Miracle-dz/UniFAR-FTUs huggingface dataset:
Global diurnal and nocturnal parameters of stomatal conductance in woody plants and major crops

Aim: stomata regulate CO₂ uptake, water-vapour loss and uptake of gaseous pollutants. Jarvis-type models that apply multiple-constraint functions are commonly used to estimate stomatal conductance (gs), but most parameters for plant functional types (PFTs) have been estimated using limited information. We refined the data set of key components of the gs response to environmental factors in global PFTs. - Location: global. - Time period: data published in 1973–2015. - Major taxa studied: woody plants and major crops (rice, wheat and maize). - Methods: we reviewed 235 publications of field-observed gs for the parameterization of Jarvis-type models in global PFTs. The relationships between stomatal parameters and climatic factors [mean annual air temperature (MAT) and mean annual precipitation (MAP)] were assessed. - Results: we found that maximal stomatal conductance (gmax) in global woody plants was correlated with MAP rather than with MAT. The gmax of woody plants on average increased from 0.18 to 0.26 mol/m²/s with an increase in MAP from 0 to 2,000 mm. Models, however, can use a single gmax across major crops (0.44 mol/m²/s). We propose similar stomatal responses to light for C₃ crops and woody plants, but C₄ crops should use a higher light saturation point of gs. Stomatal sensitivity to vapour-pressure deficit (VPD) was similar across forest PFTs and crops, although desert shrubs had a relatively low sensitivity of stomata to VPD. The optimal temperature for gs increased by 1 °C for every 3.0 °C of MAT. Stomatal sensitivity to predawn water potential was reduced in hot and dry climate. The fraction of nighttime conductance to gmax (0.14 for forest trees, 0.28 for desert shrubs and 0.13 for crops) should be incorporated into the models. - Main conclusions: this analysis of global gs data provides a new summary of gs responses and will contribute to modelling studies for plant–atmosphere gas exchange and land-surface energy partitioning.
Affinity Gradient of Chimeric Antigen Receptor T-Cells Against Low-Antigen Density Target

Adoptive Cell Therapy (ACT) is a novel approach to cancer treatment, which implements the use of the patient T-cells redirected to eradicate tumour cells. The T-cells are engineered to express a Chimeric Antigen Receptor (CAR) that bestows specificity for an arbitrary antigen. CAR-T cell clinical trials have shown tumour eradication of leukaemia, but modest results against solid tumours. There is an ongoing debate regarding the correlation of CAR affinity and antigen-density recognition threshold, which we sought to investigate. Although the TCRs sensitivity against low antigen targets is superior at low-affinity, the effect of affinity in CAR efficacy and sensitivity is controversial. In order to examine the correlation between CAR efficacy and affinity, we designed a CAR against an intracellular protein in melanoma. Tyrosinase-Related Protein 1 (Tyrp1) resides in the surface of the organelles called melanosomes. However, Tyrp1 is also trafficked to the surface at a low density. We mutated an anti-Tyrp1 single-chain Variable Fragment (scFv) to acquire eight mutants of various affinities. The affinity range was 0.74nM-54.3nM. Including the wild-type scFv, these nine affinity gradient CARs were challenged with a cell line expressing low, medium and high densities of cell-surface Tyrp1. Three mutant scFv CARs were superior to the wild-type scFV. However, the affinities of those superior CARs was variant. There was no pattern observed to suggest a direct correlation between the affinity and the CAR efficacy. In contrast to previous publications, this study shows that affinity does not play a key role in determining the CAR efficacy. We hypothesise that the difference in CAR efficacy depends on a combination of factors, such as scFv stability and affinity, CAR density, and antigen density. However, the complex interaction of these parameters, as well as further confounding factors, renders the deduction of a pattern challenging. In order overcome this complexity, a multivariate analysis of all the parameters together is necessary.
Near-atomic cryo-EM structure of yeast kinesin-5-microtubule complex reveals a distinct binding footprint

Kinesin-5s are essential members of the superfamily of microtubule-dependent motors that undertake conserved roles in cell division. We investigated coevolution of the motor-microtubule interface using cryo-electron microscopy to determine the near-atomic structure of the motor domain of Cut7, the fission yeast kinesin-5, bound to fission yeast microtubules. AMPPNP-bound Cut7 adopts a kinesin-conserved ATP-like conformation, with a closed nucleotide binding pocket and docked neck linker that supports cover neck bundle formation. Compared to mammalian tubulin microtubules, Cut7’s footprint on S. pombe microtubule surface is subtly different because of their different architecture. However, the core motor-microtubule interaction that stimulates motor ATPase is tightly conserved, reflected in similar Cut7 ATPase activities on each microtubule type. The S. pombe microtubules were bound by the drug epothilone, which is visible in the taxane binding pocket. Stabilization of S. pombe microtubules is mediated by drug binding at this conserved site despite their noncanonical architecture and mechanochemistry. Highlights S. pombe Cut7 has a distinct binding footprint on S. pombe microtubules The core interface driving microtubule activation of motor ATPase is conserved The neck linker is docked in AMPPNP-bound Cut7 and the cover neck bundle is formed Epothilone binds at the taxane binding site to stabilize S. pombe microtubules eTOC text To investigate coevolution of the motor-microtubule interface, we used cryo-electron microscopy to determine the near-atomic structure of the motor domain of Cut7, the fission yeast kinesin-5, bound to microtubules polymerized from natively purified fission yeast tubulin and stabilised by the drug epothilone.
Agroforestry Can Enhance Food Security While Meeting Other Sustainable Development Goals

To achieve global food security, we need to approximately double food production over the coming decades. Conventional agriculture is the mainstream approach to achieving this target but has also caused extensive environmental and social harms. The consensus is that we now need an agriculture that can “multi-functionally” increase food production while simultaneously enhancing social and environmental goals, as committed to in the sustainable development goals (SDGs). Farming also needs to become more resilient to multiple insecurities including climate change, soil degradation, and market unpredictability, all of which reduce sustainability and are likely to exacerbate hunger. Here, we illustrate how agroforestry systems can increase yield while also advancing multiple SDGs, especially for the small developing-world agriculturalists central to the SDG framework. Agroforestry also increases resilience of crops and farm livelihoods, especially among the most vulnerable food producers. However, conventional yield-enhancement strategies have naturally dominated the debate on food production, hindering implementation of more multifunctional alternatives. Governments and institutions now have the opportunity to rebalance agricultural policy and investment toward such multigoal approaches. In doing so, they could achieve important improvements on multiple international commitments around the interlinked themes of food security, climate change, biodiversity conservation, and social well-being.
Translocations, conservation, and climate change: use of restoration sites as protorefuges and protorefugia

High levels of human activity have affected the quality and usability of the natural landscape, leading to habitat degradation, loss of connectivity between sites, and reduced chances of long‐term survival for individual species. In line with conservation policy, ecological restoration practitioners try to improve degraded sites by means of reestablishing species lost from these sites, thereby returning ecological functionality and maintaining biological diversity. It may appear difficult to integrate the long‐term potential impacts of climate change within restoration strategies. However, more refined climate projections and species distribution models provide us with better understanding of likely scenarios, enabling us to consider future proofing as an integral part of the design of restoration sites, aiding plant conservation. We believe that it is possible to go one step further with a closer integration of restoration and conservation objectives. We introduce the novel concepts of “protorefuges” and “protorefugia”—restoration sites that threatened species can be translocated to, where the restoration design can be specifically adapted to help reduce the decline of threatened species at the leading and trailing edges (respectively) of bioclimatic envelope shifts. This is particularly relevant for nuclear decommissioning sites, which may be free from human activity for decades to centuries.
Influence of biochar produced from different pyrolysis temperature on nutrient retention and leaching

ABSTRACT Biochar application has been received much attention because biochar can improve the fertilizer utilization efficiency of soil. However, the effect of biochar produced at different temperature on the nutrient retention and leaching remains poorly understood. In this study, we observed the nutrients leaching from a sandy loam soil amended with biochar produced at different temperature. The properties of biochars produced from wheat straw at four contrasting pyrolysis temperatures (250, 350, 450, and 550°C) showed that increasing pyrolysis temperature increased pH value and specific surface area but reduced the electrical conductivity and cation exchange capacity. With the temperature increased, the nitrogen loss was significant decreased (p > 0.05) from 109.6 mg to 53.3 mg in biochar amended soil. However, dissolved organic carbon (DOC), available P, Na and K were significant increased (p > 0.05). These results demonstrate that the pyrolytic temperature has a great influence on biochar properties, which in turn affect the leaching of the available nutrients.
Distribution and diversity of begomoviruses in tomato and sweet pepper plants in Costa Rica

Begomoviruses (genus Begomovirus, family Geminiviridae) have emerged as important plant pathogens in tropical and subtropical regions worldwide. Although these viruses were reported during the 1970s in Costa Rica, they are still poorly known. Therefore, the objective of this study was to analyse the diversity and distribution of begomoviruses in commercial tomato and sweet pepper fields from different agricultural production systems of the major growing regions of Costa Rica. A total of 651 plants were randomly sampled from greenhouses and open field crops during 2011 and 2012 in three different geographical locations. The bipartite begomoviruses Tomato yellow mottle virus, Tomato leaf curl Sinaloa virus and Pepper golden mosaic virus, and the monopartite begomovirus Tomato yellow leaf curl virus were detected in the collected samples. The complete genome of isolates from each species was cloned and sequenced. The frequency of detection of these four begomoviruses in the analysed samples ranged from 0 to 9%, the presence, and the prevalent virus varied largely according to the geographical location, the host (tomato and pepper), and the production system (greenhouses or open fields). An association between geographical region and begomovirus species was observed suggesting that in Costa Rica the heterogeneity on climate, topography and agricultural system might influence the distribution of begomovirus species in the country. A broader survey needs to be conducted to confirm it, although these preliminary results may contribute to the management of begomoviruses in Costa Rica.
Complementary chromosome folding by transcription factors and cohesin

The spatial organisation of interphase chromosomes is known to affect genomic function, yet the principles behind such organisation remain elusive. Here, we first compare and then combine two well-known biophysical models, the transcription factor (TF) and loop extrusion (LE) models, and dissect their respective roles in organising the genome. Our results suggest that extrusion and transcription factors play complementary roles in folding the genome: the former are necessary to compact gene deserts or “inert chromatin” regions, the latter are sufficient to explain most of the structure found in transcriptionally active or repressed domains. Finally, we find that to reproduce interaction patterns found in HiC experiments we do not need to postulate an explicit motor activity of cohesin (or other extruding factors): a model where co-hesin molecules behave as molecular slip-links sliding diffusively along chromatin works equally well.
The Basic Reproductive Number for Disease Systems with Multiple Coupled Heterogeneities

In mathematical epidemiology, a well-known formula describes the impact of heterogeneity on the basic reproductive number, R0, for situations in which transmission is separable and for which there is one source of variation in susceptibility and one source of variation in infectiousness. This formula is written in terms of the magnitudes of the heterogeneities, as quantified by their coefficients of variation, and the correlation between them. A natural question to ask is whether analogous results apply when there are multiple sources of variation in susceptibility and/or infectiousness. In this paper we demonstrate that with three or more coupled heterogeneities, R0 under separable transmission depends on details of the distribution of the heterogeneities in a way that is not seen in the well-known simpler situation. We provide explicit formulae for the cases of multivariate normal and multivariate log-normal distributions, showing that R0 can again be expressed in terms of the magnitudes of the heterogeneities and the pairwise correlations between them. The formulae, however, differ between the two multivariate distributions, demonstrating that no formula of this type applies generally when there are three or more coupled heterogeneities. We see that the results of the formulae are approximately equal when heterogeneities are relatively small and show that an earlier result in the literature (Koella, 1991) should be viewed in this light. We provide numerical illustrations of our results and discuss a setting in which coupled heterogeneities are likely to have a major impact on the value of R0. We also describe a rather surprising result: in a system with three heterogeneities, R0 can exhibit non-monotonic behavior with increasing levels of heterogeneity, in marked contrast to the familiar two heterogeneity setting in which R0 either increases or decreases with increasing heterogeneity.
Characterization of a new mitovirus OMV1c in a Canadian isolate of the Dutch Elm Disease pathogen Ophiostoma novo-ulmi 93-1224

Supervisory Committee Dr. William E. Hintz, (Department of Biology) Supervisor Dr. Paul de la Bastide, (Department of Biology) Departmental Member Dr. Barbara Hawkins, (Department of Biology) Departmental Member Dr. Juergen Ehlting, (Department of Biology) Departmental Member Dr. Delano James, (Canadian Food Inspection Agency) Additional Member The fungal pathogen Ophiostoma novo-ulmi is the causal agent of Dutch elm disease (DED) and has been responsible for the catastrophic decline of elms in North America and Europe. Double-stranded RNA (dsRNA) viruses are common to all fungal classes and although these viruses do not always cause disease symptoms, the presence of certain dsRNA viruses have been associated with reduced virulence (hypovirulence) in O. novoulmi. A new mitovirus was found in a Canadian isolate of O. novo-ulmi (93-1224) and has been named Ophiostoma mitovirus 1c (OMV1c). The positive strand of the dsRNA of OMV1c was 3,003 nucleotides in length and when the mitochondrial codon usage pattern was employed (mitochondria use UGA to encode tryptophan rather than as a chain terminator), a single large open reading frame (ORF) was found. This ORF had the potential to encode a protein of 784 amino acids, and revealed a high degree of nucleotide identity to genes encoding RNA-dependent RNA polymerase (RdRp) in other mitoviruses. The putative RdRp region of the newly characterized virus had the highest iv sequence similarity to Ophiostoma mitovirus 1b. The 5’terminal sequence of the positive strand could potentially be folded into a double-stranded stem-loop structure with a free energy of 16.6 kcal/mol. Attempts to cure the O. novo-ulmi isolate 93-1224 of virus were unsuccessful. Screening of the re-cultured isolates for the presence of OMV1c revealed that it was still present in the fungus despite repeated hyphal tip transfer, a method known to cure cytoplasmic but not mitochondrial viruses. Based on the genome size, phylogenetic analysis, and the observation that infected isolates could not be cured, it was surmised that the virus was a member of the genus Mitovirus (family Narnaviridae). To assess the distribution of the virus in O. novo-ulmi at the disease front in Winnipeg, a small sample of thirteen isolates were screened for the presence of the new mitovirus. All proved to be negative for OMV1c, which indicated this dsRNA virus was rare and that isolate 93-1224 was the only isolate identified to date infected with OMV1c. It was also discovered that the isolate O. novo-ulmi 93-1224 potentially harboured more than one virus. Electron microscopy of fractionated cells revealed the presence of two flexuous rod-shaped particles that may represent additional novel viruses.
Regulation of MicroRNA-378 expression in mature human adipose tissue cells by adiponectin, free fatty acids and dexamethasone

Purpose : To investigate the effects of adiponectin (ADPN), free fatty acids (FFAs), growth hormone (GH), and dexamethasone (DEX) on miR-378 expression in human adipose tissue cells, and their influence on regulation of obesity and insensitivity to insulin. Methods : Human pre-adipocytes were cultured and differentiated. Adipocytes were treated with ADPN, FFAs, GH and DEX. RNA was isolated and quantified by real-time polymerase chain reaction (RTPCR). Results : Stimulation with FFA led to significant up-regulation of the expression of MiR-378 (approximately 3.8-fold) relative to control at the 4th hour (p < 0.01) in human mature adipose tissue cells. The expression of MiR-378 was increased almost 1.5-fold by ADPN within 24 h, relative to untreated control (p < 0.05). Conclusion : The results of this study demonstrate that miR-378 expression is influenced by FFAs, ADPN, and DEX, the interaction of which may be involved in the pathogenesis of obesity-induced insensitivity to insulin. Thus, miR-378 is a potential biomarker for predicting the risk of complications, especially insulin resistance in obesity Keywords : MiR-378, Adipocytes, Adiponectin, Free fatty acids, Growth hormone, Dexamethasone, Obesity, Insulin resistance
Quantitative analysis of ciliary protein networks - Characterization of the intraflagellar transport complex B

The intraflagellar transport (IFT) complex is essential for ciliary transport. To gain insight into the function of the IFT complex, a method to determine its sub-structure was developed. The components of the IFT complex B (IFT-B) and its sub-structure were determined using different biochemical and mass spectrometric methods. Furthermore, the centrosomal protein 170 was identified to be associated to the IFT-B and shown to be essential for its ciliary localization.
The compound topology of a continent-wide interaction network explained by an integrative hypothesis of specialization

Is there a prevalent pattern among interaction networks: nestedness or modularity? Must consumers always trade-off generalism for average performance in resource exploitation? These two questions have been addressed in various systems, with contradictory results. A recent integrative hypothesis combines both questions within a common theoretical framework, proposing that ecological specialization is structured by different prevailing processes in smaller and larger network units. This should produce both a compound interaction network, formed by internally nested modules, and a scale-dependence on the relationship between consumer performance and generalism. Here, we confirm both predictions in a large dataset on host-parasite interactions. We show that modules indeed constrain nestedness at the whole network level, and that the relationship between parasite generalism and performance on their hosts changed from negative at large to positive at small scales. Our results shed light on both debates, and provide some clues to their integration and solution.
AN EFFECTIVE ROCOMMENDER MODEL FOR E-COMMERCE PLATFORMS

Sahte kullanici hesaplari, veri tabalarindaki seyreklik problemlerinden dolayi ozellikle yeteri kadar kullanici tarafindan puanlanmamis urunlerde tavsiye algoritmalarini kolaylikla etkileyebilmektedirler. Genellikle bu kullanici hesaplari kendi urununun puanini artirmak isteyen urun sahipleri olabildigi gibi herhangi bir urunu veya sirketi karalamak isteyen kotu niyetli kisiler de olabilmektedir. Bu durum bircok sirketin veri tabani yogunlugunun %1 den daha az oldugu dusunulurse e-ticaret ortamlarina nasil bir etki yarattigi tahmin edilebilir. Bu calismada, sahte hesaplarin e-ticaret ortamlarinda olusturduklari negatif etkilerin ustesinden gelebilmek icin, kullanicilar arasindaki iliskiler analiz edilerek diger kullanicilar uzerinde etkisi olan ve gercekten guvenilir oldugu dusunulen kullanicilar bulunarak bir tavsiye modeli olusturulmaktadir. Boylece, guvenilir kullanicilarin dusuncelerinden yola cikilarak e-ticaret ortamlarinda kullanicilara tavsiyelerde bulunan Tavsiye Sistemlerinin (TS) kalitesini artiracak bir tavsiye sistemi olusturulacaktir.