Pseudomonas aeruginosa strains belonging to phylogroup 3 frequently exhibit an atypical quorum sensing response: the case of MAZ105, a tomato rhizosphere isolate.

Pseudomonas aeruginosa is a widespread γ-proteobacterium and an important opportunistic pathogen. The genetically diverse P. aeruginosa phylogroup 3 strains are characterized by producing the pore-forming ExlA toxin and by their lack of a type III secretion system. However, like all strains of this species, they produce several virulence-associated traits, such as elastase, rhamnolipids and pyocyanin, which are regulated by quorum sensing (QS). The P. aeruginosa QS response comprises three systems (Las, Rhl and Pqs, respectively) that hierarchically regulate these virulence factors. The Pqs QS system is composed of the PqsR transcriptional factor, which, coupled with the alkyl-quinolones HHQ or PQS, activates the transcription of the pqsABCDE operon. The products of the first four genes of this operon produce HHQ, which is then converted to PQS by PqsH, while PqsE forms a complex with RhlR and stabilizes it. In this study we report that mutations affecting the Pqs system are particularly common in phylogroup 3 strains. To better understand QS in phylogroup 3 strains we studied strain MAZ105 isolated from tomato rhizosphere and showed that it contains mutations in the central QS transcriptional regulator, LasR, and in the gene encoding the PqsA enzyme involved in the synthesis of PQS. However, it can still produce QS-regulated virulence factors and is virulent in Galleria mellonella and mildly pathogenic in the mouse abscess/necrosis model; our results show that this may be due to the expression of pqsE from a different PqsR-independent promoter than the pqsA promoter. Our results indicate that using anti-virulence therapy based on targeting the PQS system will not be effective against infections by P. aeruginosa phylogroup 3 strains.

Crop genetic diversity uncovers metabolites, elements, and gene networks predicted to be associated with high plant biomass yields in maize.

Rapid population growth and increasing demand for food, feed, and bioenergy in these times of unprecedented climate change require breeding for increased biomass production on the world's croplands. To accelerate breeding programs, knowledge of the relationship between biomass features and underlying gene networks is needed to guide future breeding efforts. To this end, large-scale multiomics datasets were created with genetically diverse maize lines, all grown in long-term organic and conventional cropping systems. Analysis of the datasets, integrated using regression modeling and network analysis revealed key metabolites, elements, gene transcripts, and gene networks, whose contents during vegetative growth substantially influence the build-up of plant biomass in the reproductive phase. We found that S and P content in the source leaf and P content in the root during the vegetative stage contributed the most to predicting plant performance at the reproductive stage. In agreement with the Gene Ontology enrichment analysis, the cis-motifs and identified transcription factors associated with upregulated genes under phosphate deficiency showed great diversity in the molecular response to phosphate deficiency in selected lines. Furthermore, our data demonstrate that genotype-dependent uptake, assimilation, and allocation of essential nutrient elements (especially C and N) during vegetative growth under phosphate starvation plays an important role in determining plant biomass by controlling root traits related to nutrient uptake. These integrative multiomics results revealed key factors underlying maize productivity and open new opportunities for efficient, rapid, and cost-effective plant breeding to increase biomass yield of the cereal crop maize under adverse environmental factors.

Prospective Study in Children with Complicated Urinary Tract Infection Treated with Autologous Bacterial Lysates.

Antimicrobial bacteria resistance is an important problem in children with recurrent urinary tract infections (rUTI), thus it is crucial to search for alternative therapies. Autologous bacterial lysates (ABL) may be a potential treatment for rUTI. Twenty-seven children with rUTI were evaluated for one year, urine and stool cultures were performed, 10 colonies of each culture were selected and those identified as Escherichia coli were characterized by serology. For patients who presented ≥105 UFC/mL, an ABL was manufactured and administered orally (1 mL/day) for a month. Twelve children were monitored for ≥1-year, 218 urine and 11 stool samples were analyzed. E. coli (80.5%) was the main bacteria isolated from urine and feces (72%). E. coli of classical urinary serotypes (UPEC), O25:H4, O75:HNM, and O9:HNM were identified in patients with persistent urinary infection (pUTI). In 54% of patients treated with ABL, the absence of bacteria was observed in urine samples after 3 months of treatment, 42% of these remained without UTI between 10-12 months. It was observed that the use of ABL controlled the infection for almost 1 year in more than 60% of the children. We consider it necessary to develop a polyvalent immunogen for the treatment and control of rUTI.

Bioética en los procesos de investigación y bioprospección: relaciones con pueblos indígenas y comunidades locales en Colombia

Propósito/Contexto. En este artículo se exploran los principios bioéticos de autonomía y justicia, a la luz de tres casos de uso de la biodiversidad, tanto para fines investigativos como de aprovechamiento comercial, que involucran territorios colectivos de comunidades indígenas, afrodescendientes y predios de población campesina. Metodología/Enfoque. En cada caso se examinaron sus características, los actores, las relaciones entre los actores y los beneficios contemplados para las partes. El estudio comprendió la recopilación y análisis de documentación y la realización de 10 entrevistas semiestructuradas con investigadores, representantes de instituciones, empresas y organizaciones indígenas y afrocolombianas. La investigación se realizó entre 2015 y 2017 e incluyó comunidades del Amazonas, Risaralda, Chocó y Antioquia. Resultados/Hallazgos. Se encontró que las instituciones de investigación y los investigadores tramitan y obtienen las autorizaciones reglamentarias, mientras que las entidades del Estado registran una progresiva omisión de responsabilidades que afecta los derechos de las comunidades, por ejemplo, a través de la inobservancia del derecho a la consulta previa. Adicionalmente, en los casos de estudio, las relaciones que los actores establecen con las comunidades INAPRR-CL (sigla de indígenas, negros, afrodescendientes, palenqueros, raizales, Rrom, campesinas y locales) varían en la observancia de principios bioéticos. Discusión/Conclusiones/Contribuciones. Debido a que el régimen jurídico tiene un alcance limitado para el uso de la biodiversidad en investigación o innovación tecnológica, se evalúa y se discute si la bioética podría servir de guía para el respeto de la autonomía y la participación de beneficios de las comunidades en proyectos de investigación y bioprospección.

Purpose/Context. This article explores the bioethical principles of autonomy and justice in the light of three cases of use of biodiversity, both for research purposes and for commercial use, involving collective territories of indigenous communities, afro-descendants, and proper-ties of the peasant population. Methods/Approach. In each case, we examined the characteristics, agents, relationships be-tween agents, and benefits contemplated for the parties. The study included document compilation and analysis and ten semi-structured interviews with researchers, representatives of indigenous and Afro-Colombian institutions, companies, and organizations. The research was carried out between 2015 and 2017 and involved Amazon, Risaralda, Chocó, and Antioquia communities. Results/Findings. Research institutions and researchers process and obtain regulatory authorizations, while State entities report a progressive omission of responsibilities that adversely affects communities' rights, for example, through non-observance of the right to prior con-sultation. Besides, in the study cases, the agents' relationships with the INAPRRCL (acronym in Spanish for indigenous, black people, Afro-descendants, palenqueros, raizales, Rrom, peasants, and locals) vary regarding the application of bioethical principles. Discussion/Conclusions/Contributions. Because the legal system has a limited scope on the use of biodiversity in research or technological innovation, we assessed and discussed whether bioethics could serve as a guide for respecting communities' autonomy and benefit share in research and bioprospecting projects.

Objetivo/Contexto. Neste artigo exploram-se os princípios bioéticos de autonomia e justiça, à luz de três casos de uso da biodiversidade, tanto para fins investigativos como de aproveitamento comercial, que envolvem territórios coletivos de comunidades indígenas, afrodescendentes e prédios de população camponesa. Metodologia/Abordagem. Em cada caso, foram examinadas as suas características, os intervenientes, as relações entre os intervenientes e os benefícios previstos para as partes. O estudo incluiu a coleta e análise de documentação e a realização de 10 entrevistas semiestruturadas com pesquisadores, representantes de instituições, empresas e organizações indígenas e afro-colombianas. A pesquisa foi realizada entre 2015 e 2017 e incluiu comunidades do Amazonas, Risaralda, Chocó e Antioquia. Resultados/Descobertas. Verificou-se que as instituições de investigação e os investigadores processam e obtêm as autorizações regulamentares, no entanto que as entidades do Estado registram uma progressiva omissão de responsabilidades que afeta os direitos das comunidades, por exemplo, através da inobservância do direito à consulta prévia. Adicionalmente, nos casos de estudo, as relações que os atores estabelecem com as INAPRRCL (sigla de indígenas, negros, afrodescendentes, palenqueros, raizais, Rrom, camponesas e locais) variam na observância de princípios bioéticos. Discussão/Conclusões/Contribuições. Dado que o regime jurídico tem um âmbito limitado para a utilização da biodiversidade na investigação ou inovação tecnológica, se avalia e se discute se a bioética poderia servir de guia para o respeito da autonomia e a participação de benefícios das comunidades em projetos de pesquisa e bioprospeção.

Potenciales agentes terapéuticos contra el COVID-19 basados en el bloqueo e inhibición del ciclo de vida viral y en el síndrome de tormenta de citoquinas / Potential therapeutic agents against COVID-19 based on blocking and inhibition of the viral life cycle and the cytokine storm syndrome

La pandemia de COVID-19, causada por SARS-CoV-2, es considerara la mayor emergencia sanitaria en un siglo. Clínicamente, la mayoría de los pacientes tienen síntomas leves a moderados. Sin embargo, pacientes de edad avanzada o con comorbilidades pueden desarrollar una de las complicaciones más severas de COVID-19, es decir, el síndrome de tormenta de citoquinas. Actualmente, no existen tratamientos aprobados para SARS-CoV-2. Mientras tanto, las estrategias terapéuticas se basan en la experiencia previa con otros virus. En este artículo se revisarán los diferentes agentes terapéuticos propuestos para el tratamiento de COVID-19 basados en el bloqueo e inhibición del ciclo de vida viral de SARS-CoV-2, y para el tratamiento del síndrome de tormenta de citoquinas. Se realizó una revisión narrativa mediante búsqueda en la base de datos PubMed. Entre los principales objetivos terapéuticos contra el SARS-CoV-2 están la proteína estructural principal Spike y las enzimas virales proteasa similar a la 3-quimotripsina, la proteasa viral similar a la papaína y la ARN-polimerasa dependiente de ARN. Remdesivir, un antiviral análogo a la adenosina que inhibe a la ARN-polimerasa dependiente de ARN, es considerado el fármaco más prometedor en el tratamiento de COVID-19. No obstante, su eficacia aún no se ha determinado. En el síndrome de tormenta de citoquinas, la lesión tisular causada por el virus puede inducir la producción exagerada de citoquinas proinflamatorias como la interleucina-6. Tocilizumab, un anticuerpo monoclonal que bloquea receptores de interleucina-6 y corticosteroides como la metilprednisolona pueden ser opciones terapéuticas en el tratamiento de la severidad del síndrome.

The COVID-19 pandemic, caused by SARS-CoV-2, is considered as the major health emergency in a century. Clinically, most patients have mild to moderate symptoms. Nevertheless, elderly or with comorbidities patients may develop one of the most severe complication of COVID-19, that is, the cytokine storm syndrome. Currently, there are no approved treatments for SARS-CoV-2. Meanwhile, therapeutic strategies are based on previous experience with other viruses. This article will review the different therapeutic agents proposed for the treatment of COVID-19 based on the blocking and inhibition of the viral life cycle of SARS-CoV-2, and for the treatment of cytokine storm syndrome. A narrative review was performed by searching in the PubMed database. Among the main therapeutic target against SARS-CoV-2 are the major structural protein Spike and viral enzymes 3-chymotrypsin-like protease, viral papain-like protease, and RNA-dependent RNA polymerase. Remdesivir, an adenosine analogue antiviral that inhibits RNA-dependent RNA polymerase, is considered the most promising drug in the treatment of COVID-19. Nonetheless, its efficacy has not yet been determined. In the cytokine storm syndrome, the tissue injury caused by the virus may induce the exaggerated production of pro-inflammatory cytokines such as interleukin-6. Tocilizumab, a monoclonal antibody that blocks interleukin-6 receptors, and corticosteroids such as methylprednisolone may be therapeutic options in treating the severity of the syndrome.

Presencia y Expresión del Receptor ACE2 (Target de SARS-CoV-2) en Tejidos Humanos y Cavidad Oral. Posibles Rutas de Infección en Órganos Orales / Presence and Expression of ACE2 Receptor (Target of SARS-CoV-2) in Human Tissues and Oral Cavity. Possible Routes Infection in Oral Organs

RESUMEN: Un nuevo coronavirus (SARS-CoV-2) ha sido reconocido como el agente etiológico de una misteriosa neumonía originada en Wuhan, China. La OMS ha nombrado a la nueva enfermedad como COVID-19 y, además, la ha declarado pandemia. Taxonómicamente, SARS-CoV-2 pertenece al género de los betacoronavirus junto con SARS-CoV y MERS-CoV. SARS-CoV-2 utiliza la enzima convertidora de la angiotensina 2 (ACE2) como el receptor objetivo para el ingreso en una célula huésped. La expresión de ACE2 en células de tejidos humanos podría indicar un potencial riesgo de reconocimiento por parte del virus y, por ende, ser susceptibles a la infección. Mediante algunas técnicas de laboratorio y de bioinformática, se ha visto una alta presencia de ACE2 en células epiteliales alveolares tipo II de pulmón y en enterocitos del intestino delgado. En la cavidad oral, se ha podido identificar la presencia de ACE2, principalmente, en células epiteliale s de glándulas salivales y células epiteliales de la lengua. Además, se ha reportado la manifestación de algunos síntomas, como sequedad bucal y ambligeustia, los que podrían estar relacionadas con una infección de SARS-CoV-2 en estos órganos. Sin embargo, son necesarios mayores estudios que evidencien esta situación.

ABSTRACT: A novel coronavirus (SARS-CoV-2) has been recognized as a etiologic agent of a mysterious pneumonia originating in Wuhan, China. WHO has named the new disease as COVID-19 and, in addition, has declared it a pandemic. Taxonomically, SARS-CoV-2 belongs to the betacoronavirus genus along with SARS-CoV and MERS-CoV. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the target receptor for entry into a host cell. The expression of ACE2 in cells of human tissues could indicate a potential risk of recognition by the virus and, therefore, be susceptible to infection. Through some laboratory and bioinformatics techniques, high presence of ACE2 has been seen in type II alveolar epithelial cells of the lung and enterocytes of the small intestine. In oral cavity, mainly presence of ACE2 has been identified in epithelial cells of salivary glands and epithelial cells of tongue. In addition, manifestation of some symptoms, such as dry mouth and amblygeustia, have been reported, which could be related to a SARS-CoV-2 infection in these organs. However, further studies are needed to prove this situation.

Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.

BACKGROUND: In bacteria, pan-genomes are the result of an evolutionary "tug of war" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. RESULTS: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport. CONCLUSIONS: Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

Bases genéticas y moleculares del COVID-19 (SARS-CoV-2): mecanismos de patogénesis y de respuesta inmune / Genetic and molecular basis of COVID-19 (SARS-CoV-2) mechanisms of pathogenesis and imnune

A fines de diciembre de 2019, un nuevo coronavirus (SARS-CoV-2) fue identificado como el agente causal de una nueva enfermedad respiratoria llamada COVID-19 por la OMS. Sus síntomas incluyen fiebre, tos seca y dificultad respiratoria. Estos síntomas en general son leves, aunque, pueden ser fatales en adultos mayores y pacientes con comorbilidades. Se realizó búsqueda bibliográfica en Pubmed y Clinical Key donde se seleccionaron 22 artículos de acuerdo con los criterios de inclusión. SARS-CoV-2 pertenece al género de los Betacoronavirus y tiene similitudes genómicas con SARS-CoV y MERS-CoV. El virión de SARS-CoV-2 consta de una nucleocápside y de una envoltura externa compuesta por proteínas estructurales principales y accesorias. Su material genético consiste en una cadena de RNA monocatenario de polaridad positiva, en el que, se codifican proteínas importantes para su transcripción y replicación. El mecanismo de infección de SARS-CoV-2 comienza con la unión del virión a un receptor (ACE2) de la célula huésped y su posterior entrada por endocitosis. El genoma RNA viral se libera al citoplasma donde se transcriben y se traducen las proteínas necesarias para la producción de las proteínas estructurales y para la replicación de su material genético. Posteriormente, el RNA replicado se asocia con la nucleocápside y se ensambla junto con las proteínas estructurales para conformar las partículas víricas que serán liberadas de la célula infectada. El sistema inmune hace frente a la infección viral mediante el reconocimiento de patrones moleculares asociados a patógenos (PAMPs) por parte de la inmunidad innata y por la acción de los linfocitos T y B por parte de la inmunidad humoral. El conocimiento de las bases genéticas y moleculares de SARS-CoV-2 permite visualizar la posibilidad de establecer tratamientos farmacológicos o desarrollo de vacunas para controlar y disminuir los efectos patogénicos de la enfermedad.

In late December 2019, a new coronavirus (SARS-CoV-2) was identified as a causative agent of a new respiratory disease called COVID-19 by WHO. Its symptoms include fever, dry cough, and shortness of breath. Generally, these symptoms are mild, although, can be fatal in older adults and patients with comorbidities. A bibliographic search was carried out in Pubmed and Clinical Key. 22 articles were selected according to inclusion criteria. SARS-CoV-2 belongs to the genus of Betacoronaviruses and has genomic similarities to SARS-CoV and MERS-CoV. SARS-CoV-2 virion is made up of a nucleocapsid and external envelope composed of main structural and accesory proteins. Its genetic is a positive sense single stranded RNA in which important proteins are encoded for their transcription and replication. The mechanism of SARS-CoV-2 infection begins with the binding of the virion to (ACE2) receptor of the host cell and subsequent entry by endocytosis. This RNA genome is released into cytoplasm and the necessary proteins for the production of structural proteins and the replication of genetic material are transcribed and translated. Then, the replicated RNA associates with the nucleocapsid and assembles together with the structural proteins to form the viral particles that will be released from the infected cell. The immune system faces viral infection through the recognition of molecular patterns associated with pathogens (PAMPs) by innate immunity and the action of T cells and B cells by humoral immunity. Knowledge of the genetic and molecular basis of SARS-CoV-2 allows us to visualize the possibility of establishing pharmacological or vaccine treatments to control and reduce the pathogenic effects of the disease.

Molecular Cloning and Exploration of the Biochemical and Functional Analysis of Recombinant Glucose-6-Phosphate Dehydrogenase from Gluconoacetobacter diazotrophicus PAL5.

Gluconacetobacter diazotrophicus PAL5 (GDI) is an endophytic bacterium with potential biotechnological applications in industry and agronomy. The recent description of its complete genome and its principal metabolic enzymes suggests that glucose metabolism is accomplished through the pentose phosphate pathway (PPP); however, the enzymes participating in this pathway have not yet been characterized in detail. The objective of the present work was to clone, purify, and biochemically and physicochemically characterize glucose-6-phosphate dehydrogenase (G6PD) from GDI. The gene was cloned and expressed as a tagged protein in E. coli to be purified by affinity chromatography. The native state of the G6PD protein in the solution was found to be a tetramer with optimal activity at pH 8.8 and a temperature between 37 and 50 °C. The apparent Km values for G6P and nicotinamide adenine dinucleotide phosphate (NADP+) were 63 and 7.2 µM, respectively. Finally, from the amino acid sequence a three-dimensional (3D) model was obtained, which allowed the arrangement of the amino acids involved in the catalytic activity, which are conserved (RIDHYLGKE, GxGGDLT, and EKPxG) with those of other species, to be identified. This characterization of the enzyme could help to identify new environmental conditions for the knowledge of the plant-microorganism interactions and a better use of GDI in new technological applications.

Evolution of bacteria seen through their essential genes: the case of Pseudomonas aeruginosa and Azotobacter vinelandii.

Pseudomonas aeruginosa is a metabolically versatile bacterium and also an important opportunistic pathogen. It has a remarkable genomic structure since the genetic information encoding its pathogenicity-related traits belongs to its core-genome while both environmental and clinical isolates are part of the same population with a highly conserved genomic sequence. Unexpectedly, considering the high level of sequence identity and homologue gene number shared between different P. aeruginosa isolates, the presence of specific essential genes of the two type strains PAO1 and PA14 has been reported to be highly variable. Here we report the detailed bioinformatics analysis of the essential genes of P. aeruginosa PAO1 and PA14 that have been previously experimentally identified and show that the reported gene variability was owed to sequencing and annotation inconsistencies, but that in fact they are highly conserved. This bioinformatics analysis led us to the definition of 348 P. aeruginosa general essential genes. In addition we show that 342 of these 348 essential genes are conserved in Azotobacter vinelandii, a nitrogen-fixing, cyst-forming, soil bacterium. These results support the hypothesis of A. vinelandii having a polyphyletic origin with a Pseudomonads genomic backbone, and are a challenge to the accepted theory of bacterial evolution.

Enhancing Geometric Fidelity of 3-Dimensional Electroanatomic Mapping During Open Chest Epicardial Radiofrequency Catheter Ablation.

Although electroanatomic mapping techniques have been previously applied to open chest epicardial ablation procedures, such efforts have often been limited by significant geometric distortions introduced by the need to use nonstandard mapping patch placements and by intrathoracic conductance changes introduced by having the pericardial space exposed. In this article, we present a case of a patient with recurrent hemodynamically unstable ventricular tachycardia who underwent a successful open chest epicardial ablation procedure with electroanatomic mapping in which geometric distortions were minimized by judicious placement of mapping patches and the use of a saline bath within the pericardial space.

Two Pseudomonas aeruginosa clonal groups belonging to the PA14 clade are indigenous to the Churince system in Cuatro Ciénegas Coahuila, México.

Pseudomonas aeruginosa is a widely distributed environmental bacterium but is also an opportunistic pathogen that represents an important health hazard due to its high intrinsic antibiotic resistance and its production of virulence factors. The genetic structure of P. aeruginosa populations using whole genome sequences shows the existence of three clades, one of which (PA7 clade) has a higher genetic diversity. These three clades include clinical and environmental isolates that are very diverse in terms of geographical origins and isolation date. Here, we report the characterization of two distinct clonal P. aeruginosa groups that form a part of the PA14 clade (clade 2) sampled from the Churince system in Cuatro Ciénegas Basin (CCB). One of the clonal groups that we report here was isolated in 2011 (group 2A) and was displaced by the other clonal group (2B) in 2015. Both Churince groups are unable to produce pyoverdine but can produce other virulence-associated traits. The existence of these unique P. aeruginosa clonal groups in the Churince system is of ecological and evolutionary significance since the microbiota of this site is generally very distinct from other lineages, and this is the first time that a population of P. aeruginosa has been found in CCB.

MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis.

Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.

Corrigendum: Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli.

[This corrects the article DOI: 10.3389/fmicb.2018.01059.].

Implementation and impact analysis of a transitional care pathway for patients presenting to the emergency department with cardiac-related complaints.

BACKGROUND: Cardiac-related complaints are leading drivers of Emergency Department (ED) utilization. Although a large proportion of cardiac patients can be discharged with appropriate outpatient follow-up, inadequate care coordination often leads to high revisit rates or unnecessary admissions. We evaluate the impact of implementing a structured transitional care pathway enrolling low-risk cardiac patients on ED discharges, 30-day revisits and admissions, and institutional revenues. METHODS: We prospectively enrolled eligible patients presenting to a single-center Emergency Department over a 12-month period. Standardized risk measures were used to identify patients suitable for early discharge with cardiology follow-up within 5 days. The primary endpoints were rates of discharge from the ED and 30-day ED revisit and admission rates, with a secondary endpoint including 30-day returns for myocardial infarction. A cost analysis of the program's impact on institutional revenues was performed. RESULTS: Among patients presenting with cardiac-related complaints, rates of discharge from the ED increased from 44.4 to 56.6% (p < 0.0001). Enrollment in the transitional care pathway was associated with a reduced risk of cardiac-related ED revisits (RR 0.22, p < 0.0001), all-cause ED revisits (RR 0.30, p < 0.0001), and admission at second ED visit (RR 0.56, p = 0.0047); among enrolled patients, the 30-day rate of return with a myocardial infarction was 0.35%. No significant reductions were seen in 30-day cardiac-related and all-cause revisits in the 12-months following transitional care pathway implementation; however, there was a significant reduction in admissions at second ED visit from 45.6 to 37.7% (p = 0.0338). An early gender disparity in care delivery was identified in the first 120 days following program implementation that was subsequently eliminated through targeted intervention. There was an estimated decline in institutional revenue of $300 per enrolled patient, driven predominantly by a reduction in admissions. CONCLUSIONS: A structured transitional care pathway identifying low-risk cardiac patients who may be safely discharged from the ED can be effective in shifting care delivery from hospital-based to lower cost ambulatory settings without adversely impacting 30-day ED revisit rates or patient outcomes.

Variability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli.

The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as "non-orthologous gene displacement" that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species.