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Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.

Abstract Background DNA methylation (DNAm) is a critical regulator of both development and cellular identity and shows unique patterns in neurons. To better characterize maturational changes in DNAm patterns in these cells, we profile the DNAm landscape at single-base resolution across the first two decades of human neocortical development in NeuN+ neurons using whole-genome bisulfite sequencing and compare them to non-neurons (primarily glia) and prenatal homogenate cortex. Results We show that DNAm changes more dramatically during the first 5 years of postnatal life than during the entire remaining period. We further refine global patterns of increasingly divergent neuronal CpG and CpH methylation (mCpG and mCpH) into six developmental trajectories and find that in contrast to genome-wide patterns, neighboring mCpG and mCpH levels within these regions are highly correlated. We integrate paired RNA-seq data and identify putative regulation of hundreds of transcripts and their splicing events exclusively by mCpH levels, independently from mCpG levels, across this period. We finally explore the relationship between DNAm patterns and development of brain-related phenotypes and find enriched heritability for many phenotypes within identified DNAm features. Conclusions By profiling DNAm changes in NeuN-sorted neurons over the span of human cortical development, we identify novel, dynamic regions of DNAm that would be masked in homogenate DNAm data; expand on the relationship between CpG methylation, CpH methylation, and gene expression; and find enrichment particularly for neuropsychiatric diseases in genomic regions with cell type-specific, developmentally dynamic DNAm patterns.

Recently, the capture of carbon dioxide, the primary greenhouse gas, has attracted particular interest from researchers worldwide. In the present work, several theoretical methods have been used to study adsorption of CO2 molecules on Li+-decorated coronene (Li+@coronene). It has been established that Li+ can be strongly anchored on coronene, and then a physical adsorption of CO2 will occur in the vicinity of this cation. Moreover, such a decoration has substantially improved interaction energy (Eint) between CO2 molecules and the adsorbent. One to twelve CO2 molecules per one Li+ have been considered, and their Eint values are in the range from −5.55 to −16.87 kcal/mol. Symmetry-adapted perturbation theory (SAPT0) calculations have shown that, depending on the quantity of adsorbed CO2 molecules, different energy components act as the main reason for attraction. AIMD simulations allow estimating gravimetric densities (GD, wt.%) at various temperatures, and the maximal GDs have been calculated to be 9.3, 6.0, and 4.9% at T = 77, 300, and 400 K, respectively. Besides this, AIMD calculations validate stability of Li+@coronene complexes during simulation time at the maximum CO2 loading. Bader’s atoms-in-molecules (QTAIM) and independent gradient model (IGM) techniques have been implemented to unveil the features of interactions between CO2 and Li+@coronene. These methods have proved that there exists a non-covalent bonding between the cation center and CO2. We suppose that findings, derived in this theoretical work, may also benefit the design of novel nanosystems for gas storage and delivery.

OBJECTIVES/GOALS: It has been previously shown that pediatric high-grade glioma (pHGG) survival is different between sexes. We set out to find out whether there are sex-specific differences in the genomic landscapes of pHGG that may underlie this sex disparity. METHODS/STUDY POPULATION: We downloaded Illumina 450k DNAm data from ArrayExpress and GeneExpressionOmnibus. The minfi package was used to process raw DNAm data. Sex chromosomes and CpGs that are common SNPs were removed. Surrogate variables (SVs) were estimated via the sva Bioconductor package. Differentially methylated CpGs were identified by fitting a multiple linear regression model for the DNAm level at each CpG, with independent variables being sex (a binary variable) and the estimated SVs. RNAseq data was downloaded from Cavatica, and differential gene expression analysis was carried out via the DESeq2 package. RESULTS/ANTICIPATED RESULTS: In the pediatric glioblastoma (GBM) DNAm data [58 female & 91 male IDH wt samples; ages 0.1–21 yrs;], we found 7,371 differentially methylated cytosines (DMCs) at FDR≤0.05. Of the DMCs, 289 had DNAm differences between male and female samples ≥10%. The majority of probes (68%) were in CpG islands, shelves, or shores. We also found 4 differentially methylated regions (DMRs) between sexes (FWER≤0.1). In the adult GBM DNAm samples [32 F & 32 M IDH wt samples; ages 22–75 yrs], we found only 117 DMCs at FDR≤0.05, and no DMRs. In the RNAseq dataset [68 F & 54 M pHGG samples, ages 0.08–30.6 yrs], we found 383 differentially expressed genes (at FDR≤0.05), and 16 of them (4%) overlapped a DMC. DISCUSSION/SIGNIFICANCE OF IMPACT: Our findings demonstrate that pHGG exhibits sex-specific methylome differences. Interestingly, this difference is greater in the pediatric population as compared to adults. The pHGG transcriptome also differs by sex, which may be related to differential DNAm in a minority of cases.

ABSTRACT IMPACT: Here, we describe extensive sex-specific differences in the transcriptomes of pancreatic neuroendocrine tumors (PNETs). Given that the clinical course of PNETs differs by sex (female sex is associated with better survival), achieving a greater understanding of the specific molecular sexual dimorphisms is invaluable for advancing personalized treatment. OBJECTIVES/GOALS: Epidemiologic studies demonstrate that pancreatic neuroendocrine tumors (PNETs) exhibit sexual dimorphisms with regards to prognosis, disease recurrence, and complication rates. We sought to compare the transcription and DNA methylation landscapes of PNETs by sex, to elucidate molecular differences that may underlie this sex disparity. METHODS/STUDY POPULATION: RNAseq data was generated from PNETs surgically resected at our institution (9 Female; 12 Male patients). RNA was extracted with the RNeasy Mini Kit, stranded sequencing libraries were prepared with TruSeq, and paired end sequencing was done on the HiSeq 2500/4000 systems. Transcript-level quantification was performed with salmon, and DESeq2 was used for differential expression analysis. To account for significant variation due to covariates other than sex, surrogate variables were computed with the SVA package and adjusted for. The goseq package was used for gene set over representation analysis. Matched DNA methylation (DNAm) and RNAseq data was downloaded from GEO (16 F; 16 M). Raw DNAm data was processed with minfi. Differential methylation analysis was done with limma and bumphunter. Analysis was done in R. RESULTS/ANTICIPATED RESULTS: We found that 826 autosomal genes were differentially expressed (DE) by sex in PNETs (at FDR ≤0.1). Gene set over representation analysis performed on the DE genes revealed significant enrichment for several processes, including ‘ascorbate & aldarate metabolism’ and ‘positive regulation of ERK1 & ERK2 cascade’ (all FDR ≤0.1). When we compared DNAm profiles between sexes, we found 8 CpGs which were differentially methylated by sex (at FDR ≤0.1), 7 of which were proximal to genes. Methylation of one of the sex-associated CpGs, overlapping the gene TIMM8B, was found to be negatively correlated with gene expression (rho=-0.41; p-value=0.02). Interestingly, TIMM8B deletion has been previously reported in other non-pancreatic neuroendocrine tumors. There were no differentially methylated regions between sexes. DISCUSSION/SIGNIFICANCE OF FINDINGS: Our findings demonstrate that PNETs exhibit extensive sexual dimorphisms with regards to gene expression profiles but have largely congruent methylomes by sex. These molecular differences may contribute to the variability in clinical course between men and women, and their characterization is vital for the advancement of personalized medicine.

This article presents the results of the study of the morphological composition of municipal solid waste (MSW) from the landfill of Atyrau city, and the waste’s energy characteristics and presence of microorganisms, including bacteria, fungi and viruses. This study was carried out under a government order to determine the feasibility of recycling accumulated and incoming waste into electricity and its hazard to the environment and the workers involved in handling it. At the moment, there is no MSW recycling in Kazakhstan, which has led to the accumulation of more than 125 million tons of waste with an annual increase of 5 million tons. The research included four major cities (Almaty, Shymkent, Atyrau and Astana), which were selected not only on the basis of population, but also because the cities were located in different climatic zones. Samples were collected at the city landfills: 10 samples with an average distance of 100 m from each other were collected to provide a maximum coverage of both recently received waste and long-time stored waste. The research showed that neither climatic conditions nor the population size had a significant impact on MSW density, the values of which ranged from 120.1 kg/m3 to 145.4 kg/m3, as this indicator directly depends on the quality of life. The mass of the combustible fraction ranged from 39.41% to 54.62% and was mainly represented by plastic, textile and paper waste. The average value for the four cities was 50.30%. The higher calorific value fell in the range of 24.22–30.49 MJ/kg, with an average value of 26.71 MJ/kg. Microbiological studies showed little difference in average composition regardless of climatic conditions. Thus, no sharp differences in MSW composition, its energy characteristics and microbiological composition were found. The results of this study may be useful for optimising MSW recycling and disposal processes, as well as for developing measures to reduce their negative impact on the environment and human health.

Solid waste management is one of the main problems in large cities. The determination of the quantitative and qualitative composition of municipal solid waste is necessary for proper planning in the processing of such waste. This article presents the results of studies of the morphological composition, physico-chemical parameters and energetical potential of municipal solid waste (MSW) from the landfill of the city of Shymkent. Waste samples were taken from 10 different points of the landfill. The volume–mass parameters of the samples and their average density were determined. The combined waste samples mainly consisted of food waste, paper and cardboard, polymers and plastic, glass, metal, textiles, wood, leather, bones and rubber. Most of the waste, more than 30%, contains plastic products. The moisture of the combustible fraction of the samples is low and varies from 0.3% to 2.3%. The average ash content of the combustible fraction of the samples was determined and its average value is 18.4%. The yield of the volatile substances was determined and the average value per dry state is 78.7%. To determine the energetical potential of municipal solid waste, the gross calorific value was determined and the net calorific value was calculated, the average value of which is 24.15 MJ/kg. This shows the possibility of using solid waste as an energy source.

In the process of manufacturing products from high-temperature superconductors (HTS), quality control must be carried out. Traditionally, for HTS coils, electrical tests are carried out to determine critical current. In the case of an unacceptable result, it is necessary to determine the cause. Therefore, it is necessary to develop nondestructive testing methods. This article proposes a technology for manufacturing quality evaluation. It is based on determining the actual location of the tape and the gaps between the turns and rows of the coil and analyzing these values. For this purpose, samples were scanned using computed tomography (CT) with a Nordson Dage XD7600NT X-ray inspection system with a μCT module. The obtained data were analyzed using VolumeGraphics VGStudio 2.2 software. Furthermore, the proposed technology can be used as part of a predictive analysis of the state of HTS coils in the windings of electrical machines.

Differentiating pluripotent cells from fibroblast progenitors is a potentially transformative tool in personalized medicine. We previously identified relatively greater success culturing dura-derived fibroblasts than scalp-derived fibroblasts from postmortem tissue. We hypothesized that these differences in culture success were related to epigenetic differences between the cultured fibroblasts by sampling location, and therefore generated genome-wide DNA methylation and transcriptome data on 11 intrinsically matched pairs of dural and scalp fibroblasts from donors across the lifespan (infant to 85 years). While these cultured fibroblasts were several generations removed from the primary tissue and morphologically indistinguishable, we found widespread epigenetic differences by sampling location at the single CpG (N = 101,989), region (N = 697), "block" (N = 243), and global spatial scales suggesting a strong epigenetic memory of original fibroblast location. Furthermore, many of these epigenetic differences manifested in the transcriptome, particularly at the region-level. We further identified 7,265 CpGs and 11 regions showing significant epigenetic memory related to the age of the donor, as well as an overall increased epigenetic variability, preferentially in scalp-derived fibroblasts-83% of loci were more variable in scalp, hypothesized to result from cumulative exposure to environmental stimuli in the primary tissue. By integrating publicly available DNA methylation datasets on individual cell populations in blood and brain, we identified significantly increased inter-individual variability in our scalp- and other skin-derived fibroblasts on a similar scale as epigenetic differences between different lineages of blood cells. Lastly, these epigenetic differences did not appear to be driven by somatic mutation--while we identified 64 probable de-novo variants across the 11 subjects, there was no association between mutation burden and age of the donor (p = 0.71). These results depict a strong component of epigenetic memory in cell culture from primary tissue, even after several generations of daughter cells, related to cell state and donor age.