Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of the IDO Pathway

Chronic inflammation drives the development ofmany cancers, but a genetic definition of what con-stitutes‘cancer-associated’inflammationhasnotbeendetermined. Recently, a mouse genetic study revealeda critical role for the immune escape mediator in-doleamine 2,3-dioxygenase (IDO) in supporting in-flammatory skin carcinogenesis. IDO is generally re-garded as being immunosuppressive; however, therewas no discernable difference in generalized inflam-matory processes in IDO-null mice under conditionswhere tumor development was significantly sup-pressed, implicating IDO as key to establishing thepathogenic state of ‘cancer-associated’ inflammation.Here we review recent findings and their potential im-plications to understanding the relationship betweenimmuneescapeandinflammationincancer.Briefly,wepropose that genetic pathways of immune escape incancer are synonymous with pathways that define ‘can-cer-associated’ inflammation and that these processesmay be identical rather than distinct, as generally pre-sumed, in terms of their genetic definition.
Citrus Mycorrhizae: Potential Benefits and Interactions with Pathogens

The capability of vesicular-arbuscular mycorrhizal (VAM) fungi, symbiotically associated with roots of citrus and most other woody perennial crops, to dramatically enhance plant growth has attracted widespread interest among horticulturists. Unfortunately, too often scientists engaging in mycorrhizal research have become overly enthusiastic with growth responses that were created under artificial experimental conditions. Mycorrhizae are the “normal” condition of roots on citrus trees and most other horticultural plants in the field (44). The nonmycorrhizal condition is “abnormal” and often the consequence of “normal” horticultural practices, such as overuse of fertilizers and pesticides, soil sterilization, and plant production in sterile soilless media. These technical advances have led to rapid production of pathogen-free plants, but VAM fungi have been sacrificed in the process. The potential impact of mycorrhizal deficiency on the “quality” of citrus and other woody crops for transplant has not been fully evaluated. With the realization that VAM fungi are essential for the growth of citrus in field soils, the question of how to reintroduce and gain maximum benefit from mycorrhizae in greenhouse production of citrus and other woody plants needs to be assessed.
Overcoming physical seed dormancy in priority native species for use in arid-zone restoration programs

The relative effectiveness of wet- and dry-heat treatments on alleviating physical dormancy (PY) of seeds of seven species of Fabaceae and five species of Malvaceae was determined to optimise seed handling procedures for ecological restoration. Seeds of all species were treated at different temperatures (40−100°C) for various durations (2 and 5 min of wet heat, and 5, 10 and 30 min of dry heat). Prior to treatment, seeds of all species exhibited low germination (0–38%). As hypothesised, there was variation among species with respect to the efficacy of the heat treatments. In general, wet-heat treatments at temperatures >70°C for 2 or 5 min were effective in breaking PY for all Fabaceae species, and two Malvaceae species, with resultant germination typically >75%. For dry-heat treatments, higher temperatures and longer durations were required to achieve similar germination results. In the three Malvaceae species that were least responsive to heat (Abutilon otocarpum, Hibiscus haynaldii and Sida echinocarpa), there was a trade-off between treatment temperature and duration; lower temperatures (<70°C) failed to alleviate PY, whereas higher temperatures either rendered seeds permeable but not germinable (70−90°C), or resulted in seeds losing viability (e.g. 100°C). Therefore, combinational dormancy (PY + physiological dormancy) appears to be present in a proportion of the seeds of these Malvaceae species (i.e. those that imbibed and remained viable, but did not germinate). Scanning electron imagery established that the majority of wet-heat treatments resulted in the rupture of the water gap in the seed testa of all species. The results clearly demonstrate that optimal heat treatments for the alleviation of PY are species-specific. Restoration practitioners handling seeds of diverse species should be mindful of treating seeds at the lowest effective temperature (70−90°C) to avoid injury through inadvertent exposure to temperatures that are higher and longer than necessary to break dormancy.
Biochemical analyses of fossil enamel and dentin

Amino acid analyses of undecalcified samples of fossil crocodile and rhinoceros enamel and dentin from mature teeth revealed that the total protein content of these mineralized fossil tissues varied from ~0.01–0.007% by weight. Except in one instance, amino acid analyses of the enamel proteins revealed them to be free of collagen and to have an amino acid composition similar to the proteins obtained from the enamel of mature modern vertebrates. Molecular sieving of the acid soluble enamel proteins demonstrated that the components consisted principally of small peptides and free amino acids, as in the enamel of modern vertebrates. Based on the presence of hydroxyproline (hyp) and hydroxylysine (hyl), collagen was detected in undecalcified mature dentin of fossil rhinoceros, but not in undecalcified crocodile dentin. It was only by sequential extraction procedures that the presence of collagen in the dentin of fossil crocodile was established, emphasizing the utility and importance of analyzing the soluble components in specific extracts of the fossil. Based on these data and the concentrations of hyp and hyl in the material solubilized by the various solvents, the dentin of fossil rhinoceros contained considerably more collagen per weight and as a percentage of the total protein in the dentin than did the dentin of fossil crocodile. As with modern dentin, EDTA and dilute acid solubilize the noncollagenous proteins and peptides found in fossil enamel and dentin, some of which contain O-phosphoserine [Ser(P)], an amino acid unique to mineralized connective tissues. Similar to recent reported findings from fossil bone, less of the original content of the noncollagenous proteins, including those phosphorylated, is degraded and removed from the enamel and dentin during fossilization than the percentage of dentinal collagen and the nonphosphorylated domains of the enamel proteins which are removed. This selective resistance to degradation and removal of the noncollagenous proteins, including phosphoproteins, may reflect the strong interaction of these proteins with the mineral phase of fossilized tissues. The amount and close packing of the inorganic crystals may also inhibit the interaction of the proteins in the interior of the enamel and dentin with the geochemical environment.
Intra-annual density fluctuations in tree rings: how, when, where, and why?

Intra-annual density fluctuations (IADFs) in tree rings are generally considered structural anomalies caused by deviations from the “normal course” of xylogenesis during the growing season. This definition is based on the bias that, under “normal conditions”, cambial activity stops once a year. Each tree ring can thus be dated to one calendar year, which is one of the principles of dendrochronology. The formation of IADFs can be triggered directly by environmental changes, especially in precipitation and temperature, that affect cambial activity and cell differentiation. It can also be the result of limited photosynthesis, due to defoliation induced by biotic or abiotic constraints.Often indicated with alternative terms, IADFs were first described in the 1930s, and recently reported for many trees and shrubs from different ecosystems throughout the world, particularly for Mediterranean species. Different types of IADFs have been detected; their formation and structural properties depend on many factors including tree genotype, age, size, rooting depth, habitat, soil, climate, photosynthetic activity, and allocation strategies. Whether IADFs affect the adaptive capability of plants remains, however, unclear.We provide an overview of the main anatomical features of IADFs and their occurrence in tree rings from various environments and climatic regimes. We propose a simplified way of classifying them and discuss the hypotheses about their functional role and the factors triggering their formation. To understand the ecological role of IADFs better, we recommend a multidisciplinary approach, involving wood anatomy, dendroecology, and stable isotopes, which has already been applied for Mediterranean species. We conclude by considering that IADFs appear to be the “rule” rather than “anomalies” in some ecosystems where they help plants cope with fluctuating environmental conditions. Moreover, their anatomical structure represents a valuable proxy of past climatic conditions at a sub-seasonal resolution and may be relevant to adapt hydraulic functioning of living trees to changing climatic conditions.
Can the Heat of Ruminal Fermentation be Manipulated to Decrease Heat Stress

Introduction Ruminal fermentation gives cattle the ability to metabolize cellulose materials that would otherwise be indigestible, utilize non-protein nitrogen and harvest microbial protein as source of amino acids (Hungate, 1966). However, this fermentation also produces ammonia, methane and heat. These latter end-products represent losses of nitrogen and energy, respectively. The heat of ruminal fermentation can be advantageous in cool climates, but it represents yet another heat load on the animal if the ambient temperature is high. The question then arises, can the heat of ruminal fermentation be manipulated to decrease heat stress? Blaxter (1962) noted that “temperature measurements in the rumen certainly show that heat is evolved during microbial digestion, but such records do not allow any quantitative estimates of heat to be made. Estimates made many years ago, based on the ratio of carbon dioxide to the methane produced during the fermentation, indicated that the fermentation heat was probably 510% of the heat of combustion of food. ” Blaxter (1962) concluded that “fermentation heat exceeds the heat loss which takes place in the gut of non-ruminants by a factor of at least five. ” In the 1980’s, we used microcalorimetry measure the heat of fermentation directly and used these results to assess the efficiency of bacterial growth (Russell, 1986). By relating heat with basic concepts of ATP formation, growth and energy spilling, it was possible to develop a theoretical and more quantitative scheme of bacterial energetics.
Proposal of a population dynamics model of the Public Goods Dilemma in an Ant Colony

This paper proposes a model of the dynamics of the public goods dilemma in an ant colony of the species Pristomyrmex punctatus, based on recent experimental results of Dobata and Tsuji. The proposed model, based on two predators competing for one prey, represents the interactions between the worker ant population, the cheater ant population (predators) and the public goods (prey) in the nest. The simulation results are qualitatively very similar to the experimental results obtained by Dobata and Tsuji. The model also allows the study and analysis of the long term behavior of the colony, with regard to extinction or coexistence.
Chromium behavior in aquatic environments: a review

The fate of chromium (Cr) – a redox sensitive metal – in surface sediments is closely linked to early diagenetic processes. This review summarizes the main redox pathways that have been clearly identified over recent decades concerning the behavior of Cr(III,VI) in aquatic environments, and applies them to surface sediments where data for redox speciation remain limited. Overall, abiotic redox reactions that govern the speciation of Cr involve manganese (Mn) (III,IV) (hydr)-oxydes for Cr(III) oxidation, Cr(VI)-reducing species (dissolved iron (Fe) (II) and hydrosulfide (HS)−), and Cr(VI)-reducing phases (ferrous and sulfide minerals, as well as Fe(II)-bearing minerals). Bacterial activity is also responsible for the redox interconversion between Cr(III) and Cr(VI): biotic reduction of Cr(VI) to Cr(III) is observed through either detoxification or dissimilatory reduction. Whereas Mn(II)-oxidizing bacteria are known to promote indirect oxidation of Cr(III) to Cr(VI), the reaction mechanisms are unresolved.
Insight into “serpentine syndrome” of Albanian, endemic violets (Viola L., Melanium Ging. section) – Looking for unique, adaptive microstructural floral, and embryological characters

Abstract The genus Viola, particularly Melanium section, rich in metallophytes, is an excellent taxon for study of microevolutionary and adaptation processes. Pollen, ovule, and microstructural floral characters were investigated by LM, SEM, and CLSM in seven endemic Albanian violets, five serpentinophytes (Viola albanica, V. dukadjinica, V. albanica × V. dukadjinica, V. raunsiensis, and V. macedonica), two from chalk soil (V. aetolica and V. schariensis), and in their closest relatives (V. lutea ssp. sudetica, V. tricolor ssp. tricolor, and V. arvensis) for their taxonomic usefulness and adaptive value. Three among analyzed characters were common in all Albanian violets however not unique. Serpentinophytes, V. aetolica and V. schariensis possessed hairs deep inside the spur, developed pollen heteromorphism, both increase the chance of pollination in unpredictable conditions and had strongly developed tannin rich layer in the outer integument of the young ovules with a protective role. They also all exhibited high pollen viability (86.9 ± 10.2%), high frequency of normally developed, enlarged (fertilized) ovules in ovary (65.0 ± 24.0%), but also high frequency of degenerations in developing ovules (40.4 ± 9.8%). Several flower characters may be adaptive in the unfavorable, high altitude environment, including serpentine soils. High pollen viability and normally developed fertilized ovules are sufficient for Albanian species maintenance.
Work division of floral scent compounds in mediating pollinator behaviours

ABSTRACT Floral scents are known as an olfactory signal for attracting pollinators, but why the flowers pollinated by highly specialised pollinators emit scents consisting of mixtures of many compounds and dominated by one or a few compounds is still poorly understood. We supposed that each (especially characteristic) chemical in floral scents may play a specific role in mediating pollinator behaviours and tested this supposition in a fig-fig wasp mutualism. Ficus curtipes is obligately pollinated by an undescribed Eupristina species. In the scent of F. curtipes receptive figs, over 50 compounds have been identified, and the scent is dominated by two compounds, 6-methyl-5-hepten-2-ol (OL) and 6-methyl-5-hepten-2-one (NE). We therefore tested the roles of the two major chemicals in mediating the pollinator behaviours. Our results show that OL and NE, respectively, act as a long-distance attractant and a fig-entry behaviour stimulant to the obligate pollinator wasp. Namely, OL attracts the wasps to the figs and NE guides the wasps into the figs. This finding on the work division of floral scent compounds partially explains the maintenance mechanism of the fig-fig wasp mutualism and the significance of the chemical diversity of floral scent in plant–pollinator interactions, especially in specialised pollination systems.
REPRODUCTIVE BIOLOGY OF THE GROUND-DWELLING SQUIRRELS

IntroductionFamily Sciuridae of the order Rodentia in-cludes ground-dwelling squirrels of subfamilySciurinae represented by Spermophilus (groundsquirrels; GSs), Marmota (marmots), Tamias(chipmunks) and Cynomys (prairie dogs) genera.Most species of ground-dwelling squirrels areobligate hibernators and seasonal breeders thatlive in diverse habitats and they exhibit remark-able physiological adaptations to seasonal envi-ronmental factors. Ground-dwelling squirrels ex-hibit a variety of social systems and mating sys-Review
Oxidative stress and antioxidative system in plants

Free radicals and other active derivatives of oxygen are inevitable by-products of biological redox reactions. Reactive oxygen species inactivate enzymes and damage important cellular components. The increased production of toxic oxygen derivatives is considered to be a universal or common feature of stress conditions. Plant and other organisms have evolved a wide range of mechanisms to contend with this problem. The antioxidant defence system of the plant comprises a variety of antioxidant molecules and enzymes. The effects of the action of free radicals on membranes include the induction of lipid peroxidation and fatty acid de-esterification. Both ethylene biosynthesis and membrane breakdown, which appear to be closely linked, seem to involve free radicals, although the sequence of events generating these free radicals is still poorly understood. It is clear that the capacity and activity of the antioxidative defence system are important in limiting oxidative damage and in destroying active oxygen species that are produced in excess of those normally required for metabolism. Transgenic plants offered us a means by which to achieve complete understanding of the roles of the enzymes involved in protection against stress of many types, environmental and induced. Studies on transformed plants expressing increased activities of single enzymes of the antioxidative defence system indicate that it is possible to confer a degree of tolerance to stress by these means. The advent of plant transformation has placed within our grasp the possibility of engineering greater stress tolerance in plants by enhancements of the antioxidative defence system.
IMPACT OF ZINC FOLIAR APPLICATION ON LENTIL PLANT (Lens culimaries, Medic) GROWN ON SANDY SOIL

Two field experiments were carried out at El-Ismailia Agricultural Research Station, El-Ismailia Governorate during the two winter growing seasons, 2005/2006 and 2006/2007 to study the effect of sprayed zinc as chelate form at rates of control, 0.5, 1.0, 2.0 and 3.0 g/Liter on yield components, yield and chemical composition of lentil plant ( Lens culinaris , Medic.) grown on sandy soil. Results can be summarized as follows: Generally, foliar application of zinc achieved significant increases of lentil yield and its components, as compared with control treatment received no zinc in both growing seasons. Spraying zinc at rates of 1.0 & 2.0 g/liter led to significant increases in most parameters of yield and its components, compared to the other treatments in both seasons. Meanwhile, zinc at the rate of 3.0 g/liter gave significant decreases in the most parameters. In first season, in most cases, zinc foliar application at the rates of 1.0 and 2.0 g/liter increased significantly macro and micro nutrient contents in seed lentil plants, compared to the other treatments. Meanwhile, the control treatment and zinc application at the rate of rate of 3.0 g/liter decreased significantly such nutrients. On the other hand, foliar application at the rates of 1.0 and 2.0 g/liter increased significantly N & protein percentages. While, zinc addition did not significantly affect P& K percentages, as well as Fe, Zn and Mn concentrations in the second season.
Der Embryotest mit dem Zebrabärbling - eine neue Möglichkeit zur Prüfung und Bewertung der Toxizität von Abwasserproben

The suitability of the test system «fish-embryo» was studied in order to determine the nonacute toxic effect of industrial waste water on the embryonic development of the zebrafish (Brachydanio rerio) by dilution analysis. 29 samples of industrial effluents from 11 different sewage plants were tested. Parallel ot the tests with fish-embryos several bioassays described in the German DiN-Norm 38 412 (group L) were undertaken: the fish acute toxicity test L 31, the Daphnia acute toxicity test L 30, the green algae toxicity test L 33 and a bacterical bioluminescence test L 34. The results, described as the corresponding «Gfactors» (dilution at which no effects were no longer observed) were compared. The results of tests with fish-embryos are comparable to results from fish acute toxicity tests. Toxicological endpoints of the ontogenesis, summarized as G E I-factors can be equated with the lethality of adult fish. For this group of effects the embryo toxicity test is as sensitive as the fish test or more so. In addition, the sensitivity and significance of the test system fish-embryo can considerably be increased when the toxicological endpoints of the secound group (G E II-factors) are taken into account. These parameters can give hints for various patterns of activities in the embryo. The results of the present investigation show that the embryo test may be an alternative to fish acute toxicity tests in routine waste water control
Satellite tobacco necrosis virus: a new vector in plant genetic engineering

Cloned full-length copies . of genomes of RNA-viruses, when introduced into a permissive host cell (bacterium, animal cell), can lead to a productive infection presumably initiated by a single complete transcript. Satellite Tobacco Necrosis Virus (STNV) requires coinfection by a helper virus such as TNV for replication; it only codes for one protein, the structural coat protein. Introduction of a cloned full-length copy of STNV present on a plasmid into a plant cell and coinfection with TNV leads to productive infection as shown both at the RNA level (Northern) and at the protein level (Western). Therefore, it now becomes possible to manipulate the genetic information of a plant RNA virus. Synthetic DNA linkers were introduced at various positions of the STNV genome and the effect of these insertion mutations on the viral progeny could be established. Insertions which affect the reading frame of the coat protein block not only viral protein synthesis but also viral replication. Restoration of the reading frame may allow to recover viability, depending on the position of the inserted amino acids in the viral three-dimensional structure of the coat protein. Some linker insertions in the region following the coat gene are also detrimental to viability, while other insertions in the 3'untranslated region are stably transmitted to the progeny. This system for the genetic manipulation of an RNA virus offers many possibilities, not only to study the functional role of various regions of the genome, but perhaps also for expression of heterologous genes in plant cells.