bluuebunny/crossref_metadata_2025_split huggingface dataset:
Programmable RNA base editing with a single gRNA-free enzyme
Authors: Han Wenjian , Huang Wendi , Mao Miaowei , Wei Tong , Ye Yanwen , Wang Zefeng 
Published: September 2021

ABSTRACTProgrammable RNA editing enables rewriting gene expression without changing genome sequences. Current tools for specific RNA editing dependent on the assembly of guide RNA into an RNA/protein complex, causing delivery barrier and low editing efficiency. We report a new gRNA-free system, RNA editing with individual RNA-binding enzyme (REWIRE), to perform precise base editing with a single engineered protein. This artificial enzyme contains a human-originated programmable PUF domain to specifically recognize RNAs and different deaminase domains to achieve efficient A-to-I or C-to-U editing, which achieved 60-80% editing rate in human cells, with a few non-specific editing sites in the targeted region and a low level off-target effect globally. The RNA-binding domain in REWIREs was further optimized to improve editing efficiency and minimize off-target effects. We applied the REWIREs to correct disease-associated mutations and achieve both types of base editing in mice. As a single-component system originated from human proteins, REWIRE presents a precise and efficient RNA editing platform with broad applicability.
Age differences in aperiodic neural activity measured with resting EEG
Authors: Merkin Ashley , Sghirripa Sabrina , Graetz Lynton , Smith Ashleigh E. , Hordacre Brenton , Harris Richard , Pitcher Julia , Semmler John , Rogasch Nigel C. , Goldsworthy Mitchell 
Published: September 2021

AbstractPrevious research using electroencephalography (EEG) and magnetoencephalography (MEG) has shown that neural oscillatory activity within the alpha band (8-12 Hz) becomes slower and lower in amplitude with advanced age. However, most studies have focused on quantifying age-related differences in periodic oscillatory activity with little consideration of the influence of aperiodic activity on these measures. The aim of this study was to investigate age differences in aperiodic activity inherent in the resting EEG signal. We assessed aperiodic activity in 85 healthy younger adults (mean age: 22.2 years, SD: 3.9, age range: 18–35, 37 male) and 92 healthy older adults (mean age: 66.1 years, SD: 8.2, age range 50–86, 53 male) by fitting the 1/f-like background activity evident in EEG power spectra using the fitting oscillations & one over f (FOOOF) toolbox. Across the scalp, the aperiodic exponent and offset were smaller in older compared to younger participants, reflecting a flatter 1/f-like slope and a downward broadband shift in the power spectra with age. Before correcting for aperiodic activity, older adults showed slower peak alpha frequency and reduced peak alpha power relative to younger adults. After correcting for aperiodic activity, peak alpha frequency remained slower in older adults; however, peak alpha power no longer differed statistically between age groups. The large sample size utilized in this study, as well as the depth of analysis, provides further evidence that the aperiodic component of the resting EEG signal is altered with aging and should be considered when investigating neural oscillatory activity.
HCN1 channels mediate mu opioid receptor long-term depression at insular cortex inputs to the dorsal striatum
Authors: Munoz Braulio , Fritz Brandon M. , Yin Fuqin , Atwood Brady K. 
Published: September 2021

AbstractMu opioid receptors (MORs) are expressed in the dorsal striatum, a brain region that mediates goal-directed (via the dorsomedial striatum), and habitual (via the dorsolateral striatum, DLS) behaviors. Our previous work indicates that glutamate transmission is depressed when MORs are activated in the dorsal striatum, inducing MOR-mediated long-term synaptic depression (MOR-LTD) or short-term depression (MOR-STD), depending on the input. In the DLS, MOR-LTD is produced by MORs on anterior insular cortex (AIC) inputs and MOR-STD occurs at thalamic inputs, suggesting input-specific MOR plasticity mechanisms. Here, we evaluated the mechanisms of induction of MOR-LTD and MOR-STD in the DLS using pharmacology and optogenetics combined with patch clamp electrophysiology. We found that cAMP/PKA signaling and protein synthesis are necessary for MOR-LTD expression, similar to previous studies of cannabinoid-mediated LTD in DLS. MOR-STD does not utilize these same mechanisms. We also demonstrated that cannabinoid-LTD occurs at AIC inputs to DLS. However, while cannabinoid-LTD requires mTOR signaling in DLS, MOR-LTD does not. We characterized the role of presynaptic HCN1 channels in MOR-LTD induction as HCN1 channels expressed in AIC are necessary for MOR-LTD expression in the DLS. These results suggest a mechanism in which MOR activation requires HCN1 to induce MOR-LTD, suggesting a new target for pharmacological modulation of synaptic plasticity, providing new opportunities to develop novel drugs to treat alcohol and opioid use disorders.Key Points–Mu opioid receptor-mediated long-term depression at anterior insular cortex inputs to dorsolateral striatum involves presynaptic cAMP/PKA signaling and protein translation, similar to known mechanisms of cannabinoid long-term depression.–Dorsal striatal cannabinoid long-term depression also occurs at anterior insular cortex inputs to dorsolateral striatum. Dorsal striatal cannabinoid long-term depression requires mTOR signaling, similar to hippocampal cannabinoid long-term depression, but dorsal striatal mu opioid long-term depression does not require mTOR signaling.–Mu opioid long-term depression requires presynaptic HCN1 channels at anterior insular cortex inputs to dorsolateral striatum.
Genome-wide identification of sexual-reproduction genes in fission yeast via transposon-insertion sequencing
Authors: Billmyre R. Blake , Eickbush Michael T. , Craig Caroline J. , Lange Jeffrey J. , Wood Christopher , Helston Rachel M. , Zanders Sarah E. 
Published: September 2021

AbstractMany genes required for sexual reproduction remain to be identified. Moreover, many of the genes that are known have been characterized in distinct experiments using different conditions, which complicates understanding the relative contributions of genes to sex. To address these challenges, we developed an assay inSchizosaccharomyces pombe that couples transposon mutagenesis with high-throughput sequencing (TN-seq) to quantitatively measure the fitness contribution of nonessential genes across the genome to sexual reproduction. This approach identified 532 genes that contribute to sex, including more than 200 that were not previously annotated to be involved in the process, of which more than 150 have orthologs in vertebrates. Among our verified hits was an uncharacterized gene,ifs1(importantforsex), that is required for spore viability. In two other hits,plb1andalg9, we observed a novel mutant phenotype of poor spore health wherein viable spores are produced, but the spores exhibit low fitness and are rapidly outcompeted by wildtype. Finally, we fortuitously discovered that a gene previously thought to be essential,sdg1(socialdistancinggene), is instead required for growth at low cell densities. Our assay will be valuable in further studies of sexual reproduction inS. pombeand identifies multiple candidate genes that could contribute to sexual reproduction in other eukaryotes, including humans.
Biomarkers of Cardiovascular Toxicity of Benzene Inhalation in Mice
Authors: Malovichko Marina V. , Abplanalp Wesley T. , McFall Samantha A. , Taylor Breandon S. , Wickramasinghe Nalinie S. , Sithu Israel D. , Zelko Igor N. , Uchida Shizuka , Sutaria Saurin R. , Nantz Michael H. , Bhatnagar Aruni , Conklin Daniel J. , O’Toole Timothy E. , Srivastava Sanjay 
Published: September 2021

ABSTRACTBenzene is a ubiquitous environmental pollutant. Recent population-based studies suggest that benzene exposure is associated with an increased risk for cardiovascular disease. However, it is unclear whether benzene exposure is sufficient to induce cardiovascular toxicity. We examined the effects of benzene inhalation (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on the biomarkers of cardiovascular toxicity in male C57BL/6J mice. Benzene inhalation significantly increased the biomarkers of endothelial activation and injury including endothelial microparticles, activated endothelial microparticles, endothelial progenitor cell microparticles, lung endothelial microparticles, and activated lung and endothelial microparticles while having no effect on circulating levels of endothelial adhesion molecules, endothelial selectins, and biomarkers of angiogenesis. To understand how benzene may induce endothelial injury, we exposed human aortic endothelial cells to benzene metabolites. Of metabolites tested, trans,trans-mucondialdehyde (10 μM, 18h) was most toxic. It induced caspases-3, −7 and −9 (intrinsic pathway) activation, and enhanced microparticle formation by 2.4-fold. Levels of plateletleukocyte aggregates, platelet macroparticles, and proportion of CD4+ and CD8+ T-cells were also significantly elevated in the blood of the benzene-exposed mice. We also found that benzene exposure increased the transcription of genes associated with endothelial cell and platelet activation in the liver; and induced inflammatory genes and suppressed cytochrome P450s in the lungs and the liver. Together, these data suggest that benzene exposure induces endothelial injury, enhances platelet activation and inflammatory processes; and circulatory levels of endothelial cell and platelet-derived microparticles and platelet-leukocyte aggregates are excellent biomarkers of cardiovascular toxicity of benzene.HighlightsInhaled benzene exposure increases the levels of blood endothelial microparticles.In vitro, benzene metabolite trans, trans-mucondialdehyde induces endothelial cell apoptosis and microparticles formation.Inhaled benzene exposure decreases the levels of hematopoietic progenitor cells in the bone marrow.Inhaled benzene exposure augments the circulating levels of platelet-leukocyte adducts.
Effect of Vinyl Chloride Exposure on Cardiometabolic Toxicity
Authors: Zelko Igor N. , Taylor Breandon S. , Das Trinath P. , Watson Walter H. , Sithu Israel D. , Wahlang Banrida , Malovichko Marina V. , Cave Matthew C. , Srivastava Sanjay 
Published: September 2021

ABSTRACTVinyl chloride is an organochlorine mainly used to manufacture its polymer polyvinyl chloride, which is extensively used in the manufacturing of consumer products. Recent studies suggest that chronic low dose vinyl chloride exposure affects glucose homeostasis in high fat diet-fed mice. Our data suggest that even in the absence of high fat diet, exposure to vinyl chloride (0.8 ppm, 6h/day, 5day/week, for 12 weeks) induces glucose intolerance (1.0 g/kg, i.p) in male C57BL/6 mice. This was accompanied with the depletion of hepatic glutathione and a modest increase in lung interstitial macrophages. Vinyl chloride exposure did not affect the levels of circulating immune cells, endothelial progenitor cells, platelet-immune cell aggregates, and cytokines and chemokines. The acute challenge of vinyl chloride-exposed mice with LPS did not affect lung immune cell composition or plasma IL-6. To examine the effect of vinyl chloride exposure on vascular inflammation and atherosclerosis, LDL receptor-KO mice on C57BL/6 background maintained on western diet were exposed to vinyl chloride for 12 weeks (0.8 ppm, 6h/day, 5day/week). Unlike the WT C57BL/6 mice, vinyl chloride exposure did not affect glucose tolerance in the LDL receptor-KO mice. Plasma cytokines, lesion area in the aortic valve, and markers of lesional inflammation in vinyl chloride-exposed LDL receptor-KO mice were comparable with the air-exposed controls. Collectively, despite impaired glucose tolerance and modest pulmonary inflammation, chronic low dose vinyl chloride exposure does not affect surrogate markers of cardiovascular injury, LPS-induced acute inflammation in C57BL/6 mice, and chronic inflammation and atherosclerosis in the LDL receptor-KO mice.
Chronic Benzene Exposure Aggravates Pressure Overload-Induced Cardiac Dysfunction
Authors: Zelko Igor N. , Dassanayaka Sujith , Malovichko Marina V. , Howard Caitlin M. , Garrett Lauren F. , Shizuka Uchida , Brittian Kenneth R. , Conklin Daniel J. , Jones Steven P. , Srivastava Sanjay 
Published: September 2021

ABSTRACTBenzene is a ubiquitous environmental pollutant abundant in household products, petrochemicals and cigarette smoke. Benzene is a well-known carcinogen in humans and experimental animals; however, little is known about the cardiovascular toxicity of benzene. Recent population-based studies indicate that benzene exposure is associated with an increased risk for heart failure. Nonetheless, it is unclear whether benzene exposure is sufficient to induce and/or exacerbate heart failure. We examined the effects of benzene (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on transverse aortic constriction (TAC)-induced pressure overload in male C57BL/6J mice. Our data show that benzene exposure had no effect on cardiac function in the Sham group; however, it significantly compromised cardiac function as depicted by a significant decrease in fractional shortening and ejection fraction, as compared with TAC/Air-exposed mice. RNA-seq analysis of the cardiac tissue from the TAC/benzene-exposed mice showed a significant increase in several genes associated with adhesion molecules, cell-cell adhesion, inflammation, and stress response. In particular, neutrophils were implicated in our unbiased analyses. Indeed, immunofluorescence studies showed that TAC/benzene exposure promotes infiltration of CD11b+/S100A8+/myeloperoxidase+-positive neutrophils in the hearts by 3-fold. In vitro, the benzene metabolites, hydroquinone and catechol, induced the expression of P-selectin in cardiac microvascular endothelial cells by 5-fold and increased the adhesion of neutrophils to these endothelial cells by 1.5-2.0-fold. Benzene metabolite-induced adhesion of neutrophils to the endothelial cells was attenuated by anti-P-selectin antibody. Together, these data suggest that benzene exacerbates heart failure by promoting endothelial activation and neutrophil recruitment.
Imaging erythrocyte sedimentation in whole blood
Authors: Darras Alexis , Breunig Hans Georg , John Thomas , Zhao Renping , Koch Johannes , Kummerow Carsten , König Karsten , Wagner Christian , Kaestner Lars 
Published: September 2021

AbstractThe erythrocyte sedimentation rate (ESR) is one of the oldest medical diagnostic tools. However, currently there is some debate on the structure formed by the cells during the sedimentation process. While the conventional view is that erythrocytes sediment as separate aggregates, others have suggested that they form a percolating gel, similar to other colloidal suspensions. A direct probing of the structures formed by erythrocytes in blood at stasis is then required to settle these discrepancies. Here, we report observations performed with three different optical imaging techniques: direct light transmission through thin samples, two-photon microscopy and light-sheet microscopy. All techniques revealed a dynamic structure of a channeling gel but with differences in the resolved details. A quantitative analysis of the erythrocyte related processes and interactions during the sedimentation need a further refinement of the experimental set-ups.
Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data
Authors: Invergo Brandon M. 
Published: September 2021

AbstractPhosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Starting from a statistical model of a high-throughput, in vitro kinase-substrate assay, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE (“In vivo-Kinase Assignment for Phosphorylation Evidence”). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isoforms and they provide a robust basis for kinase activity analysis.
Cell size matters: nano- and micro-plastics preferentially drive declines of large marine phytoplankton due to co-aggregation
Authors: Dedman Craig J. , Christie-Oleza Joseph A. , Fernández-Juárez Víctor , Echeveste Pedro 
Published: September 2021

AbstractMarine plastic pollution represents a key environmental concern. Whilst ecotoxicological data for plastic is increasingly available, its impact upon marine phytoplankton remains unclear. Owing to their predicted abundance in the marine environment and likely interactions with phytoplankton, here we focus on the smaller fraction of plastic particles (∼50 nm and ∼2 µm polystyrene spheres). Exposure of natural phytoplankton communities and laboratory cultures revealed that plastic exposure does not follow traditional trends in ecotoxicological research, since large phytoplankton appear particularly susceptible towards plastics exposure despite their higher surface-to-volume ratios. Cell declines appear driven by hetero-aggregation and co-sedimentation of cells with plastic particles, recorded visually and demonstrated using confocal microscopy. As a consequence, plastic exposure also caused disruption to photosynthetic functioning, as determined by both photosynthetic efficiency and high throughput proteomics. Negative effects upon phytoplankton are recorded at concentrations orders of magnitude above those estimated in the environment. Hence, it is likely that impacts of NPs and MPs are exacerbated at the high concentrations typically used in ecotoxicological research (i.e., mg L-1).
Strain-dependent selective antimicrobial action of cationic polyelectrolytes on Gram-negative bacteria
Authors: Rybkin Iaroslav , Mirtič Janja , Majaron Hana , Hreščak Jitka , Čeh Miran , Štrancar Janez , Kristl Julijana , Rijavec Tomaž , Lapanje Aleš 
Published: September 2021

AbstractAlthough electrostatic modification of bacterial surfaces using polyelectrolytes (PEs) is a convenient and versatile tool for biotechnological processes, the ambiguities in toxicity of PEs between various bacteria and the insufficient understanding of the mechanism of action of cationic PEs and their nano-thick shells formed around the bacteria create a bottleneck of the approach. Here, we show how the viability of two bacterial strains, Escherichia coli and Pseudomonas stutzeri, both from the Gram-negative group differs, when the cells are exposed to cationic PEs under different conditions. Although the cell wall architecture of the strains should be structurally similar, we found that the viability of E. coli was not affected by the electrostatic deposition of polyethyleneimine (PEI) or poly(allylamine) hydrochloride (PAH), whereas for P. stutzeri the deposition resulted in high death rates. The cells of E. coli proved to be suitable templates for Layer-by-Layer (LbL) modification, while in P. stutzeri a modified protocol with mild conditions had to be used to ensure the viability of the cells. Super resolution stimulated emission depletion (STED) microscopy allowed us to clearly visualize that after PE deposition onto the surface of the cells, the PEs could penetrate inside the cells of P. stutzeri, while forming a capsule around E. coli as expected. Therefore, this knowledge will help us select the most appropriate combinations of strains and PEs, for biotechnological processes or biomedical application, preventing unwanted toxicity.
Integration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens
Authors: Almeida-Silva Fabricio , Venancio Thiago M. 
Published: September 2021

ABSTRACTSoybean is one of the most important legume crops worldwide. However, soybean yield is dramatically affected by fungal diseases, leading to economic losses of billions of dollars yearly. Here, we integrated publicly available genome-wide association studies and transcriptomic data to prioritize candidate genes associated with resistance to Cadophora gregata, Fusarium graminearum, Fusarium virguliforme, Macrophomina phaseolina, and Phakopsora pachyrhizi. We identified 188, 56, 11, 8, and 3 high-confidence candidates for resistance to F. virguliforme, F. graminearum, C. gregata, M. phaseolina and P. pachyrhizi, respectively. The prioritized candidate genes are highly conserved in the pangenome of cultivated soybeans and are heavily biased towards fungal species-specific defense response. The vast majority of the prioritized candidate resistance genes are related to plant immunity processes, such as recognition, signaling, oxidative stress, systemic acquired resistance, and physical defense. Based on the number of resistance alleles, we selected the five most resistant accessions against each fungal species in the soybean USDA germplasm. Interestingly, the most resistant accessions do not reach the maximum theoretical resistance potential. Hence, they can be further improved to increase resistance in breeding programs or through genetic engineering. Finally, the coexpression network generated here is available in a user-friendly web application (https://soyfungigcn.venanciogroup.uenf.br/) and an R/Shiny package (https://github.com/almeidasilvaf/SoyFungiGCN) that serve as a public resource to explore soybean-pathogenic fungi interactions at the transcriptional level.
ER-localized phosphatidylethanolamine synthase plays a conserved role in lipid droplet formation
Authors: Gok Mehmet Oguz , Speer Natalie Ortiz , Henne W. Mike , Friedman Jonathan R. 
Published: September 2021

AbstractThe asymmetric distribution of phospholipids in membranes is a fundamental principle of cellular compartmentalization and organization. Phosphatidylethanolamine (PE), a nonbilayer phospholipid that contributes to organelle shape and function, is synthesized at several subcellular localizations via semi-redundant pathways. Previously, we demonstrated in the yeast Saccharomyces cerevisiae that the PE synthase Psd1, which primarily operates on the mitochondrial inner membrane, is additionally targeted to the endoplasmic reticulum (ER). While ER-localized Psd1 is required to support cellular growth in the absence of redundant pathways, its physiological function at the ER is unclear. We now demonstrate that ER-localized Psd1 sub-localizes on the ER to lipid droplet (LD) attachment sites and further show it is specifically required for normal LD formation. We also find that the role of PSD enzymes in LD formation is conserved in other organisms. Thus, we have identified PSD enzymes as novel regulators of LDs and demonstrate that both mitochondria and LDs in yeast are organized and shaped by the spatial positioning of a single PE synthesis enzyme.