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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Analysis of Salmonella enterica Isolated from a Mixed-Use Watershed in Georgia, USA: Antimicrobial Resistance, Serotype Diversity, and Genetic Relatedness to Human Isolates

As the cases of Salmonella enterica infections associated with contaminated water are increasing, this study was conducted to address the role of surface water as a reservoir of S. enterica serotypes. We sampled rivers and streams (n = 688) over a 3-year period (2015 to 2017) in a mixed-use watershed in Georgia, USA, and 70.2% of the total stream samples tested positive for Salmonella. A total of 1,190 isolates were recovered and characterized by serotyping, antimicrobial susceptibility testing, and pulsed-field gel electrophoresis (PFGE). A wide range of serotypes was identified, including those commonly associated with humans and animals, with S. enterica serotype Muenchen being predominant (22.7%) and each serotype exhibiting a high degree of strain diversity by PFGE. About half (46.1%) of the isolates had PFGE patterns indistinguishable from those of human clinical isolates in the CDC PulseNet database. A total of 52 isolates (4.4%) were resistant to antimicrobials, out of which 43 isolates were multidrug resistant (MDR; resistance to two or more classes of antimicrobials). These 52 resistant Salmonella isolates were screened for the presence of antimicrobial resistance genes, plasmid replicons, and class 1 integrons, out of which four representative MDR isolates were selected for whole-genome sequencing analysis. The results showed that 28 MDR isolates resistant to 10 antimicrobials had blacmy-2 on an A/C plasmid. Persistent contamination of surface water with a high diversity of Salmonella strains, some of which are drug resistant and genetically indistinguishable from human isolates, supports a role of environmental surface water as a reservoir for and transmission route of this pathogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. In this paper, we used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ~1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ~1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. Finally, the results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The oncogenic role of meiosis-specific Aurora kinase C in mitotic cells

Highlights: • AURKC is expressed in meiotic cells and some cancers. • AURKC expression increases cell migration and transformation of human mitotic cells. • Deletion of AURKC in U2OS cells decreases cell migration and soft agar growth. • Transcriptome analysis reveals that AURKC alters the extracellular matrix. Aberrant expression of meiosis-specific genes in cancer has recently emerged as a driver of some cancer formation. Aurora kinase C (AURKC) is a member of the Aurora kinase family of proteins known to regulate chromosome segregation during cell divisions. AURKC is normally expressed in meiotic cells; however, elevated levels of AURKC mRNA and protein are frequently measured in cancer cells. To understand the function of AURKC in cancer cells, expression was induced in noncancerous, human retina pigmented epithelial cells. While AURKC expression did not alter cell proliferation over 72 h, it did increase cell migration and anchorage independent growth in soft agar suggesting an oncogenic role in mitotically dividing cells. To evaluate AURKC as a potential therapeutic target, a frameshift mutation in the gene was introduced in U2OS osteosarcoma cells using CRISPR-Cas9 technology resulting in a premature stop codon. Cancer cells lacking AURKC displayed no change in cell proliferation over 72 h but did migrate less and formed fewer colonies in soft agar. Whole transcriptome sequencing analysis uncovered over 400 differentially expressed genes in U2OS cells with and without AURKC. GO analysis revealed alterations in proteinaceous extracellular matrix genes including COL1A1. These data indicate that therapeutics targeting AURKC could decrease cancer cell metastasis and disease progression. Because AURKC is transcriptionally silenced in normal mitotic cells, its disruption could specifically target cancer cells limiting the toxic side effects associated with current therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Genomic dissection of anthracnose resistance response in sorghum [ Sorghum bicolor (L.) Moench]

Sorghum [ Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum . The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Genomic dissection of anthracnose resistance response in sorghum [ Sorghum bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important grain crop behind maize, wheat, rice, and barley. Today, it is of interest as a source of fermentable sugars for the production of renewable fuels and chemicals, and as a source of biomass for co-firing. The productivity and profitability of sorghum are limited by several biotic constraints, most notably anthracnose caused by the fungal pathogen Colletotrichum sublineolum. The most cost-effective and environmentally benign strategy to control anthracnose is through the incorporation of resistance genes. Over the last three years, our research efforts have been directed to identify new sources of resistance in temperate adapted and tropical germplasm, and to delimited genomic regions associated with the observe anthracnose resistant response. Three biparental mapping populations derived from the resistant lines SC112-14, QL3 and IS18760 were evaluated for anthracnose resistance response in Texas, Georgia, Florida and Puerto Rico. In parallel, three high density recombination maps were constructed and used to identify resistant loci. Anthracnose resistant response in line SC112-14 is controlled by a major locus on chromosome 5. Segregation analysis of 1,500 progenies delimited the resistance locus on chromosome 5 to a 23-kb region harboring three candidate genes, including Sobic.005G17230 identified by GWAS of the sorghum association panel (SAP). The latter gene belongs to a family of genes encoding F-box proteins indicating that this resistance response involved in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. In contrast, anthracnose resistant response in lines QL3 and IS18760 is controlled by multiple small-effect genes. Greenhouse evaluation of a representative subset of the three mapping populations against nine pathotypes found that lines susceptible in the field could be resistant to a single pathotype in the greenhouse. Thus, the activation of a resistance response system by a single pathotype could not provide a broader resistance response against multiple pathotypes. The screening of 1,801 sweet sorghum accessions from the National Plant Germplasm System identified 654 accessions with Brix value larger than 10, which in turn was used to select a subset of 233 accessions for evaluation of anthracnose resistant response. Even though most of the accessions were not completely infected by anthracnose, 28 accessions were completely resistant against pathotypes from Texas, Georgia, Florida and Puerto Rico. Genotyping-by-sequencing analysis of this subset identified 157,843 single nucleotide polymorphisms. Population structure analysis of the subset based on a subset of 2,345 unlinked SNPs found that the genetic diversity could be divided into four populations. The genetic relatedness among accessions within populations suggests most of the resistant germplasm may contain few different resistance sources. These resistance sources present in sweet sorghum germplasm could expedite the development of new resistant sweet sorghum cultivars and hybrids by avoiding time-consuming introgression breeding approaches with non-sweet sorghums serving as donor of the resistance alleles.

09 BIOMASS FUELS↗
DOE OSTI2017

Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment

We designed a universal human papillomavirus (HPV) typing assay based on target enrichment and whole-genome sequencing (eWGS). The RNA bait included 23,941 probes targeting 191 HPV types and 12 probes targeting beta-globin as a control. We used the Agilent SureSelect XT2 protocol for library preparation, Illumina HiSeq 2500 for sequencing, and CLC Genomics Workbench for sequence analysis. Mapping stringency for type assignment was determined based on 8 (6 HPV-positive and 2 HPV-negative) control samples. Using the optimal mapping conditions, types were assigned to 24 blinded samples. eWGS results were 100% concordant with Linear Array (LA) genotyping results for 9 plasmid samples and fully or partially concordant for 9 of the 15 cervical-vaginal samples, with 95.83% overall type-specific concordance for LA genotyping. eWGS identified 7 HPV types not included in the LA genotyping. Since this method does not involve degenerate primers targeting HPV genomic regions, PCR bias in genotype detection is minimized. With further refinements aimed at reducing cost and increasing throughput, this first application of eWGS for universal HPV typing could be a useful method to elucidate HPV epidemiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

Our genomic analyses promise to improve tumor characterization to optimize personalized treatment for patients with hepatocellular carcinoma (HCC). Exome sequencing analysis of 243 liver tumors identified mutational signatures associated with specific risk factors, mainly combined alcohol and tobacco consumption and exposure to aflatoxin B1. We identified 161 putative driver genes associated with 11 recurrently altered pathways. Associations of mutations defined 3 groups of genes related to risk factors and centered on CTNNB1 (alcohol), TP53 (hepatitis B virus, HBV) and AXIN1. These analyses according to tumor stage progression identified TERT promoter mutation as an early event, whereasFGF3, FGF4, FGF19 or CCND1 amplification and TP53 and CDKN2A alterations appeared at more advanced stages in aggressive tumors. In 28% of the tumors, we identified genetic alterations potentially targetable by US Food and Drug Administration (FDA)–approved drugs. Finally, we identified risk factor–specific mutational signatures and defined the extensive landscape of altered genes and pathways in HCC, which will be useful to design clinical trials for targeted therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Formation of less-known structurally complex ζ{sub b} and orthorhombic quasicrystalline approximant ε{sub n} on solidification of selected Al–Pd–Cr alloys

The evolution of phases was investigated on cooling of Al{sub 71}Pd{sub 24}Cr{sub 5}, Al{sub 73}Pd{sub 20}Cr{sub 7}, and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys from 1350 °C down to ambient temperature with the rate of 10 °C·min{sup −1}. To perform the investigation, differential thermal analysis, synchrotron X-ray powder diffraction, and scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy were used. In all the investigated alloys structurally complex phases ε{sub n} (ε{sub 6} + ε{sub 28}) and ζ{sub b}, as well as the δ-phase were identified. Based on the results of differential thermal analysis, sequences of phase transformations were determined. The Al{sub 71}Pd{sub 24}Cr{sub 5} alloy started to solidify at 1031.4 °C through β. Primary dendrites of ζ{sub b} were observed in Al{sub 73}Pd{sub 20}Cr{sub 7} and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys. In the second step of solidification δ and/or ζ{sub b} were formed. The peritectic reaction, liquid + ζ{sub b} + δ → ε{sub n} + ζ{sub b} + δ, leading to the formation of the quasicrystalline approximant ε{sub n} (ε{sub 6} + ε{sub 28}) took place in the final step of solidification at approximately 792 °C. - Highlights: • Structurally complex ε{sub n} (ε{sub 6} + ε{sub 28}), ζ{sub b} and δ-phases were identified. • The Al{sub 71}Pd{sub 24}Cr{sub 5} alloy started to solidify at 1031.4 °C through the primary β phase. • The Al{sub 73}Pd{sub 20}Cr{sub 7} and Al{sub 73}Pd{sub 23}Cr{sub 4} alloys solidified in the same way. • The quasicrystalline approximant ε{sub n} (ε{sub 6} + ε{sub 28}) was formed at approximately 792 °C.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Whole-Genome Sequencing and Bioinformatic Analysis of Environmental, Agricultural, and Human Campylobacter jejuni Isolates From East Tennessee

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter jejuni has a significant impact on human health in both the developed and developing worlds. Despite its prevalence as a human pathogen, the source of these infections remains poorly understood due to the mutation frequency of the organism and past limitations of whole genome analysis. Recent advances in both whole genome sequencing and computational methods have allowed for the high-resolution analysis of intraspecies diversity, leading multiple groups to postulate that these approaches may be used to identify the sources of Campylobacter jejuni infection. To address this hypothesis, our group conducted a regionally and temporally restricted sampling of agricultural and environmental Campylobacter sources and compared isolated C. jejuni genomes to those that caused human infections in the same region during the same time period. Through a network analysis comparing genomes from various sources, we found that human C. jejuni isolates clustered with those isolated from cattle and chickens, indicating these as potential sources of human infection in the region.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Chromosomal mutations in Escherichia coli that improve tolerance to nonvolatile side–products from dilute acid treatment of sugarcane bagasse

Lignocellulosic biomass provides attractive non-food carbohydrates for production of ethanol and dilute acid pretreatment is a biomass-independent process for access to these carbohydrates. However, this pretreatment also releases volatile and nonvolatile inhibitors of fermenting microorganisms. To identify unique gene products contributing to sensitivity/tolerance to non- volatile inhibitors, ethanologenic Escherichia coli strain LY180 was adapted for growth in vacuum-treated sugarcane bagasse acid hydrolysate (VBHz) lacking furfural and other volatile inhibitors. A mutant, strain AQ15, obtained after about 500 generations of growth in VBHz, grew and fermented the sugars in a medium with 50% VBHz. Comparative genome sequence analysis of strains AQ15 and LY180 revealed 95 mutations in strain AQ15. Six of these mutations were also found in strain SL112, an independent inhibitor-tolerant derivative of strain LY180. Among these six mutations, null mutations in mdh and bacA were identified as contributing factors to VBHz tolerance in strain AQ15, based on genetic and physiological analysis. Deletion of either gene in strain LY180 increased tolerance to VBHz from about 30% to 50% (v/v). Here, considering the location and physiological role of the two enzymes in the cell, it is likely that the two enzymes contribute to VBHz sensitivity of ethanologenic E. coli by different mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Transcriptome and phenotyping analyses support a role for chloroplast sigma factor 2 in red‐light‐dependent regulation of growth, stress, and photosynthesis

Abstract Sigma factor ( SIG ) proteins contribute to promoter specificity of the plastid‐encoded RNA polymerase during chloroplast genome transcription. All six members of the SIG family, that is, SIG 1– SIG 6, are nuclear‐encoded proteins targeted to chloroplasts. Sigma factor 2 ( SIG 2) is a phytochrome‐regulated protein important for stoichiometric control of the expression of plastid‐ and nuclear‐encoded genes that impact plastid development and plant growth and development. Among SIG factors, SIG 2 is required not only for transcription of chloroplast genes (i.e., anterograde signaling), but also impacts nuclear‐encoded, photosynthesis‐related, and light signaling‐related genes (i.e., retrograde signaling) in response to plastid functional status. Although SIG 2 is involved in photomorphogenesis in Arabidopsis, the molecular bases for its role in light signaling that impacts photomorphogenesis and aspects of photosynthesis have only recently begun to be investigated. Previously, we reported that SIG 2 is necessary for phytochrome‐mediated photomorphogenesis specifically under red (R) and far‐red light, thereby suggesting a link between phytochromes and nuclear‐encoded SIG 2 in light signaling. To explore transcriptional roles of SIG 2 in R‐dependent growth and development, we performed RNA sequencing analysis to compare gene expression in sig2‐2 mutant and Col‐0 wild‐type seedlings at two developmental stages (1‐ and 7‐day). We identified a subset of misregulated genes involved in growth, hormonal cross talk, stress responses, and photosynthesis. To investigate the functional relevance of these gene expression analyses, we performed several comparative phenotyping tests. In these analyses, strong sig2 mutants showed insensitivity to bioactive GA 3 , high intracellular levels of hydrogen peroxide (H 2 O 2 ) indicative of a stress response, and specific defects in photosynthesis, including elevated levels of cyclic electron flow ( CEF ) and nonphotochemical quenching ( NPQ ). We demonstrated that SIG 2 regulates a broader range of physiological responses at the molecular level than previously reported, with specific roles in red‐light‐mediated photomorphogenesis.

Oh, Sookyung↗
DOE OSTI2022

Registration of the sorghum carbon–partitioning nested association mapping (CP–NAM) population

The sorghum [ Sorghum bicolor (L.) Moench] carbon-partitioning nested association mapping (CP_NAM) (Reg. no. MP-4, NSL 542189 MAP) population was developed at Clemson University, SC, using 11 diverse, male founder accessions, each crossed with a recurrent female parent ‘Grassl’. The male parents represent all five major botanical races and the four major agronomic types: cellulosic (5), sweet (3), grain (2) and forage (1). A set of 11 recombinant inbred line (RIL) families CP_NAM01 to CP_NAM011 were maintained, which consisted of 2,484 (F 6 ) individuals. Each RIL family contained a minimum of 193 individuals (CP_NAM01) and a maximum of 287 individuals (CP_NAM06). For the development of this population, the founder lines were judiciously selected from the sorghum Bioenergy Association Panel based on carbon-partitioning phenotypes that make this population an ideal genetic resource for dissecting a wide range of agronomic and compositional traits for basic and applied research. The founder accessions of the CP_NAM were phenotypically characterized for various traits, including agronomic, biomass and related components, and additional compositional components. Each of the 11 F 6 RIL families of the CP_NAM were genotyped using genotyping-by-sequencing analysis, and 144,087 single nucleotide polymorphisms were generated for each individual. Genotypic information along with phenotypic data were used for the characterization of this population and to explore the range of phenotypes that permits the understanding of carbon-partitioning dynamics. This population is a unique resource for researchers to study a wide range of contrasting carbon-partitioning characteristics in sorghum to understand the genetic architecture underlying whole-plant carbon partitioning and allocation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Not as easy as π: An insertional residue does not explain the π‐helix gain‐of‐function in two‐component FMN reductases

Abstract The π‐helix located at the tetramer interface of two‐component FMN‐dependent reductases contributes to the structural divergence from canonical FMN‐bound reductases within the NADPH:FMN reductase family. The π‐helix in the SsuE FMN‐dependent reductase of the alkanesulfonate monooxygenase system has been proposed to be generated by the insertion of a Tyr residue in the conserved α4‐helix. Variants of Tyr118 were generated, and their X‐ray crystal structures determined, to evaluate how these alterations affect the structural integrity of the π‐helix. The structure of the Y118A SsuE π‐helix was converted to an α‐helix, similar to the FMN‐bound members of the NADPH:FMN reductase family. Although the π‐helix was altered, the FMN binding region remained unchanged. Conversely, deletion of Tyr118 disrupted the secondary structural properties of the π‐helix, generating a random coil region in the middle of helix 4. Both the Y118A and Δ118 SsuE SsuE variants crystallize as a dimer. The MsuE FMN reductase involved in the desulfonation of methanesulfonates is structurally similar to SsuE, but the π‐helix contains a His insertional residue. Exchanging the π‐helix insertional residue of each enzyme did not result in equivalent kinetic properties. Structure‐based sequence analysis further demonstrated the presence of a similar Tyr residue in an FMN‐bound reductase in the NADPH:FMN reductase family that is not sufficient to generate a π‐helix. Results from the structural and functional studies of the FMN‐dependent reductases suggest that the insertional residue alone is not solely responsible for generating the π‐helix, and additional structural adaptions occur to provide the altered gain of function.

McFarlane, Jeffrey S.↗
DOE OSTI2019

Advanced urothelial cancer: a radiology update

The recent genomic characterization of urothelial carcinoma by the Cancer Genome Atlas Project, made possible by the introduction of high throughput, reduced cost, and sequence analysis, has shed new insights on the biology of advanced disease. In addition, studies on imaging of advanced urothelial carcinoma have widened the knowledge on disease presentation and on pattern of metastatic spread and their correlation with the underlying biology of urothelial carcinoma. The wide range of treatments for advanced urothelial cancer, including combined chemotherapy regimens and immune checkpoint inhibitors, each result in treatment class-specific patterns of response and adverse events. Results of studies point to the need for a reliable biomarker, perhaps with imaging, that predicts prognosis and treatment response to systemic treatment, and can be used to select the most effective treatment while minimizing toxicity. This review of advanced urothelial cancer introduces the latest advances in genetic profiling, the current role of imaging, the radiographic appearance of treatment response and their toxicities, and details potential future areas of imaging research.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Statistical Optimization of Polyhydroxybutyrate Production by Bacillus Pumilus H9 Using Cow Dung as a Cheap Carbon Source by Response Surface Methodology

A gram positive bacterium (designated strain H9) found to be a potential polyhydroxybutyrate (biodegradable polymer) producer was isolated from the soil samples of a stress prone environment (municipal waste areas). This bacterium was identified as Bacillus pumilus H9 from its morphological, physiological and 16S rRNA gene sequence analysis. A four-factor central composite rotary design was employed to optimize the medium and to find out the interactive effects of four variables, viz. concentrations of cow dung, sucrose, peptone and pH on PHB production. Using response surface methodology, a second-order polynomial equation was obtained by multiple regression analysis and a yield of 2.47 g/L of PHB dry weight was achieved from the optimized medium at pH 7. Here, we report cow dung as a cheap carbon source for the production of PHB. Further, phbA, phbB and phbC genes were amplified by polymerase chain reaction which confirms the bacterium to be able to produce polyhydroxybutyrate.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Liquid Scintillation Counting of Environmental Radioisotopes: A Review of the Impact of Background Reduction

Liquid scintillation counting (LSC) is a versatile and commonplace method for radiometric measurement of charged particle emitting radionuclides. The LSC method provides utility in a range of environmental science applications including hydrological studies of water transport, anthropogenic releases of radionuclides into the environment, and vertical mixing rates within oceans. Instrumental measurement background is one limiting factor of radiometric measurement sensitivity. As part of the development of a custom low background LSC system located in a shallow underground laboratory at Pacific Northwest National Laboratory, a number of measurement applications of LSC have been considered and are summarized here. The focus is on determining which aspects of such measurements would gain the greatest benefit from the reduction of LSC backgrounds by a factor of 10-100 relative to values reported in the literature. Examples of benefits include lowering the minimum detectable activity, reducing the sample size required, and shortening the elapsed timeline of the processing and analysis sequence. In particular tritium, strontium, and actinium isotopes are examined as these isotopes cover a range of requirements related to the LSC measurement method (e.g., 3H: low energy; Sr: spectral deconvolution; Ac: alpha/beta discrimination).

actinium↗