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Horizontal gene transfer (HGT) is a well-documented strategy used by bacteria to enhance their adaptability to challenging environmental conditions. Through HGT, a group of conserved genetic elements known as mobile genetic elements (MGEs) is disseminated within bacterial communities. MGEs offer numerous advantages to the host, increasing its fitness by acquiring new functions that help bacteria contend with adverse conditions, including exposure to heavy metal and antibiotics. This study explores MGEs within microbial communities along the Yucatan coast using a metatranscriptomics approach. Prior to this research, nothing was known about the coastal Yucatan's microbial environmental mobilome and HGT processes between these bacterial communities. This study reveals a positive correlation between MGEs and antibiotic resistance genes (ARGs) along the Yucatan coast, with higher MGEs abundance in more contaminated sites. The Proteobacteria and Firmicutes groups exhibited the highest number of MGEs. It's important to highlight that the most abundant classes of MGEs might not be the ones most strongly linked to ARGs, as observed for the recombination/repair class. This work presents the first geographical distribution of the environmental mobilome in Yucatan Peninsula mangroves.
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Transferência Genética Horizontal , Sequências Repetitivas Dispersas , Microbiota , Sequências Repetitivas Dispersas/genética , Microbiota/genética , México , Bactérias/genética , Bactérias/classificação , Proteobactérias/genéticaRESUMO
The challenge of knowing the events surrounding the modern origins of the different specialties of Chilean medicine should be of interest to the specialists of these specialties. Thus, in the case of surgery, fortunately in Chile there are testimonial documents, which reviewed and analyzed can suggest this question, mentioning the one who today is considered the world father of modern surgery, whose important surgical teachings were delivered to Chilean disciples who introduced it in our country. In the context of the War of the Pacific, in the year 1879, a "blood hospital" was built in Santiago, donated by Domingo Matte, a Chilean politician, to receive the many war wounded who were transported from the north. It was Dr. Manuel Barros Borgoño, a young surgeon recently graduated from the Faculty of Medicine in Paris, with a degree revalidated in Chile, who in 1880 took charge of this hospital, and together with his team, began to apply his experience in listerian methods learned in Paris from his teacher Dr. Just Lucas Champonniere. Just Lucas Champonniere, giving beginning to the Chilean antiseptic surgery, managing to reduce the mortality of surgeries to 3%, compared to 80% of other Chilean hospitals that refused to change, and continued with the use of sponge soaked in cerato (lard).
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Humanos , História do Século XVI , História do Século XIX , Cirurgia Geral/história , Antissepsia/métodos , Cirurgia Geral/métodos , Chile , Hospitais/históriaRESUMO
Antibiotic resistance (AR) is one of the greatest human and clinical challenges associated with different pathogenic organisms. However, in recent years it has also become an environmental problem due to the widespread use of antibiotics in humans and livestock activities. The ability to resist antibiotics comes from antibiotic resistance genes (ARGs) and our understanding of their presence in coastal environments is still limited. Therefore, the objective of the present study was to explore the presence and possible differences in the microbial resistome of four sites from the Yucatan coast through the evaluation of the composition and abundance of ARGs using a high-throughput analysis of metatranscriptomic sequences. In total, 3,498 ARGs were uncovered, which participate in the resistance to tetracycline, macrolide, rifamycin, fluoroquinolone, phenicol, aminoglycoside, cephalosporin, and other antibiotics. The molecular mechanisms of these ARGs were mainly efflux pump, antibiotic target alteration and antibiotic target replacement. In the same way, ARGs were detected in the samples but showing dissimilar enrichment levels. With respect to the sampling sites, the ARGs were present in all the samples collected, either from preserved or contaminated areas. Importantly, sediments of the preserved area of Dzilam presented the second highest level of ARGs detected, probably as a consequence of the antibiotics dragged to the coast by submarine groundwater discharge. In general, the resistance to a single antibiotic was greater than multiresistance, both at the level of gene and organisms; and multiresistance in organisms is acquired mainly by recruiting different monoresistance genes. To our knowledge, this is the first study that describes and compares the resistome of different samples of the Yucatan coast. This study contributes to generating information about the current state of antibiotic resistance on the Yucatan coasts for a better understanding of ARGs dissemination and could facilitate the management of ARGs pollution in the environment.
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Marine gastropods of the genus Conus, comprising more than 800 species, have the characteristic of injecting worms and other prey with venom. These conopeptide toxins, highly diverse in structure and action, are highly potent and specific for their molecular targets (ion channels, receptors, and transporters of the prey's nervous system), and thus are important research tools and source for drug discovery. Next-generation sequencing technologies are speeding up the discovery of novel conopeptides in many of these species, but only limited information is available for Conus spurius, which inhabits sandy mud. To search for new precursor conopeptides, we analyzed the transcriptome of the venous ducts of C. spurius and identified 55 putative conotoxins. Seven were selected for further study and confirmed by Sanger sequencing to belong to the M-superfamily (Sr3.M01 and Sr3.M02), A-superfamily (Sr1.A01 and Sr1.A02), O-superfamily (Sr15.O01), and Con-ikot-ikot (Sr21.CII01 and Sr22.CII02). Six of these have never been reported. To our knowledge, this report is the first to use high-throughput RNA sequencing for the study of the diversity of C. spurius conotoxins.
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Conotoxinas/química , Caramujo Conus/genética , Animais , Sequenciamento de Nucleotídeos em Larga EscalaRESUMO
KEY MESSAGE: The moss Pseudocrossidium replicatum is a desiccation-tolerant species that uses an inducible system to withstand severe abiotic stress in both protonemal and gametophore tissues. Desiccation tolerance (DT) is the ability of cells to recover from an air-dried state. Here, the moss Pseudocrossidium replicatum was identified as a fully desiccation-tolerant (FDT) species. Its gametophores rapidly lost more than 90% of their water content when exposed to a low-humidity atmosphere [23% relative humidity (RH)], but abscisic acid (ABA) pretreatment diminished the final water loss after equilibrium was reached. P. replicatum gametophores maintained good maximum photosystem II (PSII) efficiency (Fv/Fm) for up to two hours during slow dehydration; however, ABA pretreatment induced a faster decrease in the Fv/Fm. ABA also induced a faster recovery of the Fv/Fm after rehydration. Protein synthesis inhibitor treatment before dehydration hampered the recovery of the Fv/Fm when the gametophores were rehydrated after desiccation, suggesting the presence of an inducible protective mechanism that is activated in response to abiotic stress. This observation was also supported by accumulation of soluble sugars in gametophores exposed to ABA or NaCl. Exogenous ABA treatment delayed the germination of P. replicatum spores and induced morphological changes in protonemal cells that resembled brachycytes. Transcriptome analyses revealed the presence of an inducible molecular mechanism in P. replicatum protonemata that was activated in response to dehydration. This study is the first RNA-Seq study of the protonemal tissues of an FDT moss. Our results suggest that P. replicatum is an FDT moss equipped with an inducible molecular response that prepares this species for severe abiotic stress and that ABA plays an important role in this response.
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Adaptação Fisiológica/genética , Bryopsida/genética , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Ácido Abscísico/farmacologia , Adaptação Fisiológica/efeitos dos fármacos , Alfa-Amanitina/farmacologia , Bryopsida/metabolismo , Cicloeximida/farmacologia , Desidratação , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Geografia , México , Inibidores da Síntese de Ácido Nucleico/farmacologia , Reguladores de Crescimento de Plantas/farmacologia , Inibidores da Síntese de Proteínas/farmacologia , RNA-Seq/métodos , Estresse Fisiológico , Fatores de TempoRESUMO
Resumen Introducción: el 12 de marzo del 2020 Honduras reporto el primer caso de COVID-19 producida por el SARS-CoV-2. A partir de ese momento, se adoptan medidas para ralentizar el contagio. Para junio 2020, se reportan casos en la mayoría de los municipios. Con el objetivo de identificar la presencia y circulación del SARS-CoV-2 y caracterizar e identificar sintomatología sugerente de COVID-19 en la población se realiza el presente estudio. Metodología: Se trató de un estudio descriptivo tipo transversal, bajo enfoque cuantitativo y cualitativo utilizando el método de muestreo por lote. La población de estudio fueron los habitantes de municipios en los cuales no se reportaban oficialmente casos activos de COVID-19. Se recolectaron datos mediante encuesta electrónica y se aplicaron pruebas rápidas de detección de anticuerpos (IgG e IgM). Resultados: se encuestó y realizó pruebas a 792 personas de 41 municipios del país. La positividad de contacto se encontró en el 6.2 % (49/792). De estos, el 55.1 % (27/49) son hombres. Los grupos de edad con menor cantidad de pruebas de contacto positivo por COVID-19 fueron entre los 10-19 años (3/49) y mayores de 60 años (6/49). El cuadro clínico consistió en fiebre, disminución del apetito, dificultad respiratoria y pérdida del gusto y olfato. El 49.2 % (32/49) fueron asintomáticos. Conclusiones: Se demostró que hubo circulación del virus en la población de municipios en donde no se notificaron casos activos, 96 días después del primer caso confirmado en el país. La detección de anticuerpos específicos del virus podría ser importante en encuestas para infección asintomática en zonas donde el contacto es esperado.
Abstract Introduction: In Honduras on March 12, 2020, the first case of COVID-19 caused by the SARS-CoV-2 was reported. From that moment on, a series of measures were adopted to slow down contact throughout the country. By June 2020, cases are reported across the whole country. With the objective of identifying the presence and circulation of SARS-CoV-2, characterizing and identifying suggestive symptoms of COVID-19 in the population, the present study was carried out. Methodology: A descriptive cross-sectional study was carried out, using a quantitative and qualitative approach, using the LQAS sampling method. The study population was the inhabitants of the identified municipalities, with no current circulation data for SARS-CoV-2 or the municipalities whose last confirmed case was 21 days ago. The data was collected through an electronic survey, it was possible to apply rapid antibody detection tests (IgG and IgM). Results: 792 people from 41 municipalities of the country were surveyed and tested. Positivity of contact was found in 6.2% (49/792). Of these, 55.1% (27/49) are men. 61.2% (30/49) are between 20 and 49 years old. The clinical symptoms found were fever, decreased appetite, respiratory distress, and loss of taste and smell, the 49.2% (32/49) without symptoms. Conclusions: virus circulation was demonstrated in the population of municipalities in which no cases were officially reported and after 96 days of the first confirmed case in the country. Detection of virus-specific antibodies could be important in surveys for asymptomatic infection in areas where contact is expected.
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Humanos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Teste Sorológico para COVID-19 , COVID-19 , HondurasRESUMO
The objective of this study was to evaluate feed intake and digestibility and ruminal characteristics of development-stage calves fed mulatto II (Brachiaria sp.) grass hay (MGH) and a protein supplement (PS) consisting of increasing levels of the parota (Enterolobium cyclocarpum) pod (PP). We used eight Swiss-zebu calves in growth stage with an average age of 11 months and initial average weight of 157.6 ± 8.5 kg. They were distributed in a repeated 4 × 4 Latin square design with 4 treatments (period 30 days): 0% (PP0), 25% (PP25), 50% (PP50), and 75% (PP75) of the PP. Calves in the PP0 and PP25 treatments had higher intake of PS and MGH as dry matter (DM) than those in the PP50 and PP75 treatments (p < 0.05). Organic matter intake (OMI) of the PP75 calves was lower than that of PP0 and PP25 calves. Crude protein intakes (CPI) of PP0 and PP25 calves were higher than those of PP50 and PP75 calves (p < 0.05). Apparent digestibility of crude protein was higher in the PP0, PP25, and PP50 treatments compared with that in treatment PP75 (p < 0.05). The treatments did not affect total bacterial count, cellulolytic bacterial count, cellulase enzymatic activity, volatile fatty acids, or the acetate/propionate ratio (p > 0.05). Rumen pH in the PP0 calves was higher than that of the PP25 calves, whereas the protozoa count and ammonia content were higher in PP0 calves than in PP75 (p < 0.05). In conclusion, the inclusion of 25% PP in the PS for forage-fed calves is a feeding alternative.
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Ração Animal , Rúmen , Ração Animal/análise , Animais , Bovinos , Dieta/veterinária , Fibras na Dieta/metabolismo , Digestão , Ingestão de Alimentos , Fermentação , Rúmen/metabolismo , DesmameRESUMO
Microbial communities are important players in coastal sediments for the functioning of the ecosystem and the regulation of biogeochemical cycles. They also have great potential as indicators of environmental perturbations. To assess how microbial communities can change their composition and abundance along coastal areas, we analyzed the composition of the microbiome of four locations of the Yucatan Peninsula using 16S rRNA gene amplicon sequencing. To this end, sediment from two conserved (El Palmar and Bocas de Dzilam) and two contaminated locations (Sisal and Progreso) from the coast northwest of the Yucatan Peninsula in three different years, 2017, 2018 and 2019, were sampled and sequenced. Microbial communities were found to be significantly different between the locations. The most noticeable difference was the greater relative abundance of Planctomycetes present at the conserved locations, versus FBP group found with greater abundance in contaminated locations. In addition to the difference in taxonomic groups composition, there is a variation in evenness, which results in the samples of Bocas de Dzilam and Progreso being grouped separately from those obtained in El Palmar and Sisal. We also carry out the functional prediction of the metabolic capacities of the microbial communities analyzed, identifying differences in their functional profiles. Our results indicate that landscape of the coastal microbiome of Yucatan sediment shows changes along the coastline, reflecting the constant dynamics of coastal environments and their impact on microbial diversity.
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The off-label use of antiviral and antimalarial drugs has been considered by many researchers as a fast and relatively safe alternative to provide therapeutic options to treat COVID-19, but the assessment of such drug-specific effectiveness in this regard is far from complete. Especially, the current body of knowledge about COVID-19 therapeutics needs more data regarding drug effectiveness and safety in the severely ill patients with comorbidities. In the present article, we retrospectively analyze data from 61 patients that received treatment with chloroquine, lopinavir/ritonavir, both drugs administered together, or a standard treatment with no antiviral drugs, and the study was carried in severely ill patients. We found that either drug is ineffective at treating COVID-19, as they are not able to reduce hospitalization length, mortality, C-reactive protein (CRP), lactate dehydrogenase (LDH), d-Dimer, or ferritin, or to enhance gasometric parameters, lymphocytes, total leukocytes, and neutrophil levels, whereas both drugs administered together decrease circulating lymphocytes, increase LDH and ferritin levels, and more importantly, enhance mortality. In this way, our results show that both drugs are ineffective and even potentially harmful alternatives against SARS-CoV-2.
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Tratamento Farmacológico da COVID-19 , Cloroquina/efeitos adversos , Cloroquina/uso terapêutico , Lopinavir/efeitos adversos , Lopinavir/uso terapêutico , Ritonavir/efeitos adversos , Ritonavir/uso terapêutico , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antimaláricos/efeitos adversos , Antimaláricos/uso terapêutico , Antivirais/efeitos adversos , Antivirais/uso terapêutico , Quimioterapia Combinada/efeitos adversos , Quimioterapia Combinada/métodos , Feminino , Hospitalização , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , SARS-CoV-2/efeitos dos fármacos , Índice de Gravidade de Doença , Adulto JovemRESUMO
Justificación: los centros penales constituyen escenarios donde confluyen una serie de determinantes para la aparición de enfermedades de interés en salud pública, dada la vulnerabilidad imperante y el riesgo exponencial de propagación. En el mes de junio del año 2020 el personal de salud del municipio de Gracias, departamento de Lempira, al occidente de Honduras, observó un incremento en el número de enfermedades respiratorias agudas a expensas de las atenciones brindadas en el centro penal ubicado en esta ciudad. Metodología: se integró un equipo de investigación coordinado por la Unidad de Epidemiologia del Sistema Nacional de Gestión de Riesgos para realizar un estudio de casos. Resultados: se encontraron 63 casos de COVID-19, distribuidos entre personal penitenciario y privados de libertad; el 97% eran hombres, entre 40 y 59 años de edad, que presentaron un cuadro clínico de leve a moderado, siendo los síntomas más frecuentemente observados: fiebre, anosmia y tos persistente. Se inició manejo y tratamiento normado, ninguno de los casos requirió hospitalización. Discusión: de acuerdo al tiempo de incubación descrito para la COVID-19 y los resultados de las pruebas serológicas, se dedujo que el ingreso de la enfermedad al centro penitenciario fue a través del personal de seguridad, identificando el caso índice probable en un guardia penitenciarios que realizó un traslado hacia otro centro penal. Este reporte describe las acciones realizadas para la investigación y control del primer brote de la COVID-19 documentado en un centro penitenciario de Honduras...(AU)
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Humanos , Masculino , Feminino , Adulto , Pessoa de Meia-Idade , Estabelecimentos Correcionais/legislação & jurisprudência , COVID-19/epidemiologia , Prisioneiros/legislação & jurisprudência , Doenças Respiratórias/complicações , Populações Vulneráveis , Direitos dos PrisioneirosRESUMO
Antimicrobial resistance (AR) is one of the most important public health challenges worldwide as it represents a serious complication that is able to increase the mortality, morbidity, disability, hospital stay and economic burden related to infectious diseases. As such, the spread of AR-pathogens must be considered as an emergency, and interdisciplinary approaches must be undertaken in order to develop not only drugs, but holistic strategies to undermine the epidemic and pathogenic potentials of multi-drug resistant (MDR) pathogens. One of such approaches has focused on the use of antimicrobial nanoparticles (ANPs), as they have demonstrated to possess strong antimicrobial effects on MDR pathogens. On the other hand, the ability of bacteria to develop resistance to such agents is minimal. In this way, ANPs may seem a good choice for the development of new drugs, but there is no certainty about their safety, which may delay its translation to the clinical setting. As MDR pathogens are quickly becoming more prevalent and drug development is slow and expensive, there is an increasing need for the rapid development of new strategies to control such agents. We hereby explore the possibility of designing ANP-based devices such as surgical masks and fabrics, wound dressings, catheters, prostheses, dentifrices, water filters, and nanoparticle-coated metals to exploit the potential of such materials in the combat of MDR pathogens, with a good potential for translation into the clinical setting.
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PURPOSE: To determine the anatomical variations and morphology of the external carotid artery (ECA) and its anterior branches. METHODS: Using computed tomography angiography (CTA), the origin, internal diameter, and surface laterality emergence of the superior thyroid (STA), lingual (LA), and facial (FA) arteries were evaluated retrospectively evaluated and classified. The bifurcation level of the common carotid artery (CCA) in relation to the cervical vertebrae and disc was also determined. RESULTS: A total of 76 CTA were included in the study. STA originated from the carotid bifurcation (CB) (type I), CCA (type II) and ECA (type III) in 20.4 (31/152), 17.1 (26/152) and 50.7% (77/152) cases, respectively. Also 10.5% (16/152) arose from a shared trunk with LA as a thyrolingual trunk (TLT) (type IVa), and absent in 1.3% (2/152). LA originated in the CB in only one case. A linguofacial trunk (LFT) was present in 14.5% (22/152). Mean diameters of STA, LA and FA were 1.70, 1.95 and 2.45 mm, respectively. Meanwhile, surface laterality were predominately from anteromedial, medial, and anterior, respectively. CB was mainly on C3 or C3-C4 (55.9% of cases). CONCLUSIONS: STA origin below the ECA is a common finding. Our population presented the highest percentage of TLT (10.5%) and high CB (9.8%) in literature. Considering these variations are important to prevent complications in neck surgical procedures.
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Variação Anatômica , Artéria Carótida Externa/anormalidades , Glândula Tireoide/irrigação sanguínea , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Artéria Carótida Externa/diagnóstico por imagem , Angiografia por Tomografia Computadorizada , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Glândula Tireoide/diagnóstico por imagem , Adulto JovemRESUMO
Prokaryotes represent a source of both biotechnological and pharmaceutical molecules of importance, such as nonribosomal peptides (NRPs). NRPs are secondary metabolites which their synthesis is independent of ribosomes. Traditionally, obtaining NRPs had focused on organisms from terrestrial environments, but in recent years marine and coastal environments have emerged as an important source for the search and obtaining of nonribosomal compounds. In this study, we carried out a metataxonomic analysis of sediment of the coast of Yucatan in order to evaluate the potential of the microbial communities to contain bacteria involved in the synthesis of NRPs in two sites: one contaminated and the other conserved. As well as a metatranscriptomic analysis to discover nonribosomal peptide synthetases (NRPSs) genes. We found that the phyla with the highest representation of NRPs producing organisms were the Proteobacteria and Firmicutes present in the sediments of the conserved site. Similarly, the metatranscriptomic analysis showed that 52% of the sequences identified as catalytic domains of NRPSs were found in the conserved site sample, mostly (82%) belonging to Proteobacteria and Firmicutes; while the representation of Actinobacteria traditionally described as the major producers of secondary metabolites was low. It is important to highlight the prediction of metabolic pathways for siderophores production, as well as the identification of NRPS's condensation domain in organisms of the Archaea domain. Because this opens the possibility to the search for new nonribosomal structures in these organisms. This is the first mining study using high throughput sequencing technologies conducted in the sediments of the Yucatan coast to search for bacteria producing NRPs, and genes that encode NRPSs enzymes.
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Bactérias/genética , Proteínas de Bactérias/genética , Sedimentos Geológicos/microbiologia , Microbiota , Biossíntese de Peptídeos Independentes de Ácido Nucleico/genética , Peptídeo Sintases/genética , Transcriptoma , Bactérias/classificação , Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , Peptídeo Sintases/metabolismo , Filogenia , Áreas AlagadasRESUMO
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor ß (TGF-ß) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10-3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy.
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The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins dedicated to favor and/or impede the activity of the RNA polymerase. In prokaryotes these proteins have been grouped into families that can be found in most of the different taxonomic divisions. In this work, the association between the expansion patterns of 111 protein regulatory families was systematically evaluated in 1351 non-redundant prokaryotic genomes. This analysis provides insights into the functional and evolutionary constraints imposed on different classes of regulatory factors in bacterial and archaeal organisms. Based on their distribution, we found a relationship between the contents of some TF families and genome size. For example, nine TF families that represent 43.7% of the complete collection of TFs are closely associated with genome size; i.e., in large genomes, members of these families are also abundant, but when a genome is small, such TF family sizes are decreased. In contrast, almost 102 families (56.3% of the collection) do not exhibit or show only a low correlation with the genome size, suggesting that a large proportion of duplication or gene loss events occur independently of the genome size and that various yet-unexplored questions about the evolution of these TF families remain. In addition, we identified a group of families that have a similar distribution pattern across Bacteria and Archaea, suggesting common functional and probable coevolution processes, and a group of families universally distributed among all the genomes. Finally, a specific association between the TF families and their additional domains was identified, suggesting that the families sense specific signals or make specific protein-protein contacts to achieve the regulatory roles.
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Células Procarióticas/metabolismo , Fatores de Transcrição/análise , Fatores de Transcrição/genética , Archaea/genética , Bactérias/genética , DNA/genética , Proteínas de Ligação a DNA , Tamanho do Genoma/genética , Genoma Arqueal/genética , Genoma Bacteriano/genética , Genômica/métodos , Ligação Proteica , Transcriptoma/genéticaRESUMO
The Pelibuey sheep (Ovis aries) is an indigenous breed distributed in the tropical regions of Mexico. The prolificacy of this sheep is on average from 1 to 1.5 lambs, being an important breeding characteristic that owners seek to increase with the purpose of economic improvements. New-generation RNA sequencing technology has been used to identify the genes that are expressed in the ovarian tissue of sheep that have two or more lambs per parturition, as well as to elucidate the metabolic pathways that are affected by the expression of these genes, with the purpose of better understanding the prolificacy in the sheep. In the present study, the transcriptional expression of multiparous and uniparous sheep was compared using RNA sequencing. Multiparous (M group) and uniparous (U group) sheep that had a genealogical record for three generations (M, n = 5 and U, n = 5) were selected. RNA was extracted from ovarian tissue and subsequently used to prepare the libraries that were sequenced using the Illumina NextSeq500 platform. A total of 31,575 genes were detected from the transcriptomic analysis of which 4908 were significantly expressed (p-value ≤ 0.001) in the ovary of sheep. Subsequently, a second filter was carried out to evaluate the false discovery rate (FDR) and select those genes with p-values ≤ 0.05 and values of expression ≥ 1 (log2), obtaining 354 differential expressed genes (DEG): 120 genes up-regulated and 234 genes down-regulated in the group M with respect to the group U. Through Gene Ontology (GO) and metabolic analysis, we obtained information on the function of differentially expressed genes, and its importance in the reproduction of multiparous sheep. This result suggest that genes identified in the present study participate in the development of the final stages of follicles.
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Tamanho da Ninhada de Vivíparos/genética , Ovário/metabolismo , Ovinos/genética , Animais , Feminino , RNA-SeqRESUMO
We fully sequenced the genome of Houston virus, a recently discovered mosquito-associated virus belonging to the newly established family Mesoniviridae. The isolate was recovered from Culex quinquefasciatus in southern Mexico, which shows that the geographic range of Houston virus is not restricted to the United States in North America.
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In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.
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The repertoire of 304 DNA-binding transcription factors (TFs) in Escherichia coli K-12 has been described recently, with 196 TFs experimentally characterized and 108 proteins predicted by sequence comparisons. Based on 303 expression profile patterns retrieved from the Colombos database 12 clusters were identified, including hypothetical and experimentally characterized TFs, using a spectral clustering algorithm based on a 3NN graph built using 14 principal components that represent 65% of the variance of the expression data. In a posterior step, clusters were characterized in terms of their associated overrepresented functions, based on KEGG, Supfam annotations and Pfam assignments among other functional categories using an enrichment test, reinforcing the notion that the identified clusters are functionally similar among them. Based on these data, the we identified 12 clusters in which hypothetical and known TFs share similar regulatory and physiological functions, such as module associations of toxin-antitoxin (TA) systems with DNA repair mechanisms, amino acid biosynthesis, and carbon metabolism/transport, among others. This analysis has increased our knowledge about gene regulation in E. coli K-12 and can be further expanded to other organisms.
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The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.