bluuebunny/crossref_metadata_2025 huggingface dataset:
Shelterin is a Dimeric Complex with Extensive Structural Heterogeneity
Authors: Zinder John C , Olinares Paul Dominic B , Svetlov Vladimir , Bush Martin W , Nudler Evgeny , Chait Brian T , Walz Thomas , de Lange Titia
Published: January 2022

Human shelterin is a six-subunit complex – comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1 – that binds telomeres, protects them from the DNA-damage response, and regulates the maintenance of telomeric DNA. Although high-resolution structures have been generated of the individual structured domains within shelterin, the architecture and stoichiometry of the full complex are currently unknown. Here we report the purification of shelterin subcomplexes and reconstitution of the entire complex using full-length, recombinantly produced components. By combining negative-stain electron microscopy (EM), crosslinking mass spectrometry (XLMS), mass photometry, and native mass spectrometry (MS), we obtain stoichiometries as well as domain-scale architectures of shelterin subcomplexes and determine that they are extensively conformationally heterogenous. For POT1/TPP1 and POT1/TPP1/TIN2, we observe high variability in the positioning of the POT1 DNA-binding domain, the TPP1 OB fold, and the TIN2 TRFH domain with respect to the C-terminal domains of POT1. Truncation of unstructured linker regions in TIN2, TPP1, and POT1 did not reduce the conformational variability of the heterotrimer. Both shelterin and the TRF1/TIN2/TPP1/POT1 subcomplex primarily adopt fully dimeric complexes, even in the absence of DNA substrates. TRF1/TIN2/TPP1/POT1 and shelterin complex showed extensive conformational variability, regardless of the presence of DNA substrates. We conclude that shelterin adopts a multitude of conformations and argue that its unusual architectural variability is beneficial for its many functions at telomeres.
Chemical-induced degradation of PreS2 mutant surface antigen reverses HBV-mediated hepatocarcinogenesis
Authors: Yang Joey Yi , Wu Yi-Hsuan , Pan Max Yu-Chen , Chiou Yu-Ting , Lee Richard Kuan-Lin , Li Tian-Neng , Wang Lily Hui-Ching
Published: January 2022

Naturally evolved immune-escape PreS2 mutant is an oncogenic caveat of liver cirrhosis and hepatocellular carcinoma (HCC) during chronic hepatitis B virus (HBV) infection. Notably, PreS2 mutants is prevalent in above 50% of patients with HCC. Intrahepatic expression of PreS2 mutant large surface antigen (PreS2-LHBS) induces endoplasmic reticulum stress, mitochondria dysfunction, cytokinesis failure and subsequent chromosome hyperploidy. In this study, we ask if long-term inhibition of PreS2-LHBS may act to reverse HBV-mediated hepatocarcinogenesis. We set up a stability reporter platform and identified ABT199 as an inhibitor of PreS2-LHBS from a library of 1068 FDA-approved drugs. Treatment of ABT199 induced PreS2-LHBS degradation without affecting the general cell viability, as shown in hepatoma and immortalized hepatocyte cell lines. We found that ABT199 induced the recruitment of PreS2-LHBS to ring-shaped structures in close proximity to lysosomal marker Lamp1 and multivesicular body marker Rab7. Simultaneously, inhibitions of lysosomal degradation or microautophagy restored the expression of PreS2-LHBS. Specifically, a 24-hr treatment of ABT199 reduced DNA damages and cytokinesis failure induced by PreS2-LHBS. Persistent treatment of ABT199 for 3 weeks reversed chromosome hyperploidy in PreS2-LHBS cells and suppressed anchorage-independent growth of HBV-positive hepatoma cell line. Together, we showed that ABT199 provoked selective degradation of PreS2-LHBS through the induction of microautophagy, and a long-term treatment of ABT199 reversed oncogenic mechanisms induced by HBV. Our results indicate that long-term degradation of PreS2-LHBS may serve as a novel therapeutic strategy to constrain HBV-mediated hepatocarcinogenesis.

Graphical abstract

Author summary

HBV PreS2 mutant large surface antigen (PreS2-LHBS) is an oncoprotein that induces liver cirrhosis and liver cancer. This study identified ABT199 as a potential inhibitor of PreS2-LHBS. We found that ABT199 could trigger the degradation of PreS2-LHBS through the induction of microautophagy. Moreover, a long-term treatment of ABT199 significantly reversed LHBS-induced oncogenic events including DNA damage, mitotic failure, chromosome hyperploidy, and anchorage-independent growth. This study not only identifies a specific inhibitor of PreS2-LHBS but also highlights a plausible strategy to constrain HBV-mediated hepatocarcinogenesis through targeting the degradation of PreS2-LHBS.
GAGAM: a genomic annotation-based enrichment of scATAC-seq data for Gene Activity Matrix
Authors: Martini Lorenzo , Bardini Roberta , Savino Alessandro , Di Carlo Stefano
Published: January 2022

Single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) is rapidly becoming a powerful technology to assess the epigenetic landscape of thousands of cells. However, the current great sparsity of the resulting data poses significant challenges to their interpretability and informativeness. Different computational methods are available, proposing ways to generate significant features from accessibility data and process them to obtain meaningful results. In particular, the most common way to interpret the raw scATAC-seq data is through peak-calling, generating the peaks as features. Nevertheless, this method is dataset-dependent because the peaks are related to the given dataset and can not be directly compared between different experiments. For this reason, this study wants to improve on the concept of the Gene Activity Matrix (GAM), which links the accessibility data to the genes, by proposing a Genomic-Annotated Gene Activity Matrix (GAGAM), which aims to label the peaks and link them to the genes through functional annotation of the whole genome. Using genes as features solves the problem of the feature dataset dependency allowing for the link of gene accessibility and expression. The latter is crucial for gene regulation understanding and fundamental for the increasing impact of multi-omics data. Results confirm that our method performs better than the previous GAMs.
The first horse gut microbiome gene catalog reveals that rare microbiome ensures better cardiovascular fitness in endurance horses
Authors: Mach Núria , Midoux Cédric , Leclercq Sébastien , Pennarun Samuel , Le Moyec Laurence , Rué Olivier , Robert Céline , Sallé Guillaume , Barrey Eric
Published: January 2022

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance, but the extent of their functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built the first equine gut microbial gene catalog comprising more than 25 million non-redundant genes representing 4,696 genera spanning 95 phyla. The unprecedented resolution unrevealed functional pathways relevant for both the structure of the microbiome and the host health and recovered 369 novel metagenome-assembled bacterial genomes, providing useful reference for future studies. Integration of microbial and host omic datasets suggested that microbiomes harboring rare species were functionally dissimilar from those enriched in Lachnospiraceae taxa. Moreover, they offered expanded metabolic pathways to fine-tune the cardiovascular capacity through mitochondria-mediated mechanisms. The results identify an associative link between horse endurance capability and its microbiome gene function, laying the basis for nutritional interventions that could benefit endurance athletes.
ArtSeg: Rapid Artifact Segmentation and Removal in Brightfield Cell Microscopy Images
Authors: Ali Mohammed A. S. , Hollo Kaspar , Laasfeld Tõnis , Torp Jane , Tahk Maris-Johanna , Rinken Ago , Palo Kaupo , Parts Leopold , Fishman Dmytro
Published: January 2022

Brightfield cell microscopy is a foundational tool in life sciences. The acquired images are prone to contain visual artifacts that hinder downstream analysis, and automatically removing them is therefore of great practical interest. Deep convolutional neural networks are state-of-the-art for image segmentation, but require pixel-level annotations, which are time-consuming to produce. Here, we propose ScoreCAM-U-Net, a pipeline to segment artifactual regions in brightfield images with limited user input. The model is trained using only image-level labels, so the process is faster by orders of magnitude compared to pixel-level annotation, but without substantially sacrificing the segmentation performance. We confirm that artifacts indeed exist with different shapes and sizes in three different brightfield microscopy image datasets, and distort downstream analyses such as nuclei segmentation, morphometry and fluorescence intensity quantification. We then demonstrate that our automated artifact removal ameliorates this problem. Such rapid cleaning of acquired images using the power of deep learning models is likely to become a standard step for all large scale microscopy experiments.
Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants
Authors: Wang Eric , Chakraborty Arup K.
Published: January 2022

The rise of SARS-CoV-2 variants and the history of outbreaks caused by zoonotic coronaviruses point to the need for next-generation vaccines that confer protection against variant strains. Here, we combined analyses of diverse sequences and structures of coronavirus spikes with data from deep mutational scanning to design SARS-CoV-2 variant antigens containing the most significant mutations that may emerge. We trained a neural network to predict RBD expression and ACE2 binding from sequence, which allowed us to determine that these antigens are stable and bind to ACE2. Thus, they represent viable variants. We then used a computational model of affinity maturation (AM) to study the antibody response to immunization with different combinations of the designed antigens. The results suggest that immunization with a cocktail of the antigens is likely to promote evolution of higher titers of antibodies that target SARS-CoV-2 variants than immunization or infection with the wildtype virus alone. Finally, our analysis of 12 coronaviruses from different genera identified the S2’ cleavage site and fusion peptide as potential pan-coronavirus vaccine targets.

Author Summary

SARS-CoV-2 variants have already emerged and future variants may pose greater threats to the efficacy of current vaccines. Rather than using a reactive approach to vaccine development that would lag behind the evolution of the virus, such as updating the sequence in the vaccine with a current variant, we sought to use a proactive approach that predicts some of the mutations that could arise that could evade current immune responses. Then, by including these mutations in a new vaccine antigen, we might be able to protect against those potential variants before they appear. Toward this end, we used various computational methods including sequence analysis and machine learning to design such antigens. We then used simulations of antibody development, and the results suggest that immunization with our designed antigens is likely to result in an antibody response that is better able to target SARS-CoV-2 variants than current vaccines. We also leveraged our sequence analysis to suggest that a particular site on the spike protein could serve as a useful target for a pan-coronavirus vaccine.
The monosialoganglioside GM1a protects trophoblasts, erythrocytes and endothelial cells against complement attack
Authors: Wedekind Henri , Beimdiek Julia , Rossdam Charlotte , Kats Elina , Wittek Vanessa , Schumann Lisa , Tiede Andreas , Buettner Falk F. R. , Weinhold Birgit , Münster-Kühnel Anja , Abeln Markus
Published: January 2022

The complement system is a part of the innate immune system in the fluid phase and efficiently eliminates pathogens. However, its activation requires tight regulation on the host cell surface in order not to compromise cellular viability. Previously, we showed that loss of placental cell surface sialylation in mice in vivo leads to a maternal complement attack at the fetal-maternal interface, ultimately resulting in loss of pregnancy. To gain insight into the regulatory function of sialylation in complement activation, we here generated trophoblast stem cells devoid of sialylation, which also revealed complement sensitivity and cell death in vitro. Glycolipid-analysis by xCGE-LIF allowed us to identify the monosialoganglioside GM1a as a key element of cell surface complement regulation. Exogenously administered GM1a integrated into the plasma membrane of trophoblasts, dramatically increased binding of complement factor H and was sufficient to protect the cells from complement attack and cell death. Furthermore, GM1a treatment rescued sensitized human erythrocytes and endothelial cells from complement attack in a concentration dependent manner. This study demonstrates for the first time the complement regulatory potential of exogenously administered gangliosides and paves the way for sialoglycotherapeutics as a novel substance class for membrane-targeted complement regulators.

Key points

The naturally occurring sialic acid containing glycosphingolipid GM1a is a potent regulator of complement activation on mammalian trophoblast, erythrocyte and endothelial cell surfaces.

Incorporated GM1a recruits complement factor H and thus could represent a novel membrane-targeted complement therapeutic.
Initial assessment of the spatial learning, reversal, and sequencing task capabilities of knock- in rats with humanizing mutations in the Aβ-coding region of App
Authors: Pham Hoa , Yin Tao , D’Adamio Luciano
Published: January 2022

Model organisms mimicking the pathogenesis of human diseases are useful for identifying pathogenic mechanisms and testing therapeutic efficacy of compounds targeting them. Models of Alzheimer’s disease and related dementias aim to reproduce the brain pathology associated with these neurodegenerative disorders. Transgenic models, which involve random insertion of disease-causing genes under the control of artificial promoters, are efficient means of doing so. There are confounding factors associated with transgenic approaches, however, including target gene overexpression, dysregulation of endogenous gene expression at transgenes’ integration sites, and limitations in mimicking loss-of-function mechanisms. Furthermore, the choice of species is important, and there are anatomical, physiological, and cognitive reasons for favoring the rat over the mouse, which has been the standard for models of neurodegeneration and dementia. We report an initial assessment of the spatial learning, reversal, and sequencing task capabilities of knock-in Long-Evans rats with humanizing mutations in the Aβ-coding region of App, which encodes amyloid precursor protein (Apph/h rats), using the IntelliCage, an automated operant social home cage system, at 6-8 weeks of age, then again at 4-5 months of age. These rats were previously generated as control organisms for studies on neurodegeneration involving other knock-in rat models from our lab. Apph/h rats of either sex can acquire place learning and reversal tasks. They can also acquire a diagonal sequencing task by 6-8 weeks of age, but not a more advanced serial reversal task involving alternating diagonals, even by 4-5 months of age.
Imprinted genes Cdkn1c and Igf2 interact to promote terminal differentiation of adult NSCs
Authors: Lozano-Ureña Anna , Jiménez-Villalba Esteban , Lázaro-Carot Laura , Montalbán-Loro Raquel , Martínez-Gurrea Irene , Nakayama Keiichi , Kirstein Martina , Ferrón Sacri R.
Published: January 2022

Genomic imprinting is implicated in the control of gene dosage in neurogenic niches. Insulin-like growth factor 2 (Igf2), is an imprinted gene that shows biallelic expression only in the vascular compartment contributing to neural stem cells (NSCs) maintenance in the subventricular zone (SVZ) niche. The effects of this factor in adult NSCs differentiation are not well defined. We show here that IGF2 promotes cell fate commitment of NSCs by inducing the expression of another imprinted gene, the maternally expressed gene cyclin-dependent kinase inhibitor 1c (Cdkn1c), which encodes for p57 protein, eliciting cell cycle exit and terminal differentiation into astrocytes, neurons and oligodendrocytes. Using a conditional mouse model with Cdkn1c-deficient neural progenitors, we confirm that IGF2 and p57 interact in a common pathway to regulate the differentiation program of adult NSCs. This occurs through a mechanism involving the PI3K-Akt pathway that mediates regulation of p57 expression. We also show that the imprinted state of the Cdkn1c gene is not altered after IGF2 treatment confirming maternal expression of the gene in NSCs. Our results identify a molecular mechanism by which a paracrine factor produced and secreted by the neurogenic niche compartment can modulate Cdkn1c dosage to trigger differentiation of adult NSCs.
plotsr: Visualising structural similarities and rearrangements between multiple genomes
Authors: Goel Manish , Schneeberger Korbinian
Published: January 2022

Third-generation genomic technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands for new tools for visualising their structural properties. Here we present plotsr, an efficient tool to visualize structural similarities and rearrangements between multiple genomes. It can be used to compare genomes on chromosome level or to zoom in on any selected region. In addition, plotsr can augment the visualisation with regional identifiers (e.g. genes or genomic markers) or histogram tracks for continuous features (e.g. GC content or polymorphism density).

Availability and implementation

plotsr is implemented as a python package and uses the standard matplotlib library for plotting. It is freely available under the MIT license at GitHub (https://github.com/schneebergerlab/plotsr) and bioconda (https://anaconda.org/bioconda/plotsr).

Contact

Manish Goel (manish.goel@lmu.de), Korbinian Schneeberger (k.schneeberger@lmu.de)
Genomics-based annotations help unveil the molecular composition of edible plants
Authors: Ofaim Shany , Menichetti Giulia , Sebek Michael , Barabási Albert László
Published: January 2022

Given the important role food plays in health and well-being, the past decades have seen considerable experimental efforts dedicated to mapping the chemical composition of food ingredients. As the composition of raw food is genetically predetermined, here we ask, to what degree can we rely on genome-associated metabolic annotations to predict the chemical composition of natural ingredients? To that end, we developed an approach to unveil the chemical composition of 75 edible plants’ genomes, finding that genome-associated functional annotations substantially increase the number of compounds linked to specific plants. To account for the gap between the metabolic potential represented by functional annotations and the compounds likely to be accumulated and detected experimentally, we employed a predictive thermodynamic feasibility approach to systematically identify compounds that are likely to accumulate in plants. To quantify the accuracy of our predictions, we performed untargeted metabolomics on 13 plants, allowing us to experimentally confirm the detectability of the predicted compounds. For example, we observed 59 potentially novel compounds predicted and experimentally detected in corn. Our study shows that the application of genome-associated functional annotations can lead to an integrated metabologenomics platform capable of unveiling the chemical composition of edible plants and the biochemical pathways responsible for the observed compounds.

Author Summary

Nutrition and well-being take a central role in today’s high pace life, but how much do we really know about the food we eat? Here, we harness existing metabolic knowledge encrypted in staple food ingredients’ genome to help us explore the composition of raw edible plants. We first show the benefit and value of looking into genome-associated functional annotations on a wide scale. Next, we rely on new experimental data to develop a framework that helps us reveal new, potentially bioactive compounds in staple food ingredients. This has significance in, first, extending current food composition knowledge and second in discovering newly detected bioactive compounds, shedding light on the potential impacts of common food ingredients beyond their nutritional value as described in food labels. Finally, we show that staple foods that are already included in our daily diets might have the potential to contribute to our well-being.
Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes
Authors: Aherrahrou Rédouane , Lue Dillon , Perry R Noah , Aberra Yonathan Tamrat , Khan Mohammad Daud , Soh Joon Yuhl , Örd Tiit , Singha Prosanta , Gilani Huda , Benavente Ernest Diez , Wong Doris , Hinkle Jameson , Ma Lijiang , Sheynkman Gloria M , den Ruijter Hester M , Miller Clint L , Björkegren Johan LM , Kaikkonen Minna U , Civelek Mete
Published: January 2022

Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies (GWAS) have identified over 175 loci associated with CAD. The majority of these loci are in non-coding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we hypothesized that a subset of the CAD GWAS risk loci are associated with the regulation of transcription in distinct SMC phenotypes. Here, we measured gene expression in SMCs isolated from the ascending aortas of 151 ethnically diverse heart transplant donors in quiescent or proliferative conditions and calculated the association of their expression and splicing with ∼6.3 million imputed single nucleotide polymorphism (SNP) markers across the genome. We identified 4,910 expression and 4,412 splice quantitative trait loci (sQTL) that represent regions of the genome associated with transcript abundance and splicing. 3,660 of the eQTLs had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 of the eQTLs were SMC- and sex-specific, respectively. To identify the effector transcript(s) regulated by CAD GWAS loci, we used four distinct colocalization approaches and identified 84 eQTL and 164 sQTLs that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. Two CAD loci colocalized with a SMC sex-specific eQTL (AL160313.1 and TERF2IP) and another locus colocalized with SMC-specific eQTL (ALKBH8). Also, 27% and 37% of the sQTLs were unique to quiescent or proliferative SMCs, respectively. The most significantly associated CAD locus, 9p21, was an sQTL for the long non-coding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. Collectively, these results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.
Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins
Authors: Sadeghi Mohsen
Published: January 2022

Peripheral membrane-associated proteins are known to accumulate on the surface of biomembranes as result of membrane-mediated interactions. For a pair of rotationally-symmetric curvature-inducing proteins, membrane mechanics at the low-temperature limit predicts pure repulsion. On the other hand, temperature-dependent entropic forces arise between pairs of stiff-binding proteins suppressing membrane fluctuations. These Casimir-like interactions have thus been suggested as candidates for attractive force leading to aggregation. With dense assemblies of peripheral proteins on the membrane, both these abstractions encounter multi-body complications. Here, we make use of a particle-based membrane model augmented with flexible peripheral proteins to quantify purely membrane-mediated interactions and investigate their underlying nature. We introduce a continuous reaction coordinate corresponding to the progression of protein aggregation. We obtain free energy and entropy landscapes for different surface concentrations along this reaction coordinate. In parallel, we investigate time-dependent estimates of membrane entropy corresponding to membrane undulations and coarse-grained tilt field and how they also change dynamically with protein aggregation. Congruent outcomes of the two approaches point to the conclusion that for low surface concentrations, interactions with an entropic nature may drive the aggregation. But at high concentrations, energetic contributions due to concerted membrane deformation by protein clusters are dominant.
Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA
Authors: Navarro Isabela Cunha , Suen Kin Man , Bensaddek Dalila , Tanpure Arun , Lamond Angus , Balasubramanian Shankar , Miska Eric A.
Published: January 2022

Methylation of carbon-5 of cytosines (m5C) is a post-transcriptional nucleotide modification of RNA with widespread distribution across organisms. m5C has been shown to participate in mRNA transport and maintain mRNA stability through its recognition by the reader proteins ALYREF and YBX1, respectively. We recently showed that m5C is required for Caenorhabditis elegans development and fertility under heat stress. To contribute to the understanding of how m5C and its oxidative derivatives mediate their functions, we developed RNA baits bearing modified cytosines in diverse structural contexts to pulldown potential readers in C. elegans. Our mass spectrometry analyses reveal unique binding proteins for each of the modifications. We validate our dataset by demonstrating that the nematode ALYREF homologues ALY-1 and ALY-2 preferentially bind m5C in vitro. The dataset presented here serves as an important scientific resource that will support the discovery of new functions of m5C and its derivatives.
Functional wetland loss drives emerging risks to waterbird migration networks
Authors: Donnelly J. Patrick , Moore Johnnie N. , Casazza Michael L. , Coons Shea P.
Published: January 2022

Migratory waterbirds (i.e., shorebirds, wading birds, and waterfowl) rely on a diffuse continental network of wetland habitats to support annual life cycle needs. Emerging threats of climate and land-use change raise new concerns over the sustainability of these habitat networks as water scarcity triggers cascading ecological effects impacting wetland habitat availability. Here we use important waterbird regions in Oregon and California, USA, as a model system to examine patterns of landscape change impacting wetland habitat networks in western North America. Wetland hydrology and flooded agricultural habitats were monitored monthly from 1988 to 2020 using satellite imagery to quantify the timing and duration of inundation—a key delimiter of habitat niche values associated with waterbird use. Trends were binned by management practice and wetland hydroperiods (semi-permanent, seasonal, and temporary) to identify differences in their climate and land-use change sensitivity. Wetland results were assessed using 33 waterbird species to detect nonlinear effects of network change across a diversity of life cycle and habitat needs. Pervasive loss of semi-permanent wetlands was an indicator of systemic functional decline. Shortened hydroperiods caused by excessive drying transitioned semi-permanent wetlands to seasonal and temporary hydrologies—a process that in part counterbalanced concurrent seasonal and temporary wetland losses. Expansion of seasonal and temporary wetlands associated with closed-basin lakes offset wetland declines on other public and private lands, including wildlife refuges. Diving ducks, black terns, and grebes exhibited the most significant risk of habitat decline due to semi-permanent wetland loss that overlapped important migration, breeding, molting, and wintering periods. Shorebirds and dabbling ducks were beneficiaries of stable agricultural practices and top-down processes of functional wetland declines that operated collectively to maintain habitat needs. Outcomes from this work provide a novel perspective of wetland ecosystem change affecting waterbirds and their migration networks. Understanding the complexity of these relationships will become increasingly important as water scarcity continues to restructure the timing and availability of wetland resources.
Cannabidiol increases gramicidin current in human embryonic kidney cells: An observational study
Authors: Ghovanloo Mohammad-Reza , Goodchild Samuel J. , Ruben Peter C.
Published: January 2022

Gramicidin is a monomeric protein that is thought to non-selectively conduct cationic currents and water. Linear gramicidin is considered an antibiotic. This function is considered to be mediated by the formation of pores within the lipid membrane, thereby killing bacterial cells. The main non-psychoactive active constituent of the cannabis plant, cannabidiol (CBD), has recently gained interest, and is proposed to possess various potential therapeutic properties, including being an antibiotic. We previously determined that CBD’s activity on ion channels could be, in part, mediated by altering membrane biophysical properties, including elasticity. In this study, our goal was to determine the empirical effects of CBD on gramicidin currents in human embryonic kidney (HEK) cells, seeking to infer potential direct compound-protein interactions. Our results indicate that gramicidin, when applied to the extracellular HEK cell membrane, followed by CBD perfusion, increases the gramicidin current.
Two roles for choice selective inhibition in decision-making circuits
Authors: Roach James P. , Churchland Anne K. , Engel Tatiana A.
Published: January 2022

During perceptual decision-making, the firing rates of cortical neurons reflect upcoming choices. Recent work showed that excitatory and inhibitory neurons are equally selective for choice. However, functional consequences of inhibitory choice selectivity in decision-making circuits are unknown. We developed a circuit model of decision-making which accounts for the specificity of inputs to and outputs from inhibitory neurons. We found that selective inhibition expands the space of circuits supporting decision-making, allowing for weaker or stronger recurrent excitation when connected in a competitive or feedback motif. The specificity of inhibitory outputs sets the trade-off between speed and accuracy of decisions by altering the attractor dynamics in the circuit. Recurrent neural networks trained to make decisions display the same dependence on inhibitory specificity and the strength of recurrent excitation. Our results reveal two concurrent roles for selective inhibition in decision-making circuits: stabilizing strongly connected excitatory populations and maximizing competition between oppositely selective populations.
Single cell sequencing reveals microglia induced angiogenesis by specific subsets of endothelial cells following spinal cord injury
Authors: Yao Chun , Cao Yuqi , Lv Yehua , Wang Dong , Liu Yan , Gu Xiaosong , Wang Yongjun , Wang Xuhua , Yu Bin
Published: January 2022

Spinal cord injury (SCI) results in dynamic alterations of the microenvironment at the lesion site, which inevitably leads to neuron degeneration and functional deficits. The prominent deterioration of the milieu, derived from the destruction of spinal vascular system, not only activates innate immunity but also makes cells in the lesion lose nutrient supports. Limited endogenous angiogenesis happens after SCI, but the cell events at the lesion site underpinning this process have not been delineated so far. Here, we conducted single-cell RNA sequencing (scRNA-seq) of tissues in the spinal lesion at different time points after rat SCI. After performing clustering and cell-type identification, we focused on the vascular endothelial cells (ECs), which play a pivot role in angiogenesis, and drew a comprehensive cellular and molecular atlas for endogenous angiogenesis after SCI. We found that microglia and macrophage promote endogenous angiogenesis by regulating EC subsets through SPP1 and IGF1 signal pathways. Our results indicated that immune cells promotes angiogenesis by the regulation of specific cell subsets of vascular ECs, which provides new clues for the development of interventions for SCI.
High throughput RNA sequencing discovers symptomatic and latent viruses: an example from ornamental Hibiscus
Authors: Zhou Shuyu , Richert-Pöggeler Katja R. , Wang Ziwei , Schwarzacher Trude , Heslop-Harrison J.S. (Pat) , Liu Qing
Published: January 2022

Hibiscus rosa-sinensis L. (Hibiscus, Malvaceae) is an ornamental species grown widely in amenity plantings. We collected leaves on an urban roadside pavement (sidewalk) near a market in Guangzhou which showed multiple symptoms of leaf rolling, deformation and chlorosis. Initial evaluation by electron microscopy using negative staining of drip preparations revealed the presence of tobamovirus-like particles. Total RNA was extracted, and, unusually, without any RNA selection based on sequence, was used for cDNA library construction and high-throughput survey sequencing. From the 814 Mb of clean sequence data (from 2,712,161 paired reads of 150 bp) reads representing chloroplast, ribosomal, and mitochondrial genes were filtered out, eliminating 79.1% of reads. 1,135,848 × 150 bp of the sequence was retained and screened for viral sequences. Assembly of these sequences detected nine virus species from seven virus genera comprising three tobamoviruses, namely, Tobacco mosaic virus, Tobacco mild green mosaic virus and Hibiscus latent Singapore virus, Turnip mosaic virus (Potyvirus), Potato virus M (Carlavirus), Hibiscus chlorotic ringspot virus (Betacarmovirus), Fabavirus sp (Fabavirus), Cotton leaf curl Multan virus (Begomovirus) and a putative mitoviruses replicating in mitochondria, Chenopodium quinoa mitovirus 1. Mapping the reads to complete virus reference sequences showed high and uniform coverage of the genomes from 3,729 x coverage for Turnip mosaic virus to 22 x for Cotton leaf curl Multan virus. By comparison, nuclear reference genes actin showed 14 x coverage and polyubiquitin 27 x. Notable variants from reference sequences (SNPs) were identified. With the low cost of sequencing and potential for semi-automated bioinformatic pipelines, the whole-RNA approach has huge potential for identifying multiple undiagnosed viruses in ornamental plants, resulting in the ability to take preventive measures in production facilities against spread and to product quality for the mutual benefit of producers and consumers.
The curious case of green human resource management practices in the Ghanaian manufacturing industry; a reality or a mirage?
Authors: Suleman Abdul-Razak , Amponsah-Tawiah Kwesi , Adu Isaac Nyarko , Boakye Kwame Owusu
Published: January 2022

Purpose

Based on the legitimacy theory, this study sought to explore specific Green Human Resource Management Practices implemented by manufacturing firms in Ghana.

Design/methodology/approach

The study purposively sourced data from five manufacturing firms operating in Ghana, specifically, Cocoa Processing Company, Dannex Aryton Starwin PLC, Fan Milk Limited, Guinness Ghana Breweries Limited and Unilever Ghana PLC. The qualitative data from 10 interviewees were thematically analysed.

Findings

Pervasively, it was evident that Ghanaian manufacturing firms have integrated environmental concerns into their human resource management functions, hence they place more emphasis on online tools and platforms in attracting, selecting, involving, training, paying and managing the performance of employees. Lastly, manufacturing firms operating in Ghana give priority to online job applications ahead of manual applications.

Practical implications

In an era of sustainability, green human resource management practices provide a basis for the legitimation and sustenance of businesses through enhanced environmental performance and its resultant corporate image.

Originality/value

The study highlights the extent to which green human resource management is practised in a Sub-Saharan African country and the specific practices adopted in promoting the concept.
Pharmacological interventions to diminish cognitive side effects of electroconvulsive therapy: A systematic review and meta‐analysis
Authors: Verdijk Joey P.A.J. , van Kessel Mike A. , Oud Matthijs , Kellner Charles H. , Hofmeijer Jeannette , Verwijk Esmée , van Waarde Jeroen A.
Published: January 2022

Objective

The authors conducted a systematic review and meta‐analysis of pharmacological interventions to diminish cognitive side effects of ECT.

Methods

Electronic databases of Pubmed, PsycInfo, Embase and Scopus were searched from inception through 1 April, 2021, using terms for ECT (e.g. electroconvulsive therapy), cognitive outcome (e.g. cogni*) and pharmacological intervention (e.g. calcium channel blocker and general terms, like protein). Original studies with humans receiving ECT were included, which applied pharmacological interventions in comparison with placebo or no additive intervention to diminish cognitive side effects. Data quality was assessed using Risk of Bias and GRADE. Random‐effects models were used. PROSPERO registration number was CRD42021212773.

Results

Qualitative synthesis (systematic review) showed 52 studies reporting sixteen pharmacological intervention‐types. Quantitative synthesis (meta‐analysis) included 26 studies (1387 patients) describing twelve pharmacological intervention‐types. Low‐quality evidence of efficacy was established for memantine (large effect size) and liothyronine (medium effect size). Very low‐quality evidence shows effect of acetylcholine inhibitors, piracetam and melatonin in some cognitive domains. Evidence of no efficacy was revealed for ketamine (very low‐quality), herbal preparations with anti‐inflammatory properties (very low to low‐quality) and opioid receptor agonists (low‐quality).

Conclusion

Memantine and liothyronine are promising for further research and future application. Quality of evidence was low because of differences in ECT techniques, study populations and cognitive measurements. These findings provide a guide for rational choices of potential pharmacological intervention research targets to decrease the burden of cognitive side effects of ECT. Future research should be more uniform in design and attempt to clarify pathophysiological mechanisms of cognitive side effects of ECT.
The quality and readability of online molar incisor hypomineralization patient education materials: a systematic analysis
Authors: Meade MJ , Dreyer CW
Published: January 2022

Background

Molar incisor hypomineralization (MIH) is estimated to affect 14% of children worldwide. It is crucial that patients and their families have access to easily comprehensible and reliable MIH‐relevant information. This study aims to determine the quality, reliability and readability of online patient education materials about MIH.

Methods

A systematic search strategy was adopted. Five validated tools were used to assess the content of the 21 websites that satisfied inclusion/exclusion criteria. Data analyses were applied via GraphPad Prism software version 9 (GraphPad Software, San Diego, CA, USA).

Results

Five (23.8%) websites only satisfied the criteria for understandability and two (9.5%) websites satisfied the criteria for actionability using the Patient Education Materials Assessment Tool (PEMAT). No website contained the Health on the Net (HON)Code Seal and the mean (SD) Journal of the American Medical Association number of benchmarks per website was 1.33/4 (1.02). All websites failed to reach recommended minimum readability levels. Higher PEMAT scores were associated with ‘easier’ readability.

Conclusions

Online patient education materials related to MIH are lacking in quality and reliability, and are too difficult for most to read easily. The authors of MIH‐related online content should consider reference to quality of information tools when developing patient education materials.
Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene‐doping detection considering the presence of pseudogenes
Authors: Tozaki Teruaki , Ohnuma Aoi , Kikuchi Mio , Ishige Taichiro , Kakoi Hironaga , Hirota Kei‐ichi , Kusano Kanichi , Nagata Shun‐ichi
Published: January 2022

Processed pseudogenes, also known as retrocopy genes, are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome. In this study, we identified 62 processed pseudogene candidates as intron‐less genes from whole‐genome sequencing (WGS) data of Thoroughbred horses using delly structural variation software. The 62 processed pseudogene candidates were confirmed by PCR amplification of intron‐less products. A total of 11 processed pseudogenes were confirmed in the genome of all 23 analysed horses, whereas three processed pseudogenes with structures of ATP11B, DPH3 and RPL17 were detected in only one of 115 horses by PCR amplification of intron‐less products. Currently, most of the gene doping tests proposed in human and horse sports are adapted PCR‐based methods using hydrolysis probes to detect exon/exon junctions in transgenes because the operation is simple and economical. However, when the pseudogene is present in the host genome, the PCR‐based methods may have a potential risk of detecting false positives. In this study, because processed pseudogenes that exist less frequently in the horse genome may affect PCR‐based transgene detection in gene‐doping tests, we propose and demonstrate that PCR amplification and sequencing using primers designed on transgene and promotors and/or polyadenylation signal for gene expression are useful for gene‐doping detection as an additional confirmatory test to prevent false positives.
Association of Apgar score at 5 minutes with academic performance and intelligence in youth: A cohort study
Authors: Ladelund Agnes Kielgast , Bruun Frederik Jager , Slavensky Julie Anna , Ladelund Steen , Kesmodel Ulrik Schiøler
Published: January 2022

Introduction

The Apgar score is routinely given at childbirth worldwide. A low Apgar score at 5 minutes is a strong predictor for neonatal death. Scores below 7 have been associated with higher risks of later neurologic disability. Few studies have assessed the association between Apgar score and school performance and intelligence. The existing literature points towards a possible association between Apgar score and later cognitive function, but the contradictions call for further investigation to fully understand the potential association. This study aimed to examine the possible association between Apgar score at 5 minutes and academic performance and intelligence in youth.

Material and methods

The study is a cohort study. The cohort consists of all Danish liveborn children in 1978–2000 (n = 1 450 681). Data regarding pregnancies, births, parents, school grades, and intelligence of the children were retrieved from different Danish registers. Multiple imputations were performed to avoid discarding data. After exclusion, the final cohort consisted of 1 005 241 children. Associations between Apgar score at 5 minutes and school graduation, grades and attendance, and intelligence scores from conscription were analyzed using univariate and multivariate logistic and linear regressions.

Results

No association was found between Apgar score and graduating primary school. Adjusted odds ratio (aOR) of graduating upper secondary education and attending conscription were significantly lower for children with scores below 7 compared with 7–10: graduating upper secondary education: Apgar 0–3: aOR 0.79 (95% CI 0.67–0.93), Apgar 4–6: aOR 0.86 (95% CI 0.81–0.93), attending conscription: Apgar 0–3: aOR 0.73 (95% CI 0.59–0.91), Apgar 4–6: aOR 0.73 (95% CI 0.66–0.80). The Apgar 4–6 group had significantly lower total mean primary school grade average: −0.13 (95% CI −0.21 to −0.054) and lower mean intelligence scores at conscription: −0.57 (95% CI −1.09 to −0.058). All other differences remained insignificant.

Conclusions

Performances when graduating school and attending conscription were overall equal regardless of Apgar score at 5 minutes. Chances of graduating primary school were the same irrespective of the score, but chances of graduating upper secondary education and attending conscription were significantly lower with scores below 7. The results suggest that children with scores below 7 may fail to appear at upper secondary education and conscription, but if they do, they perform equally to anyone else.
1013. TANACETUM DENSUM subsp. AMANI
Authors: Hind Nicholas , Strange Kit , King Christabel
Published: January 2022

Tanacetum densum (Labill.) Sch.Bip. subsp. amani Heywood (Compositae: Anthemideae: Anthemidinae) is illustrated and described. Notes on cultivation, propagation, pests and diseases and availability are provided. The position of Tanacetum in the tribe Anthemideae is discussed, as well as the size of the genus, and previous treatment of many of the species in Pyrethrum. The homonymy of Pyrethrum Zinn is outlined, and the likely position of P. bidens Medik. is discussed: a position in either Acmella or Spilanthes, in the tribe Heliantheae, is proposed. The phytochemistry of Tanacetum densum subsp. amani is discussed.
On the influence of environmental factors on the oviposition activity of necrophagous flies
Authors: Lutz Lena , Verhoff Marcel A. , Rosenbaum Tabea , Amendt Jens
Published: January 2022

1. Locating an optimal oviposition site can be a challenging task for female insects, especially when dealing with a patchy, unpredictable and ephemeral food source such as carrion. Understanding the biotic and abiotic parameters that influence the oviposition behaviour of necrophagous flies is not just of great biological importance but also essential for their application in legal investigations.

2. In this study, we monitored the oviposition activity of necrophagous flies (Calliphoridae, Sarcophagidae) using mouse carcasses in an urban (city) and a rural (mixed forest) habitat in Frankfurt/Germany over a 2‐year period.

3. Over 240 sampling days, 220,963 larvae of 4 blow fly species and 1 flesh fly were sampled. The most abundant species was the blow fly Lucilia ampullacea, followed by its family members Calliphora vicina and Lucilia caesar, the flesh fly Sarcophaga caerulescens and Lucilia sericata. Up to seven environmental parameters were statistically significant predictors for a colonisation of the carcasses, leading to unique patterns of seasonal and daily oviposition activity for all five species.

4. Overall, the analysis showed that the seasonal adaption (the phenology of each species), the habitat (rural vs. urban) as well as temperature are the most important factors influencing the oviposition behaviour and activity of necrophagous blow flies and flesh flies.