Detained introns are a novel, widespread class of post-transcriptionally spliced introns

Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as “detained” introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs—including those in Mdm4, a negative regulator of p53—was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.National Institutes of Health (U.S.) (Grant R01 GM34277-23)American Cancer Society (Novartis Institutes of Biomedical Research Postdoctoral Research Fellowship)National Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051

Dicer loss and recovery induce an oncogenic switch driven by transcriptional activation of the oncofetal Imp1–3 family

MicroRNAs(miRNAs) are post-transcriptional regulators of gene expressioncritical for organismal viability. Changes inmiRNAactivity arecommonin cancer, buthowthese changes relate to subsequent alterations in transcription and the process of tumorigenesis is not well understood. Here, we report a deep transcriptional, oncogenic network regulated bymiRNAs. Wepresent analysis of the gene expression and phenotypic changes associated with globalmiRNA restoration in miRNA-deficient fibroblasts. This analysis uncovers a miRNA-repressed network containing oncofetal genesImp1, Imp2, and Imp3(Imp1–3) that is up-regulated primarily transcriptionally > 100-fold uponDicer loss and is resistant to resilencing by complete restoration of miRNA activity. This Dicer-resistant epigenetic switch confers tumorigenicity to these cells. Let-7 targets Imp1–3 are required for this tumorigenicity and feed back to reinforce and sustain expression of the oncogenic network. Together, these Dicer-resistant genes constitute an mRNA expression signature that is present in numerous human cancers and is associated with poor survival.United States. Public Health Service (Grant R01CA133404)National Cancer Institute (U.S.) (Grant P01CA42063)Marie D. and Pierre Casimir-Lamber

Synthetic biology: promises and challenges

http://dx.doi.org/10.1038/msb410020

Evaluación de dimetilsulfóxido y Aloe vera como potenciadores de la penetración para la aplicación cutánea de lidocaína

Objective: The objective of the present work was to compare and verify efficacy of Aloe vera (1 to 3 %) with dimethyl sulfoxide (1 to 3 %) for its penetration enhancing property for topical delivery of lidocaine. Method: Carbopol 934 was used as gelling agent for preparation of lidocaine gel formulations containing or not dimetilsulfoxido or Aloe vera (1%, 2% and 3%). Gels were evaluated for physical appearance, rheological behavior, drug content, drug release and stability. Results: It was inferred from result that obtained gel formulation were good in appearance, homogeneity and consistency. In vitro drug release profiles showed that concentrations of Aloe vera gel increased in formulations, the drug release rate increased substantially. It was observed that F6 formulation which comprised of 3% Aloe vera as permeation enhancer exhibited 79.18 % of drug release. Similarly, for formulation F3 which comprised of 3% dimetilsulfoxido as permeation enhancer the drug release was found to be 84.52%. Use of Aloe vera may prove to be beneficial as compared to synthetic permeation enhancers. Conclusion: Based on results of the study it was concluded that the topical gel of lidocaine prepared along with Carbopol 934 by using Aloe vera as a natural penetration enhancer at a concentration of 3% can be used to enhance the penetration for lidocain across the skin.Objetivo: El objetivo del presente trabajo fue comparar y verificar la eficacia de Aloe vera (1 a 3%) con dimetilsulfoxido (1 a 3%) por su propiedad de mejora de la penetración para la administración tópica de lidocaína. Método: Carbopol 934 se usó como agente gelificante para la preparación de formulaciones de gel de lidocaína que contenían o no dimetilsulfoxido o Aloe vera (1%, 2% y 3%). Los geles se evaluaron por su aspecto físico, comportamiento reológico, contenido de fármaco, liberación de fármaco y estabilidad. Resultados: Se dedujo del resultado que la formulación del gel obtenido era adecuada en apariencia, homogeneidad y consistencia. Los perfiles de liberación de fármaco in vitro mostraron que conforme aumentaban el porcentaje de “Aloe vera” en las formulaciones, la tasa de liberación del fármaco se incrementaba sustancialmente. Se observó que la formulación F6 que contenía un 3% de Aloe vera como potenciador de la permeación exhibía un 79,18% de liberación de fármaco. De manera similar, para la formulación F3, que comprendía un 3% de DMSO como potenciador de la permeación, se encontró que la liberación del fármaco era del 84,52%. El uso de Aloe vera puede resultar beneficioso en comparación con los potenciadores de permeación sintéticos. Conclusión: Sobre la base de los resultados del estudio, se concluyó que el gel tópico de lidocaína preparado junto con Carbopol 934 mediante el uso de Aloe vera como un potenciador natural de la penetración a una concentración del 3%, se puede usar para mejorar la penetración de lidocaína en la piel

Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Global microRNA depletion suppresses tumor angiogenesis

MicroRNAs delicately regulate the balance of angiogenesis. Here we show that depletion of all microRNAs suppresses tumor angiogenesis. We generated microRNA-deficient tumors by knocking out Dicer1. These tumors are highly hypoxic but poorly vascularized, suggestive of deficient angiogenesis signaling. Expression profiling revealed that angiogenesis genes were significantly down-regulated as a result of the microRNA deficiency. Factor inhibiting hypoxia-inducible factor 1 (HIF-1), FIH1, is derepressed under these conditions and suppresses HIF transcription. Knocking out FIH1 using CRISPR/Cas9-mediated genome engineering reversed the phenotypes of microRNA-deficient cells in HIF transcriptional activity, VEGF production, tumor hypoxia, and tumor angiogenesis. Using multiplexed CRISPR/Cas9, we deleted regions in FIH1 3′ untranslated regions (UTRs) that contain microRNA-binding sites, which derepresses FIH1 protein and represses hypoxia response. These data suggest that microRNAs promote tumor responses to hypoxia and angiogenesis by repressing FIH1.Swedish Research CouncilHoward Hughes Medical Institute (International Student Research Fellowship)National Institutes of Health (U.S.) (grant number R01-CA133404)MIT-Harvard Center of Cancer Nanotechnology Excellence (grant no. U54-CA151884)David H. Koch Institute for Integrative Cancer Research at MIT (Marie D. and Pierre Casimir-Lambert Fund)National Cancer Institute (U.S.) (Koch Institute Support (core) Grant P30-CA14051))National Institutes of Health (U.S.) (grant EB016101-01A1)Damon Runyon Cancer Research Foundation (Research Fellow (DRG-2117-12)

User Persona of Mother of Preterm Neonate

This research paper presents a user persona of Indian mothers of preterm neonates. Many of these preterm neonates require hospitalization in Neona-tal Intensive Care Units (NICUs), leading to mental stress for mothers and their families. The mother’s persona is proposed based on hypothesis, user interviews and data analysis. The participant mothers of preterm neonates are graduates and homemakers from semiurban areas around Pune, India. These mothers prefer non-vegetarian diet, they visit a pediatrician more fre-quently and presently, they do not use any mobile healthcare app or YouTube videos for information about neonatal care. A mobile app will be developed for these mothers in future with due consideration to their user persona.<br/

Chronic cisplatin treatment promotes enhanced damage repair and tumor progression in a mouse model of lung cancer

Chemotherapy resistance is a major obstacle in cancer treatment, yet the mechanisms of response to specific therapies have been largely unexplored in vivo. Employing genetic, genomic, and imaging approaches, we examined the dynamics of response to a mainstay chemotherapeutic, cisplatin, in multiple mouse models of human non-small-cell lung cancer (NSCLC). We show that lung tumors initially respond to cisplatin by sensing DNA damage, undergoing cell cycle arrest, and inducing apoptosis—leading to a significant reduction in tumor burden. Importantly, we demonstrate that this response does not depend on the tumor suppressor p53 or its transcriptional target, p21. Prolonged cisplatin treatment promotes the emergence of resistant tumors with enhanced repair capacity that are cross-resistant to platinum analogs, exhibit advanced histopathology, and possess an increased frequency of genomic alterations. Cisplatin-resistant tumors express elevated levels of multiple DNA damage repair and cell cycle arrest-related genes, including p53-inducible protein with a death domain (Pidd). We demonstrate a novel role for PIDD as a regulator of chemotherapy response in human lung tumor cells.National Institutes of Health (U.S.) (grant 5-UO1-CA84306)National Cancer Institute (U.S.) (CA034992

Application of ultrasound treatments in the processing and production of high-quality and safe-to-drink kiwi juice

This study explores the potential of thermosonication as an alternative to traditional heat treatments, such as pasteurization, in the processing of fruit juices. Conventional methods often lead to undesirable quality changes in fruit juices, whereas thermosonication offers promising results regarding microbial inactivation and quality preservation. This work focused on the inactivation kinetics of Listeria innocua 2030c, a surrogate for pathogenic L. monocytogenes, in kiwifruit juice using thermosonication at 45 °C, 50 °C, and 55 °C. These treatments were compared with equivalent heat treatments. Quality attributes of the juice were also evaluated to assess process efficiency. Survival data of L. innocua were fitted with the Weibull model, estimating first decimal reduction times (δ) and shape parameters (n). The results reveal temperature and process dependencies on δ, while n remains mostly temperature and treatment independent. Thermosonication outperforms heat treatment, achieving higher L. innocua reductions while retaining quality attributes like pH, soluble solid content, and total phenolics and chlorophylls. Thermosonication at 55 °C stands out, providing a 6.2-log-cycle reduction in just 3 min with superior quality retention. These findings highlight the synergistic effect of temperature and ultrasound, making mild heat processes feasible while enhancing product quality. Thermosonication, particularly at 55 °C, emerges as an effective alternative to traditional thermal treatments for fruit juices, offering improved microbial safety without compromising product quality.info:eu-repo/semantics/publishedVersio