Investigation of endoderm marker-genes during gastrulation and gut-development in the velvet worm Euperipatoides kanangrensis

Abstract Background and Aims Vascular media calcification is frequently seen in elderly and patients with chronic kidney disease (CKD), diabetes and osteoporosis. Pyrophosphate is a well-known calcification inhibitor that binds to nascent hydroxyapatite crystals and prevents further incorporation of inorganic phosphate into these crystals. However, the enzyme tissue-nonspecific alkaline phosphatase (TNAP), which is highly expressed in calcified arteries, degrades extracellular pyrophosphate into phosphate ions, by which pyrophosphate loses its ability to block vascular calcification. Here, we aimed to evaluate whether a TNAP inhibitor is able to prevent the development of arterial calcification in a rat model of warfarin-induced vascular calcification. Method To induce vascular calcification, rats received a diet containing 0.30% warfarin and 0.15% vitamin K1 throughout the entire study and were subjected to the following daily treatments: (i) vehicle (n=10) or (ii) 10 mg/kg/day TNAP-inhibitor (n=10) administered via an intraperitoneal catheter from start of the study until sacrifice at week 7. Calcium, phosphorus and parathyroid hormone (PTH) levels were determined in serum samples as these are important determinants of vascular calcification. As TNAP is also expressed in the liver, serum alanine aminotransferase (ALT) and aspartate (AST) levels were analyzed. At sacrifice, vascular calcification was evaluated by measurement of the total calcium content in the arteries and quantification of the area % calcification on Von Kossa stained sections of the aorta. The mRNA expression of osteo/chondrogenic marker genes (runx2, TNAP, SOX9, collagen 1 and collagen 2) was analyzed in the aorta by qPCR to verify whether vascular smooth muscle cells underwent reprogramming towards bone-like cells. Bone histomorphometry was performed on the left tibia to measure static and dynamic bone parameters as TNAP also regulates physiological bone mineralization. Results No differences in serum calcium, phosphorus and PTH levels was observed between both study groups. Warfarin exposure resulted in distinct calcification in the aorta and peripheral arteries. Daily dosing with the TNAP inhibitor (10 mg/kg/day) for 7 weeks significantly reduced vascular calcification as indicated by a significant decrease in calcium content in the aorta (vehicle 3.84±0.64 mg calcium/g wet tissue vs TNAP inhibitor 0.70±0.23 mg calcium/g wet tissue) and peripheral arteries and a distinct reduction in area % calcification on Von Kossa stained aortic sections as compared to vehicle condition. The inhibitory effects of SBI-425 on vascular calcification were without altering serum liver markers ALT and AST levels. Furthermore, TNAP-inhibitor SBI-425 did not modulate the mRNA expression of osteo/chondrogenic marker genes runx2, TNAP, SOX9, collagen 1 and 2. Dosing with SBI-425 resulted in decreased bone formation rate and mineral apposition rate, and increased osteoid maturation time and this without significant changes in osteoclast- and eroded perimeter. Conclusion Dosing with TNAP inhibitor SBI-425 significantly reduced the calcification in the aorta and peripheral arteries of a rat model of warfarin-induced vascular calcification and this without affecting liver function. However, suppression of TNAP activity should be limited in order to maintain adequate physiological bone mineralization.

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Protective Effect of Psoralea corylifolia L. Seed Extract against Palmitate-Induced Neuronal Apoptosis in PC12 Cells

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2016/5410419 ◽

2016 ◽

Vol 2016 ◽

pp. 1-11 ◽

Cited By ~ 3

Author(s):

Yunkyoung Lee ◽

Hee-Sook Jun ◽

Yoon Sin Oh

Keyword(s):

Pc12 Cells ◽

Molecular Mechanisms ◽

Neuronal Cell ◽

Marker Genes ◽

Heme Oxygenase 1 ◽

Mrna Levels ◽

Protective Effects ◽

Psoralea Corylifolia ◽

Antioxidant Genes ◽

Bax Protein

The extract of Psoralea corylifolia seeds (PCE) has been widely used as a herbal medicine because of its beneficial effect on human health. In this study, we investigated the protective effects and molecular mechanisms of PCE on palmitate- (PA-) induced toxicity in PC12 cells, a neuron-like cell line. PCE significantly increased cell viability in PA-treated PC12 cells and showed antiapoptotic effects, as evidenced by decreased expression of cleaved caspase-3, cleaved poly(ADP-ribose) polymerase, and bax protein as well as increased expression of bcl-2 protein. In addition, PCE treatment reduced PA-induced reactive oxygen species production and upregulated mRNA levels of antioxidant genes such as nuclear factor (erythroid-derived 2)-like 2 and heme oxygenase 1. Moreover, PCE treatment recovered the expression of autophagy marker genes such as beclin-1 and p62, which was decreased by PA treatment. Treatment with isopsoralen, one of the major components of PCE extract, also recovered the expression of autophagy marker genes and reduced PA-induced apoptosis. In conclusion, PCE exerts protective effects against lipotoxicity via its antioxidant function, and this effect is mediated by activation of autophagy. PCE might be a potential pharmacological agent to protect against neuronal cell injury caused by oxidative stress or lipotoxicity.

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The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

Microorganisms ◽

10.3390/microorganisms9081570 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1570

Author(s):

Chien-Hsun Huang ◽

Chih-Chieh Chen ◽

Yu-Chun Lin ◽

Chia-Hsuan Chen ◽

Ai-Yun Lee ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Target Genes ◽

Marker Genes ◽

Rrna Gene ◽

Accurate Identification ◽

Discrimination Power ◽

Sequence Identity ◽

Genome Wide ◽

A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

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Secondary Trisomics and Telotrisomics of Rice: Origin, Characterization, and Use in Determining the Orientation of Chromosome Map

Genetics ◽

10.1093/genetics/143.1.517 ◽

1996 ◽

Vol 143 (1) ◽

pp. 517-529

Author(s):

Kuldeep Singh ◽

D S Multani ◽

Gurdev S Khush

Keyword(s):

Linkage Map ◽

Large Population ◽

Marker Genes ◽

Linkage Groups ◽

Breeding Behavior ◽

Specific Chromosome ◽

Chromosome Map ◽

Primary Trisomics ◽

Correct Orientation ◽

Genetic Segregation

Abstract Secondary trisomics and telotrisomics representing the 12 chromosomes of rice were isolated from the progenies of primary trisomics. A large population of each primary trisomic was grown. Plants showing variation in gross morphology compared to the primary trisomics and disomic sibs were selected and analyzed cytologically at diakinesis and pachytene. Secondary trisomics for both arms of chromosomes 1, 2, 6, 7 and 11 and for one arm of chromosomes 4, 5, 8, 9 and 12 were identified. Telotrisomics for short arm of chromosomes 1, 8, 9 and 10 and for long arms of chromosomes 2, 3 and 5 were isolated. These secondary and telotrisomics were characterized morphologically and for breeding behavior. Secondary trisomics 2n + 1S · 1S, 2n + 1L · 1L, 2n + 2S · 2S, 2n + 2L · 2L, 2n + 6S · 6S, 2n + 6L · 6L and 2n + 7L · 7L are highly sterile, and 2n + 1L · 1L, 2n + 2L · 2L and 2n + 7L · 7L do not set any seed even upon backcrossing. Telotrisomics are fertile and vigorous. Genetic segregation of 43 marker genes was studied in the F2 or backcross progenies. On the basis of segregation data, these genes were delimited to specific chromosome arms. Correct orientation of 10 linkage groups was determined and centromere positions on nine linkage groups were approximated. A revised linkage map of rice is presented.

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Crayfish hemocytes develop along the granular cell lineage

Scientific Reports ◽

10.1038/s41598-021-92473-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Fang Li ◽

Zaichao Zheng ◽

Hongyu Li ◽

Rongrong Fu ◽

Limei Xu ◽

...

Keyword(s):

Developmental Stages ◽

Cell Lineage ◽

Granular Cell ◽

Marker Genes ◽

Hematopoietic Tissue ◽

Differentiated Cells ◽

Stage Of Development ◽

Almost All ◽

Relationship Of

AbstractDespite the central role of hemocytes in crustacean immunity, the process of hemocyte differentiation and maturation remains unclear. In some decapods, it has been proposed that the two main types of hemocytes, granular cells (GCs) and semigranular cells (SGCs), differentiate along separate lineages. However, our current findings challenge this model. By tracking newly produced hemocytes and transplanted cells, we demonstrate that almost all the circulating hemocytes of crayfish belong to the GC lineage. SGCs and GCs may represent hemocytes of different developmental stages rather than two types of fully differentiated cells. Hemocyte precursors produced by progenitor cells differentiate in the hematopoietic tissue (HPT) for 3 ~ 4 days. Immature hemocytes are released from HPT in the form of SGCs and take 1 ~ 3 months to mature in the circulation. GCs represent the terminal stage of development. They can survive for as long as 2 months. The changes in the expression pattern of marker genes during GC differentiation support our conclusions. Further analysis of hemocyte phagocytosis indicates the existence of functionally different subpopulations. These findings may reshape our understanding of crustacean hematopoiesis and may lead to reconsideration of the roles and relationship of circulating hemocytes.

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scSorter: assigning cells to known cell types according to marker genes

Genome Biology ◽

10.1186/s13059-021-02281-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Hongyu Guo ◽

Jun Li

Keyword(s):

Real Data ◽

Cell Types ◽

Exact Expression ◽

Marker Genes ◽

Specific Marker ◽

Sequencing Data ◽

Reference Dataset ◽

Over Expression ◽

Higher Power ◽

Cell Type Specific

AbstractOn single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.

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Isolation and Characterization of Broad-Spectrum Disease-Resistant Arabidopsis Mutants

Genetics ◽

10.1093/genetics/160.4.1661 ◽

2002 ◽

Vol 160 (4) ◽

pp. 1661-1671

Author(s):

Klaus Maleck ◽

Urs Neuenschwander ◽

Rebecca M Cade ◽

Robert A Dietrich ◽

Jeffery L Dangl ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Systemic Acquired Resistance ◽

Acquired Resistance ◽

Constitutive Expression ◽

Firefly Luciferase ◽

Marker Genes ◽

Arabidopsis Mutants ◽

Isolation And Characterization ◽

Firefly Luciferase Gene

Abstract To identify Arabidopsis mutants that constitutively express systemic acquired resistance (SAR), we constructed reporter lines expressing the firefly luciferase gene under the control of the SAR-inducible PR-1 promoter (PR-1/luc). After EMS mutagenesis of a well-characterized transgenic line, we screened 250,000 M2 plants for constitutive expression of the reporter gene in vivo. From a mutant collection containing several hundred putative mutants, we concentrated on 16 mutants lacking spontaneous hypersensitive response (HR) cell death. We mapped 4 of these constitutive immunity (cim) mutants to chromosome arms. Constitutive expression of disease resistance was established by analyzing responses to virulent Peronospora parasitica and Pseudomonas syringae strains, by RNA blot analysis for endogenous marker genes, and by determination of salicylic acid levels in the mutants. The variety of the cim phenotypes allowed us to define distinct steps in both the canonical SAR signaling pathway and a separate pathway for resistance to Erysiphe cichoracearum, active in only a subset of the mutants.

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