bluuebunny/crossref_metadata_2025 huggingface dataset:
Wild-type FUS corrects ALS-like disease induced by cytoplasmic mutant FUS through autoregulation
Authors: Sanjuan-Ruiz Inmaculada , Govea-Perez Noé , Mcalonis-Downes Melissa , Dieterle Stéphane , Megat Salim , Dirrig-Grosch Sylvie , Picchiarelli Gina , Piol Diana , Zhu Qiang , Myers Brian , Lee Chao-Zong , Cleveland Don W , Lagier-Tourenne Clotilde , Da Cruz Sandrine , Dupuis Luc
Published: July 2021

Mutations in FUS, an RNA-binding protein involved in multiple steps of RNA metabolism, are associated with the most severe forms of amyotrophic lateral sclerosis (ALS). Accumulation of cytoplasmic FUS is likely to be a major culprit in the toxicity ofFUSmutations. Thus, preventing cytoplasmic mislocalization of the FUS protein may represent a valuable therapeutic strategy. FUS binds to its own pre-mRNA creating an autoregulatory loop efficiently buffering FUS excess through multiple proposed mechanisms including retention of introns 6 and/or 7. Here, we introduced a wild-typeFUSgene allele, retaining all intronic sequences, in mice whose heterozygous or homozygous expression of a cytoplasmically retained FUS protein (FusΔNLS) was previously shown to provoke ALS-like disease or postnatal lethality, respectively. Wild-type FUS completely rescued the early lethality caused by the twoFusΔNLSalleles, and improved age-dependent motor deficit and reduced lifespan associated with the heterozygous expression ofFusΔNLS. Mechanistically, wild-type FUS decreased the load of cytoplasmic FUS, increased exon 7 skipping and retention of introns 6 and 7 in the endogenous mouseFusmRNA, leading to decreased expression of the mutant mRNA. Thus, the wild-typeFUSallele activates the homeostatic autoregulatory loop, maintaining constant FUS levels and decreasing the mutant protein in the cytoplasm. These results provide proof of concept that an autoregulatory competent wild-type FUS expression could protect against this devastating, currently intractable, neurodegenerative disease.
Oncolytic virus treatment differentially affects the CD56dimand CD56brightNK cell subsetsin vivoand regulates a spectrum of human NK cell activity
Authors: Wantoch Michelle , Wilson Erica B. , Droop Alastair P. , Phillips Sarah L. , Coffey Matt , El-Sherbiny Yasser M. , Holmes Tim D. , Melcher Alan A. , Wetherill Laura F. , Cook Graham P.
Published: July 2021

Natural killer (NK) cells protect against intracellular infection and cancer. These properties are exploited in oncolytic virus (OV) therapy, where anti-viral responses enhance anti-tumour immunity. We have analysed the mechanism by which reovirus, an oncolytic dsRNA virus, modulates human NK cell activity. Reovirus activates NK cells in a type I interferon (IFN-I) dependent manner, resulting in STAT1 and STAT4 signalling in both CD56dimand CD56brightNK cell subsets. Gene expression profiling revealed the dominance of IFN-I responses and identified induction of genes associated with NK cell cytotoxicity and cell cycle progression, with distinct responses in the CD56dimand CD56brightsubsets. However, reovirus treatment, acting via IFN-I, inhibited NK cell proliferative responses to IL-15 and was associated with reduced AKT signalling.In vivo, human CD56dimand CD56brightNK cells responded with similar kinetics to reovirus treatment, but CD56brightNK cells were transiently lost from the peripheral circulation at the peak of the IFN-I response, suggestive of their redistribution to secondary lymphoid tissue. These results show that reovirus modulates a spectrum of NK cell activityin vivo, encompassing direct action on tumour cells and the regulation of adaptive immunity. Such activity is likely to mirror NK cell responses to natural viral infection.
Interacting brains coming in sync through their minds: An inter-brain neurofeedback study
Authors: Müller Viktor , Perdikis Dionysios , Mende Melinda A. , Lindenberger Ulman
Published: July 2021

We live in a social world where we interact with each other. Neurofeedback (NFB) is an indispensable element for such interaction. Single-person NFB studies using electroencephalography (EEG) or other neuroimaging recordings were extensively reported. However, hyperscanning studies using inter-brain synchrony (IBS) as an NFB feature are completely unknown. In this study, we present two different experimental designs where IBS was fed visually back either as two balls approaching each other (so-called“ball”design) or as two pendula reflecting oscillatory activity of two participants (so-called“pendulum”design). The NFB was provided at two EEG frequencies (2.5 and 5 Hz) and manipulated by enhanced (fake condition) and inverse feedback. We showed that the participants were able to increase IBS by using NFB, especially when it was fed back at the theta frequency. Apart from the intra- and inter-brain coupling, other oscillatory activities (e.g., power spectral density, peak amplitude and peak frequency) changed during the task compared to rest. Moreover, all the measures showed specific correlations to the subjective post-survey item scores, reflecting subjective feeling and appraisal. We conclude that hyperscanning with IBS as a feedback feature seems to be an important tool to examine neural mechanisms of social interaction and collective behavior.
Investigating the Effects of Macaque Primary Motor Cortex Multi-Unit Activity Binning Period on Behavioural Decoding Performance
Authors: Savolainen Oscar W. , Constandinou Timothy G.
Published: July 2021

This paper investigates the relationship between Multi-Unit Activity (MUA) Binning Period (BP) and Brain-Computer Interface (BCI) decoding performance using Long-Short Term Memory decoders. The motivation is to determine whether lossy compression of MUA via increasing BP has any adverse consequences for BCI Behavioral Decoding Performance (BDP). The Neural data originates from intracortical recordings from Macaque Primary Motor cortex [1]. The BDP is measured by the Pearson correlationrbetween the observed and predicted velocity of the subject’s X-Y hand coordinates in reaching tasks [1]. The results suggest a statistically significant but slight linear relationship between increasing MUA BP and decreasing BDP. For example, when using a 100 ms moving average window, increasing the BP by 10 ms on average reduces the BDP r by approximately 0.85%. This relationship may be due to the reduced number of training examples, or due to the loss of Behavioral information because of reduced MUA temporal resolution.
Tooth size apportionment, Bayesian inference, and the phylogeny ofHomo naledi
Authors: Irish Joel D. , Grabowski Mark
Published: July 2021

This study has three main objectives—two methodological and one summative, namely, further characterization ofHomo naledi(∼335–236 ka) to more firmly establish its evolutionary history. Using mathematically-corrected mesiodistal and buccolingual crown dimensions, the species was compared with samples ofPan troglodytes, Australopithecus africanus,A. afarensis,Paranthropus robustus,P. boisei,H. habilis,H. ergaster,H. erectus,H. heidelbergensis,H. neanderthalensis, andH. sapiens; the correction yields equivalently scaled samples unaffected by significant interspecific size differences. After initial cluster analysis, the data were used in tooth size apportionment analysis to determine how size is distributed relatively in each species’ dentition, while visualizing this variation in a sample scatterplot. The first main objective then, after quantitative coding, is evaluating the utility of these characters to estimate phylogenetic relationships, here using Bayesian inference with an Mkv model. The second objective, for the first time in paleoanthropological study, is estimating relationships using continuous characters, i.e., the scaled data, through Bayesian inference under a Brownian-motion model. This strategy facilitates maximum reception of potential phylogenetic signal. The final objective based on all analyses, though principally continuous Bayesian inference, is to elucidate the phylogeny ofH. naledi.Relationships are largely congruent across methods and, with markedly higher node support, most of those inferred in prior systematic studies using qualitatively discretized traits. The present results placeH. naledias a sister taxon toH. habilis(node support ∼70-99%), with a plesiomorphic pattern of relative tooth size. It is nested within a clade comprising australopiths and earlyHomodating 3.3 Ma to ∼800 ka, distinct from youngerH. erectusthroughH. sapiens.This suggests thatH. naledioriginated well before the geological date range associated with the Dinaledi Chamber, from which the remains in this study were recovered, to represent a long-lived side branch in the genus.
Abnormal Cannabidiol protects pancreatic beta cells in mouse models of experimental Type 1 diabetes
Authors: Gonzalez-Mariscal Isabel , Morales Macarena Pozo , Romero-Zerbo Silvana Yanina , Espinosa-Jimenez Vanesa , Escamilla Alejandro , Sánchez-Salido Lourdes , Cobo-Vuilleumier Nadia , Gauthier Benoit R. , Bermudez-Silva Francisco Javier
Published: July 2021

Background and Purpose

The atypical cannabinoid Abn-CBD was reported to improve the inflammatory status in preclinical models of several pathologies including autoimmune diseases. However, its potential for autoimmune diabetes, i.e. type 1 diabetes (T1D), is unknown.

Experimental Approach

We used two mouse models of T1D, streptozotocin (STZ)-injected and non-obese diabetic (NOD) mice. Eight-to-ten-week-old male C57Bl6/J mice were pre-treated with Abn-CBD (1mg/kg of body weight) or vehicle for 1 week, following STZ treatment, and euthanized 1 week later. Six-week-old female NOD mice were treated with Abn-CBD (0.1-1mg/kg) or vehicle for 12 weeks and then euthanized. Blood, pancreas, pancreatic lymph nodes and circulating T cells were collected and processed for analysis. Glycemia was also monitored.

Key Results

Abn-CBD decreased circulating proinflammatory cytokines, ameliorated islet inflammation and the autoimmune attack, showing a 2-fold decrease in CD8+ T cells infiltration and reduced Th1/Th2 ratio in pancreatic lymph nodes of STZ-injected mice. Mechanistically, Abn-CBD reduced intra-islet phospho-NF-κB and TXNIP. Concomitant reduction of islet cell apoptosis and intra-islet fibrosis were observed in Abn-CBD pre-treated mice compared to vehicle. In NOD mice, Abn-CBD reduced the expression of Ifng, Il21, Tnfa and Il10 while increased Il4 in circulating CD4+ T cells compared to vehicle, reducing the severity of insulitis and improving glucose tolerance.

Conclusion and Implications

Altogether, we found that Abn-CBD reduces intra-islet inflammation and delays the progression of insulitis in mouse models of T1D, preserving healthy functional islets. Hence, Abn-CBD and related compounds emerge as new candidates to develop pharmacological strategies to treat early stages of T1D.

WHAT IS ALREADY KNOWN

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Phytocannabinoids such as cannabidiol (CBD) have anti-inflammatory and glucose-lowering properties

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The CBD derivative Abn-CBD ameliorates inflammation in various diseases and modulates beta cell function

WHAT THIS STUDY ADDS

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Abn-CBD reduces systemic and pancreatic inflammation in mice models of type 1 diabetes

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Abn-CBD prevents beta cell damage and loss during type 1 diabetes onset

CLINICAL SIGNIFICANCE

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Synthetic cannabinoids emerge as potential treatment for type 1 diabetes
A CLEM approach to access to the ultrastructure at the graft interface in Arabidopsis thaliana
Authors: Chambaud Clément , Cookson Sarah Jane , Ollat Nathalie , Bayer Emmanuelle , Brocard Lysiane
Published: July 2021

Despite recent progress in our understanding of the graft union formation, we still know little about the cellular events underlying the grafting process. This is partially due to the difficulty of reliably targeting the graft interface in electron microscopy to study its ultrastructure and three-dimensional architecture. To overcome this technological bottleneck, we developed a correlative light electron microscopy approach (CLEM) to study the graft interface with high ultrastructural resolution. Grafting hypocotyls of Arabidopsis thaliana lines expressing YFP or mRFP in the endoplasmic reticulum allowed the efficient targeting of the grafting interface for under light and electron microscopy. To explore the potential of our method to study sub-cellular events at the graft interface, we focused on the formation of secondary plasmodesmata (PD) between the grafted partners. We showed that 4 classes of PD were formed at the interface and that PD introgression into the call wall was initiated equally by both partners. Moreover, the success of PD formation appeared not systematic with a third of PD not spanning the cell wall entirely. Characterizing the ultrastructural characteristics of these failed PD gives us insights into the process of secondary PD biogenesis. We showed that the thinning of the cell wall and the endoplasmic reticulum-plasma membrane tethering seem to be required for the establishment of symplastic connections between the scion and the rootstock. The resolution reached in this work shows that our CLEM method offer a new scale to the study for biological processes requiring the combination of light and electron microscopy.
Scalable Fabrication of 3D Structured Microparticles Using Induced Phase Separation
Authors: Lee Sohyung , de Rutte Joseph , Dimatteo Robert , Koo Doyeon , Di Carlo Dino
Published: July 2021

Microparticles with defined shapes and spatial chemical modification can enable new opportunities to interface with cells and tissues at the cellular scale. However, conventional methods to fabricate shaped microparticles have trade-offs between the throughput of manufacture and precision of particle shape and chemical functionalization. Here, we achieved scalable production of hydrogel microparticles at rates of greater than 40 million/hour with localized surface chemistry using a parallelized step emulsification device and temperature-induced phase-separation. The approach harnesses a polymerizable polyethylene glycol (PEG) and gelatin aqueous-two phase system (ATPS) which conditionally phase separates within microfluidically-generated droplets. Following droplet formation, phase separation is induced and phase separated droplets are subsequently crosslinked to form uniform crescent and hollow shell particles with gelatin functionalization on the boundary of the cavity. The gelatin localization enabled deterministic cell loading in sub nanoliter-size crescent-shaped particles, which we refer to as nanovials, with cavity dimensions tuned to the size of cells. Loading on nanovials also imparted improved cell viability during analysis and sorting using standard fluorescence activated cell sorters, presumably by protecting cells from shear stress. This localization effect was further exploited to selectively functionalize capture antibodies to nanovial cavities enabling single-cell secretion assays with reduced cross-talk in a simplified format.
Alterations in leptin signaling in Amyotrophic Lateral Sclerosis (ALS)
Authors: Ferrer-Donato Agueda , Contreras Ana , Frago Laura M. , Chowen Julie A. , Fernandez-Martos Carmen M.
Published: July 2021

Leptin has been suggested to play a role in amyotrophic lateral sclerosis (ALS), a fatal progressive and neurodegenerative disease. This adipokine has previously been shown to be associated with a lower risk of ALS disease and to confer a survival advantage in ALS patients. However, the role of leptin in the progression of ALS is unknown. Indeed, our understanding of the mechanisms underlying leptin’s effects in the pathogenesis of ALS is very limited, and it is fundamental to determine whether alterations in leptin’s actions take place in this neurodegenerative disease. To characterize the association between leptin signaling and the clinical course of ALS we assessed the mRNA and protein expression profiles of leptin, the long leptin receptor (Ob-Rb) and leptin-related signaling pathways over the time course of the disease (onset and end-stage of disease), in TDP-43A315T mice compared to age-matched WT littermates. In addition, at the selected time-points immunoassay analysis was conducted to characterize plasma levels of total ghrelin, the adipokines (resistin and leptin) and metabolic proteins (plasminogen activator inhibitor type 1 (PAI-1), gastric inhibitory peptide (GIP), glucagon like peptide 1 (GLP-1), insulin and glucagon) in TDP-43A315T mice compared to WT controls. Our results indicate alterations in leptin signaling in the spinal cord and the hypothalamus on the backdrop of TDP-43-induced deficits in mice, providing new evidence about the pathways that could link leptin signaling to ALS.
Dorsal root ganglia control nociceptive input to the central nervous system
Authors: Hao Han , Ramli Rosmaliza , Wang Caixue , Liu Chao , Shah Shihab , Mullen Pierce , Lall Varinder , Jones Frederick , Shao Jicheng , Zhang Hailin , Jaffe David B. , Gamper Nikita , Du Xiaona
Published: July 2021

Accumulating observations suggest that peripheral somatosensory ganglia may regulate nociceptive transmission, yet direct evidence is sparse. Here we show that the peripheral afferent nociceptive information undergoes dynamic filtering within the dorsal root ganglion (DRG) and suggest that this filtering occurs at the axonal bifurcations (t-junctions). Using synchronous in vivo electrophysiological recordings from the peripheral and central processes of sensory neurons (in the spinal nerve and dorsal root), ganglionic transplantation of GABAergic progenitor cells, and optogenetics we demonstrate existence of tonic and dynamic filtering of action potentials traveling through the DRG. Filtering induced by focal application of GABA or optogenetic GABA release from the DRG-transplanted GABAergic progenitor cells was specific to nociceptive fibers. Light-sheet imaging and computer modeling demonstrated that, compared to other somatosensory fiber types, nociceptors have shorter stem axons, making somatic control over t-junctional filtering more efficient. Optogenetically-induced GABA release within DRG from the transplanted GABAergic cells enhanced filtering and alleviated hypersensitivity to noxious stimulation produced by chronic inflammation and neuropathic injury in vivo. These findings support ‘gating’ of pain information by DRGs and suggest new therapeutic approaches for pain relief.
Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
Authors: Hsieh Tsung-Han S. , Cattoglio Claudia , Slobodyanyuk Elena , Hansen Anders S. , Darzacq Xavier , Tjian Robert
Published: July 2021

It remains unclear why acute depletion of CTCF and cohesin only marginally affects expression of most genes despite substantially perturbing 3D genome folding at the level of domains and structural loops. To address this conundrum, we used high-resolution Micro-C and nascent transcript profiling to find that enhancer-promoter (E-P) interactions are largely insensitive to acute (3-hour) depletion of CTCF, cohesin, and WAPL. YY1 has been proposed to be a structural regulator of E-P loops, but acute YY1 depletion also had minimal effects on E-P loops, transcription, and 3D genome folding. Strikingly, live-cell single-molecule imaging revealed that cohesin depletion reduced transcription factor binding to chromatin. Thus, although neither CTCF, cohesin, WAPL, nor YY1 are required for the short-term maintenance of most E-P interactions and gene expression, we propose that cohesin may serve as a “transcription factor binding platform” that facilitates transcription factor binding to chromatin.
HIF-dependent Neuropeptide Y Receptor Y1 and Y5 expression sensitizes hypoxic cells to NPY stimulation
Authors: Medeiros Philip J. , Pascetta Sydney , Kirsh Sarah , Al-Khazraji Baraa K. , Uniacke James
Published: July 2021

Neuropeptide Y (NPY) is an abundant neurohormone in the central and peripheral nervous system involved in feeding behavior, energy balance, nociception, and anxiety. Several NPY receptor (NPYR) subtypes display elevated expression in many cancers including in breast cancer where this is exploited for imaging and diagnosis. Here, we show that NPY1R and NPY5R mRNA abundance is induced by hypoxia in a Hypoxia Inducible Factor (HIF)-dependent manner in breast cancer cell lines MCF7 and MDA-MB-231. The HIFs bind to several genomic regions upstream of the NPY1R and NPY5R transcription start sites. The MAPK/ERK pathway is activated more rapidly upon NPY5R stimulation in hypoxic cells compared to normoxic cells. This pathway requires IGF1R activity in normoxia, but not in hypoxic cells where they display resistance to the radiosensitizer and IGF1R inhibitor AG1024. Hypoxic cells proliferate and migrate more when stimulated with NPY relative to normoxic cells, with a more robust response observed with a Y5-specific agonist. Our data suggest that hypoxia induced NPYRs render hypoxic cells more sensitive to NPY stimulation. Considering that breast tissue receives a constant supply of NPY, and hypoxia is a common feature of the tumor microenvironment, breast tumors are the perfect storm for hyperactive NPYR. This study not only highlights a new relationship between the HIFs and NPYR expression and activity, but may inform the use of chemotherapeutics targeting NPYRs and hypoxic cells.
Mapping Human Transient Transcriptomes Using Single Nucleotide Resolution 4sU Sequencing (SNU-Seq)
Authors: Lorenz Philipp , Lamstaes Anna , Fischl Harry , Xi Shidong , Saukko-Paavola Aksel , Murray Struan , Brown Thomas , George Charlotte , Furger Andre , Angel Andrew , Mellor Jane
Published: July 2021

Genomes are pervasively transcribed leading to stable and unstable transcripts that define functional regions of genomes and contribute to cellular phenotypes. Defining comprehensive nascent transcriptomes is pivotal to understand gene regulation, disease processes, and the impact of extracellular signals on cells. However, currently employed methods are laborious, technically challenging and costly. We developed single-nucleotide resolution 4sU-sequencing (SNU-Seq), involving pulse labelling, biotinylation and direct isolation of nascent transcripts. Artificial poly-(A)-tailing of the 3’ most nucleotide of nascent transcripts ensures oligo-d(T) primer-based library preparation and sequencing using commercial 3’ RNA-Seq kits. We show that SNU-Seq is a cost-effective new method generating even read profiles across transcription units. We used SNU-Seq to identify transcription elongation parameters, to map usage of polyadenylation (PAS) sites and novel enhancers. Remarkably, 4sU labelled nascent RNA accumulates short ∼100nt transcripts that map to the 5’ end of genes. We show that isolation of these short nascent RNA and sequencing the 5’ and 3’ ends using size-selected SNU-Seq (ssSNU-Seq) provides highly sensitive annotations of mapped and novel TSSs, promoter-proximal pause/termination sites. Thus, SNU-seq and ssSNU-seq combined yield comprehensive transcriptomics data at low cost with high spatial and temporal resolution.

Highlights

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SNU-Seq maps nascent transcripts at base-pair resolution, with high sensitivity and low cost

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SNU-Seq detects comprehensive polyadenylation sites.

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SNU-Seq maps the promoter proximal pause 60-80 nt from the TSS.

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Size-selected SNU-Seq yields highly sensitive and novel TSS annotations
Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis
Authors: Bhan Namita , Callisto Alec , Strutz Jonathan , Glaser Joshua , Kalhor Reza , Boyden Edward , Church George , Kording Konrad , Tyo Keith E.J.
Published: July 2021

Employing DNA as a high-density data storage medium has paved the way for next-generation digital storage and biosensing technologies. However, the multipart architecture of current DNA-based recording techniques renders them inherently slow and incapable of recording fluctuating signals with sub-hour frequencies. To address this limitation, we developed a simplified system employing a single enzyme, terminal deoxynucleotidyl transferase (TdT), to transduce environmental signals into DNA. TdT adds nucleotides to the 3’ ends of single-stranded DNA (ssDNA) in a template-independent manner, selecting bases according to inherent preferences and environmental conditions. By characterizing TdT nucleotide selectivity under different conditions, we show that TdT can encode various physiologically relevant signals like Co2+, Ca2+, Zn2+ concentrations and temperature changes in vitro. Further, by considering the average rate of nucleotide incorporation, we show that the resulting ssDNA functions as a molecular ticker tape. With this method we accurately encode a temporal record of fluctuations in Co2+ concentration to within 1 minute over a 60-minute period. Finally, we engineer TdT to allosterically turn off in the presence of physiologically relevant concentration of calcium. We use this engineered TdT in concert with a reference TdT to develop a two-polymerase system capable of recording a single step change in Ca2+ signal to within 1 minute over a 60-minute period. This work expands the repertoire of DNA-based recording techniques by developing a novel DNA synthesis-based system that can record temporal environmental signals into DNA with minutes resolution.
Single cell profiling of T and B cell repertoires following SARS-CoV-2 mRNA vaccine
Authors: Sureshchandra Suhas , Lewis Sloan A. , Doratt Brianna , Jankeel Allen , Ibraim Izabela , Messaoudi Ilhem
Published: July 2021

mRNA based vaccines for SARS-CoV-2 have shown exceptional clinical efficacy providing robust protection against severe disease. However, our understanding of transcriptional and repertoire changes following full vaccination remains incomplete. We used single-cell RNA sequencing and functional assays to compare humoral and cellular responses to two doses of mRNA vaccine with responses observed in convalescent individuals with asymptomatic disease. Our analyses revealed enrichment of spike-specific B cells, activated CD4 T cells, and robust antigen-specific polyfunctional CD4 T cell responses in all vaccinees. On the other hand, CD8 T cell responses were both weak and variable. Interestingly, clonally expanded CD8 T cells were observed in every vaccinee, as observed following natural infection. TCR gene usage, however, was variable, reflecting the diversity of repertoires and MHC polymorphism in the human population. Natural infection induced expansion of larger CD8 T cell clones occupied distinct clusters, likely due to the recognition of a broader set of viral epitopes presented by the virus not seen in the mRNA vaccine. Our study highlights a coordinated adaptive immune response where early CD4 T cell responses facilitate the development of the B cell response and substantial expansion of effector CD8 T cells, together capable of contributing to future recall responses.
The Janus-like role of neuraminidase isoenzymes in inflammation
Authors: Howlader Md. Amran , Demina Ekaterina P. , Samarani Suzanne , Guo Tianlin , Ahmad Ali , Pshezhetsky Alexey V. , Cairo Christopher W.
Published: July 2021

The processes of activation, extravasation, and migration of immune cells to a site are early and essential steps in the induction of an acute inflammatory response. These events are part of the inflammatory cascade which involves multiple regulatory steps. Using a murine air-pouch model of inflammation with LPS as an inflammation inducer we demonstrate that isoenzymes of the neuraminidase family (NEU1, 3, and 4) play essential roles in this process acting as positive or negative regulators of leukocyte infiltration. Genetically knocked-out (KO) mice for different NEU genes (Neu1KO,Neu3KO,Neu4KO, andNeu3/4double KO mice) were induced with LPS, leukocytes at the site of inflammation were counted, and the inflamed tissue was analyzed using immunohistochemistry. Our data show that leukocyte recruitment was decreased in NEU1 and NEU3-deficient mice, while it was increased in NEU4-deficient animals. Consistent with these results, systemic levels of pro-inflammatory cytokines and those in pouch exudate were reduced inNeu1and increased inNeu4KO mice. We found that pharmacological inhibitors specific for NEU1, NEU3, and NEU4 isoforms also affected leukocyte recruitment. We conclude that NEU isoenzymes have distinct – and even opposing – effects on leukocyte recruitment, and therefore warrant further investigation to determine their mechanisms and importance as regulators of the inflammatory cascade.
Cellular Pharmacology of Curcumin With and Without Piperine
Authors: Mahran Rama I , Shu Pan , Colacino Justin , Hagras Magda M , Sun Duxin , Brenner Dean E
Published: July 2021

Prior reports have suggested that piperine enhances curcumin’s anti-carcinogenesis. We tested the hypothesis that piperine increases the intracellular concentrations of curcumin by improving intracellular uptake or reducing curcumin efflux or metabolism in breast cells. We incubated SUM149, MCF10A, primary normal human breast cells, ALDH+, and ALDH-CD44+24- SUM149 cells with curcumin ± piperine at concentrations 1 μM to 15 μM for time periods of 15 minutes to 24 hours. We assayed cell viability by MTT assay and proliferation by primary mammosphere assay. Curcumin and its metabolites were assayed using liquid chromatography mass spectroscopy. Curcumin, but not piperine, showed significantly higher effects on the viability of breast cancer SUM149 cells than in non-tumorigenic MCF10A cells. Curcumin + piperine synergistically reduced viability of SUM149 cells but had a concentration dependent effect upon MCF10A cell viability. Cellular uptake of curcumin in SUM149 is significantly higher, while the efflux in SUM149 is significantly lower than in MCF10A, which correlated with cell viability. Piperine did not alter curcumin cellular uptake, efflux, or metabolism in any of the cell models. The observed synergism of piperine+curcumin in reducing breast stem cell self renewal is likely due to independent anti-carcinogenesis effects rather than any effects upon intracellular curcumin concentrations.
Mining bacterial NGS data vastly expands the complete genomes of temperate phages
Authors: Zhang Xianglilan , Wang Ruohan , Xie Xiangcheng , Hu Yunjia , Wang Jianping , Sun Qiang , Feng Xikang , Tong Shanwei , Cui Yujun , Wang Mengyao , Zhai Shixiang , Niu Qi , Wang Fangyi , Kropinski Andrew M. , Jiang Xiaofang , Peng Shaoliang , Li Shuaicheng , Tong Yigang
Published: July 2021

Temperate phages (active prophages induced from bacteria) help control pathogenicity, modulate community structure, and maintain gut homeostasis1. Complete phage genome sequences are indispensable for understanding phage biology. Traditional plaque techniques are inapplicable to temperate phages due to the lysogenicity of these phages, which curb the identification and characterization of temperate phages. Existing in silico tools for prophage prediction usually fail to detect accurate and complete temperate phage genomes2–5. In this study, by a novel computational method mining both the integrated active prophages and their spontaneously induced forms (temperate phages), we obtained 192,326 complete temperate phage genomes from bacterial next-generation sequencing (NGS) data, hence expanded the existing number of complete temperate phage genomes by more than 100-fold. The reliability of our method was validated by wet-lab experiments. The experiments demonstrated that our method can accurately determine the complete genome sequences of the temperate phages, with exact flanking sites (attPandattBsites), outperforming other state-of-the-art prophage prediction methods. Our analysis indicates that temperate phages are likely to function in the evolution of microbes by 1) cross-infecting different bacterial host species; 2) transferring antibiotic resistance and virulence genes; and 3) interacting with hosts through restriction-modification and CRISPR/anti-CRISPR systems. This work provides a comprehensive complete temperate phage genome database and relevant information, which can serve as a valuable resource for phage research.
Tuned to Learn: An anticipatory hippocampal convergence state conducive to memory formation revealed during midbrain activation
Authors: Poh Jia-Hou , Vu Mai-Anh T , Stanek Jessica K , Hsiung Abigail , Egner Tobias , Adcock R. Alison
Published: July 2021

The hippocampus has been a focus of memory research since H.M’s surgery in 1953 abolished his ability to form new memories, yet its mechanistic role in memory is still debated. Here, we identify a novel, systems-level candidate memory mechanism: an anticipatory hippocampal “convergence state”, observed while awaiting valuable information, that both predicts later memory, and accounts for the relationship between midbrain activation and enhanced learning. To reveal this state, we leveraged endogenous neuromodulation associated with motivation: During fMRI, participants viewed trivia questions eliciting high or low curiosity, each followed seconds later by its answer. We reasoned that memory encoding success requires a convergence of factors, and as such, hippocampal states associated with remembered trials would be less variable than forgotten ones. Using a novel multivariate approach, we measured convergence by quantifying the typicality of spatially distributed patterns. We found that during anticipation of trivia answers, hippocampal states showed greater convergence under high than low curiosity. Crucially, convergence in the hippocampus increased with greater midbrain activation and uniquely accounted for the association between midbrain activation and subsequent memory recall. We propose that this novel convergence state in the hippocampus reflects a mechanism of its contribution to long term memory formation and that engagement of this convergence state completes the cascade from motivation to midbrain activity to memory enhancement.
Novel municipal sewage-associated bacterial genomes and their potential in source tracking
Authors: Lindner Blake G. , Suttner Brittany , Conrad Roth E. , Rodriguez-R Luis M. , Hatt Janet K. , Zhu Kevin J. , Brown Joe , Konstantinidis Konstantinos T.
Published: July 2021

Little is known about the genomic diversity of raw municipal wastewater (sewage) microbial communities, including to what extent sewage-specific populations exist and how they can be used to improve source attribution and partitioning in sewage-contaminated waters. Herein, we used the influent of three wastewater treatment plants in Atlanta, Georgia (USA) as inoculum in multiple controlled laboratory mesocosms to simulate sewage contamination events and followed these perturbed freshwater microbial communities with metagenomics over a 7-day observational period. We describe 15 abundant non-redundant bacterial metagenome-assembled genomes (MAGs) ubiquitous within all sewage inoculum yet absent from the unperturbed freshwater control at our analytical limit of detection. Tracking the dynamics of populations represented by these MAGs revealed varied decay kinetics, depending on (inferred) phenotypes, e.g., anaerobes decayed faster under the well-aerated incubation conditions. Notably, a portion of these populations show decay patterns similar to common markers, Enterococcus and HF183. Comparisons against MAGs from different sources such as human and animal feces, revealed low cross-reactivity, indicating how genomic collections could be used to sensitively identify sewage contamination and partition signal among multiple sources. Overall, our results indicate the usefulness of metagenomic approaches for assessing sewage contamination in waterbodies and provides needed methodologies for doing so.
Induced Nanoscale Membrane Curvature Bypasses Clathrin’s Essential Endocytic Function
Authors: Cail Robert C , Shirazinejad Cyna R , Drubin David G
Published: July 2021

During membrane trafficking, flat membrane is rapidly remodeled to produce nanometer-scale vesicles. The mechanisms underlying this shape change are not completely understood, but coat proteins such as clathrin are implicated. Clathrin’s ability to bind to membranes of many different geometries casts uncertainty on its specific role in curvature generation and stabilization. Here, we used nanopatterning to produce substrates of ideal optical properties for live-cell imaging, with U-shaped features that bend a cell’s ventral plasma membrane into shapes characteristic of the energetically-unfavorable intermediate of clathrin- mediated endocytosis (CME). This induced plasma membrane curvature recruits the endocytic machinery, promoting productive endocytosis. Upon clathrin or AP2 disruption, CME sites on flat substrates are diminished. However, induced curvature rescues the localization, turnover and transferrin cargo uptake activities of CME sites after clathrin, but not AP2, disruption. These data establish that clathrin’s essential function during CME is to facilitate the evolution of membrane curvature rather than to scaffold CME protein recruitment.

Cail et al. demonstrate that induced nanoscale membrane curvature recruits endocytic sites and produces vesicles in cells lacking the coat protein clathrin, while the adaptor protein AP2 is still required, showing that clathrin’s essential function is to facilitate curvature development of the nascent vesicle.
Evolution of DNA methylation across Ecdysozoa
Authors: Engelhardt Jan , Scheer Oliver , Stadler Peter F. , Prohaska Sonja J.
Published: July 2021

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. We report here a comprehensive study of the presence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa, covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. Three of these phyla have not been investigated for the presence of DNA methylation before. We observe that the loss of individual DNMTs independently occurred multiple times across ecdysozoan phyla. We computationally predict the presence of DNA methylation based on CpG rates in coding sequences using an implementation of Gaussian Mixture Modelling, MethMod. Integrating both analysis we predict two previously unknown losses of DNA methylation in Ecdysozoa, one within Chelicerata (Mesostigmata) and one in Tardigrada. In the early-branching Ecdysozoa Priapulus caudatus we predict the presence of a full set of DNMTs and the presence of DNA methylation. We are therefore showing a very diverse and independent evolution of DNA methylation in different ecdysozoan phyla spanning a phylogenetic range of more than 700 million years.
Influence of Strain Post-Processing on Brain Injury Prediction
Authors: Fahlstedt Madelen , Meng Shiyang , Kleiven Svein
Published: July 2021

Finite element head models are a tool to better understand brain injury mechanisms. Many of the models use strain as output but with different percentile values such as 100th, 95th, 90th, and 50th percentiles. Some use the element value, whereas other use the nodal average value for the element. Little is known how strain post-processing is affecting the injury predictions and evaluation of different prevention systems. The objective of this study was to evaluate the influence of strain output on injury prediction and ranking.

Two models with different mesh densities were evaluated (KTH Royal Institute of Technology head model and the Total Human Models for Safety (THUMS)). Pulses from reconstructions of American football impacts with and without a diagnosis of mild traumatic brain injury were applied to the models. The value for 100th, 99th, 95th, 90th, and 50th percentile for element and nodal averaged element strain was evaluated based on peak values, injury risk functions, injury predictability, correlation in ranking, and linear correlation.

The injury risk functions were affected by the post-processing of the strain, especially the 100th percentile element value stood out. Meanwhile, the area under the curve (AUC) value was less affected, as well as the correlation in ranking (Kendall’s tau 0.71-1.00) and the linear correlation (Pearson’s r2 0.72-1.00). With the results presented in this study, it is important to stress that the same post-processed strain should be used for injury predictions as the one used to develop the risk function.
CEO power and R&D investment
Authors: Naaman Christine , Sun Li
Published: July 2021

Purpose

This study aims to examine whether and how the power of a chief executive officer (CEO) relates to firm-level research and development (R&D) investment.

Design/methodology/approach

The authors use clustered standard errors ordinary least squares regression using a large sample of US firms from 1994 to 2017.

Findings

The authors find a significant negative relation between CEO power and R&D investment, suggesting that firms with more powerful CEOs are less likely to invest in R&D activities. Besides, the study finds that this significant negative relation is largely driven by firms with weaker corporate governance.

Originality/value

This study contributes to the finance literature on the impact and consequences of having powerful CEOs and the financial accounting literature on the determinants of R&D expenditures.
“Building as machine”: mental image of combined cycle power plants workers
Authors: Rezaee Mohammad , Eghbali Seyed Rahman
Published: July 2021

Purpose

This paper aims to interpret the workers’ perception of combined cycle power plants through visual qualities.

Design/methodology/approach

In this qualitative research landscape image, the sketching technique is applied as a data collection method to extract participants’ mental images by asking them to draw sketches. The resulted sketches besides obtained verbal and written data were analyzed and coded in three stages to explain the workers’ perception. Visual qualities were studied as a mean which made it possible to interpret the workers’ perception of their workplace.

Findings

Careful analysis of the gathered data and the emerged concepts via open coding identify four axial categories of the concepts forming the workers’ perception of the power plants: “inconsistency with nature,” “emphasis on function and product,” “health and environmental threats” and “interpretation of the built form as a mass instead of space.” These four categories support the core category of the proposed theory which is “perceiving building as the machine.” This phrase explains how workers perceive power plants as machines, not as supportive and lively environments. This is followed by consequences, “precedence of building over human” is prominent among them.

Originality/value

In the relevant body of literature, visual impact and visual perception of conventional thermal power plants are largely missed, as well as visual relation to environment focusing on a single building or groups of adjacent buildings. This paper covers both areas via asking for sketches as a data collection method, in addition, to interview the participants to clarify their mental image of the work environment.
Barriers to lean construction implementation in Zimbabwe
Authors: Moyo Tirivavi , Chigara Benviolent
Published: July 2021

Purpose

Increased waste during projects execution has led to time and cost overruns within the Zimbabwean construction projects industry. However, contextual barriers to lean construction implementation are yet to be established for derivation of effective remedies. The purpose of this paper is to report on a study that sought to determine barriers to lean construction implementation and assess the existence of statistically significant differences because of gender, designation and educational levels of respondents.

Design/methodology/approach

A questionnaire survey was administered on construction professionals for the collection of quantitative data. Factor analysis was used to reveal interrelated significant sets of barriers to lean construction implementation. Non-parametric statistical methods were also used to determine significant differences because of demographic variables.

Findings

Integration- and performance-related, human capital management–related, quality management–related barriers were determined as the highest-ranked of the nine significant components. Significant differences because of gender, designation and educational levels were non-existent for aggregated barriers, generally indicating consensus on the barriers. However, individual barriers showed inadequacies in management requirements for lean construction implementation from architects and those with diplomas and degrees.

Research limitations/implications

The determination of barriers establishes the knowledge for construction policy evaluation for enhanced performance of the construction industry. However, because of the exploratory nature of this study, the insights of clients were not considered.

Originality/value

Context-specific barriers to lean construction implementation were determined for consequent construction policy improvements in the construction industry.
The effect of novelty in in-game advertising: examining the moderating role of interactivity and congruency
Authors: Vashisht Devika
Published: July 2021

Purpose

The motivation behind the study is to look at the impact of novelty in games on brand recall and attitude, and to dissect the directing job of game interactivity from the points of view of “contrast effect,” “engagement theory” and “transportation theory”.

Design/methodology/approach

A 2 (novelty: congruent or incongruent) × 2 (game interactivity: high or low) between-subject measures design was used. In total, 172 management students participated in the study. A 2 × 2 between-subjects measure multivariate analysis of variance (MANOVA) was utilized to test the hypotheses.

Findings

Incongruent novelty results in higher brand recall but less favorable brand attitude than congruent novelty. Interactivity moderates the relationship between novelty congruence and brand recall such that in a high-interactivity condition, incongruent novelty results in higher brand recall than that in the low-interactivity condition. But, in case of the high-interactivity condition, congruent novelty results in more favorable brand attitude than that in the low-interactivity condition.

Practical implications

Developing high brand recall rates and attitudes are the prime objectives of the marketers for choosing a medium to advertise their brands. This investigation adds knowledge to the area of interactive marketing, particularly in-game advertising as a media technique to promote brands taking novelty and game interactivity factors into thought.

Originality/value

From the perspectives of interactive marketing, psychological elaboration, mind-engagement and transportation of experience, this investigation adds to the literature of advanced media advertising, explicitly to in-game advertising by looking at the effect of novelty and game interactivity.