The presented analysis concerns the inter-domain and inter-protein interface in protein complexes. We propose extending the traditional understanding of the protein domain as a function of local compactness with an additional criterion which refers to the presence of a well-defined hydrophobic core. Interface areas in selected homodimers vary with respect to their contribution to share as well as individual (domain-specific) hydrophobic cores. The basic definition of a protein domain, i.e., a structural unit characterized by tighter packing than its immediate environment, is extended in order to acknowledge the role of a structured hydrophobic core, which includes the interface area. The hydrophobic properties of interfaces vary depending on the status of interacting domains—In this context we can distinguish: (1) Shared hydrophobic cores (spanning the whole dimer); (2) Individual hydrophobic cores present in each monomer irrespective of whether the dimer contains a shared core. Analysis of interfaces in dystrophin and utrophin indicates the presence of an additional quasi-domain with a prominent hydrophobic core, consisting of fragments contributed by both monomers. In addition, we have also attempted to determine the relationship between the type of interface (as categorized above) and the biological function of each complex. This analysis is entirely based on the fuzzy oil drop model.

Background: The aim of this study was to investigate the role of urine-derived extracellular vesicles (uEVs) in diabetic kidney disease (DKD) in patients diagnosed with type 2 diabetes mellitus (T2DM). Methods: UEVs were characterized by size distribution and microRNA content by next-generation small RNA sequencing and quantitative reverse transcription PCR. Results: A subset of sixteen miRNAs enriched in T2DM patients with DKD, including hsa-miR-514a-5p, hsa-miR‑451a, hsa-miR-126-3p, hsa-miR-214, or hsa-miR‑503 was identified. Eight miRNAs as hsa-miR-21-3p, hsa-miR-4792, hsa-miR‑375, hsa-miR-1268a, hsa-miR-501-5p, or hsa-miR-582 were downregulated. Prediction of potential target genes and pathway enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) confirmed possible functions related to cellular processes such as apoptosis, inflammation, and tissue remodeling, that promote diabetic complications, such as DKD. Among them, hsa-miR-375, hsa-miR-503, and hsa-miR-451a make important contribution. Additionally, downregulated hsa-miR-582-5p has not been reported so far in any diabetes-related pathways. Conclusions: This study revealed the most significant miRNAs in uEVs of patients with T2DM. However, as this is a bioinformatic prediction that we performed based on the putative targets of the identified miRNAs. Thus, further in vitro functional studies are needed to confirm our findings. Knowing the fact that EVs are crucial in transferring miRNAs, there is a great need toto discover their involvement in the pathomechanism of T2DM-related kidney disease.

The type of diet not only affects the composition of the oral microflora but is also one of the more critical factors associated with an increased risk of Parkinson’s disease, PD. This study compared diet preferences and oral microbiota profiles in patients with PD vs. healthy controls. This study compared the oral microbiota composition of 59 patients with PD and 108 healthy controls (without neurodegeneration) using 16S rRNA gene amplicon sequencing. According to results, oral microbiota in patients with PD is different compared from healthy controls. In particular, decreased abundance of Proteobacteria, Pastescibacteria, and Tenercutes was observed. The oral cavity of patients with PD was characterized by the high relative abundance of bacteria from the genera Prevotella, Streptococcus, and Lactobaccillus. There were also differences in food preferences between patients with PD and healthy controls, which revealed significantly higher intake of margarine, fish, red meat, cereals products, avocado, and olives in the patients with PD relative to healthy controls. Strong positive and negative correlations between specific food products and microbial taxa were identified.

The aim of the study was to evaluate the frequency of breakfast and other meal consumption by adolescents and to assess the relationship between the first and the last meal consumption and sex, body mass index (BMI), and middle school and high school students’ education level. The study was conducted in 2013–2014 among 3009 students (1658 girls and 1351 boys) from middle s and high schools in Krakow and Silesia (Poland). The data was obtained from questionnaires that were analyzed with a logistic regression model for measurable and dichotomous variables. Breakfast consumers were seen to eat other meals (second breakfast, lunch, dessert, supper) significantly more often than breakfast skippers. The main meal consumption habits depend on sex and change as adolescents age. Being a girl and a high school student predisposed participants to skip breakfast and supper more often. The BMI of breakfast consumers does not differ significantly from the BMI of breakfast skippers, so BMI might thus not be a sufficient marker of breakfast consumption regularity and dietary habits in an adolescent group. The importance of regularly eaten meals, especially breakfast, together with adequate daily dietary energy intake are beneficial for physical and psychological development and cannot be overestimated in nutritional education and it is necessary to promote healthy eating behavior for well-being in later adult life.

(1) Background: Static foot deformities, including hallux valgus, are common deformities. The subject under consideration is the role of extrinsic and intrinsic muscles working within muscular systems that shape the arches of the foot and the alignment of the toes. (2) Methods: Based on a literature review, the muscle systems were analyzed. The systems under consideration were as follows: “tendon stirrup” (system I); muscles complementary to the tendon stirrup (system II); “foot lever” (system III); muscles complementary to system III (system IV); “reins of hallux” (system V), a muscular system having distal inserts on the hallux. The shape of the foot arches was analyzed in this context. (3) Results: The correct arch architecture of the foot stabilized mainly by the extrinsic muscle systems determining the function of the intrinsic muscle systems of the foot is described. The proper function of muscular systems shaping the arches of the foot is a prerequisite for the proper function of muscles directly responsible for the alignment of the big toe (hallux) and other foot toes. (4) Conclusion: The action of muscles should be considered in groups (systems) because the action of the group of muscles results in the creation of a new quality of movement. The analysis of individual muscle-pulling forces, especially the moments of force in the weight-bearing foot, may lead to extremely incorrect conclusions. In pathological cases, the restoration of the correct arches of the foot guarantees the recovery of the correct function of the pulling forces of the foot muscles responsible for the physiological alignment of the hallux. This is especially important concerning conservative and surgical treatment of hallux valgus.

The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of “multi-omics” data. Our tool supports a range of complex analyses, including – among others – low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions. We demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses. The DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for “multi-omics” data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.