bluuebunny/crossref_metadata_2025 huggingface dataset:
TPPP Forms Liquid Condensates and Aggregates in Multiple System Atrophy
Authors: Kemal Shahrnaz , Richardson Hunter S. , McAlear Thomas S. , Kopach Andrii , Nowacki Joseph C. , Li Yan , Bechstedt Susanne , Fu Meng-meng
Published: June 2023

Oligodendrocytes have elaborate arbors of microtubules that extend toward axons and spiral around myelin sheaths. Oligodendrocytes rely on satellite organelles called Golgi outposts to nucleate new microtubules at sites far from the cell body. We now show that the Golgi outpost marker TPPP (tubulin polymerization promoting protein) forms liquid condensates that co-partition with tubulin in order to nucleate microtubules. In oligodendrocytes, TPPP forms either dynamic puncta or aberrant microtubule-associated aggregates. In Multiple System Atrophy (MSA), a sequela of histological events initiates with TPPP aggregation in myelin sheaths and terminates in perinuclear TPPP co-aggregation with alpha-synuclein (aSyn). Finally, recombinant TPPP aggregates are toxic to primary oligodendrocytes. Thus, while the liquid condensate property of TPPP facilitates microtubule nucleation, it also predisposes TPPP to aggregate in disease.
Therapeutic TNF-alpha Delivery After CRISPR Receptor Modulation in the Intervertebral Disc
Authors: Stover Joshua D. , Trone Matthew A. R. , Weston Jacob , Lewis Christian , Levis Hunter , Philippi Matthew , Zeidan Michelle , Lawrence Brandon , Bowles Robby D.
Published: June 2023

Low back pain (LBP) ranks among the leading causes of disability worldwide and generates a tremendous socioeconomic cost. Disc degeneration, a leading contributor to LBP, can be characterized by the breakdown of the extracellular matrix of the intervertebral disc (IVD), disc height loss, and inflammation. The inflammatory cytokine TNF-α has multiple pathways and has been implicated as a primary mediator of disc degeneration. We tested our ability to regulate the multiple TNF-α inflammatory signaling pathwaysin vivoutilizing CRISPR receptor modulation to slow the progression of disc degeneration in rats. Sprague-Dawley rats were treated with CRISPRi-based epigenome-editing therapeutics targeting TNFR1 and showed a decrease in behavioral pain in a disc degeneration model. Surprisingly, while treatment with the vectors alone was therapeutic, TNF-α injection itself became therapeutic after TNFR1 modulation. These results suggest direct inflammatory receptor modulation, to harness beneficial inflammatory signaling pathways, as a potent strategy for treating disc degeneration.
Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN
Authors: Powell Barrett M. , Davis Joseph H.
Published: June 2023

Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via iterative alignment and averaging are well-developed but rely on assumptions of structural homogeneity among the complexes under consideration. Recently developed downstream analysis tools allow for some assessment of macromolecular diversity but have limited capacity to represent highly heterogeneous macromolecules, including those undergoing continuous conformational changes. Here, we extend the highly expressive cryoDRGN deep learning architecture, originally created for cryo-electron microscopy single particle analysis, to sub-tomograms. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct a large, heterogeneous ensemble of structures supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET data. We additionally illustrate tomoDRGN’s efficacy in analyzing an exemplar dataset, using it to reveal extensive structural heterogeneity among ribosomes imagedin situ.
zDB: bacterial comparative genomics made easy
Authors: Marquis Bastian , Pillonel Trestan , Carrara Alessia , Bertelli Claire
Published: June 2023

The analysis and comparison of genomes relies on different tools for tasks such as annotation, orthology prediction and phylogenetic inference. Most tools are specialized for a single task and additional efforts are necessary to integrate and visualize the results. To fill this gap, we developed zDB, an application that integrates an analysis pipeline and a visualization platform. Starting from annotated Genbank files, zDB identifies orthologs and infers a phylogeny for each orthogroup. A species phylogeny is also constructed from shared single-copy orthologs. The results can be enriched with Pfam protein domain prediction, COG and KEGG annotations and Swissprot homologs. The web application allows searching for specific genes or annotations, running Blast queries and comparing genomic regions and whole genomes. The metabolic capacities of organisms can be compared at either the module or pathway levels. Finally, users can run queries to examine the conservation of specific genes or annotations across a chosen subset of genomes and display the results as a list of genes, Venn diagram or heatmaps. Those features will make zDB useful for both bioinformaticians and researchers more accustomed to laboratory research. zDB is perfectly suited to process datasets with tens to hundred of genomes on a desktop machine.

IMPORTANCE

Genome comparison and analysis rely on many independent tools, leaving to scientists the burden to integrate and visualize their results for interpretation. To alleviate this burden, we have built zDB, a comparative genomics tool that includes both an analysis pipeline and a visualization platform. The analysis pipeline automates gene annotation, orthology prediction and phylogenetic inference, while the visualization platform allows scientists to easily explore the results in a web browser. Among other features, the interface allows users to visually compare whole genomes and targeted regions, assess the conservation of genes or metabolic pathways, perform Blast searches or look for specific annotations. Altogether, this tool will be useful for a broad range of applications in comparative studies between two to hundred genomes. Furthermore, it is designed to allow sharing datasets easily at local or international scale, thereby supporting exploratory analyses for non-bioinformaticians on the genome of their favorite organisms.
Design Automation of Microfluidic Single and Double Emulsion Droplets with Machine Learning
Authors: Lashkaripour Ali , McIntyre David P. , Calhoun Suzanne G.K. , Krauth Karl , Densmore Douglas M. , Fordyce Polly M.
Published: June 2023

Droplet microfluidics enables kHz screening of picoliter samples at a fraction of the cost of other high-throughput approaches. However, generating stable droplets with desired characteristics typically requires labor-intensive empirical optimization of device designs and flow conditionsthat limit adoption to specialist labs. Here, we compile the most comprehensive droplet dataset to date and use it to train machine learning models capable of accurately predicting device geometries and flow conditions required to generate stable aqueous-in-oil and oil-in-aqueous single and double emulsions from 15 to 250μm at rates up to 12000 Hz for different fluids commonly used in life sciences. Novel device geometries predicted by our models for as-yet-unseen fluids yield accurate predictions, establishing their generalizability. Finally, we generate an easy-to-use design automation tool that yield droplets within 3μm (< 8%) of the desired diameter, facilitating tailored droplet-based platforms for new applications and accelerating their utility in life sciences.
Absence of electron transfer-associated changes in the time-dependent X-ray free-electron laser structures of the photosynthetic reaction center
Authors: Nishikawa Gai , Sugo Yu , Saito Keisuke , Ishikita Hiroshi
Published: June 2023

Using the X-ray free-electron laser (XFEL) structures of the photosynthetic reaction center fromBlastochloris viridisthat show light-induced time-dependent structural changes [Dods, R.et al. (2021) Nature589, 310-314], we investigated time-dependent changes in the energetics of the electron transfer pathway, considering the entire protein environment of the protein structures and titrating the redox active sites in the presence of all fully equilibrated titratable residues. In the dark and charge-separation intermediate structures, the calculated redox potential (Em) values for the accessory bacteriochlorophyll and bacteriopheophytin in the electron-transfer active branch (BLand HL) are higher than those in the electron-transfer inactive branch (BMand HM). However, the stabilization of the [PLPM]•+HL•–state owing to protein reorganization is not clearly observed in theEm(HL) values in the charge-separated 5-ps ([PLPM]•+HL•–state) structure. Furthermore, the expected chlorin ring deformation upon formation of HL•–(saddling mode) is absent in the HLgeometry of the original 5-ps structure. These findings suggest that there is no clear link between the time-dependent structural changes and the electron transfer events in the XFEL structures.
Characterisation of membrane protein interactions by peptidisc-mediated mass photometry
Authors: Young John William , Pfitzner Emanuel , Kukura Philipp , Robinson Carol V.
Published: June 2023

Membrane proteins perform a variety of critical functions in the cell, making many of them primary drug targets. At the same time, their preference for a lipid environment makes them challenging to study using established solution-based methods. Here, we show that peptidiscs, a recently developed membrane mimetic, provide an ideal platform to study membrane proteins and their interactions with mass photometry (MP) in detergent-free conditions. The mass resolution for membrane protein complexes is similar to that achievable with soluble proteins owing to the low carrier heterogeneity. Using two well-characterized bacterial membrane protein complexes - the ABC transporter BtuCD, and the Sec translocon - we show that MP can quantify interactions between peptidisc-reconstituted membrane protein receptors and their soluble protein binding partners. Using the BAM complex, we further show that MP reveals interactions between a membrane protein receptor and a bactericidal antibody. Our results highlight the utility of peptidiscs for membrane protein characterization in detergent-free solution and provide a rapid and powerful platform for quantifying membrane protein interactions.
Sixteen oogenesin genes are dispensable for fertilityWhat is the significance of the dispensability of genes expressed in germ-cell?
Authors: Castille Johan , Thépot Dominique , Fouchécourt Sophie , Passet Bruno , Daniel-Carlier Nathalie , Vilotte Jean-Luc , Monget Philippe
Published: June 2023

Gene knockout experiments have shown that many genes are dispensable for a given biological function. The Oogenesin/Pramel family contains almost 85 paralogs, about thirty of which are specific to female (as well as male for some of them) germ cells. In this paper, we show that the deletion of a block of around 1Mb containing sixteen paralogous genes of the Oogenesin/Pramel family specific to germ cells, including Oogenesin-2, -3 and -4, has no consequences on fertility or prolificacy in mouse both sexes. The dispensability of these genes is probably due to the compensation by the other germ-cell specific paralogs.
Mapping temperature-sensitive mutations at a genome-scale to engineer growth-switches inE. coli
Authors: Schramm Thorben , Pahl Vanessa , Link Hannes
Published: June 2023

Temperature-sensitive (TS) mutants are a unique tool to perturb and engineer cellular systems. Here, we constructed a CRISPR library with 15,120Escherichia colimutants, each with a single amino acid change in one of 346 essential proteins. 1,269 of these mutants showed temperature-sensitive growth in a time-resolved competition assay. We reconstructed 94 TS mutants and measured their metabolism under growth arrest at 42°C using metabolomics. Metabolome changes were strong and mutant-specific, showing that metabolism of non-growingE. coliis perturbation-dependent. For example, 24 TS mutants of metabolic enzymes overproduced the direct substrate-metabolite due to a bottleneck in their associated pathway. A strain with TS homoserine kinase (ThrBF267D) produced homoserine for 24 hours, and production was tunable by temperature. Finally, we used a TS subunit of DNA polymerase III (DnaXL289Q) to decouple growth from arginine overproduction in engineeredE. coli. These results provide a strategy to identify TS mutantsen masseand demonstrate their large potential to produce bacterial metabolites with non-growing cells.
Thrombospondin 2 is a key determinant of fibrogenesis in NAFLD
Authors: Kimura Takefumi , Iwadare Takanobu , Wakabayashi Shun-ichi , Kuldeep Seema , Nakajima Tomoyuki , Yamazaki Tomoo , Aomura Daiki , Zafar Hamim , Iwaya Mai , Uehara Takeshi , Pydi Sai P , Tanaka Naoki , Umemura Takeji
Published: June 2023

Hepatic overexpression of the thrombospondin 2 gene (THBS2) and elevated levels of circulating thrombospondin 2 (TSP2) have been observed in patients with chronic liver disease. The current study aimed to identify the specific cells expressing THBS2/TSP2 in non-alcoholic fatty liver disease (NAFLD) and investigate the underlying mechanism behind THBS2/TSP2 up-regulation. Comprehensive NAFLD liver gene datasets, including single-cell RNA sequencing (scRNA-seq), in-house NAFLD liver tissue, and LX-2 cells derived from human hepatic stellate cells (HSCs), were analyzed using a combination of computational biology, genetic, immunological, and pharmacological approaches. Analysis of the genetic dataset revealed the presence of 1433 variable genes in patients with advanced fibrosis NAFLD, with THBS2 ranked among the top 2 genes. Quantitative polymerase chain reaction examination of NAFLD livers showed a significant correlation between THBS2 expression and fibrosis stage (r=0.349, p<0.001). In support of this, scRNA-seq data and in situ hybridization demonstrated that the THBS2 gene was highly expressed in HSCs of NAFLD patients with advanced fibrosis. Pathway analysis of the gene dataset revealed THBS2 expression to be associated with the transforming growth factor beta (TGFβ) pathway and collagen gene activation. Moreover, the activation of LX-2 cells with TGFβ increased THBS2/TSP2 and collagen expression independently of the TGFβ-SMAD2/3 pathway. THBS2 gene knockdown significantly decreased collagen expression in LX-2 cells. In conclusion, THBS2/TSP2 is highly expressed in HSCs and plays a role in regulating fibrogenesis in NAFLD patients. THBS2/TSP2 may therefore represent a potential target for anti-fibrotic therapy in NAFLD. (241 words)

One-sentence summaries:

Thrombospondin 2 represent a potential target for anti-fibrotic therapy in NAFLD.
The strand exchange domain of tumor suppressor PALB2 is intrinsically disordered and promotes oligomerization-dependent DNA compaction.
Authors: Kyriukha Yevhenii , Watkins Maxwell B , Redington Jennifer M , Dastvan Reza , Uversky Vladimir N , Hopkins Jesse B , Pozzi Nicola , Korolev Sergey
Published: June 2023

The Partner and Localizer of BRCA2 (PALB2) is a scaffold protein that links BRCA1 with BRCA2 to initiate homologous recombination (HR). PALB2 interaction with DNA strongly enhances HR efficiency in cells. The PALB2 DNA-binding domain (PALB2-DBD) supports strand exchange, a complex multistep reaction conducted by only a few proteins such as RecA-like recombinases and Rad52. Using bioinformatics analysis, small-angle X-ray scattering, circular dichroism, and electron paramagnetic spectroscopy, we determined that PALB2-DBD is an intrinsically disordered region (IDR) forming compact molten globule-like dimer. IDRs contribute to oligomerization synergistically with the coiled-coil interaction. Using confocal single-molecule FRET we demonstrated that PALB2-DBD compacts single-stranded DNA even in the absence of DNA secondary structures. The compaction is bimodal, oligomerization-dependent, and is driven by IDRs, suggesting a novel strand exchange mechanism. Intrinsically disordered proteins (IDPs) are prevalent in the human proteome. Novel DNA binding properties of PALB2-DBD and the complexity of strand exchange mechanism significantly expands the functional repertoire of IDPs. Multivalent interactions and bioinformatics analysis suggest that PALB2 function is likely to depend on formation of protein-nucleic acids condensates. Similar intrinsically disordered DBDs may use chaperone-like mechanism to aid formation and resolution of DNA and RNA multichain intermediates during DNA replication, repair and recombination.
Scaling of an antibody validation procedure enables quantification of antibody performance in major research applications
Authors: Ayoubi Riham , Ryan Joel , Biddle Michael S , Alshafie Walaa , Fotouhi Maryam , Bolivar Sara Gonzalez , Moleon Vera Ruiz , Eckmann Peter , Worrall Donovan , McDowell Ian , Southern Kathleen , Reintsch Wolfgang , Durcan Thomas M , Brown Claire M , Bandrowski Anita , Virk Harvinder S , Edwards Aled M , McPherson Peter S , Laflamme Carl
Published: June 2023

Antibodies are critical reagents to detect and characterize proteins. It is commonly understood that many commercial antibodies do not recognize their intended targets, but information on the scope of the problem remains largely anecdotal, and as such, feasibility of the goal of at least one potent and specific antibody targeting each protein in a proteome cannot be assessed. Focusing on antibodies for human proteins, we have scaled a standardized characterization approach using parental and knockout cell lines (Laflamme et al., 2019) to assess the performance of 614 commercial antibodies for 65 neuroscience-related proteins. Side-by-side comparisons of all antibodies against each target, obtained from multiple commercial partners, demonstrates that:i)more than 50% of all antibodies failed in one or more tests,ii) yet, ∼50-75% of the protein set was covered by at least one high-performing antibody, depending on application, suggesting that coverage of human proteins by commercial antibodies is significant; andiii) recombinant antibodies performed better than monoclonal or polyclonal antibodies. The hundreds of underperforming antibodies identified in this study were found to have been used in a large number of published articles, which should raise alarm. Encouragingly, more than half of the underperforming commercial antibodies were reassessed by the manufacturers, and many had alterations to their recommended usage or were removed from the market. This first such study helps demonstrate the scale of the antibody specificity problem but also suggests an efficient strategy toward achieving coverage of the human proteome; mine the existing commercial antibody repertoire, and use the data to focus new renewable antibody generation efforts.
Estimating multiplicity of infection, allele frequencies, and prevalences accounting for incomplete data
Authors: Hashemi Meraj , Schneider Kristan A.
Published: June 2023

Background

Molecular surveillance of infectious diseases allows the monitoring of pathogens beyond the granularity of traditional epidemiological approaches and is well-established for some of the most relevant infectious diseases such as malaria. The presence of genetically distinct pathogenic variants within an infection, referred to as multiplicity of infection (MOI) or complexity of infection (COI) is common in malaria and similar infectious diseases. It is an important metric that scales with transmission intensities, potentially affects the clinical pathogenesis, and a confounding factor when monitoring the frequency and prevalence of pathogenic variants. Several statistical methods exist to estimate MOI and the frequency distribution of pathogen variants. However, a common problem is the quality of the underlying molecular data. If molecular assays fail not randomly, it is likely to underestimate MOI and the prevalence of pathogen variants.

Methods and findings

A statistical model is introduced which explicitly addresses data quality, by assuming a probability by which a pathogen variant remains undetected in a molecular assay. This is different from the assumption of missing at random, for which a molecular assay either performs perfectly or fails completely. The method is applicable to a single molecular marker and allows to estimate allele-frequency spectra, the distribution of MOI, and the probability of variants to remain undetected (incomplete information). Based on the statistical model, expressions for the prevalence of pathogen variants are derived and differences between frequency and prevalence are discussed. The usual desirable asymptotic properties of the maximum-likelihood estimator (MLE) are established by rewriting the model into an exponential family. The MLE has promising finite sample properties in terms of bias and variance. The covariance matrix of the estimator is close to the Cramér-Rao lower bound (inverse Fisher information). Importantly, the estimator’s variance is larger than that of a similar method which disregards incomplete information, but its bias is smaller.

Conclusions

Although the model introduced here has convenient properties, in terms of the mean squared error it does not outperform a simple standard method that neglects missing information. Thus, the new method is recommendable only for data sets in which the molecular assays produced poor quality results. This will be particularly true if the model is extended to accommodate information from multiple molecular markers at the same time, and incomplete information at one or more markers leads to strong depletion of sample size.
AGILE Platform: A Deep Learning-Powered Approach to Accelerate LNP Development for mRNA Delivery
Authors: Xu Yue , Ma Shihao , Cui Haotian , Chen Jingan , Xu Shufen , Wang Kevin , Varley Andrew , Ze Lu Rick Xing , Wang Bo , Li Bowen
Published: June 2023

Ionizable lipid nanoparticles (LNPs) have seen widespread use in mRNA delivery for clinical applications, notably in SARS-CoV-2 mRNA vaccines. Despite their successful use, expansion of mRNA therapies beyond COVID-19 is impeded by the absence of LNPs tailored to different target cell types. The traditional process of LNP development remains labor-intensive and cost-inefficient, relying heavily on trial and error. In this study, we present theAI-GuidedIonizableLipidEngineering (AGILE) platform, a synergistic combination of deep learning and combinatorial chemistry. AGILE streamlines the iterative development of ionizable lipids, crucial components for LNP-mediated mRNA delivery. This approach brings forth three significant features: efficient design and synthesis of combinatorial lipid libraries, comprehensive in silico lipid screening employing deep neural networks, and adaptability to diverse cell lines. Using AGILE, we were able to rapidly design, synthesize, and evaluate new ionizable lipids for mRNA delivery in muscle and immune cells, selecting from a library of over 10,000 candidates. Importantly, AGILE has revealed cell-specific preferences for ionizable lipids, indicating the need for different tail lengths and head groups for optimal delivery to varying cell types. These results underscore the potential of AGILE in expediting the development of customized LNPs. This could significantly contribute to addressing the complex needs of mRNA delivery in clinical practice, thereby broadening the scope and efficacy of mRNA therapies.

One Sentence Summary

AI and combinatorial chemistry expedite ionizable lipid creation for mRNA delivery.
Endosome-ER Interactions Define a Cellular Energy Landscape to Guide Cargo Transport
Authors: Shen Yusheng , Wen Yan , Zhao Qirui , Huang Pingbo , Lai Pik-Yin , Tong Penger
Published: June 2023

Molecular motor-driven cargo must navigate a complex intracellular environment, which is often crowded, heterogeneous and fluctuating, to fulfill their diverse functions in a cell. To meet these challenges, most cargo display qualitatively similar transport behavior, that is, random switching between states of diffusive “jiggling” movement (off-state) and states of directed “runs” (on-state). The physical picture of this 2-state motion and their regulation in a cell are not well understood. Here, by using single-particle tracking and motion-states dissection, we present a statistical analysis of the 2-state motion of epidermal growth factor receptor (EGFR)-endosomes in living cells. From a thorough analysis of a large volume of EGFR-endosome trajectories, we reveal that their lifetime in both states feature an exponential distribution with its probability density function (PDF)-amplitude varied by more than three decades. We show that their characteristic time, on-state probability, velocity and off-state diffusion coefficient are spatially regulated, and are probably contributed by the endoplasmic reticulum (ER) network via its spatially varying membrane densities and interactions with the cargo. We further propose a 2-state transport model to describe the complex, spatially varying transport dynamics of EGFR-endosomes in a cell. Our findings suggest that the ER network may play an essential role in constructing a cellular-level free-energy landscape ΔG(r) to spatially guide cargo transport.
Deep Phenotyping of the Lipidomic Response in COVID and non-COVID Sepsis
Authors: Meng Hu , Sengupta Arjun , Ricciotti Emanuela , Mrčela Antonijo , Mathew Divij , Mazaleuskaya Liudmila L. , Ghosh Soumita , Brooks Thomas G. , Turner Alexandra P. , Schanoski Alessa Soares , Lahens Nicholas F. , Tan Ai Wen , Woolfork Ashley , Grant Greg , Susztak Katalin , Letizia Andrew G. , Sealfon Stuart C. , Wherry E. John , Laudanski Krzysztof , Weljie Aalim M. , Meyer Nuala B. , FitzGerald Garret A.
Published: June 2023

Lipids may influence cellular penetrance by pathogens and the immune response that they evoke. Here we find a broad based lipidomic storm driven predominantly by secretory (s) phospholipase A2(sPLA2) dependent eicosanoid production occurs in patients with sepsis of viral and bacterial origin and relates to disease severity in COVID-19. Elevations in the cyclooxygenase (COX) products of arachidonic acid (AA), PGD2and PGI2, and the AA lipoxygenase (LOX) product, 12-HETE, and a reduction in the high abundance lipids, ChoE 18:3, LPC-O-16:0 and PC-O-30:0 exhibit relative specificity for COVID-19 amongst such patients, correlate with the inflammatory response and link to disease severity. Linoleic acid (LA) binds directly to SARS-CoV-2 and both LA and its di-HOME products reflect disease severity in COVID-19. AA and LA metabolites and LPC-O-16:0 linked variably to the immune response. These studies yield prognostic biomarkers and therapeutic targets for patients with sepsis, including COVID-19. An interactive purpose built interactive network analysis tool was developed, allowing the community to interrogate connections across these multiomic data and generate novel hypotheses.
Doublecortin restricts neuronal branching by regulating tubulin polyglutamylation
Authors: Sébastien Muriel , Paquette Alexandra L. , Prowse Emily N. P. , Hendricks Adam G. , Brouhard Gary J.
Published: June 2023

Doublecortin (DCX) is a neuronal microtubule-associated protein (MAP) that binds directly to microtubules via two Doublecortin (DC) domains. The DC domains sense the nucleotide state, longitudinal curvature, and protofilament number of the microtubule lattice, indicating a role in the regulation of microtubule structure in neurons. Mutations in DCX cause lissencephaly and subcortical band heterotopia (also known as double-cortex syndrome) due to impaired neuronal migration. To better understand the role of DCX in neuronal migration, we developed a model system based on induced pluripotent stem cells (iPSCs). We used CRISPR/Cas9 to knock-out theDcxgene in iPSCs and differentiated the cells into cortical neurons. Compared to control neurons, the DCX-KO neurons showed reduced velocities of nuclear movements. The reduced velocities coincided with an increase in the number of neurites early in neuronal development, consistent with a neuronal migration phenotype and previous findings in a DCX-KO mouse model. Neurite branching is regulated by a host of MAPs and other factors, as well as by microtubule polymerization dynamics. However, EB comet dynamics were unchanged in DCX-KO neurons, with similar growth rates, lifetimes, and numbers. Rather, we observed a significant reduction in α-tubulin polyglutamylation in DCX-KO neurons. Polyglutamylation levels and neuronal branching were rescued by expression of DCX or of TTLL11, an α-tubulin glutamylase. Using U2OS cells as an orthogonal model system, we show that DCX and TTLL11 act synergistically to promote polyglutamylation. Polyglutamylation regulates numerous MAPs, severing enzymes, and molecular motors. Consistently, we observe that lysosomes in DCX-KO neurons show a reduction of their processivity. We propose that the DCX acts as a positive regulator of α-tubulin polyglutamylation and restricts neurite branching. Our results indicate an unexpected role for DCX in the homeostasis of the tubulin code.
Terminal maturation of human reticulocytes to red blood cells by extensive remodelling and progressive liquid ordering of membrane lipids
Authors: Minetti Giampaolo , Kaestner Lars , Köfeler Harald , Perotti Cesare , Dorn Isabel
Published: June 2023

In the age of "omics", lipidomics of erythropoiesis is still missing. How reticulocytes mature in the circulation into functional erythrocytes is also largely unknown, beyond the lipidomics level. We have isolated here two populations of human circulating reticulocytes at different levels of maturation, and three subpopulations of erythrocytes of different age, and characterized the evolution of their lipidome. Sphingomyelin, cholesterol and partly phosphatidylethanolamine increase relative to total lipids, whereas phosphatidylcholine and phosphatidylserine decrease from immature reticulocytes to mature erythrocytes, at the same time as the surface area per cell decreases. The relative amounts of more than 70 phospholipid subclasses, based on the number of carbon atoms (12-24) and of double bonds (0-6) in the fatty acids linked to the phospholipid, also change in the process. As reticulocytes and erythrocytes are unable of de-novo phospholipid synthesis, lipid remodeling likely requires selective removal of phospholipids from the membrane or their exchange with plasma or both, with the possible involvement of lipid transfer proteins such as VPS13A, which is highly expressed in reticulocytes and erythrocytes. These findings not only shed light on fundamental aspects of red blood cell physiology and erythropoiesis but also raise intriguing questions surrounding protein-lipid interactions, membrane architecture, and lipid trafficking mechanisms.
A marine cryptochrome with an inverse photo-oligomerization mechanism
Authors: Vu Hong Ha , Behrmann Heide , Hanić Maja , Jeyasankar Gayathri , Krishnan Shruthi , Dannecker Dennis , Hammer Constantin , Gunkel Monika , Solov’yov Ilia A. , Wolf Eva , Behrmann Elmar
Published: June 2023

Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle wormPlatynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark,PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishesPdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight.
Social dynamics of vervet monkeys are dependent upon group identity
Authors: Kerjean Elena , van de Waal Erica , Canteloup Charlotte
Published: June 2023

Traditions are widespread across the animal realm. Here, we investigated inter-group variability of social dynamics in wild vervet monkeys (Chlorocebus pygerythrus). We analysed 84 704 social behavioural interactions involving 247 individuals collected over nine years in three neighbouring groups of wild vervet monkeys. We found that, in one group - Ankhase - individuals had a higher propensity to be affiliative (i.e., sociality) and grooming interactions were more reciprocal. Despite yearly fluctuations in sociality, differences between groups remained stable over time. Moreover, our statistical model predictions confirmed that these findings were maintained for similar sex ratios, age distributions and group sizes. Strikingly, our results suggested that dispersing males adapted their sociality to the sociality of the group they integrated with. As a whole, our study sheds light on the existence of stable social dynamics dependent upon group identity in wild vervet monkeys and suggests that at least part of this variability is socially mediated.

Graphical Abstract

Highlights

The sociality of vervet monkeys groups differs consistently across a nine years study despite similar genetic and ecological environments.

Dispersing males adapt their sociality according to the group they integrate with.

In the most social group, grooming interactions were more reciprocal.
Morphomechanic tuning of ERK by actin-TFII-IΔ regulates cell identity
Authors: Wu Qiao , Zhang Jian , Long Bing , Hu Xiao , de Faria Bruna Mafra , Scalf Stephen Maxwell , Karatepe Kutay , Cao Wenxiang , Tsopoulidis Nikolaos , Binkercosen Andres , Yagi Masaki , Weiner Aaron , Kaileh Mary , De La Cruz Enrique M. , Roy Ananda L , Hochedlinger Konrad , Guo Shangqin
Published: June 2023

Cell morphology is faithfully coupled to its identity but the coupling mechanism remains elusive. Using somatic cell reprogramming into pluripotency as a model system, we show that activity of the extracellular signal-regulated kinase (ERK) is tuned by cellular morphomechanic state to direct cell fate. Pluripotent cells and somatic cells reprogramming into pluripotency allocate large amounts of actin into their nucleus, which morphs cells to become taller than 10 μm, a minimal height required for the pluripotent identity. Accumulated nuclear actin binds to TFII-IΔ, an atypical transcription factor that translocates into the nucleus upon signaling. TFII-IΔ also binds to and activates ERK. The binding of TFII-IΔ by nuclear actin reduces ERK activity, in coordination with changes in cell/colony height. The tight coupling between cell height and nuclear actin accumulation necessitates the degree of ERK tuning to be mild. Mild ERK inhibition by chemicals recapitulates the tuning by actin-TFII-IΔ and turns most cells in reprogramming cultures into pluripotency. Thus, we uncover a novel mechanism for how cell morphology couples to its identity via the actin-TFII-IΔ-ERK axis, identifying points of intervention in cell fate manipulation.
Single-component multilayered self-assembling protein nanoparticles displaying extracellular domains of matrix protein 2 as a pan-influenza A vaccine
Authors: Gomes Keegan Braz , Zhang Yi-Nan , Lee Yi-Zong , Eldad Mor , Lim Alexander , Ward Garrett , Auclair Sarah , He Linling , Zhu Jiang
Published: June 2023

The development of a cross-protective pan-influenza A vaccine remains a significant challenge. In this study, we designed and evaluated single-component self-assembling protein nanoparticles (SApNPs) presenting the conserved extracellular domain of matrix protein 2 (M2e) as vaccine candidates against influenza A viruses. The SApNP-based vaccine strategy was first validated for human M2e (hM2e) and then applied to tandem repeats of M2e from human, avian and swine hosts (M2ex3). Vaccination with M2ex3 displayed on SApNPs demonstrated higher survival rates and lower weight loss compared to the soluble M2ex3 antigen against lethal challenges of H1N1 and H3N2 in mice. M2ex3 I3-01v9a SApNPs formulated with a squalene-based adjuvant were retained in the lymph node follicles over eight weeks and induced long-lived germinal center reactions. Notably, a single low dose of M2ex3 I3-01v9a SApNP formulated with a potent adjuvant, either a Toll-like receptor 9 (TLR9) agonist or a stimulator of interferon genes (STING) agonist, conferred 90% protection against a lethal H1N1 challenge in mice. With the ability to induce robust and durable M2e-specific functional antibody and T cell responses, the M2ex3-presenting I3-01v9a SApNP provides a promising pan-influenza A vaccine candidate.

ONE-SENTENCE SUMMARY

Single-component self-assembling protein nanoparticles (SApNPs) displaying tandem M2e elicit robust and durable immunity that may protect against influenza A viruses of diverse origins.
The basis of antigenic operon fragmentation inBacteroidotaand commensalism
Authors: Bank Nicholas C. , Singh Vaidhvi , Grubb Brandon , McCourt Blake , Burberry Aaron , Roberts Kyle D. , Rodriguez-Palacios Alex
Published: June 2023

The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylumBacteroidotaremain unclear (1, 2). Using the classical lipopolysaccharide/O-antigen ‘rfboperon’ inEnterobacteriaceaeas a surface antigen model (5-gene-clusterrfbABCDX), and a recentrfbA-typing strategy for strain classification (3), we characterized the architecture/conservancy of the entirerfboperon inBacteroidota. Analyzing complete genomes, we discovered that mostBacteroidotahave therfboperon fragmented into non-random gene-singlets and/or doublets/triplets, termed ‘minioperons’. To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantlyBacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in specific micro-niches.Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain whyBacteroidotahave fewer KEGG-pathways despite large genomes (4). DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating ‘extra-species’ abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohn’s Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFTBacteroidotastimulate macrophages with lower potency thanEnterobacteriaceae, and do not induce peritonitis in mice. The impact of ‘foreign-DNA’ insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.
Resolving conformational changes that mediate a two-step catalytic mechanism in a model enzyme
Authors: Greisman Jack B. , Dalton Kevin M. , Brookner Dennis E. , Klureza Margaret A. , Sheehan Candice J. , Kim In-Sik , Henning Robert W. , Russi Silvia , Hekstra Doeke R.
Published: June 2023

Enzymes catalyze biochemical reactions through precise positioning of substrates, cofactors, and amino acids to modulate the transition-state free energy. However, the role of conformational dynamics remains poorly understood due to lack of experimental access. This shortcoming is evident withE. colidihydro-folate reductase (DHFR), a model system for the role of protein dynamics in catalysis, for which it is unknown how the enzyme regulates the different active site environments required to facilitate proton and hydride transfer. Here, we present ligand-, temperature-, and electric-field-based perturbations during X-ray diffraction experiments that enable identification of coupled conformational changes in DHFR. We identify a global hinge motion and local networks of structural rearrangements that are engaged by substrate protonation to regulate solvent access and promote efficient catalysis. The resulting mechanism shows that DHFR’s two-step catalytic mechanism is guided by a dynamic free energy landscape responsive to the state of the substrate.
Multi-tiered actions ofLegionellaeffectors to modulate host Rab10 dynamics
Authors: Kubori Tomoko , Arasaki Kohei , Oide Hiromu , Kitao Tomoe , Nagai Hiroki
Published: June 2023

Rab GTPases are representative targets of manipulation by intracellular bacterial pathogens for hijacking membrane trafficking.Legionella pneumophilarecruits many Rab GTPases to its vacuole and exploits their activities. Here, we found that infection-associated regulation of Rab10 dynamics involves ubiquitin signaling cascades mediated by the SidE and SidC families ofLegionellaubiquitin ligases. Phosphoribosyl-ubiquitination of Rab10 catalyzed by the SidE ligases is crucial for its recruitment to the bacterial vacuole. SdcB, the previously uncharacterized SidC family effector, resides on the vacuole and contributes to retention of Rab10 at the late stages of infection. We further identified MavC as a negative regulator of SdcB. By the transglutaminase activity, MavC crosslinks ubiquitin to SdcB and suppresses its function, resulting in elimination of Rab10 from the vacuole. These results demonstrate that the orchestrated actions of manyL. pneumophilaeffectors fine-tune the dynamics of Rab10 during infection.
The sustainability awareness of banking institutions in Indonesia, its implication on profitability by the mediating role of operational efficiency
Authors: Anis Idrianita , Gani Lindawati , Fauzi Hasan , Hermawan Ancella Anitawati , Adhariani Desi
Published: June 2023

Purpose

This study aims to propose a solution to accelerate financing support low carbon (circular economy) transition. The authors developed a sustainability governance (SGOV) model and a sustainability governance (SGOV) index as a proxy for the diffusion of sustainability innovation. This study investigates the effect of SGOV practices on profitability with the mediating role of operational efficiency.

Design/methodology/approach

The SGOV index consists of 32 and 122 sub-items, constructed using content analysis of annual and sustainability reports published by banks listed on the Indonesia Stock Exchange (IDX) from 2010 to 2020 (404 bank-year observations).

Findings

Banks are at a moderate level of sustainability innovation. They are prioritizing the balance aspects of financial, social and environmental. SGOV practice negatively affects profitability. However, operational efficiency plays a positive mediating role that is robust.

Research limitations/implications

The measurement of the SGOV index uses criteria that have not been tested in previous studies. There is the potential subjectivity in interpreting qualitative data, although this has been minimized by cross-checking the analysis of five raters.

Practical implications

This study gives feedback for the Indonesia sustainable finance (SF) journey phase I to proceed into SF journey phase II.

Social implications

The SGOV model can be applied in other industry sectors to know the readiness for entering low carbon (circular economy) transition.

Originality/value

The uniqueness of the scoring technique assuming a step-by-step innovation model to sustainable finance.
Institutionalization of corporate bribery: a measurement proposal with evidence from a Latin American sample
Authors: Yepes-López Gustavo Adolfo , Camarena José Luis , Cruz-Pulido Julián Mauricio , Quintero-Campos Luz Jeannette , Lasio Virginia , Rodriguez Jorge , Zambrano-Vera Jack , García de la Torre Consuelo Adelaida , Schwalb-Helguero María Matilde , Prialé María Ángela , Solís-Sierra José , Rossi-Undurraga Maruzella , Carvajal-Ramos Roberto , Martinez Pedro Javier , González-Gutiérrez Victoria , Sánchez-Reyna Rogelio , Lassaga Griselda , Beltramino Nicolás
Published: June 2023

Purpose

This article aims to report on the development and validation of a bribery measurement index for the business sector, which, based on institutional theory, seeks to overcome the limitations of traditional measurements, recognizing the dynamics that originate the phenomenon and identifying process components.

Design/methodology/approach

To construct the index, correlational and principal component analysis techniques were used, as well as rigorous statistical tests, validating the instrument in a sample of 2,963 companies in Latin America, including Argentina, Colombia, Chile, Ecuador, Guatemala, Mexico and Peru.

Findings

The result was an instrument composed of two dimensions: (1) anti-bribery game rules, composed of regulations knowledge and anti-bribery efforts, and (2) bribery as a perceived habit, allowing an objective representation of reality due to its internal consistency, concurrent and discriminant validity.

Practical implications

This instrument is one of the few that focuses on measuring bribery in the business sector in terms of corrupt practices, applicable for both public and private institutions to promote game rules against bribery. Additionally, the proposed theoretical model can be used to measure other phenomena with similar characteristics.

Originality/value

This article empirically highlights different variables that make bribery possible. The results can be helpful in the design of strategies to prevent this type of behavior. It also highlights the importance of designing mechanisms to record information related to bribery and the different expressions of corruption in order to explain its different nuances.
Client attributes that motivate contractors' bid decision
Authors: Olatunji Oluwole Alfred , Ramanayaka Chamil Erik D.
Published: June 2023

Purpose

This study aims to investigate clients' attributes, their key decision variables and causal relationships between the decision variables. In addition, the purpose of the study is to map-out from these analyses, the attributes of project clients that motivate contractors' bid decision.

Design/methodology/approach

A total of 50 responses were obtained from a questionnaire survey. 50% of participants are contractors. 44% are claims consultants, whilst 6% are manufacturers and clients. Beyond measures of central tendencies, analysis focussed on causal relationships by way of correlation, analysis of variance and reductionism.

Findings

All 20 factors considered have significant correlations with at least one other factor. Findings also show the factors can be clustered into six: reputation, financial strength, relationship with the bidder, organisational attributes, history with project attributes and project organisation.

Practical implications

Evidence suggests stakeholders have often struggled to consider the many decision factors reported in normative literature, numbering hundreds. By clustering the factors into sub-themes, bid decisioning has been made more efficient. The study also explains how client attributes could determine project success and contractor participation. Different stakeholders can use findings of this study for training and further studies.

Originality/value

Previous studies have considered bid decisioning indexically – factors were long, analyses were largely inconclusive, and causal relationships are orthogonal. Findings in this study have shown depth: 20 originating client-specific factors were clustered into six sub-themes, and correlations were established. The methodology used for the study is confirmatory and conclusive.