Abstracts of the 5th International Conference on Lactoferrin / Résumés du 5e symposium internationeige sur la lactoferrin

2002 ◽  
Vol 80 (1) ◽  
pp. 137-168
Keyword(s):  
Gene Expression ◽  
Cancer Treatment ◽  
Structure Function ◽  
Gene Expression Regulation ◽  
Three Dimensional ◽  
Antimicrobial Properties ◽  
Dimensional Structure ◽  
International Conference ◽  
Immunological Effects ◽  
Potential Use

Sixty-three abstracts are presented from the 5th International Conference on Lactoferrin "Structure, Function and Applications" in Banff, Alberta. The conference focused on lactoferrin’s three-dimensional structure, antimicrobial properties, immunological effects, potential use in cancer treatment, gene expression regulation, and receptors.

Comparison of gene expression and activation of transcription factors in organoid-derived monolayer intestinal epithelial cells and organoids

2021 ◽  
Author(s):  
Yu Takahashi ◽  
Yu Inoue ◽  
Keitaro Kuze ◽  
Shintaro Sato ◽  
Makoto Shimizu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Gene Expression Regulation ◽  
Intestinal Epithelial Cells ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Dependent Manner ◽  
Intestinal Epithelial

Abstract Intestinal organoids better represent in vivo intestinal properties than conventionally used established cell lines in vitro. However, they are maintained in three-dimensional culture conditions that may be accompanied by handling complexities. We characterized the properties of human organoid-derived two-dimensionally cultured intestinal epithelial cells (IECs) compared with those of their parental organoids. We found that the expression of several intestinal markers and functional genes were indistinguishable between monolayer IECs and organoids. We further confirmed that their specific ligands equally activate intestinal ligand-activated transcriptional regulators in a dose-dependent manner. The results suggest that culture conditions do not significantly influence the fundamental properties of monolayer IECs originating from organoids, at least from the perspective of gene expression regulation. This will enable their use as novel biological tools to investigate the physiological functions of the human intestine.

A murrel cysteine protease, cathepsin L: bioinformatics characterization, gene expression and proteolytic activity

Biologia ◽  
2014 ◽  
Vol 69 (3) ◽  
Author(s):  
Venkatesh Kumaresan ◽  
Prasanth Bhatt ◽  
Rajesh Palanisamy ◽  
Annie Gnanam ◽  
Mukesh Pasupuleti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Infections ◽  
Cathepsin L ◽  
Three Dimensional ◽  
Structural Similarity ◽  
Data Bank ◽  
Minimum Free Energy ◽  
Dimensional Structure ◽  
Peptide Bonds ◽  
Gene Expression Studies

AbstractCathepsin L, a lysosomal endopeptidase, is a member of the peptidase C1 family (papain-like family) of cysteine proteinases that cleave peptide bonds of lysosomal proteins. In this study, we report a cathepsin L sequence identified from the constructed cDNA library of striped murrel Channa striatus (designated as CsCath L) using genome sequencing FLXTM technology. The full-length CsCath L contains three eukaryotic thiol protease domains at positions 134-145, 278-288 and 299-318. Phylogenetic analysis revealed that the CsCath L was clustered together with other cathepsin L from teleosts. The three-dimensional structure of CsCath L modelled by the I-Tasser program was compared with structures deposited in the Protein Data Bank to find out the structural similarity of CsCath L with experimentally identified structures. The results showed that the CsCath L exhibits maximum structural identity with pro-cathepsin L from human. The RNA fold structure of CsCath L was predicted along with its minimum free energy (−471.93 kcal/mol). The highest CsCath L gene expression was observed in liver, which was also significantly higher (P < 0.05) than that detected in other tissues taken for analysis. In order to investigate the mRNA transcription profile of CsCath L during infection, C. striatus were injected with fungus (Aphanomyces invadans) and bacteria (Aeromonas hydrophila) and its expression was up-regulated in liver at various time points. Similar to gene expression studies, the highest CsCath L enzyme activity was also observed in liver and its activity was up-regulated by fungal and bacterial infections.

Three-dimensional imaging of nucleosomes from transcriptionally active genes using electron spectroscopic imaging

1996 ◽  
Vol 54 ◽  
pp. 54-55
Author(s):  
G. J. Czarnota ◽  
D. P. Bazett-Jones ◽  
F. P. Ottensmeyer
Keyword(s):  
Gene Expression ◽  
Three Dimensional ◽  
Spectroscopic Imaging ◽  
Dimensional Structure ◽  
Crystallographic Structure ◽  
Electron Spectroscopic Imaging ◽  
Nucleosome Structure ◽  
Active Genes

The three-dimensional structure of the nucleosome was determined using particles purified from transcriptionally active genes in conjunction with electron spectroscopic imaging, and quaternion-assisted angular reconstitution procedures. The results reveal a configuration which is very different from the canonical compact crystallographic structure for this fundamental chromosome subunit, implying a structural disruption of the nucleosome with the activation of gene expression in accord with numerous physico-chemical observations.Previous analyses of nucleosomes purified from transcriptionally quiescent genes have indicated numerous structural states dependent on factors in vitro which modify charge based interactions in nucleoprotein complexes. Nucleosomes from transcriptionally active genes undergo chemical alterations in vivo which similarly modify charge based interactions. In order to investigate the effects of the gene expression associated chemical alterations on nucleosome structure, particles were purified from transcriptionally active genes using mercury affinity chromatography. These nucleosome particles are hyperacetylated with respect to particles from transcriptionally quiescent genes. Here additionally, sulphydryls normally buried within the protein core of the transcriptionally inactive particle are exposed to chemical modifying agents thus facilitating purification as described.

scholarly journals A proline rich protein from the gingival seal around teeth exhibits antimicrobial properties against Porphyromonas gingivalis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aurélien Fouillen ◽  
Charline Mary ◽  
Katia Julissa Ponce ◽  
Pierre Moffatt ◽  
Antonio Nanci
Keyword(s):  
Porphyromonas Gingivalis ◽  
Calcium Binding ◽  
Mammalian Cells ◽  
Three Dimensional ◽  
Antimicrobial Properties ◽  
In Silico Analysis ◽  
The Body ◽  
Dimensional Structure ◽  
Molecular Characteristics ◽  
Bacterial Number

AbstractThe gingival seal around teeth prevents bacteria from destroying the tooth-supporting tissues and disseminating throughout the body. Porphyromonas gingivalis, a major periodontopathogen, degrades components of the specialized extracellular matrix that mediates attachment of the gingiva to the tooth. Of these, secretory calcium-binding phosphoprotein proline-glutamine rich 1 (SCPPPQ1) protein has a distinctive resistance to degradation, suggesting that it may offer resistance to bacterial attack. In silico analysis of its amino acid sequence was used to explore its molecular characteristics and to predict its two- and three-dimensional structure. SCPPPQ1 exhibits similarities with both proline-rich and cationic antimicrobial proteins, suggesting a putative antimicrobial potential. A combination of imaging approaches showed that incubation with 20 μM of purified SCPPPQ1 decrease bacterial number (p < 0.01). Fluorescence intensity decreased by 70% following a 2 h incubation of Porphyromonas gingivalis with the protein. Electron microscopy analyses revealed that SCPPPQ1 induced bacterial membrane disruption and breaches. While SCPPPQ1 has no effect on mammalian cells, our results suggest that it is bactericidal to Porphyromonas gingivalis, and that this protein, normally present in the gingival seal, may be exploited to maintain a healthy seal and prevent systemic dissemination of bacteria.

scholarly journals Computational-approach understanding the structure-function prophecy of Fibrinolytic Protease RFEA1 from Bacillus cereus RSA1

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11570
Author(s):  
Chhavi Sharma ◽  
Arti Nigam ◽  
Rajni Singh
Keyword(s):  
Structure Function ◽  
Bacillus Cereus ◽  
Structural Model ◽  
Three Dimensional ◽  
Conformational Space ◽  
Dimensional Structure ◽  
After Effects ◽  
Short Life Span ◽  
Therapeutic Enzymes

Microbial fibrinolytic proteases are therapeutic enzymes responsible to ameliorate thrombosis, a fatal cardiac-disorder which effectuates due to excessive fibrin accumulation in blood vessels. Inadequacies such as low fibrin specificity, lethal after-effects and short life-span of available fibrinolytic enzymes stimulates an intensive hunt for novel, efficient and safe substitutes. Therefore, we herewith suggest a novel and potent fibrinolytic enzyme RFEA1 from Bacillus cereus RSA1 (MK288105). Although, attributes such as in-vitro purification, characterization and thrombolytic potential of RFEA1 were successfully accomplished in our previous study. However, it is known that structure-function traits and mode of action significantly aid to commercialization of an enzyme. Also, predicting structural model of a protein from its amino acid sequence is challenging in computational biology owing to intricacy of energy functions and inspection of vast conformational space. Our present study thus reports In-silico structural-functional analysis of RFEA1. Sequence based modelling approaches such as—Iterative threading ASSEmbly Refinement (I-TASSER), SWISS-MODEL, RaptorX and Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) were employed to model three-dimensional structure of RFEA1 and the modelled RFEA1 was validated by structural analysis and verification server (SAVES v6.0). The modelled crystal structure revealed the presence of high affinity Ca1 binding site, associated with hydrogen bonds at Asp147, Leu181, Ile185 and Val187residues. RFEA1 is structurally analogous to Subtilisin E from Bacillus subtilis 168. Molecular docking analysis using PATCH DOCK and FIRE DOCK servers was performed to understand the interaction of RFEA1 with substrate fibrin. Strong RFEA1-fibrin interaction was observed with high binding affinity (−21.36 kcal/mol), indicating significant fibrinolytic activity and specificity of enzyme RFEA1. Overall, the computational research suggests that RFEA1 is a subtilisin-like serine endopeptidase with proteolytic potential, involved in thrombus hydrolysis.

scholarly journals The presence of copy number variants in specific topologically associating domains has prognostic value in many cancer types

2019 ◽  
Author(s):  
Lifei Li ◽  
Nicolai K. H. Barth ◽  
Christian Pilarsky ◽  
Leila Taher
Keyword(s):  
Gene Expression ◽  
Prognostic Value ◽  
Gene Expression Regulation ◽  
Cox Regression ◽  
Three Dimensional ◽  
Regulatory Elements ◽  
Cancer Genes ◽  
Cox Regression Analysis ◽  
Topologically Associating Domains ◽  
Cancer Types

AbstractThe human genome is organized into topologically associating domains (TADs), which represent contiguous regions with a higher frequency of intra-interactions as opposed to inter-interactions. TADs contribute to gene expression regulation by restricting interactions between regulatory elements, and their disruption by genomic rearrangements can result in altered gene expression and, ultimately, in cancer. Here, we provide a proof-of-principle that mutations within TADs can be used to predict the survival of cancer patients. For this purpose, we first constructed a set of 1,467 TADs representing the three-dimensional organization of genome across 24 normal human tissues. We then used Cox regression analysis to assess the prognostic value of the TADs in different cancer types, and identified a total of 35 TADs that were prognostic for at least one of nine cancer types. Interestingly, only 46% of the prognostic TADs comprised one or more genes with a known causal association with cancer. Moreover, for those TADs encompassing such a gene, the prognostic effect of the TAD was only directed related to the presence/absence of mutations in the gene in 13% of the cases. These observations indicate that the predictive power of a large proportion of the prognostic TADs is independent of whether pan-cancer genes are mutated or not. Furthermore, 34% of the 35 prognostic TADs showed strong structural perturbations in the cancer genome, which might mediate cancer development and progression. This study has important implications for the interpretation of cancer-related non-coding mutations and offer insights to new strategies for personalizing cancer medicine.

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