GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs.

Genome search and/or classification typically involves finding the best-match database (reference) genomes and has become increasingly challenging due to the growing number of available database genomes and the fact that traditional methods do not scale well with large databases. By combining k-mer hashing-based probabilistic data structures (i.e. ProbMinHash, SuperMinHash, Densified MinHash and SetSketch) to estimate genomic distance, with a graph based nearest neighbor search algorithm (Hierarchical Navigable Small World Graphs, or HNSW), we created a new data structure and developed an associated computer program, GSearch, that is orders of magnitude faster than alternative tools while maintaining high accuracy and low memory usage. For example, GSearch can search 8000 query genomes against all available microbial or viral genomes for their best matches (n = ∼318 000 or ∼3 000 000, respectively) within a few minutes on a personal laptop, using ∼6 GB of memory (2.5 GB via SetSketch). Notably, GSearch has an O(log(N)) time complexity and will scale well with billions of genomes based on a database splitting strategy. Further, GSearch implements a three-step search strategy depending on the degree of novelty of the query genomes to maximize specificity and sensitivity. Therefore, GSearch solves a major bottleneck of microbiome studies that require genome search and/or classification.

Phycobiliprotein from Arthrospira maxima: Conversion to nanoparticles by high-energy ball milling, structural characterization, and evaluation of their anti-inflammatory effect.

Arthrospira maxima is a source of phycobiliproteins with different nutraceutical properties, e.g. antioxidant and anti-inflammatory activities. The current study was aimed at the elaboration, characterization, and evaluation of the anti-inflammatory effect of the phycobiliprotein nanoparticles extracted from Arthrospira maxima. Previously freeze-dried phycobiliproteins were milled by high-energy ball milling until reaching a nanometric size (optimal time: 4 h). Microscopy techniques were used for the characterization of the size and morphology of phycobiliproteins nanoparticles. Additionally, a spectroscopic study evidenced that nanosized reduction induced an increase in the chemical functional groups associated with its anti-inflammatory activity that was tested in a murine model, showing an immediate inflammatory effect. The novelty and importance of this contribution was to demonstrate that high energy ball milling is an emerging and green technology that can produce phycobiliprotein nanoparticles on a large-scale, without the use of organic solvents, to test their nutraceutical properties in a biological model by intragastric administration.

[GMK rotating hinge prosthesis. A valid option for complex revision knee prosthetic surgery]. / Prótesis bisagra rotatoria GMK. Una opción válida para la cirugía de revisión protésica compleja de rodilla.

INTRODUCTION: revision joint replacement surgery presents a surgical challenge. The use of rotating hinge prostheses is an option in patients with femorotibial bone defects, ligament insufficiency, or significant deformities. The aim of this study was to evaluate the clinical, functional, and radiological outcomes of a series of patients who underwent surgery using the GMK Hinge (Medacta®) rotational hinge model. MATERIAL AND METHODS: a descriptive, retrospective, and analytical study was conducted on a series of 36 patients, with a mean age of 72.5 years (47-85), operated on by the same surgical team between January 2015 and January 2022. The etiology of revision was chronic infection in 38.9% of cases, instability in 33.3%, aseptic loosening in 19.4%, and stiffness in 8.4%. The Knee Society Score (KSS) and the Forgotten Joint Score (FJS) were used to assess functional outcomes. The degree of femorotibial bone defect was evaluated using the Anderson Orthopaedic Research Institute (AORI) classification. Postoperative complications are also recorded. RESULTS: a total of 36 patients, 17 males and 19 females, were included, with a mean follow-up of 30 months (12-66). Twelve patients had type 1 defects, ten had 2A defects, ten had 2B defects, and two had type 3 defects on the femoral side, with the use of wedges required for asymmetrical defects (21 patients). The predominant tibial defect was type 1 without the need for wedges. The majority achieved a satisfactory outcome on the KSS scale (72.2 ± 9.4), with significant differences compared to the previous KSS (54.3 ± 8.9). A score of 31 (12-67) was also obtained on the FJS scale. Postoperative complications were present in 16.7% of patients. CONCLUSIONS: complex prosthetic revision surgery using a rotating hinge prosthesis represents a suitable therapeutic option, yielding appropriate clinical and functional outcomes, albeit not without complications.

INTRODUCCIÓN: la cirugía de revisión protésica constituye un reto quirúrgico. La utilización de prótesis tipo bisagra rotatoria es una opción en pacientes con defectos óseos femorotibiales, insuficiencia ligamentosa o importantes deformidades. El objetivo del presente estudio es evaluar los resultados clínicos, funcionales y radiológicos de una serie de pacientes intervenidos mediante un modelo de bisagra rotacional GMK Hinge (Medacta®). MATERIAL Y MÉTODOS: estudio descriptivo retrospectivo y analítico que incluyó una serie de 36 pacientes, con edad media de 72.5 años (47-85) intervenidos entre Enero de 2015 y Enero de 2022 por el mismo equipo quirúrgico. La etiología de revisión fue infección crónica en 38.9%, inestabilidad en 33.3%, aflojamiento aséptico en 19.4% y rigidez en 8.4%. Para la evaluación de resultados funcionales se utiliza la escala Knee Society Score (KSS), así como la escala Forgotten Joint Score (FJS). El grado de defecto óseo femorotibial se evaluó mediante la clasificación de Anderson Orthopaedic Research Institute (AORI). También se registraron las complicaciones postquirúrgicas. RESULTADOS: se analizó un total de 36 pacientes, 17 varones y 19 mujeres, con seguimiento medio de 30 meses (12-66). Se encontraron doce pacientes con defectos tipo 1, diez con defectos 2A, diez con defectos 2B y dos con defecto tipo 3 en la vertiente femoral, siendo necesario la utilización de cuñas en defectos asimétricos (21 pacientes). El defecto tibial mayoritario fue el tipo 1 sin necesidad de cuñas. La mayoría obtuvo un resultado satisfactorio en la escala KSS (72.2 ± 9.4), con diferencias significativas respecto al KSS previo (54.3 ± 8.9). Se obtuvo también una puntuación de 31 (12-67) en la escala FJS. Presentaron complicaciones postoperatorias 16.7% de los pacientes. CONCLUSIONES: la cirugía de revisión protésica compleja mediante prótesis tipo bisagra rotacional constituye una correcta opción terapéutica, presentando resultados clínicos y funcionales adecuados, no exentos de complicaciones.

Why and how to use the SeqCode.

The SeqCode, formally called the Code of Nomenclature of Prokaryotes Described from Sequence Data, is a new code of nomenclature in which genome sequences are the nomenclatural types for the names of prokaryotic species. While similar to the International Code of Nomenclature of Prokaryotes (ICNP) in structure and rules of priority, it does not require the deposition of type strains in international culture collections. Thus, it allows for the formation of permanent names for uncultured prokaryotes whose nearly complete genome sequences have been obtained directly from environmental DNA as well as other prokaryotes that cannot be deposited in culture collections. Because the diversity of uncultured prokaryotes greatly exceeds that of readily culturable prokaryotes, the SeqCode is the only code suitable for naming the majority of prokaryotic species. The start date of the SeqCode was January 1, 2022, and the online Registry (https://seqco.de/) was created to ensure valid publication of names. The SeqCode recognizes all names validly published under the ICNP before 2022. After that date, names validly published under the SeqCode compete with ICNP names for priority. As a result, species can have only one name, either from the SeqCode or ICNP, enabling effective communication and the creation of unified taxonomies of uncultured and cultured prokaryotes. The SeqCode is administered by the SeqCode Committee, which is comprised of the SeqCode Community and elected administrative components. Anyone with an interest in the systematics of prokaryotes is encouraged to join the SeqCode Community and participate in the development of this resource.

Effect of combining the methanogenesis inhibitor 3-nitrooxypropanol and cottonseeds on methane emissions, feed intake, and milk production of grazing dairy cows.

No single enteric CH4 mitigating strategy has been consistently effective or is readily applicable to ruminants in grassland systems. When CH4 mitigating strategies are effective under grazing conditions, mitigation is mild to moderate at best. A study was conducted to evaluate the potential of combining two CH4 mitigation strategies deemed feasible to apply in grazing dairy cows, the methanogenesis inhibitor 3-nitrooxypropanol additive (3-NOP) and cottonseed supplementation (CTS), seeking to enhance their individual CH4 mitigating potential. Forty-eight dairy cows were evaluated in a continuous grazing study and supplemented with either a starch-based concentrate (STA) or one that contained cottonseeds (1.75 kg DM/d; CTS), and with either 19 g/d of 10% 3-NOP (Bovaer®) or the additive's carrier (placebo), in a 2 × 2 factorial arrangement of treatments. Treatments were supplied mixed with a concentrate supplement (5 kg/d as fed) and offered in two equal rations at milking. Methane emissions were measured on weeks 4 and 8 using the sulphur hexafluoride tracer gas technique over a 5-d period. The 3-NOP and CTS treatments tended to interact on absolute CH4 such that 3-NOP decreased CH4 by 13.4% with STA, but there was no mitigation with 3-NOP and CTS. Treatment interactions were also obtained for CH4 yield, where 3-NOP tended to decrease CH4 when supplied with STA, and tended to increase it with CTS. The increase in CH4 yield with the CTS diet was driven by a numerical decrease in DM intake. Methane intensity was not affected by the 3-NOP or CTS treatments. Total volatile fatty acids in ruminal fluid were not affected by 3-NOP supplementation, but a reduction in acetate and an increase in propionate proportion occurred, resulting in decreased acetate: propionate. The 3-NOP additive decreased grass intake; however, energy-corrected milk yield and milk composition were largely unaffected. Milk urea increased with 3-NOP supplementation. Combining twice daily supplementation of 3-NOP and CTS did not enhance their CH4 mitigation potential when fed to grazing dairy cows. The relatively low inhibition of CH4 production by 3-NOP compared to studies with total mixed rations may result from the mode of delivery (pulse dosed twice daily) and time gap caused by experimental handling and moving of animals to pasture after 3-NOP supplementation in the milking parlour, which could have impaired the synchrony between the additive presence in the rumen and grass intake in paddocks.

Activation of androgen receptor-expressing neurons in the posterior medial amygdala is associated with stress resistance in dominant male hamsters.

Social stress is a negative emotional experience that can increase fear and anxiety. Dominance status can alter the way individuals react to and cope with stressful events. The underlying neurobiology of how social dominance produces stress resistance remains elusive, although experience-dependent changes in androgen receptor (AR) expression is thought to play an essential role. Using a Syrian hamster (Mesocricetus auratus) model, we investigated whether dominant individuals activate more AR-expressing neurons in the posterior dorsal and posterior ventral regions of the medial amygdala (MePD, MePV), and display less social anxiety-like behavior following social defeat stress compared to subordinate counterparts. We allowed male hamsters to form and maintain a dyadic dominance relationship for 12 days, exposed them to social defeat stress, and then tested their approach-avoidance behavior using a social avoidance test. During social defeat stress, dominant subjects showed a longer latency to submit and greater c-Fos expression in AR+ cells in the MePD/MePV compared to subordinates. We found that social defeat exposure reduced the amount of time animals spent interacting with a novel conspecific 24 h later, although there was no effect of dominance status. The amount of social vigilance shown by dominants during social avoidance testing was positively correlated with c-Fos expression in AR+ cells in the MePV. These findings indicate that dominant hamsters show greater neural activity in AR+ cells in the MePV during social defeat compared to their subordinate counterparts, and this pattern of neural activity correlates with their proactive coping response. Consistent with the central role of androgens in experience-dependent changes in aggression, activation of AR+ cells in the MePD/MePV contributes to experience-dependent changes in stress-related behavior.

Thermal damage to the skin from 8.2 and 95 GHz microwave exposures in swine.

A study of burn thresholds from superficially penetrating radio-frequency (RF) energy at 8.2 and 95 GHz for swine skin was conducted. The study determined the thresholds for superficial, partial-thickness, and full-thickness burn severities after 5 seconds of exposure at power densities of 4-30 W/cm2and 2-15 W/cm2at 8.2 and 95 GHz, respectively. There were significant differences in he burn thresholds at the different severities between the two frequencies due to the large difference in energy penetration depths. Biopsies were collected from each burn site at 1, 24, 72, and 168 hr post exposure. Each sample was assessed by a burn pathologist against 20 histological factors to characterize the damage resulting from these RF overexposures. A one-dimensional, layered digital phantom that utilized realistic values for dielectric and thermal properties was used to explain some observed thresholds. The results of the heating and cooling response of the animal model and histology scores of each exposure are provided to enhance future efforts at simulation of RF overexposures and to establish damage thresholds.

Volar dislocation of the metacarpophalangeal joint of the thumb: open reduction and repair of the ulnar collateral ligament. A case report.

INTRODUCTION: metacarpophalangeal dislocations of the thumb are not very frequent injuries, it is necessary to know the anatomy of the region to know possible causes of interposition that prevent a closed reduction of this pathology. CASE PRESENTATION: we present the case of a 75-year-old woman with a post-traumatic metacarpophalangeal dislocation of the thumb that required open reduction and surgical repair. In this procedure, we performed reduction of the dislocation, mobilization of the interposed structures, repair of the capsule and reinsertion of the ulnar collateral ligament. The early mobilization protocol helped to obtain very good results. CONCLUSION: it is imperative to consider possible associated injuries during the acute phase to achieve optimal short, medium, and long-term outcomes for our patients. A comprehensive and proactive approach to diagnosis and treatment is vital in effectively addressing this pathology and minimizing its potential sequelae.

INTRODUCCIÓN: las luxaciones metacarpofalángicas del pulgar no son lesiones muy frecuentes, es necesario conocer la anatomía de la región para conocer posibles causas de interposición que impidan una reducción cerrada de esta patología. PRESENTACIÓN DEL CASO: presentamos el caso de una mujer de 75 años con luxación metacarpofalángica postraumática del pulgar que requirió reducción abierta y reparación quirúrgica. En este procedimiento realizamos reducción de la luxación, movilización de las estructuras interpuestas, reparación de la cápsula y reinserción del ligamento colateral cubital. El protocolo de movilización temprana ayudó a obtener muy buenos resultados. CONCLUSIÓN: es imperativo considerar posibles lesiones asociadas durante la fase aguda para lograr resultados óptimos a corto, mediano y largo plazo para nuestros pacientes. Un enfoque integral y proactivo del diagnóstico y tratamiento es vital para abordar eficazmente esta patología y minimizar sus posibles secuelas.

A quality improvement intervention on surgical prophylaxis impact in antibiotic consumption and cost in selected surgical procedures.

BACKGROUND: Improper compliance with antibiotic prophylaxis (AP) in surgery is associated with an increased risk of surgical site infection (SSI), and impacts the efficiency of healthcare. OBJECTIVE: Evaluate the impact of an intervention in compliance with AP in selected surgical procedures and its effect on antibiotic consumption and cost. METHODS: A prospective interventional study was performed in a community hospital from January to December 2022. The baseline period was considered January-April 2022 and the intervention period May-December 2022. All patients who underwent cesarean section, appendectomies, hernia surgery, open reduction and internal fixation (ORIF), abdominoplasty, and cholecystectomy during the study period were selected. The intervention includes staff education, pharmacy interventions, monitoring the quality of prescriptions and feedback, and improved role of anesthesia staff, and department champions. RESULTS: The study involved 192 and 617 surgical procedures in the baseline and intervention periods respectively. The compliance with timing, selection, dose, and discontinuation achieved 100%, 99.2%, and 97.6% from baseline figures of 92.7%, 95.8%, and 81.3%, respectively. The antibiotic consumption was reduced by 55.1% during the intervention with a higher contribution of other antibiotics (94.1% reduction) in comparison with antibiotics as per policy (31.2% reduction). The cost was reduced by 47.2% (antibiotic as per policy 31.9%, other antibiotics 94.2%). CONCLUSION: The implemented strategy was effective in improving the quality of antibiotic prophylaxis with a significant impact in reducing antibiotic consumption and cost.

Efficacy of new active viscosupplements on the behavior of an experimental model of osteoarthritis. / Eficacia de nuevos viscosuplementos activos en el comportamiento de un modelo experimental de osteoartritis.

OBJECTIVE: To evaluate with an animal model of osteoarthritis (New Zealand rabbits) the effectiveness of treatment with active viscosupplements (hyaluronic acid loaded with nanoparticles (NPs) that encapsulate anti-inflammatory compounds or drugs. MATERIAL AND METHODS: Experimental study composed of 5 groups of rabbits in which section of the anterior cruciate ligament and resection of the internal meniscus were performed to trigger degenerative changes and use it as a model of osteoarthritis. The groups were divided into osteoarthrosis without treatment (I), treatment with commercial hyaluronic acid (HA) (II), treatment with HA with empty nanoparticles (III), treatment with HA with nanoparticles encapsulating dexamethasone (IV) and treatment with HA with nanoparticles that encapsulate curcumin (V). In groups II to V, the infiltration of the corresponding compound was carried out spaced one week apart. Macroscopic histological analysis was performed using a scale based on the Outerbridge classification for osteoarthritis. RESULTS: We observed that this osteoarthritis model is reproducible and degenerative changes similar to those found in humans are observed. The groups that were infiltrated with hyaluronic acid with curcumin-loaded nanoparticles (V), followed by the dexamethasone group (IV) presented macroscopically less fibrillation, exposure of subchondral bone and sclerosis (better score on the scale) than the control groups (I) (osteoarthritis without treatment), group (II) treated with commercial hyaluronic acid and hyaluronic acid with nanoparticles without drug (III). CONCLUSIONS: The use of active viscosupplements could have an additional effect to conventional hyaluronic acid treatment due to its antioxidant and anti-inflammatory effect. The most promising group was hyaluronic acid with nanoparticles that encapsulate curcumin and the second group was the one that encapsulates dexamethasone.

Uso de vasopresina en el postoperatorio de cirugía de Fontan: inferencias sobre morbimortalidad / Vasopressin use in postoperative Fontan surgery: implications for morbidity and mortality

Introducción: Se ha postulado que el uso de vasopresina tendría efectos beneficiosos en el postoperatorio de cirugía cardiovascular. Objetivo: Evaluar la respuesta a la vasopresina en el postoperatorio (POP) de cirugía de Fontan de nuestra población. Métodos: Estudio de casos y controles anidados en una cohorte retrospectiva. Se incluyeron pacientes con cirugía de Fontan entre 2014 y 2019. Se registraron variables demográficas, datos del cateterismo pre-Fontan, días de asistencia respiratoria mecánica (ARM), necesidad de inotrópicos, diuréticos, diálisis, dieta hipograsa, octreotide, sildenafil y nutrición parenteral total (NPT); balance de fluidos al primer y segundo día POP, necesidad de cateterismo en el POP, días de permanencia de tubo pleural, días de internación, necesidad de reinternación y mortalidad. Se compararon los grupos con y sin vasopresina utilizando la prueba de Mann- Whitney-Wilcoxon test. Se consideró significativa una p < 0.05. Resultados: Del total analizado, 35 pacientes recibieron vasopresina. En el grupo control fueron 58 pacientes con características similares de gravedad sin vasopresina. No se encontraron diferencias en la evolución postoperatoria entre ambos grupos. El grupo con vasopresina recibió en mayor proporción dieta hipograsa. Conclusiones: En nuestra serie el uso de vasopresina no marcó diferencias significativas en términos de morbimortalidad con relación al grupo control (AU)

Introduction: The use of vasopressin has been suggested to have beneficial effects in the postoperative period after cardiovascular surgery. Objective: To evaluate the response to vasopressin in the postoperative period (POP) of Fontan surgery in our population. Methods: Nested case-control study in a retrospective cohort. Patients who underwent Fontan surgery between 2014 and 2019 were included. Demographic variables, pre-Fontan catheterization data, days of mechanical ventilation (MRA), need for inotropics, diuretics, dialysis, low-fat diet, octreotide, sildenafil and total parenteral nutrition (TPN); fluid balance at first and second day POP, need for catheterization at POP, duration of chest tube drainage, days of hospitalization, need for readmission, and mortality were recorded. Groups with and without vasopressin were compared using the Mann-Whitney- Wilcoxon test. A p < 0.05 was considered significant. Results: Of all patients analyzed, 35 received vasopressin. The control group consisted of 58 patients with similar severity characteristics who did not receive vasopressin. No differences were found in the postoperative outcome between the two groups. The vasopressin group received a higher proportion of low-fat diet. Conclusions: In our series the use of vasopressin did not show significant differences in terms of morbidity and mortality compared to the control group (AU)

Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode.

Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of Archaea and Bacteria using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.

Cognitive rehabilitation program in patients with multiple sclerosis: A pilot study.

INTRODUCTION: In recent years, there has been an increase of studies dedicated to cognitive rehabilitation in patients with multiple sclerosis (MS); however, few of these analyze the impact on such variables as cognitive reserve. The study aims to explore the effects of a cognitive rehabilitation program comprising a combination of cognitive and physical exercises, as well as group sessions to improve cognitive performance, emotional state, and cognitive reserve index. METHOD: Fifty patients with MS were subdivided into 2 groups: the control group, which performed aerobic exercise (n=25), and the experimental group (n=25), which participated in the integrated cognitive rehabilitation program (ICRP). All participants were evaluated 3 times (baseline, post-treatment, and long-term) with the Brief Repeatable Battery of Neuropsychological Tests, Cognitive Reserve Scale, Beck Depression Inventory, and a scale evaluating trait and state anxiety. RESULTS: Compared with the control group, patients in the experimental group showed improvements in cognitive function, with significant changes in measures of information processing speed, attention, memory, cognitive reserve index, and long-term mood. CONCLUSIONS: The ICRP was effective in improving cognitive and emotional function in MS, and increased the cognitive reserve index.

Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria.

The RNA recognition motif (RRM) is the most common RNA-binding protein domain identified in nature. However, RRM-containing proteins are only prevalent in eukaryotic phyla, in which they play central regulatory roles. Here, we engineered an orthogonal post-transcriptional control system of gene expression in the bacterium Escherichia coli with the mammalian RNA-binding protein Musashi-1, which is a stem cell marker with neurodevelopmental role that contains two canonical RRMs. In the circuit, Musashi-1 is regulated transcriptionally and works as an allosteric translation repressor thanks to a specific interaction with the N-terminal coding region of a messenger RNA and its structural plasticity to respond to fatty acids. We fully characterized the genetic system at the population and single-cell levels showing a significant fold change in reporter expression, and the underlying molecular mechanism by assessing the in vitro binding kinetics and in vivo functionality of a series of RNA mutants. The dynamic response of the system was well recapitulated by a bottom-up mathematical model. Moreover, we applied the post-transcriptional mechanism engineered with Musashi-1 to specifically regulate a gene within an operon, implement combinatorial regulation, and reduce protein expression noise. This work illustrates how RRM-based regulation can be adapted to simple organisms, thereby adding a new regulatory layer in prokaryotes for translation control.

Towards estimating the number of strains that make up a natural bacterial population.

What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.

Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes.

An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.

Guidelines: basic principles of neurorehabilitation for patients with acquired brain injury. Recommendations of the Spanish Society of Neurorehabilitation.

INTRODUCTION: We present the Spanish Society of Neurorehabilitation's guidelines for adult acquired brain injury (ABI) rehabilitation. These recommendations are based on a review of international clinical practice guidelines published between 2013 and 2020. DEVELOPMENT: We establish recommendations based on the levels of evidence of the studies reviewed and expert consensus on population characteristics and the specific aspects of the intervention or procedure under research. CONCLUSIONS: All patients with ABI should receive neurorehabilitation therapy once they present a minimal level of clinical stability. Neurorehabilitation should offer as much treatment as possible in terms of frequency, duration, and intensity (at least 45-60minutes of each specific form of therapy that is needed). Neurorehabilitation requires a coordinated, multidisciplinary team with the knowledge, experience, and skills needed to work in collaboration both with patients and with their families. Inpatient rehabilitation interventions are recommended for patients with more severe deficits and those in the acute phase, with outpatient treatment to be offered as soon as the patient's clinical situation allows it, as long as intensity criteria can be maintained. The duration of treatment should be based on treatment response and the possibilities for further improvement, according to the best available evidence. At discharge, patients should be offered health promotion, physical activity, support, and follow-up services to ensure that the benefits achieved are maintained, to detect possible complications, and to assess possible changes in functional status that may lead the patient to need other treatment programmes.

An ANI gap within bacterial species that advances the definitions of intra-species units.

IMPORTANCE: Bacterial strains and clonal complexes are two cornerstone concepts for microbiology that remain loosely defined, which confuses communication and research. Here we identify a natural gap in genome sequence comparisons among isolate genomes of all well-sequenced species that has gone unnoticed so far and could be used to more accurately and precisely define these and related concepts compared to current methods. These findings advance the molecular toolbox for accurately delineating and following the important units of diversity within prokaryotic species and thus should greatly facilitate future epidemiological and micro-diversity studies across clinical and environmental settings.

A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.

Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.

Kinetic FRET Assay to Measure Binding-Induced Conformational Changes of Nucleic Acids.

The interaction of small molecules or proteins with RNA or DNA often involves changes in the nucleic acid (NA) folding and structure. A biophysical characterization of these processes helps us to understand the underlying molecular mechanisms. Here, we propose kinFRET (kinetics Förster resonance energy transfer), a real-time ensemble FRET methodology to measure binding and folding kinetics. With kinFRET, the kinetics of conformational changes of NAs (DNA or RNA) upon analyte binding can be directly followed via a FRET signal using a chip-based biosensor. We demonstrate the utility of this approach with two representative examples. First, we monitored the conformational changes of different formats of an aptamer (MN19) upon interaction with small-molecule analytes. Second, we characterized the binding kinetics of RNA recognition by tandem K homology (KH) domains of the human insulin-like growth factor II mRNA-binding protein 3 (IMP3), which reveals distinct kinetic contributions of the two KH domains. Our data demonstrate that kinFRET is well suited to study the kinetics and conformational changes of NA-analyte interactions.