Search

Understanding gene expression in different cell types within their spatial context is a key goal in genomics research. SPADE (SPAtial DEconvolution), our proposed method, addresses this by integrating spatial patterns into the analysis of cell type composition. This approach uses a combination of single-cell RNA sequencing, spatial transcriptomics, and histological data to accurately estimate the proportions of cell types in various locations. Our analyses of synthetic data have demonstrated SPADE's capability to discern cell type-specific spatial patterns effectively. When applied to real-life datasets, SPADE provides insights into cellular dynamics and the composition of tumor tissues. This enhances our comprehension of complex biological systems and aids in exploring cellular diversity. SPADE represents a significant advancement in deciphering spatial gene expression patterns, offering a powerful tool for the detailed investigation of cell types in spatial transcriptomics. SPADE integrates single-cell RNA sequencing, spatial transcriptomics, and histological data to estimate cell type composition, enhancing understanding of cellular dynamics and tumor tissue diversity. [ABSTRACT FROM AUTHOR]

We aimed to explore diagnostic biomarks and immune cell infiltration characteristics in ulcerative colitis (UC). We used the dataset GSE38713 as the training set and dataset GSE94648 as the test set. A total of 402 differentially expressed genes (DEGs) were obtained from GSE38713. Annotating, visualizing, and integrating discovery of these differential genes was performed using Gene Ontology (GO), Kyoto Gene and Genome Encyclopedia Pathway (KEGG), and Gene Set Enrichment Analysis (GSEA). Protein–protein interaction networks were constructed from the STRING database, and protein functional modules were identified using the CytoHubba plugin of Cytoscape. Random forest and LASSO regression were used to screen for UC-related diagnostic markers, and ROC curves were generated to validate their diagnostic value. The composition of 22 immune cells was analyzed, and the immune cell infiltration in UC was analyzed using CIBERSORT. Results: Seven diagnostic markers associated with UC were identified: TLCD3A, KLF9, EFNA1, NAAA,WDR4, CKAP4, and CHRNA1. Immune cell infiltration assessment revealed that macrophages M1, activated dendritic cells, and neutrophil cells infiltrated relatively more compared to normal control samples. Our results suggest a new functional feature of UC and suggest potential biomarkers for UC through comprehensive analysis of integrated gene expression data. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) have been found as novel participants in the pathophysiology of prostate cancer (PCa), which is predominantly regulated by androgen and its receptor. The biological function of androgen-responsive lncRNAs remains poorly understood. Here, we identified that lncRNA RP11-1023L17.1, which is highly expressed in PCa. RP11-1023L17.1 expression, can be directly repressed by the androgen receptor in PCa cells. RP11-1023L17.1 depletion inhibited the proliferation, migration, and cell cycle progression, and promoted the apoptosis of PCa cells, indicating that RP11-1023L17.1 acts as an oncogene in PCa cells. Microarray results revealed that RP11-1023L17.1 depletion downregulated the c-Myc transcription signature in PCa cells. RP11-1023L17.1 depletion-induced cellular phenotypes can be overcome by ectopically overexpressed c-Myc. Mechanistically, RP11-1023L17.1 represses FBXO32 mRNA expression, thereby enhancing c-Myc protein stability by blocking FBXO32-mediated c-Myc degradation. Our findings reveal the previously unrecognized roles of RP11-1023L17.1 in c-Myc-dependent PCa tumorigenesis. [ABSTRACT FROM AUTHOR]

PBX3 (Pre-B-cell leukemia homeobox 3) had been considered to be a multifunctional oncogene which involved in tumor growth, invasion, and metastasis in leukemia and some solid tumors. However, the contribution of PBX3 to papillary thyroid carcinoma (PTC) remains unclear. In this study, we found that PBX3 expression was significantly upregulated in PTC tissues compared to adjacent normal tissues, and high levels of PBX3 were correlated with tumor size, lymphatic metastasis, TMN stage, and poor prognosis of PTC patients. Overexpression of PBX3 in PTC cell lines promoted cell proliferation. Consistently, knockdown of PBX3 by shRNA induced cell cycle arrest at G0/G1 phase, and inhibited angiogenesis and tumor growth in vitro and in vivo. Furthermore, PBX3 promoted PTC cell proliferation and angiogenesis through activation of AT1R/VEGFR2 pathway while overexpression of AT1R and treatment with VEGFA reversed PBX3-shRNA-induced decreased phosphorylation of VEGFR2 and its downstream (ERK1/2, AKT and Src). It demonstrated that PBX3 could be used as a potential prognostic biomarker and therapeutic target for PTC. [ABSTRACT FROM AUTHOR]

Liver fibrosis represents a frequent event following chronic insult to trigger wound healing responses in the liver. Activation of hepatic stellate cells (HSCs), which is a pivotal event during liver fibrogenesis, is accompanied by enhanced expressions of a series of marker proteins and pro-fibrogenic signaling molecules. Artemisinin, a powerful antimalarial medicine, is extracted from the Chinese herb Artemisia annua L ., and can inhibit the proliferation of cancer cells. Dihydroartemisinin (DHA), the major active metabolite of artemisinin, is able to attenuate lung injury and fibrosis. However, the effect of DHA on liver fibrosis remains unclear. The aim of this study was to investigate the effect of DHA on bile duct ligation-induced injury and fibrosis in rats. DHA improved the liver histological architecture and attenuated collagen deposition in the fibrotic rat liver. Experiments in vitro showed that DHA inhibited the proliferation of HSCs and arrested the cell cycle at the S checkpoint by altering several cell-cycle regulatory proteins. Moreover, DHA reduced the protein expressions of a-SMA, α1 (I) collagen and fibronectin, being associated with interference of the platelet-derived growth factor β receptor (PDGF-βR)-mediated ERK pathway. These data collectively revealed that DHA relieved liver fibrosis possibly by targeting HSCs via the PDGF-βR/ERK pathway. DHA may be a therapeutic antifibrotic agent for the treatment of hepatic fibrosis. [ABSTRACT FROM AUTHOR]

Abstract: DEAD box polypeptide 43 (DDX43), a cancer/testis antigen (CTA), has been found to be overexpressed in various solid tumors and some hematologic malignancies. In the present work hypomethylation of the DDX43 gene was detected in 15% (32/214) of primary acute myeloid leukemia (AML) using real-time quantitative methylation-specific PCR (RQ-MSP). The level of DDX43 expression was correlated with DDX43 hypomethylation (R =0.277, P =0.014). Moreover, bisulfite sequencing confirmed the significant correlation between the methylation density and the level of DDX43 hypomethylation. Additionally, restoration of DDX43 expression in the K562 cell line by 5-aza-2′-deoxycytidine treatment confirmed a direct contribution of methylation in regulating the DDX43 gene. DDX43 hypomethylation was observed more frequently in favorable group (21.4%) and intermediate group (15.8%) than in poor group (0%) (P =0.009). AML patients with DDX43 hypomethylation had a better overall survival (median not obtained) than those with DDX43 methylation (median 8 months, 95% confidence interval 5.6–10.4 months) (P =0.014). In summary, the DDX43 gene is activated by promoter hypomethylation and DDX43 hypomethylation may be a favorable prognostic factor in AML. [Copyright &y& Elsevier]

Osterix (Osx) is an osteoblast-specific transcription factor which is essential for bone formation. MicroRNAs (miRNAs) have been previously shown to be involved in osteogenesis. However, it is unclear whether Osx is involved in the regulation of miRNA expression. In this study, we have identified groups of miRNAs that are differentially expressed in calvaria of the E18.5 Osx−/− embryos compared to wild type embryos. The correlation between the levels of miRNAs and Osx expression was further verified in cultured M-Osx cells in which over-expression of Osx is inducible. Our results suggest that Osx down-regulates expression of a group of miRNAs including mir-133a and -204/211, but up-regulates expression of another group of miRNAs such as mir-141/200a. Mir-133a and -204/211 are known to target the master osteogenic transcription factor Runx2. Further assays suggest that Sost, which encodes the Wnt signaling antagonist Sclerostin, and alkaline phosphatase (ALP) are two additional targets of mir-204/211. Mir-141/200a has been known to target the transcription factor Dlx5. Thus, we postulate that during the process of Osx-controlled osteogenesis, Osx has the ability to coordinately modulate Runx2, Sclerostin, ALP and Dlx5 proteins at levels appropriate for optimal osteoblast differentiation and function, at least in part, through regulation of specific miRNAs. Our study shows a tight correlation between Osx and the miRNAs involved in bone formation, and provides new information about molecular mechanisms of Osx-controlled osteogenesis. [ABSTRACT FROM AUTHOR]

Breast carcinoma (BC) remains one of the most serious health problems. It is a heterogeneous entity, and mainly classified according to receptor status for estrogen (ER), progesterone (PR) and egf (HER2/Neu), as well as the proliferation marker ki67. Gene expression in eukaryotes is regulated at the level of both gene transcription and translation, where eukaryotic initiation factors (eIFs) are key regulators of protein biosynthesis. Aberrant translation results in an altered cellular proteome, and this clearly effects cell growth supporting tumorigenesis. The relationship between various eIFs and BC entities, as well as the related regulatory mechanisms, has meanwhile become a focus of scientific interest. Here, we give an overview on the current research state of eIF function, focusing on BC. [ABSTRACT FROM AUTHOR]

Background: Most monoclonal antibodies against mouse antigens have been derived from rat spleen-mouse myeloma fusions, which are valuable tools for purposes ranging from general laboratory reagents to therapeutic drugs, and yet selecting and expressing them remains a time-consuming and inefficient process. Here, we report a novel approach for the rapid high-throughput selection and expression of recombinant functional rat monoclonal antibodies with different isotypes. Results: We have developed a robust system for generating rat monoclonal antibodies through several processes involving simultaneously immunizing rats with three different antigens expressing in a mixed cell pools, preparing hybridoma cell pools, in vitro screening and subsequent cloning of the rearranged light and heavy chains into a single expression plasmid using a highly efficient assembly method, which can decrease the time and effort required by multiple immunizations and fusions, traditional clonal selection and expression methods. Using this system, we successfully selected several rat monoclonal antibodies with different IgG isotypes specifically targeting the mouse PD-1, LAG-3 or AFP protein from a single fusion. We applied these recombinant anti-PD-1 monoclonal antibodies (32D6) in immunotherapy for therapeutic purposes that produced the expected results. Conclusions: This method can be used to facilitate an increased throughput of the entire process from multiplex immunization to acquisition of functional rat monoclonal antibodies and facilitate their expression and feasibility using a single plasmid. [ABSTRACT FROM AUTHOR]

Background. Qinghuayin (QHY) is a Chinese formula that is widely used in the treatment of chronic atrophic gastritis (CAG). This study was planned with the following objectives: (1) confirming the efficacy of QHY in a rat model of CAG and (2) performing a preliminary observation of the changes in several inflammatory signaling pathways potentially involved in the QHY mechanisms. Methods. A total of 33 rats were used in this study; they were divided into the control (n = 12) and model (n = 21) groups. QHY was administrated to both the groups. We assessed the pathological manifestations and the serum tumor necrosis factor alpha (TNF-α) level as markers of efficacy. We also performed a preliminary observation of the changes in the protein and messenger ribonucleic acid (mRNA) expression of toll-like receptors 4 (TLR4), MyD88, NF-κB, and COX-2. Results. The pathological changes induced in the rats by the establishment of the CAG models were recovered by low and high doses of QHY. Their serum TNF-α level also reduced following low- and high-dose QHY treatment. Protein and mRNA expressions of TLR4, MyD88, NF-κB, and COX-2 were upregulated by the establishment of CAG models and downregulated by the administration of low- and high-dose QHY. Conclusions. Our data confirm the efficacy of QHY as an adjuvant therapy, based on the theories in traditional Chinese medicine. The preliminary observations indicate that the downregulation of the enhanced inflammatory signaling pathways might be crucial QHY mechanisms that need further verification. [ABSTRACT FROM AUTHOR]

Summary: Submergence is an abiotic stress that limits agricultural production world‐wide. Plants sense oxygen levels during submergence and postsubmergence reoxygenation and modulate their responses. Increasing evidence suggests that completely submerged plants are often exposed to low‐light stress, owing to the depth and turbidity of the surrounding water; however, how light availability affects submergence tolerance remains largely unknown.Here, we showed that Arabidopsis thaliana MYB DOMAIN PROTEIN30 (MYB30) is an important transcription factor that integrates light signaling and postsubmergence stress responses.MYB DOMAIN PROTEIN30 protein abundance decreased upon submergence and accumulated during reoxygenation. Under submergence conditions, CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a central regulator of light signaling, caused the ubiquitination and degradation of MYB30. In response to desubmergence, however, light‐induced MYB30 interacted with MYC2, a master transcription factor involved in jasmonate signaling, and activated the expression of the VITAMIN C DEFECTIVE1 (VTC1) and GLUTATHIONE SYNTHETASE1 (GSH1) gene families to enhance antioxidant biosynthesis. Consistent with this, the myb30 knockout mutant showed increased sensitivity to submergence, which was partially rescued by overexpression of VTC1 or GSH1.Thus, our findings uncover the mechanism by which the COP1‐MYB30 module integrates light signals with cellular oxidative homeostasis to coordinate plant responses to postsubmergence stress. [ABSTRACT FROM AUTHOR]

4-coumarate: CoA ligase (4CL) is not only involved in the biosynthetic processes of flavonoids and lignin in plants but is also closely related to plant tolerance to abiotic stress. UV irradiation can activate the expression of 4CL genes in plants, and the expression of 4CL genes changed significantly in response to different phytohormone treatments. Although the 4CL gene has been cloned in potatoes, there have been fewer related studies of the 4CL gene family on the potato genome-wide scale. In this study, a total of 10 potato 4CL genes were identified in the potato whole genome. Through multiple sequence alignment, phylogenetic analysis as well as gene structure analysis indicated that the potato 4CL gene family could be divided into two subgroups. Combined with promoter cis-acting element analysis, transcriptome data, and RT-qPCR results indicated that potato 4CL gene family was involved in potato response to white light, UV irradiation, ABA treatment, MeJA treatment, and PEG simulated drought stress. Abiotic stresses such as UV, ABA, MeJA, and PEG could promote the up-regulated expression of St4CL6 and St4CL8 but inhibits the expression of St4CL5. The above results will increase our understanding of the evolution and expression regulation of the potato 4CL gene family and provide reference value for further research on the molecular biological mechanism of 4CL participating in response to diverse environmental signals in potatoes. [ABSTRACT FROM AUTHOR]

An abstract of the article "Expression of Neurotrophin-3 Promotes Axonal Plasticity in the Acute but Not Chronic Injured Spinal Cord," by Qin Chen, Lijun Zhou, and H. David Shine is presented.

Background: In aged people, tendon injuries frequently occur during sporting and daily activities. In clinical practice, typical physiotherapeutic, pharmacotherapeutic, and surgical techniques do not result in the full recovery of injured tendons, which may lead to chronic degenerative disease. Methods: We first isolated tendon stem cells (TSCs) from rats and transfected them with the TGFβ1 gene, resulting in TGFβ1-TSCs. The proliferation of TSCs was detected using the Cell Counting Kit 8, and TSCs were identified by immunofluorescence analysis and differentiation capacity analysis. Aggrecan, COL2A1, alpha smooth muscle actin (α-SMA), and p-Smad2 expression levels were detected using western blotting and quantitative reverse transcription polymerase chain reaction. Additionally, a tendon injury model was generated to explore the effect of TGFβ1 on the repair of the tendon by TSCs. Results: Compared with fibrinogen treatment, TSC + fibrinogen or TGFβ1-TSC + fibrinogen treatment significantly promoted the fibrosis of injured tendons, as evidenced by histological analyses, with TGFβ1-TSC + fibrinogen having a greater effect than TSC + fibrinogen. In TGFβ1-TSCs, increased expression levels of aggrecan and COL2A1 indicated that TGFβ1 signaling induced chondrogenic differentiation. Meanwhile, the increased collagen and α-SMA protein levels indicated that TGFβ1 promoted fibrogenesis. Additionally, TGFβ1 stimulated the production of phosphorylated Smad2 in TSCs, which suggested that the chondrogenic and fibrogenic differentiation of TSCs, as well as tissue regeneration, may be associated with the TGFβ1/Smad2 pathway. Conclusion: TGFβ1-TSC therapy may be a candidate for effective tendon fibrosis. [ABSTRACT FROM AUTHOR]

Background: Anthocyanins, which account for color variation and remove reactive oxygen species, are widely synthesized in plant tissues and organs. Using targeted metabolomics and nanopore full-length transcriptomics, including differential gene expression analysis, we aimed to reveal potato leaf anthocyanin biosynthetic pathways in different colored potato varieties. Results: Metabolomics analysis revealed 17 anthocyanins. Their levels varied significantly between the different colored varieties, explaining the leaf color differences. The leaves of the Purple Rose2 (PurpleR2) variety contained more petunidin 3-O-glucoside and malvidin 3-O-glucoside than the leaves of other varieties, whereas leaves of Red Rose3 (RedR3) contained more pelargonidin 3-O-glucoside than the leaves of other varieties. In total, 114 genes with significantly different expression were identified in the leaves of the three potato varieties. These included structural anthocyanin synthesis–regulating genes such as F3H, CHS, CHI, DFR, and anthocyanidin synthase and transcription factors belonging to multiple families such as C3H, MYB, ERF, NAC, bHLH, and WRKY. We selected an MYB family transcription factor to construct overexpression tobacco plants; overexpression of this factor promoted anthocyanin accumulation, turning the leaves purple and increasing their malvidin 3-o-glucoside and petunidin 3-o-glucoside content. Conclusions: This study elucidates the effects of anthocyanin-related metabolites on potato leaves and identifies anthocyanin metabolic network candidate genes. [ABSTRACT FROM AUTHOR]

Increased levels of oxidative stress have been found with heart failure. Whether failing hearts express antioxidant and detoxification enzymes have not been addressed systematically. Nrf2 gene encodes a transcription factor that regulates the expression of antioxidant and detoxification genes. Using RNA-Seq data set from explanted hearts of 37 patients with dilated cardiomyopathy (DCM), 13 patients with ischemic cardiomyopathy (ICM), and 14 nonfailure (NF) donors as a control, we addressed whether failing hearts change the expression of Nrf2, its negative regulator Keap1, and antioxidant or detoxification genes. Significant increases in the ratio of Nrf2 to Keap1 were found to associate with DCM or ICM. Antioxidant genes showed decreased expression in both types of heart failure, including NQO1, SOD1, GPX3, GPX4, GSR, PRDX1, and TXNRD1. Detoxification enzymes, GCLM and EPHX1, also showed decreased expression, whereas the CYP1B1 transcript was elevated in both DCM and ICM. The genes encoding metal-binding protein ferritin were decreased, whereas five out of 12 metallothionein genes showed elevated expression. Our finding on Nrf2 gene expression has been validated by meta-analysis of seven independent data sets of microarray or RNA-Seq for differential gene expression in DCM and ICM from NF controls. In conclusion, minor elevation of Nrf2 gene expression is not coupled to increases in antioxidant and detoxification genes, supporting an impairment of Nrf2 signaling in patients with heart failure. Decreases in multiple antioxidant and detoxification genes are consistent with the observed increases of oxidative stress in failing hearts. [ABSTRACT FROM AUTHOR]

Currently, the impact of electromagnetic field (EMF) exposure on the nervous system is an increasingly arousing public concern. The present study was designed to explore the effects of continuous long-term exposure to L-band high-power microwave (L-HPM) on brain function and related mechanisms. Forty-eight male Institute of Cancer Research (ICR) mice were exposed to L-HPM at various power densities (0.5, 1.0, and 1.5 W/m2) and the brain function was examined at different time periods after exposure. The morphology of the brain was examined by hematoxylin-eosin (HE) and deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) staining. Furthermore, cholinergic markers, oxidative stress markers, and the expression of c-fos were evaluated to identify a "potential" mechanism. The results showed that exposure to L-HPM at 1.5 W/m2 can cause generalized injuries in the hippocampus (CA1 and CA3) and cerebral cortex (the first somatosensory cortex) of mice, including cell apoptosis, cholinergic dysfunction, and oxidative damage. Moreover, the deleterious effects were closely related to the power density and exposure time, indicating that long-term and high-power density exposure may be detrimental to the nervous system. [ABSTRACT FROM AUTHOR]

Cotton fibre yield and quality are markedly influenced by drought and high-temperature stress. We examined the traits of the leaf stomata in 39 cotton genotypes subjected to exogenous phytohormone abscisic acid (ABA) signalling, electrolyte leakage under 40°C thermal stress, and relative GhHsfA, GhbZIP and GhHSP70 expression levels under two treatments. Stomatal density and area ranged from 66 to 182/mm2 and 663 to 1305 μm2, respectively. Under exogenous ABA signalling, the changes in stomatal aperture (ΔSAp) were in the range of 2.5–31.2%; ΔSAp and relative GhHsfA, GhbZIP and GhHSP70 expression levels were significantly correlated, respectively. Electrolyte leakage increased unequally among cotton genotypes after heat stress. The changes in electrolyte leakage (ΔEL) and relative GhHsfA, GhbZIP and GhHSP70 expression levels were very strongly correlated, respectively. Their relative expression levels could be used as references for the rapid identification of stress-tolerant cotton strains. Cluster analysis of the 39 cotton genotypes indicated that Xinluzao36, Shiyang1, shinong98-7 and Zhongmiansuo293 are heat- and drought-resistant. We integrated both analysis of physiological parameters and molecular methods to identify cotton varieties with the drought and heat tolerance, in order to provide a reference for the selection of materials and methods for the research and production of cotton. [ABSTRACT FROM AUTHOR]

Plant-specific heat shock protein 70 s (HSP70s) play crucial roles in response to various environmental stimuli. GhHSP70-26, an HSP70 member, is involved in the response to multiple abiotic stresses in cotton (Gossypium hirsutum). This study explored the relationship between the genetic diversity of GhHSP70–26 and drought resistance in cotton to aid crop breeding. Indel sites at −650 bp upstream of the GhHSP70–26 promoter were discovered in cotton and designated an M-650 marker. The M-650 marker was significantly associated with the effective boll numbers (M-650-In360 > M-650-Del) in 110 types of cotton under drought stress conditions for three years. The relative expression levels of GhHSP70–26 was linearly correlated with comprehensive drought resistance in cotton seedlings. The gene expression levels were enhanced in BC 2 F 2 (pGhHSP70–26 In360 ) of cotton and the transgenic lines pGhHSP70–26 In360 :GhHSP70–26 of Arabidopsis , and drought resistance was also enhanced. After PEG, ABA and SA treatments, the transgenic lines of M-650-In360 promoter showed higher GUS expression activity than the M-650-del promoter in Arabidopsis. The GhFLZ, GhABF3, and GhRVE8 transcription factors could regulate to In360 bp of pGhHSP70–26 to activate high levels of gene expression. These results provide important genetic information to study the natural variation of drought tolerance in cotton, and the loci or exceptional promoters identified can be used as direct targets for cotton trait improvement and genetic engineering. [ABSTRACT FROM AUTHOR]

BACKGROUND Peanut allergy is one of the most common food allergies worldwide. Studies have shown that the incidence of peanut allergies in Western‐born Asians is higher than that in Asia‐born Asians. Notably, Europeans and Americans mostly eat roasted peanuts, whereas Asians mostly eat boiled or fried peanuts. RESULTS: BALB/c mice were sensitized using purified protein from raw, roasted or boiled peanuts, then fed the same by oral gavage. The relevant allergic reactions were studied using BALB/c mice model, including a rat basophilic leukemia (RBL) cell model, simulated gastric fluid experiments, and ultraviolet (UV) and circular dichroism (CD) spectral analysis. Serological studies showed increased levels of immunoglobulin E, interleukin‐4 and interleukin‐5, and pathological studies showed mast cell degranulation and inflammatory changes in jejunal tissues, with an increase in thymic stromal lymphopoietin (TSLP) gene expression in all treatment groups compared with the control group (phosphate‐buffered saline). Compared with the raw peanut group, sera from the roasted peanut group produced a significant increase in RBL β‐hexosaminidase A release in vitro, and roasted peanuts showed increased resistance to digestion in simulated gastric fluid experiments. Ultraviolet and CD spectral analyses showed that the roasting and boiling processes altered the structure of the major peanut allergens, which may have contributed to the differences observed in peanut allergenicity. CONCLUSION: Our findings indicate that peanut allergies are related to peanut thermal processing methods. In our mouse model, the raw, roasted and boiled peanuts elicited different degrees of allergic response. Compared with raw peanut, roasted peanuts show a higher allergenicity, whereas the boiled peanuts show a lower allergenicity. © 2018 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Curcuma longa possesses powerful antifungal activity, as demonstrated in many studies. In this study, the antifungal spectrum of Curcuma longa alcohol extract was determined, and the resulting EC50 values (mg/mL) of its extract on eleven fungi, including Fusarium graminearum, Fusarium chlamydosporum, Alternaria alternate, Fusarium tricinctum, Sclerotinia sclerotiorum, Botrytis cinerea, Fusarium culmorum, Rhizopus oryzae, Cladosporium cladosporioides, Fusarium oxysporum and Colletotrichum higginsianum, were 0.1088, 0.1742, 0.1888, 0.2547, 0.3135, 0.3825, 0.4229, 1.2086, 4.5176, 3.8833 and 5.0183, respectively. Among them, F. graminearum was selected to determine the inhibitory effects of the compounds (including curdione, isocurcumenol, curcumenol, curzerene, β-elemene, curcumin, germacrone and curcumol) derived from Curcuma longa. In addition, the antifungal activities of curdione, curcumenol, curzerene, curcumol and isocurcumenol and the synergies of the complexes of curdione and seven other chemicals were investigated. Differential proteomics of F. graminearum was also compared, and at least 2021 reproducible protein spots were identified. Among these spots, 46 were classified as differentially expressed proteins, and these proteins are involved in energy metabolism, tRNA synthesis and glucose metabolism. Furthermore, several fungal physiological differences were also analysed. The antifungal effect included fungal cell membrane disruption and inhibition of ergosterol synthesis, respiration, succinate dehydrogenase (SDH) and NADH oxidase. [ABSTRACT FROM AUTHOR]

Potato dormancy is a complex process with an extensive release phase. This study investigated involvement of reactive oxygen species during tuber dormancy release. We found that tuber sprouting was delayed by treatment with diphenylene iodonium chloride, an NADPH oxidase inhibitor; NADPH oxidase catalyze the production of ROS. In situ ROS localization and ROS content estimation revealed that dormancy release was associated with an accumulation of superoxide anion and hydrogen peroxide in tuber buds. The antioxidant compounds and enzymes display important changes during the progression of dormancy. The application of Ca 2+ induced superoxide anion production and promoted in vitro tuber bud sprouting. Among the seven homologues of NADPH oxidases in potato, the expression of StrbohA and StrbohB were detected in particular when dormancy break. In addition, the expression of key genes that function in the potato dormancy release are discussed in relation to ROS metabolism in other plants. [ABSTRACT FROM AUTHOR]

WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research. [ABSTRACT FROM AUTHOR]

Objective: To implement a meta-analysis to investigate the relationship between high-mobility group box 1 (HMGB1) overexpression in the tissue and serum of ovarian cancer patients, and to evaluate its prognostic significance. Methods: Searches were made of China National Knowledge Infrastructure, EMBASE, WanFang, PubMed, MEDLINE, and Web of Science databases up to August 2015, with no language or style restrictions. Reference lists of related studies were also carefully reviewed to identify additional articles. Results: The literature search identified a total of 12 relevant studies on HMGB1 expression for inclusion in the meta-analysis: seven in ovarian tumor tissue, four in ovarian tumor patient serum, and one in both tissue and serum. HMGB1 protein levels in ovarian cancer tissues were notably higher than those in normal ovarian tissues with no evidence of heterogeneity between studies (RD=0.64, 95% confidence interval (CI): 0.57-0.70, Z=18.70, P,0.00001, I2=15%), and also higher than those in benign tumor tissues with no evidence of heterogeneity between studies (RD=0.52, 95% CI: 0.43-0.61, Z=11.14, P,0.00001, I2=0). Serum HMGB1 levels were similarly significantly higher in ovarian cancer patients than those with benign tumors or normal ovaries. Pooled mean differences of HMGB1 in ovarian cancer patients compared with patients with benign tumors or normal ovaries were 99.32 with 95% CI: 67.82-130.81, Z=6.18, P,0.00001, and 95.34 with 95% CI: 62.11-128.57, Z=5.62, P,0.0001. The pooled relative risk of ovarian cancer with high vs low HMGB1 expression levels was 1.40 with 95% CI: 1.09-1.79, Z=2.66, P=0.008, heterogeneity I2=50%. Conclusion: This meta-analysis suggested that HMGB1 levels in both tissue and serum of ovarian cancer patients were significantly higher than those of benign tumor and normal ovarian samples. High serum or tissue HMGB1 expression may therefore be an effective molecular marker for ovarian benign or malignant tumor diagnosis and patient prognosis. [ABSTRACT FROM AUTHOR]

Nrf2 is a bZIP transcription factor regulating the expression of antioxidant and detoxification genes. We have found that Nrf2 knockout mice have an increased infarction size in response to regional ischemic reperfusion and have a reduced degree of cardiac protection by means of ischemic preconditioning. With cycles of brief ischemia and reperfusion (5′I/5′R) that induce cardiac protection in wild type mice, an elevated Nrf2 protein was observed without prior increases of Nrf2 mRNA. When an mRNA species is being translated into a protein, it is occupied by multiple ribosomes. The level of ribosome-associated Nrf2 mRNA increased following cycles of 5′I/5′R, supporting de novo Nrf2 protein translation. A dicistronic reporter assay indicated a role of the 5′ untranslated region (5′ UTR) of Nrf2 mRNA in oxidative stress induced Nrf2 protein translation in isolated cardiomyocytes. Western blot analyses after isolation of proteins binding to biotinylated Nrf2 5′ UTR from the myocardium or cultured cardiomyocytes demonstrated that cycles of 5′I/5′R or oxidants caused an increased association of La protein with Nrf2 5′ UTR. Ribonucleoprotein complex immunoprecipitation assays confirmed such association indeed occurring in vivo. Knocking down La using siRNA was able to prevent Nrf2 protein elevation by oxidants in cultured cardiomyocytes and by cycles of 5′I/5′R in the myocardium. Our data point out a novel mechanism of cardiac protection by de novo Nrf2 protein translation involving interaction of La protein with 5′ UTR of Nrf2 mRNA in cardiomyocytes. [ABSTRACT FROM AUTHOR]

Danggui Buxue Decoction (DBT) is classical prescriptions, which contains two Traditional Chinese Medicines of Angelicae sinensis radix and Astragali radix. According to the preliminary work of our laboratory and numerous studies, it has been found that DBT has a therapeutic effect on diabetic nephropathy (DN). However, the mechanisms underlying its action remain unclear. The aim of this study was to evaluate the impact of DBT on kidney disease in diabetic mice and further explore its protective mechanism. DN mice model was induced by high-fat fodder and streptozotocin (STZ). Qualitative and quantitative analysis of 6 compounds in DBT was carried out by HPLC, including calycosin-7-glucoside, ferulic acid, ononin, calycosin, formononetin, and levostilide A. Hematoxylin-Eosin (HE) staining was used to determine the degree of kidney pathological damage. The UPLC-Q Exactive MS technique was used to analyze the lipids metabolism profile of kidneys samples and multiple statistical analysis methods were used to screen and identify biomarkers. Transcriptomics analyses were carried out using RNAseq. The possible molecular mechanism was unraveled by network pharmacology. Thirty-one significantly altered lipid metabolites were identified in the model group comparing with the control group. DBT improved aberrant expression of several pathways related to lipidomics, including glycerophospholipid metabolism and sphingolipid metabolism. Comprehensive analysis indicated that DBT intervention reduced the content of Cers, phosphatidylethanolamines and phosphatidylcholines in mouse kidneys by downregulating the transcription level of Degs2 and Cers , reducing lipid accumulation and promoting Akt phosphorylation by upregulating the expression of Acers and Pdk1. Network pharmacology analysis showed that components in DBT, such as kaempferol, ferulic acid and astragaloside IV, could be responsible for the pharmacological activity of DN by regulating the AGE-RAGE, PI3K/Akt, MAPK and NF-κB signaling pathways in diabetic complications. These results showed that DBT may improve DN by affecting insulin resistance, chronic inflammation and lipid accumulation. [Display omitted] • DBT treatment mainly affected glycerophospholipid and sphingolipid metabolism. • DBT improved DN by affecting the expression of the Degs2 and Cers genes. • Ceramides were important biomarkers of DN. [ABSTRACT FROM AUTHOR]

Abstract: Objective: SALL4 gene has been identified to stimulate the expansion of hematopoietic stem cell (HSCs) and enhance the self-renewal of HSCs. Overexpression of SALL4 has been found in several cancers. The present study was aimed to investigate the methylation status of SALL4 promoter region in acute myeloid leukemia (AML). Designs and methods: The methylation status of SALL4 promoter was analyzed in 84 patients with AML using methylation-specific PCR (MSP) and its clinical significance was evaluated. Results: Aberrant hypomethylation of SALL4 gene, which was correlated with SALL4 expression, was found in 17.8% (15/84) cases. The patients with SALL4 hypomethylation had significantly older age and higher WBCs than those without SALL4 hypomethylation. The incidence of SALL4 hypomethylation was higher in M1 subtype than in M2 and other subtypes (50%, 26% and 6%, respectively, P =0.001). SALL4 hypomethylation was associated with cytogenetically intermediate and poor groups. Although survival time of the SALL4-hypomethylated AML was shorter than that of SALL4-methylated group (4months vs 9months), the difference was not statistically significant (P =0.356). Conclusions: Hypomethylation of SALL4 promoter is a common event and is associated with the intermediate and poor karyotypes in AML. [Copyright &y& Elsevier]

Abstract: Salt and alkali stress are two of the main environmental factors limiting crop production. Recent discoveries show that the JAZ family encodes plant-specific genes involved in jasmonate signaling. However, there is only limited information about this gene family in abiotic stress response, and in wild soybean (Glycine soja), which is a species noted for its tolerance to alkali and salinity. Here, we isolated and characterized a novel JAZ family gene, GsJAZ2, from G. soja. Transcript abundance of GsJAZ2 increased following exposure to salt, alkali, cold and drought. Over-expression of GsJAZ2 in Arabidopsis resulted in enhanced plant tolerance to salt and alkali stress. The expression levels of some alkali stress response and stress-inducible marker genes were significantly higher in the GsJAZ2 overexpression lines as compared to wild-type plants. Subcellular localization studies using a GFP fusion protein showed that GsJAZ2 was localized to the nucleus. These results suggest that the newly isolated wild soybean GsJAZ2 is a positive regulator of plant salt and alkali stress tolerance. [Copyright &y& Elsevier]

Abstract: Doxorubicin (Dox) is an antineoplastic agent that can cause cardiomyopathy in humans and experimental animals. As an inducer of reactive oxygen species and a DNA damaging agent, Dox causes elevated expression of p21WAF1/Cip1/Sdi1 (p21) gene. Elevated levels of p21 mRNA and p21 protein have been detected in the myocardium of mice following Dox treatment. With chronic treatment of Dox, wild type (WT) animals develop cardiomyopathy evidenced by elongated nuclei, mitochondrial swelling, myofilamental disarray, reduced cardiac output, reduced ejection fraction, reduced left ventricular contractility, and elevated expression of ANF gene. In contrast, p21 knockout (p21KO) mice did not show significant changes in the same parameters in response to Dox treatment. In an effort to understand the mechanism of the resistance against Dox induced cardiomyopathy, we measured levels of antioxidant enzymes and found that p21KO mice did not contain elevated basal or inducible levels of glutathione peroxidase and catalase. Measurements of 6 circulating cytokines indicated elevation of IL-6, IL-12, IFNγ and TNFα in Dox treated WT mice but not p21KO mice. Dox induced elevation of IL-6 mRNA was detected in the myocardium of WT mice but not p21KO mice. While the mechanism of the resistance against Dox induced cardiomyopathy remains unclear, lack of inflammatory response may contribute to the observed cardiac protection in p21KO mice. [Copyright &y& Elsevier]

While gender-based differences in heart disease have raised the possibility that estrogen (ES) or progesterone (PG) may have cardioprotective effects, recent controversy regarding hormone replacement therapy has questioned the cardiac effects of these steroids. Using cardiomyocytes, we tested whether ES or PG has protective effects at the cellular level. We found that PG but not ES protects cardiomyocytes from apoptotic cell death induced by doxorubicin (Dox). PG inhibited apoptosis in a dose-dependent manner, by 12 ± 4.0% at 1 μm and 60 ± 1.0% at 10 μm. The anti-apoptotic effect of PG was also time dependent, causing 18 ± 5% or 62 + 2% decrease in caspase-3 activity within 1 h or 72 h of pretreatment. While PG causes nuclear translocation of its receptor within 20 min, the cytoprotective effect of PG was canceled by mifepristone (MF), a PG receptor antagonist. Analyses using Affymetrix high-density oligonucleotide array and RT-PCR found that PG induced Bcl-xL, metallothionine, NADPH quinone oxidoreductase 1, glutathione peroxidase-3, and four isoforms of glutathione S-transferase. Western blot analyses revealed that PG indeed induced an elevation of Bcl-xL protein in a dose- and time-dependent manner. Nuclear run-on assay indicated that PG induced Bcl-xL gene transcription. Inhibiting the expression of Bcl-xL using siRNA reduced the cytoprotective effect of PG. Our data suggests that PG induces a cytoprotective effect in cardiomyocytes in association with induction of Bcl-xL gene. [ABSTRACT FROM AUTHOR]

Abstract: Recent work from our laboratory found that corticosteroids induce transcriptional activation of cyclooxygenase-2 (COX-2) gene in cardiomyocytes. Here we report that COX-2 gene promoter mutation studies indicate a role of cAMP response element-binding protein (CREB) in corticosterone-induced COX-2 gene expression. Corticosterone causes activation of p38 MAPK and subsequent CREB phosphorylation at serine 133 in cardiomyocytes. The inhibitors of p38 MAPK, SB202190 and SB203580, block corticosterone from inducing CREB phosphorylation and COX-2 gene expression while dominant-negative p38 MAPK or CREB prevents corticosterone from activating COX-2 promoter. Corticosterone does not induce p38 MAPK activation or COX2 expression in cardiac fibroblasts or HEK293 cells transfected with glucocorticoid receptor, suggesting that p38 MAPK activation is cell specific and necessary for corticosterone-induced COX-2 expression in cardiomyocytes. While glucocorticoid receptor antagonist mifepristone inhibits COX-2 gene induction by corticosterone, mifepristone fails to inhibit p38 MAPK activation or CREB phosphorylation. In contrast, inhibition of p38 MAPK does not prevent corticosterone from activating glucocorticoid receptor. Our data suggest that two parallel signaling pathways, glucocorticoid receptor and p38 MAPK, act in concert to regulate the expression of COX-2 gene in cardiomyocytes. [Copyright &y& Elsevier]

Psychological stress increases the level of glucocorticoids in the circulating system. We found that dexamethasone administration in adult mice elevates the expression of COX-2 in the myocardium. With isolated neonatal cardiomyocytes, corticosterone (CT) at physiologically relevant doses (0.01-1 µM) induces the expression of COX-2 gene. The induction first appeared at 4 h and remained for at least 24 h with 1 µM CT treatment. This response is likely cardiomyocyte cell type specific since CT did not induce COX-2 expression in cardiac fibroblasts and glucocorticoids are known to suppress the expression of COX-2 in lymphocytes and several organs. Corticosteroids, but not estrogen or progesterone, induce COX-2 expression. The glucocorticoid receptor (GR) antagonist mifepristone (MF) prevented CT from inducing COX-2 gene, suggesting a GR-dependent induction in cardiomyocytes. COX-2 gene promoter deletion and mutation studies indicate a role of CCAAT/enhancer binding protein-β (C/EBP-β) in CT-induced COX-2 gene expression. Chromatin immunoprecipitation assays revealed that CT caused the binding of both GR and C/EBP-β to COX-2 promoter, while MF pretreatment blocked such binding. Coimmunoprecipitation experiments demonstrated that CT treatment induced the interaction of GR with C/EBP-β Small interfering RNA against C/EBP-β prevented CT from activating COX-2 promoter or elevating COX-2 protein. Our data suggest that the interaction between GR and C/EBP-β contributes to elevated COX-2 gene transcription by CT in cardiomyocytes. [ABSTRACT FROM AUTHOR]

Simple Summary: Phospholipase D is the most important kind of phospholipase in plants, which can specifically catalyze the hydrolysis of phosphodiester bonds at the end of phospholipid molecules to produce phospholipid acid and a free group. Phospholipase D is not only involved in maintaining the structural stability of plant cell membrane and the dynamic balance of lipid composition but also involved in a variety of physiological processes, such as plant growth and development and stress response, including stomatal closure, root elongation, cell senescence, high salt stress, cold stress, and drought stress. It plays a critical role in plant growth and development, as well as in hormone and stress responses. In this study, the basic information on phospholipase D gene family was comprehensively introduced, and the physical and chemical properties, systematic evolution, gene structure, conservative motif, chromosome location, gene replication, cis-acting element prediction, GO annotation, interspecific collinearity, and quantitative analysis of potato phospholipase D gene family were analyzed to gain a better understanding of potato phospholipase D gene family. Through the analysis of potato phospholipase D gene family, our results lay the foundation for further understanding of the function of phospholipase gene family in higher plants. Phospholipase D (PLD) is the most important phospholipid hydrolase in plants, which can hydrolyze phospholipids into phosphatidic acid (PA) and choline. When plants encounter low temperature, drought and high salt stress, phospholipase D and its products play an important role in regulating plant growth and development and coping with stress. In this study, 16 members of StPLD gene family were identified in potato genome, which were distributed in α, β, δ, and ζ subfamilies, and their expression patterns under salt, high temperature, drought, and ABA stress were detected by qRT-PCR method. Gene expression analysis showed that the expression of StPLD genes in potato was upregulated and downregulated to varying degrees under the four stresses, indicating that the PLD gene family is involved in the interaction of potato plant hormones and abiotic stress signals. Chromosome distribution showed that StPLD gene was unevenly distributed on 8 chromosomes, and only one pair of tandem repeat genes was found. All StPLD promoters contain hormone and stress-related cis-regulatory elements to respond to different stresses. Structural analysis showed that StPLD genes in the same subgroup had a similar exon–intron structure. Our study provides a valuable reference for further research of the function and structure of PLD gene. [ABSTRACT FROM AUTHOR]

Abstract: We detected aberrant Midkine (MK) expressions in human insulinoma and pancreatic cancer tissues by immunohistochemistry, revealing its potential role in tumorigenesis/carcinogenesis. With a nested-touchdown PCR program we were able to detect the tMK in all human tumor/cancer tissues and cancer/tumor cell lines. Detection of MK in the peripheral cells and precancerous lesions implies its potential for early cancer/tumor diagnosis. Furthermore, we have discovered two novel truncations of the MK, tMKB and tMKC, respectively, in the disease specimens. Our data not only provide an efficient methodology potentially for clinical application but also shed light on the molecular mechanism underlying the role for MK in tumorigenesis/carcinogenesis. [Copyright &y& Elsevier]

Abstract: Mild or low doses of oxidants are known to prime cells towards resistance against further damage. In cardiomyocytes, we found that pretreatment with 100 μM H2O2 prevents the cells from apoptosis induced by doxorubicin (Dox). Affymetrix microarray analyses of 28,000 genes reveal that H2O2 treated cells reduced expression of genes encoding cytochrome c, mitochondrial complex I, III, IV and V and several contractile proteins. Elevated expression of antioxidant and detoxification genes appears as a dominant feature of the gene expression profile of H2O2 treated cells. Most of the genes in this category contain an Antioxidant Response Element (ARE) in their promoters. Measurements of ARE promoter–reporter gene activity indicate a dose- and time-dependent activation of the ARE by H2O2. Since the Nrf2 transcription factor regulates ARE-mediated gene expression, we overexpressed Nrf2 to test whether activation of Nrf2 is sufficient to induce cytoprotection. High levels of Nrf2 expression were achieved via adenovirus mediated gene delivery. Transduced Nrf2 was present in the nuclei and caused an increase in the expression of NAD(P)H:quinone oxidoreductase 1 (NQO1), a representative downstream target of Nrf2. Unlike H2O2 pretreated cells, the cells expressing high levels of Nrf2 were not resistant to Dox-induced apoptosis. Therefore, the cytoprotective effect of H2O2 pretreatment is not reliant upon Nrf2 activation alone as measured by resistance against Dox-induced apoptosis. [Copyright &y& Elsevier]

Lateral organ boundaries domain (LBD) proteins belong to a particular class of transcription factors of lateral organ boundary (LOB) specific domains that play essential roles in plant growth and development. However, a potato phylogenetic analysis of the LBD family has not been fully studied by scholars and researchers. In this research, bioinformatics methods and the growth of potatoes were used to identify 43 StLBD proteins. We separated them into seven subfamilies: Ia, Ib, Ic, Id, Ie, IIa and IIb. The number of amino acids encoded by the potato LBD family ranged from 94 to 327. The theoretical isoelectric point distribution ranged from 4.16 to 9.12 Kda, and they were distributed among 10 chromosomes. The results of qRT-PCR showed that the expression levels of StLBD2-6 and StLBD3-5 were up-regulated under drought stress in the stem. The expression levels of StLBD1-5 and StLBD2-6 were down-regulated in leaves. We hypothesized that StLBD1-5 was down-regulated under drought stress, and that StLBD2-6 and StLBD3-5 up-regulation might help to maintain the normal metabolism of potato and enhance the potatoes' resistance to drought. [ABSTRACT FROM AUTHOR]

Background: Changes in metabolic pathway preferences are key events in the reprogramming process of somatic cells to induced pluripotent stem cells (iPSCs). The optimization of metabolic conditions can enhance reprogramming; however, the detailed underlying mechanisms are largely unclear. By comparing the gene expression profiles of somatic cells, intermediate-phase cells, and iPSCs, we found that carnitine palmitoyltransferase (Cpt)1b, a rate-limiting enzyme in fatty acid oxidation, was significantly upregulated in the early stage of the reprogramming process. Methods: Mouse embryonic fibroblasts isolated from transgenic mice carrying doxycycline (Dox)-inducible Yamanaka factor constructs were used for reprogramming. Various fatty acid oxidation-related metabolites were added during the reprogramming process. Colony counting and fluorescence-activated cell sorting (FACS) were used to calculate reprogramming efficiency. Fatty acid oxidation-related metabolites were measured by liquid chromatography–mass spectrometry. Seahorse was used to measure the level of oxidative phosphorylation. Results: We found that overexpression of cpt1b enhanced reprogramming efficiency. Furthermore, palmitoylcarnitine or acetyl-CoA, the primary and final products of Cpt1-mediated fatty acid oxidation, also promoted reprogramming. In the early reprogramming process, fatty acid oxidation upregulated oxidative phosphorylation and downregulated protein kinase C activity. Inhibition of protein kinase C also promoted reprogramming. Conclusion: We demonstrated that fatty acid oxidation promotes reprogramming by enhancing oxidative phosphorylation and inhibiting protein kinase C activity in the early stage of the reprogramming process. This study reveals that fatty acid oxidation is crucial for the reprogramming efficiency. [ABSTRACT FROM AUTHOR]