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S. D. Kalmykova G. P. Arapidi A. S. Urban M. S. Osetrova V. D. Gordeeva V. T. Ivanov V. M. Govorun 《Russian Journal of Bioorganic Chemistry》2018,44(4):367-385
Over the past decade, tools of omics technologies have generated a large amount of data in various repositories, which are of interest for meta-analysis today. Now, researchers in the field of proteomics and peptidomics focus not on sequencing, but on functions performed by molecules and metabolic interactions, in which the proteins or peptides participate. As a result of a single LC-MS/MS analysis, several thousand unique peptides can be identified, each of which may be bioactive. A classic technique for determining the peptide function is a direct experiment. Bioinformatics approaches as a preliminary analysis of potential biological functions are an important step and are able to significantly reduce time and cost of experimental verification. This article provides an overview of computational methods for predicting biological functions of peptides. Approaches based on machine learning, which are the most popular today, algorithms using structural, evolutionary, or statistical patterns, as well as methods based on molecular docking, are considered. Databases of bioactive peptides are reported, providing information necessary to construct new algorithms for predicting biological functions. Attention is paid to the characteristics of peptides, on the basis of which it is possible to draw conclusions about their bioactivity. In addition, the report provides a list of online services that may be used by researchers to analyze potential activities of peptides with which they work. 相似文献
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N.?A.?LogvinaEmail author V.?O.?Shender G.?P.?Arapidi T.?D.?Holina 《Russian Journal of Bioorganic Chemistry》2018,44(2):129-139
Export of biologically active compounds is essential for any living cell. Transport of bioactive molecules through a cellular membrane can be active, or passive, or vesicular. In the past decade, vesicular transduction of intercellular signals has attracted great interest in the scientific community. An extremely important role of the vesicle transduction has been established for almost all processes in a living body. Not only profiles of protein and RNA expression in a cell, but also its secretome change during various pathologies, including cancer development. The enhanced secretion of vesicles by transformed cells is one important factor in creating a special microenvironment that favors tumor progression. At present, a role of exosomes has been demonstrated for such important processes as an epithelial-mesenchymal transition, angiogenesis, metastatic niche formation, chemotherapeutic resistance, and interaction with the immune system. The special biological role of the extracellular vesicles and their basic differences depend on their molecular composition. Therefore, special protein and lipid markers are responsible for a vesicular targeted delivery with information due to the preferable interaction with cells of a definite type. The exosomes of cancer cells can facilitate apoptosis or growth of neighboring malignant cells depending on the exosome composition. These and other special features of the extracellular vesicles make studies of their composition and role especially interesting and attract significant attention from researchers. Despite the rapid progress in this field, there are still many unresolved problems, such as a search for specific markers which allow identification of different types of vesicles or vesicles secreted by distinct cells, as well as screening of vesicular markers of cancers and other diseases that are associated with disorders in a functioning immune system. This review is mainly focused on the role of intercellular vesicular transport of bioorganic molecules in cancer progression. We believe that a successful treatment of oncological diseases is impossible without an understanding of the intercellular communication of both cancer cells between each other and with other systems of an organism and with a concept of an active participation of the cell-secreted vesicles in this process. 相似文献
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CS Bedetti NC Jorge FCG Trigueiro GP Bragança LV Modolo 《Biotechnic & histochemistry》2018,93(2):149-154
We report a new method for histochemical localization of cytokinins (CKs) in plant tissues based on bromophenol blue/silver nitrate staining. The method was validated by immunohistochemistry using anti-trans-zeatin riboside antibody. Indole-3-acetic acid (auxin, IAA) was localized by anti-IAA antibody in plant tissues as a proof for IAA histolocalization. We used root sections, because they are major sites of CKs synthesis, and insect galls of Piptadenia gonoacantha that accumulate IAA. Immunostaining confirmed the presence of zeatin and sites of accumulation of IAA indicated by histochemistry. The colors developed by histochemical reactions in free-hand sections of plant tissues were similar to those obtained by thin layer chromatography (TLC), which reinforced the reactive sites of zeatin. The histochemical method for detecting CKs is useful for galls and roots, whereas IAA detection is more efficient for gall tissues. Therefore, galls constitute a useful model for validating histochemical techniques due to their rapid cell cycles and relatively high accumulation of plant hormones. 相似文献
15.
In vertebrates and the cephalochordate, amphioxus, the closest vertebrate
relative, Hox genes are linked in a single cluster. Accompanying the
emergence of higher vertebrates, the Hox gene cluster duplicated in either
a single step or multiple steps, resulting in the four-cluster state
present in teleosts and tetrapods. Mammalian Hox clusters (designated A, B,
C, and D) extend over 100 kb and are located on four different chromosomes.
Reconstructing the history of the duplications and its relation to
vertebrate evolution has been problematic due to the lack of alignable
sequence information. In this study, the problem was approached by
conducting a statistical analysis of sequences from the fibrillar-type
collagens (I, II, III, and IV), genes closely linked to each Hox cluster
which likely share the same duplication history as the Hox genes. We find
statistical support for the hypothesis that the cluster duplication
occurred as multiple distinct events and that the four-cluster situation
arose by a three- step sequential process.
相似文献
16.
The alcohol dehydrogenase (Adh) gene was isolated from Drosophila simulans
and D. mauritiana, and the DNA sequence of a 4.6-kb region, containing the
structural gene and flanking sequence, was determined for each. These
sequences were compared with the Adh region of D. melanogaster to
characterize changes that occur in the Drosophila genome during evolution
and to identify conserved sequences of functional importance. Drosophila
simulans and D. mauritiana Adh are organized in a manner similar to that of
D. melanogaster Adh, including the presence of two promoters for the single
Adh gene. This study identified conserved flanking elements that, in
conjunction with other studies, suggest regions that may be involved in the
control of Adh expression. Inter- and intraspecies comparisons revealed
differences in the kinds of sequence changes that have accumulated.
Sequence divergence in and around the Adh gene was used to assess inter-
and intraspecies evolutionary relationships. Finally, there appears to be
an unrelated structural gene located directly 3' of the Adh transcribed
region.
相似文献
17.
Central CCL2 signaling onto MCH neurons mediates metabolic and behavioral adaptation to inflammation
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Ophélia Le Thuc Céline Cansell Miled Bourourou Raphaël GP Denis Katharina Stobbe Nadège Devaux Alice Guyon Julie Cazareth Catherine Heurteaux William Rostène Serge Luquet Jean‐Louis Nahon Carole Rovère 《EMBO reports》2016,17(12):1738-1752
Sickness behavior defines the endocrine, autonomic, behavioral, and metabolic responses associated with infection. While inflammatory responses were suggested to be instrumental in the loss of appetite and body weight, the molecular underpinning remains unknown. Here, we show that systemic or central lipopolysaccharide (LPS) injection results in specific hypothalamic changes characterized by a precocious increase in the chemokine ligand 2 (CCL2) followed by an increase in pro‐inflammatory cytokines and a decrease in the orexigenic neuropeptide melanin‐concentrating hormone (MCH). We therefore hypothesized that CCL2 could be the central relay for the loss in body weight induced by the inflammatory signal LPS. We find that central delivery of CCL2 promotes neuroinflammation and the decrease in MCH and body weight. MCH neurons express CCL2 receptor and respond to CCL2 by decreasing both electrical activity and MCH release. Pharmacological or genetic inhibition of CCL2 signaling opposes the response to LPS at both molecular and physiologic levels. We conclude that CCL2 signaling onto MCH neurons represents a core mechanism that relays peripheral inflammation to sickness behavior. 相似文献
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Anufrieva K. S. Shender V. O. Arapidi G. P. Lagarkova M. A. Govorun V. M. 《Russian Journal of Bioorganic Chemistry》2019,45(1):1-8
Russian Journal of Bioorganic Chemistry - The spliceosome is necessary for the removal of intron sequences in transcribed pre-mRNA in eukaryotic cells. More than 200 proteins are involved in the... 相似文献
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Background
The Neotropical ovenbird-woodcreeper family (Furnariidae) is an avian group characterized by exceptionally diverse ecomorphological adaptations. For instance, members of the family are known to construct nests of a remarkable variety. This offers a unique opportunity to examine whether changes in nest design, accompanied by expansions into new habitats, facilitates diversification. We present a multi-gene phylogeny and age estimates for the ovenbird-woodcreeper family and use these results to estimate the degree of convergent evolution in both phenotype and habitat utilisation. Furthermore, we discuss whether variation in species richness among ovenbird clades could be explained by differences in clade-specific diversification rates, and whether these rates differ among lineages with different nesting habits. In addition, the systematic positions of some enigmatic ovenbird taxa and the postulated monophyly of some species-rich genera are evaluated. 相似文献20.
Ziganshin R Arapidi G Azarkin I Zaryadieva E Alexeev D Govorun V Ivanov V 《Journal of Proteomics》2011,74(5):595-606
This report describes a new method for desorption of low-molecular weight (LMW) peptides from abundant blood proteins for use in subsequent mass spectrometry analyses. Heating of diluted blood serum to 98°C for 15min resulted in dissociation of LMW peptides from the most abundant blood proteins. Application of blood plasma/serum fractionation using magnetic beads with a functionalized surface followed by heating of the resultant fractions significantly increases the number of LMW peptides detected by MALDI-TOF MS, enhances the general reproducibility of mass spectrometry profiles and considerably increases the number of identified blood serum peptides by LC-MS/MS using an Agilent 6520 Accurate-Mass Q-TOF. 相似文献