Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of the cAMP levels with a conserved actinobacteria phosphodiesterase enzyme reduces antimicrobial tolerance in mycobacteria

Antimicrobial tolerance (AMT) is the gateway to the development of antimicrobial resistance (AMR) and is therefore a major issue that needs to be addressed. The second messenger cyclic-AMP (cAMP), which is conserved across all taxa, is involved in propagating signals from environmental stimuli and converting these into a response. In bacteria, such as M. tuberculosis, P. aeruginosa, V. cholerae and B. pertussis, cAMP has been implicated in virulence, metabolic regulation and gene expression. However, cAMP signalling in mycobacteria is particularly complex due to the redundancy of adenylate cyclases, which are enzymes that catalyse the formation of cAMP from ATP, and the poor activity of the only known phosphodiesterase (PDE) enzyme, which degrades cAMP into 5’- AMP. Based on these two features, the modulation of this system with the aim of investigating cAMP signalling and its involvement in AMT in mycobacteria id difficult. To address this pressing need, we identified a new cAMP-degrading phosphodiesterase enzyme (Rv1339) and used it to significantly decrease the intrabacterial levels of cAMP in mycobacteria. This analysis revealed that this enzyme increased the antimicrobial susceptibility of M. smegmatis mc2155. Using a combination of metabolomics, RNA-sequencing, antimicrobial susceptibility assays and bioenergetics analysis, we were able to characterize the molecular mechanism underlying this increased susceptibility. This work represents an important milestone showing that the targeting of cAMP signalling is a promising new avenue for antimicrobial development and expands our understanding of cAMP signalling in mycobacteria.
Single-Particle Resolution Fluorescence Microscopy of Nanoplastics

Understanding of nanoplastic prevalence and toxicology is limited by imaging challenges resulting from their small size. Fluorescence microscopy is widely applied to track and identify microplastics in laboratory studies and environmental samples. However, conventional fluorescence microscopy, due to diffraction, lacks the resolution to precisely localize nanoplastics in tissues, distinguish them from free dye, or quantify them in environmental samples. To address these limitations, we developed techniques to label nanoplastics for imaging with Stimulated Emission Depletion (STED) microscopy to achieve resolution at an order of magnitude superior to conventional fluorescence microscopy. These techniques include (1) passive sorption; (2) swell incorporation; and (3) covalent coupling of STED-compatible fluorescence dyes to nanoplastics. We demonstrate that our labeling techniques, combined with STED microscopy, can be used to resolve nanoplastics of different shapes and compositions as small as 50 nm. The longevity of the dye labeling is demonstrated in different media and conditions of biological and environmental relevance. We also test STED imaging of nanoplastics in exposure experiments with the model worm C. elegans. These techniques will allow more precise localization and quantification of nanoplastics in complex matrices. Synopsis We show that Stimulated Emission Depletion (STED) microscopy can be used to image single nanoplastics of different compositions and shapes. This will allow researchers to study environmentally-relevant nanoplastics and their interactions with organisms in relevant exposure scenarios. TOC Graphic
EmpiReS: Differential Analysis of Gene Expression and Alternative Splicing

While absolute quantification is challenging in high-throughput measurements, changes of features between conditions can often be determined with high precision. Therefore, analysis of fold changes is the standard method, but often, a doubly differential analysis of changes of changes is required. Differential alternative splicing is an example of a doubly differential analysis, i.e. fold changes between conditions for different isoforms of a gene. EmpiRe is a quantitative approach for various kinds of omics data based on fold changes for appropriate features of biological objects. Empirical error distributions for these fold changes are estimated from Replicate measurements and used to quantify feature fold changes and their directions. We assess the performance of EmpiRe to detect differentially expressed genes applied to RNA-Seq using simulated data. It achieved higher precision than established tools at nearly the same recall level. Furthermore, we assess the detection of alternatively Spliced genes via changes of isoform fold changes (EmpiReS) on distribution-free simulations and experimentally validated splicing events. EmpiReS achieves the best precision-recall values for simulations based on different biological datasets. We propose EmpiRe(S) as a general, quantitative and fast approach with high reliability and an excellent trade-off between sensitivity and precision in (doubly) differential analyses.
Antioxidant activity of flaxseed proteins and their hydrolysates

Certain components of flaxseed are known to exhibit antioxidant activity. The objective of this research was to study the antioxidant activity of flaxseed proteins and protein hydrolysates. Proteins and their hydrolysates were prepared from defatted, non-defatted, and demucilaged flaxseed with and without dialysis, and the antioxidant activities were examined by DPPH scavenging assay, reducing power assay, and metal ion chelating assay. The degree of hydrolysis (DH) of the proteins using bacterial protease was higher than using trypsin. Using bacterial protease, higher DH was observed for demucilaged and defatted flaxseed protein/dialysis (DDFPD, 30% DH), defatted flaxseed protein/dialysis (DFPD, 28% DH), and non-defatted flaxseed proteins/dialysis with 14% DH, compared to flaxseed protein/non-dialysis which were DDFPND 28% DH, DFPND 25% DH, and NDFPND with 12% DH. Proteins from dialysis treatment as well as their hydrolysates showed positive effect on antioxidant activity. DDFPD hydrolysates using bacterial protease showed higher DPPH radical scavenging activity (73.23%) and reducing power activity (0.15) at the concentration of 2.5 mg/ml as well as Fe2+ chelating ability (75%) at of concentration 1 mg/ml. SDS-PAGE and native-PAGE results of non-hydrolyzed samples showed no change in electrophoretic behavior as a result of the treatments; a major band corresponding to MW 48 KDa and three minor bands with MW of 16, 23, and 34 KDa. SDS-PAGE of DDFPNDH and NDFPNDH hydrolysates obtained using trypsin showed one resistant band. %%%%Certaines composantes des graines de lin sont reconnues pour avoir des effets antioxydants. L'objectif du projet de recherche ci-present est d'etudier les effets antioxydants des proteines des graines de lin et de leurs hydrolysâtes. Les proteines et leurs hydrolysâtes ont ete prepare a partir de graines de lin degraissees ou natures et demucilaginees, avec et sans dialyse. Leurs effets antioxydants ont ete examines avec le test de scannage DPPH, le test du pouvoir de reduction, et le test des ions metalliques chelates. Le degre d'hydrolyse (DH) des proteines etait plus eleve avec l'utilisation d'une protease bacteriale qu'avec l'utilisation de trypsine. En utilisant la protease bacteriale, un DH plus eleve a ete observe avec les graines demucilaginees et degraissees avec dialyse/proteine (DDFPD, 30% DH), les graines degraissees avec dialyse/proteine (DFPD, 28% DH), et les graines nature avec dialyse/proteines (14% DH), compare aux graines proteine/sans dialyse qui ont eu comme resultat DDFPND 28%, DFPND 25% DH, et NDFPND avec 12% DH. Les proteines et leurs hydrolysâtes du traitement avec dialyse ont montre qu'il y avait bel et bien un effet antioxydant. Les hydrolysâtes, du test DDFPD et de l'utilisation du protease bacteriale, ont montre un niveau d'activite de radicaux libres plus eleve (DPPH 73.23%) ainsi qu'un pouvoir de reduction de (0.15) a une concentration de 2.5 mg/ml, de meme qu'une habilite au Fe2+ de 75% a la concentration de 1mg/ml. Les resultats de SDS-PAGE et PAGE-original des…
Genome-wide diversity and differentiation of two novel multidrug-resistant populations of Pasteurella multocida type B:2 from fowl cholera

Pasteurella multocida is the etiologic agent of fowl cholera (FC), a highly contagious and severe disease in poultry with higher mortality and morbidity. Twenty-two P. multocida strains isolated from the FC outbreaks were subjected to phenotypic and genotypic characterization. The isolates were grouped into two distinct RAPD biotypes harboring a range of pathogenic genes; exbB, ompH, ptfA, nanB, sodC, and hgbA. Among these strains, 90.90% and 36.37% were multidrug-resistant and strong biofilm formers, respectively. Whole genome sequencing of the two representative RAPD isolates confirmed as P. multocida type B:L2:ST122 harboring a number of virulence factors, and antimicrobial resistance genes. Pan-genome analysis revealed 90 unique genes in these genomes associated with versatile metabolic functions, pathogenicity, virulence, and antimicrobial resistance. This study for the first time reports the association of P. multocida genotype B:L2:ST122 in the pathogenesis of FC, and provides a genetic context for future researches on P. multocida strains.
Loud noise exposure differentially affects subpopulations of auditory cortex pyramidal cells

Loud noise-exposure generates tinnitus in both humans and animals. Macroscopic studies show that noise exposure affects the auditory cortex; however, cellular mechanisms of tinnitus generation are unclear. Here we compare membrane properties of layer 5 (L5) pyramidal cells (PCs) of the primary auditory cortex (A1) from control and noise-exposed mice. PCs were previously classified in type A or type B based on connectivity and firing properties. Our analysis based on a logistic regression model predicted that afterhyperpolatization and afterdepolarization following the injection of inward and outward current are enough to predict cell type and these features are preserved after noise trauma. One week after a noise-exposure (4-18kHz, 90dB, 1.5 hr, followed by 1.5hr silence) no passive membrane properties of type A or B PCs were altered but principal component analysis showed greater separation between control/noise-exposure recordings for type A neurons. When comparing individual firing properties, noise exposure differentially affected type A and B PC firing frequency in response to depolarizing current steps. Specifically, type A PCs decreased both initial and steady state firing frequency and type B PCs significantly increased steady state firing frequency following noise exposure. These results show that loud noise can cause distinct effects on type A and B L5 auditory cortex PCs one week following noise exposure. As the type A PC electrophysiological profile is correlated to corticofugal L5 neurons, and type B PCs correlate to contralateral projecting PCs these alterations could partially explain the reorganization of the auditory cortex observed in tinnitus patients.
TOLLIP promotes durable alveolar macrophage-mediated immunity during Mycobacterium tuberculosis infection by resolving cellular stress from lipids

TOLLIP, a ubiquitin binding protein that controls multiple macrophage functions via endoplasmic reticulum transport and autophagy, is associated with human tuberculosis (TB) susceptibility and immune responses in genetic studies. We investigated how TOLLIP influences immunity during Mycobacterium tuberculosis (Mtb) infection in the mouse model. During early infection, Tollip-/- mice had reduced mycobacterial burden and increased innate immune responses, but later, Tollip-/- mice developed worse disease and many foam cells within their lung infiltrates. The delayed immune impairment was intrinsic to alveolar macrophages, associated with cellular stress, and accompanied by lipid accumulation. Further, this phenotype was reproducible with administration of exogenous lipids. Thus, TOLLIP expression in alveolar macrophages is necessary for durable protection from prolonged Mtb infection by resolving lipid-induced cellular stress. These descriptions define a critical role for TOLLIP as part of the lipid-induced ER stress response, which is responsible for Mtb progression during post-primary infection.
Effect of host-mimicking medium and biofilm growth on the ability of colistin to kill Pseudomonas aeruginosa

In vivo biofilms cause recalcitrant infections with extensive and unpredictable antibiotic tolerance. Here, we demonstrate increased tolerance of colistin by Pseudomonas aeruginosa when grown in cystic fibrosis-mimicking medium versus standard medium in in vitro biofilm assays, and drastically increased tolerance when grown in an ex vivo CF model versus the in vitro assay. We used colistin conjugated to the fluorescent dye BODIPY to assess the penetration of the antibiotic into ex vivo biofilms and showed that poor penetration partly explains the high doses of drug necessary to kill bacteria in these biofilms. The ability of antibiotics to penetrate the biofilm matrix is key to their clinical success, but hard to measure. Our results demonstrate both the importance of reduced entry into the matrix in in vivo-like biofilm, and the tractability of using a fluorescent tag and benchtop fluorimeter to assess antibiotic entry into biofilms. This method could be a relatively quick, cheap and useful addition to diagnostic and R&D pipelines, allowing the assessment of drug entry into biofilms, in in vivo-like conditions, prior to more detailed tests of biofilm killing.
In vitro development of Encyclea cordigera in different concentrations of honey

The objective of this paper was to evaluate the effects of different honey concentrations in culture media, in comparison to sucrose medium, for the in vitro development of the epiphytic Encyclea cordigera orchid, in order to improve the process of propagation of the species. The in vitro germination was prepared on a reduced Murashige & Skoog (MS) medium. After 90 days, the seedlings were divided into different treatments, where they remained for another 90 days. Six treatments were set up (30g L-1 of sucrose; 15, 30, 45, and 60g L-1 of honey; and absence of any carbohydrates) in a completely randomized design. Plants were removed from the vials 270 days after the start of the experiment, and the number of roots, length of the largest leaf, length of the longest root, number of leaves, and fresh and dry masses were evaluated. Data concerning the number of leaves and roots were (x+1)1/2 transformed and subjected to an analysis of variance (ANOVA); the means were compared by a Tukey's test set at 5% probability. Medium containing 60g L-1 of honey proved to be superior to the sucrose medium traditionally used, favoring the in vitro growth and development of Encyclea cordigera. This medium can therefore be recommended for the propagation of this species, which is usually cultivated as an ornamental plant.
Vertebrate features revealed in the rudimentary eye of the Pacific hagfish (Eptatretus stoutii)

Hagfish eyes are markedly basic compared to the eyes of other vertebrates, lacking a pigmented epithelium, a lens, and a retinal architecture built of three cell layers – the photoreceptors, interneurons & ganglion cells. Concomitant with hagfish belonging to the earliest-branching vertebrate group (the jawless Agnathans), this lack of derived characters has prompted competing interpretations that hagfish eyes represent either a transitional form in the early evolution of vertebrate vision, or a regression from a previously elaborate organ. Here we show the hagfish retina is not extensively degenerating during its ontogeny, but instead grows throughout life via a recognizable Pax6+ ciliary marginal zone. The retina has a distinct layer of photoreceptor cells that appear to homogeneously express a single opsin of the rh1 rod opsin class. The epithelium that encompasses these photoreceptors is striking because it lacks the melanin pigment that is universally associated with animal vision; notwithstanding, we suggest this epithelium is a homolog of gnathosome Retinal Pigment Epithelium (RPE) based on its robust expression of RPE65 and its engulfment of photoreceptor outer segments. We infer that the hagfish retina is not entirely rudimentary in its wiring, despite lacking a morphologically distinct layer of interneurons: multiple populations of cells exist in the hagfish inner retina that differentially express markers of vertebrate retinal interneurons. Overall, these data clarify Agnathan retinal homologies, reveal characters that now appear to be ubiquitous across the eyes of vertebrates, and refine interpretations of early vertebrate visual system evolution. HIGHLIGHTS Hagfish eyes are degenerate but not degenerating, i.e. rudimentary but growing Retinal interneurons discovered implying ancestral hagfish had derived retinas & vision Despite lacking pigment, a Retinal Pigmented Epithelium homolog functions in hagfish Revised synapomorphies illuminate the dimly lit origins of vertebrate eye evolution GRAPHICAL ABSTRACT
Hemodynamic Responses Link Individual Differences in Informational Masking to the Vicinity of Superior Temporal Gyrus

Suppressing unwanted background sound is crucial for aural communication. Public spaces often contain a particularly disruptive background sound, called informational masking (IM). At present, IM is identified operationally: when a target should be audible, based on suprathreshold target/masker energy ratios, yet cannot be heard because perceptually similar background sound interferes. Here, behavioral experiments combined with functional near infrared spectroscopy identify brain regions that predict individual vulnerability to IM. Results show that tasked-evoked blood oxygenation changes near the superior temporal gyrus (STG) and behavioral speech detection performance covary for same-ear IM background sound, suggesting that the STG is part of an IM-dependent network. Moreover, listeners who are more vulnerable to IM show an increased metabolic need for oxygen near STG. In contrast, task-evoked responses in a region of lateral frontal cortex, the caudal inferior frontal sulcus (cIFS), do not predict behavioral sensitivity, suggesting that the cIFS belongs to an IM-independent network.
Mouse models for V103I and I251L gain of function variants of the human MC4R display reduced adiposity and are not protected from a hypercaloric diet

Objective The melanocortin 4 receptor (MC4R) is a G protein-coupled receptor that plays major roles in the central control of energy balance. Loss-of-function mutations of MC4R constitute the most common monogenic cause of early-onset extreme obesity in humans, whereas gain-of-function mutations appear to be protective. In particular, two relatively frequent alleles carrying the non-synonymous coding mutations V103I or I251L have been associated with lower risks of obesity and type-2 diabetes. Although V103I and I251L MC4Rs showed more efficient signaling in transfected cells, their specific effects in live animals remain unexplored. Here, we investigated whether the introduction of V103I and I251L mutations into the mouse MC4R leads to a lean phenotype and provides protection against an obesogenic diet. Methods Using CRISPR/Cas9, we generated two novel strains of mice carrying single nucleotide mutations into the mouse Mc4r which are identical to those present in V103I and I251L MCR4 human alleles, and studied their phenotypic outcomes in mice fed with normal chow or a high- fat diet. In particular, we measured body weight progression, food intake and adiposity. In addition, we analyzed glucose homeostasis through glucose and insulin tolerance tests. Results We found that homozygous V103I females displayed shorter longitudinal length and decreased abdominal white fat, whereas homozygous I251L females were also shorter and leaner due to decreased weight in all white fat pads examined. Homozygous Mc4rV103I/V103I and Mc4rI251L/I251L mice of both sexes showed improved glucose homeostasis when challenged in a glucose tolerance test, whereas Mc4rI251L/I251L females showed improved responses to insulin. Despite being leaner and metabolically more efficient, V103I and I251L mutants fed with a hypercaloric diet increased their fasting glucose levels and adiposity similar to their wild-type littermates. Conclusions Altogether, our results demonstrate that mice carrying V103I and I251L MC4R mutations displayed gain-of-function phenotypes that were more evident in females. However, hypermorphic MC4R mutants were as susceptible as their control littermates to the obesogenic and diabetogenic effects elicited by a long-term hypercaloric diet, highlighting the importance of healthy feeding habits even under favorable genetic conditions. Highlights Identical single nucleotide substitutions to gain-of-function mutations of the human MC4R were introduced into the genome of inbred mice using CRISPR/Cas9 technology. Homozygous female carriers of V103I Mc4r alleles are shorter and display reduced adiposity, together with improved glucose homeostasis in both sexes. Homozygous females carrying the I251L mutation in the mouse MC4R also display shorter longitudinal length, decreased weight in all abdominal white fat pads and improved glucose clearance and insulin response. Gain-of-function mutations V103I and I251L of MC4R do not protect against the diabetogenic and adipogenic effects of a high-fat diet.
Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects

Neuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome-wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a single block, while the last approach considers each haplotype independently. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.