Metabarcoding reveals that a non-nutritive sweetener and sucrose yield similar gut microbiota patterns in Wistar rats

The effects of non-nutritive sweeteners (NNS) on the gut microbiota are an area of increasing research interest due to their potential influence on weight gain, insulin resistance, and inflammation. Studies have shown that mice and rats fed saccharin develop weight gain and metabolic alterations, possibly related to changes in gut microbiota. Here, we hypothesized that chronic exposure to a commercial NNS would change the gut microbiota composition in Wistar rats when compared to sucrose exposure. To test this hypothesis, Wistar rats were fed either NNS- or sucrose-supplemented yogurt for 17 weeks alongside standard chow (ad libitum). The gut microbiome was assessed by 16S rDNA deep sequencing. Assembly and quantification were conducted using the Brazilian Microbiome Project pipeline for Ion Torrent data with modifications. Statistical analyses were performed in the R software environment. We found that chronic feeding of a commercial NNS-sweetened yogurt to Wistar rats, within the recommended dose range, did not significantly modify gut microbiota composition in comparison to sucrose-sweetened yogurt. Our findings do not support the hypothesis that moderate exposure to NNS is associated with changes in gut microbiota pattern compared to sucrose, at least in this experimental model.

A comparative approach of cuticular maturation in social and solitary bees using RNAseq, hydrocarbons\' quantification, and electron microscopy

Diferenças no timing da melanização e esclerotização do exoesqueleto são evidentes quando se compara a morfologia externa de abelhas de hábitos sociais e as solitárias. A esta diferença convencionamos chamar de heterocronia da maturação cuticular, o termo heterocronia significando variações no tempo relativo, ou ritmo, de um evento ontogenético em relação ao ancestral ou entre taxons. Propusemos que as abelhas sociais, que após a ecdise permanecem na colônia por vários dias, alcançariam a maturidade de alguns sistemas orgânicos, entre eles o tegumento, muito mais tarde que as espécies de abelhas solitárias que ao emergir partem imediatamente para atividades extra-nidais. Neste contexto, o objetivo deste trabalho consistiu em testar esta hipótese utilizando o tegumento em maturação das espécies de abelhas sociais, Apis mellifera e Frieseomelitta varia, e da espécie solitária Centris analis, em estudos comparativos de expressão gênica, ultraestrutura e quantificação de hidrocarbonetos cuticulares (CHCs). Para isto utilizamos sequenciamento de mRNA (RNA-seq), microscopia eletrônica de transmissão (MET) e cromatografia de gás e espectrometria de massas (CG/MS). Os perfis de expressão de genes da via de melanização/esclerotização cuticular (ebony e tan) diferenciaram as espécies sociais da solitária, assim como a expressão de genes com função na via de metabolismo de quitina (Cda5, Idgf4 e chitooligosacchariodolytic-domain-like) e de genes codificadores de proteínas estruturais da cutícula (CPR14, CPR17, CPR18, CPR25, CPR23, CPR26, Apd-3 e Apd-like). Genes com função na regulação da maturação cuticular (FTZ-F1, E74, Hr46 e Hr4) se mostraram co-expressos nas espécies sociais e os perfis de expressão destes genes, exceto Hr46, e de outros reguladores (Ethr, Hr38, Rickets e Ptx-1) também diferenciaram as espécies sociais da solitária. Ressaltamos em nossas análises os genes do ciclo circadiano, cuja expressão tem relação com a deposição de quitina cuticular, além de genes de vias de pigmentação não melanínicas. As análises de MET, abrangendo outras três espécies de abelhas (Bombus brasilienses: primitivamente eussocial; Euglossa cordata: facultativamente social; Tetrapedia diversipes: solitária), mostraram diferenças consistentes entre a ultraestrutura e espessura das cutículas das espécies sociais e solitárias, o que reforçou nossos resultados de RNA-seq. A quantificação absoluta dos CHCs diferenciou as abelhas sociais da solitária, consistente com a hipótese de heterocronia da maturação cuticular e com os perfis de expressão de genes envolvidos na biossíntese de CHCs. Assim, além de desvendar transcriptomas de tegumento de três espécies de abelhas, a comparação da expressão gênica aliada à análise de ultraestrutura da cutícula e quantificação de CHCs levaram à caracterização de diferenças no processo de maturação cuticular entre as espécies sociais e solitáriasDifferences in the timing of exoskeleton melanization and sclerotization processes are evident when comparing the external morphology of social and solitary bee species. Such differences may constitute a relevant example of cuticular maturation heterochrony, this term referring to a genetic change in timing of an ontogenetic process relative to an ancestor or between taxons. We proposed that social bees, which remain protected inside the colony for many days before initiating outside nest activities, would reach the maturity of some organic systems, such as the integument (epidermis and cuticle), later than solitary bees, which start such activities immediately after ecdysis. We tested this hypothesis in a comparative study of the developing integument of eusocial bees, Apis mellifera and Frieseomelitta varia, and the solitary bee Centris analis. Using RNA-seq, we verified that the expression profiles of genes involved in cuticular melanization and sclerotization (ebony and tan), chitin deposition and organization (Cda5, Idgf4, chitooligosacchariodolytic-domain-like), and cuticle formation (CPR14, CPR17, CPR18, CPR25, CPR23, CPE26, Apd-3, Apd-like) were positively, correlated between the two eusocial species, but not between the eusocial and the solitary species. Some of the genes with roles in regulating exoskeleton maturation (FTZ-F1, E74, Hr46, Hr4) were co-expressed only in the eusocial species. The expression profiles of these genes (except Hr46) and other regulatory genes (Ethr, Hr38, Rickets, Ptx-1) were also positively correlated exclusively in the eusocial bees. We also highlighted the expression of genes involved in non-melanin pigment production and the expression of circadian rhythm genes that could be related to chitin layers deposition. Transmission electron microscopy analysis of the integument of the two eusocial and the solitary bee species, in addition to other three bee species (the primitively eusocial Bombus brasilienses; the facultatively social Euglossa cordata; the solitary bee Tetrapedia diversipes), showed differences in cuticle ultrastructure and thickness, thus supporting the RNA-seq data. In agreement with our hypothesis, CHC quantifications were consistent with the expression levels of genes involved in CHC biosynthesis, thus differentiating the superficial cuticle layer of the eusocial and solitary species. Together, the integument transcriptomes, ultrastructure, and CHC quantification allowed us to characterize differences in the timing of cuticle maturation in social and solitary bee

Differential Expression and PAH Degradation: What Burkholderia vietnamiensis G4 Can Tell Us?

Petroleum is the major energy matrix in the world whose refining generates chemical byproducts that may damage the environment. Among such waste, polycyclic aromatic hydrocarbons (PAH) are considered persistent pollutants. Sixteen of these are considered priority for remediation, and among them is benzo(a)pyrene. Amid remediation techniques, bioremediation stands out. The genus Burkholderia is amongst the microorganisms known for being capable of degrading persistent compounds; its strains are used as models to study such ability. High-throughput sequencing allows researchers to reach a wider knowledge about biodegradation by bacteria. Using transcripts and mRNA analysis, the genomic regions involved in this aptitude can be detected. To unravel these processes, we used the model B. vietnamiensis strain G4 in two experimental groups: one was exposed to benzo(a)pyrene and the other one (control) was not. Six transcriptomes were generated from each group aiming to compare gene expression and infer which genes are involved in degradation pathways. One hundred fifty-six genes were differentially expressed in the benzo(a)pyrene exposed group, from which 33% are involved in catalytic activity. Among these, the most significant genomic regions were phenylacetic acid degradation protein paaN, involved in the degradation of organic compounds to obtain energy; oxidoreductase FAD-binding subunit, related to the regulation of electrons within groups of dioxygenase enzymes with potential to cleave benzene rings; and dehydrogenase, described as accountable for phenol degradation. These data provide the basis for understanding the bioremediation of benzo(a)pyrene and the possible applications of this strain in polluted environments

Metabarcoding reveals that a non-nutritive sweetener and sucrose yield similar gut microbiota patterns in Wistar rats

The effects of non-nutritive sweeteners (NNS) on the gut microbiota are an area of increasing research interest due to their potential influence on weight gain, insulin resistance, and inflammation. Studies have shown that mice and rats fed saccharin develop weight gain and metabolic alterations, possibly related to changes in gut microbiota. Here, we hypothesized that chronic exposure to a commercial NNS would change the gut microbiota composition in Wistar rats when compared to sucrose exposure. To test this hypothesis, Wistar rats were fed either NNS- or sucrose-supplemented yogurt for 17 weeks alongside standard chow (ad libitum). The gut microbiome was assessed by 16S rDNA deep sequencing. Assembly and quantification were conducted using the Brazilian Microbiome Project pipeline for Ion Torrent data with modifications. Statistical analyses were performed in the R software environment. We found that chronic feeding of a commercial NNS-sweetened yogurt to Wistar rats, within the recommended dose range, did not significantly modify gut microbiota composition in comparison to sucrose-sweetened yogurt. Our findings do not support the hypothesis that moderate exposure to NNS is associated with changes in gut microbiota pattern compared to sucrose, at least in this experimental model.

The genomes of three Bradyrhizobium sp. isolated from root nodules of Lupinus albescens grown in extremely poor soils display important genes for resistance to environmental stress

Lupinus albescens is a resistant cover plant that establishes symbiotic relationships with bacteria belonging to the Bradyrhizobium genus. This symbiosis helps the development of these plants in adverse environmental conditions, such as the ones found in arenized areas of Southern Brazil. This work studied three Bradyrhizobium sp. (AS23, NAS80 and NAS96) isolated from L. albescens plants that grow in extremely poor soils (arenized areas and adjacent grasslands). The genomes of these three strains were sequenced in the Ion Torrent platform using the IonXpress library preparation kit, and presented a total number of bases of 1,230,460,823 for AS23, 1,320,104,022 for NAS80, and 1,236,105,093 for NAS96. The genome comparison with closest strains Bradyrhizobium japonicum USDA6 and Bradyrhizobium diazoefficiens USDA110 showed important variable regions (with less than 80% of similarity). Genes encoding for factors for resistance/tolerance to heavy metal, flagellar motility, response to osmotic and oxidative stresses, heat shock proteins (present only in the three sequenced genomes) could be responsible for the ability of these microorganisms to survive in inhospitable environments. Knowledge about these genomes will provide a foundation for future development of an inoculant bioproduct that should optimize the recovery of degraded soils using cover crops

Analysis of the cancer genome atlas data reveals novel putative ncRNAs targets in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the prevalent type of primary liver malignancy. Different noncoding RNAs (ncRNAs) that negatively regulate gene expression, such as the microRNAs and the long ncRNAs (lncRNAs), have been associated with cell invasiveness and cell dissemination, tumor recurrence, and metastasis inHCC.To evaluatewhich regulatory ncRNAsmight be good candidates to disrupt HCC proliferation pathways, we performed both unsupervised and supervised analyses of HCC expression data, comparing samples of solid tumor tissue (TP) and adjacent tissue (NT) of a set of patients, focusing on ncRNAs and searching for common mechanisms that may shed light in future therapeutic options. All analyses were performed using the R software. Differential expression (total RNA and miRNA) and enrichment analyses (Gene Ontology + Pathways) were performed using the package TCGABiolinks. As a result, we improved the set of lncRNAs that could be the target of future studies in HCC, highlighting the potential of FAM170B-AS1 and TTN-AS1