IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.

Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.

Targeted bacterial conjugation mediated by synthetic cell-to-cell adhesions.

Genetic interventions on microbiomes, for clinical or biotechnological purposes, remain challenging. Conjugation-based delivery of genetic cargo is still unspecific and limited by low conjugation rates. Here we report an approach to overcome these problems, based on a synthetic bacterial adhesion system. Mating assemblers consist on a synthetic adhesion formed by the expression on the surface of donor and target cells of specific nanobodies (Nb) and their cognate antigen (Ag). The Nb-Ag bridge increased 1-3 logs transfer of a variety of plasmids, especially in liquid media, confirming that cell-cell docking is a main determinant limiting mating efficiency. Synthetic cell-to-cell adhesion allows efficient conjugation to targeted recipients, enhancing delivery of desired genes to a predefined subset of prey species, or even specific pathogenic strains such as enterohemorrhagic Escherichia coli (EHEC), within a bacterial community. The synthetic conjugation enhancer presented here optimizes plasmid delivery by selecting the target hosts with high selectivity.

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models.

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms' metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models' reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.

Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.

Short-term outcomes of laparoscopic extended hepatectomy versus major hepatectomy: a single-center experience.

INTRODUCTION: Laparoscopic major hepatectomy (LMH) remains restricted to a few specialized centers and poses a challenge to surgeons performing laparoscopic resections. Laparoscopic extended resections are even more complex and rarely conducted. METHODS: From a single-institution database, we compared the short-term outcomes of patients who underwent major and extended laparoscopic resections, stratifying the entire retrospective cohort into four groups: right hepatectomy, left hepatectomy, right extended hepatectomy, and left extended hepatectomy. Patient demographics, tumor characteristics, operative variables, and especially postoperative outcomes were evaluated. RESULTS: 250 patients underwent major and extended laparoscopic liver resections, including 160 right, 31 right extended, 36 left, and 23 left extended laparoscopic hepatectomies. The most common indication for resection was colorectal liver metastases (64%). Laparoscopic extended hepatectomy (LEH) showed significantly longer operative time, more blood loss, need for Pringle maneuver, conversion to open surgery, higher rates of liver failure, postoperative ascites, and intra-abdominal hemorrhage, R1 margins and length of stay when compared with the LMH group. Mortality rates were similar between groups. Multivariate analysis revealed intraoperative blood transfusion (OR = 5.1[CI-95%: 1.15-6.79]; p = 0.02) as an independent predictor for major complications. CONCLUSIONS: LEH showed to be feasible, however with higher blood loss and significantly associated to major complications.

Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids.

Conjugation drives the horizontal transfer of adaptive traits across prokaryotes. One-fourth of the plasmids encode the functions necessary to conjugate autonomously, the others being eventually mobilizable by conjugation. To understand the evolution of plasmid mobility, we studied plasmid size, gene repertoires, and conjugation-related genes. Plasmid gene repertoires were found to vary rapidly in relation to the evolutionary rate of relaxases, for example, most pairs of plasmids with 95% identical relaxases have fewer than 50% of homologs. Among 249 recent transitions of mobility type, we observed a clear excess of plasmids losing the capacity to conjugate. These transitions are associated with even greater changes in gene repertoires, possibly mediated by transposable elements, including pseudogenization of the conjugation locus, exchange of replicases reducing the problem of incompatibility, and extensive loss of other genes. At the microevolutionary scale of plasmid taxonomy, transitions of mobility type sometimes result in the creation of novel taxonomic units. Interestingly, most transitions from conjugative to mobilizable plasmids seem to be lost in the long term. This suggests a source-sink dynamic, where conjugative plasmids generate nonconjugative plasmids that tend to be poorly adapted and are frequently lost. Still, in some cases, these relaxases seem to have evolved to become efficient at plasmid mobilization in trans, possibly by hijacking multiple conjugative systems. This resulted in specialized relaxases of mobilizable plasmids. In conclusion, the evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology of plasmids.

Plasmid classifications.

Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).

ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range.

Plasmids, when transferred by conjugation in natural environments, must overpass restriction-modification systems of the recipient cell. We demonstrate that protein ArdC, encoded by broad host range plasmid R388, was required for conjugation from Escherichia coli to Pseudomonas putida. Expression of ardC was required in the recipient cells, but not in the donor cells. Besides, ardC was not required for conjugation if the hsdRMS system was deleted in P. putida recipient cells. ardC was also required if the hsdRMS system was present in E. coli recipient cells. Thus, ArdC has antirestriction activity against the HsdRMS system and consequently broadens R388 plasmid host range. The crystal structure of ArdC was solved both in the absence and presence of Mn2+. ArdC is composed of a non-specific ssDNA binding N-terminal domain and a C-terminal metalloprotease domain, although the metalloprotease activity was not needed for the antirestriction function. We also observed by RNA-seq that ArdC-dependent conjugation triggered an SOS response in the P. putida recipient cells. Our findings give new insights, and open new questions, into the antirestriction strategies developed by plasmids to counteract bacterial restriction strategies and settle into new hosts.

Knowledge, experience, and perception of molar incisor hypomineralisation among dentists in the metropolitan area of Mexico City: a cross-sectional study.

BACKGROUND: Molar-incisor hypomineralisation (MIH) is the most common developmental abnormality observed in teeth. Being a relatively new condition, its treatment can present a challenge for the dentist. There is currently no study available that has evaluated the knowledge of Mexican dental personnel. This study aimed to evaluate the knowledge, experience, and perceptions of dental surgeons regarding the detection, assessment, and treatment of MIH in the metropolitan area of Mexico City. METHODS: A cross-sectional study was designed. Dentists from Mexico City and its metropolitan area were invited through social networks to answer a questionnaire of 30 questions related to MIH. Participants were classified into general practice dentists, paediatric dentists, and other speciality dentists. Pearson's chi-square test was used for data analysis. RESULTS: The questionnaire was answered by 391 dentists. A total of 86% (338 out of 391) of them identified MIH lesions, while 84% of them reported having observed MIH lesions in their practice. The most frequently observed lesions were yellow-brown opacities which accounted for 47% of the lesions, 46% were white opacities, while only 7% were observed as post-eruptive fractures in the enamel as part of the manifestations of MIH. The most frequently reported problem in the management of teeth with MIH was insufficient training for treating children with MIH. A total of 84% of dentists stated that they would like more information on the treatment of MIH lesions. CONCLUSIONS: Most of the surveyed dentists recognised MIH and reported having observed MIH lesions in their practice. Most of the dentists indicated that the main problem for the management of the MIH is the lack of training.

MEWpy: a computational strain optimization workbench in Python.

SUMMARY: Metabolic Engineering aims to favour the overproduction of native, as well as non-native, metabolites by modifying or extending the cellular processes of a specific organism. In this context, Computational Strain Optimization (CSO) plays a relevant role by putting forward mathematical approaches able to identify potential metabolic modifications to achieve the defined production goals. We present MEWpy, a Python workbench for metabolic engineering, which covers a wide range of metabolic and regulatory modelling approaches, as well as phenotype simulation and CSO algorithms. AVAILABILITY AND IMPLEMENTATION: MEWpy can be installed from PyPi (pip install mewpy), the source code being available at https://github.com/BioSystemsUM/mewpy under the GPL license.

Evaluation of Chlorhexidine Concentration on the Skin After Preoperative Surgical Site Preparation in Breast Surgery-A Randomized Controlled Trial.

BACKGROUND: Although there is a rationale supporting that preoperative showering with 2% or 4% chlorhexidine gluconate (CHG) would decrease skin bacterial colonization, there is no consensus that this practice reduces the risk of surgical site infection (SSI). OBJECTIVES: Analyze the skin concentration of CHG after preoperative showering associated with the traditional skin preparation with CHG 4% for breast surgery. METHODS: Randomized controlled trial that included 45 patients, all candidates for augmentation mammaplasty, allocated into three groups (A: no preoperative showering; B: one preoperative showering; C: two preoperative showering with CHG 4%) in a 1:1:1 ratio. Skin swabs collection was performed right before the surgical incision. The samples were, then, sent to spectrophotometry in order to determine the skin concentration of CHG at the beginning of surgery. RESULTS: The age ranged from 18 to 61 years, with a mean of 37 years old. Group C had the lowest median concentration (0.057) followed by group B (0.060) and group A (0.072), however, with no statistical significance. The areola was the place with the lowest median concentration level (0.045), followed by the axilla (0.061) and the inframammary fold (IMF) (0.069). Still, when comparing the distribution of the sites, a statistically significant difference was found only between the axilla and the areola (p = 0.022). CONCLUSION: Preoperative showering with CHG 4% did not increase the concentration of this agent on the skin surface right before the surgical incision. LEVEL OF EVIDENCE IV: This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

COPLA, a taxonomic classifier of plasmids.

BACKGROUND: Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. RESULTS: We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. CONCLUSIONS: COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.

We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.

Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha.

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.

Structure and thermodynamics of empty clathrate hydrates below the freezing point of water.

Recently prepared as a new H2O phase, ice XVI was obtained by degassing a Ne-sII clathrate hydrate under vacuum, however very little is known of that crystalline solid under temperatures (T ≤ 220 K) and pressures (p ≤ 5000 bar) relevant for the Earth's environment and geochemistry. In this work, atomically detailed calculations using long time-scale molecular simulations, seldom paralelled before, are employed to probe empty sII clathrate hydrates. It is found that the volumetric response to an applied pressure-temperature gradient is accurately described by the Parsafar and Mason equation of state with an accuracy of at least 99.7%. Structural deformation induced upon the crystals is interpreted by monitoring the unit cell length and isobaric thermal expansivity, whilst benchmarked against previous neutron diffraction measurements of ice XVI and hexagonal ice under room pressure conditions; a critical comparison is established with other sII guest occupied lattices (CH4, CO2 and CnH2n+2 with n = 2, 3, 4), often found in permafrost regions and in the margins of continental shelves. Such an analysis reveals that empty sII frameworks are slightly more stable to thermal deformation than their sI analogues and that hexagonal ice is the structurally most stable of the condensed H2O phases addressed here. Of paramount importance for the oil and natural gas industries, heat capacities obtained from enthalpy profiles are identical for the sI and sII empty clathrates up to 2000 bar and diverge by only ∼7.3% at 5000 bar. The canonical tetrahedral symmetry of water-bonded networks is analysed in terms of an angular and a distance order parameters, which are observed to decrease (increase) as pressure (temperature) increases (decreases). The results now being reported constitute a landmark for future studies dealing with high-pressure and very low-temperature conditions, characteristic of the Earth's permafrost environment and other planetary interiors, whilst contributing to expand our knowledge regarding the recently discovered ice XVI phase.

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.).

BACKGROUND: Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. RESULTS: We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. CONCLUSIONS: Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.

Evaluation of Sensitivity in Specific Points of the Areola and Nipple of Patients Submitted to Reduction Mammoplasty With Periareolar Dermis Release: A Randomized Controlled Study.

BACKGROUND: To date, studies on periareolar dermis release have recorded the areola sensitivity as a mean. Despite being clinically reported by patients, specific points of the areola may present sensitivities not detected when researchers only consider mean values. OBJECTIVES: The aim of this study was to determine the pressure sensitivity at specific points of the nipple-areola complex and compare these values with the mean value measured in the areolas of patients undergoing reduction mammaplasty with periareolar dermis release. METHODS: This is a prospective, randomized controlled trial of 39 consecutive patients (78 breasts) who underwent surgery for treatment of breast hypertrophy; the same surgical technique was used for all patients. In each patient, 1 breast was assigned to a control group and the other to an experimental group. The periareolar dermis release was performed in the experimental group (39 breasts). Pressure sensitivity was tested with Semmes-Weinstein monofilaments on the papilla and at 4 specific points of the areola. The evaluations were conducted preoperatively and at 3 weeks, 6 weeks, and 1 year postoperatively. RESULTS: The group comparisons show a statistically significant difference in sensitivity at the medial point of the areola and in the papilla at 3 weeks postoperation. This difference disappeared in the 1-year evaluation. This recovery profile also occurs when areola sensitivity corresponds to a mean value. The sensitivity significantly decreased at the lower point of the areola up to 1 year postoperation in the control and experimental groups. CONCLUSIONS: The periareolar dermis release did not compromise the pressure sensitivity at the points evaluated in the nipple-areola complex. The mean areola sensitivity differed from the sensitivity at the lower point of the areola.

A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation.

The current survey aims to describe the main methodologies for extending the reconstruction and analysis of genome-scale metabolic models and phenotype simulation with Flux Balance Analysis mathematical frameworks, via the integration of Transcriptional Regulatory Networks and/or gene expression data. Although the surveyed methods are aimed at improving phenotype simulations obtained from these models, the perspective of reconstructing integrated genome-scale models of metabolism and gene expression for diverse prokaryotes is still an open challenge.

Biochemical interactions between LPS and LPS-binding molecules.

Lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, often pose a serious risk not only when delivered in the bloodstream but also in air, the environment and several industrial fields such as pharmaceutics or food. LPS is constituted of three regions; the O-specific chain, the core region and the lipid A, which is the responsible segment of the toxicity. Previous literature dealt with the study of lipid A, its potential ligands as well as the mechanisms of Lipid A interactions that, among other applications, establish the basis for detection methods such as Limulus Amebocyte Lysate (LAL) assays and emerging biosensoring techniques. However, quantifying LPS binding affinity is an urgent need that still requires thorough studies. In this context, this work reviews the molecules that bind LPS, highlighting quantitative affinity parameters. Moreover, state of the art methods to analyze the affinity and kinetics of lipid-ligand interactions are also reviewed and different techniques have been briefly described. Thus, first, we review existing information on LPS ligands, classifying them into three main groups and targeting the comparison of molecules in terms of their interaction affinities and, second, we establish the basis for further research aimed at the development of effective methods for LPS detection and removal.

treNch: Ultra-Low Power Wireless Communication Protocol for IoT and Energy Harvesting.

Although the number of Internet of Things devices increases every year, efforts to decrease hardware energy demands and to improve efficiencies of the energy-harvesting stages have reached an ultra-low power level. However, no current standard of wireless communication protocol (WCP) can fully address those scenarios. Our focus in this paper is to introduce treNch, a novel WCP implementing the cross-layer principle to use the power input for adapting its operation in a dynamic manner that goes from pure best-effort to nearly real time. Together with the energy-management algorithm, it operates with asynchronous transmissions, synchronous and optional receptions, short frame sizes and a light architecture that gives control to the nodes. These features make treNch an optimal option for wireless sensor networks with ultra-low power demands and severe energy fluctuations. We demonstrate through a comparison with different modes of Bluetooth Low Energy (BLE) a decrease of the power consumption in 1 to 2 orders of magnitude for different scenarios at equal quality of service. Moreover, we propose some security optimizations, such as shorter over-the-air counters, to reduce the packet overhead without decreasing the security level. Finally, we discuss other features aside of the energy needs, such as latency, reliability or topology, brought again against BLE.