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Abstract

Working with biodiversity data is a computationally intensive process. Numerous applications and services provide options to deal with sequencing and taxonomy data. Professional statistics software are also available to analyze these type of data. However, in-between the two processes there is a huge need to curate biodiversity sample files. Curation involves creating summed abundance values for chosen taxonomy ranks, excluding certain taxa from analysis, and finally merging and downsampling data files. Very few tools, if any, offer a solution to this problem, thus we present Taxamat, a simple data management application that allows for curation of biodiversity data files before they can be imported to other statistics software. Taxamat is a downloadable application for automated curation of biodiversity data featuring taxonomic classification, taxon filtering, sample merging, and downsampling. Input and output files are compatible with most widely used programs. Taxamat is available on the web at http://www.taxamat.com either as a single executable or as an installable package for Microsoft Windows platforms.

Open access

Abstract  

The complex of [Tb2(p-ClBA)6(PHEN)2] [(p-ClBA: p-chlorobenzoate and PHEN: 1,10-phenanthroline) was prepared and characterized by elemental analysis and IR spectroscopy. The thermal behavior of [Tb2(p-ClBA)6(PHEN)2] in dynamic nitrogen atmosphere was investigated by TG-DTG, SEM and IR techniques. By the kinetic method of processing thermal analysis data put forward by Malek et al., it is defined that the kinetic model for the first-step thermal decomposition is SB(m,n). The activation energy E and the pre-exponential factor lnA for this step reaction are 164 kJ mol-1 and 32.80, respectively. The lifetime equation at mass loss of 10% was deduced as lnτ=(-33.0569+20512.36/T by isothermal thermogravimetric analysis.

Restricted access
Acta Alimentaria
Authors: P.Y.Z. Jiang, Y.F. Tian, X.Y. Liu, L.L Wei, Y.X. Bai, X.L. Liu, and S.B. Li

Abstract

Marine organisms have attracted considerable attention in recent years. In this study, peptides with osteogenic activity from Pinctada martensii were isolated and identified. Additionally, the effects of the hydrolysates on MC3T3-E1 cell proliferation and differentiation were evaluated using the MTT and alkaline phosphatase (ALP) assays, respectively. First, trypsin, pancreatin, and neutral protease were used to hydrolyse the intact shellfish. The hydrolysates with the greatest effects on osteoblast proliferation and ALP activity were separated and purified. Second, fraction WP2 was isolated and purified using a Sephadex G-25 column. WP2, which had the highest osteogenic activity, increased cell growth by 48.57 ± 0.05% and ALP activity by 6.27 ± 0.07 mU. Finally, four novel peptides were identified in WP2 (FDNEGKGKLPEEY, IVLDSGDGVTH, IVLDSGDGVSH, and SSENSDLQRQ) by Orbitrap Fusion Lumos Tribrid orbital liquid chromatography-mass spectrometry. Our findings revealed that P. martensii contains peptides with potential osteogenic activity.

Restricted access
Physiology International
Authors: Zs. Sári, T. Kovács, T. Csonka, M. Török, É. Sebő, J. Toth, D. Tóth, E. Mikó, B. Kiss, D. Szeőcs, K. Uray, Zs. Karányi, I. Kovács, G. Méhes, P. Árkosy, and P. Bai

Abstract

Breast cancer is characterized by oncobiosis, the abnormal composition of the microbiome in neoplastic diseases. The biosynthetic capacity of the oncobiotic flora in breast cancer is suppressed, as suggested by metagenomic studies. The microbiome synthesizes a set of cytostatic and antimetastatic metabolites that are downregulated in breast cancer, including cadaverine, a microbiome metabolite with cytostatic properties. We set out to assess how the protein expression of constitutive lysine decarboxylase (LdcC), a key enzyme for cadaverine production, changes in the feces of human breast cancer patients (n = 35). We found that the fecal expression of Escherichia coli LdcC is downregulated in lobular cases as compared to invasive carcinoma of no special type (NST) cases. Lobular breast carcinoma is characterized by low or absent expression of E-cadherin. Fecal E. coli LdcC protein expression is downregulated in E-cadherin negative breast cancer cases as compared to positive ones. Receiver operating characteristic (ROC) analysis of LdcC expression in lobular and NST cases revealed that fecal E. coli LdcC protein expression might have predictive values. These data suggest that the oncobiotic transformation of the microbiome indeed leads to the downregulation of the production of cytostatic and antimetastatic metabolites. In E-cadherin negative lobular carcinoma that has a higher potential for metastasis formation, the protein levels of enzymes producing antimetastatic metabolites are downregulated. This finding represents a new route that renders lobular cases permissive for metastasis formation. Furthermore, our findings underline the role of oncobiosis in regulating metastasis formation in breast cancer.

Open access