INTERACTIONS OF HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS WITH TOBACCO TREATED STREPTOCOCCUS MUTANS

poster abstractStreptococcus mutans (S. mutans) is a major contributor to dental caries. Previous research has shown that there is a positive relationship between smoking and dental carries, however the pathway of S. mutans growth is not yet understood. Tobacco use affects the cardiovascular system and increases the rate of cardiovascular disease among smokers. However, the effects of tobacco on the endothelial cells that line blood vessels are not yet fully understood. Thus, the objective of this study was to examine some of the effects that a periodontal pathogen such as S. mutans treated with cigarette smoke condensate (CSC) and nicotine have on human umbilical vein endothelial cells (HUVEC’s). The S. mutans was grown at 37°C and then the planktonic cells were harvested, washed with saline, and then killed with formaldehyde. To standardize the samples, they were diluted to the same OD at 600nm wavelength using a spectroscope. The HUVEC were cultured in Endothelial Basal Medium-2 and plated in 12 well plates and exposed to the P. gingivalis cells and supernatants and after 72 hours, lactate dehydrogenase (LDH) assays will be used to cytotoxicity. Non-toxic amounts of the cells and supernatants will then be used to treat HUVEC cells for 72 hours before the media is collected and analyzed for cytokine/growth factor expression by protein arrays. Second messenger signaling pathways will be analyzed with ERK and JNK antagonists and agonists to determine the pathway of up regulation of S. mutans. A better understanding of the detrimental effects that tobacco has on the underlining causes of periodontal disease can advance the quest of controlling the disease

Study of Fulvic Acid: A Natural Dietary Supplement

poster abstractShilajit is a substance found in parts of Asia. Although there have been no clinical studies, it is used by the locals and is marketed because it is thought to have antiseptic, anti-inflammatory and pain suppressing effects. Fulvic acid (F-A) is a major constituent of shilajit and was used in the analysis of the anti-pathogenic tendencies of shilajit and cytotoxic effects on human cells of the oral cavity. The bacterial study was performed on Streptococcus mutans, a normal flora of the oral cavity. The idea was to test the metabolic activity of the bacteria in F-A-containing media. Menadione-XTT reagent was used for this. The bacterial biofilm was allowed to grow in TSBS in a microtiter plate of 96 wells. The F-A solution of different concentration were introduced into each well in a gradually decreasing amount and the last control wells had a zero concentration. The XTT reagent was introduced and after incubation the biofilm of S. mutans reduced the XTT to an orange color, the change in color was detected by measuring the absorbance at 490nm. Between 2.5% to 5.0% of F-A the wells showed signs of decreased activity. The numbers indicated that absorbance of the wells with concentrated F-A was lower compared to the wells with more diluted F-A solutions. From this it can be concluded that F-A had a negative effect on the growth and metabolic activity of S. mutans. For human testing, pulp and fibroblast cells were subjected to different concentrations of F-A. The cytotoxicity was measured by the amount of Lactate Dehydrogenase released from the treated cells (sign of damage). Overall, the experiment validates the potency of F.A as an effective antibacterial. Further testing is needed but the compound shows promise and can be employed as an effective ingredient of mouthwash and other such antiseptic products

Network based transcription factor analysis of regenerating axolotl limbs

<p>Abstract</p> <p>Background</p> <p>Studies on amphibian limb regeneration began in the early 1700's but we still do not completely understand the cellular and molecular events of this unique process. Understanding a complex biological process such as limb regeneration is more complicated than the knowledge of the individual genes or proteins involved. Here we followed a systems biology approach in an effort to construct the networks and pathways of protein interactions involved in formation of the accumulation blastema in regenerating axolotl limbs.</p> <p>Results</p> <p>We used the human orthologs of proteins previously identified by our research team as bait to identify the transcription factor (TF) pathways and networks that regulate blastema formation in amputated axolotl limbs. The five most connected factors, c-Myc, SP1, HNF4A, ESR1 and p53 regulate ~50% of the proteins in our data. Among these, c-Myc and SP1 regulate 36.2% of the proteins. c-Myc was the most highly connected TF (71 targets). Network analysis showed that TGF-β1 and fibronectin (FN) lead to the activation of these TFs. We found that other TFs known to be involved in epigenetic reprogramming, such as Klf4, Oct4, and Lin28 are also connected to c-Myc and SP1.</p> <p>Conclusions</p> <p>Our study provides a systems biology approach to how different molecular entities inter-connect with each other during the formation of an accumulation blastema in regenerating axolotl limbs. This approach provides an in silico methodology to identify proteins that are not detected by experimental methods such as proteomics but are potentially important to blastema formation. We found that the TFs, c-Myc and SP1 and their target genes could potentially play a central role in limb regeneration. Systems biology has the potential to map out numerous other pathways that are crucial to blastema formation in regeneration-competent limbs, to compare these to the pathways that characterize regeneration-deficient limbs and finally, to identify stem cell markers in regeneration.</p

lncRNA profile study reveals the mRNAs and lncRNAs associated with docetaxel resistance in breast cancer cells

Abstract Resistance to adjuvant systemic treatment, including taxanes (docetaxel and paclitaxel) is a major clinical problem for breast cancer patients. lncRNAs (long non-coding RNAs) are non-coding transcripts, which have recently emerged as important players in a variety of biological processes, including cancer development and chemotherapy resistance. However, the contribution of lncRNAs to docetaxel resistance in breast cancer and the relationship between lncRNAs and taxane-resistance genes are still unclear. Here, we performed comprehensive RNA sequencing and analyses on two docetaxel-resistant breast cancer cell lines (MCF7-RES and MDA-RES) and their docetaxel-sensitive parental cell lines. We identified protein coding genes and pathways that may contribute to docetaxel resistance. More importantly, we identified lncRNAs that were consistently up-regulated or down-regulated in both the MCF7-RES and MDA-RES cells. The co-expression network and location analyses pinpointed four overexpressed lncRNAs located within or near the ABCB1 (ATP-binding cassette subfamily B member 1) locus, which might up-regulate the expression of ABCB1. We also identified the lncRNA EPB41L4A-AS2 (EPB41L4A Antisense RNA 2) as a potential biomarker for docetaxel sensitivity. These findings have improved our understanding of the mechanisms underlying docetaxel resistance in breast cancer and have provided potential biomarkers to predict the response to docetaxel in breast cancer patients

Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance

Abstract Oesophageal carcinoma is the fourth leading cause of cancer-related death in China, and more than 90% of these tumours are oesophageal squamous cell carcinoma (ESCC). Although several ESCC genomic sequencing studies have identified mutated somatic genes, the number of samples in each study was relatively small, and the molecular basis of ESCC has not been fully elucidated. Here, we performed an integrated analysis of 490 tumours by combining the genomic data from 7 previous ESCC projects. We identified 18 significantly mutated genes (SMGs). PTEN, DCDC1 and CUL3 were first reported as SMGs in ESCC. Notably, the AJUBA mutations and mutational signature4 were significantly correlated with a poorer survival in patients with ESCC. Hierarchical clustering analysis of the copy number alteration (CNA) of cancer gene census (CGC) genes in ESCC patients revealed three subtypes, and subtype3 exhibited more CNAs and marked for worse prognosis compared with subtype2. Moreover, database annotation suggested that two significantly differential CNA genes (PIK3CA and FBXW7) between subtype3 and subtype2 may serve as therapeutic drug targets. This study has extended our knowledge of the genetic basis of ESCC and shed some light into the clinical relevance, which would help improve the therapy and prognosis of ESCC patients

Classification of subtypes and identification of dysregulated genes in sepsis

BackgroundSepsis is a clinical syndrome with high mortality. Subtype identification in sepsis is meaningful for improving the diagnosis and treatment of patients. The purpose of this research was to identify subtypes of sepsis using RNA-seq datasets and further explore key genes that were deregulated during the development of sepsis.MethodsThe datasets GSE95233 and GSE13904 were obtained from the Gene Expression Omnibus database. Differential analysis of the gene expression matrix was performed between sepsis patients and healthy controls. Intersection analysis of differentially expressed genes was applied to identify common differentially expressed genes for enrichment analysis and gene set variation analysis. Obvious differential pathways between sepsis patients and healthy controls were identified, as were developmental stages during sepsis. Then, key dysregulated genes were revealed by short time-series analysis and the least absolute shrinkage and selection operator model. In addition, the MCPcounter package was used to assess infiltrating immunocytes. Finally, the dysregulated genes identified were verified using 69 clinical samples.ResultsA total of 898 common differentially expressed genes were obtained, which were chiefly related to increased metabolic responses and decreased immune responses. The two differential pathways (angiogenesis and myc targets v2) were screened on the basis of gene set variation analysis scores. Four subgroups were identified according to median expression of angiogenesis and myc target v2 genes: normal, myc target v2, mixed-quiescent, and angiogenesis. The genes CHPT1, CPEB4, DNAJC3, MAFG, NARF, SNX3, S100A9, S100A12, and METTL9 were recognized as being progressively dysregulated in sepsis. Furthermore, most types of immune cells showed low infiltration in sepsis patients and had a significant correlation with the key genes. Importantly, all nine key genes were highly expressed in sepsis patients.ConclusionThis study revealed novel insight into sepsis subtypes and identified nine dysregulated genes associated with immune status in the development of sepsis. This study provides potential molecular targets for the diagnosis and treatment of sepsis

Proteomic analysis of blastema formation in regenerating axolotl limbs

BACKGROUND: Following amputation, urodele salamander limbs reprogram somatic cells to form a blastema that self-organizes into the missing limb parts to restore the structure and function of the limb. To help understand the molecular basis of blastema formation, we used quantitative label-free liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS)-based methods to analyze changes in the proteome that occurred 1, 4 and 7 days post amputation (dpa) through the mid-tibia/fibula of axolotl hind limbs. RESULTS: We identified 309 unique proteins with significant fold change relative to controls (0 dpa), representing 10 biological process categories: (1) signaling, (2) Ca2+ binding and translocation, (3) transcription, (4) translation, (5) cytoskeleton, (6) extracellular matrix (ECM), (7) metabolism, (8) cell protection, (9) degradation, and (10) cell cycle. In all, 43 proteins exhibited exceptionally high fold changes. Of these, the ecotropic viral integrative factor 5 (EVI5), a cell cycle-related oncoprotein that prevents cells from entering the mitotic phase of the cell cycle prematurely, was of special interest because its fold change was exceptionally high throughout blastema formation. CONCLUSION: Our data were consistent with previous studies indicating the importance of inositol triphosphate and Ca2+ signaling in initiating the ECM and cytoskeletal remodeling characteristic of histolysis and cell dedifferentiation. In addition, the data suggested that blastema formation requires several mechanisms to avoid apoptosis, including reduced metabolism, differential regulation of proapoptotic and antiapoptotic proteins, and initiation of an unfolded protein response (UPR). Since there is virtually no mitosis during blastema formation, we propose that high levels of EVI5 function to arrest dedifferentiated cells somewhere in the G1/S/G2 phases of the cell cycle until they have accumulated under the wound epidermis and enter mitosis in response to neural and epidermal factors. Our findings indicate the general value of quantitative proteomic analysis in understanding the regeneration of complex structures

Rapid biotic rebound during the late Griesbachian indicates heterogeneous recovery patterns after the Permian-Triassic mass extinction

New fossil data from two Early Triassic (Griesbachian to Dienerian) sections from South China show unusually high levels of both benthic and nektonic taxonomic richness occurring in the late Griesbachian. In total, 68 species (including 26 newly originated species) representing mollusks, brachiopods, foraminifers, conodonts, ostracods, and echinoderms occur in the late Griesbachian, indicating well-established and relatively complex marine communities. Furthermore, the nekton shows higher origination rates than the benthos. Analyses of the sedimentary facies and size distribution of pyrite framboids show that this high-diversity interval is associated with well-oxygenated environments. In contrast to the previously suggested scenario, which inferred that persistently harsh environmental conditions impeded the biotic recovery during the Early Triassic, our new findings, combined with recent work, indicate a fitful regional recovery pattern after the Permian-Triassic crisis, resulting in three main diversity highs: late Griesbachian–early Dienerian, early–middle Smithian, and Spathian. The transient rebound episodes were therefore influenced by both extrinsic local (e.g., redox condition, temperature) and intrinsic (e.g., biological tolerances, origination rates) parameters

Associations of Educational Attainment, Occupation, Social Class and Major Depressive Disorder among Han Chinese Women

Background The prevalence of major depressive disorder (MDD) is higher in those with low levels of educational attainment, the unemployed and those with low social status. However the extent to which these factors cause MDD is unclear. Most of the available data comes from studies in developed countries, and these findings may not extrapolate to developing countries. Examining the relationship between MDD and socio economic status in China is likely to add to the debate because of the radical economic and social changes occurring in China over the last 30 years. Principal findings We report results from 3,639 Chinese women with recurrent MDD and 3,800 controls. Highly significant odds ratios (ORs) were observed between MDD and full time employment (OR = 0.36, 95% CI = 0.25–0.46, logP = 78), social status (OR = 0.83, 95% CI = 0.77–0.87, logP = 13.3) and education attainment (OR = 0.90, 95% CI = 0.86–0.90, logP = 6.8). We found a monotonic relationship between increasing age and increasing levels of educational attainment. Those with only primary school education have significantly more episodes of MDD (mean 6.5, P-value = 0.009) and have a clinically more severe disorder, while those with higher educational attainment are likely to manifest more comorbid anxiety disorders. Conclusions In China lower socioeconomic position is associated with increased rates of MDD, as it is elsewhere in the world. Significantly more episodes of MDD occur among those with lower educational attainment (rather than longer episodes of disease), consistent with the hypothesis that the lower socioeconomic position increases the likelihood of developing MDD. The phenomenology of MDD varies according to the degree of educational attainment: higher educational attainment not only appears to protect against MDD but alters its presentation, to a more anxious phenotype