Miracle-dz/UniFAR-FTUs huggingface dataset:
Clostridial Gas Gangrene: Evidence That α and θ Toxins Differentially Modulate the Immune Response and Induce Acute Tissue Necrosis

: The rapid extension of necrosis and an absence of polymorphonuclear leukocytes (PMNL) at the site of infection are two hallmarks of Clostridium perfringens gas gangrene. While both alpha and theta toxins profoundly affect PMNL function and viability in vitro, their roles in muscle destruction and impairment of the inflammatory response in vivo have not been investigated. Comparative histopathologic examinations were performed on animals infected with either wild-type C. perfringens, or isogenic, toxin-deficient mutants of C. perfringens. Tissue destruction was modest in animals infected with the alpha toxin-deficient mutant; destruction was more pronounced in tissues infected with the theta toxin-deficient mutant or the wild-type strain. alpha and theta toxins also displayed differing abilities to modulate the inflammatory response. Histopathologic studies in which recombinant toxins were injected together with killed, washed C. perfringens further substantiated these tissue-destructive and differential antiinflammatory effects.
Susceptibility of Barleys to Bipolaris sorokiniana Seedling Blight Determined by Disease Scoring and Electrolyte Leakage

Spring (14) and winter (8) barley cultivars were examined for seedling susceptibility (root and coleoptile) to Bipolaris sorokiniana infection under a controlled environment. High susceptibility of all cultivars to root rot was observed, both in winter and spring genotypes, Coleoptile infection on average, was about three times lower than root disease score. Significant membrane injury up to 35% of maximum electrolyte leakage was observed on the 7th day after inoculation. In only 3 cultivars were the membrane injuries low-on the level of 3–6% and related with low coleoptile infection. Resistance of the barley cultivars to B. sorokiniana was not related with their resistance to Fusarium cutmorum Zusammenfassung Untersucht wurden 14 Sommer- und Wintergerstensorten auf ihre Anfalligkeit gegen Bipolaris sorokiniana als Samlinge unter kontrollierten Bedingungen. Eine hohe Anfalligkeit der Wurzeln wurde in allen Sorten beobachtet. Der Befall der Koleoptilen war im Durchschnitt ein Drittel weniger als der Wurzelbefall. Eine Infektion fuhrte zu signifikanten Zerstorungen der Zellmembranen und der maximale Elektrolytverlust wurde 7 Tage nach der Inokulation emittelt. Die Membranschaden waren nur in 3 Sorten vergleichsweise minimal-ca. 3–6%-und konnten mit einer niedrigen Koleoptylinfektion in Zusammenhang gebracht werden. Eine B. sorokiniana- Resistenz in Gerstensorten war nicht mit deren Resistenz gegen Fusarium culmorum gekoppelt.
Interleukin‐1β‐ and tumor necrosis factor‐α‐independent monocyte stimulation of fibroblast collagenase activity

To investigate the mechanism of cyclosporine (Cs)‐induced fibrous gingival enlargement, the indirect effects of Cs on fibroblast collagenolysis via the drug's effect on the synthesis of the fibroblast regulatory monokines interleukin‐1β (IL‐1β) and tumor necrosis factor‐α (TNFα) have been studied. Peripheral blood monocytes stimulated with lipopolysaccharide (LPS) for 48 h produced conditioned media (MCM‐LPS) that contained 665 pg/ml IL‐1β and 16 pg/ml TNFα and significantly (P < 0.001) enhanced the collagenase activity of a fibroblast strain (GN 23) derived from a healthy individual with clinically normal gingiva. The concurrent addition of Cs (50, 100, or 150 ng/ml) with LPS to the monocytes (MCM‐LPS‐Cs) significantly diminished their ability to enhance GN 23 collagenase activity in a dose‐dependent manner, with MCM‐LPS‐Cs (150 ng/ml) causing the greatest effect. Cs also significantly inhibited IL‐1β and TNFα production. Although the greatest inhibition of both cytokines was at 50 ng/ml Cs, the corresponding MCM‐LPS‐Cs caused the least diminution (16%) of the collagenase stimulation caused by MCM‐LPS (no Cs). This suggested that factor(s) other than or in addition to IL‐1β and TNFα might be responsible for the stimulation of GN 23 collagenase activity. MCM‐LPS depleted of IL‐1β by affinity chromatography retained its stimulatory effect on GN 23 collagenolysis, and human recombinant IL‐1β and TNFα, when tested alone or together at levels found in the stimulatory MCM‐LPS and MCM‐LPS‐Cs, did not stimulate GN 23 collagenase activity as did the crude conditioned media. This evidence suggested that the conditioned media contained the complex mixture of cytokines necessary to stimulate collagenase activity of this fibroblast strain and that IL‐1β and TNFα were not necessarily involved. Cs may alter the synthesis of other collagenase‐stimulating cytokines, accounting for the diminished ability of Cs‐treated monocytes to enhance collagenase activity of susceptible fibroblast strains. Decreased collagenase activity, therefore, resulting from Cs suppression of monokine production, may be an important factor in the development of fibrous gingival enlargement seen in some susceptible patients treated with Cs.
Nematode-Responsive Activity of the Cauliflower Mosaic Virus 35S Promoter and Its Subdomains

Root-knot and cyst nematodes are obligate plant parasites that induce complex biotrophic feeding structures in host roots. The mechanisms by which nematodes regulate host gene expression to produce feeding sites are unknown. The cauliflower mosaic virus (CaMV) 35S promoter has been reported to be repressed strongly in the feeding sites of both root-knot and cyst nematodes. In contrast, other work has indicated that this promoter is partially active in some feeding sites. Considering the importance of the 35S promoter in biotechnology, we have defined the nematoderesponsive nature of this promoter in more detail. Transgenic tobacco harboring various 35S-uidA constructs was assayed for β-glucuronidase (GUS) activity after infection by root-knot nematodes (Meloidogyne incognita) and cyst nematodes (Globodera tabacum subsp. tabacum). The entire 35S promoter (-343 to +8) was active in giant cells induced by M. incognita and, to a lesser extent, the syncytia of G. tabacum subsp. tabacum. In the latter case, act.
Morphological Differences between the "Races" of Drosophila Pseudoobscura

The use of suitable statistical analyses permits the demonstration of racial differences in the numbers of the sex-comb teeth and in certain measurements of the legs and wings, when taken on male flies. No such differences were found between females of the two races. The differences in numbers of sex-comb teeth were constant over a series of experiments even when performed at different temperatures. The use of these criteria for assignation of strains to the two races would result in 10 per cent. misclassification.
UNA NUEVA ESPECIE DE COSTUS (COSTACEAE) DE LA AMAZONIA COLOMBIANA

Se describe e ilustra Costus fissicalyx N. R. Salinas, Clavijo & Betancur, una especie nueva del sudeste de la Amazonia colombiana; ademas, se presenta informacion sobre sus relaciones taxonomicas, distribucion y habitat. Costus fissicalyx se diferencia de las otras especies del genero principalmente por la forma y el tipo de crecimiento del caliz
Diversidad de frutos de los árboles del bosque tropical perennifolio de México

Fruit morphology (color, size and type) of 881 tree species (338 genera and 85 families) that inhabit the tropical rain forest in Mexico was assessed. We found 46 fruit types and about 52.7% of species had berries (212 species), drupes (163) or loculicidal capsules (89); ten fruit types were represented by just one species. The most abundant fruit colors were ( n = 865 species) black (307 species; 35.5%), brown (227; 26.2%) and red (159; 18.4%). Berries were usually black (66%), drupes black (53.9%) or red (39.3%) and more than half of loculicidal capsules were brown (66.3%). Fruit length varied from 0.8 to 430 mm (mean 31.7 mm) and fruit width from 1 to 145 mm (mean 16.1 mm); these variables were positively correlated (r = 0.55, p 100 mm long). The largest numbers of fruit types per family was recorded for Rubiaceae (seven) and 47 of them displayed just one. Fruit type frequency and species per family were correlated (r = 0.58, p < 0.05 ; n = 85 families). Such correlation was not sustained at generic level, because 328 genera (97%) showed just one fruit type. Our results indicate that fruit morphological diversity of tree species is an important trait to understand the structure and composition of the tropical rain forest.
Spermatogenesis in Bovicola limbata Gervais, 1844 and B. caprae Gurlt, 1843 (Phthiraptera, Ischnocera)

Summary Adult males of Bovicola limbata and B. caprae were cytogenetically analyzed. Both species have n=7, holokinetic chromosomes, and achiasmatic male meiosis. As in other species of Phthiraptera, spermatogenesis follows a particular course with mitotic divisions after meiosis; consequently, cysts of 64 active spermatozoa and 64 non-functional cells (pycnotic nuclei) are encountered. In B. limbata an heteromorphic chromosome pair was observed. The results are compared with previous reports in Phthiraptera. The achiasmatic male meiosis, together with the particular course of spermatogenesis and the low chromosome numbers markedly constrain genetic variability.
Membrane forces and key protein determinants of hematopoietic cell function: Lamins and myosin-II in hematopoiesis and CD47 in immunotherapy of cancer

Hematopoiesis in human bone marrow generates every second about 105 – 106 anucleated platelets and red blood cells as well as nucleated white blood cells that are capable of infiltrating distant tissues. The thesis begins in the marrow with a description of (1) nuclear membrane ‘lamina’ physicochemical properties that influence marrow-to-circulation trafficking, and proceeds to detail (2) the physicochemical roles of membrane cortex ‘myosin’ in key marrow processes of motility and division as well as platelet biogenesis and disease. The thesis finishes with (3) studies of macrophages in peripheral tissues far from the marrow and aspects of how such cells distinguish ‘foreign’ cells from ‘self ’ cells. Collaborative studies show the lamin–A:B ratio controls nuclear viscoelasticity and in turn cell trafficking relevant to marrow escape. Additionally, differential lamin expression can direct erythroid and megakaryocyte differentiation. Secondly, xenografts show that MIIB is required for blood cell generation, while MIIA is required for long–term HSC/P engraftment. MII inhibition by blebbistatin prior to xenotransplantation enriches for long–term hematopoietic multilineage reconstituting cells, and also multi–nucleated megakaryocytes. Cone and plate rheometry demonstrates an optimal shear stress for platelet–like–particle generation from MKs that is enhanced by MII inhibition, and that MIIA heavy chain phosphorylation at S1943 is shear sensitive. Micropipette aspiration of MKs with mutations of the MIIA gene, MYH9, recapitulates MYH9–RD macrothrombocytopenia. Comparing MYH9–RD patient and normal donor platelets shows a similarity in pre/pro-platelets when normals are treated with blebbistatin. These findings provide evidence that regulation of MIIA activity through S1943 phosphorylation is critical to proper MK fragmentation and proplatelet fission to generate platelets of normal size and number. The dissertation concludes with an investigation of an immunotherapy approach to treat peripheral solid tumors by controlling tumor cell CD47 expression and administering an anti–human polyclonal IgG antibody. These in vivo xenograft models provide a mechanism of selective tumor clearance driven by FcR stimulation of macrophages. In all, this work highlights biophysical factors of cortical and nuclear membranes that govern hematopoietic differentiation and trafficking, normal and pathological thrombopoiesis, and a mechanism of phagocytic clearance of cancer cells through CD47 attenuation and species specific but epitope non–specific antibody infusion. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Chemical and Biomolecular Engineering This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1454 First Advisor Dennis E. Discher
Name that microbe: rapid identification of taxa responsible for individual fragments in fingerprints of microbial community structure

Polymerase chain reaction (PCR)-based ‘fingerprinting’ methods, such as Terminal restriction fragment length polymorphism, Length Heterogeneity-Polymerase Chain Reaction (LH-PCR) and Automated Ribosomal Intergenic Spacer Analysis (ARISA) make possible quantitative studies of microbial community structure and dynamics. Here we outline a strategy for the rapid and cost-effective isolation of 16S clones corresponding to particular fragment sizes in a fingerprint, based on applying the fingerprinting method to pools of colonies from a clone library. This allows the definitive identification of taxa responsible for the most important bands in the community fingerprint from a full 16S sequence. It offers significant advantages over random selection of clones and removes a significant barrier to the use of these methods.
Random Amplified Polymorphic DNA in Perennial Ryegrass: A Comparison of Bulk Samples vs. Individuals

The usefulness of random amplified polymorphic DNA (RAPD) in characteriz- ing two perennial ryegrass (Lolium perenne L.) synthetic cultivars, 'Accolade' and 'Caravelle', was tested. Two out of 10 arbitrary primers produced three RAPD markers that distinguished bulk samples of 30 seedlings. Additional fragments were apparent when DNA from individual seedlings was amplified. Amplification products from bulk samples were not simply the sum of amplification products of individual seedlings and did not reflect all the diversity within or between the cultivars. The study illustrates the need to screen individuals to accurately evaluate the genotypic composition of a synthetic cultivar or heterogeneous population.
Root survival of six cool-temperate wetland graminoids in autumn and early winter

Background: Timing of leaf senescence is an important ecological trait of species in cool-temperate climates. In contrast to above-ground biomass, not much is known about timing and extent of root mortality of herbaceous perennials at the end of the growing season. Aims: We undertook to assess patterns of end-of-season root mortality in species of temperate wetlands, investigate if the interspecific variation in the pattern of leaf senescence in autumn is reflected in patterns of root mortality, and determine if coarse axile roots and fine lateral roots differ in their autumn mortality pattern in wetland graminoids. Methods: For six cool-temperate perennial wetland graminoids, we assessed whether their roots die back for the winter, if the species-specific timing of senescence corresponds to interspecific variation in leaf senescence, and if fine lateral roots and axile roots differ in their mortality pattern. Survival and mortality of lateral and axile roots, and above-ground senescence was assessed in Sudbury, Ontario, Canada, from 11 September to 11 December, 2007, a period during which most of the above-ground biomass died. Root mortality was assessed using 2,3,5-triphenyltetrazolium chloride. Results: In Carex oligosperma, Carex stricta, Phalaris arundinacea and Scirpus microcarpus the majority of lateral and axile roots showed little mortality until mid-December. Axile roots of Dulichium arundinaceum showed little mortality, but its lateral roots died in October. Both lateral and axile roots of Sparganium androcladum died in October. Conclusions: These results indicate that fine roots of many species do not senesce along with the leaves for winter in cool-temperate climates. In some species, however, all roots senesce in autumn.
Pigments, total soluble phenols and lignin levels of coffee seedlings inoculated with Colletotrichum gloeosporioides

The objective of this work was to study the effects of different isolates of Colletotrichum gloeosporioides, as topigment level (chlorophyll a, b and total), total soluble phenols and soluble lignin in coffee seedlings obtained by artificially inoculatedtissue culture. The experiment was carried out in randomized block design in a 2 x 3 factorial scheme (2 genetic materials), 3 isolates(an isolate from mango fruits and another one from coffee plants), with 5 replicates and control (plants without inoculation). Theplants were inoculated with a suspension of 2 x 106 conidia.ml-1. The conidial suspension was sprayed on previously injured leaves.Leaves of inoculated plants were collected at 3 and 7 days after inoculation, except for leaves on the lower part of the plants.Afterwards, samples were prepared for the evaluation of chlorophyll, total soluble phenols and soluble lignin. The results showedthat the presence of the pathogen in healthy and diseased plants significantly reduced the amount of chlorophyll. At 7 days afterinoculation of healthy and diseased coffee plants higher total soluble phenol and soluble lignin levels were observed in response to theattack by Colletotrichum gloeosporioides.
Common pitfalls when testing additivity of treatment mixtures with chi‐square analyses

Studying interactions of multiple pesticides applied simultaneously in a mixture is a common task in phytopathology. Statistical methods are employed to test whether the treatment components influence each other's efficacy in a promotive or inhibitory way (synergistic or antagonistic interaction) or rather act independent of one another (additivity). The trouble is that widely used procedures based on chi‐square tests are often seriously flawed, either because people apply them in a preposterous way or because the method simply does not fit the problem at hand. Browsing recent volumes of entomological journals, we found that numerous researchers have (in all likelihood unwittingly) analysed their data as if they had had a sample size of 100 or, equally bad, a sample size of one! We show how to avoid such poor practices and further argue that chi‐square testing is, even if applied correctly (meaning that no technical errors are made), a limited purpose tool for assessing treatment interactions.
Effects of the Physical Environment and Primate Gut Passage on the Early Establishment of Ampelocera hottlei Standley in Rain Forest Fragments

The regeneration of many tropical trees is threatened by forest fragmentation because it produces major physical, biological and ecological changes that limit seed germination and seedling establishment. We analyzed the regenerative potential of an old growth forest tree species—Ampelocera hottlei (Ulmaceae)—in three contrasting habitats located in the Lacandona rain forest, southeastern Mexico: continuous forest, fragments occupied by black howler monkeys (Alouatta pigra) and fragments unoccupied by howlers. We tested if germination of A. hottlei seeds among habitats was affected by understory temperature, light incidence and ingestion by A. pigra. We compared seedling survival and relative growth rate in height (RGRH) for 20 d among habitats and between ingested and control seeds (from mature fruits). Germination was higher in continuous forest than in fragments (occupied or not), with higher germination rates for ingested seeds in fragments. Temperature and light incidence were lower in continuous forest than in fragments. Germination decreased with increasing temperature and light incidence with this relationship being significantly higher for ingested seeds. Seedling survival was higher in continuous forest than in fragments, whereas RGRH did not differ among habitats. In addition, survival and RGRH were higher in seedlings originating from ingested seeds. Overall, our results suggest that the populations of A. hottlei can be limited in fragments where changes in the understory physical environment and the extirpation of A. pigra will likely have deleterious consequences for the regeneration of A. hottlei and possibly for other tree species, ultimately affecting forest composition and structure.
Plasmopara obducens occurring on Impatiens walleriana hybrids and species in Hungary: Morphological and molecular characterization of the pathogen

In May 2011, young Impatiens walleriana Hook. f. plants showing downy mildew symptoms were collected from a greenhouse (Kecskemet, Hungary). The upper surface of affected leaves turned yellow and white fungal-like growth was observed on the underside. Diseased plants wilted and rapidly collapsed, resulting in losses of nearly 100%. Downy mildew of impatiens can be caused by two pathogens, Plasmopara obducens or Plasmopara constantinescui (syn: Bremiella sphaerosperma), which can be distinguished by the symptoms and by morphology of sporangiophores and sporangia. For molecular identification the 5′-end of the large subunit of ribosomal RNA gene was amplified by PCR using NL1 and NL4 primers and cloned and sequenced. The nucleotide sequence of the Hungarian isolate showed highest identity (99.72%) with two isolates of Plasmopara obducens from the United Kingdom and Serbia. On the basis of the symptoms, molecular and morphological characters, the pathogen was identified as P. obducens. The appearance of the pathogen in Hungary seriously endangers the production of I. walleriana, which is a popular ornamental in gardens and city parks. The chemical plant protection is not effective against the pathogen, by the occurrence of the first symptoms the diseased plants should be removed from the plantlet and must be destroyed.
Structure and ontogeny of Stomata in Polypodiaceae

The stomata as occurring on the fronds of the sporophytes of a large number of Polypodiaceae s.s. (Filicales) are investigated. A number of different stomatal types is recognised, (newly) described, and their ontogeny investigated. The different types of stomata are discussed in relation to their possible significance for tracing phylogenetic relationships in the Polypodiaceae following a cladistic analysis.