Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of clubroot of crucifers on canola (Brassica napus) in Alberta

Clubroot, caused by Plasmodiophora brassicae, was detected for the first time on canola in Alberta. Galling, typical of the disease, was observed on the roots of canola (Brassica napus) plants in a dozen fields near St. Albert, Alberta. The presence of resting spores of the pathogen was confirmed by light and electron microscopy. Pathogen spores were isolated from diseased tissue and used to inoculate roots of B. napus 'Westar', on which they produced symptoms similar to those observed in the field. Resting spores were recovered from galls on inoculated plants. The identification of clubroot on the Alberta canola crop is a matter of concern, as the disease is associated with appreciable yield losses and can only be managed with extended intervals between host crops because other management strategies may be too expensive to implement or are of limited effectiveness. Further studies are underway to determine the extent of the problem.
Enhancing the production of gamma-linolenic acid in Hansenula polymorpha by fed-batch fermentation using response surface methodology

Gamma-linolenic acid (GLA, C18:3Δ6,9,12) is an n-6 polyunsaturated fatty acid (PUFA) that has been used for the alleviation and treatment of a number of symptoms and diseases. Increasing GLA demand has led to a search for alternative producers and potential strategies for GLA production. Based on the successful performance of Hansenula polymorpha, a methylotrophic yeast, as a “cell factory” for the production of valuable bioproducts, a bioprocess development approach was implemented for GLA production in the recombinant yeast carrying the mutated Δ6-desaturase gene of Mucor rouxii. Using a substrate-feeding strategy under glycerol-limited conditions, the physical-chemical variables during the fed-batch fermentation of the recombinant H. polymorpha were optimised for GLA production through response surface methodology using a Box-Behnken design. The medium composition, including yeast extract and trace elements, and dissolved oxygen tension (DOT) were targeted. We found that DOT was the most effective variable for enhancing GLA yield. These results also suggest that the optimum conditions for GLA production are 28 % saturation of DOT, 1 g L−1 of yeast extract and 3.6 mL L−1 of the Pichia trace metals 1 (PTM1).
Reprogramming of the Developmental Program of Rhus javanica During Initial Stage of Gall Induction by Schlechtendalia chinensis

Insect galls are unique organs that provide shelter and nutrients to the gall-inducing insects. Although insect galls are fascinating structures for their unique shapes and functions, the process by which gall-inducing insects induce such complex structures is not well understood. Here, we performed RNA-sequencing-based comparative transcriptomic analysis of the early developmental stage of horned gall to elucidate the early gall-inducing process carried out by the aphid, Schlechtendalia chinensis, in the Chinese sumac, Rhus javanica. There was no clear similarity in the global gene expression profiles between the gall tissue and other tissues, and the expression profiles of various biological categories such as phytohormone metabolism and signaling, stress-response pathways, secondary metabolic pathways, photosynthetic reaction, and floral organ development were dramatically altered. Particularly, master transcription factors that regulate meristem, flower, and fruit development, and biotic and abiotic stress-responsive genes were highly upregulated, whereas the expression of genes related to photosynthesis strongly decreased in the early stage of the gall development. In addition, we found that the expression of class-1 KNOX genes, whose ectopic overexpression is known to lead to the formation of de novo meristematic structures in leaf, was increased in the early development stage of gall tissue. These results strengthen the hypothesis that gall-inducing insects convert source tissues into fruit-like sink tissues by regulating the gene expression of host plants and demonstrate that such manipulation begins from the initial process of gall induction.
Identification of the Optimal Light Harvesting Antenna Size for High-Light Stress Mitigation in Plants

One of the major constraints limiting biomass production in autotrophs is the low thermodynamic efficiency of photosynthesis, ranging from 1 to 4%. Given the absorption spectrum of photosynthetic pigments and the spectral distribution of sunlight, photosynthetic efficiencies as high as 11% are possible. It is well-recognized that the greatest thermodynamic inefficiencies in photosynthesis are associated with light absorption and conversion of excited states into chemical energy. This is due to the fact that photosynthesis light saturates at one quarter full sunlight intensity in plants resulting in the dissipation of excess energy as heat, fluorescence and through the production of damaging reactive oxygen species. Recently, it has been demonstrated that it is possible to adjust the size of the light harvesting antenna over a broad range of optical cross sections through targeted reductions in chlorophyll b content, selectively resulting in reductions of the peripheral light harvesting antenna size, especially in the content of Lhcb3 and Lhcb6. We have examined the impact of alterations in light harvesting antenna size on the amplitude of photoprotective activity and the evolutionary fitness or seed production in Camelina grown at super-saturating and sub-saturating light intensities to gain an understanding of the driving forces that lead to the selection for light harvesting antenna sizes best fit for a range of light intensities. We demonstrate that plants having light harvesting antenna sizes engineered for the greatest photosynthetic efficiency also have the greatest capacity to mitigate high light stress through non-photochemical quenching and reduction of reactive oxygen associated damage. Under sub-saturating growth light intensities, we demonstrate that the optimal light harvesting antenna size for photosynthesis and seed production is larger than that for plants grown at super-saturating light intensities and is more similar to the antenna size of wild-type plants. These results suggest that the light harvesting antenna size of plants is designed to maximize fitness under low light conditions such as occurs in shaded environments and in light competition with other plants.
Reorganization of Golgi Apparatus by Brefeldin A in the Embryonic Epidermal Cells of Xenopus laevis

The Golgi apparatus of Xenopus embryonic epidermal cells was examined by an inhibition experiment using brefeldin A (BFA), to know its target Golgi components since BFA caused rapid reorganization of the Golgi apparatus. Three different probes were used to identify the Golgi and Golgirelated components by fluorescence or electron microscopy: firstly anti-clathrin antibody for distinction of non-clathrin- and clathrincoated vesicles, secondly C5-DMB-Ceramide as a trans-Golgi membrane marker, and thirdly anti-chondroitin 6-sulfate for identification of immature secretory granules. BFA caused rapid disorganization of the Golgi apparatus to form small vesicle clusters. Immature secretory granules did not contribute to the formation of the Golgi-derived vesicle clusters. The vesiculation of the stacked structures of the Golgi cisternae by BFA preceded the BFA-inhibition of non-clathrinand clathrin-coated vesicle formation. Thus, the results raise a question as to whether the BFA inhibition of coated vesicle formation and the vesiculation of the Golgi cisternae by BFA are different events.
A Computational Theory of Mindfulness Based Cognitive Therapy from the “Bayesian Brain” Perspective

Mindfulness Based Cognitive Therapy (MBCT) was developed to combine methods from cognitive behavioral therapy and meditative techniques, with the specific goal of preventing relapse in recurrent depression. While supported by empirical evidence from multiple clinical trials, the cognitive mechanisms behind the effectiveness of MBCT are not well understood in computational (information processing) or biological terms. This article introduces a testable theory about the computational mechanisms behind MBCT that is grounded in “Bayesian brain” concepts of perception from cognitive neuroscience, such as predictive coding. These concepts regard the brain as embodying a model of its environment (including the external world and the body) which predicts future sensory inputs and is updated by prediction errors, depending on how precise these error signals are. This article offers a concrete proposal how core concepts of MBCT—(i) the being mode (accepting whatever sensations arise, without judging or changing them), (ii) decentering (experiencing thoughts and percepts simply as events in the mind that arise and pass), and (iii) cognitive reactivity (changes in mood reactivate negative beliefs)—could be understood in terms of perceptual and metacognitive processes that draw on specific computational mechanisms of the “Bayesian brain. ” Importantly, the proposed theory can be tested experimentally, using a combination of behavioral paradigms, computational modelling, and neuroimaging. The novel theoretical perspective on MBCT described in this paper may offer opportunities for finessing the conceptual and practical aspects of MBCT.
A hybrid method for increasing the accuracy of software development effort estimation

Since software development environments, methods and tools are changing rapidly, the importance of accurate estimations in software projects is increasing significantly. Inaccurate estimations can lead to unpleasant results in the software projects so that many projects are failed at the early stages of the project. During the recent years, numerous estimation methods have been proposed that most of which are based on statistical techniques. Among all existing methods, simplicity of analogy based method makes it so common in this field. Analogy methods usually present accurate estimations but if the level of non normality in the software project datasets is high or type of most project features is categorical, these methods are confronted with inaccurate estimation problem. In this paper, genetic algorithm has been used under a new framework to improve the performance of analogy methods. A large dataset has been employed to evaluate the performance of the proposed method and the results have been compared with the other estimation methods. The results showed that the proposed method outperformed the other methods considerably
Primulina Zixingensis (Gesneriaceae), a New Species from Hunan, China

Primulina zixingensis L.H. Yang & B. Pan (Gesneriaceae), a new species from a limestone area in southeastern Hunan, China, is described and illustrated. It is morphologically similar to P. jiangyongensis due to its yellow flower with a network of dark red stripes on the abaxial lip. The morphological differences between P. zixingensis and the latter species are discussed.
Twin-arginine translocase component TatB performs folding quality control via a general chaperone activity

The twin-arginine translocation (Tat) pathway involves an inbuilt quality control (QC) system that synchronizes proofreading of substrate protein folding with lipid bilayer transport. However, the molecular details of this QC mechanism remain poorly understood. Here, we hypothesized that the conformational state of Tat substrates is directly sensed by the TatB component of the bacterial Tat translocase. In support of this hypothesis, several TatB variants in which the cytoplasmic membrane-extrinsic domain was either truncated or mutated in the vicinity of a conserved, highly flexible α-helical domain were observed to form functional translocases in vivo that had compromised QC activity as evidenced by the uncharacteristic export of several misfolded protein substrates. In vitro folding experiments revealed that the membrane-extrinsic domain of TatB possessed general chaperone activity, transiently binding to highly structured, partially unfolded intermediates of a model protein, citrate synthase, thereby preventing its irreversible aggregation and stabilizing the active species. Collectively, these results suggest that the Tat translocase may use chaperone-like client recognition to monitor the conformational status of its substrates.
Chrna5 is Essential for a Rapid and Protected Response to Optogenetic Release of Endogenous Acetylcholine in Prefrontal Cortex

Optimal attention performance requires cholinergic modulation of corticothalamic neurons in the prefrontal cortex. These pyramidal cells express specialized nicotinic acetylcholine receptors containing the α5 subunit encoded by Chrna5. Disruption of this gene impairs attention, but the advantage α5 confers on endogenous cholinergic signaling is unknown. To ascertain this underlying mechanism, we used optogenetics to stimulate cholinergic afferents in prefrontal cortex brain slices from compound-transgenic wild-type and Chrna5 knock-out mice of both sexes. These electrophysiological experiments identify that Chrna5 is critical for the rapid onset of the postsynaptic cholinergic response. Loss of α5 slows cholinergic excitation and delays its peak, and these effects are observed in two different optogenetic mouse lines. Disruption of Chrna5 does not otherwise perturb the magnitude of the response, which remains strongly mediated by nicotinic receptors and tightly controlled by autoinhibition via muscarinic M2 receptors. However, when conditions are altered to promote sustained cholinergic receptor stimulation, it becomes evident that α5 also works to protect nicotinic responses against desensitization. Rescuing Chrna5 disruption thus presents the double challenge of improving the onset of nicotinic signaling without triggering desensitization. Here, we identify that an agonist for the unorthodox α-α nicotinic binding site can allosterically enhance the cholinergic pathway considered vital for attention. Treatment with NS9283 restores the rapid onset of the postsynaptic cholinergic response without triggering desensitization. Together, this work demonstrates the advantages of speed and resilience that Chrna5 confers on endogenous cholinergic signaling, defining a critical window of interest for cue detection and attentional processing. SIGNIFICANCE STATEMENT The α5 nicotinic receptor subunit (Chrna5) is important for attention, but its advantage in detecting endogenous cholinergic signals is unknown. Here, we show that α5 subunits permit rapid cholinergic responses in prefrontal cortex and protect these responses from desensitization. Our findings clarify why Chrna5 is required for optimal attentional performance under demanding conditions. To treat the deficit arising from Chrna5 disruption without triggering desensitization, we enhanced nicotinic receptor affinity using NS9283 stimulation at the unorthodox α-α nicotinic binding site. This approach successfully restored the rapid-onset kinetics of endogenous cholinergic neurotransmission. In summary, we reveal a previously unknown role of Chrna5 as well as an effective approach to compensate for genetic disruption and permit fast cholinergic excitation of prefrontal attention circuits.
Habitat specifity, endemism and the neotropical distribution of Amazonian white-water floodplain trees

The Amazon basin is covered by the most species-rich forests in the world and is considered to house many endemic tree species. Yet, most Amazonian ecosystems lack reliable estimates of their degree of endemism, and causes of tree diversity and endemism are intense matters of debate. We reviewed the spatial distribution of 658 of the most important floodtolerant Amazonian white-water (varzea) tree species across the entire Neotropics by using data from herbaria, floras, inventories and checklists. Our results show that 90% of the varzea tree species are partially or widely distributed across neotropical macro-regions and biomes. Chi-square analyses indicated that varzea species richness in non-varzea macro-regions was dependent on the flooding gradient and the longitudinal position. Cluster analysis combined with association tests indicated four significant patterns of varzea species distributions depending on species flood-tolerance (low vs high) and spatial distribution (restricted vs widespread). We predict that the predominance of Andean substrates is the most important factor that determines the distribution of varzea tree species within and beyond the Amazon basin and explains the high floristic similarity to the Orinoco floodplains. Distribution patterns in other extra-Amazonian macro-regions are more likely linked to climatic factors, with rainforest climates housing more varzea species than savanna climates. 130 tree species were restricted to South-American freshwater floodplains, and 68 ( 10%) were endemic to Amazonian varzea. We detected two centers of endemism, one in the western Amazon characterized by low and brief floods, and one in the central Amazon, characterized by high and prolonged floods. Differences in taxonomic composition of endemic centers in the western and central Amazon are the result of different abiotic factors (i.e. flood regimes), as well as the regional species pools from where the species are recruited from. We hypothesize that numerous morphological, physiological and biochemical adaptations permit survival of trees in flooded environments. Furthermore, these adaptations are independently derived across many taxa and result in a highly specialized flora. We attribute higher than expected levels of endemism to the great spatial extent and age of floodplain ecosystems in the Amazon basin, and highlight the role of Amazonian varzea as an potential driver in speciation and diversification processes. Freshwater floodplains cover an area of approximately 1.7
A Darwinian Selection Based Explanation of Peacock’s Tail

There is no satisfactory explanation for why peacock possesses a tail, presence and especially courtship display of which makes the organism vulnerable to predation. Here, I present a model according to which in a polygynous mating system a mechanism which increases vulnerability to predation, a Zahavian handicap, evolves when other two mechanisms to identify high-quality males are either absent or are not sufficiently strong. The two mechanisms are: 1) male resource acquisition ability, and 2) male-male competition for females. The three mechanisms are not necessarily mutually exclusive. It is shown through stochastic simulation that sexual selection, mediated by the tail (a Zahavian handicap), leads to higher rate of increase in the quality of the population of tailed peacocks and tailed-choosy peahens (which exclusively mate with tailed peacocks) as compared to the population of tailless peacocks and tailless-choosy peahens (which exclusively mate with tailless peacocks), through a positive feedback, as daughters of tailed-choosy peahens are of higher average quality and, by virtue of not carrying the tail’s handicap, also fitness than daughters of tailless-choosy peahens. Also, the fold-change in the population of tailed peacocks and tailless-choosy peahens are higher than the fold-change in the population of tailless peacocks and tailless-choosy peahens, for all combinations of the initial conditions. The same results were got, though in milder form, when tailless-choosy peahens were replaced by undiscriminating peahens (which mate with tailless and tailed peacocks in proportion to their frequencies in the population). Although sons of tailed-choosy peahens have lower average fitness than sons of undiscriminating peahens, this difference is inconsequential, because in a polygynous mating system a single male can potentially mate with every female. In peacock, increased vulnerability to predation because of tail exists throughout its life, but the model only demands the presence of heightened vulnerability to predation during mate selection process. The work presented here reconciles Zahavi’s handicap principle with Darwin’s theories of natural and sexual selection. Further, it is hypothesized that a genotype responsible for producing in males a reliable indicator of high quality (a Zahavian handicap) or paternal care ability generates mating desirability in females toward males possessing the indicator. It is demonstrated through simulation that this cross-gender pleiotropy expedites the evolution of tailed peacocks and tailed-choosy peahens and leads to higher rate of increase in their quality.
Development and optimization of a novel T7 polymerase-independent Marburg virus minigenome system

Marburg virus (MARV) is the only known pathogenic filovirus not belonging to the genus Ebolavirus. Minigenomes have proven a useful tool to study MARV, but all existing MARV minigenomes are dependent on the addition of an exogenous T7 RNA polymerase to drive minigenome expression. However, exogenous expression of a T7 polymerase is not always feasible and acts as a confounding factor in compound screening assays. We have developed an alternative minigenome that is controlled by the natively expressed RNA polymerase II. We demonstrate here the characteristics of this new system and its applicability in a wide range of cell types. Our system shows a clear concentration-dependent activity and outperforms the existing T7 polymerase-based system at higher concentrations, especially in difficult-to-transfect cell lines. In addition, we show that our system can be used for high-throughput compound screening in a 96-well format, thereby providing an attractive alternative to previously developed MARV minigenomes.
The Temporal Variability of Animal Abundances: Measures, Methods and Patterns

From first principles, the temporal variability of a time series of abundances can be defined as the average deviation of values from a mean value on a proportional scale. In this paper we review: (i) the different kinds of temporal variability; (ii) the different ways in which it can be measured; (iii) the design of appropriate sampling schemes; (iv) methods of analysing variability; and (v) patterns in temporal variability. We emphasize that some commonly applied measures are not appropriate, that several do not measure the desired feature of time series, and the importance of considerations of trend and sampling error. A number of suggestions are made for the improvement of the basis for comparative analyses of levels of variability, and some of the potential pitfalls are identified. Given the serious faults in many previous analyses of ecological patterns in the temporal variability of animal abundances, emphasis is laid on the theoretical basis for different patterns, and hence a set of hypotheses for testing is generated.
Review: Endotoxin in the environment — exposure and effects

This review deals with endotoxin in the environment and its relation to disease among exposed persons. Data are presented on levels of endotoxin in different environments with maximum values of several μg/m3. The cellular reactions of importance for inhalation exposure effects are attachment to lipopolysaccharide binding protein, CD14 cell surface protein and TLR-4 receptors. The internalisation of endotoxin in macrophages and endothelial cells results in local production of inflammatory cytokines with subsequent migration of inflammatory cells into the lung and the penetration of cytokines into the blood. These events orchestrate clinical effects in terms of toxic pneumonitis, airways' inflammation and systemic symptoms. Inhalation challenges with pure endotoxin and field studies confirm the relation between these effects and exposure to dusts containing endotoxin. It is possible that polymorphism in genes determining endotoxin reactivity, particularly TLR-4, influences the risk for disease after environmental exposures. Some data suggest that the inflammation caused by inhaled endotoxin may decrease the risk for atopic sensitisation among children and lung cancer among workers exposed to organic dust. Additional research is needed to clarify the role of other environmental agents that are present in connection with endotoxin, particularly (1→3)-β-D-glucan from mold cell walls.