Juniperus navicularis - a study of Portuguese population structure and fitness

Juniperus navicularis Gand. is a dioecious endemic conifer that constitutes the understory of seaside pine forests in Portugal, areas currently threatened by increasing urban expansion. The aim of this study is to assess the conservation status of previously known populations of this species located on its core area of distribution. The study was performed in south-west coast of Portugal. Three populations varying in size and pine density were analyzed. Number of individuals, population density, spatial distribution and individual characteristics of junipers were estimated. Female cone, seed characteristics and seed viability were also evaluated. Results suggest that J. navicularis populations are vulnerable because seminal recruitment is scarce, what may lead to a reduction of genetic variability due solely to vegetative propagation. This vulnerability seems to be strongly determined by climatic constraints toward increasing aridity. Ratio between male and female shrubs did not differ from 1:1 in any population. Deviations from 1:1 between mature and non-mature plants were found in all populations, denoting population ageing. Very low seed viability was observed. A major part of described Juniperus navicularis populations have disappeared through direct habitat loss to urban development, loss of fitness in drier and warmer locations and low seed viability. This study is the first to address J. navicularis conservation, and represents a valuable first step toward this species preservation. 

Ecophysiology of Adonis distorta, a high-mountain species endemic of the Central Apennines

Morphological, anatomical and physiological plant and leaf traits of A. distorta, an endemic species of the Central Apennines on the Majella Massif, growing at 2,675 m a.s.l, were analyzed. The length of the phenological cycle starts immediately after the snowmelt at the end of May, lasting 128 ± 10 days. The low A. distorta height  (Hmax= 64 ± 4 mm) and total leaf area (TLA= 38 ± 9 cm2) associated to a high leaf mass area (LMA =11.8±0.6 mg cm−2) and a relatively high leaf tissue density (LTD = 124.6±14.3 mg cm−3) seem to be adaptive traits to the stress factors of the environment where it grows. From a physiological point of view, the high A. distorta photosynthetic rates (PN =19.6 ± 2.3 µmol m−2 s−1) and total chlorophyll content (Chla+b = 0.88 ± 0.13 mg g−1) in July are justified by the favorable temperature. PN decreases by 87% in September at the beginning of plant senescence. Photosynthesis and leaf respiration (RD) variations allow A. distorta to maintain a positive carbon balance during the growing season becoming indicative of the efficiency of plant carbon use. The results could be an important tool for conservation programmes of the A. distorta wild populations.

Effect of galactose metabolising and non-metabolising strains of Streptococcus thermophilus as a starter culture adjunct on the properties of Cheddar cheese made with low or high pH at whey drainage

Cheddar cheese was made using control culture (Lactococcus lactis subsp. lactis), or with control culture plus a galactose-metabolising (Gal+) or galactose-non-metabolising (Gal-) Streptococcus thermophilus adjunct; for each culture type, the pH at whey drainage was either low (pH 6.15) or high (pH 6.45). Sc. thermophilus affected the levels of residual lactose and galactose, and the volatile compound profile and sensory properties of the mature cheese (270 d) to an extent dependent on the drain pH and phenotype (Gal+ or Gal-). For all culture systems, reducing drain pH resulted in lower levels of moisture and lactic acid, a higher concentration of free amino acids, and higher firmness. The results indicate that Sc. thermophilus may be used to diversify the sensory properties of Cheddar cheese, for example from a fruity buttery odour and creamy flavour to a more acid taste, rancid odour, and a sweaty cheese flavour at high drain pH.

Vitamin A supplementation enhances Senegalese sole (Solea senegalensis) early juvenile’s immunocompetence: new insights on potential underlying pathways

Senegalese sole (Solea senegalensis) has been considered since the 1990´s to be a promising flatfish species for diversifying European marine aquaculture. However, pathogen outbreaks leading to high mortality rates can impair Senegalese sole commercial production at the weaning phase. Different approaches have been shown to improve fish immunocompetence; with this in mind the objective of the work described herein was to determine whether increased levels of dietary vitamin A (VA) improve the immune response in early juveniles of Senegalese sole. For this purpose, Senegalese sole were reared and fed with Artemia metanauplii containing increased levels of VA (37,000; 44,666; 82,666 and 203,000 total VA IU Kg-1) from 6 to 60 days post-hatch (early juvenile stage). After an induced bacterial infection with a 50 % lethal dose of Photobacterium damselae subsp. damselae, survival rate, as well as underlying gene expression of specific immune markers (C1inh, C3, C9, Lgals1, Hamp, LysC, Prdx1, Steap4 and Transf) were evaluated. Results showed that fish fed higher doses of dietary VA were more resistant to the bacterial challenge. The lower mortality was found to be related with differential expression of genes involved in the complement system and iron availability. We suggest that feeding metamorphosed Senegalese sole with 203,000 total VA IU Kg-1 might be an effective, inexpensive and environmentally friendly method to improve Senegalese sole immunocompetence, thereby improving survival of juveniles and reducing economic losses.

Sistematic, population genetics, propagation and conservation of Prunus azorica (Rosaceae)

Tese de Doutoramento, Biologia (Ecologia Vegetal), 25 de Junho de 2013, Universidade dos Açores.

Performance of Sirex noctilio’s biocontrol agent Deladenus siricidicola, in known and predicted hosts

Survival of the free-living mycetophagous form of Deladenus siricidicola, the major biological control agent of Sirex woodwasp, Sirex noctilio, was tested in known (Pinus taeda) and predicted novel (P. elliottii subsp. elliottii × P. caribaea var. hondurensis) hybrid host taxa. Trials were established in the field to simulate nematode dispersal both naturally by infected wasps and following commercial inoculation, as well as in the laboratory under controlled conditions. Nematodes showed reduced survival in hybrid pine compared with P. taeda for all tree-associated treatments, but performed equivalently in petri-dish bioassays containing substrate of each taxon. Growth of Amylostereum areolatum, the food source of D. siricidicola was lower on plates containing ground hybrid substrate than on plates containing ground P. taeda. Some physical differences were found between taxa, including differences in bordered pit diameters, tracheid widths, and basic density, but these did not consistently explain reduced performance. More plant secondary compounds (predominantly oleoresins) were present in hybrid taxa than in P. taeda, and in standing trees compared with felled trees. Our results suggested that D. siricidicola may not be as effective in hybrid pine taxa for the biological control of S. noctilio as it is in its current known host taxa, possibly because of reduced growth of its food source, A. areolatum in hybrid pine.

Eficácia de películas edíveis suplementadas com componentes de óleos essenciais no controlo de Listeria monocytogenes e Salmonella enterica Typhimurium

Dissertação de Mestrado, Engenharia Biológica, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2014

Monitorização da vegetação infestante em arrozais e prospeção de resistência a herbicidas em Echinochloa spp.

Mestrado em Engenharia Agronómica - Especialização em Proteção das plantas - Instituto Superior de Agronomia - UL

Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization

BACKGROUND Lactococcus garvieae is a bacterial pathogen that affects different animal species in addition to humans. Despite the widespread distribution and emerging clinical significance of L. garvieae in both veterinary and human medicine, there is almost a complete lack of knowledge about the genetic content of this microorganism. In the present study, the genomic content of L. garvieae CECT 4531 was analysed using bioinformatics tools and microarray-based comparative genomic hybridization (CGH) experiments. Lactococcus lactis subsp. lactis IL1403 and Streptococcus pneumoniae TIGR4 were used as reference microorganisms. RESULTS The combination and integration of in silico analyses and in vitro CGH experiments, performed in comparison with the reference microorganisms, allowed establishment of an inter-species hybridization framework with a detection threshold based on a sequence similarity of >or= 70%. With this threshold value, 267 genes were identified as having an analogue in L. garvieae, most of which (n = 258) have been documented for the first time in this pathogen. Most of the genes are related to ribosomal, sugar metabolism or energy conversion systems. Some of the identified genes, such as als and mycA, could be involved in the pathogenesis of L. garvieae infections. CONCLUSIONS In this study, we identified 267 genes that were potentially present in L. garvieae CECT 4531. Some of the identified genes could be involved in the pathogenesis of L. garvieae infections. These results provide the first insight into the genome content of L. garvieae.

Genetic diversity of Mycobacterium avium isolates recovered from clinical samples and from the environment: molecular characterization for diagnostic purposes

Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR for detection of IS1245 and IS901, sequencing of the hsp65 gene, and pulsed-field gel electrophoresis) were evaluated. The same strain was found in all the environmental isolates, 21 out of 23 (91.3%) of the isolates cultured from urine samples, and 5 out of 19 (26.3%) isolates from respiratory specimens. This strain did not cause disease in the patients. Testing best characterized the strain as M. avium subsp. hominissuis, with the unusual feature that 81.4% of these isolates lacked the IS1245 element. Contamination of certain clinical samples with an environmental strain was the most likely event; therefore, characterization of the environmental mycobacteria present in health care facilities should be performed to discard false-positive isolations in nonsterile samples, mainly urine samples. Molecular techniques applied in this study demonstrated their usefulness for this purpose.

Bifidobacterium breve UCC2003 metabolises the human milk oligosaccharides lacto-N-tetraose and lacto-N-neo-tetraose through overlapping, yet distinct pathways

In this study, we demonstrate that the prototype B. breve strain UCC2003 possesses specific metabolic pathways for the utilisation of lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), which represent the central moieties of Type I and Type II human milk oligosaccharides (HMOs), respectively. Using a combination of experimental approaches, the enzymatic machinery involved in the metabolism of LNT and LNnT was identified and characterised. Homologs of the key genetic loci involved in the utilisation of these HMO substrates were identified in B. breve, B. bifidum, B. longum subsp. infantis and B. longum subsp. longum using bioinformatic analyses, and were shown to be variably present among other members of the Bifidobacterium genus, with a distinct pattern of conservation among human-associated bifidobacterial species.

Développement de stratégies et d'outils analytiques novateurs pour la détection de vaches atteintes de paratuberculose

La paratuberculose bovine est une maladie causée par la mycobactérie Mycobacterium avium subsp. paratuberculosis (MAP). Elle est responsable d’énormes pertes économiques dans le monde. En effet, cette maladie provoque la diminution de la production laitière chez les vaches ainsi qu’un état de fatigue général en raison d’une entérite chronique chez les sujets atteints. Des indices mettent également en évidence le potentiel zoonotique de MAP et malheureusement aucun traitement n’est connu à ce jour. Ainsi, les stratégies actuelles pour contrer la maladie dans les troupeaux reposent plutôt sur des actions préventives. Actuellement, le diagnostic de la paratuberculose reste difficile et la prévalence de la maladie est probablement sous-estimée dans les troupeaux en raison de la faible sensibilité des tests diagnostiques. Dans l’optique de développer une nouvelle méthode diagnostique pour la paratuberculose, ce projet de recherche s’est établi en deux étapes : la mise en place d’un système de diagnostic robuste des animaux par les méthodes de dépistage traditionnelles, incluant une étude comparative de l’efficacité de trousses commerciales, et finalement l’étude de la prolifération cellulaire spécifique des lymphocytes comme d’une épreuve diagnostique pour la maladie. Ainsi, la comparaison des trousses commerciales a démontré un écart d’efficacité qui a permis d’établir de nouvelles recommandations pour l’analyse des animaux ainsi que l’amélioration du diagnostic de la paratuberculose dans les troupeaux. Concernant le développement d’une méthode de diagnostique basée sur la prolifération lymphocytaire, de nombreuses difficultés techniques ont entravé le bon déroulement du projet mais ces travaux montrent la possibilité de caractériser de manière plus complète les différents types lymphocytaires par cytométrie de flux chez le bovin laitier.

Descripción del análisis microbológico realizado mediante maldi-tof en muestras de la fundación santa fe de Bogotá.

Introducción: La rápida detección e identificación bacteriana es fundamental para el manejo de los pacientes críticos que presentan una patología infecciosa, esto requiere de métodos rápidos para el inicio de un correcto tratamiento. En Colombia se usan pruebas microbiología convencional. No hay estudios de espectrofotometría de masas en análisis de muestras de pacientes críticos en Colombia. Objetivo general: Describir la experiencia del análisis microbiológico mediante la tecnología MALDI-TOF MS en muestras tomadas en la Fundación Santa Fe de Bogotá. Materiales y Métodos: Entre junio y julio de 2013, se analizaron 147 aislamientos bacterianos de muestras clínicas, las cuales fueron procesadas previamente por medio del sistema VITEK II. Los aislamientos correspondieron a 88 hemocultivos (60%), 28 urocultivos (19%), y otros cultivos 31 (21%). Resultados: Se obtuvieron 147 aislamientos con identificación adecuada a nivel de género y/o especie así: en el 88.4% (130 muestras) a nivel de género y especie, con una concordancia del 100% comparado con el sistema VITEK II. El porcentaje de identificación fue de 66% en el grupo de bacilos gram negativos no fermentadores, 96% en enterobacterias, 100% en gérmenes fastidiosos, 92% en cocos gram positivos, 100% bacilos gram negativos móviles y 100% en levaduras. No se encontró ninguna concordancia en bacilos gram positivos y gérmenes del genero Aggregatibacter. Conclusiones: El MALDI-TOF es una prueba rápida para la identificación microbiológica de género y especie que concuerda con los resultados obtenidos de manera convencional. Faltan estudios para hacer del MALDI-TOF MS la prueba oro en identificación de gérmenes.