Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutagenesis by O6-[4-Oxo-4-(3-pyridyl)butyl]guanine in Escherichia coli and Human Cells

Site-specific mutagenesis by O6-[4-oxo-4-(3-pyridyl)butyl]guanine (O6-pobGua), a product of DNA pyridyloxobutylation by metabolites of the tobacco-specific nitrosamines N-nitrosonornicotine (NNN) and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), was studied in Escherichia coli strain DH10B and human kidney cells (293) when the modified base was incorporated in either a double-stranded or a gapped shuttle vector. In the repair-competent E. coli strain, less than 3% of the colonies produced by double-stranded vectors harboring the modified base were mutant whereas 96% were mutant when DH10B cells were transformed with modified gapped vectors. By contrast, transformation of DH10B cells with plasmids derived from O6-pobGua-containing double-stranded and gapped vectors previously replicated in 293 cells produced 7 and 16% mutant colonies, respectively. These percentages increased to 42 and 82%, respectively, when the 293 cells were pretreated with O6-benzylguanine to inactivate the O6-alkylguanine−DNA .
Larger hatching fractions in avian dispersed anostracan eggs (Branchiopoda)

Anostracan crustacean eggs were collected from various materials leaving and entering branchiopod habitats. The eggs were cultured from allochthonous dust and mud, bird faeces and stomach contents. Eggs that passed through aquatic bird digestive tracts hatched in significantly larger fractions than eggs dispersed by other vectors and eggs from resident habitat egg banks. Predator dispersed eggs would necessarily have a greater chance of reaching suitable habitat than eggs that are randomly dispersed (such as by wind). This larger hatching fraction would amplify the priority effects of habitat monopolisation should the eggs be deposited in unoccupied habitat.
Quasi–static deformation of particulate media

Quasi–static shear deformation of granular media is examined by performing numerical simulations on polydisperse systems of elastic spheres in a periodic cell. Results of axisymmetric compression test simulations are reported for both a dense and a loose system of spheres sheared under constant mean stress conditions. At the macroscopic scale, the simulated stress–strain–dilation responses are in excellent qualitative agreement with the mechanical behaviour of sand observed in real experiments. Numerical simulation permits a detailed examination of the evolution of internal variables associated with the micromechanical processes occurring at the particle scale. In this context, we present and discuss the evolution of the induced structural anisotropy, the percentage of sliding contacts, the average coordination number and the normal and tangential contact–force contributions to the stress tensor. Encouraged by recent research published by physicists working on granular media, we show how the distribution of normal contact forces evolves during shear, and how it is affected by changing the particle modulus and stress level. This work has led us to consider two types of interparticle contacts: (1) the contacts carrying below–average normal contact forces; and (2) the contacts carrying above–average normal contact forces. We examine how these two different categories contribute to the stress tensor and the structural anisotropy tensor. As a consequence, we present information that provides new insights into the physics of granular media and clarifies some previous findings.
The Need for Consideration of Fire Behavior and Effects in Prescribed Burning

Prescribed burns are increasingly being used in ecological restoration and vegetation management. Despite the accumulation of scientific information on fire behavior and fire effects, however, in many cases fires are prescribed without consideration of such information and often simply because of evidence of past fires. Rather than basing fire management plans on ideas of the historical “natural” occurrence of fire, we present the case for fire management being based on the fire effects desired. Effective fire management and development of proper fire prescriptions require an understanding of fire processes and heat transfer that explain fire behavior characteristics, as well as an understanding of how fire behavior is coupled to specific fire effects. We provide a basic introduction to these concepts and processes, which will help in understanding the importance of having a more technical understanding of fire. The discussion includes the processes of heat transfer and the relative role of various fuel variables in these processes, as well as the concepts of fire intensity, rate of spread, fuel consumption, duff consumption, fire frequency, and the ecological effects associated with variation in these characteristics of fire behavior.
Nuclear Pre-mRNA Splicing in Plants

Referee: Dr. Gabor Lazar, Chief, Dept. of Molecular Biology, Massachsetts General Hospital, Harvard Medical School, Wellman Eleven, Boston, MA 02114 The coding regions of about 80% of plant nuclear genes contain one or more noncoding intervening sequences (introns). The transcription of these genes results in a precursor mRNA (pre-mRNA) with coding sequences (exons) and introns. The noncoding intervening sequences are then accurately removed and the coding regions are joined in the nucleus to generate functional mRNAs by a process called pre-mRNA splicing. In addition to basic/constitutive splicing, many plant pre-mRNAs, like metazoan pre-mRNAs, undergo alternative splicing, thereby contributing to proteomic complexity. The splicing of pre-mRNAs takes place in a large RNA-protein complex named the spliceosome, which is made up of several small nuclear ribonucleoprotein (snRNP) particles and other associated proteins. Until recently, it was thought that there is only one type of spliceosome in all eukaryotes. However, it is now established that most metazoans have a second (minor) type of spliceosome that is compositionally different from the widely studied major spliceosome and functions in splicing of some rare introns. Based on the conservation of many components of major and minor spliceosomes in plants, it is likely that plants contain both types of spliceosomes and the basic mechanisms involved in spliceosome formation and intron removal are likely to be similar between plants and animals. However, a number of reports using in vivo splicing assays have shown that the cis-elements that are necessary for intron recognition and proper splicing of plant introns differ considerably from yeast and animals. These studies suggest that the mechanisms of intron recognition in plants are likely to differ from yeast and animals and involve novel proteins that recognize the plant-specific cis-elements. In recent years, several proteins that are implicated in plant pre-mRNA splicing have been characterized, including some novel ones that are not present in metazoans. The recent completion of the Arabidopsis and other eukaryotic genomes sequence should facilitate the identification of plant orthologs of various animal spliceosomal proteins in the near future. However, identification and functional analysis of the splicing proteins that are specific to plants will demand novel approaches.
Effects of Historical Selective Logging on Anuran Communities in a Wet Evergreen Forest, South India

Vast areas of tropical evergreen forests have been selectively logged in the past, and many areas continue to be logged. The impacts of such logging on amphibians are poorly understood. I examined the response of anuran communities to historical selective logging in a wet evergreen forest in south India. Anuran assemblages in unlogged forest were compared with assemblages in selectively logged forest. Forty 10 m × 10 m quadrats in forest, riparian zones, and streams of unlogged and selectively logged forests were searched at night for anurans. Species richness did not appear to be affected by logging. However, anuran density varied significantly and was 42 percent lower in selectively logged forests compared to unlogged forests. Anuran densities also varied significantly across microhabitats, with highest densities in streams of both selectively logged and unlogged forests. Patterns of niche overlap varied with selective logging as niche breadth either expanded, contracted, or remained neutral for different species. Ordination analysis explained 95 percent of the variation in species assemblage across selectively logged and unlogged forests. The assemblage in selectively logged forest was nested within unlogged forest. Among the habitat characteristics, litter thickness and water depth had the highest influence on the assemblage. This was followed by litter/water temperature, air temperature, and lastly relative humidity. It appears that species richness and composition of anurans in selectively logged forests is converging with unlogged forests, but the effects of historical logging seem to persist on anuran densities and their niche characteristics even ca 40 yr since logging ceased.
Possible Role of Bone γ-Carboxyglutamic Acid-Containing Protein in the Pathogenesis of Vitamin K Deficiency in Early Infancy

(Gla) by high performance liquid chromatography, plasma and urinary bone Gla-containing protein (BGP) by radioimmunoassay, and vitamin K-dependent coagulation activity by Normotest, in newborn and 1-3month-old infants. The infants were divided into two groups, one of which received vitamin K orally at birth and at the 7th day thereafter, and the other, which did not receive vitamin K, was taken as the control. Urinary Gla level in the control group was fairly steady during early infancy, whereas in the vitamin K-administered group urinary Gla increased with age and was significantly higher than that of the control
Can plants absorb and utilize phosphate buffer extractable soil organic nitrogen without its prior mineralization?

Abstract Several researchers have hypothesized that organic nitrogen extracted using neutral phosphate buffer, termed phosphate buffer extractable organic nitrogen (PEON), is absorbed and utilized by some plant species as a nitrogen source without prior mineralization. Earlier reports have suggested that leaf lettuce (Lactuca sativa L.) depends mainly on inorganic nitrogen, whereas qing-geng-cai (Brassica chinensis L.) can absorb PEON. We tested leaf lettuce and qing-geng-cai growth under aseptic conditions using three nitrogen sources under different light conditions to investigate this hypothesis. Nitrate, amino acids or purified PEON were supplied as the sole nitrogen source. Five different levels of light intensity were used to detect the contribution of carbon to plant growth supplied from PEON. Leaf lettuce growth was promoted only by nitrate, whereas growth of qing-geng-cai was promoted by nitrate and amino acids. The positive effect of amino acids on qing-geng-cai was pronounced at higher light intensity. However, PEON imparted no significant effect on either of the plants under any of the light conditions. Our results do not support the hypothesis that PEON is used as a nitrogen source by plants.
On the True Role of Oxygen Free Radicals in the Living State, Aging, and Degenerative Disorders

Abstract: Oxyradicals are generally considered harmful byproducts of oxidative metabolism, causing molecular damage in living systems. They are implicated in various processes such as mutagenesis, aging, and series of pathological events. Although all this may be justified, evidence is accumulating that it is an oversimplified view of the real situation. We can assume nowadays that the living state of cells and organisms implicitly requires the production of oxyradicals. This idea is supported by experimental facts and arguments as follows. (1) Complete inhibition of the oxyradical production by KCN (or by any block of respiration) kills the living organisms much before the energy reserves would be exhausted. (2) Construction of the supramolecular organization of the cells (especially of their membranous compounds) requires the cross‐linking effect of oxyradicals, particularly that of OH· radicals. (3) Blast type cells produce much fewer oxyradicals than do differentiated ones, and interventions increasing the production of OH· radicals induce differentiation of various lines of leukemic (HL‐60 and K562) and normal (fibroblasts, chondroblasts, etc.) cells, while SOD expression increases greatly. (4) It is reasonable to assume that the continuous flux of OH· radicals is prerequisite to maintenance of constant electron delocalization on the proteins, which is a semiconductive phenomenon suggested in 1941 by Szent‐Györgyi, but it has never been proven experimentally. It is theoretically possible to describe the function of the synapses as that of a single p‐n‐p transistor, assuming that the free radical flux maintains electron movements on the subsynaptic structures, while the actual membrane potential is governing the electron flux. This theoretical approach may open completely new possibilities for our understanding of the normal functions of living organisms, such as basic memory mechanisms in brain cells, their aging processes, and therapeutic approaches to many degenerative disorders, such as various types of dementia.
Selecting for floral character associations in wild radish, Raphanus sativus L.

ESS models of reproductive allocation have been used extensively to explain patterns of floral diversity in angiosperms. These theoretical explorations assume that proportional allocation to pollen, ovules, and seeds, as well as to secondary features such as showy petals and nectar rewards, can evolve independently within the limits set by total resource availability. In populations of California wild radish, we have shown previously that petal size, a strong determinant of visitation by honey bee pollinators, is positively correlated with both pollen and nectar production, but not with ovule or seed number per flower. These phenotypic associations may reflect selection, environmental correlation, and/or genetic constraint. By exerting selection on the petal size : pollen number ratio over two generations, we eliminated the positive correlation between petal size and pollen production, with both characters showing significant change after a single selection episode. Once these two floral traits became uncoupled, nectar sugar production was significantly correlated only with petal size. Our results suggest that natural selection could readily alter reproductive allocation in these flowers, and that the phenotypic correlations observed in nature may be maintained by selection for effective reproductive phenotypes.
A three‐dimensional model of CO2 transport in airspaces and mesophyll cells of a silver birch leaf

A realistic numerical three-dimensional (3D) model was constructed to study CO2 transport inside a birch leaf. The model included chloroplasts, palisade and spongy mesophyll cells, airspaces, stomatal opening and the leaf boundary layer. Diffusion equations for CO2 were solved for liquid(mesophyll) and gaseous(air) phases. Simulations were made in typical ambient field conditions varying stomatal opening, photosynthetic capacity and temperature. Doubled ambient CO2 concentration was also considered. Changes in variables caused non-linear effects in the total flux, especially when compared with the results of double CO2 concentration. The reduction in stomatal opening size had a smaller effect on the total flux in doubled concentrations than ambient CO2. The reduced photosynthetic capacity had a similar effect on the flux in both cases. The palisade and spongy mesophyll cells had unequal roles mainly due to the light absorption profile. Results from the 3D simulation were also compared to the classical one-dimensional resistance approach. Liquid and gas phase resistances were estimated and found strongly variable according to changes in temperature and degree of stomatal opening. For the birch leaves modelled, intercellular airspace resistance was small (2% of the total resistance in saturating irradiance conditions at 25 °C at stomatal opening diameter of 4 µm) whereas the liquid phase resistance was significant (23% for mesophyll and chloroplasts in the same ‘base case’). The absorption of CO2 into water at cell surfaces caused additional (strongly temperature dependent) resistance which accounted for 36% of the total resistance in the base case.
Evolution of sex determining mechanisms

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Flower and Fruit Characteristics in Small and Isolated Populations of a Fleshy‐Fruited Shrub

: During a warm period after the last glaciation the fleshy-fruited shrub, Prunus mahaleb, extended its area of distribution from the Mediterranean basin towards central Europe. Under a subsequent cooler climate, and probably increased competition from trees, the species became restricted to steep, south-facing cliffs and scree slopes with a particularly sunny and warm microclimate. Thus, the small relict populations in central Europe have been isolated for about 5000 - 6000 years. To investigate whether or not reproductive traits of P. mahaleb are affected by isolation and population size, several flower and fruit characteristics were sampled in ten populations in Switzerland. A Canonical Correlation Analysis (CCA) based on these reproductive characteristics differentiated the populations. The first CCA axis was determined by flower size, pollination frequency, pulp and seed mass. This ran parallel to increasing precipitation and decreasing altitude. The second axis correlated with the number of fruits per raceme and seed viability, and ran parallel to increasing sunshine. None of the six flower and fruit variables correlated with population size or with the degree of isolation. However, flower size, pollination frequency, pulp and seed mass showed a negative correlation with altitude. The results suggest that, in populations of P. mahaleb in central Europe, climatic conditions explain more of the observed variation in flower and fruit characteristics than population size or degree of isolation.
Gut ph and digestive strategies in estuarine grey mullet (Mugilidae) and tilapia (Cichlidae)

Tilapia guineensis, which feeds on leafy material, and Sarotherodon melanothron, which utilizes blue-green algae, were both capable of producing a pH 2 or less in the stomach which could contribute to the lysis and digestion of blue-green algae and bacteria. Of the grey mullets investigated, Liza falcipinnis had a gastric pH 3.3–4.5, which may not be low enough to cause cell lysis, whilst Liza dumerili, Mugil cephalus and Mugil curema all had stomach, caecal and intestinal pH's of 7–8.5. Grey mullet appear to have a different digestive strategy to tilapia and may rely upon the establishment of a ‘colloid mill’ in the stomach.
Trace Elements in Edible Rocky Shore Species: Effect of Sewage Discharges and Human Health Risk Implications

ABSTRACT Sewage pollution is a worldwide concern and can result in increasing levels of trace elements in the environment that can pose serious risks both to wildlife and human health. This highlights the importance of studying the role of sewage discharges in the contamination of aquatic systems, especially in rocky shores, since part of our food resources is directly collected from coastal waters. For this purpose, the accumulation of trace elements (Cu, Zn, Pb, Ni, Co, Cd, Fe, Mn, and As) by edible molluscs (Mytilus galloprovincialis, Patella ulyssiponensis, and Phorcus lineatus) was compared between one sewage-impacted area and two reference areas. This study suggests that the concentrations of trace elements in the soft tissues of the selected molluscs can be affected by the presence of sewage discharges, and that limpets seem to be the best bioindicator. Moreover, the sewage pollution increased the concentrations of As in the mollusc species, emphasizing its potential damaging effects on natural systems and on edible species.
Biomarkers of oxidative status associated with metal pollution in the blood of the white stork (Ciconia ciconia) in Spain

The aim of this study was to determine the impact of specific environmental contaminants on the activities of antioxidant enzymes in terrestrial, free-living birds. To investigate this, several biomarkers and the levels of lead, mercury, and arsenic were determined in blood of white stork (Ciconia ciconia) nestlings from two different colonies located in the west of Spain that were exposed to different environmental conditions and human activities. Different biomarker and contaminant patterns were observed between the two colonies, suggesting different levels of environmental contamination. In comparison to nestlings from a natural reference area, the levels of the three hazardous elements Pb, As, and Hg were significantly higher in the colony nearby a landfill. Analysis of antioxidant biomarkers revealed significantly higher levels of glutathione and glutathione S-transferase activity in birds from the colony close to the landfill site than were found in those from the “control” area. In contrast, the levels of malondialdehyde did not significantly differ between the two sampling sites. In addition, a positive correlation between glutathione and both Hg and As has been observed. Taken together, exposure to the three hazardous elements is reflected by enhanced activity of glutathione S-transferases, and elevated levels of glutathione and malondialdehyde. White storks can therefore be considered as a suitable model species for environmental monitoring programs.
BIOLOGICAL APPLICATIONS OF IONOPHORES: THEORY AND PRACTICE fn1

The discovery of the ion~phores'-~ has provided the means for studying a wide range of ion-selective processes. These compounds of moderate molecular weight (ca. 500-1500) form lipid-soluble complexes which provide a vehicle for a wide variety of cations to transverse lipid barriers, hence the term ionophore signifying i~n-bearer . ~ A series of representative ionophores is shown in FIGURE 1. Ionophore-mediated transport has not only been employed to perturb biological systems for study, but has also provided clues to the molecular mechanisms by which the biological membranes themselves transport and
Purification and properties of isocitrate lyase from Aspergillus nidulans, a model enzyme to study catabolite inactivation in filamentous fungi

In order to facilitate the purification of isocitrate lyase from Aspergillus nidulans , the isocitrate lyase overexpressing strain JCB4a was derived. Isocitrate lyase was purified to homogeneity by the criterion of polyacrylamide gel electrophoresis and anti-isocitrate lyase polyclonal antibodies were raised. Stabilization of purified enzyme, when stored at – 20 °C, required the addition of 1 mM dithiothreitol (DTT) plus 1 mM ethylenediaminetetraacetate (EDTA). Aspergillus nidulans isocitrate lyase is a multimeric enzyme with a native molecular weight of 240 kDa and composed of four monomers of 59 kDa. The enzyme required 5 mM Mg and 1 mM DTT or cysteine for full activity. EDTA at 1 mM replaced the requirement of a thiol compound for activity. The K m for threo -D s -isocitrate was 0·050 mM, and the enzyme activity was inhibited by succinate, itaconate and structural analogs of glyoxylate as well as by fructose-1,6-bisphosphate.