for breast radiologists' attire and appearance. MATERIALS AND METHODS: A multi-institutional anonymous, voluntary 19-question survey was administered to patients undergoing screening and diagnostic mammography examinations over a 5-week period. Using a 5-point Likert scale, respondents were asked about their preferences for gender-neutral attire (white coat), male-presenting attire (scrubs, dress shirt with tie, or dress shirt without tie), and female-presenting attire (scrubs, dress, blouse with pants, and blouse with skirt). Patient responses were compared to demographic data using bivariable analysis and multivariable regression. RESULTS: Response rate was 84.7% (957/1130). Mean respondent age was 57.2 years±11.9. Most respondents agreed/strongly agreed that the breast radiologist's appearance mattered (52.5%, 502/956) followed by being indifferent (28.1%, 269/956). Respondents with greater education levels felt less strongly (p=0.001) about the radiologist's appearance: 63.3% (70/110) less than college cared about appearance compared to 53.5% (266/497) college/vocational and 47.4% (165/348) graduate. Most respondents felt indifferent about a breast radiologist wearing a white coat (68.9%, 657/954) or about male-presenting breast radiologists wearing a tie (77.1%, 734/952) without significant demographic differences. Almost all respondents either prefer/strongly prefer (60.1%, 572/951) or were indifferent (39.6%, 377/951) to all breast radiologists wearing scrubs when performing procedures. While respondents approved of all attire choices overall, most respondents preferred scrubs for both male- and female-presenting breast radiologists (64.0%, 612/957 and 64.9%, 621/957, respectively). CONCLUSION: A variety of breast radiologists' attire can be worn while maintaining provider professionalism and without compromising patient expectations.


Assuntos
Preferência do Paciente , Relações Médico-Paciente , Humanos , Masculino , Feminino , Pessoa de Meia-Idade , Vestuário , Estudos Transversais , Radiologistas , Inquéritos e Questionários
5.
J Am Coll Radiol ; 21(3): 415-424, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37820836

RESUMO

PURPOSE: The aim of this study was to determine differences in patient satisfaction and anxiety among women undergoing core-needle breast biopsies performed the same day as recommended versus a future date. METHODS: After institutional review board exemption was granted, a survey was administered to patients at four sites on the day of imaging-guided core-needle breast biopsy. The survey was available from November 2020 through January 2022. Questions pertained to biopsy timing (same day versus later day), pre- and postbiopsy satisfaction with overall breast-care experience, biopsy wait-time satisfaction, pre- and postbiopsy anxiety, radiologist-patient communication, demographics, life stressors, breast cancer history, and risk factors. Comparisons were made between same-day and later-day biopsies by multivariable analysis. RESULTS: Of 974 respondents (response rate 65.6%), almost half were scheduled for same-day biopsies (47.8% [466 of 974]). In multivariate analyses, same-day biopsies were associated with higher prebiopsy overall breast-care satisfaction (P < .001), higher wait-time satisfaction (P < .001), and higher prebiopsy (P = .001) and postbiopsy anxiety (P = .001). Better radiologist-patient communication was associated with lower prebiopsy anxiety (P < .001) and greater prebiopsy overall (P < .001) and wait-time (P < .001) satisfaction. Compared with White women, Black women reported lower postbiopsy anxiety (P < .001) but also lower prebiopsy satisfaction (P = .03) and wait-time satisfaction (P < .001). CONCLUSIONS: Same-day versus later-day biopsies resulted in better prebiopsy overall breast-care and wait-time patient satisfaction scores; however, no satisfaction differences were noted after biopsy. Clinically significant anxiety was associated with both same- and later-day biopsies but was higher for same-day biopsies. Higher anxiety levels correlated with lower overall satisfaction, suggesting that interventions to reduce anxiety and improve communication could improve patient experiences during same-day biopsies.


Assuntos
Mama , Satisfação do Paciente , Humanos , Feminino , Ansiedade/epidemiologia , Transtornos de Ansiedade , Biópsia/efeitos adversos
6.
J Am Coll Radiol ; 2023 Dec 04.
Artigo em Inglês | MEDLINE | ID: mdl-38056581

RESUMO

OBJECTIVE: To assess the impact of interruptions on radiologists' efficiency, accuracy, and job satisfaction in interpreting screening mammograms. METHODS: This institutional review board-approved retrospective reader study recruited nine breast radiologists from a single academic institution [name withheld] to interpret 150 screening mammograms performed between December 1, 2008, and December 31, 2015 under two different reading conditions, as follows: (1) uninterrupted batch reading and (2) interrupted reading. The 150 cases consisted of 125 normal mammograms and 25 mammograms with subtle breast cancers. Cases were divided into two groups of 75 cases each (cohort 1 and cohort 2), with a comparable distribution of cancer cases. Four rounds of 75 cases each were conducted with a 6-week washout period between rounds 2 and 3. After completing each interpretation session, readers completed a seven-question survey, assessing perceptions of mental and physical effort, level of frustration, and performance satisfaction. Clinical performance metrics (reading time, recall rate, sensitivity, specificity, accuracy, and positive predictive value 1) were calculated. RESULTS: Recall rates were significantly (P = .04) higher during interrupted reading sessions (35.4%) than they were during uninterrupted batch reading sessions (31.4%). Accuracy was significantly (P = .049) worse in the interrupted reading sessions (69.5%), compared with uninterrupted sessions (73.6%). Differences in overall image interpretation times were not statistically significant (P = .065). Compared with uninterrupted batch reading sessions, readers during interrupted sessions reported feeling busier (P < .001), encountered higher levels of cognitive demand (P = .005), experienced elevated levels of physical fatigue (P = .004), and expressed lower levels of satisfaction with their performance (P = .041). CONCLUSION: Interruptions during interpretation of screening mammography have deleterious effects on physician performance and their sense of well-being.

7.
PeerJ ; 11: e15680, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37483986

RESUMO

Background: Ultramicrobacteria (UMB), also known as ultra-small bacteria, are tiny bacteria with a size less than 0.1 µm3. They have a high surface-to-volume ratio and are found in various ecosystems, including the human body. UMB can be classified into two types: one formed through cell contraction and the other that maintains a small size. The ultra-small microbiome (USM), which may contain UMB, includes all bacteria less than 0.2 µm in size and is difficult to detect with current methods. However, it poses a potential threat to food hygiene, as it can pass through sterilization filters and exist in a viable but non-culturable (VBNC) state. The data on the USM of foods is limited. Some bacteria, including pathogenic species, are capable of forming UMB under harsh conditions, making it difficult to detect them through conventional culture techniques. Methods: The study described above focused on exploring the diversity of USM in fermented cabbage samples from three different countries (South Korea, China, and Germany). The samples of fermented cabbage (kimchi, suancai, and sauerkraut) were purchased and stored in chilled conditions at approximately 4 °C until filtration. The filtration process involved two steps of tangential flow filtration (TFF) using TFF cartridges with different pore sizes (0.2 µm and 100 kDa) to separate normal size bacteria (NM) and USM. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction. The extracted DNA was then amplified using PCR and the full-length 16S rRNA gene was sequenced using single-molecule-real-time (SMRT) sequencing. The transmission electron microscope (TEM) was used to confirm the presence of microorganisms in the USM of fermented cabbage samples. Results: To the best of our knowledge, this is the first study to identify the differences between USM and NM in fermented cabbages. Although the size of the USM (average 2,171,621 bp) was smaller than that of the NM (average 15,727,282 bp), diversity in USM (average H' = 1.32) was not lower than that in NM (average H' = 1.22). In addition, some members in USM probably underwent cell shrinkage due to unfavorable environments, while others maintained their size. Major pathogens were not detected in the USM in fermented cabbages. Nevertheless, several potentially suspicious strains (genera Cellulomonas and Ralstonia) were detected. Our method can be used to screen food materials for the presence of USM undetectable via conventional methods. USM and NM were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The USM of fermented vegetables exhibited differences in size, diversity, and composition compared with the conventional microbiome. This study could provide new insights into the ultra-small ecosystem in fermented foods, including fermented cabbages.


Assuntos
Brassica , Microbiota , Bactérias/genética , Brassica/genética , DNA , Microbiota/genética , RNA Ribossômico 16S/genética , Verduras/genética
8.
Nature ; 620(7972): 209-217, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37438531

RESUMO

The human genome functions as a three-dimensional chromatin polymer, driven by a complex collection of chromosome interactions1-3. Although the molecular rules governing these interactions are being quickly elucidated, relatively few proteins regulating this process have been identified. Here, to address this gap, we developed high-throughput DNA or RNA labelling with optimized Oligopaints (HiDRO)-an automated imaging pipeline that enables the quantitative measurement of chromatin interactions in single cells across thousands of samples. By screening the human druggable genome, we identified more than 300 factors that influence genome folding during interphase. Among these, 43 genes were validated as either increasing or decreasing interactions between topologically associating domains. Our findings show that genetic or chemical inhibition of the ubiquitous kinase GSK3A leads to increased long-range chromatin looping interactions in a genome-wide and cohesin-dependent manner. These results demonstrate the importance of GSK3A signalling in nuclear architecture and the use of HiDRO for identifying mechanisms of spatial genome organization.


Assuntos
Cromatina , Posicionamento Cromossômico , Cromossomos Humanos , Genoma Humano , Quinases da Glicogênio Sintase , Ensaios de Triagem em Larga Escala , Análise de Célula Única , Humanos , Cromatina/efeitos dos fármacos , Cromatina/genética , Cromatina/metabolismo , Posicionamento Cromossômico/efeitos dos fármacos , Cromossomos Humanos/efeitos dos fármacos , Cromossomos Humanos/genética , Cromossomos Humanos/metabolismo , DNA/análise , DNA/metabolismo , Genoma Humano/efeitos dos fármacos , Genoma Humano/genética , Quinases da Glicogênio Sintase/antagonistas & inibidores , Quinases da Glicogênio Sintase/deficiência , Quinases da Glicogênio Sintase/genética , Ensaios de Triagem em Larga Escala/métodos , Interfase , Reprodutibilidade dos Testes , RNA/análise , RNA/metabolismo , Transdução de Sinais/efeitos dos fármacos , Análise de Célula Única/métodos , Coesinas
9.
Immunity ; 56(7): 1451-1467.e12, 2023 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-37263273

RESUMO

Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.


Assuntos
Hipersensibilidade , Linfócitos T , Humanos , Camundongos , Animais , Diferenciação Celular/genética , Hematopoese , Inflamação/genética , Sequências Reguladoras de Ácido Nucleico , Hipersensibilidade/genética , Elementos Facilitadores Genéticos/genética
10.
Nat Commun ; 14(1): 1570, 2023 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-36944632

RESUMO

Integration of single-cell RNA sequencing data between different samples has been a major challenge for analyzing cell populations. However, strategies to integrate differential expression analysis of single-cell data remain underinvestigated. Here, we benchmark 46 workflows for differential expression analysis of single-cell data with multiple batches. We show that batch effects, sequencing depth and data sparsity substantially impact their performances. Notably, we find that the use of batch-corrected data rarely improves the analysis for sparse data, whereas batch covariate modeling improves the analysis for substantial batch effects. We show that for low depth data, single-cell techniques based on zero-inflation model deteriorate the performance, whereas the analysis of uncorrected data using limmatrend, Wilcoxon test and fixed effects model performs well. We suggest several high-performance methods under different conditions based on various simulation and real data analyses. Additionally, we demonstrate that differential expression analysis for a specific cell type outperforms that of large-scale bulk sample data in prioritizing disease-related genes.


Assuntos
Benchmarking , Análise de Dados , Análise de Sequência de RNA/métodos , Benchmarking/métodos , Simulação por Computador , Fluxo de Trabalho , Análise de Célula Única/métodos , Perfilação da Expressão Gênica/métodos
11.
Nat Immunol ; 24(1): 42-54, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36050414

RESUMO

Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.


Assuntos
Imunidade Inata , Linfócitos , Humanos , Inflamação/genética , Inflamação/metabolismo , Linhagem da Célula , Regiões Promotoras Genéticas
12.
J Breast Imaging ; 5(2): 159-166, 2023 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38416937

RESUMO

OBJECTIVE: To examine time from screening to diagnostic workup, biopsy, and surgery for non-Hispanic White (NHW) and Black women following implementation of a same-day biopsy program. METHODS: All NHW and Black women with BI-RADS category 0 screening mammogram at Duke University Hospital were identified between August 1, 2020, and August 1, 2021. Patient characteristics were recorded. Time between screening mammogram, diagnostic workup, breast biopsy, surgical consultation, and surgery were recorded. Comparisons were made between NHW and Black women using a multivariable regression model. Diagnostic imaging to biopsy time interval was compared to historical averages before same-day biopsy implementation. RESULTS: There were 2156 women: 69.9% NHW (1508/2156) and 30.1% Black (648/2156). Mean ± standard deviation time from screening to diagnostic imaging overall was 13.5 ±â€…32.5 days but longer for Black (18.0 ±â€…48.3 days) than for NHW women (11.5 ±â€…22.2 days) (P < 0.001). The mean time from diagnostic mammogram to biopsy was 5.9 ±â€…18.9 days, longer for Black (9.0 ±â€…27.9 days) than for NHW women (4.4 ±â€…11.8 days) (P = 0.017). The same-day biopsy program shortened the time from diagnostic imaging to biopsy overall (12.5 ±â€…12.4 days vs 5.9 ±â€…18.9 days; P < 0.001), with a significant reduction for NHW women (12.4 ±â€…11.7 days vs 4.4 ±â€…11.8 days) (P < 0.001) but not Black women (11.5 ±â€…9.9 days vs 9.0 ±â€…27.9 days) (P = 0.527). CONCLUSION: Disparities exist along the breast imaging pathway. A same-day biopsy program benefited NHW women more than Black women.


Assuntos
Biópsia , Neoplasias da Mama , Disparidades em Assistência à Saúde , Mamografia , Listas de Espera , Feminino , Humanos , Mamografia/métodos , Grupos Raciais , Brancos , Negro ou Afro-Americano , Neoplasias da Mama/diagnóstico
13.
J Breast Imaging ; 5(2): 167-173, 2023 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38416938

RESUMO

OBJECTIVE: Evaluate the effectiveness of alcohol sclerotherapy in postoperative breast and axillary seromas. METHODS: This was an IRB-approved retrospective review of consecutive patients from 2017 to 2021. The procedure involves aspiration of seroma fluid, injection of ethanol for 15 to 30 minutes, and then aspiration of the injected ethanol. Following review of the medical record, patient and procedure data were recorded. Success was defined as no recurrence of seroma. Statistical analysis was performed using a chi-square or t-test, as appropriate. RESULTS: Twenty seromas were treated in 19 patients (mean age, 63 years; range, 49-79) following mastectomy (9/20, 45%), lumpectomy (25%, 5/20), axillary nodal dissection (5/20, 25%), or chest wall surgery (1/20, 5%). The mean seroma volume was 146 ±â€…165 mL. There was a mean of 1.4 prior aspiration attempts (range, 0-3). Mean injected ethanol volume was 39 mL (range, 8-60 mL) for a mean of 26 ±â€…5 minutes. Seromas recurred in 85% (17/20) of cases, and repeat aspiration was performed in 35% (6/17). The mean recurrence time was 34 ±â€…29 days. The recurrent seromas were 31% smaller (mean, 80 ±â€…48 mL). Only a smaller pre-ablation seroma was associated with successful ablation (P < 0.01), as the mean pre-ablation volume was 36 ± 24 mL for successful ablations and 119 ±â€…56 mL for unsuccessful ablations. There were no post-procedural complications. CONCLUSION: Single-treatment ethanol sclerotherapy is typically unsuccessful in ablating breast and axillary seromas. Only a smaller pre-ablation seroma size was associated with successful ablation.


Assuntos
Neoplasias da Mama , Seroma , Humanos , Pessoa de Meia-Idade , Feminino , Seroma/etiologia , Mastectomia/efeitos adversos , Escleroterapia/efeitos adversos , Etanol/efeitos adversos , Axila , Neoplasias da Mama/cirurgia , Complicações Pós-Operatórias/terapia
14.
Front Microbiol ; 13: 1026513, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36274711

RESUMO

Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 µm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to "protein metabolism," and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the "cell wall and capsule" of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.

15.
Sci Rep ; 12(1): 14707, 2022 08 29.
Artigo em Inglês | MEDLINE | ID: mdl-36038711

RESUMO

Identification of soft rot disease in napa cabbage, an essential ingredient of kimchi, is challenging at the industrial scale. Therefore, nondestructive imaging techniques are necessary. Here, we investigated the potential of hyperspectral imaging (HSI) processing in the near-infrared region (900-1700 nm) for classifying napa cabbage quality using nondestructive measurements. We determined the microbiological and physicochemical qualitative properties of napa cabbage for intercomparison of HSI information, extracted HSI characteristics from hyperspectral images to predict and classify freshness, and established a novel approach for classifying healthy and rotten napa cabbage. The second derivative Savitzky-Golay method for data preprocessing was implemented, followed by wavelength selection using variable importance in projection scores. For multivariate data of the classification models, partial least square discriminant analysis (PLS-DA), support vector machine (SVM), and random forests were used for predicting cabbage conditions. The SVM model accurately distinguished the cabbage exhibiting soft rot disease symptoms from the healthy cabbage. This study presents the potential of HSI systems for separating soft rot disease-infected napa cabbages from healthy napa cabbages using the SVM model, especially under the most effective wavelengths (970, 980, 1180, 1070, 1120, and 978 nm), prior to processing. These results are applicable to industrial multispectral images.


Assuntos
Brassica , Imageamento Hiperespectral , Análise dos Mínimos Quadrados , Espectroscopia de Luz Próxima ao Infravermelho/métodos , Máquina de Vetores de Suporte
16.
Front Microbiol ; 13: 885413, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35663872

RESUMO

Processes in the food industry that use large amounts of water have been an important cause of waterborne disease outbreaks, as they expose individuals to risks for waterborne disease transmission. Developing technologies to ensure the hygiene and safety of food-processing steps is an urgent concern from an economic perspective. Furthermore, economic benefits can be derived if the processed water can be reused under microbiologically safe conditions. Among the major manufacturing processes in the kimchi industry, the brining process for salted kimchi cabbages requires a considerable amount of brine (approximately 2,000-2,500 l/1,000 kg of raw cabbage). The aim of this study was to establish virucidal conditions with ultraviolet-C light-emitting diodes (UVC LEDs) that can ensure the microbiological safety of brine water samples with various turbidities for reuse after disinfection. For quantitative analysis, first of all, magnetic bead separation (MBS) technique was used to capture and recover the human norovirus (HuNoV) virus particles; propidium monoazide (PMA) combined with RT-qPCR (PMA-RT-qPCR) was subsequently used to selectively detect infectious norovirus. Overall, as the turbidity of the brine water samples increased, the reduction in the HuNoV genogroup II genotype 4 (HuNoV GII.4) levels by UVC LED disinfection decreased. The derived inactivation rate constant (kinac ) and inactivation curves (calculated using the log-linear model) were studied as a function of turbidity based on the exponential one-phase inactivation kinetics of HuNoV. Using an impeller system set at 100 rotations/min (rpm) with an eight-nephelometric turbidity unit (NTU) sample (the lowest turbidity studied), the kinact based on the levels of viral genomic RNA concentrations was approximately 2.15-fold higher than that observed without rotation (0 rpm). Moreover, the kinact increased 1.69-fold with a 56-NTU sample (the highest turbidity studied) when the impeller system was set at 100 rpm. UVC LED treatment decreased the HuNoV GII.4 population more effectively in conjunction with the impeller system (100 rpm) than without the impeller system. Our novel findings and model provide fundamental and scientific data that may help reuse brine water and ensure its microbiological safety through disinfection. Our study highlights the benefits of UVC LED treatment in successfully eliminating waterborne viruses in a prompt, resistance-reducing, and energy-efficient approach at the laboratory scale, which lays the foundation for future plant-scale studies of UVC LED-disinfection systems.

17.
Nat Immunol ; 23(7): 1052-1062, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35726060

RESUMO

The high mobility group (HMG) transcription factor TCF-1 is essential for early T cell development. Although in vitro biochemical assays suggest that HMG proteins can serve as architectural elements in the assembly of higher-order nuclear organization, the contribution of TCF-1 on the control of three-dimensional (3D) genome structures during T cell development remains unknown. Here, we investigated the role of TCF-1 in 3D genome reconfiguration. Using gain- and loss-of-function experiments, we discovered that the co-occupancy of TCF-1 and the architectural protein CTCF altered the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes at late stages of T cell development. The TCF-1-dependent gain in long-range interactions was linked to deposition of active enhancer mark H3K27ac and recruitment of the cohesin-loading factor NIPBL at active enhancers. These data indicate that TCF-1 has a role in controlling global genome organization during T cell development.


Assuntos
Cromatina , Elementos Facilitadores Genéticos , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo , Proteínas de Ciclo Celular/metabolismo , Elementos Facilitadores Genéticos/genética , Regulação da Expressão Gênica , Linfócitos T/metabolismo
18.
Nat Commun ; 13(1): 1602, 2022 03 24.
Artigo em Inglês | MEDLINE | ID: mdl-35332165

RESUMO

Architectural stripes tend to form at genomic regions harboring genes with salient roles in cell identity and function. Therefore, the accurate identification and quantification of these features are essential for understanding lineage-specific gene regulation. Here, we present Stripenn, an algorithm rooted in computer vision to systematically detect and quantitate architectural stripes from chromatin conformation measurements using various technologies. We demonstrate that Stripenn outperforms existing methods and highlight its biological applications in the context of B and T lymphocytes. By comparing stripes across distinct cell types and different species, we find that these chromatin features are highly conserved and form at genes with prominent roles in cell-type-specific processes. In summary, Stripenn is a computational method that borrows concepts from widely used image processing techniques to demarcate and quantify architectural stripes.


Assuntos
Cromatina , Processamento de Imagem Assistida por Computador , Algoritmos , Cromatina/genética , Computadores , Genoma
19.
Diabetes ; 71(8): 1746-1762, 2022 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-35167651

RESUMO

Dysregulation of extracellular matrix proteins in obese adipose tissue (AT) induces systemic insulin resistance. The metabolic roles of type VI collagen and its cleavage peptide endotrophin in obese AT are well established. However, the mechanisms regulating endotrophin generation remain elusive. Herein, we identified that several endotrophin-containing peptides (pre-endotrophins) were generated from the COL6A3 chain in a stepwise manner for the efficient production of mature endotrophin, partly through the action of hypoxia-induced matrix metalloproteinases (MMPs), including MMP2, MMP9, and MMP16. Hypoxia is an upstream regulator of COL6A3 expression and the proteolytic processing that regulates endotrophin generation. Hypoxia-inducible factor 1α (HIF1α) and the hypoxia-associated suppression of microRNA-29 (miR-29) cooperatively control the levels of COL6A3 and MMPs, which are responsible for endotrophin generation in hypoxic ATs. Adipocyte-specific Hif1α knock-out (APN-HIF1αKO) mice fed a chronic high-fat diet exhibited the significant amelioration of both local fibro-inflammation in AT and systemic insulin resistance compared with their control littermates, partly through the inhibition of endotrophin generation. Strikingly, adenovirus-mediated miR-29 overexpression in the ATs of APN-HIF1αKO mice in obesity significantly decreased endotrophin levels, suggesting that miR-29, combined with HIF1α inhibition in AT, could be a promising therapeutic strategy for treating obesity and related metabolic diseases.


Assuntos
Subunidade alfa do Fator 1 Induzível por Hipóxia , Resistência à Insulina , MicroRNAs , Tecido Adiposo/metabolismo , Animais , Colágeno Tipo VI/metabolismo , Hipóxia/genética , Hipóxia/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/deficiência , Inflamação/genética , Inflamação/metabolismo , Resistência à Insulina/genética , Camundongos , MicroRNAs/genética , MicroRNAs/metabolismo , Obesidade/genética , Obesidade/metabolismo
20.
Food Sci Biotechnol ; 31(1): 131-138, 2022 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-35059237

RESUMO

This study aimed to evaluate the virucidal effect and potential use as a disinfectant of undiluted and diluted slightly acidic electrolyzed water (SAEW) on human noroviruses (HuNoVs) using the in vitro suspension test and in food test. The oxidization reduction potential of SAEW gradually decreased with the increase in distilled water volume. Moreover, as the volume of distilled water and the dilution ratio increased, the available chlorine concentration of the samples significantly decreased from 31.2 ± 0.63 (SAEW) to 1.3 ± 0.21 (1:10 dilution of SAEW solution) (p < 0.05). Undiluted SAEW presented the lowest pH (5.56 ± 0.02) and as SAEW was diluted in distilled water, the pH of the sample increased. Considering the standard reduction values of pathogenic virus (> 4.00 log reduction), the reduction value of HuNoVs in cabbage samples was 4.65 (GI.6) and 4.28 (GII.4) log. These results suggest the potential application of SAEW for inactivating HuNoVs in the food industry. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-01011-w.

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