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At least 1,531 records · Page 85
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Molecular cloning, genomic organization, chromosome mapping, tissues expression pattern and identification of a novel splicing variant of porcine CIDEb gene

Cell death-inducing DNA fragmentation factor-α-like effector b (CIDEb) is a member of the CIDE family of apoptosis-inducing factors, CIDEa and CIDEc have been reported to be Lipid droplets (LDs)-associated proteins that promote atypical LD fusion in adipocytes, and responsible for liver steatosis under fasting and obese conditions, whereas CIDEb promotes lipid storage under normal diet conditions [1], and promotes the formation of triacylglyceride-enriched VLDL particles in hepatocytes [2]. Here, we report the gene cloning, chromosome mapping, tissue distribution, genetic expression analysis, and identification of a novel splicing variant of the porcine CIDEb gene. Sequence analysis shows that the open reading frame of the normal porcine CIDEb isoform covers 660bp and encodes a 219-amino acid polypeptide, whereas its alternative splicing variant encodes a 142-amino acid polypeptide truncated at the fourth exon and comprised of the CIDE-N domain and part of the CIDE-C domain. The deduced amino acid sequence of normal porcine CIDEb shows an 85.8% similarity to the human protein and 80.0% to the mouse protein. The CIDEb genomic sequence spans approximately 6KB comprised of five exons and four introns. Radiation hybrid mapping demonstrated that porcine CIDEb is located at chromosome 7q21 and at a distance of 57cR from the most significantly linked marker, S0334, regions that are syntenic with the corresponding region in the human genome. Tissue expression analysis indicated that normal CIDEb mRNA is ubiquitously expressed in many porcine tissues. It was highly expressed in white adipose tissue and was observed at relatively high levels in the liver, lung, small intestine, lymphatic tissue and brain. The normal version of CIDEb was the predominant form in all tested tissues, whereas the splicing variant was expressed at low levels in all examined tissues except the lymphatic tissue. Furthermore, genetic expression analysis indicated that CIDEb mRNA levels were significantly higher in the white adipose tissue of lean pigs than their obese counterparts, in contrast to porcine CIDEa and CIDEc [3]. We therefore speculate that CIDEb may play a contrary role to the other CIDEs. The basic molecular information we provide here will be useful for further investigations of the physiological function of the gene, which will be helpful in better understanding the role of the CIDE family in lipid metabolism in pig models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Molecular cloning and expression analysis of cytochrome c oxidase subunit II from Sitophilus zeamais

Cytochrome c oxidase subunit II (COX II) containing a dual core CuA active site is one of the core subunits of mitochondrial Cytochrome c oxidase (Cco), which plays a significant role in the physiological process. In this report, the full-length cDNA of COXII gene was cloned from Sitophilus zeamais, which had an open reading frame (ORF) of 684 bp encoding 227 amino acids residues. The predicted COXII protein had a molecular mass of 26.2 kDa with pI value of 6.37. multiple sequence alignment and phylogenetic analysis indicated that Sitophilus zeamais COXII had high sequence identity with the COXII of other insect species. The gene was subcloned into the expression vector pET-32a, and induced by isopropyl β-D-thiogalactopyranoside (IPTG) in E. coli Transetta (DE3) expression system. Finally the recombinant COXII with 6-His tag was purified using affinity chromatography with Ni{sup 2+}-NTA agarose. Western Blotting (WB) showed the recombinant protein was about 44 kD, and the concentration of fusion protein was 50 μg/mL. UV-spectrophotometer and infrared spectrometer analysis showed that recombinant COXII could catalyze the oxidation of substrate Cytochrome C (Cyt c), and influenced by allyl isothiocyanate (AITC). By using molecular docking method, It was found that a sulfur atom of AITC structure could form a length of 2.9 Å hydrogen bond with Leu-31. These results suggested that tag-free COXII was functional and one of the action sites of AITC, which will be helpful to carry out a point mutation in binding sites for the future research. - Highlights: • A full-length cDNA of COXII was cloned from the Sitophilus zeamais. • We were successfully expressed the recombinant COXII and optimized the expression conditions. • After enterokinase digesting, the tag-free COXII was functional and affected by AITC. • Through the relevant data analysis, The COXII of Sitophilus zeamais might be one of the action sites of AITC.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Interaction of Alpha-synuclein with Cytogaligin, a protein encoded by the proapoptotic gene GALIG

Highlights: • Cytogaligin interacts with αSynuclein, a major protein of Parkinson's disease. • Cytogaligin is an intracellular protein also secreted in the extracellular medium. • Cytogaligin-αSynuclein interaction decreases αSynuclein homodimerization. GALIG, an internal gene to the human galectin-3 gene, encodes two distinct proteins, Mitogaligin and Cytogaligin through translation of a unique mRNA in two overlapping alternative reading frames. When overexpressed GALIG induces apoptosis. In cultured cells, Mitogaligin destabilizes mitochondria membranes through interaction with cardiolipin. Little is known regarding the role of Cytogaligin. This protein displays multiple subcellular localizations; cytosol, nucleus, and mitochondria. We illustrate here that Cytogaligin is also secreted in the extracellular medium. Cytogaligin is shown to interact with α-Synuclein, the major component of Lewy bodies in Parkinson's disease. Overexpression of Cytogaligin reduces α-Synuclein dimerization raising a possible role in the evolution of α-Synuclein aggregation, a key molecular event underlying the pathogenesis of Parkinson's disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Molecular cloning and characterization of the glutathione reductase gene from Stipa purpurea

Reactive oxygen species (ROS) are a key factor in abiotic stresses; excess ROS is harmful to plants. Glutathione reductase (GR) plays an important role in scavenging ROS in plants. Here, a GR gene, named SpGR, was cloned from Stipa purpurea and characterized. The full-length open reading frame was 1497 bp, encoding 498 amino acids. Subcellular localization analysis indicated that SpGR was localized to both the plasma membrane and nucleus. The expression of SpGR was induced by cold, salt, and drought stresses. Functional analysis indicated that ectopic expression of SpGR in Arabidopsis thaliana resulted in greater tolerance to salt stress than that of wild-type plants, but no difference under cold or drought treatments. The results of GR activity and GSSG and GSH content analyses suggested that, under salt stress, transgenic plants produced more GR to reduce GSSG to GSH for scavenging ROS than wild-type plants. Therefore, SpGR may be a candidate gene for plants to resist abiotic stress.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Transcription of blunt snout bream (Megalobrama amblycephala) HIF3α and its localization in the nucleus under both normoxic and hypoxic conditions

Highlights: • HIF3α cDNA was characterized the in hypoxia-sensitive blunt snout bream. • HIF3α mRNA was stably expressed during embryogenesis and different adult tissues. • HIF3α mRNA was upregulated in the liver, brain, and kidney under hypoxia. • HIF3α was distributed in the nucleus under normoxic and hypoxic conditions. • Hypoxia simulation caused a significant increase in HIF3α protein levels. • There was a nuclear localization signal (NLS) sequence at the C-terminus of HIF3α. Although hypoxia-inducible factor (HIF) 1α and 2α function as master regulators of the transcriptional response to hypoxia, the function of HIF3α and its responses to hypoxic stress remain unclear in teleost fish. Here, we characterized the HIF3α cDNA in hypoxia-sensitive blunt snout bream (Megalobrama amblycephala), with 3059 bp length, consisting of an open reading frame (ORF) encoding 643 amino acid residues. Blunt snout bream HIF3α mRNA was stably expressed during stages of embryonic development and in adult tissues. After a 4 h hypoxia stress, HIF3α mRNA of the juvenile fish was significantly upregulated in the liver, brain, and kidney, and restored to the pretreatment levels after a 24 h recovery. When tagged with enhanced green fluorescent protein (EGFP) and transfected into cultured HeLa cells, blunt snout bream HIF3α was mainly distributed in the nucleus under normoxia. Treatment of the cells with CoCl{sub 2} to mimic hypoxic conditions showed that there was no effect about the nuclear localization of HIF3α but a statistically significant increase in HIF3α protein levels. A nuclear localization signal (NLS) sequence at the C-terminus of HIF3α may exert positive effects in the process of nuclear localization. These results suggest that blunt snout bream HIF3α could be involved in different physiological functions under normoxia and hypoxia conditions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Codon usage revisited: Lack of correlation between codon usage and the number of tRNA genes in enterobacteria

Highlights: • Average number of tRNA genes correlate with codon usage in highly expressed genes. • Changes in the number of tRNA genes do not correlate to codon usage. • Altered tRNA gene copy numbers do not correlate to changes of codon translation. • Our data indicates that tRNA gene copies adapt to codon usage, but not the contrary. It is widely believed that if a high number of genes are found for any tRNA in a rapidly replicating bacteria, then the cytoplasmic levels of that tRNA will be high and an open reading frame containing a higher frequency of the complementary codon will be translated faster. This idea is based on correlations between the number of tRNA genes, tRNA concentration and the frequency of codon usage observed in a limited number of strains as well as from the fact that artificially changing the number of tRNA genes alters translation efficiency and consequently the amount of properly folded protein synthesized. tRNA gene number may greatly vary in a genome due to duplications, deletions and lateral transfer which in turn would alter the levels and functionality of many proteins. Such changes are potentially deleterious for fitness and as a result it is expected that changes in tRNA gene numbers should be accompanied by a modification of the frequency of codon usage. In contrast to this model, when comparing the number of tRNA genes and the frequency of codon usage of several Salmonella enterica and Escherichia coli strains we found that changes in the number of tRNA genes are not correlated to changes in codon usage. Furthermore, these changes are not correlated with a change in the efficiency of codon translation. These results suggest that once a genome gains or loses tRNA genes, it responds by modulating the concentrations of tRNAs rather than modifying its frequency of codon usage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Mutant cytoskeletal and ECM peptides sensitive to the ST14 protease are associated with a worse outcome for glioblastoma multiforme

Highlights: • In GBM, mutant ECM proteins appear largely resistant to the ST14 protease. • Patients with resistant proteins have a better survival. • The few patients with sensitive mutants have T-cell infiltrates. We previously identified a set of the most frequently mutated cytoskeleton- and extracellular matrix-related proteins (CECMPs) in numerous cancer datasets. In this report, we used a bioinformatics approach to assess the impact of amino acid (AA) substitutions on the sensitivity of CECMPs to the ST14 protease (matriptase I), a transmembrane serine protease previously implicated in cancer development. Results indicated that AA substitutions in glioblastoma multiforme (GBM) CECMPs are skewed toward increased resistance to the ST14 protease, in comparison to the wild-type peptide sequence. Furthermore, the protease resistant AA substitutions represent relatively high binding affinities to HLA class I proteins, when assessing the binding specificities using HLA class I alleles matched to the source of the mutant AA. Moreover, samples representing AA substitutions that increased protease sensitivity also represented reduced overall and disease-free survival periods for patients with glioblastoma. To assess tumor specimen immunogenicity, we identified T-cell receptor (TCR) V(D)J recombinations in GBM exome files. The overlap between ST14 protease sensitive mutant barcodes and the TCR V(D)J recombination read positive barcodes represented significantly reduced survival.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Molecular cloning and characterization of a novel Y-box gene from planarian Dugesia japonica

Highlights: • A novel gene encoding a Y-box protein named DjY2 was cloned from Dugesia japonica. • DjY2 protein was structurally different from other Y-box proteins in planarians. • The expression patterns of DjY2 transcripts are different from DjY1 and DeY1. • DjY2 gene might participate in the regeneration process in planarian. Y-box binding protein (YB protein) is an ancient conserved multifunctional DNA/RNA-binding protein. A novel YB protein DjY2 gene from planarian Dugesia japonica was cloned by RACE method and characterized. This cDNA contains 689 bp with a putative open reading frame of 197 amino acids. It has a predicted molecular mass of 22.14 kDa and an isoelectric point of 9.67. Whole-mount in situ hybridization and relative quantitative real-time PCR were used to study the spatial and temporal expression pattern of DjY2 in the process of planarian regeneration. Results showed that DjY2 was expressed in many parts of the body in intact planarian, but the expression level was low in head and pharynx. The transcripts of DjY2 was significantly increased both at the head parts and the tail parts after amputation, especially at the site of cutting. The spatial expression gradually recovered to the state of intact planarian with the time of regeneration. Our results indicated that DjY2 might participate in the process of regeneration in planarian.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2026

Corrigendum to “Cool Rooms for Indoor Heat Resilience: Evaluating Affordable Cooling Strategies in Heat-Stressed California Homes” [Building and Environment 287 (2026) 113877]

The authors regret an error in the acknowledgments section regarding the U.S. Department of Energy Solar Energy Technologies Office award number. The previously listed grant number, 2597–1625, was incorrect. The corrected acknowledgment should read: “This work was supported by the Assistant Secretary for Energy Efficiency and Renewable Energy, Office of Building Technologies of the United States Department of Energy (DOE), under Contract No. DE-AC02–05CH11231. This material is based upon work supported by the U.S. Department of Energy's Office of Energy Efficiency and Renewable Energy (EERE) under the Solar Energy Technologies Office Award Number DE-EE00040384. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the Department of Energy.” The authors would like to apologise for any inconvenience caused.

Malik, Jeetika↗
DOE OSTI2019

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast

Here, we developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae , which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating, 15 barcoded plasmid libraries containing split selectable markers (URA3 AI , KanMX AI , HphMX AI , and NatMX AI ), and an array of ~24,000 “double-barcoder” strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performing many new combinatorial screens by short-read sequencing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Non-intrusive temperature measurements in the vicinity of a thermocouple using synchrotron x-ray fluorescence

A highly spatially resolved synchrotron x-ray fluorescence (XRF) thermometry technique has been used to map temperature fields around a 125 mu m type R thermocouple immersed in a stoichiometric premixed methane flame. The high spatial resolution of the XRF technique allowed temperatures to be measured close to the thermocouple and the impact of the thermocouple on the flame to be assessed. This paper discusses some of the nontrivial challenges of these measurements including the recovery of spectral features from the krypton fluorescent agent that are overlapped by those from the thermocouple metals at locations near the bead surface. The calculated temperatures from 1D premixed flame simulations are in excellent agreement with measurements along the centerline. The results show that the 125 mu m thermocouple induces minimal disturbances to the gas flow and any catalytic effects originating from the bare wires are also inconsequential. Here, the methodology has advanced to a stage where it enables comparisons between the gas temperature in the vicinity of the thermocouple and the actual thermocouple reading.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Microbial spies and bloggers: programming cells to convert environmental information into discernible signals

Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. Here, in this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.

analyte↗
DOE OSTI2014

Improved cache performance in Monte Carlo transport calculations using energy banding

We present an energy banding algorithm for Monte Carlo (MC) neutral particle transport simulations which depend on large cross section lookup tables. In MC codes, read-only cross section data tables are accessed frequently, exhibit poor locality, and are typically too much large to fit in fast memory. Thus, performance is often limited by long latencies to RAM, or by off-node communication latencies when the data footprint is very large and must be decomposed on a distributed memory machine. The proposed energy banding algorithm allows maximal temporal reuse of data in band sizes that can flexibly accommodate different architectural features. The energy banding algorithm is general and has a number of benefits compared to the traditional approach. In the present analysis we explore its potential to achieve improvements in time-to-solution on modern cache-based architectures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

PyProcar: A Python library for electronic structure pre/post-processing

The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each k-point in the Brillouin zone and band in an electronic structure calculation. This can be performed on top of any electronic structure code, as long as the band and projection information is written in the PROCAR format, as done by the VASP and ABINIT codes. PyProcar can be easily modified to read other formats as well. This package is particularly suitable for understanding atomic effects into the band structure, Fermi surface, spin texture, etc. PyProcar can be conveniently used in a command line mode, where each one of the parameters define a plot property. In the case of Fermi surfaces, the package is able to plot the surface with colors depending on other properties such as the electron velocity or spin projection. Furthermore, the mesh used to calculate the property does not need to be the same as the one used to obtain the Fermi surface. A file with a specific property evaluated for each k-point in a k-mesh and for each band can be used to project other properties such as electron–phonon mean path, Fermi velocity, electron effective mass, etc. Another existing feature refers to the band unfolding of supercell calculations into predefined unit cells.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Thermo4PFM: Facilitating Phase-field simulations of alloys with thermodynamic driving forces

Phase-field modeling is a popular front-tracking approach used to model solidification. Its time-evolution equations are often coupled to alloy composition and/or thermal diffusion in high-resolution multiphysics approaches. Materials thermodynamic properties tabulated in CALPHAD databases can be used for phase-field modeling to parameterize bulk energies of alloys. In addition, they can be naturally integrated into models such as the Kim-Kim-Suzuki (KKS) model where driving forces depend on the differences between chemical potentials of co-existing phases. In that case, a small system of coupled nonlinear equations needs to be solved at every point in space where the phase-field order parameter is to be updated and evolved in time. Here we present Thermo4PFM, a solver for the KKS equations for binary and ternary alloys, with two or three phases, and parameterized with CALPHAD models. Thermo4PFM is open source, written in C++, and can take advantage of Graphics Processing Units (GPU) accelerators. Using OpenMP offload capabilities for C++ classes, an excellent performance is demonstrated on GPU using the LLVM compiler. CALPHAD data is read from simple JSON files using an open source parser from the boost library.

36 MATERIALS SCIENCE↗
DOE OSTI2023

The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses

Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.50 years ago, "herpes-type" viral particles were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes, but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ~300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Discovery of additional ancient genome duplications in yeasts

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi. The oldest of these occurred ∼100 million years ago (mya) and is shared by ∼60 extant Saccharomycetales species, including the baker’s yeast Saccharomyces cerevisiae. Notably, this is the only known ancient WGD event in the yeast subphylum Saccharomycotina. The dearth of ancient WGD events in fungi remains a mystery. Some studies have suggested that fungal lineages that experience chromosome and genome duplication quickly go extinct, leaving no trace in the genomic record, while others contend that the lack of known WGDs is due to an absence of data. Under the second hypothesis, additional sampling and deeper sequencing of fungal genomes should lead to the discovery of more WGD events. Coupling hundreds of recently published genomes from nearly every described Saccharomycotina species, with three additional long-read assemblies, we discovered three novel WGD events. Although the functions of retained duplicate genes originating from these events are broad, they bear similarities to the well-known WGD that occurred in the Saccharomycetales. In conclusion, our results suggest that WGD may be a more common evolutionary force in fungi than previously believed.

convergent evolution↗