Predicting Risk of Ammonia Exposure in Broiler Housing: Correlation with Incidence of Health Issues.

The study aimed to forecast ammonia exposure risk in broiler chicken production, correlating it with health injuries using machine learning. Two chicken breeds, fast-growing (Ross®) and slow-growing (Hubbard®), were compared at different densities. Slow-growing birds had a constant density of 32 kg m-2, while fast-growing birds had low (16 kg m-2) and high (32 kg m-2) densities. Initial feeding was uniform, but nutritional demands led to varied diets later. Environmental data underwent selection, pre-processing, transformation, mining, analysis, and interpretation. Classification algorithms (decision tree, SMO, Naive Bayes, and Multilayer Perceptron) were employed for predicting ammonia risk (10-14 pmm, Moderate risk). Cross-validation was used for model parameterization. The Spearman correlation coefficient assessed the link between predicted ammonia risk and health injuries, such as pododermatitis, vision/affected, and mucosal injuries. These injuries encompassed trachea, bronchi, lungs, eyes, paws, and other issues. The Multilayer Perceptron model emerged as the best predictor, exceeding 98% accuracy in forecasting injuries caused by ammonia. The correlation coefficient demonstrated a strong association between elevated ammonia risks and chicken injuries. Birds exposed to higher ammonia concentrations exhibited a more robust correlation. In conclusion, the study effectively used machine learning to predict ammonia exposure risk and correlated it with health injuries in broiler chickens. The Multilayer Perceptron model demonstrated superior accuracy in forecasting injuries related to ammonia (10-14 pmm, Moderate risk). The findings underscored the significant association between increased ammonia exposure risks and the incidence of health injuries in broiler chicken production, shedding light on the importance of managing ammonia levels for bird welfare.

Nuclear-capture of endosomes depletes nuclear G-actin to promote SRF/MRTF activation and cancer cell invasion.

Signals are relayed from receptor tyrosine kinases (RTKs) at the cell surface to effector systems in the cytoplasm and nucleus, and coordination of this process is important for the execution of migratory phenotypes, such as cell scattering and invasion. The endosomal system influences how RTK signalling is coded, but the ways in which it transmits these signals to the nucleus to influence gene expression are not yet clear. Here we show that hepatocyte growth factor, an activator of MET (an RTK), promotes Rab17- and clathrin-dependent endocytosis of EphA2, another RTK, followed by centripetal transport of EphA2-positive endosomes. EphA2 then mediates physical capture of endosomes on the outer surface of the nucleus; a process involving interaction between the nuclear import machinery and a nuclear localisation sequence in EphA2's cytodomain. Nuclear capture of EphA2 promotes RhoG-dependent phosphorylation of the actin-binding protein, cofilin to oppose nuclear import of G-actin. The resulting depletion of nuclear G-actin drives transcription of Myocardin-related transcription factor (MRTF)/serum-response factor (SRF)-target genes to implement cell scattering and the invasive behaviour of cancer cells.

Comprehensive NGS Panel Validation for the Identification of Actionable Alterations in Adult Solid Tumors.

The increasing identification of driver oncogenic alterations and progress of targeted therapies addresses the need of comprehensive alternatives to standard molecular methods. The translation into clinical practice of next-generation sequencing (NGS) panels is actually challenged by the compliance of high quality standards for clinical accreditation. Herein, we present the analytical and clinical feasibility study of a hybridization capture-based NGS panel (Action OncoKitDx) for the analysis of somatic mutations, copy number variants (CNVs), fusions, pharmacogenetic SNPs and Microsatellite Instability (MSI) determination in formalin-fixed paraffin-embedded (FFPE) tumor samples. A total of 64 samples were submitted to extensive analytical validation for the identification of previously known variants. An additional set of 166 tumor and patient-matched normal samples were sequenced to assess the clinical utility of the assay across different tumor types. The panel demonstrated good specificity, sensitivity, reproducibility, and repeatability for the identification of all biomarkers analyzed and the 5% limit of detection set was validated. Among the clinical cohorts, the assay revealed pathogenic genomic alterations in 97% of patient cases, and in 82.7%, at least one clinically relevant variant was detected. The validation of accuracy and robustness of this assay supports the Action OncoKitDx's utility in adult solid tumors.

Mitochondria-to-nucleus retrograde signaling drives formation of cytoplasmic chromatin and inflammation in senescence.

Cellular senescence is a potent tumor suppressor mechanism but also contributes to aging and aging-related diseases. Senescence is characterized by a stable cell cycle arrest and a complex proinflammatory secretome, termed the senescence-associated secretory phenotype (SASP). We recently discovered that cytoplasmic chromatin fragments (CCFs), extruded from the nucleus of senescent cells, trigger the SASP through activation of the innate immunity cytosolic DNA sensing cGAS-STING pathway. However, the upstream signaling events that instigate CCF formation remain unknown. Here, we show that dysfunctional mitochondria, linked to down-regulation of nuclear-encoded mitochondrial oxidative phosphorylation genes, trigger a ROS-JNK retrograde signaling pathway that drives CCF formation and hence the SASP. JNK links to 53BP1, a nuclear protein that negatively regulates DNA double-strand break (DSB) end resection and CCF formation. Importantly, we show that low-dose HDAC inhibitors restore expression of most nuclear-encoded mitochondrial oxidative phosphorylation genes, improve mitochondrial function, and suppress CCFs and the SASP in senescent cells. In mouse models, HDAC inhibitors also suppress oxidative stress, CCF, inflammation, and tissue damage caused by senescence-inducing irradiation and/or acetaminophen-induced mitochondria dysfunction. Overall, our findings outline an extended mitochondria-to-nucleus retrograde signaling pathway that initiates formation of CCF during senescence and is a potential target for drug-based interventions to inhibit the proaging SASP.

Sphingomonas paucimobilis keratitis in a patient with neurotrophic keratopathy and severe neurosensory hypoacusis: Treatment with penetrating keratoplasty and amniotic membrane grafting.

We describe a case of a man with neurotrophic keratitis of unknown ethiology, who developed a massive stromal melting during treatment of a persistent epithelial defect. A tectonic keratoplasty combined with amniotic membrane grafting was made. Host cornea specimen was analyzed, and Sphingomonas paucimobilis was isolated.

WebLEC: a test to assess adolescents' Internet reading literacy skills / WebLEC: una prueba para evaluar la competencia lectora en Internet de los adolescentes

BACKGROUND: Reading on the Internet requires specific skills (e.g., navigation), apart from comprehension abilities, but there is no test in Spanish to assess these skills in adolescents. The goal of this study is to fill this gap with a test called WebLEC, inspired by the PISA framework. METHOD: WebLEC was validated with secondary education students (n = 941). It includes 28 items of three types (access & retrieve, integrate & interpret, and reflect & evaluate) applied to four reading scenarios (e.g., web portal, search engines, Internet forums, and Wikipedia). WebLEC provides a general reading literacy index, plus two navigation indices. RESULTS: The validity and reliability of WebLEC was confirmed, and a scale to diagnose reading literacy skills is provided. CONCLUSIONS: WebLEC assesses adolescents' Internet reading literacy skills. Given the growing importance of the Internet in daily life and learning situations, assessing these skills is the first step in implementing instructional interventions to foster Internet reading

ANTECEDENTES: leer en Internet requiere habilidades específicas (e.g., navegación) aparte de habilidades de comprensión. No existe en español un test para evaluar estas habilidades en población adolescente. El propósito de este trabajo es cubrir esta laguna con el test WebLEC, desarrollado a partir del marco de PISA. MÉTODO: WebLEC fue validado con estudiantes de Educación Secundaria Obligatoria (ESO) (n = 941). Incluye 28 ítems o tareas de tres tipos (acceso y recuperación, integrar e interpretar, y reflexionar y evaluar) aplicadas a 4 escenarios de lectura (portal web, buscador, foro de internet y Wikipedia). WebLEC proporciona un índice general de competencia lectora y dos índices de navegación. RESULTADOS: se confirma la validez y fiabilidad de WebLEC, y se proporciona un baremo para los diferentes cursos de ESO. CONCLUSIONES: WebLEC sirve para evaluar la competencia lectora en Internet de estudiantes de ESO. Dada la creciente importancia de Internet para la vida ordinaria y el aprendizaje, evaluar estas habilidades es el primer paso para implementar intervenciones para la mejora de la competencia lectora en Internet

WebLEC: a test to assess adolescents' Internet reading literacy skills.

BACKGROUND: Reading on the Internet requires specific skills (e.g., navigation), apart from comprehension abilities, but there is no test in Spanish to assess these skills in adolescents. The goal of this study is to fill this gap with a test called WebLEC, inspired by the PISA framework. METHOD: WebLEC was validated with secondary education students (n = 941). It includes 28 items of three types (access & retrieve, integrate & interpret, and reflect & evaluate) applied to four reading scenarios (e.g., web portal, search engines, Internet forums, and Wikipedia). WebLEC provides a general reading literacy index, plus two navigation indices. RESULTS: The validity and reliability of WebLEC was confirmed, and a scale to diagnose reading literacy skills is provided. CONCLUSIONS: WebLEC assesses adolescents’ Internet reading literacy skills. Given the growing importance of the Internet in daily life and learning situations, assessing these skills is the first step in implementing instructional interventions to foster Internet reading.

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets.

Activation-induced deaminase (AID) initiates antibody diversification in germinal center (GC) B cells through the deamination of cytosines on immunoglobulin genes. AID can also target other regions in the genome, triggering mutations or chromosome translocations, with major implications for oncogenic transformation. However, understanding the specificity of AID has proved extremely challenging. We have sequenced at very high depth >1,500 genomic regions from GC B cells and identified 275 genes targeted by AID, including 30 of the previously known 35 AID targets. We have also identified the most highly mutated hotspot for AID activity described to date. Furthermore, integrative analysis of the molecular features of mutated genes coupled to machine learning has produced a powerful predictive tool for AID targets. We also have found that base excision repair and mismatch repair back up each other to faithfully repair AID-induced lesions. Finally, our data establish a novel link between AID mutagenic activity and lymphomagenesis.

CCCTC-Binding Factor Locks Premature IgH Germline Transcription and Restrains Class Switch Recombination.

In response to antigenic stimulation B cells undergo class switch recombination (CSR) at the immunoglobulin heavy chain (IgH) to replace the primary IgM/IgD isotypes by IgG, IgE, or IgA. CSR is initiated by activation-induced cytidine deaminase (AID) through the deamination of cytosine residues at the switch (S) regions of IgH. B cell stimulation promotes germline transcription (GLT) of specific S regions, a necessary event prior to CSR because it facilitates AID access to S regions. Here, we show that CCCTC-binding factor (CTCF)-deficient mice are severely impaired in the generation of germinal center B cells and plasma cells after immunization in vivo, most likely due to impaired cell survival. Importantly, we find that CTCF-deficient B cells have an increased rate of CSR under various stimulation conditions in vitro. This effect is not secondary to altered cell proliferation or AID expression in CTCF-deficient cells. Instead, we find that CTCF-deficient B cells harbor an increased mutation frequency at switch regions, probably reflecting an increased accessibility of AID to IgH in the absence of CTCF. Moreover, CTCF deficiency triggers premature GLT of S regions in naïve B cells. Our results indicate that CTCF restricts CSR by enforcing GLT silencing and limiting AID access to IgH.

Activation-induced cytidine deaminase targets SUV4-20-mediated histone H4K20 trimethylation to class-switch recombination sites.

Activation-induced cytidine deaminase (AID) triggers antibody diversification in B cells by catalysing deamination and subsequently mutating immunoglobulin (Ig) genes. Association of AID with RNA Pol II and occurrence of epigenetic changes during Ig gene diversification suggest participation of AID in epigenetic regulation. AID is mutated in hyper-IgM type 2 (HIGM2) syndrome. Here, we investigated the potential role of AID in the acquisition of epigenetic changes. We discovered that AID binding to the IgH locus promotes an increase in H4K20me3. In 293F cells, we demonstrate interaction between co-transfected AID and the three SUV4-20 histone H4K20 methyltransferases, and that SUV4-20H1.2, bound to the IgH switch (S) mu site, is replaced by SUV4-20H2 upon AID binding. Analysis of HIGM2 mutants shows that the AID truncated form W68X is impaired to interact with SUV4-20H1.2 and SUV4-20H2 and is unable to bind and target H4K20me3 to the Smu site. We finally show in mouse primary B cells undergoing class-switch recombination (CSR) that AID deficiency associates with decreased H4K20me3 levels at the Smu site. Our results provide a novel link between SUV4-20 enzymes and CSR and offer a new aspect of the interplay between AID and histone modifications in setting the epigenetic status of CSR sites.

CTCF orchestrates the germinal centre transcriptional program and prevents premature plasma cell differentiation.

In germinal centres (GC) mature B cells undergo intense proliferation and immunoglobulin gene modification before they differentiate into memory B cells or long-lived plasma cells (PC). GC B-cell-to-PC transition involves a major transcriptional switch that promotes a halt in cell proliferation and the production of secreted immunoglobulins. Here we show that the CCCTC-binding factor (CTCF) is required for the GC reaction in vivo, whereas in vitro the requirement for CTCF is not universal and instead depends on the pathways used for B-cell activation. CTCF maintains the GC transcriptional programme, allows a high proliferation rate, and represses the expression of Blimp-1, the master regulator of PC differentiation. Restoration of Blimp-1 levels partially rescues the proliferation defect of CTCF-deficient B cells. Thus, our data reveal an essential function of CTCF in maintaining the GC transcriptional programme and preventing premature PC differentiation.

3' Uridylation controls mature microRNA turnover during CD4 T-cell activation.

Activation of T lymphocytes requires a tight regulation of microRNA (miRNA) expression. Terminal uridyltransferases (TUTases) catalyze 3' nontemplated nucleotide addition (3'NTA) to miRNAs, which may influence miRNA stability and function. Here, we investigated 3'NTA to mature miRNA in CD4 T lymphocytes by deep sequencing. Upon T-cell activation, miRNA sequences bearing terminal uridines are specifically decreased, concomitantly with down-regulation of TUT4 and TUT7 enzymes. Analyzing TUT4-deficient T lymphocytes, we proved that this terminal uridyltransferase is essential for the maintenance of miRNA uridylation in the steady state of T lymphocytes. Analysis of synthetic uridylated miRNAs shows that 3' addition of uridine promotes degradation of these uridylated miRNAs after T-cell activation. Our data underline post-transcriptional uridylation as a mechanism to fine-tune miRNA levels during T-cell activation.

Empagliflozin in combination with oral agents in young and overweight/obese Type 2 diabetes mellitus patients: A pooled analysis of three randomized trials.

AIMS: This analysis aimed to evaluate efficacy and safety of empagliflozin in combination therapy in <65 y.o. patients, overweight/obese, and with uncontrolled T2DM. METHODS: Pooled analysis from three phase-III trials, in <65 y.o. patients, with BMI 25-35kg/m2, and HbA1c ≥8% at baseline. Patients (N=439) were randomized to placebo (n=138), empagliflozin 10mg (n=160), or empagliflozin 25mg (n=141) once daily (24weeks) as add-on to metformin, to metformin plus sulfonylurea, or to pioglitazone ± metformin. RESULTS: At week 24, adjusted mean (SE) changes from baseline in HbA1c were -0.19% (0.07) for placebo vs. -1.10% (0.07) and -1.10% (0.07) for empagliflozin 10 and 25mg, respectively (both p<0.001). Adjusted mean (SE) changes from baseline in weight were -0.33kg (0.21) for placebo vs. -1.94kg (0.19) and -2.14kg (0.20) for empagliflozin 10 and 25mg, respectively (both p<0.001). Adverse events were reported in 57.2% on placebo, 64.4% on empagliflozin 10mg and 59.6% on empagliflozin 25mg. Genital infection AEs were reported in 1.4% on placebo, 3.8% on empagliflozin 10mg, and 5.0% on empagliflozin 25mg. CONCLUSIONS: In this specific population, empagliflozin in combination with other oral agents, significantly reduced HbA1c and body weight and was well tolerated.

Effectiveness, Good Tolerability, and High Compliance of Doses of Risperidone Long-Acting Injectable Higher Than 75 mg in People With Severe Schizophrenia: A 3-Year Follow-Up.

Tolerability and effectiveness of antipsychotics are important to increase treatment compliance in people with schizophrenia. The aim of this study was to evaluate effectiveness, tolerability, and adherence to treatment with high doses of risperidone long-acting injectable (RLAI) in patients with severe schizophrenia.It is a 3-year prospective, observational study of patients with severe (Clinical Global Impression Severity scale [CGI-S] score of ≥5) schizophrenia according to International Classification of Diseases (ICD-10) criteria. Subjects were the consecutive 60 who first underwent treatment with RLAI with doses of 75 mg or higher every 14 days to get clinical stabilization.Assessment included the following: CGI-S, World Health Organization Disability Assessment Schedule, Camberwell Assessment of Need (CAN), Medication Adherence Rating Scale, laboratory tests, weight, and hospital admissions.The mean (SD) dose of RLAI was 111.2 (9.1) mg per 14 days. Tolerability was good and there were almost no interruptions due to adverse effects or to relevant biological parameters alterations. Also, weight gain was not significant.Retention rate in treatment after 3 years was 95%. Clinical Global Impression Severity (P < 0.01) and Camberwell Assessment of Need (P < 0.01) decreased and also Disability Assessment Schedule in the 4 areas (P < 0.01). Medication Adherence Rating Scale score increased from 3.6 (0.7) to 8.9 (0.9) (P < 0.001). There were significantly few hospital admissions than during the previous 36 months (1.9 [1.3] vs 0.31 [0.2], P < 0.001).As a conclusion, we highlight that the effectiveness and tolerability of 75 mg or higher every 14 days of RLAI were high, being useful in improving treatment adherence in patients with severe schizophrenia, getting good clinical and functional outcomes.

AID-expressing epithelium is protected from oncogenic transformation by an NKG2D surveillance pathway.

Activation-induced deaminase (AID) initiates secondary antibody diversification in germinal center B cells, giving rise to higher affinity antibodies through somatic hypermutation (SHM) or to isotype-switched antibodies through class switch recombination (CSR). SHM and CSR are triggered by AID-mediated deamination of cytosines in immunoglobulin genes. Importantly, AID activity in B cells is not restricted to Ig loci and can promote mutations and pro-lymphomagenic translocations, establishing a direct oncogenic mechanism for germinal center-derived neoplasias. AID is also expressed in response to inflammatory cues in epithelial cells, raising the possibility that AID mutagenic activity might drive carcinoma development. We directly tested this hypothesis by generating conditional knock-in mouse models for AID overexpression in colon and pancreas epithelium. AID overexpression alone was not sufficient to promote epithelial cell neoplasia in these tissues, in spite of displaying mutagenic and genotoxic activity. Instead, we found that heterologous AID expression in pancreas promotes the expression of NKG2D ligands, the recruitment of CD8(+) T cells, and the induction of epithelial cell death. Our results indicate that AID oncogenic potential in epithelial cells can be neutralized by immunosurveillance protective mechanisms.

Litter aeration and spread of Salmonella in broilers.

Litter quality in the poultry sector is one of the main parameters of health, productivity, and animal welfare. Therefore, innovative management methods have been developed to improve the quality of litter. One of them is litter aeration (LA) by tumbling. However, there is little information related to the effect of this technique on the spreading of pathogens of public health importance such as Salmonella. In this context, the objective of this study was to determine the epidemiology of Salmonella in poultry farms, when serial LA were implemented during the rearing cycle of broilers. For this purpose, an experimental broiler farm with 3 identical rooms was used in the study. Two rooms were assigned to the LA treatment, and the other one served as the control room. Environmental samples were taken in poultry houses after LA in 4 consecutive weeks at the end of the cycle. All samples collected were analyzed according to the standards of the International Organization for Standardization (ISO 6579:2002, Annex D). The results of this study showed that in the control and treated rooms, the percentage of positive samples for Salmonella decreased in the first 3 LA sessions (LA 1, LA 2, and LA 3). However, in the last LA session of rearing (LA 4), the percentage of positive samples increased from 8.2 to 33.2% in the control room instead the treated rooms where the positive samples decreased (P = 0.017). Thus, the aeration of the litter as litter management technique in poultry broiler production does not increase the shedding or the spread of Salmonella throughout broiler houses. In addition, it could be an effective technique to reduce the infective pressure of this bacterium in several areas of the farm or in certain moments of the rearing period with more risk of multiplication and spreading of Salmonella.

Cancer-initiating enriched cell lines from human glioblastoma: preparing for drug discovery assays.

Glioblastoma multiforme (GBM) is the most lethal type of brain tumour in the adult humans. The cancer-initiating cell (CIC) hypothesis supports the notion that failures in current approaches to GBM treatment might be attributed to the survival of the CIC subpopulation. Recent evidence shows the idea that using CIC-enriched cell lines derived from human GBM as new targets for drug discovery programs, may improve the chance of successfully translating the basic research findings into clinical trials. Although this approach appears promising, many important biological and technical issues (characterization of functional CIC markers, inter- and intra-tumoral CIC heterogeneity, and isolation and maintenance inconsistency) need to be resolved.

Genomic instability of surgical sample and cancer-initiating cell lines from human glioblastoma.

Glioblastoma multiforme (GBM) is the most aggressive brain tumor in the adult human, with an average survival of 16 months. A small population of cells within the GBM termed cancer-initiating cells is responsible for the initiation and maintenance of the tumor mass. The traditional glioblastoma cancer cells, grown with serum containing media, display increased rate of genomic instability events, which in turn renders the cell cultures with little resembling to the original tumor, making doubtful their use as preclinical models for screening therapeutic agents. On the contrary, the cancer-initiating cells grown in serum-free media seems to show lower rate of genomic instability processes. However, considering the diversity of genetic and/or epigenetic background, we will need to evaluate the possibility of using different culture conditions to allow for the isolation and culture of such cancer-initiating cells diversity, keeping, at the same time, the genomic instability rate as the original tumor. We summarized the main genetic and epigenetic mechanisms that are driving genomic instability in cancer-initiating cells from human glioblastoma.

Cambiando un programa de posgrado en neurociencia. Historia de una propuesta abierta elaborada por y para estudiantes de doctorado / Changing the curriculum of a postgraduated program in neuroscience. The story of an open proposal elaborated by and for Ph.D students

Introducción: El curso académico 1999-2000, siguiendo las directrices del nuevo Real Decreto para los Estudios de Posgrado, el programa de Doctorado en Neurociencia de la Universitat Autònoma de Barcelona se vio obligado a adaptar su currículo a la nueva legislación (RD778/1998). Material y métodos: Considerando las diferencias de conocimientos existentes entre los futuros doctorandos e evitando la hiperespecialización de los contenidos, la Asociación de Estudiantes de Neurociencias elaboró una propuesta curricular basada en 8 cursos fundamentales y 5 cursos metodológicos. Según la base de conocimientos de la licenciatura, los estudiantes deberían superar 5 cursos fundamentales y entre 2 y 3 cursos metodológicos para completar los 20 créditos mínimos de formación. Se elaboraron programas detallados para cada curso y la propuesta fue enviada a 24 profesionales relacionados con la neurociencia, con la intención de recoger críticas, comentarios y sugerencias en un formato abierto. Resultados: Se recibieron un total de 9 respuestas (37 per cent), 7 de ellas consideraron la propuesta totalmente positiva (78 per cent) mientras que 2/9 (22 per cent) consideraron los contenidos de los programas demasiado elementales para estudiantes graduados y mostraban su desacuerdo general con el proyecto. Además, 3 profesores expresaban algunas críticas sobre aspectos puntuales del contenido de los programas, mientras que cuatro se ofrecían para impartir cursos específicos adaptados. Conclusiones: La propuesta sirvió para abrir un debate sobre modelos generalistas y especializados de currículo de doctorado y para estimular la discusión sobre la enseñanza de la neurociencia en la Universidad Autónoma de Barcelona (AU)