Miracle-dz/UniFAR-FTUs huggingface dataset:
Employing marine invertebrate cell culture media for isolation and cultivation of thraustochytrids

Abstract Thraustochytrids, a common group of marine eukaryotic protists, have drawn considerable scientific and industrial interest due to their ability to synthesize high levels of bioactive compounds, including polyunsaturated fatty acids, docosahexaenoic acid, squalene and carotenoids, and their new applications for biofuels. The pharmaceutical and industrial potential of thraustochytrids necessitate effective isolation of new strains and establishment of axenic cultures. To date, existing isolation protocols have used baiting and direct plating methods to generate axenic cultures with varied media compositions that contain peptone and yeast extracts as nitrogen sources, glucose as carbon source, seawater and antibiotics. Here we reveal a new approach for the isolation of thraustochytrids from tissues of marine invertebrates using (a) primary cell cultures in a liquid medium containing basal medium, 50% artificial seawater, vitamins, proteins and antibiotics, and (b) cultivation in the same cell culture medium. Using the colonial tunicate Botryllus schlosseri as a model system, thraustochytrid cells thrived in the medium from the day of extraction, grew and proliferated for the next five weeks (five-passages, up to 1.9 × 106 cells ml−1 in passage 5; 1.45-fold multiplication week−1). This new approach for isolation and cultivation of axenic thraustochytrid cultures enables the isolation of new species with promising bioactive compounds.
New targets of morphine postconditioning protection of the myocardium in ischemia/reperfusion injury: Involvement of HSP90/Akt and C5a/NF-κB

Abstract Background Activation of the complement component 5a (C5a) and nuclear factor κB (NF-κB) signaling is an important feature of myocardial ischemia/reperfusion (I/R) injury and recent studies show that morphine postconditioning (MP) attenuates the myocardial injury. However, the mediating cardioprotective mechanisms remain unclear. The present study explores the role and interaction of heat shock protein 90 (HSP90), Akt, C5a, and NF-κB in MP-induced cardioprotection. Methods Male Sprague Dawley rats (n = 160) were randomized into eight groups (n = 20 per group). Rats in the sham group underwent thoracotomy, passing the ligature through the heart but without tying it (150 min), and the other seven groups were subjected to 30 min of anterior descending coronary artery occlusion followed by 2 h of reperfusion and the following treatments: I/R (30 min of ischemia and followed by 2 h of reperfusion); ischemic postconditioning (IPostC, 30 s of ischemia altered with 30 s of reperfusion, repeated for three cycles, and followed by reperfusion for 2 h); MP (0.3 mg/kg morphine administration 10 min before reperfusion); MP combined with the HSP90 inhibitor geldanamycin (GA, 1 mg/kg); MP combined with the Akt inhibitor GSK-690693 (GSK, 20 mg/kg); and MP combined with the C5a inhibitor PMX205 (PMX, 1 mg/kg/day, administration via drinking water for 28 days) and MP combined with the NF-κB inhibitor EVP4593 (QNZ, 1 mg/kg). All inhibitors were administered 10 min before morphine and followed by 2 h reperfusion. Results MP significantly reduced the I/R-induced infarct size, the apoptosis, and the release of cardiac troponin I, lactate dehydrogenase (LDH), and creatine kinase-MB. These beneficial effects were accompanied by increased expression of HSP90 and p-Akt, and decreased expression of C5a, NF-κB, tumor necrosis factor α, interleukin-1β, and intercellular cell adhesion molecule 1. However, HSP90 inhibitor GA or Akt inhibitor GSK increased the expression of C5a and NF-κB and prevented MP-induced cardioprotection. Furthermore, GA inhibited the MP-induced upregulation of p-Akt, while GSK did not affect HSP90, indicating that p-Akt acts downstream of HSP90 in MP-induced cardioprotection. In addition, C5a inhibitor PMX enhanced the MP-induced downregulation of NF-κB, while NF-κB inhibitor QNZ had no effect on C5a, indicating that the C5a/NF-κB signaling pathway is involved in MP-induced cardioprotection. Conclusion HSP90 is critical for MP-mediated cardioprotection possibly by promoting the phosphorylation of Akt and inhibiting the activation of C5a and NF-κB signaling and the subsequent myocardial inflammation, ultimately attenuating the infarct size and cardiomyocyte apoptosis.
Fe3+ and Ce3+ modified nano-TiO2 for degradation of exhaust gas in tunnels

Abstract To solve the environmental pollution caused by automobile exhaust in a tunnel, this study has developed a modified nano-TiO2 based on Fe3+ and Ce3+. The modified nano-TiO2 is prepared by the sol–gel method, and the modification adopts Fe3+ single-doping, Ce3+ sing-doping, and co-doping. The properties were also characterized by X-ray diffraction analysis, UV-vis diffuse reflectance analysis, fluorescence spectroscopy analysis, specific surface area analysis, and paramagnetic resonance popper analysis. The analyses showed that the doping of ions would change the energy band structure of nano-TiO2 and produce crystal defects, thus improving the photocatalytic activity. Then, a self-fabricated exhaust gas degradation device was used to carry out the exhaust gas degradation experiments. The results showed that the modification improves the catalytic efficiency of nano-TiO2, and Fe3+, Ce3+ co-doping > Ce3+ single-doping > Fe3+ single-doping > pure TiO2. At the dosage of 0.5%, the maximum degradation efficiencies of NO and CO before compensation are 53.85% and 16.39%, respectively, and the maximum degradation rates are 1.04 and 0.93 ppm·min−1. After compensation, the maximum degradation efficiencies of NO and CO are 20.14% and 6.04%, respectively. The maximum degradation rate is 0.40 and 0.41 ppm·min−1, respectively.
Universal inequalities of the poly-drifting Laplacian on smooth metric measure spaces

Abstract In this paper, we study the eigenvalue problem of poly-drifting Laplacian on complete smooth metric measure space ( M , ⟨ , ⟩ , e − ϕ d v ) \left(M,\langle ,\rangle ,{e}^{-\phi }{\rm{d}}v) , with nonnegative weighted Ricci curvature Ric ϕ ≥ 0 {{\rm{Ric}}}^{\phi }\ge 0 for some ϕ ∈ C 2 ( M ) \phi \in {C}^{2}\left(M) , which is uniformly bounded from above, and successfully obtain several universal inequalities of this eigenvalue problem.
Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii

Agrobacterium tumefaciens is considered a prominent phytopathogen, though most isolates are nonpathogenic. Agrobacteria can inhabit plant tissues interacting with other microorganisms. Yeasts are likewise part of these communities. We analyzed the quorum sensing (QS) systems of A. tumefaciens strain 6N2, and its relevance for the interaction with the yeast Meyerozyma guilliermondii, both sugarcane endophytes. We show that strain 6N2 is nonpathogenic, produces OHC8-HSL, OHC10-HSL, OC12-HSL and OHC12-HSL as QS signals, and possesses a complex QS architecture, with one truncated, two complete systems, and three additional QS-signal receptors. A proteomic approach showed differences in QS-regulated proteins between pure (64 proteins) and dual (33 proteins) cultures. Seven proteins were consistently regulated by quorum sensing in pure and dual cultures. M. guilliermondii proteins influenced by QS activity were also evaluated. Several up- and down- regulated proteins differed depending on the bacterial QS. These results show the importance of the QS regulation in the bacteria-yeast interactions. Highlights The avirulent A. tumefaciens 6N2 has two replicons and a complex QS architecture The profile of QS-regulated proteins is modified in dual cultures with Pa. laurentii The bacterial QS activity alters the proteome of the yeast Pa. laurentii
Intratumoral and extratumoral synapses are required for glioblastoma progression in Drosophila

Glioblastoma (GB) is the most aggressive, lethal and frequent primary brain tumor. It originates from glial cells and is characterized by rapid expansion through infiltration. GB cells interact with the microenvironment and healthy surrounding tissues, mostly neurons and vessels. GB cells project tumor microtubes (TMs) that contact with neurons and exchange signaling molecules related to Wingless/WNT, JNK, Insulin or Neuroligin-3 pathways. This cell to cell communication promotes GB expansion and neurodegeneration. Moreover, healthy neurons form glutamatergic functional synapses with GB cells which facilitate GB expansion and premature death in mouse GB xerograph models. Targeting signaling and synaptic components of GB progression may become a suitable strategy against glioblastoma. In a Drosophila GB model, we have determined the post-synaptic nature of GB cells with respect to neurons, and the contribution of post-synaptic genes expressed in GB cells to tumor progression. In addition, we document the presence of intratumoral synapses between GB cells, and the functional contribution of pre-synaptic genes to GB calcium dependent activity and expansion. Finally, we explore the relevance of synaptic genes in GB cells to the lifespan reduction caused by GB advance. Our results indicate that both presynaptic and postsynaptic proteins play a role in GB progression and lethality.
SURFMAP: a software for mapping in two dimensions protein surface features

Molecular cartography using two-dimensional (2D) representation of protein surfaces has been shown to be very promising for protein surface analysis. Here, we present SURFMAP, a free standalone and easy-to-use software that enables the fast and automated 2D projection of either predefined features of protein surface (i.e., electrostatic potential, Kyte-Doolittle hydrophobicity, stickiness, and surface relief) or any descriptor encoded in the temperature factor column of a PDB file. SURFMAP uses a pseudo-cylindrical sinusoidal “equal-area” projection that has the advantage of preserving the area measures. It provides the user with (i) 2D maps that enable the easy and visual analysis of protein surface features of interest and (ii) maps in a text file format allowing the fast and straightforward quantitative comparison of 2D maps of homologous proteins.
CellTools algorithm for mapping scRNA-seq query cells to the reference dataset improves the classification of resilient and susceptible retinal ganglion cell types

The clustering of single cell RNA-sequencing (scRNA-seq) data enables the classification of cell types, and the development of integration mapping algorithms has enabled the tracing of altered-from-baseline transcriptomes to their respective cell type origins. Here, we developed an algorithm that removes sources of noise from scRNA-seq reference dataset, and in the next step optimizes weight-assignment to anchors, cumulatively improving the accuracy of query cells mapping to reference dataset. The denoising step of our algorithm also improved the performance of other mapping algorithms. To further demonstrate biological relevance, using our algorithm we determined the type-origin of the 17% of injured retinal ganglion cells (RGCs) that a prior algorithm did not identify. As we found that most of the originally unassigned cells belonged to only some RGC types, a consequent change in the proportions of the surviving types resulted in an amended ranking of resiliency to injury. We also identified new cluster-markers for RGC types, validated two novel markers by immunostaining in retinas, and developed a website for cluster-by-cluster comparison of gene expression between uninjured and injured RGC types. Additional bioinformatic analyses contributed new insights into the global characteristics of RGC types and how axonal injury affects them, showing how dissimilarity between transcriptomes of RGC types increases during maturation and after injury. We further characterized the correspondence between the neonatal and adult RGC types, and showed which cluster markers change expression developmentally or after injury. We also show, for the first time, that global properties of the transcriptome can predict the resilience to injury of at least some cell types. The R-package, CellTools, for the algorithms we developed, will assist scRNA-seq studies across biological fields.
The ESX-1 secretion system senses bacterial contact and prepares mycobacteria for environmental adaptation

The ESX-1 system (6-kDa early secretory antigenic target (ESAT-6) secretion system-1) is essential for Mycobacterium tuberculosis pathogenesis and conjugal transfer in Mycobacterium smegmatis, yet little is known about how its function is regulated. Live-cell fluorescence microscopy showed natively expressed ESX-1 was organized into distinct foci predominantly observed at cell-cell contacts. These foci formed when two cells touched and required a fully assembled ESX-1 system in both bacteria, suggesting the generation of an ESX-1 megacomplex across multiple membranes. The emergence of ESX-1 foci and ESX-1 secretion was environmentally dependent: foci formed in low nitrogen environments in which secretion was suppressed, yet with increasing concentrations of nitrogen, ESX-1 systems diffused along the plasma membrane and secretion was activated. Genome-wide transcriptional profiling revealed ESX-1 dependent induction of genes required for the SOS response and error prone DNA replication in high nitrogen. Based on these findings, we propose a new model of ESX-1 function where ESX-1 localization and secretion are responsive to nitrogen levels and form an integral node in the mycobacterial response to neighboring cells and environmental adaptation.
In situ architecture of the ciliary base reveals the stepwise assembly of IFT trains

The cilium is an antenna-like organelle that performs numerous cellular functions, including motility, sensing, and signaling. The base of the cilium contains a selective barrier that regulates the entry of large intraflagellar transport (IFT) trains, which carry cargo proteins required for ciliary assembly and maintenance. However, the native architecture of the ciliary base and the process of IFT train assembly remain unresolved. Here, we use in situ cryo-electron tomography to reveal native structures of the transition zone region and assembling IFT trains at the ciliary base. We combine this direct cellular visualization with ultrastructure expansion microscopy to describe the front-to-back stepwise assembly of IFT trains: IFT-B forms the backbone, onto which IFT-A, then dynein-1b, and finally kinesin-2 sequentially bind before entry into the cilium. Highlight Native molecular structure of the ciliary transition zone and hierarchical order of IFT assembly visualized within Chlamydomonas cells.
Accounting for animal movement improves vaccination strategies against wildlife disease in heterogeneous landscapes

Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife like raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting strategies that match raccoon movement patterns perform better than currently employed baiting strategies in an oral rabies vaccination zone in greater Burlington, Vermont, USA. Habitat selection patterns estimated from locally radio-collared raccoons were used to parameterize movement simulations. We then used our simulations to estimate raccoon population rabies seroprevalence under currently used baiting strategies (actual baiting) relative to habitat selection-based baiting strategies (habitat baiting). We conducted simulations on the Burlington landscape and artificial landscapes that varied in heterogeneity relative to Burlington in the proportion and patch size of preferred habitats. We found that the benefits of habitat baiting strongly depended on the magnitude and variability of raccoon habitat selection and the degree of landscape heterogeneity within the baiting area. Habitat baiting improved seroprevalence over actual baiting for raccoons characterized as habitat specialists but not for raccoons that displayed weak habitat selection similar to radio-collared individuals—except when baits were delivered off roads where preferred habitat coverage and complexity was more pronounced. In contrast, in artificial landscapes with either more strongly juxtaposed favored habitats and/or higher proportions of favored habitats, habitat baiting performed better than actual baiting, even when raccoons displayed weak habitat preferences and where baiting was constrained to roads. Our results suggest that habitat selection-based baiting could increase raccoon population seroprevalence in urban-suburban areas, where practical, given the heterogeneity and availability of preferred habitat types in those areas. Our novel simulation approach provides a flexible framework to test alternative baiting strategies in multiclass landscapes to optimize bait distribution strategies.
Into the range: a latitudinal gradient or a center-margins differentiation of ecological strategies in Arabidopsis thaliana?

Background and Aims Determining within-species large-scale variation in phenotypic traits is central to elucidate the drivers of species’ ranges. Intraspecific comparisons offer the opportunity to understand how trade-offs and biogeographical history constrain adaptation to contrasted environmental conditions. Here we test whether functional traits, ecological strategies and phenotypic plasticity in response to abiotic stress vary along a latitudinal or a center-margins gradient within the native range of Arabidopsis thaliana. Methods The phenotypic outcomes of plant adaptation at the center and margins of its geographic range were experimentally examined in 30 accessions from southern, central and northern Europe. The variation of traits related to stress tolerance, resource use, colonization ability as well as survival and fecundity was determined in response to high temperature (34°C) or frost (- 6°C), in combination with response to water deficit. Key Results Both evidence for a latitudinal and a center-margins differentiation was found. Traits related to the acquisitive/conservative strategy trade-off varied along a latitudinal gradient. Northern accessions presented a greater survival to stress than central and southern accessions. Traits related to a colonization-competition trade-off followed a center-margin differentiation. Central accessions presented a higher phenotypic plasticity and trait values associated with a higher colonization ability than northern and southern accessions which instead had a higher competition ability. Conclusions Intraspecific phenotypic variation helps us understand how the distribution range has evolved in Arabidopsis thaliana, which is shaped both by climate and the population migratory history. We advocate to consider intraspecific trait variation in species range studies instead of species means only as classically done in macroecology.
1 14-3-3 z constrains insulin secretion in pancreatic b-cells by regulating mitochondrial function

1Department of Medicine, Université de Montréal, Montréal, QC, Canada 2Cardiometabolic axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada. 3Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden 4Immunopathology axis, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada. 5The University of Ottawa, Faculty of Medicine, Department of Biochemistry, Microbiology and Immunology, Ottawa, Ontario, K1H 8M5, Canada 6 The University of Ottawa Heart Institute, 40 Ruskin Street, Ottawa, Ontario, Canada, K1Y4W7 7Institute of Metabolism and Systems Research (IMSR), Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham UK 8Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners Birmingham UK 9Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Chemical Biology
Single-Shot Optical Projection tomography for high-speed volumetric imaging

We present a single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic samples. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio but the sequential acquisition of projection images required for volumetric reconstruction typically requires samples to be immobilised during the acquisition of an OPT data set. We present a proof-of-principle system capable of single-shot imaging of a 1 mm diameter volume, demonstrating camera-limited rates of up to 62.5 volumes/second, which we have applied to 3D imaging of a freely-swimming zebrafish embryo. This is achieved by recording 8 projection views simultaneously on 4 low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5,000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including fluid dynamics.
Antibiotic Resistance via Bacterial Cell Shape-Shifting

Bacteria have evolved to develop multiple strategies for antibiotic resistance by effectively reducing intracellular antibiotic concentrations or antibiotic binding affinities, but the role of cell morphology in antibiotic resistance remains poorly understood. By analyzing cell morphological data for different bacterial species under antibiotic stress, we find that bacteria increase or decrease the cell surface-to-volume ratio depending on the antibiotic target. ABSTRACT Bacteria have evolved to develop multiple strategies for antibiotic resistance by effectively reducing intracellular antibiotic concentrations or antibiotic binding affinities, but the role of cell morphology in antibiotic resistance remains poorly understood. By analyzing cell morphological data for different bacterial species under antibiotic stress, we find that bacteria increase or decrease the cell surface-to-volume ratio depending on the antibiotic target. Using quantitative modeling, we show that by reducing the surface-to-volume ratio, bacteria can effectively reduce the intracellular antibiotic concentration by decreasing antibiotic influx. The model further predicts that bacteria can increase the surface-to-volume ratio to induce the dilution of membrane-targeting antibiotics, in agreement with experimental data. Using a whole-cell model for the regulation of cell shape and growth by antibiotics, we predict shape transformations that bacteria can utilize to increase their fitness in the presence of antibiotics. We conclude by discussing additional pathways for antibiotic resistance that may act in synergy with shape-induced resistance.