Notes

A case report regarding bilateral pseudo-doubling with the optic cds.
The InterPro database (https//www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.Long non-coding RNAs (lncRNAs) act as versatile regulators of many biological processes and play vital roles in various diseases. lncRNASNP is dedicated to providing a comprehensive repository of single nucleotide polymorphisms (SNPs) and somatic mutations in lncRNAs and their impacts on lncRNA structure and function. Since the last release in 2018, there has been a huge increase in the number of variants and lncRNAs. Thus, we updated the lncRNASNP to version 3 by expanding the species to eight eukaryotic species (human, chimpanzee, pig, mouse, rat, chicken, zebrafish, and fruitfly), updating the data and adding several new features. SNPs in lncRNASNP have increased from 11 181 387 to 67 513 785. The human mutations have increased from 1 174 768 to 2 387 685, including 1 031 639 TCGA mutations and 1 356 046 CosmicNCVs. Compared with the last release, updated and new features in lncRNASNP v3 include (i) SNPs in lncRNAs and their impacts on lncRNAs for eight species, (ii) SNP effects on miRNA-lncRNA interactions for eight species, (iii) lncRNA expression profiles for six species, (iv) disease & GWAS-associated lncRNAs and variants, (v) experimental & predicted lncRNAs and drug target associations and (vi) SNP effects on lncRNA expression (eQTL) across tumor & normal tissues. The lncRNASNP v3 is freely available at http//gong_lab.hzau.edu.cn/lncRNASNP3/.A nickel-catalyzed reductive cross-coupling of cyclopropylamine NHP esters with (hetero)aryl halides is reported. This efficient protocol provides direct access to 1-arylcyclopropylamines, a bioisosteric motif commonly used in small molecule drug discovery. The reaction proceeds rapidly ( less then 2 h) with excellent functional group tolerance and without requiring heat- or air-sensitive reagents. The method can also be extended to the arylation of four-membered strained rings. The NHP esters are easily obtained from the corresponding commercially available carboxylic acids in one step with high yields and no column chromatography.
Given the reported effects of nuclear paraspeckle assembly transcript 1 (NEAT1) on kidney injury, a study is worth formulating to investigate whether and how NEAT1 impacts podocytes.

A mouse podocyte injury model was established using the adriamycin (ADR)-induced mouse podocyte cell line (MPC5). The target relationships between NEAT1 and microRNA (miR)-23b-3p and between miR-23b-3p and Bcl-2 interacting protein 3 like (BNIP3L) were verified by dual-luciferase reporter assay and RNA immunoprecipitation assay. After ADR-induced MPC5 cells were transfected with NEAT1 overexpression plasmid (oe-NEAT1) or shNEAT1, the viability and apoptosis of MPC5 cells were evaluated by Cell Counting Kit-8 (CCK-8) assay and flow cytometry, respectively. The expressions of MPC5, miR-23b-3p, BNIP3L and the factors related to podocyte injury, apoptosis and epithelial-mesenchymal transition were determined using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot.

NEAT1 was high-expressed in ADR-induced cell model. After transfection with oe-NEAT1, the expression of NEAT1, the levels of marker (Desmin) and apoptosis were promoted, while the viability and the levels of podocyte injury markers (WT1, Nephrin) were inhibited in ADR-induced cells. However, shNEAT1 generated the effects opposite to oe-NEAT1. Besides, miR-23b-3p competitively bound to NEAT1 and targeted BNIP3L. MiR-23b-3p inhibitor reversed the effect of shNEAT1, while its effect could be further offset by shBNIP3L. Furthermore, miR-23b-3p inhibitor affected mouse podocyte injury through downregulating Bcl-2 and E-cadherin levels and upregulating Cleaved-caspase-3, Bax, N-cadherin, Vimentin and Snail levels, but shBNIP3L did oppositely.

NEAT1 promotes the podocyte injury
targeting miR-23b-3p/BNIP3L axis.
NEAT1 promotes the podocyte injury via targeting miR-23b-3p/BNIP3L axis.DNA methyltransferase inhibitor zebularine was proven to induce regeneration in the ear pinna in mice. We utilized a dorsal skin wound model to further evaluate this epigenetic inhibitor in wound healing. Full-thickness excisional wounds were made on the dorsum of 2 and 10-month-old healthy BALB/c and 3 and 8-month-old diabetic (db/db) mice, followed by topical or intraperitoneal zebularine delivery. Depending on the strain, age, dose, and delivery, the zebularine treatments either had no effect or accelerated or delayed wound closure. In principle, zebularine applied topically moderately promoted wound closure in the healthy but markedly delayed in the diabetic mice, which was in line with decreased viability of cultured keratinocytes from diabetic patients exposed to zebularine. The histological analysis revealed an improvement in the architecture of restored skin in zebularine-treated mice, manifested as a distinct layered pattern resembling panniculus carnosus. The finding corresponds with the zebularine-mediated activation of the Wnt5a gene, an essential regulator of Wnt signaling, the pathway involved in hair follicle development, the process which in turn is connected with regenerative skin healing. Although zebularine did not remarkably accelerate wound healing, zebularine and other epigenetic inhibitors deserve further testing as potential drugs to improve the quality of restored skin.
Exposome research aims to describe and understand the extent to which all the exposures in human environments may affect our health over the lifetime. However, the way in which humans interact with their environment is socially patterned. Failing to account for social factors in research exploring the exposome may underestimate the magnitude of the effect of exposures or mask inequalities in the distribution of both exposures and outcomes.

We aimed to describe the extent to which social factors appear in the exposome literature, the manner in which they are used in empirical analyses and statistical modeling, and the way in which they are considered in the overall scientific approach.

We conducted a scoping review of the literature using three databases (PubMed, Embase, and Web of Science) up to January 2022. We grouped studies based on the way in which the social variables were used in the analyses and quantified the type and frequency of social variables mentioned in the articles. We also qualitativelsms of construction and, potentially, alleviate social inequalities in health and mitigate the emergence of new ones. https//doi.org/10.1289/EHP11015.
Social factors in exposome research should be considered in a more systematic way, considering their role in structuring both the specific external and the internal exposome. Doing so could help to understand the mechanisms of construction and, potentially, alleviate social inequalities in health and mitigate the emergence of new ones. https//doi.org/10.1289/EHP11015.A flowing gas experiment using a Knudsen flow reactor was performed on a series of seven semivolatile probe gases interacting with two often used mineral dust materials, namely, coarse Arizona test dust (ATD-C) and kaolinite. The semivolatile probe gases used were applinate (acetate ester), pipol (ethyl ester of 2-methylvaleric acid), benzylacetate (acetate ester of benzylalcohol), menthol (alcohol), toluene, limonene, and γ-terpinene (terpene hydrocarbon). Uptake experiments under molecular flow conditions resulted in absolute coverages and initial uptake coefficients γ0 based on the geometric sample surface. Integration of a simple Langmuir adsorption model afforded an analytical solution of the desorption kinetics of the semivolatile hydrocarbon upon spontaneous desorption from the solid mineral dust substrate at ambient temperature. Numerical fitting of the desorption rate resulted in adsorption (ka) and desorption (kd) rate constants, where 1/kd represented the surface residence time of the adsorbed semio undergo chemical reactions on both mineral substrates.Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. learn more We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https//TEDD.obg.cuhk.edu.hk/.OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity. This update of the underlying data to over 18 000 prokaryotes and almost 2000 eukaryotes with over 100 million genes propels the coverage to another level. This achievement also demonstrates the scalability of the underlying OrthoLoger software for delineation of orthologs, freely available from https//orthologer.ezlab.org. In addition to the ab-initio computations of gene orthology used for the OrthoDB release, the OrthoLoger software allows mapping of novel gene sets to precomputed orthologs and thereby links to their annotations. The LEMMI-style benchmarking of OrthoLoger ensures its state-of-the-art performance and is available from https//lemortho.
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