Miracle-dz/UniFAR-FTUs huggingface dataset:
Accompanying ions of ammonium sources and nitrate : ammonium ratios in tomato plants

The tomato (Solanum lycopersicum L.) cultivar Micro-Tom (MT) is widely used in physiological studies, but the effects of nitrate ( NO3 - ) and ammonium ( NH4 + ) ratios ( NO3 - : NH4 + ratios) and, in particular, the effects of the accompanying ions in NH4 + sources are unknown. To determine whether the accompanying ions in NH4 + sources influence NH4 + toxicity, the effects of NO3 - : NH4 + ratios on the physiology, electrolyte leakage index, nutrition, and dry weight were studied using hydroponics. The NH4 + sources were ammonium chloride (NH4Cl) or ammonium sulfate [(NH4)2SO4], and five NO3 - : NH4 + ratios were used: 100 : 0, 75 : 25, 50 : 50, 25 : 75, and 0 : 100. The NO3 - source was calcium nitrate [Ca(NO3)2], and the nitrogen (N) concentration was 15 mmol L−1. The results indicate that NH4Cl or (NH4)2SO4 can be used in studies on NH4 + toxicity because the accompanying ions did not influence the tomato plants. In addition, NO3 - : NH4 + ratios of 100 : 0 and 75 : 25 resulted in the highest dry weight of tomato plants, whereas ratios of 25 : 75 or 0 : 100 were toxic.
Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs), of which polyhydroxybutyrate (PHB) is the most abundant, are bacterial carbon and energy reserve materials of widespread occurrence. They are composed of 3-hydroxyacid monomer units and exist as a small number of cytoplasmic granules per cell. The properties of the C4 homopolymer PHB as a biodegradable thermoplastic first attracted industrial attention more than 20 years ago. Copolymers of C4 (3-hydroxybutyrate [3HB]) and C5 (3-hydroxyvalerate [3HV]) monomer units have modified physical properties; e.g., the plastic is less brittle than PHB, whereas PHAs containing C8 to C12 monomers behave as elastomers. This family of materials is the centre of considerable commercial interest, and 3HB-co-3HV copolymers have been marketed by ICI plc as Biopol. The known polymers exist as 2(1) helices with the fiber repeat decreasing from 0.596 nm for PHB to about 0.45 nm for C8 to C10 polymers. Novel copolymers with a backbone of 3HB and 4HB have been obtained. The native granules contain noncrystalline polymer, and water may possibly act as a plasticizer. Although the biosynthesis and regulation of PHB are generally well understood, the corresponding information for the synthesis of long-side-chain PHAs from alkanes, alcohols, and organic acids is still incomplete. The precise mechanisms of action of the polymerizing and depolymerizing enzymes also remain to be established. The structural genes for the three key enzymes of PHB synthesis from acetyl coenzyme A in Alcaligenes eutrophus have been cloned, sequenced, and expressed in Escherichia coli. Polymer molecular weights appear to be species specific. The factors influencing the commercial choice of organism, substrate, and isolation process are discussed. The physiological functions of PHB as a reserve material and in symbiotic nitrogen fixation and its presence in bacterial plasma membranes and putative role in transformability and calcium signaling are also considered.
Identification of the sequences controlling cyclic AMP regulation and cell-type-specific expression of a prestalk-specific gene in Dictyostelium discoideum

We have cloned and analyzed a developmentally and spatially regulated prestalk cell-specific gene from Dictyostelium discoideum. The gene encodes a protein highly homologous to the lysosomal cysteine proteinases cathepsin H and cathepsin B. Amino acid comparisons between these enzymes showed that the active-site amino acids were conserved, as were amino acids known to be important for catalysis and residues which form the intramolecular cysteine bridges. We have constructed a series of internal deletions, duplications, and linker scanner mutations within the region 300 base pairs 5' to the cap site. Analysis of expression of the mutations in transformants identified a approximately 35-base pair GC-rich region containing a dAdC/dGdT palindromic repeat and a G-rich box which is homologous to the 3' GT half of the palindromic repeat. Deletion or disruption of the G box resulted in a approximately 50-fold drop in the level of expression of the gene fusion in transformants in response to cyclic AMP in single-cell culture but did not affect the temporal pattern of regulation or control by cyclic AMP. The expression of such constructs during normal multicellular differentiation paralleled that of the endogenous gene; however, the level of RNA from the constructs was only approximately 10-fold lower than that of constructs containing the G box. Deletion of the 3' half of the palindromic sequence and the G box region resulted in a dramatic decrease in the level of transcription, although the constructs still showed proper temporal expression. These results suggest that this 35-base-pair region acts as an important part of the regulatory region for cell type and cyclic AMP regulation.
Water retention characteristics of coarse porous materials to construct purpose-designed plant growing media

ABSTRACT Among potential components to construct Technosols for urban greening purposes, the commercially available geogenic coarse porous materials (CPMs) are mainly used in practice because of their high porosity. However, the knowledge of the hydraulic behavior of CPMs as well as of their mixtures with other substrates is limited, provoking their suboptimal usage. Therefore, we determined the water retention characteristics, including the available water capacity (AWC) of six geogenic CPMs: porlith, expanded shale, expanded clay, tuff, pumice, and lava. In order to obtain the water retention characteristics of the CPMs as well as of their mixture with sand (1:4 per volume), the following methods adapted from soil physics were applied over a wide range of pressure heads: Equi-pF apparatus, ceramic tension plates, pressure plate extractors, WP4C apparatus, and water vapor adsorption. The results were used to parametrize the modified Kosugi model (using SHYPFIT 2.0). Porlith and tuff have the highest AWC (0.37 m3 m−3 and 0.17 m3 m−3, respectively) and are the only ones which can be recommended as effective water-retaining materials. Further materials exhibit an AWC less than 0.10 m3 m−3. The CPMs exhibit a bimodal pore size distribution, which can be well described by the applied model, except for pumice and expanded shale. The mixtures present overall low AWCs up to 0.07 m3 m−3, with the pure sand having less than 0.03 m3 m−3. For practical application a quite high ratio of CPM is needed, and the mixing material must be adapted to the hydraulic properties of the CPMs. The water inside the CPMs may be easily available for plant roots able to penetrate in the CPMs’ coarse pores.
Effect of insertions, deletions, and double-strand breaks on homologous recombination in mouse L cells

We have used DNA-mediated gene transfer to study homologous recombination in cultured mammalian cells. A family of plasmids with insertion and deletion mutations in the coding region of the herpes simplex type 1 thymidine kinase (tk) gene served as substrates for DNA-mediated gene transfer into mouse Ltk- cells by the calcium phosphate technique. Intermolecular recombination events were scored by the number of colonies in hypoxanthine-aminopterin-thymidine selective medium. We used supercoiled plasmids containing tk gene fragments to demonstrate that an overlap of 62 base pairs (bp) of homologous DNA was sufficient for intermolecular recombination. Addition of 598 bp of flanking homology separated from the region of recombination by a double-strand gap, deletion, or insertion of heterologous DNA increased the frequency of recombination by 300-, 20-, or 40-fold, respectively. Linearizing one of the mutant plasmids in a pair before cotransfer by cutting in the area of homology flanking a deletion of 104 bp or an insertion of less than 24 bp increased the frequency of recombination relative to that with uncut plasmids. However, cutting an insertion mutant of greater than or equal to 24 bp in the same manner did not increase the frequency. We show how our data are consistent with models that postulate at least two phases in the recombination process: homologous pairing and heteroduplex formation.
PHENOLIC COMPOUNDS AND ANTIOXIDANT ACTIVITY OF WILD GRAPE (VITIS TILIIFOLIA)

Vitis tiliifolia is a tropical grape with a deep purple colour and a high content of pigments. Total polyphenols content in the skin and pulp was 400.35 and 171.26 mg GAE/g extract of Vitis tiliifolia, respectively, which coincides with DPPH radical scavenging for skin (91.39 %) and in the pulp (19.57%). The predominant individual phenolic compounds found in the skin were quercetin-3-glucoside (39.86 µg/g), rutin (37.01 µg/g) and trans-resveratrol (32.88 µg/g). The DPPH radical scavenging and reducing power revealed a high antioxidant activity. This study demonstrates that wild grape can thus be utilised as a novel functional resource.
Plasmon-Enhanced Self-Powered UV Photodetectors Assembled by Incorporating Ag@SiO2 Core–Shell Nanoparticles into TiO2 Nanocube Photoanodes

A novel photoelectrochemical self-powered ultraviolet photodetector (UVPD) has been assembled employing Ag@SiO2 core–shell nanoparticles (NPs) incorporated TiO2 nanocubes (NCs) as the photoanode. The incorporation of the plasmonic core–shell NPs can boost the photocurrent of the self-powered UVPD. Finite difference time domain (FDTD) and transient absorption spectroscopy (TAS) were employed to understand plasmonic enhancement processes. By optimizing the incorporated ratio of Ag@SiO2 NPs, the photocurrent of UVPD with 2 wt % Ag@SiO2 NPs reaches the maximum value in view of the enhanced light harvesting and effective inhibition of charge recombination. More importantly, the UVPD with 2 wt % Ag@SiO2 NPs achieves a high on/off ratio of 8212 and a remarkable responsivity of 0.151 A W–1, combined with a rapid response time, prominent spectral selectivity, and photosensitivity linearity response.
Parvovirus replication

The members of the family Parvoviridae are among the smallest of the DNA viruses, with a linear single-stranded genome of about 5 kilobases. Currently the family is divided into three genera, two of which contain viruses of vertebrates and a third containing insect viruses. This review concentrates on the vertebrate viruses, with emphasis on recent advances in our insights into the molecular biology of viral replication. Traditionally the vertebrate viruses have been distinguished by the presence or absence of a requirement for a coinfection with a helper virus before productive infection can occur, hence the notion that the dependoviruses (adeno-associated viruses [AAV]) are defective. Recent data would suggest that not only is there a great deal of structural and genetic organizational similarity between the two types of vertebrate viruses, but also there is significant similarity in the molecular biology of productive replication. What differs is the physiological condition of the host cell that renders it permissive. Healthy dividing cells are permissive for productive replication by autonomous parvoviruses; such cells result in latent infection by dependoviruses. For a cell to become permissive for productive AAV replication, it must have been exposed to toxic conditions which activate a latent AAV genome. Such conditions can be caused by helper-virus infection or exposure to physical (UV light) or chemical (some carcinogens) agents. In this paper the molecular biology of replication is reviewed, with special emphasis on the role of the host and the consequences of viral infection for the host.
Bacterial scission of ether bonds

INTRODUCTION . 216 PROBLEM POLLUTANTS AND ETHER SCISSION.217 Agrochemicals.217 Polyethers.218 Polyethylene glycols . 218 Polypropylene glycols and polytetramethylene glycols . 219 Detergents . 219 Builder compounds.219 Alcohol ethoxylates . 219 Alkylphenol ethoxylates.220 Alkylethoxy sulfate surfactants . 220 BIOCHEMICAL MECHANISMS OF ETHER CLEAVAGE.221 Oxygenation . 221 Oxidation by Cytochromes P-450 . 221 Hydroxyl Shift Mechanisms . 223 Hydrolysis . 225 Anaerobic O Dealkylation of Alkyl-Aryl Ethers . 225 Oxidation to Carboxylic Acids . 226 Reduction . 227 Carbon-Oxygen Bond Cleavage by Lyases . 228 CONCLUDING REMARKS.228 State of Knowledge and Prospects . 228 Pathways.228 Enzymes.229 Emerging Themes . 229 Natural Substrates for Ether Cleavage Systems . 229 ACKNOWLEDGMENT.230 REFERENCES . 230
Translating Information into Action: A Public Health Experiment in Bangladesh

Standard models of technology adoption posit learning as the basis of adoption. However, hygiene campaigns centered around information provision have been overwhelmingly unsuccessful in changing behavior and improving child health across the developing world. We design a low cost and scalable information campaign which we randomly distribute to poor households in rural Bangladesh. The campaign embeds hygiene-related edutainment within popular dramas and disseminates the material on SD cards for mobile phones, a commonly used entertainment medium across the infrastructurally weak subcontinent. First, we document improvements in handwashing behavior among exposed households, which translate into substantial reductions in symptoms of diarrheal disease (54%) and acute respiratory infection (29%) among exposed children. However, we find no change in self-reported hygiene knowledge, suggesting that the translation of information to behavior change involves tacit knowledge acquisition or behavioral nudges rather than conscious knowledge gains. Using minute-level data on handwashing behavior paired with minute-level data on mobile phone exposure to the campaign, we utilize machine learning techniques to investigate how the temporal nature of information exposure translates to behavioral change. We find that cumulative exposure to the campaign over the one month prior to a washing opportunity is highly predictive of washing, followed by any exposure immediately prior to a washing opportunity. Importantly, while behavioral changes eventually dissipate, health improvements remain over the course of the ten month experiment. This investigation establishes a framework for designing future public health campaigns to maximize information internalization and behavior change. ∗We are indebted to research assistant Mohammed Helal Uddin and Nayamat Tasnim Ullah, as well as the survey firm MOMODa in Gaibandha, Bangladesh. Experiment registered in the AEA Registry under AEARCTR-XXXXX. This work was supported by Japan Society for the Promotion of Science (JSPS) KAKENHI Grant Number 25101002. ” †Harvard Business School; corresponding author: rhussam@hbs.edu. (617) 495-6378. Address: Morgan Hall, 15 Harvard Way, Boston, MA 02163. ‡Department of Economics, Florida International University, shonchoy@fiu.edu §GRIPS, c-yamauchi@grips.edu ¶Harvard Business School; kpandey@hbs.edu
Solid Suspension Characteristics in a Dished Base Tank for a Range of Geometric and Solids Properties

Just-suspension conditions were studied in a dished base ba ed cylindrical tank with internal diameter, T=155 mm using two variables of impeller-to-tank geometry, D=0.3T and 0.5T. The performance of the alternative geometries was studied using a conventional down-pumping 45° four pitched blade turbine (4PBT) impeller in comparison to the novel SATAKE SUPERMIX® HR100 and HS604 impellers. The slurry comprised of 18.0, 75.3 and 195.5 μm PMMA particles in concentrations ranging from 5–40% by weight. The performance of solid suspension was assessed in a dished base tank, which was found to be not as e cient as the at base tank when used with the D=0.5T impellers. However, it is interesting to note that, when used with a suitable impeller, namely the HS604 impeller, the dished base tank was more superior to the at base tank. This indicates that impeller-to-tank geometry is critical in determining the e ciency of solid suspension. Additionally, solid suspension performance in a dished base tank was markedly enhanced with D=0.3T impellers by approximately 60 to 80% reduction in the speci c energy at just suspension (εjs) compared with D=0.5T, resulting from the uid ow pattern generated inside the stirred tank. This suggests that the dished base tank is not a poor option for solid suspension if it is used with the right impeller geometry.
Ash Fusion Characteristics and Transformation Behaviors during Bamboo Combustion in Comparison with Straw and Poplar

In this work, the bamboo ash fusion and sintering characteristics were studied to evaluate its potential application in combustion for the production of heat and power. Poplar and wheat straw were used in the experimental test as the reference fuels for comparison. Standard ash fusion tests and ash sintering tests were carried out at elevated temperatures. The results indicate that bamboo has a low ash melting temperature of 862 °C, much lower than that of poplar. In spite of the high K content in bamboo ash, no severe melting and sintering was observed under the temperature lower than 1000 °C. The ashes after the tests were analyzed using SEM/EDX, XRF, and XRD techniques to illustrate the ash transformation behavior. Standard ash fusion tests indicated that the melting temperatures of bamboo, wheat straw, and poplar ashes are 862 °C, 770 °C, and 1088 °C, respectively. No severe sintering can be observed for poplar due to the large existence of refractory compounds. Ash sintering occurred when the tempera.
Differences in oncogenic potency but not target cell specificity distinguish the two forms of the BCR/ABL oncogene

Two forms of activated BCR/ABL proteins, P210 and P185, that differ in BCR-derived sequences, are associated with Philadelphia chromosome-positive leukemias. One of these diseases is chronic myelogenous leukemia, an indolent disease arising in hematopoietic stem cells that is almost always associated with the P210 form of BCR/ABL. Acute lymphocytic leukemia, a more aggressive malignancy, can be associated with both forms of BCR/ABL. While it is virtually certain that BCR/ABL plays a central role in both of these diseases, the features that determine the association of a particular form with a given disease have not been elucidated. We have used the bone marrow reconstitution leukemogenesis model to test the hypothesis that BCR sequences influence the ability of activated ABL to transform different types of hematopoietic cells. Our studies reveal that both P185 and P210 induce a similar spectrum of hematological diseases, including granulocytic, myelomonocytic, and lymphocytic leukemias. Despite the similarity of the disease patterns, animals given P185-infected marrow developed a more aggressive disease after a shorter latent period than those given P210-infected marrow. These data demonstrate that the structure of the BCR/ABL oncoprotein does not affect the type of disease induced by each form of the oncogene but does control the potency of the oncogenic signal.
Biology of bacterial deoxyribonucleic acid topoisomerases

INTRODUCTION . DNA SUPERCOILING AND TOPOISOMERASES . CONTROL OF TOPOISOMERASE GENE EXPRESSION . ROLE OF TOPOISOMERASES AND SUPERCOILING IN DNA REPLICATION. Elongation Phase of Replication . Initiation of Replication . Termination of Replication . Plasmid Replication In Vivo . ROLE OF TOPOISOMERASES AND SUPERCOILING IN GENE EXPRESSION. CELLULAR RESPONSES TO NALIDIXIC ACID. TOPOISOMERASES, RECOMBINATION, AND REPAIR . Generalized Recombination. Site-Specific Recombination. Gyrase-Mediated Illegitimate Recombination. DNA Repair. CONCLUDING REMARKS . ACKNOWLEDGMENTS . LITERATURE CITED. 273 274 276 277 277 279 279 280 280 281 282 282 282 283 284 285 285 285
The intron-containing gene for yeast profilin (PFY) encodes a vital function

The gene coding for profilin (PFY), an actin-binding protein, occurs as a single copy in the haploid genome of Saccharomyces cerevisiae and is required for spore germination and cell viability. Displacement of one gene copy in a diploid cell by a nonfunctional allele is recessively lethal: tetrad analysis yields only two viable spores per ascus. The PFY gene maps on chromosome XV and is linked to the ADE2 marker. The primary transcript of about 1,000 bases contains an intron of 209 bases and is spliced into a messenger of about 750 bases. The intron was identified by comparison with a cDNA clone, which also revealed the 3' end of the transcript. The 5' end of the mRNA was mapped by primer elongation. The gene is transcribed constitutively and has a coding capacity for a protein of 126 amino acids. The deduced molecular weight of
Cell biology and molecular basis of denitrification

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.