Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus

Phylogenies based on four loci confirmed the relatedness of all nine validly published species type strains within the Pseudomonas syringae species complex. To further establish the phylogenetic structure within the complex, all 67 pathovar type strains (with defined host ranges) were sequenced using a 578-nucleotide rpoD locus. Since this locus encompassed that used in a previous seven-locus study, it was possible to relate these strains to the existing phylogroup, genomospecies and binomial classifications. All species type strains were distinguished by relatively long branch lengths with all four loci, except for P. savastanoi, P. ficuserectae, P. meliae, P. amygdali and P. tremae, which were attributed to phylogroup 3. The grouping of P. tremae with these genomospecies-2 species was surprising since this species was previously designated as the sole representative of genomospecies 5. The oat pathogen P. syringae pv. coronafaciens was also distinguished by relatively long branch lengths with all four loci. The rpoD phylogeny grouped all the pathovar type strains into major clades that corresponded to previously defined phylogroups, except for two genomospecies-7 strains and P. caricapapayae, which were identified as a new phylogroup (6). There was good correlation between phylogroup and genomospecies classifications, except that two genomospecies-8 strains (P. avellanae and P. syringae pv. theae) were found as a distinct clade within phylogroup 1 along with P. syringae pvs morsprunorum and actinidiae. The rpoD locus will provide a common reference framework to improve monitoring and surveillance of these important pathogens.
Machine learning in systems biology at different scales : from molecular biology to ecology

Machine learning has been a source for continuous methodological advances in the eld of computational learning from data. Systems biology has pro ted in various ways from machine learning techniques but in particular from network inference, i.e. the learning of interactions given observed quantities of the involved components or data that stem from interventional experiments. Originally this domain of system biology was con ned to the inference of gene regulation networks but recently expanded to other levels of organization of biological and ecolgical systems. Especially the application to species interaction networks in a varying environment is of mounting importance in order to improve our understanding of the dynamics of species extinctions, invasions, and population behaviour in general. The aim of this thesis is to demonstrate an extensive study of various state-of-art machine learning techniques applied to a genetic regulation system in plants and to expand and modify some of these methods to infer species interaction networks in an ecological setting. The rst study attempts to improve the knowledge about circadian regulation in the plant Arabidopsis thaliana from the view point of machine learning and gives suggestions on what methods are best suited for inference, how the data should be processed and modelled mathematically, and what quality of network learning can be expected by doing so. To achieve this, I generate a rich and realistic synthetic data set that is used for various studies under consideration of di erent e ects and method setups. The best method and setup is applied to real transcriptional data, which leads to a new hypothesis about the circadian clock network structure. The ecological study is focused on the development of two novel inference methods that exploit a common principle from transcriptional time-series, which states that expression pro les over time can be temporally heterogeneous. A correponding concept in a spatial domain of 2 dimensions is that species interaction dynamics can be spatially heterogeneous, i.e. can change in space dependent on the environment and other factors. I will demonstrate the expansion from the 1-dimensional time domain to the 2-dimensional spatial domain, introduce two distinct space segmentation schemes, and consider species dispersion e ects with spatial autocorrelation. The two novel methods display a signi cant improvement in species interaction inference compared to competing methods and display a high con dence in learning the spatial structure of di erent species neighbourhoods or environments.
Improving the power of pasture cultivar trials to discriminate cultivars on the basis of differences in herbage yield

A review of 7 recently published perennial ryegrass cultivar trials (from 6 contrasting environments) with data expressed as an aggregate of seasonal harvests (autumn, winter, spring, and summer) revealed that the l.s. d. (P = 0.05) varied between 4 and 255% of the mean herbage yield of the trial in a given season, with 56 of 72 data points having an l.s. d. (P = 0.05) >10% of the trial mean. Power analysis of a perennial ryegrass trial that was conducted at Heywood (Vic.) from 1997 to 1998, with a 16% apparent difference in the total yield of a new synthetic and commercial cultivars, demonstrated that this difference would have only been detected 45% of the time. However, if the number of replications in the trial was increased from 4 to 8, then it was predicted that this difference would have been detected 70% of the time. In response to the data from this experiment, a trial was sown in 1999 that compared 4, 6, and 8 replicates to detect differences in the herbage yield of perennial ryegrass cultivars. In this trial, differences that were detected (P < 0.05) with 8 replicates would have routinely gone undetected when 4 or 6 replicate combinations were used. The use of a row–column design on the 8 replicates of the trial reduced the error variance of the trial by 5–12%, depending on the harvest. It was concluded that current pasture cultivar trials are routinely failing to detect differences between cultivars at an adequate level, given the rates of genetic gain in pasture species. In order to increase this precision, the number of replicates in a trial should be optimised on the basis of past data and the likely difference between control and test cultivars. Once the number of replications in a trial has been optimised then the use of row–column, or nearest neighbour designs, and analysis, will further increase precision for little extra cost.
Ultrastructural analyses of the rat esophageal stratified epithelium under normal conditions and in chronic reflux esophagitis

Address for correspondence: Dr. Hiroki Mori, Department of Gastroenterology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan Tel: +81-3-3813-3111, Fax: +81-3-3813-8862 E-mail: hmori@juntendo.ac. jp TJ structures only in the stratum granulosum (SG) of the esophageal epithelia in control rats, and the number of TJ structures seemed to be decreased in the RE model. Most of the TJs were composed of only one "kissing point. " Freeze-fracture electron microscopy did not allow identification of typical TJ strands, suggesting that TJs in the rat esophageal mucosa were not well-developed. Immunoelectron microscopy confirmed our previous immunohistochemical results indicating that claudin-3 was located on the surface of esophageal epithelial cells in control rats and that the immunoreactivity decreased in the RE group. However, claudin-3 was diffusely localized on the plasma membrane and not concentrated on the TJ structures. These results indicate that claudin-3 is not directly involved in the composition of the TJ structure.
Epidemiology and control of groundnut bud necrosis and other diseases of legume crops in India caused by tomato spotted wilt virus

Tomato spotted wilt virus (TSWV) was first reported in India in tomato in 1964 (Todd et dl., 1975). The occurrence of TSWV on a legume in ~India was first recorded in 1968 (Reddy et dl., 1968). The "bud necrosis disease" of groundnut, caused by TSWV, is now considered to be one of the most damaging groundnut diseases in India (Ghanekar et al., 1979a; Reddy, 1980). Bud necrosis is likely to have been present in India for some time although it has only recently become economically important. TSWV has also been reported on groundnuts in Brazil (Costa, 1941), the United States of America (Halliwell & Philley, 1974), South Africa (Klesser, 1966) and Australia (Helms et al., 1961). This chapter considers the epidemiology and control of bud necrosis and gives a brief account of other economically important diseases of legumes in India caused by TSWV.
Pinching for Flower Regulation in Sim Carnation

For a crop planted in 1st week of January under mid hills of Himachal Predesh, flowering can be spread over a period of five months [April, (2nd week) to mid-Sept. ] by employing various piehing methods. Double pinching produced maximum number of cut blooms/m2 (177.77) and delayed flowering, but the stems were weak and short (21.10 cm). The unpinched plants were early to flower (100.53 days), had longest stems (48.77 cm) and maximum flower size (6.98 cm), but the flower yield/m2 was very low (11.11). The best treatment appeared to be pinch and a half method (with 6 laterals) which staggered the flower production in two flushes (3rd week of May to July end) and yielded 66.66 flowers/m2 of good quality in a cropping season.
Autocrine and paracrine regulation of endothelial cell function by F-Prostanoid receptor signalling.

Endometrial adenocarcinoma, originating from the glandular epithelial cells of the uterine endometrial lining, is one of the most prevalent cancers amongst women in the Western world. The prostaglandin F2α (PGF2α) receptor (FP) is upregulated in endometrial adenocarcinoma. A previous microarray analysis of endometrial adenocarcinoma cells (Ishikawa) identified numerous targets of PGF2α-FP signalling including angiogenic factors, VEGF-A, FGF-2, CXCL1 and CXCL8 and antiangiogenic factors ADAMTS1. The regulation of VEGF-A, FGF-2, CXCL1 and CXCL8 was confirmed by previous studies using an in vitro model system, of Ishikawa cells stably expressing the FP receptor to levels observed in cancer (FPS cells). In this thesis, ADAMTS1 expression was found to be upregulated in endometrial adenocarcinoma samples compared to normal endometrium. Using FPS cells, ADAMTS1 expression was regulated in an extracellular signal regulated kinase 1/2 (ERK1/2) independent manner involving activation of nuclear factor of activated T cells (NFAT). Angiogenic and antiangiogenic proteins secreted by epithelial cells, in response to PGF2α-FP receptor signalling, could therefore regulate vascular function in a paracrine manner. Hence this thesis examines the role of angiogenic factors FGF2, CXCL1 and CXCL8, secreted into PGF2α-treated FPS cell conditioned medium (P CM), in the regulation of endothelial cell function in vitro. Firstly, using an in vitro model system, treatment of human umbilical vein endothelial cells (HUVECs) with P CM increased endothelial network formation and proliferation, compared to control CM. Immunoneutralisation of FGF2, CXCL1 and CXCL8 from the P CM reduced endothelial cell network formation and proliferation (P<0.05). In addition, inhibition of their receptors (FGFR1 and CXCR2) with chemical antagonists decreased endothelial cell network formation and proliferation (P<0.05) in response to treatment with P CM. This indicates that FGF2, CXCL1 and CXCL8 are paracrine effectors of FP-mediated endothelial cell network formation and proliferation. Next, the mechanisms by which FGF2 regulates P CM-induced endothelial cell network formation and proliferation were investigated. Using specific inhibitors of cell signalling, FGF2-FGFR1 was found to regulate endothelial cell proliferation via the mTOR pathway. In contrast, FGF2-FGFR1 signalling mediated endothelial cell network formation via the regulation of COX-2 expression and PGF2α synthesis in endothelial cells.
Natural enemies of sugarcane longhorn stem borer, Dorysthenes buqueti Guerin (Coleoptera: Cerambycidae), in Thailand.

THE SUGARCANE longhorn stem borer, Dorysthenes buqueti Guerin, is a major soil insect pest of sugarcane on many plantations in Thailand. Survey and evaluation of natural enemies of sugarcane longhorn stem borer were conducted and only a mite, Caloglyphus sp. , and the pathogen Metarhizium anisopliae were found as natural enemies. Caloglyphus sp. is an ectoparasite of the larva, pupa and adult sugarcane longhorn stem borer, but it is not effective as a biological agent. M. anisopliae is an entomopathogenic fungus in soil and is frequently found infecting D. buqueti in nature. In the laboratory, a symptom of infected larva of sugarcane longhorn stem borer is its slow movement 6 days after inoculation. There was no visible external fungal development on the larva before death. Death of larva occurred 7 days after inoculation. The pathogen can infect eggs, larvae, pupae and adults of sugarcane longhorn stem borer. The mortality of larva was 100% at 14 days after inoculation with a conidial suspension of 1x10 conidia/mL. In the greenhouse, data showed that 80–100% of sugarcane longhorn stem borer were killed 20 days after application. Our investigation showed that M. anisopliae is an efficient natural enemy and appropriate for biological control of the sugarcane longhorn stem borer in Thailand.
Characterization of the dolphinfish (Coryphaenidae) fishery of the United States western north Atlantic Ocean

Fishery dependent data from various commercial and recreational sampling programs form the basis for characterizing the fishery for dolphinfish ( Coryphaenus hippurus ) in the waters of the Gulf of Mexico and off the southeastern U.S. coast. Three states in the region have implemented size and bag limits for dolphinfishes, but there are no federal regulations in place at this time. Commercial landings were relatively small in comparison to recreational landings from 1984 through 1996. In 1995 however, commercial landings in the Atlantic Ocean of the southeastern U.S. were almost twice the weight of the previous years. The average weight per fish was calculated for each water body and fishing sector and there appear to have been significant increases in the average weight of fish landed both in the commercial and recreational sectors in the Atlantic and the Gulf of Mexico. Catch per unit of effort is measured as numbers of fish caught per angler per hour in the recreational fishery and has been variable since the early 1980s. In light of increasing landings and average weights of fish landed since the 1980s, the sustainability of this fishery must be fully evaluated.
The effect of acute milk-based carbohydrate/protein supplementation on the attenuation of exercise-induced muscle damage

i Peer reviewed publications.iv Conference communications and published abstracts.iv Table of contents.v List of Figures.xii List of Tables.xiii List of Appendices.xiv Table of abbreviations.xv Acknowledgements.xvii Declaration.xviii
High-content array based screening technology for the identification of factors that regulate cell fate

High throughput screens (HTS) of biological and synthetic molecules has become a useful tool in drug discovery and basic biology. However, traditional HTS can be cost- prohibitive given the costs of purified biological molecules and the rarity of certain cell types. Additionally, these approaches employ a candidate based strategy ignoring the complex crosstalk that occurs between combinations of biological molecules. To that end, we have developed a technology platform, called arrayed cellular microenvironments (ACME), which allows for the real-time simultaneous screening of thousands of biological and synthetic physiochemical parameters on cell attachment, proliferation, differentiation and gene expressions. We demonstrate that our platform provides data comparable to that obtained from traditional multi- well based assays while using 1,000-10,000 times fewer cells and reagents. As proof of principle, we applied this technology to identify combinations of microenvironment components that differentially modulate the phenotype of hepatic stellate cells (HSCs), a progenitor cell population of the liver that are involved in liver homeostasis. Next, we modified the ACME technology to screen the full complement of factors that may regulate human embryonic stem cell (hESC) proliferation and maintenance of pluripotency. Through the systematic screening of extracellular matrix proteins (ECMPs) and other signaling molecules, we developed and characterized a completely defined culture system for the long-term self -renewal of three independent hESC lines. Finally, we extended the ACME technology to screen synthetic polymers and peptides to identify artificial matrices that support self-renewal of hESCs. This system will be useful for future stem cell research, including the elucidation of differentiation protocols, as well as the identification of culture conditions of rare and recalcitrant primary cell populations, such as progenitor, adult stem, and cancer stem cells.
Il calcolo della data di scadenza degli alimenti: La funzione shelf life e la propagazione degli errori sperimentali

The aim of this work was to discuss the calculus of foods Shelf Life on the basis of a new mathematical approach (Parisi, 2002a-2003b). The Authors mean to define a correct study about the foods Shelf Life like a mathematical function: the final goal is to understand the time-based development of this equation and the exact nature of the dependence on the storage temperature. A linear approach for calculating a correct durability on the basis of temperature values was previously suggested (Parisi, 2002a) through the so-called "Degradation Speed". Nevertheless, some subsequent assays demonstrated that final results are always incorrect (Parisi, 2003b). In fact the Shelf Life, exponentially depends on the storage temperature, even though related mathematical function is not equal to that about Degradation Speed; every simplification is then incorrect and possibly dangerous (possible overestimated values).
Sequential immunohistochemical detection of infectious bursal disease virus antigen in experimental chicken

The distribution of infectious bursal disease (IBD) virus antigen in experimentally infected lymphoid and non lymphoid formalin fixed paraffin embedded tissues were studied sequentially from 0 hours post infection (HPI) to 28 days post infection (DPI)using immunoperoxidase (IPT) and immunofluoresence (IFT) staining techniques. A scoring pattern was adopted to study the distribution of viral antigen histologically in the tissues.The viral antigen was noticed in the cortical lymphocytes and plical epithelium of bursa of Fabricius, thymus, spleen, caecal tonsils, Harderian gland within 12 HPI. The macrophages present in interfollicular stromal tissue of bursa, proventriculus and liver showed presence of viral antigen by 24 HPI. The intensity of reaction decreased by 10 DPI to 14 DPI in bursa of Fabricius, thymus and spleen. The antigen started disappearing from Harderian gland, proventriculus, spleen and thymus in that order and persisted for longer time in bursa of Fabricius and caecal tonsils.
Notes on the sexual condition of Myriophyllum aquaticum, Haloragaceae.

Resumen. Myriophyllum aquaticum (Vell.) Verdc. es nativa de Sudamérica con distribución pantropical. Esta especie ha sido citada como dioica, monoica y polígama. El objetivo de este trabajo es contribuir a la discusión sobre su condición sexual, basada en material de herbario, y apoyada por observaciones de campo. Se examinó material de herbario de Argentina. En la Reserva Natural de Punta Lara (Buenos Aires, Argentina), se muestrearon periódicamente veinte ramas para registrar el sexo de las flores presentes en cada verticilo durante el período de floración de 2002. Tanto en material de herbario, como en el campo, observamos especímenes con ramas con flores femeninas, especímenes con ramas con flores masculinas y especímenes con flores femeninas y masculinas en la misma rama. Algunos de estos materiales presentan frutos. Nuestras observaciones apoyan la idea que M. aquaticum no es una especie estrictamente dioica, al menos en Argentina.
The use of digital image analysis and real-time PCR fine-tunes bioassays for quantification of Cercospora leaf spot disease in sugar beet breeding

Cercospora leaf spot, caused by the fungus Cercospora beticola, is a major fungal sugar beet disease worldwide and the cause of significant yield losses. The disease is most successfully countered by the introduction of genetic tolerance into elite sugar beet hybrids. To this end, breeding programmes require high quality biological assays allowing discrimination of minor differences between plants within a segregating population. This study describes the successful implementation of image analysis software in the bioassays for quantification of necrotic lesions at different stages of C. beticola infection, allowing selection on minor phenotypic differences during the sugar beet breeding process for C. beticola resistance. In addition, a real-time PCR assay was developed for the quantification of C. beticola pathogen biomass in infected beet canopy. The use of both techniques, even in an early stage of infection, fine-tunes current bioassays, allowing more accurate and efficient selection of resistant breeding material.
Isolation, characterization of ethanol tolerant yeast.

The present study was conducted to isolate the yeast strain ( Saccharomyces cerevisiae ) from the sources such as Grapes, Molasses, Musambi, Cashew Apple, Distillary Effluent, Sorghum, Sugarcane and it is used for the study of ethanol tolerance at various concentrations from 6-14.5%. Among these the yeast strains isolated from Molasses and Cashew apple showed highest tolerance upto 12.5% and strains from Sorghum had least with 10%. Molecular characterization of yeast strain also studied using RAPD-PCR, among 63 bands produced, 6 bands were monomorphic and 57 bands were polymorphic and genetic distance of yeast strains were performed based on cluster analysis reveals that the highest genetic difference between Sugarcane and Molasses at average of 0.5 and the least genetic difference showed between Sorghum, Cashew apple and Distillary effluent at average of 0.10.