Miracle-dz/UniFAR-FTUs huggingface dataset:
Where are the short-range endemics among Western Australian macrofungi?

There are 491 Western Australian (WA) basidiomycete macrofungi, most of which are found also in eastern Australia (78.4%) or overseas. Only 52 (10.6%) endemic WA species have been identified. Of the 32 WA endemics known from more than one location, most (25) have ranges greater than 100 km, even though they are usually represented by few collections (average 4.2). It is considered likely that further collecting will extend ranges. Only Torrendia grandis and T. inculta are known from several collections from the one restricted area, in the Kellerberrin district. Otherwise there is no conclusive evidence for short-range endemism or for any particular centres of narrow endemism for macrofungi. This also appears to be the case for eastern Australia, with the only exceptions being a few fungi of very narrow host range or very specific substratum requirements. Where sufficient collections are available to determine distribution, most Australian macrofungi seem to be very widespread. A model to explain the lack of short-range endemism in macrofungi will need to draw on detailed knowledge of the phylogeny and population genetics of macrofungi, which is currently lacking. The absence of short-range endemic macrofungi also necessitates reconsideration of conservation strategies for macrofungi, since such species are prime candidates for listing on conservation schedules.
Role of molecular motors and maps in spindle dynamics and chromosome segregation in the fission yeast Schizosaccharomyces pombe

Mitosis is a key event in the life of a cell, where duplicated chromosomes are separated into the daughter cells. Defects associated with chromosome segregation can lead to aneuploidy, a hallmark of cancer. Chromosome segregation is achieved by the mitotic spindle, which is composed of microtubules (MTs), motors and microtubule associated protein (MAPs). Motors such as kinesins generate forces within the spindle while MAPs perform functions such as organize the spindle pole and maintain the bipolar spindle. Both motors and MAPs contribute to spindle mechanics. Here I used the relatively simple fission yeast to address how defects in spindle mechanics affect chromosome segregation. The metaphase spindle is maintained at a constant length by an antagonistic force-balance model yet how the regulation of metaphase spindle length contribute to subsequent chromosome segregation remains unexplored. To test the force-balance model, I applied gene deletion and fast microfluidic temperature-control with live-cell imaging to monitor the effect of deleting or switching off different combinations of antagonistic forces in the fission yeast metaphase spindle. I show that kinesin-5 cut7p and MT bundler ase1p contribute to outward pushing forces, and kinesin-8 klp5/6p and dam1p contribute to inward pulling forces. Removing these proteins individually led to aberrant metaphase spindle length and chromosome segregation defects. Removing these proteins in antagonistic combination rescued the defective spindle length and, in some combinations, also partially rescued chromosome segregation defects. Motors and MAPs cooperate to focus MTs at the spindle pole. Defects in MT focusing lead to defects in chromosome segregation, resulting in aneuploidy. The mechanism behind these observations is not well understood. Here I identified a new mechanism for aneuploidy in fission yeast. Kinesin-14 pkl1p and MAP msd1p localize to the spindle poles and focus the MT minus ends. Their absence leads to pole and MT defocusing, resulting in protrusion of MT minus ends due to cut7p-dependent pushing forces at the spindle midzone. Infrequent long MT minus end protrusions can push the already separated chromosome mass back to the cell center, where cytokinesis will `cut' the chromosome mass, creating two daughter cells with unequal chromosome content. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Phong Tran This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1150
Agricultural intensification drives landscape‐context effects on host–parasitoid interactions in agroecosystems

Summary 1. Agricultural land use threatens ecosystem services such as biological control by natural enemies because of simplification of habitat structure and intensification of disturbance and agrochemical inputs. Low parasitism rates of agricultural pests have typically been attributed to a lack of resources for parasitoids in highly simplified landscapes, but this could be confounded by the nearly ubiquitous correlation between landscape complexity and the cover of intensively farmed agricultural crops. 2. Here, we disentangle the mechanisms driving landscape-scale effects on host–parasitoid interactions by taking advantage of a landscape modification gradient in which the diversity of habitat types and annual crop cover in the landscape were uncorrelated. We quantified herbivore densities and parasitism and hyperparasitism rates on two important crop pests (aphids and Plutella xylostella) across 30 landscapes. We used structural equation modelling (SEM) to test whether land-use intensity (insecticide application and habitat disturbance) or resource availability for parasitoids (floral resources and alternative host plants) was mediating the effects of habitat diversity and annual crop cover on the landscape. 3. Rates of primary- and hyperparasitism of aphids and primary parasitism of P. xylostella decreased with increasing annual crop cover, whereas decreasing habitat diversity in the landscape had little effect on parasitism rates. These effects were mediated almost entirely by greater habitat disturbance and greater frequency of insecticide application, rather than by changes in resource availability. 4. Parasitoids were more sensitive to intensive farming practices than were their herbivore hosts, and in turn hyperparasitoids were more sensitive than were primary parasitoids. This supports the theoretical prediction that higher trophic levels should be increasingly sensitive to the disturbances associated with land-use change. 5. Synthesis and applications. Our work suggests that increased land-use intensity (e.g. higher insecticide inputs and greater levels of disturbance associated with increasing area of annual crops) has been underestimated as a driver of landscape effects on host–parasitoid interactions. These findings have important implications for the maintenance of ecosystem services such as biological control. The promotion of low-intensity farming practices that limit the extent and frequency of agrochemical inputs and habitat disturbances will be essential for the maintenance of effective biological control by parasitoids in agroecosystems.
A relict in New Caledonia: phylogenetic relationships of the family Troglosironidae (Opiliones: Cyphophthalmi)

The species richness and endemism of New Caledonia are traditionally held to result from the main island’s Gondwanan origin and progressive diversification subsequent to extended isolation. Recent studies have challenged this hypothesis, promoting a scenario of recent origins and diversifications of New Caledonian arthropod groups. In the present study, the phylogeny of the endemic harvestman family Troglosironidae (Opiliones: Cyphophthalmi) is investigated using DNA sequence data from two nuclear ribosomal genes (18S rRNA and 28S rRNA) and two mitochondrial genes (the protein‐coding cytochrome c oxidase subunit I and the ribosomal 16S rRNA). Phylogenetic analyses support the monophyly of Troglosironidae and a scenario of an ancient (> 200 Ma) origin of the family, with subsequent diversification of extant lineages in the Eocene. These results corroborate the relictual nature of taxa among New Caledonia’s biota while being consistent with diversification in accordance with geological events in the Eocene.
A comparison of wing length and primary length as size measures for small passerines

The length of primary 3 (ascendent) has been strongly promoted in some countries as a better measure of body size than wing length for small passerines. This is because it is believed to offer a more repeatable measure and to be safer for the bird. New data from the British ringing scheme suggest that, for trained observers, repeatability of primary 3 length is no better than that for maximum chord wing length. Furthermore, sexual dimorphism in primary 3 length is perhaps less marked than that in wing length, so that it may be a poorer metric to use to discriminate sexes. We can find no evidence supporting the use of primary 3 length in preference to wing length on grounds of bird welfare.
Development and evaluation of a recombinant DNA vaccine candidate expressing porcine circovirus 2 structural protein

Porcine circovirus 2 (PCV2) is generally associated with the porcine circovirosis syndrome, which is considered an important disease of swine and has potentially serious economic impact on the swine industry worldwide. This article describes the construction of a recombinant plasmid expressing the PCV2 structural protein and the evaluation of cellular and humoral immune responses produced by this recombinant vaccine in BALB/c mice. The vaccine candidate was obtained and analyzed in vivo, in an effort to determine the ability to induce a specific immune response in mice. DNA was extracted from a Brazilian PCV2 isolate and the gene coding for Cap protein was amplified by PCR and inserted into an expression plasmid. Groups of BALB/c mice were inoculated intra-muscularly and intradermally in a 15-day interval, with 100 µg and 50 µg of the vaccine construct, respectively. Another group was inoculated intramuscularly with 100 µg of empty plasmid, corresponding to the control group. Seroconversion and cellular response in BALB/c mice were compared and used for vaccine evaluation. Seroconversion was analyzed by ELISA. After a series of 3 immunizations the spleen cells of the immunized animals were used to perform lymphocyte proliferation assays. Seroconversion to PCV2 was detected by ELISA in the animals inoculated with the vaccine construct when compared with control groups. Lymphocyte proliferation assays showed a stronger cell proliferation in the inoculated animals compared with the control group. Thus, the vaccine candidate construct demonstrated to be able to induce both humoral and cellular responses in inoculated mice.
Branch Yield Components Controlling Soybean Yield Stability across Plant Populations

Soybean [Glycine max (L.) Merr. ] optimizes yield over a broad range of plant populations, but mechanisms responsible for compensation have not been fully elucidated. Identification of these factors would help in selecting cultivars-genotypes having low optimal plant populations (minimal plant population required for best yield) and provide agronomists and farmers with indicators of optimal plant population. Our objective was to determine the mechanism for plant yield compensation across a range of plant populations. Soybean cultivar DeltaPine 415 (Maturity Group V) was planted at an optimal date at low (70 000 plants ha⁻ˡ), medium (164 000 plants ha⁻ˡ), medium-high (189 000 plants ha⁻ˡ), and high (234 000 plants ha⁻ˡ) plant populations on a Commerce silt loam (fine-silty, mixed, nonacid, thermic Aeric, Fluvaquent Haplaquepts) near Baton Rouge, LA(30°N Lat.). A 58% population decrease from 164 000 plants ha⁻ˡ resulted in a yield decrease of only 12%, while a 43% increase resulted in no significant yield change. Yield per plant was primarily regulated by changes in branch dry matter per plant, which averaged 14.0, 5.3, and 3.6 g per plant for the low, medium, and high populations, respectively. Greater branch dry matter per plant created more branch nodes, branch reproductive nodes, and branch pods. Pod per reproductive branch node also affected yield in some cases. High correlation between branch dry matter per plant and yield (r² = 0.95; P ≤ 0.001) demonstrated the usefullness of this yield component for identifying cultivars or genotypes with low optimal plant populations. Approved for publication by the Director of the Louisiana Agric. Exp. Stn. as manuscript no. 96-09-0137.
Tradeoffs between foliar silicon and carbon‐based defences: evidence from vegetation communities of contrasting soil types

Silica is ubiquitous in plants and can constitute up to 10% of plant dry mass, varying with phylogeny and soil silicon availability. Plant silicon is an important alleviator of abiotic (salinity, heavy metal, drought) and biotic (herbivore and fungal pathogen) stress. As well as playing an important role in reducing the impact of abiotic stresses, silicon may be an alternative to carbon-based and other chemical defences. Knowledge of silicon function is predominantly derived from agricultural species and model systems. We investigated the abundance and role of plant silicon at a community level by comparing leaf silicon concentration with defence chemicals, carbon compound concentrations and invertebrate assemblages in vegetation communities from two different soil types with contrasting levels of plant available silicon. We found that the concentrations of silicon in the leaves did not reflect the silicon availability in the soil at a community level. The leaf silica concentration range in the vegetation communities was comparable to other diverse communities reported in the literature, suggesting that the species rather than the environment determine leaf silica concentration. Across sites, leaf silica concentration was significantly negatively correlated with concentrations of carbon, total phenols and weakly with tannins but not with other measured defence compounds. Leaf silica concentration was also negatively correlated with Coleoptera abundance, but not the abundance of any other invertebrate groups measured. Our results suggest that tradeoffs exist between phenolic- and tannin-based defences and provide evidence that leaf silicification may be a more effective defence against some chewing herbivore groups than others.
The effect of food dry matter intake on the flow of amino acids at the terminal ileum for rats fed an enzyme-hydrolysed casein-based diet

The aim of the study was to determine whether food dry matter intake had an effect on endogenous ileal amino acid flows in the rat when the flows were expressed in units of mg g−1 dry matter. Eighty 200 g body weight rats were trained for 7 days to consume a casein-based diet over a daily 3 h feeding period, and then an enzyme-hydrolysed casein (MW 0.05). There were significant slopes (P < 0.05) for the other eight amino acids, although the magnitudes of the effect were small. When the data were re-examined after removing the lowest feeding level, the slopes for most of these amino acids were no longer statistically significant. The results showed that the measures of amino acid flow (mg g−1 dry matter), except for isoleucine and cystine, over a wide range of food intakes were not materially affected by food intake. From the perspective of bioassay logistics the results indicate that expressing ileal amino acid flows proportional to dry matter intake is justified over the range of intakes found in practice for determining true ileal amino acid digestibility by the enzyme-hydrolysed casein method. © 2002 Society of Chemical Industry
Health Effects of Toxin-Producing Cyanobacteria: “The CyanoHABs”

Increasingly, harmful algal blooms (HABs) are being reported worldwide due to several factors, primarily eutrophication, climate change and more scientific monitoring. All but cyanobacteria toxin poisonings (CTPs) are mainly a marine occurrence. CTPs occur in fresh (lakes, ponds, rivers and reservoirs) and brackish (seas, estuaries, and lakes) waters throughout the world. Organisms responsible include an estimated 40 genera but the main ones are Anabaena, Aphanizomenon, Cylindrospermopsis, Lyngbya, Microcystis, Nostoc, and Oscillatoria (Planktothrix). Cyanobacteria toxins (cyanotoxins) include cytotoxins and biotoxins with biotoxins being responsible for acute lethal, acute, chronic and sub-chronic poisonings of wild/domestic animals and humans. The biotoxins include the neurotoxins; ana-toxin-a, anatoxin-a(s) and saxitoxins plus the hepatotoxins; microcystins, nodularins and cylindrospermopsins. Confirmations of human deaths from cyanotoxins are limited to exposure through renal dialysis at a haemodialysis center in Caruaru, Brazil, in 1996. A major effort to compile all available information on toxic cyanobacteria including issues of human health, safe water practices, management, prevention and remediation have been published by the World Health Organization. This paper will review our current understanding of CTP's including their risk to human health.
The status of Botryosphaeriaceae species infecting grapevines.

Normal 0 MicrosoftInternetExplorer4 Normal 0 MicrosoftInternetExplorer4 Species in the Botryosphaeriaceae have a cosmopolitan distribution, and occur on a wide range of annual and perennial hosts including grapevines. To date, morphological and taxonomic studies, as well as analyses of nucleotide sequences of multiple genes, have allowed the identification of at least 21 different species in the Botryosphaeriaceae occurring in grapevines worldwide. Grapevine disease symptoms caused by members of this family include leaf spots, fruit rots, shoot dieback, bud necrosis, vascular discoloration of the wood, and perennial cankers, and their current status as pathogens is reviewed. Additionally, the disease name Botryosphaeria dieback is proposed here to describe the different grapevine trunk disease symptoms caused by species of Botryosphaeriaceae. Much has been written during the last decade about the association between species in the Botryosphaeriaceae and grapevine trunk diseases, which has contributed to a better understanding of the role that these fungal taxa play in grapevine diseases. Although virulence has been shown to vary between species and isolates of the same species in different countries, these fungi have become well-recognized as important grapevine pathogens worldwide. Latest and novel findings from studies conducted in different countries, on disease etiology and species distribution, epidemiology and biology are discussed. Much progress has been achieved in the development and implementation of novel diagnostic and detection techniques.Vineyard sanitation techniques, as well as chemical, biological, and cultural control strategies available at the present time to reduce the infection caused by botryosphaeriaceous fungi, are presented in this review.
Direct and indirect effects of climate change on soil microbial and soil microbial‐plant interactions: What lies ahead?

Global change is altering species distributions and thus interactions among organisms. Organisms live in concert with thousands of other species, some beneficial, some pathogenic, some which have little to no effect in complex communities. Since natural communities are composed of organisms with very different life history traits and dispersal ability it is unlikely they will all respond to climatic change in a similar way. Disjuncts in plant-pollinator and plant-herbivore interactions under global change have been relatively well described, but plant-soil microorganism and soil microbe-microbe relationships have received less attention. Since soil microorganisms regulate nutrient transformations, provide plants with nutrients, allow co-existence among neighbors, and control plant populations, changes in soil microorganism-plant interactions could have significant ramifications for plant community composition and ecosystem function. In this paper we explore how climatic change affects soil microbes and soil microbe-plant interactions directly and indirectly, discuss what we see as emerging and exciting questions and areas for future research, and discuss what ramifications changes in these interactions may have on the composition and function of ecosystems.
Cultivares tradicionales mixtecos de Stenocereus pruinosus y S. stellatus (Cactaceae)

A TOTAL OF 40 CULTIVATED VARIANTS OF STENOCEREUS PRUINOSUS (OTTO) BUXB. AND S. STELLATUS (PFEIFF.) RICCOB. WERE RECOGNIZED IN THE MIXTECA BAJA REGION. IN ORDER TO EXPLORE INFRASPECIFIC FOLK CLASSIFICATION, SELECTIVE MOTIVES AND VARIATION PATTERNS OF THESE VARIANTS, 19 MORPHOLOGICAL ATTRIBUTES WERE MEASURED ON 230 FRUITS (2-10 FRUITS PER VARIANT), AND 44 CHARACTERISTICS OF STEMS, FLOWERS AND FRUITS ON 5 INDIVIDUALS OF EACH SPECIES AND OF ONE PUTATIVE HYBRID BETWEEN THEM. THE FOLK INFRAESPECIFIC CLASSIFICATION IS CLOSELY RELATED TO THE HUMAN SELECTIVE PRESSURES. THESE PRESSURES APPEAR TO HAVE BEEN GREATER IN S. PRUINOSUS, SINCE THIS SPECIES HAS MORE THAN 30 VARIANTS (10 AND MORE COMMERCIAL) WHICH ARE RECOGNIZED BY COLOR, SIZE AND SHAPE OF FRUITS, SIZE AND COLOR OF SPINES, SIZE AND NUMBER OF SEEDS, SWEETNESS, FLAVOR AND PRODUCTION SEASON. IN S. STELLATUS, ONLY NINE VARIANTS WERE MEASURED, WHICH ARE CLASSIFIED MAINLY BY THE COLOR, SIZE AND SWEETNESS OF FRUIT, PRODUCTION SEASON, AND SIZE AND NUMBER OF SEEDS. IT IS POSSIBLE THAT ONE OF THESE VARIANTS WERE A HYBRID BETWEEN THE TWO SPECIES OF STENOCEREUS, BUT ITS MORPHOLOGY SEEMS MORE SIMILAR TO THAT OF S. STEL! ATUS.
Surface soil moisture and stubble management practice effects on the progress of infection of wheat by Fusarium pseudograminearum

The influence of surface soil moisture and stubble management practices on the progress of infection of wheat by Fusarium pseudograminearum, the cause of crown rot, was assessed in a field trial at Moree in northern New South Wales during the growing seasons of 1994, 1995 and 1996 by analysis of infection progress curves. During the dry season of 1994, wheat was sown into dry surface soil. Increases in incidence of infection followed rainfall events that raised the water content of the surface soil above the equivalent of a water potential of –1.5 MPa. The rate of increase in incidence of infection was more uniform in the 1995 and 1996 seasons, which had more regular rainfall. The area under the infection progress curve (AUIPC) was consistently greater when stubble was retained on the surface compared with incorporation with a disc plough, and this difference was significant in 2 out of 3 years. Comparison of AUIPCs indicated greater epidemiological differences between stubble management treatments than did comparisons of incidence of infection at single points during the season.
Temperament traits and microhabitat use in bullhead, **Cottus perifretum** : fish associated with complex habitats are less aggressive

Temperament traits have been linked to fitness-related functional contexts such as dispersal or mating attractiveness, but few studies have linked inter-individual differences in habitat use to temperament traits. Therefore, we conducted a three-month field study with weekly tracking to define the individual microhabitat use of bullhead (Cottus perifretum). The species is known for its dependence on structured habitats. At the end of the field-survey, bullhead were recaptured and tested in the laboratory for five temperament traits: boldness, interest in novel food, novel environment activity, aggressiveness and activity. Repeated trait tests (activity, r = 0.439; novel environment activity, r = 0.422) and habitat complexity use (r = 0.568) indicated behavioural consistency. Overall, bullhead significantly preferred complex habitats, such as branch jams, while avoiding open water. Individual frequency in the use of complex habitats could not be attributed to size or sex differences, but was significantly negatively correlated to the level of aggressiveness. We hypothesize that this relationship was caused by a higher level of aggressive defence of less structured territories. Other temperament traits were not significantly linked to individual habitat use. To our knowledge, this study is the first to show a relationship between aggressiveness measured under laboratory conditions and the use of complex habitats in situ.