Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine‐scale quantification of floral and faunal breaks and their geographic correlates, with an example from south‐eastern Australia

Aim We introduce a method to quantify shared breaks in aggregate biotic distributions and their relationships to geographic variables. The method is based on quantification of distributional taxic and abiotic data that can be applied over multiple spatial scales. We aim to show biogeographic breaks and varying transition zones at a fine level of detail (5‐km resolution) and develop an approach to assess existing bioregionalization schemes.
Analysis of arsenic resistance in the biomining bacterium, Acidithiobacillus caldus

In this study the chromosomal arsenic resistance (ars) genes shown to be present in all Acidithiobacillus. caldus isolates were cloned and sequenced from At. caldus #6. Ten open reading frames (ORFs) were identified on a clone conferring arsenic resistance, with three homologs to arsenic genes, arsC (arsenate reductase), arsR (regulator) and arsB (arsenite export). This ars operon is divergent, with the arsRC and arsB genes transcribed in opposite directions. Analysis of the putative amino acid sequences of these arsRC and arsB genes revealed that they are the most closely related to the ars genes of Acidithiobacillus ferrooxidans. These ars genes were functional when transformed into an Escherichia coli ars deletion mutant ACSH50I, and conferred increased levels of resistance to arsenate and arsenite. ArsC was required for resistance to arsenate, but not for resistance to arsenite. None of the other ORFs enhanced arsenic resistance in E. coli. A transposon located arsenic resistance system (TnAtcArs) has been described for highly arsenic resistant strains of the moderately thermophilic, sulfur-oxidizing, biomining bacterium At . caldus #6. In the latter study it was shown that TnAtcArs confers higher levels of resistance to arsenate and arsenite than the chromosomal operon. TnAtcArs was conjugated into a weakly ars resistant At. caldus strain (C-SH12) and resulted in greatly increased arsenite resistance. RT-PCR analysis revealed that arsR and arsC are co-transcribed. Despite ORF1 (cadmium inducible-like protein) and ORF5 (putative integrase for prophage CP-933R) not being involved in resistance to arsenic, ORF1 was co-transcribed with arsRC and ORF5 with arsB. Using arsR-lacZ and arsB-lacZ fusions it was shown that the chromosomal ArsR-like regulator of At. caldus acts as a repressor of the arsR and arsB promoter expression. Induction of gene expression took place when either arsenate or arsenite was added. The chromosomal located ArsR was also able to repress TnAtcArs, but the transposon-located ArsR was unable to regulate the chromosomal system.
Genes of the serotonergic system & susceptibility to psychiatric disorders : A gene-based haplotype approach

Psychiatric disorders are complex, non-mendelian disorders. Complex disorders are ultimately determined by a number of genetic and environmental factors, and the effect of each factor may be obscured or confounded by others. Although detection and precise characterization of the relationship and interactions between genes involved and/or environmental factors may not be ascertained by any available methods, several strategies of investigation may be used. Candidate gene analysis is one disclosing approach, which was used in this thesis to test for associations between a particular gene variant and a disease. This thesis work aimed to design a simple strategy to construct sets of polymorphic loci limited by gene boundaries, referred to as gene-based haplotypes, to be applied in casecontrol clinical studies, as opposed to the classical, ancestral haplotype block approach, which is mostly used for genome-wide and large scale population analyses. The genebased haplotype approach developed here is not influenced by parental transmission data, is cost and time effective, and is more informative than single locus associations. Also, linkage disequlibrium (LD) analysis within the gene and between the markers increases the likelihood to detect concealed causative alleles. This strategy was applied to two candidate susceptibility genes of the serotonergic system implicated in the pathophysiology of several psychiatric disorders: (i) the serotonin transporter (5-HTT) gene, and (ii) the tryptophan hydroxylase 1 (TPH-1) gene. Focusing on these genes, the strategy was adapted to a classical case-control design to seek for association between specific gene-based haplotypes that are common in the population while potentially carrying risk for the disorder. Three different psychiatric disorders were explored: Major Depressive Disorder (MDD), Schizophrenia (SCZ) and Borderline Personality Disorder (BPD). Single locus analyses provided a few positive associations with the disorders, which were mostly weak especially after correction for multiple testing. This was expected, as it is often the case for single-locus association studies. However, when multi-loci sets were constructed using a population genetics algorithm, several haplotypes were identified that displayed strong statistical associations with disease. The significance level obtained for haplotype markers in association studies was substantially higher than that observed for single loci.
A Survey of the Invasive Aquatic and Riparian Plants of the Lower Rio Grande

Abstract : Hydrilla has exhibited extensive range expansion along the Rio Grande since it was first discovered in early 1990 and is now found in areas far removed from the original infestation in Brownsville, TX. Hydrilla, a nonindigenous aquatic plant species, has been implicated in restricted water delivery, inaccurate water accounting, and an overall breakdown of system maintenance. The presence of hydrilla also has had a decided impact on native flora by the formation of extensive monocultures in many areas. In 2004, surveys were conducted starting below Amistad Reservoir to immediately below Falcon Reservoir to assess the distribution and expansion of hydrilla infestations and document the presence of other invasive aquatic and riparian plant species. A total of seven nonindigenous plant species were observed. Hydrilla infestations that were originally discovered during 2003 had increased in size through localized stolon expansion. Also, new hydrilla sites were discovered in 2004, including several directly below Amistad Reservoir. No hydrilla was discovered immediately south of Laredo; however, hydrilla infestations had dramatically increased below Falcon Reservoir. Giant cane continues to spread down river, even displacing well-established common cane. While no new Eurasian watermilfoil sites were discovered in 2004, existing infestations near Del Rio remain stable, extending bank-to-bank and considerable distances down the river. Eurasian watermilfoil fragments, which could lead to the formation of new infestations downstream, were observed in the river. Numerous new sites of parrotfeather, elephant-ear and salt cedar were found during the 2004 survey, and all sites identified in 2003 had increased in localized spread. One endangered wetland plant species, Correll's false dragonhead (Physostegia correllii), was tentatively identified.
BIOECOLOGIA DE Oncideres cervina (COLEOPTERA: CERAMBYCIDAE) EM CANELA-GUAICÁ ( Ocotea puberula : Lauraceae) NA REGIÃO CENTRAL DO RIO GRANDE DO SUL, BRASIL

The insect fauna knowledge of forest ecosystems have their importance in relation to damage caused by their different segments. The bioecology of the Oncideres cervina(Coleoptera: Cerambycidae) in Ocotea puberula(Lauraceae) was studied in the central region of Rio Grande do Sul state, Brazil. In 49 cut twigs were analyzed the cutoff frequency, the diameter of cut twigs and sections, twig length, posture incisions frequency, adult emergence, exit orifice size, length and volume of the larvae gallery of this species. The cut twigs period extends from February to March and this species is fit as thick cutter twigs. The incisions posture number is variable, but the highest concentration is found on sections 20 to 40 cm from the cut, with an average value of 11 incisions. Two hundred adults emerged from 27 twigs, with the most emergent on the first half of December. In order to complete its development, this species requires less wood volume if compared to other twig girdlers species.
Dynamic QTL mapping for plant height in Upland cotton (Gossypium hirsutum)

Plant height served as one of model traits to analyse dynamic development. The objective of this research was to investigate quantitative trait loci (QTL) and dynamic QTL for plant height trait using an intraspecific recombinant inbred line (RIL) population and a constructed genetic map in Upland cotton (Gossypium hirsutum L.). Totally, 41 QTL and 23 conditional QTL controlling plant height were detected at two experimental environments, respectively. Four stable QTL were identified simultaneously in both environments. Some QTL identified at the early stage could not be detected at the final stage at plant maturity. Conditional QTL with different genetic effects were identified at certain stages, demonstrating that the expression of QTL had temporal characteristic during plant growth. Therefore, the study of dynamic QTL could unravel temporal genetic patterns controlling complex developmental quantitative traits.
Produtividade de melancia em diferentes níveis de adubação química e orgânica

O experimento teve o objetivo de avaliar a resposta da melancieira a diferentes niveis de adubacao quimica e orgânica. O delineamento empregado foi em blocos casualizados, em esquema fatorial 5 x 4, sendo 5 doses de adubo quimico na formulacao 4-30-16 e 4 niveis de adubo orgânico - esterco de gado. Foram utilizadas 4 repeticoes e 10 plantas por parcela da variedade Crimson Sweet. Os niveis de adubacao quimica testados foram de 0, 150, 300, 450 e 600 gramas por cova e para a adubacao orgânica os niveis avaliados foram 0, 3, 6 e 9 litros de esterco de gado por cova. Houve correlacao linear positiva entre todos os parâmetros avaliados. O adubo quimico nao teve interacao significativa com o esterco de gado, exceto na relacao C/D, nas doses de 0, 3 e 6 litros por cova. A melhor produtividade (22989,61 kg.ha-1) foi obtida com 450g/cova de 4-30-16 (NPK). O incremento na produtividade da melancia foi limitado pelo fosforo quando cultivada somente com fertilizacao orgânica. O incremento na produtividade da melancia foi limitado pelo nitrogenio quando cultivada somente com fertilizante quimico NPK. Para a cultivar Crimson Sweet, quanto maior a relacao C/D, maior o peso medio do fruto.
Landscape structure and climatic variation determine Atlantic salmon genetic connectivity in the Northwest Atlantic

The identification of landscape or climatic correlates of genetic connectivity can reveal the processes that regulate spatial diversity and inform the management and conservation of exploited or endangered species. Increasingly, the role of local adaptation in regulating spatial structure is gaining recognition, though disentangling its influence from that of dispersal and genetic drift remains challenging. We examined genetic connectivity using 15 microsatellite loci in 3546 Atlantic salmon (Salmo salar) from 47 locations in Newfoundland and Labrador. Cluster analysis revealed regional associations, but examples of unexpectedly high divergence over small spatial scales ( 500 km) were common with little evidence of isolation by distance (R2 = 0.04). We evaluated the hypothesis that spatial structure is less influenced by straying and more by adaptation and (or) drift using sample-associated data on 22 landscape and climate variables and both stepwise multiple r.
Expansion of Vγ9Vδ2 T Cells Is Triggered byFrancisella tularensis-Derived Phosphoantigens in Tularemia but Not after Tularemia Vaccination

ABSTRACT Tularemia is a disease caused by the facultative intracellular bacterium Francisella tularensis. Here we demonstrate that during the first weeks of infection, a significant increase in levels of Vγ9Vδ2 cells occurred in peripheral blood: in 13 patients analyzed 7 to 18 days after the onset of disease, these lymphocytes represented, on average, 30.5% of CD3+ cells and nearly 100% of γδ+ T cells. By contrast, after vaccination with the live vaccine strain (LVS) of F. tularensis, only a minor increase occurred. Eleven days after vaccination, γδ T cells represented an average of 6.7% and Vγ9Vδ2 cells represented an average of 5.3% of T cells, as in control subjects. Since derivatives of nonpeptidic pyrophosphorylated molecules, referred to as phosphoantigens, are powerful stimuli for Vγ9Vδ2 cells, this observation prompted an investigation of phosphoantigens in F. tularensis strains. The F. tularensis phosphoantigens triggered in vitro a proliferative response of human Vγ9Vδ2 peripheral blood leukocytes as well as a cytotoxic response and tumor necrosis factor release from a Vγ9Vδ2 T-cell clone. Quantitatively similar phosphoantigenic activity was detected in acellular extracts from two clinical isolates (FSC171 and Schu) and from LVS. Taken together, the chemical nature of the stimulus from the clinical isolates and the significant increase in levels of Vγ9Vδ2 cells in peripheral blood of tularemia patients indicate that phosphoantigens produced by virulent strains of F. tularensis trigger in vivo expansion of γδ T cells in tularemia.
Unravelling the malaria mosquito's sense of smell: neural and behavioural responses to human-derived compounds

9 Chapter 1: General introduction 12 Chapter 2: Electrophysiological characterisation of olfactory receptor neurons 34 innervating antennal trichoid sensilla B and D in Anopheles gambiae s.s. Chapter 3: Comparing heterologous expression system responses with in vivo 74 responses from maxillary palp olfactory sensilla of Anopheles gambiae s.s. to binary odour mixtures Chapter 4: Physiological state of Anopheles gambiae influences the responsiveness 92 of palpal olfactory receptor neurons to human microbiota-derived odorants Chapter 5: Behavioural consequences of extensively sustained olfactory receptor 116 neuron responses Chapter 6: Summarising discussion 142
MORPHOLOGICAL AND MOLECULAR ANALYSIS OF THE ENDANGERED SPECIES PORPHYRA TENERA (BANGIALES, RHODOPHYTA) 1

Porphyra tenera Kjellman, widely cultivated in nori farms before the development of artificial seeding, is currently listed as an endangered species in Japan. To confirm whether a wild‐collected gametophytic blade was P. tenera or the closely related species P. yezoensis Ueda, morphological observations and molecular analyses were made on the pure line HGT‐1 isolated from a wild blade. This pure line was identified as P. tenera based on detailed morphological features. Sequences of the nuclear internal transcribed spacer region 1 and the plastid RUBISCO spacer revealed that P. tenera HGT‐1 was clearly different from P. yezoensis f. narawaensis Miura, the main species cultivated in Japan. PCR‐RFLP analysis of the internal transcribed spacer region was found to be a convenient method for rapid discrimination between P. tenera and cultivated P. yezoensis. The restriction patterns generated by the endonucleases Dra I and Hae III were useful for differentiating between both gametophytic and conchocelis stages of P. tenera HGT‐1 and P. yezoensis f. narawaensis strains. Thus, PCR‐RFLP analysis will serve as a valuable tool for rapid species identification of cultivated Porphyra strains, culture collections of Porphyra strains for breeding material and conservation of biodiversity, and, as codominant cleaved amplified polymorphic sequence markers for interspecific hybridization products between P. tenera and P. yezoensis f. narawaensis. Under the same culture conditions, rate of blade length increase and the blade length‐to‐width ratio were lower in P. tenera HGT‐1 than in P. yezoensis f. narawaensis HG‐4. The HGT‐1 became mature more rapidly than HG‐4 and had thinner blades.
Coevolution of Rhagoletis hosts and their parasitic wasps

iii ACKNOWLEDGEMENTS I am deeply indebted to my advisor, Andrew Forbes, whose encouragement and support over the years has been invaluable. I wish to thank my committee, for their guidance, support and feedback. A special thanks goes to my lab-mates Amanda Nelson, Alaine Hippee, Kristina Ottens and Eric Tvedte for driving me crazy while keeping me sane over the past five years. Thank you to Eileen, Misty and the rest of the Biology Department administrative staff for making life so much easier for all of us. The same can be said for the Graduate College and the OGI staff. Thank you for all of your years of support – I don't know what I would have done without it. The biggest thank you goes to my parents. I would be lost without your continuous love and support. Thank you for driving me to zoo camp and letting me travel all around the world. Thank you for letting me make mistakes and helping me learn from them. And thank you for listening to my practice talks and telling me I did a great job, even if you didn't understand a word. Finally, to my science friends and my best friends – I couldn't have done this without you: ABSTRACT Phytophagous (plant-feeding) insects are extremely species-rich and typically display tight host associations (meeting and mating on or near their host plant) with one or a small number of hosts. This specialized lifestyle can promote diversification through assortative mating, ultimately leading to genetically differentiated host races (host associated differentiation; HAD). It has been shown that HAD can cascade up to the parasitic wasps (parasitoids) that utilize the phytophagous insects as hosts. Cascading HAD occurs when there is genetic differentiation among parasitoids as a result of differential host plant use by their host insects. Thus, host switching can promote parasitoid diversification as well. Here, I present three studies designed to help understand aspects of parasitoid shifts to novel hosts and environments. All of the studies in this dissertation utilize the Rhagoletis complex of flies and their associated parasitoids. Specifically, I address i) the role of subtle trait variation and environmental context in predicting successful parasitoid host shifts; ii) whether parasitoid host discrimination (a trait that can influence host shifts) is an innate or learned behavior; and iii) whether contemporary patterns of host shifts among parasitoids are echoed by historical host shifts in cophylogenetic analyses …
Variation in size and condition of neonate pygmy bluetongue lizards, Tiliqua adelaidensis

Phenotypic variation among offspring of individual animals is an important life-history trait. In viviparous lizards, it could result from genetic variation of individuals and also differences in environments experienced by mothers during gestation. We investigated variation in phenotype and survival of neonate pygmy bluetongue lizards, Tiliqua adelaidensis, over three sampling years. We explored changes in body condition, using body size residuals as an index, and body size (snout-vent length (SVL) and mass) of neonates. For litters that were captured with their mothers, we hypothesised that body condition and size of offspring are influenced by the condition and size of their mothers, the presence of mothers in the burrow and litter size. We found that there were significant variations in body condition and mass of neonates among years. There was no significant relationship between neonate body condition, mass and SVL and post-partum body condition of their mothers. Results revealed that females with higher SVL produced larger litters. None of the analyses showed any effect of mother’s presence on neonate body condition, SVL or mass. Neither was there any effect of observed litter size on these parameters. Our findings have important conservation implications for this endangered species, given that the aim of conservation managers is to encourage conditions that promote optimum body condition and fitness in offspring in order to maximise their survival in fragmented habitats.
Resistência em germoplasma de Coffea ao crestamento bacteriano incitado por Pseudomonas garcae AMARAL et al

O germoplasma de cafeeiros, constituido por cultivares comerciais, linhagens e progenies resistentes a ferrugem, variedades de Coffea arabica, C. canephora, cruzamentos interespecificos de C . arabica x C . canephora, C. eugenioides e C. stenophylla foi avaliado na casa de vegetacao contra o crestamento bacteriano incitado por Pseudomonas garcae (AMARAL et al). Tambem as introducoes de C. arabica originadas da Etiopia foram avaliadas no campo. Todas as cultivares comerciais - Mundo Novo, Catuai e Bourbon - foram altamente susceptiveis. Encontrou-se, dentro do material resistente a ferrugem, as progenies EP95-1520 C133, EP24-1168-18 C590, 7002-H6963 C328 como resistentes e M7846 como altamente resistente. As variedades, Coffea arabica var. semierecta, C. arabica var. ennarea e C. arabica var. geisha apresentaram-se imunes ou altamente resistentes. Em C. canephora encontram-se 2 fontes moderadamente resistentes: Guarini LC1598-14 e Robusta 1598-11EP119. Em hibridos interespecificos de C. arabica x C. canephora , a progenie Icatu H4782-7MBR (E) foi moderadamente resistente. Nas progenies resultantes do cruzamento de Hibrido de Timor com Caturra, (F 3 ) PI 34 foi resistente e (F 3 ) PI 44 foi moderadamente resistente. A progenie do Hibrido de Timor com Blue Mountain, (F 2 ) PI 50 se mostrou imune. As especies, C. eugenioides e C. stenophylla tambem foram altamente resistentes. Nas 138 introducoes de C. arabica provenientes da Etiopia, identificaram-se 38 fontes de alta resistencia.
Using an energetic cost–benefit approach to identify ecological traps: the case of the African wild dog

In a natural environment, there are high‐quality habitats that produce a surplus of animals (sources), facilitating migration into low‐quality habitats in which mortality exceeds natality (sinks). Human alterations can increase the attractiveness of a low‐quality habitat and/or decrease the suitability of a high‐quality habitat, herewith creating an ecological trap. In an ecological trap, animals prefer to stay in habitats where mortality exceeds natality, which can result in extirpation of a population. It is important to distinguish ecological traps from sinks; however, relative population densities do not necessarily give reliable information. In order to identify ecological traps and set appropriate conservation priorities, it is necessary to gain insight into the relationship between habitat preference, quality and suitability. In this study, we used African wild dog hunt data and energetic cost–benefit analysis to determine whether the preferred habitat outside Hwange National Park (HNP) serves as an ecological trap. This analysis enabled us to take several ecological factors into account while assessing habitat quality. Although outside HNP anthropogenic mortality exceeded natality, per capita energetic intake was higher. This indicates that the habitat outside HNP serves as an ecological trap where human alterations have decreased the suitability of the high quality habitat. In order to ensure the recovery of the African wild dog population, conservation efforts should therefore focus on improving the suitability of the habitat outside HNP. This study shows that an energetic cost–benefit analysis can assist with identifying ecological traps and setting conservation priorities. Moreover, in cases of social territorial species, the cost–benefit analysis may also help to identify ecological traps before source populations are depleted, thus increasing the likelihood of population recovery.