Abstract Gut microbiota establishment and further microbiota shifts are very important for maintaining host health throughout life. There are some factors, including genetics, the mother's health and ...diet, delivery mode, breast or formula feeding, that may influence the gut microbiota. By the end of approximately the first 3 y of life, the gut microbiota becomes an adult-like stable system. Once established, 60 to 70% of the microbiota composition remains stable throughout life, but 30 to 40% can be altered by changes in the diet and other factors such as physical activity, lifestyle, bacterial infections, and antibiotic or surgical treatment. Diet-related factors that influence the gut microbiota in people of all ages are of great interest. Nutrition may have therapeutic success in gut microbiota correction. This review describes current evidence concerning the links between gut microbiota composition and dietary patterns throughout life.
A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model ...analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging type of genomic data - containing sequences of all genes from the totality of a complex microbial community. Recently, researchers started to analyze metagenomes using reference-free methods based on the analysis of oligonucleotides (k-mers) frequency spectrum previously applied to isolated genomes. However, little is known about their correlation with the existing approaches for metagenomic feature extraction, as well as the limits of applicability. Here we evaluated a metagenomic pairwise dissimilarity measure based on short k-mer spectrum using the example of human gut microbiota, a biomedically significant object of study.
We developed a method for calculating pairwise dissimilarity (beta-diversity) of "shotgun" metagenomes based on short k-mer spectra (5 ≤ k ≤ 11). The method was validated on simulated metagenomes and further applied to a large collection of human gut metagenomes from the populations of the world (n=281). The k-mer spectrum-based measure was found to behave similarly to one based on mapping to a reference gene catalog, but different from one using a genome catalog. This difference turned out to be associated with a significant presence of viral reads in a number of metagenomes. Simulations showed limited impact of bacterial genetic variability as well as sequencing errors on k-mer spectra. Specific differences between the datasets from individual populations were identified.
Our approach allows rapid estimation of pairwise dissimilarity between metagenomes. Though we applied this technique to gut microbiota, it should be useful for arbitrary metagenomes, even metagenomes with novel microbiota. Dissimilarity measure based on k-mer spectrum provides a wider perspective in comparison with the ones based on the alignment against reference sequence sets. It helps not to miss possible outstanding features of metagenomic composition, particularly related to the presence of an unknown bacteria, virus or eukaryote, as well as to technical artifacts (sample contamination, reads of non-biological origin, etc.) at the early stages of bioinformatic analysis. Our method is complementary to reference-based approaches and can be easily integrated into metagenomic analysis pipelines.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Temperature flammability limits are one of the key indicators of fire and explosion hazard and are used in the development of measures, ensuring fire and explosion safety of production facilities, in ...the calculation of safe temperature conditions for storage, transportation, and processing of highly flammable and combustible liquids. Along with the standard methods for determination of the temperature limits of flammability, researchers apply non-standard instruments. This work considers the devices by Eitner, Bradley-Hale, Mack, Fricke, Jones, the US Bureau of Mines, the US Naval Research Laboratory, the All-Russian Research Fire Protection Institute, Yagyu, Gordon, Kong, Hasegawa-Kashiki, Brandes, and a 20-L spherical bomb. It is demonstrated that in many cases non-standard apparatuses make it possible to determine the temperature flammability limits with acceptable accuracy.
We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is ...represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
We report on a measurement of Spin Density Matrix Elements (SDMEs) in hard exclusive Formula omitted meson muoproduction on the proton at COMPASS using 160 GeV/c polarised Formula omitted and Formula ...omitted beams impinging on a liquid hydrogen target. The measurement covers the range 5.0 GeV/ Formula omitted Formula omitted 17.0 GeV/ Formula omitted, with the average kinematics Formula omitted 2.1 (GeV/c) Formula omitted, Formula omitted GeV/ Formula omitted, and Formula omitted (GeV/c) Formula omitted. Here, Formula omitted denotes the virtuality of the exchanged photon, W the mass of the final hadronic system and Formula omitted the transverse momentum of the Formula omitted meson with respect to the virtual-photon direction. The measured non-zero SDMEs for the transitions of transversely polarised virtual photons to longitudinally polarised vector mesons ( Formula omitted) indicate a violation of s-channel helicity conservation. Additionally, we observe a sizeable contribution of unnatural-parity-exchange (UPE) transitions that decreases with increasing W. The results provide important input for modelling Generalised Parton Distributions (GPDs). In particular, they may allow to evaluate in a model-dependent way the contribution of UPE transitions and assess the role of parton helicity-flip GPDs in exclusive Formula omitted production.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The aim of this paper was to study gut microbiota composition in patients with different metabolic statuses.
92 participants aged 25⁻76 years (26 of whom were men), with confirmed absence of ...cardiovascular and other chronic diseases (but with the possible presence of cardiovascular risk factors) were included. Carotid ultrasound examinations, 16
rRNA sequencing of stool samples and diet assessments were performed. Statistical analysis was performed using R programming language, 3.1.0.
Enterotyping yielded two clusters differentiated by alpha-diversity. Intima-media thickness was higher in the cluster with lower diversity (adj.
< 0.001). Obesity was associated with higher
(adj.
= 0.003) and
(adj.
< 0.0003) in relative abundance. Abdominal obesity was associated with higher abundance of
(adj.
= 0.004) and
(adj.
= 0.0008) and lower levels of
(adj.
= 0.0005). Glucose metabolism disturbances were associated with higher
(adj.
= 0.0007) and
(adj.
= 0.003) prevalence. Arterial hypertension was associated with high
levels (adj.
= 0.002). The
genus strongly correlated with low resistant starch consumption (adj.
= 0.007). A combination of high-fat diet and elevated
levels was very common for diabetes mellitus type 2 patients (adj.
= 0.0001).
The results show that there is a relationship between metabolic changes and higher representation of opportunistic pathogens and low diversity of gut microbiota even in apparently healthy participants.
Alcohol abuse has deleterious effects on human health by disrupting the functions of many organs and systems. Gut microbiota has been implicated in the pathogenesis of alcohol-related liver diseases, ...with its composition manifesting expressed dysbiosis in patients suffering from alcoholic dependence. Due to its inherent plasticity, gut microbiota is an important target for prevention and treatment of these diseases. Identification of the impact of alcohol abuse with associated psychiatric symptoms on the gut community structure is confounded by the liver dysfunction. In order to differentiate the effects of these two factors, we conducted a comparative "shotgun" metagenomic survey of 99 patients with the alcohol dependence syndrome represented by two cohorts-with and without liver cirrhosis. The taxonomic and functional composition of the gut microbiota was subjected to a multifactor analysis including comparison with the external control group.
Alcoholic dependence and liver cirrhosis were associated with profound shifts in gut community structures and metabolic potential across the patients. The specific effects on species-level community composition were remarkably different between cohorts with and without liver cirrhosis. In both cases, the commensal microbiota was found to be depleted. Alcoholic dependence was inversely associated with the levels of butyrate-producing species from the Clostridiales order, while the cirrhosis-with multiple members of the Bacteroidales order. The opportunist pathogens linked to alcoholic dependence included pro-inflammatory Enterobacteriaceae, while the hallmarks of cirrhosis included an increase of oral microbes in the gut and more frequent occurrence of abnormal community structures. Interestingly, each of the two factors was associated with the expressed enrichment in many Bifidobacterium and Lactobacillus-but the exact set of the species was different between alcoholic dependence and liver cirrhosis. At the level of functional potential, the patients showed different patterns of increase in functions related to alcohol metabolism and virulence factors, as well as pathways related to inflammation.
Multiple shifts in the community structure and metabolic potential suggest strong negative influence of alcohol dependence and associated liver dysfunction on gut microbiota. The identified differences in patterns of impact between these two factors are important for planning of personalized treatment and prevention of these pathologies via microbiota modulation. Particularly, the expansion of Bifidobacterium and Lactobacillus suggests that probiotic interventions for patients with alcohol-related disorders using representatives of the same taxa should be considered with caution. Taxonomic and functional analysis shows an increased propensity of the gut microbiota to synthesis of the toxic acetaldehyde, suggesting higher risk of colorectal cancer and other pathologies in alcoholics.
The investigation is focused on solving the problems of protein deficiency in the diets of the megacities population and on the cost-effective utilization of the offal from processing salmon fishes ...through the development of energy efficient and environmentally friendly technology for the potato snacks production. The aim of the work is to study the process of obtaining extruded expanded potato-based snacks in a single-screw extruder and to develop through an empirical research a method of industrial production of potato snacks enriched with proteins from the offal of processing salmon fishes. As a result of the study, it was established that the addition of 10% of offal salmon fish powder processing to potato flakes provided a fairly high nutritional value, good organoleptic and physic-chemically parameters in all extrudate samples. We also established the kinetics of extrusion of the fish-potato mixture, more specifically, we found out that the dependences between the initial moisture content in the mixture and the pressure in the extruder chamber, and between the initial humidity and the temperature in the chamber are inversely proportional; the dependence between the expansion ratio and the starch content in the extruded mixture is directly proportional, and the dependence between the expansion ration and the molding channel diameter is inversely proportional. Solutions obtained in the investigation can be used by enterprises engaged in the production of extruded snacks in order to optimize the working conditions of extrusion of potato extrudates and to reduce production costs.
The American oil revolution of 1859 and the invention of a kerosene lamp contributed to the onset of the kerosene era when candle lighting was replaced by kerosene. The side effect of this was the ...growth of fires and explosions due to the use of unsafe kerosene. There was a need to develop criteria for safe kerosene. The fire (burning) and flash point of kerosene were chosen as such indicators. The first stage of creating instruments to determine these indicators began in 1862 and ended at the beginning of the 20th century. This stage is characterized by the development of apparatuses of various designs, one of which were “open cup” testers. The first naphthometers (by Abel, Tag, Pease, Shaw, Saybolt, Pinkney, Squier, Indiana state, Millochau, Ettele, Cleveland, Courtois, Kissling, Brenken, Treumann, Marcusson, Schluter and “Sommer and Runge” company) are considered in the article. Many of these devices have not survived to our days and are undeservedly forgotten.
Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase ...part of Ty3/gypsy centromeric retrotransposon (RT-CR) is highly conservative in the segmental hexaploid Thinopyrum intermedium (JrJvsSt) and its possible diploid progenitors Th. bessarabicum (Jb), Pseudoroegneria spicata (St) and Dasypyrum villosum (V) but the abundance of the repeats varied to a large extent. Fluorescence in situ hybridization (FISH) showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In Th. intermedium, the strongest signal of RT-CR probe was detected on the chromosomes of Jv, intermediate on Jr and faint on Js and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in Th. bessarabicum is ~ 2 times and P. spicata is ~ 1,5 times higher than in genome of D. villosum. The possible burst of Ty3/gypsy centromeric retrotransposon in Th. intermedium during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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