Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequence variability and expression pattern of the dehydrin gene family in Populus alba × P. tremula var. glandulosa

The dehydrin (Dhn) genes occur as multi-gene families in the plant genome and are suggested to play a protective role in cold and drought tolerance. Here, we have identified 10 unique dehydrin genes (PoDhn) from poplar (Populus alba × P. tremula var. glandulosa), 6 of which have the full ORF. The PoDhn1 encodes for SK2-type, PoDhn2 and PoDhn7 for Kn-type, PoDhn3 for K3Stype, and PoDhn5 and PoDhn6 for the Y3SKn-type dehydrins, respectively. Results of gene expression analysis demonstrated that most of the PoDhn genes were expressed under normal growth conditions and the transcription level of the PoDhns increased by abiotic stress treatment. In particular, PoDhn2 and PoDhn7 transcripts increased dramatically by both cold and drought treatment and PoDhn5 was up-regulated by only drought stress. These results may be useful in further studies of PoDhn genes, including investigations into the mechanisms underlying gene expression, the nature of their variation, and their physiological functions.
The Two‐Culture Problem: Ecological Restoration and the Integration of Knowledge

The terms “ecological restoration” and “restoration ecology” are frequently interchanged. Restoration ecology is the suite of scientific practices that constitute an emergent subdiscipline of ecology. Ecological restoration is the ensemble of practices that constitute the entire field of restoration, including restoration ecology as well as the participating human and natural sciences, politics, technologies, economic factors, and cultural dimensions. This paper is motivated by the concern that the broader practice of restoration may become narrowed over the next decade as a result of zealous attention to scientific and technological considerations, and that restoration ecology will trump ecological restoration. Scientific and technological acumen is necessary for successful restoration, but insufficient. Maintaining a broader approach to restoration requires respect for other kinds of knowledge than science, and especially the recognition of a moral center that is beyond the scope of science to address fully. An example of integrated restoration is presented: the ecological and cultural restoration of Discovery Island (near Victoria, British Columbia, Canada) by the Lekwungen people (Songhees First Nation).
Synthese des Mannose-6-Phosphat-Erkennungsmarkers lysosomaler Enzyme: Molekulare Analyse der humanen UDP-N-Acetylglucosamin:lysosomales Enzym-N- Acetylglucosamin-1-Phosphotransferase

Die GlcNAc-Phosphotransferase katalysiert den initialen Schritt bei der Generierung von Mannose-6-Phosphat (M6P)-Resten, die wichtig fur den Transport lysosomaler Enzyme entlang des Biosynthese- und Endozytoseweges zum Lysosom sind. Die GlcNAc-Phosphotransferase stellt ein Heterohexamer dar, das aus drei Untereinheiten, alpha2beta2gamma2, zusammengesetzt ist. Die alpha/beta-Untereinheiten werden durch ein unbekanntes Gen, die gamma-Untereinheit durch ein separates GNPTAG-Gen kodiert. In der vorliegenden Arbeit konnte gezeigt werden, das humane Makrophagen, die nur wenige lysosomale Enzyme sezernieren, die M6P-Reste tragen, die GNPTAG zwar exprimieren, aber diese Untereinheit neben N-gebundenen Oligosaccharidketten weitere Makrophagen-spezifische posttranslationale Modifikationen tragen, die moglicherweise die Formierung von M6P-Resten behindern. Fur die lysosomale Protease Cathepsin D wurde ein M6P-unabhangiger intrazellularer Transport nachgewiesen, bei dem die verschiedenen Cathepsin D-Formen Membran-assoziiert sind. Defekte im GNPTAG-Gen werden verantwortlich gemacht fur die lysosomale Speicherkrankheit Mukolipidose III (ML III). Die molekularen Analysen des GNPTAG-Gens bei 10 ML III-Patienten ergab aber nur bei einem Geschwisterpaar eine Mutation, die eine N-Glykosylierungsstelle betraf und zur Fehlsortierung lysosomaler Enzyme sowie zu zellularen Umverteilung der GNPTAG fuhrte. Mit Hilfe einer GNPTAG-Affinitatschromatographie konnte aus Extrakten von Golgi-Membranen aus humaner Plazenta ein unbekanntes Protein isoliert und identifiziert werden, das durch das MGC4170-Gen kodiert wird. Das Gen ist auf Chromosom 12q23.3 lokalisiert und besteht aus 21 Exons. Das Genprodukt umfast 1256 Aminosauren, besitz zwei Transmembrandomanen und weist eine komplexe Modulstruktur auf, die aus mindestens 6 Domanen besteht. Die N-terminale Domane weist Ahnlichkeiten zu bisher nicht charakterisierten bakteriellen Proteinen auf, die an der Bildung von Zucker-1-Phosphat-Verbindungen bei der Kapselpolysaccharidsynthese beteiligt sind. Im MGC4170-Gen wurde bei 2 Patienten mit Mukolipidose II (I-cell disease) und bei 2 Patienten mit ML III (pseudo-Hurler-Polydystropie) Mutationen identifiziert. Die Daten zeigen, das es sich bei MGC4170 um das kodierende Gen der alpha/beta-Untereinheiten der GlcNAc-Phosphotransferase handelt.
Chemical Data on Pituitary Gonadotropins and Their Implication to Evolution

Chemical data on gonadotropins from several vertebrate species are summarized and discussed from an evolutionary point of view. A high degree of homology has been observed between mammalian gonadotropins (LH and FSH) and thyrotropin (TSH). In non-mammalian species the existence of LH and FSH-like hormones has been demonstrated except for squamate and fish species. Especially in fish the number of GTHs is still controversial. One pituitary glycoprotein assumes various gonadotropic functions of the pituitary, and a second pituitary hormone (carbohydrate-poor) acts on fish ovarian growth. GTHs from bird, reptile, amphibian, and fish pituitaries have been purified and chemically characterized (amino acid composition, carbohydrate content). The existence of a quaternary structure has been demonstrated for several tetrapod LHs and fish GTHs. The amino acid composition of α and β subunits purified from turkey (Meleagris gallopavo), and turtle (Chelydra serpentira, Chelonia mydas) LHs and from common carp (Cyprin.
Who are the innovators? A field experiment with 2 passerine species

Ecological and evolutionary drivers of innovativeness among species are relatively well studied, but the significance of similar variation within species is much less well understood. Using automated foraging devices, we conducted the first large-scale study of novel problem-solving performance in a wild bird population to test whether variation in innovativeness can be explained by inherent individual differences and by factors related to the "necessity drives innovation" hypothesis. We detected 20145 visits by 236 great tits (Parus major) and blue tits (Cyanistes caeruleus) and found consistent individual differences in the propensity to solve and in the time spent at devices between successive solutions in the field. Although individuals that were successful in a similar version of the task in captivity solved 3 times faster in the wild than those that were unsuccessful in captivity, success in captivity did not predict success in the wild. Thus, innovative propensity varies among individuals but it is also context dependent. Juveniles were more likely to solve the problem in the wild than adults, supporting the necessity drives innovation hypothesis. We found no evidence for social learning at problem-solving devices in the wild. The consistent individual differences in novel problem-solving performance we report suggest that innovativeness may be of adaptive significance within our population. Our results also suggest that selection for innovativeness may occur primarily among juveniles. Copyright 2011, Oxford University Press.
Development of a field test kit for coliphage detection in natural waters

Coliphages may be suitable alternative indicators of fecal pollution in natural waters. The relationship between coliphage and fecal coliform numbers may be expressed by log10 transformed linear regression equations in surface waters (correlation coefficient, r2 = 0.5872; p < 0.001) and in well waters (r2 = 0.4767; p < 0.001). Using the American Public Health Association 919C single agar layer method, coliphages can be enumerated easily and at less cost and more rapidly than coliform enumeration methods. In adapting this test for use in a field test kit, however, further modifications and simplifications are required. The use of 2,3,5-triphenyl tetrazolium chloride (TPTZ) to enhance plaque visibility while helpful, was not essential. Matched-pair t-test analysis showed no significant difference between the plaque numbers enumerated with or without TPTZ to help plaque visibility. The Escherichia coli C host bacteria can be maintained either as a frozen preparation or dried on to paper disks with protective milk colloids. In the latter procedure, a resuscitation period of 18–24 h in broth at 30°C was found to be satisfactory in giving plaque numbers in the test that were not significantly different than when frozen host was used. A portable field kit has been designed to carry out a total of eight tests. The kit includes the media, the bacterial host, petri dishes, syringes, receptacles, and a camping gas cylinder. It measures 38 cm by 25.5 cm by 33.5 cm and weighs about 6.4 kg. Using the kit, the test procedure for a water sample can be carried out in under 15 min.
Validation of computationally predicted substrates for laccase

Present study reports the validation (oxidation) of computationally predicted oxidation of xenobiotic contaminants by commercially available pure laccase from Trametes versicolor. Selected contaminants were predicted as potential targets for laccase oxidation by using in-silico docking tool. The oxidation by laccase was measured by change in absorbance at specific λ max of each compound. Sinapic acid and tyrosine were taken as positive and negative controls, respectively. Oxidation was observed in m-chlorophenol, 2,4 di-chlorophenol, 2,4,6 tri-chlorophenol, captan, atrazine and thiodicarb, except malathion, which showed no activity. It could be speculated that the predicted substrates showing oxidation shared homology at structural and chemical level with positive control compounds. In case of malathion, structural non-homology with sinapic acid could be attributed to its inactivity towards laccase that required further structural analysis. Thus, a remediation tool proposing an advanced remediation approach combining the application of theoretical in-silico method and subsequent experimental validation using pure laccase could be proposed. As number and type of xenobiotics increase, the unfeasibility to screen them experimentally for bioremediation also rise. This approach would be useful to reduce the time and cost required in other screening methods.
PHOTOADAPTATION, GROWTH AND PRODUCTION OF BOTTOM ICE ALGAE IN THE ANTARCTIC 1

Biomass, chemical composition, growth rates and the photosynthetic response of natural populations of sea ice algae in McMurdo Sound, Antarctica were followed over most of the spring bloom to examine temporal variability under a relatively constant incident irradiance (ca. 1500–1700 μE · m‐2· s‐1 at solar noon). Collection were restricted to bottom 20 cm of the ice sheet in an area with little or no snow (0–5 cm). At low temperature and irradiance these algae normally exhibited low assimilation numbers (ca. 0.1–0.4 mg C · mg Chl‐1· h‐1). Average growth rates (0.02–0.45 d‐1), based on changes in standing stocks, were also low. Biomass, biochemical composition, growth rates, assimilation numbers and photosynthetic efficiencies (mg C · mg Chl‐1· h‐1 (μE · m‐2· s‐1)‐1) displayed large fluctuations over periods of several days during the growth season. On the other hand, Ik which is an index of photoadaptation, and Im, the optimal irradiance for photosynthesis, were relatively constant with less than twofold variation throughout our study.
The inhibition of ammonium uptake by nitrate in wheat

summary The improvement of root growth in hydroponically grown crop plants such as wheat when nitrate is added to an ammonium-only nitrogen source is possibly brought about by a suppression of the over-rapid absorption of ammonium by nitrate, thus alleviating the stress imposed by root-based ammonium assimilation on the supply of carbon skeletons required for root growth. The degree of suppression of ammonium absorption by nitrate in hydroponically grown wheat was investigated by measuring the relative rates of absorption of 15N from nutrient solutions containing 2 mM l6N nitrate, 2 HIM 15N ammonium, 2 mM 14N nitrate + 2 mM 15N ammonium, 2 mM 14N nitrate + 2mM 14N ammonium or 3 mM 14N nitrate + 1 mM 15N ammonium. After 8 h 15N feeding, 24% more 15N was found in ammonium-only fed plants than in nitrate-only fed plants. The l5N content of plants fed equal concentrations of 14N nitrate and l5N ammonium was 44 % lower than that of 15N ammonium-only fed plants; those fed a 3:1 mixture of 14N nitrate and l5N ammonium had a 15N content 68%, lower than that of 15N ammonium-only fed plants. The l5N nitrate +14N ammonium fed plants possessed a 15N content 32% below that of 15N nitrate-only fed plants. It thus appears that not only is there a measure-able suppressive effect of ammonium on the uptake of nitrate ions by wheat plants but that the inverse effect is even more pronounced and could account for observed effects of mixed ammonium + nitrate nutrition on root growth.
Coyote (Canis latrans) Food Habits in a Tropical Deciduous Forest of Western Mexico

Abstract We studied the food habits of the coyote (Canis latrans) in a tropical deciduous forest along the Mexican Pacific coast during 1996 and 1997. Small mammals, chiefly the Jaliscan cotton rat (Sigmodon mascotensis), were the main prey items during the dry season. Cultivated fruits, like mango and papaya, were the most important food for coyotes during the wet season. Given the importance in our study area of human related food items like the Jaliscan cotton rat, mango and papaya, we expect the expansion of coyote populations due to deforestation of the tropical deciduous forest.
Associative effects between forages and grains: Consequences for feed utilisation

Intake of metabolisable energy (ME) when forages and grains are fed together to ruminants may, due to digestive and metabolic interactions, be lower or higher than expected from feeding these components separately. These interactions, or associative effects, are due primarily to changes in the intake and/or the digestibility of the fibrous components of forage. Effects on voluntary forage intake (substitution effects) are usually much larger than on the digestibility of fibrous components, although the changes in forage intake may be a consequence of changes in the rate of digestion of the fibrous components. Positive associative effects, where grains increase voluntary intake and/or digestion of forage, are usually due to the provision of a limiting nutrient (eg. nitrogen, phosphorus) in the grain which is deficient in the forage. Negative associative effects, where grains decrease voluntary intake and/or digestion of forage, occur frequently and can cause low efficiency of utilisation of grain. Rate of substitution of grain for forage is related to forage intake, forage digestibility, the proportion of grain in the diet, and the maturity of the animal. Substitution rates are usually high in ruminants consuming high intakes of forage of high digestibility, probably due to the metabolic mechanisms which control voluntary intake reducing forage intake. Substitution rates are often low when animals are consuming forage of low to medium digestibility. Since voluntary intake of such forages is most likely determined by the capacity of the rumen to accommodate and pass to the lower gastrointestinal tract undigested forage residues, and of the rate of forage fibre digestion in the rumen, substitution is likely to be determined by changes in these processes. Reduced rate of fibre digestion in the rumen is often due to low rumen pH and/or an insufficiency of essential substrates for rumen microorganisms. Use of grains for lactating dairy cows involves an additional constraint since dietary grain may severely reduce milk fat content. Negative associative effects can be alleviated by ensuring supply of essential microbial substrates, feeding management, and modification of grain to minimise their adverse effects on fibre digestion, while ensuring satisfactory digestion of the grain and efficient microbial protein production.
Effects of enhanced UV‐B radiation on a weedy forb (Plantago lanceolata) and its interactions with a generalist and specialist herbivore

Assessments of potential impacts of global climate change often focus exclusively on plants; however, as the base of most food webs, plants generally experience abiotic stresses concomitantly with biotic stresses. Longleaf plantain, Plantago lanceolata L. , is a cosmopolitan temperate perennial weed that experiences a wide range of environmental conditions throughout its range. We examined the impacts of elevated levels of exposure to shortwave (UV‐B) radiation on this plant, on two herbivores associated with this plant, and on the plant‐herbivore interaction. Plantains were grown at 6 and 12 kJ m−2 d−1 BE300 UV‐B radiation and concentrations of iridoid glycosides (aucubin and catalpol), verbascosides, and nitrogen were measured. In terms of plant impacts, we found that iridoid glycoside concentrations were unchanged by elevated UV‐B radiation, whereas, in one experiment, the concentration of verbascosides in young leaves and levels of nitrogen in old leaves increased under elevated UV‐B radiation. Variation in plant chemistry due to leaf age and maternal family was greater than variation due to UV‐B exposure. When caterpillars were fed excised leaves from plants grown under elevated UV‐B, growth and survivorship of the specialist herbivore, Precis coenia Hbn. (Lepidoptera: Nymphalidae), were unaltered and growth of the generalist herbivore, Trichoplusia ni (Hbn.) (Lepidoptera: Noctuidae), was accelerated. When the caterpillars were reared on potted plants at high and low levels of UV‐B radiation, growth and survivorship of P. coenia were unchanged while growth of T. ni was significantly depressed by elevated UV‐B. Elevated UV‐B altered allocation patterns of above‐ground biomass in these plants; masses of crowns and reproductive tissue were reduced. UV‐B levels, however, did not affect distribution of damage to foliage inflicted by either species. In two additional experiments with artificial diet, designed to test the direct effect of UV‐B radiation on caterpillars, growth and survivorship of P. coenia were unaltered while survivorship of T. ni was significantly depressed when caterpillars were exposed to elevated UV‐B radiation. These studies collectively demonstrate that higher trophic level impacts of UV‐B‐induced changes in plants depend on the identity of the herbivore and its degree of adaptation not only to variation in hostplant quality but also variation in its light environment.
Histochemical characterisation of unextractable seed coat pigments and quantification of extractable lignin in the Brassicaceae

The differences determined by in situ histochemical staining and thioglycolic lignin analyses provided a new view of seed coat composition in a range of yellow- and brown-seeded germplasm of the Brassicaceae. Unextractable seed coat pigments were composed of proanthocyanidin (condensed tannin) polymers. Anthocyanins were absent in all seed coat tissues. Proanthocyanidin was deposited over the entire seed coat in dark-seeded germplasm and in patches in some yellow-seeded germplasm. The seed coat and hilum of Crambe abyssinica cv Prophet and some yellow-seeded accessions contained an unidentified, unreactive brown pigment. Several new pigmentation patterns, occurring as spots and patches and surrounding the hilum, became apparent from this analysis. Thioglycolic lignin was significantly lower in yellow-seeded samples compared with the dark-seeded accessions, and the majority of the lignin occurred in the seed coat. These discoveries provide new and useful data for plant breeders and indicate the need to use more detailed analytical methods in breeding programmes that have the goal of improving seed meal quality by reducing fibre and phenolics. Copyright © 2004 Society of Chemical Industry
Isolation of grapevine promoters with special emphasis on the vacuolar pyrophosphatase

Understanding the complex nature of grapevine molecular biology is of great importance for viticulturists. Progress in the elucidation of key events on a genetic level could provide further insight into the underlying cues responsible for the precise control of physiological and metabolic changes during a specific condition such as fruit development. The use and analysis of molecular ‘tools’, such as promoters controlling the site and level of gene activity, could assist in the understanding of grapevine biology and serve as a platform for the future design and development of recombinant DNA protocols and strategies for Vitis vinifera L. A high-throughput gene expression system, cDNA-AFLPs, was successfully used to analyse large-scale transcriptional activity during berry ripening. Candidate cDNA fragments were selected on the basis of desired expression patterns and/or known gene function for subsequent promoter isolation. From three candidate cDNAs selected, the promoter of a gene encoding vacuolar pyrophosphatase (V-PPase) was isolated for computational and comparative analyses. Promoter activity was evaluated on a transient level using the green fluorescent protein (GFP) reporter gene. Comparative integration has allowed for putative correlation of cis-elements, acting as receptors within promoter regions, to regulate V-PPase gene expression in response to development, environmental stress and tissue-specificity. In this study, integration of genetic data have advanced the understanding and transcriptional role of a key enzyme (V-PPase) during grape ripening. Although never a replacement for experimental verification, this integrative strategy of combining gene expression profiles with bioinformatics and regulatory data will greatly assist in further elucidation of various other key components and regulatory cues associated with grapevine molecular biology. This study has allowed us to use molecular tools that could assist in gaining further insight into genetic complexities and could serve as a platform for a more refined genetic manipulation strategy in Vitis vinifera L.
Somatic mutation-mediated evolution of herbicideresistance in the nonindigenous invasive plant hydrilla( Hydrilla verticillata )And Franck E. Dayan

Hydrilla ( Hydrilla verticillata L.f. Royle) was introduced to the surface water of Florida in the 1950s and is today one of the most serious aquatic weed problems in the USA. As a result of concerns associated with the applications of pesticides to aquatic systems, fluridone is the only USEPA-approved chemical that provides systemic control of hydrilla. After a decrease in fluridone’s efficacy at controlling hydrilla, 200 Florida water bodies were sampled to determine the extent of the problem and the biological basis for the reduced efficacy. Our studies revealed that hydrilla phenotypes with twoto six-fold higher fluridone resistance were present in 20 water bodies. Since fluridone is an inhibitor of the enzyme phytoene desaturase (PDS), the gene for PDS ( pds ) was cloned from herbicidesusceptible and -resistant hydrilla plants. We report for the first time in higher plants three independent herbicide-resistant hydrilla biotypes arising from the selection of somatic mutations at the arginine 304 codon of pds . The three PDS variants had specific activities similar to the wild-type enzyme but were two to five times less sensitive to fluridone. In vitro activity levels of the enzymes correlated with in vivo resistance of the corresponding biotypes. As hydrilla spread rapidly to lakes across the southern United States in the past, the expansion of resistant biotypes is likely to pose significant environmental challenges in the future.