Miracle-dz/UniFAR-FTUs huggingface dataset:
Salmonella enterica interactions with tomato: Plant genotype effects and Salmonella genetic responses

Title of Document: SALMONELLA ENTERICA INTERACTIONS WITH TOMATO: PLANT GENOTYPE EFFECTS AND SALMONELLA GENETIC RESPONSES Sanghyun Han, Ph. D. , 2015 Directed By: Dr. Shirley Ann Micallef, Assistant Professor, Department of Plant Science and Landscape Architecture Several outbreaks of Salmonella enterica infections have been linked to tomatoes. One cost-effective way to complement on-farm preventive Good Agricultural Practices would be to identify cultivars with inherent decreased susceptibility to Salmonella colonization. Various tomato cultivars with distinct phenotypes were screened to evaluate their susceptibility to Salmonella epiphytic colonization. The potential role of plant exudates, collected from the same cultivars, on the growth kinetics of Salmonella was examined. These investigations were supplemented with Salmonella genome-wide transcriptomics that showed bacterial responses to colonization of tomato shoots and roots. Epiphytic colonization of fruit by S. enterica was cultivar-dependent and serotype-specific, but did not correlate with leaf colonization. Fruit and leaves of the same cultivar differed in their ability to support Salmonella growth. Quantitative and qualitative analysis of tomato exudates provided a possible explanation for the differential susceptibility to bacterial colonization among tomato cultivars. Tomato exudates alone were capable of supporting Salmonella growth, and the growth kinetics of Salmonella in tomato exudates differed by cultivar. Characterization of the chemical composition of primary and secondary metabolites in tomato exudates pointed to potential causes for the differential growth of Salmonella observed in the exudates of various tomato cultivars. Key transcriptomic signals that were downand up-regulated in Salmonella upon interacting with tomato were identified, enabling us to elucidate the molecular mechanisms underlying this enteric pathogen-plant interaction. Overall, the identified signals lead to a proposed model that depicts the cellular processes needed to preserve cell viability when multiple abiotic stresses in conjunction with low nutrient availability are encountered, while simultaneously repressing unnecessary energy demands or maintaining them at a level equivalent to growth in a nutritious medium. These findings strongly support the hypothesis that plant-regulated mechanisms influence enteric pathogen colonization. It is clear that Salmonella can sense subtle environmental cues brought about by the genotype or physiological state of plants and can respond with distinct patterns of gene expression. Future work should focus on whether this bacterial behavior on plants results from an evolutionary adaptation to use plants as a vector to re-enter animal hosts. SALMONELLA ENTERICA INTERACTIONS WITH TOMATO: PLANT GENOTYPE EFFECTS AND SALMONELLA GENETIC RESPONSES
Effect of Carbon Tetrachloride Administration on Serum Aromatic L-Amino Acid Decarboxylase Activity of the Rat

Administration of carbon tetrachloride to rats by intraperitoneal injection caused significant increases in serum aromatic L-amino acid decarboxylase activity and serum glutamate oxaloacetate and glutamate pyruvate transaminase levels. Moreover, a significant positive correlation coefficient was obtained between the decarboxylase activity and glutamate oxaloacetate transaminase activity.The increment of the decarboxylase activity in the serum caused by carbon tetrachloride was found to be accompanied by a decrease in the decarboxylase activity of the liver, and a significant negative correlation was found between the two enzyme activities. In contrast, no change was found in the decarboxylase activity of the kidney.These observations suggest that aromatic L-amino acid decarboxylase occurs in the serum at least in part as a result of the leakage of the enzyme from the liver into the blood.
The field pea crop in S.W. Australia. I. Patterns of growth, biomass production and photosynthetic performance in genotypes of contrasting morphology

Biological yield and photosynthetic performance of six field pea genotypes of contrasting foliar morphology and growth habit were studied in a water-limited field environment at Wongan Hills, Western Australia. Dundale and Wirrega were tall, indeterminate, scrambling and conventionally leaved; Dinkum, L82 and L80 (semi-leafless) and Progreta (tare-leaved) were semi-dwarf and more erect. Green area index (green leaf area per unit of ground area), green area duration (time integral of green area), crop growth rate (rate of dry matter accumulation per unit ground area) during early spring, net photosynthetic rate (CO2 exchange rate per unit green area or unit green weight) and net assimilation rate (rate of dry matter accumulation per unit green area) all influenced crop productivity. Shoot and root biomass was highest in Wirrega, due mainly to superior green area index, extended green area duration and maintenance of high growth rate during pod fill. Inverse relationships amongst genotypes were evident between green area index and net assimilation rate, and between green area index and CO2 exchange rate of green area. Total net photosynthesis of the tendrils of semi-leafless types was similar to that of leaflets of conventional types, due mainly to larger biomass of tendrils compensating for poor photosynthetic rates. The poor growth of semi-leafless and tare-leaved types was attributed to lower vigour, green area, ground cover and photosynthate production. Future selection of such types for water-limited environments should concentrate on increasing shoot height, node number per plant, stipule and tendril size and photosynthetic efficiency of green area.
Effects of Superheated Steam Fluidized Bed Drying on the Quality of Parboiled Germinated Brown Rice

The parboiled germinated brown rice (PGBR) was produced using a superheated steam fluidized bed dryer. Grains with an initial moisture content of 58.16 ± 0.25% dry basis (d.b.) were steamed and dried in a single stage at steam temperatures of 110–150C. After superheated steam drying, grains were tempered for 2 h and then ventilated with ambient air until the moisture content reached 16% d.b. as two-stage drying. During superheated steam drying, the results revealed that moisture content, white belly and γ-aminobutyric acid (GABA) content significantly decreased with increasing drying temperature and time, whereas internal fissuring, yellowness and peak viscosity increased. The moisture content of grains after drying should be no lower than 19.19–22.00% d.b. to prevent internal fissuring of grains. Two-stage drying resulted in better quality grains and prevented GABA content reduction. In addition, the cooking quality of PGBR differed significantly from that of germinated brown rice (GBR) because of starch gelatinization in PGBR. Practical Applications PGBR is a functional food. The superheated steam fluidized bed drying can be used to produce PGBR. In the dryer, the grains were steamed and dried as a single state to reduce the number of operating steps. Results of this research revealed the effects of superheated steam drying on the quality of PGBR. The superheated steam fluidized bed drying represents a good practice in the production of PGBR with high GABA content.
Mise en évidence immunologique de la protéine tau au niveau des lésions de dégénérescence neurofibrillaire de la maladie d'Alzheimer

The abnormal filaments of neurofibrillary tangles of Alzheimer's disease have been studied by immunocytochemistry with a serum raised against the isolated filaments, and with a serum anti-tau, a microtubule-associated protein. The two antisera give a similar labelling of the cellular lesions. Moreover, the anti-abnormal filaments serum contains anti-tau antibodies.
Control of termites and other soil pests of groundnuts with special reference to controlled release formulations of non-persistent insecticides in India and Sudan

Trials for the control of soil pests, particularly of termites (Isoptera:Termitidae), in groundnuts (Arachis hypogaea) in India and Sudan used chlorpyrifos and isofenphos granules, chlorpyrifos, phorate, carbosulfan and carbofuran in controlled release formulations, and chlorpyrifos seed dressing. Their effects on foliar pests were also noted. Chlorpyrifos controlled release pellets were as effective as aldrin, used as a standard, in reducing root and pod attack and, like aldrin, doubled yields. Isofenphos and chlorpyrifos granules increased yields and reduced pod damage, but to a lesser extent. Other treatments were less effective. Carbosulfan and phorate controlled release and isofenphos granules reduced leaf miner attack. These trials establish the efficacy of controlling termites and other soil pests with controlled release formulations of otherwise non-persistent insecticides. However, the expensive formulation is unlikely to be cost-effective for rural farmers in developing countries and, in the case of chlorpyrifos , residue levels in kernels may be unacceptable. Future work should investigate other insecticides in the formulation and development of cheaper controlled release matrices
Factors Influencing Within-Vine Variation in the Cold Resistance of Cane and Primary Bud Tissues

The cold resistance of bud and cane tissues on the same grapevine varied up to 12°C depending on the presence of periderm, periderm color, cane diameter, persistent-lateral status, and leaf exposure to the sky during the growing season. The conditions that consistently favored greatest cold resistance were exposure to sunlight, dark-colored periderm, medium cane diameter (6-7 mm), and lack of persistent lateral canes. The value of understanding cold resistance mechanisms is discussed from three viewpoints: 1) as the basis for solving the problem; 2) as a basis for cultural decisions; and 3) as a basis for sampling procedures when doing cold-resistance studies in grapevine canopies.
Pseudopodosira kosugii : A new Holocene diatom found to be a useful indicator to identify former sea-levels

A heavily silicified sub-spherical diatom occurring abundantly close to the upper limits of marine facies in the sedimentary sequences recording a Holocene transgression is named and described; Pseudopodosira kosugii sp. nov. Observations on this form in a recent habitat and growing in cultures show that it grows vegetatively by normal cell division, although its thick spiny hemispherical valves in the Holocene sequences are suggestive of resting spore valves rather than valves of vegetative cells. Variation in frustule morphology is revealed and discussed. This new species is highly variable in morphology, and a pair of watch-glass shaped spiny valves is the most common combination of vegetative cells. Its peak abundances being close to marine limits have made the species a useful indicator of the former sea-level during the Holocene.
An Oviposition Deterrent Associated with Frass from Feeding Larvae of the Cabbage Looper, Trichoplusia ni (Lepidoptera: Noctuidae)

First-instar Trichoplusia ni larvae feeding on cabbage deterred oviposition by adult moths in laboratory assays.The effect remained for at least 3 days after removal of larvae from plants.When cabbage plants were treated with a dispersion of larval frass in water, oviposition was also deterred. The results suggest that larval frass can serve as a signal of occupancy to gravid females searching for oviposition sites.
Temporal Spawning Distribution of Largemouth Bass and Young-of-Year Growth, Determined from Daily Otolith Rings

Abstract Age and growth of young-of-year largemouth bass Micropterus salmoides in Lake Shelbyville, Illinois, were determined from daily growth rings in otoliths of fish collected in September of 1980 and 1981. Otolith ages, adjusted for the interval from spawning to the start of feeding (swim-up), revealed that spawning of largemouth bass occurred during 45 days from late April until early June in both years. Spawning occurred at temperatures of 12 to 20 C. In mid-September, 60–75% of the variation in largemouth bass lengths was attributable to age. Older individuals had increased their initial length advantage through faster average daily growth. Back-calculated lengths at 5-day intervals indicated that growth was most rapid to early August and had decreased by mid-September. Growth of individuals that reached swim-up in mid-June declined much more rapidly than growth of individuals that reached swim-up in late May. Differences in growth between largemouth bass that reached swim-up on different dates we.
Big six of the individual adaptive ability of the sleep-wake cycle: Explanation and measurement

Abstract Research is directed at understanding the nature of differences between individuals in the adaptive abilities of their sleep–wake cycles. We proposed a three-dimensional model that reduces the subjectively assessed variation of the sleep–wake patterns to three underlying physiological variables. This model explains the results of factor analysis of chronotypological questionnaires and predicts the hierarchical structure of the sleep–wake adaptability with three most general abilities at the top level, six basic abilities at the middle level, and 18 primary (most specific) abilities at the bottom level. Any such subjectively assessed trait of any of these three hierarchical levels might be located in the space of three physiological parameters (namely, these are amplitude of circadian modulation of sleep–wake states, rate of accumulation of sleep debt and intensity of circadian arousal). The present study is aimed at generation and testing a particular prediction of the model. It points to the features of one basic and five primary abilities that are not accounted by the 52-item Sleep–Wake Pattern Assessment Questionnaire. Twenty new questionnaire items relevant to these predicted abilities were produced and corrected through a series of three questionnaire surveys of the residents of Novosibirsk (n = 150, 180 and 200). The results of factor analysis of the intermediate and final versions of the questionnaire provided evidence of applicability of the model for identification of the abilities that have not yet been measured by means of the questionnaire and for improvement of measurement of already identified abilities.
Characterization of Black and Green Tea from Local Market

The leaves from Camellia sinensis are used from ancient times for preparation of tea but also as raw material for different extracts which are used in food industry as well as in pharmaceutical or cosmetic products. Due to the increasing interest in tea health benefits, the aim of the present study was to characterize several brands of green and black tea found on local market, regarding their content in total phenolic compounds, flavonoids and antioxidant capacity. Total phenolics and flavonoids were determined spectrophotometrically using a modified Folin-Ciocalteu method, respectively a chromogenic system of NaNO 2 -Al(NO3) 3 -NaOH based method. The antioxidant capacity of each tea sample was assessed through the evaluation of free radical scavenging effect on 2,2-diphenyl-1-picrylhydrazyl. The results obtained for the green and black tea samples varied widely, depending on the tea variety. The antioxidant capacity of the analyzed teas ranged between 12.10 and 40.03%RSA, while the total phenolic content was within 2090 and 6080 mg GA/ 100g. The concentrantion in flavonoids was between 9.04 and 15.34 g/100g of tea.
Distribution Fitting 2. Pearson-Fisher, Kolmogorov-Smirnov, Anderson-Darling, Wilks-Shapiro, Cramer-von-Misses and Jarque-Bera Statistics

The methods measuring the departure between observation and the model were reviewed. The following statistics were applied on two experimental data sets: Chi- Squared, Kolmogorov-Smirnov, Anderson-Darling, Wilks-Shapiro, and Jarque-Bera. Both investigated sets proved not to be normal distributed. The Grubbs' test identified one outlier and after its removal the normality of the set of 205 chemical active compounds was accepted. The second data set proved not to have any outliers. Kolmogorov-Smirnov statistic is less affected by the existence of outliers (positive variation expressed as percentage smaller than 2). The outliers bring to Kolmogorov-Smirnov statistic errors of type II and to the Anderson- Darling statistic errors of type I.
Characterization of internal airflow within tissues of mangrove species from Australia: leaf pressurization processes1

Abstract Mangroves are a diverse group of plants that inhabit tidal zones in the tropics and sub-tropics. Some mangrove species occupy the lower tidal zone in which the substrate is anoxic for long time periods while some mangroves inhabit the upper tidal zone in which the substrate should be less anoxic. The purpose of this study was to determine if twenty-four species of mangroves have a mechanism of internal airflow to provide air to roots within anoxic substrates. Results show that 11 species pressurize air in leaves and move this air internally in aerenchyma tissues in stems and eventually to roots while 13 mangrove species do not move air internally from leaves to roots. Quantitative data showed that the internal airflow from leaves to roots for these 11 mangrove species was correlated with 1) number of cork warts on leaves, 2) volume of aerenchyma tissues within leaves, and 3) the volume of aerenchyma tissues in stems relative to the number of leaves on stems. Higher values of these three parameters were negatively related (y = 64.8 x −0.36 with an r2 of 0.93) with the minimum air pressure required to release air pressure from foliage when air pressure was applied to cut stems of whole plants. Each of the three characteristics above is required for air conductance from leaves to roots. Indeed, relative internal airflow from roots to stems in these 11 mangrove species can be accounted for by these three factors alone. Some mangrove species only have aerenchyma in their roots and can move air internally from pneumatophores to other roots within the anoxic substrate. Some mangrove species that occupy the upper tidal zone do not have aerenchyma tissues to move air internally. To our knowledge, this is the first report that 1) provides extensive air pressure testing of tissues for many mangrove species, 2) extensively quantifies morphological and anatomical data to account for internal air movement from leaves to roots, and 3) quantifies internal air movement and provides anatomical data to help explain the predominant location that many mangrove species occupy in the tidal and estuary zones of Australia.
Opposing actin networks modulate the mechano-activation of the integrin LFA-1 during immunological synapse formation

Formation of a functional immune response requires the regulated transfer of information between T cells, and APCs, which leads to a variety of functional outcomes. In many cases this information transfer occurs at a regulated area of cell cell contact termed the immunological synapse (IS). In T cells responding to APCs there is a robust accumulation of F-actin on the T cell side of the synapse. This F-actin response is characterized by robust polymerization at the periphery of the contact site followed by centripetal flow of the network towards the center of the IS. While it is well known that this F-actin flow is required for the maintenance of signaling at the IS, the mechanism behind this observation has remained elusive. Recent evidence has suggested that the TCR and the integrin LFA-1 are regulated through the application of force on the receptor ligand bond. This raises the distinct possibility that the robust F-actin flow provides the mechanical force to activate these receptors, thereby enhancing and maintaining signaling at the IS. I demonstrate that the robust F-actin flow at the T cell side of the IS is required for LFA-1 accumulation to and maintenance of conformational changes associated with affinity maturation at the IS. Furthermore I find that full induction of LFA-1 conformational change requires binding to immobilized ligand, and is enhanced through the induced fit of ligand binding, alongside the enhanced tension provided by pulling on immobilized ICAM-1. Furthermore, I find that Dendritic Cells (DCs) are capable of modulating the lateral mobility of ICAM-1 on their plasma membrane during TLR induced maturation. Mature DCs greatly restrict the lateral mobility of ICAM through the increased expression and activity of the actin binding proteins moesin and αactinin-1. The limitation of ICAM-1 mobility is critical for ICAM-1 mediated adhesion of T cells to DCs, through the regulation of LFA-1 affinity maturation, and is essential for full T cell proliferation. Our results therefore indicate that the actin cytoskeletons on both sides of the T cell DC IS coordinately function to maximize conformational change of LFA-1 and promote synapse stability at the IS. Additionally, these data demonstrate that one role of the T cell F-actin centripetal flow may be to provide the force required for the activation of mechano-sensitive molecules, thus propagating signal transduction at the IS. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Immunology First Advisor Janis K. Burkhardt Second Advisor Terri M. Laufer This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1242
Evaluating Solarization and Cultivated Fallow for Johnsongrass (Sorghum halepense) Control and Nitrogen Cycling on an Organic Farm

ABSTRACT A two-year field study evaluating efficacy of two weed control techniques on the noxious weed johnsongrass (Sorghum halepense L. Pers.) was conducted in Lexington KY. The weed control treatments were soil solarization, accomplished by covering the soil with clear plastic for 8 weeks, and cultivated bare fallow. Both treatments, along with a control treatment (mowing), were applied during the summers of 2003 and 2004 to a field heavily infested with johnsongrass (40–50% coverage). Effects of solarization on soil microbial activity and nitrogen (N) cycling were also evaluated. In both years, half of each treatment plot was lightly tilled 8 months after initial treatment application, and johnsongrass populations were characterized 2 months later. At the end of the experiment, the solarized-untilled treatment had lower johnsongrass populations than the cultivated-tilled and control treatments. Shallow tillage resulted in significantly more johnsongrass in the cultivated treatment in 2003, and in both cultivated and solarized treatments in 2004, compared with their untilled counterparts. At the conclusion of the experiment the johnsongrass populations were considerably reduced in both treatments compared with the original infestation. Solarization resulted in significant increases of both NH4-N and NO3-N in the soil during the time the plastic was in place, likely due to release of labile NH4-N from soil microbial biomass and subsequent nitrification. Substrate-induced respiration rates were also reduced during solarization, indicating a reduction of microbial biomass. However, these soil indicators were not persistent and should not prohibit the use of this weed management technique by organic growers.