Diseño de una red de dispositivos inalámbricos para monitorear la calidad del aire en interiores

FRIDA JENNY DE LA ROSA ANDRADE (2023, [Tesis de maestría])

No cabe duda de que la contaminación ambiental siempre a existido, y es una consecuencia

producida por las diferentes actividades que el ser humano ha realizado a lo largo de su

desarrollo y evolución tecnológica, por lo que conlleva a muchas repercusiones en la

integridad física del ambiente. Las actividades de desarrollo, como la construcción, el

transporte y la fabricación, no solo agotan los recursos naturales, sino que también producen

una gran cantidad de desechos que conducen a la contaminación del aire, el agua, el suelo y

los océanos, dando pie a los problemas más preocupantes del ser humano, tal es el caso del

calentamiento global, las lluvias acidas. Hoy en día la contaminación del aire se considera

un tema de gran importancia puesto que, es uno de los principales problemas en las zonas

más urbanizadas del mundo, y se encuentra presente tanto en los países desarrollados como

en los no desarrollados, por ello surge la necesidad de conocer que tan contaminado se

encuentra el aire que se respira.

El estándar de calidad del aire es una táctica para establecer las condiciones del aire desde un

grado de pureza, hasta una calidad critica perjudicial para el deterioro de la salud humana,

haciendo referencia a la cantidad de contaminación presente en el aire, definiéndola ya sea

de alta calidad con un nivel bajo de contaminación o una mala calidad con un nivel elevado

de concentración de contaminación en el aire.

En este proyecto se diseñará una Red de dispositivos inalámbricos para el análisis y

monitoreo de la calidad del aire en interiores, con la finalidad de fungir como un medidor de

contaminación que le permita a las personas darse cuenta de que tan contaminados están sus

hogares. Por tal motivo en el desarrollo de este proyecto se hará uso de un microcontrolador

Arduino IDE, un Node-red y un phpMyadmin para el análisis y monotoreo constante de

diversos gases como CO, CO2, metano, nitrógeno y O2. Cabe mencionar que este escrito se

ha dividido en 4 capítulos en los cuales se explica detalladamente todos y cada uno de los

procesos llevado a cabo para la elaboración y el desarrollo de este proyecto.

There is no doubt that environmental pollution has always existed, and is a consequence

produced by the different activities that human beings have carried out throughout their

development and technological evolution, which leads to many repercussions on the physical

integrity of the environment. Development activities such as construction, transportation and

manufacturing not only deplete natural resources but also produce a large amount of waste

leading to pollution of air, water, soil and oceans, giving rise to to the most worrying problems

of human beings, such as global warming and acid rain. Nowadays, air pollution is considered

an issue of great importance since it is one of the main problems in the most urbanized areas

of the world, and is present in both developed and undeveloped countries, which is why the

need to know how contaminated the air you breathe is.

The air quality standard is a tactic to establish air conditions from a degree of purity to a

critical quality harmful to the deterioration of human health, referring to the amount of

pollution present in the air, defining it either high quality with a low level of contamination

or poor quality with a high level of concentration of contamination in the air.

In this project, a network of wireless devices will be designed for the analysis and monitoring

of indoor air quality, with the purpose of serving as a pollution meter that allows people to

realize how polluted their homes are. For this reason, in the development of this project, an

Arduino IDE microcontroller, a Node-red and a phpMyadmin will be used for the analysis

and constant monitoring of various gases such as CO, CO2, methane, nitrogen and O2. It is

worth mentioning that this writing has been divided into 4 chapters in which each and every

one of the processes carried out for the preparation and development of this project is

explained in detail.

BIOLOGÍA Y QUÍMICA QUÍMICA Red de dispositivos inalámbricos, análisis monitoreo, calidad, riesgo, contaminación. Network of wireless devices, monitoring analysis, quality, risk, contamination.

PROPUESTA DE MANEJO DE LA PESQUERÍA EMERGENTE DE MERLUZA DEL PACÍFICO NORTE Merluccius productus EN EL GOLFO DE ULLOA, BAJA CALIFORNIA SUR

PABLO MORA ZAMACONA (2023, [Tesis de doctorado])

"La merluza del Pacífico Merluccius productus se distribuye desde Alaska hasta el sur de México, con una población particular descrita al sur de la península de Baja California conocida como merluza enana, de la que poco se sabe. Dicha población actualmente no es pescada comercialmente, por lo que representa un recurso con potencial de explotación. Las pesquerías potenciales y emergentes crean desafíos y oportunidades para los administradores pesqueros que necesitan tomar decisiones sobre cómo gestionar de forma sostenible una pesquería previa a su inicio. Este trabajo propone y analiza posibles medidas alternativas de gestión pesquera para esta potencial pesquería, bajo incertidumbre biológica y de mercado. Debido al desconocimiento de diversos aspectos de la biología del recurso primeramente se analizó el crecimiento individual del stock y posteriormente se realizó un análisis bioeconómico de la potencial pesquería.

Para el análisis del crecimiento individual se utilizó un total de 240 otolitos y datos de longitud patrón de 932 especímenes muestreados de mayo a diciembre de 2015. La formación anual de incrementos en los otolitos se verificó mediante la relación de incremento marginal y el análisis de borde. La edad se estimó a partir de recuentos de anillos en secciones sagitales de otolitos y el crecimiento se analizó mediante un enfoque de inferencia multimodelo. Se consideraron los modelos de crecimiento de von Bertalanffy (VBGM), VBGM generalizado, Gompertz, Logístico y Johnson, los cuales se ajustaron a conjuntos de datos de talla a la edad observados y retrocalculados agrupados por sexo. Según el criterio de información de Akaike, el VBGM generalizado fue el más apropiado para las hembras (L∞= 31.36 cm, k= 0.15 cm año-1), mientras que el VBGM proporcionó el mejor ajuste para los machos (L∞= 25.35 cm, k= 0.28 cm año-1).

El análisis bioeconómico de alternativas de manejo para una potencial pesquería de merluza enana indicó que una nueva pesquería de dicho stock podría ser biológicamente sostenible y económicamente rentable, bajo un conjunto de estrategias de gestión y reglas de control. Se recomienda un acceso limitado con bajo esfuerzo pesquero ya que resulta más redituable por barco y biológicamente precautorio, considerando la alta incertidumbre asociada con la explotación de una población virgen..."

"The Pacific hake Merluccius productus is distributed from Alaska to southern Mexico, with a particular population described south of the Baja California peninsula known as dwarf hake, about which little is known. This population is not currently commercially fished; hence it represents a resource with potential for exploitation. Potential and emerging fisheries create challenges and opportunities for fishery managers who need to make decisions about how to sustainably manage a fishery prior to its initiation. This work proposes and analyzes possible alternative fishery management measures for this potential fishery, under biological and market uncertainty. Due to the lack of knowledge of various aspects of the biology of the resource, the individual growth of the stock was first analyzed and subsequently a bioeconomic analysis of the potential fishery was carried out.

A total of 240 otoliths and standard-length data from 932 specimens sampled from May to December 2015 were used for the analysis of individual growth. The annual formation of otolith increments was verified using the marginal increment analysis and the edge analysis. Age was estimated from annuli counts in sagittal sections of otoliths and growth was analyzed using a multi-model inference approach. The von Bertalanffy growth models (VBGM), generalized VBGM, Gompertz, Logistic and Johnson growth models were considered, which were fitted to observed and back calculated length-at-age data sets grouped by sex. According to Akaike's information criterion, the generalized VBGM was the most appropriate for females (L∞= 31.36 cm, k= 0.15 cm year-1), while the VBGM provided the best fit for males (L∞= 25.35 cm, k= 0.28 cm year-1).

The bioeconomic analysis of management alternatives for a potential dwarf hake fishery indicated that a new fishery for said stock could be biologically sustainable and economically profitable, under a set of management strategies and control rules. Limited access with low fishing effort is recommended as it is more profitable by boat and biologically precautionary, considering the high uncertainty associated with the exploitation of an unfished stock. Despite the combination of high fishing costs and low prices, the fishery could still be profitable in the long term, although there is risk of overexploitation if high fishing effort is allowed..."

Merluza enana, stock no explotado, crecimiento individual, análisis bioeconómico, pesquería potencial Dwarf hake, unexploited stock, individual growth, bioeconomic analysis, potential fishery CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE REGLAMENTACIÓN Y CONTROL REGLAMENTACIÓN Y CONTROL

Diferenciación gonadal e identificación del período lábil para el control del sexo en la lobina rayada, Morone saxatilis

Gonadal differentiation and identification of the labile period for sex control in striped bass, Morone saxatilis

Estefanía de los Ángeles Murillo Núñez (2024, [Tesis de maestría])

La lobina rayada (Morone saxatilis) es un pez teleósteo perciforme anádromo que pertenece a la familia Moronidae. Esta especie se destaca por sus notables cualidades para la acuicultura. La empresa Pacífico Aquaculture, S. A. P. I. de C. V., agregó a sus cultivos a la lobina rayada, puesto que es de gran valor comercial y tiene una gran demanda en el mercado local, nacional e internacional. Aunque existe un creciente interés en intensificar el cultivo de la lobina rayada con el fin de mejorar las prácticas productivas, hasta el momento se han llevado a cabo relativamente pocos estudios que describan su proceso de gonadogénesis o que identifiquen el período crítico en el ciclo reproductivo de esta especie. Dado su parentesco con la especie Dicentrarchus labrax, en este estudio, utilizamos esta última como modelo para el diseño de experimentos y la descripción del desarrollo gonadal de la lobina rayada. En este trabajo, se presenta el proceso de diferenciación de las gónadas de la lobina rayada durante su etapa larval y juvenil, que abarca desde 0 hasta 300 días después de la eclosión (dde), utilizando técnicas histológicas. A partir de 32 dde (2.03 cm LT) se desarrolló el primordio gonadal indiferenciado con células germinales. La diferenciación ovárica se determinó con la formación de la cavidad ovárica a los 52 dde (4.97 cm LT). Los primeros ovocitos primarios se desarrollaron a los 102 dde (11.99 cm LT). La diferenciación testicular se identificó a los 140 dde (13.75 cm) con la presencia y proliferación de espermatogonias. El periodo lábil de la lobina rayada es entre los 32 y 52 dde. M. saxatilis es más precoz que D. labrax. Este estudio representa el primer intento sistemático y detallado de describir el proceso de diferenciación de la lobina rayada. Los hallazgos de este trabajo serán de gran utilidad al proporcionar información crucial para el desarrollo de estrategias de manipulación reproductiva con el fin de mejorar los rendimientos biológicos de esta especie en el contexto acuícola.

The striped bass (Morone saxatilis) is an anadromous teleost perciform fish belonging to the Moronidae family. This species stands out for its remarkable qualities in aquaculture. Pacífico Aquaculture, S. A. P. I. de C. V., has incorporated striped bass into its aquaculture operations due to its significant commercial value and high demand in the local, national, and international markets. Although there is a growing interest in intensifying striped bass farming to enhance production practices, relatively few studios have been conducted to describe its gonadogenesis process or identify the critical period in the reproductive cycle of this species. Given its relationship with the Dicentrarchus labrax species, in this study, we used the latter as a model for experimental design and the description of striped bass gonadal development. This work presents the process of gonad differentiation in striped bass during its larval and juvenile stages, spanning from 0 to 300 days post hatching (dph), using histological techniques. The undifferentiated gonadal primordium with germ cells developed starting from 32 dph (2.03 cm TL). Ovarian differentiation was determined with the formation of the ovarian cavity at 52 dph (4.97 cm TL). The first primary oocytes developed at 102 dph (11.99 cm TL). Testicular differentiation was identified at 140 dph (13.75 cm) with the presence and proliferation of spermatogonia. The critical period for striped bass is between 32 and 52 dph. M. saxatilis differentiates earlier than D. labrax. This study represents the first systematic and detailed attempt to describe the striped bass differentiation process. The findings of this work will be of great utility by providing crucial information for the development of reproductive manipulation strategies aimed at enhancing the biological yields of this species in the aquacultural context.

Morone saxatilis, diferenciación sexual, análisis histológico, período lábil, gonadogénesis Morone saxatilis, sex differentiation, histological analysis, labile period, gonadogenesis CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE PISCICULTURA PISCICULTURA

Variability of Microcirculation Detected by Blood Pulsation Imaging

Alexei Kamshilin (2013, [Artículo])

The non-invasive assessment of blood flow is invaluable for the diagnostic and monitoring treatment of numerous vascular and neurological diseases. We developed a non-invasive and non-contact method of blood pulsation imaging capable of visualizing and monitoring of the two-dimensional distribution of two key parameters of peripheral blood flow: the blood pulsation amplitude and blood pulsation phase. The method is based on the photoplethysmographic imaging in the reflection mode. In contrast with previous imaging systems we use new algorithm for data processing which allows two dimensional mapping of blood pulsations in large object's areas after every cardiac cycle. In our study we carried out the occlusion test of the arm and found (i) the extensive variability of 2D-distribution of blood pulsation amplitude from one cardiac cycle to another, and (ii) existence of the adjacent spots to which the blood is asynchronously supplied. These observations show that the method can be used for studying of the multicomponent regulation of peripheral blood circulation. The proposed technique is technologically simple and cost-effective, which makes it applicable for monitoring the peripheral microcirculation in clinical settings for example, in diagnostics or testing the efficiency of new medicines. © 2013 Kamshilin et al.

algorithm, article, blood analysis, heart cycle, human, human experiment, image analysis, imaging system, male, microcirculation, peripheral circulation, photoelectric plethysmography, process development, Algorithms, Diagnostic Imaging, Diagnostic T CIENCIAS FÍSICO MATEMÁTICAS Y CIENCIAS DE LA TIERRA MATEMÁTICAS ANÁLISIS NUMÉRICO ANÁLISIS NUMÉRICO

Assessing the Spatiotemporal Relationship between Coastal Habitats and Fish Assemblages at Two Neotropical Estuaries of the Mexican Pacific

VICTOR MANUEL MURO TORRES FELIPE AMEZCUA MARTINEZ Gerogina Ramírez Ortiz FRANCISCO JAVIER FLORES DE SANTIAGO Felipe Amezcua Linares Yareli Hernández Álvarez (2022, [Artículo])

"Differences in fish assemblages’ structures and their relations with environmental variables (due to the variations in sampled seasons, habitats, and zones) were analyzed in two adjacent estuaries on the north Pacific coast of Mexico. Environmental variables and fish catches were registered monthly between August 2018 and October 2020. Multivariate analyses were conducted to define habitats and zones based on their environmental characteristics, and the effect of this variability on fish assemblages’ composition, biomass, and diversity (α and β) was evaluated. A total of 12,008 fish individuals of 143 species were collected using different fishing nets. Multivariate analyses indicated that fish assemblages’ structures were different between zones due to the presence, height, and coverage of distinct mangrove species. Additionally, depth and salinity showed effects on fish assemblages’ diversity (α and β-nestedness), which presented higher values in the ocean and remained similar in the rest of the analyzed zones and habitats. These results and the differences in species replacement (β-turnover) indicate the singularity of fish assemblages at estuaries (even in areas close to the ocean) and the necessity to establish local management strategies for these ecosystems."

mangrove forests, marine protected areas, alpha diversity, beta diversity, multivariate analyses CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE DINÁMICA DE LAS POBLACIONES DINÁMICA DE LAS POBLACIONES

A Comparison of Multi-Label Text Classification Models in Research Articles Labeled With Sustainable Development Goals

Roberto Carlos Morales-Hernández Joaquín Gutiérrez Jaguey David Becerra-Alonso (2022, [Artículo])

"The classification of scientific articles aligned to Sustainable Development Goals is crucial for research institutions and universities when assessing their influence in these areas. Machine learning enables the implementation of massive text data classification tasks. The objective of this study is to apply Natural Language Processing techniques to articles from peer-reviewed journals to facilitate their classification according to the 17 Sustainable Development Goals of the 2030 Agenda. This article compares the performance of multi-label text classification models based on a proposed framework with datasets of different characteristics. The results show that the combination of Label Powerset (a transformation method) with Support Vector Machine (a classification algorithm) can achieve an accuracy of up to 87% for an imbalanced dataset, 83% for a dataset with the same number of instances per label, and even 91% for a multiclass dataset."

Classification algorithm, multi-label text classification, problem transformation method, scientific articles, sustainable development goals, text classification INGENIERÍA Y TECNOLOGÍA CIENCIAS TECNOLÓGICAS TECNOLOGÍA DE LOS ORDENADORES LENGUAJES ALGORÍTMICOS LENGUAJES ALGORÍTMICOS

Estudios de genética en poblaciones de abulón y sus aplicaciones en ordenamiento pesquero

RICARDO PEREZ ENRIQUEZ NOE DIAZ VILORIA JOSE LUIS GUTIERREZ GONZALEZ ALEJANDRA ARCINIEGA DE LOS SANTOS ADRIANA MAX AGUILAR Pedro Cruz Hernández Fernando Aranceta Garza (2016, [Artículo])

"Se presenta la integración de más de 10 años de investigación científica en genética de las poblaciones de abulón en México realizada en el CIBNOR. Esta investigación muestra cómo se pueden aplicar los marcadores genéticos tanto en estudios de genética poblacional como en identificación forense con la finalidad de contribuir al conocimiento aplicado para manejo de la pesquería. Se desarrollaron marcadores genéticos tipo microsatélites de ADN enfocados tanto al abulón azul Haliotis fulgens como amarillo Haliotis corrugata para diferenciación de poblaciones y análisis de parentesco. Un análisis de estructura genética de las poblaciones silvestres de ambas especies de abulón mostró homogeneidad genética en la costa del Pacífico en la región centro-sur de la Península de Baja California, México, pero con diferenciación genética en localidades distantes debido a un flujo genético limitado producto del aislamiento reproductivo. Por ello, no existen elementos que den soporte a un manejo pesquero delimitado por bancos en ambas especies. De manera particular, el abulón amarillo mostró una menor de diversidad genética que el azul, posiblemente debido a una mayor explotación pesquera histórica. Los resultados obtenidos en pruebas de parentesco han indicado que la retención larvaria en bancos específicos es reducida, por lo que ni la agregación de reproductores ni la liberación de larvas han mostrado ser estrategias eficientes para favorecer el incremento de reclutas en bancos definidos. Un análisis de perfiles genéticos con el gen de la lisina permitió la identificación de las especies de abulón que se capturan y enlatan en México. El análisis comparativo de perfi les genéticos, basado en el gen nuclear 18S de abulón y otros moluscos, detectó producto enlatado conteniendo especies de moluscos comercializadas falsamente como abulón, lo que puede constituirse como una herramienta forense en futuras disputas legales. Este tipo de aplicación es potencialmente utilizable con otros productos comestibles en los cuales se sospecha de prácticas fraudulentas, ya sea por captura o comercialización ilegal o por sustitución de contenidos en productos procesados."

"This is an integrative work of more than 10 years of research in population genetics of abalone in Mexico performed at CIBNOR. It shows how molecular tools have the potential to support abalone fisheries management through population genetics and forensic analyses. Microsatellite DNA markers were developed on blue (green for its name in English) Haliotis fulgens and yellow abalone (pink for its name in English) H. corrugata to be used for genetic differentiation on populations and for parentage analysis. The analysis of genetic structure on wild populations of both species revealed genetic homogeneity in the Pacific coast of the central region of the Baja California Peninsula, Mexico, with genetic differentiation on distant localities due to a limited gene flow as a result of reproduction isolation. From this result we suggest that no evidences were found supporting the management of the fishery based on individual abalone beds. Pink abalone shows lower genetic diversity than green abalone, possibly due to higher historical fishery exploitation. The parentage analysis suggested that larval retention within beds is reduced, indicating that neither broodstockaggregation nor the release of abalone larvae for stock enhancement are efficient strategies to increase recruitment in specific beds.

An analysis of the genetic profiles with the lysine gene allowed the identification of abalone species captured and processed in Mexico. The comparative analysis, based on the 18S gene, among abalone and other mollusks, detected canned product containing mollusks that are commercialized allegedly as abalone or ‘abalone type’, which could constitute a forensic tool in future legal disputes. This type of application can also be used with other edible products in which fraudulent practices are suspected either because of illegal catch or commercialization or substitution in processed products."

Análisis forense, diversidad genética, gen 18S, genética de poblaciones, marcadores genéticos, retención larvaria Forensic analysis, genetic diversity, 18S gene, genetic markers, population genetics, larval retention BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA DE POBLACIONES GENÉTICA DE POBLACIONES

Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis

ELIANA VALENCIA LOZANO LISSET HERRERA ISIDRON Osiel Salvador Recoder-Meléndez Aarón Barraza Celis JOSE LUIS CABRERA PONCE (2022, [Artículo])

"Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interaction (PPI) network analyses performed in the STRING database (v11.5), we found 299 genes tightly associated in 14 clusters. Two major clusters of up-regulated proteins fundamental for life growth and development were found: 29 ribosomal proteins (RPs) interacting with 6 PEBP family members and 117 cell cycle (CC) proteins. The PPI network of up-regulated transcription factors (TFs) revealed that at least six TFs–MYB43, TSF, bZIP27, bZIP43, HAT4 and WOX9–may be involved during MTs development. The PPI network of down-regulated genes revealed a cluster of 83 proteins involved in light and photosynthesis, 110 in response to hormone, 74 in hormone mediate signaling pathway and 22 related to aging."

transcriptome-wide analysis, microtubers, potato, Solanum tuberosum, darkness, cell cycle, ribosomal proteins, PEBP family genes, cytokinin BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA MOLECULAR DE PLANTAS GENÉTICA MOLECULAR DE PLANTAS

The Pacific harbor seal gut microbiota in Mexico: Its relationship with diet and functional inferences

ARLETTE MARIMAR PACHECO SANDOVAL (2019, [Artículo])

Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway. © 2019 Pacheco-Sandoval et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

RNA 16S, RNA 18S, amino acid analysis, animal food, Article, bacterium colony, Bacteroidetes, basal metabolic rate, biodegradation, controlled study, DNA barcoding, feces analysis, Firmicutes, Fusobacteria, intestine flora, metabolism, Mexico, microb BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) BIOLOGÍA ANIMAL (ZOOLOGÍA)

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA