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Improving litter size at birth (TNB) and the number of piglets born alive (NBA) are the main breeding goals related to litter traits, which are economically important. A better understanding of genetic architecture underlying TNB and NBA traits could increase pig production efficiency. However, most previous studies on these traits focus on additive genetic effects, while epistatic interactions underlying TNB and NBA traits has not yet been well investigated, which are essential to understand how traits-related genes interact. Herein, we conducted genome scans of epistatic interactions underlying TNB and NBA traits in a total of 150 Chinese indigenous pigs (75 Jinhua and 75 Shengxian Spotted pigs) with high throughput genomic data. Based on SNPs with high interaction values and connectivity scores, we identified eight promising candidate genes (AKT2, TSC1, MTOR, PIK3R5, TIAM1, FGF14, RALB and ROR2) potentially associated with litter traits in pigs. Moreover, the underlying pathways, e.g., calcium ion transport, pointed out their roles in litter size-related traits. Our findings provide new insight into genetic architecture of litter traits in pigs and will benefit economic profits in pig production.

The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGF&beta, 2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of &ldquo, circadian sleep/wake cycle process,&rdquo, &ldquo, negative regulation of transforming growth factor-&beta, secretion,&rdquo, positive regulation of calcium ion transport&rdquo, in BH-vs-WH and &ldquo, cell surface receptor signaling pathway,&rdquo, Notch signaling pathway&rdquo, and &ldquo, calcium ion transport&rdquo, in BL-vs-BH. Besides, &ldquo, steroid biosynthetic process,&rdquo, granulosa cell development&rdquo, egg coat formation&rdquo, were mainly enriched in BL-vs-WL and &ldquo, reproduction,&rdquo, MAPK cascade&rdquo, mitotic cell cycle&rdquo, were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.

Protein phosphorylation is an important post-translational modification (PTM) involved in diverse cellular functions. It is the most prevalent PTM in both Toxoplasma gondii and Plasmodium falciparum, but its status in Eimeria tenella has not been reported. Herein, we performed a comprehensive, quantitative phosphoproteomic profile analysis of four stages of the E. tenella life cycle: unsporulated oocysts (USO), partially sporulated (7 h) oocysts (SO7h), sporulated oocysts (SO), and sporozoites (S). A total of 15,247 phosphorylation sites on 9514 phosphopeptides corresponding to 2897 phosphoproteins were identified across the four stages. In addition, 456, 479, and 198 differentially expressed phosphoproteins (DEPPs) were identified in the comparisons SO7h vs. USO, SO vs. SO7h, and S vs. SO, respectively. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DEPPs suggested that they were involved in diverse functions. For SO7h vs. USO, DEPPs were mainly involved in cell division, actin cytoskeleton organization, positive regulation of transport, and pyruvate metabolism. For SO vs. SO7h, they were related to the peptide metabolic process, translation, and RNA transport. DEPPs in the S vs. SO comparison were associated with the tricarboxylic acid metabolic process, positive regulation of ATPase activity, and calcium ion binding. Time course sequencing data analysis (TCseq) identified six clusters with similar expression change characteristics related to carbohydrate metabolism, cytoskeleton organization, and calcium ion transport, demonstrating different regulatory profiles across the life cycle of E. tenella. The results revealed significant changes in the abundance of phosphoproteins during E. tenella development. The findings shed light on the key roles of protein phosphorylation and dephosphorylation in the E. tenella life cycle.

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.

Objective: To tentatively investigate the mechanism of uncaria rhynchophylla (UR) in treatment of Alzheimer's disease (AD). Methods: The targets and pathways of UR against AD were obtained from network pharmacology analysis. Results: We analyzed and obtained 7 active ingredients of UR, 29 targets of UR for treatment of AD, of which 26.9% targets were protein-modifying enzymes. The core active ingredients of UR were C3, C6, C7 and C5. The core targets of UR in the treatment of AD are AKT1, CASP3 and MTOR. The enrichment analysis of GO biological process suggests that the biological function of UR in the treatment of AD mainly involves regulation of neurotransmitter levels, rhythmic process, cellular response to nitrogen compound, calcium ion transport, response to toxic substance, response to oxygen levels, maintenance of location, positive regulation of cell death, and apoptotic signaling pathway, etc. KEGG pathway enrichment analysis showed that the most significant enrichment signaling pathways were neuroactive ligand-receptor interaction, calcium signaling pathway, cAMP signaling pathway, PI3K-Akt signaling pathway and so on. Conclusion: UR against AD may be related to its multiple components, multiple targets and biological functions. This study can provide a theoretical basis for further experimental and clinical research.

Introduction: Despite the availability of new vaccines for SARS-CoV-2, there has been slow uptake and problems with supply in some parts of the world. Hence, there is still a necessity for drugs that can prevent hospitalization of patients and reduce the strain on health care systems. Drugs with sigma affinity potentially provide protection against the most severe symptoms of SARS-COV-2 and could prevent mortality via interactions with the sigma-1 receptor. Areas covered: This review examines the role of the sigma-1 receptor and autophagy in SARS-CoV-2 infections and how they may be linked. The authors reveal how sigma ligands may reduce the symptoms, complications, and deaths resulting from SARS-CoV-2 and offer insights on those patient cohorts that may benefit most from these drugs. Expert opinion: Drugs with sigma affinity potentially offer protection against the most severe symptoms of SARS-CoV-2 via interactions with the sigma-1 receptor. Agonists of the sigma-1 receptor may provide protection of the mitochondria, activate mitophagy to remove damaged and leaking mitochondria, prevent ER stress, manage calcium ion transport, and induce autophagy to prevent cell death in response to infection.

The active component-target network and protein-protein interaction network of Compound Anshen essential oil were constructed. The target functions and related pathways were analyzed to explore the mechanism of Compound Anshen essential oil in the treatment of insomnia. GC-MS was used to detect the chemical composition of Compound Anshen essential oil, and the TCMSP, STITCH, TTD, and DrugBank databases were searched to predict and screen the targets of Compound Anshen essential oil in the treatment of insomnia. Cytoscape software was used to construct the network diagrams of the active component-action target and protein-protein interaction networks, ClueGO software was used to analyze the GO enrichment and KEGG pathway of the target, and the systemsDock website database was used for molecular docking. The analysis of the network results showed that the activity of Compound Anshen essential oil mainly involves biological processes such as the phospholipase C-activating G protein-coupled receptor signaling pathway, response to ammonium ions, calcium ion transport into the cytosol, and chloride transport. The results of molecular docking showed that linalool, caryophyllene, dibutyl phthalate, (-)-4-terpineol, and (-)-α-terpineol have good binding activity with ADRB2, DRD2, ESR1, KCNH2, NR1H4, NR1I2, NR1I3, and TRPV1 targets. This study demonstrates the multicomponent, multitarget, and multichannel characteristics of Compound Anshen essential oil and provides a new therapeutic idea and method for further research on the mechanism of Compound Anshen essential oil in the treatment of insomnia.

Diabetic neuropathic pain (DNP), an early symptom of diabetic neuropathy, involves complex mechanisms. Long non-coding RNA (lncRNA) dysregulation contributes to the pathogenesis of various human diseases. Here, we investigated the genome-wide expression patterns of lncRNAs and genes in the spinal dorsal horn of mice with streptozotocin-induced DNP. Microarray analysis identified 1481 differentially expressed (DE) lncRNAs and 1096 DE mRNAs in DNP mice. Functional analysis showed that transforming growth factor-beta receptor binding was the most significant molecular function and retrograde endocannabinoid signaling was the most significant pathway of DE mRNAs. Calcium ion transport was the second most significant biological process of DE lncRNAs. Finally, we found 289 neighboring and 57 overlapping lncRNA-mRNA pairs, including ENSMUST00000150952-Mbp and AK081017-Usp15, which may be involved in DNP pathogenesis. Microarray data were validated through quantitative PCR of selected lncRNAs and mRNAs. These results suggest that aberrant expression of lncRNAs may contribute to the pathogenesis of DNP.

The onset of lactation results in a sudden irreversible loss of Ca for colostrum and milk synthesis. Some cows are unable to quickly adapt to this demand and succumb to clinical hypocalcemia, whereas a larger proportion of cows develop subclinical hypocalcemia that predisposes them to other peripartum diseases. The objective of this study was to perform a comprehensive genomic analysis of blood total Ca concentration in periparturient Holstein cows. We first performed a genomic scan and a subsequent gene-set analysis to identify candidate genes, biological pathways, and molecular mechanisms affecting postpartum Ca concentration. Then, we assessed the prediction of postpartum Ca concentration using genomic information. Data consisted of 7,691 records of plasma or serum concentrations of Ca measured in the first, second, and third day after parturition of 959 primiparous and 1,615 multiparous cows that calved between December 2015 and June 2020 in 2 dairy herds. All cows were genotyped with 80k SNPs. The statistical model included lactation (1 to 5+), calf category (male, females, twins), and day as fixed effects, and season-treatment-experiment, animal, and permanent environmental as random effects. Model predictive ability was evaluated using 10-fold cross-validation. Heritability and repeatability estimates were 0.083 (standard error = 0.017) and 0.444 (standard error = 0.028). The association mapping identified 2 major regions located on Bos taurus autosome (BTA)6 and BTA16 that explained 1.2% and 0.7% of additive genetic variance of Ca concentration, respectively. Interestingly, the region on BTA6 harbors the GC gene, which encodes the vitamin D binding protein, and the region on BTA16 harbors LRRC38, which is actively involved in K transport. Other sizable peaks were identified on BTA5, BTA2, BTA7, BTA14, and BTA9. These regions harbor genes associated with Ca channels (CACNA1S, CRACR2A), K channels (KCNK9), bone remodeling (LRP6), and milk production (SOCS2). The gene-set analysis revealed terms related to vitamin transport, calcium ion transport, calcium ion binding, and calcium signaling. Genomic predictions of phenotypic and genomic estimated breeding values of Ca concentration yielded predictive correlations up to 0.50 and 0.15, respectively. Overall, the present study contributes to a better understanding of the genetic basis of postpartum blood Ca concentration in Holstein cows. In addition, the findings may contribute to the development of novel selection and management strategies for reducing periparturient hypocalcemia in dairy cattle.

The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.

We evaluated the impact of genetic variance on biomarker levels in a population of workers in the automotive repair and refinishing industry who were exposed to respiratory sensitizers 1,6-hexamethylene diisocyanate (HDI) monomer and one of its trimers, HDI isocyanurate. The exposures and respective urine and plasma biomarkers 1,6-diaminohexane (HDA) and trisaminohexyl isocyanurate (TAHI) were measured in 33 workers; and genome-wide microarrays (Affymetrix 6.0) were used to genotype the workers’ single-nucleotide polymorphisms (SNPs). Linear mixed model analyses have indicated that interindividual variations in both inhalation and skin exposures influenced these biomarker levels. Using exposure values as covariates and a false discovery rate < 0.10 to assess statistical significance, we observed that seven SNPs were associated with HDA in plasma, five were associated with HDA in urine, none reached significance for TAHI in plasma, and eight were associated with TAHI levels in urine. The different genotypes for the 20 significant SNPs accounted for 4- to 16-fold changes observed in biomarker levels. Associated gene functions include transcription regulation, calcium ion transport, vascular morphogenesis, and transforming growth factor beta signaling pathway, which may impact toxicokinetics indirectly by altering inflammation levels. Additionally, in an expanded analysis using a minor allele cutoff of 0.05 instead of 0.10, there were biomarker-associated SNPs within three genes that have been associated with isocyanate-induced asthma: ALK, DOCK2, and LHPP. We demonstrate that genetic variance impacts the biomarker levels in workers exposed to HDI monomer and HDI isocyanurate and that genetics can be used to refine exposure predictions in small cohorts when quantitative personal exposure and biomarker measurements are included in the models.

In the present study, we report the effects of extracellular medium conductivity on cell response in the context of sub-microsecond range (100 ns–900 ns) electroporation, calcium electroporation and cell size. The effects of 25 ns and microsecond range (100 μs) pulses were also covered. As a model, three different cancer cell lines of various size (C32, MCF-7/DX and MC38/0) were used and the results indicated different size-dependent susceptibility patterns to the treatment. The applied pulsed electric field (PEF) protocols revealed a significant decrease of cell viability when calcium electroporation was used. The dependence of calcium ion transport and finally the anticancer effect on the external medium conductivity was determined. It was shown that small differences in conductivity do not alter viability significantly, however, mostly affect the permeabilization. At the same, MC38/0 cell line was the least susceptible to calcium electroporation, while the C32 line the most. In all cases calcium electroporation was mostly dependent on the sensitivity of cells to electroporation and could not be effectively improved by the increase of CaCl2 concentration from 2 mM to 5 mM. Lastly, sub-microsecond PEF stimulated aquaporin-4 and VDAC1/Porin immunoreactions in all treated cells lines, which indicated that cell water balance is affected, ions exchange is increased and release of mitochondrial products is occurrent.

Developing synthetic biological devices to allow the noninvasive control of cell fate and function, in vivo can potentially revolutionize the field of regenerative medicine. To address this unmet need, we designed an artificial biological &ldquo, switch&rdquo, that consists of two parts: (1) the electromagnetic perceptive gene (EPG) and (2) magnetic particles. Our group has recently cloned the EPG from the Kryptopterus bicirrhis (glass catfish). The EPG gene encodes a putative membrane-associated protein that responds to electromagnetic fields (EMFs). This gene&rsquo, s primary mechanism of action is to raise the intracellular calcium levels or change in flux through EMF stimulation. Here, we developed a system for the remote regulation of [Ca2+]i (i.e., intracellular calcium ion concentration) using streptavidin-coated ferromagnetic particles (FMPs) under a magnetic field. The results demonstrated that the EPG-FMPs can be used as a molecular calcium switch to express target proteins. This technology has the potential for controlled gene expression, drug delivery, and drug developments.

Understanding the molecular mechanisms of plant response to unfavorable conditions is necessary for the effective selection of tolerant genotypes. Earlier, using high-throughput transcriptome sequencing of flax plants after exposure to aluminum ions (Al3+) and high soil acidity, we detected stress-induced alteration in the expression of several genes, including CAX3, which encodes Ca2+/H+-exchanger involved in calcium ion transport. Here we describe CAX3 mRNA levels in flax cultivars either tolerant (Hermes and TMP1919) or sensitive (Lira and Orshanskiy) to Al3+. Stress-induced increased expression of CAX3 was detected only in aluminum-tolerant flax cultivars. The product of CAX3 gene may participate in flax response to high soil acidity and high Al3+ concentration through Ca2+-mediated intracellular regulation.

The hypothalamus plays a central role in controlling poultry endocrine and reproductive activities. So far there is limited information focused on the proteome profiles of the hypothalamus from geese during different stages of the egg-laying cycle. In order to identify proteins regulating the egg-laying process of Huoyan geese, we investigated the proteome profiles of the hypothalamus from Huoyan geese during the laying period and pre-laying period by applying an isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic technology. A total number of 3,337 were identified and quantified, of which 18 were significantly up-regulated and 16 were significantly down-regulated. These differentially expressed proteins were subjected to bioinformatics analyses based on the Gene Ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathway. Some of these were revealed to be involved in hormone and neurotransmitter secretion, exocytosis, calcium ion transport and synaptic transmission. Subsequently, excitatory amino acid transporter 2, complexin-1 and inositol 1,4,5-trisphosphate receptor, type 3 were confirmed at the messenger RNA level using quantitative real-time RT-PCR. Then, the abundance change of these proteins was verified further using Western blotting analysis. These data may aid in elucidating the molecular mechanism of higher laying performance in Huoyan geese.

Objectives We aimed to identify the effect of lncRNAs in CD4+ T cells on Allergic rhinitis (AR). Methods The present study conducted a microarray to identify the expression profiles of lncRNA and mRNA in CD4+ T cells in both AR murine models and normal controls. And qRT-PCR was used to confirm the results. GO and KEGG enrichment analysis were used to show all related pathways and a co-expression network was conducted to find lncRNAs which have high correlation with these pathways. Results The results showed that the two groups contained a total of 158 deregulated lncRNAs, of which 110 were upregulated and 48 were downregulated. And positive regulation of calcium ion transport, B cell activation, chemokine-signaling pathways and calcium-signaling pathways may be involved in the development of T cells in AR pathology. Finally, we can find the differentially expressed mRNA in the pathways related to T cell differentiation correlated with many deregulated lncRNAs. Conclusions The present study was the first to show the differential expression profiles of lncRNAs in the CD4+ T cells of an AR murine model, which may provide significant insights into AR pathogenesis and offer new treatment targets to alleviate it.

Low-intensity pulsed ultrasound (LIPUS) is known for its positive effect on bone healing and reparative regeneration. This study investigated whether LIPUS affects reparative progression of the tooth and the expression of calcium ion transport-related proteins in odontoblasts and dental pulp cells using a rat dentin-pulp complex injury model. Forty male adult Sprague-Dawley rats underwent cavity preparation in the right maxillary first molar: 20 received LIPUS irradiation on the cavity-prepared tooth; 20 received LIPUS irradiation on the left maxillary first molar. Rats were randomly allocated into four groups: blank control group, LIPUS group, cavity-prepared group, cavity-prepared + LIPUS group. LIPUS irradiation (frequency: 1.5 MHz, 200-µs pulse width, 1-kHz pulse repetition frequency, 30 mW/cm2 spatial averaged temporal averaged intensity) was administered individually for 20 min daily. Rats were sacrificed 1, 3, 7 and 14 d post-operation. The histopathological and cellular morphologic changes in the dentin-pulp complex were detected with hematoxylin and eosin staining. Expression of calcium ion transport-related proteins (Cav1.2, NCX1 and TRPV1) was determined with immunohistochemical staining and imaging analysis. Histopathological analysis revealed obvious reparative dentin formation at day 14 in the cavity-prepared + LIPUS group compared with the other groups. Expression levels of Cav1.2, NCX1 and TRPV1 increased significantly by 22%, 53% and 23%, respectively, at day 1 and increased significantly by 23%, 27% and 22%, respectively, at day 3 in the cavity-prepared + LIPUS group (p

WRKY transcription factors (TFs) are important regulators in the complex stress response signaling networks in plants, but the detailed mechanisms underlying these regulatory networks have not been fully characterized. In the present study, we identified a Group III WRKY gene (PsnWRKY70, Potri.016G137900) from Populussimonii × Populusnigra and explored its function under salt and pathogen stresses. The promoter sequence that is located 2471-bp upstream from the start codon (SC) of PsnWRKY70 contained many stress-responsive cis-elements. Yeast one-hybrid assay suggested the upstream regulators, PsnWRKY70, PsnNAM (Potri.009G141600), PsnMYB (Potri.006G000800) and PsnGT1 (Potri.010G055000), probably modulate the expression of the PsnWRKY70 gene by specifically binding to the W-box or GT1GMSCAM4 (GT1) element. Yeast two-hybrid assay and transcriptome analysis revealed that HP1 (Potri.004G092100), RRM (Potri.008G146700), Ulp1 (Potri.002G105700) and some mitogen-activated protein kinase cascade members probably interact with PsnWRKY70 TF to response to salt stress. Compared with non-transgenic (NT) plants, PsnWRKY70-overexpressing (OEX) plants exhibited improved leaf blight disease resistance, while PsnWRKY70-repressing (REX) plants displayed enhanced salt stress tolerance. PsnWRKY70, PsnNAM, PsnMYB and PsnGT1 exhibited similar expression patterns in NT under salt and leaf blight disease stresses. The differentially expressed genes (DEGs) from NT vs OEX1 and the DEGs from NT vs REX1 exhibited considerable diversification. Most of the DEGs between NT and OEX1 were involved in aromatic amino acid biosynthesis, secondary metabolism, programmed cell death, peroxisomes and disease resistance. Most of the DEGs between NT and REX1 were related to desiccation response, urea transmembrane transport, abscisic acid response, calcium ion transport and hydrogen peroxide transmembrane transport. Our findings not only revealed the salt stress response signal transduction pathway of PsnWRKY70, but also provided direct evidence for the opposite biological functions of PsnWRKY70 TF in response to salt stress and leaf blight disease in P. simonii × P. nigra.

The syncytiotrophoblast (STB) plays a key role in maintaining the function of the placenta during human pregnancy. However, the molecular network that orchestrates STB development remains elusive. The aim of this study was to obtain broad and deep insight into human STB formation via transcriptomics. We adopted RNA sequencing (RNA-Seq) to investigate genes and isoforms involved in forskolin (FSK)-induced fusion of BeWo cells. BeWo cells were treated with 50 μM FSK or dimethyl sulfoxide (DMSO) as a vehicle control for 24 and 48 h, and the mRNAs at 0, 24 and 48 h were sequenced. We detected 28,633 expressed genes and identified 1902 differentially expressed genes (DEGs) after FSK treatment for 24 and 48 h. Among the 1902 DEGs, 461 were increased and 395 were decreased at 24 h, whereas 879 were upregulated and 763 were downregulated at 48 h. When the 856 DEGs identified at 24 h were traced individually at 48 h, they separated into 6 dynamic patterns via a K-means algorithm, and most were enriched in down–even and up–even patterns. Moreover, the gene ontology (GO) terms syncytium formation, cell junction assembly, cell fate commitment, calcium ion transport, regulation of epithelial cell differentiation and cell morphogenesis involved in differentiation were clustered, and the MAPK pathway was most significantly regulated. Analyses of alternative splicing isoforms detected 123,200 isoforms, of which 1376 were differentially expressed. The present deep analysis of the RNA-Seq data of BeWo cell fusion provides important clues for understanding the mechanisms underlying human STB formation.

Spica Prunellae is an important Chinese herbal medicine. Because of its good curative effect on various diseases, this herb is consumed in large quantities in clinical applications. The metabolites of Spica Prunellae are known to change under salt stress; however, the difference in protein levels of Spica Prunellae between saline and normal conditions is unclear. In this study, we used proteomics techniques to identify differentially expressed proteins in Spica Prunellae under different saline conditions. (iTRAQ) MS/MS was used to detect statistically significant changes in protein between salt stress and normal conditions. Ultimately, we detected 1,937 proteins, 89 of which were detected in two different comparison. Based on GO, STRING and KEGG analyses, 35 significantly differentially expressed proteins were selected for further analysis. The results of functional and signal pathway analyses indicated that the cellular protein and carbohydrate metabolism of Spica Prunellae was weaker, calcium ion transport was higher, photosynthesis was higher, and protein production was faster under saline conditions than under normal conditions. This study provides useful information for studying the causes of differences in secondary metabolites in Spica Prunellae under salt stress and the protein mechanisms related to their quality.

Bladder cancer (BCa) is a tumor associated with high morbidity and mortality and its incidence is increasing worldwide. However, the pathogenesis of bladder cancer is not well understood. To further illustrate the molecular mechanisms involved in the pathogenesis of BCa and identify potential therapeutic targets, we combined the transcriptomic analysis with RNA sequencing and tandem mass tags (TMT)-based proteomic methods to quantitatively screen the differentially expressed genes and proteins between bladder cancer tissues (BC) and adjacent normal tissues (AN). Transcriptome and proteome studies indicated 7094 differentially expressed genes (DEGs) and 596 differentially expressed proteins (DEPs) between BC and AN, respectively. GO enrichment analyses revealed that cell adhesion, calcium ion transport, and regulation of ATPase activity were highly enriched in BCa. Moreover, several key signaling pathway were identified as of relevance to BCa, in particular the ECM-receptor interaction, cell adhesion molecules (CAMs), and PPAR signaling pathway. Interestingly, 367 genes were shared by DEGs and DEPs, and a significant positive correlation between mRNA and translation profiles was found. In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the disease status of BCa.

A set of six new 4-pyridinio-1,4-dihydropyridine (1,4-DHP) compounds has been synthesized. The calcium channel modulating activity of these compounds was evaluated in an aorta vascular smooth muscle cell line (A7R5), in an isolated rat aortic ring model, and in human neuroblastoma cell lines (SH-SY5Y). The antagonistic effect of these 1,4-DHP was tested by modulating the impact of carbachol-dependent mobilization of intracellular Ca2+in SH-SY5Y cells. The intracellular free Ca2+concentration was measured in confluent monolayers of SH-SY5Y cells and A7R5 cells with the Ca2+-sensitive fluorescent indicator Fluo-4 NW. Only four compounds showed calcium channel blocking activity in SH-SY5Y and A7R5 cells as well as in the aortic ring model. Among them, compound 3 was the most active calcium channel antagonist, which had 3 times higher activity on carbachol-activated SH-SY5Y cells than amlodipine. Two of the compounds were inactive. Compound 4 had 9 times higher calcium agonist activity than the classic DHP calcium agonist Bay K8644. The intracellular mechanism for the action of compound 4 using inhibitor analysis was elucidated. Nicotinic as well as muscarinic receptors were not involved. Sarcoplasmic reticulum (ER) Ca2+(SERCA) stores were not affected. Ryanodine receptors (RyRs), another class of intracellular Ca2+releasing channels, participated in the agonist response evoked by compound 4. The electrooxidation data suggest that the studied compounds could serve as antioxidants in OS.

The potential association between the prognosis of the pancreatic adenocarcinoma (PAAD) and its microenvironment is unclear. This study aims to construct a prognostic index (PI) model of the PAAD microenvironment to predict PAAD patient survival outcomes. The mRNA sequencing and the clinical parameters data were obtained from The Cancer Genome Atlas. Immune and stromal scores were computed using the expression data algorithm to capture infiltration of immune and stromal cells in the PAAD tissue, where patients were categorized as high and low score groups according to these scores. Differentially expressed genes were identified using the R package LIMMA. Univariate and multivariate Cox regression analysis were conducted to select candidate survival-correlated gene signatures from the tumor microenvironment for constructing a model. The Kaplan-Meier method was used to access overall survival of the primary and validation cohorts. The immunological features of the PI model was explored using the Tumor Immune Estimation Resource (TIMER) database. Bioinformatic analyses were conducted based on the DAVID database. A total of 1266 overlapping differentially expressed genes and 49 prognosis-associated genes were identified. A 7-mRNA signature (GBP5, BICC1, SLC7A14, CYSLTR1, P2RY6, VENTX, and RAB39B) was screened for the construction of a PI model (area under the curve = 0.791). In both the primary and validation cohorts, Kaplan Meier analysis revealed that the overall survival of the high-risk group was significantly worse compared to the low-risk group (P

In Rosaceae, incompatible pollen can penetrate into the style during the gametophytic self-incompatibility response. It is therefore considered a stylar event rather than a stigmatic event. In this study, we explored the differences in gene expression between compatibility and incompatibility in the early stage of pollination. The self-compatible pear variety “Jinzhuili” is a naturally occurring bud mutant from “Yali”, a leading Chinese native cultivar exhibiting typical gametophytic self-incompatibility. We collected the styles of ‘Yali’ and ‘Jinzhuili’ at 0.5 and 2 h after self-pollination and then performed high-throughput sequencing. According to the pathway enrichment analysis of the differentially expressed genes, “plant-pathogen interaction” was the most represented pathway. Quantitative PCR was used to validate these differential genes. The expression levels of genes related to pollen growth and disease inhibition, such as LRR (LEUCINE-RICH REPEAT EXTENSIN), resistance, and defensin, differed significantly between compatible and incompatible pollination. Interestingly, at 0.5 h, most of these genes were upregulated in the compatible pollination system compared with the incompatible pollination system. Calcium ion transport, which requires ATPase, also demonstrated upregulated expression. In summary, the self-incompatibility reaction was initiated when the pollen came into contact with the stigma.

New Findings What is the central question of this study? What are the molecular underpinnings of the seasonal adaptation in a latitudinal migratory songbird? What is the main finding and its importance? We found changes in mRNA levels after a photoperiod-induced alteration of seasonal state in a captive long-distance latitudinal avian migrant. The hypothalamus and liver transcriptomes revealed genes involved in the regulatory and functional pathways between non-migratory and migratory states. Our results provide insights into mechanisms underlying homeostasis during seasonal changes that are conserved across most species, including humans. Abstract Very little is understood about genetic mechanisms underlying the onset of spring migration in latitudinal avian migrants. To gain insight into the genetic architecture of the hypothalamus and liver tissues of a long-distance migrant, we examined and compared the transcriptome profile of captive night-migratory black-headed buntings (Emberiza melanocephala) between photoperiod-induced winter non-migratory (WnM) and spring migratory (SM) life-history states under short and long days, respectively. High-throughput 454 pyrosequenced transcripts were mapped initially with reference to the genome of two phylogenetically close species, Taeniopygia guttata and Ficedula albicollis. The F. albicollis genome gave higher annotation results and was used for further analysis. A total of 216 (78 in hypothalamus; 138 in liver) genes were found to be expressed differentially between the WnM and SM life-history states. These genes were enriched for physiological pathways that might be involved in the regulation of seasonal migrations in birds. For example, genes for the ATP binding pathway in the hypothalamus were expressed at a significantly higher level in SM than in the WnM life-history state. Likewise, upregulated genes associated with the myelin sheath and focal adhesion were enriched in the hypothalamus, and those with cell-to-cell junction, intracellular protein transport, calcium ion transport and small GTPase-mediated signal transduction were enriched in the liver. Many of these genes are a part of physiological pathways potentially involved in the regulation of seasonal migration in birds. These results show molecular changes at the regulatory and metabolic levels associated with seasonal transitions in a long-distance migrant and provide the basis for future studies aimed at unravelling the genetic control of migration in birds.

Gram-positive bacteria are an important pathogenic factor for bacterial pneumonia. The aim of the present study was to identify the differentially expressed genes (DEGs) and to explore their associated pathways or expression patterns. Expression profiling of gene arrays from two independent datasets, GSE6269 and GSE35716, were downloaded from the Gene Expression Omnibus. The DEGs between peripheral blood samples from healthy controls and patients with bacterial pneumonia were identified. The Functional Annotation Tool in the Database for Annotation, Visualization and Integrated Discovery was used to annotate and analyze the DEGs in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Multiple proteins were used to generate a protein-protein interaction (PPI) network. A total of 624 (621 annotated) were identified in the GSE6269 dataset and 398 (295 annotated) DEGs were identified in the GSE35716 dataset between pneumonia and healthy samples. A total of 40 common DEGs were identified between the 2 datasets, including 4 downregulated and 32 upregulated DEGs. In the GO category cellular component, melanosome was highly enriched among 11 genes; in the category biological process, the three most enriched items were regulation of ruffle assembly, negative regulation of calcium ion transport and necroptotic process. In the KEGG terms, only the nuclear factor-κB signaling pathway (Homo sapiens 04064) was significantly enriched. In the PPI network, five genes (CCL4, TIMP metallopeptidase inhibitor 1, intercellular adhesion molecule 1, plasminogen activator, urokinase receptor and cathepsin B) were identified to have a high degree of interaction with other DEGs. In conclusion, these five genes may represent key genes associated with pneumonia caused by Gram-positive bacteria. All of these results provide primary information and basic knowledge to understand the mechanisms of the pathogenesis.

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real bacterial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic versus abiotic) involved. In this work we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originatingStreptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3deposition. The metabolic activities involved in CaCO3transformation were furthermore assessedin vitroamong the collection of moonmilkStreptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally,in silicosearch for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2allowed to identify genetic predispositions for carbonate precipitation inStreptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.

Dysregulation of intracellular trafficking system plays a fundamental role in the progression of cardiovascular disease. Up-regulation of miR-1 contributes to arrhythmia, we sought to elucidate whether intracellular trafficking contributes to miR-1-driven arrhythmia. By performing microarray analyses of the transcriptome in the cardiomyocytes-specific over-expression of microRNA-1 (miR-1 Tg) mice and the WT mice, we found that these differentially expressed genes in miR-1 Tg mice were significantly enrichment with the trafficking-related biological processes, such as regulation of calcium ion transport. Also, the qRT-PCR and western blot results validated that Stx6, Braf, Ube3a, Mapk8ip3, Ap1s1, Ccz1 and Gja1, which are the trafficking-related genes, were significantly down-regulated in the miR-1 Tg mice. Moreover, we found that Stx6 was decreased in the heart of mice after myocardial infarction and in the hypoxic cardiomyocytes, and further confirmed that Stx6 is a target of miR-1. Meanwhile, knockdown of Stx6 in cardiomyocytes resulted in the impairments of PLM and L-type calcium channel, which leads to the increased resting ([Ca2+]i). On the contrary, overexpression of Stx6 attenuated the impairments of miR-1 or hypoxia on PLM and L-type calcium channel. Thus, our studies reveals that trafficking-related gene Stx6 may regulate intracellular calcium and is involved in the occurrence of cardiac arrhythmia, which provides new insights in that miR-1 participates in arrhythmia by regulating the trafficking-related genes and pathway.

We data-analyzed and constructed the high-expression CAMK1 phosphoinositide signal-mediated protein sorting and transport network in human hepatocellular carcinoma (HCC) compared with low-expression (fold change ≥ 2) no-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) in GEO data set, using integration of gene regulatory network inference method with gene ontology (GO). Our result showed that CAMK1 transport subnetwork upstream KCNQ3, LCN2, NKX2_5, NUP62, SORT1, STX1A activated CAMK1, and downstream CAMK1-activated AFP, ENAH, KPNA2, SLC4A3; CAMK1 signal subnetwork upstream BRCA1, DKK1, GPSM2, LEF1, NR5A1, NUP62, SORT1, SSTR5, TBL3 activated CAMK1, and downstream CAMK1-activated MAP2K6, SFRP4, SSTR5, TSHB, UBE2C in HCC. We proposed that CAMK1 activated network enhanced endosome to lysosome transport, endosome transport via multivesicular body sorting pathway, Golgi to endosome transport, intracellular protein transmembrane transport, intracellular protein transport, ion transport, mRNA transport, plasma membrane to endosome transport, potassium ion transport, protein transport, vesicle-mediated transport, anion transport, intracellular transport, androgen receptor signaling pathway, cell surface receptor-linked signal transduction, hormone-mediated signaling, induction of apoptosis by extracellular signals, signal transduction by p53 class mediator resulting in transcription of p21 class mediator, signal transduction resulting in induction of apoptosis, phosphoinositide-mediated signaling, Wnt receptor signaling pathway, as a result of inducing phosphoinositide signal-mediated protein sorting, and transport in HCC. Our hypothesis was verified by CAMK1 functional regulation subnetwork containing positive regulation of calcium ion transport via voltage gated calcium channel, cell proliferation, DNA repair, exocytosis, I-kappaB kinase/NF-kappaB cascade, immunoglobulin-mediated immune response, mast cell activation, natural killer cell-mediated cytotoxicity directed against tumor cell target, protein ubiquitination, sodium ion transport, survival gene product activity, T cell-mediated cytotoxicity, transcription, transcription from RNA polymerase II promoter, transcription initiation from RNA polymerase II promoter, transcription via serum response element binding, exit from mitosis, ubiquitin ligase activity during mitotic cell cycle, regulation of angiogenesis, apoptosis, cell growth, cell proliferation, cyclin-dependent protein kinase activity, gene expression, insulin secretion, steroid biosynthesis, transcription from RNA polymerase II promoter, transcription from RNA polymerase III promoter, cell cycle, cell migration, DNA recombination, and protein metabolism; also by CAMK1 negative functional regulation subnetwork including negative regulation of apoptosis, cell proliferation, centriole replication, fatty acid biosynthesis, lipoprotein lipase activity, MAPK activity, progression through cell cycle, transcription, transcription from RNA polymerase II promoter, cell growth, phosphorylation, and ubiquitin ligase activity during mitotic cell cycle in HCC.

Inhibitors of the sarco/endoplasmic reticulum calcium ATPase (SERCA) are valuable research tools and hold promise as a new generation of anti-prostate cancer agents. Based on previously determined potencies of phenolic SERCA inhibitors, we created quantitative structure–activity relationship (QSAR) models using three independent development strategies. The obtained QSAR models facilitated virtual screens of several commercial compound collections for novel inhibitors. Sixteen compounds were subsequently evaluated in SERCA activity inhibition assays and 11 showed detectable potencies in the micro- to millimolar range. The experimental results were then incorporated into a comprehensive master QSAR model, whose physical interpretation by partial least squares analysis revealed that properly positioned substituents at the central phenyl ring capable of forming hydrogen bonds and of undergoing hydrophobic interactions were prerequisites for effective SERCA inhibition. The established SAR was in good agreement with findings from previous structural studies, even though it was obtained independently using standard QSAR methodologies.

Background Schizophrenia (SZ) is a severe neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. About 20% of SZ patients are resistant to the commonly-prescribed antipsychotic medications used to treat disease symptoms. Clozapine is an atypical antipsychotic drug often prescribed to treatment-resistant SZ patients, although the functional pathways mediating its action are not well understood. Importantly, 40–70% of patients treated with clozapine show an inadequate response and there are sever side-effects. Understanding the molecular pathways involved in antipsychotic response will help in the development of new improved therapeutics that act on pathogenicity rather than just treating the acute manifestations of SZ. Methods We exposed wild type zebrafish to high and low doses of the antipsychotic drug clozapine over 72 hours. Relevant controls were included at all stages of the experiment. We recorded the animals and analysed changes in behavior associated with clozapine exposure. We then performed RNA-sequencing in the brain and identified changes in gene expression in response to clozapine exposure. Network analysis was performed to identify modules of co-expressed genes sensitive to clozapine exposure and pathway analysis was employed to identify overrepresentation of GO terms in each of the clozapine exposure-associated modules Results The fish showed a dose-sensitive shift in behaviour in response to clozapine. We identified five genes showing significant gene expression changes in response to clozapine, including ODC1, a gene previously implicated in SZ which shows changes in expression during brain development. Using network analysis, we identified fifteen modules of co-expressed genes which present a striking change in module connectivity in response to the drug. These modules show overrepresentation of key gene ontology terms, implicating processes such as calcium ion transport, cell-cell signalling, G-protein coupled receptor activity, ribosomal activity, and the regulation of transcription. Discussion Our study highlights the utility of zebrafish as a model for assessing the molecular consequences of antipsychotic medications. Our data show marked behavioural effects induced by clozapine and significant transcriptomic alterations in important functional pathways in the brain.

Hexabromocyclododecane (HBCD) is one of the most widely used brominated flame retardants. In the present study, zebrafish embryos were exposed to HBCD at the low concentrations of 0, 2, 20 and 200 nM. The results showed HBCD exposure resulted in an increase in heart rate and cardiac arrhythmia after exposure for 72 h, though the survival rate and the whole malformation rate were not significantly affected. These results demonstrated that the heart might be a target of HBCD. Low-level HBCD exposure may not share the same mechanisms as exposure to high concentrations, since no obvious increase of apoptotic cells around the heart was observed in the HBCD-treated groups. It was observed that the expression of Tbx5 and Nkx2.5 was significantly elevated by HBCD treatment in a dose-dependent manner using real-time quantitative PCR, which may be mainly responsible for the alteration of heart rate, given that Tbx5 and Nkx2.5 are two factors regulating ventricle conduction. The mRNA expression of RyR2 and Atp2a2b (SERCA2a) was up-regulated in the exposure group, which may be one of reasons to affect the normal heart rate, since SERCA2a and RyR2 play an important role in calcium ion transport of cadiomyocytes. However, HBCD exposure did not significantly change the expression of Actc1l, Tnnt2, and Myh6, which are mainly muscle contractile genes that play key roles in the formation of cardiac structure. These results were consistent with the lack of effect seen on the other measurements of cardiac function, end diastolic volume, end-systolic volume, stroke volume, and cardiac output.

In the present study, a comparison of the biological processes and gene ontology (GO) in human hepatocellular carcinoma (HCC) with high expression (fold change ≥2) of amelogenin Y-linked (AMELY)-activated upstream regulation networks with non-tumor hepatitis/cirrhotic tissues (HBV or HCV infection) with low expression of activated networks was performed. The principle biological processes involved in non-tumor hepatitis/cirrhotic tissues include positive regulation of mismatch repair, regulation of transcription from RNA polymerase II promoters, negative regulation of cell-cell adhesion, protein ubiquitinatin and protein catabolism. The main biological processes involved in the development of HCC include positive regulation of calcium ion transport into the cytosol, cell proliferation, DNA replication, fibroblast proliferation, immune response, microtubule polymerization and protein secretion. Specific transcription from RNA polymerase II promoters, regulation of angiogenesis, cell growth, protein metabolism, Wnt receptor signaling pathways, negative regulation of endothelial cell differentiation, microtubule depolymerization, peptidase activity and progression through the cell cycle are also involved. Positive regulation of transcription is involved in both processes. An activated AMELY-coupled upstream positive regulation of immune response-mediated protein secretion to Wnt signaling and calcium into cytosol-induced regulation of cell growth and angiogenesis in HCC is proposed. The AMELY upstream regulation molecular network model was constructed with BUB1B, CST6, ESM1, HOXA5, LEF1, MAPT, MYBL2, NOTCH3, PLA2G1B, PROK1, ROBO1, SCML2 and UBE2C in HCC from a Gene Expression Omnibus (GEO) dataset by gene regulation network inference methods and our programming methods.

The present study aimed to screen for differentially expressed extracellular microRNAs (miRNAs) during the development of acute pancreatitis (AP) and validate the miRNA expression in the plasma of patients with AP. The culture medium of taurolithocholic acid‑3 sulfate‑treated rat pancreatic acinar AR42J cells was collected to extract total RNA for miRNA microarray analysis. Compared with the miRNA test results of the AP rats in the GEO databases, the differentially expressed extracellular miRNAs were screened. The TargetScan, miRanda, and PicTar programs were used for target gene prediction of the identified miRNAs, and gene ontology‑biological processes (GO‑BP) functional annotation was performed. Finally, the results from the combined microarray analyses (in vitro cell line and in vivo rat samples) were validated using plasma samples from patients with mild and moderately severe AP by reverse transcription‑polymerase chain reaction. The results demonstrated that extracellular miR‑24 was differentially expressed by microarray and bioinformatics analysis in both the cell line and the animal model of AP. Bioinformatics prediction analysis revealed that downstream target genes of miR‑24 included Vav2, Syk, Lhcgr, Slc9a3r1, Cacnb1, Cacna1b, Bcl10, and Fgd3. Functional enrichment analysis revealed that the main GO‑BP predicted functional presentations were positive regulation of calcium‑mediated signaling, activation of c‑Jun N‑terminal kinase activity, calcium ion transport, regulation of Rho protein signal transduction, negative regulation of the protein kinase B signaling cascade, and the T cell receptor signaling pathway. Validation analysis for the plasma miR‑24 expression in humans revealed a significant upregulation of miR‑24 in the plasma samples of AP patients compared with the healthy controls, while no significant difference was observed in the miR‑24 expression between the mild and the moderately severe AP groups. The present study confirmed the high expression of miR‑24 in peripheral blood during AP, suggesting that miR‑24 might have an intercellular communication role contributing to the AP‑associated distant organ injury.

Made available in DSpace on 2018-12-11T17:02:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2016-05-21 Background: Some plants had been used in the treatment of cancer and one of these has attracted scientific interest, the Euphorbia tirucalli (E. tirucalli), used in the treatment of asthma, ulcers, warts has active components with activities scientifically proven as antimutagenic, anti-inflammatory and anticancer. Methods: We evaluate the influence of the antitumoral fraction of the E. tirucalli latex in the larynx squamous cell carcinoma (Hep-2), on the morphology, cell proliferation and gene expression. The Hep-2 cells were cultivated in complete medium (MEM 10%) and treated with E.tirucalli latex for 1, 3 ,5 and 7days. After statistically analyzing the proliferation of the tested cells, the cells were cultivated again for RNA extraction and the Rapid Subtractive Hybridization (RaSH) technique was used to identify genes with altered expression. The genes found using the RaSH technique were analyzed by Gene Ontology (GO) using Ingenuity Systems. Results: The five genes found to have differential expression were validated by real-time quantitative PCR. Though treatment with E. tirucalli latex did not change the cell morphology in comparison to control samples, but the cell growth was significantly decreased. The RaSH showed change in the expression of some genes, including ANXA1, TCEA1, NGFRAP1, ITPR1 and CD55, which are associated with inflammatory response, transcriptional regulation, apoptosis, calcium ion transport regulation and complement system, respectively. The E. tirucalli latex treatment down-regulated ITPR1 and up-regulated ANXA1 and CD55 genes, and was validated by real-time quantitative PCR. Conclusions: The data indicate the involvement of E. tirucalli latex in the altered expression of genes involved in tumorigenic processes, which could potentially be applied as a therapeutic indicator of larynx cancer. Institute of Biosciences Letters and Science - IBILCE/UNESP Department of Biology Foundation Blood Center of Ribeirão Preto Faculty of Medicine of Ribeirão Preto University of São Paulo - FCFRP/USP Department of Clinical Medical Faculty of Medicine of São José do Rio Preto - FAMERP Department of Molecular Biology Faculty of Engineering of Ilha Solteira - FEIS/UNESP Department of Biology and Animal Science, Av. Brasil, 56 Institute of Biosciences Letters and Science - IBILCE/UNESP Department of Biology Faculty of Engineering of Ilha Solteira - FEIS/UNESP Department of Biology and Animal Science, Av. Brasil, 56

Human pharmaceutical drugs have been found in surface waters worldwide, and represent an increasing concern since little is known about their possible effects on wildlife. Propranolol is a common beta-adrenergic receptor antagonist (β-blocker) typically prescribed to people suffering from heart disease and hypertension. Propranolol has been detected in United States wastewater effluents at concentrations ranging from 0.026 to 1.90 μg/l. In mammals, there is evidence that β-blockers can cause sexual dysfunction, and alter serotonergic pathways which may impact reproductive behavior but little is known about the effects on fish behavior. The present study tested the effects of propranolol on fecundity, on brain gene expression and on reproductive behavior of the fathead minnow, Pimephales promelas, a fish that exhibits male parental care. Sexually mature fathead minnows were housed at a ratio of one male and two females per tank and exposed to nominal concentrations of 0, 0.1, 1, 10 μg/l for 21 days. Measured concentrations (±SD) of propranolol were 0.003±0.004, 0.05±0.02, 0.88±0.34 and 4.11±1.19 μg/l. There were no statistically significant differences in fecundity, fertilization rate, hatchability and time to hatch. Propranolol exposure was not associated with a change in nest rubbing behavior, time spent in the nest or approaching the females. There was a significant difference in the number of visits to the nest with males receiving low and medium propranolol treatments. The microarray analysis showed that there were 335 genes up-regulated and 400 genes down-regulated in the brain after exposure to the highest dose of propranolol. Among those genes, myoglobin and calsequestrin transcripts (fold change=10.84 and 5.49, respectively) were highly up-regulated. Ontological analyses indicated changes in genes involved in calcium ion transport, transcription, proteolysis and apoptosis/anti-apoptosis. Pathway analysis indicated that the reduced expression of caspases may lead to impaired neurite outgrowth, neurotransmitter secretion and brain function in developing organisms. The results showed that exposure to propranolol at concentrations as high as 4.11 μg/l did not significantly impact reproductive behavior or spawning abilities of fathead minnow but did alter the regulation of genes within the brain of fish.

Intrinsic disorder in proteins has been explored to study lack of structure-function aspects of many proteins. The current study focuses on coiled coils which are often linked to intrinsic disorder. We present a sequence level analysis of human coiled coils to find out if this is universally true for all coiled coils. When annotated coiled-coil regions were collected from UniProt and investigated with disorder prediction tools namely-IUPred and DISpro, three patterns were commonly observed-disordered coiled coils (DisCCs), ordered coiled coils (OCCs) and the last one having a disordered region outside the coiled-coil region (DOCCs). Differential enrichment in the gene ontology was seen in these three categories. We found that OCCs are enriched in structural components of the extracellular space including the fibrinogen complex and laminin complex. On the contrary, DisCCs were found to be exclusively over-represented in proteins involved in actin filament, lamellipodium, cell junction, macromolecule complexes, ciliary rootlet and nucleolus. DOCCs are found to be associated with many regulatory and adaptor functions including positive regulation of calcium ion transport via store-operated calcium channel activity, cytoskeletal adaptor activity etc. Other than the GO-based analysis, sequence level analysis showed that disordered coiled-coil regions bear a high proportion of low-complexity regions as compared to ordered coiled coils. The former also has a higher probability of forming a dimer as compared to the ordered counterpart. Our study shows that the in silico approach of mapping of disorder in or around coiled coils in other biological systems or organisms can be applied to understand and rationalize the mode of action of these dynamic motifs.

A major germacranolide sesquiterpene lactone, deoxyelephantopin, identified from Elephantopus scaber L. (known as "Didancao" in Chinese medicine) showed significant antitumor growth and antimetastatic effect on murine mammary adenocarcinoma TS/A cells in vitro and in vivo in mice. Deoxyelephantopin exhibited a superior effect to that of the paclitaxel in prolonging median survival time of tumor-bearing animals in our recent study. To investigate the molecular mechanisms underlying the difference in efficacy between deoxyelephantopin and paclitaxel, we used 2-D DIGE and LC-ESI-MS/MS to profile proteins differentially expressed in the nucleus and cytoplasm of TS/A cells and used the MetaCore database to determine the functional protein networks affected by both treatments. Deoxyelephantopin and paclitaxel treatment produced regulation of molecules involved in proteolysis and calcium ion transport, suggesting the possible effects of both drugs on proteasome and endoplasmic reticulum machinery in TS/A cells. Western blot analysis of marker proteins (e.g., PDI, GRP78, TXND5, caspase-12, caspase-3 and PARP) further verified that induction of endoplasmic reticulum stress was associated with apoptosis induced by both deoxyelephantopin and paclitaxel, but only deoxyelephantopin inhibited proteasomal proteolysis in TS/A cells. The novel effects on targeting ER machinery and suppressing proteasome activity suggest the great potential of deoxyelephantopin for mammary cancer therapy.

Deep tissue injury (DTI) is a serious pressure ulcer, involving a mass of necrotic soft tissue under bony prominences as a consequence of sustained tissue deformations. Though several processes are thought to participate in the onset and development of DTI (e.g., cellular deformation, ischemia, and ischemia-reperfusion), the specific mechanisms responsible for it are currently unknown. Recent work indicated that pathological processes at the cell level, which relate to cell deformation, are involved in the etiology. We hypothesized that sustained tissue deformations can lead to elevated intracellular concentration of cell metabolites, e.g., calcium ion (Ca2+), due to a stretch-induced increase in the local permeability of plasma membranes. This may ultimately lead to cell death due to intracellular cytotoxic concentrations of metabolites. In order to investigate this hypothesis, computational models were developed, for determining compression-induced membrane stretches and trends of times for reaching intracellular cytotoxic Ca2+ levels due to uncontrolled Ca2+ influx through stretched membranes. The simulations indicated that elevated compressive cell deformations exceeding 25% induce large tensional strains (>5%, and up to 11.5%) in membranes. These are likely to increase Ca2+ influx from the extracellular space into the cytosol through the stretched sites. Consistent with this assumption, the Ca2+ transport model showed high sensitivity of times for cell death to changes in membrane resistance. These results may open a new path in pressure ulcer research, by indicating how global tissue deformations are transformed to plasma membrane deformations, which in turn, affect transport properties and eventually, cell viability.

Eggshell damages lead to economic losses in the egg production industry and are a threat to human health. We examined 49-wk-old Rhode Island White hens (Gallus gallus) that laid eggs having shells with significantly different strengths and thicknesses. We used HiSeq 2000 (Illumina) sequencing to characterize the chicken transcriptome and whole genome to identify the key genes and genetic mutations associated with eggshell calcification. We identified a total of 14,234 genes expressed in the chicken uterus, representing 89% of all annotated chicken genes. A total of 889 differentially expressed genes were identified by comparing low eggshell strength (LES) and normal eggshell strength (NES) genomes. The DEGs are enriched in calcification-related processes, including calcium ion transport and calcium signaling pathways as revealed by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Some important matrix proteins, such as OC-116, LTF and SPP1, were also expressed differentially between two groups. A total of 3,671,919 single-nucleotide polymorphisms (SNPs) and 508,035 Indels were detected in protein coding genes by whole-genome re-sequencing, including 1775 non-synonymous variations and 19 frame-shift Indels in DEGs. SNPs and Indels found in this study could be further investigated for eggshell traits. This is the first report to integrate the transcriptome and genome re-sequencing to target the genetic variations which decreased the eggshell qualities. These findings further advance our understanding of eggshell calcification in the chicken uterus.

Microbially influenced corrosion (MIC) in concrete results in significant cost for infrastructure maintenance. Prior studies have employed molecular techniques to identify microbial community species in corroded concrete, but failed to explore bacterial activity and functionality during deterioration. In this study, biofilms of different sulfur-oxidizing bacteria compositions were developed on the surface of cement paste samples to simulate the natural ecological succession of microbial communities during MIC processes. Noninvasive, self-referencing (SR) microsensors were used to quantify real time changes of oxygen, hydrogen ion and calcium ion flux for the biofilm to provide more information about bacterial behavior during deterioration. Results showed higher transport rates in oxygen consumption, and hydrogen ion at 4 weeks than 2 weeks, indicating increased bacterial activity over time. Samples with five species biofilm had the highest hydrogen ion and calcium ion transport rates, confirming attribution of acidophilic sulfur-oxidizing microorganisms (ASOM). Differences in transport rates between three species samples and two species samples confirmed the diversity between Thiomonas intermedia and Starkeya novella. The limitations of SR sensors in corrosion application could be improved in future studies when combined with molecular techniques to identify the roles of major bacterial species in the deterioration process.

Bcl-2 family proteins are key regulators for cellular homeostasis in response to apoptotic stimuli. Bcl-xL, an antiapoptotic Bcl-2 family member, undergoes conformational transitions, which leads to two conformational states: the cytoplasmic and membrane-bound. Here we present the crystal and small-angle X-ray scattering (SAXS) structures of Bcl-xL treated with the mild detergent n-Octyl β-D-Maltoside (OM). The detergent-treated Bcl-xL forms a dimer through three-dimensional domain swapping (3DDS) by swapping helices α6-α8 between two monomers. Unlike Bax, a proapoptotic member of the Bcl-2 family, Bcl-xL is not converted to 3DDS homodimer upon binding BH3 peptides and ABT-737, a BH3 mimetic drug. We also designed Bcl-xL mutants which cannot dimerize and show that these mutants reduced mitochondrial calcium uptake in MEF cells. This illustrates the structural plasticity in Bcl-xL providing hints toward the probable molecular mechanism for Bcl-xL to play a regulatory role in mitochondrial calcium ion transport.