Polysensitisation is associated with more severe symptoms: The reality of patients with allergy.

BACKGROUND: Studying the sensitisation profiles of patients with allergies allows for a deeper understanding of the disease which may facilitate the selection of the best-personalised allergen immunotherapy. This observational, cross-sectional, multicentre study aimed to demonstrate the heterogeneity of the German population with allergies by analysing specific immunoglobulin E (sIgE) patterns towards aeroallergens and exploring the relationship between sensitisation and clinical symptoms. METHODS: In total, 500 patients with allergies from different regions of Germany were recruited based on their case histories, clinical allergic symptoms and skin prick test data for aeroallergens. Serum samples were analysed using ImmunoCAP assays to determine sIgE levels for 33 allergenic sources and 43 molecular allergens. RESULTS: Most patients (81%) were polysensitised. Betula verrucosa pollen was the most common cause of sensitisation (59%), followed by Phleum pratense (58%) and Dermatophagoides pteronyssinus (44%). The highest prevalence rates of molecular allergens were observed for Bet v 1 (84%) from birch pollen, Phl p 1 from grass pollen (82%), Der p 2 (69%) from mites and Fel d 1 (69%) from cat. Polysensitisation was significantly associated with the presence of asthma and the severity of rhinitis symptoms. CONCLUSIONS: Our findings show a high rate of polysensitisation and emphasise the importance of molecular diagnosis for more precise and comprehensive insights into sensitisation patterns and their association with clinical symptoms. These data may help improve personalised diagnosis and immunotherapy adapted to the needs of individual patients in the region.

Datasets of Iso-Seq transcripts for decoding transcriptome complexity in four Leishmania species.

The Iso-Seq technology, based on PacBio sequencing, enables the generation of high-quality, full-length transcripts, providing insights into transcriptome complexity. In this study, total RNA from promastigotes of four Leishmania species (Leishmania braziliensis, Leishmania donovani, Leishmania infantum and Leishmania major) was sequenced using Single Molecule, Real-Time (SMRT) Sequencing (PacBio) methodology. The Iso-seq transcripts were categorized as either complete or truncated according to the presence or absence of the Spliced-Leader (SL) sequence at their 5'-end, respectively. Moreover, only transcripts having a poly-A+ at their 3'-end were considered. Supplied datasets represent valuable information that may help to uncover novel transcripts and alternative splicing events in a parasite that regulates its gene expression at the post-transcriptional level. A better knowledge of gene expression regulation in Leishmania will open avenues for the development of new drugs to treat leishmaniasis, a devastating disease that has worldwide distribution. Additionally, the bioinformatics pipeline followed here may guide the analysis of Iso-Seq data derived from related trypanosomatids like Trypanosoma cruzi (Chagas disease agent) and Trypanosoma brucei (sleeping disease). © 2023 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Refinement of Leishmania donovani Genome Annotations in the Light of Ribosome-Protected mRNAs Fragments (Ribo-Seq Data).

Advances in next-generation sequencing methodologies have facilitated the assembly of an ever-increasing number of genomes. Gene annotations are typically conducted via specialized software, but the most accurate results require additional manual curation that incorporates insights derived from functional and bioinformatic analyses (e.g., transcriptomics, proteomics, and phylogenetics). In this study, we improved the annotation of the Leishmania donovani (strain HU3) genome using publicly available data from the deep sequencing of ribosome-protected mRNA fragments (Ribo-Seq). As a result of this analysis, we uncovered 70 previously non-annotated protein-coding genes and improved the annotation of around 600 genes. Additionally, we present evidence for small upstream open reading frames (uORFs) in a significant number of transcripts, indicating their potential role in the translational regulation of gene expression. The bioinformatics pipelines developed for these analyses can be used to improve the genome annotations of other organisms for which Ribo-Seq data are available. The improvements provided by these studies will bring us closer to the ultimate goal of a complete and accurately annotated L. donovani genome and will enhance future transcriptomics, proteomics, and genetics studies.

Cognitive decline in diabetic mice predisposed to Alzheimer's disease is greater than in wild type.

In this work, we tested the hypothesis that the development of dementia in individuals with type 2 diabetes (T2DM) requires a genetic background of predisposition to neurodegenerative disease. As a proof of concept, we induced T2DM in middle-aged hAPP NL/F mice, a preclinical model of Alzheimer's disease. We show that T2DM produces more severe behavioral, electrophysiological, and structural alterations in these mice compared with wild-type mice. Mechanistically, the deficits are not paralleled by higher levels of toxic forms of Aß or by neuroinflammation but by a reduction in γ-secretase activity, lower levels of synaptic proteins, and by increased phosphorylation of tau. RNA-seq analysis of the cerebral cortex of hAPP NL/F and wild-type mice suggests that the former could be more susceptible to T2DM because of defects in trans-membrane transport. The results of this work, on the one hand, confirm the importance of the genetic background in the severity of the cognitive disorders in individuals with T2DM and, on the other hand, suggest, among the involved mechanisms, the inhibition of γ-secretase activity.

Frequencies of variants in genes associated with dyslipidemias identified in Costa Rican genomes.

Dyslipidemias are risk factors in diseases of significant importance to public health, such as atherosclerosis, a condition that contributes to the development of cardiovascular disease. Unhealthy lifestyles, the pre-existence of diseases, and the accumulation of genetic variants in some loci contribute to the development of dyslipidemia. The genetic causality behind these diseases has been studied primarily on populations with extensive European ancestry. Only some studies have explored this topic in Costa Rica, and none have focused on identifying variants that can alter blood lipid levels and quantifying their frequency. To fill this gap, this study focused on identifying variants in 69 genes involved in lipid metabolism using genomes from two studies in Costa Rica. We contrasted the allelic frequencies with those of groups reported in the 1000 Genomes Project and gnomAD and identified potential variants that could influence the development of dyslipidemias. In total, we detected 2,600 variants in the evaluated regions. However, after various filtering steps, we obtained 18 variants that have the potential to alter the function of 16 genes, nine variants have pharmacogenomic or protective implications, eight have high risk in Variant Effect Predictor, and eight were found in other Latin American genetic studies of lipid alterations and the development of dyslipidemia. Some of these variants have been linked to changes in blood lipid levels in other global studies and databases. In future studies, we propose to confirm at least 40 variants of interest from 23 genes in a larger cohort from Costa Rica and Latin American populations to determine their relevance regarding the genetic burden for dyslipidemia. Additionally, more complex studies should arise that include diverse clinical, environmental, and genetic data from patients and controls and functional validation of the variants.

Leishmania infantum (JPCM5) Transcriptome, Gene Models and Resources for an Active Curation of Gene Annotations.

Leishmania infantum is one of the causative agents of visceral leishmaniases, the most severe form of leishmaniasis. An improved assembly for the L. infantum genome was published five years ago, yet delineation of its transcriptome remained to be accomplished. In this work, the transcriptome annotation was attained by a combination of both short and long RNA-seq reads. The good agreement between the results derived from both methodologies confirmed that transcript assembly based on Illumina RNA-seq and further delimitation according to the positions of spliced leader (SAS) and poly-A (PAS) addition sites is an adequate strategy to annotate the transcriptomes of Leishmania, a procedure previously used for transcriptome annotation in other Leishmania species and related trypanosomatids. These analyses also confirmed that the Leishmania transcripts boundaries are relatively slippery, showing extensive heterogeneity at the 5'- and 3'-ends. However, the use of RNA-seq reads derived from the PacBio technology (referred to as Iso-Seq) allowed the authors to uncover some complex transcription patterns occurring at particular loci that would be unnoticed by the use of short RNA-seq reads alone. Thus, Iso-Seq analysis provided evidence that transcript processing at particular loci would be more dynamic than expected. Another noticeable finding was the observation of a case of allelic heterozygosity based on the existence of chimeric Iso-Seq reads that might be generated by an event of intrachromosomal recombination. In addition, we are providing the L. infantum gene models, including both UTRs and CDS regions, that would be helpful for undertaking whole-genome expression studies. Moreover, we have built the foundations of a communal database for the active curation of both gene/transcript models and functional annotations for genes and proteins.

Gingival state and presence of red complex bacteria in 12-Year-Old schoolchildren / Estado gingival y presencia de bacterias del complejo rojo en escolares de 12 años

Abstract The objective of this study was to determine the gingival state and presence of red complex bacteria in saliva samples of 12-year-old schoolchildren. A calibrated periodontist evaluated biofilm index (BI) (Silness and Löe, 1964), presence of calculus, and gingival index (GI) (Silness and Löe, 1967) in sixty two 12-year-old students of Carmen Lyra School. Saliva samples were collected from each student. The DNA of each sample was extracted and amplified by the polymerase chain reaction (PCR) technique, using specific primers. The BI was 1.18. Calculus was present in 40.40% of the schoolchildren examined; 19.4% was supragingival calculus and 21% both supragingival and subgingival calculus. The GI was 0.97, which according to Silness and Löe is mild gingivitis. Gingivitis was present in 96.8% of the children examined. Regarding the PCR tests: 18 of the samples (31.58%) did not present any of the bacteria analyzed and the remaining 39 samples (68.42%) were positive for at least the presence of red complex bacteria. Within the limitations of this study, it is concluded that the prevalence of gingivitis and calculus is high in the sample examined, and the gingival state observed in the study population, may be related to the presence of red complex bacteria.

Resumen El objetivo de este estudio era determinar el estado gingival y la presencia de bacterias del complejo rojo en muestras de saliva de niños de 12 años de la Escuela Carmen Lyra. Una periodoncista calibrada evaluó en 62 estudiantes de 12 años de la Escuela Carmen Lyra, el índice de biofilme (IB) (Silness y Löe, 1964), la presencia de cálculo y el índice gingival (IG) (Silness y Löe, 1967). Se recolectaron muestras de saliva de cada estudiante. El ADN de cada muestra fue extraído y amplificado por medio de la prueba PCR, empleando primers específicos, para determinar la presencia de bacterias del complejo rojo. El IB fue de 1.18. El cálculo estuvo presente en el 40.40% de la muestra, se encontró 19.4% de cálculo en supragingival y 21% tanto en supragingival como en subgingival. El IG fue de 0.97, que de acuerdo con Silness y Löe es una gingivitis leve. La gingivitis estuvo presente en el 96.8 % de los niños examinados. Con respecto a las pruebas PCR: 18 de las muestras (31.58 %) no presentaron ninguna de las bacterias analizadas y las 39 muestras restantes (68.42%) fueron positivas por lo menos a la presencia de las bacterias del complejo rojo. Dentro de las limitaciones de este estudio, se concluye que la prevalencia de gingivitis y cálculo es alta en la muestra examinada y el estado gingival observado puede estar relacionado con la presencia de bacterias del complejo rojo.

Hematological reference values for Alouatta palliata (Primates: Atelidae) and Cebus imitator (Primates: Cebidae) from the Pacific Coast of Costa Rica / Valores de referencia hematológicos para Alouatta palliata (Primates: Atelidae) y Cebus imitator (Primates: Cebidae) de la costa Pacífica de Costa Rica

Abstract Introduction: Wildlife hematological patterns are fundamental for health monitoring, and allows elucidating variations both within and between populations. Among these, hematological parameters are particularly valuable to evaluate the health status of neotropical primate species in the wild. Objective: To define hematological reference values for two species of monkeys in Costa Rica. Methods: During 2014, we collected blood samples from free-ranging mantled howler monkeys, Alouatta palliata (17 females, 18 males) and white-faced capuchin monkeys, Cebus imitator (5 females, 7 males) in seven localities of the Costa Rican Pacific coast. Results: For both species, the hematological values were higher in males, and howler monkey populations differed significantly except for platelets. Conclusions: These hematological values, which differ by sex and locality, will help evaluate the health status of these neotropical primate populations.

Resumen Introducción: Los patrones hematológicos de la vida silvestre son fundamentales para el monitoreo de la salud y permiten dilucidar las variaciones tanto dentro como entre poblaciones. Entre estos, los parámetros hematológicos son particularmente valiosos para evaluar el estado de salud de las especies de primates neotropicales en la naturaleza. Objetivo: Definir valores de referencia hematológicos para dos especies de monos en Costa Rica. Métodos: Durante el 2014 recolectamos muestras de sangre de monos aulladores de manto, Alouatta palliata (17 hembras, 18 machos) y monos capuchinos cariblancos, Cebus imitador (5 hembras, 7 machos) en siete localidades de la costa Pacífica de Costa Rica. Resultados: Para ambas especies, los valores hematológicos fueron mayores en los machos, y las poblaciones de monos aulladores difirieron significativamente con excepción de las plaquetas. Conclusiones: Estos valores hematológicos, que difieren según el sexo y la localidad, ayudarán a evaluar el estado de salud de estas poblaciones de primates neotropicales.

Vitamin D Treatment Prevents Uremia-Induced Reductions in Aortic microRNA-145 Attenuating Osteogenic Differentiation despite Hyperphosphatemia.

In chronic kidney disease, systemic inflammation and high serum phosphate (P) promote the de-differentiation of vascular smooth muscle cells (VSMC) to osteoblast-like cells, increasing the propensity for medial calcification and cardiovascular mortality. Vascular microRNA-145 (miR-145) content is essential to maintain VSMC contractile phenotype. Because vitamin D induces aortic miR-145, uremia and high serum P reduce it and miR-145 directly targets osteogenic osterix in osteoblasts, this study evaluated a potential causal link between vascular miR-145 reductions and osterix-driven osteogenic differentiation and its counter-regulation by vitamin D. Studies in aortic rings from normal rats and in the rat aortic VSMC line A7r5 exposed to calcifying conditions corroborated that miR-145 reductions were associated with decreases in contractile markers and increases in osteogenic differentiation and calcium (Ca) deposition. Furthermore, miR-145 silencing enhanced Ca deposition in A7r5 cells exposed to calcifying conditions, while miR-145 overexpression attenuated it, partly through increasing α-actin levels and reducing osterix-driven osteogenic differentiation. In mice, 14 weeks after the induction of renal mass reduction, both aortic miR-145 and α-actin mRNA decreased by 80% without significant elevations in osterix or Ca deposition. Vitamin D treatment from week 8 to 14 fully prevented the reductions in aortic miR-145 and attenuated by 50% the decreases in α-actin, despite uremia-induced hyperphosphatemia. In conclusion, vitamin D was able to prevent the reductions in aortic miR-145 and α-actin content induced by uremia, reducing the alterations in vascular contractility and osteogenic differentiation despite hyperphosphatemia.

Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain.

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

¿Es la proteína C reactiva un indicador de riesgo periodontal? / Is C Reactive Protein a Risk Indicator for Periodontal Disease?

RESUMEN: La periodontitis es una enfermedad inflamatoria crónica, multifactorial, causada por microorganismos y caracterizada por la destrucción progresiva del tejido de soporte dental. En los últimos años se han realizado estudios que señalan cierta similitud y asociación entre la periodontitis y la enfermedad cardiovascular aterosclerótica. Esta relación se ha establecido por tener ciertos factores de riesgo en común y por producir incremento plasmático de la proteína C reactiva (P-CR). A esta proteína se le atribuyen características favorables como marcador inflamatorio. Este estudio busca establecer si existe algún tipo de relación, entre la periodontitis y los valores de la P-CR antes de iniciar el tratamiento periodontal, en un grupo de pacientes de la Facultad de Odontología de la Universidad de Costa Rica. Se hicieron exámenes periodontales a 30 pacientes y se obtuvo una muestra de sangre de cada uno para determinar la concentración de P-CR. Con respecto al valor de la P-CR, se encontró que el promedio fue de 3.72mg/L (IC95%: 2.06-5.38), lo que constituye un marcador de riesgo de moderado a severo. El 54% de los pacientes presentó enfermedad periodontal crónica generalizada, sin que se encontrara diferencia estadísticamente significativa por sexo (p=0.416), ni edad (p=0.477). El 43% de los pacientes padecía de enfermedad periodontal crónica localizada y el 3% de los pacientes presentaron gingivitis. Se observó que el género femenino mostró relativamente, un mayor riesgo cardiovascular respecto al género opuesto (p=0.640). No se encontró diferencia estadísticamente significativa en el valor de P-CR por sexo, edad o la presencia de otras enfermedades, aunque esta cifra fue mayor en los que presentaron enfermedades metabólicas (5.5mg/L) con respecto a quienes no las padecían (2.7mg/L).

ABSTRACT: Periodontitis is an inflammatory multifactorial chronic disease, caused by microorganisms that destroys periodontal tissues. In the last years, several studies have described an association between periodontitis and atherosclerotic cardiovascular disease. This relationship has been made since both diseases share the same risk factors and they both increase C reactive proteins levels. C-reactive protein (C-RP) is a well-known inflammatory marker. This study was designed to try to stablish the relationship between C-RP levels and periodontitis in a group of patients that need periodontal treatment at Odontology Faculty in Universidad de Costa Rica. Periodontal examinations were done to 30 patients and blood samples were taken. The mean value of C-RP found was 3.72mg/L (IC95%: 2.06-5.38) which represents a medium- high risk level. 54% of the patients had generalized chronic periodontitis, without statistical difference when compared gender (p=0.416) or age (p=0.477). 43% had chronic localized periodontitis and 3% gingivitis. Females showed a higher risk for cardiovascular disease (p=0.640). No statistical differences were found between C-RP values relating gender, age or other comorbilities, even though mean values were always higher in those suffering metabolic diseases (5.5mg/L) compared to those values from patients not suffering the same diseases (2.7mg/L).

Spinal Muscular Atrophy autophagy profile is tissue-dependent: differential regulation between muscle and motoneurons.

Spinal muscular atrophy (SMA) is a neuromuscular genetic disease caused by reduced survival motor neuron (SMN) protein. SMN is ubiquitous and deficient levels cause spinal cord motoneurons (MNs) degeneration and muscle atrophy. Nevertheless, the mechanism by which SMN reduction in muscle contributes to SMA disease is not fully understood. Therefore, studies evaluating atrophy mechanisms in SMA muscles will contribute to strengthening current knowledge of the pathology. Here we propose to evaluate autophagy in SMA muscle, a pathway altered in myotube atrophy. We analized autophagy proteins and mTOR in muscle biopsies, fibroblasts, and lymphoblast cell lines from SMA patients and in gastrocnemius muscles from a severe SMA mouse model. Human MNs differentiated from SMA and unaffected control iPSCs were also included in the analysis of the autophagy. Muscle biopsies, fibroblasts, and lymphoblast cell lines from SMA patients showed reduction of the autophagy marker LC3-II. In SMA mouse gastrocnemius, we observed lower levels of LC3-II, Beclin 1, and p62/SQSTM1 proteins at pre-symptomatic stage. mTOR phosphorylation at Ser2448 was decreased in SMA muscle cells. However, in mouse and human cultured SMA MNs mTOR phosphorylation and LC3-II levels were increased. These results suggest a differential regulation in SMA of the autophagy process in muscle cells and MNs. Opposite changes in autophagy proteins and mTOR phosphorylation between muscle cells and neurons were observed. These differences may reflect a specific response to SMN reduction, which could imply diverse tissue-dependent reactions to therapies that should be taken into account when treating SMA patients.

Intracellular pathways involved in cell survival are deregulated in mouse and human spinal muscular atrophy motoneurons.

Spinal Muscular Atrophy (SMA) is a severe neuromuscular disorder caused by loss of the Survival Motor Neuron 1 gene (SMN1). Due to this depletion of the survival motor neuron (SMN) protein, the disease is characterized by the degeneration of spinal cord motoneurons (MNs), progressive muscular atrophy, and weakness. Nevertheless, the ultimate cellular and molecular mechanisms leading to cell loss in SMN-reduced MNs are only partially known. We have investigated the activation of apoptotic and neuronal survival pathways in several models of SMA cells. Even though the antiapoptotic proteins FAIM-L and XIAP were increased in SMA MNs, the apoptosis executioner cleaved-caspase-3 was also elevated in these cells, suggesting the activation of the apoptosis process. Analysis of the survival pathway PI3K/Akt showed that Akt phosphorylation was reduced in SMA MNs and pharmacological inhibition of PI3K diminished SMN and Gemin2 at transcriptional level in control MNs. In contrast, ERK phosphorylation was increased in cultured mouse and human SMA MNs. Our observations suggest that apoptosis is activated in SMA MNs and that Akt phosphorylation reduction may control cell degeneration, thereby regulating the transcription of Smn and other genes related to SMN function.

Integrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus.

Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended "donor" strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation.

Estimación del rendimiento máximo sostenible del recurso tiburón-cazón en México / Estimation of maximum sustainable yield of the shark resource from Mexico

Resumen En México, la captura del recurso pesquero tiburón-cazón (RTC) ocupa el décimo lugar de las 22 pesquerías más representativas del país, con un volumen anual promedio estimado en 29 772 T, y una derrama económica de 437 millones de pesos mexicanos. La captura máxima que se puede obtener sin agotar el recurso en ningún plazo, se denomina rendimiento máximo sostenible (RMS), y es uno de los principales puntos de referencia en la evaluación de pesquerías. El objetivo del presente estudio fue estimar el rendimiento máximo sostenible del recurso pesquero tiburón-cazón, agrupándolo en 26 regiones (México, océano Pacífico, golfo de México, 6 regiones de la NOM-029-PESC-2006 y 17 estados costeros). Se utilizaron series de tiempo de captura (STC), en toneladas por año de captura reportada (Cr) y captura total (Ct) (captura reportada + captura no reportada) del periodo de 1976 a 2014, y se aplicaron modelos empíricos que relacionan la captura máxima de la STC con el RMS. No hubo diferencias significativas entre los modelos. Con base en la Ct y el RMS estimados (T x 103) se evidencia una sobreexplotación del RTC en México (Ct = 51 417, RMS = 29 040), en el océano Pacífico (Ct = 38 654, RMS = 20 840) y en el golfo de México (Ct = 15 737, RMS = 14 540); en la Región 2 (golfo de California) (Ct = 22 664, RMS = 14 330) y Región 5 (línea costera de Tamaulipas, Veracruz y Tabasco) (Ct = 9 202, RMS = 8 510), y en la costa de los estados de Baja California (Ct = 5 781, RMS = 4 880) y Baja California Sur (Ct = 5 950, RMS = 5 510). Es necesario atender de forma urgente la problemática del aprovechamiento de este recurso pesquero en la república mexicana.

Abstract In Mexico, shark catch ranks 10th place out of the 22 most representative fisheries in the country, with an estimated annual average number of 29 772 T and an economic income of approximately MXN 437 million. The maximum sustainable yield (MSY), which means the maximum catch that can be obtained without the depletion of the fishing resource at any given time is one of the main points of reference in the evaluation of fisheries. In this study, the MSY of sharks in Mexico was estimated for 26 coastal areas (Mexico, Pacific ocean, gulf of Mexico, 6 regions of the NOM-029-PESC-2006 and 17 coastal States). Catch time series (CTS) were used in tons per year of reported catch (Rc) and total catch (Tc) (reported catch + non-reported catch) over the 1976 to 2014 period. In addition, empirical models that relate the maximum catch of the STM to the MSY were applied. There were no significant differences between the models applied. Based on the estimated Tc and MSY (T x 103) there is an over-exploitation of sharks in Mexico (Tc = 51 417, MSY = 29 040), in the Pacific ocean (Tc = 38 654, MSY = 20 840) and in the gulf of Mexico (Tc = 15 737, MSY = 14 540); in Regions 2 (gulf of California) (Tc = 22 664, MSY = 14 330) and 5 (coastal line of Tamaulipas, Veracruz and Tabasco) (Tc = 9 202, MSY = 8 510) and on the coast of the States of Baja California (Tc = 5 781, MSY = 4 880) and Baja California Sur (Tc = 5 950, MSY = 5 510). It is recommended to urgently address the problem of using this fishery resource in the Mexican Republic.

The Experimental Proteome of Leishmania infantum Promastigote and Its Usefulness for Improving Gene Annotations.

Leishmania infantum causes visceral leishmaniasis (kala-azar), the most severe form of leishmaniasis, which is lethal if untreated. A few years ago, the re-sequencing and de novo assembling of the L. infantum (JPCM5 strain) genome was accomplished, and now we aimed to describe and characterize the experimental proteome of this species. In this work, we performed a proteomic analysis from axenic cultured promastigotes and carried out a detailed comparison with other Leishmania experimental proteomes published to date. We identified 2352 proteins based on a search of mass spectrometry data against a database built from the six-frame translated genome sequence of L. infantum. We detected many proteins belonging to organelles such as glycosomes, mitochondria, or flagellum, as well as many metabolic enzymes and many putative RNA binding proteins and molecular chaperones. Moreover, we listed some proteins presenting post-translational modifications, such as phosphorylations, acetylations, and methylations. On the other hand, the identification of peptides mapping to genomic regions previously annotated as non-coding allowed for the correction of annotations, leading to the N-terminal extension of protein sequences and the uncovering of eight novel protein-coding genes. The alliance of proteomics, genomics, and transcriptomics has resulted in a powerful combination for improving the annotation of the L. infantum reference genome.

Calpain system is altered in survival motor neuron-reduced cells from in vitro and in vivo spinal muscular atrophy models.

Spinal muscular atrophy (SMA) is a severe neuromuscular disorder caused by loss of the survival motor neuron 1 (SMN1) gene. SMA is characterized by the degeneration of spinal cord motoneurons (MNs), progressive skeletal muscle atrophy, and weakness. The cellular and molecular mechanisms causing MN loss of function are only partially known. Recent advances in SMA research postulate the role of calpain protease regulating survival motor neuron (SMN) protein and the positive effect on SMA phenotype of treatment with calpain inhibitors. We analyzed the level of calpain pathway members in mice and human cellular SMA models. Results indicate an increase of calpain activity in SMN-reduced MNs. Spinal cord analysis of SMA mice treated with calpeptin, a calpain inhibitor, showed an increase of SMN, calpain, and its endogenous inhibitor calpastatin in MNs. Finally, in vitro calpeptin treatment prevented microtubule-associated protein 1A/1B-light chain 3 (LC3) increase in MNs neurites, indicating that calpain inhibition may reduce autophagosome accumulation in neuron prolongations, but not in soma. Thus, our results show that calpain activity is increased in SMA MNs and its inhibition may have a beneficial effect on SMA phenotype through the increase of SMN in spinal cord MNs.

Leishmania Mitochondrial Genomes: Maxicircle Structure and Heterogeneity of Minicircles.

The mitochondrial DNA (mtDNA), which is present in almost all eukaryotic organisms, is a useful marker for phylogenetic studies due to its relative high conservation and its inheritance manner. In Leishmania and other trypanosomatids, the mtDNA (also referred to as kinetoplast DNA or kDNA) is composed of thousands of minicircles and a few maxicircles, catenated together into a complex network. Maxicircles are functionally similar to other eukaryotic mtDNAs, whereas minicircles are involved in RNA editing of some maxicircle-encoded transcripts. Next-generation sequencing (NGS) is increasingly used for assembling nuclear genomes and, currently, a large number of genomic sequences are available. However, most of the time, the mitochondrial genome is ignored in the genome assembly processes. The aim of this study was to develop a pipeline to assemble Leishmania minicircles and maxicircle DNA molecules, exploiting the raw data generated in the NGS projects. As a result, the maxicircle molecules and the plethora of minicircle classes for Leishmania major, Leishmania infantum and Leishmania braziliensis have been characterized. We have observed that whereas the heterogeneity of minicircle sequences existing in a single cell hampers their use for Leishmania typing and classification, maxicircles emerge as an extremely robust genetic marker for taxonomic studies within the clade of kinetoplastids.

Complete assembly of the Leishmania donovani (HU3 strain) genome and transcriptome annotation.

Leishmania donovani is a unicellular parasite that causes visceral leishmaniasis, a fatal disease in humans. In this study, a complete assembly of the genome of L. donovani is provided. Apart from being the first published genome of this strain (HU3), this constitutes the best assembly for an L. donovani genome attained to date. The use of a combination of sequencing platforms enabled to assemble, without any sequence gap, the 36 chromosomes for this species. Additionally, based on this assembly and using RNA-seq reads derived from poly-A + RNA, the transcriptome for this species, not yet available, was delineated. Alternative SL addition sites and heterogeneity in the poly-A addition sites were commonly observed for most of the genes. After a complete annotation of the transcriptome, 2,410 novel transcripts were defined. Additionally, the relative expression for all transcripts present in the promastigote stage was determined. Events of cis-splicing have been documented to occur during the maturation of the transcripts derived from genes LDHU3_07.0430 and LDHU3_29.3990. The complete genome assembly and the availability of the gene models (including annotation of untranslated regions) are important pieces to understand how differential gene expression occurs in this pathogen, and to decipher phenotypic peculiarities like tissue tropism, clinical disease, and drug susceptibility.

Into the Thermus Mobilome: Presence, Diversity and Recent Activities of Insertion Sequences Across Thermus spp.

A high level of transposon-mediated genome rearrangement is a common trait among microorganisms isolated from thermal environments, probably contributing to the extraordinary genomic plasticity and horizontal gene transfer (HGT) observed in these habitats. In this work, active and inactive insertion sequences (ISs) spanning the sequenced members of the genus Thermus were characterized, with special emphasis on three T. thermophilus strains: HB27, HB8, and NAR1. A large number of full ISs and fragments derived from different IS families were found, concentrating within megaplasmids present in most isolates. Potentially active ISs were identified through analysis of transposase integrity, and domestication-related transposition events of ISTth7 were identified in laboratory-adapted HB27 derivatives. Many partial copies of ISs appeared throughout the genome, which may serve as specific targets for homologous recombination contributing to genome rearrangement. Moreover, recruitment of IS1000 32 bp segments as spacers for CRISPR sequence was identified, pointing to the adaptability of these elements in the biology of these thermophiles. Further knowledge about the activity and functional diversity of ISs in this genus may contribute to the generation of engineered transposons as new genetic tools, and enrich our understanding of the outstanding plasticity shown by these thermophiles.