bluuebunny/crossref_metadata_2025 huggingface dataset:
The effect of external lateral stabilization on energy cost of walking – A systematic review and meta-analysis
Authors: Mahaki Mohammadreza , Hoozemans Marco J M , Houdijk Han , van Dieën Jaap H. , Bruijn Sjoerd M
Published: September 2021

Previous studies have estimated the energy cost required for the control of medio-lateral stability in human walking by means of external lateral stabilization. Results were inconsistent, possibly due to differences in task constraints or stabilization devices. To better understand the effects of lateral stabilization on energy cost, we conducted a systematic review with meta-analysis of studies, which directly assessed effects of lateral stabilization on energy cost in healthy young adult participants (18-41 years old). We obtained individual participant data on net energy cost (J kg-1 m-1) from previously published studies. Across all studies reviewed, the net energy cost reduction during stabilized walking at preferred and zero step widths equaled to 0.05 ± 0.35 (~2-3% reduction) and 0.25 ± 0.29 J kg-1 m-1 (mean ± s.d.) (~8-9% reduction), respectively. The effect of external lateral stabilization was significant only for walking at zero step width and without arm swing. Lateral stabilization devices with short rope length increased energy cost reduction. However, spring stiffness and habituation time did not influence energy cost reduction. We provide recommendations for improvement of lateral stabilization devices to avoid some of the confounding effects. External lateral stabilization reduces energy cost during walking by a small amount. It can be concluded that a small proportion of total energy cost is required to control medio-lateral stability; this proportion is larger when walking with narrow steps and without arm swing.
Differentially optimized cell-free buffer enables robust expression from unprotected linear DNA in exonuclease-deficient extracts
Authors: Batista Angelo Cardoso , Levrier Antoine , Soudier Paul , Voyvodic Peter L. , Achmedov Tatjana , Reif-Trauttmansdorff Tristan , DeVisch Angelique , Gonsaud Martin Cohen , Faulon Jean-Loup , Beisel Chase L. , Bonnet Jerome , Kushwaha Manish
Published: September 2021

The use of linear DNA templates in cell-free systems promises to accelerate the prototyping and engineering of synthetic gene circuits. A key challenge is that linear templates are rapidly degraded by exonucleases present in cell extracts. Current approaches tackle the problem by adding exonuclease inhibitors and DNA-binding proteins to protect the linear DNA, requiring additional time- and resource-intensive steps. Here, we delete the recBCD exonuclease gene cluster from the Escherichia coli BL21 genome. We show that the resulting cell-free systems, with buffers optimized specifically for linear DNA, enable near-plasmid levels of expression from σ70 promoters in linear DNA templates without employing additional protection strategies. When using linear or plasmid DNA templates at the buffer calibration step, the optimal potassium glutamate concentrations obtained when using linear DNA were consistently lower than those obtained when using plasmid DNA for the same extract. We demonstrate the robustness of the exonuclease deficient extracts across seven different batches and a wide range of experimental conditions across two different laboratories. Finally, we illustrate the use of the ΔrecBCD extracts for two applications: toehold switch characterization and enzyme screening. Our work provides a simple, efficient, and cost-effective solution for using linear DNA templates in cell-free systems and highlights the importance of specifically tailoring buffer composition for the final experimental setup. Our data also suggest that similar exonuclease deletion strategies can be applied to other species suitable for cell-free synthetic biology.
Transcriptome-informed reduction of protein databases: an analysis of how and when proteogenomics enhances eukaryotic proteomics
Authors: Fancello Laura , Burger Thomas
Published: September 2021

Background

Proteogenomics aims to identify variant or unknown proteins in bottom-up proteomics, by searching transcriptome- or genome-derived custom protein databases. However, empirical observations reveal that these large proteogenomic databases produce lower-sensitivity peptide identifications. Various strategies have been proposed to avoid this, including the generation of reduced transcriptome-informed protein databases (i.e., built from reference protein databases only retaining proteins whose transcripts are detected in the sample-matched transcriptome), which were found to increase peptide identification sensitivity. Here, we present a detailed evaluation of this approach.

Results

First, we established that the increased sensitivity in peptide identification is in fact a statistical artifact, directly resulting from the limited capability of target-decoy competition to accurately model incorrect target matches when using excessively small databases. As anti-conservative FDRs are likely to hamper the robustness of the resulting biological conclusions, we advocate for alternative FDR control methods that are less sensitive to database size. Nevertheless, reduced transcriptome-informed databases are useful, as they reduce the ambiguity of protein identifications, yielding fewer shared peptides. Furthermore, searching the reference database and subsequently filtering proteins whose transcripts are not expressed reduces protein identification ambiguity to a similar extent, but is more transparent and reproducible.

Conclusion

In summary, using transcriptome information is an interesting strategy that has not been promoted for the right reasons. While the increase in peptide identifications from searching reduced transcriptome-informed databases is an artifact caused by the use of an FDR control method unsuitable to excessively small databases, transcriptome information can reduce ambiguity of protein identifications.
Ustilago maydis telomere protein Pot1 harbors an extra N-terminal OB fold and regulates homology-directed DNA repair factors in a dichotomous and context-dependent manner
Authors: Zahid Syed , Aloe Sarah , Sutherland Jeanette H. , Holloman William K. , Lue Neal F.
Published: September 2021

The telomere G-strand binding protein Pot1 plays multifaceted roles in telomere maintenance and protection. We examined the structure and activities of Pot1 in Ustilago maydis, a fungal model that recapitulates key features of mammalian telomere regulation. Compared to the well-characterized primate and fission yeast Pot1 orthologs, UmPot1 harbors an extra N-terminal OB-fold domain (OB-N), which was recently shown to be present in most metazoans. UmPot1 binds directly to Rad51 and regulates the latter’s strand exchange activity. Deleting the OB-N domain, which is implicated in Rad51-binding, caused telomere shortening, suggesting that Pot1-Rad51 interaction facilitates telomere replication. Depleting Pot1 through transcriptional repression triggered growth arrest as well as rampant recombination, leading to multiple telomere aberrations. In addition, telomere repeat RNAs transcribed from both the G- and C-strand were dramatically up-regulated, and this was accompanied by elevated levels of telomere RNA-DNA hybrids. Telomere abnormalities of pot1-deficient cells were suppressed, and cell viability was restored by the deletion of genes encoding Rad51 or Brh2 (the BRCA2 ortholog), indicating that homology-directed repair (HDR) proteins are key mediators of telomere aberrations and cellular toxicity. Together, these observations underscore the complex physical and functional interactions between Pot1 and DNA repair factors, leading to context-dependent and dichotomous effects of HDR proteins on telomere maintenance and protection.
Three-dimensional label-free histological imaging of whole organs by microtomy-assisted autofluorescence tomography
Authors: Zhang Yan , Kang Lei , Yu Wentao , Tsang Victor Tsz Chun , Wong Terence T. W.
Published: September 2021

Three-dimensional (3D) histology is vitally important to characterize disease-induced tissue heterogeneity at the individual cell level. However, it remains a scientific challenge for both high-quality 3D imaging and volumetric reconstruction. Here we propose a label-free, automated, and ready-to-use 3D histological imaging technique, termed microtomy-assisted autofluorescence tomography with ultraviolet excitation (MATE). With the combination of block-face imaging and serial microtome sectioning, MATE can achieve rapid and label-free imaging of paraffin-embedded whole organs at an acquisition speed of 1 cm3 per 4 hours with a voxel resolution of 1.2 × 1.2 × 10 μm3. We demonstrate that MATE enables simultaneous visualization of cell nuclei, fiber tracts, and blood vessels in mouse/human brains without tissue staining or clearing. Moreover, diagnostic features, such as nuclear size and packing density, can be quantitatively extracted with high accuracy. MATE is augmented to the current slide-based 2D histology, holding great promise for facilitating histopathological interpretation at the cell level to analyze complex tissue heterogeneity in 3D.

Significance Statement

Conventional 3D histology based on spatial registration of serial histochemically-stained thin tissue slices is fundamentally labor-intensive and inaccurate. Here, we propose a rapid and label-free 3D histological imaging technique (i.e., MATE) that enables high-resolution imaging of complex whole organs without tissue staining or clearing. MATE is fully automated to provide a series of distortion- and registration-free images with intrinsic absorption-based contrast, demonstrating great potential as a routine tissue analysis tool that can seamlessly fit into the current clinical practice to facilitate the applications of histopathological interpretation at the subcellular level.
Motivations, concerns and selection biases when posting preprints: a survey of bioRxiv authors
Authors: Fraser Nicholas , Mayr Philipp , Peters Isabella
Published: September 2021

Since 2013, the usage of preprints as a means of sharing research in biology has rapidly grown, in particular via the preprint server bioRxiv. Recent studies have found that journal articles that were previously posted to bioRxiv received a higher number of citations or mentions/shares on other online platforms compared to articles in the same journals that were not posted. However, the exact causal mechanism for this effect has not been established, and may in part be related to authors’ biases in the selection of articles that are chosen to be posted as preprints. We aimed to investigate this mechanism by conducting a mixed-methods survey of 1,444 authors of bioRxiv preprints, to investigate the reasons that they post or do not post certain articles as preprints, and to make comparisons between articles they choose to post and not post as preprints. We find that authors are most strongly motivated to post preprints to increase awareness of their work and increase the speed of its dissemination; conversely, the strongest reasons for not posting preprints centre around a lack of awareness of preprints and reluctance to publicly post work that has not undergone a peer review process. We additionally find weak evidence that authors preferentially select their highest quality, most novel or most significant research to post as preprints, however, authors retain an expectation that articles they post as preprints will receive more citations or be shared more widely online than articles not posted.
Honest cues contribute to male choice for female guarding in a herbivorous spider mite
Authors: Goossens Steven F. , Mortier Frederik , Parmentier Thomas , Batsleer Femke , Van Leeuwen Thomas , Wybouw Nicky , Bonte Dries
Published: September 2021

Mate choice is a wide-spread phenomenon with important effects on ecological and evolutionary dynamics of successive generations. Increasing evidence shows that males can choose females if females vary in quality and these mating choices can strongly impact fitness. In the herbivorous spider mite Tetranychus urticae males engage in precopulatory mate guarding of quiescent females, and it is known that females vary in their time to sexual maturity and fecundity. However, our understanding of how males maximize their reproductive success and which female phenotypic traits are important cues for their mating decisions are still limited. In many arthropod species, female body size and pheromones are well known proxies for fecundity. These traits—and thus possibly male mating decisions—are however sensitive to environmental (dietary) stress. By allowing males to freely choose amongst many (synchronized) females in a controlled semi natural environment, we found that guarded females have a higher fecundity and are closer to sexual maturity than non-guarded females. Despite the fact that female body size was positively correlated with fecundity and significantly influenced by the environment, males did not discriminate on body size nor did we find evidence that they used other cues like cuticular pheromones or copying behavior (social cues). In conclusion we were able to show male mate preference for females that are closer to sexual maturity and have higher fecundity, but we were unable to identify the female traits that signal this information
Improved Docking of Protein Models by a Combination of Alphafold2 and ClusPro
Authors: Ghani Usman , Desta Israel , Jindal Akhil , Khan Omeir , Jones George , Hashemi Nasser , Kotelnikov Sergey , Padhorny Dzmitry , Vajda Sandor , Kozakov Dima
Published: September 2021

It has been demonstrated earlier that the neural network based program AlphaFold2 can be used to dock proteins given the two sequences separated by a gap as the input. The protocol presented here combines AlphaFold2 with the physics based docking program ClusPro. The monomers of the model generated by AlphaFold2 are separated, re-docked using ClusPro, and the resulting 10 models are refined by AlphaFold2. Finally, the five original AlphaFold2 models are added to the 10 AlphaFold2 refined ClusPro models, and the 15 models are ranked by their predicted aligned error (PAE) values obtained by AlphaFold2. The protocol is applied to two benchmark sets of complexes, the first based on the established protein-protein docking benchmark, and the second consisting of only structures released after May 2018, the cut-off date for training AlphaFold2. It is shown that the quality of the initial AlphaFold2 models improves with each additional step of the protocol. In particular, adding the AlphaFold2 refined ClusPro models to the AlphaFold2 models increases the success rate by 23% in the top 5 predictions, whereas considering the 10 models obtained by the combined protocol increases the success rate to close to 40%. The improvement is similar for the second benchmark that includes only complexes distinct from the proteins used for training the neural network.
Selective activation of BK channels in small-headed dendritic spines suppresses excitatory postsynaptic potentials
Authors: Tazerart Sabrina , Blanchard Maxime G. , Miranda-Rottmann Soledad , Mitchell Diana E. , Pina Bruno Navea , Thomas Connon I. , Kamasawa Naomi , Araya Roberto
Published: September 2021

Dendritic spines are the main receptacles of excitatory information in the brain. Their particular morphology, with a small head connected to the dendrite by a slender neck, has inspired theoretical and experimental work to understand how these structural features affect the processing, storage and integration of synaptic inputs in pyramidal neurons (PNs).

The activation of glutamate receptors in spines triggers a large voltage change as well as calcium signals at the spine head. Thus, voltage-gated and calcium-activated potassium channels located in the spine head likely play a key role in synaptic transmission. Here we study the presence and function of large conductance calcium-activated potassium (BK) channels in spines from layer 5 PNs. We find that BK channels are localized to dendrites and spines regardless of their size, but their activity can only be detected in spines with small head volumes (≤ 0.09 µm3), which reduces the amplitude of two-photon (2P) uncaging (u) excitatory postsynaptic potentials (EPSPs) recorded at the soma. In addition, we find that calcium signals in spines with small head volumes are significantly larger than those observed in spines with larger head volumes. In accordance with our experimental data, numerical simulations predict that synaptic inputs impinging onto spines with small head volumes generate voltage responses and calcium signals within the spine head itself that are significantly larger than those observed in spines with bigger head volumes, which are sufficient to activate spine BK channels. These results show that BK channels are selectively activated in small-headed spines, suggesting a new level of dendritic spine-mediated regulation of synaptic processing, integration, and plasticity in cortical PNs.
CBEA: Competitive balances for taxonomic enrichment analysis
Authors: Nguyen Quang P. , Hoen Anne G. , Frost H. Robert
Published: September 2021

Research in human associated microbiomes often involves the analysis of taxonomic count tables generated via high-throughput sequencing. It is difficult to apply statistical tools as the data is high-dimensional, sparse, and compositional. An approachable way to alleviate high-dimensionality and sparsity is to aggregate variables into pre-defined sets. Set-based analysis is ubiquitous in the genomics literature, and has demonstrable impact in improving interpretability and power of downstream analysis. Unfortunately, there is a lack of sophisticated set-based analysis methods specific to microbiome taxonomic data, where current practice often employs abundance summation as a technique for aggregation. This approach prevents comparison across sets of different sizes, does not preserve inter-sample distances, and amplifies protocol bias. Here, we attempt to fill this gap with a new single sample taxon enrichment method that uses a novel log-ratio formulation based on the competitive null hypothesis commonly used in the enrichment analysis literature. Our approach, titled competitive balances for taxonomic enrichment analysis (CBEA), generates sample-specific enrichment scores as the scaled log ratio of the subcomposition defined by taxa within a set and the subcomposition defined by its complement. We provide sample-level significance testing by estimating an empirical null distribution of our test statistic with valid p-values. Herein we demonstrate using both real data applications and simulations that CBEA controls for type I error even under high sparsity and high inter-taxa correlation scenarios. Additionally, it provides informative scores that can be inputs to downstream analyses such as prediction tasks.

Author summary

The study of human associated microbiomes relies on genomic surveys via high-throughput sequencing. However, microbiome taxonomic data is sparse and high dimensional which prevents the application of standard statistical techniques. One approach to address this problem is to perform analyses at the level of taxon sets. Set-based analysis has a long history in the genomics literature, with demonstrable impact in improving both power and interpretability. Unfortunately, there is limited interest in developing new set-based tools tailored for microbiome taxonomic data given its unique features compared to other ‘omics data types. We developed a new tool to generate taxon set enrichment scores at the sample level through a novel log-ratio formulation based on the competitive null hypothesis. Our scores can be used for statistical inference at both the sample and population levels, as well as inputs to other downstream analyses such as prediction models. We demonstrate the performance of our method against competing approaches across both real data analyses and simulation studies.
Neurophysiological evidence for cognitive map formation during sequence learning
Authors: Stiso Jennifer , Lynn Christopher W. , Kahn Ari E. , Rangarajan Vinitha , Szymula Karol P. , Archer Ryan , Revell Andrew , Stein Joel M. , Litt Brian , Davis Kathryn A. , Lucas Timothy H. , Bassett Dani S.
Published: September 2021

Humans deftly parse statistics from sequences. Some theories posit that humans learn these statistics by forming cognitive maps, or underlying representations of the latent space which links items in the sequence. Here, an item in the sequence is a node, and the probability of transitioning between two items is an edge. Sequences can then be generated from walks through the latent space, with different spaces giving rise to different sequence statistics. Individual or group differences in sequence learning can be modeled by changing the time scale over which estimates of transition probabilities are built, or in other words, by changing the amount of temporal discounting. Latent space models with temporal discounting bear a resemblance to models of navigation through Euclidean spaces. However, few explicit links have been made between predictions from Euclidean spatial navigation and neural activity during human sequence learning. Here, we use a combination of behavioral modeling and intracranial encephalography (iEEG) recordings to investigate how neural activity might support the formation of space-like cognitive maps through temporal discounting during sequence learning. Specifically, we acquire human reaction times from a sequential reaction time task, to which we fit a model that formulates the amount of temporal discounting as a single free parameter. From the parameter, we calculate each individual’s estimate of the latent space. We find that neural activity reflects these estimates mostly in the temporal lobe, including areas involved in spatial navigation. Similar to spatial navigation, we find that low dimensional representations of neural activity allow for easy separation of important features, such as modules, in the latent space. Lastly, we take advantage of the high temporal resolution of iEEG data to determine the time scale on which latent spaces are learned. We find that learning typically happens within the first 500 trials, and is modulated by the underlying latent space and the amount of temporal discounting characteristic of each participant. Ultimately, this work provides important links between behavioral models of sequence learning and neural activity during the same behavior, and contextualizes these results within a broader framework of domain general cognitive maps.
Arg-tRNA synthetase links inflammatory metabolism to RNA splicing and nuclear trafficking via SRRM2
Authors: Cui Haissi , Diedrich Jolene K. , Wu Douglas C. , Lim Justin J. , Nottingham Ryan M. , Moresco James J. , Yates John R. , Blencowe Benjamin J. , Lambowitz Alan M. , Schimmel Paul
Published: September 2021

Cells respond to perturbations like inflammation by sensing changes in metabolite levels. Especially prominent is arginine, which has known connections to the inflammatory response. Here, we found that depletion of arginine during inflammation decreased levels of a nuclear form of arginyl-tRNA synthetase (ArgRS). Surprisingly, we found that nuclear ArgRS interacts with serine/arginine repetitive matrix protein 2 (SRRM2), a spliceosomal protein and nuclear speckle component and that arginine depletion impacted both condensate-like nuclear trafficking of SRRM2 and splice-site usage in certain genes. These splice-site usage changes cumulated in synthesis of different protein isoforms that altered cellular metabolism and peptide presentation to immune cells. Our findings uncover a novel mechanism whereby a tRNA synthetase cognate to a key amino acid that is metabolically controlled during inflammation modulates the splicing machinery.
Cumulative effects of mutation and selection on susceptibility to bacterial pathogens inCaenorhabditis elegans
Authors: Saber Sayran , Johnson Lindsay M. , Rifat Md. Monjurul Islam , Rouse Sydney , Baer Charles F.
Published: September 2021

Understanding the evolutionary and genetic underpinnings of susceptibility to pathogens is of fundamental importance across a wide swathe of biology. Much theoretical and empirical effort has focused on genetic variants of large effect, but pathogen susceptibility often appears to be a polygenic complex trait. Here we investigate the quantitative genetics of survival over 120 hours of exposure ("susceptibility") ofC. elegansto three bacterial pathogens of varying virulence, along with the standard laboratory food, the OP50 strain ofE. coli. We compare the genetic (co)variance input by spontaneous mutations accumulated under minimal selection to the standing genetic (co)variance in a set of 47 wild isolates. Three conclusions emerge. First, mutations increase susceptibility to pathogens, and susceptibility is uncorrelated with fitness in the absence of pathogens. Second, the orientation in trait space of the heritable (co)variance of wild isolates is sufficiently explained by mutation. However, with the possible exception ofS. aureus, pathogen susceptibility is clearly under purifying, directional, selection of magnitude roughly similar to that of competitive fitness in the MA conditions. The results provide no evidence for fitness tradeoffs between pathogen susceptibility and fitness in the absence of pathogens.
Canopy health, but not Candidatus Liberibacter asiaticus Ct values, are correlated with fruit yield in Huanglongbing affected sweet orange trees
Authors: Levy Amit , Livingston Taylor , Wang Chunxia , Achor Diann , Vashisth Tripti
Published: September 2021

In Florida, almost all citrus trees are infected with Huanglongbing (HLB), caused by the gram-negative, intracellular phloem limited bacteria Candidatus liberibacter asiaticus (CLas). Distinguishing between the severely and mildly sick trees is important for managing the groves and testing new HLB therapies. A mildly sick tree is one that produces higher fruit yield, compared to a severely sick tree, but measuring yields is laborious and time consuming. Here we characterized HLB affected sweet orange trees in the field in order to identify the specific traits that are correlated with the yields. We found that canopy volume, fruit detachment force (FDF) and the percentage of photosynthetically active radiation interception in the canopy (%INT) were positively correlated with fruit yields. Specifically, %INT measurements accurately distinguished between mild and severe trees in independent field trials. We could not find a difference in the Ct value between high and low producing HLB trees. Moreover, Ct values did not always agree with the number of CLas in the phloem that were visualized by transmission electron microscopy. Overall, our work identified an efficient way to distinguish between severe and mild HLB trees in Florida by measuring %INT and suggests that health of the canopy is more important for yields than the Ct value.
Antidepressant Sertraline Hydrochloride Inhibits the Growth of HER2+ AU565 Breast Cancer Cell Line through Induction of Apoptosis, and Arrest of Cell Cycle
Authors: Wahab Atia-tul- , Fayyaz Sharmeen , Irshad Rimsha , Siddiqui Rafat A. , Rahman Atta-ur- , Choudhary M. Iqbal
Published: September 2021

Breast cancer is one the most aggressive cancer worldwide, especially Pakistan due to limited therapeutic options. This study was conducted to repurpose the use of selective serotonin reuptake inhibitors (SSRIs), in the treatment of breast cancers, and merit to pursue drug re-positioning in oncology. Anti-proliferative activity of SSRIs, such as fluoxetine, paroxetine, and sertraline hydrochloride on the growth of AU-565, MCF-7, MDA-MB-231, and BT-474 breast cancer cell lines, along with human fibroblast BJ cells was determined in vitro. Changes in nuclear morphology (DAPI staining), and induction of apoptosis (flow cytometry, and caspase-3 activation) were also studied. Sertraline hydrochloride most effectively inhibited the growth of breast cancer cells in vitro. Therefore, pharmacological mechanism involved in sertraline mediated cell death was investigated in HER2+ AU565 cell line. Enhanced nuclear fragmentation, increased Annexin (+) cells, and caspase-3/7 activation indicated that sertraline-mediated cell death could be a result of BCl2-independent apoptosis as evidenced by expression of Bax, and BCl2 genes. Taken together, our results identified sertraline hydrochloride, as a potential candidate for the treatment of HER2-positive breast cancer. Even though these are in vitro results, this study opens great opportunity in the field of drug repurposing for the development of chemotherapeutic agents.
Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex
Authors: Liu Shuang , Won Hyejung , Clarke Declan , Matoba Nana , Khullar Saniya , Mu Yudi , Wang Daifeng , Gerstein Mark
Published: September 2021

Psychiatric disorders exact immense human and economic tolls in societies globally. Underlying many of these disorders is a complex repertoire of genomic variants that influence the expression of genes involved in pathways and processes in the brain. Identifying such variants and their associated brain functions is thus essential for understanding the molecular underpinnings of psychiatric disorders. Genome-wide association studies (GWASes) have provided many variants associated with these disorders; however, our knowledge of the precise biological mechanisms by which these contribute to disease remains limited. In connection with this, expression quantitative trait loci (eQTLs) have provided useful information linking variants to genes and functions. However, most eQTL studies on human brain have focused exclusively on cis-eQTLs. A complete understanding of disease etiology should also include trans-regulatory mechanisms. Thus, we conduct one of the first genome-wide surveys of trans-eQTLs in the dorsolateral prefrontal cortex (DLPFC) by leveraging the large datasets from the PsychENCODE consortium. We identified ∼80,000 trans-eQTLs. We found that a significant number of these overlap with cis-eQTLs, thereby implicating cis-mediators as key players in trans-acting regulation. We show, furthermore, that trans-regulatory mechanisms provide novel insights into psychiatric disease. Particularly, colocalization analysis between trans-eQTLs and schizophrenia (SCZ) GWAS loci identified 90 novel SCZ risk genes and 23 GWAS loci previously uncharacterized by cis-eQTLs. Moreover, these 90 genes tend to be more central in transcriptome-wide co-expression networks and more susceptible to rare variants than SCZ-risk genes associated by cis-variation.
The activation of a Suv39h1-repressive antisense lncRNA by OCT4 couples the control of H3K9 methylation to pluripotency
Authors: Bernard Laure D. , Dubois Agnès , Heurtier Victor , Chervova Almira , Tachtsidi Alexandra , Gil Noa , Owens Nick , Vandormael-Pournin Sandrine , Ulitsky Igor , Cohen-Tannoudji Michel , Navarro Pablo
Published: September 2021

Histone H3 Lysine 9 (H3K9) methylation, a characteristic mark of heterochromatin, is progressively implemented during development to contribute to cell fate restriction as differentiation proceeds. For instance, in pluripotent mouse Embryonic Stem (ES) cells the global levels of H3K9 methylation are rather low and increase only upon differentiation. Conversely, H3K9 methylation represents an epigenetic barrier for reprogramming somatic cells back to pluripotency. How global H3K9 methylation levels are coupled with the acquisition and loss of pluripotency remains largely unknown. Here, we identify SUV39H1, a major H3K9 di- and tri-methylase, as an indirect target of the pluripotency network of Transcription Factors (TFs). We find that pluripotency TFs, principally OCT4, activate the expression of an uncharacterized antisense long non-coding RNA to Suv39h1, which we name Suv39h1as. In turn, Suv39h1as downregulates Suv39h1 transcription in cis via a mechanism involving the modulation of the chromatin status of the locus. The targeted deletion of the Suv39h1as promoter region triggers increased SUV39H1 expression and H3K9me2 and H3K9me3 levels, leading to accelerated and more efficient commitment into differentiation. We report, therefore, a simple genetic circuitry coupling the global levels of H3K9 methylation to pluripotency in mouse ES cells.
Tafazzin deficiency in mouse mesenchymal stem cells potentiates their immunosuppression and impairs activated B lymphocyte immune function
Authors: Zegallai Hana M. , Abu-El-Rub Ejlal , Olayinka-Adefemi Folayemi , Cole Laura K. , Sparagna Genevieve C. , Marshall Aaron J. , Hatch Grant M.
Published: September 2021

Barth Syndrome (BTHS) is a rare X-linked genetic disorder caused by mutation in the TAFAZZIN gene which encodes the cardiolipin (CL) transacylase tafazzin (Taz). Taz deficiency in BTHS patients results in reduced CL in their tissues and a neutropenia which contributes to the risk of infections. However, the impact of Taz deficiency in other cells of the immune system is poorly understood. Mesenchymal stem cells (MSCs) are well known for their immune inhibitory function. We examined whether Taz-deficiency in murine MSCs impacted their ability to modulate lipopolysaccharide (LPS)-activated wild type (WT) murine B lymphocytes. MSCs from tafazzin knockdown (TazKD) mice exhibited a 50% reduction in CL compared to wild type (WT) MSCs. However, mitochondrial oxygen consumption rate and membrane potential were unaltered. In contrast, TazKD MSCs exhibited increased glycolysis compared to WT MSCs and this was associated with elevated proliferation, phosphatidylinositol-3-kinase expression and expression of the immunosuppressive markers indoleamine-2,3-dioxygenase, cytotoxic T-lymphocyte-associated protein 4, interleukin-10, and cluster of differentiation 59. When co-cultured with LPS-activated WT B cells, TazKD MSCs inhibited B cell proliferation and growth rate and reduced B cell secretion of IgM to a greater extent than B cells co-cultured with WT MSCs. In addition, co-culture of LPS-activated WT B cells with TazKD MSCs induced B cell differentiation toward potent immunosuppressive phenotypes including interleukin-10 secreting plasma cells and B regulatory cells compared to activated B cells co-cultured with WT MSCs. These results indicate that Taz deficiency in MSCs enhances MSCs-mediated immunosuppression of activated B lymphocytes.
Effects of bacterial lipopolysaccharide and Shiga Toxin on induced Pluripotent Stem Cell-derived Mesenchymal Stem Cells
Authors: Martire-Greco Daiana , La Greca Alejandro , Castillo Montañez Luis , Biani Celeste , Lombardi Antonella , Birnberg-Weiss Federico , Norris Alessandra , Sacerdoti Flavia , Amaral María Marta , Rodrigues-Rodriguez Nahuel , Pittaluga José Ramón , Furmento Verónica Alejandra , Landoni Verónica Inés , Miriuka Santiago Gabriel , Luzzani Carlos D , Fernández Gabriela Cristina
Published: September 2021

Background: Mesenchymal Stem Cells can be activated and respond to different bacterial toxins. Lipopolysaccharides (LPS) and Shiga Toxin (Stx) are the two main bacterial toxins present in Hemolytic Uremic Syndrome (HUS) that cause endothelial damage. In this work we aimed to study the response of iPSC-MSC to LPS and/or Stx and its effect on the restoration of injured endothelial cells. Methods: iPSC-MSC were used as a source of mesenchymal stem cells (MSC) and Human Microvascular Endothelial Cells-1 (HMEC-1) as a source of endothelial cells. iPSC-MSC were treated or not with LPS and or/Stx. For some experiments, Conditioned Media (CM) were collected from each plate and incubated with an anti-Stx antibody to block the direct effect of Stx, or Polymyxin to block the direct effect of LPS. In CM from both treatments, anti-Stx and Polymyxin were used. Results are expressed as mean ± S.E.M. Significant differences (p<0.05) were identified using one way analysis of variance (ANOVA) and Bonferroni's Multiple comparison test. Results: The results obtained showed that LPS induced a pro-inflammatory profile on iPSC-MSC, but not Stx, even though they expressed Gb3 receptor. Moreover, LPS induced on iPSC-MSC an increment in migration and adhesion to gelatin substrate. Also, the addition of CM of iPSC-MSC treated with LPS+Stx, decreased the capacity of HMEC-1 to close a wound, and did not favor the formation of new tubes. Proteomic analysis of iPSC-MSC treated with LPS and/or Stx revealed specific protein secretion patterns that support many of the functional results described here. Conclusions: In conclusion, these results suggest that iPSC-MSC activated by LPS acquired a pro-inflammatory profile that induces migration and adhesion to extracellular matrix proteins (ECM), but the combination LPS+Stx decreased the repair of endothelial damage. The importance of this work is that it provides knowledge to understand the context in which iPSC-MSC could benefit or not the restoration of tissue injury, taking into account that the inflammatory context in response to a particular bacterial toxin is relevant for iPSC-MSC immunomodulation.
Magnetic fluctuations affect circadian patterns of locomotor activity in zebrafish
Authors: Krylov Viacheslav V. , Izvekov Evgeny I. , Pavlova Vera V. , Pankova Natalia A. , Osipova Elena A.
Published: September 2021

The locomotor activity of zebrafish (Danio rerio) has a pronounced, well-studied circadian rhythm. Under constant illumination, the period of free-running locomotor activity in this species usually becomes less than 24 hours. To evaluate the entraining capabilities of slow magnetic variations, zebrafish locomotor activity was evaluated at constant illumination and fluctuating magnetic field with a period of 26.8 hours. Lomb-Scargle periodogram revealed significant free-running rhythms of locomotor activity and related behavioral endpoints with a period close to 27 hours. Obtained results reveal the potential of slow magnetic fluctuations for entrainment of the circadian rhythms in zebrafish. The putative mechanisms responsible for the entrainment are discussed, including the possible role of cryptochromes.
Crystal structure of a constitutive active mutant of adenosine A2A receptor
Authors: Cui Min , Zhou Qingtong , Weng Yuan , Yao Deqiang , Zhao Suwen , Song Gaojie
Published: September 2021

Previously we reported a common activation pathway of the class A G protein-coupled receptors (GPCRs) in which a series of conserved residues/motifs undergo conformational change during extracellular agonist binding and finally induce the coupling of intracellular G protein, and successfully predicted several novel constitutive active or inactive mutations for A2A adenosine receptor (A2AAR) through this mechanism (Zhou et al., 2019). Here we determined the crystal structure of a typical A2AAR constitutive active mutant I92N in complex with agonist UK-432097 to reveal the molecular mechanism of mutation-induced constitutive activity. The mutated I92N forms a hydrophilic interaction network with nearby residues including W6.48 of the CWxP motif, which is absent in the wild type A2AAR. Although the mutant structure is overall similar to the previously determined intermediate state A2AAR structure (PDB ID: 3QAK), the molecular dynamics simulations suggested that the I92N mutant stabilizes the metastable intermediate state through the hydrophilic interaction network and favors the receptor conformational transition towards the active state. This research provides a structural template toward the special pharmacological outcome triggered by conformational mutation and sheds light on future structural or pharmacological studies among class A GPCRs.
cDNA display coupled with next-generation sequencing for rapid activity-based screening: Comprehensive analysis of transglutaminase substrate preference
Authors: Damnjanović Jasmina , Odake Nana , Fan Jicheng , Jia Beixi , Kojima Takaaki , Nemoto Naoto , Hitomi Kiyotaka , Nakano Hideo
Published: September 2021

cDNA display is an in vitro display technology based on a covalent linkage between a protein and its corresponding mRNA/cDNA, where a stable complex is formed suitable for a wide range of selection conditions. A great advantage of cDNA display is the ability to handle enormous library size (1012) in a microtube scale, in a matter of days. To harness its benefits, we aimed at developing a platform which combines the advantages of cDNA display with high-throughput and accuracy of next-generation sequencing (NGS) for the selection of preferred substrate peptides of transglutaminase 2 (TG2), a protein cross-linking enzyme. After the optimization of the platform by the repeated screening of binary model libraries consisting of the substrate and non-substrate peptides at different ratios, screening and selection of combinatorial peptide library randomized at positions -1, +1, +2, and +3 from the glutamine residue was carried out. Enriched cDNA complexes were analyzed by NGS and bioinformatics, revealing the comprehensive amino acid preference of the TG2 at targeted positions of the peptide backbone. This is the first report on the cDNA display/NGS screening system to yield comprehensive data on TG substrate preference. Although some issues remain to be solved, this platform can be applied to the selection of other TGs and easily adjusted for the selection of other peptide substrates and even larger biomolecules.
Stress corrosion cracking of A517 steel in marine environments
Authors: Chen Lin , Yang Huisheng , Su Yanjing , Qiao Lijie
Published: September 2021

Purpose

The purpose of this study is to develop the existence and mechanism of stress corrosion cracking (SCC) for A517 steel in marine environments.

Design/methodology/approach

Slow strain rate test (SSRT) and constant load tests were used to investigate the SCC susceptibility of A517 steel. In addition, the additive stresses caused by the corrosion film and hydrogen entering into steel were applied to reveal the fundamental mechanism of the SCC.

Findings

The SCC susceptibility increased due to anodic dissolution and additive stress caused by the corrosion-produced film under anode polarization. Furthermore, the SCC susceptibility increased with increasing cathodic polarization, which is due to the increased additional stress caused by hydrogen entering into the steel. However, when the cathode polarization further increased, the additional stress remained due to the constant hydrogen content, thus the SCC susceptibility did not vary. Moreover, the SCC susceptibility of A517 steel under an alternate immersion environment (AIE) was lower than that under a full immersion environment and the steel under the AIE with 0.5 W/D had the lowest SCC susceptibility.

Originality/value

The stress corrosion behaviors of A517 in marine environments under various conditions were systematically analyzed.
Predicting the response and perforation of fibre metal laminates subjected to projectile impact
Authors: Liu Y.J. , Wang Z.H. , Wen H.M.
Published: September 2021

Purpose

The purpose of this paper is to predict the response and perforation of fibre metal laminates (FMLs) subjected to impact by projectiles at different velocities.

Design/methodology/approach

A finite element (FE) model is constructed in which recently proposed dynamic constitutive models for fibre reinforced plastic (FRP) laminates and metals are used. Moreover, a recently developed dynamic cohesive element constitutive model is also used to simulate the debonding between FRP laminates and metal sheets. The FE model is first validated against the test data for glass laminate aluminum reinforced epoxy (GLARE) both under dropped object loading and ballistic impact, then used to perform a parametric study on the influence of projectile nose shape on the perforation of FMLs.

Findings

It is found that the present model predicts well the response and perforation of GLARE subjected to impact loading in terms of load-time history, load-displacement curve, residual velocity and failure pattern. It is also found that projectile nose shape has a considerable effect on the perforation of GLARE FMLs and that the ballistic limit is the highest for a flat-ended projectile whilst for a conical-nosed missile the resistance to perforation is the least.

Originality/value

Recently developed constitutive models for FRPs and metals, together with cohesive element model which considers strain rate effect, are used in the FE model to predict the behaviour of FMLs struck by projectiles in a wider range of impact velocities; the present model is advantageous over such existing models as Johnson-Cook (JC) + Chang-Chang and JC (+BW) + MAT162 in terms of failure pattern though they produce similar results for residual velocity.
Estimation of the virtual masses of a large unconventional airship based on purely analytical method to aid in the preliminary design
Authors: Chaabani Said , Azouz Naoufel
Published: September 2021

Purpose

This paper presents preliminary results of the modeling of a large autonomous quad-rotor airship, with flying wing shape. This airship is supposed to be a flexible body. This study promotes an entirely analytical methodology with some assumptions. In this study and as first assumption, the shape of the careen is supposed to be an elliptic cone. To retrieve the velocity potential shapes, this paper solved the Laplace’s equation by using the sphero-conal coordinates. This leads to the Lamé’s equations. The whole system equations governing the interaction of air–structure, including the boundary conditions, is solved in an analytical setting.

Design/methodology/approach

This paper opted for a modeling and determination of the added masses of a flexible airship by an analytical method illustrated by a comparison with a geometric method. This analytical method includes the study of complex functions which are the Lamé functions.

Findings

This paper provides an analytical way to estimate an aerodynamic phenomenon which acts on the airship and in particular on its envelope and known as the phenomenon of added masses or virtual masses, as well as the means of defining it and the calculation analytically for the case of the flexible airship.

Research limitations/implications

Considering that the calculation of the added masses is very difficult and the numerical methods increase the number of degrees of freedom, the analytical method established in this paper has become a solution of calculations of these virtual masses.

Practical implications

This paper includes an application for determining the added masses of a new generation MC500 airship.

Originality/value

This paper allows defining an analytical method which determines the added masses of an airship, which helps the automation engineer to develop a control strategy to stabilize this airship.