Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellular and molecular signatures of motherhood in the adult and ageing rat brain

Pregnancy is marked by robust changes, including brain changes to volume, structure, connectivity and neuroplasticity. Although some brain changes are restricted to pregnancy and the postpartum, others are long-lasting. Few studies have examined possible mechanisms of these changes or the effects of multiple pregnancies. We characterized various cellular and molecular signatures of parity (nulliparous, primiparous, biparous) in the rat hippocampus. We investigated density of neural stems cells (Sox2), microglia (Iba-1) and levels of a synaptic protein (PSD-95), cell signalling pathways, neuroinflammation, and the tryptophan–kynurenine (TRP–KYN) pathway, one week after weaning their pups from the last pregnancy (age of dam: seven months) and in middle-age (age of dam: 13 months). Parity increased PSD-95 levels in both age groups and prevented the age-related decrease in neural stem cell density observed in nulliparous rats. Biparity increased cell signalling phosphoproteins (pp70S6K, S6RP) and number of microglia in the dentate gyrus, regardless of age. Parity resulted in transient changes to the TRP–KYN system. Thus, previous parity has lasting effects on synaptic plasticity with fewer lasting effects on inflammation and cell signalling phosphoproteins in the whole hippocampus.
Function of the bacteriophage P2 baseplate central spike Apex domain in the infection process

The contractile tail of bacteriophage P2 functions to drive the tail tube across the outer membrane of its host bacterium, a prerequisite event for subsequent translocation of phage genomic DNA into the host cell. The tube is equipped with a spike-shaped protein (product of P2 gene V, gpV or Spike) that contains a membrane-attacking Apex domain carrying a centrally positioned Fe ion. The ion is enclosed in a histidine cage that is formed by three symmetry-related copies of a conserved HxH (histidine, any residue, histidine) sequence motif. Here, we used solution biophysics and X-ray crystallography to characterize the structure and properties of Spike mutants in which the Apex domain was either deleted or its histidine cage was either destroyed or replaced with a hydrophobic core. We found that the Apex domain is not required for the folding of full-length gpV or its middle intertwined β-helical domain. Furthermore, despite its high conservation, the Apex domain is dispensable for infection in laboratory conditions. Collectively, our results show that the diameter of the Spike but not the nature of its Apex domain determines the efficiency of infection, which further strengthens the earlier hypothesis of a drill bit-like function of the Spike in host envelope disruption.
Parental childhood maltreatment associates with offspring left amygdala volume at early infancy

Background Childhood maltreatment exposure (CME) and related trauma could be considered some of psychiatry’s greatest public health challenges. CME and early adversity have been associated with increased amygdala volume in exposed individuals. Emerging evidence implies that CME could also affect prenatal development of the offspring. Methods As part of the FinnBrain Birth Cohort Study, we measured bilateral amygdala volumes from MR images in 76 healthy infants at 2–5 weeks of gestation corrected age and obtained the Trauma and Distress Scale (TADS) questionnaire from both parents. The associations between neonatal amygdala volumes and TADS scores were examined in stepwise regression models. Results We found that maternal CME associated positively with infant left amygdala volume (p = .045) while the positive association for the paternal trauma score was only marginally significant (p = .099). Similar associations were not observed for the right amygdala. In the exploratory analyses, we used age ranges (0–6, 7–12, and 13–18 years) as estimate of the timing of the CME and included all three time points from both parents using left amygdala volume into the stepwise regression models. We found that maternal TADS scores from 13–18 years of age associated positively with infant left amygdala volumes (p = .008). Correspondingly, paternal TADS scores from 0–6 years of age associated positively with the infant left amygdala volumes (p = .014). Conclusions Our link the infant offspring amygdala volume with parental CME with some agreement with prior findings, and they also imply links paternal CME to infant amygdala volumes. Amygdala is one of the key brain structures associated with both early life exposures and later psychiatric health, which makes it crucially important to elucidate both the underlying mechanisms and the later relevance of these associations in future studies.
Dissecting neuron-specific functions of circadian genes using modified cell-specific CRISPR approaches

Circadian behavioral rhythms in Drosophila melanogaster are regulated by about 75 pairs of brain neurons. They all express the core clock genes but have distinct functions and gene expression profiles. To understand the importance of these distinct molecular programs, neuron-specific gene manipulations are essential. Although RNAi based methods are standard to manipulate gene expression in a cell-specific manner, they are often ineffective, especially in assays involving smaller numbers of neurons or weaker Gal4 drivers. We and others recently exploited a neuron-specific CRISPR-based method to mutagenize genes within circadian neurons. Here we further explore this approach to mutagenize three well-studied clock genes: the transcription factor gene vrille, the photoreceptor gene Cryptochrome (cry) and the neuropeptide gene Pdf. The CRISPR-based strategy not only reproduced their known phenotypes but also assigned cry function for different light mediated phenotypes to discrete, different subsets of clock neurons. We further tested two recently published methods for temporal regulation in adult neurons, inducible Cas9 and auxin-inducible gene expression system (AGES). The results were not identical, but both approaches successfully showed that the adult-specific knockout of the neuropeptide Pdf reproduces the canonical loss-of-function mutant phenotypes. In summary, a CRISPR-based strategy is a highly effective, reliable, and general method to temporally manipulate gene function in specific adult neurons. Significance statement Most animals have specific brain neurons that regulate sleep-wake cycles and other aspects of circadian behavior. Drosophila has only about 150 of these clock neurons. Despite their small numbers, they have remarkably diverse anatomy and gene expression profiles. To address the different functions of these neurons, we used highly specific and efficient CRISPR-based methods to create cell type-specific disruptions of three traditional circadian genes. We were able to assign the function of the photoreceptor cryptochrome to two tiny subsets of clock neurons. In addition, two independent methods assigned the neuropeptide PDF to the adult stage. In summary, we find that the CRISPR-based methods are very efficient at studying adult specific functions of genes in small, discrete sets of neurons.
A conformational-dependent interdomain redox relay at the core of Protein Disulfide Isomerase activity

Protein disulfide isomerases (PDIs) are a family of molecular chaperones resident in the endoplasmic reticulum (ER) emerging as important factors in disease. In addition to an holdase function, some members catalyse disulfide bond formation and isomerization, a crucial step for native folding and prevention of aggregation of misfolded proteins. PDIs are characterized by a modular arrangement of thioredoxin-like domains, with the canonical, first identified PDIA1, organized as four thioredoxin-like domains forming a horseshoe with two active sites at the extremities. Using two fluorescent redox sensors, roGFP2 and HyPer, as client substrates either unfolded or native, and the in vitro reconstitution of the full pathways of oxidative protein in the ER, we clarified important aspects underlying the catalytic cycle of PDIA1. The N-terminal a active site is the main oxidant of thiols and can transfer electrons to the C-terminal a’ active site relying on the redox-dependent conformational flexibility of PDIA1 that allows the formation of an interdomain disulfide bond. The a’ active site act then as a crossing point to redirect electrons to the ER downstream oxidases or back to client proteins. The two active sites of PDIA1 work cooperatively as an interdomain redox relay that explains PDIA1 oxidative activity to form native disulfides and PDIA1 reductase activity to resolve scrambled disulfides. Moreover, this mechanism reveals a new rational for shutting down oxidative protein folding under ER redox imbalance or when the levels of unfolded proteins and folding intermediates exceed the folding capacity of the system.
Polarimetric response of second harmonic generation in microscopy of chiral fibrillar structures

Polarimetric second harmonic generation (SHG) microscopy is employed to study partially oriented fibrillar structures. The polarimetric SHG parameters are influenced by three-dimensional (3D) configuration of C6 symmetry fibrilar structures in the focal volume (voxel) of a microscope. The achiral and chiral susceptibility tensor components ratios (R and C, respectively) are extracted from the linear polarization-in polarization-out (PIPO) measurements. The analytical derivations along with the polarimetric SHG microscopy results obtained from rat tail tendon, rabbit cornea, pig cartilage and meso-tetra (4-sulfonatophenyl) porphine (TPPS4) cylindrical aggregates demonstrate that SHG intensity is affected by parallel/antiparallel arrangements of the fibers, and R and C ratio values change by tilting the fibers out of image plane, as well as by crossing the fibers in 2D and 3D. The polarimetric microscopy results are consistent with the digital microscopy modeling of fibrillar structures. These results facilitate the interpretation of polarimetric SHG microscopy images in terms of 3D organization of fibrilar structures in each voxel of the samples. Statement of Significance Polarimetric second harmonic generation (SHG) microscopy is used to study partially oriented C6 symmetry chiral fibrillar structures. The linear polarization-in polarization-out (PIPO) SHG imaging is performed on rat tail tendon, rabbit cornea, pig cartilage tissues and meso-tetra (4-sulfonatophenyl) porphine (TPPS4) cylindrical aggregates. The study demonstrates that SHG intensity is affected by parallel/antiparallel arrangements of the fibers, and the achiral and chiral susceptibility component ratio values change by tilting the fibers out of image plane, as well as by crossing the fibers in 2D and 3D. The polarimetric microscopy results are consistent with the digital microscopy modeling of fibrillar structures. These results facilitate the interpretation of polarimetric SHG microscopy images in terms of 3D organization of fibrillar structures in each voxel of the samples.
Incomplete transcriptional dosage compensation of vertebrate sex chromosomes is balanced by post-transcriptional compensation

Heteromorphic sex chromosomes (XY or ZW) present problems of gene dosage imbalance between the sexes, and with the autosomes. Mammalian X chromosome inactivation was long thought to imply a critical need for dosage compensation in vertebrates. However, the universal importance of sex chromosome dosage compensation was questioned by mRNA abundance measurements that demonstrated sex chromosome transcripts are neither balanced between the sexes or with autosomes in monotreme mammals or birds. Here, we demonstrate unbalanced mRNA levels of X genes in platypus males and females that correlate with differential loading of histone modifications, and confirm that transcripts of Z genes are unbalanced between males and females also in chicken. However, we found that in both species, median male to female protein abundance ratios were 1:1, implying an additional level of post-transcriptional control. We conclude that parity of sex chromosome output is achieved in birds, as well as all mammal groups, by a combination of transcriptional and post-transcriptional control, consistent with an essential role for sex chromosome dosage compensation in vertebrates.
Cooperativity between H3.3K27M and PDGFRA poses multiple therapeutic vulnerabilities in human iPSC-derived diffuse midline glioma avatars

Diffuse midline glioma (DMG) is a leading cause of brain tumor death in children. In addition to hallmark H3.3K27M mutations, significant subsets also harbor alterations of other genes, such as TP53 and PDGFRA. Despite the prevalence of H3.3K27M, the results of clinical trials in DMG have been mixed, possibly due to the lack of models recapitulating its genetic heterogeneity. To address this gap, we developed human iPSC-derived tumor models harboring TP53R248Q with or without heterozygous H3.3K27M and/or PDGFRAD842V overexpression. The combination of H3.3K27M and PDGFRAD842V resulted in more proliferative tumors when gene-edited neural progenitor (NP) cells were implanted into mouse brains compared to NP with either mutation alone. Transcriptomic comparison of tumors and their NP cells of origin identified conserved JAK/STAT pathway activation across genotypes as characteristic of malignant transformation. Conversely, integrated genome-wide epigenomic and transcriptomic analyses, as well as rational pharmacologic inhibition, revealed targetable vulnerabilities unique to the TP53R248Q; H3.3K27M; PDGFRAD842V tumors and related to their aggressive growth phenotype. These include AREG-mediated cell cycle control, altered metabolism, and vulnerability to combination ONC201/trametinib treatment. Taken together, these data suggest that cooperation between H3.3K27M and PDGFRA influences tumor biology, underscoring the need for better molecular stratification in DMG clinical trials.
In vitro and in vivo effects of zoledronic acid on senescence and senescence-associated secretory phenotype markers

In addition to reducing fracture risk, zoledronic acid has been found in some studies to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple co-morbidities, the non-skeletal actions of zoledronic acid could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype [SASP]) actions. To test this, we first performed in vitro senescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronic acid killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronic acid or vehicle for 8 weeks, zoledronic acid significantly reduced circulating SASP factors, including CCL7, IL-1β, TNFRSF1A, and TGFβ1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronic acid demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronic acid, we used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronic acid significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. Collectively, our findings demonstrate that zoledronic acid has senolytic effects in vitro and modulates senescence/SASP biomarkers in vivo. These data point to the need for additional studies testing zoledronic acid and/or other bisphosphonate derivatives for senotherapeutic efficacy.
Shape measurement system for single point incremental forming (SPIF) manufacts by using trinocular vision and random pattern

Many contemporary works show the interest of the scientific community in measuring the shape of artefacts made by single point incremental forming. In this paper, we will present an algorithm able to detect feature points with a random pattern, check the compatibility of associations exploiting multi-stereo constraints and reject outliers and perform a 3D reconstruction by dense random patterns. The algorithm is suitable for a real-time application, in fact it needs just three images and a synchronous relatively fast processing. The proposed method has been tested on a simple geometry and results have been compared with a coordinate measurement machine acquisition.
Bioenergetic-Related Gene Expression in the Hippocampus Predicts Internalizing vs. Externalizing Behavior in a F2 Cross of Selectively-Bred Rats

Using selective breeding, we have produced two rat lines with highly divergent behaviors: bred Low Responders (bLR) are extremely inhibited and anxious in a novel environment, whereas bred High Responders (bHR) are exploratory and sensation-seeking. These traits map onto temperamental extremes predictive of internalizing vs. externalizing psychiatric disorders in humans and model two divergent paths to drug abuse. To elucidate gene expression underlying these heritable behavioral differences, bHR and bLR rats from the 37th generation of selection were used to produce F0, F1 cross, and F2 intercross generations. We measured exploratory locomotion, anxiety-like behavior, and sensitivity to reward cues (Pavlovian Conditioned Approach) and performed hippocampal RNA sequencing in both F0s (n=24, n=6/phenotype/sex) and F2s (n=250, n=125/sex). Behaviors that diverged during selective breeding remained correlated in F2s, implying a shared genetic basis. F0 bHR/bLR differences in gene expression were robust, surpassing differences associated with sex, and predicted expression patterns associated with F2 behavior. Among the bHR/bLR differentially expressed genes (DEGs), 17 were associated with exploratory locomotion in the F2s, seven of which were located within related quantitative trait loci we previously identified in F2s. Convergence between our study and others targeting similar behavioral traits revealed an additional 26 genes related to behavioral temperament. Gene set enrichment analysis pointed to growth and proliferation being upregulated with bHR-like behavior, and mitochondrial function, oxidative stress, and microglial activation being upregulated with bLR-like behavior. Our findings implicate bioenergetic regulation of hippocampal function in shaping temperamental differences, thereby modulating vulnerability to psychiatric and addictive disorders.
A hyperthermic seizure unleashes a surge of spreading depolarizations in Scn1a-deficient mice

Spreading depolarization (SD) is a massive wave of cellular depolarization that slowly migrates across the brain gray matter. Cortical SD is frequently generated following brain injury, while less is understood about its potential contribution to genetic disorders of hyperexcitability, such as SCN1A deficient epilepsy in which febrile seizure often contributes to disease initiation. Here we report that spontaneous SD waves are a predominant EEG abnormality in the Scn1a deficient mouse (Scn1a+/R1407X) and undergo sustained intensification following a single hyperthermic seizure. Chronic DC-band EEG recording detected spontaneous SDs, seizures, and seizure-SD complexes in Scn1a+/R1407X mice but not wild-type littermates. The SD events were infrequent, while a single hyperthermia-induced seizure robustly increased SD frequency over four-fold during the initial postictal week. This prolonged neurological aftermath could be suppressed by memantine administration. Video, electromyogram (EMG), and EEG spectral analysis revealed distinct neurobehavioral patterns; individual seizures were associated with increased motor activities, while SDs were generally associated with immobility. We also identified a stereotypic SD prodrome, detectable over a minute before the onset of the DC potential shift, characterized by increased motor activity and bilateral EEG frequency changes. Our study suggests that cortical SD is a pathological manifestation in SCN1A deficient epileptic encephalopathy.
On spread extent of sessile droplet into porous medium: Numerical solution and comparisons with experiments

The spread of a wetting liquid sessile droplet into porous medium is solved numerically using the capillary network model with a microforce balance boundary condition at the liquid/gas free interface in the porous medium. The spread starts as the porous medium imbibes the sessile liquid, followed by liquid additionally being spread inside the porous medium itself. After there is no remaining sessile liquid, the net flow across the porous medium boundaries is equal to zero. Either spread, with or without sessile liquid present at the porous medium surface, is rendered by local differences in capillary pressure. These local differences are accounted for by implementing the numerical solution over a heterogeneous capillary network, consisting of pores connected by throats. Both pores and throats follow predefined distribution functions. Once there is no sessile liquid present on the porous medium surface, it is found from a numerical solution that the liquid front can extend significantly in time, wetting ve.
Stimulated Raman scatter analyses of experiments conducted at the National Ignition Facility a)

Recent experiments conducted at the National Ignition Facility achieved two main goals: providing radiation drive and symmetry suitable for subsequent ignition experiments. Of the many diagnostics fielded, one provided a time-resolved wavelength spectrum of light reflected from the target by stimulated Raman scatter (SRS). SRS occurs when incident light reflects off self-generated electron plasma waves. Analyses indicate that synthetic SRS spectra better match those of experiments when an atomic physics model with greater emissivity is utilized in target modeling, along with less inhibited electron transport (higher flux, with, ideally, nonlocal electron transport). With these models, SRS occurs in a target region where nearest-neighbor quads of laser beams significantly overlap the diagnosed quad. This increases SRS gain at lower density (lower wavelength), a feature consistent with experimental results. Inclusion of this effect of multiple quads sharing a reflected SRS light wave has resulted in improved capabilities used to successfully predict (preshot) the SRS spectrum from the first target driven with 1.25 MJ of laser energy. Additional resonant amplification of SRS light in the overlap intensity region is demonstrated in beam propagation simulations. Such effects will be reduced in a target optimized for these less dense and cooler plasma conditions.