bluuebunny/crossref_metadata_2025 huggingface dataset:
Autism excitation-inhibition imbalance linked to brain hyperconnectivity: An analysis based on 657 autistic subjects
Authors: Rasero Javier , Jimenez-Marin Antonio , Diez Ibai , Toro Roberto , Hasan Mazahir T. , Cortes Jesus M.
Published: July 2022

The large heterogeneity in autism spectrum disorder (ASD) is a major drawback for the development of therapies. Here, we apply consensus-subtyping strategies based on functional connectivity patterns to a population of N=657 quality-assured autistic subjects. We found two major subtypes (each divided hierarchically into several minor subtypes): Subtype 1 exhibited hypoconnectivity (less average connectivity than typically developing controls) and subtype 2, hyperconnectivity. The two subtypes did not differ in structural imaging metrics in any of the regions analyzed (64 cortical and 14 subcortical), nor in any of the behavioral scores (including Intelligence Quotient, ADI and ADOS). Finally, we used the Allen Human Brain Atlas of gene transcription to show that subtype 2, corresponding with about 42% of all patients, had significant enrichment (after multiple comparisons correction) to excitation-inhibition (E/I) imbalance, a leading reported mechanism in the developmental pathophysiology of ASD. Altogether, our results support a link between E/I imbalance and brain hyperconnectivity in ASD, an association that does not exist in hypoconnected autistic subjects.
Identifiability analysis and noninvasive online estimation of the first-order neural activation dynamics in the brain with closed-loop transcranial magnetic stimulation
Authors: Alavi Seyed Mohammad Mahdi , Mahdi Adam , Vila-Rodriguez Fidel , Goetz Stefan M
Published: July 2022

Background

Neurons demonstrate very distinct nonlinear activation dynamics, influenced by the neuron type, morphology, ion channel expression, and various other factors. The measurement of the activation dynamics can identify the neural target of stimulation and detect deviations, e.g., for diagnosis. This paper describes a tool for closed-loop sequential parameter estimation (SPE) of the activation dynamics through transcranial magnetic stimulation (TMS). The proposed SPE method operates in real time, selects ideal stimulus parameters, detects and processes the response, and concurrently estimates the input–output (IO) curve and the first-order approximation of the activated neural target.

Objective

To develop a method for concurrent SPE of the first-order activation dynamics and IO curve with closed-loop TMS.

Method

First, identifiability of an integrated model of the first-order neural activation dynamics and IO curve is assessed, demonstrating that at least two IO curves need to be acquired with different pulse widths. Then, a two-stage SPE method is proposed. It estimates the IO curve by using Fisher information matrix (FIM) optimization in the first stage and subsequently estimates the membrane time constant as well as the coupling gain in the second stage. The procedure continues in a sequential manner until a stopping rule is satisfied.

Results

The results of 73 simulation cases confirm the satisfactory estimation of the membrane time constant and coupling gain with average absolute relative errors (AREs) of 6.2% and 5.3%, respectively, with an average of 344 pulses (172 pulses for each IO curve or pulse width). The method estimates the IO curves’ lower and upper plateaus, mid-point, and slope with average AREs of 0.2%, 0.7%, 0.9%, and 14.5%, respectively. The conventional time constant estimation method based on the strength-duration (S–D) curve leads to 33.3% ARE, which is 27.0% larger than 6.2% ARE obtained through the proposed real-time FIM-based SPE method in this paper.

Conclusions

SPE of the activation dynamics requires acquiring at least two IO curves with different pulse widths, which needs a controllable TMS (cTMS) device with adjustable pulse duration.

Significance

The proposed SPE method enhances the cTMS functionality, which can contribute novel insights in research and clinical studies.
DeepInsight-3D for precision oncology: an improved anti-cancer drug response prediction from high-dimensional multi-omics data with convolutional neural networks
Authors: Sharma Alok , Lysenko Artem , Boroevich Keith A , Tsunoda Tatsuhiko
Published: July 2022

Modern oncology offers a wide range of treatments and therefore choosing the best option for particular patient is very important for optimal outcomes. Multi-omics profiling in combination with AI-based predictive models have great potential for streamlining these treatment decisions. However, these encouraging developments continue to be hampered by very high dimensionality of the datasets in combination with insufficiently large numbers of annotated samples. In this study, we propose a novel deep learning-based method to predict patient-specific anticancer drug response from three types of multiomics data. The proposed DeepInsight-3D approach relies on structured data-to-image conversion that then allows use of convolutional neural networks, which are particularly robust to high dimensionality of the inputs while retaining capabilities to model highly complex relationships between variables. Of particular note, we demonstrate that in this formalism additional channels of an image can be effectively used to accommodate data from different ‘omics layers while explicitly encoding the connection between them. DeepInsight-3D was able to outperform two other state-of-the-art methods proposed for this task. These advances can facilitate the development of better personalized treatment strategies for different cancers in the future.
Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology
Authors: MacDonald Samual , Foley Helena , Yap Melvyn , Johnston Rebecca L. , Steven Kaiah , Koufariotis Lambros T. , Sharma Somwya , Wood Scott , Addala Venkateswar , Pearson John V. , Roosta Fred , Waddell Nicola , Kondrashova Olga , Trzaskowski Maciej
Published: July 2022

Trust and transparency are critical for deploying deep learning (DL) models into the clinic. DL application poses generalisation obstacles since training/development datasets often have different data distributions to clinical/production datasets that can lead to incorrect predictions with underestimated uncertainty. To investigate this pitfall, we benchmarked one pointwise and three approximate Bayesian DL models used to predict cancer of unknown primary with three independent RNA-seq datasets covering 10,968 samples across 57 primary cancer types. Our results highlight simple and scalable Bayesian DL significantly improves the generalisation of uncertainty estimation (e.g., p-value = 0.0013 for calibration). Moreover, we demonstrate Bayesian DL substantially improves accuracy under data distributional shifts when utilising ‘uncertainty thresholding’ by designing a prototypical metric that evaluates the expected (accuracy) loss when deploying models from development to production, which we call the Area between Development and Production curve (ADP). In summary, Bayesian DL is a hopeful avenue of research for generalising uncertainty, which improves performance, transparency, and therefore safety of DL models for deployment in real-world.
Rapid protein stability prediction using deep learning representations
Authors: Blaabjerg Lasse M. , Kassem Maher M. , Good Lydia L. , Jonsson Nicolas , Cagiada Matteo , Johansson Kristoffer E. , Boomsma Wouter , Stein Amelie , Lindorff-Larsen Kresten
Published: July 2022

Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate predictions of changes in protein stability by leveraging deep learning representations. RaSP performs on-par with biophysics-based methods and enables saturation mutagenesis stability predictions in less than a second per residue. We use RaSP to calculate ∼ 300 million stability changes for nearly all single amino acid changes in the human proteome, and examine variants observed in the human population. We find that variants that are common in the population are substantially depleted for severe destabilization, and that there are substantial differences between benign and pathogenic variants, highlighting the role of protein stability in genetic diseases. RaSP is freely available—including via a Web interface—and enables large-scale analyses of stability in experimental and predicted protein structures.
A role for brassinosteroid signaling in decision-making processes in the Arabidopsis seedling
Authors: Kalbfuß Nils , Strohmayr Alexander , Kegel Marcel , Le Lien , Grosseholz Friederike , Brunschweiger Barbara , Stöckl Katharina , Wiese Christian , Franke Carina , Schiestl Caroline , Prem Sophia , Sha Shuyao , Franz-Oberdorf Katrin , Hafermann Juliane , Thiemé Marc , Facher Eva , Palubicki Wojciech , Bolle Cordelia , Assaad Farhah F.
Published: July 2022

Plants often adapt to adverse conditions via differential growth, whereby limited resources are discriminately allocated to optimize the growth of one organ at the expense of another. Little is known about the decision-making processes that underly differential growth. In this study, we developed a screen to identify decision making mutants by deploying two tools that have been used in decision theory: a well-defined yet limited budget, as well as conflict-of-interest scenarios. A forward genetic screen that combined light and water withdrawal was carried out. This identified BRASSINOSTEROID INSENSITIVE 2 (BIN2) alleles as decision mutants with “confused” phenotypes. An assessment of organ and cell length suggested that hypocotyl elongation occurred predominantly via cellular elongation. In contrast, root growth appeared to be regulated by a combination of cell division and cell elongation or exit from the meristem. Brassinosteroid signalling mutants were most severely impaired in their ability to adjust cell geometry in the hypocotyl and cell elongation as a function of distance from the quiescent centre in the root tips. This study describes a novel paradigm for root growth under limiting conditions, which depends not only on hypocotyl-versus-root trade-offs in the allocation of limited resources, but also on an ability to deploy different strategies for root growth in response to multiple stress conditions.
Rare Ribosomal RNA Sequences from Archaea Stabilize the Bacterial Ribosome
Authors: Nissley Amos J. , Penev Petar I. , Watson Zoe L. , Banfield Jillian F. , Cate Jamie H. D.
Published: July 2022

Ribosomes serve as the universally conserved translators of the genetic code into proteins and must support life across temperatures ranging from below freezing to above the boiling point of water. Ribosomes are capable of functioning across this wide range of temperatures even though the catalytic site for peptide bond formation, the peptidyl transferase center, is nearly universally conserved. Peptide bond formation by the ribosome requires correct positioning of the 3’
s-end of the aminoacylated tRNA (aa-tRNA) substrate, which is aided by an RNA hairpin in the ribosomal RNA (rRNA) of the large subunit, termed the A loop. Here we find that Thermoproteota, a phylum of thermophilic Archaea, substitute cytidine for uridine at large subunit rRNA positions 2554 and 2555 (Escherichia coli numbering) in the A loop, immediately adjacent to the binding site for the 3′-end of A-site tRNA. We show by cryo-EM that E. coli ribosomes with uridine to cytidine mutations at these positions retain the proper fold and post-transcriptional modification of the A loop. Additionally, these mutations do not exert a dominant negative effect on cellular growth, protect the large ribosomal subunit from thermal denaturation, and increase the mutational robustness of nucleotides in the peptidyl transferase center. This work identifies sequence variation in the peptidyl transferase center of the archaeal ribosome that likely confers stabilization of the ribosome at high temperatures and develops a stable mutant bacterial ribosome that can act as a scaffold for future ribosome engineering efforts.
Antibiotic-tolerant persisters are pervasive among clinical Streptococcus pneumoniae isolates and show strong condition-dependence
Authors: Geerts Nele , De Vooght Linda , Passaris Ioannis , Van den Bergh Bram , Cos Paul
Published: July 2022

Streptococcus pneumoniae is an important human pathogen, being one of the most common causes of community-acquired pneumonia and otitis media. Antibiotic resistance in S. pneumoniae is an emerging problem as it depletes our arsenal of effective drugs. In addition, persistence also contributes to the antibiotic crisis in many other pathogens, yet, in S. pneumoniae nothing is known about antibiotic-tolerant persisters. Persister cells are phenotypic variants that exist as a subpopulation within a clonal culture. Being tolerant to lethal antibiotics, they underly the chronic nature of a variety of infections and even help in acquiring genetic resistance. Here, we set out to identify and characterize persistence in S. pneumoniae. Specifically, we followed different strategies to overcome the self-limiting nature of S. pneumoniae as confounding factor in the prolonged monitoring of antibiotic survival needed to study persistence. In optimized conditions, we identified genuine persisters in various growth phases and for four relevant antibiotics through biphasic survival dynamics and heritability assays. Finally, we detected a high variety in antibiotic survival levels across a diverse collection of S. pneumoniae clinical isolates, which shows that a high natural diversity in persistence is widely present in S. pneumoniae. Collectively, this proof-of-concept significantly progresses the understanding of the importance of antibiotic persistence in S. pneumoniae infections which will set stage for characterizing its relevance to clinical outcomes and advocates for increased attention to the phenotype in both fundamental and clinical research.

IMPORTANCE

S. pneumoniae is considered a serious threat by the Centers of Disease Control and Prevention through arising antibiotic resistance. In addition to resistance, bacteria can also survive lethal antibiotic treatment by developing antibiotic tolerance and more specifically by antibiotic tolerance through persistence. This phenotypic variation seems omnipresent among bacterial life, is linked to therapy failure and acts as a catalyst for resistance development. This study gives the first proof of the presence of persister cells in S. pneumoniae and shows a high variety in persistence levels among diverse strains, suggesting persistence is a general trait in S. pneumoniae cultures and that a broad range of genetic elements are controlling the phenotype. Together, our work advocates for higher interest for persistence in S. pneumoniae as a contributing factor for therapy failure and resistance development.
The difference in FRET efficiency fluctuation at each end of the actin filament
Authors: Mitani Takahiro , Mashiko Ryota , Nezasa Miku , Nishikata Ichiro , Kamimura Kenji , Honda Hajime , Fujiwara Ikuko
Published: July 2022

Actin filaments are involved in various cell motility processes. Actin polymerisation is primarily governed by monomer association and dissociation occurring at the rapid-growing end called the barbed end, which generates the force to push the plasma membrane forward. Individual actin filaments bind to one nucleotide and its hydrolysis energy is used to maintain the filamentous form by changing the characteristics of the subunits. The asymmetry of the individual actin filaments is also important for detecting the asymmetry of the cell. However, asymmetry at the subunit level including conformational and temporal changes in actin filaments has not been visualized yet. Here, we used “Förster (or fluorescence) resonance energy transfer (FRET)-actin filament” by copolymerising an equal amount of donor and acceptor labelled actin. FRET efficiency change was measured along each actin filament under a light microscope. The FRET efficiency was lower near the end region than in the interior regions. Fluctuations in the FRET efficiency (fFRET) were used to monitor local flexibilities along each actin filament. The fFRET was larger near the end region than the interior region. Our quantified data showed that spatial change of fFRET along actin filaments was rapidly decayed from the barbed end from near the pointed end toward internal region, suggesting that the behaviour of actin subunits near ends is affected from each end. Our result revealed that actin filaments have different orientations locally. These orientations appear when actin forms filaments, which may contribute the cell motility.
Regulated Degradation of the Inner Nuclear Membrane Protein SUN2 Maintains Nuclear Envelope Architecture and Function
Authors: Krshnan Logesvaran , Siu Wingyan Skyla , Van de Weijer Michael , Hayward Daniel , Guerrero Elena Navarro , Gruneberg Ulrike , Carvalho Pedro
Published: July 2022

Nuclear architecture and functions depend on dynamic interactions between nuclear components (such as chromatin) and inner nuclear membrane (INM) proteins. Mutations in INM proteins interfering with these interactions result in disease. However, mechanisms controlling the levels and turnover of INM proteins remain unknown. Here, we describe a mechanism of regulated degradation of the INM SUN domain-containing protein 2 (SUN2). We show that Casein Kinase II and the C-terminal domain Nuclear Envelope Phosphatase 1 (CTDNEP1) have opposing effects on SUN2 levels by regulating SUN2 binding to the ubiquitin ligase Skp/Cullin1/F-BoxβTrCP(SCFβTrCP). Upon binding to phosphorylated SUN2, SCFβTrCPpromotes its ubiquitination. Ubiquitinated SUN2 is membrane extracted by the AAA ATPase p97 and delivered to the proteasome for degradation. Importantly, accumulation of non-degradable SUN2 results in aberrant nuclear architecture, vulnerability to DNA damage and increased lagging chromosomes in mitosis. These findings uncover a central role of proteolysis in INM protein homeostasis.
Immunological contributions to age-dependent variations in behavioural responses to cutaneous inflammation
Authors: Dayman Emma , Bennett Andrew , Hathway Gareth J.
Published: July 2022

Systemic responses to immune challenge are immature at birth. However exposure to experimental inflammogens are able to produce an immunologic response which is characterised by swelling and oedema but, unlike in adults, does not result in sensory hypersensitivity. We sought to investigate whether the lack of nociceptive hypersensitivity was as a result of altered hemapoietic immune cell recruitment to the site of inflammation and/or differences in the cytokine and chemokine profile released by tissue invading cells. Postnatal (day of birth) and young adult (40-days old) Sprague-Dawley rats were used. Inflammation was induced by s.c. injection of Complete Freunds Adjuvant (CFA) unilaterally into the one hind paw. Mechanical withdrawal thresholds were measured before and after injection (2-168hrs). In adults a significant hyperalgesia was evoked which was absent in neonates. Immunohistochemical analysis of invading immune cells present in the perfusion fixed skin showed that although total cell numbers in the paw were the same in both age groups, neonates recruited more cells positive for both cell surface markers CD68 and Mannose-receptor (MR) whereas adults recruited significantly more cells positive for MR alone. There were no differences in neutrophil recruitment (as measured with H&E staining). TaqMan qPCR demonstrated that the temporal profile of cytokine production in the skin differed between ages with neonates responding faster than adults and that neonates produced significantly more IL-1b and IL-27 then adults who expressed significantly more IL-6 and IL-10. This study illustrates that in neonates the cell recruitment and cytokine profiles are markedly different to those seen in adults; this may in part explain why behavioural responses to inflammation are suppressed relative to adults.
Whole exome sequencing study identifies candidate loss of function variants and locus heterogeneity in familial cholesteatoma
Authors: Cardenas Ryan , Prinsley Peter , Philpott Carl , Bhutta Mahmood F , Wilson Emma , Brewer Daniel S. , Jennings Barbara A.
Published: July 2022

Cholesteatoma is a rare progressive disease of the middle ear. Most cases are sporadic, but some patients report a positive family history. Identifying functionally important gene variants associated with this disease has the potential to uncover the molecular basis of cholesteatoma pathology with implications for disease prevention, surveillance, or management.

We performed an observational WES study of 21 individuals treated for cholesteatoma who were recruited from ten multiply affected families. These family studies were complemented with gene-level mutational burden analysis. We also applied functional enrichment analyses to identify shared properties and pathways for candidate genes and their products.

Filtered data collected from pairs and trios of participants within the ten families revealed 398 rare, loss of function (LOF) variants co-segregating with cholesteatoma in 389 genes. We identified six genesDENND2C, DNAH7, NBEAL1, NEB, PRRC2C, andSHC2, for which we found LOF variants in two or more families. The parallel gene-level of mutation-burden identified a significant mutation burden for the genes in theDNAHgene family, which encode products involved in ciliary structure. Functional enrichment analyses identified common pathways for the candidate genes which included GTPase regulator activity, calcium ion binding, and degradation of the extracellular matrix.

The number of candidate genes identified and the locus heterogeneity that we describe within and between multiply affected families suggest that the genetic architecture for familial cholesteatoma is complex.
Differentiating interactions of antimicrobials with Gram-negative and Gram-positive bacterial cell walls using molecular dynamics simulations
Authors: Vaiwala Rakesh , Sharma Pradyumn , Ayappa K. Ganapathy
Published: July 2022

Developing molecular models to capture the complex physicochemical architecture of the bacterial cell wall and to study the interaction with antibacterial molecules is an important aspect of assessing and developing novel antimicrobial molecules. We carried out molecular dynamics simulations using an atomistic model of peptidoglycan (PGN) to represent the architecture for Gram-positive Staphylococcus aureus. The model is developed to capture various structural features of the staphylococcal cell wall, such as the peptide orientation, area per disaccharide, glycan length distribution, crosslinking, and pore size. A comparison of the cell wall density and electrostatic potentials is made with a previously developed cell wall model of Gram-negative bacteria, Escherichia coli, and properties for both a single and multilayered structures of the Staphylococcal cell wall are studied. We investigated the interactions of the antimicrobial peptide melittin with the PGN structures. The depth of melittin binding to PGN is more pronounced in E. coli than S. aureus, and consequently the melittin has greater contacts with glycan units of E. coli. Contacts of melittin with the amino acids of peptidoglycan are comparable across both the strains, and the D-Ala residues, which are sites for transpeptidation, show enhanced interactions with melittin. A low energetic barrier is observed for translocation thymol with the four-layered peptidoglycan model. The molecular model developed for Gram-positive PGN allows us to compare and contrast the cell wall penetrating properties with Gram-negative strains and assess for the first time binding and translocation of antimicrobial molecules for Gram-positive cell walls.
Novel exotic alleles of EARLY FLOWERING 3 determine plant development in barley
Authors: Zahn Tanja , Zhu Zihao , Ritoff Niklas , Krapf Jonathan , Junker Astrid , Altmann Thomas , Schmutzer Thomas , Tüting Christian , Kastritis Panagiotis L. , Babben Steve , Quint Marcel , Pillen Klaus , Maurer Andreas
Published: July 2022

EARLY FLOWERING 3(ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation which will be substantial for future plant breeding. To expand the limited knowledge on barleyELF3in determining agronomic traits, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at theELF3locus, were compared for ten developmental and yield-related traits. We determine novel exoticELF3alleles and show that HIF lines, carrying the exoticELF3allele, accelerated plant development compared to the cultivatedELF3allele, depending on the genetic background. Remarkably, the most extreme phenotypic effects could be attributed to one exoticELF3allele, differing in only one SNP from the cultivated BarkeELF3allele. This SNP causes an amino acid change, which predictively has an impact on the protein structure of ELF3, thereby possibly affecting phase separation behaviour and nano-compartment formation of ELF3 and, potentially, also affecting its local cellular interactions causing significant trait differences between HIF sister lines.
Mapping PTBP splicing in human brain identifies targets for therapeutic splice switching including SYNGAP1
Authors: Dawicki-McKenna Jennine M. , Felix Alex J. , Waxman Elisa A. , Cheng Congsheng , Amado Defne A. , Ranum Paul T. , Bogush Alexey , Dungan Lea V. , Heller Elizabeth A. , French Deborah L. , Davidson Beverly L. , Prosser Benjamin L.
Published: July 2022

Alternative splicing of neuronal genes is controlled in part by the coordinated action of the polypyrimidine tract binding proteins (PTBP1 and PTBP2). While PTBP1 is ubiquitously expressed, PTBP2 is predominantly neuronal, controlling the expression of such targets as DLG4, which encodes PSD95, a protein important in synaptic function whose deficiency causes neurodevelopmental disorders. Here, we fully define the PTBP2 footprint in the human transcriptome using both human brain tissue and neurons derived from human induced pluripotent stem cells (iPSC-neurons). We identify direct PTBP2 binding sites and define PTBP2-dependent alternative splicing events, finding novel targets such as STXBP1 and SYNGAP1, which are synaptic genes also associated with neurodevelopmental disorders. The resultant PTBP2 binding and splicing maps were used to test if PTBP2 binding could be manipulated to increase gene expression in PTBP-targeted genes that cause disease when haploinsufficient. We find that PTBP2 binding to SYNGAP1 mRNA promotes alternative splicing and non-sense mediated decay. Antisense oligonucleotides that disrupt PTBP binding sites on SYNGAP1 redirect splicing and increase gene and protein expression. Collectively, our data provide a comprehensive view of PTBP2-dependent alternative splicing in human neurons and human cerebral cortex, guiding the development of novel therapeutic tools that may benefit a range of neurodevelopmental disorders.
Limitations of Busulfan to Create Humanize Mice with an Innate Immune System
Authors: Alhawiti Ohud , Hu Bin , Kobilinski Jennifer , Guo Chunqing , Landry Joseph W.
Published: July 2022

Humanized mouse models have improved biomedical research by providing a tractable system with which to perform in vivo experiments on human tissues. Use of irritators is the standard method for establishing high levels of stem cell engraftment, however not all institutes have access to this instrumentation in the animal facility. The use of busulfan has been successfully used to precondition for stem cell engraftment on a limited number of mouse backgrounds. In this report we further test the utility of busulfan as a means to successfully engraft hIL15-Tg-NSG and SGM3-NSG mouse stains which are capable of establishing the innate NK cell and myeloid immune compartments. Results from our studies show that busulfan can successfully precondition hIL15-Tg-NSG mice but not SGM3-NSG mice for high levels of human immune cell engraftment. SGM3-NSG mice preconditioned with busulfan exhibited only 10-20% human CD45 cells in the bone marrow or spleen, where as NSG and hIL15-Tg-NSG mice routinely achieved ∼80%. Busulfan preconditioned SGM3-NSG mice showed elevated levels of granulocytic MDSC, and cDC1 and cDC2 myeloid populations. This is in contrast with hIL15-TG-NSG which showed robust reconstitution of mature CD16 expressing NK cells. We conclude from our studies that busulfan is an effective means to precondition mice for CD34+ stem cell engraftment, but it may have limitations when use to precondition the SGM3-NSG model.
A Toxin-Antidote Selfish Element Increases Fitness of its Host
Authors: Long Lijiang , Xu Wen , Paaby Annalise B. , McGrath Patrick T.
Published: July 2022

Selfish genetic elements can promote their transmission at the expense of individual survival, creating conflict between the element and the rest of the genome. Recently, a large number of toxin-antidote (TA) post-segregation distorters have been identified in non-obligate outcrossing nematodes. Their origin and the evolutionary forces that keep them at intermediate population frequencies are poorly understood. Here, we study a TA element in C. elegans called peel-1/zeel-1. Two major haplotypes of this locus, with and without the selfish element, segregate in C. elegans. Here we study the fitness consequences of the peel-1/zeel-1 element outside of its role in gene drive in non-outcrossing animals. We demonstrate that loss of the toxin peel-1 decreased fitness of hermaphrodites and resulted in reductions in fecundity and body size. This fitness advantage is independent of the antidote zeel-1, suggesting that a distinct peel-1 pathway plays a biological role. This work demonstrates that a TA element can provide a fitness benefit to its hosts, either during their initial evolution or by being co-opted by the animals following their selfish spread. These findings guide our understanding on how TA elements can remain in a population where gene drive is minimized, helping resolve the mystery of prevalent TA elements in selfing animals.
Melanoma cells appropriate pericyte:endothelial cell crosstalk during perivascular invasion in the brain
Authors: Zhang Yu , Riedstra Caroline P. , Wang Sarah , Patel Sonia , Bald Tobias , Kumar Pankaj , Rohani Ali , Kashatus David F. , Moschos Stergios J. , Dudley Andrew C.
Published: July 2022

Post brain colonization, cancer cells may adhere to and spread along the abluminal surface of the vasculature providing advantageous access to oxygen, nutrients, and vessel-derived paracrine factors. For example, brain-tropic melanoma cells are well-known to invade along or within blood vessels at the invasive front, but the molecular mechanisms that guide this process are not well-characterized. We have used melanoma cells of different phenotypic states (melanocytic versus mesenchymal) to characterize different modes of perivascular invasion in the brain. We find that Sox9hi mesenchymal state melanoma cells undergo pericyte-like spreading along brain blood vessels via a Snail1-dependent process; in contrast, Sox10hi melanocytic state melanoma form proliferative, perivascular clusters. Snai1 deletion in mesenchymal-state melanoma cells diminishes Tgfβ-induced expression of Pdgfrβ which impairs Tgfβ/Pdgf ligand-driven motility along the brain microvasculature and dramatically reduces perivascular dispersal of melanoma cells throughout the brain post-colonization. These data suggest that, depending on their transcriptional/phenotypic state, some melanoma cells may appropriate signals that typically mediate endothelial cell:pericyte cross talk as an adaptive mechanism for maintaining vessel proximity and motility within the brain microenvironment.
Cortical polarity ensures its own asymmetric inheritance in the stomatal lineage to pattern the leaf surface
Authors: Muroyama Andrew , Gong Yan , Hartman Kensington S. , Bergmann Dominique
Published: July 2022

Asymmetric cell divisions (ACDs) specify differential cell fates across kingdoms. In metazoans, preferential inheritance of fate determinants into one daughter cell frequently depends on polarity-cytoskeleton interactions (1, 2). Despite the prevalence of ACDs during plant development, evidence for analogous mechanisms that segregate fate determinants during ACD remain elusive. Here, we describe a mechanism in the Arabidopsis thaliana leaf epidermis that ensures unequal inheritance of a fate-enforcing polarity domain during the creation of stomata, essential two-celled valves that mediate gas exchange between the plant and environment. Formation of a plasma membrane-associated polarity domain, defined by BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL), overrides default division patterns in stomatal precursors. The polarity domain exerts this control by constraining formation of the preprophase band of microtubules that mark the cortical division site and are a hallmark of plant mitosis. Experimentally uncoupling preprophase band establishment from the polarity domain results in aberrant polarity inheritance and subsequent fate errors. Mechanistically, our analyses of the interactions between microtubules and BASL in native and heterologous contexts revealed that the stomatal lineage polarity domain locally depletes cortical microtubules by altering microtubule stability. As the inherited cortical BASL crescent scaffolds a MAPK cascade to suppress progenitor identity in one daughter post-division, we propose that BASL-microtubule interactions represent a novel strategy to link cell identity to division orientation. Together, our data highlight how a common biological module, coupling the cytoskeleton to fate segregation via cell polarity, has been configured to accommodate the unique features of plant development.
Different inhibition of Nrf2 by two Keap1 isoforms α and β to shape malignant behaviour of human hepatocellular carcinoma
Authors: Chen Feilong , Xiao Mei , Feng Jing , Wufur Reziyamu , Liu Keli , Hu Shaofan , Zhang Yiguo
Published: July 2022

Nrf2 (nuclear factor E2-related factor 2, encoded by Nfe2l2) acts as a master transcriptional regulator in mediating antioxidant, detoxification and cytoprotective responses against oxidative, electrophilic and metabolic stress, but also plays a crucial role in cancer metabolism and multiple oncogenic pathways, whereas the redox sensor Keap1 functions as a predominant inhibitor of Nrf2 and hence changes in its expression abundance directly affect the Nrf2 stability and transcriptional activity. However, nuanced functional isoforms of Keap1α and β have rarely been identified to date. Herein, we have established four distinct cell models stably expressing Keap1-/-, Keap1β (Keap1Δ1-31), Keap1-Restored and Keap1α-Restored, aiming to gain a better understanding of similarities and differences of two Keap1 isoforms between their distinct regulatory profiles. Our experimental evidence revealed that although Keap1 and its isoforms are still localized in the cytoplasmic compartments, they elicited differential inhibitory effects on Nrf2 and its target HO-1. Furtherly, transcriptome sequencing unraveled that they possess similar but different functions. Such functions were further determined by multiple experiments in vivo (i.e. subcutaneous tumour formation in nude mice) and in vitro (e.g., cell cloning, infection, migration, wound healing, cell cycle, apoptosis, CAT enzymatic activity and intracellular GSH levels). Of note, the results obtained from tumorigenesis experiments in xenograft model mice were verified based on the prominent changes in the PTEN signaling to the PI3K-AKT-mTOR pathways, in addition to substantially aberrant expression patterns of those typical genes involved in the EMT (epithelial-mesenchymal transition), cell cycle and apoptosis.
Intralumenal docking of Cx36 channels in the ER isolates mis-trafficked protein
Authors: Tetenborg Stephan , Liss Viktoria , Breitsprecher Leonhard , Timonina Ksenia , Kotova Anna , Acevedo Harnecker Alejandra Jesús , Yuan Chunxu , Shihabeddin Eyad , Dedek Karin , Zoidl Georg , Hensel Michael , O’Brien John
Published: July 2022

The intracellular domains of connexins are essential for the assembly of gap junctions. For connexin 36 (Cx36), the major neuronal connexin, it has been shown that a dysfunctional PDZ binding motif interferes with electrical synapse formation. However, it is still unknown how this motif coordinates the transport of Cx36. In the present study, we characterize a phenotype of Cx36 mutants that lack a functional PDZ binding motif using HEK293T cells as an expression system. We provide evidence that an intact PDZ binding motif is critical for proper ER export of Cx36. Removing the PDZ binding motif of Cx36 results in ER retention and the formation of multi-membrane vesicles containing gap junction-like connexin aggregates. Using a combination of site directed mutagenesis and electron micrographs we reveal that these vesicles consist of Cx36 channels that docked prematurely in the ER. Our data suggest a model in which ER-retained Cx36 channels reshape the ER membrane into concentric whorls that are released into the cytoplasm.
Structural basis for RNA slicing by a plant Argonaute
Authors: Xiao Yao , Maeda Shintaro , Otomo Takanori , MacRae Ian J.
Published: July 2022

Argonaute (AGO) proteins use small RNAs to recognize transcripts targeted for silencing in plants and animals. Many AGOs possess an endoribonuclease activity termed RNA slicing, which catalyzes rapid turnover of target RNAs. The nuclease activity of Thermus thermophilus AGO (TtAgo)1,2 is often used as a model for RNA slicing, but how well DNA-guided slicing by this bacterial thermophile resembles RNA-guided slicing by eukaryotic AGOs is not known. We present cryo-EM structures of the Arabidopsis thaliana Argonaute10 (AtAgo10)-guide RNA complex with and without a target RNA representing a slicing substrate. Like TtAgo, AtAgo10 conformation expands in response to target binding. However, the AtAgo10-guide-target complex adopts slicing-competent and -incompetent conformations that are distinct from structures of TtAgo. AtAgo10 slicing activity is licensed by docking target (t) nucleotides t9-t13 into a surface channel containing the AGO endoribonuclease active site. A ß-hairpin, conserved in the L1 domain of eukaryotic AGOs, secures the t9-t13 segment and coordinates t9-t13 docking with extended guide-target pairing, preventing the complex from becoming trapped in slicing-incompetent conformations. Results show the mechanism for achieving RNA slicing in eukaryotes is distinct from that of bacteria and provide insights for controlling small interfering RNA (siRNA) potency.
smalldisco, a pipeline for siRNA discovery and 3’ tail identification
Authors: Caldas Ian V. , Kelley Leanne H. , Ahmed-Braimah Yasir H. , Maine Eleanor M.
Published: July 2022

Capturing and sequencing small RNAs is standard practice, however identification of a group of these small RNAs—small interfering RNAs (siRNAs)—has been more difficult. We present smalldisco, a command-line tool forsmallinterfering RNAdiscovery and annotation from small RNA-seq datasets. smalldisco can distinguish short reads that map antisense to an annotated genomic feature (e.g., exons or mRNAs), annotate these siRNAs, and quantify their abundance. smalldisco also uses the program Tailor to quantify 3’ non-templated nucleotides of siRNAs or any small RNA species. smalldisco and supporting documentation are available for download from GitHub (https://github.com/ianvcaldas/smalldisco).
Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system
Authors: Dazzoni Régine , Li Yuanyuan , López-Castilla Aracelys , Brier Sébastien , Mechaly Ariel , Cordier Florence , Haouz Ahmed , Nilges Michael , Francetic Olivera , Bardiaux Benjamin , Izadi-Pruneyre Nadia
Published: July 2022

Type II secretion systems (T2SS) allow diderm bacteria to secrete hydrolytic enzymes, adhesins or toxins important for growth and virulence. In T2SS, secretion of folded proteins from the periplasm to the cell surface requires assembly of periplasmic filaments called pseudopili. Like the related type IV pili, pseudopili are polymerized in the inner membrane through addition of subunits at the filament base, mediated by the essential assembly platform (AP). To understand the structure and molecular role of the AP, we focused on its components PulL and PulM from the Klebsiella oxytoca T2SS. By combining biophysical methods, NMR and X-ray crystallography we studied the structure and associations of their periplasmic domains. We describe the first structure of the heterodimer complex formed by the PulL and PulM ferredoxin-like domains and show how their structural complementarity and plasticity favor their association during the secretion process. Cysteine scanning and cross-linking of transmembrane segments provided additional constraints to build a structural model of the PulL–PulM complex and assembly in the cellular context. Together with the relative abundance of PulL, PulM and their partners our findings suggest a model of the AP as a dynamic hub that orchestrates pseudopilus polymerization.
Managing strategies for mitigating interacting barriers to sustainable online e-waste collection platforms in India
Authors: Chandra Pratistha , Yeh Chung-Hsing , Dutta Pankaj
Published: July 2022

Purpose

This study identifies barriers faced by online e-waste collection platforms in India and proposes a novel approach to manage strategies that contribute towards making such online platforms economically, socially, and environmentally sustainable by mitigating their interacting barriers.

Design/methodology/approach

The approach consists of a barrier assessment process and a strategy evaluation and planning process. The barrier assessment process uses multiple criteria decision making (MCDM) based method to evaluate the interactive effects of the barriers to derive their direct and indirect impacts on sustainability. The strategy evaluation and planning process evaluates the overall contribution value of strategies for mitigating interacting barriers and then categorizes them into planning zones based on their contribution and feasibility.

Findings

The interaction among the barriers is a significant component of the overall impact of the barriers on sustainability. The most impactful barriers are the lack of dissemination of information, lack of government support, insufficient infrastructure, and awareness and attitude of consumers. Lack of government support is the most influential causal barrier. Lack of information dissemination is a significant causal barrier with the highest overall impact on sustainability. Priority strategies that must be implemented to ensure sustainability include government support, offering higher prices or discounts for giving up e-waste, and increasing information dissemination.

Originality/value

Different from existing approaches for evaluating sustainability strategies, the strategies in this study are identified and evaluated based on their overall contribution towards mitigating interacting barriers to sustainability. The approach is applied in the Indian context to reveal the most influential barriers to the sustainability of online e-waste collection platforms and the most effective strategies for mitigating these barriers. The outcomes of this study contribute to strategy planning for sustainable online e-waste collection platforms in India.
The framing of plastic pollution responsibility: comparing corporate versus environmental movement discursive evaluations
Authors: Ravazzani Silvia , Maier Carmen Daniela
Published: July 2022

Purpose

This article aims to investigate evaluative framing of global plastic pollution as discursively performed by two opposed categories of social actors, namely corporations versus environmental movements.

Design/methodology/approach

The article builds on the literature related to framing, issue arenas and moral evaluations to unravel how evaluative framing and counterframing are implemented in multimodal digital spaces and how social practices get legitimized or delegitimized according to different communicative purposes. It presents a longitudinal critical discourse analysis of the issue-related webpages and press releases of PepsiCo, one of the worst global plastic polluters, and of the global environmental movement #breakfreefromplastic.

Findings

Findings suggest that the systematic recurrence of specific evaluative strategies has a double macro-function: (a) organizing discourses strategically through its presence or absence; (b) signalling the moral significance of recontextualized social practices by conferring legitimacy to remedial actions and/or illegitimacy to deviant actions.

Social implications

This study contributes to increasing accountable environmental action and trustful communication for overcoming global sustainability issues.

Originality/value

The article offers a nuanced understanding of the role of evaluative framing in communicating global sustainability issues. Methodologically, it extends existing categories of moral evaluations and articulates a framework for future studies.
Boundary-spanning search and business model innovation: the joint moderating effects of innovative cognitive imprinting and environmental dynamics
Authors: Zhu Peiyu , Miao Xiaoming , Jin Shumo
Published: July 2022

Purpose

Business model innovation (BMI) is an important channel of enterprise innovation, and BMI's antecedents have attracted extensive attention. The purpose of this paper is to address a substantial gap in the extant literature by developing a moderate model to explain the effects of boundary-spanning search on BMI as well as whether and how innovative cognitive imprinting (ICI) and environmental dynamics (ED) affect the above relationship.

Design/methodology/approach

A total of 239 usable questionnaires from different enterprises in China were collected to obtain firm-level data. Then multiple regression analyses were used by SPSS software to test hypotheses.

Findings

Boundary-spanning search extensity (BSE) and focus have inverted U-shaped impacts on BMI; ICI moderates the relationship between boundary-spanning search and BMI and steepens the curves; ED weakens the moderating role of ICI.

Originality/value

By identifying two antecedents of BMI, this paper contributes to the literature on the antecedents of BMI. Meanwhile, the joint moderating effect of ICI and ED is introduced into the emergent analysis framework of the relationship between boundary-spanning search and BMI and examined through empirical analysis for the first time.