Investigating volatile compounds in the Bacteroides secretome

Microorganisms and their hosts communicate with each other by secreting numerous components. This cross-kingdom cell-to-cell signaling involves proteins and small molecules, such as metabolites. These compounds can be secreted across the membrane via numerous transporters and may also be packaged in outer membrane vesicles (OMVs). Among the secreted components, volatile compounds (VOCs) are of particular interest, including butyrate and propionate, which have proven effects on intestinal, immune, and stem cells. Besides short fatty acids, other groups of volatile compounds can be either freely secreted or contained in OMVs. As vesicles might extend their activity far beyond the gastrointestinal tract, study of their cargo, including VOCs, is even more pertinent. This paper is devoted to the VOCs secretome of the Bacteroides genus. Although these bacteria are highly presented in the intestinal microbiota and are known to influence human physiology, their volatile secretome has been studied relatively poorly. The 16 most well-represented Bacteroides species were cultivated; their OMVs were isolated and characterized by NTA and TEM to determine particle morphology and their concentration. In order to analyze the VOCs secretome, we propose a headspace extraction with GC–MS analysis as a new tool for sample preparation and analysis of volatile compounds in culture media and isolated bacterial OMVs. A wide range of released VOCs, both previously characterized and newly described, have been revealed in media after cultivation. We identified more than 60 components of the volatile metabolome in bacterial media, including fatty acids, amino acids, and phenol derivatives, aldehydes and other components. We found active butyrate and indol producers among the analyzed Bacteroides species. For a number of Bacteroides species, OMVs have been isolated and characterized here for the first time as well as volatile compounds analysis in OMVs. We observed a completely different distribution of VOC in vesicles compared to the bacterial media for all analyzed Bacteroides species, including almost complete absence of fatty acids in vesicles. This article provides a comprehensive analysis of the VOCs secreted by Bacteroides species and explores new perspectives in the study of bacterial secretomes in relation the intercellular communication

The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment

Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m(7)G) cap and a poly(A) tail at their 5' and 3' extremities, respectively. The hydrolysis of the m(7)G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners

Late Replication Domains in Polytene and Non-Polytene Cells of Drosophila melanogaster

In D. melanogaster polytene chromosomes, intercalary heterochromatin (IH) appears as large dense bands scattered in euchromatin and comprises clusters of repressed genes. IH displays distinctly low gene density, indicative of their particular regulation. Genes embedded in IH replicate late in the S phase and become underreplicated. We asked whether localization and organization of these late-replicating domains is conserved in a distinct cell type. Using published comprehensive genome-wide chromatin annotation datasets (modENCODE and others), we compared IH organization in salivary gland cells and in a Kc cell line. We first established the borders of 60 IH regions on a molecular map, these regions containing underreplicated material and encompassing ∼12% of Drosophila genome. We showed that in Kc cells repressed chromatin constituted 97% of the sequences that corresponded to IH bands. This chromatin is depleted for ORC-2 binding and largely replicates late. Differences in replication timing between the cell types analyzed are local and affect only sub-regions but never whole IH bands. As a rule such differentially replicating sub-regions display open chromatin organization, which apparently results from cell-type specific gene expression of underlying genes. We conclude that repressed chromatin organization of IH is generally conserved in polytene and non-polytene cells. Yet, IH domains do not function as transcription- and replication-regulatory units, because differences in transcription and replication between cell types are not domain-wide, rather they are restricted to small “islands” embedded in these domains. IH regions can thus be defined as a special class of domains with low gene density, which have narrow temporal expression patterns, and so displaying relatively conserved organization

Microbial Degradation of Poly-3-Hydroxybutyrate in Samples of Agrogenically Changed Soils

Исследована деградация поли-3-гидроксибутирата (П3ГБ) в лабораторных условиях в полевой и огородной почвах с различной структурой микробиоценозов. В огородной почве с высоким содержанием элементов питания общая численность органотрофных бактерий и микромицетов существенно превосходила аналогичные показатели в полевой почве. Выявлены различия в микробных сообществах образцов почв, показано, что в полевой почве доминировали актинобактерии, Arthrobacter и Corynebacterium. В огородной почве доминировали представители родов Bacillus, Micrococcus, Corynebacterium и Pseudomonas. В ходе экспозиции плёнок П3ГБ в почвах микробный состав менялся, в обоих образцах почв увеличивалось количество грамотрицательных палочек. Процесс биоразрушения плёночных образцов П3ГБ в огородной почве протекал в 1,5-1,7 раза активнее по сравнению с полевой почвой (по различию времени достижения одного уровня деградации)Degradation of poly-3-hydroxybutyrate (P3HB) under laboratory conditions was investigated in field and garden soils with different structure of microbial communities. In the vegetable garden soil with a high content of nutrients the total number of organotrophic bacteria and micromycetes was significantly higher than in field soil. The differences in microbial communities of soil samples were estimated. Domination of actinobacteria of Arthrobacter and Corynebacterium genera was found in field soil. In the vegetable garden soil representatives of the genera Bacillus, Micrococcus, Corynebacterium and Pseudomonas dominated. Microbial composition of both soils was changing during the exhibition of P3HB films, with increasing the number of Gram-negative rods. The rate of biodegradation of P3HB film samples in garden soil was 1.5-1.7 times higher then in field soi

Pedagogical tact as a component of a teacher’s moral culture

The research objective was to describe the phenomenon of pedagogical tact in the context of the cultural and moral traditions of Russian and foreign pedagogical practices. The authors used comparative historical analysis of scientific-pedagogical and historical-pedagogical sources, chronological and comparative methods, and generalization of historical and pedagogical data. According to deontological approach, pedagogical tact is a professional agreement on teacher’s standards of conduct, while the moral-cultural approach views pedagogical tact as a component of teacher’s moral culture and manners. Thus, there is a contradiction in these interpretations of pedagogical tact, which is aggravated in Russia by standardization of pedagogical activityLa meta de la investigación fue describir el tacto pedagógico en el marco de las tradiciones pedagógicas culturales y éticas de Rusia y otros países. Los autores hicieron un análisis comparativo histórico de recursos científicos históricos y pedagógicos, usaron métodos cronológicos y comparativos y generalizaron los datos pedagógicos. En el enfoque deontológico el tacto pedagógico es un acuerdo profesional sobre las normas de conducta de maestros, mientras que en el enfoque ético cultural es un componente del ademán y de la cultura de maestros. Así hay una contradicción entre las interpretaciones y en Rusia eso se empeora por la estandarización de actividades pedagógica

Dual Effect of Low-Molecular-Weight Bioregulators of Bacterial Origin in Experimental Model of Asthma

Asthma is one of the most common noncommunicable diseases, affecting over 200 million people. A large number of drugs control asthma attacks, but there is no effective therapy. Identification of reasons for asthma and preventing this disease is a relevant task. The influence of bacterial components is necessary for the normal development of the immune system and the formation of an adequate immune response to antigens. In the absence of microorganisms or their insufficient exposure, the prerequisites are formed for excessive reactivity to harmless antigens. In the present study, we analyzed cellular and humoral factors in a standard mouse model of OVA-induced asthma modified by 5-fold intraperitoneal injection of bacterial cell wall fragments of glucosaminylmuramyl dipeptide (GMDP) 5 μg/animal or 1 μg lipopolysaccharide (LPS) per animal for 5 days before sensitization by ovalbumin (OVA). Preliminary administration of LPS or GMDP to animals significantly reduced goblet cells as well as the number of neutrophils, lymphocytes, and eosinophils in bronchoalveolar lavage, wherein GMDP corrected neutrophilia to a 2-fold degree, and LPS reduced the severity of eosinophilia by 1.9 times. With OVA administration of GMDP or LPS at the sensitization stage, an increase in the total number of bronchoalveolar lavage cells due to neutrophils, macrophages, lymphocytes, and eosinophils in relation to the group with asthma without GMDP or LPS was observed. The administration of GMDP or LPS to normal mice without asthma for 5 days had no statistically significant effect on the change in the number and population composition of cells in bronchoalveolar lavage in comparison with the control group receiving PBS. As a result of a study in a mouse model of asthma, a dual effect of LPS and GMDP was established: the introduction of LPS or GMDP before sensitization reduces neutrophilia and eosinophilia, while the introduction of LPS or GMDP together with an allergen significantly increases neutrophilia and eosinophilia. The study of the immunoglobulin status shows that in normal-asthma mice, GMDP and LPS slightly increase IgA in bronchoalveolar lavage; at the same time, in the asthma model, injections of GMDP or LPS before sensitization contribute to a significant decrease in IgA (2.6 times and 2.1 times, respectively) in BALF and IgE (2.2 times and 2.0 times, respectively) in blood serum. In an experimental model of asthma, the effect of GMDP and LPS was multidirectional: when they are repeatedly administered before sensitization, the bacterial components significantly reduce the severity of the allergic process, while in the case of a joint injection with an allergen, they increase the influx of macrophages, lymphocytes, and neutrophils into the lungs, which can aggravate the course of pathological process. Thus, the insufficient effect of antigens of a bacterial nature, in particular, with prolonged use of antibiotics can be compensated for by substances based on low-molecular-weight bioregulators of bacterial origin to establish the missing signals for innate immunity receptors, whose constant activation at a certain level is necessary to maintain homeostasis

Dual Effect of Low-Molecular-Weight Bioregulators of Bacterial Origin in Experimental Model of Asthma

Asthma is one of the most common noncommunicable diseases, affecting over 200 million people. A large number of drugs control asthma attacks, but there is no effective therapy. Identification of reasons for asthma and preventing this disease is a relevant task. The influence of bacterial components is necessary for the normal development of the immune system and the formation of an adequate immune response to antigens. In the absence of microorganisms or their insufficient exposure, the prerequisites are formed for excessive reactivity to harmless antigens. In the present study, we analyzed cellular and humoral factors in a standard mouse model of OVA-induced asthma modified by 5-fold intraperitoneal injection of bacterial cell wall fragments of glucosaminylmuramyl dipeptide (GMDP) 5 μg/animal or 1 μg lipopolysaccharide (LPS) per animal for 5 days before sensitization by ovalbumin (OVA). Preliminary administration of LPS or GMDP to animals significantly reduced goblet cells as well as the number of neutrophils, lymphocytes, and eosinophils in bronchoalveolar lavage, wherein GMDP corrected neutrophilia to a 2-fold degree, and LPS reduced the severity of eosinophilia by 1.9 times. With OVA administration of GMDP or LPS at the sensitization stage, an increase in the total number of bronchoalveolar lavage cells due to neutrophils, macrophages, lymphocytes, and eosinophils in relation to the group with asthma without GMDP or LPS was observed. The administration of GMDP or LPS to normal mice without asthma for 5 days had no statistically significant effect on the change in the number and population composition of cells in bronchoalveolar lavage in comparison with the control group receiving PBS. As a result of a study in a mouse model of asthma, a dual effect of LPS and GMDP was established: the introduction of LPS or GMDP before sensitization reduces neutrophilia and eosinophilia, while the introduction of LPS or GMDP together with an allergen significantly increases neutrophilia and eosinophilia. The study of the immunoglobulin status shows that in normal-asthma mice, GMDP and LPS slightly increase IgA in bronchoalveolar lavage; at the same time, in the asthma model, injections of GMDP or LPS before sensitization contribute to a significant decrease in IgA (2.6 times and 2.1 times, respectively) in BALF and IgE (2.2 times and 2.0 times, respectively) in blood serum. In an experimental model of asthma, the effect of GMDP and LPS was multidirectional: when they are repeatedly administered before sensitization, the bacterial components significantly reduce the severity of the allergic process, while in the case of a joint injection with an allergen, they increase the influx of macrophages, lymphocytes, and neutrophils into the lungs, which can aggravate the course of pathological process. Thus, the insufficient effect of antigens of a bacterial nature, in particular, with prolonged use of antibiotics can be compensated for by substances based on low-molecular-weight bioregulators of bacterial origin to establish the missing signals for innate immunity receptors, whose constant activation at a certain level is necessary to maintain homeostasis

Microbial Degradation of Poly-3-Hydroxybutyrate in Samples of Agrogenically Changed Soils

Исследована деградация поли-3-гидроксибутирата (П3ГБ) в лабораторных условиях в полевой и огородной почвах с различной структурой микробиоценозов. В огородной почве с высоким содержанием элементов питания общая численность органотрофных бактерий и микромицетов существенно превосходила аналогичные показатели в полевой почве. Выявлены различия в микробных сообществах образцов почв, показано, что в полевой почве доминировали актинобактерии, Arthrobacter и Corynebacterium. В огородной почве доминировали представители родов Bacillus, Micrococcus, Corynebacterium и Pseudomonas. В ходе экспозиции плёнок П3ГБ в почвах микробный состав менялся, в обоих образцах почв увеличивалось количество грамотрицательных палочек. Процесс биоразрушения плёночных образцов П3ГБ в огородной почве протекал в 1,5-1,7 раза активнее по сравнению с полевой почвой (по различию времени достижения одного уровня деградации)Degradation of poly-3-hydroxybutyrate (P3HB) under laboratory conditions was investigated in field and garden soils with different structure of microbial communities. In the vegetable garden soil with a high content of nutrients the total number of organotrophic bacteria and micromycetes was significantly higher than in field soil. The differences in microbial communities of soil samples were estimated. Domination of actinobacteria of Arthrobacter and Corynebacterium genera was found in field soil. In the vegetable garden soil representatives of the genera Bacillus, Micrococcus, Corynebacterium and Pseudomonas dominated. Microbial composition of both soils was changing during the exhibition of P3HB films, with increasing the number of Gram-negative rods. The rate of biodegradation of P3HB film samples in garden soil was 1.5-1.7 times higher then in field soi