Miracle-dz/UniFAR-FTUs huggingface dataset:
Biotic and abiotic soil factors in the succession of sea buckthorn, Hippophae rhamnoides L. in coastal sand dunes

Decline and succession in dune scrub vegetation of sea buckthorn, Hippophae rhamnoides L. in the Netherlands was previously found to be stimulated by biotic soil factors. In the present study, the role of plant-parasitic nematodes and root fungi was investigated. A field survey showed that during the ageing of H. rhamnoides vegetation there was a change in the plant-feeding nematode fauna. Certain nematode species, such as Tylenchorhynchus microphasmis Loof, were present in different stages and their population increased from stage to stage when expressed per unit of root length. The fraction of root length infected by VA-mycorrhizal fungi increased, as did soil concentrations of nitrogen and organic matter. Pot experiments with selective inhibition of groups of soil organisms indicated that soil fungi could be harmful to H . rhamnoides in the presence of nematodes, although fungi were not harmful on their own. The impact of various densities of T . microphasmis, either alone or in combination with the nitrogen-fixing actinorhizal symbiont Frankia or the fungus Cylindrocarpon destructans Zinnsm. Scholten, was assessed in pot experiments with controlled soil moisture conditions. Results showed inhibitory effects of the nematode on growth and on the acquisition of certain nutrients (especially phosphate). Although root nodulation and nitrogen fixation by Frankia were reduced, this did not appear to be the primary cause of growth reduction. No synergic interaction was found between T . microphasmis and C. destructans in their effect on growth of H . rhamnoides. The results of this study support the hypothesis that the increase in the concentration of soil nitrogen in the field stimulates nematode activity which in its turn impedes the acquisition of phosphate by H. rhamnoides. This reduces the competitive ability of this shrub and gives way to other plant species in the vegetation which are less sensitive to root damage.
The molecular mechanism for vegetative phase change: Regulation of miR156 expression and action

The timing of the transitions between the juvenile and adult vegetative stages (vegetative phase change) is important for shoot maturation in plants. The juvenile and adult vegetative stages are defined by a difference in reproductive competence (incompetent versus competent), but they are also associated with a variety of other morphological and physiological differences. An evolutionarily conserved microRNA, miR156, plays a central role in promoting the juvenile phase through its repression of ten adult-phase-inducing SPL family transcription factors. A decrease in miR156 abundance and a concomitant increase in SPL expression are correlated with the onset of adult traits. However, despite the importance of miR156 in regulating vegetative phase change, very little is known about the regulation of miR156 itself at either transcriptional or posttranscriptional levels. The aim of this work is to further the understanding of the factors that contribute to the regulation of miR156. To identify the source of signals that repress miR156 and promote vegetative phase change, I performed organ ablation experiments in Arabidopsis. I discovered that defoliation, but not root or cotyledon ablation, delayed phase change, and this effect was attributable to an increase in the expression of MIR156. Defoliation also delayed phase change in Nicotiana benthamiana, Zea mays (maize), and Acacia mangium. Based on these results, I concluded that vegetative phase change is mediated by a leaf-derived signal that represses the transcription of MIR156. Furthermore, the possibility that sugar is the leaf signal was explored. Exogenous sugar repressed the expression of MIR156, resulting in an increase in SPL expression and early phase change. Consistent with this observation, mutants with reduced abundance of endogenous sugars had elevated miR156 expression and delayed phase change. This sugar response was dependent on the signaling function of the glucose sensor HXK1. To identify additional modifiers of the miR156 pathway, I performed a genetic screen using an SPL3-GFP translational reporter, identifying mutants that have either higher or lower GFP expression. This screen produced mutations in SUO, a BAH domain containing protein. SUO is a Processingbody (P-body) component and is specifically required for miR156-mediated translational repression, but not for miR156-mediated transcript cleavage. These results indicate that miR156-mediated translational repression plays an important role in regulating vegetative phase change. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biology First Advisor R. Scott Poethig This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/390
Physiological responses to water stress and temperature on the pine wilt disease development in Pinus spp.

Four to five-years-old Pinus pinaster, P. pinea and P. radiata trees were inoculated with 6000 pinewood nematodes (PWN) and symptoms evolution, trees physiological responses and PWN population densities were assessed under high and low water availability conditions, at 25 and 30oC. Pine wilt disease symptoms were observed in all infected P. pinaster and P. radiata leading to a decrease in photosynthetic activity and water potential values, under the highest temperature and low water availability. Pinus pinea did not develop symptoms and no significant changes in physiological status were detected. Nematodes were found in higher numbers, in high temperatures and low water availability, in P. pinaster followed by P. radiata and P. pinea.
Abiotic Stress Tolerance in Plants: towards the improvement of global environment and food. Edited by K. Rai and T. Takabe. Dordrecht, The Netherlands: Springer (2006), pp. 267. £77.00. ISBN 10-1-4020-4388-0

This textbook aims to present a state of the art description of the physiological, biochemical and molecular status of the understanding of abiotic stress in plants and the application of biotechnology to crop and environmental improvement. The text, which is a collection of monograph papers produced by experts in the field, mainly from Asia, achieves some of its objectives but is left lacking in others. For salt stress and to a lesser extent osmotic stress and photo-induced stress there are several papers that cover the topic in good depth and with plenty of cross-references. For other stresses, notably temperature (both cold and heat), there is little in this textbook to advance the knowledge base. The book concentrates its examples on the application of stress gene modifications to crop improvement and forestry, but it is difficult to see where the references to the ‘improvement of global environment’ are in the text. Whilst the book is divided into themes (signal transduction, temperature stress, oxidative stress, phytoremediation, osmotic stresses, ion homeostasis, nutrition, structural responses and developments in biotechnology), there is little attempt to overview the individual papers together under each theme. Similarly the whole text lacks an overview to put the book into perspective. Given the comments above and the price of the text, it is clear that it is unlikely to become an undergraduate text, but could serve postgraduates, academics and researchers alike as a reference to the current state of the art of (some of ) the research in the field of abiotic stress of plants.
Structural shift of planktonic communities in seawater enclosures: from autotrophic to heterotrophic communities

An outdoor enclosure experiment was carried out near the southern coast of Korea in order to investigate the effect of enclosed environments on planktonic community structure. The experiment was conducted in 6 floating, 220-liter cylindrical enclosures maintained for short periods (17 days). Rapid decreases of inorganic nutrients (N. P, Si), and in the abundance of large diatoms, Coscinodiscus spp. , were observed after only one day from the start of the experiment. Decreases in chlorophyll a progressed through the experimental period, although the small diatoms, Chaetoceros spp. and Thalassiosira sp. , increased considerably during the initial days. The continuous supply of dissolved organic carbon from crashing stocks of planktonic organisms sustained rapid growth of heterotrophic bacteria. The bacterial increase was followed by increase of heterotrophic nanoflagellates and ciliated protozoa. Noctiluca scintillans flourished as a dominant zooplankter until the end of the experiment, feeding on phytoplankton during the first half of the observations and on the abundant heterotrophic microorganisms during the second half. The results suggested that the enclosed environment provoked a structural shift of the plankton community from autotrophy to heterotrophy and indicated additionally that the trophic status in plankton communities was reflected by an enclosed environment formed by artificial structures in the coastal zone.
IFN-γ-Inducible Protein 10 (CXCL10) Contributes to Airway Hyperreactivity and Airway Inflammation in a Mouse Model of Asthma1

Allergic asthma is an inflammatory disease of the airways characterized by eosinophilic inflammation and airway hyper-reactivity. Cytokines and chemokines specific for Th2-type inflammation predominate in asthma and in animal models of this disease. The role of Th1-type inflammatory mediators in asthma remains controversial. IFN-γ-inducible protein 10 (IP-10; CXCL10) is an IFN-γ-inducible chemokine that preferentially attracts activated Th1 lymphocytes. IP-10 is up-regulated in the airways of asthmatics, but its function in asthma is unclear. To investigate the role of IP-10 in allergic airway disease, we examined the expression of IP-10 in a murine model of asthma and the effects of overexpression and deletion of IP-10 in this model using IP-10-transgenic and IP-10-deficient mice. Our experiments demonstrate that IP-10 is up-regulated in the lung after allergen challenge. Mice that overexpress IP-10 in the lung exhibited significantly increased airway hyperreactivity, eosinophilia, IL-4 levels, and CD8+ lymphocyte recruitment compared with wild-type controls. In addition, there was an increase in the percentage of IL-4-secreting T lymphocytes in the lungs of IP-10-transgenic mice. In contrast, mice deficient in IP-10 demonstrated the opposite results compared with wild-type controls, with a significant reduction in these measures of Th2-type allergic airway inflammation. Our results demonstrate that IP-10, a Th1-type chemokine, is up-regulated in allergic pulmonary inflammation and that this contributes to the airway hyperreactivity and Th2-type inflammation seen in this model of asthma.
Detection of the Electrical Surface Charge Induced by Treatment of the Membrane Lipid Bilayer of Human Erythrocytes

The lipid bilayer of the membrane of human erythrocytes from which most sialic acid residues on the outer surface had been removed was digested by phospholipase from outside the medium or treated by the incorpora-tion of exogenous amphiphilic lipid, then it was electrophoresed. After treat-ments that caused the additional exposure of the dissociable polar head group of the amphiphilic lipid to the outer medium, the electrophoretic mobility of the treated cells increased as the pH of the suspending medium rose. This show-ed that there was an increase in the negative charges in the immediate vicinity of the lipid bilayer surface of the membrane. The possible effect of the dissocia-tion of exposed head groups in the lipids on the morphology of the membrane is discussed.
Molecular biotechnology : principles and applications ofrecombinant DNA

A unique, adaptable textbook for upper-level undergraduate and graduate courses emphasizing particular aspects of modern biotechnology. Allows instructors to easily tailor the content to courses focusing on the fundamentals of biotechnology as well as courses dedicated to medical, agricultural, environmental, or industrial applications. URI http://dspace.fue. edu.eg/xmlui/handle/123456789/4507 Description Includes bibliographical references and index. xvii, 1000 p. : Collections Books Summaries [1560] DSpace software copyright © 2002-2016 DuraSpace Contact Us | Send Feedback All rights reserved to Molecular biotechnology: principles and applications of recombinant DNA  
Does the stress‐gradient hypothesis hold water? Disentangling spatial and temporal variation in plant effects on soil moisture in dryland systems

Summary The nature of the relationship between water limitation and facilitation has been one of the most contentious debates surrounding the stress-gradient hypothesis (SGH), which states that plant-plant interactions shift from competition to facilitation with increasing environmental stress. We take a closer look at the potential role of soil moisture in mediating plant-plant interaction outcomes by assessing effects of climate and soil texture on plant modulation of soil moisture. Using an empirically-parameterized soil moisture model, we simulated soil moisture dynamics beneath shrubs and in un-vegetated coarse and fine soils for 1000 sites in the Western United States with <700 mm mean annual precipitation. This threshold reflects the transition from dryland (<600 mm precipitation) to mesic ecosystems. Positive effects of shrubs on shallow soil moisture (i.e. the difference between shrub and interspace soil moisture) decreased along the aridity gradient when long-term average conditions were considered, contrary to expectations based on the SGH. Negative effects of shrubs on deeper soil moisture also increased with aridity. However, when extreme years were considered, positive effects of shrub on soil moisture were greatest at intermediate points along the spatial aridity gradient, consistent with a hump-backed model of plant-plant interactions. When viewed through time within a site, shrub effects on shallow soil moisture were positively related to precipitation, with more complex relationships exhibited in deeper soils Taken together, the results of this simulation study suggest that plant effects on soil moisture are predictable based on relatively general relationships between precipitation inputs and differential evaporation and transpiration rates between plant and interspace microsites that are largely driven by temperature. In particular, this study highlights the importance of differentiating between temporal and spatial variation in weather and climate, respectively, in determining plant effects on available soil moisture. Rather than focusing on the somewhat coarse-scale predictions of the SGH, it may be more beneficial to explicitly incorporate plant effects on soil moisture into predictive models of plant-plant interaction outcomes in drylands.
Influence of aquatic plant-specific habitat on an assemblage of small neotropical floodplain fishes

Dibble ED, Pelicice FM. Influence of aquatic plant-specific habitat on an assemblage of small neotropical floodplain fishes. Ecology of Freshwater Fish 2010: 19: 381–389. © 2010 John Wiley & Sons A/S Abstract – This study investigated the effects of plant-specific habitat on the distribution of young and small adult fishes in lagoons of the Upper Parana River floodplain, Brazil. We compared fish catch per unit effort (CPUE) and species richness and used an indirect gradient analysis to investigate fish-plant relationships within three aquatic macrophytes beds (Cabomba furcata, Eichhornia azurea, Nymphaea amazonum), and explored microhabitat influence (indexed by eight variables related to physical structure and water quality) on the structure of fish assemblages. Rarefaction analysis was used to compare fish species richness among the vegetated habitats. We captured a total of 1599 fish constituting 23 species, 7 families and 3 orders. Fish CPUE and species richness increased relative to microhabitat structure innate to the macrophytes; higher CPUE and richness were observed in C. furcata beds, a submerged aquatic macrophyte with finely dissected leaves. On the contrary, N. amazonum, a species that provides low microhabitat complexity, harbored fewer individual fish and number of species. Reproduction dynamics, hydrology and the amount of available plant-generated habitat structure (surface effect) contributed to the disproportionally high number of individuals captured during the dry season. Our data suggest that the microhabitat physical structure (e.g., edge distance, stem density and patch size) provided by macrophyte beds in the lagoons of the Upper Parana River may play a more important role than physicochemistry (e.g., oxygen, temperature and pH) at mediating distribution patterns of small-sized fishes.
Inheritance of resistance to pathotypes QCC and MCC of Puccinia graminis f. sp. tritici in barley line Q21861 and temperature effects on the expression of resistance

Barley line Q21861 is one of several accessions that possess resistance to pathotypes QCC and MCC of Puccinia graminis f. sp. tritici. Crosses were made between Q21861 and several barley cultivars to study the inheritance of resistance to pathotypes QCC and MCC. Progeny evaluations indicated that resistance to pathotype QCC in Q21861 was conferred by a recessive gene that conditioned low infection types at low incubation temperatures (18-20 C). This gene was ineffective against pathotype QCC at incubation temperatures greater than 27 C. Resistance to pathotype MCC in Q21861 was controlled by two genes, one dominant and one recessive, that segregated independently. The dominant gene is allelic to Rpg 1, and the recessive gene identified is the same one conferring resistance to pathotype QCC [. ]
Fruit Quality of Organic Food: Experimental Evidence

The public opinion has a growing concern for food health issues and is interested in the consumption of food of improved quality, which is defined by several aspects, like the internal composition, appearance of the produce, technological/commercial issues, and social and environmental criteria. In this respect, conventional agriculture has resulted in a reduction of the internal quality, resulting from a decrease in the concentrations of nutrients and bioactive substances, as well as in some non sustainable practices that have a profound impact in the environment. Organic agriculture allows the production of food without the use of chemical synthesis products and with practices that are friendlier to the environment than conventional agriculture. In addition, organic food usually has a higher concentration of nutrients and bioactive substances. In order to guarantee that the organic foods have been produced according to adequate practices, in the EU only the foods produced according to specific regulations can be labeled as organic. Several experiments, of which we summarize the results show that organic food is healthier than conventionally produced food as, depending on the crops, organic fruits and vegetables have lower concentration of nitrates, higher concentration of relevant minerals (e.g., K, Ca, Fe), and more vitamin C and total phenolics. We have also found that organic meat has more protein and less fat than conventionally produced meat. Organic eggs also have a better quality than conventionally produced eggs, with more protein and oleic acid and also keep freshness for longer time. All these results show that organic food is healthier than conventional food for human health and at the same time is produced using methodologies that are friendlier for the environment.
LIGHT‐INDUCED RESPONSES OF OXYGEN PHOTOREDUCTION, REACTIVE OXYGEN SPECIES PRODUCTION AND SCAVENGING IN TWO DIATOM SPECIES 1

Diatoms are frequently exposed to high light (HL) levels, which can result in photoinhibition and damage to PSII. Many microalgae can photoreduce oxygen using the Mehler reaction driven by PSI, which could protect PSII. The ability of Nitzschia epithemioides Grunow and Thalassiosira pseudonana Hasle et Heimdal grown at 50 and 300 μmol photons · m−2 · s−1 to photoreduce oxygen was examined by mass spectrometric measurements of 18O2. Both species exhibited significant rates of oxygen photoreduction at saturating light levels, with cells grown in HL exhibiting higher rates. HL‐grown T. pseudonana had maximum rates of oxygen photoreduction five times greater than N. epithemoides, with 49% of electrons transported through PSII being used to reduce oxygen. Exposure to excess light (1,000 μmol photons · m−2 · s−1) produced similar decreases in the operating quantum efficiency of PSII (Fq′/Fm′) of low light (LL)‐ and HL‐grown N. epithemoides, whereas HL‐grown T. pseudonana exhibited much smaller decreases in Fq′/Fm′ than LL‐grown cells. HL‐grown T. pseudonana and N. epithemioides exhibited greater superoxide and hydrogen peroxide production, higher activities (in T. pseudonana) of superoxide dismutase (SOD) and ascorbate peroxidase (APX), and increased expression of three SOD‐ and one APX‐encoding genes after 60 min of excess light compared to LL‐grown cells. These responses provide a mechanism that contributes to the photoprotection of PSII against photodamage.
Keragaman genetik ikan tuna sirip kuning (Thunnus albacares) dari dua populasi di Laut Maluku, Indonesia

Abstract. Yellowfin tuna (Thunnus albacores) is a large, pelagic, and migratory species of tuna that inhabits Moluccas Sea in Indonesia, and most sea environment worldwide. However, high fishing activities tend to happen in the Indonesia region and catch product appear to be decreasing. A better understanding of yellowfin tuna genetic diversity is required to plan better conservation strategy of tuna. The study was conducted to infer the genetic diversity of yellowfin tuna (T. albacores) in the Moluccas Sea. A total of 41 tissue samples of yellowfin tuna were collected from two regions in the Moluccas Sea (North Moluccas and Ambon) during an expedition in February 2013. The results showed that genetic diversity and nucleotide diversity of yellowfin tuna from North Moluccas population was 0.984 and 0.021, respectively; while in Ambon population, the genetic and nucleotide diversities were 1.00 and 0.018, respectively. The high genetic diversity (0.990) and nucleotide diversity (0.020) between two populations were observed. Based on phylogenetic analysis, no genetic differentiation between the two populations in Moluccas Sea was revealed . Keywords : Population genetics ; Haplotype diversity ; Coral Triangle ; Phylogenetics ; Polymerase Chain Reactions (PCRs) Abstrak. Tuna sirip kuning ( Thunnus albacores ) adalah ikan komersial penting dan ditemukan di Laut Maluku, Indonesia. Tetapi, aktivitas penangkapan ikan tuna sirip kuning dapat menurunkan kualitas dan kuantitas stok ikan, sehingga perlu adanya pengkajian keragaman genetik ikan tuna sirip kuning. Pemahaman yang baik tentang keragaman genetika dibutuhkan untuk merencanakan strategi konservasi tuna yang lebih baik. Penelitian ini bertujuan untuk mengetahui keragaman genetik ikan tuna sirip kuning dari dua populasi di Laut Maluku. Sebanyak 41 sampel jaringan dari tuna sirip kuning dikumpulkan dari dua populasi di Laut Maluku (Maluku Utara dan Ambon) selama ekspedisi pada bulan Februari 2013. Hasil penelitian menunjukkan bahwa keragaman genetik populasi tuna sirip kuning pada perairan Maluku Utara dan Ambon masing-masing sebesar 0,984 dan 1,00 sedangkan nilai keragaman nukleotida masing-masing bernilai 0,021 dan 0,018. Nilai keragaman genetik dan keragaman nukloetida yang tinggi didaptkan antar kedua populasi masing-masing sebesar 0,990 dan 0,020. Berdasarkan analisis filogenetik, dua populasi di Laut Maluku ini memiliki kedekatan secara genetik. Kata kunci : Genetika populasi; Keragaman haplotipe; Segitiga Terumbu Karang; Filogenetika; Polymerase Chain Reaction (PCR)