Miracle-dz/UniFAR-FTUs huggingface dataset:
Cyanate distribution and uptake above and within the Eastern Tropical South Pacific oxygen deficient zone

Cyanate is a simple reduced nitrogen (N) compound that can be a source of N and carbon (C) for marine organisms and may also be a substrate for dissimilatory N processes such as nitrification and anammox. We measured cyanate distributions and cyanate and urea uptake in the Eastern Tropical South Pacific, a region defined by coastal upwelling, high primary productivity, a shallow oxic layer, and rapid N loss from a large oxygen deficient zone (ODZ). Cyanate concentrations ranged from below the limit of detection (0.4 nM) to 45 nM in the oxic upper water column. Below the oxycline, cyanate concentrations were largely below detection except for small cyanate peaks (2–8.3 nM) within the core of the ODZ at some stations. The majority of N taken up in the shallow oxic layer was from ammonium and urea (78% ± 8%); cyanate uptake was < 2% of these. Uptake of cyanate fluctuated diurnally with the highest rates of cyanate N uptake in the early afternoon. In the ODZ, rates of cyanate, urea, and ammonium uptake were similar to each other (0.1–14 nmol N L−1 d−1) and to previously reported rates of 29N2 production supported by cyanate and ammonium (3–14 nmol N2 L−1 d−1). This suggests a role for cyanate in the metabolism of anaerobic microbes and a potential role for cyanate in the anammox reaction (cyanammox). To our knowledge, these represent the first rates of N uptake in a marine anoxic water column.
Organization of regionally expressed silkmoth chorion genes

We described the organization of two silkmoth chorion genes, called E1 and E2, whose expression is largely restricted in time to the very late period of choriogenesis and in space to one of two major subpopulations of follicle cells. Using E1 and E2 clone cDNAs as probes, we showed that gene copy numbers per haploid genome remain constant throughout silkmoth development despite major changes in total DNA content per nucleus. Furthermore, gene copy numbers are the same in both cellular regions of the choriogenic follicle despite differences in nuclear size and levels of E gene expression. Southern analysis indicated between two and four copies each for E1 and E2 genes. Analysis of chromosomal clones showed that single copies of E1 and E2 are separated by about 7.5 kilobases and are transcribed from the same DNA strand. Two distinct pairs of cloned E1 and E2 genes were characterized. No other chorion genes were in their immediate vicinity.
RNA Polymerases from Bacillus subtilis andEscherichia coli Differ in Recognition of Regulatory Signals In Vitro

Adaptation of bacterial cells to diverse habitats relies on the ability of RNA polymerase to respond to various regulatory signals. Some of these signals are conserved throughout evolution, whereas others are species speciﬁc. In this study we present a comprehensive comparative analysis of RNA polymerases from two distantly related bacterial species, Escherichia coli and Bacillus subtilis , using a panel of in vitro transcription assays. We found substantial species-speciﬁc differences in the ability of these enzymes to escape from the promoter and to recognize certain types of elongation signals. Both enzymes responded similarly to other pause and termination signals and to the general E. coli elongation factors NusA and GreA. We also demonstrate that, although promoter recognition depends largely on the s subunit, promoter discrimination exhibited in species-speciﬁc fashion by both RNA polymerases resides in the core enzyme. We hypothesize that differences in signal recognition are due to the changes in contacts made between the b and b * subunits and the downstream DNA duplex.
Control of BEK and K-SAM splice sites in alternative splicing of the fibroblast growth factor receptor 2 pre-mRNA

The fibroblast growth factor receptor 2 gene pre-mRNA can be spliced by using either the K-SAM exon or the BEK exon. The exon chosen has a profound influence on the ligand-binding specificity of the receptor obtained. Cells make a choice between the two alternative exons by controlling use of both exons. Using fibroblast growth factor receptor 2 minigenes, we have shown that in cells normally using the K-SAM exon, the BEK exon is not used efficiently even in the absence of the K-SAM exon. This is because these cells apparently express a titratable repressor of BEK exon use. In cells normally using the BEK exon, the K-SAM exon is not used efficiently even in the absence of a functional BEK exon. Three purines in the K-SAM polypyrimidine tract are at least in part responsible for this, as their mutation to pyrimidines leads to efficient use of the K-SAM exon, while mutating the BEK polypyrimidine tract to include these purines stops BEK exon use.
Direct and indirect gene replacements in Aspergillus nidulans

We performed three sets of experiments to determine whether cloned DNA fragments can be substituted for homologous regions of the Aspergillus nidulans genome by DNA-mediated transformation. A linear DNA fragment containing a heteromorphic trpC+ allele was used to transform a trpC- strain to trpC+. Blot analysis of DNA from the transformants showed that the heteromorphic allele had replaced the trpC- allele in a minority of the strains. An A. nidulans trpC+ gene was inserted into the argB+ gene, and a linear DNA fragment containing the resultant null argB allele was used to transform a trpC- argB+ strain to trpC+. Approximately 30% of the transformants were simultaneously argB-. The null argB allele had replaced the wild-type allele in a majority of these strains. The A. nidulans SpoC1 C1-C gene was modified by removal of an internal restriction fragment and introduced into a trpC- strain by transformation with a circular plasmid. A transformant containing a tandem duplication of the C1-C region separated by plasmid DNA was self-fertilized, and trpC- progeny were selected. All of these had lost the introduced plasmid DNA sequences, whereas about half had retained the modified C1-C gene and lost the wild-type copy. Thus, it is possible with A. nidulans to replace chromosomal DNA sequences with DNA fragments that have been cloned and modified in vitro by using either one- or two-step procedures similar to those developed for Saccharomyces cerevisiae.
The effect of initial pH on surface properties of ferric ion precipitates formed during microbial oxidation of ferrous ion by Leptospirillum ferriphilum in a CSTR

iii DEDICATION . v ACKNOWLEDGEMENTS . vi LIST OF PRESENTATION . viii TABLE OF CONTENTS . ix LIST OF FIGURES . xiv LIST OF TABLES . xv Chapter 1 .
Regulation of nitrogen metabolism and gene expression in fungi

ITROD 04 UCTON . 437 NITREAT E . E.D. E.438 NiRATE REDUCTASE AND AUTOGENOUS CONTROL . 440 TURNOVER OF NiREATE REDUCTABSE.441 PURINlNE CATABO-LISM . 4.441 PRO11UN4E CATABOLISML . 446. 446 ACETAMEDE UTILIZATION AND INTEGRATOR GENE.448 NrIROGEN CATABOLIE REPRESSIONN: GENgI'IC STUDIE . 450 PATHWAY-SPECIFIC CONTROL . 451 REGULATORY RECOGNIMION SEQUENCES? 451 GLUTAMATE DEHDROGENASE . 452 GLUTAMATE DMElHYDROGENASE: A REGULATORY PROTEIN? 453 GLUTAMIMMNE E . NTH. A.S3E 454 MERCHANISRM OF NIROGEN CATABOIXTE REPRESSION . 455 CLOSING SAND FUTURE PROSPECTS . 457 LITERATURE, CYRE ITED 458
Specific growth inhibitory sequences in genomic DNA from quiescent human embryo fibroblasts

We used HeLa cells as recipients in a gene transfer assay to characterize DNA sequences that negatively regulate mammalian cell growth. In this assay, genomic DNA from quiescent human embryo fibroblasts was more inhibitory for HeLa replication than was DNA from either Escherichia coli or HeLa cells. Surprisingly, growth inhibitory activity depended on the growth state of the cells from which genomic DNA was prepared; it was strongest in DNA prepared from serum-deprived, quiescent embryo fibroblasts. This latter observation implies a role for DNA modification(s) in regulating the activity of the inhibitory sequences detected in our assay. The level of the observed growth inhibitory activity was sometimes high, suggesting that the relevant sequences may be abundantly represented in the mammalian genome. We speculate that these findings may provide new insights into the molecular mechanisms involved in cellular quiescence and in vitro senescence.
Band engineering in Mg_3Sb_2 by alloying with Mg_3Bi_2 for enhanced thermoelectric performance

Mg_3Sb_2–Mg_3Bi_2 alloys show excellent thermoelectric properties. The benefit of alloying has been attributed to the reduction in lattice thermal conductivity. However, Mg_3Bi_2-alloying may also be expected to significantly change the electronic structure. By comparatively modeling the transport properties of n- and p-type Mg_3Sb_2–Mg_3Bi_2 and also Mg_3Bi_2-alloyed and non-alloyed samples, we elucidate the origin of the highest zT composition where electronic properties account for about 50% of the improvement. We find that Mg_3Bi_2 alloying increases the weighted mobility while reducing the band gap. The reduced band gap is found not to compromise the thermoelectric performance for a small amount of Mg_3Bi_2 because the peak zT in unalloyed Mg_3Sb_2 is at a temperature higher than the stable range for the material. By quantifying the electronic influence of Mg_3Bi_2 alloying, we model the optimum Mg_3Bi_2 content for thermoelectrics to be in the range of 20–30%, consistent with the most commonly reported composition Mg_3Sb_(1.5)Bi_(0.5).
Cellular Targets for Activation by the E2F1 Transcription Factor Include DNA Synthesis- and G1/S-Regulatory Genes

Although a number of transfection experiments have suggested potential targets for the action of the E2F1 transcription factor, as is the case for many transcriptional regulatory proteins, the actual targets in their normal chromosomal environment have not been demonstrated. We have made use of a recombinant adeno- virus containing the E2F1 cDNA to infect quiescent cells and then measure the activation of endogenous cellular genes as a consequence of E2F1 production. We ﬁnd that many of the genes encoding S-phase-acting proteins previously suspected to be E2F targets, including DNA polymerase (cid:97) , thymidylate synthase, proliferating cell nuclear antigen, and ribonucleotide reductase, are indeed induced by E2F1. Several other candi- dates, including the dihydrofolate reductase and thymidine kinase genes, were only minimally induced by E2F1. In addition to the S-phase genes, we also ﬁnd that several genes believed to play regulatory roles in cell cycle progression, such as the cdc2 , cyclin A, and B- myb genes, are also induced by E2F1. Moreover, the cyclin E gene is strongly induced by E2F1, thus deﬁning an autoregulatory circuit since cyclin E-dependent kinase activity can stimulate E2F1 transcription, likely through the phosphorylation and inactivation of Rb and Rb family members. Finally, we also demonstrate that a G 1 arrest brought about by (cid:103) irradiation is overcome by the overexpression of E2F1 and that this coincides
Intracellular precursors and secretion of alkaline extracellular protease of Yarrowia lipolytica

Processing and secretion of the alkaline extracellular protease (AEP) from the yeast Yarrowia lipolytica was studied by pulse-chase and immunoprecipitation experiments. Over half of newly synthesized AEP was secreted by 6 min. Over 99% of AEP activity which was external to the cytoplasmic membrane was located in the supernatant medium. Polypeptides of 55, 52, 44, 36, and 32 kilodaltons (55K, 52K, 44K, 36K, and 32K polypeptides) were immunoprecipitated from [3H]leucine-labeled cell extracts by rabbit antibodies raised against mature, secreted AEP (32K polypeptide). Experiments with tunicamycin and endoglycosidase H indicated that the 55K, 52K, and 44K polypeptides contained about 2 kilodaltons of N-linked oligosaccharide and that the 36K and 32K polypeptides contained none. Results of pulse-chase experiments did not fit a simple precursor-product relationship of 55K----52K----44K----36K----32K. In fact, maximum labeling intensity of the 52K polypeptide occurred later than for the 44K and 36K polypeptides. Secretion of polypeptides of 19 and 20 kilodaltons derived from the proregion of AEP indicated that one major processing pathway was 55K----52K----32K. The gene coding for AEP (XPR2) was cloned and sequenced. The sequence and the immunoprecipitation results suggest that AEP is originally synthesized with an additional preproI-proII-proIII amino-terminal region. Processing definitely involves cleavage(s) after pairs of basic amino acids and the addition of one N-linked oligosaccharide. Signal peptidase cleavage, dipeptidyl aminopeptidase cleavages, and at least one additional proteolytic cleavage may also be involved.
Potential virulence factors of Proteus bacilli

The object of this review is the genus Proteus, which contains bacteria considered now to belong to the opportunistic pathogens. Widely distributed in nature (in soil, water, and sewage), Proteus species play a significant ecological role. When present in the niches of higher macroorganisms, these species are able to evoke pathological events in different regions of the human body. The invaders (Proteus mirabilis, P. vulgaris, and P. penneri) have numerous factors including fimbriae, flagella, outer membrane proteins, lipopolysaccharide, capsule antigen, urease, immunoglobulin A proteases, hemolysins, amino acid deaminases, and, finally, the most characteristic attribute of Proteus, swarming growth, enabling them to colonize and survive in higher organisms. All these features and factors are described and commented on in detail. The questions important for future investigation of these facultatively pathogenic microorganisms are also discussed.
Genetic competence in Bacillus subtilis

Genetic competence may be defined as a physiological state enabling a bacterial culture to bind and take up high-molecular-weight exogenous DNA (transformation). In Bacillus subtilis, competence develops postexponentially and only in certain media. In addition, only a minority of the cells in a competent culture become competent, and these are physiologically distinct. Thus, competence is subject to three regulatory modalities: growth stage specific, nutritionally responsive, and cell type specific. This review summarizes the present state of knowledge concerning competence in B. subtilis. The study of genes required for transformability has permitted their classification into two broad categories. Late competence genes are expressed under competence control and specify products required for the binding, uptake, and processing of transforming DNA. Regulatory genes specify products that are needed for the expression of the late genes. Several of the late competence gene products have been shown to be membrane localized, and others are predicted to be membrane associated on the basis of amino acid sequence data. Several of these predicted protein sequences show a striking resemblance to gene products that are involved in the export and/or assembly of extracellular proteins and structures in gram-negative organisms. This observation is consistent with the idea that the late products are directly involved in transport of DNA and is equally consistent with the notion that they play a morphogenetic role in the assembly of a transport apparatus. The competence regulatory apparatus constitutes an elaborate signal transduction system that senses and interprets environmental information and passes this information to the competence-specific transcriptional machinery. Many of the regulatory gene products have been identified and partially characterized, and their interactions have been studied genetically and in some cases biochemically as well. These include several histidine kinase and response regulator members of the bacterial two-component signal transduction machinery, as well as a number of known transcriptionally active proteins. Results of genetic studies are consistent with the notion that the regulatory proteins interact in a hierarchical way to make up a regulatory pathway, and it is possible to propose a provisional scheme for the organization of this pathway. It is remarkable that almost all of the regulatory gene products appear to play roles in the control of various forms of postexponential expression in addition to competence, e.g., sporulation, degradative-enzyme production, motility, and antibiotic production. This has led to the notion of a signal transduction network which transduces environmental information to determine the levels and timing of expression of the ultimate products characteristic of each of these systems.
Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress

The existence of multiple heat shock factor (HSF) genes in higher eukaryotes has promoted questions regarding the functions of these HSF family members, especially with respect to the stress response. To address these questions, we have used polyclonal antisera raised against mouse HSF1 and HSF2 to examine the biochemical, physical, and functional properties of these two factors in unstressed and heat-shocked mouse and human cells. We have identified HSF1 as the mediator of stress-induced heat shock gene transcription. HSF1 displays stress-induced DNA-binding activity, oligomerization, and nuclear localization, while HSF2 does not. Also, HSF1 undergoes phosphorylation in cells exposed to heat or cadmium sulfate but not in cells treated with the amino acid analog L-azetidine-2-carboxylic acid, indicating that phosphorylation of HSF1 is not essential for its activation. Interestingly, HSF1 and HSF2 overexpressed in transfected 3T3 cells both display constitutive DNA-binding activity, oligomerization, and transcriptional activity. These results demonstrate that HSF1 can be activated in the absence of physiological stress and also provide support for a model of regulation of HSF1 and HSF2 activity by a titratable negative regulatory factor.
Gender Differences in Student Comfort Voluntarily Asking and Answering Questions in Large-Enrollment College Science Courses

Allowing students to ask and answer questions is a common practice employed by college science instructors. However, recent literature has identified that women participate in whole-class discussions less often than men. One hypothesized reason for this gender gap is that women may be less comfortable participating. ABSTRACT Allowing students to ask and answer questions is a common practice employed by college science instructors. However, recent literature has identified that women participate in whole-class discussions less often than men. One hypothesized reason for this gender gap is that women may be less comfortable participating. However, no studies have examined students’ comfort with asking and answering questions in large-enrollment science courses, identified what about these practices might make students uncomfortable, or explored whether there are gender differences with regard to student comfort. To answer these questions, we surveyed 417 undergraduates at an R1 institution about their experiences asking and answering questions in large-enrollment college science courses. Students answered questions about the extent to which they felt comfortable both asking and answering questions and selected possible factors that could make them uncomfortable participating. Using binary logistic regression, we tested whether student demographics predicted their opinions about these practices. Over half of students reported feeling uncomfortable both asking and answering questions in front of college science classes, and women were significantly less comfortable than men both asking and answering questions. Furthermore, we identified student confidence regarding their knowledge of the material and a concern that other students would judge them as some of the primary factors that could cause students to feel uncomfortable asking and answering questions in front of the whole class. This work highlights factors that instructors can target in hopes of maximizing student comfort participating in large-enrollment college science courses.
Polyamines in microorganisms

INTRODUCTION. 82 POLYAMINES IN ESCHERICHIA COLI 82 Biosynthesis of Putrescine, Agmatine, and Cadaverine 8 Biodegradative (induced) ornithine decarboxylase. Biosynthetic (constitutive) ornithine decarboxylase . 82 Mutants lacking ornithine decarboxylase . ,, 82 Biodegradative arginine decarboxylase 83 Biosynthetic arginine decarboxylase 4 Mutants lacking biosynthetic arginine decarboxylase . 84 Agmatine ureohydrolase. 84 Lysine decarboxylase 8 Biosynthesis of Spermidine 4 Methionine adenosyltransferase (S-adenosylmethionine synthetase). 84 S-Adenosylmethionine decarboxylase. , 85 Spermidine synthase (putrescine aminopropyltransferase). 85 Polyamine Concentrations in E. coli 85 Influence of culture conditions Transport of polyamines into E. coli Intracellular localization of polyamines. 85 Regulation of Biosynthetic Enzymes 86 Control by intracellular concentrations of ornithine and arginine. 86 Control by intracellular concentrations of polyamines.86 Control by guanine nucleotides and by cyclic AMP . 86 Control by antizyme. 86 Metabolism . , . 86 Formation of glutathionylspermidine 86 Acetylation of putrescine and spermidine 7 Effects of Polyamines In Vivo. 87 Effects on protein biosynthesis in vivo 8 Effects on DNA replication in vivo. 87 Effects on osmotic fragility of spheroplasts and protoplasts 87 Polyamines in bacteriophages Effects of spermidine analogs in vivo.88 Toxicity of spermine.8 Effects of Polyamines In Vitro. 88 POLYAMINES IN SACCHAROMYCES CEREVISIAE 89 Concentration of Amines. 0 89 Biosynthesis of Putrescine 8 Purification of ornithine decarboxylase 89 Mutants lacking ornithine decarboxylase activity.8 Regulation of ornithine decarboxylase . 9. 90 Effects of polyamines on ornithine decarboxy! ase 90 Biosynthesis of Spermidine and Spermine Methionine adenosyltransferase (S-adenosylmethionine synthetase). 90 S-Adenosylmethionine decarboxylase.90 Mutants lacking S-adenosylmethionine decarboxylase.9 Mutants lacking putrescine aminopropyltransferase and spermidine aminopropyltransferase. 90 Effects of Polyamines In Vitro on tRNA of S. cerevisiae 1 POLYAMINES IN PHYSARUM POLYCEPHALUM 9 Polyamine concentrations.91 Ornithine decarboxylase and adenosylmethionine decarboxylase.91 Regulation of polyamine biosynthesis in P. polycephalum. POLYAMINES IN NEUROSPORA CRASSA 92 POLYAMINES IN ASPERGILLUS NIDULANS UNUSUAL AMINES AND AMI NE D RIVATIVES INMICROORGANISMS.92 Thermophilic organisms. 92
Perspective of safflower (Carthamus tinctorius) as a potential biodiesel feedstock in Turkey: characterization, engine performance and emissions analyses of butanol–biodiesel–diesel blends

ABSTRACT Safflower (Carthamus tinctorius) is widely farmed in Turkey. This study investigates the physicochemical properties of safflower biodiesel and its blends with Euro diesel and butanol. A polynomial curve-fitting method was used to predict kinematic viscosity and density of the ternary blends. Furthermore, characteristics such as DSC, FT-IR, UV-Vis and TGA were adopted to evaluate the influence of butanol addition on biodiesel–diesel blends. Engine performance parameters such as BP, torque and BSFC and emissions such as CO, HC, NOx and EGT were studied. Safflower methyl ester satisfied both EN 14214 and ASTM D 6751 standards regarding viscosity, flash point and density. However, iodine value was quite high. Oxidation stability fails to satisfy either standard. This is due to the high level of unsaturated fatty acids (91.05%). A reduction in BP, torque, HC and CO coupled with an increase in BSFC, NOx emissions and EGT was observed for all blends compared to Euro diesel. Overall, all blends appear to be good alternatives to biodiesel–diesel blends. This work supports that biodiesel can be blended with diesel and butanol as ternary blends (up to 20%) for use as a fuel in compression ignition (CI) engines. Therefore, combustion characteristics of blends shall be further investigated.