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[This corrects the article DOI: 10.1371/journal.pbio.2001272.].

The generation of new adipocytes from precursor cells (adipogenesis) has implications for systemic metabolism and is a commonly used model for studying the process of cell differentiation in vitro. Previous studies from us and others suggested that the peripheral circadian clock can influence adipogenesis in vitro, but the mechanisms driving this activity and the relevance for adipogenesis in vivo are unknown. Here we reveal that mouse adipocyte precursor cells (APCs) contain a circadian clock that oscillates in vivo. We expose context-specific features of the clock in APCs: expression of the canonical core clock component Per1 does not significantly oscillate, whereas the lesser-understood paralog Per3 has a prominent rhythm. We discovered that deletion of Per3 promotes adipogenesis in vivo by a clock output pathway in which PER3 and BMAL1 directly regulate Klf15 expression. These findings demonstrate that Per3 has a major role in the APC clock and regulates adipogenesis in vivo.

The degradation of small RNAs in plants and animals is associated with small RNA 3' truncation and 3' uridylation and thus relies on exonucleases and nucleotidyl transferases. ARGONAUTE (AGO) proteins associate with small RNAs in vivo and are essential for not only the activities but also the stability of small RNAs. AGO1 is the microRNA (miRNA) effector in Arabidopsis, and its closest homolog, AGO10, maintains stem cell homeostasis in meristems by sequestration of miR165/6, a conserved miRNA acting through AGO1. Here, we show that SMALL RNA DEGRADING NUCLEASES (SDNs) initiate miRNA degradation by acting on AGO1-bound miRNAs to cause their 3' truncation, and the truncated species are uridylated and degraded. We report that AGO10 reduces miR165/6 accumulation by enhancing its degradation by SDN1 and SDN2 in vivo. In vitro, AGO10-bound miR165/6 is more susceptible to SDN1-mediated 3' truncation than AGO1-bound miR165/6. Thus, AGO10 promotes the degradation of miR165/6, which is contrary to the stabilizing effect of AGO1. Our work identifies a class of exonucleases responsible for miRNA 3' truncation in vivo and uncovers a mechanism of specificity determination in miRNA turnover. This work, together with previous studies on AGO10, suggests that spatially regulated miRNA degradation underlies stem cell maintenance in plants.

Mitochondrial dysfunction, inflammation, and mutant bone morphogenetic protein receptor 2 (BMPR2) are associated with pulmonary arterial hypertension (PAH), an incurable disease characterized by pulmonary arterial (PA) endothelial cell (EC) apoptosis, decreased microvessels, and occlusive vascular remodeling. We hypothesized that reduced BMPR2 induces PAEC mitochondrial dysfunction, promoting a pro-inflammatory or pro-apoptotic state. Mice with EC deletion of BMPR2 develop hypoxia-induced pulmonary hypertension that, in contrast to non-transgenic littermates, does not reverse upon reoxygenation and is associated with reduced PA microvessels and lung EC p53, PGC1α and TFAM, regulators of mitochondrial biogenesis, and mitochondrial DNA. Decreasing PAEC BMPR2 by siRNA during reoxygenation represses p53, PGC1α, NRF2, TFAM, mitochondrial membrane potential, and ATP and induces mitochondrial DNA deletion and apoptosis. Reducing PAEC BMPR2 in normoxia increases p53, PGC1α, TFAM, mitochondrial membrane potential, ATP production, and glycolysis, and induces mitochondrial fission and a pro-inflammatory state. These features are recapitulated in PAECs from PAH patients with mutant BMPR2.

Stem cells are crucial in morphogenesis in plants and animals. Much is known about the mechanisms that maintain stem cell fates or trigger their terminal differentiation. However, little is known about how developmental time impacts stem cell fates. Using Arabidopsis floral stem cells as a model, we show that stem cells can undergo precise temporal regulation governed by mechanisms that are distinct from, but integrated with, those that specify cell fates. We show that two microRNAs, miR172 and miR165/166, through targeting APETALA2 and type III homeodomain-leucine zipper (HD-Zip) genes, respectively, regulate the temporal program of floral stem cells. In particular, we reveal a role of the type III HD-Zip genes, previously known to specify lateral organ polarity, in stem cell termination. Both reduction in HD-Zip expression by over-expression of miR165/166 and mis-expression of HD-Zip genes by rendering them resistant to miR165/166 lead to prolonged floral stem cell activity, indicating that the expression of HD-Zip genes needs to be precisely controlled to achieve floral stem cell termination. We also show that both the ubiquitously expressed ARGONAUTE1 (AGO1) gene and its homolog AGO10, which exhibits highly restricted spatial expression patterns, are required to maintain the correct temporal program of floral stem cells. We provide evidence that AGO10, like AGO1, associates with miR172 and miR165/166 in vivo and exhibits "slicer" activity in vitro. Despite the common biological functions and similar biochemical activities, AGO1 and AGO10 exert different effects on miR165/166 in vivo. This work establishes a network of microRNAs and transcription factors governing the temporal program of floral stem cells and sheds light on the relationships among different AGO genes, which tend to exist in gene families in multicellular organisms.

Visual place recognition (VPR) is considered among the most challenging problems due to the extreme variations in appearance and viewpoint. Essentially, appearance-based VPR can be considered as an image retrieval task, thus the key is to accurately and efficiently describe the images. Recently, global descriptor methods have attracted substantial attention from the VPR community, which has contributed to numerous important outcomes. Despite the growing number of global descriptors presented, little attention has been paid to the comparison and evaluation of these methods and so it remains difficult for researchers to disentangle the factors that led to better performance. This study provided comprehensive insight into global descriptors from a practical application perspective. We present a systematic evaluation that integrates 15 commonly used global descriptors, 6 benchmark datasets, and 5 evaluation metrics, and subsequently extended this evaluation to discuss the key factors impacting the matching performance and computational efficiency. We also report practical suggestions for constructing promising CNN descriptors, based on the experimental conclusions. Our analysis reveals both advantages and limitations of three different types of global descriptors, including handcrafted features-based ones, off-the-shelf CNN-based ones, and customized CNN-based ones. Finally, we evaluate the practicality of reported global descriptors to mediate the trade-offs between matching performance and computational efficiency. [ABSTRACT FROM AUTHOR]

The analytical validation is reported for a targeted methylation-based cell-free DNA multi-cancer early detection test designed to detect cancer and predict the cancer signal origin (tissue of origin). A machine-learning classifier was used to analyze the methylation patterns of >105 genomic targets covering >1 million methylation sites. Analytical sensitivity (limit of detection [95% probability]) was characterized with respect to tumor content by expected variant allele frequency and was determined to be 0.07%-0.17% across five tumor cases and 0.51% for the lymphoid neoplasm case. Test specificity was 99.3% (95% confidence interval, 98.6–99.7%). In the reproducibility and repeatability study, results were consistent in 31/34 (91.2%) pairs with cancer and 17/17 (100%) pairs without cancer; between runs, results were concordant for 129/133 (97.0%) cancer and 37/37 (100%) non-cancer sample pairs. Across 3- to 100-ng input levels of cell-free DNA, cancer was detected in 157/182 (86.3%) cancer samples but not in any of the 62 non-cancer samples. In input titration tests, cancer signal origin was correctly predicted in all tumor samples detected as cancer. No cross-contamination events were observed. No potential interferent (hemoglobin, bilirubin, triglycerides, genomic DNA) affected performance. The results of this analytical validation study support continued clinical development of a targeted methylation cell-free DNA multi-cancer early detection test. [ABSTRACT FROM AUTHOR]

RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes (1). Small silencing RNAs of ~20-30 nucleotides and their associated effector proteins, the Argonaute family proteins, are the central components in RNA silencing (2). A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide (3-6). A conserved S-adenosyl-L-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification (3-5,7,8). Here we report the 3.1 Å crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-L-homocysteine. Highly cooperative recognition of the small RNA substrate by multiple RNA binding domains and the methyltransferase domain in HEN1 measures the length of the RNA duplex and determines the substrate specificity. Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel [Mg.sup.2+]-dependent 2'-O-methylation mechanism., HEN1 was first identified in a genetic screen as a floral pattering gene and later found to be essential for Arabidopsis microRNA (miRNA) accumulation in vivo (9,10). Subsequently, HEN1 was [...]

Purpose: To investigate the values of gemstone spectral imaging (GSI)-dual-energy computed tomography (DECT) in differentiation of renal cell carcinoma (RCC) and minimal-fat renal angiomyolipoma (MF-RAML).Patients and Methods: Twenty-one patients with ischemic RCC and 19 patients with MF-RAML were enrolled in this study. GSI was performed on them, and the spectrum signs were analyzed.Results: I(H2O), H2O(I), I(fat), and fat(I) concentrations, normalized I concentration, and effective atomic number of corticomedullary phase and parenchymal phase in enhanced GSI-DECT in ischemic RCC group were all significantly lower than those in MF-RAML group (P < 0.05). CT value and absolute slope rate of spectral attenuation curve in two phases in ischemic RCC group were also significantly lower than those in MF-RAML group (P < 0.05).Conclusion: GSI-DECT has provided a new idea and method for differential diagnosis of ischemic RCC and MF-RAML, with high-clinical values. [ABSTRACT FROM AUTHOR]

Aims Icariin ( ICA), a flavonoid isolated from epimedii, has been reported to have potential protective effects on the cardiovascular system. This study is to investigate the effect and the underlying mechanisms of ICA on ischemia/reperfusion (I/R) injury. Methods Wister rat hearts were subjected to I/R using Langendorff perfusion system. Cardiac function, myocardial infarct size, lactate dehydrogenase ( LDH), and creatine kinase- MB ( CK- MB) activities in coronary effluent, and superoxide dismutase ( SOD) and malondialdehyde ( MDA) content in heart tissue and cardiomyocyte apoptosis were assayed. Results Compared with the I/R group, ICA treatment significantly improved cardiac function, decreased myocardial infarct size, enzyme activity, oxidative stress, and apoptosis. In addition, ICA treatment lead to an increased p-Akt level, which was partially reversed by LY294002, a PI3 K pathway inhibitor. Conclusion Our study suggests that ICA has a cardioprotective effect against I/R injury, which is associated with its antioxidative and anti-apoptotic effect, at least partially, through the activation of PI3 K-Akt signaling pathway. [ABSTRACT FROM AUTHOR]

As central components of RNA silencing, small RNAs play diverse and important roles in many biological processes in eukaryotes. Aberrant reduction or elevation in the levels of small RNAs is associated with many developmental and physiological defects. The in vivo levels of small RNAs are precisely regulated through modulating the rates of their biogenesis and turnover. 2′-O-methylation on the 3′ terminal ribose is a major mechanism that increases the stability of small RNAs. The small RNA methyltransferase HUA ENHANCER1 (HEN1) and its homologs methylate microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs (piRNAs) in animals, and siRNAs in Drosophila. 3′ nucleotide addition, especially uridylation, and 3′-5′ exonucleolytic degradation are major mechanisms that turnover small RNAs. Other mechanisms impacting small RNA stability include complementary RNAs, cis-elements in small RNA sequences and RNA-binding proteins. Investigations are ongoing to further understand how small RNA stability impacts their accumulation in vivo in order to improve the utilization of RNA silencing in biotechnology and therapeutic applications. [ABSTRACT FROM AUTHOR]

A quantitative proteomic analysis of the response to dry needling combined with static stretching treatment was performed in a rat model of active myofascial trigger points (MTrPs). 36 rats were divided into a model group (MG), a stretching group (SG) and a dry needling combined with stretching group (SDG). We performed three biological replicates to compare large-scale differential protein expression between groups by tandem mass tag (TMT) labeling technology based on nanoscale liquid chromatography mass spectrometry analysis (LC–MS/MS). Hierarchical clustering, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and protein-protein interaction network analyses were performed for the general characterization of overall enriched proteins. For validation of the results of TMT, the candidate proteins were verified by parallel reaction monitoring (PRM) analysis. 285 differentially expressed proteins between groups were identified and quantified. Tight junction pathway played a dominant role in dry needling combined with static stretching treatment for the rat model of active MTrPs. Three candidate proteins, namely actinin alpha 3, calsequestrin-1 and parvalbumin alpha, were further validated, consistent with the results of LC–MS/MS. This is the first proteomics-based study to report the therapeutic mechanism underlying dry needling and static stretching treatment for MTrPs. Further functional verification of the potential signaling pathways and the enriched proteins is warranted. [ABSTRACT FROM AUTHOR]

Summary: Translation inhibition is a major but poorly understood mode of action of microRNAs (miRNAs) in plants and animals. In particular, the subcellular location where this process takes place is unknown. Here, we show that the translation inhibition, but not the mRNA cleavage activity, of Arabidopsis miRNAs requires ALTERED MERISTEM PROGRAM1 (AMP1). AMP1 encodes an integral membrane protein associated with endoplasmic reticulum (ER) and ARGONAUTE1, the miRNA effector and a peripheral ER membrane protein. Large differences in polysome association of miRNA target RNAs are found between wild-type and the amp1 mutant for membrane-bound, but not total, polysomes. This, together with AMP1-independent recruitment of miRNA target transcripts to membrane fractions, shows that miRNAs inhibit the translation of target RNAs on the ER. This study demonstrates that translation inhibition is an important activity of plant miRNAs, reveals the subcellular location of this activity, and uncovers a previously unknown function of the ER. PaperClip: Display Omitted [ABSTRACT FROM AUTHOR]

This study was designed to clarify the role of matrix metalloproteinases (MMPs) in coronary artery lesions (CAL). Serum samples were acquired from healthy, febrile, and Kawasaki disease (KD) children with or without CAL. Standard blood parameters were examined and enzyme-linked immunosorbent assay (ELISA) was used to assess the levels of MMP-2 and MMP-9. Intravenous immunoglobulin (IVIG) therapy was conducted on the KD patients and the changes of MMPs before and after treatment were compared. The correlations between MMP levels and clinical parameters were also evaluated. Compared to febrile and healthy controls, KD patients demonstrated clinical signs characteristic of abnormal immunoregulation. However, the clinical parameters of KD patients with or without CAL were not significantly different. MMP-2 and MMP-9 levels, however, were significantly higher in KD patients with CAL than those without CAL. IVIG treatment effectively downregulated the levels of MMPs in KD patients, which was more prominent in those with CAL. Significant correlations were found between MMP levels and some clinical parameters of KD, such as fever time, white blood cell count, etc. The upregulation of MMPs significantly correlates with coronary artery aneurysms (CAAs) in KD patients, making it important biomarkers of CAL in KD patients., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Tian, Ma, Zhao, Ji, Wang, Sun and Jiang.)

BACKGROUND Serine hydroxymethyltransferase 2 (SHMT2) is a key enzyme in one-carbon cell metabolism, including in liver cancer. However, the associations between SHMT2 expression at the gene and protein level and prognosis in patients with hepatocellular carcinoma (HCC) remains unknown. This study aimed to investigate the expression levels of SHMT2 in tumor tissue samples from patients with HCC and clinical outcome and the effects of silencing the expression of the SHMT2 gene in HepG2 cells. MATERIAL AND METHODS Expression levels of SHMT2 were evaluated in 144 cases of HCC using immunohistochemistry and correlated with clinicopathological factors using the chi-squared (χ²) test. The prognostic significance of SHMT2 expression was analyzed by univariate analysis and multivariate analysis. Twenty pairs of HCC tissue and adjacent normal liver tissue were compared for SHMT2 expression levels using quantitative reverse transcription polymerase chain reaction (qRT-PCR). HepG2 cells underwent SHMT2 gene silencing and MTT and transwell assays investigated cell proliferation and migration. Western blot was used to detect the expression of markers of epithelial-mesenchymal transition (EMT). RESULTS Expression levels of SHMT2 in HCC tissues were significantly correlated with tumor grade and hepatitis B virus (HBV) infection, and increased expression was an independent negative prognostic factor in patients with HCC (P=0.003). Increased expression of the SHMT2 gene promoted the proliferation and migration of the HepG2 HCC cell line. CONCLUSIONS Increased expression of SHMT2 was a negative prognostic biomarker in patients with HCC. Expression of the SHMT2 gene promoted the proliferation and migration of HepG2 HCC cells.

BACKGROUND Ubiquitin-specific peptidase 33 (USP33) is a deubiquitinase that balances the ubiquitin status of proteins. It has been reported to act as a tumor suppressor in colorectal cancer and lung cancer. However, the expression pattern and clinical significance of USP33 have not been investigated in gastric adenocarcinoma (GAC). MATERIAL AND METHODS We explored the USP33 protein and RNA levels by immunohistochemistry (IHC), Western blot analysis, and qRT-PCR. The Pearson chi-square test was performed to evaluate the statistical associations between USP33 level and patient characteristics. Additionally, the relationship between USP33 expression and patient survival was investigated. Cellular studies, including proliferation assay, migration assay, and invasion assay, were conducted to demonstrate the underlying mechanisms of USP33 in GAC progression. RESULTS This study included 121 patients with GAC. USP33 showed a decreased expression in GAC tissues compared to adjacent normal gastric tissues. Low expression of USP33 was correlated with invasion depth and advanced TNM stage. According to survival analysis, upper location of tumor (P=0.003), invasion depth (P=0.048), advanced TNM stage (P=0.001), and low USP33 level (P=0.001) were all associated with poor overall survival of GAC patients. Cox analysis confirmed the independent role of USP33 in predicting patient survival. Cell experiments showed that USP33 overexpression significantly inhibited the proliferation, migration, and invasion of GAC cells. CONCLUSIONS USP33 was downregulated in GAC, and was an independent prognostic factor. In vitro results demonstrated the role of USP33 in suppressing tumor progression, suggesting that the developing an agonist of USP33 may be a novel direction for chemotherapy development.