Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis.

Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.

Expanding amphiphilic architectures by ring-opening of epoxides and polyepoxides with N-methyl-d-glucamine: Structure, chiral bias and gelation.

The facile reaction of a readily available aminopolyol from the chiral pool, N-methyl-d-glucamine, which avoids the side reactions usually associated to anomers of amino sugars, with epoxide and polyepoxide derivatives, enables the preparation of new non-ionic surfactant-like structures combining hydrophilic and hydrophobic moieties. The molecular architectures thus obtained range from linear to tripodal and pyramidal structures. The resulting substances containing multiple chiral centers exist as diastereomeric mixtures, for which various conformations are likewise possible by virtue of inter-chain interactions. The stability and chirality preferences of all possible stereoisomers have been evaluated in detail by DFT methods. Given the amphiphilic structure of both protected and O-protected derivatives obtained by acetylation, self-aggregation could eventually lead to solvent entrapment. Unfortunately, only one compound behaves as efficient hydrogelator and DMSO-gelator at low concentrations. The issue is also discussed in terms of the different molecular arrangements.

The immunogenetic diversity of the HLA system in Mexico correlates with underlying population genetic structure.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) allele groups and alleles by PCR-SSP based typing in a total of 15,318 mixed ancestry Mexicans from all the states of the country divided into 78 sample sets, providing information regarding allelic and haplotypic frequencies and their linkage disequilibrium, as well as admixture estimates and genetic substructure. We identified the presence of 4268 unique HLA extended haplotypes across Mexico and find that the ten most frequent (HF > 1%) HLA haplotypes with significant linkage disequilibrium (Δ'≥0.1) in Mexico (accounting for 20% of the haplotypic diversity of the country) are of primarily Native American ancestry (A*02~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*08~DQB1*04, A*68~B*39~DRB1*04~DQB1*03:02, A*02~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*14~DQB1*03:01, A*24~B*35~DRB1*04~DQB1*03:02, A*24~B*39~DRB1*04~DQB1*03:02, A*02~B*40:02~DRB1*04~DQB1*03:02, A*68~B*35~DRB1*04~DQB1*03:02, A*02~B*15:01~DRB1*04~DQB1*03:02). Admixture estimates obtained by a maximum likelihood method using HLA-A/-B/-DRB1 as genetic estimators revealed that the main genetic components in Mexico as a whole are Native American (ranging from 37.8% in the northern part of the country to 81.5% in the southeastern region) and European (ranging from 11.5% in the southeast to 62.6% in northern Mexico). African admixture ranged from 0.0 to 12.7% not following any specific pattern. We were able to detect three major immunogenetic clusters correlating with genetic diversity and differential admixture within Mexico: North, Central and Southeast, which is in accordance with previous reports using genome-wide data. Our findings provide insights into the population immunogenetic substructure of the whole country and add to the knowledge of mixed ancestry Latin American population genetics, important for disease association studies, detection of demographic signatures on population variation and improved allocation of public health resources.

Genetic diversity of HLA system in two populations from Hidalgo, Mexico: Pachuca and rural Hidalgo.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 122 Mexicans from the state of Hidalgo living in the city of Pachuca (N = 41) and rural communities (N = 81), to obtain information regarding allelic and haplotypic frequencies. We find that the most frequent haplotypes in Hidalgo include eight Native American and one European haplotypes. Admixture estimates revealed that the main genetic components in Hidalgo are Native American (58.93 ±â€¯2.16% by ML; 54.51% of Native American haplotypes) and European (32.49 ±â€¯2.88% by ML; 28.69% of European haplotypes), and a relatively high African genetic component (8.58 ±â€¯0.93% by ML; 6.97% of African haplotypes).

Genetic diversity of HLA system in seven populations from Veracruz, Mexico: Veracruz city, Coatzacoalcos, Córdoba, Orizaba, Poza Rica, Xalapa and rural Veracruz.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 1113 Mexicans from the state of Veracruz living in the cities of Coatzacoalcos (N = 55), Orizaba (N = 60), Córdoba (N = 56), Poza Rica (N = 45), Veracruz (N = 171), Xalapa (N = 187) and rural communities (N = 539) to obtain information regarding allelic and haplotypic frequencies. We found that the most frequent haplotypes include 12 Native American haplotypes. Admixture estimates revealed that the main genetic components are Native American (64.93 ±â€¯1.27% by ML; 55.10% of Native American haplotypes) and European (26.56 ±â€¯0.89% by ML; 28.38% of European haplotypes), and a relatively high African genetic component (8.52 ±â€¯1.82% by ML; 8.78% of African haplotypes).

Genetic diversity of HLA system in two populations from Oaxaca, Mexico: Oaxaca city and rural Oaxaca.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 636 Mexicans from the state of Oaxaca living in the city of Oaxaca (N = 151) and rural communities (N = 485), to obtain information regarding allelic and haplotypic frequencies. We found that the 13 most frequent haplotypes in Oaxaca are all of putative Native American origin. Admixture estimates revealed that the main genetic components in the state of Oaxaca are Native American (73.12 ±â€¯2.77% by ML; 61.52% of Native American haplotypes) and European (17.36 ±â€¯2.07% by ML; 20.69% of European haplotypes), and a relatively high African genetic component (9.52 ±â€¯0.88% by ML; 8.94% of African haplotypes).

Genetic diversity of HLA system in two populations from Puebla, Mexico: Puebla city and rural Puebla.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 2827 Mexicans from the state of Puebla living in the city of Puebla (N = 1994) and rural communities (N = 833), to obtain information regarding allelic and haplotypic frequencies. We found that the 16 most frequent haplotypes in Puebla are all of them Native American. Admixture estimates revealed that the main genetic components in the state of Puebla are Native American (72.21 ±â€¯1.25% by ML; 63.30% of Native American haplotypes) and European (21.05 ±â€¯1.92% by ML; 23.86% of European haplotypes), and a less prominent African genetic component (6.74 ±â€¯2.20% by ML; 6.20% of African haplotypes).

Genetic diversity of HLA system in two populations from Tlaxcala, Mexico: Tlaxcala city and rural Tlaxcala.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 1011 Mexicans from the state of Tlaxcala residing in the city of Tlaxcala (N = 181) and rural communities (N = 830), to obtain information regarding allelic and haplotypic frequencies. We find that the ten most frequent haplotypes in Tlaxcala are all of Native American origin. Admixture estimates revealed that the main genetic components are Native American (75.13 ±â€¯1.56% by ML; 69.24% based on of Native American haplotypes) and European (16.10 ±â€¯4.98% by ML; 19.74% of European haplotypes), with a less prominent African genetic component (8.78 ±â€¯4.09% by ML; 4.35% of African haplotypes).

Genetic diversity of HLA system in six populations from Mexico City Metropolitan Area, Mexico: Mexico City North, Mexico City South, Mexico City East, Mexico City West, Mexico City Center and rural Mexico City.

We studied HLA class I (HLA-A, -B) and class II (HLA-DRB1, -DQB1) alleles by PCR-SSP based typing in 1217 Mexicans from the Mexico City Metropolitan Area living in the northern (N = 751), southern (N = 52), eastern (N = 79), western (N = 33), and central (N = 152) Mexico City, and rural communities (N = 150), to obtain information regarding allelic and haplotypic frequencies. We found that the most frequent haplotypes include 11 Native American haplotypes. Admixture estimates revealed that the main genetic components are Native American (63.85 ±â€¯1.55% by ML; 57.19% of Native American haplotypes) and European (28.53 ±â€¯3.13% by ML; 28.40% of European haplotypes), and a less apparent African genetic component (7.61 ±â€¯1.96% by ML; 7.17% of African haplotypes).

Proteomic analysis of porcine mesenteric lymph-nodes after Salmonella typhimurium infection.

In this study we employed for the first time an in vivo approach coupled to DIGE-based proteomics to explore the response of porcine mesenteric lymph nodes (MLN) to Salmonella typhimurium infection. MLN samples were collected from four control and twelve infected pigs (at 1, 2 and 6 days post infection) for histological analysis, protein and RNA purification. Afterwards, expressed proteins were screened by differential in gel analysis and data were analyzed by bioinformatic tools to generate interaction networks, and identify enriched signaling pathways and biological annotations. S. typhimurium labeling in tissue and phagocyte infiltration were analyzed by immunohistochemistry and RNA was employed to determine the relative expression of immune-related genes by quantitative RNA analysis. The proteome response of porcine MLN to infection was associated to the induction of processes such as phagocyte infiltration, cytoskeleton remodeling and pyroptosis. Moreover, our results suggest that S. typhimurium antigens are cross-presented via MHC-I in a proteasome-dependent manner in porcine MLN. Since pathogen burden in tissue was noticeably reduced at the end of the time course, we infer that host innate and adaptive immunity act in association in MLN to control S. typhimurium dissemination in swine infections.

[Urodynamic paradigms: from renaissance fibrilar theory to current Doppler-flowmetry]. / Paradigmas urodinamicos. Desde la teoria fibrilar renacentista, hasta la flujometría-Doppler actual.

UNLABELLED: To perform a historical introduction and a review of the mathematical model, emphasizing that our mathematical model may be the solution to the viscoelastic model. It is evident that the same experiment has been repeated over half a century, with similar results in all cases. We also show one of the projects we are working on: the electro-vesicogram for the evaluation of the filling phase, and Doppler uroflowmetry for the study of the voiding phase. METHODS: We have chosen and studied in depth the results Dr. Virseda presents in his thesis of one of the experiments performed in relation to the viscoelastic model. After applying analytical methods we reach a differential equation we suppose defines detrusor behaviour, as it has been explained by the viscoelastic model. The solution of this equation by means of the Laplace's transform enables to obtain the values of the incognitas set by urodynamics. Besides, we analyzed the behaviour of solutions' stability using a matricial method following the Lyapunov theory. The former may solve the incognitas for the voiding phase. We used urethral Doppler with simultaneous uroflowmetry to obtain the data equations demanded; this is what we named "Doppler uroflowmetry". The filling phase was studied by superficial electromiography. We named it "electrovesicogram". We attach images for both Doppler wave and electrovesicogram. They both are the projects we are working on. RESULTS: Currently we can only explain the methodology we are following. Indeed, this article is the first of a series in which we aim to explain the methodology we are following in detail: Doppler wave capture; mounting process photogram by photogram, and vectorization and cleaning of the wave, either Doppler or flow waves; treatment in autocad to obtain the vector; and management of the vector with the matalab software, which gives us the results we are looking for. CONCLUSIONS: It is intuitive to deduct the usefulness of these methods as not invasive techniques in the urodynamic diagnosis. We have our illusions in these projects which open a window to the future.

Paradigmas urodinámicos. Desde la teoría fibrilar renacentista hasta la flujometría-Doppler actual / Urodynamic paradigms: from renaissance fibrilar theory to current Doppler-flowmetry

OBJETIVO: Hacer una introducción histórica y una revisión del modelo matemático en la que se destaca fundamentalmente que nuestro modelo matemático puede ser la solución del modelo viscoelástico. Es evidente que durante medio siglo se ha estado repitiendo el mismo experimento, y en todas las ocasiones con resultados similares. También exponemos uno de los proyectos en los trabajamos: el electrovesicograma, para la exploración de la fase de llenado y la uroflujometría doppler para el estudio de la fase miccional. MÉTODOS: Basándonos en los resultados de uno de los experimentos realizados en relación con el modelo viscoelástico hemos elegido y estudiado en profundidad los resultados que el Dr. Virseda, presenta en su tesis. Y tras aplicar métodos analíticos, llegamos a una ecuación diferencial que suponemos define el comportamiento del detrusor según nos ha estado diciendo que lo hace el modelo viscoelástico. La solución de esta ecuación mediante la transformada de Laplace, nos permite obtener los valores de las incógnitas que la urodinámica plantea. Por otra parte, mediante el método matricial, analizamos el comportamiento de la estabilidad de las soluciones, según la teoria de Lyapunov. Lo anterior puede resolver las incógnitas de la fase miccional. Para obtener los datos que las ecuaciones nos demandan, utilizamos el doppler uretral, simultaneandolo con la flujometría, en lo que hemos dado en llamar la "Flujometría doppler". La fase de llenado la estudiamos mediante métodos de electromiografía superficial. El "Electrovesicograma", como lo llamamos nosotros. Adjuntamos imágenes tanto de la onda doppler como de la del electrovesicograma. Ambos son proyectos en los que estamos trabajando en la actualidad. RESULTADOS: De momento sólo podemos explicar la metodología que estamos siguiendo. De hecho este es el primero de una serie de artículos en los que nos proponemos detallar la metodología que seguimos: la captura de la onda doppler, su montaje fotograma a fotograma y la vectorización y limpieza de la onda, doppler y de flujo. Su tratamiento en autocad, para obtener el vector y el manejo del vector con el programa matalab, que nos da los resultados buscados. CONCLUSIONES: Es intuitivo deducir la utilidad de estos métodos, como técnicas no invasivas en el diagnóstico urodinámico. Tenemos puestas nuestras ilusiones en estos proyectos que no son otra cosa que abrir una puerta al futuro (AU)

To perform a historical introduction and a review of the mathematical model, emphasizing that our mathematical model may be the solution to the viscoelastic model. It is evident that the same experiment has been repeated over half a century, with similar results in all cases. We also show one of the projects we are working on: the electro-vesicogram for the evaluation of the filling phase, and Doppler uroflowmetry for the study of the voiding phase. METHODS: We have chosen and studied in depth the results Dr. Virseda presents in his thesis of one of the experiments performed in relation to the viscoelastic model. After applying analytical methods we reach a differential equation we suppose defines detrusor behaviour, as it has been explained by the viscoelastic model. The solution of this equation by means of the Laplace'S transform enables to obtain the values of the incognitas set by urodynamics. Besides, we analyzed the behaviour of solutions' stability using a matricial method following the Lyapunov theory. The former may solve the incognitas for the voiding phase. We used urethral Doppler with simultaneous uroflowmetry to obtain the data equations demanded; this is what we named "Doppler uroflowmetry". The filling phase was studied by superficial electromiography. We named it "electrovesicogram". We attach images for both doppler wave and electrovesicogram. They both are the projects we are working on. RESULTS: Currently we can only explain the methodology we are following. Indeed, this article is the first of a series in which we aim to explain the methodology we are following in detail: Doppler wave capture; mounting process photogram by photogram, and vectorization and cleaning of the wave, either Doppler or flow waves; treatment in autocad to obtain the vector; and management of the vector with the matalab software, which gives us the results we are looking for. CONCLUSIONS: It is intuitive to deduct the usefulness of these methods as not invasive techniques in the urodynamic diagnosis. We have our illusions in these projects which open a window to the future (AU)