bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of different immunomodulating liposome-based adjuvants and injection sites on immunogenicity in pigs
Authors: Šťastná Evelína , Erbs Gitte , Skovgaard Kerstin , Jakobsen Jeanne Toft , Pedersen Gabriel Kristian , Jungersen Gregers
Published: June 2023

Vaccine adjuvants are able to boost immune responses and steer immunity towards a desired direction. Liposome-based cationic adjuvant formulations (CAFs) are effective in inducing cell-mediated immune responses in mice, non-human primates and humans. In the translation from mouse to humans, pigs could play an important role. In this study, we thus used commercial pigs housed under field conditions to investigate the effects of four different CAFs incorporating distinct immunomodulators: C-type lectin receptor ligands trehalose-6,6’-dibehenate and monomycolyl glycerol, toll-like receptor ligand Poly(I:C) or retinoic acid. The vaccines were formulated with a recombinantChlamydiamodel protein antigen and administered via distinct injection routes. All adjuvants significantly increased antigen-specific IgA and IgG in serum, compared to non-adjuvanted antigen. Administering the vaccines through intramuscular and intraperitoneal routes induced significantly higher antigen-specific IgA and IgG serum antibodies, than the perirectal route. Although the immunizations triggered cell-mediated immunity, no significant differences between the adjuvants or injection sites were detected by intracellular flow cytometry or cytokine-release assays. Genes depicting T cell subtypes were monitored by qPCR, which revealed minor differences only. Our findings suggest that the adjuvant-specific signature of the tested adjuvant immunomodulation does not translate well from mice to pigs. This study provides new insights into immune responses to CAFs in the pig model, and highlights that adjuvant studies should be ideally carried out in the intended species of interest.
Integrative Analysis of Epilepsy-Associated Genes Reveals Expression-Phenotype Correlations
Authors: Chi Wanhao , Kiskinis Evangelos
Published: June 2023

Epilepsy is a highly prevalent neurological disorder characterized by recurrent seizures. Patients exhibit broad genetic, molecular, and clinical diversity involving mild to severe comorbidities. The factors that contribute to this phenotypic diversity remain unclear. We used publicly available datasets to systematically interrogate the expression pattern of 247 epilepsy-associated genes across human tissues, developmental stages, and central nervous system (CNS) cellular subtypes. We grouped genes based on their curated phenotypes into 3 broad classes: core epilepsy genes (CEG), where seizures are the core syndrome, developmental and epileptic encephalopathy genes (DEEG) that are associated with developmental delay, and seizure-related genes (SRG), which are characterized by developmental delay and gross brain malformations. We find that DEEGs are highly expressed within the CNS, while SRGs are most abundant in non-CNS tissues. DEEGs and CEGs exhibit highly dynamic expression in various brain regions across development, spiking during the prenatal to infancy transition. Lastly, the abundance of CEGs and SRGs is comparable within cellular subtypes in the brain, while the average expression level of DEEGs is significantly higher in GABAergic neurons and non-neuronal cells. Our analysis provides an overview of the expression pattern of epilepsy-associated genes with spatiotemporal resolution and establishes a broad expression-phenotype correlation in epilepsy.
KIF1A neurodegenerative disease mutations modulate motor motility and force generation
Authors: Shewale Dipeshwari J. , Soppina Pushpanjali , Soppina Virupakshi
Published: June 2023

KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and dense-core vesicle, essential for neuronal development and maintenance. Several point mutations in the KIF1A motor domain have been identified in patients with various motor neuron diseases. Recent studies have shown that these mutations affected the motor and cargo localization in cultured hippocampal andC.elegansneurons. However, a detailed analysis of these mutations on KIF1A motility, force generation, and cargo transport is largely unexplored. Here, we have analyzed the effect of 16 point mutations and showed that these mutations significantly decreased the motor velocity and landing rates compared to wild-type motors. Except for A255V, mutations V144F, V220I, and E233D mildly affected motor mechanical outputs. S58L, A202P, R216P, R216H, L249Q, T312M, and R316W mutants exhibited drastic impairments in the motility properties, force generation, and cargo transport. Notably, T46M, T99M, G102D, S215R, and E253K mutants showed strong microtubule binding, resulting in complete disruption of cargo transport. Our study provides the first comprehensive demonstration of KIF1A disease mutations at the molecular level. The observed changes in motility properties and cargo transport align with the severity of disease phenotype observed in KIF1A-associated neurological disorders)
Machine Learning to Predict Continuous Protein Properties from Simple Binary Sorting and Deep Sequencing Data
Authors: Case Marshall , Smith Matthew , Vinh Jordan , Thurber Greg
Published: June 2023

Proteins are a diverse class of biomolecules responsible for wide-ranging cellular functions, from catalyzing reactions and recognizing pathogens to forming dynamic cellular structure. The ability to evolve proteins rapidly and inexpensively towards improved properties is a common objective for protein engineers. Powerful high-throughput methods like fluorescent activated cell sorting (FACS) and next-generation sequencing (NGS) have dramatically improved directed evolution experiments. However, it is unclear how to best leverage this data to characterize protein fitness landscapes more completely and identify lead candidates. In this work, we develop a simple yet powerful framework to improve protein optimization by predicting continuous protein properties from simple directed evolution experiments using interpretable machine learning. Evaluated across five diverse protein engineering tasks, continuous properties are consistently predicted from readily available deep sequencing data. To prospectively test the utility of this approach, we generated a library of stapled peptides and applied the framework to predict and optimize both affinity and specificity. We coupled integer linear programming with the interpretable machine learning model coefficients to identify new variants from experimentally unseen sequence space that have desired properties. This approach represents a versatile tool for improved analysis and identification of protein variants across many domains of protein engineering.
Dose optimization of an adjuvanted peptide-based personalized neoantigen melanoma vaccine
Authors: Valega-Mackenzie Wencel , Rodriguez Messan Marisabel , Yogurtcu Osman N. , Nukala Ujwani , Sauna Zuben E. , Yang Hong
Published: June 2023

The advancements in next-generation sequencing have made it possible to effectively detect somatic mutations, which has led to the development of personalized neoantigen cancer vaccines that are tailored to the unique variants found in a patient’s cancer. These vaccines can provide significant clinical benefit by leveraging the patient’s immune response to eliminate malignant cells. However, determining the optimal vaccine dose for each patient is a challenge due to the heterogeneity of tumors. To address this challenge, we formulated a mathematical dose optimization problem that aims to find the optimal personalized vaccine doses for a given fixed vaccination schedule, based on a previous mathematical model that encompasses the immune response cascade produced by the vaccine in a patient. To validate our approach, we performedin silicoexperiments on six patients with advanced melanoma. We compared the results of applying an optimal vaccine dose to those of a suboptimal dose (dose used in the clinical trial and its deviations). Our simulations revealed that an optimal vaccine may lead to a reduction in tumor size for certain patients, with higher initial doses and lower final doses. Our mathematical dose optimization offers a promising approach to determining the optimal vaccine dose for each patient and improving clinical outcomes.
Novel topological methods for identifying surprising protein tertiary structure relationships
Authors: Bale Arron , Rambo Robert , Prior Christopher
Published: June 2023

We present fast and simple-to-implement measures of the entanglement of protein tertiary structures which are appropriate for highly flexible structure comparison. These quantities are based on the writhing and crossing numbers heavily utilised in DNA topology studies which and which have shown some promising results when applied to proteins recently. Here we show how they can be applied in a novel manner across various scales of the protein’s backbone to identify similar topologies which can be missed by more common RMSD, secondary structure or primary sequence based comparison methods. We derive empirical bounds on the entanglement implied by these measures and show how they can be used to constrain the search space of a protein for solution scattering, a method highly suited to determining the likely structure of proteins in solution where crystal structure or machine learning based predictions often fail to match experimental data. In addition we identify large scale helical geometries present in a large array of proteins, which are consistent across a number of different protein structure types and sequences. This is used in one specific case to demonstrate significant structural similarity between Rossmann fold and TIM Barrel proteins, a link which is potentially significant as attempts to engineer the latter have in the past produced the former. Finally we provide the SWRITHE python notebook to calculate these metrics.

Author summary

There is much interest in developing quantitative methods to compare different protein structures or identify common sub-structures across protein families. We present novel methods for studying and comparing protein structures based on the entanglement of their amino-acid backbone and demonstrate a number of their critical properties. First, they are shown to be especially useful in identifying similar protein entanglement for structures which may be seen as distinct via more established methods. Second, by studying the distribution of entanglement across a wide sample of proteins, we show that there exists a minimum expected amount (a lower bound) of entanglement given the protein’s length. This bound is shown to be useful in ensuring realistic predictions from experimental structural determination methods. Third, using fundamental properties of this entanglement measure, we identify two common classes of protein sub-structure. The first are large scale helices, which provide stability to the structure. These helical structures indicate strong structural similarity of two protein families usually regarded as differing significantly. The second class of substructure is one which, though complex, has a small net entanglement. This configuration is physically useful in other disciplines, but its function in proteins is not yet clear. Finally, we provide an interactive python notebook to compute these measures for a given protein.
The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes
Authors: Frascarelli Giulia , Galise Teresa R. , D’Agostino Nunzio , Cafasso Donata , Cozzolino Salvatore , Cortinovis Gaia , Sparvoli Francesca , Bellucci Elisa , Vittori Valerio Di , Nanni Laura , Pieri Alice , Rossato Marzia , Vincenzi Leonardo , Benazzo Andrea , Delledonne Massimo , Bitocchi Elena , Papa Roberto
Published: June 2023

The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main genepools corresponding to three different ecogeographic areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios and the northern Peru/Ecuador population has been described as a new species calledP. debouckii,rekindling the debate about the origin ofP. vulgaris. Here we shed light on the origin ofP. vulgarisby analysing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms. We assembled 37 chloroplast genomesde novoand used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador genepools occurred ∼0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recentP. deboukiihypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account recombination events when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.
African Swine Fever Virus major capsid p72 Trimers function as a pH sensor during uncoating process of virus endocytosis
Authors: Meng Kaiwen , Huyan Yangnan , Liu Qi , Li Junyi , Xiang Ye , Meng Geng
Published: June 2023

African swine fever virus (ASFV) belongs to nucleocytoplasmic large DNA viruses (NCLDVs), the only member of Asfarviridae. So far, it is revealed that the ASFV uncoating is a pH-dependent process undergone in late endosomes. But, the research on how pH affects capsid stability is limited, and which protein plays an essential role in pH sensing remains unknown. In this study, we identified the main component of the ASFV capsid -- major capsid protein p72, as a pH sensitive residue abundance protein, and it is speculated that the conformational change of the p72 trimer is possibly responsible for the ASFV uncoating process. To test this speculation, we obtained recombinant p72 trimers, treated with the acidic environment that simulated endosomes and displayed structural analysis. The results showed that the p72 trimer depolymerized at low pH. The depolymerization of trimers rationally explains the disassembly mechanism of the ASFV icosahedral capsid in endosomes.
mRNA vaccine induces protective immunity against the type III secretory virulence ofPseudomonas aeruginosa
Authors: Kawaguchi Ken , Kinoshita Mao , Sudo Kazuki , Inoue Keita , Naito Yoshifumi , Oba Makoto , Uchida Satoshi , Sawa Teiji
Published: June 2023

Few studies have addressed mRNA vaccination against bacteria despite the desperate need to control antimicrobial resistance. Herein, we developed mRNA vaccines targeting the type III secretion system ofPseudomonas aeruginosa, which plays a critical role in the pathogenesis. Vaccination with a nucleoside-modified mRNA encapsulated in lipid nanoparticles improved mouse survival, reduced the bacterial load in the lung, and alleviated pathological changes in the lungs after bacterial challenge.
Information-theoretic analysis of a model of CAR-4-1BB-mediated NFκB activation
Authors: Tserunyan Vardges , Finley Stacey
Published: June 2023

Systems biology utilizes computational approaches to examine an array of biological processes, such as cell signaling, metabolomics and pharmacology. This includes mathematical modeling of CAR T cells, a modality of cancer therapy by which genetically engineered immune cells recognize and combat a cancerous target. While successful against hematologic malignancies, CAR T cells have shown limited success against other cancer types. Thus, more research is needed to understand their mechanisms of action and leverage their full potential. In our work, we set out to apply information theory on a mathematical model of cell signaling of CAR-mediated activation following antigen encounter. First, we estimated channel capacity for CAR-4-1BB-mediated NFκB signal transduction. Next, we evaluated the pathway’s ability to distinguish contrasting “low” and “high” antigen concentration levels, depending on the amount of intrinsic noise. Finally, we assessed the fidelity by which NFκB activation reflects the encountered antigen concentration, depending on the prevalence of antigen-positive targets in tumor population. We found that in most scenarios, fold change in the nuclear concentration of NFκB carries a higher channel capacity for the pathway than NFκB’s absolute response. Additionally, we found that most errors in transducing the antigen signal through the pathway skew towards underestimating the concentration of encountered antigen. Finally, we found that disabling IKKβ deactivation could increase signaling fidelity against targets with antigen-negative cells. Our information-theoretic analysis of signal transduction can provide novel perspectives on biological signaling, as well as enable a more informed path to cell engineering.
Innovative approach for vaccinating Nile tilapia,Oreochromis niloticusagainstStreptococcus agalactiaeusing an ozone nanobubble pre-treatment, VAC in BAG and VAC in FEED
Authors: Vinh Nguyen Tien , Dong Ha Thanh , Senapin Saengchan , Pumpuang Suntree , Lan Nguyen Giang Thu , Wilairat Bulakorn , Garud Pradnya R. , St-Hilaire Sophie , Linh Nguyen Vu , Phanphut Wattana , Shinn Andrew P.
Published: June 2023

The treatment of Nile tilapia with ozone nanobubbles (ONb) prior to vaccination with an immersible heat-killedStreptococcus agalactiae(Sa) vaccine has been reported to modulate and enhance both innate and specific immunity. The efficacy of this novel vaccination strategy is explored further in field trials. This strategy involved a short-term treatment of ONb to activate the fish’s immunity prior to immersion vaccination during their transportation in oxygenated plastic bags (VAC in BAG), followed by two oral boosters during the grow-out stage mixing vaccine in feed (VAC in FEED). The field trial was conducted over 112 days in open cages, comprising four groups: normal aeration control (AC), normal aeration + vaccine (AV), ONb control (NC), and ONb + vaccine (NV). The efficacy of the vaccine was evaluated by measuring specific antibodies forS. agalactiae, monitoring expressions ofIgMandIgTtranscripts in the gills and head kidney every two weeks, and a laboratory pathogen challenge. Results found that fish in the NV group had significant increases in anti-S. agalactiaeantibodies after the primary dose, whereas fish in the AV group required an oral booster dose to produce significant anti-S. agalactiaeantibodies. In the vaccinated groups (AV and NV), onlyIgMwas observed to be upregulated at 14 days post-immersion (dpi), while this gene was upregulated in both gills and head kidney in the NC group. No statistically significant upregulation ofIgTwas recorded in any group at any time point. Despite a decline in the levels of specific antibodies among the vaccinated groups at the time of challenge (88 dpi), the NV and AV groups demonstrated a relative percent survival (RPS) of 50% and 46.7%, respectively, following a relatively high injection dose ofS. agalactiaeinjection (0.1 mL of 108CFU/mL). In summary, this ONb, VAC in BAG and VAC in FEED vaccination strategy represents a promising alternative to the undesirable handling and costly injection approach used within the Nile tilapia industry.
Trained immunity in human monocyte enhances myeloid-T-cell pathogenic crosstalk in Ankylosing Spondylitis
Authors: Zhao Jinyi , Liu Feng , Worth Claudia , Simone Davide , Penkava Frank , Shi Hui , Li Jiaqi , Lama Shristi , Fang Hai , Lee Jeong Seok , Kim Tae-Jong , Duan Lihua , Bowness Paul , Chen Liye
Published: June 2023

Recent studies in infectious, cardiovascular and neurodegenerative diseases have established the presence of memory in innate immune cells. This “trained immunity (TI)” leads to an enhanced response to a second challenge. Monocytes in Ankylosing Spondylitis (AS), a common form of inflammatory arthritis, are known to be hyper-responsive to microbial stimulus lipopolysaccharide (LPS). We asked if TI is present in AS monocytes and, if so, how it contributes to disease pathology.

Using Single-cell RNA sequencing (scRNA-seq), flow cytometry and enzyme-linked immunosorbent assays (ELISA), we identify a subset of monocytes from AS patients exhibiting features of trained immunity and being hyperresponsive to LPS stimulation. Surprisingly, both trained monocytes in AS and β-glucan-trained monocytes from healthy donors are hyper-responsive to T-cell-induced activation. scRNA-seq of AS synovial mononuclear cells shows enrichment of a monocyte population with these/analogous features. Additionally, T cell-stimulated monocytes act back on T-cells to support Th17 responses (of established pathology in AS). Lastly, using genetic and chemical perturbations we show that ERN1, an AS risk gene enriched in this trained monocyte population, contributes to T-cell-induced monocyte activation.

Our data provide strong evidence for the first time for the key role of TI in common human inflammatory arthritis.
Modulation of neuronal activity in cortical organoids with bioelectronic delivery of ions and neurotransmitters
Authors: Park Yunjeong , Hernandez Sebastian , Hernandez Cristian O. , Schweiger Hunter E. , Li Houpu , Voitiuk Kateryna , Dechiraju Harika , Hawthorne Nico , Muzzy Elana M. , Selberg John A. , Sullivan Frederika N. , Urcuyo Roberto , Salama Sofie R. , Aslankoohi Elham , Teodorescu Mircea , Mostajo-Radji Mohammed A. , Rolandi Marco
Published: June 2023

Precise modulation of brain activity is fundamental for the proper establishment and maturation of the cerebral cortex. To this end, cortical organoids are promising tools to study circuit formation and the underpinnings of neurodevelopmental disease. However, the ability to manipulate neuronal activity with high temporal resolution in brain organoids remains limited. To overcome this challenge, we introduce a bioelectronic approach to control cortical organoid activity with the selective delivery of ions and neurotransmitters. Using this approach, we sequentially increased and decreased neuronal activity in brain organoids with the bioelectronic delivery of potassium ions (K+) and γ-aminobutyric acid (GABA), respectively, while simultaneously monitoring network activity. This works highlights bioelectronic ion pumps as tools for high-resolution temporal control of brain organoid activity toward precise pharmacological studies that can improve our understanding of neuronal function.
Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome
Authors: Wu Christine C. , Tsantilas Kristine A. , Park Jea , Plubell Deanna , Sanders Justin A. , Naicker Previn , Govender Ireshyn , Buthelezi Sindisiwe , Stoychev Stoyan , Jordaan Justin , Merrihew Gennifer , Huang Eric , Parker Edward D. , Riffle Michael , Hoofnagle Andrew N. , Noble William S. , Poston Kathleen L. , Montine Thomas J. , MacCoss Michael J.
Published: June 2023

Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ∼1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a “liquid biopsy,” while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer’s disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson’s disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
eIF4E1b is a non-canonical eIF4E required for maternal mRNA dormancy
Authors: Lorenzo-Orts Laura , Strobl Marcus , Steinmetz Benjamin , Leesch Friederike , Pribitzer Carina , Schutzbier Michael , Dürnberger Gerhard , Pauli Andrea
Published: June 2023

Maternal mRNAs are essential for protein synthesis during oogenesis and early embryogenesis. To adapt translation to specific needs during development, maternal mRNAs are translationally repressed by shortening the polyA tails. While mRNA deadenylation is associated with decapping and degradation in somatic cells, maternal mRNAs with short polyA tails are stable. Here we report an essential role for the germline-specific paralog of the mRNA cap-binding factor eIF4E, known as eIF4E1b, in the storage and repression of maternal mRNAs with short polyA tails. eIF4E1b binds to the mRNA cap and is targeted to ribonucleoprotein complexes through its direct interaction with eIF4ENIF1/4E-T. In early embryos, eIF4E1b binds to a specific set of translationally repressed mRNAs with short or no polyA tails, such as histone mRNAs, which are translated later on during embryogenesis. Consistent with an important role in maternal mRNA dormancy, mutation ofeIF4E1bin zebrafish impairs female germline development. Understanding the mechanism and function of eIF4E1B provides new insights into fundamental post-transcriptional regulatory principles governing early vertebrate development.
Roadmap For The Expression Of Canonical and Extended Endocannabinoid System Receptors and Proteins in Peripheral Organs of Preclinical Animal Models
Authors: Rosado-Franco JJ , Ellison AL , White CJ , Price AS , Moore CF , Williams RE , Fridman LB , Weerts EM , Williams DW
Published: June 2023

The endocannabinoid system is widely expressed throughout the body and is comprised of receptors, ligands, and enzymes that maintain metabolic, immune, and reproductive homeostasis. Increasing interest in the endocannabinoid system has arisen due to these physiologic roles, policy changes leading to more widespread recreational use, and the therapeutic potential ofCannabisand phytocannabinoids. Rodents have been the primary preclinical model of focus due to their relative low cost, short gestational period, genetic manipulation strategies, and gold-standard behavioral tests. However, the potential for lack of clinical translation to non-human primates and humans is high as cross-species comparisons of the endocannabinoid system has not been evaluated. To bridge this gap in knowledge, we evaluate the relative gene expression of 14 canonical and extended endocannabinoid receptors in seven peripheral organs of C57/BL6 mice, Sprague-Dawley rats, and non-human primate rhesus macaques. Notably, we identify species- and organ-specific heterogeneity in endocannabinoid receptor distribution where there is surprisingly limited overlap among the preclinical models. Importantly, we determined there were only five receptors (CB2, GPR18, GPR55, TRPV2, and FAAH) that had identical expression patterns in mice, rats, and rhesus macaques. Our findings demonstrate a critical, yet previously unappreciated, contributor to challenges of rigor and reproducibility in the cannabinoid field, which has profound implications in hampering progress in understanding the complexity of the endocannabinoid system and development of cannabinoid-based therapies.
Liquid-liquid phase separation and aggregation of a globular folded protein SUMO1
Authors: Arora Simran , Roy Debsankar Saha , Maiti Sudipta , Koti Ainavarapu Sri Rama
Published: June 2023

Many studies in recent years have investigated the phenomenon of liquid-liquid phase separation (LLPS) in proteins. LLPS is reported in intrinsically disordered proteins (IDPs) or in proteins with intrinsically disordered regions (IDRs) lacking a well-defined three-dimensional structure. However, the occurrence of LLPS in folded proteins, that lacks IDRs is not widely known. It is generally assumed that the compact structure and limited flexibility of folded proteins hinder their ability to establish weak and dynamic interactions crucial for LLPS. Contrary to the prevailing understanding, we present direct evidence of rapid phase separation of a globular protein, SUMO1, occurring under crowded conditions at physiological pH and room temperature. The protein molecules in the liquid droplets undergo conformational changes with time, monitored by intrinsic tryptophan fluorescence. We also demonstrate the phase transition of SUMO1 droplets from liquid to solid state with maturation, ultimately leading to aggregation. The SUMO1 aggregates contain a significant amount of beta-sheet structure but have amorphous morphology, probed by several spectroscopic techniques (Thioflavin T fluorescence, Raman Spectroscopy, and TEM). Our findings provide insights into the behaviour of SUMO1 protein in crowded environment, albeit, the underlying mechanism is not well understood and may differ from those of IDPs. Furthermore, SUMO1 protein is known to colocalize in inclusion bodies of IDPs, and therefore, LLPS of SUMO1 may have important biological implications in neurodegenerative diseases.
Excitatory neurons derived from human induced Pluripotent Stem Cells show transcriptomic differences in Alzheimer’s patients from controls
Authors: Sagar Ram , Azoidis Ioannis , Zivko Cristina , Xydia Ariadni , Oh Esther , Rosenberg Paul , Lyketsos Constantine G. , Mahairaki Vasiliki , Avramopoulos Dimitrios
Published: June 2023

The recent advances in creating pluripotent stem cells from somatic cells and differentiating them into a variety of cell types is allowing us to study them without the caveats associated with disease related changes. We have generated induced Pluripotent Stem Cells (iPSCs) from eight Alzheimer’s disease (AD) patients and six controls and used lentiviral delivery to differentiate them into excitatory glutamatergic neurons. We have performed RNA sequencing on these neurons and compared the Alzheimer’s and control transcriptomes. We find that 621 genes show differences in expression levels at adjusted p<0.05 between the case and control derived neurons. These genes show significant overlap and direction concordance with genes reported from a Single cell transcriptome study of Alzheimer’s patients, they contain 5 genes implicated with AD from genome wide association studies and they appear to be part of a larger functional network as indicated by an excess of interactions between them observed in the protein-protein interaction database STRING. Exploratory analysis with Uniform Manifold Approximation and Projection (UMAP) suggests distinct clusters of patients, based on gene expression, who maybe clinically different. If confirmed this finding will to contribute to precision medicine approaches to subgroup Alzheimer’s disease.
Senescent Subtypes Transition Model
Authors: Singh Ghanendra
Published: June 2023

Senescence has both beneficial and detrimental roles across the tissues over time. This dual nature is mediated by the senescence-associated secretory phenotype (SASP). Still, transient and persistent SASP secretion is poorly understood. There are some unknown mechanisms through which phenotypic transition takes place from beneficial helper (H) senescent cells to deleterious (D) senescent cell states. NOTCH1 is suggested to mediate switching between the different SASP secretomes. NOTCH1 also suppresses a transcription factor C/EBPβduring the SASP secretion. Therefore, a hypothesis is proposed about the existence of negative feedback from C/EBPβto NOTCH1 together forming a senescence-switching circuit that might be mediating this phenotypic transition at the molecular level. Using a population dynamics model with competitive interaction to decipher the underlying transition mechanism between the senescent cell subtypes and a mechanistic model to explain the underlying molecular mechanisms of NOTCH1 signaling in modulating the two waves of SASP secretion. By designing effective senescence therapies with selective removal of deleterious senescent cells and maintaining sufficient helper senescent cells can enhance health span and reduce age-related effects.
NMR structure verifies the eponymous degenerate zinc finger domain of transcription factor ZNF750
Authors: Rua Antonio J. , Whitehead Richard D. , Alexandrescu Andrei T.
Published: June 2023

ZNF750 is a nuclear transcription factor that activates skin differentiation and has tumor suppressor roles in several cancers. Unusually, ZNF750 has only a single zinc-finger (ZNF) domain, Z*, with an amino acid sequence that differs markedly from the CCHH family consensus. Because of its sequence differences Z* is classified as degenerate, presumed to have lost the ability to bind the zinc ion required for folding. AlphaFold predicts an irregular structure for Z* with low confidence. Low confidence predictions are often inferred to be intrinsically disordered regions of proteins, which would be the case if Z* did not bind Zn2+. We use NMR and CD spectroscopy to show that a 25-51 segment of ZNF750, corresponding to the Z* domain, folds into a well-defined antiparallel ββα tertiary structure with a pM dissociation constant for Zn2+, and a thermal stability >80 °C. Of three alternative Zn2+ligand sets, Z* uses a CCHC rather than the expected CCHH motif. The switch in the last ligand maintains the folding topology and hydrophobic core of the classical ZNF motif. CCHC ZNFs are associated with protein-protein interactions but Z* binds DNA. Since the metal chelating site is on the other side of the molecule, it suggests functional preferences are a result of divergent evolution rather than physical constraints on the structure. The structure of Z* provides a context for understanding the domain’s DNA-binding properties and mutations associated with cancers. We expect other ZNFs currently classified as degenerate, are CCHC-type structures like Z*.
RNA Helicase DDX3 Regulates RAD51 Localization and DNA Damage Repair in Ewing Sarcoma
Authors: Randolph Matthew E. , Afifi Marwa , Gorthi Aparna , Weil Rachel , Wilky Breelyn A. , Weinreb Joshua , Ciero Paul , ter Hoeve Natalie , van Diest Paul J. , Raman Venu , Bishop Alexander J. R. , Loeb David M.
Published: June 2023

We previously demonstrated that RNA helicase DDX3X (DDX3) can be a therapeutic target in Ewing sarcoma (EWS), but its role in EWS biology remains unclear. The present work demonstrates that DDX3 plays a unique role in DNA damage repair (DDR). We show that DDX3 interacts with several proteins involved in homologous recombination, including RAD51, RECQL1, RPA32, and XRCC2. In particular, DDX3 colocalizes with RAD51 and RNA:DNA hybrid structures in the cytoplasm of EWS cells. Inhibition of DDX3 RNA helicase activity increases cytoplasmic RNA:DNA hybrids, sequestering RAD51 in the cytoplasm, which impairs nuclear translocation of RAD51 to sites of double-stranded DNA breaks thus increasing sensitivity of EWS to radiation treatment, bothin vitroandin vivo. This discovery lays the foundation for exploring new therapeutic approaches directed at manipulating DDR protein localization in solid tumors.
AGpr35tuned gut-brain metabolic axis regulates depressive-like behavior
Authors: Cheng Lingsha , Wu Haoqian , Cai Xiaoying , Wang Qiong , Zhang Youying , Yin Zhe , Yan Qingyuan , Hou Yuanlong , Yuan Yonggui , Wang Guangji , Zhang Xueli , Hao Haiping , Zheng Xiao
Published: June 2023

Gene-environment interactions shape animal behavior and the susceptibility to neurobehavioral symptoms such as depression. However, little is known about the signaling pathway that integrates genetic and environmental inputs with neurobehavioral outcomes, preventing the development of targeted therapies. Here we report thatGpr35engages a gut microbe-to-brain metabolic pathway to modulate neuronal plasticity and depressive behavior in mice. Chronic stress decreases gut epithelialGpr35, the genetic deletion of which induces despair and social impairment in a microbiome-dependent manner. We identify a dominant role for the imbalance of microbe-derived indole-3-carboxaldehyde (IAld) and indole-3-lactate (ILA) in the behavioral symptoms withGpr35deficiency. Mechanistically, these bacterial metabolites counteractively modulate dendritic spine density and synaptic transmission in the nucleus accumbens. Supplementation of IAld, which is similarly decreased in depressive patients, produce anti-depressant effects in mice with stress or gut epithelialGpr35deficiency. Together, these findings identify a genetics-shaped gut-brain connection underlying the susceptibility to depression and suggest a microbial metabolite-based therapeutic strategy to genetic predisposition.
Genome-wide association studies reveal a rapidly evolving candidate avirulence effector in the Cercospora leaf spot pathogenCercospora beticola
Authors: Chen Chen , Keunecke Harald , Bemm Felix , Gyetvai Gabor , Neu Enzo , Kopisch-Obuch Friedrich J. , McDonald Bruce A. , Stapley Jessica
Published: June 2023

The major resistance geneBvCR4recently bred into sugar beets provides a high level of resistance to Cercospora leaf spot caused by the fungal pathogenCercospora beticola. The occurrence of pathogen strains virulent toBvCR4was studied using field trials in Switzerland. Virulence of a subset of these strains was evaluated in a field trial conducted under elevated artificial disease pressure. We created a newC. bet colareference genome and mapped whole genome sequences of 256 field-collected isolates. These were combined with virulence phenotypes to conduct three separate GWAS to identify candidate avirulence genes. We identified a locus associated with avirulence containing a single candidate avirulence effector gene namedAvrCR4. All virulent isolates either lackedAvrCR4or had non-synonymous mutations within the gene.AvrCR4was present in all 74 isolates from non-BvCR4hybrids, whereas 33 of 89 isolates fromBvCR4hybrids carried a deletion. We also mapped genomic data from 190 publicly available U.S. isolates to our new reference genome. TheAvrCR4deletion was found in only one of 95 unique isolates from non-BvCR4hybrids in the U.S.AvrCR4presents a unique example of an avirulence effector in which virulent alleles have only recently emerged. Most likely these were selected out of standing genetic variation after deployment ofBvCR4. Identification ofAvrCR4will enable real-time screening ofC. beticolapopulations for the emergence and spread of virulent isolates.
Opening the black box between strategic vision on digitalization and SMEs digital transformation: the mediating role of resource orchestration
Authors: Cheng Songsong , Fan Qunpeng , Dagestani Abd Alwahed
Published: June 2023

Purpose

In the digital era, the competitiveness of an enterprise is highly dependent on the success of its digital transformation. The effectiveness of such transformation, in turn, relies heavily on the organization's strategic vision and resource fitness. Accordingly, the authors aim to explore the impact of strategic vision on digitalization (SVD) on the digital transformation of small- and medium-sized enterprises (SMEs), drawing on the perspective of resource orchestration theory.

Design/methodology/approach

Based on first-hand interview data from 347 Chinese SMEs, the research model was tested empirically by both Structural Equation Modeling and Fuzzy Set Qualitative Comparative Analysis (fsQCA).

Findings

The study results supported that the positive effect of SVD on digital transformation, and the mediating effect of resource orchestration (resource structuring, resource bundling and resource leveraging) accounts for the relationship between SVD and digital transformation. Further, the fsQCA showed that neither SVD nor resource orchestration alone constitutes a necessary condition for high digital transformation in SMEs, and that SVD and resource orchestration elements constitute three configuration paths that drive SMEs to achieve high-level digital transformation.

Originality/value

To the authors knowledge, this is the first study of its kind to theorize and empirically examine how SVD affects SMEs digital transformation. In addition, the authors have highlighted the importance of resource orchestration in forging a link between SVD and digital transformation. The research contributes to the resource orchestration theory and digitalization literature and provides guidelines on how SMEs can realize digital transformation.
A conceptual framework of the perceived marketability of independent professionals
Authors: Ghosh Koustab , McDonnell Anthony , Irum Ayesha
Published: June 2023

Independent professionals represent a highly skilled contractual based workforce. In this paper, we propose a conceptual framework that explains the career construction mechanism of independent professionals. Specifically, we theorize that their boundaryless career orientation favorably influences the perception of their marketability via their involvement in career construction activities. Additionally, we elucidate the intervening role of their career competencies, physical and psychological mobility in augmenting or dampening perceived marketability as a career outcome. Differing to traditionally employed professionals, we argue that independent professional careers can be better explained conjointly, rather than separately, by boundaryless career theory and career construction theory. This paper has practical relevance in highlighting the significance of career construction activities by independent professionals for achieving positive career outcomes while pursuing a boundaryless career.
Research output of radiologists in Australia and New Zealand: Strengths, weaknesses and future directions
Authors: Clements Warren , So Joanne , Koukounaras Jim , Lau Gabes , Lukies Matthew W
Published: June 2023

Introduction

Clinical radiology is a popular career. However, academic radiology in Australia and New Zealand (ANZ) has not traditionally been a strength of the specialty which has a focus on clinical medicine and has been influenced by corporatisation of the specialty. The aim of this study was to review the source(s) of radiologist‐led research in Australia and New Zealand, to identify areas of relative deficiency and propose plans to improve research output.

Methods

A manual search was performed of all manuscripts in seven popular ANZ journals, where the corresponding or senior author was a radiologist. Publications between January 2017 and April 2022 were included.

Results

There were 285 manuscripts from ANZ radiologists during the study period. This equates to 10.7 manuscripts per 100 radiologists based on RANZCR census data. Radiologists in Northern Territory, Victoria, Western Australia, South Australia and the Australian Capital Territory all produced manuscripts above the corrected mean incidence rate of 10.7 manuscripts per 100 radiologists. However, locations including Tasmania, New South Wales, New Zealand and Queensland were below the mean. The majority of manuscripts arose from public teaching hospitals with accredited trainees (86%), and there were a higher proportion of manuscripts published by female radiologists (11.5 compared to 10.4 per 100 radiologists).

Conclusion

Radiologists in ANZ are academically active; however, interventions aimed at increasing output could be targeted at certain locations and/or areas within a busy private sector. Time, culture, infrastructure and research support are vital, but personal motivation is also extremely important.
Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome
Authors: Stamatas Georgios N. , Roux Pierre‐Francois , Boireau‐Adamezyk Elise , Lboukili Imane , Oddos Thierry
Published: June 2023

Infant and adult skin physiology differ in many ways; however, limited data exist for older children. To further investigate the maturation processes of healthy skin during childhood. Skin parameters were recorded in 80 participants of four age groups: babies (0–2 years), young children (3–6 years), older children (7–<10 years) and adults (25–40 years). Overall, skin barrier function continues to mature, reaching adult levels of transepidermal water loss (TEWL), lipid compactness, stratum corneum (SC) thickness and corneocyte size by the age of about 6 years. Higher levels of lactic acid and lower levels of total amino acids in the SC of babies and young children further indicate higher cell turnover rates. In all age groups, TEWL and skin surface hydration values remain higher on the face compared with the arm. Skin becomes darker and contains higher levels of melanin with increasing age. The composition of skin microbiome of the dorsal forearm in all children groups is distinct from that in adults, with Firmicutes predominating in the former and Proteobacteria in the latter. Skin physiology, along with the skin microbiome, continues to mature during early childhood in a site‐specific manner.
Editors’ introduction to Sound “Repatriation” in South America: The Politics of Collaborative Archive Reactivations
Authors: Kummels Ingrid , Cánepa Gisela
Published: June 2023

The introduction first gives insights into the state of the art of sound “repatriation” concerning the way historical and current recordings of verbal arts, music, and dance are brought back into circulation in originating communities. Sound restitution also seeks to level the epistemological divide resulting from conventional archiving. The groundbreaking, collaborative reactivations taking place in South America explored within the three articles in this journal issue are presented. External researchers and local co‐researchers join forces to create shared soundscapes on an equitable basis; they develop innovative research designs for restitution and participate in webs of collaboration that take into account the recuperation of sound traditions that expert vocalists and instrumentalists, grassroots researchers, Indigenous leaders, and cultural entrepreneurs have independently initiated. Finally, the inclusion of co‐researchers in the curatorship of museum exhibitions and the need to identify anyone who may claim rights to oratory, music, and dance is addressed.
Long‐distance transfer of unwell neonates: A case series
Authors: Bills Hannah , Woodward Louise , Martin Simone
Published: June 2023

Aim

The Northern Territory Neonatal Emergency Transport Service (NETS NT) pilot was created in April 2018 to expedite the transfer of critically unwell neonates to specialised interstate centres. The aim of this paper is to describe long‐distance retrievals undertaken during the first 3 years of operation of the service.

Methods

A case series is described comprising neonates requiring long‐distance aeromedical transfer (>2500 km) by NETS NT between April 2018 and June 2021. Data were obtained from hospital and transport service documentation. This was supplemented by four semi‐structured interviews with transport staff.

Results

Thirty neonates were transferred via NETS NT during the investigation period, including 19 transfers >2500 km. Of these, 18/19 (94.7%) required respiratory support, 8/19 (42.1%) were intubated and 4/19 (21.1%) required inotropic support. The average length of transport was 7.5 h (5.6–8.9). Twelve patients had in‐flight documentation available. Eight required increased oxygen administration 8/12 (66.6%). The median change in FiO2 was an increase of 0.02 (−0.05 to 0.45).

Conclusions

The NETS NT has been successfully established to transport high‐risk neonates to interstate quaternary health services when required. Future recommendations for the service include ongoing implementation of systems and processes to strengthen all aspects of governance and operations using suitably adapted resources from established Australian retrievals services.