De Novo assembly and annotation of the Pacific calico scallop (Argopecten ventricosus) transcriptome for immune-related gene discovery

RUTH ESCAMILLA MONTES GENARO DIARTE PLATA GABRIELA BERENICE MENDOZA MALDONADO Aarón Barraza Celis Carlos Eliud Angulo Valadez Seyed Hossein Hoseinifar Jesús Arturo Fierro Coronado ANTONIO LUNA GONZALEZ (2022, [Artículo])

"Invertebrates' immune defense mechanisms play a critical role in pathogen recognition and elimination. De novo assembly and annotation of the Argopecten ventricosus transcriptome were performed for the immune-related gene identification. Scallops (height: 4.4 cm) were challenged with inactivated Vibrio parahaemolyticus IPNGS16. The RNA from different tissues was pooled for a single cDNA library construction sequenced by NextSeq 500 platform 2×75 paired‐end chemistry. Before de novo assembling with Trinity, reads were analyzed with FastQC, Trimmomatic, and Prinseq. Assembled sequences were analyzed by CD-HIT-EST and TransDecoder. The corresponding annotation was performed against NCBI-nr, RefSeq protein, and KAAS (KEGG) databases. The Trinity assembly yielded 107,516 contigs. TransDecoder yielded 25,285 sequences as CDSs of which, 16,123 were annotated against the NCBI-nr protein, most of them scored with Crassostrea gigas data. Gene ontology mapped sequences (15,262) were classified in molecular functions (~13,000), cellular components (~11,000), and biological processes (~13,000). The KAAS analysis showed biological categories for metabolism (13%), cellular processes (12%), genetic information processing (10%), organismal systems (19%), environmental information (13%), and human diseases (33 %). Within the organismal systems, 467 immune-related genes (KO) were identified. Sixty-four immune-related genes were annotated/blasted against the NCBI-nr and RefSeq protein databases. An RT-qPCR was performed to analyze the expression level of immune-related genes obtained in the transcriptome analysis in scallops (height 4.5 cm) treated with probiotic bacilli added to culture water. Bacilli significantly increased the expression of the HSP70 and PGRP genes. The gene transcripts analysis of A. ventricosus will better understand its immune response against pathogens in culture systems."

Argopecten ventricosus, calico scallop, transcriptome, bivalve, immune genes BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) INMUNOLOGÍA INMUNOLOGÍA

Expansión poblacional reciente en la historia evolutiva de la anchoveta de California Engraulis mordax

Recent population expansion in the evolutionary history of the Californian anchovy Engraulis mordax

NOE DIAZ VILORIA LAURA SANCHEZ VELASCO RICARDO PEREZ ENRIQUEZ (2012, [Artículo])

"La anchoveta de California Engraulis mordax, es una especie templada que pudo haber pasado por un proceso de disyunción poblacional, debido al proceso postglacial de calentamiento del agua alrededor de la punta de la península de Baja California, hace unos 10,000 años. Se realizó un análisis genético para probar la hipótesis nula de homogeneidad genética entre el Golfo de California, México y el sur de California, EUA y si este era el caso, estimar el tiempo de surgimiento de haplotipos en términos de coalescencia. Se analizaron en total 80 secuencias de la región control hipervariable (ADNmt) de E. mordax, capturadas en la región central del Golfo de California (n = 40) y el sur de California (n = 40). A pesar del gran número de haplotipos únicos, no se observó diferenciación genética significativa entre localidades (FST = –0.0025, p = 0.686). Una distribución unimodal en la frecuencia del número de diferencias entre haplotipos indica un modelo de expansión rápida en el tamaño poblacional, que basado en una tasa mutacional de 3.6% por millón de años para la región control, indicó un tiempo de diferenciación nucleotídica relativamente reciente de aproximadamente 61,000 años. Este periodo de tiempo corresponde al Pleistoceno tardío, después de la formación de la península de Baja California, sugiriendo expansiones poblacionales en cada una de las localidades, seguidas del último episodio de glaciación, el cual quizás contribuyó a la migración de esta especie de afinidad templada entre las dos localidades y a su homogenización genética. Sin embargo este único evento reciente de flujo genético en la historia evolutiva de la especie, no explica por sí solo los patrones de distribución encontrados en las frecuencias de diferencias nucleotídicas."

"The Californian anchovy Engraulis mordax, a temperate species, may have undergone a process of population disjunction from experiencing post-glacial water heating processes around the tip of the Baja California Peninsula, Mexico about 10,000 b.p. A genetic analysis was performed to test the null hypothesis of genetic homogeneity between the Gulf of California and Southern California, U. S. A., and if this is the case, to estimate the time of haplotype emergence in terms of coalescence. A total of 80 sequences of the mtDNA hypervariable control region of E. mordax captured in the central Gulf of California (n = 40) and Southern California (n = 40) were analyzed. In spite of the large number of private haplotypes, no significant genetic differentiation among sites (FST = –0.0025, p = 0.686) was observed. An unimodal distribution of mismatch frequency between haplotypes indicated a model of rapid expansion in population size that, based on a mutation rate of 3.6% per million years in the control region, indicates a relatively recent nucleotide differentiation

time of approximately 61,000 years. This time period corresponds to the late Pleistocene, suggesting population expansions at each locality, followed by the last episode of glaciation, which may have contributed to migration of this temperate-affinity species between two locations and the genetic homogenization. However this unique recent event of gene flow in the evolutionary history of species does not explain by itself the mismatch distribution patterns found."

ADN mitocondrial, expansión poblacional reciente, flujo genético, región control, reloj molecular. Control region, gene flow, mitochondrial DNA, molecular clock, recent population expansion. BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) ZOOLOGÍA MARINA ZOOLOGÍA MARINA

Parques vemos, biodiversidad no sabemos: el caso de la herpetofauna de la ciudad de Mérida

Roberto Carlos Barrientos Medina (2023, [Artículo])

La herpetofauna, constituida por las diferentes especies de anfibios y reptiles que se pueden encontrar en un hábitat, es un buen grupo indicador de diversidad, ya que presenta características de movilidad que los hacen ser más dependientes del hábitat (lugar en el que viven). En este trabajo se analizan los patrones de diversidad de los anfibios y reptiles que se pueden encontrar en los parques ecológicos de Mérida, en distintos niveles de expresión (alfa, beta y gamma). Los resultados señalan la influencia del grado de urbanización, de acuerdo con los patrones encontrados en las diversidades beta y gamma.

AMBIENTES ANTROPIZADOS ECOLOGIA URBANA NIVELES DE DIVERSIDAD PATRONES ECOLOGICOS YUCATAN BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) HERPETOLOGÍA HERPETOLOGÍA

Influencia de las fases lunares en fertilidad, tasa de preñez y partos de vacas mestizas en el trópico seco.

CANUTO MUÑOZ GARCIA ROSENDO CUICAS HUERTA JUAN GONZALEZ MALDONADO EFREN ESTRADA PAQUI ISIDRO JAUREGUI PLATA JULIO CESAR GOMEZ VARGAS (2023, [Artículo])

There is speculation about moon phases influencing animal reproductive performance. A study was carried out to shed light on the influence of moon phases on estrus presentation, pregnancy rate, calving presentation, and offspring sex in cows from the Mexican dry tropical region. The reproductive data of 580 crossbred cows from 2010 to 2021 was organized according to reproductive events (estrus presentation, gestation, calving presentation, and offspring sex) occurrence during moon phases (new moon, first quarter, full moon, and last quarter). The data were analyzed by Chi-squared test and logistic regression. The full moon reduced the estrus presentation (p0.05). It is concluded that the full moon reduces estrus presentation in crossbred cows. Moon phases do not influence the gestation, calving presentation, and offspring sex.

estrus calving offspring sex CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS CIENCIAS VETERINARIAS FISIOLOGÍA ANIMAL

Forest proximity positively affects natural enemy mediated control of fall armyworm in Southern Africa

Frédéric Baudron Terence Sunderland (2022, [Artículo])

Insectivorous Birds Bat Predation Maize Cultivation CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA FALL ARMYWORMS BIOLOGICAL PEST CONTROL INSECTIVOROUS ANIMALS MAIZE PREDATOR PREY RELATIONS

Multiple approaches to understanding the taxonomic status of an enigmatic new scorpion species of the genus Tityus (Buthidae) from the biogeographic island of Paraje Tres Cerros (Argentina)

Andres Alejandro Ojanguren Affilastro (2017, [Artículo])

Tityus curupi n. sp., belonging to the bolivianus complex, is described from the biogeographically distinct area of Paraje Tres Cerros in north-eastern Argentina. We also present a molecular species delimitation analysis between Tityus curupi n. sp. and its sister species Tityus uruguayensis Borelli 1901 to confirm species integrity. Furthermore, a cytogenetic analysis is presented for these two species which contain different multivalent associations in meiosis, as a consequence of chromosome rearrangements, and the highest chromosome numbers in the genus. © 2017 Ojanguren-Affilastro 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.

Argentina, chromosome analysis, chromosome rearrangement, genus, human, meiosis, sister, species, anatomy and histology, animal, Argentina, chemistry, chromosome, classification, ecosystem, fluorescence in situ hybridization, genetics, geography, isl BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA DE INSECTOS (ENTOMOLOGÍA) BIOLOGÍA DE INSECTOS (ENTOMOLOGÍA)

Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover

OMAR VALENCIA MENDEZ (2018, [Artículo])

Gobies are the most diverse marine fish family. Here, we analysed the gamma-diversity (γ-diversity) partitioning of gobiid fishes to evaluate the additive and multiplicative components of α and β-diversity, species replacement and species loss and gain, at four spatial scales: sample units, ecoregions, provinces and realms. The richness of gobies from the realm Eastern Tropical Pacific (ETP) is represented by 87 species. Along latitudinal and longitudinal gradients, we found that the γ-diversity is explained by the β-diversity at both spatial scales, ecoregions and provinces. At the ecoregion scale, species are diverse in the north (Cortezian ecoregion) and south (Panama Bight ecoregion) and between insular and coastal ecoregions. At the province scale, we found that the species turnover between the warm temperate Northeast Pacific (WTNP), Tropical East Pacific (TEaP) and the Galapagos Islands (Gala) was high, and the species nestedness was low. At the ecoregion scale, historical factors, and phylogenetic factors have influenced the hotspots of gobiid fish biodiversity, particularly in the Cortezian, Panama Bight and Cocos Island ecoregions, where species turnover is high across both latitudinal and longitudinal gradients. At the provincial level, we found that the contributions of the β-diversity from north to south, in the WTNP, TEaP and Gala were high, as result of the high number of unique species. Species turnover was also high at this scale, with a low contribution from species nestedness that was probably due to the low species/gene flow within the provinces. These results highlight the importance and successful inclusion of a cryptobenthic fish component in ecological and biogeographical studies. © 2018 Valencia-Méndez 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, biodiversity, biogeographic region, biogeography, gene flow, goby fish, nonhuman, phylogeny, species distribution, species diversity, taxonomic identification, teleost, animal, animal dispersal, fish, Pacific Ocean, phylogeography, Animal Di CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CIENCIAS AGRARIAS PECES Y FAUNA SILVESTRE PECES Y FAUNA SILVESTRE

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

Reubicación de enjambres de abejas de Apis mellifera en zonas urbanas y periurbanas

JOSÉ CHAVIER DE ARAUJO FREITAS (2023, [Artículo])

Hoy día podemos encontrar poblaciones silvestres de Apis mellifera de origen africanizado en todo el país, siendo además la abeja que la mayoría de los apicultores tienen en sus apiarios. Estas abejas africanizadas tuvieron su origen en un proceso de hibridación entre abejas africanizadas y europeas que ocurrió en México, pero que tuvo su origen en Brasil. Estos enjambres en zonas urbanas son un riesgo para la salud pública, ya que su presencia puede ocasionar accidentes y víctimas fatales, por lo cual es necesario saber qué hacer cuando se está ante la presencia de ellos.

ABEJAS MELIFERAS ENJAMBRE DEFENSIVIDAD AFRICANIZACION YUCATAN MEXICO BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) INVERTEBRADOS INVERTEBRADOS

Compuestos bioactivos presentes en geopropóleos de Melipona beecheii y su potencial uso en la medicina tradicional

ANGEL DANIEL HERRERA ESPAÑA OMAR ARISTEO PEÑA MORAN ROGER GASPAR CAUICH KUMUL (2023, [Artículo])

El interés actual por estudios con productos naturales, ha llevado a realizar investigaciones con geopropóleos. Este producto natural producido por especies de abejas sin aguijón (meliponinos), resulta de una mezcla de material resinoso vegetal, arcilla y secreciones salivales. Estudios farmacológicos realizados con extractos de geopropóleos de Melipona beecheii, han demostrado sus propiedades anticancerígenas, antimicrobianas y antioxidantes, las cuales se relacionan con la presencia de diversos compuestos bioactivos. Debido a sus propiedades terapéuticas, este producto natural puede ser considerado como una potencial alternativa dentro de la medicina tradicional maya.

ABEJA SIN AGUIJON ACTIVIDAD ANTIMICROBIANA FENOLES FLAVONOIDES PROPIEDADES TERAPEUTICAS BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA ANIMAL (ZOOLOGÍA) INVERTEBRADOS INVERTEBRADOS