Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis-Insect Interactions

1.1 Plant-Insect Interactions Insects are the most species-rich class of eukaryotes on earth and roughly half of all insect species are herbivores. Besides being species-rich, insects are also quite abundant, making up more biomass than any other animal class. It is therefore likely that during their life, most plants will encounter herbivorous insects chewing on their tissue, sucking up their cell content and/or passively feeding on their vascular sap. Not surprisingly, plants are not defenseless against these herbivores. Plants have evolved a wide range of defense mechanisms which can be constitutively present and/or induced by herbivory. Many of these defense mechanisms have a direct effect on the herbivore by negatively affecting its physiology (e.g. through toxins or anti-nutritional compounds) or by interfering with its behavior (e.g. through repelling or deterring compounds) (Schoonhoven et al., 1998). Besides direct defense mechanisms, plants can make use of ‘bodyguards’ to protect themselves against herbivorous insects. Often, these bodyguards are insects themselves: predators or parasitoids preying or parasitizing on the herbivores. Plants can reward these bodyguards by providing them shelter, additional food and/or information (Van Poecke and Dicke, 2004). But plants do not only rely on insects as bodyguards. For many plant species insects form an essential part of plant reproduction by transporting their pollen (Pichersky and Gershenzon, 2002). Clearly, insects play an important part in the ecology of plants, whether considered from a natural, agricultural or an evolutionary perspective. In the last decade, Arabidopsis thaliana has been introduced to studies on plant-insect interactions, especially with the aim to get a better understanding of the plant molecular mechanisms underlying this interaction. As the number of publications on Arabidopsis - insect interactions is steadily increasing, this review aims to summarize their most important findings.
Crossing barriers: The new dimension of 2D cell migration assays

In our body cells move in three dimensions, embedded in an extracellular matrix that varies in composition, density and stiffness, and this movement is fundamental to life. Next to 3D cell migration assays, representing these physiological circumstances, still we need 2D migrations assays to perform detailed studies on the contribution of matrix‐components and (extra)cellular proteins to cell movements. Next to the debate on differences between 3D and 2D migration, there also are many new perspectives on the use and development of novel or modified 2D cell migration assays. Of special significance is the introduction of so‐called barrier migration assays, methods that avoid cell and matrix damage, as complementation or replacement of scratch/wound healing assays. Here, we discuss the possibilities and limitations of different 2D barrier migration assays. J. Cell. Physiol. 226: 288–290, 2010. © 2010 Wiley‐Liss, Inc.
Sulfate‐reducing bacteria in littoral sediment of Lake Constance

Abstract The viable population of sulfate-reducing bacteria (SRB) in littoral sediments of Lake Constance was investigated using enrichment and enumeration techniques. Enrichment studies established that most types of SRB grew best in media with low salt concentrations (max. 0.4 g Cl − /1), consistent with the low salinity of the freshwater habitat. Enumerations were based on an adequate medium with the following electron donors: H 2 , lactate, acetate, propionate, butyrate, caprylate, succinate, benzoate, or S 2 O 3 2− for thiosulfate-disproportionating bacteria. Cultures were incubated for 6 weeks to obtain maximum counts. A maximum cell density of 6.3 × 10 6 cells per ml sediment was estimated, which is the highest number of SRB ever reported for anoxic sediments. A comparison with measured sulfate reduction rates showed that the enumeration techniques were about 10–100-fold more efficient than those previously used. The population of SRB had a characteristic structure consisting of 87.7% H 2 -utilizing SRB (physiologically resembling the classical Desulfovibrio species); 12.0% propionate utilizers (tentatively identified as Desulfobulbus species); 0.3% long chain fatty acid-oxidizing Desulfovibrio sapovorans species. Acetate-utilizing SRB ( Desulfotomaculum acetoxidans ) constituted ⩽ 0.05% of the total estimated population. Moreover, the latter species was only present as inactive spores. Benzoate-degrading SRB were not detected.
Comparative embryology of Bambusa tulda Roxb. and Thyrsostachys siamensis Gamble (Poaceae: Bambuseae)

Abstract Bambusa tulda and Thyrsostachys siamensis resemble each other in having an obovate ovary which is hairy and thickened along the apex, a pseudo-crassinucellate ovule with a wide region of attachment, poorly-developed and ephemeral outer integument, an inner integument which fails to grow beyond the nucellus, «Polygonum» type of embryo sac ontogeny, parallel orientation of embryo sac to the long axis of the ovule, multiple antipodals which retain apical position in the embryo sac even during post-fertilization phase of development, an ephemeral nucellus, relatively small «bambusoid» embryos, and many-layered and apically thickened pericarp. However, they differ from each other in their gynoecial structure, the extent of the development of the outer integument, organization of megaspore tetrads and development-stage-related behaviour of the inner integument in the fertilized ovules. These taxa also differ from other members of the subfamily Bambusoideae in the structure of the mature ovule, endosperm and pericarp.
The specificity of the interaction with intestinal bacterial fermentation by prebiotics determines their physiological efficacy

The concept of prebiotic food ingredients is an important recent development in nutrition. The concept has attracted a great deal of attention, and many food ingredients (mainly dietary carbohydrates) have been claimed to be ‘prebiotic’. It is emphasised that in order to be called prebiotic, a compound should be: (1) non-digestible; (2) fermentable; (3) fermentable in a selective way. These properties should be demonstrated in human volunteers in at least two independent dietary intervention trials. On the basis of published and unpublished results, it is shown in the present paper that the way in which a prebiotic influences intestinal fermentation is the key to its physiological properties. This statement is illustrated mainly by considering an established group of prebiotics, the β(2–1) fructans. These linear molecules show a strong discontinuity in physicochemical properties as the chains become longer. The β(2–1) fructans with a chain length of up to ten monomer units are very soluble and are particularly ‘bifidogenic’. Longer chains (ten to sixty-five monomer units) are poorly soluble in water, they have less pronounced bifidogenic properties, and they are fermented more slowly. It was observed that a combination of short-chain and long-chain fructans (Synergy1) is physiologically (for example, increasing mineral absorption, suppressing carcinogenesis, modulating lipid metabolism, etc) more active than the individual fractions. A possible mechanism is described in the present review. From an in-depth overview of the literature it is confirmed that for prebiotic action, the ‘selectivity principle’ for intestinal fermentation is determinative for the type and for the efficiency of physiological activity. It is confirmed that prebiotics act through their influence on intestinal fermentation.
EFFECT OF ZONAL TRANSPORT AND METABOLISM ON HEPATIC REMOVAL: ENALAPRIL HYDROLYSIS IN ZONAL, ISOLATED RAT HEPATOCYTES IN VITRO AND CORRELATION WITH PERFUSION DATA

Previous studies showed that the transport of enalapril occurred homogeneously among zonal rat hepatocytes. However, the metabolism of hepatic arterially delivered enalapril, swept into the rat liver by the portal or hepatic venous flow (HAPV and HAHV perfusion), was more abundant in the perivenous (PV) than the periportal (PP) region. Hence, metabolic activities toward enalapril in 9000 g supernatant (S9) fractions of enriched rat PP and PV hepatocytes were examined. Although Michaelis-Menten kinetics were invariably observed, the metabolic activity toward enalapril (intrinsic clearance or V max met / K m met of 0.008 ml/min/mg of S9 protein, V max met of 21 ± 6 nmol/min/mg of S9 protein, and K m met of 2612 ± 236 μM) was greater in PV than in PP ( V max met of 5.5 ± 3.1 nmol/min/mg of S9 protein and K m met of 1049 ± 335 μM; intrinsic clearance of 0.0052 ml/min/mg of S9 protein) hepatocytes. These metabolic intrinsic clearances were much lower than the sinusoidal influx clearances observed from previous transport studies, revealing metabolism as the rate-limiting step. Substitution of the scaled-up transport and metabolic intrinsic clearances into the “well stirred”, “parallel-tube”, and “dispersion” models predicted higher steady-state extraction ratios for HAHV perfusion. By contrast, integration of the scaled-up in vitro parameters on zonal metabolism and homogeneous transport into a “zonal-compartment” model of three zonal subcompartments (1, 2, and 3) provided an improved description of the extraction ratios during HAPV and HAHV. Zonal factors are important for the scale-up of data in vitro to the whole organ.
Circularity and Independence in Phylogenetic Tests of Ecological Hypotheses

It has been asserted that in order to avoid circularity in phylogenetic tests of ecological hypotheses, one must exclude from the cladistic analysis any characters that might be correlated with that hypothesis. The argument assumes that selective correlation leads to lack of independence among characters and may thus bias the analysis. This argument conflates the idea of independence between the ecological hypothesis and the phylogeny with independence among characters used to construct the tree. We argue that adaptation or selection does not necessarily result in the non‐independence of characters, and that characters for a cladistic analysis should be evaluated as homology statements rather than functional ones. As with any partitioning of data, character exclusion may lead to weaker phylogenetic hypotheses, and the practice of mapping characters onto a tree, rather than including them in the analysis, should be avoided. Examples from pollination biology are used to illustrate some of the theoretical and practical problems inherent in character exclusion.
Determination of mitochondrial fragmentation and autophagosome formation in C2C12 skeletal muscle cells

Durum wheat (Triticum durum) is primarily used for the production of high-quality pasta products because of its certain superior characteristics. Wheat landraces are locally adapted diverse populations evolved through natural selection and are invaluable genetic resources for breeding programs. The search for new genetic resources all around the world has been underway to develop high-quality durum wheats. The purpose of this study was therefore to determine the pasta quality-associated characteristics of 12 durum wheat landraces (Bagacak, Beyaziye, Iskenderiye, Sorgul, Karakilcik, Beyaz Bugday, Ag Bugdayi, Bintepe, Havrani, Calibasan, Haci Halil, and Akcakale) compared to 2 well-established high-quality durum wheat cultivars, Kyle and Zenit. Protein content and quality, pigment content, activities of oxidative enzymes (lipoxygenase, polyphenol oxidase, and peroxidase), kernel size, and endosperm vitreousness were measured as the major quality parameters. The landraces had significant differences (P < 0.05) in their quality characteristics. Of the landraces, Akcakale, Havrani, and Calibasan were found to be quite promising for the processing of so-called al dente cooking pasta products, as judged by their elevated protein quantity and gluten quality. With respect to pigment content and oxidative enzymes that are central to the bright yellow color of pasta products, however, the landraces Havrani, Haci Halil, and Sorgul were found to have great potential. In brief, several landraces have potential for high-quality pasta processing, while a few others can be used for breeding purposes.
Estimating the effect of competition on trait evolution using maximum likelihood inference

Many classical ecological and evolutionary theoretical frameworks posit that competition between species is an important selective force. For example, in adaptive radiations, resource competition between evolving lineages plays a role in driving phenotypic diversification and exploration of novel ecological space. Nevertheless, current models of trait evolution fit to phylogenies and comparative datasets are not designed to incorporate the effect of competition. The most advanced models in this direction are diversity-dependent models where evolutionary rates depend on lineage diversity. However, these models still treat changes in traits in one branch as independent of the value of traits on other branches, thus ignoring the effect of species similarity on trait evolution. Here, we consider a model where the evolutionary dynamics of traits involved in interspecific interactions are influenced by species similarity in trait values and where we can specify which lineages are in sympatry. We develop a maximum-likelihood based approach to fit this model to combined phylogenetic and phenotypic data. Using simulations, we demonstrate that the approach accurately estimates the simulated parameter values across a broad range of parameter space. Additionally, we develop tools for specifying the biogeographic context in which trait evolution occurs. In order to compare models, we also apply these biogeographic methods to specify which lineages interact sympatrically for two diversity-dependent models. Finally, we fit these various models to morphological data from a classical adaptive radiation (Greater Antillean Anolis lizards). We show that models that account for competition and geography perform better than other models. The matching competition model is an important new tool for studying the influence of interspecific interactions, in particular competition, on phenotypic evolution. More generally, it constitutes a step toward a better integration of interspecific interactions in many ecological and evolutionary processes.
Effect of temperature on in vitro adhesion of potential fish probiotics

As fish are poikilothermic animals, i.e. the temperature of their body is dependent on the external environment, we aimed to investigate the effect of temperature on the in vitro adhesive ability of potential fish probiotics. The tested strains were Bifidobacterium animalis Bb12, Lactobacillus rhamnosus GG, L. rhamnosus LC 705, L. rhamnosus LCR 1/83 and Enterococcus faecium M74. The in vitro adhesive ability of the five strains to two types of rainbow trout mucus (skin and intestinal mucus) was determined at temperatures ranging from 4°C to 25°C. Three of the tested strains, B. animalis Bb12, L. rhamnosus GG and L. rhamnosus LCR 1/83, showed high adhesion to both types of mucus at all temperatures studied (19–30% and 11–29% of the added bacteria to skin and intestinal mucus, respectively). The adhesive abilities of the remaining strains were low in comparison with the above-mentioned group at all temperatures tested (3–10% and 2–19% to skin and intestinal mucus, respectively). In the case of skin mucus, three strains showed significant differences in adhesion depending on the incubation temperature, while two strains exhibited significant temperature-related differences in adhesion to intestinal mucus. The quartic polynomial fit was the best model to describe the changes in the adhesive ability related to the temperature changes. In conclusion, in order to optimize probiotic functionality in aquaculture, the dose may have to be adjusted with regard to the water temperature.
Observational study on hospital building heritage and microbiological air quality in the orthopedic operating theater: the IM.PA.C.T. Project.

BACKGROUND The study investigated 35 orthopedic OTs [17 with mixed flow (M-OTs), 18 with turbulent flow (T-OTs)]. METHODS The OTs were divided into two categories based on recurring architectural and construction solutions, collected by a survey form: type-A (recently built or renovated rooms), and type-B (other OTs). Assessment of microbial air contamination (colony forming units (cfu)/m3 obtained by active sampling via Surface Air System) was then performed. RESULTS In 97% of the OTs, a Total Viable Count (TVC) was within the limits recommended by ISPESL 2009; all A-type OTs, and 94% of B-type passed. The TVC of type-A OTs [median 15 cfu/m3, range 3-158] was lower than that of type-B OTs [median 28 cfu/m3, range 6-206], although the difference was not significant. The number of people in type-A [mean 8.6, range 6-11] was lower than in type-B [mean 9.6, range 7-13] OTs, and when adjusted to the volume of the OT (person/m3), showed a significant correlation with TVC (ρ = 0.383, p <0.05). CONCLUSIONS In conclusion, the structural factors examined do not appear to significantly affect the microbiological air quality at the specific sampling point. However, further investigations are required to identify the factors that have the greatest effect on TVC.
Inhibiting PGGT1B Disrupts Function of RHOA, Resulting in T-cell Expression of Integrin α4β7 and Development of Colitis in Mice.

BACKGROUND AND AIMS It is not clear how regulation of T-cell function is altered during development of inflammatory bowel diseases (IBD). We studied the mechanisms by which geranylgeranyltransferase-mediated prenylation controls T-cell localization to the intestine and chronic inflammation. METHODS We generated mice with T-cell specific disruption of the geranylgeranyltransferase type I, beta subunit gene (Pggt1b), called Pggt1bΔCD4 mice, or the ras homolog family member A gene (Rhoa), called RhoaΔCD4 mice. We also studied mice with knockout of CDC42 or RAC1 and wild-type mice (controls). Intestinal tissues were analyzed by histology, multiphoton and confocal microscopy, and real-time PCR. Activation of CDC42, RAC1, and RHOA were measured with G-LISA, cell fractionation, and immunoblots. T cells and lamina propria mononuclear cells from mice were analyzed by flow cytometry or transferred to Rag1-/- mice. Mice were given injections of antibodies against integrin alpha4beta7 or gavaged with the RORC antagonist GSK805. We obtained peripheral blood and intestinal tissue samples from patients with and without IBD and analyzed them by flow cytometry. RESULTS Pggt1bΔCD4 mice developed spontaneous colitis, characterized by thickening of the intestinal wall, edema, fibrosis, accumulation of T cells in the colon, and increased expression of inflammatory cytokines. Compared with control CD4+ T cells, PGGT1B-deficient CD4+ T cells expressed significantly higher levels of integrin alpha4beta7, which regulates their localization to the intestine. Inflammation induced by transfer of PGGT1B-deficient CD4+ T cells to Rag1-/- mice was blocked by injection of an antibody against integrin alpha4beta7. Lamina propria of Pggt1bΔCD4 mice had increased numbers of CD4+ T cells that expressed RORC and higher levels of cytokines produced by T-helper 17 cells (GM-CSF, IL17A, IL17F, IL22, and TNF). The RORC inverse agonist GSK805, but not antibodies against IL17A or IL17F, prevented colitis in Pggt1bΔCD4 mice. PGGT1B-deficient CD4+ T cells had decreased activation of RHOA. RhoaΔCD4 mice had a similar phenotype to Pggt1bΔCD4 mice, including development of colitis, increased numbers of CD4+ T cells in colon, increased expression of integrin alpha4beta7 by CD4+ T cells, and increased levels of IL17A and other inflammatory cytokines in lamina propria. T cells isolated from intestinal tissues from patients with IBD had significantly lower levels of GGT1B than tissues from individuals without IBD. CONCLUSION Loss of PGGT1B from T cells in mice impairs RHOA function, increasing CD4+ T-cell expression of integrin alpha4beta7 and localization to colon, resulting in increased expression of inflammatory cytokines and colitis. T cells isolated from gut tissues from patients with IBD have lower levels of PGGT1B than tissues from patients without IBD.
Cloning and identification of the Frigocyclinone biosynthetic gene cluster from Streptomyces griseus strain NTK 97

ABSTRACT Frigocyclinone is a novel antibiotic with antibacterial and anticancer activities. It is produced by both Antarctica-derived Streptomyces griseus NTK 97 and marine sponge-associated Streptomyces sp. M7_15. Here, we first report the biosynthetic gene cluster of frigocyclinone in the S. griseus NTK 97. The frigocyclinone gene cluster spans a DNA region of 33-kb which consists of 30 open reading frames (ORFs), encoding minimal type II polyketide synthase, aromatase and cyclase, redox tailoring enzymes, sugar biosynthesis-related enzymes, C-glycosyltransferase, a resistance protein, and three regulatory proteins. Based on the bioinformatic analysis, a biosynthetic pathway for frigocyclinone was proposed. Second, to verify the cloned gene cluster, CRISPR-Cpf1 mediated gene disruption was conducted. Mutant with the disruption of beta-ketoacyl synthase encoding gene frig20 fully loses the ability of producing frigocyclinone, while inactivating the glycosyltransferase gene frig1 leads to the production of key intermediate of anti-MRSA anthraquinone tetrangomycin. Graphical Abstract Cloning and identification of the frigocylinone biosynthetic gene cluster provide a deep insight into the biosynthetic pathway and will contribute to development of novel antibiotics via genetic engineering.
Evaluation of vaccination against infectious laryngotracheitis (ILT) with recombinant herpesvirus of turkey (rHVT-LT) and chicken embryo origin (CEO) vaccines applied alone or in combination

ABSTRACT The chicken embryo origin (CEO) infectious laryngotracheitis (ILT) live attenuated vaccines, although capable of protecting against disease and reducing challenge virus replication, can regain virulence. Recombinant ILT vaccines do not regain virulence but are partially successful at blocking challenge virus replication. The objective of this study was to evaluate the effect of rHVT-LT vaccination on CEO replication and how this vaccination strategy enhances protection and limits challenge virus transmission to naïve contact chickens. The rHVT-LT vaccine was administered at 1 day of age subcutaneously and the CEO vaccine was administered at 6 weeks of age via eye-drop or drinking water. CEO vaccine replication post vaccination, challenge virus replication and transmission post challenge were evaluated. After vaccination, only the group that received the CEO via eye-drop developed transient conjunctivitis. A significant decrease in CEO replication was detected for the rHVT-LT + CEO groups as compared to groups that received CEO alone. After challenge, reduction in clinical signs and challenge virus replication were observed in all vaccinated groups. However, among the vaccinated groups, the rHVT-LT group presented higher clinical signs and challenge virus replication. Transmission of the challenge virus to naïve contact chickens was only observed in the rHVT-LT vaccinated group of chickens. Overall, this study found that priming with rHVT-LT reduced CEO virus replication and the addition of a CEO vaccination provided a more robust protection than rHVT alone. Therefore, rHVT-LT + CEO vaccination strategy constitutes an alternative approach to gain better control of the disease.