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1.
Plant Physiol ; 196(2): 1674-1690, 2024 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-38713768

RESUMO

Synechococcus sp. PCC 11901 (PCC 11901) is a fast-growing marine cyanobacterial strain that has a capacity for sustained biomass accumulation to very high cell densities, comparable to that achieved by commercially relevant heterotrophic organisms. However, genetic tools to engineer PCC 11901 for biotechnology applications are limited. Here we describe a suite of tools based on the CyanoGate MoClo system to unlock the engineering potential of PCC 11901. First, we characterized neutral sites suitable for stable genomic integration that do not affect growth even at high cell densities. Second, we tested a suite of constitutive promoters, terminators, and inducible promoters including a 2,4-diacetylphloroglucinol (DAPG)-inducible PhlF repressor system, which has not previously been demonstrated in cyanobacteria and showed tight regulation and a 228-fold dynamic range of induction. Lastly, we developed a DAPG-inducible dCas9-based CRISPR interference (CRISPRi) system and a modular method to generate markerless mutants using CRISPR-Cas12a. Based on our findings, PCC 11901 is highly responsive to CRISPRi-based repression and showed high efficiencies for single insertion (31% to 81%) and multiplex double insertion (25%) genome editing with Cas12a. We envision that these tools will lay the foundations for the adoption of PCC 11901 as a robust model strain for engineering biology and green biotechnology.


Assuntos
Synechococcus , Synechococcus/genética , Synechococcus/crescimento & desenvolvimento , Regiões Promotoras Genéticas/genética , Sistemas CRISPR-Cas , Engenharia Genética/métodos , Edição de Genes/métodos
2.
Mol Cancer ; 23(1): 222, 2024 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-39367409

RESUMO

Ewing sarcoma (ES) poses a significant therapeutic challenge due to the difficulty in targeting its main oncodriver, EWS::FLI1. We show that pharmacological targeting of the EWS::FLI1 transcriptional complex via inhibition of P300/CBP drives a global transcriptional outcome similar to direct knockdown of EWS::FLI1, and furthermore yields prognostic risk factors for ES patient outcome. We find that EWS::FLI1 upregulates LMNB1 via repetitive GGAA motif recognition and acetylation codes in ES cells and EWS::FLI1-permissive mesenchymal stem cells, which when reversed by P300 inhibition leads to senescence of ES cells. P300-inhibited senescent ES cells can then be eliminated by senolytics targeting the PI3K signaling pathway. The vulnerability of ES cells to this combination therapy suggests an appealing synergistic strategy for future therapeutic exploration.


Assuntos
Senescência Celular , Proteínas de Fusão Oncogênica , Proteína Proto-Oncogênica c-fli-1 , Proteína EWS de Ligação a RNA , Sarcoma de Ewing , Fatores de Transcrição de p300-CBP , Sarcoma de Ewing/metabolismo , Sarcoma de Ewing/patologia , Sarcoma de Ewing/tratamento farmacológico , Sarcoma de Ewing/genética , Humanos , Proteína Proto-Oncogênica c-fli-1/metabolismo , Proteína Proto-Oncogênica c-fli-1/genética , Proteína EWS de Ligação a RNA/genética , Proteína EWS de Ligação a RNA/metabolismo , Senescência Celular/efeitos dos fármacos , Fatores de Transcrição de p300-CBP/metabolismo , Fatores de Transcrição de p300-CBP/antagonistas & inibidores , Proteínas de Fusão Oncogênica/genética , Proteínas de Fusão Oncogênica/metabolismo , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos , Células-Tronco Mesenquimais/metabolismo , Células-Tronco Mesenquimais/efeitos dos fármacos , Proteína p300 Associada a E1A
3.
Hum Mol Genet ; 31(19): 3207-3215, 2022 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-34791233

RESUMO

Transcriptome-wide association studies increase the yield of loci associated with disease phenotypes by focusing on expression quantitative trait loci (eQTL). The major source of eQTL data for is the Gene and Tissue Expression (GTEx) project, which is comprised entirely of adults, mainly those >50 years of age at death. Since gene expression levels differ by developmental stage, it is not clear whether eQTLs derived from adult data sources are best suited for use in young-onset diseases such as pediatric cancers. To fill in this knowledge gap, we performed a large-scale eQTL mapping analysis in the GenCord study with newborn samples and compared it with GTEx. Under matched conditions, we found around 80% of the eQTLs in one study can be replicated in the other. However, among all eQTLs identified in GenCord (GTEx), 584 (1045) showed statistically significant differences in effect sizes in GTEx (GenCord). We further investigated how using fetal eQTL data can facilitate the genetic association study of acute lymphoblastic leukemia. GenCord and GTEx identified the same genetic loci with statistical significance; however, the overall association pattern was only weakly correlated. Our paper demonstrates age-differential eQTLs and shows their potential influence on childhood leukemia research.


Assuntos
Leucemia , Locos de Características Quantitativas , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Leucemia/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Transcriptoma/genética
4.
Pediatr Emerg Care ; 40(9): 665-667, 2024 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-38776429

RESUMO

OBJECTIVES: The aim of this study was to identify the incidence of adverse events of ketamine administration in the pediatric emergency department in patients aged 90 days or younger in order to demonstrate the safety and efficacy of administration in this patient population. METHODS: An 8-year retrospective chart review of patients aged 90 days or younger who received ketamine in the pediatric emergency department was conducted. All patients who met the age criteria were included in this study. Identified routes of ketamine administration included oral, intramuscular, and intravenous. RESULTS: Fourteen patients were identified who met the inclusion criteria and were included in the final analysis. The median age was 45 days old. Indications for ketamine administration included 7 cases for procedural sedation, 5 cases for RSI, and 2 cases for postintubation sedation. The average dose amount (mg/kg) of ketamine administered was 10, 4.43, and 1.59 for oral, intramuscular, and intravenous routes, respectively. Of the 14 patients, 1 patient was identified to have an adverse event to ketamine administration. A transient desaturation and bradycardic event due to laryngospasm was observed during laryngoscopy performed for RSI that was resolved with administration of anticholinergics and paralytics as well as successful intubation and ventilation. CONCLUSIONS: In this study, 1 patient suffered an adverse event due to laryngospasm during intubation. In the pediatric population, the incidence of adverse events of ketamine administration has been found to be variable in the current literature, ranging from 0.71% to 7.26%. In our study, an adverse event occurred in 1 out of 14 administrations (7.1%). The incidence of adverse events associated with ketamine administration in our patients aged 90 days or less appeared to be similar to that reported in the general pediatric population.


Assuntos
Serviço Hospitalar de Emergência , Ketamina , Humanos , Ketamina/administração & dosagem , Ketamina/efeitos adversos , Estudos Retrospectivos , Masculino , Feminino , Lactente , Recém-Nascido , Injeções Intramusculares , Anestésicos Dissociativos/efeitos adversos , Anestésicos Dissociativos/administração & dosagem , Administração Oral , Analgésicos/efeitos adversos , Analgésicos/administração & dosagem , Analgésicos/uso terapêutico , Laringismo/induzido quimicamente , Laringismo/epidemiologia , Incidência
5.
PLoS Biol ; 17(2): e3000153, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30807574

RESUMO

The transcriptional mechanisms driving lineage specification during development are still largely unknown, as the interplay of multiple transcription factors makes it difficult to dissect these molecular events. Using a cell-based differentiation platform to probe transcription function, we investigated the role of the key paraxial mesoderm and skeletal myogenic commitment factors-mesogenin 1 (Msgn1), T-box 6 (Tbx6), forkhead box C1 (Foxc1), paired box 3 (Pax3), Paraxis, mesenchyme homeobox 1 (Meox1), sine oculis-related homeobox 1 (Six1), and myogenic factor 5 (Myf5)-in paraxial mesoderm and skeletal myogenesis. From this study, we define a genetic hierarchy, with Pax3 emerging as the gatekeeper between the presomitic mesoderm and the myogenic lineage. By assaying chromatin accessibility, genomic binding and transcription profiling in mesodermal cells from mouse and human Pax3-induced embryonic stem cells and Pax3-null embryonic day (E)9.5 mouse embryos, we identified conserved Pax3 functions in the activation of the skeletal myogenic lineage through modulation of Hedgehog, Notch, and bone morphogenetic protein (BMP) signaling pathways. In addition, we demonstrate that Pax3 molecular function involves chromatin remodeling of its bound elements through an increase in chromatin accessibility and cooperation with sine oculis-related homeobox 4 (Six4) and TEA domain family member 2 (Tead2) factors. To our knowledge, these data provide the first integrated analysis of Pax3 function, demonstrating its ability to remodel chromatin in mesodermal cells from developing embryos and proving a mechanistic footing for the transcriptional hierarchy driving myogenesis.


Assuntos
Montagem e Desmontagem da Cromatina , Proteínas de Ligação a DNA/genética , Proteínas de Homeodomínio/genética , Mesoderma/metabolismo , Células Musculares/metabolismo , Desenvolvimento Muscular/genética , Fator de Transcrição PAX3/genética , Transativadores/genética , Fatores de Transcrição/genética , Animais , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Diferenciação Celular , Linhagem Celular , Proteínas de Ligação a DNA/metabolismo , Embrião de Mamíferos , Células-Tronco Embrionárias/citologia , Células-Tronco Embrionárias/metabolismo , Fatores de Transcrição Forkhead/genética , Fatores de Transcrição Forkhead/metabolismo , Regulação da Expressão Gênica no Desenvolvimento , Proteínas de Homeodomínio/metabolismo , Humanos , Mesoderma/citologia , Mesoderma/crescimento & desenvolvimento , Camundongos , Camundongos Transgênicos , Células Musculares/citologia , Músculo Esquelético/citologia , Músculo Esquelético/crescimento & desenvolvimento , Músculo Esquelético/metabolismo , Fator Regulador Miogênico 5/genética , Fator Regulador Miogênico 5/metabolismo , Fator de Transcrição PAX3/metabolismo , Transdução de Sinais , Proteínas com Domínio T , Fatores de Transcrição de Domínio TEA , Transativadores/metabolismo , Fatores de Transcrição/metabolismo
6.
Proc Natl Acad Sci U S A ; 116(7): 2640-2645, 2019 02 12.
Artigo em Inglês | MEDLINE | ID: mdl-30679280

RESUMO

Established T cell dysfunction is a barrier to antitumor responses, and checkpoint blockade presumably reverses this. Many patients fail to respond to treatment and/or develop autoimmune adverse events. The underlying reason for T cell responsiveness remains elusive. Here, we show that susceptibility to checkpoint blockade is dependent on the activation status of T cells. Newly activated self-specific CD8 T cells respond to checkpoint blockade and cause autoimmunity, which is mitigated by inhibiting the mechanistic target of rapamycin. However, once tolerance is established, self-specific CD8 T cells display a gene signature comparable to tumor-specific CD8 T cells in a fixed state of dysfunction. Tolerant self-specific CD8 T cells do not respond to single or combinatorial dosing of anti-CTLA4, anti-PD-L1, anti-PD-1, anti-LAG-3, and/or anti-TIM-3. Despite this, T cell responsiveness can be induced by vaccination with cognate antigen, which alters the previously fixed transcriptional signature and increases antigen-sensing machinery. Antigenic reeducation of tolerant T cells synergizes with checkpoint blockade to generate functional CD8 T cells, which eliminate tumors without concomitant autoimmunity and are transcriptionally distinct from classic effector T cells. These data demonstrate that responses to checkpoint blockade are dependent on the activation state of a T cell and show that checkpoint blockade-insensitive CD8 T cells can be induced to respond to checkpoint blockade with robust antigenic stimulation to participate in tumor control.


Assuntos
Linfócitos T CD8-Positivos/citologia , Linfócitos T CD8-Positivos/imunologia , Reprogramação Celular , Animais , Antígenos/imunologia , Antígeno B7-H1/antagonistas & inibidores , Antígeno B7-H1/imunologia , Proliferação de Células , Tolerância Imunológica , Ativação Linfocitária , Camundongos , Camundongos Endogâmicos C57BL
7.
Lab Invest ; 101(12): 1585-1596, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34489559

RESUMO

Osteosarcoma has a guarded prognosis. A major hurdle in developing more effective osteosarcoma therapies is the lack of disease-specific biomarkers to predict risk, prognosis, or therapeutic response. Exosomes are secreted extracellular microvesicles emerging as powerful diagnostic tools. However, their clinical application is precluded by challenges in identifying disease-associated cargo from the vastly larger background of normal exosome cargo. We developed a method using canine osteosarcoma in mouse xenografts to distinguish tumor-derived from host-response exosomal messenger RNAs (mRNAs). The model allows for the identification of canine osteosarcoma-specific gene signatures by RNA sequencing and a species-differentiating bioinformatics pipeline. An osteosarcoma-associated signature consisting of five gene transcripts (SKA2, NEU1, PAF1, PSMG2, and NOB1) was validated in dogs with spontaneous osteosarcoma by real-time quantitative reverse transcription PCR (qRT-PCR), while a machine learning model assigned dogs into healthy or disease groups. Serum/plasma exosomes were isolated from 53 dogs in distinct clinical groups ("healthy", "osteosarcoma", "other bone tumor", or "non-neoplastic disease"). Pre-treatment samples from osteosarcoma cases were used as the training set, and a validation set from post-treatment samples was used for testing, classifying as "osteosarcoma detected" or "osteosarcoma-NOT detected". Dogs in a validation set whose post-treatment samples were classified as "osteosarcoma-NOT detected" had longer remissions, up to 15 months after treatment. In conclusion, we identified a gene signature predictive of molecular remissions with potential applications in the early detection and minimal residual disease settings. These results provide proof of concept for our discovery platform and its utilization in future studies to inform cancer risk, diagnosis, prognosis, and therapeutic response.


Assuntos
Biomarcadores Tumorais/metabolismo , Osteossarcoma/metabolismo , Animais , Linhagem Celular Tumoral , Cães , Exossomos/metabolismo , Feminino , Humanos , Aprendizado de Máquina , Camundongos Nus , Transplante de Neoplasias , Osteossarcoma/diagnóstico , Cultura Primária de Células , Prognóstico , Células Estromais/fisiologia
8.
Plant Physiol ; 181(4): 1721-1738, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31578229

RESUMO

Cyanobacteria are complex prokaryotes, incorporating a Gram-negative cell wall and internal thylakoid membranes (TMs). However, localization of proteins within cyanobacterial cells is poorly understood. Using subcellular fractionation and quantitative proteomics, we produced an extensive subcellular proteome map of an entire cyanobacterial cell, identifying ∼67% of proteins in Synechocystis sp. PCC 6803, ∼1000 more than previous studies. Assigned to six specific subcellular regions were 1,712 proteins. Proteins involved in energy conversion localized to TMs. The majority of transporters, with the exception of a TM-localized copper importer, resided in the plasma membrane (PM). Most metabolic enzymes were soluble, although numerous pathways terminated in the TM (notably those involved in peptidoglycan monomer, NADP+, heme, lipid, and carotenoid biosynthesis) or PM (specifically, those catalyzing lipopolysaccharide, molybdopterin, FAD, and phylloquinol biosynthesis). We also identified the proteins involved in the TM and PM electron transport chains. The majority of ribosomal proteins and enzymes synthesizing the storage compound polyhydroxybuyrate formed distinct clusters within the data, suggesting similar subcellular distributions to one another, as expected for proteins operating within multicomponent structures. Moreover, heterogeneity within membrane regions was observed, indicating further cellular complexity. Cyanobacterial TM protein localization was conserved in Arabidopsis (Arabidopsis thaliana) chloroplasts, suggesting similar proteome organization in more developed photosynthetic organisms. Successful application of this technique in Synechocystis suggests it could be applied to mapping the proteomes of other cyanobacteria and single-celled organisms. The organization of the cyanobacterial cell revealed here substantially aids our understanding of these environmentally and biotechnologically important organisms.


Assuntos
Compartimento Celular , Proteoma/metabolismo , Proteômica , Synechocystis/citologia , Synechocystis/metabolismo , Arabidopsis/metabolismo , Proteínas de Bactérias/metabolismo , Fracionamento Celular , Membrana Celular/metabolismo , Parede Celular/metabolismo , Cloroplastos/metabolismo , Cloroplastos/ultraestrutura , Redes e Vias Metabólicas , Análise de Componente Principal , Subunidades Ribossômicas/metabolismo , Synechocystis/ultraestrutura
10.
J Pediatr Gastroenterol Nutr ; 69(3): 383-387, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31107793

RESUMO

OBJECTIVES: Behavioral intervention is the only treatment for pediatric feeding problems with well documented empirical support. However, parents may be hesitant to pursue behavioral intervention because of concerns about possible negative side effects on child behavioral health and the parent-child relationship. This study investigated associations between behavioral feeding treatment and parenting stress, internalizing and externalizing behavior problems in young children, and parent-child attachment quality. METHODS: Participants included 16 mother-child dyads seeking treatment from a behavioral feeding clinic at a large Midwestern university medical center. Children were between the ages of 30 and 45 months (adjusted) at baseline. Caregivers completed the Child Behavior Checklist for ages 1.5 to 5 (CBCL/1.5-5), the Parenting Stress Index, 3rd Edition Short Form (PSI/SF), and mother-child dyads participated in the Strange Situation procedure at baseline and again after 6 months. The treatment group (n = 12) began outpatient behavioral feeding intervention following the baseline evaluation, whereas the control group (n = 12) remained on the clinic waitlist until after the 6-month follow-up. RESULTS: The treatment group demonstrated decreases in internalizing and externalizing child behavior problems and parenting stress compared with the control group. No significant differences were demonstrated in parent-child attachment quality within or between groups. CONCLUSIONS: Behavioral feeding intervention had positive effects on perceptions of child emotional and behavioral functioning and maternal parenting stress. Intervention also did not impact the quality of the mother-child attachment relationship. Further research with a larger sample size and additional observational measures of behavior is needed to support the replicability and generalizability of these results.


Assuntos
Transtornos da Alimentação e da Ingestão de Alimentos/psicologia , Relações Pais-Filho , Pais/psicologia , Estresse Psicológico , Adulto , Terapia Comportamental , Pré-Escolar , Feminino , Humanos , Masculino , Psicometria , Resultado do Tratamento
11.
Nucleic Acids Res ; 45(10): e78, 2017 Jun 02.
Artigo em Inglês | MEDLINE | ID: mdl-28130425

RESUMO

The detailed analysis of the impact of deletions on proteins or nucleic acids can reveal important functional regions and lead to variants with improved macromolecular properties. We present a method to generate large libraries of mutants with deletions of varying length that are randomly distributed throughout a given gene. This technique facilitates the identification of crucial sequence regions in nucleic acids or proteins. The approach utilizes in vitro transposition to generate 5΄ and 3΄ fragment sub-libraries of a given gene, which are then randomly recombined to yield a final library comprising both terminal and internal deletions. The method is easy to implement and can generate libraries in three to four days. We used this approach to produce a library of >9000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible deletions. The quality of the library was assessed by next-generation sequencing and detailed bioinformatics analysis. Finally, we subjected this library to in vitro selection and obtained fully functional variants with deletions of up to 18 amino acids of the parental enzyme that had been 95 amino acids in length.


Assuntos
Sequência de Aminoácidos , DNA/genética , Biblioteca Gênica , Deleção de Sequência , Transposases/genética , Região 3'-Flanqueadora , Região 5'-Flanqueadora , Biologia Computacional , DNA/metabolismo , Primers do DNA/genética , Primers do DNA/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Diester Fosfórico Hidrolases/genética , Diester Fosfórico Hidrolases/metabolismo , Plasmídeos/química , Plasmídeos/metabolismo , Reação em Cadeia da Polimerase , RNA Ligase (ATP)/genética , RNA Ligase (ATP)/metabolismo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Transposases/metabolismo , beta-Lactamases/genética , beta-Lactamases/metabolismo
12.
Br J Cancer ; 119(7): 864-872, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30287918

RESUMO

BACKGROUND: Abnormal DNA methylation may be important in germ cell tumour (GCT) aetiology, as germ cells undergo complete epigenetic reprogramming during development. GCTs show differences in global and promoter methylation patterns by histologic subtype. We conducted an epigenome-wide study to identify methylation differences by GCT histology. METHODS: Using the Illumina HumanMethylation450K array we measured methylation in 154 paediatric GCTs (21 germinomas/seminomas/dysgerminoma, 70 yolk sac tumours [YST], 9 teratomas, and 54 mixed histology tumours). We identified differentially methylated regions (DMRs) between GCT histologies by comparing methylation beta values. RESULTS: We identified 8,481 DMRs (FWER < 0.05). Unsupervised hierarchical clustering of individual probes within DMRs resulted in four high level clusters closely corresponding to tumour histology. Clusters corresponding to age, location, sex and FFPE status were not observed within these DMRs. Germinomas displayed lower levels of methylation across the DMRs relative to the other histologic subtypes. Pathway analysis on the top 10% of genes with differential methylation in germinomas/seminomas/dysgerminoma compared to YST suggested angiogenesis and immune cell-related pathways displayed decreased methylation in germinomas/seminomas/dysgerminoma relative to YST. CONCLUSIONS: Paediatric GCT histologies have differential methylation patterns. The genes that are differentially methylated may provide insights into GCT aetiology including the timing of GCT initiation.


Assuntos
Metilação de DNA , Tumor do Seio Endodérmico/genética , Epigenômica/métodos , Germinoma/genética , Neoplasias Embrionárias de Células Germinativas/genética , Neoplasias Ovarianas/genética , Neoplasias Testiculares/genética , Adolescente , Criança , Pré-Escolar , Aprendizado Profundo , Disgerminoma/genética , Epigênese Genética , Feminino , Humanos , Lactente , Recém-Nascido , Masculino , Análise de Componente Principal , Regiões Promotoras Genéticas , Seminoma/genética
13.
Cultur Divers Ethnic Minor Psychol ; 23(4): 595-600, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28333478

RESUMO

OBJECTIVE: To determine whether geographic access to licensed mental health providers in California is a barrier for underserved populations. METHOD: Data from the master file of the California Board of Psychology and Board of Behavioral Sciences were merged with U.S. Census data to determine the correlations between the concentration of providers and the corresponding sociodemographic characteristics of places in California. RESULTS: This article shows that the concentration of licensed mental health providers in the communities of California varies systematically with the racial, ethnic, age, education, and economic characteristics of those places. Specifically, licensed mental health providers are more concentrated in places that are wealthier, Whiter, older, and more educated. CONCLUSIONS: Policy and advocacy efforts in health service psychology can help assure more equitable distribution of mental health services. (PsycINFO Database Record


Assuntos
Serviços Comunitários de Saúde Mental/provisão & distribuição , Pessoal de Saúde/estatística & dados numéricos , Acessibilidade aos Serviços de Saúde/estatística & dados numéricos , Transtornos Mentais/terapia , Área de Atuação Profissional/estatística & dados numéricos , Adulto , California , Etnicidade , Feminino , Setor de Assistência à Saúde/estatística & dados numéricos , Humanos , Masculino , Pessoa de Meia-Idade , Fatores Socioeconômicos
14.
Bioinformatics ; 29(23): 3007-13, 2013 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-23995390

RESUMO

MOTIVATION: Sequence similarity searches performed with BLAST, SSEARCH and FASTA achieve high sensitivity by using scoring matrices (e.g. BLOSUM62) that target low identity (<33%) alignments. Although such scoring matrices can effectively identify distant homologs, they can also produce local alignments that extend beyond the homologous regions. RESULTS: We measured local alignment start/stop boundary accuracy using a set of queries where the correct alignment boundaries were known, and found that 7% of BLASTP and 8% of SSEARCH alignment boundaries were overextended. Overextended alignments include non-homologous sequences; they occur most frequently between sequences that are more closely related (>33% identity). Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries. In addition, the scoring matrix that produced a correct alignment could be reliably predicted based on the sequence identity seen in the original BLOSUM62 alignment. Realigning with the predicted scoring matrix corrected 37% of all overextended alignments, resulting in more correct alignments than using BLOSUM62 alone.


Assuntos
Biologia Computacional/métodos , Matrizes de Pontuação de Posição Específica , Proteínas/química , Alinhamento de Sequência/métodos , Análise de Sequência de Proteína/métodos , Algoritmos , Sequência de Aminoácidos , Bases de Dados de Proteínas , Dados de Sequência Molecular , Homologia de Sequência de Aminoácidos
15.
HGG Adv ; : 100356, 2024 Sep 26.
Artigo em Inglês | MEDLINE | ID: mdl-39340156

RESUMO

The aim of this study was to scan phenotypes in adulthood associated with polygenic risk scores (PRS) for childhood cancers with well-articulated genetic architectures: acute lymphoblastic leukemia (ALL), Ewing sarcoma, and neuroblastoma to examine genetic pleiotropy. Furthermore, we aimed to determine which single nucleotide polymorphisms (SNPs) could drive associations. Per-SNP summary statistics were extracted for PRS calculation. Participants with white British ancestry were exclusively included for analyses. SNPs were queried from the UK biobank genotype imputation data. Records from the cancer registry, death registry, and inpatient diagnoses were abstracted for phenome-wide scans. Firth logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) alongside corresponding p-values, adjusting for age at recruitment and sex. A total of 244,332 unrelated white British participants were included. We observed a significant association between ALL-PRS and ALL (OR: 1.20e+24, 95% CI: 9.08e+14-1.60e+33). In addition, we observed a significant association between high-risk neuroblastoma PRS and nonrheumatic aortic valve disorders (OR: 43.9, 95% CI: 7.42-260). There were no significant phenotype associations with Ewing sarcoma and neuroblastoma PRS. Regarding individual SNPs, rs17607816 increased the risk of ALL (OR: 6.40, 95% CI: 3.26-12.57). For high-risk neuroblastoma, rs80059929 elevated the risk of atrioventricular block (OR: 3.04, 95% CI: 1.85-4.99). Our findings suggest that individuals with genetic susceptibility to ALL may face a lifelong risk for developing ALL, along with a genetic pleiotropic association between high-risk neuroblastoma and circulatory diseases.

16.
HGG Adv ; 5(1): 100254, 2024 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-37919896

RESUMO

Knowledge of Ewing sarcoma (EWS) risk factors is exceedingly limited; however, multiple small, independent studies have suggested a possible connection between hernia and EWS. By leveraging hernia summary statistics from the UK Biobank and a recently published genome-wide association study of EWS (733 EWS cases and 1,346 controls), we conducted a genetic investigation of the relationship of 5 hernia types (diaphragmatic, inguinal, umbilical, femoral, and ventral) and EWS. We discovered a positive causal relationship between inguinal hernia and EWS (OR 1.27, 95% confidence interval [CI] 1.01-1.59, and p = 0.041) through Mendelian randomization analysis. Further analyses suggested shared pathways through three genes: HMGA2, LOX, and FBXW7. Diaphragmatic hernia showed a stronger causal relationship with EWS among all of the hernia types (OR 2.26, 95% CI 1.30-3.95, p = 0.004), but no statistically significant local correlation pattern was observed. No evidence of a causal or genetic relationship was observed between EWS and the other three hernia types, including umbilical hernia, despite a previous report indicating an OR as high as 3.3. The finding of our genetic analysis provided additional support to the hypothesis that EWS and hernias may share a common origin.


Assuntos
Hérnia Inguinal , Sarcoma de Ewing , Humanos , Sarcoma de Ewing/epidemiologia , Estudo de Associação Genômica Ampla , Hérnia Inguinal/epidemiologia
17.
Nat Commun ; 15(1): 2025, 2024 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-38448455

RESUMO

The timing and fitness effect of somatic copy number alterations (SCNA) in cancer evolution remains poorly understood. Here we present a framework to determine the timing of a clonal SCNA that encompasses multiple gains. This involves calculating the proportion of time from its last gain to the onset of population expansion (lead time) as well as the proportion of time prior to its first gain (initiation time). Our method capitalizes on the observation that a genomic segment, while in a specific copy number (CN) state, accumulates point mutations proportionally to its CN. Analyzing 184 whole genome sequenced samples from 75 patients across five tumor types, we commonly observe late gains following early initiating events, occurring just before the clonal expansion relevant to the sampling. These include gains acquired after genome doubling in more than 60% of cases. Notably, mathematical modeling suggests that late clonal gains may contain final-expansion drivers. Lastly, SCNAs bolster mutational diversification between subpopulations, exacerbating the circle of proliferation and increasing heterogeneity.


Assuntos
Variações do Número de Cópias de DNA , Mutação Puntual , Humanos , Variações do Número de Cópias de DNA/genética , Mutação , Cognição , Exercício Físico
18.
J Athl Train ; 2024 Sep 17.
Artigo em Inglês | MEDLINE | ID: mdl-39287079

RESUMO

CONTEXT: Majority of research surrounding the predictive value of clinical measurements and assessments for future athletic injury does not differentiate between contact and non-contact injuries. OBJECTIVE: We assessed the association between clinical measures and questionnaire data collected prior to sport participation and the incidence of non-contact lower extremity (LE) injuries among Division III collegiate athletes. DESIGN: Prospective cohort study. SETTING: University setting, NCAA Division III. PARTICIPANTS: 488 Division III freshmen athletes were recruited to participate in the study during their preseason physical examinations. PATIENTS OR OTHER PARTICIPANTS: 10,983 public schools. MAIN OUTCOME MEASURE: Prospective incidence of non-contact Lower extremity Injury. METHODS: Athletes completed questionnaires to collect demographics and musculoskeletal pain history. Clinical tests, performed by trained examiners, included hip provocative tests, visual appraisal of a single leg squat to identify dynamic knee valgus, and hip range of motion (ROM). Injury surveillance for each athlete's collegiate career was performed. The athletic training department documented each athlete-reported, new onset injury and documented the injury location, type, and outcome (days lost, surgery performed). Univariable Generalized Estimating Equations (GEE) models were used to analyze the relationship between each clinical measure and the first occurrence of non-contact LE injury. An exchangeable correlation structure was used to account for repeated measurements within athletes (right and left limbs). RESULTS: Of the 488 athletes, 369 athletes (75%) were included in the final analysis. 69 non-contact LE injuries were reported. Responding "Yes" to "Have you ever had pain or an injury to your low back" was associated with an increased risk of non-contact LE, odds ratio = 1.59 (95%CI 1.03- 2.45, p=.04). No other clinical measures were associated with increased injury risk. CONCLUSION: A history of prior low back pain or injury was associated with an increased risk of sustaining a non-contact LE injury while participating in NCAA Division III athletics.

19.
J Heart Lung Transplant ; 43(2): 303-313, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37783299

RESUMO

BACKGROUND: Right ventricular failure (RVF) is a leading cause of morbidity and mortality in multiple cardiovascular diseases, but there are no treatments for RVF as therapeutic targets are not clearly defined. Contemporary transcriptomic/proteomic evaluations of RVF are predominately conducted in small animal studies, and data from large animal models are sparse. Moreover, a comparison of the molecular mediators of RVF across species is lacking. METHODS: Transcriptomics and proteomics analyses defined the pathways associated with cardiac magnetic resonance imaging (MRI)-derived values of RV hypertrophy, dilation, and dysfunction in control and pulmonary artery banded (PAB) pigs. Publicly available data from rat monocrotaline-induced RVF and pulmonary arterial hypertension patients with preserved or impaired RV function were used to compare molecular responses across species. RESULTS: PAB pigs displayed significant right ventricle/ventricular (RV) hypertrophy, dilation, and dysfunction as quantified by cardiac magnetic resonance imaging. Transcriptomic and proteomic analyses identified pathways associated with RV dysfunction and remodeling in PAB pigs. Surprisingly, disruptions in fatty acid oxidation (FAO) and electron transport chain (ETC) proteins were different across the 3 species. FAO and ETC proteins and transcripts were mostly downregulated in rats but were predominately upregulated in PAB pigs, which more closely matched the human response. All species exhibited similar dysregulation of the dilated cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy pathways. CONCLUSIONS: The porcine metabolic molecular signature was more similar to human RVF than rodents. These data suggest there may be divergent molecular responses of RVF across species, and pigs may more accurately recapitulate metabolic aspects of human RVF.


Assuntos
Insuficiência Cardíaca , Disfunção Ventricular Direita , Humanos , Ratos , Animais , Suínos , Multiômica , Proteômica , Hipertrofia Ventricular Direita/diagnóstico por imagem , Hipertrofia Ventricular Direita/etiologia , Hipertrofia Ventricular Direita/patologia , Função Ventricular Direita , Modelos Animais de Doenças , Remodelação Ventricular/fisiologia
20.
J Clin Nurs ; 22(19-20): 2838-48, 2013 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-23311643

RESUMO

AIMS AND OBJECTIVES: To develop and test strategies to reduce interruptions to enteral feeding to improve practice and promote attainment of nutritional goals. BACKGROUND: Enteral nutrition is preferred for feeding patients in the intensive care unit who are unable to have oral nutrition. Interruption to feeding is likely to be a major contributor to patients not receiving their prescribed nutrition goals. DESIGN: Prospective before (May-November 2009) and after (March-September 2010) study. METHOD: Patients admitted to the intensive care unit (except cardiac surgery) and who were eligible to receive enteral nutrition were enrolled. After gaining Ethics Committee approval, baseline data were collected to identify interruptions to enteral nutrition. Nurse-led multidisciplinary teams developed interventions to target specific reasons for interruption. Change champions implemented the improvements after staff were provided with an education package. Postintervention data were then collected. RESULTS: Six hundred and fifty-three patients received enteral nutrition with the majority (88%) fed within 48 hours. Considering the first 28 days of feeding for patients fed longer than 24 hours (505 patients), the number of interruptions for patients who had an interruption decreased from 907-662. Interruptions due to gastrointestinal issues decreased (14 vs 10%), while those due to airway issues, enteral nutrition delivery system problems and other interruptions were similar before-and-after the practice change. Time lost to feeding because of interruptions was similar between groups. CONCLUSION: Targeted strategies to enteral feeding practice resulted in a reduction to the number of interruptions but not the duration of enteral nutrition lost to interruption. Reducing unnecessary interruption of feeding circuits is likely to minimise the risk for splash injury and contamination of feeding sets through less manipulation and interruption to enteral nutrition flow. RELEVANCE TO CLINICAL PRACTICE: Review of practice may reveal opportunities for improvement. Nurse champions can facilitate change processes to improve care.


Assuntos
Nutrição Enteral/métodos , Unidades de Terapia Intensiva/organização & administração , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade
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