Integrative Analysis of Metabolomic,Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein “phosphoglycerate mutase 2” and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.     

Effect of pretreatment temperature on the surface modification of diatomite with trimethylchlorosilane

Diatomite samples from Costa Rica were purified using acidic treatments with hydrochloric acid, thermally treated (400–1000 °C) and then silylated with trimethylchlorosilane in toluene under inert atmosphere. The purification process allows to decrease the concentration of metals presented in the crude diatomite, as is confirmed by X-ray Fluorescence (XRF) Analysis. The silylated materials were analyzed by using Hyperpolarized ¹²⁹Xe Nuclear Magnetic Resonance Spectroscopy (HP ¹²⁹Xe NMR), Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), Scanning Electron Microscopy (SEM), Thermogravimetric Analysis (TGA), rehydration tests, and contact angle measurements. XRD measurements indicate that diatomite is mainly amorphous, but presents several crystalline phases (kaolinite, cristobalite, and quartz). Pretreatments at high temperatures cause changes in those crystalline phases, resulting in more amorphous materials. However, there is no difference in the overall structure of purified and thermally treated diatomite samples with respect to the silylation products. In addition, SEM measurements show no effect over the pore structure of the materials. On the other hand, TGA measurements and rehydration tests show lower losses of water for silylated materials prepared using higher pretreatment temperatures. Moreover, HP ¹²⁹Xe NMR, FTIR, and contact angle measurements evidence a modification due to covalent attachment of Si(CH₃)₃-groups to the surface, which increases for higher pretreatment temperatures. The results provide valuable information about external factors that influence the surface modification of diatomite. This can be useful to control modifications that can be achieved in a similar way.     

Microwave-assisted synthesis and characterization of bioactive chitosan scaffolds doped with Au nanoparticles for mesenchymal stem cells culture

In this work we present a novel strategy for chitosan-based scaffolds. Chitosan is a versatile biopolymer obtained from waste biomass known of its favorable biological properties. Thus it can replace other polymers in the preparation of bioactive scaffolds. To increase its durability chitosan can be crosslinked into form of the hydrogel yet application of toxic crosslinkers may lead to loss of biocompability. Mesenchymal stem cells can be used in cell therapy for advanced wound treatment. However their culture requires special biomaterials application. In this article a novel microwave-assisted synthesis method for bioactive chitosan scaffolds is presented.     

Screening of different agroindustrial by-products for industrial enzymes production by fermentation processes

Agroindustrial by-products are an abundant source of biocompounds that contain valuable nutrients, which are not exploited. In this work, lignocellulosic wastes (LW) were used in submerged fermentation (SmF) and solid-state fermentation (SSF) by Aspergillus niger NRRL3 to obtain valuable enzymes required in industries. SmF using soya bean hulls (SH), wheat bran (WB) and a by-product of wheat flour (F) produced the highest activities of endo-1,4-β-xylanase (Xyl) and endo-1,4-β-D-glucanase (EG) being at least 3 times lower than those obtained by SSF. The highest ratio of Xyl to EG was obtained in SmF with F. Xyl obtained by SmF with WB was the most thermally resistant. The enzymatic extract obtained in SmF using SH presented a high power of saccharification. The production of enzymes for further application such as bioethanol generation process revalue these LW and can help offset growing environmental problems.     

Porous ceramics with tailored pore size and morphology as substrates for coral larval settlement

The growing demand for stony corals as ornamental aquarium animals requires defined aquacultural breeding strategies. For the sexual propagation of corals, material substrates are needed, that attract larvae and support their settlement and development. In this study, five types of highly porous ceramic materials were developed following the example of coral skeleton. The applicability of these settlement substrates was tested using larvae of the stony coral Pocillopora damicornis. Partial sintering of pressed clay pellets, freeze casting of clay and alumina-mullite based slurries and direct foaming of high alkane phase emulsified suspensions (HAPES) using alumina were employed. By the addition of mm-sized spherical polystyrene beads as sacrificial templates during freeze casting (alumina-mullite), superficial pores in the size of the larvae were created. The inorganic substrates featured open porosities between 35% (pressed clay) and 83% (foamed alumina), pore sizes ranging from nm to mm-scale and pore morphologies dominated by interparticle porosity (pressed), lamellar pores (freeze casting) and cellular pore types (direct foaming). The ceramic substrates were incubated in artificial sea water for 3 months to induce necessary biofilm formation and algae growth. Afterwards, individual substrates were exposed to 5 coral larvae, and their settlement behavior was monitored over 14 days. At the end of this period, all ceramic materials were successfully accepted as settlement substrates, with a mean settlement rate of 46.2%, and no significant differences between the substrate types. On samples with large surface superficial pores, a significantly reduced survival of settled larvae (79%) compared to the other porous materials (93–98%) was determined, suggesting a non-ideal surface topography. While alumina foam samples (HAPES) exhibit the most promising results in terms of settlement and survival of larvae, clay-based substrates provide a more economic solution for the sexual propagation of corals in aquaculture.     

Myocardial infarction classification with multi-lead ECG using hidden Markov models and Gaussian mixture models

This study presented a new diagnosis system for myocardial infarction classification by converting multi-lead ECG data into a density model for increasing accuracy and flexibility of diseases detection. In contrast to the traditional approaches, a hybrid system with HMMs and GMMs was employed for data classification. A hybrid approach using multi-leads, i.e., lead-V1, V2, V3 and V4 for myocardial infarction were developed and HMMs were used not only to find the ECG segmentations but also to calculate the log-likelihood value which was treated as statistical feature data of each heartbeat's ECG complex. The 4-dimension feature vector extracted by HMMs was clustered by GMMs with different numbers of distribution (disease and normal data). SVMs classifier was also examined for comparison with our system in experimental result. There were total 1129 samples of heartbeats from clinical data, including 582 data with myocardial infarction and 547 normal data. The sensitivity of this diagnosis system achieved 85.71%, specificity achieved 79.82% and accuracy achieved 82.50% statistically.