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At least 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern

Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several variants of concern emerged globally, including the UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California variants of interest (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On the basis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. Finally, as vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2018

Isolation and characterization of ventricular-like cells derived from NKX2-5 eGFP/w and MLC2v mCherry/w double knock-in human pluripotent stem cells

Highlights: • NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSC double knock-ins were established. • Culture conditions mimic in vivo cardiac developmental process. • Subtype-specific cardiac development and functional analysis were possible. Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) are a promising source for cell transplantation into the damaged heart, which has limited regenerative ability. Many methods have been developed to obtain large amounts of functional CMs from hPSCs for therapeutic applications. However, during the differentiation process, a mixed population of various cardiac cells, including ventricular, atrial, and pacemaker cells, is generated, which hampers the proper functional analysis and evaluation of cell properties. Here, we established NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSC double knock-ins that allow for labeling, tracing, purification, and analysis of the development of ventricular cells from early to late stages. As with the endogenous transcriptional activities of these genes, MLC2v-mCherry expression following NKX2-5-eGFP expression was observed under previously established culture conditions, which mimic the in vivo cardiac developmental process. Patch-clamp and microelectrode array electrophysiological analyses showed that the NKX2-5 and MLC2v double-positive cells possess ventricular-like properties. The results demonstrate that the NKX2-5{sup eGFP/w} and MLC2v{sup mCherry/w} hPSCs provide a powerful model system to capture region-specific cardiac differentiation from early to late stages. Our study would facilitate subtype-specific cardiac development and functional analysis using the hPSC-derived sources.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Immunomodulatory effects of polysaccharide fraction isolated from Fagopyrum esculentum on innate immune system

Highlights: • Immunomodulatory activities of BPF on the enhancement of immune response. • BPF was stimulated of murine macrophages and NK cells related to immune reactions. • BPF will have an effect on CTX-induced immunosuppression mouse model. The present study investigates the immunomodulatory activities of buckwheat polysaccharide fraction (BPF) from the seed of Fagopyrum esculentum on RAW 264.7 macrophage cell line and Cyclophosphamide-induced immunosuppressed conditions in mice models. The results of in vitro showed that treatment with 0.5–10 μg/mL of BPF can modulate immune responses. MTT assay and nitric oxide production and immune-related cytokine levels were conducted. Treatment with BPF at a dose of 10 μg/mL of BPF increased immune responses on macrophages. Moreover, natural killer (NK) cell cytotoxicity was conducted. The apoptosis of YAC-1 cells increased as the co-culture ratio between spleen cells and YAC-1 cells increased approximately 4- fold compared to the control group from 12.5:1 to 50.0:1. The in-vivo immunomodulatory effects of BPF were evaluated by cyclophosphamide-induced mice model. The immune response of BPF was determined against cyclophosphamide (100 mg/kg) immunosuppressed mice at doses of 50 mg/kg and 100 mg/kg of BPF as compared to control. The results of this study showed that BPF administration increased spleen and thymus indices as well as the leukocytes count in the blood of immunosuppressed mice. All of results suggested that BPF are potentially acts as immunomodulator for activation of immune responses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Isolation of a novel protein phosphatase2C in rice and its response to gibberellin

Highlights: • OsPP2C34 is highly inducible by gibberellin (GA) and expressed in various tissues. • OsPP2C34 is localized to the cytosol and involved in α-amylase genes inducible by GA. • OsPP2C34 has dephosphorylation activity at its serine/threonine residues. • OsPP2C34 is a positive regulator of the GA-dependent signaling transduction pathway. Protein phosphatase 2Cs (PP2Cs) have been referred to act as negative modulators of the protein kinase pathways involved in different environmental stress responses and developmental processes. In Arabidopsis, PP2Cs have been extensively studied and some are known to negatively regulate abscisic acid signaling. In rice, PP2Cs are scarcely characterized functionally. Here, we identified a novel PP2C from rice (OsPP2C34), which is highly inducible by gibberellin (GA) and expressed in various tissues. Subcellular localization analysis in maize protoplasts using a green fluorescence protein fusion vector localized OsPP2C34 to the cytosol. Genetic analysis of T-DNA insertional mutants revealed that plant height and internode length were significantly shorter in mutants than in corresponding wild types under GA treatment. The induction of the GA-inducibleα-amylase genes RAmy3E and OsAmy was delayed in mutant plants. The substrate of OsPP2C34 was identified by immunoblotting using anti serine/threonine antibodies. A 65 kDa protein was phosphorylated in Ospp2c34-1 but dephosphorylated in the wild type during early germination stage. Overall, the present results indicated that OsPP2C34 is involved inα-amylase expression of GA signal transduction pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Characterization of fractional cuts of co-solvent enhanced lignocellulosic fractionation lignin isolated by sequential precipitation

We report that lignin valorization is significantly hindered by the intrinsic heterogeneity of its complex structures and variability of biomass feedstocks. Fractionation of lignin can overcome these challenges by producing functionally distinct lignin cuts that can be further tailored to end products. Herein, lignin was extracted and depolymerized from poplar by the co-solvent enhanced lignocellulosic fractionation method with renewable THF to obtain CELF lignin. Several solvents were screened to separate soluble and insoluble fractions from the parent CELF lignin. The ethanol soluble portion was then fractionated into different molecular weight cuts via sequential precipitation of the lignin by reducing the concentration of THF. The physicochemical structures of different CELF lignin cuts were elucidated by GPC and NMR techniques. In conclusio, these results suggest that CELF lignin cuts with lower molecular weight contain progressively higher phenolic and carboxylic acid OH groups, which can be more suitable as green antioxidants than the parent lignin.

09 BIOMASS FUELS↗
DOE OSTI2026

Three pairs of fungal Trametes strains isolated from distinct geographic origins show conserved genomic features and adaptive response to plant biomass

The genomes of white-rot fungi hold extended repertoires of enzymes active on virtually all the chemical bonds that intertwine lignocellulose polymers, and several Trametes species have been identified as powerful tools for biorefinery or bioremediation. However, only few studies have addressed the intra-species polymorphism one would expect from fungal strains collected in contrasted environments. We compared the genome sequence of pairs of strains collected in different geographic areas, for each of three fungal species. Using an updated list of the predicted functions for fungal ligno- and cellulolytic enzymes (CAZymes), we observed a high conservation of the gene repertoires among the six strains. We compared the adaptative response of the fungi grown on crystalline cellulose, wheat straw, aspen or pine sawdust by transcriptomics and secretomics. The gene regulation profiles were determined by the species and the substrates, rather than the strain. The secretomes did not show marked differences in the sets of secreted CAZymes after 3 day-growth on the substrates. We identified five transcription factor genes and two sesquiterpenoid synthesis genes induced during growth on lignocellulose. Wider studies using larger sets of strains will be necessary to evaluate the genericity of our findings, and to assess the phenotype diversity one could expect from geographic diversity as compared to taxonomic diversity in Trametes fungi.

Drula, E. [French National Research Institute for ↗