Miracle-dz/UniFAR-FTUs huggingface dataset:
THE ROLE OF SHEARING IN THE TRANSMISSION OF DIPLODIA PINEA IN SCOTS PINE CHRISTMAS TREES IN KENTUCKY

OF THESIS THE ROLE OF SHEARING IN THE TRANSMISSION OF DIPLODIA PINEA IN SCOTS PINE CHRISTMAS TREES IN KENTUCKY Diplodia tip blight is an important disease of pines, especially Scots pine Christmas trees in Kentucky. The hypothesis for my thesis work was that D. pinea could be acquired and transmitted on the tools during annual shearing of the Christmas trees. Samples taken from tools after shearing on two different Christmas tree farms in Kentucky in 2005 and 2006 yielded D. pinea colony forming units, but in very low quantities; typically less than 10 CFUs per collection. Diplodia-associated dieback from the sheared tips was never found in the field, suggesting that transmission and subsequent infections were not occurring via these sheared tips. Controlled infections indicated that a minimum of 100 spores was necessary to create symptomatic infections on sheared tips. Lysol Disinfectant Spray did not remove D. pinea from tools when sprayed on them after shearing, but it did effectively prevent spore germination in vitro. Observations of Diplodia lesion development on one Scots pine Christmas tree farm in Kentucky during the springs of 2006 and 2007 suggested that D. pinea infections occurred primarily via the bases of needle bundles on elongating shoots. The most likely source of inoculum was dead infested pine tissues within and beneath the canopy. The use of a protectant fungicide may have resulted in an observed dramatic decrease of disease on this farm.
The Sea Urchin Diadema antillarum (Echinodermata, Equinoidea), algal cover and juvenile coral densities in La Parguera, Puerto Rico

Grazing by the black sea urchin Diadema antillarum reduces algal cover and enhances coral recruitment. The overall goal of this project was to examine if there is a relationship between densities of D. antillarum with algal cover and abundance of juvenile corals. Population densities of the black sea urchin, juvenile coral abundances and algal cover were assessed along four 20m2 transects at two depth intervals (0-3 and 3-8m) within each of two inner shelf coral reefs off La Parguera Natural Reserve (San Cristobal and Enrique) in southwest, Puerto Rico using a 1m2 quadrat (divided into 100 areas of 100cm2, each area encompassing 1% of the quadrat). Juvenile coral densities were counted and identified to genus or species. Algal cover and composition was measured using each 1% square of the 1m2 quadrat. Urchin population densities were significantly higher at 0-3m at the two sites studied. Population densities were higher at Enrique at 0-3m than at San Cristobal but at 3-8m Diadema was not seen at Enrique. A total of 30 juvenile corals belonging to eight different genera were found. Juvenile coral densities were higher at 3-8m at the two reef sites studied. Algal cover and composition was mainly composed by crustose coralline algae at 0-3m at both reef sites. Macroalgal cover was low at both reefs. The results of this study suggest that densities of coral recruits at inner shelf reefs in La Parguera, Puerto Rico are driven mainly by differences in habitats (depth). KEY WORDScoral recruitment, abundance, Diadema antillarum, densities, composition, correlation
Constructive tissue remodeling by extracellular matrix bioscaffolds within the aging skeletal muscle microenvironment

Adult mammalian skeletal muscle tissue retains inherent regenerative capability in response to injury. This regenerative response is contingent upon an activated progenitor cell population and a temporal transition from pro-inflammatory M1 to immunomodulatory and constructive M2 polarized macrophages at the site of injury. Specifically, pro-inflammatory effector molecules secreted by M1 macrophages promote the expansion of skeletal muscle progenitor cells, while resolution of the inflammatory response and myogenic differentiation of skeletal muscle progenitor cells is dependent upon immunomodulatory effector molecules secreted by M2 macrophages. The decline in the regenerative capacity of skeletal muscle tissue associated with advanced age is largely a consequence of progenitor cell dysfunction. Furthermore, advanced age is accompanied with immunosenesence of the innate immune system resulting in an impaired macrophage polarization potential. Biologic scaffold materials composed of mammalian extracellular matrix (ECM) have been successfully used in both pre-clinical animal studies and in human clinical applications to promote constructive tissue remodeling in a variety of anatomic locations including skeletal muscle. The presence of ECM bioscaffolds at sites of skeletal muscle injury has been associated with a predominant M2 macrophage phenotype and downstream site-appropriate or constructive, functional tissue remodeling. The mechanisms responsible for this constructive tissue remodeling response are only partially understood. The present dissertation shows that the age of source animals from which ECM bioscaffold materials are harvested represents a determinant factor of the constructive tissue remodeling potential induced by these materials. The present work also shows that degradation products of mammalian ECM promote the constructive M2 macrophage phenotype in both young and age-impaired macrophages. Moreover, effector molecules from macrophages exposed to ECM degradation products are chemotactic and myogenic for skeletal muscle progenitor cells. The present dissertation describes a new rodent model of volumetric muscle loss (VML) and an ECM bioscaffold based approach for tissue replacement associated with modulation of macrophage phenotype and the endogenous recruitment of perivascular stem cells.
Complex Regional Pain Syndrome Type 1 is a Disorder to Prevent and Treat

The typical areas that CRPS can affect are the arms, legs, hands, or feet. The condition usually occurs after some kind of injury or trauma to the area. It is a syndrome characterized by pain at even rest, functional impotence, edema, micro vascular alterations skin, alloying and hyperalgesia. The clinical criteria currently used for the diagnosis of CRPS 1 are those defined by Harden and Bruehel in 2007 (“Budapest clinical diagnostic criteria for CRPS“) [2] [Table 1].
Adaptability and stability of soybean yield in two soybean producing regions = Adaptabilidade e estabilidade da produtividade de soja em duas regiões sojícolas

The aim of this study was to evaluate the adaptability and stability of soybean genotypes grown in two soybean producing micro-regions (301 and 401), in the harvest seasons of 2006/2007 and 2007/2008. 16 soybean genotypes were studied (six soybean lines of the breeding program of Monsoy Ltda. and 10 cultivars). The experiments were conducted in a randomized complete block design, with three replications. Individual and group analyses were performed and the parameters of adaptability and stability were estimated by the methods proposed by Eberhart and Russel, Annicchiarico, Linn and Binn and Centroide. The results showed interaction of genotypes and environments showing different behavior of the genotypes according to environmental fluctuations. The methods of Annicchiarico, Linn and Binns modified by Carneiro and Centroid, were consistent with each other and allowed to identify among the genotypes, the highest stability and adaptability. The cultivars M-SOY 7908 RR, M-SOY 8199 RR and BRS Valiosa RR have general adaptability and stability. The Strains LG4 and LG5, and cultivar M-SOY 7908 RR showed high adaptability and stability in favorable environments and the control M-SOY 8199 RR for unfavorable environments and the strain CC4 showed high stability and adaptability in favorable environments. The cultivars MSoy 8199 RR and BRS Valiosa RR had adaptation to unfavorable and general environments, considering the four methods that were evaluated in this study.
Olfactory orientation of the truffle beetle, Leiodes cinnamomea

Although the truffle beetle, Leiodes cinnamomea, inflicts substantial damage to the ripe stage of fruiting bodies of the economically important black truffle (Tuber melanosporum), it is not attracted by ripe truffle odours. Rather, male beetles are attracted to infested truffles only in the presence of female beetles, suggesting that the former employ a pheromone to locate truffles over short distances. In contrast, female beetles show no attraction to infested or uninfested truffles, suggesting that they employ other cues, possibly linked to odours emitted by truffles prior to the ripe stage. We hypothesize that the chemical composition of truffle volatiles changes over the life of the truffle fruiting body, being attractive to insects early on and to mammals just prior to decomposition.
Biology Today: An Issues Approach

1. Biology: Science and Ethics 2. Genes, Chromosomes, and DNA 3. Human Genetics 4. Genetic Engineering and Genomics 5. Evolution 6. Classifying Nature 7. Human Variation 8. Sociobiology 9. The Population Explosion 10. Nutrition and Health 11. Plants to Feed the World 12. Stem Cells, Cell Division and Cancer 13. The Nervous System and Senses 14. Drugs and Addiction 15. Mind and Body 16. HIV and AIDS 17. New Infectious Threats 18. Biodiversity and Threatened Habitats 19. Protecting the Biosphere
Análisis de sistemas pectinolíticos bacterianos. Aislamiento y caracterización de las pectinasas PelA de "Paenibacillus" sp. BP-23 E YvpA de "Bacillus subtilis"

La aplicacion de enzimas en la industria constituye una de las aportaciones mas recientes en las tecnologias de produccion, debido a su elevada eficiencia catalitica, a que su uso no dana el medio ambiente y a su alta rentabilidad economica. En los ultimos anos ha aumentado de forma importante la aplicacion de enzimas microbianos en la industria. La mayoria de estos enzimas son degradadores de polisacaridos de la pared celular vegetal, como celulosas, hemicelulosas y pectinas. La pectina es un polimero formado principalmente por cadenas de acido galacturonico, parcialmente esterificado. Las pectinasas son las enzimas que degradan la pectina. El principal objetivo de la tesis fue caracterizar pectinasas con potencial aplicacion industrial. Para ello, primero se realizo el analisis de los sistemas degradadores de pectina de las cepas bacterianas "Paenibacillus" sp. BP-23 y "Bacillus" sp. BP-7, aisladas previamente por el grupo de investigacion a partir de suelo de arrozal del Delta del Ebro. El sistema pectinolitico de ambas cepas mostro una multiplicidad de bandas, motivo por el cual, se procedio a la clonacion, purificacion y caracterizacion de pectinasas a partir de las cepas analizadas y de "Bacillus subtilis" 168. Los estudios realizados indican que PelA de "Paenibacillus" sp. BP-23 e YvpA de "Bacillus subtilis" son enzimas nuevos, con caracteristicas diferentes a las pectato liasas conocidas, que permiten identificar un subgrupo de enzimas dentro de las pectato liasas de la familia PL3. La inusual elevada actividad sobre pectina de los dos enzimas estudiados en este trabajo los hace buenos candidatos para aplicaciones biotecnologicas relacionadas con la degradacion de pectina de sustratos naturales. En el contexto de la utilizacion creciente de enzimas en la industria se planteo la produccion del mas activo de ellos, la pectato liasa PelA, en cantidades elevadas para poder realizar ensayos de aplicacion industrial, utilizando cepas huesped de "Bacillus subtilis". Con este fin se construyeron vectores lanzadera que replican tanto en "Bacillus subtilis" como en "Escherichia coli". Los resultados obtenidos en este trabajo suponen una aproximacion a la tarea de sobreproducir pectato liasas, lo que ha permitido la identificacion de problemas especificos de la expresion de los enzimas en estudio y posibilitaran la construccion futura de nuevas cepas recombinantes de productividad y rendimiento aumentado. ENGLISH
The roles of surface ultrastructures in the predatory life cycle of Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is a ubiquitous Gram-negative 8-proteobacterium that is predatory on other Gram negative bacteria. It's prey includes many pathogenic bacteria, including E. coli, Salmonella, Proteus and Pseudomonas species; as such, there is much interest in the study of Bdellovibrio with a view to its potential use as an alternative antimicrobial therapy. Key to any future research into medical applications of this bacterium is an understanding of its predatory life cycle. Attack phase Bdellovibrio uses rapid flagellar motility through liquid environments to find its prey; upon collision with a suitable prey cell, it forms a strong attachment to the cell and generates a pore in the prey outer membrane. The predator then squeezes through this pore, loses its flagellum and establishes itself in the prey periplasm; the entry pore is then resealed, the prey rapidly killed with its peptidoglycan being modified to produce a rounded, osmotically stable structure termed the bdelloplast. Once safely within the bdelloplast, the Bdellovibrio secretes an arsenal of lytic enzymes into the prey cytoplasm which allow transport of the constituent monomers of DNA, RNA, protein et cetera from the prey back into the growing Bdellovibrio. The predator elongates as a spiral shaped filament within the periplasm of the prey and once the contents of the cytoplasm are exhausted, the filament septates into progeny Bdellovibrio which then re-synthesise flagella and lyse the remains of the prey cell to become free swimming attack phase predators. In this thesis, the role of flagellar motility in the predatory lifestyle of Bdellovibrio was studied through individual insertional inactivation of each of the 6 genes found in the B. bacteriovorus HDIOO genome that encode the flagellar filament protein, FliC. Only one was found to be essential for filament formation yet, contrary to previous hypotheses, this non-motile mutant was still found to be predatory when applied to immobilised prey in a novel fluorescence assay. Thus, the role of Type IV pili in predation was investigated through both microscopic, mutational and transcriptional means. Abolition of the Type IV pilus fibre forming protein, PilA, resulted in a mutant that had no pilus fibres and was incapable of predation using the same assay as in the non-motile FliC mutant strain. Throughout this work, experimental challenges have necessitated the continuing development of electron microscopic techniques for whole cell, flagella, pili and bdelloplast imaging and development of fluorescence methods for use in Bdellovibrio, such as novel use of GFP-encoding transposon mutagenesis and chemical dye-based assays. Work presented here has demonstrated that pili, not flagella, are the bacterial nanomachines required for prey entry and that GFP is a viable tool for future study of this fascinating and potentially therapeutic predator.
Mapping a path towards improved coccidial control in poultry.

Coccidiosis is a disease caused by the Eimeria species (phylum Apicomplexa), most notably in poultry. The annual cost of coccidiosis has been estimated to exceed US$ 2.4 billion per annum and control is essential for effective poultry production (Shirley et al. 2005). Control of the Eimeria species has largely been based upon chemotherapy, although resistance is rife. Vaccination with live parasites is effective but relatively expensive. Sustainable alternatives including novel recombinant vaccines are being sought but, in common with other protozoan parasites, the identification of genuinely immunoprotective antigens has proven difficult. The majority of screens for vaccine candidates protective against protozoan infection have been largely empirical, based upon criteria other than protection. In response to this problem we have developed a population based genetic mapping strategy using a combination of host and parasite genetics as well as deleterious parasite strain-specific selection (Blake et al. 2011a).
The application of High Resolution Melting Analysis (HRMA) for rapid detection of bacteria responsible for bloodstream infections

Abstract: Background: The diagnosis of bloodstream infection is a significant challenge for healthcare providers and is often associated with severe illness (sepsis) and poor outcomes. Rapid detection and identification of pathogens followed by characterisation of antibiotic resistance could help direct early treatment and improve patient care. Standard blood culture methods, which usually take 2-5 days to complete, can confirm if there is a bacteraemia or not in suspected patients. However, molecular approaches have been developed and are being increasingly investigated to overcome disadvantages of culture. One of the main potentials of molecular techniques is that they should be able to identify pathogens within a short time which could help clinicians treat patients earlier with rational antimicrobial therapy and limit overuse of antibiotic exposure.Objectives: To present the development and optimisation of a simple, rapid and cost-effective Real Time PCR methods combined with a High Resolution Melting Analysis (HRMA) approach, to detect and identify common bacteria associated with bloodstream infections.Approach: 16S rRNA and Gram classification primers were used on a broad range real-time PCR for molecular Gram typing and HRMA in a single run. Differentiation of bacterial species was achieved using a multi-parameter, decision-tree approach based on Gram typing, grouping according to melting temperature (Tm) and sequential comparisons of melting profiles (Curve shapes) against reference organisms.Findings: A preliminary validation was undertaken by blinded analysis of 53 consecutive bloodstream isolates from a clinical microbiology laboratory. 50 isolates contained organisms present on the panel and 96% of these were identified correctly at genus or species level. A correct Gram classification was reported for all 53 isolates. The strategy of amplification of the bacterial signal to an appropriate level using a short term pre-culture system (STPCS) for up to 12 hours prior to HRMA analysis significantly improved the overall sensitivity of the assay in spiked blood.Conclusion: This study suggests that a PCR-HRMA approach could be used as an alternative cheap approach to other molecular approaches for rapid detection and identification of bacteria responsible for >95% of bloodstream infections especially when combined with a Short Term Pre-Culture System (STPCS). Such development together with the current standard culture-based methods could allow clinicians to establish more effective management and treatment of patients with suspected bloodstream infection at an earlier stage than is possible with only current culture-based approaches.
Individual and environmental drivers of the foraging behaviour in a long-lived coastal seabird

To study the impact of environmental changes in a coastal marine ecosystem, it is necessary to use indicator species. It is crucial to understand the foraging performances that proceed from environmental changes. The aim of my thesis was to examine the influence of intrinsic and extrinsic factors on the foraging activity of the little penguins (Eudyptula minor). The thermocline allowed birds to approach optimal behaviour. However, the thermocline is an unstable element. I did not find any effect of individual characteristics on their foraging behaviour and success. My work suggests that environmental conditions are major factors that will influence the behaviour of little penguins, allowing me to conclude that little penguins are good ecological indicators.
Effects of an Intervention Program with and without Pretest Assessment on Schoolchildren' s Self-efficacy to Create a Smoke-free Home

Background: A school-based smoke free home (SFH) program is useful in empowering the mother and child to reduce secondhand smoke exposure or create a smoke-free home but the effects of pretesting on knowledge and attitude has been largely ignored. We aimed to test whether such a program can be effective in Southern Thailand with an additional assessment of the net effect of the pretest. Methods: A Solomon four-group design was conducted in 12 out of 50 schools of Hatyai district, Songkhla province, Thailand. Schools were assigned to receive an immediate intervention with and without pretest assessment; or control group with and without pretest assessment. Four hundred and eighty-two households participated. Four classroom sessions taught by a trained teacher over a 1-month period were implemented. Outcome variables included smoke-free home status, knowledge and attitude towards the harms of exposure to secondhand smoke and smoking, selfconfidence in creating a smoke-free home, avoiding exposure to secondhand smoke, encouraging the smoker to not smoke in the home, and number of cigarettes smoked per day. The outcomes were assessed at baseline and 3 months after the intervention using self-administered questionnaires.
Does Dispersal Limit Beetle Re‐colonization of Restored Fenland? A Case Study Using Direct Measurements of Dispersal and Genetic Analysis

Dispersal ability is known to limit the colonization by many fenland species onto restored habitat but factors determining colonization by wetland invertebrates onto restored fenland have not been previously examined. We used mark‐release‐recapture and harmonic radar tracking coupled with genetic analysis (ISSR‐PCR, inter‐simple sequence repeat—polymerase chain reaction) to assess the population structure and colonization of a brachypterous wetland carabid (Carabus granulatus) onto restored fenland. The first two methods were used to determine the dispersal rate of C. granulatus in the absence of barriers, while the genetic analysis was used to examine whether populations were separated by either distance or the water channels and drainage ditches that intersect fenland landscapes. Mark‐release‐recapture and harmonic radar tracking indicated that the most active 6% of individuals could travel over 25 m in a day and individuals found to be traveling these distances remained atypically active throughout the season. Thus, C. granulatus can disperse at a rate great enough to colonize all areas of restored fenland in the study site within 1 year in the absence of barriers. We found no evidence of genetically distinct sub‐populations of C. granulatus showing that distance and water barriers did not limit the movement of individuals from potential source populations to the restored habitat. This research indicates that where fenland is created with nearby established fenland, colonization opportunities should not be considered a limiting factor to colonization by wetland carabids, even where waterways divide sites.