Identification of the ATPase Subunit of the Primary Maltose Transporter in the Hyperthermophilic Anaerobe \u3ci\u3eThermotoga maritima\u3c/i\u3e

Thermotoga maritima is a hyperthermophilic anaerobic bacterium that produces molecular hydrogen (H2) by fermentation. It catabolizes a broad range of carbohydrates through the action of diverse ABC transporters. However, in T. maritima and related species, highly similar genes with ambiguous annotation obscure a precise understanding of genome function. In T. maritima, three putative malK genes, all annotated as ATPase subunits, exhibited high identity to each other. To distinguish between these genes, malK disruption mutants were constructed by gene replacement, and the resulting mutant cell lines were characterized. Only a disruption of malK3 produced a defect in maltose catabolism. To verify that the mutant phenotype arose specifically from malK3 inactivation, the malK3 mutation was repaired by recombination, and maltose catabolism was restored. This study demonstrates the importance of a maltose ABC-type transporter and its relationship to sugar metabolism in T. maritima. IMPORTANCE: The application and further development of a genetic system was used here to investigate gene paralogs in the hyperthermophile Thermotoga maritima. The occurrence of three ABC transporter ATPase subunits all annotated as malK was evaluated using a combination of genetic and bioinformatic approaches. The results clarify the role of only one malK gene in maltose catabolism in a nonmodel organism noted for fermentative hydrogen production. Includes supplemental material

Comparative kinetic modeling of growth and molecular hydrogen overproduction by engineered strains of \u3ci\u3eThermotoga maritima \u3c/i\u3e

Thermotoga maritima is an anaerobic hyperthermophilic bacterium known for its high amounts of hydrogen (H2) production. In the current study, the kinetic modeling was applied on the engineered strains of T. maritima that surpassed the natural H2 production limit. The study generated a kinetic model explaining H2 overproduction and predicted a continuous fermentation system. A Leudking-Piret equation-based model predicted that H2 production by Tma200 (0.217 mol-H2 g–1-biomass) and Tma100 (0.147 mol-H2 g–1-biomass) were higher than wild type (0.096 mol-H2 g–1 -biomass) with reduced rates of maltose utilization. Sensitivity analysis confirmed satisfactory fitting of the experimental data. The slow growth rates of Tma200 (0.550 h–1) and Tma100 (0.495 h–1) are compared with the wild type (0.663 h–1). A higher maintenance energy along with growth and non-growth H2 coefficients corroborate the higher H2 productivity of the engineered strains. The modeled data established a continuous fermentation system for the sustainable H2 production. (Inludes 2 supplemental figures

Comparative kinetic modeling of growth and molecular hydrogen overproduction by engineered strains of \u3ci\u3eThermotoga maritima \u3c/i\u3e

Thermotoga maritima is an anaerobic hyperthermophilic bacterium known for its high amounts of hydrogen (H2) production. In the current study, the kinetic modeling was applied on the engineered strains of T. maritima that surpassed the natural H2 production limit. The study generated a kinetic model explaining H2 overproduction and predicted a continuous fermentation system. A Leudking-Piret equation-based model predicted that H2 production by Tma200 (0.217 mol-H2 g–1-biomass) and Tma100 (0.147 mol-H2 g–1-biomass) were higher than wild type (0.096 mol-H2 g–1 -biomass) with reduced rates of maltose utilization. Sensitivity analysis confirmed satisfactory fitting of the experimental data. The slow growth rates of Tma200 (0.550 h–1) and Tma100 (0.495 h–1) are compared with the wild type (0.663 h–1). A higher maintenance energy along with growth and non-growth H2 coefficients corroborate the higher H2 productivity of the engineered strains. The modeled data established a continuous fermentation system for the sustainable H2 production. (Inludes 2 supplemental figures

All-thermal switching of amorphous Gd-Fe alloys: analysis of structural properties and magnetization dynamics

In recent years, there has been an intense interest in understanding the microscopic mechanism of thermally induced magnetization switching driven by a femtosecond laser pulse. Most of the effort has been dedicated to periodic crystalline structures while the amorphous counterparts have been less studied. By using a multiscale approach, i.e. first-principles density functional theory combined with atomistic spin dynamics, we report here on the very intricate structural and magnetic nature of amorphous Gd-Fe alloys for a wide range of Gd and Fe atomic concentrations at the nanoscale level. Both structural and dynamical properties of Gd-Fe alloys reported in this work are in good agreement with previous experiments. We calculated the dynamic behavior of homogeneous and inhomogeneous amorphous Gd-Fe alloys and their response under the influence of a femtosecond laser pulse. In the homogeneous sample, the Fe sublattice switches its magnetization before the Gd one. However, the temporal sequence of the switching of the two sublattices is reversed in the inhomogeneous sample. We propose a possible explanation based on a mechanism driven by a combination of the Dzyaloshiskii-Moriya interaction and exchange frustration, modeled by an antiferromagnetic second-neighbour exchange interaction between Gd atoms in the Gd-rich region. We also report on the influence of laser fluence and damping effects in the all-thermal switching.Comment: Accepted in Physical Review B as a regular article. It contains 14 pages and 14 figure

Contribution of Pentose Catabolism to Molecular Hydrogen Formation by Targeted Disruption of Arabinose Isomerase (\u3ci\u3earaA\u3c/i\u3e) in the Hyperthermophilic Bacterium \u3ci\u3eThermotoga maritima\u3c/i\u3e

Thermotoga maritima ferments a broad range of sugars to form acetate, carbon dioxide, traces of lactate, and near theoretic yields of molecular hydrogen (H2). In this organism, the catabolism of pentose sugars such as arabinose depends on the interaction of the pentose phosphate pathway with the Embden-Myerhoff and Entner-Doudoroff pathways. Although the values for H2 yield have been determined using pentose-supplemented complex medium and predicted by metabolic pathway reconstruction, the actual effect of pathway elimination on hydrogen production has not been reported due to the lack of a genetic method for the creation of targeted mutations. Here, a spontaneous and genetically stable pyrE deletion mutant was isolated and used as a recipient to refine transformation methods for its repair by homologous recombination. To verify the occurrence of recombination and to assess the frequency of crossover events flanking the deleted region, a synthetic pyrE allele, encoding synonymous nucleotide substitutions, was used. Targeted inactivation of araA (encoding arabinose isomerase) in the pyrE mutant was accomplished using a divergent, codon-optimized Thermosipho africanus pyrE allele fused to the T. maritima groES promoter as a genetic marker. Mutants lacking araA were unable to catabolize arabinose in a defined medium. The araA mutation was then repaired using targeted recombination. Levels of synthesis of H2 using arabinose-supplemented complex medium by wild-type and araA mutant cell lines were compared. The difference between strains provided a direct measurement of H2 production that was dependent on arabinose consumption. Development of a targeted recombination system for genetic manipulation of T. maritima provides a new strategy to explore H2 formation and life at an extremely high temperature in the bacterial domain

Mapping Text: Automated Geoparsing and Map Browser for Electronic Theses and Dissertations

Presented at the Digital Humanities 2013 International Conference at the University of Nebraska-Lincoln, 16-19 July, 201

Bundling up carbon nanotubes through Wigner defects

We show, using ab initio total energy density functional theory, that the so-called Wigner defects, an interstitial carbon atom right besides a vacancy, which are present in irradiated graphite can also exist in bundles of carbon nanotubes. Due to the geometrical structure of a nanotube, however, this defect has a rather low formation energy, lower than the vacancy itself, suggesting that it may be one of the most important defects that are created after electron or ion irradiation. Moreover, they form a strong link between the nanotubes in bundles, increasing their shear modulus by a sizeable amount, clearly indicating its importance for the mechanical properties of nanotube bundles.Comment: 5 pages and 4 figure

Regulation of Stat5 by FAK and PAK1 in Oncogenic FLT3 and KIT driven Leukemogenesis

Oncogenic mutations of FLT3 and KIT receptors are associated with poor survival in patients with acute myeloid leukemia (AML) and myeloproliferative neoplasms (MPN) and currently available drugs are largely ineffective. Although Stat5 has been implicated in regulating several myeloid and lymphoid malignancies, how precisely Stat5 regulates leukemogenesis, including its nuclear translocation to induce gene transcription is poorly understood. In leukemic cells, we show constitutive activation of focal adhesion kinase (FAK), whose inhibition represses leukemogenesis. Downstream of FAK, activation of Rac1 is regulated by RacGEF Tiam1, whose inhibition prolongs the survival of leukemic mice. Inhibition of the Rac1 effector PAK1 prolongs the survival of leukemic mice in part by inhibiting the nuclear translocation of Stat5. These results reveal a leukemic pathway involving FAK/Tiam1/Rac1/PAK1 and demonstrate an essential role for these signaling molecules in regulating the nuclear translocation of Stat5 in leukemogenesis

Class IA PI3Kinase Regulatory Subunit, p85α, Mediates Mast Cell Development through Regulation of Growth and Survival Related Genes

Stem cell factor (SCF) mediated KIT receptor activation plays a pivotal role in mast cell growth, maturation and survival. However, the signaling events downstream from KIT are poorly understood. Mast cells express multiple regulatory subunits of class 1A PI3Kinase (PI3K) including p85α, p85β, p50α, and p55α. While it is known that PI3K plays an essential role in mast cells; the precise mechanism by which these regulatory subunits impact specific mast cell functions including growth, survival and cycling are not known. We show that loss of p85α impairs the growth, survival and cycling of mast cell progenitors (MCp). To delineate the molecular mechanism (s) by which p85α regulates mast cell growth, survival and cycling, we performed microarray analyses to compare the gene expression profile of MCps derived from WT and p85α-deficient mice in response to SCF stimulation. We identified 151 unique genes exhibiting altered expression in p85α-deficient cells in response to SCF stimulation compared to WT cells. Functional categorization based on DAVID bioinformatics tool and Ingenuity Pathway Analysis (IPA) software relates the altered genes due to lack of p85α to transcription, cell cycle, cell survival, cell adhesion, cell differentiation, and signal transduction. Our results suggest that p85α is involved in mast cell development through regulation of expression of growth, survival and cell cycle related genes

Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): Their expression during early embryonic development

<p>Abstract</p> <p>Background</p> <p>Current literature and our previous results on expression patterns of oocyte-specific genes and transcription factors suggest a global but highly regulated maternal mRNA degradation at the time of embryonic genome activation (EGA). MicroRNAs (miRNAs) are small, non-coding regulatory RNAs (19–23 nucleotides) that regulate gene expression by guiding target mRNA cleavage or translational inhibition. These regulatory RNAs are potentially involved in the degradation of maternally inherited mRNAs during early embryogenesis.</p> <p>Results</p> <p>To identify miRNAs that might be important for early embryogenesis in rainbow trout, we constructed a miRNA library from a pool of unfertilized eggs and early stage embryos. Sequence analysis of random clones from the library identified 14 miRNAs, 4 of which are novel to rainbow trout. Real-time PCR was used to measure the expression of all cloned miRNAs during embryonic development. Four distinct expression patterns were observed and some miRNAs showed up-regulated expression during EGA. Analysis of tissue distribution of these miRNAs showed that some are present ubiquitously, while others are differentially expressed among different tissues. We also analyzed the expression patterns of Dicer, the enzyme required for the processing of miRNAs and Stat3, a transcription factor involved in activating the transcription of miR-21. Dicer is abundantly expressed during EGA and Stat3 is up-regulated before the onset of EGA.</p> <p>Conclusion</p> <p>This study led to the discovery of 14 rainbow trout miRNAs. Our data support the notion that Dicer processes miRNAs and Stat3 induces expression of miR-21 and possibly other miRNAs during EGA. These miRNAs in turn guide maternal mRNAs for degradation, which is required for normal embryonic development.</p