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Fanning Harboe posted an update 1 month ago
Cellular membrane asymmetry is a hallmark characteristic of all eukaryotic cells. The balance of phospholipid composition within the cytoplasmic inner leaflet and the extracellular outer leaflet of the plasma membrane (PM) maintains cellular function and vitality. The proper exposure of particular phospholipids is necessary to maintain cellular signalling, controlled apoptosis, and vesicle transportation among other roles. Phospholipid asymmetry is coordinated by P4-type phospholipid transferases (flippases or ATPases). ATP11A, ATP11B, and ATP11C belong to class VI of the P4-flippase family (vertebrates) and are responsible for the movement of phosphatidylserine (PS) from the outer leaflet to the inner leaflet of the PM. To date, there is a lack of knowledge of the tissue specific expression of these three flippases on a whole-organism level in a vertebrate system. Here we have determined the spatial-temporal expression profiles of each gene in a zebrafish model using in situ hybridization and performed comparative phylogenetic analyses with other vertebrates. Our data reveals sequence similarity between vertebrate flippases and specific synteny of zebrafish and human chromosomes. Both atp11b and atp11c are maternally expressed in zebrafish, while zygotic expression analysis demonstrates tissue and temporal specificity for all three genes. atp11a is expressed in the neural crest cells as well as in the developing eye and ear, while atp11b is expressed early in the ventricular epithelial lining and later in the ear. atp11c is expressed in the anterior most rhombomeres of the hindbrain, pharyngeal arches, and liver. Our expression data suggests that each of the three flippases are integral for the development of specific tissues, and aberrant function of either could lead to visual, hearing, neural, or liver dysfunction. DNA copy number variants (CNVs) account for approximately 300 Mb of sequence variation in the normal human genome. Significant numbers of pathogenic CNVs contribute toward human genetic disorders. Recent studies suggest a higher diagnostic and clinical significance of low-pass genome sequencing (LP-GS) compared with chromosomal microarrays (CMAs). The performance metrics of the 5X LP-GS was compared with CMA to validate a low-cost and high-throughput method. LP-GS test performed on 409 samples (including 78 validation and 331 clinical) was evaluated using American College of Medical Genetics and Genomics guidelines. The CNV accuracy, precision, specificity, and sensitivity were calculated to be 100% for all previously characterized CNVs by CMA. Samples (n = 6) run at both approximately 30X GS and approximately 5X GS (LP-GS) average depth detected a concordance of 89.43% to 91.8% and 77.42% to 89.86% for overall single-nucleotide variants and insertions/deletions, respectively. In the 331 clinical samples, 17.2% each were classified as pathogenic/likely pathogenic and uncertain clinical significance. In addition, several cases with pathogenic CNVs were detected that were missed by CMA. Hedgehog inhibitor This study demonstrates that LP-GS (5X GS) was able to reliably detect absence of heterozygosity, microdeletion/microduplication syndromes, and intragenic CNVs with higher coverage and resolution over the genome. Because of lower cost, higher resolution, and greater sensitivity of this test, our study in combination with other reports could be used in an evidence-based review by professional societies to recommend replacing CMAs. The Chinese sturgeon (Acipenser sinensis) is one of the critically endangered aquatic species in China. It is also among the oldest extant actinopterygian fish species. To advance the characterization of the Chinese sturgeon immune system, we identified the gene encoding the macrophage migration inhibitory factor (MIF), a multifunctional cytokine that contributes to both innate and adaptive immune responses. Molecular and phylogenic analysis indicates the Chinese sturgeon (cs) MIF share a high degree of structural conservation with other MIF sequences and is closely related to other bony fish MIF. At steady state, cs-mif gene is expressed at relatively high levels in the brain, and to a lesser but significant level in liver, spleen, kidney, gut and skin. The spatial expression patterns determined by in situ hybridization indicates a preferential distribution of cs-mif transcripts in the cerebral cortex, the gut epithelium, hematopoietic tissues of kidney, spleen and liver parenchyma, and skin epidermis. Marked increase of cs-mif gene expression was induced by lipopolysaccharide (LPS) stimulation and Aeromonas hydrophila infection in all tested tissues. Furthermore, higher cs-mif transcript levels were detected in the liver, spleen, kidney, gut and skin during stress response resulting from hyperthermia. These results are not only consistent with the expected role of cs-mif gene in innate immunity but also suggest a potential role of this gene in stress response to hyperthermia in the Chinese sturgeon. Hepatocellular carcinoma (HCC) is the liver’s most common primary malignancy, with over half a million new cases diagnosed each year and being the fourth leading cause of cancer death, worldwide. The poor prognosis of HCC is largely related to late diagnosis. Historically, serum alpha-fetoprotein and diagnostic imaging have been primary diagnostic modalities. However, the poor prognosis due to late diagnosis of HCC has proven unacceptable and, recently, significant efforts have been devoted to identifying patients with early stage HCC. Molecular biomarkers can provide additional and relevant information about the biological behavior of these tumors. Research in biomarker combinations may provide more accurate and valuable information for the future individualized HCC diagnosis and/or prognosis. Several biomarkers with prognostic significance have been identified, however all of them have been studied retrospectively. Furthermore, of all different molecular signatures that have been published, very few have been externally validated. The aim of this review is to analyze the most relevant emerging biomarkers of HCC.