The transcription factor Bach2 negatively regulates murine natural killer cell maturation and function

BTB domain And CNC Homolog 2 (Bach2) is a transcription repressor that actively participates in T and B lymphocyte development, but it is unknown if Bach2 is also involved in the development of innate immune cells, such as natural killer (NK) cells. Here, we followed the expression of Bach2 during murine NK cell development, finding that it peaked in immature CD2

WashU Epigenome Browser update 2022

WashU Epigenome Browser (https://epigenomegateway.wustl.edu/browser/) is a web-based genomic data exploration tool that provides visualization, integration, and analysis of epigenomic datasets. The newly renovated user interface and functions have enabled researchers to engage with the browser and genomic data more efficiently and effectively since 2018. Here, we introduce a new integrated panel design in the browser that allows users to interact with 1D (genomic features), 2D (such as Hi-C), 3D (genome structure), and 4D (time series) data in a single web page. The browser can display three-dimensional chromatin structures with the 3D viewer module. The 4D tracks, called \u27Dynamic\u27 tracks, animatedly display time-series data, allowing for a more striking visual impact to identify the gene or genomic region candidates as a function of time. Genomic data, such as annotation features, numerical values, and chromatin interaction data can all be viewed in the dynamic track mode. Imaging data from microscopy experiments can also be displayed in the browser. In addition to software development, we continue to service and expand the data hubs we host for large consortia including 4DN, Roadmap Epigenomics, TaRGET and ENCODE, among others. Our growing user/developer community developed additional track types as plugins, such as qBed and dynseq tracks, which extend the utility of the browser. The browser serves as a foundation for additional genomics platforms including the WashU Virus Genome Browser (for COVID-19 research) and the Comparative Genome Browser. The WashU Epigenome Browser can also be accessed freely through Amazon Web Services at https://epigenomegateway.org/

Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome

Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection

Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi)

Abstract Background MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play important roles in the regulation of diverse biological processes in eukaryotes. Chinese perch (Siniperca chuatsi) is one of the most economically important fish species widely cultured in China. Growth is an extremely important characteristic in fish. Individual differences in body size are common in Siniperca chuatsi, which significantly influence the aquaculture production of Siniperca chuatsi. However, the underline growth-related regulatory factors, such as miRNAs, are still unknown. Results To investigate the growth-related miRNAs in Siniperca chuatsi, two RNA libraries from four growth-related tissues (brain, pituitary, liver, and muscle) of Siniperca chuatsi at 6-month stage with relatively high or low growth rates (big-size group or small-size group) were obtained and sequenced using Solexa sequencing. A total of 252 known miRNAs and 12 novel miRNAs were identified. The expression patterns of these miRNAs in big-size group and small-size group were compared, and the results showed that 31 known and 5 novel miRNAs were differently expressed (DE). Furthermore, to verify the Solexa sequencing, five DE miRNAs were randomly selected and quantified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The results showed that their expression patterns were consistent with those of Solexa sequencing. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of target genes of DE miRNAs was performed. It showed that the target genes were involved in multiple biological processes including metabolic process, suggesting that metabolic process played an important role in growth of fish. Conclusions Siniperca chuatsi is a popular and economically important species in aquaculture. In this study, miRNAs in Siniperca chuatsi with different growth rates were identified, and their expression profiles were compared. The data provides the first large-scale miRNA profiles related to growth of Siniperca chuatsi, which is expected to contribute to a better understanding of the role of miRNAs in regulating the biological processes of growth and possibly useful for Siniperca chuatsi breeding

A Review of Coating Materials Used to Improve the Performance of Optical Fiber Sensors

In order to improve the performance of fiber sensors and fully tap the potential of optical fiber sensors, various optical materials have been selectively coated on optical fiber sensors under the background of the rapid development of various optical materials. On the basis of retaining the original characteristics of the optical fiber sensors, the coated sensors are endowed with new characteristics, such as high sensitivity, strong structure, and specific recognition. Many materials with a large thermal optical coefficient and thermal expansion coefficients are applied to optical fibers, and the temperature sensitivities are improved several times after coating. At the same time, fiber sensors have more intelligent sensing capabilities when coated with specific recognition materials. The same/different kinds of materials combined with the same/different fiber structures can produce different measurements, which is interesting. This paper summarizes and compares the fiber sensors treated by different coating materials

Isobaric Vapor–Liquid Equilibrium for Binary and Ternary Systems of <i>tert</i>-Butanol + <i>tert</i>-Butyl Acetate + Chlorobenzene at 101.33 kPa

Isobaric vapor–liquid equilibria of <i>tert</i>-butanol + chlorobenzene and <i>tert</i>-butyl acetate + chlorobenzene binary systems and the <i>tert</i>-butanol + <i>tert</i>-butyl acetate + chlorobenzene ternary system at 101.33 kPa were measured using a circulation VLE still. The data of binary systems passed the thermodynamic consistency test of the Herington method and the Van Ness point test, and the experimental data of the ternary system also passed the Wisniak consistency test. These binary systems’ VLE data were fitted by the Wilson, nonrandom two-liquid (NRTL), and universal quasichemical (UNIQUAC) activity coefficient models with minor deviations. Furthermore, the obtained binary interaction parameters from the binary systems were used to predict the VLE behavior of the <i>tert</i>-butanol + <i>tert</i>-butyl acetate + chlorobenzene ternary system. The rmsd of vapor and the temperature between the experimental and predicted values for the ternary system were smaller than 0.0304 and 0.81K, respectively. The results indicated that the relative volatility between <i>tert</i>-butanol and <i>tert</i>-butyl acetate obviously increased when adding chlorobenzene as a solvent. Thus, chlorobenzene is a promising solvent for the separation of the <i>tert</i>-butanol and <i>tert</i>-butyl acetate mixture system by extractive distillation

Additional file 1: of Identification and profiling of growth-related microRNAs in Chinese perch (Siniperca chuatsi)

Target gene prediction and analysis of miRNAs. (XLS 1498 kb

Enhancing rice production sustainability and resilience via reactivating small water bodies for irrigation and drainage

Abstract Rice farming threatens freshwater resources, while also being increasingly vulnerable to drought due to climate change. Rice farming needs to become more sustainable and resilient to climate change by improving irrigation drainage systems. Small water bodies, used to store drainage water and supply irrigation in traditional rice farming systems have gradually been abandoned in recent decades. This has resulted in a higher water footprint (WF) associated with rice farming due to increased freshwater usage and wastewater release, also leaving rice production more vulnerable to extreme weather events. Here, we propose how protecting and reactivating small water bodies for rice irrigation and drainage can decrease rice production WF in China by 30%, save 9% of China’s freshwater consumption, increase irrigation self-sufficiency from 3% to 31%, and alleviate yield loss in dry years by 2–3%. These findings show that redesigning rice irrigation drainage systems can help meet water scarcity challenges posed by climate change