Brucella NpeA is a secreted Type IV effector containing an N-WASP-binding short linear motif that promotes niche formation.

The modulation of actin polymerization is a common theme among microbial pathogens. Even though microorganisms show a wide repertoire of strategies to subvert the activity of actin, most of them converge in the ones that activate nucleating factors, such as the Arp2/3 complex. Brucella spp. are intracellular pathogens capable of establishing chronic infections in their hosts. The ability to subvert the host cell response is dependent on the capacity of the bacterium to attach, invade, avoid degradation in the phagocytic compartment, replicate in an endoplasmic reticulum-derived compartment and egress. Even though a significant number of mechanisms deployed by Brucella in these different phases have been identified and characterized, none of them have been described to target actin as a cellular component. In this manuscript, we describe the identification of a novel virulence factor (NpeA) that promotes niche formation. NpeA harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP and stabilizes the autoinhibited state. Our results show that NpeA is secreted in a Type IV secretion system-dependent manner and that deletion of the gene diminishes the intracellular replication capacity of the bacterium. In vitro and ex vivo experiments demonstrate that NpeA binds N-WASP and that the short linear motif is required for the biological activity of the protein.IMPORTANCEThe modulation of actin-binding effectors that regulate the activity of this fundamental cellular protein is a common theme among bacterial pathogens. The neural Wiskott-Aldrich syndrome protein (N-WASP) is a protein that several pathogens target to hijack actin dynamics. The highly adapted intracellular bacterium Brucella has evolved a wide repertoire of virulence factors that modulate many activities of the host cell to establish successful intracellular replication niches, but, to date, no effector proteins have been implicated in the modulation of actin dynamics. We present here the identification of a virulence factor that harbors a short linear motif (SLiM) present within an amphipathic alpha helix that has been described to bind the GTPase-binding domain (GBD) of N-WASP stabilizing its autoinhibited state. We demonstrate that this protein is a Type IV secretion effector that targets N-WASP-promoting intracellular survival and niche formation.

Uncovering novel bacterial and archaeal diversity: genomic insights from metagenome-assembled genomes in Cuatro Cienegas, Coahuila.

A comprehensive study was conducted in the Cuatro Ciénegas Basin (CCB) in Coahuila, Mexico, which is known for its diversity of microorganisms and unique physicochemical properties. The study focused on the "Archaean Domes" (AD) site in the CCB, which is characterized by an abundance of hypersaline, non-lithifying microbial mats. In AD, we analyzed the small domes and circular structures using metagenome assembly genomes (MAGs) with the aim of expanding our understanding of the prokaryotic tree of life by uncovering previously unreported lineages, as well as analyzing the diversity of bacteria and archaea in the CCB. A total of 325 MAGs were identified, including 48 Archaea and 277 Bacteria. Remarkably, 22 archaea and 104 bacteria could not be classified even at the genus level, highlighting the remarkable novel diversity of the CCB. Besides, AD site exhibited significant diversity at the phylum level, with Proteobacteria being the most abundant, followed by Desulfobacteria, Spirochaetes, Bacteroidetes, Nanoarchaeota, Halobacteriota, Cyanobacteria, Planctomycetota, Verrucomicrobiota, Actinomycetes and Chloroflexi. In Archaea, the monophyletic groups of MAGs belonged to the Archaeoglobi, Aenigmarchaeota, Candidate Nanoarchaeota, and Halobacteriota. Among Bacteria, monophyletic groups were also identified, including Spirochaetes, Proteobacteria, Planctomycetes, Actinobacteria, Verrucomicrobia, Bacteroidetes, Candidate Bipolaricaulota, Desulfobacteria, and Cyanobacteria. These monophyletic groups were possibly influenced by geographic isolation, as well as the extreme and fluctuating environmental conditions in the pond AD, such as stoichiometric imbalance of C:N:P of 122:42:1, fluctuating pH (5-9.8) and high salinity (5.28% to saturation).

Maxillary sinus angiolymphoid hyperplasia with eosinophilia associated to orbital and cutaneous lesion.

INTRODUCTION: We describe the first case of ALHE in the orbit with extension to the maxillary sinus and the importance of a multidisciplinary approach to achieve removal of the lesion. CASE STUDY: A 72-year-old man presented with epiphora of the left eye and several episodes of recurrent acute dacryocystitis. Magnetic resonance imaging revealed a solid homogeneous mass located in the inferomedial region of the left orbit. In addition, it was associated with destruction of the adjacent ethmoidal wall and upper wall of the left maxillary sinus. Incisional biopsy of the orbital mass was compatible with ALHE. RESULTS: It was decided to perform surgery using an orbital floor approach, left medial wall via subconjunctival and caruncular approach together with an endoscopic nasal approach (ESS), achieving complete removal of the orbital mass and cleaning of the maxillary sinus. After one year of treatment, no tumor recurrence was evident through endoscopy and imaging tests and the patient is asymptomatic. CONCLUSIONS: ALHE is a very rare benign vascular tumor that presents subcutaneous nodules in the head and neck region. We do not know of any case of ALHE in the paranasal sinuses described in the literature, either in isolation or together with orbital or cutaneous ALHE. In conclusion, ALHE disease should be considered as a diagnosis when faced with an orbital mass with extension to the paranasal sinuses, and a complete excision through a combined endonasal and orbital approach prevents recurrence in most cases.

Magnetic-Dielectric Cantilevers for Atomic Force Microscopy.

Atomic force microscopy (AFM) is a technique that relies on detecting forces at the nanonewton scale. It involves using a cantilever with a tiny tip at one end. This tip interacts with the short- and long-range forces of material surfaces. These cantilevers are typically manufactured with Si or Si3N4 and synthesized using a lithography technique, which implies a high cost. On the other hand, through simple chemical methods, it is possible to synthesize a magneto-dielectric composite made up of artificial SiO2 opals infiltrated with superparamagnetic nanoparticles of Fe3O4. From these materials, it is possible to obtain tipless cantilevers that can be used in AFM analysis. Tipless cantilevers are an alternative tool in nanoscale exploration, offering a versatile approach to surface analysis. Unlike traditional AFM probes, tipless versions eliminate the challenges associated with tip wear, ensuring prolonged stability during measurements. This makes tipless AFM particularly valuable for imaging delicate or soft samples, as it prevents sample damage and provides precise measurements of topography and mechanical and electromechanical properties. This study presents the results of the characterization of known surfaces using magneto-dielectric cantilevers and commercial cantilevers based on Si. The characterization will be carried out through contact and non-contact topography measurements.

HIV Risk Behaviors and the Use of Geosocial Networking Dating Apps among Men Who have Sex with Men and Transgender Women in Lima, Peru: a Cross-Sectional Study.

Geosocial networking dating apps (GSN apps) are an increasingly widespread technology used by populations throughout the world to facilitate sexual encounters. Studies from a variety of settings suggest a possible association between GSN app use and HIV risk behaviors, including among sexual and gender minority populations such as men who have sex with men (MSM) and transgender women (TW). However, it remains unclear to what extent GSN apps play a causal role. We explored the relationship between GSN app use and sexual risk behaviors among MSM and TW in Lima, Peru by analyzing data from a multi-site cross-sectional survey assessing both general and partner-specific sexual behaviors. We performed bivariate analysis to estimate the association of GSN app use with different individual and partner-specific factors, then fit multivariable regression models adjusting for age and education. Among 741 total participants (698 MSM, 43 TW), 64% met at least one sex partner in the prior three months using a GSN app. GSN app users were significantly more likely to report engaging in HIV risk behaviors in general, including condomless receptive anal sex, group sex, transactional sex, and sex under the influence of alcohol or drugs. Having condomless anal sex with a given partner was not associated with meeting that partner via GSN app. These findings highlight GSN app users as a particularly vulnerable subpopulation among MSM and TW in Lima. GSN apps could provide a useful vehicle for targeted HIV prevention efforts for priority populations in Peru.

RESUMEN: Las aplicaciones de citas de redes geosociales (aplicaciones GSN) son una tecnología con creciente alcance en todo el mundo usadas para facilitar encuentros sexuales. Diferentes estudios sugieren una posible relación entre uso de aplicaciones GSN y comportamientos de riesgo para VIH entre hombres que tienen sexo con hombres (HSH) y mujeres transgénero (MT). No es claro hasta qué punto aplicaciones GSN tendrían un papel causal directo. Exploramos la relación entre uso de aplicaciones GSN y comportamientos sexuales de riesgo entre HSH y MT en Lima, Perú, analizando datos de una encuesta transversal que evaluó comportamientos sexuales en general y en parejas específicas. Realizamos análisis bivariable para estimar la asociación del uso de aplicaciones GSN con diferentes factores individuales y específicos de la pareja. También aplicamos modelos de regresión multivariables ajustados por edad y educación. Entre 741 participantes totales (698 HSH, 43 MT), 64% conoció al menos a una pareja sexual en los últimos tres meses mediante una aplicación GSN. Los usuarios de aplicaciones GSN fueron significativamente más propensos a reportar comportamientos de riesgo de VIH en general, incluyendo sexo anal receptivo sin condón, y sexo grupal, transaccional y bajo influencia de alcohol o drogas. Tener sexo anal sin condón con una pareja determinada no se asoció con conocer a esa pareja mediante aplicación GSN. Estos hallazgos muestran a usuarios de aplicaciones GSN como una subpoblación particularmente vulnerable entre HSH y MT en Lima. Aplicaciones GSN podrían ser útiles para iniciativas de prevención del VIH en poblaciones prioritarias en Perú.

Comprehensive comparative analysis of the periodontal pathogen Porphyromonas gingivalis: exploring the pan-genome, the reconstruction of the gene regulatory network and genome-scale metabolic network.

Porphyromonas gingivalis is a nonmotile, obligate anaerobic, Gram-negative bacterium known for its association with periodontal disease and its involvement in systemic diseases such as atherosclerosis, cardiovascular disease, colon cancer, and Alzheimer's disease. This bacterium produces several virulence factors, including capsules, fimbriae, lipopolysaccharides, proteolytic enzymes, and hemagglutinins. A comparative genomic analysis revealed the open pangenome of P. gingivalis and identified complete type IV secretion systems in strain KCOM2805 and almost complete type VI secretion systems in strains KCOM2798 and ATCC49417, which is a new discovery as previous studies did not find the proteins involved in secretion systems IV and VI. Conservation of some virulence factors between different strains was observed, regardless of their genetic diversity and origin. In addition, we performed for the first time a reconstruction analysis of the gene regulatory network, identifying transcription factors and proteins involved in the regulatory mechanisms of bacterial pathogenesis. In particular, QseB regulates the expression of hemagglutinin and arginine deaminase, while Rex may suppress the release of gingipain through interactions with PorV and the formatum/nitrate transporter. Our study highlights the central role of conserved virulence factors and regulatory pathways, particularly QseB and Rex, in P. gingivalis and provides insights into potential therapeutic targets.

Acceptability of venue-based HIV testing and prevention interventions for men who have sex with transgender women and transgender women in Lima, Perú: a formative, qualitative study.

BACKGROUND: Despite being at elevated risk for HIV, men who have sex with transgender women (MSTW) are an overlooked population in the global HIV response. Venue-based HIV interventions have previously had success reaching other HIV priority populations, including transgender women (TW). Similar approaches could be applied for MSTW. OBJECTIVE: To evaluate the prospective acceptability of venue-based HIV testing and prevention interventions for MSTW and TW in Lima, Peru. METHODS: In this exploratory qualitative study, we conducted in-depth interviews (IDI) and focus group discussions (FGD) with three types of participants: MSTW (7 IDIs, 1 FGD), TW (1 FGD), and owners of social venues frequented by MSTW/TW in Lima (2 IDIs). We elicited participants' attitudes and perceptions related to the following four hypothetical interventions delivered at social venues in Lima: rapid HIV testing; HIV self-test distribution; condom/lubricant distribution; and enrolment in a mobile app supporting HIV prevention. We performed a mixed deductive-inductive thematic analysis using the framework method, then applied the Theoretical Framework of Acceptability to classify the overall acceptability of each intervention. RESULTS: Condom/lubricant distribution and app-based HIV prevention information were highly acceptable among all participant types. The two HIV testing interventions had relatively lower acceptability; however, participants suggested this could be overcome if such interventions focused on ensuring discretion, providing access to healthcare professionals, and offering appropriate incentives. CONCLUSIONS: Overall, MSTW and TW shared similar favourable attitudes towards venue-based HIV interventions. Venue-based outreach warrants further exploration as a strategy for engaging MSTW and TW in HIV prevention activities.

Corrosion of an Additively Manufactured Ti6Al4V Alloy in Saline and Acidic Media.

The present work aims to provide corrosion performance data for an additively manufactured Ti6Al4V alloy in saline and polluted environments. The as-received additively manufactured material underwent heat treatment at 850 °C for 3 h to transform the acicular α' microstructure into a lamellar α microstructure. Comparative corrosion assessments were conducted between the heat-treated substrates, the as-received condition, and a conventionally mill-annealed alloy. Potentiodynamic polarization experiments were carried out in saline (3.5 wt.% NaCl) and acid aqueous media ((NH4)2SO4 containing Harrison's solution). The corrosion performance of additively manufactured substrates matched or surpassed that of the conventional alloy in Harrison's solutions while remaining inferior in saline medium, despite forming a thicker passive film. Overall, the XY plane showed better corrosion performance, particularly after the elimination of the acicular α' martensite by the applied heat treatment. The results also suggested that the presence of the coarse ß phase was beneficial in 3.5 wt.% NaCl solution and detrimental in Harrison's solutions, more so in acidified and fluorinated conditions.

Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System.

Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.

Vastus Lateralis Muscle Flap for High-Risk Patients Undergoing Orthopaedic Hip Surgery.

INTRODUCTION: Chronic infections and soft-tissue defects are serious complications after total hip arthroplasties (THAs) that may require hip disarticulation (HD). HD is a relatively high-risk procedure with poor long-term outcomes and survival. This is the first study to analyze the effect of an ipsilateral, pedicled vastus lateralis (VL) muscle flap in preventing HD in patients with recurrent complications after THA. METHODS: This retrospective case review analyzed the 6-month postoperative outcomes of 14 patients who underwent soft-tissue hip reconstruction with a VL muscle flap by a single surgeon. RESULTS: Most (86%) patients fully recovered after 6 months with preserved hip range of motion, no pain, and no weakness on ambulation. Two (14%) patients ultimately required HD despite introducing a VL flap. DISCUSSION: A VL muscle flap is an effective treatment of nonhealing THA and prophylactic intervention for patients at high risk for HD. The VL muscle is optimal because of its large size allowing reduction of soft-tissue dead space, its local anatomical location to the hip, and its exceptional vascularity. Additional prospective studies are necessary to determine the most appropriate population for this technique.

Biomechanical Factors Predisposing to Knee Injuries in Junior Female Basketball Players.

This cross-sectional observational study aims to determine isokinetic normality data at different speeds, and isometric data of ankle and knee joints, in healthy basketball players aged 15-16 years old. The participants were recruited through non-probabilistic convenience sampling. Sociodemographic, anthropometric, and biomechanical variables were collected. The study involved 42 participants. Right-leg dominance was higher in women (85.7%) than in men (78.6%). Men had a higher weight, height, and body mass index compared to women. Statistically significant differences were observed between sex and height (p < 0.001). Significant differences were found between sexes in knee flexor and extensor strength at different isokinetic speeds (30°, 120°, and 180°/s), except for the maximum peak strength knee flexion at 180°/s in the right leg. In the ankle, the variables inversion, eversion, and work strength values at different isokinetic speeds and full RoM, by sex, were not significantly different, except for the right (p = 0.004) and the left (p = 0.035) ankle full RoM. The study found lower knee extensor strength in women, indicating the need to improve knee flexor/extensor strength in women to match that of men, as seen in other joints. The results can guide the development of preventive and therapeutic interventions for lower limb injuries in basketball players.

Campylobacter prophage diversity reveals pervasive recombination between prophages from different Campylobacter species.

IMPORTANCE: Prophages play an important role in shaping the genetic diversity and evolution of their hosts. Acquisition or loss of prophages can lead to genomic variations, including changes in the bacterial phenotype promoted by recombination events, genetic repertoire exchanges and dissemination of virulence factors, and antibiotic resistance. By studying prophages in Campylobacter species, scientists can gain insights into the evolutionary patterns, pathogenicity mechanisms, epidemiology, and population dynamics of these species. This has implications for public health, antibiotic resistance surveillance, and the development of targeted therapeutic approaches.

Genetic insights into the microevolutionary dynamics and early introductions of human monkeypox virus in Mexico.

The recent global outbreak of mpox, caused by monkeypox virus (MPV) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. In this study, we analyzed 880 MPV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than single-nucleotide polymorphisms (SNPs), which do not contribute significantly to genome diversity. Although the genome contains multiple SNPs in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is amino acid position 63 of the protein encoded by the Cop-A4L gene, which is intricately related to viral maturity, which we found to be under strong positive selection. Ancestral state reconstruction indicated that the ancestral state at position 63 corresponds to the amino acid valine, which is present only in isolates of clade I. However, the isolates from the current outbreak contained threonine at position 63. Our findings contribute new information about the evolution of monkeypox virus.

Relación del apoyo social percibido y el logro de las metas de compensación de los pacientes con hipertensión arterial y diabetes mellitus / Relationship of perceived social support and the compensation goals of patients with arterial hypertension and diabetes mellitus

INTRODUCCIÓN: Las enfermedades crónicas son un problema actual que presentan altos porcentajes de descompensación en pacientes hipertensos y diabéticos, que hace interesante evaluar los determinantes sociales que influyen en la situación, como el apoyo social. OBJETIVO DEL ESTUDIO: fue relacionar el apoyo social percibido, adherencia a medicamentos, literacidad y variables sociodemográficas con el logro de compensación en pacientes con hipertensión arterial y diabetes mellitus. METODOLOGÍA: De tipo descriptivo correlacional de corte transversal. RESULTADOS: Se estudió a 600 personas, con un promedio de edad de 62,9 años, 63,5% mujeres. Un 64,66% son diabéticos y 89,5% hipertensos (46,9% y 43,33% descompensados respectivamente). El apoyo social percibido fue alto y presentan una inadecuada adherencia al tratamiento farmacológico y una adecuada literacidad en salud (57,6%). Se realiza un análisis de relaciones que demuestran relación significativa entre una menor percepción de apoyo instrumental y ser mujer; la percepción del apoyo de interacción social disminuye con el aumento de la edad y en relación con el apoyo afectivo, disminuye la percepción a mayores años de estudios. Al realizar una regresión logística, entre la percepción de apoyo social baja y los niveles de compensación de los parámetros de compensación no se evidencia una relación estadísticamente significativa. Se evidencia una asociación entre las personas con menos de 8 años de estudio y presentar presiones arteriales elevadas. DISCUSIÓN: Existe dificultad en la medición del concepto de apoyo social, dado que el sentido y significancia es personal. Las patologías crónicas como estresores debe ser un elemento que continúe estudiándose con estudios longitudinales y experimentales. Las estrategias clínicas para la compensación de la hipertensión y la diabetes deben ir más allá del apoyo social, considerando las crecientes complicaciones y proyecciones de mortalidad. CONCLUSIÓN: Se destaca la importancia de abordar el apoyo social considerando su naturaleza subjetiva y contextual, aunque no se estableció una correlación directa con el logro terapéutico. Se señala la inadecuada adherencia al tratamiento farmacológico, la asociación entre baja escolaridad y presiones arteriales elevadas.

INTRODUCTION: Chronic diseases are a current problem since there are high percentages of decompensation in hypertensive and diabetic patients, which makes it interesting to evaluate the social determinants that influence and social support as a multidimensional concept. OBJECTIVE: To relate the perceived social support, medication adherence, literacy and sociodemographic variables with the achievement of compensation in patients with arterial hypertension and / or diabetes mellitus. METHODOLOGY: Descriptive correlational descriptive study is performed methodologically. RESULTS: 600 people were studied, with an average age of 62.9 years, 63.5% women. 64.66% are diabetic and 89.5% hypertensive (46.9% and 43.33% decompensated respectively). The perceived social support was high and showed inadequate adherence to drug treatment and adequate literacy (57.6%). An analysis of relationships that are significantly related between a lower perception of instrumental support and being a woman is performed; the perception of social interaction support with increasing age and in relation to affective support, the perception of older years of studies. When performing a logistic regression, there is no statistically significant relationship between the perception of low social support and the compensation levels of the compensation parameters. There is evidence of an association between children under 8 years of study and presentation of high arterial references. DISCUSSION: There is difficulty in measuring the concept of social support, since the meaning and meaning is personal. Chronic pathologies as stressors should be an element that continues to study with longitudinal and experimental studies. Clinical strategies for the compensation of hypertension and diabetes must go beyond social support, considering the increasing complications and mortality projections. CONCLUSION: Emphasizes the importance of addressing social support considering its subjective and contextual nature, though no direct correlation with therapeutic achievement was established. Highlights inadequate adherence to pharmacological treatment, the association between low education and elevated blood pressure.

Skeletal and Dentoalveolar Changes in Growing Patients Treated with Rapid Maxillary Expansion Measured in 3D Cone-Beam Computed Tomography.

The skeletal and dental effects of rapid maxillary expansion (RME) have been extensively studied, but high-quality research is still needed to determine the three-dimensional (3D) effects of RME. The aim of this study was to compare skeletal and dentoalveolar parameters through cone-beam computed tomography (CBCT) pre- (T1) and post-treatment (T2) with respect to RME. Twenty growing patients (mean age 10.7 years) were treated with a Hyrax-type expander. A 3D CBCT was performed at T1 and T2, measuring nasal width, maxillary width, palatal height, maxillary arch perimeter, angulation of the upper first molar, and intermolar width. The mean palatal suture opening was 2.85 ± 0.62 mm (p < 0.0001). Nasal width increased 1.28 ± 0.64 mm and maxillary width 2.79 ± 1.48 mm (p < 0.0001). In contrast, palatal height was reduced 0.65 ± 0.64 mm (p < 0.0001). Regarding arch perimeter, the radicular perimeter increased 2.89 ± 1.80 mm, while the coronal perimeter increased 3.42 ± 2.09 mm (p < 0.0001). Molar angulation increased 5.62 ± 3.20° for the right molar and 4.74 ± 2.22° for the left molar (p < 0.0001). Intermolar width increased 5.21 ± 1.55 mm (p < 0.0001). Treatment with Hyrax produced a significant opening in the mean palatal suture. Also, a significant increase in nasal width, maxillary width, arch perimeter, molar angulation, and intermolar width, and a decrease in palatal height, were observed.

HADEG: A curated hydrocarbon aerobic degradation enzymes and genes database.

Databases of genes and enzymes involved in hydrocarbon degradation have been previously reported. However, these databases specialize on only a specific group of hydrocarbons and/or are constructed partly based on enzyme sequences with putative functions indicated by in silico research, with no experimental evidence. Here, we present a curated database of Hydrocarbon Aerobic Degradation Enzymes and Genes (HADEG) containing proteins and genes involved in alkane, alkene, aromatic, and plastic aerobic degradation and biosurfactant production based solely on experimental evidence, which are present in bacteria, and fungi. HADEG includes 259 proteins for petroleum hydrocarbon degradation, 160 for plastic degradation, and 32 for biosurfactant production. This database will help identify and predict hydrocarbon degradation genes/pathways and biosurfactant production in genomes.

Using Linear Motif Database Resources to Identify SH2 Domain Binders.

The SH2-binding phosphotyrosine class of short linear motifs (SLiMs) are key conditional regulatory elements, particularly in signaling protein complexes beneath the cell's plasma membrane. In addition to transmitting cellular signaling information, they can also play roles in cellular hijack by invasive pathogens. Researchers can take advantage of bioinformatics tools and resources to predict the motifs at conserved phosphotyrosine residues in regions of intrinsically disordered protein. A candidate SH2-binding motif can be established and assigned to one or more of the SH2 domain subgroups. It is, however, not so straightforward to predict which SH2 domains are capable of binding the given candidate. This is largely due to the cooperative nature of the binding amino acids which enables poorer binding residues to be tolerated when the other residues are optimal. High-throughput peptide arrays are powerful tools used to derive SH2 domain-binding specificity, but they are unable to capture these cooperative effects and also suffer from other shortcomings. Tissue and cell type expression can help to restrict the list of available interactors: for example, some well-studied SH2 domain proteins are only present in the immune cell lineages. In this article, we provide a table of motif patterns and four bioinformatics strategies that introduce a range of tools that can be used in motif hunting in cellular and pathogen proteins. Experimental followup is essential to determine which SH2 domain/motif-containing proteins are the actual functional partners.

Emergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance.

Purpose: The purpose of this study was to highlight the clinical and molecular features of 13 Raoultella ornithinolytica strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of Raoultella spp. As Raoultella is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments. Methods: We analyzed 13 strains of Raoultella ornithinolytica isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing. Results: Polymerase chain reaction revealed that seven isolates were positive isolates for blaOXA-48 and one for blaKPC-2 gene. Of the seven strains that presented the blaOXA-48 gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The blaKPC gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene blaOXA-48, originating from Ecuador. Moreover, all R. ornithinolytica strains contained the ORN-1 gene, which confers resistance for ß-lactams, such as penicillins and cephalosporins. Comparative genome analysis of the strains showed that the pangenome of R. ornithinolytica is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes. Conclusion: These results reveal the genome plasticity of R. ornithinolytica, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico.

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.

Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses.

Comparing the evolution of distantly related viruses can provide insights into common adaptive processes related to shared ecological niches. Phylogenetic approaches, coupled with other molecular evolution tools, can help identify mutations informative on adaptation, although the structural contextualization of these to functional sites of proteins may help gain insight into their biological properties. Two zoonotic betacoronaviruses capable of sustained human-to-human transmission have caused pandemics in recent times (SARS-CoV-1 and SARS-CoV-2), although a third virus (MERS-CoV) is responsible for sporadic outbreaks linked to animal infections. Moreover, two other betacoronaviruses have circulated endemically in humans for decades (HKU1 and OC43). To search for evidence of adaptive convergence between established and emerging betacoronaviruses capable of sustained human-to-human transmission (HKU1, OC43, SARS-CoV-1, and SARS-CoV-2), we developed a methodological pipeline to classify shared nonsynonymous mutations as putatively denoting homoplasy (repeated mutations that do not share direct common ancestry) or stepwise evolution (sequential mutations leading towards a novel genotype). In parallel, we look for evidence of positive selection and draw upon protein structure data to identify potential biological implications. We find 30 candidate mutations, from which 4 (codon sites 18121 [nsp14/residue 28], 21623 [spike/21], 21635 [spike/25], and 23948 [spike/796]; SARS-CoV-2 genome numbering) further display evolution under positive selection and proximity to functional protein regions. Our findings shed light on potential mechanisms underlying betacoronavirus adaptation to the human host and pinpoint common mutational pathways that may occur during establishment of human endemicity.