Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigation of two native Australian perennial forage legumes for their potential use in agriculture: Indigofera australis subsp. hesperia and Glycyrrhiza acanthocarpa

Abstract. In order to investigate the potential for domestication of native pasture legumes, a seed collecting mission was undertaken between Kalbarri and Esperance in the south of Western Australia followed by establishment of a field nursery at Northam, Western Australia. Indigofera australis subsp. hesperia Peter G.Wilson & Rowe was collected from eight sites, Indigofera brevidens Benth. from one site, and Glycyrrhiza acanthocarpa (Lindl.) J.M. Black from six sites. The field nursery was an irrigated, replicated trial designed to produce seed for future field testing and to provide preliminary information on plant agronomic characteristics. Over 12 months, I. australis produced herbage dry matter (DM) of 2.1–4.4 t/ha compared with 3.4 t/ha for a composite line of tedera (Bituminaria bituminosa C.H. Stirton vars. albomarginata and crassiuscula) and 1.0 t/ha DM for G. acanthocarpa. Most lines had digestibility and crude protein (15–25%) values that would support moderate growth of sheep or cattle. The best line of G. acanthocarpa produced >400 kg/ha of seeds, whereas I. australis had poor production most likely due to poor adaptation to the nursery site. The severity of cutting of I. australis plants had no significant effect on visual assessments of herbage growth. Most plants of I. australis died within 3 years, whereas most plants of G. acanthocarpa, I. brevidens and tedera survived for 3 years. Both I. australis and G. acanthocarpa have potential for use in broadacre agriculture as grazing plants, most likely in niches specifically suited to each, and demonstrate that native plants can contribute to pasture production currently dominated by exotic species.
LEAF HAIR TUFTS FUNCTION AS DOMATIA FOR MITES IN QUERCUS AGRIFOLIA (FAGACEAE)

Abstract An identifying feature of Quercus agrifolia Née (Fagaceae) is the presence of hair tufts on lower leaf surfaces. In other plant species, hair tufts act as domatia for arthropods such as mites, which in turn feed on leaf fungi or small herbivores and possibly benefit plant health. However, this mutualistic relationship remains untested in Q. agrifolia. In this study two primary questions were addressed within a natural stand of Q. agrifolia in San Luis Obispo, CA: 1) Do hair tufts act as domatia for mites? and 2) Does the removal of hair tufts impact mite abundance, herbivory or fungal pathogens on leaves? In an observational study of 377 leaves from 20 trees, we found a significant association between the presence of hair tufts and the presence of mites. When we experimentally removed hair tufts, we found a significant reduction in mites, yet there was no impact on leaf herbivory or necrosis. We conclude leaf hair tufts on Q. agrifolia serve as domatia for mites, but we found no evidence that mites reduce herbivory or fungal pathogens. Thus, while mites likely benefit from housing provided by hair tufts on Q. agrifolia, it is unclear that the tree benefits from the mites, i.e., whether this is a mutually beneficial relationship.
Carbon Emission Evaluation in Jinan Western New District Based on Multi-Source Data Fusion

Abstract: Carbon emissions caused by human activities are closely related to the process of urbanization, and urban land utilization, function vitality and traffic systems are three important factors that may influence the emission levels. For clarifying the space structure of a low-carbon eco-city, and combining the concept of “Combining Assessment with Construction” to track and contrast the construction of the low-carbon eco-city, this research selects quantifiable low-carbon eco-city spatial characteristics as indicators, and evaluates and analyzes the potential carbon emissions. Taking the Jinan Western New District as an example, diversity of construction land, travel carbon emission potential, and density and accessibility of adjacent road networks in the overall urban planning were measured. After the completion of the new urban area, the evaluation mainly reflected certain factors, such as the mixed degree of urban functions, the density of urban functions, the walking distance to bus stops and the density and number of bus stops. Dividing the levels and adding equal weights after index normalization, the carbon emission potential is evaluated at the two levels of the overall and fragmented areas. The results show that: (1) The low-carbon emission potential areas in the planning scheme basically reached the planned goals. (2) There is inconsistency between districts and indicators in the planning scheme. The diversity of construction land and the accessibility of the adjacent road network are relatively small; however, there is a large difference between the travel carbon emission potential and the road network accessibility. (3) Carbon emission potential after completion did not reach the planned expectation, and the low-carbon emission potential plots were concentrated in the Changqing Old City Area and Central Area of Dangjia Town Area. (4) The carbon emission indicators varied greatly in different areas, and there were serious imbalances in the density of public transportation lines and the mixed degree of urban functions.
TAXONOMIC REVISION OF MENTZELIA SECTION BICUSPIDARIA (LOASACEAE) IN MEXICO

Abstract Results from molecular phylogenetic analyses have indicated that the two southernmost species in Mentzelia section Bicuspidaria, M. hirsutissima sensu lato and M. involucrata, form a clade in which M. hirsutissima is paraphyletic with respect to M. involucrata. Here we elevate M. hirsutissima S.Watson var. nesiotes I.M. Johnst. to specific rank, recognizing it as M. nesiotes (I.M.Johnst.) Brokaw & J.J.Schenk, thus rendering all three taxa monophyletic. Mentzelia nesiotes is allopatric relative to M. involucrata and M. hirsutissima sensu stricto, with all known populations of M. nesiotes occurring in northern Baja California Sur and nearby Pacific islands. Multivariate analyses of morphological differences determined that M. nesiotes and M. hirsutissima are best distinguished by capsule length, calyx length, and leaf intersinus width. Estimation of climate niches with MaxEnt inferred that M. nesiotes and M. hirsutissima showed minimal overlap in climate tolerances, with M. nesiotes inhabiting the Vizcaíno fog desert west of the Peninsular Ranges and M. hirsutissima inhabiting areas further north with higher precipitation and temperature fluctuations primarily east of the Peninsular Ranges. We provide updated circumscriptions of all three species, reduce M. hirsutissima var. stenophylla and M. involucrata var. megalantha to synonymy with their respective species, and designate the lectotype of M. hirsutissima.
: Suitable reference genes selection for reliable normalization of gene expression in melanoma: implementation of an innovative GenExpA software

Melanoma is characterized by a high mutation rate and the proper reference selection is a serious problem. The algorithms commonly used to select the best stable reference gene or pair of genes in RT-qPCR data analysis have their limitations which affects the interpretation of the results and drawing conclusions. For reliable assessment of the B4GALT genes expression changes in melanoma and comparing them to their expression levels in melanocytes, we implemented an innovative GenExpA software. We proposed selection of the best reference by combining the NormFinder algorithm with progressive removal of the least stable gene from the candidate genes in a given experimental model and the set of daughter models assigned to it. The reliability of references is validated by normalizing of target gene expression level through all models and is described by the coherence score. The software performs statistical analyses and generates results in the form of ready-to-use graphs and tables. GenExpA is a promising tool for basic research; it produces analyses of target gene expression in a manner independent of the experimental model and the normalizer. GenExpA and its manual is freely available at https://drive.google. com/drive/folders/1FcpBtEc_bKPvEnM5GcPZerBb_Tw_fCkt? usp=shari ng or https://www.sciencemarket. pl/baza-programow-open-source#oferty. Supplemental materials are deposited under DOI number: 10.5281/zenodo.4544296.
metID: an R package for automatable compound annotation for LC−MS-based data

Summary Accurate and efficient compound annotation is a long-standing challenge for LC−MS-based data (e.g. untargeted metabolomics and exposomics). Substantial efforts have been devoted to overcoming this obstacle, whereas current tools are limited by the sources of spectral information used (in-house and public databases) and are not automated and streamlined. Therefore, we developed metID, an R package that combines information from all major databases for comprehensive and streamlined compound annotation. metID is a flexible, simple, and powerful tool that can be installed on all platforms, allowing the compound annotation process to be fully automatic and reproducible. A detailed tutorial and a case study are provided in Supplementary Materials. Availability and implementation https://jaspershen.github. io/metID/. Contact jiangzhu@sioc.ac. cn and mpsnyder@stanford.edu
Comprehensive analysis of meiosis-derived cDNA libraries reveals gene isoforms and mitochondrial proteins important for competitive fitness

Gametogenesis is a highly regulated and dynamic developmental program where a diploid progenitor cell differentiates into haploid gametes, the precursors for sexual reproduction. During meiosis, several pathways converge to initiate ploidy reduction and organelle remodelling to render gametes competent for zygote formation and subsequent organismal development. Additionally, meiosis inherently rejuvenates the newly formed gametes resulting in lifespan resetting. Here, we construct five stage-specific, inducible meiotic cDNA libraries that represent over 84% of the yeast genome. We employ computational strategies to detect stage-specific meiotic transcript isoforms in each library and develop a robust screening pipeline to test the effect of each cDNA on competitive fitness. Our multi-day proof-of-principle time course reveals gene isoforms that are important for competitive fitness as well as mitochondrial proteins that cause dose-dependent disruption of respiration. Together, these novel meiotic cDNA libraries provide an important resource for systematically studying meiotic genes and gene isoforms in future studies. HIGHLIGHTS Construction of five stage-specific, inducible meiotic cDNA libraries in budding yeast that collectively represent 5563 genes, which is over 84% of the genome Analysis of the cDNA libraries reveal the presence of meiosis-specific transcript isoforms that are largely uncharacterized Development of a robust gain-of-function screening pipeline identifies previously characterized genes and novel gene isoforms important for competitive fitness Multi-day proof-of-principle screen reveals mitochondrial proteins that cause dosage-specific respiration defects
Human iPSC-derived mesodermal progenitor cells preserve their vasculogenesis potential after extrusion and form hierarchically organized blood vessels

Post-fabrication formation of a proper vasculature remains an unresolved challenge in bioprinting. Established strategies focus on the supply of the fabricated structure with nutrients and oxygen and either rely on the mere formation of a channel system using fugitive inks or additionally use mature endothelial cells and/or peri-endothelial cells such as smooth muscle cells for the formation of blood vessels in vitro. Functional vessels, however, exhibit a hierarchical organization and multilayered wall structure that is important for their function. Human induced pluripotent stem cell-derived mesodermal progenitor cells (hiMPCs) have been shown to possess the capacity to form blood vessels in vitro, but have so far not been assessed for their applicability in bioprinting processes. Here, we demonstrate that hiMPCs, after formulation into an alginate/collagen type I bioink and subsequent extrusion, retain their ability to give rise to the formation of complex vessels that display a hierarchical network in a process that mimics the embryonic steps of vessel formation during vasculogenesis. Histological evaluations at different time points of extrusion revealed the initial formation of spheres, followed by lumen formation and further structural maturation as evidenced by building a multilayered vessel wall and a vascular network. These findings are supported by immunostainings for endothelial and peri-endothelial cell markers as well as electron microscopic analyses at the ultrastructural level. Moreover, endothelial cells in capillary-like vessel structures deposited a basement membrane-like matrix at the basal side between the vessel wall and the alginate-collagen matrix. After transplantation of the printed constructs into the chicken chorioallantoic membrane (CAM) the printed vessels connected to the CAM blood vessels and get perfused in vivo. These results evidence the applicability and great potential of hiMPCs for the bioprinting of vascular structures mimicking the basic morphogenetic steps of de novo vessel formation during embryogenesis.
Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified 30 new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA Partitiviridae, as well as a single negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.
Cortical alpha-synuclein preformed fibrils do not affect interval timing in mice

One hallmark feature of Parkinson’s disease (PD) is Lewy body pathology associated with misfolded alpha-synuclein. Previous studies have shown that striatal injection of alpha-synuclein preformed fibrils (PFF) can induce misfolding and aggregation of native alpha-synuclein in a prion-like manner, leading to cell death and motor dysfunction in mouse models. Here, we tested whether alpha-synuclein PFFs injected into the medial prefrontal cortex results in cognitive deficits in mouse models as measured by interval timing, which is reliably disrupted in PD patients and in rodent models. We injected human alpha-synuclein PFF or monomers in the medial prefrontal cortex pre-injected with adeno-associated virus (AAV) overexpressing human alpha-synuclein. Despite notable medial prefrontal cortical synucleinopathy, we did not observe consistent deficits in fixed-interval timing. These results suggest that cortical alpha-synuclein does not reliably disrupt interval timing in rodent models. Highlights Cortical injection of alpha-synuclein preformed fibrils (PFF) induces diffuse synucleinopathy Cortical injection of PFFs does not affect interval timing in mice Medial prefrontal cortical synucleinopathy does not reliably disrupt interval timing
Tree diversity effects on forest productivity: disentangling the effects of tree species addition vs. substitution

Mixture effect on stand productivity is usually apprehended through a substitutive approach, whereby productivity in mixed stands is compared to productivity in monocultures, at equivalent stand density. This approach has proved that in many cases mixed stands perform better than monospecific forests, however, we do not yet have a solid theory about species behaviour in the mixture or even guidelines for combining species. The addition of a second tree species to an existing mono-specific stand has received much less consideration. Yet, this approach has the potential to separate the facilitation effect from the complementarity effect. We compared the effect of tree species substitution vs. addition on the productivity of maritime pine and silver birch in a young tree diversity experiment implemented in 2008 in SW France. Substituting pines with birches to create two-species mixtures resulted in an increase of tree productivity at stand level beyond what was expected from monocultures (i.e., overyielding). In contrast, creating mixture through the addition of birches to pine stands had no effect on the maritime pine stand productivity (transgressive mixture effect not significant). This absence of effect is produced by two distinct density-dependence responses at an individual level. Our results allow clarifying the cases in which a mixed stand can be considered as an alternative to a monoculture of a productive species. In particular, the addition of a pioneer and soil low-demanding species during young developmental stages is a possibility to diversify the stand and potentially to increase ecosystem services without altering the productivity of the target species.
Can the lack of fibrillar form of alpha-synuclein in Lewy bodies be explained by its catalytic activity?

Finding the causative pathophysiological mechanisms for Parkinson’s disease (PD) is important for developing therapeutic interventions. Until recently, it was believed that Lewy bodies (LBs), the hallmark of PD, are mostly composed of alpha-synuclein (α-syn) fibrils. Recent results (Shahmoradian et al., Lewy pathology in Parkinson’s disease consists of crowded organelles and lipid membranes, Nature Neuroscience 22 (2019) 1099-1109) demonstrated that the fibrillar form of α-syn is lacking from LBs. Here we propose that this surprising observation can be explained by the catalytic activity of the fibrillar form of α-syn. We assumed that α-syn fibrils catalyze the formation of LBs, but do not become part of them. We developed a mathematical model based on this hypothesis. By using the developed model, we investigated the consequences of this hypothesis. In particular, the model suggests that the long incubation time of PD can be explained by a two-step aggregation process that leads to its development: (i) aggregation of monomeric α-syn into α-syn oligomers and fibrils and (ii) clustering of membrane-bound organelles, which may cause disruption of axonal trafficking and lead to neuron starvation and death. The model shows that decreasing the rate of destruction of α-syn aggregates in somatic lysosomes accelerates the formation of LBs. Another consequence of the model is the prediction that removing α-syn aggregates from the brain after the aggregation of membrane-bound organelles into LBs has started may not stop the progression of PD because LB formation is an autocatalytic process; hence, the formation of LBs will be catalyzed by aggregates of membrane-bound organelles even in the absence of α-syn aggregates. The performed sensitivity study made it possible to establish the hierarchy of model parameters with respect to their effect on the formation of vesicle aggregates in the soma.
The Polar Flagellar Transcriptional Regulatory Network in Vibrio campbellii Deviates from Canonical Vibrio Species

Vibrio campbellii is a Gram-negative bacterium that is free-living and ubiquitous in marine environments and is an important global pathogen of fish and shellfish. Disruption of the flagellar motor significantly decreases host mortality of V. campbellii, suggesting that motility is a key factor in pathogenesis. ABSTRACT Swimming motility is a critical virulence factor in pathogenesis for numerous Vibrio species. Vibrio campbellii DS40M4 is a wild-type isolate that has been recently established as a highly tractable model strain for bacterial genetics studies. We sought to exploit the tractability and relevance of this strain for characterization of flagellar gene regulation in V. campbellii. Using comparative genomics, we identified homologs of V. campbellii flagellar and chemotaxis genes conserved in other members of the Vibrionaceae and determined the transcriptional profile of these loci using differential RNA-seq. We systematically deleted all 63 predicted flagellar and chemotaxis genes in V. campbellii and examined their effects on motility and flagellum production. We specifically focused on the core regulators of the flagellar hierarchy established in other vibrios: RpoN (σ54), FlrA, FlrC, and FliA. Our results show that V. campbellii transcription of flagellar and chemotaxis genes is governed by a multitiered regulatory hierarchy similar to other motile Vibrio species. However, there are several critical differences in V. campbellii: (i) the σ54-dependent regulator FlrA is dispensable for motility; (ii) the flgA, fliEFGHIJ, flrA, and flrBC operons do not require σ54 for expression; and (iii) FlrA and FlrC coregulate class II genes. Our model proposes that the V. campbellii flagellar transcriptional hierarchy has three classes of genes, in contrast to the four-class hierarchy in Vibrio cholerae. Our genetic and phenotypic dissection of the V. campbellii flagellar regulatory network highlights the differences that have evolved in flagellar regulation across the Vibrionaceae. IMPORTANCE Vibrio campbellii is a Gram-negative bacterium that is free-living and ubiquitous in marine environments and is an important global pathogen of fish and shellfish. Disruption of the flagellar motor significantly decreases host mortality of V. campbellii, suggesting that motility is a key factor in pathogenesis. Using this model organism, we identified >60 genes that encode proteins with predicted structural, mechanical, or regulatory roles in function of the single polar flagellum in V. campbellii. We systematically tested strains containing single deletions of each gene to determine the impact on motility and flagellum production. Our studies have uncovered differences in the regulatory network and function of several genes in V. campbellii compared to established systems in Vibrio cholerae and Vibrio parahaemolyticus.