RESUMO
Peptides are bioactive molecules whose functional versatility in living organisms has led to successful applications in diverse fields. In recent years, the amount of data describing peptide sequences and function collected in open repositories has substantially increased, allowing the application of more complex computational models to study the relations between the peptide composition and function. This work introduces AMP-Detector, a sequence-based classification model for the detection of peptides' functional biological activity, focusing on accelerating the discovery and de novo design of potential antimicrobial peptides (AMPs). AMP-Detector introduces a novel sequence-based pipeline to train binary classification models, integrating protein language models and machine learning algorithms. This pipeline produced 21 models targeting antimicrobial, antiviral, and antibacterial activity, achieving average precision exceeding 83%. Benchmark analyses revealed that our models outperformed existing methods for AMPs and delivered comparable results for other biological activity types. Utilizing the Peptide Atlas, we applied AMP-Detector to discover over 190,000 potential AMPs and demonstrated that it is an integrative approach with generative learning to aid in de novo design, resulting in over 500 novel AMPs. The combination of our methodology, robust models, and a generative design strategy offers a significant advancement in peptide-based drug discovery and represents a pivotal tool for therapeutic applications.
Assuntos
Peptídeos Antimicrobianos , Aprendizado de Máquina , Peptídeos Antimicrobianos/química , Peptídeos Antimicrobianos/farmacologia , Algoritmos , Descoberta de Drogas/métodos , Sequência de Aminoácidos , Peptídeos Catiônicos Antimicrobianos/química , Peptídeos Catiônicos Antimicrobianos/farmacologia , Biologia Computacional/métodosRESUMO
Tracking cell death in vivo can enable a better understanding of the biological mechanisms underlying tissue homeostasis and disease. Unfortunately, existing cell death labeling methods lack compatibility with in vivo applications or suffer from low sensitivity, poor tissue penetration, and limited temporal resolution. Here, we fluorescently labeled dead cells in vivo with Trypan Blue (TBlue) to detect single scattered dead cells or to generate whole-mount three-dimensional maps of large areas of necrotic tissue during organ regeneration. TBlue effectively marked different types of cell death, including necrosis induced by CCl4 intoxication in the liver, necrosis caused by ischemia-reperfusion in the skin, and apoptosis triggered by BAX overexpression in hepatocytes. Moreover, due to its short circulating lifespan in blood, TBlue labeling allowed in vivo "pulse and chase" tracking of two temporally spaced populations of dying hepatocytes in regenerating mouse livers. Additionally, upon treatment with cisplatin, TBlue labeled dead cancer cells in livers with cholangiocarcinoma and dead thymocytes due to chemotherapy-induced toxicity, showcasing its utility in assessing anticancer therapies in preclinical models. Thus, TBlue is a sensitive and selective cell death marker for in vivo applications, facilitating the understanding of the fundamental role of cell death in normal biological processes and its implications in disease.
Assuntos
Morte Celular , Azul Tripano , Animais , Camundongos , Morte Celular/efeitos dos fármacos , Hepatócitos/efeitos dos fármacos , Hepatócitos/patologia , Hepatócitos/metabolismo , Humanos , Neoplasias/patologia , Camundongos Endogâmicos C57BL , Regeneração Hepática/efeitos dos fármacos , Fígado/patologia , Fígado/efeitos dos fármacos , Rastreamento de Células/métodos , Apoptose/efeitos dos fármacos , Imageamento Tridimensional , Regeneração/efeitos dos fármacos , Necrose , MasculinoRESUMO
Hyperactivation of YAP/TAZ, the Hippo pathway downstream effectors, is common in human cancer. The requirement of YAP/TAZ for cancer cell survival in preclinical models, prompted the development of pharmacological inhibitors that suppress their transcriptional activity. However, systemic YAP/TAZ inhibition may sometimes have unpredictable patient outcomes, with limited or even adverse effects because YAP/TAZ action is not simply tumor promoting but also tumor suppressive in some cell types. Here, we review the role of the Hippo pathway in distinct tumor cell populations, discuss the impact of inhibiting Hippo output on tumor growth, and examine current developments in YAP/TAZ inhibitors.
Assuntos
Neoplasias , Transdução de Sinais , Humanos , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Fatores de Transcrição/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Proteínas de Sinalização YAP , Neoplasias/tratamento farmacológico , Neoplasias/genéticaRESUMO
The Hippo pathway and its downstream effectors, the transcriptional co-activators Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), regulate organ growth and cell plasticity during animal development and regeneration. Remarkably, experimental activation of YAP/TAZ in the mouse can promote regeneration in organs with poor or compromised regenerative capacity, such as the adult heart and the liver and intestine of old or diseased mice. However, therapeutic YAP/TAZ activation may cause serious side effects. Most notably, YAP/TAZ are hyperactivated in human cancers, and prolonged activation of YAP/TAZ triggers cancer development in mice. Thus, can the power of YAP/TAZ to promote regeneration be harnessed in a safe way? Here, we review the role of Hippo signalling in animal regeneration, examine the promises and risks of YAP/TAZ activation for regenerative medicine and discuss strategies to activate YAP/TAZ for regenerative therapy while minimizing adverse side effects.
Assuntos
Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transdução de Sinais/fisiologia , Fatores de Transcrição/metabolismo , Animais , Humanos , Medicina Regenerativa/métodosRESUMO
The current understanding of Xenopus laevis development provides a comparative background for the analysis of frog developmental modes. Our analysis of development in various frogs reveals that the mode of gastrulation is associated with developmental rate and is unrelated to egg size. In the gastrula of the rapidly developing embryos of the foam-nesting frogs Engystomops coloradorum and Engystomops randi, archenteron and notochord elongation overlapped with involution at the blastopore lip, as in X. laevis embryos. In embryos of dendrobatid frogs and in the frog without tadpoles Eleutherodactylus coqui, which develop somewhat more slowly than X. laevis, involution and archenteron elongation concomitantly occurred during gastrulation; whereas elongation of the notochord and, therefore, dorsal convergence and extension, occurred in the postgastrula. In contrast, in the slow developing embryos of the marsupial frog Gastrotheca riobambae, only involution occurred during gastrulation. The processes of archenteron and notochord elongation and convergence and extension were postgastrulation events. We produced an Ab against the homeodomain protein Lim1 from X. laevis as a tool for the comparative analysis of development. By the expression of Lim1, we were able to identify the dorsal side of the G. riobambae early gastrula, which otherwise was difficult to detect. Moreover, the Lim1 expression in the dorsal lip of the blastopore and notochord differed among the studied frogs, indicating variation in the timing of developmental events. The variation encountered gives evidence of the modular character of frog gastrulation.
Assuntos
Anuros/embriologia , Animais , Embrião não Mamífero/citologia , Fertilização , Gástrula/citologia , Gástrula/metabolismo , Proteínas de Homeodomínio/metabolismo , Sistema Nervoso/citologia , Sistema Nervoso/embriologia , Notocorda/citologia , Óvulo/citologia , Somitos/citologia , Xenopus laevis/embriologiaRESUMO
Blastopore formation, the embryonic disk, archenteron and notochord elongation, and Brachyury expression in the marsupial frog Gastrotheca riobambae was compared with embryos of Xenopus laevis and of the dendrobatids Colostethus machalilla and Epipedobates anthonyi. In contrast with X. laevis embryos, the blastopore closes before elongation of the archenteron and notochord in the embryos of G. riobambae and of the dendrobatid frogs. Moreover, the circumblastoporal collar (CBC) thickens due to the accumulation of involuted cells. An embryonic disk, however, is formed only in the G. riobambae gastrula. We differentiate three gastrulation patterns according to the speed of development: In X. laevis, elongation of the archenteron and notochord begin in the early to mid gastrula, whereas in the dendrobatids C. machalilla and E. anthonyi the archenteron elongates at mid gastrula and the notochord elongates after gastrulation. In G. riobambae, only involution takes place during gastrulation. Archenteron and notochord elongation occur in the post gastrula. In the non-aquatic reproducing frogs, the margin of the archenteron expands anisotropically, resulting in an apparent displacement of the CBC from a medial to a posterior location, resembling the displacement of Hensen's node in the chick and mouse. The differences detected indicate that amphibian gastrulation is modular.
Assuntos
Anuros/embriologia , Gástrula/fisiologia , Animais , Anuros/metabolismo , Embrião não Mamífero/citologia , Embrião não Mamífero/metabolismo , Embrião não Mamífero/fisiologia , Proteínas Fetais/biossíntese , Gástrula/citologia , Gástrula/metabolismo , Notocorda/citologia , Notocorda/metabolismo , Notocorda/fisiologia , Proteínas com Domínio T/biossínteseRESUMO
To provide a developmental correlate with other frogs, we prepared a normal table of development for the dendrobatid, Colostethus machalilla and analyzed the morphology of its early development. This frog reproduces in captivity and deposits moderately sized eggs (1.6 mm in diameter) in terrestrial nests. The father guards the embryos until tadpole hatching. We divided development until hatching into 25 stages and implemented methods for in vitro culture of the embryos. The external and internal morphology of embryos were evaluated by observations in whole mount and in sections. Neural, notochord and somite specific antibodies were used to analyze gene expression patterns by immunostaining of embryos. Embryonic development of C. machalilla is slow and deviates from Xenopus laevis. In C. machalilla the elongation of the notochord, neural plate and somite formation occur after blastopore closure, possibly due to a delay in the dorsal convergence and extension movements. The gastrula of C. machalilla also deviates from X. laevis. The archenteron remains small until blastopore closure, where small cells accumulate at the blastopore lips. Simultaneously, the blastocoel roof thins until it becomes a monolayer of cells. Although C. machalilla does not form an embryonic disk, its thick blastopore lips resemble the embryonic disk of the marsupial frog Gastrotheca riobambae and represent an interesting deviation from the gastrulation pattern observed in X. laevis.
Assuntos
Anuros/embriologia , Embrião não Mamífero , Desenvolvimento Embrionário , Regulação da Expressão Gênica no Desenvolvimento , Animais , Blástula/fisiologia , Gástrula/fisiologia , Modelos Biológicos , Especificidade da Espécie , Fatores de Tempo , Xenopus laevisRESUMO
La deficiencia de hierro es el trastorno nutricional más frecuente, especialmente en los países subdesarrollados. El establecimiento de los puntos de corte para clasificar a la población en anemíca o no anémica, han sido cuestionados. En el presente trabajo analizamos los efectos de la suplementación marcial en el tercer trimestre gestacional, evaluando los efectos mediante el Método de Garby y cols., que registra la inevitable regresión hacia la media que ocurre entre dos medidas de una misma variable. Estudiamos 143 pacientes divididas en dos grupos: Grupo tratamiento (n=99) que recibió una tableta diaria de 200 mg de Sulfato Ferroso y 250 ug de ácido fólico; y el grupo Control (n=44) que recibió placebo. La suplementación se inició a las 28 semanas de edad gestacional, en un estudio longuitudinal, prospectivo, ciego, y termino a las 37 semanas de embarazo. Se mide los efectos en cada nivel de hemoglobina, se determina el punto de corte, y se estudia sensibilidad, especificidad, valores predictivos positivo y negativo. Finalmente analizamos los datos en el recien nacido. El 66 por ciento de las pacientes respondieron a la suplementación marcial. El punto de corte para establecer deficiencia de hierro fue 12.5 g/dl de hemoglobina, con una sensibilidad de 53.8, especificidad de 52.9, un valor predictivo positivo de 68.6, un valor predictivo negativo de 37.5, y una prevalencia medida de 51.5 por ciento, que al ser corregida determina una verdadera prevalencia de 58.2 por ciento Algunos indicadores bioquímicos y antropométricos de los recien nacidos del grupo tratamiento son significativamente favorables, frente a los recien nacidos del grupo control. Se concluye que el punto de corte de hemoglobina, establecido por la OMS, identifica solamente los casos que presenten anemia. Se destaca la importancia de poder estimar oportunamente la deficiencia de hierro, en especial en pacientes gestantes.