Search

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Tinea capitis is a dermatophytosis, which is more common in children. It is caused by dermatophytes that vary according to the region; the most frequently isolated dermatophyte in our setting is Microsporum canis. Given its anthropophilic nature, its dissemination via interpersonal transmission and through the use of hair care tools is very common. In the course of the past year, an increase has been reported in the incidence of a pathogen that was very rare in our setting: Trichophyton tonsurans. Here we describe a retrospective study of cases of tinea capitis caused by Trichophyton tonsurans identified between September 2021 and March 2023 in the Department of Pediatric Dermatology at a general hospital of the City of Buenos Aires., (Sociedad Argentina de Pediatría.)

Introduction: Newborn filiform periungual hyperkeratosis (NFPH) incidence and prevalence during the neonatal period remain unknown and have not been described in current literature. Timely diagnosis and treatment are essential to avoid complications during the neonatal period, such as acute paronychia., Objective: The aim of our prospective observational study was to describe the characteristics of NFPH in neonates born in a referral hospital in Buenos Aires., Results: One hundred patients were included. Most of them were male (60%). NFPH consists of hard, filiform elements, mostly present bilaterally in lateral nail folds. It was found in 46% of included patients. Prevalence was higher in the right hand. Due to a trend towards easy detachment and fracture, erosions were seen in several cases. Two cases of acute paronychia secondary to NFPH were diagnosed, with favorable outcomes after topical antibiotic treatment., Conclusion: The importance of clinical examination for screening of this local predisposing factor for infection in neonatal patients is highlighted., (© 2024 Wiley Periodicals LLC.)

Objetives: Obtain a version to validate it in a population of adults with AD., Materials and Methods: 1) Translation into Spanish and cross-cultural adaptation of the questionnaire from the original version in English, through a seven-step process. 2) Evaluation of the unidimensionality of the resulting scale by means of an exploratory factor analysis (EFA), of its reliability by means of Cronbach's alpha coefficient, and of its validity by evaluating the correlation of its score with those of the POEM and DLQI questionnaires. (external reference criteria)., Results: The version resulting from the translation and cross-cultural adaptation process was well understood by the target population. The AFE of the 66 questionnaires documented the unidimensionality of the scale based on compliance with all the criteria used for its verification. Its reliability was excellent (Cronbach's Alpha: 0.917) and its score had a very high correlation with the external reference criteria (POEM: Spearman's Rho 0.85; p < 0.0001; DLQI Spearman's Rho = 0.81; p < 0 .0001)., Conclusions: The version translated into Spanish and adapted for transculturation of the ADCT questionnaire has appropriate psychometric characteristics, which will contribute to optimizing the care processes of Spanish-speaking patients., (UNIVERSIDAD NACIONAL DE CORDOBA)

The majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales , repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses., Competing Interests: The authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Background: Idiopathic aseptic facial granuloma (IAFG) is an underrecognized pediatric skin disease, currently considered within the spectrum of rosacea. It usually manifests as a solitary, reddish, asymptomatic nodule on the cheek that resolves spontaneously., Methods: Retrospective and descriptive observational study of 43 pediatric patients with a clinical diagnosis of IAFG, followed between 2004 and 2022, at two general hospitals in Argentina., Results: IAFG predominated in girls (65%) and the average age of onset was about 6 years. A single asymptomatic nodule was seen in 79% of patients. The most common localization was the cheek (58%) followed by lower eyelids (41%). Family history of rosacea was present in 16% of patients. A concomitant diagnosis of rosacea and periorificial dermatitis was made in 14% and 9% of our population, respectively. Past or present history of chalazia was detected in 42% of the children. IAFG diagnosis was mainly clinical (88% of cases). Oral antibiotics were the most common indicated treatment (84%). Complete healing was achieved by the majority, but 18% of those with eyelid compromise healed with scars., Conclusions: IAFG is a benign pediatric condition that physicians should recognize in order to manage correctly. We herein refer to a particular morphologic aspect of IAFG lesions affecting the lower eyelids, where nodules adopt a linear distribution and have a higher probability of involute leaving a scar. Also, we consider that the concomitant findings of rosacea, periorificial dermatitis and chalazia in our patients, reinforce the consideration of IAFG within the spectrum of rosacea., (© 2024 Wiley Periodicals LLC.)

Introduction: in one third of patients with psoriasis, symptoms start during childhood and adolescence, with a strong emotional and psychosocial impact., Objective: to develop a guideline for the systemic treatment of psoriasis in pediatric patients by means of recommendations based on the best available evidence., Materials and Methods: Sources: articles indexed in PubMed, Epistemonikos, Google Scholar, Cochrane Library and Scielo, published between January 2010 and May 2022, in English, Spanish and Portuguese. Study selection: evidence-based clinical practice guidelines, systematic reviews, meta-analyses, randomized controlled studies, observational studies (case-control, cohort studies, real-life registries) and evaluations of biosimilar drugs in patients up to and including 17 years of age were considered. The keywords "psoriasis" and "treatment" were used in all three languages. Data extraction: the literature was evaluated using Grading of Recommendations Assessment, Development and Evaluation (GRADE) recommendations. Data synthesis: evidence tables were developed and analyzed by the expert committee. The questions for the development of recommendations were based on the PICO system (population, intervention, comparison, outcome)., Results: A total of 8 recommendations and 7 points of good practice were developed. The direction and strength of the recommendations were expressed according to the GRADE system., Conclusions: the final decision on a specific therapy should be based on the best opinion of the treating physician, the individual characteristics, and the values and preferences of the patients and their caregivers., (Universidad Nacional de Córdoba)

Summary: PyHMMER provides Python integration of the popular profile Hidden Markov Model software HMMER via Cython bindings. This allows the annotation of protein sequences with profile HMMs and building new ones directly with Python. PyHMMER increases flexibility of use, allowing creating queries directly from Python code, launching searches, and obtaining results without I/O, or accessing previously unavailable statistics like uncorrected P-values. A new parallelization model greatly improves performance when running multithreaded searches, while producing the exact same results as HMMER., Availability and Implementation: PyHMMER supports all modern Python versions (Python 3.6+) and similar platforms as HMMER (x86 or PowerPC UNIX systems). Pre-compiled packages are released via PyPI (https://pypi.org/project/pyhmmer/) and Bioconda (https://anaconda.org/bioconda/pyhmmer). The PyHMMER source code is available under the terms of the open-source MIT licence and hosted on GitHub (https://github.com/althonos/pyhmmer); its documentation is available on ReadTheDocs (https://pyhmmer.readthedocs.io)., (© The Author(s) 2023. Published by Oxford University Press.)

The interpretation of genomic, transcriptomic and other microbial 'omics data is highly dependent on the availability of well-annotated genomes. As the number of publicly available microbial genomes continues to increase exponentially, the need for quality control and consistent annotation is becoming critical. We present proGenomes3, a database of 907 388 high-quality genomes containing 4 billion genes that passed stringent criteria and have been consistently annotated using multiple functional and taxonomic databases including mobile genetic elements and biosynthetic gene clusters. proGenomes3 encompasses 41 171 species-level clusters, defined based on universal single copy marker genes, for which pan-genomes and contextual habitat annotations are provided. The database is available at http://progenomes.embl.de/., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Background: Atopic dermatitis (AD) is a chronic, recurrent, inflammatory skin condition that is associated with detrimental effects on the lives of patients and their families, including an impact on quality of life (QOL). Studies about QOL on Latin American AD patients are scarce and have generally included few patients., Objective: describing AD impact on the QOL in a large cohort in Argentina., Methods: a structured web-based survey including 1,650 AD pediatric and adult patients was performed., Results: according to retrieved data, AD symptoms onset started during childhood in most patients, but 20 % of participants reported that manifestations of AD were initially perceived during late adolescence and adulthood. Important differences were observed among country regions, with a shorter time-to-diagnosis in most populated and richer districts. Main affected domains included frustration, anger, mood alterations, stress, sleep alterations, routine alterations, pain and economic impact of AD., Limitations: biases inherent to survey design., Conclusions: we consider that our study contributes to a better understanding of AD in Argentina, as well as its physical, social and financial impact on affected patients., (Universidad Nacional de Córdoba)

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community. Database URL: https://github.com/INCATools/ontology-development-kit., (© The Author(s) 2022. Published by Oxford University Press.)

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups 1 , this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds 2,3 . However, studying this diversity to identify genomic pathways for the synthesis of such compounds 4 and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments., (© 2022. The Author(s).)

Trichophyton benhamiae is a zoonotic dermatophyte that can cause tinea corporis, tinea faciei and tinea capitis, producing inflammatory lesions, especially in children. In this publication, we describe 7clinical cases of pediatric patients that occurred in our institution between July 2019 and January 2020. All patients underwent a conventional mycological study. The identification of fungi isolates was confirmed by MALDI-TOF MS and sequencing of the ribosomal DNA. T. benhamiae was identified as the etiological agent, whose epidemiological link in all cases was the contact with Guinea pigs. This is the first description of infections caused by T. benhamiae in Argentina. This dermatophyte can be misidentified as other more frequent dermatophytes when performing conventional studies. Molecular technology should be used to reach a definitive diagnosis. It is important to have epidemiological data from patients such as contact with non-traditional pets, especially Guinea pigs, for an adequate presumptive diagnosis of this dermatophytosis., (Copyright © 2021 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)

Importance: Ichthyoses are clinically and genetically heterogeneous disorders characterized by scaly skin. Despite decades of investigation identifying pathogenic variants in more than 50 genes, clear genotype-phenotype associations have been difficult to establish., Objective: To expand the genotypic and phenotypic spectra of ichthyosis and delineate genotype-phenotype associations., Design, Setting, and Participants: This cohort study recruited an international group of individuals with ichthyosis and describes characteristic and distinguishing features of common genotypes, including genotype-phenotype associations, during a 10-year period from June 2011 to July 2021. Participants of all ages, races, and ethnicities were included and were enrolled worldwide from referral centers and patient advocacy groups. A questionnaire to assess clinical manifestations was completed by those with a genetic diagnosis., Main Outcomes and Measures: Genetic analysis of saliva or blood DNA, a phenotyping questionnaire, and standardized clinical photographs. Descriptive statistics, such as frequency counts, were used to describe the cases in the cohort. Fisher exact tests identified significant genotype-phenotype associations., Results: Results were reported for 1000 unrelated individuals enrolled from around the world (mean [SD] age, 50.0 [34.0] years; 524 [52.4%] were female, 427 [42.7%] were male, and 49 [4.9%] were not classified); 75% were from the US, 12% from Latin America, 4% from Canada, 3% from Europe, 3% from Asia, 2% from Africa, 1% from the Middle East, and 1% from Australia and New Zealand. A total of 266 novel disease-associated variants in 32 genes were identified among 869 kindreds. Of these, 241 (91%) pathogenic variants were found through multiplex amplicon sequencing and 25 (9%) through exome sequencing. Among the 869 participants with a genetic diagnosis, 304 participants (35%) completed the phenotyping questionnaire. Analysis of clinical manifestations in these 304 individuals revealed that pruritus, hypohydrosis, skin pain, eye problems, skin odor, and skin infections were the most prevalent self-reported features. Genotype-phenotype association analysis revealed that the presence of a collodion membrane at birth (odds ratio [OR], 6.7; 95% CI, 3.0-16.7; P < .001), skin odor (OR, 2.8; 95% CI, 1.1-6.8; P = .02), hearing problems (OR, 2.9; 95% CI, 1.6-5.5; P < .001), eye problems (OR, 3.0; 95% CI, 1.5-6.0; P < .001), and alopecia (OR, 4.6; 95% CI, 2.4-9.0; P < .001) were significantly associated with TGM1 variants compared with other ichthyosis genotypes studied. Skin pain (OR, 6.8; 95% CI, 1.6-61.2; P = .002), odor (OR, 5.7; 95% CI, 2.0-19.7; P < .001), and infections (OR, 3.1; 95% CI, 1.4-7.7; P = .03) were significantly associated with KRT10 pathogenic variants compared with disease-associated variants in other genes that cause ichthyosis. Pathogenic variants were identified in 869 (86.9%) participants. Most of the remaining individuals had unique phenotypes, enabling further genetic discovery., Conclusions and Relevance: This cohort study expands the genotypic and phenotypic spectrum of ichthyosis, establishing associations between clinical manifestations and genotypes. Collectively, the findings may help improve clinical assessment, assist with developing customized management plans, and improve clinical course prognostication.