bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of diagnosis delay and disease activity with burden on Daily life in 4150 European patients with Systemic Lupus Erythematosus
Authors: Cornet Alain , Andersen Jeanette , Marchiori Francesca , Rubio Blanca , Mertz Philippe , Arnaud Laurent ,   the patient association Lupus Europe
Published: November 2022

Objective

Despite significant improvements in diagnosis delay and treatment strategies, the burden of Systemic Lupus Erythematosus (SLE) remains high. The objective of the study was to assess the association between diagnosis delay, disease activity and burden on daily life (BoDL) in a large sample of European patients with SLE.

Methods

In May 2020, Lupus Europe, the European umbrella patient association for SLE, conducted a multilingual anonymous online cross-sectional study to individuals with a self-reported physician’s diagnosis of SLE living in Europe. The BoDL score was computed using 1 to 5 Likert scales on 5 domains (mobility, anxiety/depression, self-care, daily activities and pain/discomfort) and the sum was rescaled on a 0 (minimum Burden on daily life) to 100 (maximum BoDL) scale. Comparisons between independent groups were made using the Mann-Whitney test for continuous outcomes and the Chi-2 test (or Fisher’s exact test) for quantitative data.

Results

Data of 4,150 SLE patients from 35 European countries were analysed. Those with a diagnosis of SLE within 2 years of first symptoms had significantly lower mean BoDL scores than those diagnosed after 5 years (33.6 versus 44.0, p<0.001). The BoDL score was better in SLE patients feeling that their lupus had been under control during the last 3 months versus the others (34.0% versus 47.6%, p<0.001).

Conclusion

This large international study highlights the association between diagnosis delay and self-perceived disease activity with the burden of the disease on the daily life of people living with SLE. Healthcare pathways, which may accelerate diagnosis and optimize therapeutic management, are necessary to improve patients’ outcomes in SLE.
Exploration of wastewater surveillance for Monkeypox virus
Authors: Mejia Edgard M , Hizon Nikho A , Dueck Codey E , Lidder Ravinder , Daigle Jade , Wonitowy Quinn , Medina Nestor G , Mohammed Umar P , Cox Graham W , Safronetz David , Hagan Mable , Strong Jim , Nichani Anil , Mulvey Michael R , Mangat Chand S
Published: November 2022

The sudden emergence and spread of Monkeypox in non-endemic parts of the world is currently not well understood. Infections are often mis-diagnosed and surveillance strategies are scarce. Wastewater-based surveillance (WBS) of human Monkeypox virus (MPXV) can help supplement our current clinical surveillance and mitigation efforts. WBS has shown to be an effective tool in monitoring the spread of other infectious pathogens, such as SARS-CoV-2 and its variants, and has helped guide public health actions. In this study, we describe how WBS can be used to detect MPXV in wastewater. We conducted WBS for MPXV in 22 wastewater treatment plants (WWTPs) over a period of 14 weeks. Nucleic acids were extracted using the MagAttract PowerMicrobiome DNA/RNA extraction kit. Three real-time qPCR assays were assessed for the detection of MPXV in wastewater. These included the G2R assays (G2R_WA and G2R_G) developed by the Centers for Disease Control and Prevention (CDC) in 2010, as well as an in-house-developed assay (G2R_NML). The G2R_G (generic) assay was designed to detect both the Congo and West African clades (re-named to Clades one and two, respectively) of viruses while the G2R_WA assay was designed to detect the West African clade (Clade one). The G2R_NML assay was designed using reference genomes of the 2022 MPXV outbreak. Our results show that all three assays have similar limits of detection and are all able to detect the presence of MPXV in wastewater. Following detection through real time qPCR, Sanger sequencing was performed on the resulting amplicon products, with the assembled contigs then undergoing analysis using nucleotide Basic Local Alignment Search Tool (BLAST). Due in part to the longer amplicon size of the G2R_NML assay, a significantly greater number of positive detections were identified as originating from MPXV compared to the CDC G2R assays. The ability to detect trace amounts of MPXV in wastewater as well as obtain Sanger sequence confirmation, has allowed for the successful surveillance of this virus in wastewater.
Pentameric assembly of glycine receptor intracellular domains provides insights into gephyrin clustering
Authors: Macha Arthur , Grünewald Nora , Havarushka Nastassia , Burdina Nele , Toelzer Christine , Merkler Yvonne , Cabrera-Orefice Alfredo , Brandt Ulrich , Pauly Thomas , Nagel-Steger Luitgard , Niefind Karsten , Schwarz Guenter
Published: November 2022

Pentameric ligand-gated ion channels represent a large family of receptors comprising an extracellular domain, four transmembrane helices and a cytosolic intracellular domain (ICD). ICDs play important roles in receptor localization and trafficking, thus regulating synaptic activity and plasticity. Glycine and GABA type A receptor ICDs bind to the scaffolding protein gephyrin, a master regulator of inhibitory synapses. Here we report the use of yeast lumazine synthase as soluble pentameric protein scaffold for the study of receptor ICDs derived from GlyR α1− and β-subunits. We were able to create ICDs assemblies in a homo- (LS-βICD) and hetero-pentameric state (LS-αβICD) and provide first-in-class structural insights on their high structural flexibility using small angle X-ray scattering. We report a high-affinity interaction between the LS-αβICD and gephyrin leading to thein vitroformation of high-molecular mega-Dalton complexes composed of three gephyrin trimers and three pentamers as basic building block. Depending on the stoichiometric ratios between gephyrin and LS-ICDs the formed complexes grow or shrink in size. In cells, LS-ICDs efficiently recruited gephyrin and were able to accumulate gephyrin at GABAergic synapses in neurons. Our findings collectively propose a new, potentially general, mechanistic concept for a gephyrin-dependent bridging of GlyRs at the inhibitory synapse.
A tracheal aspirate-derived airway basal cell model reveals a proinflammatory epithelial defect in congenital diaphragmatic hernia
Authors: Wagner Richard , Amonkar Gaurang M. , Wang Wei , Shui Jessica E. , Bankoti Kamakshi , Tse Wai Hei , High Frances A. , Zalieckas Jill M. , Buchmiller Terry L. , Zani Augusto , Keijzer Richard , Donahoe Patricia K. , Lerou Paul H. , Ai Xingbin
Published: November 2022

Rationale

Congenital diaphragmatic hernia (CDH) is characterized by incomplete closure of the diaphragm and lung hypoplasia. The pathophysiology of lung defects in CDH is poorly understood.

Objectives

To establish a translational model of human airway epithelium in CDH for pathogenic investigation and therapeutic testing.

Methods

We developed a robust methodology of epithelial progenitor derivation from tracheal aspirates of newborns. Basal stem cells (BSCs) from CDH patients and preterm and term, non-CDH controls were derived and analyzed by bulk RNA-sequencing, ATAC-sequencing, and air-liquidinterface differentiation. Lung sections from fetal human CDH samples and the nitrofen rat model of CDH were subjected to histological assessment of epithelial defects. Therapeutics to restore epithelial differentiation were evaluated in human epithelial cell culture and the nitrofen rat model of CDH.

Measurements and Main Results

Transcriptomic and epigenetic profiling of CDH and non-CDH basal stem cells reveals a disease-specific, proinflammatory signature independent of severity or hernia size. In addition, CDH basal stem cells exhibit defective epithelial differentiationin vitrothat recapitulates epithelial phenotypes found in fetal human CDH lung samples and fetal tracheas of the nitrofen rat model of CDH. Furthermore, steroid treatment normalizes epithelial differentiation phenotypes of human CDH basal stem cellsin vitroand in nitrofen rat tracheasin vivo.

Conclusions

Our findings have identified an underlying proinflammatory signature and BSC differentiation defects as a potential therapeutic target for airway epithelial defects in CDH.
Investigating vaccine uptake dynamics of neutrophils using HIV-1 Envelope glycoprotein trimer
Authors: Ngo Philip Y.X.
Published: November 2022

Rhesus macaques were previously immunized with two distinct subunit vaccine candidates, to monitor antigen trafficking by immune cells infiltrating the site of injection. The first, a formulation based on the HIV-1 envelope glycoprotein (Env) and the other based on the RSV-fusion (F) protein. Neutrophil and monocyte uptake profiles were vastly different between the vaccine candidates despite similar cell infiltration numbers, hinting that antigen characteristics could orchestrate different innate responses. Notably, the Env trimer is significantly more glycosylated than RSV-F.

Recapitulating thesein vivoobservations under reliablein vitroconditions is thus of importance in exploring uptake dynamics and insights into the manipulation of innate responses. The study later demonstrated a complement component, Mannose Binding Lectin (MBL), to be resistant to heat-inactivation and binds Env in a CRDdependent manner. Interestingly, the data suggests a heat-labile component of the serum hinders MBL from binding to Env, which corresponded to a weaker uptake profile. Also, the generation of 3 differentially glycosylated Env variants to study glycan-mediated uptake by neutrophils derived contrary observations. In all, modulation of MBL interactions could potentially target specific innate immune cells, particularly neutrophils, and the later development of adaptive immune responses after immunization.
Nucleus accumbens dopamine release reflects the selective nature of pair bonds
Authors: Pierce Anne F. , Protter David S.W. , Chapel Gabriel D. , Cameron Ryan T. , Donaldson Zoe R.
Published: November 2022

In monogamous species, prosocial behaviors directed towards partners are dramatically different from those directed towards unknown individuals and potential threats. Dopamine release in the nucleus accumbens plays an important role in guiding social behavior, however, its role in real time social decision making in a monogamous species remains largely unknown. We used monogamous prairie voles to investigate how dopamine release differs in voles when seeking and interacting with a pair bonded partner or a novel vole. Employing the sub-second temporal resolution of the fluorescent biosensor, GRABDA, during a social operant task, we found that partner seeking, anticipation, and interaction resulted in more dopamine release than the same events directed towards a novel vole. Furthermore, partner-elicited dopamine release decreases after prolonged partner separation. Thus, differences in partner- and novel-elicited dopamine release reflect the selective nature of pair bonds and may drive the social behaviors that reinforce and cement bonds over time, eroding after partner loss to facilitate new bond formation.
Transcriptome dynamics ofPseudomonas aeruginosaduring transition from replication-uncoupled to -coupled growth
Authors: Alpers Kathrin , Vatareck Elisabeth , Gröbe Lothar , Müsken Mathias , Scharfe Maren , Häussler Susanne , Tomasch Jürgen
Published: November 2022

In bacteria, either chromosome duplication is coupled to cell division with only one replication round per cell cycle or DNA is replicated faster than the cells divide thus both processes are uncoupled. Here, we show that the opportunistic pathogenPseudomonas aeruginosaswitches from fast uncoupled to sustained coupled growth when cultivated under standard laboratory conditions. The transition was characterized by fast-paced, sequential changes in transcriptional activity along theori-teraxis of the chromosome reflecting adaptation to the metabolic needs during both growth phases. Quorum sensing (QS) activity was highest at the onset of the coupled growth phase during which only a quarter of the cells keeps replicating. RNA sequencing of subpopulations of these cultures sorted based on their DNA content, revealed a strong gene dosage effect as well as specific expression patterns for replicating and non-replicating cells. Expression of flagella andmexE, involved in multi drug efflux was restricted to cells that did not replicate, while those that did showed a high activity of the cell division locus and recombination genes. A possible role of QS in the formation of these subpopulations upon switching to coupled growth could be a subject of further research.

Significance statement

The coordination of gene expression with the cell cycle has so far been studied only in a handful of bacteria, the bottleneck being the need for synchronized cultures. Here, we determined replication-associated effects on transcription by comparingPseudomonas aeruginosacultures that differ in their growth mode and number of replicating chromosomes. We further show that cell cycle-specific gene regulation can be principally identified by RNA sequencing of subpopulations from cultures that replicate only once per cell division and that are sorted according to their DNA content. Our approach opens the possibility to study asynchronously growing bacteria from a wide phylogenetic range and thereby enhance our understanding of the evolution of cell-cycle control on the transcriptional level.
The Nature of Race in Germany: A systematic literature review of human classifications in German life sciences
Authors: Bartram Isabelle , Schnieder Laura , Ellebrecht Nils , Ruland Florian , Plümecke Tino , Nieden Andrea zur
Published: November 2022

The use of human diversity classifications like race, ethnicity, ancestry, or migration background entails a range of scientific as well as social consequences, therefore, a careful application is vital. In this article, we present results from a systematic literature review and subsequent quantitative content analysis based on 546 papers focusing on classifications applied in life sciences studies at German research institutions. Our aim is to capture a snap-shot of current classification practices applied to categorize humans across various disciplines and fields in a specific national context that remains underexposed in this regard. The review substantiates a) the results from earlier studies that point to heterogeneity, inconsistency and vagueness of human classifications used in the life sciences, and b) underlines the presumed specificity of the German science context, where the term “race” is comparatively little used. Our findings stress the need for German researchers to partake in the ongoing international debate on the practice of human classification in the life sciences to advance the international and interdisciplinary transferability of scientific results and, first and foremost, to avoid unintended effects such as overgeneralization, racialization, and stigmatization.
Male mammalian meiosis and spermiogenesis is critically dependent on the shared functions of the katanins KATNA1 and KATNAL1
Authors: Dunleavy Jessica EM , Graffeo Maddison , Wozniak Kathryn , O’Connor Anne E , Merriner D. Jo , Nguyen Joseph , Schittenhelm Ralf B , Houston Brendan J , O’Bryan Moira K
Published: November 2022

Katanin microtubule severing enzymes are potent M-phase regulators in oocytes and somatic cells. How the complex, and evolutionarily critical, male mammalian meiotic spindle is sculpted remains unknown. Here, using multiple single and double gene knockout mice, we reveal that the canonical katanin A-subunit, KATNA1, and its close paralogue, KATNAL1, together execute multiple aspects of meiosis. We show KATNA1 and KATNAL1 collectively regulate the male meiotic spindle, cytokinesis and midbody abscission, in addition to diverse spermatid remodelling events, including Golgi organisation, and acrosome and manchette formation. We also define KATNAL1-specific roles in sperm flagella development, manchette regulation, and sperm-epithelial disengagement. Finally, using proteomic approaches we define the KATNA1, KATNAL1, and KATNB1 mammalian testis interactome, which includes a network of cytoskeletal and vesicle trafficking proteins. Collectively, we reveal the presence of multiple katanin A-subunit paralogs in mammalian spermatogenesis allows for ‘customized cutting’ via neofunctionalization and protective buffering via gene redundancy.
Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone
Authors: Muratore Daniel , Bertagnolli Anthony D. , Bristow Laura A. , Thamdrup Bo , Weitz Joshua S. , Stewart Frank J.
Published: November 2022

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter- and even micron-level spatial scales. It is unclear if such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions distinguishing free-living versus particle-associated microbes. We find a substantial increase in nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size-fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in modulating the C:N ratio of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers.

IMPORTANCE

The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses using metagenomes from the nitracline of the eastern tropical North Pacific OMZ including both particle-associated and non-associated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micro- to millimeter scale associated with particle-associated versus free-living lifestyles.
Structural Assessment of the Full-Length Wild-Type Tumor Suppressor Protein p53 by Mass Spectrometry-Guided Computational Modeling
Authors: Di Ianni Alessio , Tüting Christian , Kipping Marc , Ihling Christian H. , Köppen Janett , Iacobucci Claudio , Arlt Christian , Kastritis Panagiotis L. , Sinz Andrea
Published: November 2022

The tetrameric tumor suppressor p53 represents a great challenge for 3D-structural analysis due to its high degree of intrinsic disorder (ca. 40%). We aim to shed light on the structural and functional roles of p53’s C-terminal region in full-length, wild-type human p53 tetramer and their importance for DNA binding. For this, we employed complementary techniques of structural mass spectrometry (MS) in an integrated approach with AI-based computational modeling. Our results show no major conformational differences in p53 between DNA-bound and DNA-free states, but reveal a substantial compaction of p53’s C-terminal region. This supports the proposed mechanism of unspecific DNA binding to the C-terminal region of p53 prior to transcription initiation by specific DNA binding to the core domain of p53. The synergies between complementary structural MS techniques and computational modeling as pursued in our integrative approach is envisioned to serve as general strategy for studying intrinsically disordered proteins (IDPs) and intrinsically disordered region (IDRs).
Fluid flow structures gut microbiota biofilm communities by distributing public goods
Authors: Wong Jeremy P. H. , Fischer-Stettler Michaela , Zeeman Samuel C. , Battin Tom J. , Persat Alexandre
Published: November 2022

Bacterial gut commensals experience a biologically and physically complex mucosal environment. While many chemical factors mediate the composition and structure of these microbial communities, less is known about the role of mechanics. Here, we demonstrate that fluid flow impacts the spatial organization and composition of gut biofilm communities by shaping how different species interact metabolically. We first demonstrate that a model community composed ofBacteroides thetaiotaomicron(Bt) andBacteroides fragilis(Bf), two representative human commensals, can form robust biofilms in flow. We identified dextran as a polysaccharide readily metabolized byBtbut notBf, but whose fermentation generates a public good enablingBfgrowth. We demonstrate that in flow,Btbiofilms share dextran metabolic by-products, promotingBfbiofilm formation. By transporting this public good, flow structures the spatial organization of the community, positioning theBfpopulation downstream fromBt. We show that sufficiently strong flows abolishBfbiofilm formation by limiting the effective public good concentration at the surface. Physical factors such as flow may therefore contribute to the composition of intestinal microbial communities, potentially impacting host health.
Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless
Authors: Jagtap Pravin Kumar Ankush , Müller Marisa , Kiss Anna E. , Thomae Andreas W. , Lapouge Karine , Beck Martin , Becker Peter B. , Hennig Janosch
Published: November 2022

Unwinding RNA secondary structures by RNA helicases is essential for RNA metabolism. How the basic unwinding reaction of DExH-type helicases is regulated by their accessory domains is unresolved. Here, we combine structural and functional analyses to address this challenge for the prototypic DExH RNA helicase maleless (MLE) fromDrosophila.

We captured the helicase cycle of MLE with multiple structural snapshots. We discovered that initially, dsRBD2 flexibly samples substrate dsRNA and aligns it with the open helicase tunnel. Subsequently, dsRBD2 releases RNA and associates with the helicase core, leading to closure of the tunnel around ssRNA. Structure-based MLE mutations confirm the functional relevance of the structural model in cells. We propose a molecular model in which the dsRBD2 domain of MLE orchestrates large structural transitions that depend on substrate RNA but are independent of ATP.

Our findings reveal the fundamental mechanics of dsRNA unwinding by DExH helicases with high general relevance for dosage compensation and specific implications for MLE’s human orthologue DHX9/RHA mechanisms in disease.
Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profiles
Authors: Touizer Emma , Alrubbayi Aljawharah , Ford Rosemarie , Hussain Noshin , Gerber Pehuén Pereyra , Shum Hiu-Long , Rees-Spear Chloe , Muir Luke , Gea-Mallorquí Ester , Kopycinski Jakub , Jankovic Dylan , Pinder Christopher , Fox Thomas A , Williams Ian , Mullender Claire , Maan Irfaan , Waters Laura , Johnson Margaret , Madge Sara , Youle Michael , Barber Tristan , Burns Fiona , Kinloch Sabine , Rowland-Jones Sarah , Gilson Richard , Matheson Nicholas J , Morris Emma , Peppa Dimitra , McCoy Laura E
Published: November 2022

People living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can have residual immune dysfunction and often display poorer responses to vaccination. We assessed in a cohort of PLWH (n=110) and HIV negative controls (n=64) the humoral and spike-specific B-cell responses following 1, 2 or 3 SARS-CoV-2 vaccine doses. PLWH had significantly lower neutralizing antibody (nAb) titers than HIV-negative controls at all studied timepoints. Moreover, their neutralization breadth was reduced with fewer individuals developing a neutralizing response against the Omicron variant (BA.1) relative to controls. We also observed a delayed development of neutralization in PLWH that was underpinned by a reduced frequency of spike-specific memory B cells (MBCs) and pronounced B cell dysfunction. Improved neutralization breadth was seen after the third vaccine dose in PLWH but lower nAb responses persisted and were associated with global, but not spike-specific, MBC dysfunction. In contrast to the inferior antibody responses, SARS-CoV-2 vaccination induced robust T cell responses that cross-recognized variants in PLWH. Strikingly, a subset of PLWH with low or absent neutralization had detectable functional T cell responses. These individuals had reduced numbers of circulating T follicular helper cells and an enriched population of CXCR3+CD127+CD8+T cells after two doses of SARS-CoV-2 vaccination, which may compensate for sub-optimal serological responses in the event of infection. Therefore, normalisation of B cell homeostasis could improve serological responses to vaccines in PLWH and evaluating T cell immunity could provide a more comprehensive immune status profile in these individuals and others with B cell imbalances.
Modeling multiphage-bacteria kinetics to predict phage therapy potency and longevity
Authors: Yu Zhiyuan , Luong Tiffany , Banuelos Selenne , Sue Andrew , Horn Mary Ann , Ryu Hwayeon , Roach Dwayne , Segal Rebecca , Huang Qimin
Published: November 2022

Pseudomonas aeruginosais a frequent cause of life-threatening opportunistic infections in the critically ill and immunocompromised. Its treatment is challenging due to the increasing prevalence of resistance to most conventional antibiotics. Although numerous alternative therapies are currently under investigation, bacteriophage (phage) cocktail therapy appears poised for long-term success. Here, we investigate potency and longevity of individualPseudomonasphages in cocktail to determine viral co-factors that promote optimal treatment efficacy. We combinedin vitroandin silicomodels to predict sixty-eight treatment permutations with three phages that adsorb symmetrically and asymmetrically when administered singly, double simultaneously, or double sequentially. We showed that simultaneously administering two asymmetrically binding phages with high cell lysis efficiencies improved cocktail potency. Use of a higher-potency cocktail, along with a reduction in the net probability of independent gene mutations was associated with prolonged bacterial suppression. Nevertheless,in vitrowe almost always observed evolution of multiphage resistance. Simulations also predict that when combining phages with polar potencies, susceptible host cells are monopolized by the more efficiently replicating phage. Thus, further perpetuating the growth demise of the weaker phage in cocktail. Our mathematical model was used to explore and predict changes in phage and bacterial populations that were difficult to measure experimentally. This framework has many inferential and exploratory uses for clinical investigation such as identifying the most sensitive parameters for phage selection and exploring different treatment regimens. Collectively, our findings attempt to dissect the mechanisms of phage cocktails combatingP. aeruginosainfections and highlight the viral co-factors necessary for treatment efficacy.
Pyrophosphoproteomics: extensive protein pyrophosphorylation revealed in human cell lines
Authors: Morgan Jeremy A. M. , Singh Arpita , Kurz Leonie , Nadler-Holly Michal , Penkert Martin , Krause Eberhard , Liu Fan , Bhandari Rashna , Fiedler Dorothea
Published: November 2022

Reversible protein phosphorylation is a central signaling mechanism in eukaryotic cells. While the identification of canonical phosphorylation sites using mass-spectrometry (MS) based proteomics has become routine, annotation of non-canonical phosphorylation has remained a challenge. Here, we report a tailored pyrophosphoproteomics workflow to detect and reliably assign protein pyrophosphorylation in two human cell lines, providing the first direct evidence of endogenous protein pyrophosphorylation. Detection of protein pyrophosphorylation was reproducible, specific and consistent with previous biochemical evidence relating the installation of the modification to inositol pyrophosphates (PP-InsPs). We manually validated 148 pyrophosphosites across 71 human proteins, the most heavily pyrophosphorylated of which were the nucleolar proteins NOLC1 and TCOF1. A predictive workflow based on the MS data set was established to recognize putative pyrophosphorylation sequences, and UBF1, a nucleolar protein incompatible with the proteomics method, was biochemically shown to undergo pyrophosphorylation. When the biosynthesis of PP-InsPs was perturbed in a model cell line, proteins expressed in this background exhibited lower levels of pyrophosphorylation. Disruption of PP-InsP biosynthesis also significantly reduced rDNA transcription, potentially by lowering pyrophosphorylation on regulatory proteins NOLC1, TCOF1, and UBF1. Overall, protein pyrophosphorylation emerges as an archetype of non-canonical phosphorylation, and should be considered in future phosphoproteomic analyses.
PRRC2 proteins regulate translation initiation by promoting leaky scanning
Authors: Bohlen Jonathan , Roiuk Mykola , Teleman Aurelio A.
Published: November 2022

Roughly half of animal mRNAs contain upstream Open Reading Frames (uORFs). These uORFs represent an impediment to translation of the main ORF since ribosomes usually bind the mRNA cap at the 5’ end and then scan for ORFs in a 5’-to-3’ fashion. One way for ribosomes to bypass uORFs is via leaky scanning, whereby the ribosome disregards the uORF start codon. Hence leaky scanning is an important instance of post-transcriptional regulation that affects gene expression. Few molecular factors regulating or facilitating this process are known. Here we show that the PRRC2 proteins PRRC2A, PRRC2B and PRRC2C regulate translation initiation. We find that they bind eukaryotic translation initiation factors and preinitiation complexes, and are enriched on ribosomes translating mRNAs with uORFs. We find that PRRC2 proteins promote leaky scanning past translation start codons, thereby promoting translation of mRNAs containing uORFs. Since PRRC2 proteins have been associated with cancer, this provides a mechanistic starting point for understanding their physiological and pathophysiological roles.
Trans-eQTL mapping in gene sets identifies network effects of genetic variants
Authors: Wang Lili , Babushkin Nikita , Liu Zhonghua , Liu Xuanyao
Published: November 2022

Nearly all trait-associated variants identified in GWAS are non-coding. Thecisregulatory effects of these variants have been extensively characterized, but how they impact gene regulation intranshas been the subject of much fewer studies. Mappingtransgenetic effects is very challenging because their effect sizes tend to be small and a large multiple testing burden reduces the power to detect them. In addition, read mapping biases can lead to many false positives. To reduce mapping biases and substantially improve power to maptrans-eQTLs, we developed a pipeline called trans-PCO, which combines careful read and gene filters with a principal component (PC)-based multivariate association test. Our simulations demonstrate that trans-PCO substantially outperforms existingtrans-eQTL mapping methods, including univariate and primary PC-based methods. We applied trans-PCO to two gene expression datasets from whole blood, DGN (N= 913) and eQTLGen (N= 31,684), to identifytrans-eQTLs associated with gene co-expression networks and hallmark gene sets representing well-defined biological processes. In total, we identified 14,985 high-qualitytrans-eSNPs–module pairs associated with 197 co-expression gene modules and biological processes. To better understand the effects of trait-associated variants on gene regulatory networks, we performed colocalization analyses between GWAS loci of 46 complex traits andtrans-eQTLs identified in DGN. We highlight several examples where our map oftranseffects helps us understand how trait-associated variants impact gene regulatory networks and biological pathways. For example, we found that a locus associated with platelet traits nearARHGEF3 trans-regulates a set of co-expressed genes significantly enriched in the platelet activation pathway. Additionally, six red blood cell trait-associated locitrans-regulate a gene set representing heme metabolism, a crucial process in erythropoiesis. In conclusion, trans-PCO is a powerful and reliable tool that detectstransregulators of cellular pathways and networks, which opens up new opportunities to learn the impact of trait-associated loci on gene regulatory networks.
Escherichia colicells are primed for survival before lethal antibiotic stress
Authors: Hossain Tahmina , Singh Abhyudai , Butzin Nicholas C.
Published: November 2022

Non-genetic factors can cause significant fluctuations in gene expression levels. Regardless of growing in a stable environment, this fluctuation leads to cell-to-cell variability in an isogenic population. This phenotypic heterogeneity allows a tiny subset of bacterial cells in a population, referred to as persister cells, to tolerate long-term lethal antibiotic effects by entering into a non-dividing, metabolically altered state. One fundamental question is whether this heterogeneous persister population is due to a pre-existing genetic mutation or a result of a transiently-primed reversible cell state. To explore this, we tested clonal populations starting from a single cell using a modified Luria–Delbrück fluctuation test. Through we kept the conditions the same, the diversity in persistence level among clones was relatively consistent: varying from ∼60-100 and ∼40-70 fold for ampicillin (Amp) and apramycin (Apr), respectively. Then we divided and diluted each clone to observe whether the same clone had comparable persister levels for more than one generation. Replicates had similar persister levels even when clones were divided, diluted by 1:20, and allowed to grow for ∼5 generations. This result explicitly shows a cellular memory passed on for generations and eventually lost when cells are diluted to 1:100 and regrown (>7 generations). Our result demonstrates 1) the existence of a small population prepared for stress (“primed cells”) resulting in higher persister numbers, 2) the primed memory state is reproducible and transient, passed down for generations but eventually lost, and 3) a heterogeneous persister population is a result of a transiently-primed reversible cell state and not due to a pre-existing genetic mutation.
Circuit dissection and functional validation of a cross-species emotional biomarker
Authors: Jackson Adam , Cohen Joshua , Phensy Aarron , Chang Edward , Dawes Heather , Sohal Vikaas S.
Published: November 2022

Emotional responses arise from limbic circuits including the hippocampus and amygdala. In the human brain, beta-frequency communication between these structures correlates with self-reported mood and anxiety. However, both the mechanism and significance of this biomarker as a readout vs. driver of emotional state remain unknown. Here we show that beta-frequency communication between the ventral hippocampus and basolateral amygdala also predicts anxiety-related behavior in mice on both long timescales (∼30 min) and immediately preceding behavioral choices. Genetically encoded voltage indicators reveal that this biomarker reflects synchronization between somatostatin interneurons across both structures. Indeed, synchrony between these neurons dynamically predicts approach vs. avoidance, and optogenetically shifting this synchronization by just 25 msec is sufficient to bidirectionally modulate anxiety-related behaviors. Thus, back-translation establishes a human biomarker as a causal determinant (not just predictor) of emotional state, revealing a novel mechanism whereby interregional synchronization that is frequency-, phase- and cell type-specific controls anxiety processing.
Comparisons of healthcare resource utilisation and costs between Brugada syndrome and congenital long QT syndrome: a territory-wide study
Authors: Lee Sharen , Chung Cheuk To , Radford Danny , Chou Oscar Hou In , Lee Teddy Tai Loy , Leung Keith Sai Kit , Roever Leonardo , Rajan Rajesh , Bazoukis George , Letsas Konstantinos P , Zeng Shaoying , Liu Fang Zhou , Wong Wing Tak , Liu Tong , Tse Gary
Published: November 2022

Introduction

Healthcare resource utilisation and costs are important metrics of healthcare burden, but they have rarely been explored in the setting of cardiac ion channelopathies.

Purpose

The aim of this study is to compare HCRUs and costs between patients with Brugada syndrome (BrS) and congenital long QT syndrome (LQTS) in a single city of China.

Methods

This was a territory-wide retrospective cohort study of consecutive BrS and LQTS patients at public hospitals or clinics in Hong Kong, China. HCRUs and costs (in USD) for accident and emergency (A&E), inpatient, general outpatient and specialist outpatient attendances were analysed over a 19-year period (2001-2019) at the cohort level. Comparisons were made between BrS and LQTS cohorts using incidence rate ratios (IRRs [95% confidence intervals]).

Results

Over the 19-year study period, 516 BrS (median age of initial presentation: 51 [interquartile range: 38-61] years, 92% male) and 134 LQTS (median age of initial presentation: 21 [9-44] years, 32% male) patients were included. BrS patients had lower total costs compared to LQTS patients (2,008,126 [2,007,622-2,008,629] vs. 2,343,864 [2,342,828-2,344,900]; IRR: 0.857 [0.855-0.858]). For specific attendance types, BrS patients had higher costs for A&E attendances (83,113 [83,048-83,177] vs. 70,604 [70,487-70,721]; IRR: 1.177 [1.165-1.189]) and general outpatient services (2,176 [2,166-2,187] vs. 921 [908-935]; IRR: 2.363 [2.187-2.552]). However, they had lower costs for inpatient stay (1,391,624 [1,391,359-1,391,889] vs. 1,713,742 [1,713,166-1,714,319]; IRR: 0.812 [0.810-0.814]) and to a smaller extent, lower costs for specialist outpatient services (531213 [531049-531376] vs. 558597 [558268-558926]; IRR: 0.951 [0.947-0.9550]) compared to LQTS patients.

Conclusion

Overall, BrS patients consume 14% less healthcare resources compared to LQTS patients in terms of attendance costs. BrS patients require more A&E and general outpatient services, but less inpatient and specialist outpatient services than LQTS patients. Further studies are needed to examine patient-based attendances and costs to identify subgroups of high HCRU users for both cohorts.
Toxin-mediated downregulation of absorptive ion transporters NHE3, DRA, and SGLT1 in the colon contributes to diarrhea associated withClostridioides difficileinfection
Authors: Peritore-Galve F. Christopher , Kaji Izumi , Smith Anna , Walker Lauren M. , Shupe John A. , Dudeja Pradeep K. , Goldenring James R. , Lacy D. Borden
Published: November 2022

Background & Aim

Clostridioides difficileinfection (CDI) is the leading cause of hospital-acquired diarrhea and pseudomembranous colitis. Two protein toxins, TcdA and TcdB, produced byC. difficileare the major determinants of disease. However, the physiological cause of diarrhea associated with CDI is not well understood. We investigated the effects of CDI on paracellular permeability and apical ion transporters.

Methods

We studied intestinal permeability and apical membrane transporters in female C57BL/6J mice. Üssing chambers were used to measure regional differences in paracellular permeability and ion transporter function in intestinal mucosa. Intestinal tissues were collected from mice and analyzed by immunofluorescence microscopy and RNA-sequencing.

Results

CDI increased intestinal permeability through the size-selective leak pathwayin vivo, but permeability was not increased at the sites of pathological damage. Chloride secretion was reduced in the cecum during infection by decreased CaCC function. Infected mice had decreased SGLT1 (also called SLC5A1) activity in the cecum and colon along with diminished apical abundance and an increase in luminal glucose. SGLT1 and DRA (also called SLC26A3) expression was ablated by either TcdA or TcdB, but NHE3 (also called SLC9A3) was decreased in a TcdB-dependent manner. Finally, expression of these three ion transporters was drastically reduced at the transcriptional level.

Conclusions

CDI increases intestinal permeability and decreases apical abundance of NHE3, SGLT1, and DRA. This combination may cause a dysfunction in water and solute absorption in the lower gastrointestinal tract, leading to osmotic diarrhea. These findings may open novel pathways for attenuating CDI-associated diarrhea.

GRAPHICAL ABSTRACT
High-Contrast PET imaging with [18F]-NT160, a Class-IIa Histone Deacetylase (Class-IIa HDAC) Probe for In Vivo Imaging of Epigenetic Machinery in the Central Nervous System
Authors: Turkman Nashaat , Xu Sulan , Huang Chun-Han , Eyermann Christopher , Salino Julia , Khan Palwasha
Published: November 2022

We utilized positron emission tomography (PET) imagingin vivoto map the spatiotemporal biodistribution/expression (protein density) of class-IIa histone deacetylases (class-IIa HDACs) in the brain. Herein, we report an improved radiosynthesis of [18F]-NT160 using 4-hydroxy-TEMPO which led to a significant improvement in radiochemical yield and molar activity. PET imaging with [18F]-NT160, a highly potent class-IIa HDAC inhibitor with sub-nM affinity for HDAC4 and 5 isoforms, led to high-quality and high-contrast images among various brain regions. [18F]-NT160 displayed excellent pharmacokinetic and imaging characteristics: brain uptake is high in gray matter regions, leading to high-quality PET images; tissue kinetics are appropriate for an18F tracer and specific binding for class-IIa HDACs is demonstrated by self-blockade. Higher uptake with [18F]-NT160 was observed in the hippocampus, thalamus, and cortex while there was relatively lower uptake in the cerebellum and striatum. Overall, our current studies with [18F]-NT160 will likely facilitate the development and clinical translation of class-IIa HDACs of the next generation of PET tracers for imaging and targeted therapy of cancer and the diseases of the central nervous system (CNS).
CORRELATION BETWEEN AGE-RELATED CHANGES IN SKIN MORPHOLOGY AND TROPHIC FUNCTION OF THE TRIGEMINAL NERVE
Authors: Kolomiytsev A. K. , Bazilevich A. V. , Peshkov M.V.
Published: November 2022

Huge advancements in the field of cosmetology and numerous methods of skin restoration have kept the studies of skin aging continually relevant and up-to-date. Age-related changes in the physiological parameters of skin cover might be related to a trophic innervation disorder, which, in its turn, is caused by aging manifesting itself in the corresponding structures of the vegetative nervous system. The present article aims at describing this particular skin aging mechanism. Reduction of the amount of cells inn. sensorius superiorof the trigeminal nerve has been proven to be connected with a decrease in the amount of cells in the innervated areas of skin. This process may be considered one of the mechanisms of aging realized as a systemic phenomenon.
For an early and strong immune response in the monomerization of polymeric immunoglobulins intermonomeric interaction relationship of potassium hydroxide
Authors: Zumrutdal Emin
Published: November 2022

Immunoglobulins (Ig), which are an integral part of the immune system in humans and animals, continue to surprise people with their effectiveness and importance every day since they were discovered for 2 centuries. Although the avidity of polymeric immunoglobulins (pIg) in the lumen in the respiratory system is high, its mobility is limited and unlike monomeric immunoglobulins (Ig), it can carry the antigenic (Ag) structure to the lamina propria by active transport. pIg's have a high weight because they have a large number of monomers. Disulfide bonds are important in the bonds that connect Ig monomers, and disulfide bonds have critical functions in construction, both in the J chain and in the intermonomeric domain. Disulfide bonds can interact quite easily with hydroxyl(OH-) ions. It is a strong molecular structure that gives OH- ions in potassium hydroxide (KOH). In our study, the potential of pIg to be made monomeric was investigated in order to increase the mobilization, antigen affinity and antigen avidity of pIgs (IgM and IgA) in the secretion in the lumen. For this purpose, intermonomeric disulfide bonds were determined by investigating cysteine locations in the J chain and on the monomers. In this study, by targeting these disulfide bonds, the intermolecular interaction energies with KOH for the destruction of these bonds were evaluated by in silico studies. Exergonic intermolecular free energy interactions were detected between the disulfide bonds in the J chain and in the intermonomeric domain and the KOH molecule.
Identification of a novel large multigene deletion and a frameshift indel inPDE6Bas the underlying cause of early-onset recessive rod–cone degeneration
Authors: Sangermano Riccardo , Biswas Pooja , Sullivan Lori S. , Place Emily M. , Borooah Shyamanga , Straubhaar Juerg , Pierce Eric A. , Daiger Stephen P. , Bujakowska Kinga M. , Ayaggari Radha
Published: November 2022

A family, with two affected identical twins with early-onset recessive inherited retinal degeneration, was analyzed to determine the underlying genetic cause of pathology. Exome sequencing revealed a rare and previously reported causative variant (c.1923_1969delinsTCTGGG; p.Asn643Glyfs*29) in thePDE6Bgene in the affected twins and their unaffected father. Further investigation, using genome sequencing, identified a novel ∼7.5-kb deletion (Chr 4:670,405–677,862del) encompassing theATP5MEgene, part of the 5′ UTR ofMYL5, and a 378-bp (Chr 4:670,405–670,782) region from the 3′ UTR ofPDE6Bin the affected twins and their unaffected mother. Both variants segregated with disease in the family. Analysis of the relative expression ofPDE6B, in peripheral blood cells, also revealed a significantly lower level ofPDE6Btranscript in affected siblings compared to a normal control.PDE6Bis associated with recessive rod–cone degeneration and autosomal dominant congenital stationary night blindness. Ophthalmic evaluation of these patients showed night blindness, fundus abnormalities, and peripheral vision loss, which are consistent withPDE6B-associated recessive retinal degeneration. These findings suggest that the loss ofPDE6Btranscript resulting from the compound heterozygous pathogenic variants is the underlying cause of recessive rod–cone degeneration in the study family.