Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Immune Responses to Adeno-Associated Virus (AAV) Vectors

Recombinant adeno-associated virus (rAAV) vectors are one of the most promising in vivo gene delivery tools. Several features make rAAV vectors an ideal platform for gene transfer. However, the high homology with the parental wild-type virus, which often infects humans, poses limitations in terms of immune responses associated with this vector platform. Both humoral and cell-mediated immunity to wild-type AAV have been documented in healthy donors, and, at least in the case of anti-AAV antibodies, have been shown to have a potentially high impact on the outcome of gene transfer. While several factors can contribute to the overall immunogenicity of rAAV vectors, vector design and the total vector dose appear to be responsible of immune-mediated toxicities. While preclinical models have been less than ideal in predicting the outcome of gene transfer in humans, the current preclinical body of evidence clearly demonstrates that rAAV vectors can trigger both innate and adaptive immune responses. Data gathered from clinical trials offers key learnings on the immunogenicity of AAV vectors, highlighting challenges as well as the potential strategies that could help unlock the full therapeutic potential of in vivo gene transfer.
A Neuron-Specific Antiviral Mechanism Modulates the Persistent Infection of Rice Rhabdoviruses in Leafhopper Vectors

Many plant rhabdoviruses are neurotropic and can persistently infect the central nervous system (CNS) of their insect vectors without causing significant cytopathology. The mechanisms by which the insect CNS resists infection by plant rhabdoviruses are largely unknown. Here, we report that the neural factor Hikaru genki homolog of the leafhopper Nephotettix cincticeps (NcHig) limits the spread of the nucleorhabdovirus rice yellow stunt virus (RYSV) in vector CNS. NcHig is predominantly expressed in the CNS of N. cincticeps, and the knockdown of NcHig expression by RNA interference enhances RYSV infection of the CNS. Furthermore, immuno-blockade of NcHig function by microinjection of N. cincticeps with NcHig antibody also enhances viral infection of the CNS. Thus, we conclude that the neuron-specific factor NcHig can control RYSV propagation in the CNS. Interestingly, we find the Hig homolog of the leafhopper Recilia dorsalis also has antiviral activity during the persistent infection of the cytorhabdovirus rice stripe mosaic virus (RSMV) in vector CNS. We further determine that RYSV and RSMV matrix proteins specifically interact with the complement control protein (CCP) domains of Higs. Thus, the matrix protein-binding ability of Hig is potentially essential for its antiviral activity in rice leafhoppers. Our results demonstrate an evolutionarily conserved antiviral mechanism for Hig to mediate the persistent infection of rice rhabdoviruses in the CNS of leafhopper vectors.
In addition to their well-recognized function in the phagocytosis and digestion of foreign materials which enter their environment, alveolar macrophages may also participate in the turnover of surfactant, as indicated by recent evidence

In addition to their well-recognized function in the phagocytosis and digestion of foreign materials which enter their environment, alveolar macrophages may also participate in the turnover of surfactant, as indicated by recent evidence from kinetic investigations (1-3). Moreover, it has recently been clearly documented that macrophages of the lung ingest tubular myelin and incorporate it into cytoplasmic vacuoles (4). But whether these are ultimately destined to become secondary lysosomes has not yet been established beyond question, since, to date, the intracellular distribution of digestive enzymes in these phagocytes has not been carefully analyzed. Thus, the possibility that there are cytochemical differences between the inclusions of macrophages cannot yet be ruled out. This project was undertaken, therefore, to investigate the subcellular localization of two lysosomal enzymes, acid phosphatase and arylsulfatase, in normal rabbit alveolar macrophages. The major objective of this study was twofold: (a) to ascertain whether the vacuoles containing surfactant are indeed secondary lysosomes or whether subpopulations of inclusions exist, and (b) to define the pathway of lysosomal enzyme transport from sites of production to sites of utilization in digestive vacuoles.
Bats Possess Unique Variants of the Antiviral Restriction Factor Tetherin

aHealth Security Program, Life Sciences Discipline, Burnet Institute, Life Sciences, Melbourne, VIC 3004, Australia; bDepartment of Microbiology, Monash University, Clayton, VIC 3168, Australia; cCSIRO, Australian Animal Health Laboratory, Health and Biosecurity Business Unit, Geelong, VIC 3220, Australia; dCAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, China; eCenter for Biosafety Mega-Science, Chinese Academy of Sciences, China; fProgramme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; gDepartment of Microbiology and Immunology, The University of Melbourne, at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.
A Rapid Pathogenicity Assay of R. solanacearum in 10-12 Days Old Eggplant (Solanum melongena) Seedlings by Root Inoculation Approach

This study has reported standardization of pathogenicity assay of Ralstonia solancearum in eggplant seedlings by root inoculation approach. Though the approach is similar to my earlier published work that done with tomato seedlings, in case of eggplant, duration of the seed germination, age of the seedlings, symptom timing and progression rate of the disease are different. In an introductory observation, R. solanacearum F1C1 inoculation was performed in to 10-12 days old eggplant seedlings resulted in lethal infection in eggplant seedlings and subsequently most of these infected seedlings got wilted within 10 days of post-inoculation. Colonization studies of R. solanacearum in wilted as well as infected eggplant seedlings were confirmed by GUS staining as well as fluorescence microscopy. In addition, we also observed that wrapping of the eggplant seedlings root by a thin layer of cotton soon after the pathogen inoculation in the root, enhanced the disease progression and wilting of the inoculated seedlings. The standardized root inoculation protocol in eggplant seedlings was found to be efficient to distinguish mutant strains of different virulence genes such as hrpB, phcA and pilT from wild-type R. solanacearum. Due to its reproducibility and consistency in different eggplant cultivars, the standardized protocol described here is practically observed as an useful and rapid approach to investigate R. solanacearum pathogenicity and disease progression at the early seedling stage of eggplant.
ArlCDE form the archaeal switch complex

Cells require a sensory system and a motility structure to achieve directed movement. Bacteria and archaea both possess rotating filamentous motility structures that work in concert with the sensory chemotaxis system. This allows microorganisms to move along chemical gradients. The central response regulator protein CheY can bind to the motor of the motility structure, the flagellum in bacteria and the archaellum in archaea. Both motility structures have a fundamentally different protein composition and structural organization. Yet, both systems receive input from the chemotaxis system. We applied a fluorescent microscopy approach in the model euryarchaeon Haloferax volcanii, and shed light on the sequence order in which signals are transferred from the chemotaxis system to the archaellum. Our findings indicate that the euryarchaeal specific ArlCDE are part of the archaellum motor and that they directly receive input from the chemotaxis system via the adaptor protein CheF. Hence, ArlCDE are an important feature of the archaellum of euryarchaea, are essential for signal transduction during chemotaxis and represent the archaeal switch complex.
Transcription-coupled repair in Drosophila melanogaster is independent of the mismatch repair pathway

Transcription-coupled repair (TCR) removes base damage on the transcribed strand of a gene to ensure a quick resumption of transcription. Based on the absence of key enzymes for TCR and empirical evidence, TCR was thought to be missing in Drosophila melanogaster. The recent demonstration of TCR in S2 cells raises the question about the involved genes. Since the mismatch repair (MMR) pathway serves a central role in TCR, at least in Escherichia coli, we studied the mutational signatures in flies with a deletion of the MMR gene spellchecker1 (spel1), a MutS homolog. Whole-genome sequencing of mutation accumulation (MA) lines obtained 7,345 new single nucleotide variants (SNVs) and 5,672 short indel mutations, the largest data set from an MA study in D. melanogaster. Based on the observed mutational strand-asymmetries, we conclude that TCR is still active without spel1. The operation of TCR is further confirmed by a negative association between mutation rate and gene expression. Surprisingly, the TCR signatures are detected for introns, but not for exons. We propose that an additional exon-specific repair pathway is masking the signature of TCR. This study presents the first step towards understanding the molecular basis of TCR in Drosophila melanogaster.
Normative models of enhancer function

In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.
Age dependent effects of protein restriction on dopamine release

Despite the essential role of protein intake for health and development, very little is known about the impact of protein restriction on neurobiological functions, especially at different stages of the lifespan. The dopamine system is a central actor in the integration of food-related processes and is influenced by physiological state and food-related signals. Moreover, it is highly sensitive to dietary effects during early life periods such as adolescence due to its late maturation. In the present study, we investigated the impact of protein restriction either during adolescence or adulthood on the function of the mesolimbic (nucleus accumbens) and nigrostriatal (dorsal striatum) dopamine pathways using fast-scan cyclic voltammetry in rat brain slices. In the nucleus accumbens, protein restriction in adults increased dopamine release in response to low and high frequency trains of stimulation (1-20 Hz). By contrast, protein restriction performed at adolescence decreased nucleus accumbens dopamine release. In the dorsal striatum, protein restriction has no impact on dopamine release when performed at adulthood but in adolescent rats we observed frequency-dependent increases in stimulated dopamine release. Taken together, our results highlight the sensitivity of the different dopamine pathways to the effect of protein restriction, as well as their vulnerability to deleterious diet effects at different life stages.
Structural dynamics of non-synonymous SNPs of histone methyltransferase EZH2 involved in Weaver Syndrome

Enhancer of zeste homolog 2 (EZH2) is a histone H3 lysine 27 methyltransferases. Non-synonymous SNPs (nsSNPs) in the ezh2 gene may cause Weaver Syndrome that is a prominent and rare congenital disorder. Several EZH2 genetic variants have been characterized and reported, but there is no information available on their structural dynamics. Our study employs an in silico approach for structural and functional characterization of EZH2 nsSNPs. We identified 19 EZH2 nsSNPs majorly associated with Weaver Syndrome, among which four SET-domain nsSNPs including V621M, A677T, R679C, and H689Y significantly affected EZH2 structure. We conducted the triplicate of 100 ns of molecular dynamics simulations (MDS) to compare the dynamic interaction behaviors between wild-type and mutants of EZH2 with their substrate, H3K27me0 peptide. The simulation results revealed that the mutants had higher levels of structural variations as evidenced by secondary structure, density, distance plots, and principal component analysis. Compared to EZH2-WT, the mutants A677T and H689Y have shown lower binding energy with H3K27me0 peptide due to the denaturing of 310 helixes as exemplified by MM/PBSA calculations and secondary structure analysis. Our analysis shed light on mechanisms of structural variations of EZH2 nsSNPs and lay a stone to develop mutant-based therapeutic strategies for the design of target-specific scaffolds against Weaver Syndrome.
Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays

Axonal connections are widely regarded as faithful transmitters of neuronal signals with fixed delays. The reasoning behind this is that extra-cellular potentials caused by spikes travelling along axons are too small to have an effect on other axons. Here we devise a computational framework that allows us to study the effect of extracellular potentials generated by spike volleys in axonal fibre bundles on axonal transmission delays. We demonstrate that, although the extracellular potentials generated by single spikes are of the order of microvolts, the collective extracellular potential generated by spike volleys can reach several millivolts. As a consequence, the resulting depolarisation of the axonal membranes increases the velocity of spikes, and therefore reduces axonal delays between brain areas. Driving a neural mass model with such spike volleys, we further demonstrate that only ephaptic coupling can explain the reduction of stimulus latencies with increased stimulus intensities, as observed in many psychological experiments. Author summary Axonal fibre bundles that connect distant cortical areas contain millions of densely packed axons. When synchronous spike volleys travel through such fibre bundles, the extracellular potential within the bundles is perturbed. We use computer simulations to examine the magnitude and shape of this perturbation, and demonstrate that it is sufficiently strong to affect axonal transmission speeds. Since most spikes within a spike volley are positioned in an area where the extracellular potential is negative (relative to a distant reference), the resulting depolarisation of the axonal membranes accelerates the spike volley on average. This finding is in contrast to previous studies of ephaptic coupling effects between axons, where ephaptic coupling was found to slow down spike propagation. Our finding has consequences for information transmission and synchronisation between cortical areas.
M2 cortex-dorsolateral striatum stimulation reverses motor symptoms and synaptic deficits in Huntington’s disease

Huntington’s disease (HD) is a neurological disorder characterized by motor disturbances. HD pathology is most prominent in the striatum, the central hub of basal ganglia. The cortex is the main striatal afference and progressive cortico-striatal disconnection characterizes HD. We mapped cortico-striatal dysfunction in HD mice to ultimately modulate the activity of selected cortico-striatal circuits to ameliorate motor symptoms and recover synaptic plasticity. Multimodal MRI in vivo suggested prominent functional network deficits in fronto-striatal compared to motor-striatal pathways, which were accompanied by reduced glutamate levels in the striatum of HD mice. Moreover, optogenetically-stimulated glutamate release from fronto-striatal terminals was reduced in HD mice and electrophysiological responses in striatal neurons were blunted. Remarkably, repeated M2 Cortex-dorsolateral striatum optogenetic stimulation normalized motor behavior in HD mice and evoked a sustained increase of synaptic plasticity. Overall, these results reveal that the selective stimulation of fronto-striatal pathways can become an effective therapeutic strategy in HD.
Mouse Classical and Non-Classical Monocytes Express Comparable Levels of Chemokine Receptor CX3CR1

Human and mouse monocytes are divided into two subpopulations, classical (C-Mo) and non-classical (NC-Mo) monocytes. CC-chemokine receptor 2 (CCR2) and CX3C-chemokine receptor 1 (CX3CR1) are common features of monocyte subsets between humans and mice, i.e., C-Mo and NC-Mo are characterized as CCR2highCX3CR1low and CCR2lowCX3CR1high. Since many studies utilize mouse models to investigate roles of monocytes in human diseases, it is important to understand the similarities and differences between human and mouse monocytic subsets. In this study, we show that the expression of Cx3cr1 mRNA and CX3CR1 cell surface protein are different between circulating monocytic subsets in human but not in mice. We analyzed monocyte subsets in the blood using wild type C57BL/6 and Cx3cr1-GFP knock-in (Cx3cr1GFP/+) reporter mice. We observed higher Cx3cr1 promoter activity indicated by GFP expression in NC-Mo compared to C-Mo. However, there were no differences between the subsets in CX3CR1 mRNA nor surface protein expression determined by anti-CX3CR1 antibody or binding of fluorophore-conjugated ligand. However in the bone marrow of Cx3cr1GFP/+ mice, CX3CR1 expression was higher in NC-Mo compared to C-Mo, suggesting that mouse NC-Mo express higher level of CX3CR1 than C-Mo in the bone but this difference disappears in the blood. In contrast, human NC-Mo differentially expressed CX3CR1 compared to C-Mo in both blood and bone marrow. Given these findings, the discrepancy between promoter activity and protein levels should be considered when the roles of CX3CR1 are investigated in mouse models of human diseases. Summary sentence In this study, we show that the expression of Cx3cr1 mRNA is different between circulating monocytic subsets in human but not in mice.
New Insights Into the Effect of Residue Mutation on the Rotavirus VP1 Function Using Molecular Dynamic Simulations

Rotavirus group A remains a major cause of diarrhea in infants and young children worldwide. The permanently emergence of new genotypes puts the potential effectiveness of vaccines under serious question. Thirteen VP1 mutants were analyzed using molecular dynamic simulations and the results were combined with the experimental findings, reported previously. The results revealed structural fluctuations and secondary structure change of VP1 protein that may alter its function during viral replication/transcription. Altogether, the structural analysis of VP1 may boost efforts to develop antivirals, as they might complement the available vaccines.
5’ UTR recruitment of eIF4GI or DAP5 drives cap-independent translation for a subset of human mRNAs

During unfavorable human cellular conditions (e.g., tumor hypoxia, viral infection, etc.), canonical, cap-dependent mRNA translation is suppressed. Nonetheless, a subset of physiologically important mRNAs (e.g., HIF-1α, FGF-9, and p53) is still translated by an unknown, cap-independent mechanism. Additionally, expression levels of eIF4G and its homolog, death associated protein 5 (DAP5), are elevated. Using fluorescence anisotropy binding studies, luciferase reporter-based in vitro translation assays, and mutational analyses, here we demonstrate that eIF4GI and DAP5 specifically bind to the 5’ UTRs of these cap-independently translated mRNAs. Surprisingly, we find that the eIF4E binding domain of eIF4GI increases not only the binding affinity, but also the selectivity among these mRNAs. We further demonstrate that the affinities of eIF4GI and DAP5 binding to these 5’ UTRs correlate with the efficiency with which these factors drive cap-independent translation of these mRNAs. Integrating the results of our binding and translation assays, we show that eIF4GI and/or DAP5 are critical for recruitment of a specific subset of mRNAs to the ribosome and provide mechanistic insight into their cap-independent translation.
The effect of device configuration and patient’s body composition on image artifact and RF heating of deep brain stimulation devices during MRI at 1.5T and 3T

BACKGROUND Patients with deep brain stimulation (DBS) implants have limited access to MRI due to safety concerns associated with RF-induced heating. Currently, MRI in these patients is allowed only in 1.5T horizontal scanners and with pulse sequences with reduced power. Nevertheless, off-label use of MRI at 3T is increasingly reported based on limited safety assessments. Here we present results of systematic RF heating measurements for two commercially available DBS systems during MRI at 1.5T and 3T. PURPOSE To assess the effect of imaging landmark, DBS lead configuration, and patient body composition on RF heating of DBS leads during MRI at 1.5 T and 3T. STUDY TYPE Phantom study. POPULATION/SUBJECTS/PHANTOM/SPECIMEN/ANIMAL MODEL Gel phantoms and cadaver brain. FIELD STRENGTH/SEQUENCE 1.5T and 3T, T1-weighted turbo spin echo. ASSESSMENT RF heating was measured at tips of DBS leads implanted in brain-mimicking gel. STATISTICAL TESTS None. RESULTS We observed substantial fluctuation in RF heating mainly affected by phantom composition and DBS lead configuration, ranging from 0.14°C to 23.73°C at 1.5 T, and from 0.10°C to 7.39°C at 3T. The presence of subcutaneous fat substantially altered RF heating at electrode tips (−3.06°C < ΔT < 19.05°C). Introducing concentric loops in the extracranial portion of the lead at the surgical burr hole reduced RF heating by up to 89% at 1.5T and up to 98% at 3T compared to worst case heating scenarios. DATA CONCLUSION Device configuration and patient body composition significantly altered the RF heating of DBS leads during MRI at 1.5T and 3T. Interestingly, certain lead trajectories consistently reduced RF heating and image artifact over different imaging landmarks, RF frequencies, and phantom compositions. Such trajectories could be implemented in patients with minimal disruption to the surgical workflow.