Miracle-dz/UniFAR-FTUs huggingface dataset:
Neuronal Nitric Oxide Synthase Knockdown Within Basolateral Amygdala Induces Autistic-Related Phenotypes and Decreases Excitatory Synaptic Transmission in Mice

Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental disorders characterized by deficits in communication, impaired social interaction, and repetitive or restricted interests and behaviors. We have recently shown that neuronal nitric oxide synthase (nNOS) expression was reduced in the basolateral amygdala of mice after postnatal valproic acid exposure. However, the specific role of nNOS downregulation in mice remains to be elucidated. Herein, we investigated the behavioral alternations of naive mice with a recombinant adeno-associated virus (rAAV)-mediated knockdown of nNOS in a comprehensive test battery, including the social interaction, marble burying, self-grooming, and open field tests. Further, the electrophysiological and surface expression changes induced by nNOS deficiency of the basolateral amygdala in these animals were examined. Our results show that nNOS knockdown displayed typical symptoms of ASD-like behaviors, such as reduced social interaction and communication, elevated stereotypes, and anxiety in mice. Surprisingly, we found that nNOS knockdown exhibited greatly reduced excitatory synaptic transmission concomitant with the lower surface expression of GluN2B-containing N-methyl-D-aspartate receptors and postsynaptic density protein 95 in mice. These findings support a notion that dysregulation of nNOS might contribute to ASD-associated phenotypes, with disease pathogenesis most likely resulting from deficits in excitatory synaptic transmission.
Blood Pressure in Different Dementia Disorders, Mild Cognitive Impairment, and Subjective Cognitive Decline

The aim of the study was to investigate whether blood pressure (BP) differed among people with different dementia diagnoses, mild cognitive impairment, and subjective cognitive decline and whether BP differences were observed across age and sex. Our study population comprised clinical data from 6,236 patients (53.5% women) aged 45–97 years (Mean = 73.9, SD = 9.6) referred to dementia assessment in 42 outpatient clinics across Norway during 2009–2019. Patients with the following diagnoses were included: Subjective cognitive decline (SCD), Mild cognitive impairment (MCI), dementia due to Alzheimer’s disease (AD), Vascular dementia (VaD), mixed AD and VaD, and dementia in Parkinson’s disease/Lewy body disease (PDD/LBD). For all diagnostic groups, SBP increased with age until about 80 years, after which it trended downward, whereas DBP declined after 60 years of age for all diagnostic groups. Patients aged 65 years and younger with SCD had lower SBP compared to AD patients at the same age, but SBP increased rapidly with increasing age, resulting in a substantially higher SBP at 80 + years compared with all other diagnostic groups. No other differences in SBP or diastolic blood pressure (DBP) were found among patients with the different dementia diagnosis. Neither SBP nor DBP differed between MCI and AD groups. An interaction between age and gender was found for SBP at younger ages, as women started out with a lower pressure than men did but ended up with higher SBP. Conclusion Among 80+ patients, blood pressure did not differ as a function of the various dementia disorders. The SBP for the SCD patients of various age groups differed from all other diagnostic groups, indicating either that internal regulation of BP in older people is a risk factor for dementia or that brain damage causing dementia or MCI may led to changes in blood pressure. Brain aging seems to influence SBP differently in men and women.
Elucidating the role of endothelial αvβ3-integrin in tumour growth and angiogenesis

Angiogenesis, the formation of new vessels from pre-existing ones, is essential for primary tumour growth as well as for metastasis, and endothelial cells play a central role in this process: they drive blood vessel formation in response to signals from the local environment by a mechanism that is integrin-dependent. αvβ3-integrin seemingly poses an ideal anti-angiogenic target. Its expression is vastly up-regulated in neo-angiogenic vessels, while its expression in quiescent vasculature is minimal. However, anti-angiogenic therapy targeting αvβ3-integrin has proven somewhat disappointing. In part, this may relate to the fact that αvβ3-integrin is not expressed solely by endothelial cells, but across a wide range of cell types that each contribute to angiogenesis. In this thesis, I describe my studies on understanding the role of αvβ3-integrin as expressed specifically by endothelial cells in tumour growth and angiogenesis using endothelial specific β3-integrin deficient mice. I have shown that inducible deletion of endothelial β3-integrin inhibits tumour growth and angiogenesis preventatively, while its constitutive deletion is ineffective; furthermore, I have found that even the inducible deletion does not alter angiogenesis in already established tumours. The findings described in this thesis re-establish αvβ3-integrin as good antiangiogenic target, but imply that timing and length of inhibition are critical factors to be considered when targeting endothelial β3-integrin-expression.
A comparison of several media types and basic techniques used to assess outdoor airborne fungi in Melbourne, Australia

Despite the recent increase in interest in indoor air quality regarding mould, there is no single widely accepted standard media for the detection of airborne fungi, nor verification of many commonly used techniques. Commonly used media including malt-extract agar (MEA), Sabouraud dextrose agar (Sab, SDA, SabCG), potato dextrose agar (PDA) with and without antibiotics chloramphenicol & gentamycin (CG) were compared for their suitability in detecting a range of common airborne fungi by collecting 150 L outdoor air on a number of different days and seasons via an Anderson 400-hole sampler in suburban Melbourne, Australia. There was relatively little variation in mean numbers of colony forming units (CFU) and types of fungi recovered between MEA, PDA, SabCG media groups relative to variation within each group. There was a significant difference between SabCG, Dichloran-18% glycerol (DG18) and V8® Original juice agar media, however. Antibiotics reliably prevented the growth of bacteria that typically interfered with the growth and appearance of fungal colonies. There was no significant evidence for a growth enhancing factor from potato, mineral supplements or various vegetable juices. Differing glucose concentrations had modest effects, showing a vague ideal at 2%-4% with peptone. Sanitisation/sterilisation of the aluminium Andersen 400-hole sampler top-plate by flame is possible, but not strictly required nor advisable. The use of SabCG as a standard medium was generally supported.
CRISPR/Cas9-mediated gene editing induces neurological recovery in an A53T-SNCA overexpression rat model of Parkinson’s disease

To date, no publicly available disease-modifying therapy for Parkinson’s disease has been developed. This can be partly attributed to the absence of techniques for in vivo deletion of the SNCA gene (encoding α-synuclein), which is one of the key players in Parkinson’s disease pathology. In particular, A53T-mutated SNCA (A53T-SNCA) is one of the most studied familial pathologic mutations in Parkinson’s disease. Here we utilized a recently discovered genome editing technique, CRISPR/Cas9, to delete A53T-SNCA in vitro and in vivo. Among various CRISPR/Cas9 systems, SaCas9-KKH with a single guide RNA (sgRNA) targeting A53T-SNCA was packaged into adeno-associated virus. Adeno-associated virus carrying SaCas9-KKH significantly reduced A53T-SNCA levels in A53T-SNCA-overexpressed HEK293T cells, without off-target effects on wild-type SNCA. Furthermore, we tested the technique’s in vivo therapeutic potential in a viral A53T-SNCA overexpression rat model of Parkinson’s disease. Gene deletion of A53T-SNCA significantly prevented the overexpression of α-synuclein, dopaminergic neurodegeneration, and parkinsonian motor symptoms, whereas a negative control without sgRNA did not. Our findings propose CRISPR/Cas9 system as a potential therapeutic tool for A53T-SNCA familial Parkinson’s disease.
Myomixer is expressed during embryonic and post-larval hyperplasia, muscle regeneration and fusion of myoblats in rainbow trout (Oncorhynchus mykiss)

In contrast to mice or zebrafish, trout exhibits post-larval muscle growth through hypertrophy and formation of new myofibers (hyperplasia). The muscle fibers are formed by the fusion of mononucleated cells (myoblasts) regulated by several muscle-specific proteins such as myomaker or myomixer. In this work, we identified a unique gene encoding a myomixer protein of 77 amino acids (aa) in the trout genome. Sequence analysis and phylogenetic tree, showed moderate conservation of the overall protein sequence across teleost fish (61% of aa identity between trout and zebrafish myomixer sequences). Nevertheless, the functionally essential motif, AxLyCxL is perfectly conserved in all studied sequences of vertebrates. Using in situ hybridization, we observed that myomixer was highly expressed in the embryonic myotome, particularly in the hyperplasic area. Moreover, myomixer remained readily expressed in white muscle of juvenile (1 and 20 g) although its expression decreased in mature fish. We also showed that myomixer is up-regulated during muscle regeneration and in vitro myoblasts fusion. Together, these data indicate that myomixer expression is consistently associated with the formation of new myofibers during somitogenesis, post-larval growth and muscle regeneration in trout.
CREB-binding protein gene, HAC701, negatively regulates WRKY45-dependent immunity in rice

CREB-binding protein (CBP) is a known transcriptional coactivator and an acetyltransferase that functions in several cellular processes by regulating gene expression. However, how it functions in plant immunity remains unexplored. By characterizing hac701, we demonstrate that HAC701 negatively regulates the immune responses in rice. hac701 shows enhanced disease resistance against a bacterial pathogen, Pseudomonas syringae pv. oryzae (Pso), which causes bacterial halo blight of rice. Our transcriptomic analysis revealed that rice WRKY45, one of the main regulators of rice immunity, is upregulated in hac701 and possibly conferring the resistance phenotype against Pso. The morphological phenotypes of hac701 single mutants were highly similar to WRKY45 overexpression transgenic lines reported in previous studies. In addition, we also compared the list of genes in these studies when WRKY45 is overexpressed and chemically induced transiently with the differentially expressed genes (DEGs) in hac701, and found that they largely overlap. When we investigated for cis-elements found 1kb upstream of WRKY45 gene and WRKY45-dependent DEGs, we found that WRKY45 promoter contains the CRE motif, a possible target of HAC701-mediated regulation. Genome-wide H3K9 acetylation profiling showed depletion of acetylation at large set of genes in hac701. However, consistent with the upregulation of WRKY45 gene expression, our ChIP-sequencing analysis demonstrated that regions of WRKY45 promoter are enriched in H3K9 acetylation in hac701 compared to the segregated wild type control in the mock condition. WRKY45 promoter might be on the receiving end for possible genome-wide compensatory effects when a global regulator like HAC701 is mutated. Finally, we show that HAC701 may have roles in systemic immune signaling. We therefore propose that wild type HAC701 negatively regulates WRKY45 gene expression, thereby suppressing immune responses. SIGNIFICANCE HAC701 is a member of CREB-binding protein (CBP) family that acts as transcriptional coactivator and acetyltransferase. However, little is known how it regulates innate immunity in plants. Herein we reported that rice HAC701 suppresses WRKY45-dependent defense pathway. Our study showed that HAC701 seemingly interacts genetically with WRKY45 in rice to modulate immune responses against pathogens.
Distinct evolutionary trajectories in asexual populations through an interplay of their size, resource availability and mutation rates

Asexually reproducing populations of single cells evolve through mutation, natural selection, and genetic drift to enhance their reproductive fitness. The environment provides the contexts that allow and regulate their fitness dynamics. In this work, we used Avida - a digital evolution framework - to uncover the effect of mutation rates, maximum size of the population, and the relative abundance of resources, on evolutionary outcomes in asexually reproducing populations of digital organisms. We observed that over extended simulations, the population evolved predominantly to one of several discrete fitness classes, each with distinct sequence motifs and/or phenotypes. For a low mutation rate, the organisms acquired either of four fitness values through an enhancement in the rate of genomic replication. Evolution at a relatively higher mutation rate presented a more complex picture. While the highest fitness values at a high mutation rate were achieved through enhanced genome replication rates, a suboptimal one was achieved through organisms sharing information relevant to metabolic tasks with each other. The information sharing capacity was vital to fitness acquisition and frequency of the genotype associated with it increased with greater resource levels and maximum population size. In addition, populations optimizing their fitness through such means exhibited a greater degree of genotypic heterogeneity and metabolic activity than those that improved replication rates. Our results reveal a minimal set of conditions for the emergence of interdependence within evolving populations with significant implications for biological systems in appropriate environmental contexts.
Regulation of Decay Accelerating Factor Primes Human Germinal Center B Cells for Phagocytosis

Germinal centers (GC) are sites for extensive B cell proliferation and homeostasis is maintained by programmed cell death. The complement regulatory protein Decay Accelerating Factor (DAF) blocks complement deposition host cells and therefore also phagocytosis of cells. Here, we show that B cells downregulate DAF upon BCR engagement and that T cell-dependent stimuli preferentially led to activation of DAFlo B cells. Consistent with this, a majority of light and dark zone GC B cells were DAFlo and susceptible to complement-dependent phagocytosis, as compared with DAFhi GC B cells. We could also show that the DAFhi GC B cell subset had increased expression of the plasma cell marker Blimp-1. DAF expression was also modulated during B cell hematopoiesis in the human bone marrow. Collectively, our results reveal a novel role of DAF to pre-prime activated human B cells for phagocytosis prior to apoptosis.
Measuring Orthopedic Plate Strain to Track Bone Healing Using a Fluidic Sensor Read via Plain Radiography

We describe a fluidic X-ray visualized strain indicator under applied load (X-VISUAL) to quantify orthopedic plate strain and inform rehabilitative care. This sensor uses a liquid-level gauge with hydro-mechanical amplification and is visualized in plain radiographs which are routinely acquired during patient recovery to find pathologies but are usually insufficient to quantify fracture stiffness. The sensor has two components: a stainless-steel lever which attaches to the plate, and an acrylic fluidic component which sits between the plate and lever. The fluidic component has a reservoir filled with radio-dense solution and an adjoining capillary wherein the fluid level is measured. When the plate bends under load, the lever squeezes the reservoir, which pushes the fluid along the channel. A tibial osteotomy model (5 mm gap) was used to simulate an unstable fracture, and allograft repair used to simulate a stiffer healed fracture. A cadaveric tibia and a mechanically equivalent composite tibia mimic were cyclically loaded five times (0 – 400 N axial force) while fluid displacement was measured from radiographs. The sensor displayed reversible and repeatable behavior with a slope of 0.096 mm/kg and fluid level noise of 50 to 80 micrometers (equivalent to 5-10 N). The allograft-repaired composite fracture was 13 times stiffer than the unstable fracture. An analysis of prior external fracture fixation studies and fatigue curves for internal plates indicates that the threshold for safe weight bearing should be 1/5th −1/10th of the initial bending for an unstable fracture. The precision of our device (<2% body weight) should thus be sufficient to track fracture healing from unstable through safe weight bearing.
Many ways to make darker flies: Intra‐ and interspecific variation in Drosophila body pigmentation components

Body pigmentation is an evolutionarily diversified and ecologically relevant trait that shows variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution and its ecological and genetic bases. Yet, while pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, its study frequently focuses on one single aspect. Here, we develop a method to quantify color and color pattern in Drosophila body pigmentation, decomposing thorax and abdominal pigmentation into distinct measurable traits, and we quantify different sources of variation in those traits. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate the two body parts. By focusing on two standard D. melanogaster laboratory populations, we show that pigmentation components vary and co-vary in different manners depending on sex, genetic background, and developmental temperature. By studying three natural populations of D. melanogaster along a latitudinal cline and five other Drosophila species, we then show that evolution of lighter or darker bodies can be achieved by changing distinct component traits. Our study underscores the value of detailed phenotyping for a better understanding of phenotypic variation and diversification, and the ecological pressures and genetic mechanisms underlying them.
Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

Massively parallel reporter assays (MPRAs) are useful tools to discover and characterize regulatory elements in human genomes. Partly because enhancer function is assumed to be orientation independent with respect to each strand of the DNA helix, most reported MPRA results ignore stranded information. However, we find pervasive strand asymmetry of MPRA signals in datasets from multiple reporter configurations and in both published and newly reported data. These effects are reproducible across different cell types and in different treatments within a cell type, and are observed both within and outside of annotated regulatory elements. From elements in gene bodies, MPRA strand asymmetry favors the sense strand, suggesting that biological function related to endogenous transcription is driving the phenomenon. Similarly, within Alu mobile element insertions, we find that strand asymmetry favors the transcribed strand of the ancestral retrotransposon. The effect is consistent across the multiplicity of Alu elements in human genomes, and is more pronounced in younger, less diverged Alu elements. We find sequence features driving MPRA strand asymmetry and demonstrate its prediction from sequence alone. We see some evidence for both RNA stabilization and transcriptional activation mechanisms, and hypothesize that the effect is driven by natural selection favoring efficient transcription. Our results indicate that strand asymmetry, as a pervasive and reproducible feature, should be accounted for in analysis of MRPA data. More importantly, the fact that MPRA asymmetry favors naturally transcribed strands suggests that it stems from preserved biological functions that have a substantial, global impact on gene and genome evolution.
Chemokines act as phosphatidylserine-bound “find-me” signals in apoptotic cell clearance

Chemokines are positively charged cytokines that attract leukocytes by binding to anionic glycosaminoglycans (GAGs) on endothelial cells for efficient presentation to leukocyte G protein-coupled receptors (GPCRs). The atypical chemokine CXCL16 has been reported to also bind the anionic phospholipid phosphatidylserine (PS), but the biological relevance of this interaction remains poorly understood. Here we demonstrate that PS binding is in fact a widely shared property of chemokine superfamily members that, like GAG binding, induces chemokine oligomerization. PS is an essential phospholipid of the inner leaflet of the healthy cell plasma membrane but it is exposed in apoptotic cells to act as an ‘eat-me’ signal that promotes engulfment of dying cells by phagocytes. We found that chemokines can bind PS in pure form as well as in the context of liposomes and on the surface of apoptotic cells and extracellular vesicles released by apoptotic cells, which are known to act as ‘find-me’ signals that chemoattract phagocytes during apoptotic cell clearance. Importantly, we show that GAGs are severely depleted from the surface of apoptotic cells and that extracellular vesicles extracted from apoptotic mouse thymus bind endogenous thymic chemokines and activate cognate chemokine receptors. Together these results indicate that chemokines tethered to surface-exposed PS may be responsible for the chemotactic and find-me signal activity previously attributed to extracellular vesicles, and that PS may substitute for GAGs as the anionic scaffold that regulates chemokine oligomerization and presentation to GPCRs on the GAG-deficient membranes of apoptotic cells and extracellular vesicles. Here, we present a new mechanism by which extracellular vesicles, currently recognized as essential agents for intercellular communication in homeostasis and disease, can transport signaling cytokines.