Miracle-dz/UniFAR-FTUs huggingface dataset:
The genetic basis of Drosophila melanogaster defense against Beauveria bassiana explored through evolve and resequence and quantitative trait locus mapping

Many of the molecular mechanisms for antifungal immunity in Drosophila melanogaster have been defined, but relatively little is known about the genetic basis for variation in antifungal immunity in natural populations. Using two population genetic approaches, Quantitative Trait Locus (QTL) Mapping and Evolve and Resequence (E&R), we explored the genetics underlying D. melanogaster immune defense against infection with the fungus Beauveria bassiana. Immune defense was highly variable both in the recombinant inbred lines from the Drosophila Synthetic Population Resource used for our QTL Mapping and in the synthetic outbred populations used in our E&R study. Survivorship of infection improved dramatically over just 10 generations in the E&R study, and continued to increase for an additional 9 generations, revealing a trade-off with uninfected longevity. Populations selected for increased defense against B. bassiana evolved cross resistance to a second, distinct B. bassiana strain but not to bacterial pathogens. The QTL mapping study revealed that sexual dimorphism in defense depends on host genotype, and the E&R study indicated that dimorphism also depends on the specific pathogen to which the host is exposed. Both the QTL Mapping and E&R experiments generated lists of potentially causal candidate genes, although these lists were non-overlapping.
Plant Metabolic Network: A multi-species resource of plant metabolic information

Plant metabolism is a pillar of our ecosystem, food security, and economy. To understand and engineer plant metabolism, we first need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we previously created the Plant Metabolic Network (PMN), an online resource of curated and computationally predicted information about the enzymes, compounds, reactions, and pathways that make up plant metabolism. Here we report PMN 15, which contains genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants, and new tools for analyzing and viewing metabolism information across species and integrating omics data in a metabolic context. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell-type specific metabolic pathways. This work shows the continued growth and refinement of the PMN resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology. One-sentence Summary The Plant Metabolic Network is a collection of databases containing experimentally-supported and predicted information about plant metabolism spanning many species.
Title: Inter-chromosomal linkage disequilibrium and linked fitness cost loci influence the evolution of nontarget site herbicide resistance in an agricultural weed

The adaptation of weedy plants to herbicide is both a significant problem in agriculture and a model for the study of rapid adaptation under regimes of strong selection. Despite recent advances in our understanding of simple genetic changes that lead to resistance, a significant gap remains in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance over time. Here, we perform a multi-level analysis involving whole genome sequencing and assembly, resequencing and gene expression analysis to both uncover putative loci involved in nontarget herbicide resistance and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification, stress sensing, and alterations in the shikimate acid pathway to be under selection, and confirmed that detoxification is responsible for glyphosate resistance using a functional assay. Furthermore, we found interchromosomal linkage disequilibrium (ILD), most likely associated with epistatic selection, to influence NTSR loci found on separate chromosomes thus potentially mediating resistance through generations. Additionally, by combining the selection screen, differential expression and LD analysis, we identified fitness cost loci that are strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work strongly suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are maintained through generations via ILD, and that the fitness cost associated with resistance in this species is a by-product of genetic-hitchhiking.
Single-Molecule Tracking of Chromatin-Associated Proteins in the C. elegans Gonad

Biomolecules are distributed within cells by molecular-scale diffusion and binding events that are invisible in standard fluorescence microscopy. These molecular search kinetics are key to understanding nuclear signaling and chromosome organization, and can be directly observed by single-molecule tracking microscopy. Here, we report a method to track individual proteins within intact C. elegans gonads and apply it to study the molecular dynamics of the axis, a proteinaceous backbone that organizes meiotic chromosomes. Using either fluorescent proteins or enzymatically ligated dyes, we obtain multi-second trajectories with a localization precision of 15-25 nm in nuclei actively undergoing meiosis. Correlation with a reference channel allows for accurate measurement of protein dynamics, compensating for movements of the nuclei and chromatin within the gonad. We find that axis proteins exhibit either static binding to chromatin or free diffusion in the nucleoplasm, and we separately quantify the motion parameters of these distinct populations. Freely diffusing axis proteins selectively explore chromatin-rich regions, suggesting they are circumventing the central phase-separated region of the nucleus. This work demonstrates that single-molecule microscopy can infer nanoscale-resolution dynamics within living tissue, expanding the possible applications of this technique.
Temporal dynamics of base excision / single-strand break repair protein complex assembly and disassembly are modulated by the PARP1/NAD+/SIRT6 axis

Assembly and disassembly of DNA repair protein complexes at sites of DNA damage is essential to maintain genomic integrity. We investigated factors coordinating assembly of the base excision repair (BER) proteins, DNA polymerase β (Polβ) and XRCC1, to DNA lesion sites, identifying a new role for Polβ in regulating XRCC1 disassembly from DNA repair complexes and conversely, demonstrating Polβ’s dependence on XRCC1 for complex assembly. RealPAR, a genetically-encoded probe for live cell imaging of poly(ADP-ribose) (PAR), reveals that Polβ and XRCC1 require PAR for repair complex assembly and PAR degradation for disassembly. We find that BER complex assembly is further modulated by attenuation / augmentation of NAD+ biosynthesis. Finally, SIRT6 does not regulate PARP1 activation but impairs XRCC1 recruitment, leading to diminished Polβ abundance at sites of DNA damage. These findings highlight coordinated yet independent roles for both PARP1 and SIRT6 and their regulation by NAD+ bioavailability to facilitate BER.
A Tool for Reliable Detection of Aflatoxin Biosynthetic Gene Clusters in Aflatoxigenic and Atoxigenic Aspergillus flavus Isolates

Molecular techniques and phenotypic characterisation have been used to differentiate aflatoxigenic and atoxigenic Aspergillus flavus strains. However, there is a lack of a consistent and reliable tool for discrimination between these strains of A. flavus. Here we report, an optimised real-time qPCR-based tool for reliable differentiation between aflatoxigenic and atoxigenic strains of A. flavus. Accordingly, expression profiles and deletion patterns of genes responsible for aflatoxin production in five representative aflatoxigenic and atoxigenic A. flavus strains (KSM012, KSM014, HB021, HB026 and HB027) were examined using the optimised real-time qPCR tool. We observed that under induced conditions, aflP, aflS, aflR and aflO transcripts were the most upregulated genes across the tested isolates while aflS and aflO were always expressed in both induced and uninduced isolates. However, aflR and aflP did not give clear distinctions between non-toxin and toxin producing isolates. The deletion patterns were prominent for aflD and aflR whereas alfO, aflS and aflP had no deletions among the isolates. Significant variation in transcript abundance for aflD, aflR and aflS were observed for aflatoxigenic isolate KSM014 under induced and uninduced states. False detection of aflD gene transcript in atoxigenic strain KSM012 was evident in both induced and uninduced conditions. With the exception of KSM012, aflP gene did not exhibit significant variation in expression in the isolates between induced and uninduced conditions. One-way ANOVA and Post-test analysis for linear trends revealed that aflatoxin biosynthetic cluster genes show significant (P < 0.05) differences between atoxigenic and aflatoxigenic isolates. Our optimized qPCR-based tool reliably discriminated between aflatoxigenic and atoxigenic A. flavus isolates and could complement existing detection methods.
Species-area relationships emerge from multiple coexistence mechanisms

The increase of species richness with area is a universal phenomenon on Earth. However, this observation contrasts with our poor understanding of how these species-area relationships (SARs) emerge from the collective effects of area, spatial heterogeneity, and local interactions. By combining a structuralist approach with five years of empirical observations in a highly-diverse grassland, we show that, contrary to expectations, spatial heterogeneity plays a little role in the accumulation of species richness with area in our system. Instead, as we increase the sampled area more species combinations are realized, and they coexist mainly due to direct pairwise interactions rather than by changes in single-species dominance or by indirect interactions. We also identify a small set of transient species with small population sizes that are consistently found across spatial scales. These findings empirically support the importance of the architecture of species interactions together with demographic stochasticity for driving SARs.
Serum CSF1 levels are elevated in patients following partial hepatectomy and acetaminophen induced acute liver failure: Reanalysis of previous data

A previous study analysed serum CSF1 concentration in patients who had undergone partial hepatectomy and patients with acute liver failure (ALF) induced by acetaminophen. A correlation between low CSF1 and poor prognosis was reported in ALF. In May 2018, an allegation of research misconduct was made against the second author of the published study, D.J.Antoine, who carried out the CSF1 analysis. The current study describes the independent reanalysis of circulating CSF1 concentration in sera from the same patient cohorts. Patient serum CSF1 levels increased following partial hepatectomy. By contrast to the published report, serum CSF1 concentration was greatest in ALF patients who died compared to survivors. The results confirm the relationship between liver injury and circulating serum CSF1.
Antagonistic inhibitory subnetworks control cooperation and competition across cortical space

The cortical microcircuit can dynamically adjust to dramatic changes in the strength, scale, and complexity of its input. In the primary visual cortex (V1), pyramidal cells (PCs) integrate widely across space when signals are weak, but integrate narrowly when signals are strong, a phenomenon known as contrast-dependent surround suppression. Theoretical work has proposed that local interneurons could mediate a shift from cooperation to competition of PCs across cortical space, underlying this computation. We combine calcium imaging and electrophysiology to constrain a stabilized superlinear network model that explains how the four principal cell types in layer 2/3 (L2/3) of mouse V1– somatostatin (SST), parvalbumin (PV), and vasoactive intestinal peptide (VIP) interneurons, and PCs transform inputs from layer 4 (L4) PCs to encode drifting gratings of varying size and contrast. Using bidirectional optogenetic perturbations, we confirm key predictions of the model. Our data and modeling show that network nonlinearities set up by recurrent amplification mediate a shift from a positive PC-VIP feedback loop at small size and low contrast to a negative PC-SST feedback loop at large size and high contrast to support this flexible computation. This may represent a widespread mechanism for gating competition across cortical space to optimally meet task demands.
A new High-Throughput-Screening-assay for Photoantimicrobials Based on EUCAST Revealed Photoantimicrobials in Cortinariaceae

A spark of light might unravel antimicrobial activity of colored compounds, which otherwise would have been classified as inactive. While many mushrooms contain such colorful pigments but lack antimicrobial activity, we wondered if a controlled irradiation is needed to unleash their effect. To explore such photoantimicrobial actions in the Kingdom Fungi, an efficient high-throughput-screening (HTS) assay is needed. Here we report on the establishment of a reliable photoantimicrobial assay based on the EUCAST recommendations, which was validated with known photosensitzers (i.e., curcumin, phenalenone, rose bengal, an hypericum extract, and methylene blue). Furthermore, an improved LED-irradiation setup enabling with only 24 LEDs a homogenous irradiation of a 96-well plate is presented. The established HTS-assay was utilized to screen six colorful Cortinarius extracts unrevealing C. xanthophyllus and C. rufo-olivaceus as promising sources for new photoantimicrobials.
Simulations of turbulent acetone spray flames using the conditional source term estimation (CSE) approach

Turbulent dilute acetone spray flames are simulated in an Eulerian–Lagrangian framework using Conditional Source-term Estimation (CSE) for closure of the mean reaction rate. The objective of this work is to assess the performance of the coupled CSE-spray approach, investigated for the first time for the selected configuration. One non-reacting case and four non-premixed flames, AcF1–AcF3 and AcF5 are chosen. Detailed tabulated chemistry is included. Predictions of mean axial velocity, gas temperature and spray statistics are compared with available experimental data. Good agreement between the predicted gas temperatures and experimental values is found. The peak temperature tends to be overpredicted and shifted radially outwards in the simulations, in particular farther downstream. Same trends are observed in all flames, but the predictions deteriorate with flame AcF5. Possible sources of discrepancy are inaccurate turbulent mixing field, increased level of premixing for flame AcF5, the neglect of spray effect in the chemistry tabulation and a larger experimental uncertainty in the temperatures in the high-temperature regions. The mean droplet velocity profiles are in good agreement with the experiments for the four flames. However, the velocity was underpredicted, in particular near the centreline, for flames AcF1 and AcF2.
The use of computer vision to estimate tree diameter and circumference in homogeneous and production forests using a non-contact method

Abstract Tree diameter and circumference measurements are important metrics that should be monitored periodically and which can be used to determine rates of plant growth, timber production (wood), rubber tapping time, and to estimate the nutrient content of the soil in agroforestry especially for rubber and Albizia sp. trees. In this study, we evaluated the use of optical sensors, including a smartphone camera, which were analyzed by an image processing technology to estimate tree circumference of homogeneous and production forests especially rubber and Albizia forest plantations, through a real-time tree diameter measurement approach. Camera measurements were carried out for the diameter at breast height (DBH) and a certain distance of each tree (with the diameter of tree range of ∼6–50 cm). The results show that the use of smartphone camera measurements is highly correlated with manual measurements obtained using a tree caliper or meter tape in estimating tree circumference with coefficient of determination (R 2) and RMSE of 0.95 and 7.9 cm, respectively. Thus, this tool can be employed as an alternative method for measuring tree diameter and circumference.
Immigrant students’ minority language learning: an analysis of language ideologies

ABSTRACT This paper focuses on language ideologies in relation to identity in Basque secondary education, in a context where the teaching of a minority language is part of the curriculum. More precisely, it addresses the views held by teachers and immigrant students in relation to Basque, which is a minority language in the Basque Country. The aim is to analyse these views in their discourses both separately and in interaction. Methods include documentary analysis, participant observation, individual interviews and focus groups. Results indicate that there are engrained ideologies indexing identity in tension: those of teachers as Basque supporters and those adopted by students as Basque detractors, which come into conflict during classroom interaction when it involves learning Basque. The article concludes that these two ideologies constitute opposing identities and provides educational guidelines to improve classroom dynamics when acrimonious interactions such as these occur.
A first-principle study on photoelectric characteristics of Ce-doped ZnO

Abstract The influence of Ce on the properties of ZnO was elaborately investigated based on first-principles. The doping structures were set to: Zn0.9687Ce0. 0313O, Zn0.9583Ce0. 0417O, Zn0.9375Ce0. 0625O, and their property changes were compared to pure ZnO. The corresponding bandgaps are 2.444 eV, 2.529 eV and 2.571 eV, respectively. The peak value of the imaginary part of the dielectric function presents a trend of gradual increase. The optical absorption edge of Ce-doped ZnO has a clear red-shift to a lower energy region. The peaks of energy loss function are much lower, indicating that the introduction of Ce reduces the excitation energy of the plasma.
Man of contradictions: Joko Widodo and the struggle to remake Indonesia

Ben Bland’s Man of Contradictions: Joko Widodo and the Struggle to Remake Indonesia is as ambitious in scope as it is a page-turner. The most reviewed book on Indonesia for 2020, bar none, it is smartly and succinctly written, and provides an accessible account of Indonesian President Joko Widodo’s (‘Jokowi’) meteoric rise and his presidency to the present day (more or less). As Jakarta-based correspondent for the Financial Times between 2012 and 2016, Bland covered Indonesia and enjoyed a sizeable degree of access to the President. In this book, he draws on four years of covering Indonesia and the anecdotes that go with it, as well as a raft of other journalistic and scholarly sources, in a noble attempt to make sense of the psyche and leadership style, as well as the many contradictions, of Indonesia’s seventh president. Accounting for the life of a man whose presidency is not even halfway through its second term, however, has its limitations and challenges. Bland is acutely aware of this; indeed, he acknowledges that his biography of Jokowi is by no means a ‘conventional biography’, because he ‘could not possibly tell [Jokowi’s] whole life story in such a short work’ (8). Nevertheless, Bland attempts to comprehend, if not theorize, the countless contradictions of Jokowi the man, as well as the ever-changing and often-contradictory nature of his presidency and leadership style. Bland muses:
Non-timber forest product utilization under community forest management in northern Thailand

Abstract Forest resources are a salient and critical issue requiring ongoing attention by the Thai government. Community forest management (CFM) is a practice used to, among other things, resolve land use issues and regulate the extraction and use of non-timber forest product (NTFPs). Managing as a community forest can not only enhance the livelihoods of the local people but also improve their socio-economic condition. This research was conducted at the Ban Mae Chiang Rai Lum Community Forest located in Pa Mae Phrik National Forest Reserve in Thailand’s northern province of Lampang. We collected species biodiversity data of the forest’s total area of 3,925 ha using a systematic sampling method, and twenty-five 40 × 40 m (0.16 ha) survey plots were established in the community forest. Interviews of 159 household heads and/or other household representatives were conducted using a designed questionnaire. The questionnaire focused on information regarding the households’ NTFP utilization habits and engagement in CFM processes. A forest survey was conducted which found that there were 197 plant species, 144 genera, and 62 families in the community forest. Of these, 160 plant species were classified as having medicinal uses, 89 were used as food, 37 as extractives, 32 for firewood, and 12 for fibers. This study also revealed that unmonitored over-exploitation of NTFPs may negatively impact forest biodiversity. As surveyed, 68.55% of households depended on NTFPs. The value of the harvested NTFPs was 6.35% of the total community income. A positive correlation between NTFP income and CFM suggests that utilization of NTFPs combined with CFM can create income opportunities and promote participation in CFM. In addition, income earned from NTFPs and participation in CFM were directly related to the socio-economics of identifiable groups in this community. Laborers, merchants, and low-income families utilized NTFPs to a lesser degree. Single people, household heads, those with a bachelor’s degree, and low income families were less likely to participate in CFM while land owners were more likely to do so. This study implies that the harvesting of NTFPs should not go unchecked, especially of species that are threatened or likely to be threatened if over-harvested. Efforts to enhance lower income household utilization, to more equitably distribute the benefits, and to incentivize community involvement should be prioritized as doing so is crucial to maintaining a healthy supply of NTFPs and safeguarding the community forest biodiversity.