Miracle-dz/UniFAR-FTUs huggingface dataset:
A constitutive promoter directs expression of the nerve growth factor receptor gene

Expression of nerve growth factor receptor is normally restricted to cells derived from the neural crest in a developmentally regulated manner. We analyzed promoter sequences for the human nerve growth factor receptor gene and found that the receptor promoter resembles others which are associated with constitutively expressed genes that have housekeeping and growth-related functions. Unlike these other genes, the initiation of transcription occurred at one major site rather than at multiple sites. The constitutive nature of the nerve growth factor receptor promoter may account for the ability of this gene to be transcribed in a diverse number of heterologous cells after gene transfer. The intron-exon structure of the receptor gene indicated that structural features are precisely divided into discrete domains.
The complete general secretory pathway in gram-negative bacteria

The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins.
Mutational analysis of the SNF3 glucose transporter of Saccharomyces cerevisiae

The SNF3 gene of Saccharomyces cerevisiae encodes a high-affinity glucose transporter that is homologous to mammalian glucose transporters. Point mutations affecting the function of the transporter were recovered from the genomes of four snf3 mutants and characterized. Two of the mutations introduced a charged amino acid into the first and second predicted membrane-spanning regions, respectively. The analogs of a bifunctional SNF3-lacZ fusion containing these two mutations were constructed, and the mutant fusion proteins were not localized to the plasma membrane, as judged by immunofluorescence microscopy. The third mutation produced a valine-to-isoleucine substitution in hydrophobic region 8, and the corresponding mutant fusion protein was correctly localized. The finding that this conservative change causes a transport defect is consistent with the possibility that this transmembrane region, which could exist as an amphipathic alpha-helix, forms part of the glucose channel through the membrane. The fourth snf3 allele harbored an ochre mutation midway through the coding sequence. We have also constructed mutations in the cloned SNF3 gene. A major difference between the yeast SNF3 protein and mammalian glucose transporters is the presence in the SNF3 protein of an additional 303 amino acids at the C terminus. Analysis of a series of C-terminal deletions and fusions to lacZ showed that this C-terminal region is important, but not essential, for transport function. We also report the genetic mapping of the SNF3 locus on the left arm of chromosome IV.
RNA editing intermediates of cox2 transcripts in maize mitochondria

Eighteen cytidines are changed to uridines in the coding sequence of transcripts for cytochrome c oxidase subunit 2 (cox2) in maize mitochondria. The temporal relationship of editing and splicing was examined in cox2 transcripts by sequence analysis of spliced and unspliced cDNAs. Cloned cDNAs of unspliced cox2 transcripts ranged from clones with no edited nucleotides to completely edited forms, while spliced cDNAs were nearly completely edited. Incompletely edited transcripts in the nascent pool of unspliced transcripts represent intermediates of the editing process. These results indicate that editing proceeds without a strong directional bias and suggest that RNA editing is a posttranscriptional process.
Inactivation of YME1, a member of the ftsH-SEC18-PAS1-CDC48 family of putative ATPase-encoding genes, causes increased escape of DNA from mitochondria in Saccharomyces cerevisiae

The yeast nuclear gene YME1 was one of six genes recently identified in a screen for mutations that elevate the rate at which DNA escapes from mitochondria and migrates to the nucleus. yme1 mutations, including a deletion, cause four known recessive phenotypes: an elevation in the rate at which copies of TRP1 and ARS1, integrated into the mitochondrial genome, escape to the nucleus; a heat-sensitive respiratory-growth defect; a cold-sensitive growth defect on rich glucose medium; and synthetic lethality in rho- (cytoplasmic petite) cells. The cloned YME1 gene complements all of these phenotypes. The gene product, Yme1p, is immunologically detectable as an 82-kDa protein present in mitochondria. Yme1p is a member of a family of homologous putative ATPases, including Sec18p, Pas1p, Cdc48p, TBP-1, and the FtsH protein. Yme1p is most similar to the Escherichia coli FtsH protein, an essential protein involved in septum formation during cell division. This observation suggests the hypothesis that Yme1p may play a role in mitochondrial fusion and/or division.
Mutational mapping of RAS-responsive domains of the Saccharomyces cerevisiae adenylyl cyclase

Large deletion and small insertion mutations in the adenylyl cyclase gene of Saccharomyces cerevisiae were used to map regions required for activation by RAS protein in vitro. The amino-terminal 605 amino acids were found to be dispensable for responsiveness to RAS protein. All other deletions in adenylyl cyclase destroyed its ability to respond to RAS. Small insertion mutations within the leucine-rich repeat region also prevented RAS responsiveness, while other insertions did not.
Cellular nucleotide measurements and applications in microbial ecology

INTRODUCTION . 740 NUCLEOTIDES, NUCLEOSIDES, AND RELATED INTRACELLULAR COMEPOUNDS . 741 Cellular Bioenergetics . 741 Regulation of Cellular Metabolism . 742 Adenylate energy charge . 742 Phosphorylation state . 742 Oxidation-reduction state 742 Indirect energy coupling. 3 Cyclic adenosine 3',5'-monophosphate, guanosine 5'-triphosphate, and guanosine tetraphosphate.743 Analytical Procedures . 743 Sampling 744 Extraction.745 Measurement 50 (i) Firefly bioluminescence . 750 (ii) Bacterial bioluminescence 751 (iii) Renilla biolumnescence. (iv) Immobilized enzymes . 751 NUCLEOTIDE LEVELS IN MICROBIAL CELLS: EFFECTS OFGROWTH RATE, CULTURE CONDMONS, NUTRIENT STRESS, AND ENVIRONMENTAL PERTURBATIONS . 751 Adenine Nucleotides and Energy Charge Ratios 751 Procaryotes . 751 Unicellular eucaryotes . 755 Metazoa . 755 Environmental Perturbations and Nutrient Limitations . 756 Transient states. 756 Nutrient limitation and starvation. 757 (i) Carbon. 757 (ii) Nitrogen, sulfur, and iron. 758 (iii) Phosphorus . 758 Nonadenine Nucleotide Triphosphates . 760 Diel Rhythms and Specific Cell-Cycle-Related Events . 760 Nicotinamide and Flavin Nucleotides . 761 NUCLEOTIDE FINGERPRINTS IN NATURE . 761 Detection of Life . 761 Adenosine 5'-Triphosphate (ATP) asa Biomass Indicator. 763 Obligate association ofATP with living organisms . 763 C/ATP ratios . 764 Correlations of ATP with other measures of biomass and activity . 766 Selected Environmental ATP Applications . 767 Partitioning of bacterial, algal, and metazoan carbon . 767 ATP applications in oceanography . 769 (i) Geographical and vertical distributions of ATP in the ocean. 769 (ii) Sedimentary ATP distributions.771 (iii) ATP-based biochemical indices of physiological state.772 (iv) ATP and respiration rates.774 (v) ATP and growth rates (vi) Downward vertical flux ofATP in the ocean.774 Terrestrial and aquatic decomposition studies . 775 Wastewater treatment, disinfection control, and pollution assessment . 776 Environmental Adenylate Energy Charge.777 Guanosine 5'-Triphosphate and Cellular Biosynthesis.780 Cyclic Adenosine 3',5'-Monophosphate.782
Structural and functional characterization of mouse U7 small nuclear RNA active in 3' processing of histone pre-mRNA

Oligonucleotides derived from the spacer element of the histone RNA 3' processing signal were used to characterize mouse U7 small nuclear RNA (snRNA), i.e., the snRNA component active in 3' processing of histone pre-mRNA. Under RNase H conditions, such oligonucleotides inhibited the processing reaction, indicating the formation of a DNA-RNA hybrid with a functional ribonucleoprotein component. Moreover, these oligonucleotides hybridized to a single nuclear RNA species of approximately 65 nucleotides. The sequence of this RNA was determined by primer extension experiments and was found to bear several structural similarities with sea urchin U7 snRNA. The comparison of mouse and sea urchin U7 snRNA structures yields some further insight into the mechanism of histone RNA 3' processing.
An efficient approach to 4-chloro quinolines via TMSCl-mediated cascade cyclization of ortho-propynol phenyl azides

A novel and efficient strategy for the synthesis of 4-chloro quinolines via the TMSCl-mediated cascade cyclization of easily prepared ortho-propynol phenyl azides is developed. This reaction proceeds smoothly in moderate to excellent yields with a wide range of substrate compatibility. TMSCl acted not only as a promoter, but also as a chloro source in this transformation. Moreover, the obtained 4-chloro quinolines could be further derivated in an array of palladium-catalyzed coupling and nucleophilic substitution reactions to construct potential biologically active and pharmaceutical molecules.
Regulation of tubulin and actin mRNA production in rat brain: expression of a new beta-tubulin mRNA with development

The expression of alpha-tubulin, beta-tubulin, and actin mRNA during rat brain development has been examined by using specific cDNA clones and in vitro translation techniques. During brain maturation (0 to 80 days postnatal), these mRNA species undergo a significant decrease in abundance. The kinetics of this decrease varies between the cerebrum and the cerebellum. These mRNAs are most abundant in both tissues during week 1 postnatal, each representing 10 to 15% of total mRNA activity. Both alpha- and beta-tubulin mRNA content decreases by 90 to 95% in the cerebrum after day 11 postnatal, and 70 to 80% decreases in the cerebellum after day 16. Actin sequences also decrease but to a lesser extent in both tissues (i.e., 50%). These decreases coincide with the major developmental morphological changes (i.e., neurite extension) occurring during this postnatal period. These studies have also identified the appearance of a new 2.5-kilobase beta-tubulin mRNA species, which is more predominant in the cerebellar cytoplasm. The appearance of this form occurs at a time when the major 1.8-kilobase beta-tubulin mRNA levels are declining. The possibility that the tubulin multigene family is phenotypically expressed and then this expression responds to the morphological state of the nerve cells is discussed.
Selective Isolation of Aerobic Actinomycetes

The composition of an arginine-glycerol-salt medium (AGS), suitable for the selective isolation of aerobic actinomycetes, was given. When soil samples were treated with calcium carbonate and plated on the AGS medium, higher total and relative plate counts of actinomycetes were obtained than when other media and methods were used.
The gene encoding the transcription factor SCIP has features of an expressed retroposon

SCIP is a POU domain transcription factor expressed by glial progenitor cells in the peripheral and central nervous systems (dividing Schwann cells and O-2A cells, respectively), where it appears to act as a repressor of myelin-specific genes. We have isolated genomic clones encoding the rat SCIP gene. Comparison of the structure of these clones with genomic Southern blots and SCIP cDNAs demonstrates that SCIP is encoded in a single-copy, intronless gene that has the general features of an expressed retroposon. This gene contributes to an extended CpG island. It is transcribed to produce a 3.1-kb mRNA that encodes a 451-amino-acid protein with a predicted molecular mass of 45 kDa. Immunopurified SCIP antibodies specifically recognize a nuclear protein of this size in cultured proliferating Schwann cells, and gel shift analyses demonstrate that this protein is the predominant octamer-binding protein in these cells.
Tetanus Toxin Production in the Absence of Protein

A modification of the Mueller medium for tetanus toxin production is presented, on which an adapted strain produces high yields of toxin (70 to 90 flocculating units per ml) in the absence of animal protein extracts. The range of iron concentration in the medium was established within which the toxigenic activity of the culture can be made to vary, and the mathematical nature of the variation is presented. Darkening of cultures during incubation indicates departure from optimal conditions. Heat input to the medium during autoclaving, originally undertaken solely for purposes of sterilization, is an important physicochemical factor in the toxigenicity of the culture.
Mechanisms of genome propagation and helper exploitation by satellite phage P4

Temperate coliphage P2 and satellite phage P4 have icosahedral capsids and contractile tails with side tail fibers. Because P4 requires all the capsid, tail, and lysis genes (late genes) of P2, the genomes of these phages are in constant communication during P4 development. The P4 genome (11,624 bp) and the P2 genome (33.8 kb) share homologous cos sites of 55 bp which are essential for generating 19-bp cohesive ends but are otherwise dissimilar. P4 turns on the expression of helper phage late genes by two mechanisms: derepression of P2 prophage and transactivation of P2 late-gene promoters. P4 also exploits the morphopoietic pathway of P2 by controlling the capsid size to fit its smaller genome. The P4 sid gene product is responsible for capsid size determination, and the P2 capsid gene product, gpN, is used to build both sizes. The P2 capsid contains 420 capsid protein subunits, and P4 contains 240 subunits. The size reduction appears to involve a major change of the whole hexamer complex. The P4 particles are less stable to heat inactivation, unless their capsids are coated with a P4-encoded decoration protein (the psu gene product). P4 uses a small RNA molecule as its immunity factor. Expression of P4 replication functions is prevented by premature transcription termination effected by this small RNA molecule, which contains a sequence that is complementary to a sequence in the transcript that it terminates.
Genetic regulation of human immunodeficiency virus

Human immunodeficiency virus (HIV) has a complex life cycle in which both cellular and virus-encoded factors participate to determine the level of virus production. Two of the viral genes, tat and rev, are essential for virus replication and encode novel trans-activators that interact specifically with their cognate RNA target elements. Elucidation of their mechanisms of action is likely to expand our knowledge of gene regulation at transcriptional and posttranscriptional levels in the eukaryotic cell. Several viral genes (vif, vpu, and vpr) facilitate virus infection and/or release and may play a role in target cell tropism and infection in vivo. The functions of yet other viral genes (nef, vpt) remain unclear. Recent data also suggest that the tat gene product may have a role in HIV pathogenesis that goes beyond trans-activating virus expression. It can potentially impact on uninfected cells as a diffusible molecule and alter the growth of different cell types.
Ribosylnicotinamide Kinase Domain of NadR Protein: Identification and Implications in NAD Biosynthesis

NAD is an indispensable redox cofactor in all organisms. Most of the genes required for NAD biosynthesis in various species are known. Ribosylnicotinamide kinase (RNK) was among the few unknown (missing) genes involved with NAD salvage and recycling pathways. Using a comparative genome analysis involving recon- struction of NAD metabolism from genomic data, we predicted and experimentally veriﬁed that bacterial RNK is encoded within the 3 (cid:1) region of the nadR gene. Based on these results and previous data, the full-size multifunctional NadR protein (as in Escherichia coli ) is composed of (i) an N-terminal DNA-binding domain involved in the transcriptional regulation of NAD biosynthesis, (ii) a central nicotinamide mononucleotide adenylyltransferase (NMNAT) domain, and (iii) a C-terminal RNK domain. The RNK and NMNAT enzymatic activities of recombinant NadR proteins from Salmonella enterica serovar Typhimurium and Haemophilus inﬂuenzae were quantitatively characterized. We propose a model for the complete salvage pathway from exogenous N -ribosylnicotinamide to NAD which involves the concerted action of the PnuC transporter and NRK, after
Activation of c-myc and c-K-ras oncogenes in primary rat tumors induced by ionizing radiation

An activated K-ras oncogene was detected by transfection in NIH 3T3 cells and by Southern blot analysis in 6 of 12 rat skin tumors induced by ionizing radiation. The DNA from 10 of the 12 tumors also showed c-myc gene amplification and restriction polymorphisms. Evidence for tissue specificity was observed in patterns of oncogene activation, with each of three clear cell carcinomas exhibiting activation of both c-myc and K-ras oncogenes.
Modeling Electrochemical Performance of the Hierarchical Morphology of Precious Group Metal-Free Cathode for Polymer Electrolyte Fuel Cell

This paper presents a two-dimensional (2D) computational model of a polymer electrolyte fuel cell (PEFC) with a platinum group metal-free (PGM-free) catalyst cathode that can significantly reduce PEFC costs by eliminating the need for expensive platinum catalysts. Due to their comparatively low volumetric activity, PGM-free cathodes are an order of magnitude thicker than their Pt-based counterpart. The resulting need for greater electrode thickness to achieve sufficient power density requires careful attention to the transport losses across the thicker cathodes. The presented model is used to correlate the composition and morphology of the cathode to PEFC performance. The model is a complete cell, continuum model that includes an advanced agglomerate model for a microstructurally consistent representation of the cathode. A unique feature of the approach is the integration of morphology and transport parameter statistics extracted from nano-scale resolution X-ray computed tomography (nano-CT) imaging of PGM-free cathodes. The model was validated with experimental results of PGM-free cathodes with varying Nafion loading. Our key findings are a need for increased cathode hydrophobicity and increased ionomer conductivity through either reduced tortuosity or increased bulk conductivity. We further use the model to evaluate targets for the volumetric activity and active site density for future catalysts. © The Author(s) 2017. Published by ECS. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 License (CC BY, http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse of the work in any medium, provided the original work is properly cited. [DOI: 10.1149/2.0041712jes] All rights reserved.
Simulation of diesel spray combustion using LES and a multicomponent vapourisation model

Diesel spray and combustion in a constant-volume engine cylinder was simulated by a large eddy simulation (LES) approach coupling with a multicomponent vapourisation (MCV) modelling. The simulation focused on the inclusion of the interaction between fuel spray and gas-phase turbulence flow at the sub-grid scale. The LES was based on the dynamic structure sub-grid model, and an additional source term was added to the filtered momentum equation to account for the effect of drop motion on the gas-phase turbulence. The multicomponent drop vapourisation modelling was based on the continuous thermodynamics approach using a gamma distribution to describe the complex diesel fuel composition and was capable of predicting a more complex drop vapourisation process. The effect of gas-phase turbulence flow on the fuel drop vapourisation process was evaluated through the solution of the gas-phase moments of the distribution in the present LES framework. A non-evaporative spray in a constant-volume engine cylinder was first simulated to examine the behaviours of LES, in comparison with a Reynolds-averaged Navier–Stokes (RANS) simulation based on the RNG k–ϵ model. More realistic diesel spray structures and improved agreement on liquid penetration length with the corresponding experimental data were predicted by the LES, using a grid resolution close to that of RANS. A more comprehensive simulation of diesel spray and combustion in cylindrical combustor was also performed. Predicted distributions of soot particles were compared to the experimental image, and improved agreement with the experimental data was also observed by using the present LES and MCV models. Consequently, results of the present models proved that improved overall performance of the fuel spray simulation can be achieved by the LES without a significant increase in the computational load compared to the RANS.
DNA-binding protein activated by gamma radiation in human cells

DNA damage-inducible responses in mammalian cells tend to lack specificity and can be activated by any one of a number of damaging agents. Although a number of different induced proteins have been described, their involvement in DNA processing and transcriptional control remains unresolved. We describe the appearance of a previously unreported, specific DNA-binding protein in nuclei from human cells exposed to ionizing radiation, which was not detected in nuclear extracts from unperturbed cells. The distal part of the simian virus 40 enhancer (without the AP-1 site) and oligonucleotide sequences derived from that sequence were used in binding studies. The appearance of this activity was dose dependent and transient, reaching a maximum at 1 h postirradiation and disappearing from nuclei by 9 h. This protein was induced in cells by a mechanism not requiring de novo protein synthesis, and the response was specific for ionizing radiation and radiomimetic agents; neither UV nor heat shock invoked a response. The DNA-binding protein was present in the cytoplasm of untreated cells, apparently being translocated to the nucleus only after radiation exposure. Southwestern (DNA-protein) analysis demonstrated that the nuclear and cytoplasmic proteins were approximately the same size, 43,000 daltons. The protected DNA-binding motif, using the distal fragment of the simian virus 40 enhancer as the substrate, was shown by DNase I footprint analysis to be pTGTCAGTTAGGGTACAGTCAATCCCAp. This was confirmed by dimethyl sulfate footprinting.