Bioaugmentation and vermicompost facilitated the hydrocarbon bioremediation: scaling up from lab to field for petroleum-contaminated soils.

The biodegradation of total petroleum hydrocarbon (TPH) in soil is very challenging due to the complex recalcitrant nature of hydrocarbon, hydrophobicity, indigenous microbial adaptation and competition, and harsh environmental conditions. This work further confirmed that limited natural attenuation of petroleum hydrocarbons (TPHs) (15% removal) necessitates efficient bioremediation strategies. Hence, a scaling-up experiment for testing and optimizing the use of biopiles for bioremediation of TPH polluted soils was conducted with three 500-kg pilots of polluted soil, and respective treatments were implemented: including control soil (CT), bioaugmentation and vermicompost treatment (BAVC), and a combined application of BAVC along with bioelectrochemical snorkels (BESBAVC), all maintained at 40% field capacity. This study identified that at pilot scale level, a successful application of BAVC treatment can achieve 90.3% TPH removal after 90 days. BAVC's effectiveness stemmed from synergistic mechanisms. Introduced microbial consortia were capable of TPH degradation, while vermicompost provided essential nutrients, enhanced aeration, and, potentially, acted as a biosorbent. Hence, it can be concluded that the combined application of BAVC significantly enhances TPH removal compared to natural attenuation. While the combined application of a bioelectrochemical snorkel (BES) with BAVC also showed a significant TPH removal, it did not differ statistically from the individual application of BAVC, under applied conditions. Further research is needed to optimize BES integration with BAVC for broader applicability. This study demonstrates BAVC as a scalable and mechanistically sound approach for TPH bioremediation in soil.

Role of extracellular matrix components in biofilm formation and adaptation of Pseudomonas ogarae F113 to the rhizosphere environment.

Regulating the transition of bacteria from motile to sessile lifestyles is crucial for their ability to compete effectively in the rhizosphere environment. Pseudomonas are known to rely on extracellular matrix (ECM) components for microcolony and biofilm formation, allowing them to adapt to a sessile lifestyle. Pseudomonas ogarae F113 possesses eight gene clusters responsible for the production of ECM components. These gene clusters are tightly regulated by AmrZ, a major transcriptional regulator that influences the cellular levels of c-di-GMP. The AmrZ-mediated transcriptional regulation of ECM components is primarily mediated by the signaling molecule c-di-GMP and the flagella master regulator FleQ. To investigate the functional role of these ECM components in P. ogarae F113, we performed phenotypic analyses using mutants in genes encoding these ECM components. These analyses included assessments of colony morphology, dye-staining, static attachment to abiotic surfaces, dynamic biofilm formation on abiotic surfaces, swimming motility, and competitive colonization assays of the rhizosphere. Our results revealed that alginate and PNAG polysaccharides, along with PsmE and the fimbrial low molecular weight protein/tight adherence (Flp/Tad) pilus, are the major ECM components contributing to biofilm formation. Additionally, we found that the majority of these components and MapA are needed for a competitive colonization of the rhizosphere in P. ogarae F113.

An Orphan VrgG Auxiliary Module Related to the Type VI Secretion Systems from Pseudomonas ogarae F113 Mediates Bacterial Killing.

The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector-immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.

A Motivational Approach to Sexual Desire: A Model for Self-Regulation

The main objective in this article was to identify the links between classical theories on motivation and postulates on the nature and workings of erotic desire, capturing these links in a model of the motivational processing of desire. The paper reviews the most relevant motivation theories identifying their links to the nature of erotic desire, relating the main variables of these motivation theories to the concept of desire, identifying the similarities between the elements of these constructs. The outcome was a theoretical model of the motivational processing of sexual desire that also includes processes for regulating desire in which a highlight is the interaction between external and internal factors in its development. We understand that these implications underpin the need to adopt a motivational and affective approach to erotic desire, as a process that can be self-regulated. This approach stress the need to continue analyzing the affective experience and the motivational process encapsulated in desire in order to increase our understanding of its activation and development (AU)

In Vivo Confocal Microscopy in Limbal Stem Cell Deficiency After Mesenchymal Stem Cell Transplantation: A Sub-analysis from a Phase I-II Clinical Trial.

INTRODUCTION: The aim of this work is to evaluate the effect of mesenchymal stem cell transplantation (MSCT) and cultivated limbal epithelial transplantation (CLET) therapies on the limbus of patients suffering from limbal stem cell deficiency (LSCD). METHODS: A sub-analysis of a phase I-II randomized, controlled, and double-masked clinical trial was performed to assess the changes in the anatomical structures of the limbus. In vivo confocal microscopy (IVCM) analysis was carried out in LSCD eyes before and 12 months after allogeneic MSCT or CLET. Epithelial phenotype of the central cornea, as well as the presence of transition zones and palisades of Vogt in the limbus, were assessed using Wilcoxon test. RESULTS: Twenty-three LSCD (14 MSCT and nine CLET) eyes were included. The epithelial phenotype of the central cornea improved significantly (p < 0.001) from 15 (eight MSCT, seven CLET) and eight (six MSCT, two CLET) LSCD eyes showing conjunctival and mixed phenotypes, respectively, to eight (five MSCT, three CLET), five (two MSCT, three CLET), and ten (seven MSCT, three CLET) eyes showing conjunctival, mixed, and corneal phenotypes, respectively. Transition areas and palisades of Vogt were observed in at least one quadrant in nine (five MSCT, four CLET) and 16 (nine MSCT, seven CLET), and in four (two MSCT, two CLET) and six (three MSCT, three CLET) LSCD eyes before and after surgery, respectively. Changes in the transition zones and palisades were solely significant (p = 0.046) for the nasal and inferior quadrants, respectively. CONCLUSIONS: MSCT and CLET improved the central corneal epithelial phenotype despite only minor changes in the anatomical structures of the limbus, as detected by IVCM technology. TRIAL REGISTRATION: ClinicalTrials.gov identifier, NCT01562002.

Unveiling changes in rhizosphere-associated bacteria linked to the genotype and water stress in quinoa.

Drought is among the main abiotic factors causing agronomical losses worldwide. To minimize its impact, several strategies have been proposed, including the use of plant growth-promoting bacteria (PGPBs), as they have demonstrated roles in counteracting abiotic stress. This aspect has been little explored in emergent crops such as quinoa, which has the potential to contribute to reducing food insecurity. Thus, here we hypothesize that the genotype, water environment and the type of inoculant are determining factors in shaping quinoa rhizosphere bacterial communities, affecting plant performance. To address this, two different quinoa cultivars (with contrasting water stress tolerance), two water conditions (optimal and limiting water conditions) and different soil infusions were used to define the relevance of these factors. Different bacterial families that vary among genotypes and water conditions were identified. Certain families were enriched under water stress conditions, such as the Nocardioidaceae, highly present in the water-sensitive cultivar F15, or the Pseudomonadaceae, Burkholderiaceae and Sphingomonadaceae, more abundant in the tolerant cultivar F16, which also showed larger total polyphenol content. These changes demonstrate that the genotype and environment highly contribute to shaping the root-inhabiting bacteria in quinoa, and they suggest that this plant species is a great source of PGPBs for utilization under water-liming conditions.

Field scale biodegradation of total petroleum hydrocarbons and soil restoration by Ecopiles: microbiological analysis of the process.

Ecopiling is a method for biodegradation of hydrocarbons in soils. It derives from Biopiles, but phytoremediation is added to biostimulation with nitrogen fertilization and bioaugmentation with local bacteria. We have constructed seven Ecopiles with soil heavily polluted with hydrocarbons in Carlow (Ireland). The aim of the study was to analyze changes in the microbial community during ecopiling. In the course of 18 months of remediation, total petroleum hydrocarbons values decreased in 99 and 88% on average for aliphatics and aromatics, respectively, indicating a successful biodegradation. Community analysis showed that bacterial alfa diversity (Shannon Index), increased with the degradation of hydrocarbons, starting at an average value of 7.59 and ending at an average value of 9.38. Beta-diversity analysis, was performed using Bray-Curtis distances and PCoA ordination, where the two first principal components (PCs) explain the 17 and 14% of the observed variance, respectively. The results show that samples tend to cluster by sampling time instead of by Ecopile. This pattern is supported by the hierarchical clustering analysis, where most samples from the same timepoint clustered together. We used DSeq2 to determine the differential abundance of bacterial populations in Ecopiles at the beginning and the end of the treatment. While TPHs degraders are more abundant at the start of the experiment, these populations are substituted by bacterial populations typical of clean soils by the end of the biodegradation process. Similar results are found for the fungal community, indicating that the microbial community follows a succession along the process. This succession starts with a TPH degraders or tolerant enriched community, and finish with a microbial community typical of clean soils.

Adaption of Pseudomonas ogarae F113 to the Rhizosphere Environment-The AmrZ-FleQ Hub.

Motility and biofilm formation are two crucial traits in the process of rhizosphere colonization by pseudomonads. The regulation of both traits requires a complex signaling network that is coordinated by the AmrZ-FleQ hub. In this review, we describe the role of this hub in the adaption to the rhizosphere. The study of the direct regulon of AmrZ and the phenotypic analyses of an amrZ mutant in Pseudomonas ogarae F113 has shown that this protein plays a crucial role in the regulation of several cellular functions, including motility, biofilm formation, iron homeostasis, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, controlling the synthesis of extracellular matrix components. On the other hand, FleQ is the master regulator of flagellar synthesis in P. ogarae F113 and other pseudomonads, but its implication in the regulation of multiple traits related with environmental adaption has been shown. Genomic scale studies (ChIP-Seq and RNA-Seq) have shown that in P. ogarae F113, AmrZ and FleQ are general transcription factors that regulate multiple traits. It has also been shown that there is a common regulon shared by the two transcription factors. Moreover, these studies have shown that AmrZ and FleQ form a regulatory hub that inversely regulate traits such as motility, extracellular matrix component production, and iron homeostasis. The messenger molecule c-di-GMP plays an essential role in this hub since its production is regulated by AmrZ and it is sensed by FleQ and required for its regulatory role. This regulatory hub is functional both in culture and in the rhizosphere, indicating that the AmrZ-FleQ hub is a main player of P. ogarae F113 adaption to the rhizosphere environment.

Shotgun proteomics of quinoa seeds reveals chitinases enrichment under rainfed conditions.

Quinoa is an Andean crop whose cultivation has been extended to many different parts of the world in the last decade. It shows a great capacity for adaptation to diverse climate conditions, including environmental stressors, and, moreover, the seeds are very nutritious in part due to their high protein content, which is rich in essential amino acids. They are gluten-free seeds and contain good amounts of other nutrients such as unsaturated fatty acids, vitamins, or minerals. Also, the use of quinoa hydrolysates and peptides has been linked to numerous health benefits. Altogether, these aspects have situated quinoa as a crop able to contribute to food security worldwide. Aiming to deepen our understanding of the protein quality and function of quinoa seeds and how they can vary when this crop is subjected to water-limiting conditions, a shotgun proteomics analysis was performed to obtain the proteomes of quinoa seeds harvested from two different water regimes in the field: rainfed and irrigated conditions. Differentially increased levels of proteins determined in seeds from each field condition were analysed, and the enrichment of chitinase-related proteins in seeds harvested from rainfed conditions was found. These proteins are described as pathogen-related proteins and can be accumulated under abiotic stress. Thus, our findings suggest that chitinase-like proteins in quinoa seeds can be potential biomarkers of drought. Also, this study points to the need for further research to unveil their role in conferring tolerance when coping with water-deficient conditions.

Energy-Efficient Routing Protocol for Selecting Relay Nodes in Underwater Sensor Networks Based on Fuzzy Analytical Hierarchy Process.

The use of underwater sensor networks (UWSNs) offers great advantages in many automatic observation services such as water monitoring (ocean, sea, etc.) and registering of geological events (landslides, earthquakes). However, UWSNs have many more limitations than terrestrial sensor networks (smaller bandwidth, higher delays, etc.) with new requirements such as low power consumption by nodes or being able to select appropriate routes in a dynamic topology due to water currents and movements. To cope with these problems, the use of a routing protocol is very important. In this paper we propose a routing technique that adapts to changes in the network topology, avoiding multiple retransmissions that would affect its overall performance. This protocol is energy-efficient and is implemented using a fuzzy analytical hierarchical process (FAHP) under multi-criteria decision making (MCDM) to make an intelligent routing decision based on objectives, criteria and alternatives. To select the next node on the route, several comparison matrices are used: number of hops, distances to the sink node, and number of neighbors. The results show that the proposed setup behaves similarly to other existing underwater sensor network routing schemes using fuzzy schemes such as SPRINT.

Corneal Regeneration Using Adipose-Derived Mesenchymal Stem Cells.

Adipose-derived stem cells are a subtype of mesenchymal stem cell that offers the important advantage of being easily obtained (in an autologous manner) from low invasive procedures, rendering a high number of multipotent stem cells with the potential to differentiate into several cellular lineages, to show immunomodulatory properties, and to promote tissue regeneration by a paracrine action through the secretion of extracellular vesicles containing trophic factors. This secretome is currently being investigated as a potential source for a cell-free based regenerative therapy for human tissues, which would significantly reduce the involved costs, risks and law regulations, allowing for a broader application in real clinical practice. In the current article, we will review the existing preclinical and human clinical evidence regarding the use of such adipose-derived mesenchymal stem cells for the regeneration of the three main layers of the human cornea: the epithelium (derived from the surface ectoderm), the stroma (derived from the neural crest mesenchyme), and the endothelium (derived from the neural crest cells).

Regulation of extracellular matrix components by AmrZ is mediated by c-di-GMP in Pseudomonas ogarae F113.

The AmrZ/FleQ hub has been identified as a central node in the regulation of environmental adaption in the plant growth-promoting rhizobacterium and model for rhizosphere colonization Pseudomonas ogarae F113. AmrZ is involved in the regulation of motility, biofilm formation, and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) turnover, among others, in this bacterium. The mutants in amrZ have a pleiotropic phenotype with distinguishable colony morphology, reduced biofilm formation, increased motility, and are severely impaired in competitive rhizosphere colonization. Here, RNA-Seq and qRT-PCR gene expression analyses revealed that AmrZ regulates many genes related to the production of extracellular matrix (ECM) components at the transcriptional level. Furthermore, overproduction of c-di-GMP in an amrZ mutant, by ectopic production of the Caulobacter crescentus constitutive diguanylate cyclase PleD*, resulted in increased expression of many genes implicated in the synthesis of ECM components. The overproduction of c-di-GMP in the amrZ mutant also suppressed the biofilm formation and motility phenotypes, but not the defect in competitive rhizosphere colonization. These results indicate that although biofilm formation and motility are mainly regulated indirectly by AmrZ, through the modulation of c-di-GMP levels, the implication of AmrZ in rhizosphere competitive colonization occurs in a c-di-GMP-independent manner.

Winter diet of Burrowing Owls in the Llano La Soledad, Galeana, Nuevo León, México.

The dietary niche breadth of the Burrowing Owl was determined (Athene cunicularia Molina, 1782) in Llano La Soledad, Galeana, Nuevo Leon in northern Mexico, by considering prey type, numerical percentage, weight, weight percentage, frequency of occurrence percentage, and IRI percentage. The study compared data from three winters (2002-2003, 2003-2004, 2004-2005) by analyzing 358 pellets, identifying 850 prey items. Invertebrates constituted 90% of prey items, which mostly included insects (85%); beetles were the most common insects found in pellets (70%). Vertebrates made up 84% of consumed weight, of which 83% were mammals. Most of the mammals were cricetid rodents (41%). Niche breadth based on the numerical and weight percentage confirmed the Burrowing Owl as a generalist species with mean values per year ranging between 0.65 and 0.82. Additionally, there was a strong association between the weight of rodent species in winter. This association was mainly driven by changes in composition and frequency of these prey species during the second winter, probably caused by high annual rainfall. The second season also showed a statistically significant narrower niche (Ro = 0.96) and the smallest overlap (0.45 vs. 0.76) among the three winters.

Detectando caras en un contexto de sorpresa e incertidumbre / Detecting facial expressions within a context of surprise and uncertainty

Las expresiones de amenaza son detectadas con rapidez y precisión, advirtiendo a quienes las observan de la presencia de un potencial peligro. Durante el proceso de detección, la expresión de sorpresa podría jugar un papel importante como clave de orientación en condiciones de incertidumbre donde se requiere una respuesta rápida y precisa. Con el objetivo de analizar este supuesto se plateó un experimento en el que participaron 70 sujetos que realizaron una tarea de señalización espacial, donde se utilizaron expresiones faciales de sorpresa (vs. neutra) como claves de orientación, y expresiones faciales de miedo, ira, alegría y neutras como estímulos objetivo. Los resultados mostraron un efecto facilitador de la expresión de sorpresa solo en la detección de la expresión de ira, reduciendo los tiempos de respuesta y el porcentaje de errores. Los datos apuntan a que la expresión de sorpresa, cuando se procesa como un estímulo independiente, podría facilitar la detección de aquellos estímulos que supongan una amenaza directa, como la expresión de ira, siendo esta distinción clave para entender en qué condiciones se detecta más eficazmente la expresión de ira respecto a otro tipo de expresiones.(AU)

Threatening expressions are detected quickly and accurately, warning the observer of the presence of a potential danger. During the de-tection process, a facial expression of surprise could play an important role as a cue for orientation in conditions of uncertainty that call for a swift and precise response. With a view to analysing this contingency, an experiment was conducted in which 70 subjects undertook a spatial cueing task that involved facial expressions of surprise (vs. neutral ones) as orientation cues, and facial expressions of fear, anger and happiness as target stimuli. The results revealed a priming effect of the expression of surprise solely in the detection of the expression of anger, reducing response times and the percentage of errors. Thedata indicate that the expression of surprise, when processed as an independent stimulus, could prime the detection of those stimuli that constitute a direct threat, such as the expression of anger, with this being a crucial distinction for understanding the circumstances in which the expression of anger is detected more effectively than other kinds of expressions.(AU)

Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption.

Rhizosphere colonization by bacteria involves molecular and cellular mechanisms, such as motility and chemotaxis, biofilm formation, metabolic versatility, or biosynthesis of secondary metabolites, among others. Nonetheless, there is limited knowledge concerning the main regulatory factors that drive the rhizosphere colonization process. Here we show the importance of the AmrZ and FleQ transcription factors for adaption in the plant growth-promoting rhizobacterium (PGPR) and rhizosphere colonization model Pseudomonas ogarae F113. RNA-Seq analyses of P. ogarae F113 grown in liquid cultures either in exponential and stationary growth phase, and rhizosphere conditions, revealed that rhizosphere is a key driver of global changes in gene expression in this bacterium. Regarding the genetic background, this work has revealed that a mutation in fleQ causes considerably more alterations in the gene expression profile of this bacterium than a mutation in amrZ under rhizosphere conditions. The functional analysis has revealed that in P. ogarae F113, the transcription factors AmrZ and FleQ regulate genes involved in diverse bacterial functions. Notably, in the rhizosphere, these transcription factors antagonistically regulate genes related to motility, biofilm formation, nitrogen, sulfur, and amino acid metabolism, transport, signalling, and secretion, especially the type VI secretion systems. These results define the regulon of two important bifunctional transcriptional regulators in pseudomonads during the process of rhizosphere colonization.

Comparative Analysis of Three Bradyrhizobium diazoefficiens Genomes Show Specific Mutations Acquired during Selection for a Higher Motility Phenotype and Adaption to Laboratory Conditions.

Microbial genomes are being extensively studied using next-generation sequencing technologies in order to understand the changes that occur under different selection regimes. In this work, the number and type of mutations that have occurred in three Bradyrhizobium diazoefficiens USDA 110T strains under laboratory conditions and during selection for a more motile phenotypic variant were analyzed. Most of the mutations found in both processes consisted of single nucleotide polymorphisms, single nucleotide deletions or insertions. In the case of adaptation to laboratory conditions, half of the changes occurred within intergenic regions, and around 80% were insertions. When the more motile phenotypic variant was evaluated, eight single nucleotide polymorphisms and an 11-bp deletion were found, although none of them was directly related to known motility or chemotaxis genes. Two mutants were constructed to evaluate the 11-bp deletion affecting the alpha subunit of 2-oxoacid:acceptor oxidoreductase (AAV28_RS30705-blr6743). The results showed that this single deletion was not responsible for the enhanced motility phenotype. IMPORTANCE The genetic and genomic changes that occur under laboratory conditions in Bradyrhizobium diazoefficiens genomes remain poorly studied. Only a few genome sequences of this important nitrogen-fixing species are available, and there are no genome-wide comparative analyses of related strains. In the present work, we sequenced and compared the genomes of strains derived from a parent strain, B. diazoefficiens USDA 110, that has undergone processes of repeated culture in the laboratory environment, or phenotypic selection toward antibiotic resistance and enhanced motility. Our results represent the first analysis in B. diazoefficiens that provides insights into the specific mutations that are acquired during these processes.

Goals and Challenges of Stem Cell-Based Therapy for Corneal Blindness Due to Limbal Deficiency.

Corneal failure is a highly prevalent cause of blindness. One special cause of corneal failure occurs due to malfunction or destruction of the limbal stem cell niche, upon which the superficial cornea depends for homeostatic maintenance and wound healing. Failure of the limbal niche is referred to as limbal stem cell deficiency. As the corneal epithelial stem cell niche is easily accessible, limbal stem cell-based therapy and regenerative medicine applied to the ocular surface are among the most highly advanced forms of this novel approach to disease therapy. However, the challenges are still great, including the development of cell-based products and understanding how they work in the patient's eye. Advances are being made at the molecular, cellular, and tissue levels to alter disease processes and to reduce or eliminate blindness. Efforts must be coordinated from the most basic research to the most clinically oriented projects so that cell-based therapies can become an integrated part of the therapeutic armamentarium to fight corneal blindness. We undoubtedly are progressing along the right path because cell-based therapy for eye diseases is one of the most successful examples of global regenerative medicine.

Energy-Efficient Packet Forwarding Scheme Based on Fuzzy Decision-Making in Underwater Sensor Networks.

Underwater Wireless Sensor Networks (UWSNs) are subjected to a multitude of real-life challenges. Maintaining adequate power consumption is one of the critical ones, for obvious reasons. This includes proper energy consumption due to nodes close to and far from the sink node (gateway), which affect the overall energy efficiency of the system. These wireless sensors gather and route the data to the onshore base station through the gateway at the sea surface. However, finding an optimum and efficient path from the source node to the gateway is a challenging task. The common reasons for the loss of energy in existing routing protocols for underwater are (1) a node shut down due to battery drainage, (2) packet loss or packet collision which causes re-transmission and hence affects the performance of the system, and (3) inappropriate selection of sensor node for forwarding data. To address these issues, an energy efficient packet forwarding scheme using fuzzy logic is proposed in this work. The proposed protocol uses three metrics: number of hops to reach the gateway node, number of neighbors (in the transmission range of a node) and the distance (or its equivalent received signal strength indicator, RSSI) in a 3D UWSN architecture. In addition, the performance of the system is also tested with adaptive and non-adaptive transmission ranges and scalable number of nodes to see the impact on energy consumption and number of hops. Simulation results show that the proposed protocol performs better than other existing techniques or in terms of parameters used in this scheme.

Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.

Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.

Advanced Therapy Medicinal Products for the Eye: Definitions and Regulatory Framework.

Advanced therapy medicinal products (ATMPs) are a group of innovative and complex biological products for human use that comprises somatic cell therapy medicinal products, tissue engineered products, gene therapy medicinal products, and the so-called combined ATMPs that consist of one of the previous three categories combined with one or more medical devices. During the last few years, the development of ATMPs for the treatment of eye diseases has become a fast-growing field as it offers the potential to find novel therapeutic approaches for treating pathologies that today have no cure or are just subjected to symptomatic treatments. Therefore, it is important for all professionals working in this field to be familiar with the regulatory principles associated with these types of innovative products. In this review, we outline the legal framework that regulates the development of ATMPs in the European Union and other international jurisdictions, and the criteria that each type of ATMP must meet to be classified as such. To illustrate each legal definition, ATMPs that have already completed the research and development stages and that are currently used for the treatment of eye diseases are presented as examples.