A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells

In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference

A central partition of molecular conformational space. II. Embedding 3D structures

A combinatorial model of molecular conformational space that was previously developped (J. Gabarro-Arpa, Comp. Biol. and Chem. 27, (2003) 153-159), had the drawback that structures could not be properly embedded beacause it lacked explicit rotational symmetry. The problem can be circumvented by sorting the elementary 3D components of a molecular system into a finite set of classes that can be separately embedded. This also opens up the possibility of encoding the dynamical states into a graph structure

Evaluating Differential Gene Expression Using RNA-Sequencing: A Case Study in Diet-Induced Mouse Model Associated with Non-Alcoholic Fatty Liver Disease (NAFLD) and CXCL12-Vs- TGFβ Induced Fibroblast to Myofibroblast Phenoconversion

Unlike the genome, cell transcriptome is dynamic and specific for a given cell developmental stage. Transcriptomics study is crucial to understand the functional elements of the genome to divulge molecular constituents of cells. The recent development of high-throughput sequencing technologies has provided an unprecedented method to sequence RNA and it has been emerging as the preferred technology for both characterization and quantification of the cell transcripts. Using “Tailor_Pipeline” we have analyzed diet-induced mouse and stromal fibroblast RNA-Seq samples and deciphers the differentially expressed genes that were significantly up- and downregulated and associated with several metabolic immune responses that presumably associated with liver disease. Analyzing the diet-induced mice model allowed us to encapsulate the transcriptional differences between diet-induced mice that can aid in the understanding of NAFLD and consequent liver pathogenesis. Identification of genes downregulated in metabolic processes and upregulated in immune responses indicate that mice model exhibiting liver disease. Moreover, the finding of a premalignant signature suggests that NAFLD may begin to progress towards hepatocellular carcinoma much earlier than earlier consideration. Tissue fibrosis arises due to overgrowth, scarring of various tissues and is attributed to deposition of the extracellular matrix including collagen, influenced by the actions of several pro-fibrotic proteins that can induce myofibroblast phenoconversion. Though recent transcriptomics analysis reveals the cellular identity, its ability to provide biologically meaningful insights in fibrosis is largely unexplored. To unravel the mechanisms at the genetic level, we have considered TGFβ/TGFβR and CXCL12/CXCR4 transcriptomes in human stromal fibroblasts. Transcriptome profiling technology revealed CXCL12/CXCR4 axis is responsible for the activation of COPII vesicle formation, ubiquitination, and Golgi/ER localization/targeting. Especially, identification of CUL3 and KLHL12 are responsible for the transportation of procollagen from ER to the Golgi. Interestingly, over-expression of CUL3 and KLHL12 are highly correlated with procollagen secretion by CXCL12-treated cells, but not in TGFβ-, treated cells. Moreover, this analysis showed how activation of the CXCL12/CXCR4 axis promotes procollagen I secretion that responsible for the deposition of ECM which is a characteristic of fibrosis

Perbedaan Jumlah Koloni Staphylococcus Epidermidis Pada Media Nutrient Agar Yang Menggunakan Pelarut Akuades Dan Air Minum Dalam Kemasan

Background : The regrowing process is conducted to investigate the contamination of Staphylococcus epidermidis. The inoculation in the specific culture media can be used to regrow the microorganism. Nutrient agaris one of the culture medium used to inoculate. In the preparation of microbiology medium, distilled water is the most-used solvent due to its purity and hygienist. However, pure distilled water is sometimes hard to find and relatively has a high price. The alternative solvent such as bottled-drinking water should be made to substitute the use of distilled water as the solvent. The distilled water and bottled-drinking water have a similar characteristic and both types of water are obtained by almost similar technology process such as filtration and sterilization. Moreover, the small amount of mineral which possibly contains in the bottled-drinking water is safe for microorganism cultivation and it also can not contaminate the culture medium. Thus, the substitution of distilled water with bottled-drinking water is possible as the alternative solvent. The present research aims to investigate the different number of Staphylococcus epidermidis colonies regrowth in nutrient agar which dissolved in distilled water and bottled-drinking water. Method : The present research is categorized as the pre-experiment with comparative statics study. The sample which is the pure colonies suspension of Staphylococcus epidermidisis diluted to 1 million times and inoculated on nutrient agar with a specific solvent. To investigate the effect of solvent, distilled water, and bottled-drinking water are used as the solvent. The inoculated-medium is incubated at 37oC for 48 hours. After 48 hours, the number of colonies is calculated, and the obtained data is parametrically analyzed using the paired t-test. Result: The research has been conducted for 20 times to ensure that the obtained data is repeatable. The result showed that the colonies number of Staphylococcus epidermidisregrowth in nutrient agar which dissolved in distilled water and bottled-drinking water is 113 and 114. The statistical analysis using Paired Sample T-Test supports that there is no significant difference of colonies number in nutrient agar dissolved in distilled water and bottled-drinking water. Conclusion: The research and the statistical analysis show that there is no significant difference of colonies number in nutrient agar dissolved in distilled water and bottled-drinking water