Prediction of 1p/19q Codeletion in Diffuse Glioma Patients Using Pre-operative Multiparametric Magnetic Resonance Imaging

Kim D, Wang N, Ravikumar V, Raghuram DR, Li J, Patel A, Wendt RE III, Rao G and Rao A (2019) Prediction of 1p/19q Codeletion in Diffuse Glioma Patients Using Pre-operative Multiparametric Magnetic Resonance Imaging. Front. Comput. Neurosci. 13:52. doi: 10.3389/fncom.2019.00052https://openworks.mdanderson.org/mdacc_imgphys_pubs/1005/thumbnail.jp

Lithosphere thinning beneath west North China Craton: Evidence from geochemical and Sr-Nd-Hf isotope compositions of Jining basalts

This study shows lithosphere evolution history in the west North China Craton (NCC) from the early Cretaceous to Quaternary by studying the major element, trace element and Sr-Nd-Hf isotope compositions in Jining basalts of 119.6-108.6. Ma, 23.5-21.9. Ma and 1.3-0.11. Ma.The early Cretaceous basalts (119.6-108.6Ma) display enriched characteristics with high contents of incompatible elements, high 87Sr/86Sri, low εNd(t) and low εHf(t). These basalts resulted from partial melting of ancient metasomatized lithospheric mantle, and we consider the 119.6-108.6Ma magmatism as indicating lithosphere thinning in the west NCC. Although the Pacific slab seen seismically in the mantle transition zone beneath eastern China is no older than 60Ma, there exists convincing evidence for the presence of the Paleo-Pacific slab in the transition-zone in the Mesozoic. Thus we propose that the water released from the transition-zone slab hydrated the overlying lithosphere and further converted the base of the lithosphere into asthenosphere. This is the most likely mechanism responsible for the lithosphere thinning in the west NCC and the petrogenesis of the Jining 119.6-108.6Ma basalts.The Jining 23.5-21.9Ma basalts also have high contents of incompatible elements, but they display high εNd(t), high εHf(t) and variably low 87Sr/86Sri. We propose that these Miocene basalts were derived from the asthenosphere with contributions from ancient metasomatized lithospheric mantle during melt ascent. The Jining Quaternary basalts (1.3-0.11Ma) represent the melt of upwelling asthenosphere with low 87Sr/86Sri, high εNd(t) and high εHf(t). Upwelling and decompression melting of the eastward flowing asthenosphere from beneath western plateaus to beneath eastern hilly plains in the Cenozoic is the most plausible mechanism for the petrogenesis of Jining Cenozoic basalts (both of 23.5-21.9Ma and 1.3-0.11Ma), but the Jining 1.3-0.11Ma basalts must have been produced beneath even thinner lithosphere.Taken together geophysical studies and our petrological and geochemical studies of all these three episodes of the Jining basalts, we propose that the lithosphere in the west NCC has been thinning since the early Cretaceous and the thinning continues to the present

Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance

Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future

TRPV4-Mediated Calcium Influx into Human Bronchial Epithelia upon Exposure to Diesel Exhaust Particles

BACKGROUND: Human respiratory epithelia function in airway mucociliary clearance and barrier function and have recently been implicated in sensory functions. OBJECTIVE: We investigated a link between chronic obstructive pulmonary disease (COPD) pathogenesis and molecular mechanisms underlying Ca2+ influx into human airway epithelia elicited by diesel exhaust particles (DEP). METHODS AND RESULTS: Using primary cultures of human respiratory epithelial (HRE) cells, we determined that these cells possess proteolytic signaling machinery, whereby proteinase-activated receptor-2 (PAR-2) activates Ca2+-permeable TRPV4, which leads to activation of human respiratory disease-enhancing matrix metalloproteinase-1 (MMP-1), a signaling cascade initiated by diesel exhaust particles (DEP), a globally relevant air pollutant. Moreover, we observed ciliary expression of PAR-2, TRPV4, and phospholipase-Cβ3 in human airway epithelia and their DEP-enhanced protein-protein complex formation. We also found that the chronic obstructive pulmonary disease (COPD)-predisposing TRPV4P19S variant enhances Ca2+ influx and MMP 1 activation, providing mechanistic linkage between man-made air pollution and human airway disease. CONCLUSION: DEP evoked protracted Ca2+ influx via TRPV4, enhanced by the COPD-predisposing human genetic polymorphism TRPV4P19S. This mechanism reprograms maladaptive inflammatory and extracellular-matrix-remodeling responses in human airways. The novel concept of air pollution-responsive ciliary signal transduction from PAR-2 to TRPV4 in human respiratory epithelia will accelerate rationally targeted therapies, possibly via the inhalatory route

Individual based model links thermodynamics, chemical speciation and environmental conditions to microbial growth

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·105 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances

Metabolomics-Based Identification of Bleached Shellac in Liquid Fruit Wax

The purpose of this study was to identify whether liquid fruit waxes could be added with bleached shellac. The compounds of bleached shellac from different sources were analyzed by targeted metabolomics based on liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) combined with liquid chromatography with evaporative light scattering detection. Twelve target compounds were selected by multivariate statistical analysis including unsupervised principal component analysis (PCA) and supervised partial least squares discriminant analysis (PLS-DA). According to variable importance in the projection (VIP) value, five differential compounds and seven shared compounds were identified. Finally, the viability of this method in the detection of commercial liquid fruit wax products was verified using the shared compounds as biomarkers. These results showed that chromatography combined with mass spectrometry can identify whether bleached shellac could be added in liquid fruit wax

Liver Imaging Reporting and Data System (LI-RADS) v2018: differential diagnostic value of ADC values for benign and malignant nodules with moderate probability (LR-3)

ObjectiveTo evaluate the usefulness of the apparent diffusion coefficient (ADC) in differentiating between benign and malignant LR-3 lesions classified by Liver Imaging Reporting and Data System 2018 (LI-RADS v2018).MethodsRetrospectively analyzed 88 patients with liver nodules confirmed by pathology and classified as LR-3 by LI-RADS. All patients underwent preoperative contrast-enhanced MR examination, and the following patient-related imaging features were collected: tumor size,nonrim APHE, nonperipheral “washout”, enhancing “capsule”, mild-moderate T2 hyperintensity, fat in mass, restricted diffusion, and nodule-in-nodule architecture. We performed ROC analysis and calculated the sensitivity and specificity.ResultsA total of 122 lesions were found in 88 patients, with 68 benign and 54 malignant lesions. The mean ADC value for malignant and benign lesions were 1.01 ± 0.15 × 103 mm2/s and 1.41 ± 0.31 × 103 mm2/s, respectively. The ADC value of malignant lesions was significantly lower than that of benign lesions, p < 0.0001. Compared with other imaging features, ADC values had the highest AUC (AUC = 0.909), with a sensitivity of 92.6% and a specificity of 74.1% for the differentiation of benign and malignant lesions.ConclusionsADC values are useful for differentiating between benign and malignant liver nodules in LR-3 classification, it improves the sensitivity of LI-RADS in the diagnosis of HCC while maintaining high specificity, and we recommend including ADC values in the standard interpretation of LI-RADSv2018

Diesel Exhaust Particles Activate the Matrix-Metalloproteinase-1 Gene in Human Bronchial Epithelia in a β-Arrestin–Dependent Manner via Activation of RAS

BACKGROUND: Diesel exhaust particles (DEPs) are globally relevant air pollutants that exert a detrimental human health impact. However, mechanisms of damage by DEP exposure to human respiratory health and human susceptibility factors are only partially known. Matrix metalloproteinase-1 (MMP-1) has been implied as an (etio)pathogenic factor in human lung and airway diseases such as emphysema, chronic obstructive pulmonary disease, chronic asthma, tuberculosis, and bronchial carcinoma and has been reported to be regulated by DEPs. OBJECTIVE: We elucidated the molecular mechanisms of DEPs' up-regulation of MMP-1. METHODS/RESULTS: Using permanent and primary human bronchial epithelial (HBE) cells at air-liquid interface, we show that DEPs activate the human MMP-1 gene via RAS and subsequent activation of RAF-MEK-ERK1/2 mitogen-activated protein kinase signaling, which can be scaffolded by beta-arrestins. Short interfering RNA mediated beta-arrestin1/2 knockout eliminated formation, subsequent nuclear trafficking of phosphorylated ERK1/2, and resulting MMP-1 transcriptional activation. Transcriptional regulation of the human MMP-1 promoter was strongly influenced by the presence of the -1607GG polymorphism, present in 60-80% of humans, which led to striking up-regulation of MMP-1 transcriptional activation. CONCLUSION: Our results confirm up-regulation of MMP-1 in response to DEPs in HBE and provide new mechanistic insight into how these epithelia, the first line of protection against environmental insults, up-regulate MMP-1 in response to DEP inhalation. These mechanisms include a role for the human -1607GG polymorphism as a susceptibility factor for an accentuated response, which critically depends on the ability of beta-arrestin1/2 to generate scaffolding and nuclear trafficking of phosphorylated ERK1/2

The Chemical Composition and Nitrogen Distribution of Chinese Yak (Maiwa) Milk

The paper surveyed the chemical composition and nitrogen distribution of Maiwa yak milk, and compared the results with reference composition of cow milk. Compared to cow milk, yak milk was richer in protein (especially whey protein), essential amino acids, fat, lactose and minerals (except phosphorus). The contents of some nutrients (total protein, lactose, essential amino acids and casein) were higher in the warm season than in the cold season. Higher ratios of total essential amino acids/total amino acids (TEAA/TAA) and total essential amino acids/total non essential amino acids (TEAA/TNEAA) were found in the yak milk from the warm season. However its annual average ratio of EAA/TAA and that of EAA/NEAA were similar to those of cow milk. Yak milk was rich in calcium and iron (p < 0.05), and thus may serve as a nutritional ingredient with a potential application in industrial processing