bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overcoming the Blood-Brain Barrier for Gene Therapy via Systemic Administration of GSH-Responsive Silica Nanocapsules
Authors: Wang Yuyuan , Wang Xiuxiu , Xie Ruosen , Burger Jacobus C. , Tong Yao , Gong Shaoqin 
Published: October 2022

AbstractCRISPR genome editing has demonstrated great potential to treat the root causes of many genetic diseases, including central nervous system (CNS) disorders. However, the promise of brain-targeted therapeutic genome editing relies on the efficient delivery of biologics bypassing the blood-brain barrier (BBB), which represents a substantial challenge in the development of CRISPR therapeutics. In this study, we created a library of GSH-responsive silica nanocapsules (SNCs) and screened them for brain targeting via systemic delivery of nucleic acids and CRISPR genome editors.In vivostudies demonstrated that systemically delivered SNCs conjugated with glucose and RVG peptide under glycemic control can efficiently bypass the intact BBB, enabling brain-wide delivery of various biologics (mRNA, Cas9 mRNA/sgRNA, and Cas9/sgRNA ribonucleoprotein) targeting both exogenous genes (i.e., Ai14 stop cassette) and disease-relevant endogenous genes (i.e.,AppandThgenes) in Ai14 reporter mice and wild-type mice, respectively. In particular, we observed up to 28% neuron editing via systemic delivery of Cre mRNA in Ai14 mice, up to 6.1% amyloid precursor protein (App) gene editing (resulting in 19.1% reduction in the expression level of intact APP), and up to 3.9% tyrosine hydroxylase (Th) gene editing (resulting in 30.3% reduction in the expression level of TH) in wild-type mice. This versatile SNC nanoplatform may offer a novel strategy for the treatment of CNS disorders including Alzheimer’s, Parkinson’s, and Huntington’s disease.
Genome-wide mapping of fluoroquinolone-stabilized DNA gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence
Authors: Tang Juechun , Brynildsen Mark P. 
Published: October 2022

AbstractPersisters are rare phenotypic variants that are suspected to be culprits of recurrent infections. Fluoroquinolones (FQs) are a class of antibiotic that facilitate DNA damage by stabilizing type II topoisomerases when they are in a complex with cleaved DNA. InEscherichia coli, DNA gyrase is the primary FQ target, and previous work has demonstrated that persisters are not spared from FQ-induced DNA damage. Since DNA gyrase cleavage sites (GCSs) largely govern the sites of DNA damage from FQ treatment, we hypothesized that GCS characteristics (e.g., number, strength, location) may influence persistence. To test this hypothesis, we measured genome-wide GCS distributions after treatment with a panel of FQs. We found drug-specific effects on the GCS distribution and discovered a strong negative correlation between the cumulative cleavage strength across the chromosome and FQ persister levels. Further experiments and analyses suggested that persistence was not governed by cleavage to individual sites, but rather survival was a function of the cumulative GCS distribution. Together, these findings demonstrate FQ-specific differences in GCS distribution that correlate with persister levels and suggest that FQs that better stabilize DNA gyrase in cleaved complexes with DNA will lead to lower levels of persistence.
The small non-coding RNA B11 regulates multiple facets ofMycobacterium abscessusvirulence
Authors: Bar-Oz Michal , Martini Maria Carla , Alonso Maria Natalia , Meir Michal , Lore Nicola Ivan , Miotto Paolo , Riva Camilla , Xiao Junpei , Masiello Catherine S. , Misiakou Maria-Anna , Sun Huaming , Moy Justin K. , Johansen Helle Krogh , Cirillo Daniela Maria , Shell Scarlet S. , Barkan Daniel 
Published: October 2022

ABSTRACTMycobacterium abscessuscauses severe, virtually incurable disease in young patients with cystic fibrosis. Little is known inM. abscessusabout the roles of small regulatory RNAs (sRNA) in gene expression regulation. Here, we show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough colony morphology, increased pro-inflammatory signaling and virulence inin-vivoinfection models, and increased resistance to clinically relevant antibiotics. Examination of clinical isolate cohorts revealed some isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of two mutations found in clinical isolates. Approximate 230 genes were differentially expressed in the B11 deletion mutant. Strains with the clinical B11 mutations showed similar expression trends to the deletion mutant but of a lesser magnitude, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with a model of translational repression via base-pairing of B11 to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences in their RBS, consistent with B11 functioning as a negative regulator through direct binding of target mRNAs. Intriguingly, the genes upregulated in the absence of B11 included components of the ESX-4 secretion system, known to be critical forM. abscessusvirulence. One of these genes had a B11-complementary sequence at its RBS, and fusing the UTR of this gene to a reporter was sufficient to make the reporter suppressible by B11. Taken together, our data show that B11 may act as either a negative or positive regulator with pleiotropic effects on gene expression and clinically important phenotypes inM. abscessus. The presence of hypomorphic B11 mutations in clinical strains supports the idea that lower B11 activity may be advantageous forM. abscessusin some clinical contexts. To our knowledge, this is the first report of the role of an sRNA inM. abscessus.
Cortically-evoked movement in humans reflects history of prior executions, not plan for upcoming movement
Authors: Suleiman Abdelbaset , Solomonow-Avnon Deborah , Mawase Firas 
Published: October 2022

AbstractHuman motor behavior involves planning and execution, but we often perform some actions more frequently. Experimentally manipulating the probability distribution of a movement through intensive repetition toward a certain direction causes physiological bias toward that direction, which can be cortically-evoked by transcranial magnetic stimulation (TMS). However, because movement execution and plan histories were indistinguishable to date, to what extent TMS-evoked biases are due to more frequently executed movement, or recent planning of movement, is unclear. Here, we use novel experimentation to separately manipulate recent history of movement plans and execution, and probe the effects of this on physiological biases using TMS, and on default plan for goal-directed actions using a behavioral timed-response task. At baseline, physiological biases shared similar low-level kinematic properties (direction) to default plan for upcoming movement. However, when recent movement execution history was manipulated via thumb movement repetitions toward a specific direction, we found a significant effect on physiological biases, but not plan-based goal-directed movement. To further determine if physiological biases reflect ongoing motor planning, we biased movement plan history by increasing the likelihood of a specific target location, and found a significant effect on the default plan for goal-directed movements. However, TMS-evoked movement during the preparation period did not become biased toward the most frequent plan. This suggests that physiological biases provide a readout of the default state of M1 population activity in the movement-related space, but not ongoing neural activation in the planning-related space, potentially ruling out relevance of cortically-evoked physiological biases to voluntary movements.HighlightsStimulating the human motor cortex selectively evoked thumb movements toward a specific direction (physiological bias)At baseline, these physiological biases shared similar low-level kinematics with default plan for voluntary goal-directed movementsModulating the probability distribution of prior movements had a significant effect on physiological biasesHowever, biasing history of plans for upcoming movement toward a specific direction had no effect on evoked movement directionDuring ongoing planning of voluntary movement, evoked movements maintained the distinct and robust baseline bias, regardless of change in probability distribution of history of upcoming plans
Origin, exposure routes and xenobiotics impart nanoplastics with toxicity on freshwater bivalves
Authors: Arini Adeline , Muller Sandra , Coma Véronique , Grau Etienne , Sandre Olivier , Baudrimont Magalie 
Published: October 2022

AbstractVarious environmental aged plastic wastes were collected in the environment and crushed to the nanometric scale to get a mix of nanoplastics (NPs) of different natures – mostly polyolefins (PE, PP), polyesters (PET) and polyvinylics (PS and PVC) – and undefined shapes (noted NP-L, mean hydrodynamic diameter at 285 nm). We aimed to test the toxicity of NPs of environmentally relevance on freshwater bivalves and compare results to commonly used styrenic NP-PS (206 nm).Corbicula flumineawere exposed to four different conditions with NPs (0.008 to 10 μg/L), for 21 days and kept under depuration conditions for 21 additional days: 1) waterborne exposure to NP-L, 2) diet borne exposure to NP-L, 3) synergic waterborne exposure to NP-L and AlCl3salt (1 mg/L), 4) waterborne exposure to NP-PS. Enzyme activities, gene expressions and behavioural tests were assessed. Trophic and synergic exposures with Al triggered more gene modulations than direct exposure to NP-L (namely on12s, atg12, gal, segpx, p53andache). NP-PS were also more harmful than NP-L, but only at high concentrations (10 μg/L). The effects of each treatment lasted until 7 days of depuration and no more gene inductions were observed after 21 days in clean water. Very few effects were shown on phenol-oxidase (PO), and glutathione S-transferase (GST). However, the inhibition of acetylcholinesterase (AchE) was concomitant with an increase of the filtration activity of bivalves exposed to NP-L (trophic route) and NP-PS, suggesting neurotoxic effects. By disturbing the ventilatory activity, NPs could have direct effects on xenobiotic accumulation and excretion capacities. The results point out how the structure, aging, exposure routes and additional xenobiotics can interact with adverse outcomes of NPs in bivalves. These findings underline the importance to consider naturally aged environmental NPs in ecotoxicological studies rather than synthetic latexes,i.e. crosslinked nanospheres prepared from virgin polymers.This manuscript presents the first data of toxicity on freshwater organisms exposed to nanoplastics coming from natural sources. Whereas the majority of papers are dealing with non-environmentally representative plastics (mainly commercially-available polystyrene latexes) to evaluate nanoplastic effects on organisms, this study develops methods to prepare model nanoplastics from plastic wastes collected in rivers, and to assess their real adverse effects on aquatic organisms. Our results show significant differences between the inflammatory effects triggered by nanoplastics coming from natural sources and polystyrene nanobeads. This work suggests that the data published so far in the literature may underestimate the toxicity of nanoplastics spread into the environment on the aquatic organisms at the bottom of the food chain, which might consequently impart halieutic resources on the long term.
Transcriptomic analyses of differentially expressed genes, micro RNAs and long-non-coding RNAs in severe, symptomatic and asymptomatic malaria infection
Authors: Oboh Mary A. , Morenikeji Olanrewaju B. , Ojurongbe Olusola , Thomas Bolaji N. 
Published: October 2022

BackgroundMalaria transmission and endemicity in Africa remains hugely disproportionate compared to the rest of the world. The complex life cycle ofP. falciparum(Pf) between the vertebrate human host and the anopheline vector results in differential expression of genes within and between hosts. An in-depth understanding ofPfinteraction with various human genes through regulatory elements will pave way for identification of additional tool in the arsenal for malaria control. Therefore, the regulatory elements (REs) involved in the over- or under-expression of various host immune genes hold a key to alternative control measures that can be applied for prompt diagnosis and treatment.MethodsWe carried out an RNAseq analysis to identify differentially expressed genes and network analysis of non-coding RNAs and target genes associated with immune response in individuals with different clinical outcomes. Raw RNAseq datasets, retrieved for analyses include individuals with severe (Gambia - 20), symptomatic (Burkina Faso - 15), asymptomatic (Mali - 16) malaria as well as uninfected controls (Tanzania - 20; Mali - 36).ResultsOf the total 107 datasets retrieved, we identified 5534 differentially expressed genes (DEGs) among disease and control groups. A peculiar pattern of DEGs was observed, with individuals presenting with severe/symptomatic malaria having the highest and most diverse upregulated genes, while a reverse phenomenon was recorded among the asymptomatic and uninfected individuals. In addition, we identified 141 differentially expressed (DE) miRNA, of which 78 and 63 were upregulated and downregulated respectively. Interactome analysis revealed a moderate interaction between DEGs and miRNAs. Of all identified miRNA, five were unique (hsa-mir-32, hsa-mir-25, hsa-mir-221, hsa-mir-29 and hsa-mir-148) because of their connectivity to several genes, including hsa-mir-221 connected to 16 genes. Six-hundred and eight DE lncRNA were identified, including SLC7A11, LINC01524 among the upregulated ones.ConclusionOur study provides important insights into host immune genes undergoing differential expression under different malaria conditions. It also identified unique miRNAs and lncRNAs that modify and/or regulate the expression of various immune genes. These regulatory elements, we surmise have the potential to serve a diagnostic purpose in discriminating between individuals with severe/symptomatic malaria and those with asymptomatic infection or uninfected.
Comparing 10x Genomics single-cell 3’ and 5’ assay in short-and long-read sequencing
Authors: Hsu Justine , Jarroux Julien , Joglekar Anoushka , Romero Juan P. , Nemec Corey , Reyes Daniel , Royall Ariel , He Yi , Belchikov Natan , Leo Kirby , Taylor Sarah E.B. , Tilgner Hagen U 
Published: October 2022

AbstractBarcoding strategies are fundamental to droplet-based single-cell sequencing, and understanding the biases and caveats between approaches is essential. Here, we comprehensively evaluated both short and long reads of the cDNA obtained through the two marketed approaches from 10x Genomics, the “3’ assay” and the “5’ assay”, which attach barcodes at different ends of the mRNA molecule. Although the barcode detection, cell-type identification, and gene expression profile are similar in both assays, the 5’ assay captured more exonic molecules and fewer intronic molecules compared to the 3’ assay. We found that 13.7% of genes sequenced have longer average read lengths and are more complete (spanning both polyA-site and TSS) in the long reads from the 5’ assay compared to the 3’ assay. These genes are characterized by long average transcript length, high intron number, and low expression overall. Despite these differences, cell-type-specific isoform profiles observed from the two assays remain highly correlated. This study provides a benchmark for choosing the single-cell assay for the intended research question, and insights regarding platform-specific biases to be mindful of when analyzing data, particularly across samples and technologies.
Wnt signaling regulates passive cell competition in the retina by inducing differential cell adhesion
Authors: Min Xuanyu , Mao Yingyu , Wu Hao , Bock Josh , Tao Chenqi , Zhang Xin 
Published: October 2022

AbstractSelf-assortation of progenitor cells during development is essential for establishment of distinct tissue identity. This is exemplified in the eye, where the early optic cup is divided into the neural retina (NR) in the center and the ciliary margin (CM) in the periphery. Previous studies have demonstrated that Wnt signaling is required for specification of the CM, but here we show that genetic ablation of Wnt signaling mediator β-catenin in the peripheral optic cup failed to prevent the formation of the CM-derived ciliary body and iris in adult animals. Mosaic analysis revealed that this was only partially due to loss of adherens junctions among β-catenin deficient cells, which were preferentially excluded from the CM. Even in β-catenin mutant cells that can maintain adherens junctions, their inability to mediate Wnt signaling resulted in a change from P-cadherin to N-cadherin expression. We showed that this cadherin switch was sufficient to segregate otherwise identical cells into separate clusters. As a result, the ciliary body and iris were still formed after inactivation of Wnt signaling in the peripheral retina. These results showed that the dual functions of β-catenin in adherens junction and Wnt signaling are required for the passive cell competition to constitute retinal compartments.
Long-Range Hopping Conductivity in Proteins
Authors: Krishnan Siddharth , Aksimentiev Aleksei , Lindsay Stuart , Matyushov Dmitry 
Published: October 2022

AbstractSingle molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1V. In the conventional fast transport scenario where the free energy barrier is zero, the hopping rate is determined by the reorganization energy of approximately 0.8 eV, which sets the time scale of a single hopping event to at least 1μs. Furthermore, the Fermi energies of metal electrodes used in experiments are far-removed from the equilibrium redox states of the aromatic residues of the protein, which should additionally slow down the electron transfer. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transfer. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the nonergodic sampling of molecular configurations by the protein results in reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ~ 0.2 eV, which is small enough to enable long-range hopping. Using the MD values of the reorganization energies we calculate a current decay with distance that is in agreement with experiment.SignificanceElectron transfer is fundamental to biology, facilitating a range of metabolic processes and efficient energy conversion. Conventionally, electron transfer through proteins is thought to occur via a chain of metal or organic co-factors connecting one side of the protein to another. Recent experiments, however, show that proteins lacking any co-factors can nonetheless transport electrons with high efficiency if properly connected to metal electrodes. This study provides a theoretical model of such cofactor-less transfer, showing that transient occupation of non-equilibrium states of the protein’s aromatic residues reduces the barrier to electron hopping, facilitating long range and rapid transport. Our results widen the pool of proteins potentially involved in biological electron transport and provide theoretical underpinning to design of protein molecular electronics.
Iterative remodeling of the mouse uterus requires Hedgehog signaling
Authors: Roberson Elle C. , Tran Ngan Kim , Godambe Anushka N. , Rust Trinity , Nguimtsop Michelle , Mark Harrison , Fitch Rebecca D. , Wallingford John B. 
Published: October 2022

AbstractThe adult uterus regenerates in the human during the menstrual cycle, and remodels in the mouse during the estrous cycle. Decades of work has demonstrated that this process is controlled by cycling steroid hormones, estrogen and progesterone. However, downstream signaling pathways that link hormonal action to this regeneration and remodeling are yet to be identified in the cycling uterus. We set out to identify these pathways, with the overarching hypothesis that developmental signaling pathways are redeployed in the adult uterus to control remodeling in the mouse. We were surprised to find that the majority of Hedgehog signaling components were transcriptionally co-regulated throughout the estrous cycle. To test the role of Hh signaling in cyclical uterine remodeling, we conditionally knocked out the major activator of the pathway,smoothened(Smo) using theprogesterone receptor cre(PR-Cre). In the absence of Hh signaling, the uterus no longer remodels throughout the estrous cycle. We also show that the smooth muscle fibers of the uterus are significantly larger in the conditional knockouts compared to the controls suggesting hypertrophy of the smooth muscle. Our findings support the possibility that this smooth muscle homeostasis may underlie important aspects of uterine function such as contractility during late-stage pregnancy or the development of uterine smooth muscle tumors.
Convection-enhanced diffusion and directed withdrawal of methylene blue in agarose hydrogel using finite element analyses
Authors: Shaw C. , Hossain K. , Riviere-Cazaux Cecile , Burns Terry , Khan M. Rashed 
Published: October 2022

ABSTRACTPrecision drug delivery for optimized therapeutic targeting requires knowledge of momentum transport and molecular diffusion of molecules within the patient’s interstitial tissue, especially for tumor treatment within the brain. Dispersion in the interstitial space is impacted by delivery method, tissue material properties, individual-specific fluid flow, and particle size of the input solute. Knowledge of a drug’s dispersion allows for optimizing solute delivery, concentration, and flow rates to maximize drug distribution and biomarker recovery. For delivering drugs, increased knowledge of drug location after delivery can improve therapeutic treatment by optimizing the dosing of healthy and unhealthy tissue. Finite element methods (FEM) tools, such as COMSOL Multiphysics, can simulate molecular distribution inside-individual specific shapes and porous material properties. Furthermore, an additional unmet need is delivery methods that can be adjusted to manipulate diffusion regions through tissue via techniques such as directed flow. This would be especially valuable in targeted drug delivery within tumors to increase the cancerous surface area covered while limiting damage to surrounding tissues. In this project, the directed flow was induced by perfusing the injected solution at an input probe while withdrawing fluid at an output probe, enabling targeted flow through the desired region. FEM computation faithfully replicated these conditions and could be used to determine the effective concentrations perfused over the region of interest. We leveraged COMSOL Multiphysics to perform a computational study simulating convection-enhanced delivery (CED) with an output probe pulling the concentration profile over the region of interest. This simulation system can be applied to therapeutics targeting, vaccine subcutaneous injection, and waste and media diffusion in tissue engineering.