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1.
Am J Med Genet A ; : e63818, 2024 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-39041659

RESUMO

Despite advances in next generation sequencing (NGS), genetic diagnoses remain elusive for many patients with neurologic syndromes. Long-read sequencing (LRS) and optical genome mapping (OGM) technologies improve upon existing capabilities in the detection and interpretation of structural variation in repetitive DNA, on a single haplotype, while also providing enhanced breakpoint resolution. We performed LRS and OGM on two patients with known chromosomal rearrangements and inconclusive Sanger or NGS. The first patient, who had epilepsy and developmental delay, had a complex translocation between two chromosomes that included insertion and inversion events. The second patient, who had a movement disorder, had an inversion on a single chromosome disrupted by multiple smaller inversions and insertions. Sequence level resolution of the rearrangements identified pathogenic breaks in noncoding sequence in or near known disease-causing genes with relevant neurologic phenotypes (MBD5, NKX2-1). These specific variants have not been reported previously, but expected molecular consequences are consistent with previously reported cases. As the use of LRS and OGM technologies for clinical testing increases and data analyses become more standardized, these methods along with multiomic data to validate noncoding variation effects will improve diagnostic yield and increase the proportion of probands with detectable pathogenic variants for known genes implicated in neurogenetic disease.

2.
J Pediatr ; 261: 113483, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37192722

RESUMO

OBJECTIVE: To evaluate the neurodevelopmental outcomes at 5.5 years of age in children who were previously randomized to cow milk-based infant formula (control) or similar formula (milk fat globule membrane + lactoferrin) with added sources of bovine milk fat globule membrane and bovine lactoferrin through 12 months of age. DESIGN: Children who completed study feeding were invited to participate in follow-up assessments: cognitive development across multiple domains (primary outcome; Wechsler Preschool & Primary Scale of Intelligence, 4th Edition), inhibitory control/rule learning (Stroop Task), flexibility/rule learning (Dimensional Change Card Sort), and behavior/emotion (Child Behavior Checklist). RESULTS: Of 292 eligible participants (control: 148, milk fat globule membrane + lactoferrin: 144), 116 enrolled and completed assessments (control: 59, milk fat globule membrane + LF: 57). There were no group demographic differences except family income (milk fat globule membrane + lactoferrin significantly higher). Wechsler Preschool & Primary Scale of Intelligence, 4th Edition composite scores (mean ± standard error) for Visual Spatial (100.6 ± 1.7 vs 95.3 ± 1.7; P = .027), Processing Speed (107.1 ± 1.4 vs 100.0 ± 1.4; P < .001), and Full-Scale IQ (98.7 ± 1.4 vs 93.5 ± 1.5; P = .012) were significantly higher for milk fat globule membrane + lactoferrin versus control, even after controlling for demographic/socioeconomic factors. Stroop Task scores were significantly higher in milk fat globule membrane + lactoferrin versus control (P < .001). Higher Dimensional Change Card Sort scores (P = .013) in the border phase (most complex/challenging) were detected, and more children passed the border phase (32% vs 12%; P = .039) for milk fat globule membrane versus control. No group differences in Child Behavior Checklist score were detected. CONCLUSIONS: Children who received infant formula to 12 months of age with added bovine milk fat globule membrane and bovine lactoferrin versus standard formula demonstrated improved cognitive outcomes in multiple domains at 5.5 years of age, including measures of intelligence and executive function. TRIAL REGISTRATION: Clinicaltrials.gov: https://clinicaltrials.gov/ct2/show/NCT04442477.


Assuntos
Fórmulas Infantis , Lactoferrina , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Glicolipídeos , Glicoproteínas , Lactoferrina/farmacologia
3.
J Nutr ; 153(2): 511-522, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36894243

RESUMO

BACKGROUND: Bovine milk fat globule membrane (MFGM) added in infant formula supports typical growth and safety through 24 mo of age in term infants. OBJECTIVES: To assess micronutrient (zinc, iron, ferritin, transferrin receptor), metabolic [glucose, insulin, Homeostatic Model Assessment of Insulin Resistance (HOMA-IR), insulin-like growth factor-1 (IGF-1), triglycerides (TGs), total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C)], and inflammatory (leptin, adiponectin, high sensitivity C-reactive protein) secondary outcomes through 24 mo of age in infants who received standard cow's milk-based infant formula (SF), similar formula with added bovine MFGM (EF), or human milk (HM) through 1 y. METHODS: Infants whose parents agreed to a blood draw at baseline (<120 d of age) (SF = 80; EF = 80; HM = 83) were included. Subsequent collections (2-4 h fasting) occurred at D180, D365, and D730. Biomarker concentrations were analyzed and group changes tested using generalized estimating equations models. RESULTS: Only serum iron (+22.1 µg/dL) and HDL-C (+2.5 mg/dL) were significantly higher for EF compared with SF at D730. Prevalence of zinc deficiency for EF (-17.4%) and SF (-16.6%) at D180 and depleted iron stores for SF (+21.4%) at D180 and EF (-34.6%) and SF (-28.0%) at D365 were significantly different compared with HM. IGF-1 (ng/mL) for EF and SF was significantly higher at D180 (+8.9) and for EF (+8.8) at D365, and (+14.5) at D730 compared with HM. Insulin (µUI/mL) for EF (+2.5) and SF (+5.8) and HOMA-IR for EF (+0.5) and SF (+0.6) were significantly higher compared with HM at D180. TGs (mg/dL) for SF (+23.9) at D180, for EF (+19.0) and SF (+17.8) at D365, and EF (+17.3) and SF (+14.5) at D730 were significantly higher compared with HM. Zinc, ferritin, glucose, LDL-C and total cholesterol changes were higher in formula groups compared with HM between various time points. CONCLUSIONS: Micronutrient, metabolic, and inflammatory biomarkers were generally similar through 2 y in infants who received infant formula with or without added bovine MFGM. Over the 2 y, differences were observed between infant formulas and HM reference group. This trial was registered at clinicaltrials.gov as NTC02626143.


Assuntos
Insulinas , Oligoelementos , Animais , Feminino , Bovinos , Humanos , Lactente , Fator de Crescimento Insulin-Like I , Micronutrientes , LDL-Colesterol , Fórmulas Infantis , Biomarcadores , Leite Humano , Zinco , Ferro
4.
PLoS Biol ; 18(12): e3001001, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33362208

RESUMO

Histone variants expand chromatin functions in eukaryote genomes. H2A.B genes are testis-expressed short histone H2A variants that arose in placental mammals. Their biological functions remain largely unknown. To investigate their function, we generated a knockout (KO) model that disrupts all 3 H2A.B genes in mice. We show that H2A.B KO males have globally altered chromatin structure in postmeiotic germ cells. Yet, they do not show impaired spermatogenesis or testis function. Instead, we find that H2A.B plays a crucial role postfertilization. Crosses between H2A.B KO males and females yield embryos with lower viability and reduced size. Using a series of genetic crosses that separate parental and zygotic contributions, we show that the H2A.B status of both the father and mother, but not of the zygote, affects embryonic viability and growth during gestation. We conclude that H2A.B is a novel parental-effect gene, establishing a role for short H2A histone variants in mammalian development. We posit that parental antagonism over embryonic growth drove the origin and ongoing diversification of short histone H2A variants in placental mammals.


Assuntos
Desenvolvimento Embrionário/genética , Histonas/genética , Animais , Cromatina/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento/genética , Variação Genética , Genoma/genética , Histonas/metabolismo , Infertilidade Masculina/genética , Masculino , Camundongos/embriologia , Camundongos Knockout , Testículo/embriologia , Testículo/metabolismo
5.
Analyst ; 148(4): 863-868, 2023 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-36651278

RESUMO

Semiconducting polymer dots (Pdots) have received much attention due to their unique characteristics, including high water solubility, good light stability, excellent biocompatibility, and low cost. Herein, we report a ratiometric nanoprobe based on Pdots-Eu for temperature sensing in vitro. The Pdots-Eu thermometer was composed of a blue temperature-insensitive semiconducting polymer, poly(9-vinylcarbazole) (PVK), a red temperature-sensitive complex tris(dibenzoylmethane)mono(5-amino-1,10-phenanthroline)europium (III) (Eu complex), and an amphiphilic polymer polystyrene graft ethylene oxide functionalized with carboxyl groups (PS-PEG-COOH). The Pdots-Eu thermometer showed two peaks at 368 nm from PVK and 611 nm from the Eu complex. The red/blue fluorescence intensity ratio of Pdots-Eu decreased with an increase in temperature, which could be used for the ratiometric monitoring of temperature change. The results showed that the red/blue fluorescence intensity ratio demonstrated a good linear relationship to the change of temperature from 25 °C to 55 °C. Impressively, the ratiometric probe featured good accuracy and high sensitivity for temperature detection in vitro, which could be used for monitoring temperature change in cells.

6.
Molecules ; 28(5)2023 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-36903280

RESUMO

Semiconductiong polymer nanoparticles (Pdots) have a wide range of applications in biomedical fields including biomolecular probes, tumor imaging, and therapy. However, there are few systematic studies on the biological effects and biocompatibility of Pdots in vitro and in vivo. The physicochemical properties of Pdots, such as surface modification, are very important in biomedical applications. Focusing on the central issue of the biological effects of Pdots, we systematically investigated the biological effects and biocompatibility of Pdots with different surface modifications and revealed the interactions between Pdots and organisms at the cellular and animal levels. The surfaces of Pdots were modified with different functional groups, including thiol, carboxyl, and amino groups, named Pdots@SH, Pdots@COOH, and Pdots@NH2, respectively. Extracellular studies showed that the modification of sulfhydryl, carboxyl, and amino groups had no significant effect on the physicochemical properties of Pdots, except that the amino modification affected the stability of Pdots to a certain extent. At the cellular level, Pdots@NH2 reduced cellular uptake capacity and increased cytotoxicity due to their instability in solution. At the in vivo level, the body circulation and metabolic clearance of Pdots@SH and Pdots@COOH were superior to those of Pdots@NH2. The four kinds of Pdots had no obvious effect on the blood indexes of mice and histopathological lesions in the main tissues and organs. This study provides important data for the biological effects and safety assessment of Pdots with different surface modifications, which pave the way for their potential biomedical applications.


Assuntos
Nanopartículas , Semicondutores , Animais , Polímeros/química , Imagem Óptica/métodos
7.
New Phytol ; 234(5): 1832-1847, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35263447

RESUMO

Mosses harbor fungi whose interactions within their hosts remain largely unexplored. Trophic ranges of fungal endophytes from the moss Dicranum scoparium were hypothesized to encompass saprotrophism. This moss is an ideal host to study fungal trophic lability because of its natural senescence gradient, and because it can be grown axenically. Dicranum scoparium was co-cultured with each of eight endophytic fungi isolated from naturally occurring D. scoparium. Moss growth rates, and gene expression levels (RNA sequencing) of fungi and D. scoparium, were compared between axenic and co-culture treatments. Functional lability of two fungal endophytes was tested by comparing their RNA expression levels when colonizing living vs dead gametophytes. Growth rates of D. scoparium were unchanged, or increased, when in co-culture. One fungal isolate (Hyaloscyphaceae sp.) that promoted moss growth was associated with differential expression of auxin-related genes. When grown with living vs dead gametophytes, Coniochaeta sp. switched from having upregulated carbohydrate transporter activity to upregulated oxidation-based degradation, suggesting an endophytism to saprotrophism transition. However, no such transition was detected for Hyaloscyphaceae sp. Individually, fungal endophytes did not negatively impact growth rates of D. scoparium. Our results support the long-standing hypothesis that some fungal endophytes can switch to saprotrophism.


Assuntos
Ascomicetos , Briófitas , Bryopsida , Ascomicetos/genética , Briófitas/genética , Bryopsida/genética , Técnicas de Cocultura , Endófitos , Fungos/genética , Transcriptoma/genética
8.
PLoS Comput Biol ; 17(9): e1008949, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34516547

RESUMO

A current strategy for obtaining haplotype information from several individuals involves short-read sequencing of pooled amplicons, where fragments from each individual is identified by a unique DNA barcode. In this paper, we report a new method to recover the phylogeny of haplotypes from short-read sequences obtained using pooled amplicons from a mixture of individuals, without barcoding. The method, AFPhyloMix, accepts an alignment of the mixture of reads against a reference sequence, obtains the single-nucleotide-polymorphisms (SNP) patterns along the alignment, and constructs the phylogenetic tree according to the SNP patterns. AFPhyloMix adopts a Bayesian inference model to estimate the phylogeny of the haplotypes and their relative abundances, given that the number of haplotypes is known. In our simulations, AFPhyloMix achieved at least 80% accuracy at recovering the phylogenies and relative abundances of the constituent haplotypes, for mixtures with up to 15 haplotypes. AFPhyloMix also worked well on a real data set of kangaroo mitochondrial DNA sequences.


Assuntos
Código de Barras de DNA Taxonômico , Filogenia , Algoritmos , Teorema de Bayes , DNA Mitocondrial/genética , Humanos , Cadeias de Markov , Método de Monte Carlo , Polimorfismo de Nucleotídeo Único
9.
Dig Dis Sci ; 67(11): 5309-5314, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-35244827

RESUMO

BACKGROUND: Chronic hepatitis B virus (HBV) is a major public health concern. Transient elastrography (TE) is a reliable method in assessing hepatic fibrosis in patients with liver disease. We assess the potential clinical associations between HBsAg seroclearance and the severity of liver fibrosis. METHODS: We retrospectively performed a matched analysis of 23 consecutive HBsAg seroclearance patients who underwent TE between March 2008 and August 2021 from a community practice at a 1:3 ratio based on clinic visit date. Baseline laboratory and clinical data were collected. Fisher's exact test and Chi-square test for proportions, and Wilcoxon rank-sum test for median were performed. RESULTS: Twenty-three cases and 69 controls were identified. Median follow up (interquartile range) for the cases and controls was 24,314 (1402) and 2332 (1587) days (p = 0.15), respectively. All patients were Asian. Median age of cases was higher than controls (64 vs 52, p < 0.01, respectively). While most comorbidities were similar, diabetes and hyperlipidemia were more prevalent in cases. Baseline HBV DNA was detectable in 78% of cases and 97% of controls (p < 0.01). More cases had baseline HBsAg titers below 1000 IU/mL than controls (81% vs 8.7%, p < 0.01). Other baseline laboratory values were similar. Few cases had a fibrosis score greater than 1, while control had over a quarter of patients with a fibrosis score of 2 or 3. CONCLUSION: Spontaneous HBsAg seroclearance remains rare in patients with chronic HBV infection. It is associated with low baseline HBsAg, and lower level of liver fibrosis as detected by TE.


Assuntos
Hepatite B Crônica , Humanos , Hepatite B Crônica/complicações , Antígenos de Superfície da Hepatite B , DNA Viral/análise , Estudos Retrospectivos , Cirrose Hepática/diagnóstico , Cirrose Hepática/epidemiologia
10.
J Clin Gastroenterol ; 54(6): 573-576, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32049690

RESUMO

BACKGROUND: The cure for hepatitis B is defined as the hepatitis B surface antigen (HBsAg) seroclearance and/or seroconversion. Predictors of spontaneous seroconversion are not well described. The objective of this study is to identify predictors of spontaneous HBsAg seroconversion from community practice. METHODS: We performed a matched analysis of patients who HBsAg seroconverted (cases) and patients who did not HBsAg seroconvert (control) in a 1:5 ratio according to date of clinic visit between 2014 and 2019 in a large community practice situated in Los Angeles area. Baseline laboratory and clinical data were collected. Univariate analysis and 2-sided t tests were performed, χ test for proportions, and logistic regression. RESULTS: We identified 14 cases and 70 controls. The mean (±SD) ages of the cases and controls were 53.6 (±12.2) and 49.5 (±13.1), respectively (P=0.45). Most patients were women, and all patients were of Asian descent. There were statistically significant mean (±SD) baseline differences between cases and controls in HBsAg titers (459.8±311.0 and 782.0±393.3 IU/mL, P=0.01) and alanine aminotransferase (ALT) values (17.6±4.4 and 25.1±16.7 IU/mL, P<0.01), respectively. Baseline hepatitis B virus DNA and other pertinent laboratory values did not differ between cases and controls. Eleven of 14 cases (79%) and 11 of 70 controls (16%) baseline HBsAg titers were <1000 IU/mL (P<0.01). The results of a logistic regression demonstrated that HBsAg titers and ALT values were predictor variables for HBsAg seroconversion (P=0.01 and <0.01, respectively). CONCLUSIONS: Spontaneous HBsAg seroclearance and seroconversion is an uncommon event in patients with chronic hepatitis B. The most important predictors of seroconversion are HBsAg titers<1000 IU/mL and low baseline ALT values.


Assuntos
Hepatite B Crônica , Hepatite B , Antivirais/uso terapêutico , DNA Viral , Feminino , Hepatite B/diagnóstico , Hepatite B/tratamento farmacológico , Antígenos de Superfície da Hepatite B , Antígenos E da Hepatite B , Vírus da Hepatite B/genética , Hepatite B Crônica/diagnóstico , Hepatite B Crônica/tratamento farmacológico , Humanos , Los Angeles , Soroconversão
11.
BMC Pediatr ; 20(1): 225, 2020 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-32423392

RESUMO

BACKGROUND: A central aim for pediatric nutrition is to develop infant formula compositionally closer to human milk. Milk fat globule membranes (MFGM) have shown to have functional components that are found in human milk, suggesting that addition of bovine sources of MFGM (bMFGM) to infant formula may promote beneficial outcomes potentially helping to narrow the gap between infants who receive human breast milk or infant formula. The objective of the current study is to determine how the addition of bMFGM in infant formula and consumption in early infancy affects physical growth and brain development when compared to infants fed with a standard formula and a reference group of infants fed with mother's own milk. METHODS: Single center, double-blind, and parallel randomized controlled trial. Planned participant enrollment includes: infants exclusively receiving breast milk (n = 200; human milk reference group; HM) and infants whose mothers chose to initiate exclusive infant formula feeding before 4 months of age (n = 340). The latter were randomized to receive one of two study formulas until 12 months of age: 1) cow's milk based infant formula that had docosahexaenoic (DHA) (17 mg/100 kcal) and arachidonic acid (ARA) (25 mg/100 kcal); 1.9 g protein/100 kcal; 1.2 mg Fe/100 kcal (Standard formula; SF) or 2) a similar infant formula with an added source of bovine MFGM (whey protein-lipid concentrate (Experimental formula; EF). Primary outcomes will be: 1) Physical growth (Body weight, length, and head circumference) at 730 days of age; and 2) Cognitive development (Auditory Event-Related Potential) at 730 days of age. Data will be analyzed for all participants allocated to each study feeding group. DISCUSSION: The results of this study will complement the knowledge regarding addition of bMFGM in infant formula including support of healthy growth and improvement of neurodevelopmental outcomes. TRIAL REGISTRATION: NCT02626143, registered on December 10th 2015.


Assuntos
Fórmulas Infantis , Fenômenos Fisiológicos da Nutrição do Lactente , Animais , Aleitamento Materno , Bovinos , Criança , Pré-Escolar , Chile , Cognição , Feminino , Humanos , Lactente , Leite Humano , Ensaios Clínicos Controlados Aleatórios como Assunto
12.
J Mol Cell Cardiol ; 127: 67-73, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30528765

RESUMO

G protein-coupled receptors that signal through Gαq (GqPCRs), like α1-adrenergic and angiotensin receptors (α1-AR, AT-R), are traditionally thought to mediate pathologic remodeling in heart failure, including cardiac myocyte death. However, we previously demonstrated that α1- ARs are cardioprotective and identified an α1A-subtype-ERK survival-signaling pathway in adult cardiac myocytes. Recently, we demonstrated that α1-ARs localize to and signal from the nucleus, whereas AT-R localize to and signal from the sarcolemma in adult cardiac myocytes. Thus, we proposed a novel paradigm, predicated on compartmentalization of GqPCR signaling, to explain the phenotypic diversity of GqPCRs. Here, we tested the hypothesis that differential subcellular compartmentalization of α1-AR and AT-R mediated activation of ERK might explain the differential effects of these receptors on cardiac myocyte survival. Using a fluorescent ERK activity FRET-based biosensor, EKAR, to measure subcellular localization and extent of receptor-mediated ERK activation in single adult cardiac myocytes, we found that α1-ARs induced ERK activity at the nucleus and in the cytosol in 60% of cardiac myocytes, whereas AT-Rs showed no consistent ERK activation. The cell-specific α1-mediated activation of ERK in 60% of adult cardiac myocytes showed concordance with previous studies indicating that the α1A-subtype is expressed in only 60% of cardiac myocytes. Consistent with the ability to activate ERK, we found that only α1-ARs induced phosphorylation of Bcl-2 family member Bad, improved mitochondrial membrane stability, and promoted cardiac myocyte survival. In summary, our results suggest that compartmentalization of GqPCRs dictate activation of ERK and cardiac myocyte survival in adult cardiac myocytes.


Assuntos
Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/metabolismo , Sistema de Sinalização das MAP Quinases , Miócitos Cardíacos/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Envelhecimento , Animais , Morte Celular , Núcleo Celular/metabolismo , Sobrevivência Celular , Citosol/metabolismo , Feminino , Potencial da Membrana Mitocondrial , Camundongos Endogâmicos C57BL , Fosforilação , Frações Subcelulares/metabolismo , Proteína de Morte Celular Associada a bcl/metabolismo
13.
J Biol Chem ; 293(23): 8734-8749, 2018 06 08.
Artigo em Inglês | MEDLINE | ID: mdl-29610273

RESUMO

G protein-coupled receptors that signal through Gαq (Gq receptors), such as α1-adrenergic receptors (α1-ARs) or angiotensin receptors, share a common proximal signaling pathway that activates phospholipase Cß1 (PLCß1), which cleaves phosphatidylinositol 4,5-bisphosphate (PIP2) to produce inositol 1,4,5-trisphosphate (IP3) and diacylglycerol. Despite these common proximal signaling mechanisms, Gq receptors produce distinct physiological responses, yet the mechanistic basis for this remains unclear. In the heart, Gq receptors are thought to induce myocyte hypertrophy through a mechanism termed excitation-transcription coupling, which provides a mechanistic basis for compartmentalization of calcium required for contraction versus IP3-dependent intranuclear calcium required for hypertrophy. Here, we identified subcellular compartmentalization of Gq-receptor signaling as a mechanistic basis for unique Gq receptor-induced hypertrophic phenotypes in cardiac myocytes. We show that α1-ARs co-localize with PLCß1 and PIP2 at the nuclear membrane. Further, nuclear α1-ARs induced intranuclear PLCß1 activity, leading to histone deacetylase 5 (HDAC5) export and a robust transcriptional response (i.e. significant up- or down-regulation of 806 genes). Conversely, we found that angiotensin receptors localize to the sarcolemma and induce sarcolemmal PLCß1 activity, but fail to promote HDAC5 nuclear export, while producing a transcriptional response that is mostly a subset of α1-AR-induced transcription. In summary, these results link Gq-receptor compartmentalization in cardiac myocytes to unique hypertrophic transcription. They suggest a new model of excitation-transcription coupling in adult cardiac myocytes that accounts for differential Gq-receptor localization and better explains distinct physiological functions of Gq receptors.


Assuntos
Cardiomegalia/patologia , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/metabolismo , Miócitos Cardíacos/patologia , Fosfatidilinositol 4,5-Difosfato/metabolismo , Fosfolipase C beta/metabolismo , Receptores Adrenérgicos alfa 1/metabolismo , Transdução de Sinais , Transporte Ativo do Núcleo Celular , Animais , Cardiomegalia/genética , Cardiomegalia/metabolismo , Núcleo Celular/metabolismo , Núcleo Celular/patologia , Feminino , Subunidades alfa Gq-G11 de Proteínas de Ligação ao GTP/análise , Histona Desacetilases/análise , Histona Desacetilases/metabolismo , Masculino , Camundongos Endogâmicos C57BL , Miócitos Cardíacos/metabolismo , Membrana Nuclear/metabolismo , Membrana Nuclear/patologia , Fenótipo , Fosfatidilinositol 4,5-Difosfato/análise , Fosfolipase C beta/análise , Receptores Adrenérgicos alfa 1/análise , Sarcolema/metabolismo , Sarcolema/patologia , Ativação Transcricional
14.
Mol Plant Microbe Interact ; 32(7): 853-864, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-30699306

RESUMO

Mortierella and Ilyonectria genera include common species of soil fungi that are frequently detected as root endophytes in many plants, including Populus spp. However, the ecological roles of these and other endophytic fungi with respect to plant growth and function are still not well understood. The functional ecology of two key taxa from the P. trichocarpa rhizobiome, M. elongata PMI93 and I. europaea PMI82, was studied by coupling forest soil bioassays with environmental metatranscriptomics. Using soil bioassay experiments amended with fungal inoculants, M. elongata was observed to promote the growth of P. trichocarpa. This response was cultivar independent. In contrast, I. europaea had no visible effect on P. trichocarpa growth. Metatranscriptomic studies revealed that these fungi impacted rhizophytic and endophytic activities in P. trichocarpa and induced shifts in soil and root microbial communities. Differential expression of core genes in P. trichocarpa roots was observed in response to both fungal species. Expression of P. trichocarpa genes for lipid signaling and nutrient uptake were upregulated, and expression of genes associated with gibberellin signaling were altered in plants inoculated with M. elongata, but not I. europaea. Upregulation of genes for growth promotion, downregulation of genes for several leucine-rich repeat receptor kinases, and alteration of expression of genes associated with plant defense responses (e.g., jasmonic acid, salicylic acid, and ethylene signal pathways) also suggest that M. elongata manipulates plant defenses while promoting plant growth.


Assuntos
Endófitos , Fungos , Regulação da Expressão Gênica de Plantas , Populus , Biodiversidade , Endófitos/fisiologia , Fungos/fisiologia , Fenótipo , Raízes de Plantas/microbiologia , Populus/microbiologia , Rizosfera
15.
Bioinformatics ; 34(15): 2659-2660, 2018 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-29566129

RESUMO

Summary: Mutation accumulation (MA) is the most widely used method for directly studying the effects of mutation. By sequencing whole genomes from MA lines, researchers can directly study the rate and molecular spectra of spontaneous mutations and use these results to understand how mutation contributes to biological processes. At present there is no software designed specifically for identifying mutations from MA lines. Here we describe accuMUlate, a probabilistic mutation caller that reflects the design of a typical MA experiment while being flexible enough to accommodate properties unique to any particular experiment. Availability and implementation accuMUlate is available from https://github.com/dwinter/accuMUlate. Supplementary information: Supplementary data are available at Bioinformatics online.


Assuntos
Genômica/métodos , Acúmulo de Mutações , Software , Sequenciamento Completo do Genoma/métodos , Arabidopsis/genética , Biologia Computacional/métodos
16.
J Pediatr ; 215: 24-31.e8, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31668885

RESUMO

OBJECTIVE: To evaluate neurodevelopment, growth, and health outcomes in infants receiving bovine milk fat globule membrane (MFGM) and lactoferrin in infant formula. STUDY DESIGN: Healthy term infants were randomized to a cow's milk-based infant formula or MFGM + LF (a similar infant formula, with an added source of bovine milk fat globule membrane [bMFGM; whey protein-lipid concentrate, 5 g/L] and bovine lactoferrin [0.6 g/L]) through 365 days of age. The Bayley Scales of Infant Development, 3rd edition cognitive composite score at day 365 was the primary outcome. Secondary outcomes included tolerance measures through day 365, additional neurodevelopmental and language outcomes, growth, and medically confirmed adverse events through day 545. RESULTS: Of 451 infants enrolled (control, 228; MFGM + LF, 223), 291 completed study feeding and Bayley-III testing at day 365 (control, 148; MFGM + LF, 143). The mean cognitive (+8.7), language (+12.3), and motor (+12.6) scores were higher (P < .001) for the MFGM + LF group; no differences were observed at day 545. Global development scores from day 120 to day 275 and attention at day 365 were significantly improved. Few group differences in day 545 neurodevelopmental outcomes were detected, however scores of some subcategories of the MacArthur-Bates Communicative Development Inventories were higher (P < .05) in the MFGM + LF group. The overall incidence of respiratory-associated adverse events and diarrhea were significantly lower for the MFGM + LF group through day 545. CONCLUSIONS: Infants receiving formula with added bovine MFGM and bovine lactoferrin had an accelerated neurodevelopmental profile at day 365 and improved language subcategories at day 545. Formulas were associated with age-appropriate growth and significantly fewer diarrhea and respiratory-associated adverse events through 545 days of age. TRIAL REGISTRATION CLINICALTRIALS.GOV:: NCT02274883.


Assuntos
Desenvolvimento Infantil/fisiologia , Cognição/fisiologia , Glicolipídeos/farmacologia , Glicoproteínas/farmacologia , Fórmulas Infantis/química , Lactoferrina/farmacologia , Leite , Transtornos do Neurodesenvolvimento/prevenção & controle , Animais , Pré-Escolar , Método Duplo-Cego , Feminino , Seguimentos , Humanos , Lactente , Recém-Nascido , Gotículas Lipídicas , Masculino , Transtornos do Neurodesenvolvimento/fisiopatologia , Transtornos do Neurodesenvolvimento/psicologia , Prognóstico , Valores de Referência , Estudos Retrospectivos
17.
Bioinformatics ; 33(15): 2322-2329, 2017 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-28334373

RESUMO

MOTIVATION: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-number-variation, paralogous sequences, library preparation, sequencing error and reference-mapping biases, among others. RESULTS: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models. In most cases the best model was comprised of two distributions. The major-component distribution is similar to a binomial distribution with low error and low reference bias. The minor-component distribution is overdispersed with higher error and reference bias. We also found that sites fitting the minor component are enriched for copy number variants and low complexity regions, which can produce erroneous genotype calls. By removing sites that do not fit the major component, we can improve the accuracy of genotype calls. AVAILABILITY AND IMPLEMENTATION: Methods and data files are available at https://github.com/CartwrightLab/WuEtAl2017/ (doi:10.5281/zenodo.256858). CONTACT: cartwright@asu.edu. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.


Assuntos
Variações do Número de Cópias de DNA , Genoma Humano , Modelos Estatísticos , Sequenciamento Completo do Genoma/métodos , Genômica/métodos , Genômica/normas , Técnicas de Genotipagem/métodos , Técnicas de Genotipagem/normas , Humanos , Sensibilidade e Especificidade , Distribuições Estatísticas , Sequenciamento Completo do Genoma/normas
18.
Anal Chem ; 89(18): 10104-10110, 2017 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-28817769

RESUMO

An inexpensive and disposable paper-based lateral flow strip (PLFS) has been developed as an immunoassay, in which surface-enhanced Raman scattering (SERS) is utilized for sensing signal transduction. The Au nanostar@Raman Reporter@silica sandwich nanoparticles are developed as the SERS probes, which is the key to the high sensitivity of the device. Compared with a colorimetric PLFS, the SERS-PLFS exhibits superior performance in terms of sensitivity and limit of detection (LOD) in a blood plasma-containing sample matrix. In addition, the SERS-PLFS has been successfully used for detection of neuron-specific enolase (NSE), a traumatic brain injury (TBI) protein biomarker, in diluted blood plasma samples, achieving a LOD of 0.86 ng/mL. Moreover, the SERS-PLFS was successfully employed to measure the NSE level in clinical blood plasma samples taken from deidentified TBI patients. This work demonstrates that the SERS-PLFS has great potential in assisting screening of TBI patients in the point-of-care setting.


Assuntos
Papel , Fosfopiruvato Hidratase/sangue , Ouro/química , Humanos , Nanopartículas Metálicas/química , Análise Espectral Raman , Propriedades de Superfície
19.
PLoS Comput Biol ; 11(7): e1004365, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-26200800

RESUMO

There has been an explosion of research on host-associated microbial communities (i.e.,microbiomes). Much of this research has focused on surveys of microbial diversities across a variety of host species, including humans, with a view to understanding how these microbiomes are distributed across space and time, and how they correlate with host health, disease, phenotype, physiology and ecology. Fewer studies have focused on how these microbiomes may have evolved. In this paper, we develop an agent-based framework to study the dynamics of microbiome evolution. Our framework incorporates neutral models of how hosts acquire their microbiomes, and how the environmental microbial community that is available to the hosts is assembled. Most importantly, our framework also incorporates a Wright-Fisher genealogical model of hosts, so that the dynamics of microbiome evolution is studied on an evolutionary timescale. Our results indicate that the extent of parental contribution to microbial availability from one generation to the next significantly impacts the diversity of microbiomes: the greater the parental contribution, the less diverse the microbiomes. In contrast, even when there is only a very small contribution from a constant environmental pool, microbial communities can remain highly diverse. Finally, we show that our models may be used to construct hypotheses about the types of processes that operate to assemble microbiomes over evolutionary time.


Assuntos
Evolução Biológica , Ecossistema , Variação Genética/genética , Especificidade de Hospedeiro/genética , Microbiota/genética , Modelos Genéticos , Simulação por Computador
20.
BMC Bioinformatics ; 16: 357, 2015 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-26536860

RESUMO

BACKGROUND: Over the last decade, next generation sequencing (NGS) has become widely available, and is now the sequencing technology of choice for most researchers. Nonetheless, NGS presents a challenge for the evolutionary biologists who wish to estimate evolutionary genetic parameters from a mixed sample of unlabelled or untagged individuals, especially when the reconstruction of full length haplotypes can be unreliable. We propose two novel approaches, least squares estimation (LS) and Approximate Bayesian Computation Markov chain Monte Carlo estimation (ABC-MCMC), to infer evolutionary genetic parameters from a collection of short-read sequences obtained from a mixed sample of anonymous DNA using the frequencies of nucleotides at each site only without reconstructing the full-length alignment nor the phylogeny. RESULTS: We used simulations to evaluate the performance of these algorithms, and our results demonstrate that LS performs poorly because bootstrap 95% Confidence Intervals (CIs) tend to under- or over-estimate the true values of the parameters. In contrast, ABC-MCMC 95% Highest Posterior Density (HPD) intervals recovered from ABC-MCMC enclosed the true parameter values with a rate approximately equivalent to that obtained using BEAST, a program that implements a Bayesian MCMC estimation of evolutionary parameters using full-length sequences. Because there is a loss of information with the use of sitewise nucleotide frequencies alone, the ABC-MCMC 95% HPDs are larger than those obtained by BEAST. CONCLUSION: We propose two novel algorithms to estimate evolutionary genetic parameters based on the proportion of each nucleotide. The LS method cannot be recommended as a standalone method for evolutionary parameter estimation. On the other hand, parameters recovered by ABC-MCMC are comparable to those obtained using BEAST, but with larger 95% HPDs. One major advantage of ABC-MCMC is that computational time scales linearly with the number of short-read sequences, and is independent of the number of full-length sequences in the original data. This allows us to perform the analysis on NGS datasets with large numbers of short read fragments. The source code for ABC-MCMC is available at https://github.com/stevenhwu/SF-ABC.


Assuntos
Evolução Molecular , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Algoritmos , Sequência de Bases , Teorema de Bayes , Simulação por Computador , Intervalos de Confiança , Humanos , Análise dos Mínimos Quadrados , Cadeias de Markov , Método de Monte Carlo , Densidade Demográfica
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