PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targetedpanel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations

Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly

Mutations of genes within the phosphatidylinositol-3-kinase (PI3K)-AKT-MTOR pathway are well known causes of brain overgrowth (megalencephaly) as well as segmental cortical dysplasia (such as hemimegalencephaly, focal cortical dysplasia and polymicrogyria). Mutations of the AKT3 gene have been reported in a few individuals with brain malformations, to date. Therefore, our understanding regarding the clinical and molecular spectrum associated with mutations of this critical gene is limited, with no clear genotype–phenotype correlations. We sought to further delineate this spectrum, study levels of mosaicism and identify genotype–phenotype correlations of AKT3-related disorders. We performed targeted sequencing of AKT3 on individuals with these phenotypes by molecular inversion probes and/or Sanger sequencing to determine the type and level of mosaicism of mutations. We analysed all clinical and brain imaging data of mutation-positive individuals including neuropathological analysis in one instance. We performed ex vivo kinase assays on AKT3 engineered with the patient mutations and examined the phospholipid binding profile of pleckstrin homology domain localizing mutations. We identified 14 new individuals with AKT3 mutations with several phenotypes dependent on the type of mutation and level of mosaicism. Our comprehensive clinical characterization, and review of all previously published patients, broadly segregates individuals with AKT3 mutations into two groups: patients with highly asymmetric cortical dysplasia caused by the common p.E17K mutation, and patients with constitutional AKT3 mutations exhibiting more variable phenotypes including bilateral cortical malformations, polymicrogyria, periventricular nodular heterotopia and diffuse megalencephaly without cortical dysplasia. All mutations increased kinase activity, and pleckstrin homology domain mutants exhibited enhanced phospholipid binding. Overall, our study shows that activating mutations of the critical AKT3 gene are associated with a wide spectrum of brain involvement ranging from focal or segmental brain malformations (such as hemimegalencephaly and polymicrogyria) predominantly due to mosaic AKT3 mutations, to diffuse bilateral cortical malformations, megalencephaly and heterotopia due to constitutional AKT3 mutations. We also provide the first detailed neuropathological examination of a child with extreme megalencephaly due to a constitutional AKT3 mutation. This child has one of the largest documented paediatric brain sizes, to our knowledge. Finally, our data show that constitutional AKT3 mutations are associated with megalencephaly, with or without autism, similar to PTEN-related disorders. Recognition of this broad clinical and molecular spectrum of AKT3 mutations is important for providing early diagnosis and appropriate management of affected individuals, and will facilitate targeted design of future human clinical trials using PI3K-AKT pathway inhibitors

Genome-enabled insights into the biology of thrips as crop pests

Background The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. Results We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. Conclusions Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Recovery of Laryngeal Closure in Post-stroke Survivors

© 2017 The Korean Association of Speech- Language Pathologists. Objectives: The purpose of this study was to examine whether traditional swallowing intervention improves the initiation or duration of laryngeal closure in post-stroke survivors using the initial and follow-up videofluoroscopic swallowing study (VFSS). Methods: Twelve post-stroke survivors completed traditional swallowing intervention such as postural changes and swallowing exercises. The initial VFSS was performed at the acute or subacute stage and the follow-up VFSS occurred at 3 to 5 weeks after the initial VFSS. Temporal measurements of laryngeal closure were analyzed for 2 mL and 5 mL thin liquids. Statistical comparisons were made by paired t-test. The significance level was set at p\u3c0.05. Results: The initiation of laryngeal closure of post-stroke survivors was significantly shorter after the traditional swallowing intervention; however, the duration of laryngeal closure did not differ after the intervention. In addition, the post-stroke survivors showed reduced occurrences of penetration or aspiration after the intervention. Conclusions: Shorter initiation of laryngeal closure after the intervention indicates that the traditional swallowing intervention at the acute or subacute stage of stroke may help poststroke survivors protect the airway effectively

Recovery of laryngeal closure in post-stroke survivors

© 2017 The Korean Association of Speech- Language Pathologists. Objectives: The purpose of this study was to examine whether traditional swallowing intervention improves the initiation or duration of laryngeal closure in post-stroke survivors using the initial and follow-up videofluoroscopic swallowing study (VFSS). Methods: Twelve post-stroke survivors completed traditional swallowing intervention such as postural changes and swallowing exercises. The initial VFSS was performed at the acute or subacute stage and the follow-up VFSS occurred at 3 to 5 weeks after the initial VFSS. Temporal measurements of laryngeal closure were analyzed for 2 mL and 5 mL thin liquids. Statistical comparisons were made by paired t-test. The significance level was set at p\u3c0.05. Results: The initiation of laryngeal closure of post-stroke survivors was significantly shorter after the traditional swallowing intervention; however, the duration of laryngeal closure did not differ after the intervention. In addition, the post-stroke survivors showed reduced occurrences of penetration or aspiration after the intervention. Conclusions: Shorter initiation of laryngeal closure after the intervention indicates that the traditional swallowing intervention at the acute or subacute stage of stroke may help poststroke survivors protect the airway effectively

Exercise Training Improved Plasma Glucose and Lipid Profiles in Obese Hispanic Women

Obesity is strongly associated with increased morbidity and mortality, notably among Hispanic women. Exercise may improve cardiovascular health by positively altering plasma lipids and lipoproteins; however, the effects of different intensities of exercise on plasma glucose and lipid profiles have not been extensively studied within Hispanic women. PURPOSE: The current study examined the effects of a 12-week aerobic exercise training at either high or low intensity on plasma glucose and lipid profiles in obese Hispanic females. METHODS: Thirty physically inactive, obese females (age= 26.07±4.4 years, height= 161.4±4.1 cm, weight= 89.8±8.1 kg and %body fat= 40.9 ±4.9%) were randomly assigned to three groups: control (n= 10, no exercise), low-intensity exercise (LI, n= 10, 50% VO2max) and high-intensity exercise (HI, n=10, 70% VO2max). Both LI and HI groups participated in supervised exercise training on a treadmill for 12 weeks with the following exercise protocol: weeks 1-4 (3 days per week to expend 13.5 METs×hr/w), weeks 5-8 (4 days per week to expend 18.0 METs×hr/w), and weeks 9-12 (5 days per week to expend 22.5 METs×hr/w). Overnight fasting plasma samples were taken at before (PRE) and after the 12-weeks of exercise training (POST). A 3 x 2 analysis of variance with a Tukey post-hoc test (p RESULTS: Both LI and HI groups decreased body weight up to 2.1 and 3.4kg, respectively. TC at POST in the LI group (116.53±5.32 mg/dL) was significantly lower (p p=0.036 and 67.17±5.24 mg/dL, p=0.006), respectively. Plasma glucose at POST in both LI (75.32±2.71 mg/dL, p= .024) and control groups (80.1±2.71 mg/dL, p=0.001) was lower than in the HI group (90.77±2.78 mg/dL). CONCLUSION: Regardless of exercise intensity, both low and high intensity aerobic exercise training for 12 weeks improved body weight and body composition in obese Hispanic women. However, the low-intensity exercise provided a more favorable effect than the high-intensity exercise on the plasma glucose and lipid profiles of obese Hispanic women

Scalable High Tensile Modulus Composite Laminates Using Carbon Nanotube Yarns

A novel approach is established for fabricating high-strength and high-stiffness composite laminates with continuous carbon nanotube (CNT) yarns for scaled-up mechanical tests and potential engineering applications. Continuous CNT yarns with up to 80% degree of nanotube alignment and a unique self-assembled graphitic CNT packing result in their specific tensile strengths up to 1.9 N/tex. Unidirectional CNT yarn reinforced composite laminates with a CNT concentration of greater than 80 wt.% and minimal microscale voids are fabricated using filament winding and aerospace-grade resin matrices. A specific tensile strength of up to 1.71 GPa/(g cm-3) and a specific modulus of 256 GPa/(g cm-3) are realized; the specific modulus exceeds current state-of-the-art IM7, T1100G and even M60J unidirectional carbon fiber composite laminates. The results demonstrate an effective approach transferring high-strength CNT yarns into composites for applications that require specific tensile modulus properties that are significantly beyond state-of-the-art carbon fiber composites, and potentially open a new performance region in the Ashby chart for composite material applications