Identification of SARS-CoV-2 in urban rodents from Southern Mexico City at the beginning of the COVID-19 pandemic

Currently, there are some concerns about the situation and, in particular, about the future of the COVID-19 pandemic and the new emerging variants of SARS-CoV-2. Rodents are an example of synanthropic animals in urban environments that harbor important zoonoses. Although the molecular identification of SARS-CoV-2 in Rattus norvegicus from New York City had been reported, in other studies, urban wild rodents infected with this virus have not been found. This study aimed to molecularly identify the presence of SARS-CoV-2 in urban wild rodents from Mexico City, trapped along a water channel of a public park as part of a pest control program, at the beginning of the COVID-19 pandemic, during the fall and winter of 2020. Up to 33 Mus musculus and 52 R. norvegicus were captured and euthanized, large intestine samples with feces from the animals were obtained. RNAs were obtained and subjected to qRT-PCR for SARS-CoV-2 identification and threshold cycle (Ct) values were obtained. Four mice (12.1%) and three rats (5.8%) were positive, three rodents exhibited Ct<30. Our results on the frequency of SARS-CoV-2 in urban rats are in line with other previous reports. Thus, similar to other authors, we suggest that surveillance for the detection of SARS-CoV-2 in urban wild rodents, as sentinel animals, should be maintained.

A conserved role for frizzled in sleep architecture

Previous studies of natural variants in Drosophila melanogaster implicated the Wnt signaling receptor frizzled in sleep. Given that the Wnt signaling pathway is highly conserved across species, we hypothesized that frizzled class receptor 1 (Fzd1), the murine homolog of frizzled, would also have a role in sleep. Using a CRISPR transgenic approach, we removed most of the Fzd1 coding region from C57BL/6N mice. We used a video assay to measure sleep characteristics in Fzd1-deficient mice. As Wnt signaling is known to affect visuospatial memory, we also examined the impact of the deletion on learning and memory using the novel object recognition (NOR) paradigm. Fzd1-deficient mice had altered sleep compared to littermate controls. The mice did not respond differently to the NOR paradigm compared to controls but did display anxiety-like behavior. Our strategy demonstrates that the study of natural variation in Drosophila sleep translates into candidate genes for sleep in vertebrate species such as the mouse.

The negative adipogenesis regulator Dlk1 is transcriptionally regulated by Ifrd1 (TIS7) and translationally by its orthologue Ifrd2 (SKMc15)

Delta-like homolog 1 (Dlk1), an inhibitor of adipogenesis, controls the cell fate of adipocyte progenitors. Experimental data presented here identify two independent regulatory mechanisms, transcriptional and translational, by which Ifrd1 (TIS7) and its orthologue Ifrd2 (SKMc15) regulate Dlk1 levels. Mice deficient in both Ifrd1 and Ifrd2 (dKO) had severely reduced adipose tissue and were resistant to high-fat diet-induced obesity. Wnt signaling, a negative regulator of adipocyte differentiation, was significantly upregulated in dKO mice. Elevated levels of the Wnt/β-catenin target protein Dlk1 inhibited the expression of adipogenesis regulators Pparg and Cebpa, and fatty acid transporter Cd36. Although both Ifrd1 and Ifrd2 contributed to this phenotype, they utilized two different mechanisms. Ifrd1 acted by controlling Wnt signaling and thereby transcriptional regulation of Dlk1. On the other hand, distinctive experimental evidence showed that Ifrd2 acts as a general translational inhibitor significantly affecting Dlk1 protein levels. Novel mechanisms of Dlk1 regulation in adipocyte differentiation involving Ifrd1 and Ifrd2 are based on experimental data presented here.

Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome

The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated by O-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevated O-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that is O-GlcNAcylated on human DNMT1. Functional studies in human and mouse cells further revealed that O-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that preferentially occurs at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establish O-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.

Potential of Leave and Fruit Ethanolic Extract of Etlingera hemisphaerica as Antihyperuricemic in Mice (Mus musculus)

&lt;b&gt;Background and Objective:&lt;/b&gt; Hyperuricemia is a disease triggered by disorders of uric acid metabolism. Therefore, this study evaluated the potential of leaves ethanolic extract of &lt;i&gt;Etlingera hemisphaerica&lt;/i&gt; (LE3H) and fruits ethanolic extract &lt;i&gt;E. hemisphaerica&lt;/i&gt; (FE3H) to restore hyperuricemia in mice. &lt;b&gt;Materials and Methods:&lt;/b&gt; Six groups (A0, A1, A2, A3, A4 and A5) each consisted of four male mice. Hyperuricemia in mice was induced by giving 0.3 mL of fresh chicken liver juice (FCLJ) for seven days (A1, A2, A3, A4 and A5). The condition of hyperuricemia in A1 is not neutralized. Meanwhile, hyperuricemia conditions in A2, A3, A4 and A5 were neutralized for seven days by giving 0.01 mg g&lt;sup&gt;&lt;/sup&gt;&lt;sup&gt;1&lt;/sup&gt; body weight (BW) allopurinol, 0.13, 0.26 and 0.36 mg g&lt;sup&gt;&lt;/sup&gt;&lt;sup&gt;1&lt;/sup&gt; BW LE3H. The control group (A0) only received double-distilled water in the same way. Blood uric acid levels were measured with the GCU Meter Device before and after the induction of hyperuricemia and after efforts to neutralize the hyperuricemia condition. Six groups (B0, B1, B2, B3, B4, B5) each consisting of four male mice were also provided to test the potential of FE3H. The recovery potential FE3H against hyperuricemia was tested separately in the same way as was done for LE3H. &lt;b&gt;Results:&lt;/b&gt; Giving FCLJ significantly increased (140.00-187.00%) uric acid compared to the control, so hyperuricemia was achieved. Doses of 0.13, 0.26 and 0.36 mg g&lt;sup&gt;&lt;/sup&gt;&lt;sup&gt;1&lt;/sup&gt; BW LE3H significantly recovered hyperuricemia as much as 54.09, 56.14 and 60.88%, respectively. Meanwhile, doses of 0.13, 0.26 and 0.36 mg g&lt;sup&gt;&lt;/sup&gt;&lt;sup&gt;1&lt;/sup&gt; FE3H significantly recovered hyperuricemia as much as 60.37, 62.24 and 65.572%, respectively. The LE3H and FE3H at the same dose showed that FE3H had a higher potential to restore hyperuricemia than LE3H. &lt;b&gt;Conclusion:&lt;/b&gt; Leave and fruit ethanolic extract of &lt;i&gt;E. hemisphaerica&lt;/i&gt; can potentially restore hyperuricemia in mice.

Creating Detailed Metadata for an R Shiny Analysis of Rodent Behavior Sequence Data Detected Along One Light-Dark Cycle

Automated mouse phenotyping through the high-throughput analysis of home cage behavior has brought hope of a more effective and efficient method for testing rodent models of diseases. Advanced video analysis software is able to derive behavioral sequence data sets from multiple-day recordings. However, no dedicated mechanisms exist for sharing or analyzing these types of data. In this article, we present a free, open-source software actionable through a web browser (an R Shiny application), which performs an analysis of home cage behavioral sequence data, which is designed to spot differences in circadian activity while preventing p-hacking. The software aligns time-series data to the light/dark cycle, and then uses different time windows to produce up to 162 behavior variables per animal. A principal component analysis strategy detected differences between groups. The behavior activity is represented graphically for further explorative analysis. A machine-learning approach was implemented, but it proved ineffective at separating the experimental groups. The software requires spreadsheets that provide information about the experiment (i.e., metadata), thus promoting a data management strategy that leads to FAIR data production. This encourages the publication of some metadata even when the data are kept private. We tested our software by comparing the behavior of female mice in videos recorded twice at 3 and 7 months in a home cage monitoring system. This study demonstrated that combining data management with data analysis leads to a more efficient and effective research process.

Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

Gene expression alterations occurring with aging have been described for a multitude of species, organs, and cell types. However, most of the underlying studies rely on static comparisons of mean gene expression levels between age groups and do not account for the dynamics of gene expression throughout the lifespan. These studies also tend to disregard the pairwise relationships between gene expression profiles, which may underlie commonly altered pathways and regulatory mechanisms with age. To overcome these limitations, we have combined segmented regression analysis with weighted gene correlation network analysis (WGCNA) to identify high-confidence signatures of aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice in a publicly available RNA-Seq dataset (GSE132040). Functional enrichment analysis of the overlap of genes identified in both approaches showed that immune- and inflammation-related responses are prominently altered in the brain and the liver, while in the heart and the muscle, aging affects amino and fatty acid metabolism, and tissue regeneration, respectively, which reflects an age-related global loss of tissue function. We also explored sexual dimorphism in the aging mouse transcriptome and found the liver and the muscle to have the most pronounced gender differences in gene expression throughout the lifespan, particularly in proteostasis-related pathways. While the data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, which we highlight as important features of murine tissue physiological aging.

Who's the Boss? Assessing Convergent Validity of Aggression Based Dominance Measures in Male Laboratory Mice, Mus Musculus

Aggression among group housed male mice continues to challenge laboratory animal researchers because mitigation strategies are generally applied at the cage level without a good understanding of how it affects the dominance hierarchy. Aggression within a group is typically displayed by the dominant mouse targeting lower ranking subordinates; thus, the strategies for preventing aggression may be more successful if applied specifically to the dominant mouse. Unfortunately, dominance rank is often not assessed because of time intensive observations or tests. Several correlates of dominance status have been identified, but none have been directly compared to home cage behavior in standard housing. This study assessed the convergent validity of three dominance correlates (urinary darcin, tube test score, preputial gland to body length ratio) with wound severity and rankings based on home cage behavior, using factor analysis. Discriminant validity with open field measures was assessed to determine if tube test scores are independent of anxiety. Cages were equally split between SJL and albino C57BL/6 strains and group sizes of 3 or 5 (N = 24). Home cage behavior was observed during the first week, and dominance measures were recorded over the second. After controlling for strain and group size, darcin and preputial ratio had strong loadings on the same factor, which was a significant predictor of home cage ranking showing strong convergent validity. Tube test scores were not significantly impacted by open field data, showing discriminant validity. Social network analysis revealed that despotic power structures were prevalent, aggressors were typically more active and rested away from cage mates, and the amount of social investigation and aggression performed by an individual were highly correlated. Data from this study show that darcin and preputial ratio are representative of home cage aggression and provide further insight into individual behavior patterns in group housed male mice.

Multiplex shRNA Screening of Germ Cell Development by in Vivo Transfection of Mouse Testis

Spermatozoa are one of the few mammalian cell types that cannot be fully derived in vitro, severely limiting the application of modern genomic techniques to study germ cell biology. The current gold standard approach of characterizing single-gene knockout mice is slow as generation of each mutant line can take 6–9 months. Here, we describe an in vivo approach to rapid functional screening of germline genes based on a new nonsurgical, nonviral in vivo transfection method to deliver nucleic acids into testicular germ cells. By coupling multiplex transfection of short hairpin RNA (shRNA) constructs with pooled amplicon sequencing as a readout, we were able to screen many genes for spermatogenesis function in a quick and inexpensive experiment. We transfected nine mouse testes with a pilot pool of RNA interference (RNAi) against well-characterized genes to show that this system is highly reproducible and accurate. With a false negative rate of 18% and a false positive rate of 12%, this method has similar performance as other RNAi screens in the well-described Drosophila model system. In a separate experiment, we screened 26 uncharacterized genes computationally predicted to be essential for spermatogenesis and found numerous candidates for follow-up studies. Finally, as a control experiment, we performed a long-term selection screen in neuronal N2a cells, sampling shRNA frequencies at five sequential time points. By characterizing the effect of both libraries on N2a cells, we show that our screening results from testis are tissue-specific. Our calculations indicate that the current implementation of this approach could be used to screen thousands of protein-coding genes simultaneously in a single mouse testis. The experimental protocols and analysis scripts provided will enable other groups to use this procedure to study diverse aspects of germ cell biology ranging from epigenetics to cell physiology. This approach also has great promise as an applied tool for validating diagnoses made from medical genome sequencing, or designing synthetic biological sequences that can act as potent and highly specific male contraceptives.

Crohn's disease-associated adherent invasive Escherichia coli modulate levels of microRNAs in intestinal epithelial cells to reduce autophagy

BACKGROUND & AIMS

Levels of microRNAs are altered in intestinal tissues of patients with Crohn's disease (CD). The adherent-invasive Escherichia coli (AIEC), which colonize the ileal mucosa of patients with CD, adhere to and invade intestinal epithelial cells. We investigated the mechanism by which AIEC infection alters the expression of microRNAs and the host immune response.

METHODS

Levels of microRNAs in human intestinal epithelial T84 cells and in mouse enterocytes were measured using quantitative reverse-transcription polymerase chain reaction. Luciferase assays were used to measure binding of microRNAs to the 3'-untranslated region of messenger RNA targets. Binding of nuclear factor-κB to promoters of genes encoding microRNAs was assessed by chromatin immunoprecipitation assays. Autophagy was measured by immunoblot analyses and immunofluorescent labeling of LC3. Anti-microRNAs were transferred to mice using ileal loops. Biopsy specimens from the terminal ileum of patients with ulcerative colitis (n = 20), CD (n = 20), or individuals without inflammatory bowel disease undergoing surveillance colonoscopies (controls, n = 13) were collected during endoscopic examination.

RESULTS

AIEC infection up-regulated levels of microRNA (MIR) 30C and MIR130A in T84 cells and in mouse enterocytes by activating nuclear factor-κB. Up-regulation of these microRNAs reduced the levels of ATG5 and ATG16L1 and inhibited autophagy, leading to increased numbers of intracellular AIEC and an increased inflammatory response. In ileal biopsy samples of patients with CD, there was an inverse correlation between levels of MIR30C and MIR130A and those of ATG5 and ATG16L1, supporting in vitro findings. Inhibition of MIR30C and MIR130A in cultured intestinal epithelial cells and in mouse enterocytes blocked AIEC-induced inhibition of ATG5 and ATG16L1 expression and restored functional autophagy. This resulted in more effective clearance of intracellular AIEC and reduced AIEC-induced inflammation.

CONCLUSIONS

Infection with AIEC up-regulates microRNAs to reduce expression of proteins required for autophagy and autophagy response in intestinal epithelial cells. Ileal samples from patients with CD have increased levels of these same microRNAs and reduced levels of ATG5 and ATG16L1.

Controlled insertional mutagenesis using a LINE-1 (ORFeus) gene-trap mouse model

A codon-optimized mouse LINE-1 element, ORFeus, exhibits dramatically higher retrotransposition frequencies compared with its native long interspersed element 1 counterpart. To establish a retrotransposon-mediated mouse model with regulatable and potent mutagenic capabilities, we generated a tetracycline (tet)-regulated ORFeus element harboring a gene-trap cassette. Here, we show that mice expressing tet-ORFeus broadly exhibit robust retrotransposition in somatic tissues when treated with doxycycline. Consistent with a significant mutagenic burden, we observed a reduced number of double transgenic animals when treated with high-level doxycycline during embryogenesis. Transgene induction in skin resulted in a white spotting phenotype due to somatic ORFeus-mediated mutations that likely disrupt melanocyte development. The data suggest a high level of transposition in melanocyte precursors and consequent mutation of genes important for melanoblast proliferation, differentiation, or migration. These findings reveal the utility of a retrotransposon-based mutagenesis system as an alternative to existing DNA transposon systems. Moreover, breeding these mice to different tet-transactivator/reversible tet-transactivator lines supports broad functionality of tet-ORFeus because of the potential for dose-dependent, tissue-specific, and temporal-specific mutagenesis.