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Based on more than 11 billion geolocated cell phone records from 33 million different devices, daily mobility networks were constructed over a 15-month period for Greater Mexico City, one of the largest and most diverse metropolitan areas globally. The time frame considered spans the entire year of 2020 and the first three months of 2021, enabling the analysis of population movement dynamics before, during, and after the COVID-19 health contingency. The nodes within the 456 networks represent the basic statistical geographic areas (AGEBs) established by the National Institute of Statistics, Geography, and Informatics (INEGI) in Mexico. This framework facilitates the integration of mobility data with numerous indicators provided by INEGI. Edges connecting these nodes represent movement between AGEBs, with edge weights indicating the volume of trips from one AGEB to another. This extensive dataset allows researchers to uncover travel patterns, cross-reference data with socio-economic indicators, and conduct segregation studies, among other potential analyses.

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The Goss's wilt and leaf blight is a disease of maize (Zea mays) caused by Clavibacter nebraskensis, which was widespread in the last several years throughout the Midwest in the United States, south in Texas, and north to Canada. The bacterium is included within the high-risk list of quarantine pathogens by many plant protection organizations and countries including Mexico. Severe blight symptoms on maize plants were found in different provinces from Coahuila and Tlaxcala, Mexico, in 2012 and 2021, respectively. Twenty bacterial isolates with morphology similar to C. nebraskensis were obtained from the diseased maize leaves. The isolates were confirmed by phenotypic tests and 16S rRNA and gyrB sequencing. Two strains were tested for pathogenicity tests on seven hybrid sweet corn cultivars available in Mexico, and the most sensitive cultivar was tested for all the strains to fulfill Koch's postulates. The phylogenetic reconstruction based on two single loci reveals a remarkable clustering of Mexican strains to American strains reported approximately 50 years ago. The presence of this pathogen represents a risk and a significant challenge for plant protection strategies in Mexico and maize diversity.

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Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

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Human mobility networks are widely used for diverse studies in geography, sociology, and economics. In these networks, nodes usually represent places or regions and links refer to movement between them. They become essential when studying the spread of a virus, the planning of transit, or society's local and global structures. Therefore, the construction and analysis of human mobility networks are crucial for a vast number of real-life applications. This work presents a collection of networks that describe the human travel patterns between municipalities in Mexico in the 2020-2021 period. Using anonymized mobile location data, we constructed directed, weighted networks representing the volume of travels between municipalities. We analysed changes in global, local, and mesoscale network features. We observe that changes in these features are associated with factors such as COVID-19 restrictions and population size. In general, the implementation of restrictions at the start of the COVID-19 pandemic in early 2020, induced more intense changes in network features than later events, which had a less notable impact in network features. These networks will result very useful for researchers and decision-makers in the areas of transportation, infrastructure planning, epidemic control and network science at large.

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Viroids are single-stranded, circular RNA molecules (234-406 nt) that infect a wide range of crop species and cause economic losses in agriculture worldwide. They are characterized by the existence of a population of sequence variants, attributed to the low fidelity of RNA polymerases involved in their transcription, resulting in high mutation rates. Therefore, these biological entities exist as quasispecies. This feature allows them to replicate within a wide range of host plants, both monocots and dicots. Viroid hosts include economically important crops such as tomato, citrus, and fruit trees such as peach and avocado. Given the high risk of introducing viroids to viroid disease-free countries, these pathogens have been quarantined globally. As discussed herein, Mexico represents a geographical landscape of viroids linked to their origin and comprises considerable biodiversity. The biological features of viroid species endemic to Mexico are highlighted in this communication. In addition, we report the phylogenetic relationships among viroid and viroid strains, their economic impact, geographical distribution, and epidemiological features, including a broad host range and possible long-distance, seed, or insect-mediated transmission. In summary, this review could be helpful for a better understanding of the biology of viroid diseases and future programs on control of movement and spread to avoid economic losses in agricultural industries.

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Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.

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The structure of eukaryotic genes is generally a combination of exons interrupted by intragenic non-coding DNA regions (introns) removed by RNA splicing to generate the mature mRNA. A fraction of genes, however, comprise a single coding exon with introns in their untranslated regions or are intronless genes (IGs), lacking introns entirely. The latter code for essential proteins involved in development, growth, and cell proliferation and their expression has been proposed to be highly specialized for neuro-specific functions and linked to cancer, neuropathies, and developmental disorders. The abundant presence of introns in eukaryotic genomes is pivotal for the precise control of gene expression. Notwithstanding, IGs exempting splicing events entail a higher transcriptional fidelity, making them even more valuable for regulatory roles. This work aimed to infer the functional role and evolutionary history of IGs centered on the mouse genome. IGs consist of a subgroup of genes with one exon including coding genes, non-coding genes, and pseudogenes, which conform approximately 6% of a total of 21,527 genes. To understand their prevalence, biological relevance, and evolution, we identified and studied 1,116 IG functional proteins validating their differential expression in transcriptomic data of embryonic mouse telencephalon. Our results showed that overall expression levels of IGs are lower than those of MEGs. However, strongly up-regulated IGs include transcription factors (TFs) such as the class 3 of POU (HMG Box), Neurog1, Olig1, and BHLHe22, BHLHe23, among other essential genes including the ß-cluster of protocadherins. Most striking was the finding that IG-encoded BHLH TFs fit the criteria to be classified as microproteins. Finally, predicted protein orthologs in other six genomes confirmed high conservation of IGs associated with regulating neural processes and with chromatin organization and epigenetic regulation in Vertebrata. Moreover, this study highlights that IGs are essential modulators of regulatory processes, such as the Wnt signaling pathway and biological processes as pivotal as sensory organ developing at a transcriptional and post-translational level. Overall, our results suggest that IG proteins have specialized, prevalent, and unique biological roles and that functional divergence between IGs and MEGs is likely to be the result of specific evolutionary constraints.

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Glioblastoma (GBM) is the most aggressive and common brain cancer in adults with the lowest life expectancy. The current neuro-oncology practice has incorporated genes involved in key molecular events that drive GBM tumorigenesis as biomarkers to guide diagnosis and design treatment. This study summarizes findings describing the significant heterogeneity of GBM at the transcriptional and genomic levels, emphasizing 18 driver genes with clinical relevance. A pattern was identified fitting the stem cell model for GBM ontogenesis, with an upregulation profile for MGMT and downregulation for ATRX, H3F3A, TP53 and EGFR in the mesenchymal subtype. We also detected overexpression of EGFR, NES, VIM and TP53 in the classical subtype and of MKi67 and OLIG2 genes in the proneural subtype. Furthermore, we found a combination of the four biomarkers EGFR, NES, OLIG2 and VIM with a remarkable differential expression pattern which confers them a strong potential to determine the GBM molecular subtype. A unique distribution of somatic mutations was found for the young and adult population, particularly for genes related to DNA repair and chromatin remodelling, highlighting ATRX, MGMT and IDH1. Our results also revealed that highly lesioned genes undergo differential regulation with particular biological pathways for young patients. This multi-omic analysis will help delineate future strategies related to the use of these molecular markers for clinical decision-making in the medical routine.

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Due to the environmental conditions presented in arid zones, it is expected to have a high influence of deterministic processes over the community assemblages. Symbiotic interactions with microorganisms could increase colonization and survival of plants in difficult conditions, independent of the plants physiological and morphological characteristics. In this context, the microbial communities associated to plants that inhabit these types of areas can be a good model to understand the community assembly processes. We investigated the influence of stochastic and deterministic processes in the assemblage of rhizosphere microbial communities of Agave lechuguilla and bulk soil on the Cuatro Cienegas Basin, a site known for its oligotrophic conditions. We hypothesize that rhizospheric microbial communities of A. lechuguilla differ from those of bulk soil as they differ in physicochemical properties of soil and biotic interactions, including not only the plant, but also their microbial co-occurrence networks, it is expected that microbial species usually critical for plant growth and health are more common in the rhizosphere, whereas in the bulk soil microbial species related to the resistance to abiotic stress are more abundant. In order to confirm this hypothesis, 16S rRNA gene was sequenced by Illumina from rhizospheric and bulk soil samples in two seasons, also the physicochemical properties of the soil were determined. Our results showed differences in bacterial diversity, community composition, potential functions, and interaction networks between the rhizosphere samples and the ones from bulk soil. Although community structure arises from a complex interplay between deterministic and stochastic forces, our results suggest that A. lechuguilla recruits specific rhizospheric microbes with functional traits that benefits the plant through growth promotion and nutrition. This selection follows principally a deterministic process that shapes the rhizospheric microbial communities, directed by the plant modifications around the roots but also subjected to the influence of other environmental variables, such as seasonality and soil properties. Interestingly, keystone taxa in the interactions networks, not necessarily belong to the most abundant taxonomic groups, but they have an important role by their functional traits and keeping the connections on the community network.

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To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.

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BACKGROUND: Transfer RNAs (tRNAs) are ubiquitous in all living organism. They implement the genetic code so that most genomes contain distinct tRNAs for almost all 61 codons. They behave similar to mobile elements and proliferate in genomes spawning both local and non-local copies. Most tRNA families are therefore typically present as multicopy genes. The members of the individual tRNA families evolve under concerted or rapid birth-death evolution, so that paralogous copies maintain almost identical sequences over long evolutionary time-scales. To a good approximation these are functionally equivalent. Individual tRNA copies thus are evolutionary unstable and easily turn into pseudogenes and disappear. This leads to a rapid turnover of tRNAs and often large differences in the tRNA complements of closely related species. Since tRNA paralogs are not distinguished by sequence, common methods cannot not be used to establish orthology between tRNA genes. RESULTS: In this contribution we introduce a general framework to distinguish orthologs and paralogs in gene families that are subject to concerted evolution. It is based on the use of uniquely aligned adjacent sequence elements as anchors to establish syntenic conservation of sequence intervals. In practice, anchors and intervals can be extracted from genome-wide multiple sequence alignments. Syntenic clusters of concertedly evolving genes of different families can then be subdivided by list alignments, leading to usually small clusters of candidate co-orthologs. On the basis of recent advances in phylogenetic combinatorics, these candidate clusters can be further processed by cograph editing to recover their duplication histories. We developed a workflow that can be conceptualized as stepwise refinement of a graph of homologous genes. We apply this analysis strategy with different types of synteny anchors to investigate the evolution of tRNAs in primates and fruit flies. We identified a large number of tRNA remolding events concentrated at the tips of the phylogeny. With one notable exception all phylogenetically old tRNA remoldings do not change the isoacceptor class. CONCLUSIONS: Gene families evolving under concerted evolution are not amenable to classical phylogenetic analyses since paralogs maintain identical, species-specific sequences, precluding the estimation of correct gene trees from sequence differences. This leaves conservation of syntenic arrangements with respect to "anchor elements" that are not subject to concerted evolution as the only viable source of phylogenetic information. We have demonstrated here that a purely synteny-based analysis of tRNA gene histories is indeed feasible. Although the choice of synteny anchors influences the resolution in particular when tight gene clusters are present, and the quality of sequence alignments, genome assemblies, and genome rearrangements limits the scope of the analysis, largely coherent results can be obtained for tRNAs. In particular, we conclude that a large fraction of the tRNAs are recent copies. This proliferation is compensated by rapid pseudogenization as exemplified by many very recent alloacceptor remoldings.

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Con el propósito de establecer la frecuencia de anticuerpos IgA e IgM anti-C-trachomatis en mujeres embarazadas se realizó un estudio en 84 mujeres con esa condición, en edades comprendidas entre 14 y 43 años, que acudieron a la consulta prenatal, del Servicio Autónomo Hospital Universitario “Antonio Patricio de Alcalá”, en Cumaná, estado Sucre, Venezuela, durante el período marzo-junio de 2006. Para ello se obtuvieron 84 muestras de suero para la determinación de anticuerpos IgA e IgM anti C-trachomatis a través del método de inmunoabsorción ligado a enzimas ELISA (Diagnostic Automation INC). Del total de muestras analizadas 16 (19,05 por ciento) y 55 (65,48 por ciento) resultaron positivas para la determinación de anticuerpos IgA e IgM anti C-trachomatis respectivamente. No se encontró asociación entre la presencia de estos anticuerpos con la edad de las pacientes, aunque el mayor número de pacientes positivas se ubicó en el intervalo de edades comprendidas entre 14 a 23 años. Asimismo al asociarse las manifestaciones clínicas genitales con la presencia de anticuerpos IgA e IgM anti C- trachomatis no se encontraron valores estadísticamente significativos. Por lo anteriormente expuesto se concluye que la infección genital por Chlamydia trachomatis en mujeres embarazadas es extremadamente frecuente, de manera especial en las edades comprendidas entre 24 a 33 años, y ocurre habitualmente en forma asintomática con las graves repercusiones que esto acarrea a la paciente, al feto y a su pareja.

In order to establish the frequency of IgA and IgM anti-C. Trachomatis antibodies in expectant women, a study was made of 84 women between the ages of 14 and 43, who attended prenatal consults in the Autonomous Service at the University Hospital “Antonio Patricio of Alcalá,” Cumaná, State of Sucre, during the March-June period, 2006. 84 serum samples were obtained to determine IgA and IgM anti-C. trachomatis antibodies using the immunoabsorption method connected to ELISA enzymes (Diagnostic Automation INC). Of the total samples studied, 16 (19.05 percent) and 55 (65.48 percent) resulted positive for the IgA and IgM anti-C. trachomatis antibodies, respectively. No association was found between the presence of these antibodies and the age of the patients, although the greater number of positive patients was in the 14 to 23 year age interval. Likewise, no statistically significant values were found between the association of clinical genital manifestations and the presence of IgA and IgM anti C- trachomatis antibodies; therefore, it was shown that Chlamydia trachomatis is presented asymptomatically in most cases. Conclusions were that genital infection by Chlamydia trachomatis in pregnant women is extremely frequent, especially for ages between 24 and 33 years, and it occurs habitually in an asymptomatic form with the serious repercussions that this produces on the patient, the fetus and the partner.

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Debido a la ausencia de publicaciones de trabajos de investigación venezolanos sobre valores de referencia de los parámetros bioquímicos que evalúan la función hepática en población infantil sana, los profesionales del área de la salud se basan en su propia experiencia y en la de sus colegas, para interpretar los resultados de estas pruebas o simplemente utilizan los valores establecidos para las casas comerciales o los de la literatura internacional; los cuales no son adecuados, porque pertenecen a poblaciones de otros países en donde existen condiciones ambientales, dieta, estilo de vida, entre otros factores, diferentes a los de nuestra región, y en su mayoría corresponden a adultos. Por lo que se propuso establecer los valores de referencia de los niveles séricos de la albúmina, bilirrubina total, bilirrubina directa, bilirrubina indirecta y de la actividad enzimática de la alanino aminotransferasa, aspartato aminotransferasa, gamma glutamiltransferasa y fosfatasa alcalina en la población infantil sana del municipio Sucre, estado Sucre y compararlos con los valores de referencia establecidos para la casa comercial de los reactivos utilizados (Olympus Diagnostica), cuantificando cada uno de estos parámetros, en sueros de 486 niños, con edades entre los 3–11 años, clasificados según la edad y sexo para determinar el efecto y la interacción de éstos dos factores a través de un análisis de varianza de dos vías y una prueba a posteriori, el cálculo de los intervalos de referencia se realizó mediante los percentiles 2,5 y 97,5. Encontrando que para establecer los valores de referencia para los niveles séricos de albúmina, bilirrubina total, directa e indirecta se consideró solo la variable edad; mientras que para los valores de referencia de la aspartato aminotransferasa y la fosfatasa alcalina fueron consideradas las dos variables (edad y sexo), y en el caso de la alanino aminotransferasa y gamma glutamiltransferasa no se consideraron...

Due to absence of publications in Venezuela of investigation paperwork on reference values of biochemical parameters that evaluate the hepatic function in infantile healthy population, the health professionals base on their own experience and on his colleagues, to interpret the results of these tests, simply there use the values established by the business firms or those found on the international literature, which are not adapted, because they belong to populations of other countries where there exist environmental conditions, diet, way of life, among other factors, different from those of our region, and mainly they correspond to adults. Because of this, it was proposed to establish the reference values of the serum levels of the albumin, total bilirubin, direct bilirubin, indirect bilirubin and of the enzymatic activity alanine aminotransferase, aspartate aminotransferase, gamma glutamyltransferase and alkaline phosphatase in the infantile healthy population of the Sucre municipality at Sucre State and compare them with the established reference values of the business firm of the used reagents (Olympus Diagnostic), quantifying each of these parameters, in 486 children’s serum, with ages between 3-11 years classified according to the age and sex to determine the effect and the interaction of these two factors through a analysis of variance of two lines and a posteriori tests, the calculation of the intervals of reference fulfilled by means of the percentiles 2,5 and 97,5. Finding that, to establish the values of reference of the serum levels of albumin, total, direct and indirect bilirubin was considered only the age variable; whereas for the reference values of the aspartate aminotransferase were considered both variables (age and sex), and in the case of alanino aminotransferasa and gamma glutamiltransferasa age and sex were not considered. Concluding that the established reference values differ from the recommended...

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