Quantifying the fitness effects of resistance alleles with and without anthelmintic selection pressure using Caenorhabditis elegans.

Albendazole (a benzimidazole) and ivermectin (a macrocyclic lactone) are the two most commonly co-administered anthelmintic drugs in mass-drug administration programs worldwide. Despite emerging resistance, we do not fully understand the mechanisms of resistance to these drugs nor the consequences of delivering them in combination. Albendazole resistance has primarily been attributed to variation in the drug target, a beta-tubulin gene. Ivermectin targets glutamate-gated chloride channels (GluCls), but it is unknown whether GluCl genes are involved in ivermectin resistance in nature. Using Caenorhabditis elegans, we defined the fitness costs associated with loss of the drug target genes singly or in combinations of the genes that encode GluCl subunits. We quantified the loss-of-function effects on three traits: (i) multi-generational competitive fitness, (ii) fecundity, and (iii) development. In competitive fitness and development assays, we found that a deletion of the beta-tubulin gene ben-1 conferred albendazole resistance, but ivermectin resistance required the loss of two GluCl genes (avr-14 and avr-15). The fecundity assays revealed that loss of ben-1 did not provide any fitness benefit in albendazole conditions and that no GluCl deletion mutants were resistant to ivermectin. Next, we searched for evidence of multi-drug resistance across the three traits. Loss of ben-1 did not confer resistance to ivermectin, nor did loss of any single GluCl subunit or combination confer resistance to albendazole. Finally, we assessed the development of 124 C. elegans wild strains across six benzimidazoles and seven macrocyclic lactones to identify evidence of multi-drug resistance between the two drug classes and found a strong phenotypic correlation within a drug class but not across drug classes. Because each gene affects various aspects of nematode physiology, these results suggest that it is necessary to assess multiple fitness traits to evaluate how each gene contributes to anthelmintic resistance.

Gene duplication and evolutionary plasticity of lin-12/Notch gene function in Caenorhabditis.

Gene duplication is an important substrate for the evolution of new gene functions, but the impacts of gene duplicates on their own activities and on the developmental networks in which they act are poorly understood. Here, we use a natural experiment of lin-12/Notch gene duplication within the nematode genus Caenorhabditis, combined with characterization of loss- and gain-of-function mutations, to uncover functional distinctions between the duplicate genes in 1 species (Caenorhabditis briggsae) and their single-copy ortholog in Caenorhabditis elegans. First, using improved genomic sequence and gene model characterization, we confirm that the C. briggsae genome includes 2 complete lin-12 genes, whereas most other genes encoding proteins that participate in the LIN-12 signaling pathway retain a one-to-one orthology with C. elegans. We use CRISPR-mediated genome editing to introduce alleles predicted to cause gain-of-function (gf) or loss-of-function (lf) into each C. briggsae gene and find that the gf mutations uncover functional distinctions not apparent from the lf alleles. Specifically, Cbr-lin-12.1(gf), but not Cbr-lin-12.2(gf), causes developmental defects similar to those observed in Cel-lin-12(gf). In contrast to Cel-lin-12(gf), however, the Cbr-lin-12.1(gf) alleles do not cause dominant phenotypes as compared to the wild type, and the mutant phenotype is observed only when 2 gf alleles are present. Our results demonstrate that gene duplicates can exhibit differential capacities to compensate for each other and to interfere with normal development, and uncover coincident gene duplication and evolution of developmental sensitivity to LIN-12/Notch activity.

Quantitative tests of albendazole resistance in beta-tubulin mutants.

Benzimidazole (BZ) anthelmintics are among the most important treatments for parasitic nematode infections in the developing world. Widespread BZ resistance in veterinary parasites and emerging resistance in human parasites raise major concerns for the continued use of BZs. Knowledge of the mechanisms of resistance is necessary to make informed treatment decisions and circumvent resistance. Benzimidazole resistance has traditionally been associated with mutations and natural variants in the C. elegans beta-tubulin gene ben-1 and orthologs in parasitic species. However, variants in ben-1 alone do not explain the differences in BZ responses across parasite populations. Here, we examine the roles of five C. elegans beta-tubulin genes (tbb-1, mec-7, tbb-4, ben-1, and tbb-6) to identify the role each gene plays in BZ response. We generated C. elegans strains with a loss of each beta-tubulin gene, as well as strains with a loss of tbb-1, mec-7, tbb-4, or tbb-6 in a genetic background that also lacks ben-1 to test beta-tubulin redundancy in BZ response. We found that only the individual loss of ben-1 conferred a substantial level of BZ resistance, although the loss of tbb-1 was found to confer a small benefit in the presence of albendazole (ABZ). The loss of ben-1 was found to confer an almost complete rescue of animal development in the presence of 30 µM ABZ, likely explaining why no additive effects caused by the loss of a second beta-tubulin were observed. We demonstrate that ben-1 is the only beta-tubulin gene in C. elegans where loss confers substantial BZ resistance.

Quantifying the fitness effects of resistance alleles with and without anthelmintic selection pressure using Caenorhabditis elegans.

Albendazole and ivermectin are the two most commonly co-administered anthelmintic drugs in mass-drug administration programs worldwide. Despite emerging resistance, we do not fully understand the mechanisms of resistance to these drugs nor the consequences of delivering them in combination. Albendazole resistance has primarily been attributed to variation in the drug target, a beta-tubulin gene. Ivermectin targets glutamate-gated chloride channel (GluCl) genes, but it is unknown whether these genes are involved in ivermectin resistance in nature. Using Caenorhabditis elegans, we defined the fitness costs associated with loss of the drug target genes singly or in combinations of the genes that encode GluCl subunits. We quantified the loss-of function effects on three traits: (i) multi-generational competitive fitness, (ii) fecundity, and (iii) development. In competitive fitness and development assays, we found that a deletion of the beta-tubulin gene ben-1 conferred albendazole resistance, but ivermectin resistance required loss of two GluCl genes (avr-14 and avr-15) or loss of three GluCl genes (avr-14, avr-15, and glc-1). The fecundity assays revealed that loss of ben-1 did not provide any fitness benefit in albendazole and that no GluCl deletion mutants were resistant to ivermectin. Next, we searched for evidence of multi-drug resistance across the three traits. Loss of ben-1 did not confer resistance to ivermectin, nor did loss of any single GluCl subunit or combination confer resistance to albendazole. Finally, we assessed the development of 124 C. elegans wild strains across six benzimidazoles and seven macrocyclic lactones to identify evidence of multi-drug resistance between the two drug classes and found a strong phenotypic correlation within a drug class but not across drug classes. Because each gene affects various aspects of nematode physiology, these results suggest that it is necessary to assess multiple fitness traits to evaluate how each gene contributes to anthelmintic resistance.

CaeNDR, the Caenorhabditis Natural Diversity Resource.

Studies of model organisms have provided important insights into how natural genetic differences shape trait variation. These discoveries are driven by the growing availability of genomes and the expansive experimental toolkits afforded to researchers using these species. For example, Caenorhabditis elegans is increasingly being used to identify and measure the effects of natural genetic variants on traits using quantitative genetics. Since 2016, the C. elegans Natural Diversity Resource (CeNDR) has facilitated many of these studies by providing an archive of wild strains, genome-wide sequence and variant data for each strain, and a genome-wide association (GWA) mapping portal for the C. elegans community. Here, we present an updated platform, the Caenorhabditis Natural Diversity Resource (CaeNDR), that enables quantitative genetics and genomics studies across the three Caenorhabditis species: C. elegans, C. briggsae and C. tropicalis. The CaeNDR platform hosts several databases that are continually updated by the addition of new strains, whole-genome sequence data and annotated variants. Additionally, CaeNDR provides new interactive tools to explore natural variation and enable GWA mappings. All CaeNDR data and tools are accessible through a freely available web portal located at caendr.org.

Novel and improved Caenorhabditis briggsae gene models generated by community curation.

BACKGROUND: The nematode Caenorhabditis briggsae has been used as a model in comparative genomics studies with Caenorhabditis elegans because of their striking morphological and behavioral similarities. However, the potential of C. briggsae for comparative studies is limited by the quality of its genome resources. The genome resources for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans. The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of software-derived gene predictions that contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 gene models and underlying transcriptomic data to repair software-derived errors. RESULTS: We designed a detailed workflow to train a team of nine students to manually curate gene models using RNA read alignments. We manually inspected the gene models, proposed corrections to the coding sequences of over 8,000 genes, and modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality and showed that manual curation led to substantial improvements in the protein sequence length accuracy of QX1410 genes. Additionally, collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. CONCLUSIONS: Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. Our manual curation efforts have brought the QX1410 gene models to a comparable level of quality as the extensively curated AF16 gene models. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.

Novel and improved Caenorhabditis briggsae gene models generated by community curation.

Background: The nematode Caenorhabditis briggsae has been used as a model for genomics studies compared to Caenorhabditis elegans because of its striking morphological and behavioral similarities. These studies yielded numerous findings that have expanded our understanding of nematode development and evolution. However, the potential of C. briggsae to study nematode biology is limited by the quality of its genome resources. The reference genome and gene models for the C. briggsae laboratory strain AF16 have not been developed to the same extent as C. elegans . The recent publication of a new chromosome-level reference genome for QX1410, a C. briggsae wild strain closely related to AF16, has provided the first step to bridge the gap between C. elegans and C. briggsae genome resources. Currently, the QX1410 gene models consist of protein-coding gene predictions generated from short- and long-read transcriptomic data. Because of the limitations of gene prediction software, the existing gene models for QX1410 contain numerous errors in their structure and coding sequences. In this study, a team of researchers manually inspected over 21,000 software-derived gene models and underlying transcriptomic data to improve the protein-coding gene models of the C. briggsae QX1410 genome. Results: We designed a detailed workflow to train a team of nine students to manually curate genes using RNA read alignments and predicted gene models. We manually inspected the gene models using the genome annotation editor, Apollo, and proposed corrections to the coding sequences of over 8,000 genes. Additionally, we modeled thousands of putative isoforms and untranslated regions. We exploited the conservation of protein sequence length between C. briggsae and C. elegans to quantify the improvement in protein-coding gene model quality before and after curation. Manual curation led to a substantial improvement in the protein sequence length accuracy of QX1410 genes. We also compared the curated QX1410 gene models against the existing AF16 gene models. The manual curation efforts yielded QX1410 gene models that are similar in quality to the extensively curated AF16 gene models in terms of protein-length accuracy and biological completeness scores. Collinear alignment analysis between the QX1410 and AF16 genomes revealed over 1,800 genes affected by spurious duplications and inversions in the AF16 genome that are now resolved in the QX1410 genome. Conclusions: Community-based, manual curation using transcriptome data is an effective approach to improve the quality of software-derived protein-coding genes. Comparative genomic analysis using a related species with high-quality reference genome(s) and gene models can be used to quantify improvements in gene model quality in a newly sequenced genome. The detailed protocols provided in this work can be useful for future large-scale manual curation projects in other species. The chromosome-level reference genome for the C. briggsae strain QX1410 far surpasses the quality of the genome of the laboratory strain AF16, and our manual curation efforts have brought the QX1410 gene models to a comparable level of quality to the previous reference, AF16. The improved genome resources for C. briggsae provide reliable tools for the study of Caenorhabditis biology and other related nematodes.

[Erythema induratum of Bazin as a reactivation of latent tuberculosis infection in a patient receiving anti-tumor necrosis factor treatment]. / Eritema indurado de Bazin como una reactivación de una tuberculosis latente en una paciente con tratamiento biológico anti-factor de necrosis tumoral.

Erythema induratum of Bazin is a rare form of cutaneous tuberculosis, considered as part of the spectrum of tuberculids or hipersensitivity reactions to Mycobacterium tuberculosis. Treatment with biologic agents is a known risk factor for tuberculosis reactivation, especially in areas of high incidence like Latin America, which is why screening and treatment protocols must be followed before these therapies are initiated. We present a case of erythema induratum of Bazin as a reactivation of latent tuberculosis infection in a patient with rheumatoid arthritis treated with golimumab.

Chromosome-Level Reference Genomes for Two Strains of Caenorhabditis briggsae: An Improved Platform for Comparative Genomics.

The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome-conformation capture data to generate chromosome-level reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.

Eritema indurado de Bazin como una reactivación de una tuberculosis latente en una paciente con tratamiento biológico anti-factor de necrosis tumoral / Erythema induratum of Bazin as a reactivation of latent tuberculosis infection in a patient receiving anti-tumor necrosis factor treatment

Resumen El eritema indurado de Bazin es una tuberculosis cutánea rara, considerada una tuberculide o reacción de hipersensibilidad a Mycobacterium tuberculosis. El tratamiento con agentes biológicos es un factor de riesgo conocido para la reactivación de tuberculosis, especialmente en áreas de alta incidencia como Latinoamérica, por lo que existen protocolos de búsqueda y tratamiento antes del inicio de este tipo de terapias. Se presenta un caso clínico de eritema indurado de Bazin como reactivación de una infección tuberculosa latente en una paciente con artritis reumatoide que recibía tratamiento con golimumab.

Abstract Erythema induratum of Bazin is a rare form of cutaneous tuberculosis, considered as part of the spectrum of tuberculids or hipersensitivity reactions to Mycobacterium tuberculosis. Treatment with biologic agents is a known risk factor for tuberculosis reactivation, especially in areas of high incidence like Latin America, which is why screening and treatment protocols must be followed before these therapies are initiated. We present a case of erythema induratum of Bazin as a reactivation of latent tuberculosis infection in a patient with rheumatoid arthritis treated with golimumab.

Selfing is the safest sex for Caenorhabditis tropicalis.

Mating systems have profound effects on genetic diversity and compatibility. The convergent evolution of self-fertilization in three Caenorhabditis species provides a powerful lens to examine causes and consequences of mating system transitions. Among the selfers, Caenorhabditis tropicalis is the least genetically diverse and most afflicted by outbreeding depression. We generated a chromosomal-scale genome for C. tropicalis and surveyed global diversity. Population structure is very strong, and islands of extreme divergence punctuate a genomic background that is highly homogeneous around the globe. Outbreeding depression in the laboratory is caused largely by multiple Medea-like elements, genetically consistent with maternal toxin/zygotic antidote systems. Loci with Medea activity harbor novel and duplicated genes, and their activity is modified by mito-nuclear background. Segregating Medea elements dramatically reduce fitness, and simulations show that selfing limits their spread. Frequent selfing in C. tropicalis may therefore be a strategy to avoid Medea-mediated outbreeding depression.

Relación entre el estado nutricional de niños de kínder y primero básico de dos colegios municipales de la Región del Maule y la percepción de sus padres sobre la Actividad Física y Hábitos Alimentarios / Relationship between the nutritional status of kindergarten and first grade children from two municipal schools in the Maule Region and their parents' perception of Physical Activity and Eating Habits

En el presente estudio se utilizaronlas recomendaciones de la Organización Mundial de la Salud para medir el estado nutricionalde alumnos(as) de kínder y primero básico de dos colegios municipales de la región del Maule, a través del índice de masa corporal. Tiene como propósito relacionarel estado nutricional con los hábitos alimenticios y la actividad física percibida por los padres. Se evaluaron a 87 alumnos de kínder y primero básico. Los resultados muestran que, en kínder, el sobrepeso y obesidad alcanzó un 76,2% y en primero básico un sobrepeso y obesidad del 70,6%,sin embargo, no se encontró mayor relación entre el conocimiento de los padres sobre la importancia de la actividad físicay loshábitos alimentarios en la vida de sus hijos y su estado nutricional. Los alumnos se encuentran en un estado nutricional de riesgo y la percepción de los padres es baja en cuantoa la influencia estos factores, relacionándose directamente con el mal estado nutricional que estos presentan

The present study used the recommendations of the World Health Organization to measure nutritional status, doing so through the body mass index. The purpose of the study is to relate the nutritional status of kindergarten and first grade students from two municipal schools in the Maule region with the eating habits and physical activity perceived by the parents. 87 kindergarten and first grade students were evaluated. The results show that in kindergarten overweight and obesity reached (76.2%) respectively, and in first grade an overweight and obesity of (70.6%), however, no greater relationship was found between knowledge of the parents of the importance of physical activity in the life of their children and their nutritional status as well as in the eating habits that they reported of their children in relation to nutritional status. Students are in a nutritional state of risk and the perception of parents is low in terms of the knowledge they have regarding the practice of physical activity and eating habits, being directly related to the poor nutritional status that they present

Caracterización de sífilis en embarazadas controladas en la unidad de atención y control en salud sexual del hospital San José (HSJ), Santiago de Chile (2010-2016) / Characterization of syphilis in controlled pregnant women in the sexual health care and control unit of hospital San José (HSJ), Santiago de Chile (2010-2016)

Introducción: La sífilis gestacional continúa sien-do un problema de salud pública en el mundo. Produce severos efectos adversos en la madre y en el feto de no ser tratada. En Chile, el Ministerio de Salud ha establecido un tamizaje para esta infección cada 3 meses en el embarazo y al momento del parto. Un tratamiento adecuado y oportuno es capaz de prevenir todos los efectos adversos de la sífilis en el embarazo. Métodos: Este fue un estudio transversal retrospectivo que incluyó a 406 embarazadas controladas en la Unidad de Atención y Control en Salud Sexual (UNACESS) del Hospital San José (HSJ) entre los años 2010-2016. Resultados: Los resultados del estudio fueron que un 87,7% de las embarazadas eran chilenas y un 12,3% de otras nacionalidades. Las nacionalidades más frecuentes para el grupo de extranjeras fueron: 54% peruanas y 18% haitianas. Al ingreso al estudio, 47,5% de las embarazadas se encontraban en el segundo trimestre de embarazo. De todas las participantes, un 38,7% se encontraba en riesgo de sífilis congénita. Discusión: En total, un 23% de las participantes presentó un falso positivo biológico, cifra similar a la reportada en otros estudios. En este estudio encontramos que, en gestantes extranjeras, había mayor proporción de diagnóstico tardío en que chilenas. Esto podría deberse a dificultades para ingresar a la atención en salud. Conclusión: Pese a que en Chile contamos con buenas tasas de diagnóstico, el manejo de la sífilis gestacional podría ser mejorado con una detección y tratamiento temprano. Las extranjeras buscaron atención en salud más tarde que las chilenas, por lo tanto, recibieron tratamiento más tardío y con mayor riesgo de sífilis congénita. Esto se puede explicar por dificultades para ingresar al sistema de salud.

Introduction: Syphilis in pregnancy remains a global public health problem with severe outcomes if it is not treated properly. The Chilean Ministry of Health has established syphilis screening at three times during pregnancy, with a final retest is during labor. An adequate treatment can prevent all side effects of syphilis in pregnancy. Methods: This was a descriptive, transversal study which included 406 pregnant women who consulted for potential syphilis at the Control and Treatment of Sexual Health Unit (UNACESS in Spanish) of San José Hospital (HSJ) in Santiago, Chile from 2010 to 2016.Results: A 87,7% of the pregnant women were Chilean, while 12,3% had a different nationality. Among immigrants, the most frequent nationalities were: peruvian 54% and Haitian 18%. At enrol-ment, 47,5% of the pregnant women were in their second trimester. 38,4% was at risk of congenital syphilis.Discussion: Overall, 23,1% of the participants had a false positive test, which is congruent with pre-viously reported data. In this study, we found a higher rate of late diagnosis, mainly in the immigrant pregnant women, which could be due to difficulties in accessing healthcare and cultural matters. Conclusion: Despite a high overall treatment rate, antenatal syphilis management in this population could be improved by earlier detection and treatment. Immigrant women sought attention later in pregnancy, thus receiving delayed treatment with higher risk of congenital syphilis. This could be explained by obstacles in their access to healthcare.

2-(Aminomethyl)phenyl complexes of Au(III), mixed Au(III)/Ag(I), and Pd(II) with the 2,2-diacetyl-1,1-ethylenedithiolato ligand: dancing of palladacycles around a juggler ligand.

The reaction of [Tl(2){mu-S,S-S(2)C=C{C(O)Me}(2)}] with [Au(C,N-C(6)H(4)CH(2)NMe(2)-2)Cl(2)] (1:1) gives [{Au(C,N-C(6)H(4)CH(2)NMe(2)-2)}{S,S-S(2)C=C{C(O)Me}(2)}] (1) which, in turn, reacts with AgClO(4) (1:1) to give [{Au(C,N-C(6)H(4)CH(2)NMe(2)-2)}{Ag(OClO(3))}{S(2)C=C{C(O)Me}(2)}] (2). Complexes [{Au(C,N-C(6)H(4)CH(2)NMe(2)-2)}{Ag(X)(PPh(3))}{S(2)C=C{C(O)Me}(2)}] [X = OClO(3) (3), ONO(2) (4)] have been obtained by reaction of 1 with PPh(3) and AgClO(4) or AgNO(3), respectively (1:1:1). Complex 3 can also be obtained by reacting 2 with PPh(3) (1:1). Complexes [Pd(C,N-C(6)H(4)CH(2)NR(2)-2)(mu-Cl)](2) (R = Me, H) react (i) with [Tl(2){S(2)C=C{C(O)Me}(2)}] and [PPN]Cl (0.5:1:1, PPN = Ph(3)P=N=PPh(3)) to form PPN[Pd(C,N-C(6)H(4)CH(2)NR(2)-2){S,S-S(2)C=C{C(O)Me}(2)}] [R = H (5a), Me (5b)], or (ii) with [Tl(2){S(2)C=C{C(O)Me}(2)}] (1:1) to form [{Pd(C,N-C(6)H(4)CH(2)NR(2)-2)}(2){mu-S,S,O-S(2)C=C{C(O)Me}(2)}] [R = H (6a), Me (6b)]. The trinuclear complexes [{Pd(C,N-C(6)H(4)CH(2)NR(2)-2)}(3){mu(3)-O,S,S,O-S(2)C=C{C(O)Me}(2)}]ClO(4) [R = H (7a), Me (7b)] can be prepared by reacting the corresponding dinuclear complex 6a or 6b with [Pd(C,N-C(6)H(4)CH(2)NR(2)-2)(NCMe)(2)]ClO(4) (1:1). The crystal structures of 1, 6b x CH(2)Cl(2), and 7b x CH(2)Cl(2) have been determined. NMR studies have been carried out to explain the solution behavior of these complexes. VT-NMR and line shape analysis for the species where R = Me (5b, 6b, 7b) have allowed the estimation of the activation parameters for these exchange processes.