scholarly journals Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons

2021 ◽  
Vol 9 (8) ◽  
pp. 1713
Author(s):  
Mingjie Li ◽  
Xingya Zhou ◽  
Catherine Stanton ◽  
R. Paul Ross ◽  
Jianxin Zhao ◽  
...  
Keyword(s):  
Theoretical Basis ◽  
Human Subjects ◽  
Phylogenetic Analyses ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Functional Genes ◽  
Human Intestine ◽  
Large Variability ◽  
Subspecies Level ◽  
Similarities And Differences

Bifidobacterium longum is one of the most widely distributed and abundant Bifidobacterium in the human intestine, and has been proven to have a variety of physiological functions. In this study, 80 strains of B. longum isolated from human subjects were classified into subspecies by ANI and phylogenetic analyses, and the functional genes were compared. The results showed that there were significant differences in carbohydrate metabolism between the two subspecies, which determined their preference for human milk oligosaccharides or plant-derived carbohydrates. The predicted exopolysaccharide (EPS) gene clusters had large variability within species but without difference at the subspecies level. Four subtype CRISPR-Cas systems presented in B. longum, while the subtypes I-U and II-C only existed in B. longum subsp. longum. The bacteriocin operons in B. longum subsp. infantis were more widely distributed compared with B. longum subsp. longum. In conclusion, this study revealed the similarities and differences between B. longum subsp. infantis and B. longum subsp. longum, which could provide a theoretical basis for further exploring the probiotic characteristics of B. longum.

scholarly journals LOVE in English and Polish

2017 ◽  
Author(s):  
Małgorzata Brożyna Reczko
Keyword(s):  
Analytical Method ◽  
Theoretical Basis ◽  
Abstract Concept ◽  
Contrastive Analysis ◽  
The World ◽  
Similarities And Differences ◽  
British National Corpus ◽  
National Corpus

LOVE in English and PolishThe paper presents a sample contrastive analysis of the linguistic picture of love in English and Polish. The material used in the survey is drawn from lexicographic data, including the British National Corpus and Narodowy Korpus Języka Polskiego [National Corpus of Polish]. The paper focuses on the similarities and differences in conceptualizing the abstract concept of love in the English and Polish languages. An analytical method, developed by Bartmiński and associates, serves as the theoretical basis for the reconstruction of the linguistic picture of the world. MIŁOŚĆ w języku angielskim i polskimNiniejszy artykuł to próba kontrastywnego porównania językowego obrazu świata MIŁOŚCI w języku angielskim i polskim. Materiał badawczy pochodzi głównie ze źródeł leksykograficznych: słowników oraz korpusów (Narodowego Korpusu Języka Polskiego oraz z korpusu języka angielskiego British National Corpus). Celem badania było poszukiwanie podobieństw i różnic w konceptualizacji MIŁOŚCI w tych dwóch językach. Metoda badawcza została zaczerpnięta z prac J. Bartmińskiego i dotyczy rekonstrukcji językowego obrazu świata różnych pojęć.

scholarly journals Pan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Isaiah Paolo A. Lee ◽  
Cheryl P. Andam
Keyword(s):  
Phylogenetic Analyses ◽  
Gene Clusters ◽  
Genomic Diversity ◽  
Ecological Niches ◽  
Cronobacter Sakazakii ◽  
Type Vi Secretion System ◽  
Accessory Gene ◽  
Pan Genome ◽  
Accessory Genes ◽  
Mannose Metabolism

Abstract Background Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources. Results The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination. Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production. Conclusions Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.

scholarly journals Multiple Transporters and Glycoside Hydrolases Are Involved in Arabinoxylan-Derived Oligosaccharide Utilization in Bifidobacterium pseudocatenulatum

2020 ◽  
Vol 86 (24) ◽  
Author(s):  
Yuki Saito ◽  
Akira Shigehisa ◽  
Yohei Watanabe ◽  
Naoki Tsukuda ◽  
Kaoru Moriyama-Ohara ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Binding Proteins ◽  
Molecular Mechanisms ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Glycoside Hydrolases ◽  
Glycoside Hydrolase Family ◽  
Carbohydrate Utilization ◽  
Bifidobacterium Adolescentis ◽  
Content Type

ABSTRACT Arabinoxylan hydrolysates (AXH) are the hydrolyzed products of the major components of the dietary fiber arabinoxylan. AXH include diverse oligosaccharides varying in xylose polymerization and side residue modifications with arabinose at the O-2 and/or O-3 position of the xylose unit. Previous studies have reported that AXH exhibit prebiotic properties on gut bifidobacteria; moreover, several adult-associated bifidobacterial species (e.g., Bifidobacterium adolescentis and Bifidobacterium longum subsp. longum) are known to utilize AXH. In this study, we tried to elucidate the molecular mechanisms of AXH utilization by Bifidobacterium pseudocatenulatum, which is a common bifidobacterial species found in adult feces. We performed transcriptomic analysis of B. pseudocatenulatum YIT 4072T, which identified three upregulated gene clusters during AXH utilization. The gene clusters encoded three sets of ATP-binding cassette (ABC) transporters and five enzymes belonging to glycoside hydrolase family 43 (GH43). By characterizing the recombinant proteins, we found that three solute-binding proteins of ABC transporters showed either broad or narrow specificity, two arabinofuranosidases hydrolyzed either single- or double-decorated arabinoxylooligosaccharides, and three xylosidases exhibited functionally identical activity. These data collectively suggest that the transporters and glycoside hydrolases, encoded in the three gene clusters, work together to utilize AXH of different sizes and with different side residue modifications. Thus, our study sheds light on the overall picture of how these proteins collaborate for the utilization of AXH in B. pseudocatenulatum and may explain the predominance of this symbiont species in the adult human gut. IMPORTANCE Bifidobacteria commonly reside in the human intestine and possess abundant genes involved in carbohydrate utilization. Arabinoxylan hydrolysates (AXH) are hydrolyzed products of arabinoxylan, one of the most abundant dietary fibers, and they include xylooligosaccharides and those decorated with arabinofuranosyl residues. The molecular mechanism by which B. pseudocatenulatum, a common bifidobacterial species found in adult feces, utilizes structurally and compositionally variable AXH has yet to be extensively investigated. In this study, we identified three gene clusters (encoding five GH43 enzymes and three solute-binding proteins of ABC transporters) that were upregulated in B. pseudocatenulatum YIT 4072T during AXH utilization. By investigating their substrate specificities, we revealed how these proteins are involved in the uptake and degradation of AXH. These molecular insights may provide a better understanding of how resident bifidobacteria colonize the colon.

scholarly journals Readings and Versions of Peter Pan in the Discursive Perspective

2020 ◽  
Vol 10 (2) ◽  
pp. 14
Author(s):  
VALÉRIA ANDRÉ DOS SANTOS ◽  
JÚLIO CÉSAR ANDRÉ ◽  
LOIANE LETÍCIA DOS SANTOS ◽  
LORENA ALINE SANTOS ALMEIDA ◽  
ELIANE LUIZ DOS SANTOS ◽  
...  
Keyword(s):  
Discourse Analysis ◽  
Theoretical Basis ◽  
School Community ◽  
Peter Pan ◽  
Reading And Writing ◽  
Similarities And Differences ◽  
Production Conditions

This article aims to present a practice of reading and writing in the discursive perspective, from versions of children’s and young adult’s literature and cinema, on reconstruction of stories. The theoretical basis supporting this reflection is Discourse Analysis (DA), anchored in the studies of Michel Pêcheux, in France, and Eni Puccinelli Orlandi, in Brazil. We started with the reading project Ler, contar e recontar (Reading, telling and retelling) in 2012, motivated by the concern about students presenting difficulties in writing and interpreting texts in all disciplines. The project’s purpose is to perform DA on literary and cinematographic works in activities that lead to the establishment of similarities and differences among such materials. We provided visibility to the effects of meaning produced in the passage from the book to films and to drawings, considering the different processes of constitution, formulation and circulation of each significant materiality. By an approach involving reading the book, watching movies and examining drawings, added by discussions on effects of meaning of each and among them, it was possible to build the final product: a new version for the Peter Pan story, which was brought to the current days. Such story was presented on a festive night to the school community, showing the effects of authorship. It is worth remembering that it is not possible to invent a recipe. Our project is unique and even if someone wants to copy it, i.e., use the same methodology, the results will be different, as the subjects will be different, just like the production conditions, the time, the teacher, the activities etc. The unique production conditions of the conceived activities and the specific chosen class are responsible for the particular result of any proposal.

scholarly journals Expanding magnetic organelle biogenesis in the domain Bacteria

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Lin ◽  
Wensi Zhang ◽  
Greig A. Paterson ◽  
Qiyun Zhu ◽  
Xiang Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Biological Significance ◽  
Gene Clusters ◽  
Magnetic Sensors ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Organelle Biogenesis ◽  
Taxonomic Distribution ◽  
Origin And Evolution ◽  
Bacterial Phyla

Abstract Background The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. Results Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. Conclusions These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.

Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights

Gene ◽  
1997 ◽  
Vol 205 (1-2) ◽  
pp. 73-94 ◽  
Author(s):  
Ross Hardison ◽  
Jerry L. Slightom ◽  
Deborah L. Gumucio ◽  
Morris Goodman ◽  
Nikola Stojanovic ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Globin Gene ◽  
Gene Clusters ◽  
Experimental Results ◽  
Locus Control Regions ◽  
Control Regions

scholarly journals Characterization of the Nodularin Synthetase Gene Cluster and Proposed Theory of the Evolution of Cyanobacterial Hepatotoxins

2004 ◽  
Vol 70 (11) ◽  
pp. 6353-6362 ◽  
Author(s):  
Michelle C. Moffitt ◽  
Brett A. Neilan
Keyword(s):  
Gene Cluster ◽  
Rational Design ◽  
Polyketide Synthase ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Cyanobacterial Bloom ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Microcystin Synthetase

ABSTRACT Nodularia spumigena is a bloom-forming cyanobacterium which produces the hepatotoxin nodularin. The complete gene cluster encoding the enzymatic machinery required for the biosynthesis of nodularin in N. spumigena strain NSOR10 was sequenced and characterized. The 48-kb gene cluster consists of nine open reading frames (ORFs), ndaA to ndaI, which are transcribed from a bidirectional regulatory promoter region and encode nonribosomal peptide synthetase modules, polyketide synthase modules, and tailoring enzymes. The ORFs flanking the nda gene cluster in the genome of N. spumigena strain NSOR10 were identified, and one of them was found to encode a protein with homology to previously characterized transposases. Putative transposases are also associated with the structurally related microcystin synthetase (mcy) gene clusters derived from three cyanobacterial strains, indicating a possible mechanism for the distribution of these biosynthetic gene clusters between various cyanobacterial genera. We propose an alternative hypothesis for hepatotoxin evolution in cyanobacteria based on the results of comparative and phylogenetic analyses of the nda and mcy gene clusters. These analyses suggested that nodularin synthetase evolved from a microcystin synthetase progenitor. The identification of the nodularin biosynthetic gene cluster and evolution of hepatotoxicity in cyanobacteria reported in this study may be valuable for future studies on toxic cyanobacterial bloom formation. In addition, an appreciation of the natural evolution of nonribosomal biosynthetic pathways will be vital for future combinatorial engineering and rational design of novel metabolites and pharmaceuticals.

scholarly journals Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 63 ◽  
Author(s):  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Core Genome ◽  
Position Effect ◽  
Genome Structure ◽  
Enrichment Analysis ◽  
Gene Clusters ◽  
Gene Cassette ◽  
Etiologic Agent ◽  
Functional Genes ◽  
The Core ◽  
Core Genes

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.

scholarly journals Dream as a subject of psychological research

2014 ◽  
Vol 6 (1) ◽  
pp. 19-27
Author(s):  
P.A. Egorova
Keyword(s):  
Activity Theory ◽  
Theoretical Basis ◽  
Empirical Studies ◽  
Psychological Research ◽  
Theoretical Concepts ◽  
Adolescents And Adults ◽  
Similarities And Differences ◽  
Definition Of ◽  
Subjective Significance

We discuss the main theoretical concepts of a dream: dream definitions, ideas about its genesis, functions, dream location in the structure of activity. We analyze the similarities and differences between the approaches. The results of empirical studies of adolescent and adult dreams are generalized, dream functions in adolescence are analyzed. Based on the analysis of different approaches, we chose theoretical basis of our own research – A. Leontiev activity theory, L.S. Vygotsky concept, K. Lewin's model. We formulated and substantiated the definition of dream as emotionally colored image of the desired future, having a subjective significance. We show the significance and hypotheses of our research: 1) the content of dreams is connected not only with a situation of frustration, but also with the teenager abilities, 2) the dream is involved in regulating of values choice; 3) restoration and development of the ability to dream can be used in the practice of counseling and psychotherapy as an effective tool to help adolescents and adults.

scholarly journals Targeted high-resolution taxonomic identification of Bifidobacterium longum subsp. infantis using human milk oligosaccharide metabolizing genes

2021 ◽  
Author(s):  
Lauren Tso ◽  
Kevin S Bonham ◽  
Alyssa Fishbein ◽  
Sophie Rowland ◽  
Vanja Klepac-Ceraj ◽  
...  
Keyword(s):  
Human Milk ◽  
Bifidobacterium Longum ◽  
Gene Clusters ◽  
Species Group ◽  
Human Breast Milk ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Specific Primers ◽  
Breastfed Infants ◽  
Shotgun Metagenomic Sequencing

Bifidobacterium longum subsp. infantis (B. infantis) is one of few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis, by molecular methods. These two organisms are classified in the same species group as B. infantis but do not share the ability to metabolize human milk oligosaccharides (HMOs). Here, we compared HMO-metabolizing genes across different Bifidobacterium genomes to develop B. infantis specific primers and determine if they alone can be used to quickly characterize B. infantis with shotgun metagenomic sequencing data. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, used this characterization to test for its prevalence in infants, and validated the results using the B. infantis-specific primers. By examining stool samples from a cohort of US children and pregnant women using shotgun metagenomic sequencing, we observed that only 18 of 204 (8.8%) of children under 2 years old harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.

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