Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components

In this paper, the Escherichia coli cell is considered as a system designed for rapid growth, but limited by the medium. We propose that this very design causes the cell to become subsaturated with precursors and catalytic components at all levels of macromolecular biosynthesis and leads to a molecular sharing economy at a high level of competition inside the cell. Thus, the promoters compete with each other in the binding of a limited amount of free RNA polymerase and the ribosome binding sites on the mRNA chains compete with each other for the free ribosomes. The macromolecular chain elongation reactions sequester a considerable proportion of the total amount of RNA polymerase and ribosomes in the cells. We propose that the degree of subsaturation of the macromolecular biosynthetic apparatus renders a variable fraction of RNA polymerase and ribosomes unavailable for the initiation of new chain synthesis and that this, at least in part, determines the composition of the cell as a function of the growth rate. Thus, at rapid growth, the high speed of the elongation reactions enables the cell to increase the concentrations of free RNA polymerase and ribosomes for initiation purposes. Furthermore, it is proposed that the speed of RNA polymerase movement is adjusted to the performance speed of the ribosomes. Mechanistically, this adjustment of the coupling between transcription and translation involves transcriptional pause sites along the RNA chains, the adjustment of the saturation level of RNA polymerase with the nucleoside triphosphate substrates, and the concentration of ppGpp, which is known to inhibit RNA chain elongation. This model is able to explain the stringent response and the control of stable RNA and of ribosome synthesis in steady states and in shifts, as well as the rate of overall protein synthesis as a function of the growth rate.
Molecular cloning and characterization of an activated human c-raf-1 gene

Results of previous studies have shown that a raf-related transforming DNA sequence is present in NIH 3T3 transformants that are derived from GL-5-JCK human glioblastoma DNA transfection. The transforming DNA was molecularly cloned by using cosmid vector pJB8 to determine its structure and origin. Analyses of selected clones revealed that the transforming DNA consisted of three portions of human DNA sequences, with the 3' half of the c-raf-1 gene as its middle portion. This raf region was about 20 kilobases long and contained exons 8 to 17 and the poly(A) addition site. RNA blot analysis showed that the raf-related transforming DNA was transcribed into 5.3-, 4.8-, and 2.5-kilobase mRNAs; the 2.5-kilobase transcript was thought to be the major transcript. Immunoprecipitation analyses revealed that a 44-kilodalton raf-related protein was specifically expressed in the NIH 3T3 transformants. The raf-related transforming DNA was considered to be activated when its amino-terminal sequence was truncated and the DNA was coupled with a foreign promoter sequence. On hybridization analysis of the original GL-5-JCK glioblastoma DNA, no rearrangement of c-raf-1 was detectable in the tumor DNA. The rearrangement of c-raf-1 may have occurred during transfection or may have been present in a small population of the original tumor cells as a result of tumor progression.
Constitutive expression of a c-myb cDNA blocks Friend murine erythroleukemia cell differentiation

A full-length human c-myb cDNA clone has been isolated from a CCRF-CEM leukemia cell cDNA library. The plasmid vector contains simian virus 40-derived promotor, splice, and polyadenylation sequences as well as a transcription unit for a dihydrofolate reductase cDNA. We have introduced this construct into Friend erythroleukemia (F-MEL) cells and have isolated a number of clones which contain intact and transcriptionally active human c-myb sequences. F-MEL clones expressing the highest levels of the human c-myb mRNA differentiate poorly in response to dimethyl sulfoxide. Two clones which initially expressed low levels of human c-myb transcripts and which differentiated normally were subsequently inhibited in their ability to differentiate when grown in successively higher concentrations of methotrexate, due to amplification and enhanced expression of plasmid sequences. The inhibitory effect on F-MEL differentiation appeared to be independent of the early decline in c-myc transcripts which were normally regulated in all cases examined. Our results indicate that constitutive expression of a nontruncated human c-myb cDNA can exert profound effects on erythroid differentiation and argue for a causal role of c-myb in the F-MEL differentiation process.
Genetic elements of plant viruses as tools for genetic engineering

Viruses have developed successful strategies for propagation at the expense of their host cells. Efficient gene expression, genome multiplication, and invasion of the host are enabled by virus-encoded genetic elements, many of which are well characterized. Sequences derived from plant DNA and RNA viruses can be used to control expression of other genes in vivo. The main groups of plant virus genetic elements useful in genetic engineering are reviewed, including the signals for DNA-dependent and RNA-dependent RNA synthesis, sequences on the virus mRNAs that enable translational control, and sequences that control processing and intracellular sorting of virus proteins. Use of plant viruses as extrachromosomal expression vectors is also discussed, along with the issue of their stability.
Characterization of cyclic olefin copolymer‐coated chitosan bilayer films containing nanocellulose and grape seed extract

This study evaluated the effect of applying cyclic olefin copolymer (COC) on the physico‐mechanical properties of chitosan (CH) film. Grape seed extract (GSE) (15%, w/w) was added to the CH film solutions to develop an active bilayer, while also adding nanocellulose (NC) (0% to 2%, w/w) to obtain better mechanical properties for CH. Characterization was carried out by contact angle measurements, scanning electron microscopy (SEM), optical analysis, and tensile and water permeability tests. SEM images showed that there was a functional adhesion layer between the CH and the COC, while a detachment occurred for bilayer films with GSE. The formation of a COC layer on the CH surface with the addition of NC improved the water vapor permeability, while the addition of GSE had an adverse effect on the water vapor permeability. The addition of NC into the CH films reduced their water uptake and solubility. The CH film surface showed lower contact angle values, whereas higher contact angle values were observed for CH film surfaces with GSE and NC. The inclusion of NC resulted in an increased elastic modulus and a decrease in TS and ε (%) values. All film samples showed antimicrobial activity against Escherichia coli and Listeria monocytogenes. Moreover, film samples with added GSE showed antioxidant properties with 2,2‐Diphenyl‐1‐picrylhydrazyl scavenging activity ranging from 14.33 ± 0.24 to 20.45 ± 0.07%. The bilayer films will have a potential use in transferring functional compounds as an active packaging material layer along with conventional polymers.
Oxidative stress responses in Escherichia coli and Salmonella typhimurium

Oxidative stress is strongly implicated in a number of diseases, such as rheumatoid arthritis, inflammatory bowel disorders, and atherosclerosis, and its emerging as one of the most important causative agents of mutagenesis, tumorigenesis, and aging. Recent progress on the genetics and molecular biology of the cellular responses to oxidative stress, primarily in Escherichia coli and Salmonella typhimurium, is summarized. Bacteria respond to oxidative stress by invoking two distinct stress responses, the peroxide stimulon and the superoxide stimulon, depending on whether the stress is mediated by peroxides or the superoxide anion. The two stimulons each contain a set of more than 30 genes. The expression of a subset of genes in each stimulon is under the control of a positive regulatory element; these genes constitute the OxyR and SoxRS regulons. The schemes of regulation of the two regulons by their respective regulators are reviewed in detail, and the overlaps of these regulons with other stress responses such as the heat shock and SOS responses are discussed. The products of Oxy-R- and SoxRS-regulated genes, such as catalases and superoxide dismutases, are involved in the prevention of oxidative damage, whereas others, such as endonuclease IV, play a role in the repair of oxidative damage. The potential roles of these and other gene products in the defense against oxidative damage in DNA, proteins, and membranes are discussed in detail. A brief discussion of the similarities and differences between oxidative stress responses in bacteria and eukaryotic organisms concludes this review.
Position effects on the timing of replication of chromosomally integrated simian virus 40 molecules in Chinese hamster cells

Simian virus 40 (SV40) DNA molecules chromosomally integrated at different sites in three Chinese hamster lung fibroblast lines replicated during the middle portion of S phase but not precisely at the same time in all three cell lines. The time of replication was unrelated to the presence of T antigen or to its relative activity in promoting SV40 replication. SV40 sequences and chromosomal DNA sequences adjacent to the SV40 insert in one cell line expressing a temperature-sensitive T antigen showed a T-antigen-independent difference in replication timing from the homologous, allelic locus not linked to SV40. Our results indicate that the timing of replication of these integrated SV40 molecules is dependent upon the site of integration and is not determined by the level of T antigen replication-promoting activity.
Alpha-toxin of Staphylococcus aureus

Alpha-toxin, the major cytotoxic agent elaborated by Staphylococcus aureus, was the first bacterial exotoxin to be identified as a pore former. The protein is secreted as a single-chain, water-soluble molecule of Mr 33,000. At low concentrations (less than 100 nM), the toxin binds to as yet unidentified, high-affinity acceptor sites that have been detected on a variety of cells including rabbit erythrocytes, human platelets, monocytes and endothelial cells. At high concentrations, the toxin additionally binds via nonspecific absorption to lipid bilayers; it can thus damage both cells lacking significant numbers of the acceptor and protein-free artificial lipid bilayers. Membrane damage occurs in both cases after membrane-bound toxin molecules collide via lateral diffusion to form ring-structured hexamers. The latter insert spontaneously into the lipid bilayer to form discrete transmembrane pores of effective diameter 1 to 2 nm. A hypothetical model is advanced in which the pore is lined by amphiphilic beta-sheets, one surface of which interacts with lipids whereas the other repels apolar membrane constitutents to force open an aqueous passage. The detrimental effects of alpha-toxin are due not only to the death of susceptible targets, but also to the presence of secondary cellular reactions that can be triggered via Ca2+ influx through the pores. Well-studied phenomena include the stimulation of arachidonic acid metabolism, triggering of granule exocytosis, and contractile dysfunction. Such processes cause profound long-range disturbances such as development of pulmonary edema and promotion of blood coagulation. (ABSTRACT TRUNCATED AT 250 WORDS)
The bacterial nucleoid revisited

This review compares the results of different methods of investigating the morphology of nucleoids of bacteria grown under conditions favoring short generation times. We consider the evidence from fixed and stained specimens, from phase-contrast and fluorescence microscopy of growing bacteria, and from electron microscopy of whole as well as thinly sectioned ones. It is concluded that the nucleoid of growing cells is in a dynamic state: part of the chromatin is "pulled out" of the bulk of the nucleoid in order to be transcribed. This activity is performed by excrescences which extend far into the cytoplasm so as to reach the maximum of available ribosomes. Different means of fixation provide markedly different views of the texture of the DNA-containing plasm of the bulk of the nucleoid. Conventional chemical fixatives stabilize the cytoplasm of bacteria but not their protein-low chromatin. Uranyl acetate does cross-link the latter well but only if the cytoplasm has first been fixed conventionally. In the interval between the two fixations, the DNA arranges itself in liquid-crystalline form, supposedly because of loss of supercoiling. In stark contrast, cryofixation preserves bacterial chromatin in a finely granular form, believed to reflect its native strongly negatively supercoiled state. In dinoflagellates the DNA of their permanently visible chromosomes (also low in histone-like protein) is natively present as a liquid crystal. The arrangement of chromatin in Epulocystis fishelsoni, one of the largest known prokaryotes, is briefly described.
Vertical transmission of viruses

INTRODUCTION . 267 Perinatal and Postnatal Transmission . 268 TRANSMISSION DURING FETAL DEVELOPMENT IN MAMMALS.269 Rubela . 269 Cytomegaloviruses . 271 Other Herpesviruses . 271 Parvovirunses . 272 Arenaviruses . 272 PapovaVruses . 273 Mfiscellaneous Persistent Viruses . 273 Scrapie. 273 Conclusions . 273 TRANSMISSION VIA THE GERM LINE-VERTEBRATES.273 Retroviruses . 274 Oncoviruses . 274 Oncoviruses as parasites 276 Parasitic deoxyribonucleic acid . 276 Spumaviruses . 277 Lentiviruses 277 Equine infectious anemia . 278 Parvoviruses . 278 Adenoviruses. 278 Papovaviruses. 279 Arenaviruses . 279 Conclusions and Comments 279 TRANSMISSION VIA THE GERM LINE-ARTHROPODS.280 Sigmavirus . 280 Mosquitoes . 281 Ticks and sandflies 281 Plant viruses 281 TRANSMISSION VIA THE GERM LINE-PIANTS.281 Seed Transmission.281 Integration of Plant Viruses into Host Cell Genome.282 VERTICAL TRANSMISSION IN SINGLE-CELE-1T D ORGANISMS.282 EPIDEMIOLOGICAL CONSIDERATIONS IN VERTICAL TRANSMISSION . 282 SUJMMARY.283 LITERATURE CITED.2
Neutron capture cross section measurements of 151,153Eu using a pair of C6D6 detectors

ABSTRACT We have measured the neutron capture cross sections of 151Eu and 153Eu by the time-of-flight (TOF) method in the range from 0.005 eV to keV region using the Kyoto University Research Reactor Institute - Linear Accelerator (KURRI-LINAC). We employed a pair of C6D6 liquid scintillators for the prompt capture γ-ray measurement. The pulse-height weighting technique was employed to obtain the capture yields from the γ-ray spectra of 151,153Eu. The obtained thermal cross sections at 0.0253 eV are 9051 ± 683 b for 151Eu and 364 ± 44 b for 153Eu, respectively. The resonance integrals have been derived as 3490 ± 162 b for 151Eu and 1538 ± 106 b for 153Eu. The obtained capture cross sections were compared with the previously reported experimental data and the evaluated data. The evaluated data in JENDL-4.0 and JEFF-3.2 show good agreement with the present experiment results of 151Eu, however, the evaluated data in ENDF/B-VII.1 are larger than the present experiment results of 151Eu about 10% to 20% in the energy region from 0.03 to 0.2 eV. For the neutron capture cross sections of 153Eu, the evaluated data in ENDF/B-VII.1 and Widder's data are in good agreement with the present results in the energy region below 0.35 eV.
Ferret Interferon (IFN)-Inducible Transmembrane Proteins Are Upregulated by both IFN-α and Influenza Virus Infection

IFITM proteins can prevent the entry of several pH-dependent viruses, including high-consequence viruses such as HIV, influenza viruses, and SARS-coronaviruses. Mutations in these genes have been associated with worsened disease outcomes with mutations in their IFITM genes, highlighting these genes as potential disease risk factors. ABSTRACT The current fears of a future influenza pandemic have resulted in an increased emphasis on the development and testing of novel therapeutic strategies against the virus. Fundamental to this is the ferret model of influenza infection, which is critical in examining pathogenesis and treatment. Nevertheless, a precise evaluation of the efficacy of any treatment strategy in ferrets is reliant on understanding the immune response in this model. Interferon-inducible transmembrane proteins (IFITMs) are interferon-stimulated proteins shown to be critically important in the host immune response against viral infections. These proteins confer intrinsic innate immunity to pH-dependent viruses such as influenza viruses and can inhibit cytosolic entry of such viruses to limit the severity of infection following interferon upregulation. Mutations in IFITM genes in humans have been identified as key risk factors for worsened disease progression, particularly in the case of avian influenza viruses such as H7N9. While the IFITM genes of humans and mice have been well characterized, no studies have been conducted to classify the IFITM locus and interferon-driven upregulation of IFITMs in ferrets. Here, we show the architecture of the ferret IFITM locus and its synteny to the IFITM locus of other mammalian and avian species. Furthermore, we show that ferret IFITM1, -2, and -3 are functionally responsive to both interferon-α (IFN-α) and influenza virus stimulation. Thus, we show that ferret IFITMs exhibit interferon-stimulated properties similar to those shown in other species, furthering our knowledge of the innate immune response in the ferret model of human influenza virus infections. IMPORTANCE IFITM proteins can prevent the entry of several pH-dependent viruses, including high-consequence viruses such as HIV, influenza viruses, and SARS-coronaviruses. Mutations in these genes have been associated with worsened disease outcomes with mutations in their IFITM genes, highlighting these genes as potential disease risk factors. Ferrets provide a valuable tool to model infectious diseases; however, there is a critical shortage of information regarding their interferon-stimulated genes. We identified the putative ferret IFITM genes and mapped their complete gene locus. Thus, our study fills a critical gap in knowledge and supports the further use of the ferret model to explore the importance of IFITMs in these important diseases.
Interaction of chlamydiae and host cells in vitro

The obligately intracellular bacteria of the genus Chlamydia, which is only remotely related to other eubacterial genera, cause many diseases of humans, nonhuman mammals, and birds. Interaction of chlamydiae with host cells in vitro has been studied as a model of infection in natural hosts and as an example of the adaptation of an organism to an unusual environment, the inside of another living cell. Among the novel adaptations made by chlamydiae have been the substitution of disulfide-bond-cross-linked polypeptides for peptidoglycans and the use of host-generated nucleotide triphosphates as sources of metabolic energy. The effect of contact between chlamydiae and host cells in culture varies from no effect at all to rapid destruction of either chlamydiae or host cells. When successful infection occurs, it is usually followed by production of large numbers of progeny and destruction of host cells. However, host cells containing chlamydiae sometimes continue to divide, with or without overt signs of infection, and chlamydiae may persist indefinitely in cell cultures. Some of the many factors that influence the outcome of chlamydia-host cell interaction are kind of chlamydiae, kind of host cells, mode of chlamydial entry, nutritional adequacy of the culture medium, presence of antimicrobial agents, and presence of immune cells and soluble immune factors. General characteristics of chlamydial multiplication in cells of their natural hosts are reproduced in established cell lines, but reproduction in vitro of the subtle differences in chlamydial behavior responsible for the individuality of the different chlamydial diseases will require better in vitro models.
Biochemical Changes in the Serum of Experimental Animals Treated with Acorus calamus Rhizome

ABSTRACT The present study was undertaken to examine the effect of Acorus calamus rhizome on serum biochemical parameters in experimental animals. Tumor was induced in mice intraperitoneally using Dalton’s ascites lymphoma cells. Methanol extract of Acorus calamus (MEAC) was administered to the mice at the dose of 100 and 200 mg/kg/day. The effect of the extract on serum enzyme levels was evaluated by analyzing the serum hematology and clinical biochemistry of experimental animals. Inoculation of Dalton’s ascites lymphoma cells caused significant decrease in the serum levels of alkaline phosphatise (ALP), serum glutamate oxaloacetate transaminase (SGOT) and serum glutamate pyruvate transaminase (SGPT) in the treated mice when compared with the control group. Urea, uric acid, creatinine and triglyceride levels were controlled significantly. The results clearly indicated that the rhizome extract has the ability to retain the altered biochemical parameters as normal in induced mice supporting its potent anticancer and hepatoprotective effects.
Changes in the stability of a human H3 histone mRNA during the HeLa cell cycle

A major component of the regulation of histone protein synthesis during the cell cycle is the modulation of the half-life of histone mRNA. We have uncoupled transcriptional and posttranscriptional regulation by using a Drosophila hsp70-human H3 histone fusion gene that produces a marked human H3 histone mRNA upon heat induction. Transcription of this gene can be switched on and off by raising and lowering cell culture temperatures, respectively. HeLa cell lines containing stably integrated copies of the fusion gene were synchronized by double thymidine block. Distinct populations of H3 histone mRNA were produced by heat induction in early S-phase, late S-phase, or G2-phase cells, and the stability of the induced H3 histone mRNA was measured. The H3 histone mRNA induced during early S phase decayed with a half-life of 110 min, whereas the same transcript induced during late S phase had a half-life of 10 to 15 min. The H3 histone mRNA induced in non-S-phase cells is more stable than that induced in late S phase, with a half-life of 40 min. Thus, the stability of histone mRNA is actively regulated throughout the cell cycle. Our results are consistent with an autoregulatory model in which the stability of histone mRNA is determined by the level of free histone protein in the cytoplasm.
Genome comparison in yeast systematics: delimitation of species within the genera Schwanniomyces, Saccharomyces, Debaryomyces, and Pichia

INTRODUCTION . 161 NUCLEIC ACID STUDIES IN YEAST SYSTEMATICS 162 Classes of Cellular DNA in Yeasts . 162 DNA Base Composition Determinations . 163 Polynucleotide Sequence Relatedness Studies 163 TAXONOMIC STATUS OF THE GENERA DEBARYOMYCES, PICHIA, SACCHAROMYCES, AND SCHWANNIOMYCES 164 MATERIALS AND METHODS . 165 Organisms Used . 165 Cultivation of Cells . 165 Isolation and Purification of Unlabeled DNA . 165 DNA Fragmentation . 167 Isolation and Purification of Labeled DNA . 167 Removal ofRapidly Renaturing Sequences from Radiolabeled Reference DNA 168 Base Composition Determination 168 Determination of DNA Concentrations . 168 Kinetics of DNA Renaturation 168 Heterologous Reannealing Reactions 168 Separation of Singleand Double-Stranded DNA on HA 168 Interaction of Yeast DNA and HA . 169 Scintillation Counting . 170 Calculation of Sequence Complementarity . 170 RESULTS AND DISCUSSION . 170 Genus Schwanniomyces . 170 Genus Saccharomyces . 173 Genera Debaryomyces and Pichia . 179 Filiation Among the Haploid, Round-Spored, Nitrate-Negative Yeasts . 184 Evaluation of Current Approaches to Yeast Systematics . 186 CONCLUSIONS . 188 LITERATURE CITED 189