Miracle-dz/UniFAR-FTUs huggingface dataset:
Phytoplasma diseases of papaya (Carica papaya L.) in Australia : phytoplasma classification, pathology and transmission

In Australia, phytoplasmas have consistently been associated with the papaya (Carica papaya L.) diseases known as papaya dieback (PpDB), yellow crinkle (PpYC) and mosaic (PpM). PpDB is the most economically important of these diseases, followed by PpYe. The investigations presented in this thesis have therefore focused primarily onPpDB. Analysis of the DNA sequences of the 168 rRNA gene and the 168-238 rRNA intergenic spacer region (8R) of the PpDB, PpYC and PpM phytoplasmas showed that the PpYC and PpM phytoplasma DNA sequences were identical to each other, but were distinctly different to that of the PpDB phytoplasma. A phylogenetic tree based on 168 rDNA sequences revealed that PpDB is most closely related to the Australian grapevine yellows (AGY) phytoplasma and the Phormiuln yellow leaf (PYL) phytoplasma from New Zealand, forming a distinct group within subclade xii. PpYC and PpM phytoplasmas are most closely related to the tomato big bud (TBB) phytoplasma from Australia, within subclade iii. It was proposed that the PpDB phytoplasma be included in the taxon "Candidatus Phytoplasma australiense", and that the ppye and PpM phytoplasmas be assigned to a new taxon, "Candidatus P. australasiense". Histological studies and mapping of phytoplasma distribution using peR revealed that it is likely that phytoplasma cells are present in very low titre and that, while the plant appears to limit proliferation of the PpDB phytoplasma, this defence response is associated with a rapid decline of the papaya plant. Immature leaf material was sampled weekly for eight months from 60 plants in a commercial papaya plantation, to estimate the minimum time between inoculation and symptom expression of PpDB,
The application of zeta diversity as a continuous measure of compositional change in ecology

Zeta diversity provides the average number of shared species across n sites (or shared operational taxonomic units (OTUs) across n cases). It quantifies the variation in species composition of multiple assemblages in space and time to capture the contribution of the full suite of narrow, intermediate and wide-ranging species to biotic heterogeneity. Zeta diversity was proposed for measuring compositional turnover in plant and animal assemblages, but is equally relevant for application to any biological system that can be characterised by a row by column incidence matrix. Here we illustrate the application of zeta diversity to explore compositional change in empirical data, and how observed patterns may be interpreted. We use 10 datasets from a broad range of scales and levels of biological organisation – from DNA molecules to microbes, plants and birds – including one of the original data sets used by R.H. Whittaker in the 1960’s to express compositional change and distance decay using beta diversity. The applications show (i) how different sampling schemes used during the calculation of zeta diversity may be appropriate for different data types and ecological questions, (ii) how higher orders of zeta may in some cases better detect shifts, transitions or periodicity, and importantly (iii) the relative roles of rare versus common species in driving patterns of compositional change. By exploring the application of zeta diversity across this broad range of contexts, our goal is to demonstrate its value as a tool for understanding continuous biodiversity turnover and as a metric for filling the empirical gap that exists on spatial or temporal change in compositional diversity.
Deleterious variation mimics signatures of genomic incompatibility and adaptive introgression

While it is appreciated that population size changes can impact patterns of deleterious variation in natural populations, less attention has been paid to how population admixture affects the dynamics of deleterious variation. Here we use population genetic simulations to examine how admixture impacts deleterious variation under a variety of demographic scenarios, dominance coefficients, and recombination rates. Our results show that gene flow between populations can temporarily reduce the genetic load of smaller populations, especially if deleterious mutations are recessive. Additionally, when fitness effects of new mutations are recessive, between-population differences in the sites at which deleterious variants exist creates heterosis in hybrid individuals. This can lead to an increase in introgressed ancestry, particularly when recombination rates are low. Under certain scenarios, introgressed ancestry can increase from an initial frequency of 5% to 30-75% and fix at many loci, even in the absence of beneficial mutations. Further, deleterious variation and admixture can generate correlations between the frequency of introgressed ancestry and recombination rate or exon density, even in the absence of other types of selection. The direction of these correlations is determined by the specific demography and whether mutations are additive or recessive. Therefore, it is essential that null models include both demography and deleterious variation before invoking reproductive incompatibilities or adaptive introgression to explain unusual patterns of genetic variation.
Reviews: Parasite Cell Biology: 2 Biogenesis and function of peroxisomes and glycosomes

Peroxisomes of higher eukaryotes, glycosomes of kinetoplastids, and glyoxysomes of plants are related microbody organelles that perform differing metabolic functions tailored to their cellular environments. The close evolutionary relationship of these organelles is most clearly evidenced by the conservation of proteins involved in matrix protein import and biogenesis. The glycosome can be viewed as an offshoot of the peroxisomal lineage with additional metabolic functions, specifically glycolysis and purine salvage. Within the parasitic protozoa, only kinetoplastids have been conclusively demonstrated to possess glycosomes or indeed any peroxisome-like organelle. The importance of glycosomal pathways and their compartmentation emphasizes the potential of the glycosome and glycosomal proteins as drug targets. © 2001 Elsevier Science B.V. All rights reserved.
Effect of the addition of a fungicide to glyphosate applied postemergence on crop injury, disease control, and corn yield

Abstract: The addition of pyraclostrobin, pyraclostrobin/fluxapyroxad, pyraclostrobin/metconazole, trifloxystrobin/propiconazole, azoxystrobin/propiconazole, and trifloxystrobin/prothioconazole fungicides to glyphosate reduced disease incidence up to 19% and disease severity up to 4% compared with glyphosate alone. Fungicides evaluated can be safely mixed with glyphosate for corn production, but fungicide use was not associated with increased corn yield.
Quantitative changes of forest landscapes over the last century across Italy

Abstract A key topic in landscape ecology and vegetation science is the quantitative analysis of changes in forest cover over time, through the use of geomatics monitoring tools. Ecologists and landscape researchers are pointing out that a full understanding of ecosystems and landscapes should be based on the analysis of their functioning over long time series. Under this perspective, a long-term historical reconstruction of forest cover is essential. This study has aimed at examining the long-term dynamics of forest landscapes in Italy, over the last century, using recent remote-sensing based map (2012) and an accurate historical map (1936). A forest-non forest approach has been followed by the computation of a variety of landscape metrics using two analysis tools, with the final objective of quantifying changes in forest cover patterns and in the composition of specific landscape elements. Results show that forest landscape structure has significantly changed across Italy, resulting in a general trend of decreasing fragmentation and patchiness, mainly through enlargement of existing forest patches, which have also assumed a more geometrically regular shape. In relative terms, the greatest expansion of forest areas has occurred mainly in lowland districts characterised by the highest level of human pressure in the country.
Fish movement in an Atlantic Forest stream

Given the importance of fish movement to the dynamics and maintenance of stream dwelling fish communities from the Atlantic Forest, we analysed patterns of fish movement in a coastal stream from Southeastern Brazil, using mark-recapture technique. Displacement distance of each species were presented and discussed considering seasonal (rainy and dry) and body size patterns. We marked 10 species along the stream and recaptured 440 (34.6%) of the 1,270 marked fishes. The species with significant number of upstream moving individuals were Astyanax janeiroensis, Characidium interruptum, Astyanax hastatus, Parotocinclus maculicauda and Awaous tajasica. Only Pimelodella lateristriga presented significant differences between resident and moving individuals. Characidium interruptum and A. tajasica demonstrated greater downstream and upstream movement, respectively, moving up to 2,100 m. Even after controlling for species identity we found no significant correlation between fish length and individual displacement distance. Fishes moved longer distances during the rainy season, in accordance to the breeding season. Patterns of fish movement were in agreement to life-history traits of many of the studied species and can be reflecting specific behaviour and morphologies.
How to provide scientific advice for ecosystem‐based management now

: n this paper, I argue that we have at hand what is needed to provide scientific advice for ecosystem-based management of small pelagics and other species groups now. The ingredients for this advice are (i) large marine ecosystems as spatial management units; (ii) maintaining ecosystem productivity and exploiting at multispecies maximum yield as overarching management objectives; (iii) assessment of ecosystems by evaluating changes in primary productivity; (iv) an operational management procedure in which single-species catch proposals are adjusted to ecosystem productivity using a set of control rules. Inspection of historic landings for small pelagics and other small species in the Northeast Atlantic (ICES area) reveals that most likely fisheries exploitation does not, and never did, exceed system productivity in most LMEs and is therefore overall sustainable, although not necessarily for individual stocks.
Influence of corn-dried distiller’s grain with solubles on growth performance and blood metabolites of Awassi lambs offered a concentrate diet

Abstract Objective of this study was to evaluate the effect of partial replacement of soybean meal and barley grain with corn-dried distiller’s grains with solubles (DDGS) on growth performance of Awassi lambs. Thirty lambs (3 to 4 months of age; 24.9 ± 1.93 kg; initial BW) were randomly assigned to three diets; (1) control diet (CON), (2) treatment diet containing 75 g DDGS/kg dietary dry matter (DM) (DDGS75) or treatment diet containing 150 g/kg DDGS/kg dietary DM (DDGS150). The study lasted for 63 days. Lamb BW and blood samples were measured on day 0, 21, 42, and 63 before the morning feeding. At the end of the feeding trial, 6 lambs from each treatment group were chosen at random and housed in metabolic cages to evaluate nutrient digestibility and N balance. Intakes, nutrient digestibility and N balance measures were similar (p > .05) among dietary treatments. Initial BW, final BW, ADG as well as feed efficiency were similar (p > .05) among the dietary treatment diets. Cost of gain reduced (p ≤ .05) in lambs fed DDGS150 compared with the CON and DDGS75 diets. Serum concentrations of urea N, glucose, total protein, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase and albumin were similar (p >.05) among diets. Results demonstrated that inclusion the DDGS at 75 or 150 g/kg of diet DM could replace part of the soybean meal and barley grain without affecting nutrient intake and growth performance while it reduced the cost of feed and cost of gain.
Prey selection and digestive processing in terrestrial carnivorous mammals

s in conference proceedings Cools, A. , A. De Cuyper, J. Pauwels, and G. P. J. Janssens. 2014. Animal fiber: a key nutrient to carnivores, but how to determine this dietary fraction analytically? 10th Biennial symposium of the Comparative Nutrition Society. North Carolina, USA Cools, A. , A. De Cuyper, J. Pauwels, and G. P. J. Janssens, G. 2015. Animal fibre: a key nutrient to carnivores, but how to determine this dietary fraction analytically. 8th European zoo nutrition conference. Arnhem, The Netherlands Dermauw, V. , A. De Cuyper, L. Duchateau, A. Waseyehon, E. Dierenfeld, M. Clauss, I. R. Peters, G. Du Laing, and G. Janssens. 2013. Feeding a Cu deficient diet to zebu (Bos indicus) and crossbreed (Bos indicus × Bos taurus): do they cope differently? 17th congress of the European Society of Veterinary and Comparative Nutrition. Ghent, Belgium De Cuyper, A. , M. Clauss, M. Hesta, W. H. Hendriks, G. Bosch, and G. P. J. Janssens. 2017. Are carnivore digestive separation mechanisms revealed on texture-rich diets? : An explorative study. 21st congress of the European Society of Veterinary and Comparative Nutrition. Cirencester, UK De Cuyper, A. , M. Clauss, M. Hesta and G. P. J. Janssens. 2015a. Do feeding strategies differ between large and small wild carnivores? 40th Animal Nutrition Research (ANR) forum, Merelbeke, Belgium De Cuyper, A. , M. Clauss, M. Hesta and G. P. J. Janssens. 2015b. Feeding strategies in wild carnivores : progress report of a model approach. 11th Conference on Zoo and Wildlife Nutrition, Nutrition Advisory group (NAG). Portland, USA
Genus Cercospora in Thailand: Taxonomy and Phylogeny (with a dichotomous key to species)

Cercospora Fresen. is one of the most importance genera of plant pathogenic fungi in agriculture and is commonly associated with leaf spots. The genus is a destructive plant pathogen and a major agent of crop losses worldwide as it is nearly universally pathogenic, occurring on a wide range of hosts in almost all major families of dicotyledonous, most monocotyledonous families, some gymnosperms and ferns. The information regarding Cercospora leaf spots in Thailand is scattered and mainly based on Chupp’s generic concepts. Therefore, this paper provides an update that includes synonyms, morphological descriptions, illustrations, host range, geographical distribution and literature related to the species. This will benefit mycologists, plant pathologists and quarantine officials who need to study this group of fungi. The present study represents a compilation of 52 species of Cercospora s. str. associated with 29 families of host plants collected from several provinces in Thailand between 2004 and 2008. Twenty-four species represent C. apii s. lat. Plant families of Asteraceae, Amaranthaceae, Convolvulaceae, Euphorbiaceae, Fabaceae, Lamiaceae and Solanaceae, are commonly found infected with Cercospora s. str. Three species, Cercospora arecacearum, C. habenariicola and C. neobougainvilleae, have been validity published as new species from Thailand.
Geographical and sexual differences in body size of common genets, Genetta genetta (Viverridae, Carnivora), in south-western Europe (Iberian Peninsula)

Abstract. Animals' body size varies intra-specifically and geographically among populations, and many species (including small carnivores) show sexual dimorphism and larger individuals (lower superficial area/volume ratio) inhabiting cooler climates complying with Bergman's rule. In the present study we analyse data of common genets wild-caught in three different regions of the Iberian Peninsula, searching for variations in size and weight between males and females, testing for sexual dimorphism, as well as for micro-scale geographical variations among populations in biometrics and sexual dimorphism. We use field measurements such as length (body and tail) and weight, to characterise the three populations in the Iberian Peninsula. Our results show that Iberian genets present significant differences between sexes, although sexual dimorphism is lower than in other small carnivores, and that they comply with Rensch's rule, males size showing greater variation. Iberian genets also follow the Bergman's rule, being bigger and heavier in colder and northern regions. Although we have detected morphometric differences among studied populations, sexual dimorphism indexes varied little. We discuss our results in the light of the different hypotheses given to explain the sexual dimorphism in carnivores, trying to identify the mechanisms that might play a role in the dimorphism of genets.
Connecting transcriptional regulation and microbial growth kinetics in cultures of Pseudomonas putida

Bioprocesses performance is monitored using microbial growth kinetics models. However most of them are empirical and unstructured ignoring molecular and transcriptional interactions thus failing in accurate prediction. Pseudomonas putida mt-2, which harbours the TOL plasmid, is a strain of great biotechnological potential. M-xylene and toluene are commonly utilised by TOL pathway while toluene enables chromosomal ortho-cleavage pathway activation. Herein, the transcriptional kinetics of TOL and key ortho-cleavage promoters which control substrate bioconversion resulting in biomass formation was consistently studied. Thus, revealing the interconnection of the two pathways and promoters’ specific expression patterns. The experimental observations lead to a dynamic model coupling transcriptional regulation to microbial growth kinetics by providing upstream quantitative information. This model enables adequate predicition capability of substrate utilisation and biomass growth under a wide range of initial conditions. However in nature it is uncommon for bacteria to degrade a sole substrate. Therefore P. putida mt-2 cells induction with succinate-toluene, m-xylene-toluene mixtures is studied. The transcriptional kinetics revealed promoters’ bi-modal expression pattern and carbon catabolite repression regardless of the growth conditions. Transcriptional regulation upon entry of m-xylene-toluene mixture was modelled resulting in a mechanistic microbial growth kinetic model development which accurately predicts substrate(s) utilisation and biomass growth patterns. The current double substrate microbial growth kinetic model can more accurately predict the macroscopic phenomena compared to the Monod, Monod-type and competitive enzymatic interaction models.
Keeping an eye on coloration: ecological correlates of the evolution of pitcher traits in the genus Nepenthes (Caryophyllales)

Nepenthes is a genus of carnivorous pitcher plants with high intra- and interspecific morphological diversity. Many species produce dimorphic pitchers, and the relative production rate of the two morphs varies interspecifically. Despite their likely ecological importance to the plants, little is known about the selective context under which various pitcher traits have evolved. This is especially true of color-related traits, which have not been examined in a phylogenetic context. Using field observations of one polymorphic species ( N. gracilis ) and phylogenetic comparative analysis of 85 species across the genus, we investigate correlations between color polymorphism and ecological factors including altitude, light environment, and herbivory. In N. gracilis , color does not correlate to amount of prey-capture, but red pitchers experience less herbivory. Throughout the genus, color polymorphism with redder lower pitchers appears to be evolutionarily favored. We found a lack of phylogenetic signal for most traits, either suggesting that most traits are labile or reflecting the uncertainty regarding the underlying tree topology. This work highlights ecological correlates of the vast phenotypic diversity of this group of tropical plants. We point to a need for future work examining herbivores of Nepenthes and experimental investigations on color polymorphism.
Callose-mediated regulation of Plasmodesmata during the establishment of Medicago truncatula-Sinorhizobium meliloti symbiotic interaction

Legumes, such as Medicago truncatula, can fix atmospheric nitrogen by forming symbiotic associations with soil-borne bacteria collectively called rhizobia. As a result of this relationship, specific roots organs called nodules, are developed that houses rhizobia and where the nitrogen fixation process occurs. Nodule formation is tightly regulated by complex signalling mechanisms and environmental cues, such as nitrate availability. Molecular signals move between the site of infection and the cortex/pericycle to coordinate nodule organogenesis and also systemically along the vascular system to coordinate root and shoot responses. Despite recent progress in the identification of some of these signals very little is known about the pathways for intercellular transport. In this project, the role of the cell-wall polysaccharide callose in the establishment of symbiotic interaction between Medicago truncatula and Sinorhizobium meliloti was addressed. Callose metabolism regulates transport through plasmodesmata: intercellular channels that form a symplastic path for transport. Using immuno-histochemistry we found that callose is downregulated as early as 16 hours post-bacterial inoculation. Concomitantly, the expression of a plasmodesmata located callose degrading enzyme (Medtr3g083580), identified using phylogeny, was induced. Roots constitutively expressing either Medtr3g083580 or its Arabidopsis orthologue PdBG1, showed reduced callose levels and a higher rate of infection and nodulation, even when grown in nitrate concentrations that inhibit nodulation. The effects were stronger when using a promoter active early after rhizobial infection and were mimicked, in high nitrate conditions, by the ectopic expression of a novel plasmodesmata receptor-like kinase (Medtr1g073320). The results suggest an important role for callose in the control of nodulation, both under nitrate deprived or sufficient conditions, likely associated with the regulation of transport via plasmodesmata. The relevance of the findings is discussed in light of potential applications in crop improvement and in reducing the use of nitrogen fertilizers.
Causal Discovery of Feedback Networks with Functional Magnetic Resonance Imaging

We test the adequacies of several proposed and two new statistical methods for recovering the causal structure of systems with feedback that generate noisy time series closely matching real BOLD time series. We compare: an adaptation for time series of the first correct method for recovering the structure of cyclic linear systems; multivariate Granger causal regression; the GIMME algorithm; the Ramsey et al. non-Gaussian methods; two non-Gaussian methods proposed by Hyv¨arinen and Smith; a method due to Patel, et al.; and the GlobalMIT algorithm. We introduce and also compare two new methods, the Fast Adjacency Skewness (FASK) and Two-Step, which exploit non-Gaussian features of the BOLD signal in different ways. We give theoretical justifications for the latter two algorithms. Our test models include feedback structures with and without direct feedback (2-cycles), excitatory and inhibitory feedback, models using experimentally determined structural connectivities of macaques, and empirical resting state and task data. We find that averaged over all of our simulations, including those with 2-cycles, several of these methods have a better than 80% orientation precision (i.e., the probability a directed edge is in the true generating structure given that a procedure estimates it to be so) and the two new methods also have better than 80% recall (probability of recovering an orientation in the data generating model). Recovering inhibitory direct feedback loops between two regions is especially challenging.