Miracle-dz/UniFAR-FTUs huggingface dataset:
Top-soil translocation as a technique in the re-creation of species-rich meadows

Abstract In France, most civil engineering and excavation projects are at present accompanied by compensatory measures with the aim of preserving biodiversity. In order to avoid the destruction of a habitat of high conservation interest in NE France, harbouring two legally protected plant species, an experiment of soil translocation was conducted on an area of 1 ha. The donor site was an extensively managed mesophilic meadow and the receiving site was a neighbouring arable land. The vegetation of the translocated meadow was described 8 and 17 months after soil translocation, and compared (1) with vegetation resulting from more classical restoration techniques tested on the arable land (natural regeneration and seed mixture sowing) and (2) with the soil seed bank and vegetation previously present on the donor site. Results showed that the soil translocation technique permitted the development of many meadow species, including two legally protected species, and few ruderal species despite a large area of bare ground. This technique seems effective in terms of number and abundance of meadow species compared to natural regeneration and commercial seed sowing. In the case of the two classical methods, species richness was lower and only widespread species were present. Topsoil translocation provides a good compensatory method to avoid habitat and species destruction. However, the study should be continued, with the aim of assessing the longer term development and stabilization of the vegetation of the translocated meadow. Nomenclature: Lambinon et al. (1992).
Aggression and growth depression in juvenile Atlantic salmon: the consequences of individual variation in standard metabolic rate

In aquaculture, competitive interactions for food are a major source of growth rate variation, since they result in aggressive individuals acquiring a disproportionate amount of food and growing faster. Consequently, such competition increases the variance and skew of the size distribution of fish. In Atlantic salmon Salmo salar acquaculture, rearing is often initiated with juveniles of uniform size. However, the initial factors allowing fish to out-compete others of the same size is unclear. This study shows that individual differences in standard metabolic rate (SMR) may contribute to differences in aggression between juvenile Atlantic salmon. Fish were segregated into three holding tanks on the basis of differences in relative SMR aggression was highest in the tank containing high SMR fish, and lowest in a low SMR group. However, there were no significant differences in mean growth between the three treatments, although the skew of the size distribution was much less in the low SMR group than in the high SMR group. Therefore, although mean growth was not improved in the low SMR group by excluding high SMR fish, their growth subsequently showed less variability, possibly as a consequence of fewer despotic individuals gaining disproportionate access to food.
Deep Sequencing and Functional Analyses Identify a Role of Fusobacterium Species in Colorectal Tumorigenesis

The tumor microenvironment is a complex community consisting of neoplastic cells, surrounding stromal cells, a broad array of immune cells, and a microbiota. By sheer numbers, the microbiota has its greatest manifestation in colorectal cancer (CRC) because the colon contains up to 100 trillion bacteria, outnumbering human cells by a factor of 10 and encoding a gene-content that is 100-fold larger than that of the human genome. Indeed, previous studies using germ-free mice in a variety of genetic backgrounds have demonstrated that the microbiota can impact colorectal tumorigenesis. In addition, specific strains of enterotoxigenic bacteria have been shown to promote colitis-associated cancer in mice. Here, we explore the composition of the tissue-associated microbiota in human CRC and evaluate the role of tumor-enriched microbes in potentiating colorectal tumorigenesis in mice. Advances in DNA sequencing technology have fueled a renaissance in the microbiome field. Deep sequencing metagenomics enables rapid, culture-independent characterization of a microbial community. We present PathSeq, a highly scalable software tool that performs computational subtraction on high-throughput sequencing data to identify nonhuman nucleic acids. PathSeq makes it possible to analyze sequence datasets as large as human whole-genomes for the purpose of metagenomics and also to discover previously unsequenced microorganisms. We used PathSeq to characterize the composition of the microbiota in human CRC using whole-
On the So‐called Mantle Muscle Scars on Shells of the Margaritiferidae (Mollusca, Pelecypoda), with Observations on Mantle‐Shell Attachment in the Unionoida and Trigonioida

Mantle attachment scars on the inner surface of shells of the Margaritiferidae have been traditionally regarded as sites of mantle muscle attachment; however, the actual occurrence of muscle tissue at points of attachment has never been verified. Mantle attachment scars occur on shells of seven examined species of margaritiferids. Gross and histological investigation of the mantle of five species reveals that mantle attachment involves modification of mantle epithelial cells and associated connective fibers within the mantle. The connective fibers within the mantle do not appear to have contractile properties, but along with the attachment cells probably provide support for the mantle. Mantle‐shell attachment scars similar to those of margaritiferids also occur in shells of recent trigonids, thus strengthening arguments for a phylogentic link between the Unionoida and Trigonioida.
Bermudagrass putting green growth, color, and nutrient partitioning influenced by nitrogen and trinexapac-ethyl

Plant growth regulators (PGRs) improve turf color by inhibiting leaf growth and may reduce fertilization requirements of bermudagrass [Cynodon dactylon (L.) Pers. X C. transvaalensis Burtt-Davy] golf greens by reducing nutrients removed through clipping collection. To test this hypothesis, growth, color, and nutrient allocation of 'TifEagle' bermudagrass maintained at 3.2 mm were investigated in field experiments conducted in Clemson, SC, from April to August in 2003 and 2004. Ammonium nitrate was applied at 6,12,18, or 24 kg N ha -1 wk -1 with a PGR, trinexapac-ethyl {[4-(cydopropyl-[α]-hydroxymethylene)- 3,5-dioxo-cydohexane carboxylic add ethyl ester]) (TE), at 0 or 0.05 kg a.i. ha -1 3 wk -1 . Turf required 18 to 24 kg N ha -1 wk -1 from May to June and ≤12 kg N ha -1 wk -1 from July to August to maintain acceptable color (≥-7, 1-9 scale). Trinexapac-ethyl initially caused discoloration but bermudagrass recovered and had color enhanced 10 to 25% from nontreated. Trinexapac-ethyl reduced clippings 67% from nontreated while clippings, percentage of lateral regrowth, and aerification recovery increased with N rate. Bermudagrass treated with TE had similar root mass to nontreated but 5% greater stolon and rhizome mass, 18% higher chlorophyll concentration, up to 67% reduced lateral regrowth, and up to 38% reduced aerification recovery. Trinexapac-ethyl reduced leaf N, P, K, Mg, S, and Fe concentrations 10 to 25% and increased rhizome concentrations 8 to 36%. Nutrients recovered through clippings were reduced ≈70% from TE applications while TE-treated turf had increased N, P, K, Ca, Mg, S, Mn, and Fe retention in stolons and rhizomes. Overall, TE enhanced color while redudng nutrient translocation from rhizomes to leaves, thus increasing bermudagrass nutrient retention.
Screening of Marine Algal Extracts for Anti-settlement Activities against Microalgae and Macroalgae

The ban on the use of TBT-based antifouling paints for boats under 25 m in length has lead to a search for new non-toxic antifoulants. One of the most promising alternative technologies to heavy metal based antifouling paint is the development of antifouling coatings whose active ingredients are naturally occurring compounds from marine organisms. This is based on the principle that marine organisms also face the problem of the presence of epibionts on their own surfaces. In this study, the antifouling activity of a series of aqueous, ethanolic and dichloromethane extracts from thirty algae from the North East Atlantic coast was investigated. The extracts were tested in laboratory assays against species representative of two major groups of fouling organisms, viz . macroalgae and microalgae. The activity of several extracts was comparable to that of heavy metals and biocides (such as TBTO and CuSO 4 ) currently used in antifouling paints and their lack of toxicity with respect to the larvae of oysters and sea urchins suggests a potential for novel active ingredients.
Phenotypic Characterization of Pink Pigmented Facultative Methylotrophic Bacteria from Soil Exposed to Vehicular Soot

33 multi-carbon compounds which explain their ubiquitous distribution. They are involved in many biological interactions as some strains can enhance plant growth (Ivanova et al., 2001; Koenig et al., 2001; Lidstrom and Chistoserdova, 2002) and protect some plants against fungal pathogens (Madhaiyan et al., 2004). Green (2001) observed that PPFM bacteria can be isolated from vehicular exhaust and soot, as these bacteria are able to degrade aliphatic and aromatic hydrocarbons. Furthermore, Popp et al. (2006) revealed that PPFM bacteria may be part of the consortia of microorganisms involved in the degradation of mineral oil in soil. These characteristic features give PPFM bacteria as possible pollution indicators. Considering the potential of this group of microorganisms to be utilized in bioremediation and biotechnology, study on this group is needed (Lee, 2007). Hence, this study was conducted to answer the dearth of information regarding local PPFM bacteria. The objective of this study was to isolate and characterize PPFM bacterial isolates from soil samples exposed to vehicular soot. Specifically, it was aimed at describing PPFM bacteria from soil collected along the island pavement of Taft Avenue fronting DLSU-Manila campus.
The influence of wildfire boundary delineation on our understanding of burning patterns in the Alberta foothills11This article is one of a selection of papers from the 7th International Conference on Disturbance Dynamics in Boreal Forests.

Under the auspices of ecosystem-based management, historical disturbance patterns are promoted as a means of providing benchmarks for ecosystem sustainability. The associated research in support of this strategy in the boreal forest has substantially increased our understanding of frequencies, sizes, shapes, and severities of wildfires. However, despite the fact that different spatial definitions of wildfires exist in both research and practice, we have not considered the significance or impact of those differences on observed patterns. This study addresses this gap by conducting a sensitivity analysis on the influence of 11 spatial definitions of a wildfire on six pattern metrics for 24 wildfires in the Foothills Natural Region of Alberta. The results suggest that all pattern metrics were sensitive to changes to wildfire delineation, but in particular the total amount of remnants, wildfire shape, and the relationship between pre-burn fuel types and the probability of burning. The results also suggest tha.
The use of the Biological Diatom Index (BDI) for the assessment of water quality in the Pilica River, Poland

The main aim of this study was to assess the usefulness of the Biological Diatom Index (BDI) (Lenoir & Coste 1996) for the estimation of water quality in the central section of the Pilica River, located in central Poland in Łódź province. The BDI has never been used before to monitor Polish surface waters. An analysis of the correlations between the values of the BDI and selected physico-chemical parameters was performed, as was an assessment of water quality using the BDI. On the basis of value ranges proposed by Descy and Ector (1996), a good ecological status in the Pilica River was obtained, but this did not correspond with the results achieved from the physico-chemical analysis. This study proposes new value ranges for the BDI. With these new values, the ecological state of the Pilica River changed from good to moderate, which corresponded with the physico-chemical analysis of the water. The new, proposed value ranges for the BDI assess more precisely the quality of water in lowland Polish rivers.
Towards redefining the regional division of Poland for faunistic studies

Towards redefining the regional division of Poland for faunistic studies For summaries and inventories of fauna of Poland, especially insects, research professionals and amateurs apply a division of the country into regions that became a functional standard in the 1960s when Catalogus Faunae Poloniae was published. Despite its long tradition in the local entomological literature, this approach should be treated as inadequate and provisional. The present article gives an overview of the roots of the traditional division, discusses its limitations and proposes a new, more precise and informative division, together with a description of the requirements and tools needed for the transition. Based on the "Physico-Geographical Regionalization of Poland" by Kondracki, this proposal redefines the borders of most of the KFP regions and presents a solution compatible with the widely used regionalization system, approved by geographers. In consequence of this direct connection with physical geography, some of the KFP regions have been removed or rearranged and new ones formed. The new system is not meant to be treated as a zoogeographical regionalization; rather, it aims to replace the unclearly defined objects of the old division, facilitating regional comparisons of fauna. Used with appropriate caution, it may also be helpful in analyses involving elements of biogeographical inference that were not justified in the old system.
Native IgG2ab is barely antigenic to major histocompatibility complexclass II‐restricted T cells owing to inefficient internalization by professionalantigen‐presenting cells

Peptide epitopes derived from immunoglobulin variable regions represent tumour‐specific antigens on B‐cell neoplasms and can be recognized by syngeneic, major histocompatibility complex (MHC) class II‐restricted T cells. Immunoglobulin peptide/MHC class II complexes may also be involved in autoimmunity and CD4+ T‐cell‐mediated B‐cell regulation. Thus, the IgG2ab H‐chain allopeptide γ2ab 435–451 presented on I‐Ad mimics the epitope implicated in herpes simplex virus‐induced autoimmune stromal keratitis and is the target of T helper 1 (Th1) clones that suppress IgG2ab production in vivo. We here report that spleen and thymus cells constitutively present the autologous γ2ab epitope to a γ2ab 435–451/I‐Ad reactive T‐cell hybridoma as a function of the animal housing conditions (specific pathogen‐free or not) and the serum levels of IgG2ab. Constitutive presentation in the spleen was predominantly performed by dendritic cells. Whereas spleen cells poorly presented native IgG2ab to a γ2ab 435–451/I‐Ad reactive T‐cell hybridoma, IgG2ab in the form of immune complexes were presented > 200‐fold more efficiently owing to internalization via low‐affinity FcγR on macrophages. The antigenicity could also be improved by homotypic aggregation and by targeting IgG2ab to complement receptors on the A20 B‐cell lymphoma. Mice without detectable IgG2ab‐containing immune complexes typically exhibited minimal constitutive presentation. Nevertheless, native IgG2ab can sensitize antigen‐presenting cells in vivo, as mice that were devoid of immune complexes and carried an IgG2ab‐producing tumour did present constitutively, even at physiological IgG2ab serum levels. Whereas the amounts of IgG released from most B‐cell lymphomas may be too low to allow spontaneous priming of tumour‐specific MHC class II‐restricted T cells, administration of tumour immunoglobulin in aggregated form might improve the efficacy of idiotype vaccination.
Synthesis of fructooligosaccharides using extracellular enzymes from Rhodotorula sp.

ABSTRACT Considering the great biodiversity of the still unexploited Brazilian environment, efforts were made to select microorganisms capable of producing fructooligosaccharide (FOS). Amongst 495 interesting isolated yeast strains, one in particular, identified as a Rhodotorula red yeast strain isolated from flowers from the Brazilian tropical biomass, was able to produce an effective thermostable extracellular enzyme, with both sucrose hydrolytic and transfructosylating activities. The best operational conditions for this enzyme were determined to be in a pH range from 3.8 to 4.3 and at temperatures of around 65C. Under these conditions, the transfructosylating activity reached its maximum, being more than 10 times higher than the hydrolytic activity. The synthesis of fructooligosaccharides from sucrose resulted in total conversion of the substrate into FOS (48%), glucose (31.3%) and fructose (20.7%). In addition, it was shown that the synthesized FOS had a prebiotic effect, promoting the growth of probiotic bacteria. PRACTICAL APPLICATIONS The search for new enzymes for oligosaccharide production, using either microbial screening or molecular engineering, became necessary as a result of the increasing number of applications of these carbohydrates in the cosmetic, agrochemical, pharmaceutical and food industries. In this work, the Rhodotorula sp. isolated from Brazilian biomes was shown to be capable of producing an extracellular fructosyltransferase enzyme with good prospects for further studies aiming an industrial application, because it can convert sucrose into fructooligosaccharide (FOS), giving high yields (50%). It is worthwhile to emphasize the high optimum temperature and low pH value of the enzyme operation, which make it possible to work in a nonsterile environment for FOS production. It is also remarkable the ability of this yeast type (Rhodotorula), of growing on diverse alternative media and agricultural by-products (molasses, corn steel liquor, grape must, whey ultrafiltrate).
Inhibition of expression of tomato-ripening genes at high temperature

Abstract. Ripening tomato fruits incubated at 35°C fail to achieve normal pigmentation, soften little and show a marked decline in ethylene evolution. Labelling studies in vivo indicate that protein synthesis continues throughout incubation at 35°C although the spectrum of labelled proteins is different to that observed at 25°C. Translation of mRNAs in vitro shows traces of several ‘heat-shock’ mRNAs at 35°C and the loss of several others normally found in fruit ripened at 25°C. Using ripening-related cDNA clones as hybridization probes the expression of 12 ripening-related genes was followed during incubation at 25°C and 35°C. In general, there was a marked decline in the amounts of these mRNAs following incubation of ripening fruit at 35°C. In particular, mRNA homologous to pTOM 6, a cDNA clone coding for polygalacturonase, a major cell wall degrading enzyme, showed a rapid decline following incubation at 35°C and after 72-h at elevated temperature was undetectable. There was no recovery of expression during 120 h at 35°C and the application of exogenous ethylene did not overcome the inhibition of ripening or lead to the renewed accumulation of polygalacturonase mRNA. It is proposed that the failure to soften normally at elevated temperature is due, in part, to the suppression of polygalacturonase mRNA and that the inhibition of other facets of ripening at 35°C is due to the inhibition or reduced expression of other, as yet unidentified, ripening-related genes.
Validation of Molecular Markers for Pre-harvest Sprouting Resistance in Bread Wheat

Pre-harvest sprouting (PHS) in bread wheat (Triticum aestivum L.) is one of the major abiotic constraints influencing production of high quality grain. Selection for pre-harvest sprouting (PHS) resistance in bread wheat (Triticum aestivum L.) in early generations is difficult because it is expressed as a quantitatively inherited trait and subject to environmental effects. The objectives of this study were to validate a major quantitative trait locus (QTL) for PHS resistance on chromosome 4A in bread wheat and to isolate near-isogenic lines for this QTL using marker-assisted selection. A total of 60 Canadian wheat cultivars and experimental lines were screened with three SSR markers in a QTL region for PHS resistance. The SSR markers DuPw004, barc170 and wmc650 explained 67%, 75% and 60% of total variation in germination (%), respectively, among different wheat genotypes. Marker assisted back crossing with DuPw004 reduced the population size in BC1 F1 and BC2 F1 generation by 41% and 59%, respectively. A survey of pedigrees of different genotypes revealed that the parental line RL4137 is a major source of increased PHS resistance in a number of western Canadian wheat cultivars. Microsatellite markers (DuPw004, barc170 and wmc650) will be useful for plant breeders to pyramid QTL from different PHS resistance sources.
14C translocation in orange plants

Translocation patterns were studied by supplying 14CO2 to selected source leaves under glasshouse conditions and preparing whole plant autoradiographs. The chemical nature of 14CO2 fixation products was also examined. Within the actively growing shoots all currently expanding leaves showed strong import of 14C assimilates but no export. Fully expanded leaves, borne either on a fruitful growth cycle or on a previous growth cycle, exported assimilates principally to nearby fruits. Sharp differences existed between adjacent fruits during their early development with respect to the level of 14C incorporation. Mature leaves some distance from sites of current growth activity exported principally to the root system. Old leaves between the source leaf and roots failed to import. 14C-labelled sugars comprised the bulk of radioactive assimilates in leaf, stem, and fruit 24 hr after the commencement of feeding. In the roots, amino acids were the most heavily labelled fraction. 14C photosynthate appeared to be translocated as sucrose and it was this metabolite which occurred within the outer peel of the fruit.
Origin and spread of the cat, Felis catus, on mainland Australia, with a discussion of the magnitude of its early impact on native fauna

A comprehensive search of historical sources found no evidence that the cat, Felis catus, was present on mainland Australia prior to settlement by Europeans. Nor were records of cats found in journals of expeditions of exploration beyond settled areas, undertaken in the period 1788–1883. Cats did not occupy Australia from the earliest point of entry (Sydney, 1788), but instead diffused and were spread from multiple coastal introductions in the period 1824–86. By 1890 nearly all of the continent had been colonised. This new chronology for the feline colonisation of Australia necessitates a re-appraisal of the early impact of the cat on native mammal and bird species. The evidence for early impacts of cats causing major and widespread declines in native fauna is considered tenuous and unconvincing.