Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution.

DNA methylation is essential for a wide variety of biological processes, yet the development of a highly efficient and robust technology remains a challenge for routine single-cell analysis. We developed a multiplex scalable single-cell reduced representation bisulfite sequencing (msRRBS) technology. It allows cell-specific barcoded DNA fragments of individual cells to be pooled before bisulfite conversion, free of enzymatic modification or physical capture of the DNA ends, and achieves read mapping rates of 62.5 ± 3.9%, covering 60.0 ± 1.4% of CpG islands and 71.6 ± 1.6% of promoters in K562 cells. Its reproducibility is shown in duplicates of bulk cells with close to perfect correlation (R = 0.97-0.99). At a low 1 Mb of clean reads, msRRBS provides highly consistent coverage of CpG islands and promoters, outperforming the conventional methods with orders of magnitude reduction in cost. Here, we use this method to characterize the distinct methylation patterns and cellular heterogeneity of six cell lines, plus leukemia and hepatocellular carcinoma models. Taking 4 h of hands-on time, msRRBS offers a unique, highly efficient approach for dissecting methylation heterogeneity in a variety of multicellular systems.

Differences in particulate matter retention and leaf microstructures of 10 plants in different urban environments in Lanzhou City.

Particulate matter (PM) is a major primary environmental air pollutant and poses a threat to human health. Differences in the environment and leaf microstructures of plants will result in varying abilities to retain PM, but the effects of changes in these factors on PM retention are not yet well understood. This study selected 10 plant species in four urban areas (sports field, park, residential green space, and greenway) as the study objects. The amount of retained PM by the different species was measured, and the leaf microstructures were observed. It was found that the environment significantly affected both PM retention and leaf microstructure. The ranking of PM retention in the 10 species in four areas was greenway > residential green space > park > sports field. The ranking of average stomatal width and length was park > sports field > residential green space > greenway, while that of average stomatal density was greenway > residential green space > park > sports field. Different environments affected the length and density of trichomes in the leaves. These changes represented the adaptation of plant species to the growth environment. The stomata and grooves of the leaf surface significantly affected the ability of plants to retain PM. The amount of PM retained by different species varied. In all four urban areas, Prunus × cistena N. E. Hansen ex Koehne (purple leaf sand cherry), Prunus cerasifera Ehrhart f. atropurpurea (Jacq.) Rehd. (cherry plum), Buxus sinica var. parvifolia M. Cheng (common boxwood), and Ligustrum × vicaryi Rehder (golden privet) showed strong PM retention. The results of this study will provide information for planners and urban managers for the selection of plant species.

Exercise resistance effect on adverse reaction rate in heart failure / Efeito de resistência ao exercício na taxa de reação adversa da insuficiência cardíaca / Efecto de la resistencia al ejercicio en la tasa de reacción adversa en la insuficiencia cardíaca

ABSTRACT Introduction: Heart Failure is a common disease in the elderly. In the end stage, patients usually accompany a reduction in fat content and lean body mass in addition to heart failure. Objective: Study the exercise resistance effects and adverse reaction rate in patients with heart failure. Methods: 52 patients with chronic heart failure (38 males, age 67 ± 2.2 years) were randomly divided into two groups. According to New York Heart Association Functional Classification, 27 patients with grade II and 25 with grade I was randomly divided. The experimental group was submitted to aerobic exercises under heart rate control for seven months and the control group with no exercise prescription. In the comparison, the 6-minute walk test and a cardiac function test were employed by Agilent 4500 EcoDoppler at a frequency of 2.5MHz. The indices of systolic and left ventricular function were recorded on ECG simultaneously using the improved Simpsons method, and the following indices were measured: left ventricular systolic and end-diastolic; left ventricular ejection fraction; left ventricular diastolic function; early, late peak velocity and its ratio; mitral valve diastole. Results: Compared to the control group, heart rate decreased to different degrees (P < 0.05), exercise endurance increased significantly (P < 0.01), and left ventricular function index improved significantly (P < 0.01). Conclusion: We observed a positive impact of aerobic exercise directed at the rehabilitation of the cardiovascular system and mental health in elderly patients. Evidence Level II; Therapeutic Studies - Investigating the results.

RESUMO Introdução: A insuficiência cardíaca é uma doença comum em idosos. No estágio final, além da disfunção cardíaca, os pacientes geralmente acompanham uma redução no teor de gordura e da massa magra. Objetivo: Estudar os efeitos da resistência ao exercício e da taxa de reação adversa em pacientes com insuficiência cardíaca. Métodos: 52 pacientes com insuficiência cardíaca crônica (38 homens, idade de 67 ± 2,2 anos) foram divididos aleatoriamente em dois grupos. Segundo a classificação funcional da IC NYHA, 27 pacientes com grau II e 25 com grau I foram divididos aleatoriamente. O grupo experimental foi submetido a exercícios aeróbicos sob controle da frequência cardíaca por 7 meses e comparado ao grupo controle sem prescrição de exercício algum. Na comparação, foram utilizados o teste de caminhada de 6 minutos, teste de função cardíaca por EcoDoppler Agilent 4500 em frequência de 2,5MHz. Os índices de função sistólica e ventricular esquerda foram registrados no eCG simultaneamente utilizando o método Simpsons melhorado e os seguintes índices foram medidos: sistólica ventricular esquerda e diastólica final; fração de ejeção ventricular esquerda; função diastólica ventricular esquerda; velocidade de pico precoce, tardio e sua razão; diástole da válvula mitral. Resultados: Comparado ao grupo controle, a frequência cardíaca diminuiu em diferentes graus (P<0,05), a resistência ao exercício aumentou significativamente (P < 0,01) e o índice de função ventricular esquerda melhorou significativamente (P < 0,01). Conclusão: Observou-se um impacto positivo do exercício aeróbico direcionado à reabilitação do sistema cardiovascular e da saúde mental nos pacientes idosos. Nível de evidência II; Estudos terapêuticos - investigação dos resultados do tratamento.

RESUMEN Introducción: La insuficiencia cardíaca es una enfermedad común en los ancianos. En la fase final, además de la disfunción cardíaca, los pacientes suelen acompañar una reducción del contenido de la grasa y de la masa magra. Objetivo: Estudiar los efectos de la resistencia al ejercicio y la tasa de reacción adversa en pacientes con insuficiencia cardíaca. Métodos: 52 pacientes con insuficiencia cardíaca crónica (38 varones, edad de 67 ± 2,2 años) fueron divididos aleatoriamente en dos grupos. Según la clasificación funcional de la IC de la NYHA, se dividieron aleatoriamente 27 pacientes con grado II y 25 con grado I. El grupo experimental fue sometido a ejercicios aeróbicos bajo control de la frecuencia cardíaca durante 7 meses y comparado con el grupo de control sin prescripción de ejercicios. En la comparación se utilizó la prueba de marcha de 6 minutos y la prueba de función cardíaca mediante el EcoDoppler Agilent 4500 a una frecuencia de 2,5MHz. Los índices de la función sistólica y del ventrículo izquierdo se registraron en la eCG simultáneamente mediante el método mejorado de Simpsons y se midieron los siguientes índices: sistólica y diastólica final del ventrículo izquierdo; fracción de eyección del ventrículo izquierdo; función diastólica del ventrículo izquierdo; velocidad máxima temprana y tardía y su relación; diástole de la válvula mitral. Resultados: En comparación con el grupo de control, la frecuencia cardíaca disminuyó en diferentes grados (P < 0,05), la resistencia al ejercicio aumentó significativamente (P < 0,01) y el índice de función ventricular izquierda mejoró significativamente (P < 0,01). Conclusión: Se observó un impacto positivo del ejercicio aeróbico dirigido a la rehabilitación del sistema cardiovascular y la salud mental en pacientes de edad avanzada. Nivel de evidencia II; Estudios terapéuticos - Investigación de resultados.

Sample-multiplexing approaches for single-cell sequencing.

Single-cell sequencing is widely used in biological and medical studies. However, its application with multiple samples is hindered by inefficient sample processing, high experimental costs, ambiguous identification of true single cells, and technical batch effects. Here, we introduce sample-multiplexing approaches for single-cell sequencing in transcriptomics, epigenomics, genomics, and multiomics. In single-cell transcriptomics, sample multiplexing uses variants of native or artificial features as sample markers, enabling sample pooling and decoding. Such features include: (1) natural genetic variation, (2) nucleotide-barcode anchoring on cellular or nuclear membranes, (3) nucleotide-barcode internalization to the cytoplasm or nucleus, (4) vector-based barcode expression in cells, and (5) nucleotide-barcode incorporation during library construction. Other single-cell omics methods are based on similar concepts, particularly single-cell combinatorial indexing. These methods overcome current challenges, while enabling super-loading of single cells. Finally, selection guidelines are presented that can accelerate technological application.