Miracle-dz/UniFAR-FTUs huggingface dataset:
Bioseedling: a chain approach to the production of healthier seeds and seedlings of Lamb’s lettuce Valerianella locusta

The project BIOSEEDLING “Robust planting material from seeds to young plants - an implementation oriented chain approach” aims to find improved production procedures for vegetable seedlings of lamb’s lettuce. First, the production of lamb’s lettuce seeds of a professional seed producer was analyzed and the effect of harvest time and seed size on the germination and disease rate in the seeds was studied. Then, using seeds naturally infected by Peronospora valerianellae and Acidovorax valerianellae, several seed disinfection methods were compared: aerated steam, hot water, sodium hypochlorite, ethanol, Calcium hydroxide, and compost pellet. After testing methods for the identification of the seed pathogens and the quantification of the infection, an assessment on how the different treatments reduce the pathogens and whether they alter the seeds germination capacity was made. In a third step, substrates suppressive of the soil borne pathogens Rhizoctonia solanii and Pythium ultimum were developed and several plant protection agents were tested against Peronospora valerianellae. Furthermore, the effect of night interruption on the sporulation of lamb’s lettuce downy mildew (Peronospora valerianellae) using periods of lighting in the red and blue regions was tested. The aim is to combine the best methods resulting from all the experiments cited above in a future experiment and compare them to the standard methods in an on-farm experiment.
Epidemiological studies on Non-O157 Shiga toxin-producing Escherichia coli

ii Acknowledgments. iv Vita . vi Publications . vii List of Tables . ix List of Figures . x Chapter 1: Literature Review: Shiga-toxin producing Escherichia coli . 1 Chapter 2: Escherichia coli in Ohio specialty-crop soils contaminated with deer feces. 133 Chapter 3: Isolation of non-O157 Shiga toxin – producing Escherichia coli from ruminant manure. 156 Chapter 4: Shiga toxin (stx) encoding genes in sheep and goats reared in Trinidad and Tobago. 179 Bibliography: . 214 Appendix A: Identification and subtyping of Salmonella isolates using Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF) . 270
The Analysis of Pandanus Relationship of Purwodadi Botanical Garden Collections Based on Morphological Character and Molecular Marker (trnL and trnL-F)

The morphological characteristics of plant vegetative organ has the potential to be the defining factor of pandanus family collection at Purwodadi Botanical Garden (PBG). However, the information is not enough to confirm the identity of pandanus at the type-level. This problem happened at the collection of PBG. It is an urgent issue considering PBG as one of the most important ex-situ plant conservation institute that also has function as a study source for plant taxonomy science in Indonesia. Therefore, the use of molecular technology analysis using molecular marker (primer) is incredibly important to identify the member of pandanus family by identifying its family relationship pattern. This information was expected to give a clarity about the identity of Pandanus family at PBG which will support further research and activity for pandanus conservation. The plant sample includes 16 specimens of pandanus with one member of the family from Freycinetia as the outgroup. Morphological analysis of the 50 characteristics of vegetative organs (leaf, stem, and root) was conducted. Molecular analysis of DNA using primer of trnL and trnL-F . The data sequence as a result of the analysis was then tested using homology test with BLAST. All of the DNA sequence was paralleled using Clustal W analysis, the tree construction relationship was analysed using Maximum Parsimony (MP) method with MEGA 6.0 program. The results of morphological studies showed the character vegetative that is the position of the spines on the leaves, the shape of apex leaf and the condition of the root surface above the soil. Molecularly, appears 1 new genera that has not been previously identified by PBG researcher is Benstonea.
Genetic Variability Analysis for Grain Yield and its Components Traits in Traditional Rice Varieties (TRVs)

Traditional Rice Varieties (TRVs) are an important component of crop genetic resources and are valued by rice breeders and farmers because of diversity, rarity and adaptability (Brush and Meng, 1998; FAO, 1998; Smale, 2006 and Gauchan et al., 2006). TRVs are often highly variable in appearance, but they are each identifiable morphologically and have a certain genetic integrity. Farmers assign them local names based on their distinct properties or particular characteristics as each TRVs has a reputation for adaptation to specific ecosystem. Hence farmers and researchers throughout the world continue to maintain and manage these TRVs within their production systems (FAO, 2010). Yet, their complete genetic potential has not yet been exploited in crop breeding programme (Gyawali et al., 2010). International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 6 Number 8 (2017) pp. 494-502 Journal homepage: http://www.ijcmas. com
Identification of promising sources for fodder traits in the world collection of pearl millet at the ICRISAT genebank

Abstract A total of 326 pearl millet accessions selected for fodder traits from the world collection at ICRISAT genebank, India were evaluated in rainy, postrainy and summer seasons to identify promising sources for fodder yield. In rainy season, majority of accessions grew significantly tall, produced thick stems, long and broad leaves compared with postrainy and summer seasons. Total tillers per plant were significantly more in rainy and summer seasons than in postrainy season. Significant (P = 0.05) positive correlations were observed among all traits in all seasons except total tillers, which showed significant negative correlation with all other traits but for a few cases. Accessions of cluster 1 flowered early and produced more tillers per plant, while those of cluster 3 flowered late, grew tall, produced thick stems, more leaves per plant, which were long and broad. Promising sources identified include IP 11839 and IP 11840 for plant height and number of leaves per plant, IP 15710, IP 15735 and IP 15752 for stem thickness and leaf width, and IP 3628, IP 15285, IP 15288, IP 15302, IP 15342, IP 15351, IP 15290, IP 20347 and IP 20350 for total tillers per plant. Further testing of these sources of fodder traits at different locations will be very useful.
Modelling the multi-step process of tumorigenesis in pigs

The pig has gained much interest as an alternative animal model for human cancers due to its shared anatomical and physiological characteristics with humans. This work describes the neoplastic transformation of stepwise genetically modified porcine mesenchymal stem cells (MSCs) in vitro. Expression of oncogenic p53 and Kras in combination with p16INK4α gene silencing and deregulated cMyc expression resulted in immortalised, transformed porcine MSCs. Several in vitro and in vivo assays confirmed the neoplastic transformation of these genetically modified porcine MSCs.
QUALITY OF REACTION WOOD IN Eucalyptus TREES TILTED BY WIND FOR PULP PRODUCTION

: This study aims to evaluate the quality of normal, tension and opposite wood of eucalyptus trees lengthwise, in straight and inclined stems,affected by wind action. It also aims to explain the pulping parameters resultant from the quality of the wood. The trees were grouped into four tilt ranges, ranging from 0 to 50o, and the basic density, chemical composition of the wood, and performance in kraft pulping were assessed. Normal and tension wood had similar basic densities; while for opposite wood, the densitywas lower, being responsible for a decrease in reaction wood density. The chemical composition of the wood was influenced by the presence ofreaction wood in the stem. Tension and opposite wood showed lower levels of extractives and lignin and higher holocellulose content when compared to normal wood, with favorable woodquality for pulping. The increase in holocellulose content and thereduction of lignin and extractives content contributed positively to a more delignified pulp andreduction of the Kappa number. However, after cooking the reaction woodunder the same conditions as those of normal wood,reaction wood pulping tends to have a lower screen yields. Due to differences in basic density and chemical constituents between opposite and normal wood, it is recommended not to designate the opposite wood as normal wood.
Do metacommunities vary through time? Intermittent rivers as model systems

Metacommunity assembly mechanisms have been traditionally considered stable through time. However, in highly dynamic systems with varying local environmental conditions and patch connectivity, communities are likely to experience temporal shifts in their assembly mechanisms. Here, we used a set of perennial (PR) and intermittent (IR) rivers to assess if assembly mechanisms vary seasonally in response to flow intermittence.
The bifunctional flavokinase/FAD synthetase from Streptomyces davawensis produces inactive flavin cofactors and is not involved in resistance to the antibiotic roseoflavin

1 2 Streptomyces davawensis synthesizes the antibiotic roseoflavin, one of the few known 3 natural riboflavin-analogs, and is roseoflavin resistant. It is thought that the endogenous 4 flavokinase (EC 2.7.1.26)/FAD synthetase (EC 2.7.7.2) activities of roseoflavin-sensitive 5 organisms are responsible for the antibiotic effect of roseoflavin producing the inactive 6 cofactors roseoflavin-5'-monophosphate (RoFMN) and roseoflavin adenine dinucleotide 7 (RoFAD) from roseoflavin. To confirm this, the FAD-dependent Sus scrofa D-amino-acid 8 oxidase (EC 1.4.3.3) was tested with RoFAD as a cofactor and found to be inactive. It was 9 hypothesized that a flavokinase/FAD synthetase (RibC) highly specific for riboflavin may be 10 present in S. davawensis, which would not allow the formation of toxic RoFMN/RoFAD. 11 The gene ribC from S. davawensis was cloned. RibC from S. davawensis was overproduced 12 in Escherichia coli and purified. Analysis of the flavokinase activity of RibC revealed that 13 the S. davawensis enzyme is not riboflavin-specific (roseoflavin, k cat /K m = 1.7 10-2 µM-1 s-1 ; 14 riboflavin, k cat /K m = 7.5 10-3 µM-1 s-1). Similar results were obtained for RibC from the 15 roseoflavin-sensitive bacterium Bacillus subtilis (roseoflavin, k cat /K m = 1.3 10-2 µM-1 s-1 ; 16 riboflavin, k cat /K m = 1.3 10-2 µM-1 s-1). Both RibC enzymes synthesized RoFAD and 17 RoFMN. The functional expression of S. davawensis ribC did not confer roseoflavin 18 resistance to a ribC defective B. subtilis strain.
A Field Guide to The Limb Progenitor

The primary goal of this thesis was to characterize the embryonic limb progenitor, a cell type that populates the early limb bud during the onset of limb morphogenesis. Two features of the limb progenitor were explored 1) the identity of a potential set of minimal transcription factors that are sufficient to instantiate limb progenitor identity and 2) the limb progenitor gene expression response to signaling molecules that are critical for regulating the ultimate morphology of the developing limb. The limb bud consists of mesenchymal progenitor cells, or limb progenitors, that originate from the lateral plate mesoderm (LPM). In addition to the limb progenitors of the limb bud, the LPM also gives rise to mesenchyme that will form the mesodermal components of the trunk, flank and neck. However, only the cells of the limb are capable of forming the patterned skeletal structures observed in arms and legs. The other LPM-derived mesenchymal progenitor cells are unable to form such structures, even when placed in the context of the organizing signals found in the limb bud. To determine which genes are responsible for specifying a limb progenitor identity that is distinct from the identity of neighboring mesenchymal tissues, a screen of transcription
Evaluation of Bio-insecticidal Property of Bacillus thuringiensis Strains Isolated from Western Ghats Soil

Morphological and cultural characterization of the native twenty isolates obtained from Western Ghats of Kerala, produced creamy white and puffy colonies. The colonies were circular or irregular and flat. Margins were either entire or undulate. Biochemical characterization of native Bacillus thuringiensis (Bt) isolates showed that all the isolates were positive for esculinase and starch hydrolysis tests and gave negative response to gelatin hydrolysis and Voges-Proskauer (VP) test. Shape of crystal proteins were studied in native Bt isolates by staining with Coomassie brilliant blue. The shape of proteins varied from irregular, spherical and composite, but the spherical shape was more common. Of the total of 20 isolates analyzed, 12 isolates produced spherical crystal proteins and 6 isolates produced composite crystal protein. Bioassay of selected four native Bt isolates (Bt23 Bt-133 Bt-190 Bt-242) and reference strain 4Q1 was done against Drosophila melanogaster. Original Research Article Sivaji and Girija; MRJI, 21(2): 1-12, 2017; Article no.MRJI. 32594 2 Lethal Concentration (LC50) value was the lowest with the reference strain 4Q1 (6.05 × 10 8 spores per mL), indicating high level of toxicity. Among the native isolates, Bt-23 recorded the lowest value of LC50 (7.39 × 10 8 spores per mL). Highest LC50 value of 8.64 × 10 8 spores per mL was recorded by Bt-242.
The impact of fisheries on vulnerable habitats: the case of trawling on circa-littoral grounds in the Strait of Sicily (central Mediterranean Sea)

ABSTRACT The Council Regulation (EC) no. 1967/2006 introduced the adoption of the 40 mm square-mesh or alternatively a 50 mm diamond-mesh codend for trawlers of EU Member States. In this context, the main aim of the current study was to compare the catch composition of Lampedusa’s shallow-water trawl fishery, in terms of retained and discarded fraction, using the 24 mm square-mesh codend (illegal and supposed unselective) and the 50 mm current diamond-mesh codend (legal and supposed selective). During 2012, 21 hauls were performed, under commercial conditions, with the 24 mm square mesh codend and 27 with the 50 mm diamond mesh codend in an area of the Strait of Sicily at depths from 40 to 80 m. The introduction of a 50 mm diamond-mesh, although not significantly, reduced the CPUEs of retained and discarded fraction compared with the 24 mm mesh. Moreover, for most target species and their size classes (especially immature individuals), the legal mesh recorded a lower mean number of specimens than the banned mesh size. All these advantages aside, the discard of the shallow-water trawl fishery, in Lampedusa, represented a very important part of the total catch (more than three-quarters) by both mesh sizes and a large amount of this was represented by species and habitat of conservation concern. Our results suggest that spatial restrictions, such as no-take zones, could be a more effective management tool to protect this sensitive ecosystem in the area than the technical measures (e.g. reduction of mesh size) imposed today by the EU.
Copper and zinc interactions: morphophysiological responses in sweet potato plants ( Ipomoea batatas L.)

Interacao cobre e zinco: respostas morfofisiologicas em plantas de batata-doce ( Ipomoea batatas L.) O objetivo do estudo foi avaliar o efeito conjunto de cobre (Cu) e zinco (Zn) sobre batata-doce, segundo parâmetros morfologicos, perfi l mineral e metabolismo antioxidante. Para tanto, as mesmas foram colocadas em sistema hidroponico e cultivadas em diferentes combinacoes de micronutrientes: T1 (0,041 mM Cu + 0,085 mM Zn [controle]); T2 (0,041 mM Cu + 0,850 mM Zn); T3 (0,123 mM Cu + 0,085 mM Zn) e T4 (0,123 mM Cu + 0,850 mM Zn). As plantas cultivadas em T2, T3 e T4 apresentaram reducao dos parâmetros morfologicos, aumento do conteudo de H2O2 e da peroxidacao lipidica quando comparadas ao controle. O aumento de Zn independente da concentracao de Cu (T2 e T4) causou diminuicao na absorcao e transporte de macronutrientes na planta; promoveu mecanismos de competicao, sequestro e compartimentalizacao de micronutrientes nas raizes e ativou a atividade das enzimas antioxidantes.
Halal tourism research bibliometric analysis in Scopus, ProQuest and Ebscohost / Mohd Nasir Ismail ...[et al.]

With the emerging and increasing interest toward halal product and services, a variety of halal based research can be found in online databases. Halal tourism in research is a quite recent topics in journal articles. Halal tourism subtopics has evolved into many subtopics such as halal culinary, halal destination, halal friendly hotel, halal lodging and halal tourism supply chain. With the use of bibliometric analysis and using Scopus analyzer and VOSviewer, this paper attempts to analyse and visualize research output made in the topic of halal tourism. Data are citations from Scopus, ProQuest and Ebscohost databases using 'halal tourism' as keyword. The data corpus are set for research articles in English and the date range set for 1987 to 2019. Total data collection is 383 citations. This paper aims to discover the subject relation of halal tourism research topics in Scopus, ProQuest and Ebscohost. From this research, related topics of halal tourism can be identified and analysed. Authors and journals of halal tourism would also be analysed
Microbial consortia in meat processing environments

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The description of the microbial consortia in the meat processing environment is important since it is a first step in understanding possible routes of product contamination. Furthermore, it may contribute in the development of sanitation programs for effective pathogen removal. The purpose of this study was to characterize the type of microbiota in the environment of meat processing plants: the microbiota of three different meat plants was studied by both traditional and molecular methods (PCR-DGGE) in two different periods. Different levels of contamination emerged between the three plants as well as between the two sampling periods. Conventional methods of killing free-living bacteria through antimicrobial agents and disinfection are often ineffective against bacteria within a biofilm. The use of gas-discharge plasmas potentially can offer a good alternative to conventional sterilization methods. The purpose of this study was to measure the effectiveness of Atmospheric Pressure Plasma (APP) surface treatments against bacteria in biofilms. Biofilms produced by three different L. monocytogenes strains on stainless steel surface were subjected to three different conditions (power, exposure time) of APP. Our results showed how most of the culturable cells are inactivated after the Plasma exposure but the RNA analysis by qPCR highlighted the entrance of the cells in the viable-but non culturable (VBNC) state, confirming the hypothesis that cells are damaged after plasma treatment, but in a first step, still remain alive. The understanding of the effects of APP on the L. monocytogenes biofilm can improve the development of sanitation programs with the use of APP for effective pathogen removal.
Separating an allele associated with late flowering and slow maturation of Arabidopsis thaliana from population structure

Genome-wide association (GWA) analysis is a powerful tool to identify individual loci underlying the complex traits. However, application of GWAS in natural population comes with challenges, especially power loss due to population stratification. Here, we introduce a bivariate analysis approach to a public GWAS dataset of Arabidopsis thaliana. Using this powerful approach, a common allele, strongly confounded with population structure, is discovered to be associated with late flowering and slow maturation of the plant. The discovered genetic effect on flowering time is further replicated in independent datasets. Using Mendelian randomization analysis based on summary associated statistics from our GWAS and expression QTL (eQTL) scans, we predicted and replicated a candidate gene AT1G11560 that potentially causes this association. Further analysis with flowering-time-related genes indicates that this locus is also co-selected with many flowering-time-related genes. Our study demonstrates the efficiency of multi-phenotype analysis to uncover hidden genetic loci masked by population structure. The discovered pleiotropic genotype-phenotype map provides new insights into understanding the genetic correlation of complex traits.
Analysis of mitochondrial DNA restriction fragment patterns in killer whales, Orcinus orca

This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu. Recommended Citation Stevens, Tracy Alison, "Analysis of mitochondrial DNA restriction fragment patterns in killer whales, Orcinus orca" (1989). Dissertations and Theses. Paper 3928.
An Optimised Protocol for Fluorescent-dUTP Based SSR Genotyping and its Application to Genetic Mapping in Eucalyptus

Abstract Integration of fluorescent-dUTP in polymerase chain reaction (PCR) appears to be a sound method for fluorescence labelling of amplicons in genotyping with simple sequence repeats (SSRs) using an automated sequence analyser. However, the method has not been explored in terms of performance optimisation and cost control. In this paper, we optimised the protocol for fluorescent-dUTP based SSR genotyping in a case study with Eucalyptus. A combination of low dNTP concentration (25 μM each) in PCR reaction and a touchdown PCR programme contributed to increase dramatically the fluorescent intensity of SSR amplicons, thereby facilitating accurate and multiplexed scoring of SSR alleles. The usefulness of the optimised protocol was demonstrated in its application to genetic mapping of SSR loci onto E. urophylla and E. tereticornis linkage maps constructed previously. The protocol optimised here would provide a reliable and economical assay for sequencer-based SSR genotyping in a wide range of biological applications.
Pathogenicity of three formulations of Beauveria bassiana and efficacy of autoinoculation devices and sterile fruit fly males for dissemination of conidia for the control of Ceratitis capitata

This study reports the pathogenicity of three formulations of Beauveria bassiana (Balsamo) Vuillemin (Hypocreales) – Bb‐ET, GHA, and Bb‐AES – and their application in panel‐type and cylinder‐type autoinoculation devices, and using sterile males as vectors for the control of Ceratitis capitata (Wiedemann) (Diptera: Tephritidae) in coffee‐producing areas of the Central Highlands of Guatemala. Using sterile adults of C. capitata under laboratory bioassays, mean lethal concentrations (LC50) of 1.4 × 107, 2.4 × 106, and 8.2 × 105 conidia ml−1, and median survival times of 4.1 ± 0.1, 4.2 ± 0.1, and 3.8 ± 0.1 days, were recorded for the strains GHA, Bb‐AES, and Bb‐ET, respectively. These values indicate that the three strains were sufficiently pathogenic and that their period of biological activity was considered adequate for using sterile flies as vectors of the inoculum. Observed percentages of sporulated wild C. capitata flies were 57.3, 44.7, and 44.3% for sterile fly vectors, panel devices, and cylinder devices, respectively. The total population reduction at the end of the study period was over 90% for the three treatments. Our results show that sterile males used as vectors or disseminator devices may represent a new control method for area‐wide integrated management of Mediterranean fruit flies. The potential of this new approach and its integration with other control methods, including the sterile insect technique, is discussed.