bluuebunny/crossref_metadata_2025 huggingface dataset:
CBGTPy: An extensible cortico-basal ganglia-thalamic framework for modeling biological decision making
Authors: Clapp Matthew , Bahuguna Jyotika , Giossi Cristina , Rubin Jonathan E. , Verstynen Timothy , Vich Catalina
Published: September 2023

Here we introduce CBGTPy, a virtual environment for designing and testing goal-directed agents with internal dynamics that are modeled on the cortico-basal-ganglia-thalamic (CBGT) pathways in the mammalian brain. CBGTPy enables researchers to investigate the internal dynamics of the CBGT system during a variety of tasks, allowing for the formation of testable predictions about animal behavior and neural activity. The framework has been designed around the principle of flexibility, such that many experimental parameters in a decision making paradigm can be easily defined and modified. Here we demonstrate the capabilities of CBGTPy across a range of single and multi-choice tasks, highlighting the ease of set up and the biologically realistic behavior that it produces. We show that CBGTPy is extensible enough to apply to a range of experimental protocols and to allow for the implementation of model extensions with minimal developmental effort.

Author summary

We introduce a toolbox for producing biologically realistic simulations of the cortico-basal ganglia-thalamic dynamics during a variety of experimental tasks. The purpose is to foster the theory-experiment cycle, offering a tool for generating testable predictions of behavioral and neural responses that can be validated experimentally, in a framework that allows for simple updating as new experimental evidence emerges. We outline how our toolbox works and demonstrate its performance on a set of normative cognitive tasks.
The potential of plasma HLA peptides beyond neoepitopes
Authors: Wahle Maria , Thielert Marvin , Zwiebel Maximilian , Skowronek Patricia , Zeng Wen-Feng , Mann Matthias
Published: September 2023

Distinction of non-self from self is the major task of the immune system. Immunopeptidomics studies the peptide repertoire presented by the human leukocyte antigen (HLA) protein, usually on tissues. However, HLA peptides are also bound to plasma soluble HLA (sHLA), but little is known about their origin and potential for biomarker discovery in this readily available biofluid. Currently, immunopeptidomics is hampered by complex workflows and limited sensitivity, generally requiring several mL of plasma for the detection of hundreds of HLA peptides. Here, we take advantage of recent improvements in the throughput and sensitivity of mass spectrometry (MS)-based proteomics to develop a highly-sensitive, automated and economical workflow for HLA peptide analysis, termed Immunopeptidomics by Biotinylated Antibodies and Streptavidin (IMBAS). IMBAS-MS quantifies more than 5,000 HLA class I peptides from only 200 μL of plasma, in just 30 minutes. Our technology revealed that the plasma immunopeptidome of healthy donors is remarkably stable throughout a year and strongly correlated between individuals with overlapping HLA types. Immunopeptides originating from diverse tissues, including the brain, are proportionately represented. We conclude that sHLAs are a promising avenue for immunology and precision oncology.
High-confidence 3D template matching for cryo-electron tomography
Authors: Cruz-León Sergio , Majtner Tomáš , Hoffmann Patrick C. , Kreysing Jan Philipp , Tuijtel Maarten W , Schaefer Stefan L , Geißler Katharina , Beck Martin , Turoňová Beata , Hummer Gerhard
Published: September 2023

Cryo-electron tomography (CryoET) resolves individual macromolecules inside living cells. However, the complex composition and high density of cells challenge the faithful identification of features in tomograms. Here, we capitalize on recent advances in electron tomography and demonstrate that 3D template matching (TM) localizes a wide range of structures inside crowded eukaryotic cells with confidence 10 to 100-fold above the noise level. We establish a TM pipeline with systematically tuned parameters for automated, objective and comprehensive feature identification. High-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, lipid membranes and microtubules, and individual subunits, demonstrate that TM is generic. We resolve ∼100-kDa proteins, connect the functional states of complexes to their cellular localization, and capture vaults carrying ribosomal cargoin situ. By capturing individual molecular events inside living cells with defined statistical confidence, high-confidence TM greatly speeds up the CryoET workflow and sets the stage for visual proteomics.
International and regional spread of carbapenem-resistantKlebsiella pneumoniaein Europe
Authors: Silva Mabel Budia , Kostyanev Tomislav , Montaño Stefany Ayala , Ferrer-Acosta Jose Bravo , Garcia-Castillo Maria , Cantón Rafael , Goossens Herman , Rodriguez-Baño Jesus , Grundmann Hajo , Reuter Sandra
Published: September 2023

Klebsiella pneumoniae,an opportunistic pathogen able to cause hospital- and community-acquired infections, is of particular concern due to the active spread of antibiotic resistance genes associated with mobile genetic elements such as plasmids and transposons. Carbapenem-resistantK. pneumoniae(CRKP) exhibit a higher mortality rate than carbapenem-susceptibleK. pneumoniaeinfections. In this COMBACTE-EURECA study, we present genomic data of 687 carbapenem-resistant strains recovered among clinical samples from 41 hospitals in nine Southern European countries (2016-2018) and compared these with the previous EuSCAPE collection (2013-2014). All isolates were resistant (EUCAST criteria) to at least one carbapenem antibiotic. We identified 11 clonal complexes (CCs), with most isolates belonging to the high-risk clones CC258, CC101, CC11, and CC307.blaKPC-likewas the most prevalent carbapenemase-encoding gene (45%), along with the dominance of the CC258 lineage. Equally,blaOXA-48had a wide-ranging spread (39%), andblaNDMwas present in half of the ST11 isolates representing a particular lineage circulating in Greece. Two carbapenemase genes were found in 38 isolates (5.5%). Through the combination of both EURECA and EuSCAPE collections, we elucidated the evolution ofK. pneumoniaehigh-risk clones circulating in Europe. Dominating clones and their associated carbapenemase genes exhibit relevant regional differences, namely CC258 in Greece, Italy, and Spain, CC101 present in Serbia and Romania and CC14 in Türkiye. Due to the wide expansion of CRKP, genomic surveillance across Europe with projects such as EURECA provides crucial insights for risk mapping at geo-temporal scales and informs necessary adaptions to the local settings for implementation of control strategies.
Astrocytes modulate neuronal development by S100A6 signaling
Authors: Cinquina Valentina , Calvigioni Daniela , Piscitelli Fabiana , Keimpema Erik , Marzo Vincenzo Di , Verkhratsky Alexei , Harkany Tibor
Published: September 2023

Neuronal morphogenesis relies on intercellular signaling. Astrocytes release metabolites, trophic, and guidance factors to promote neuronal differentiation. In contrast, the mechanisms by which astrocytes could limit and stabilize neuronal connectivity remain less explored. Here, we show cortical astrocytes to express and release S100A6, a Ca2+-binding protein (‘calcyclin’). Simultaneously, the majority of cortical neurons express abona fidebinding partner for S100A6, calcyclin-binding protein (CaCyBp). In neurons, CaCyBp maintains unfolded protein response, thereby controlling proteostasis. When released, S100A6 inhibits CaCyBp signaling, thus slowing protein turnover, and inhibiting neuritogenesis. S100A6-CaCyBp signaling during gestation and lactation is sensitive to the mother’s nutritional status, particularly eicosapentaenoic acid intake. Thus, a member of the S100 protein family acts as an astroglia-derived morphogen, whose action on neurons is modulated by environmental factors.
Distinct basal ganglia contributions to learning from implicit and explicit value signals in perceptual decision-making
Authors: Balsdon Tarryn , Pisauro M. Andrea , Philiastides Marios G.
Published: September 2023

Metacognitive evaluations of confidence provide an estimate of decision accuracy that could guide learning in the absence of explicit feedback. We examine how humans might learn from this implicit feedback in direct comparison with that of explicit feedback, using simultaneous EEG-fMRI. Participants performed a motion direction discrimination task where stimulus difficulty was increased to maintain performance, with intermixed explicit- and no-feedback trials. We isolate single-trial estimates of post-decision confidence using EEG decoding, and find these neural signatures re-emerge at the time of feedback together with separable signatures of explicit feedback. We identified these signatures of implicit versus explicit feedback along a dorsal-ventral gradient in the striatum, a finding uniquely enabled by an EEG-fMRI fusion. These two signals are then integrated into an aggregate representation in the external globus pallidus, which broadcasts updates to improve cortical decision processing via the thalamus and insular cortex, irrespective of the source of feedback.
Nighttime-specific gene expression changes in suprachiasmatic nucleus and habenula are associated with resiliency to chronic social stress
Authors: Narain Priyam , Petković Aleksa , Šušić Marko , Haniffa Salma , Drou Nizar , Arnoux Marc , Anwar Mariam , Chaudhury Dipesh
Published: September 2023

The molecular mechanisms that link stress and circadian rhythms still remain unclear. The habenula (Hb) is a key brain region involved in regulating diverse types of emotion-related behaviours while the suprachiasmatic nucleus (SCN) is the body’s central clock. To investigate the effects of chronic social stress on transcription patterns, we performed gene expression analysis in the Hb and SCN of stress naive and stress exposed mice. Our analysis revealed a large number of differentially expressed genes and enrichment of synaptic and cell signalling pathways between resilient and stress-naïve mice at ZT16 in both the Hb and SCN. This transcriptomic signature was nighttime-specific and observed only in stress-resilient mice. In contrast, there were relatively few differences between the stress-susceptible and stress-naïve groups across timepoints. Our results reinforce the functional link between diurnal gene expression patterns and differential responses to stress, thereby highlighting the importance of temporal expression patterns in homeostatic stress responses.
Distinct neural states encode task identity in frontal eye field and interact with its core spatial properties
Authors: Mouille A. , Gaillard C. , Astrand E. , Wardak C. , Hamed S. Ben , Amengual J.L.
Published: September 2023

The prefrontal cortex (PFC) plays a key role in selecting, maintaining and representing sensory information, and in its integration with our current internal goals and expectations, implementing such cognitive processes as executive functions, attention, decision making and working memory. Performing computation over all of these functional cognitive processes and dynamically shifting from one to the other based on task demands requires a complex functional organization and a high degree of coding flexibility. The PFC cells show a non-linear mixed selectivity characterized by specific tuning for multiple task- and behaviour related parameters. This non-linear mixed selectivity thought to allow for a high-dimensional representation of information. Here, we asked if the PFC is mainly involved in specific task-parameters representation, or if it additionally holds a higher order representation for task-identity. We thus trained two macaques to perform three different tasks: a memory guided saccade task and two detection tasks involving different attention mechanisms. Multi-unit activity was recorded in the frontal eye field, bilaterally, while monkeys performed these three tasks in a same session. Using demixed Principal Component Analysis, we found a two-dimensional neural state that characterized each of these tasks. The lower dimensional representation of the activity recorded during the performance of the two attentional tasks were more similar to each other than to the memory-guided saccade task. Furthermore, we report that task and spatial information are non-linearly mixed, a signature of a high-dimensional neural representation. Overall, this indicates that PFC encodes task identity information and flexibly adjusts its sensory processes as a function of the specific ongoing task.

Significance Statement

One long lasting question in cognitive neuroscience is whether PFC mainly represents the different parameters that are needed to perform any given task, or if it additionally holds a higher order representation for task-identity. We recorded from the macaque frontal eye fields while monkeys performed a memory guided saccade task and two detection tasks involving different attention mechanisms. We found a task-identity neural state in which the two attentional tasks were represented similarly to each other but differently from the memory-guided saccade task. We also report that task and spatial information are non-linearly mixed, a signature of a high-dimensional neuronal representation. Overall, this indicates that PFC encodes task identity information and flexibly adjusts its sensory processes as a function of the specific ongoing task.
Thermodynamic Forces from Protein and Water Govern Condensate Formation of an Intrinsically Disordered Protein Domain
Authors: Mukherjee Saumyak , Schäfer Lars V.
Published: September 2023

Liquid-liquid phase separation (LLPS) can drive a multitude of cellular processes by compartmentalizing biological cells via the formation of dense liquid biomolecular condensates, which can function as membraneless organelles. Despite its importance, the molecular-level understanding of the underlying thermodynamics of this process remains incomplete. In this study, we use atomistic molecular dynamics simulations of the low complexity domain (LCD) of human fused in sarcoma (FUS) protein to investigate the contributions of water and protein molecules to the free energy changes that govern LLPS. Both protein and water components are found to have comparably sizeable thermodynamic contributions to the formation of FUS condensates. Moreover, we quantify the counteracting effects of water molecules that are released into the bulk upon condensate formation and the waters retained within the protein droplets. Among the various factors considered, solvation entropy and protein interaction enthalpy are identified as the most important contributions, while solvation enthalpy and protein entropy changes are smaller. These insights provide detailed molecular insights on the intricate thermodynamic interplay between protein- and solvation-related forces underlying the formation of biomolecular condensates.
Analytical strength-duration curve for the spiking response of the LIF neuron to an alpha-function-shaped excitatory current pulse
Authors: Paraskevov Alexander
Published: September 2023

Whether or not the neuron emits a spike in response to stimulation by an excitatory current pulse is determined by a strength-duration curve (SDC) for the pulse parameters. The SDC is a dependence of the minimal pulse amplitude required to elicit the spiking response on either the pulse duration or its decay time. Excitatory neurons affect the others through pulses of excitatory postsynaptic current. A simple yet plausible approximation for the time course of such a pulse is the alpha function, with linear rise at the start and exponential decay at the end. However, an exact analytical SDC for this case is hitherto not known, even for the leaky integrate- and-fire (LIF) neuron, the simplest spiking neuron model used in practice. We have obtained general SDC equations for the LIF neuron. Using the Lambert W function — a widely-implemented special function, we have found the exact analytical SDC for the spiking response of the LIF neuron stimulated by an excitatory current pulse in the form of the alpha function. To compare results in a unified way, we have also derived the analytical SDCs for (i) rectangular pulse, (ii) ascending ramp pulse, and (iii) instantly rising and exponentially decaying pulse. In the limit of no leakage, we show that the SDC is reduced to the classical hyperbola for all considered cases.
Virion-associated US28 rapidly modulates Akt activity to suppress HCMV lytic replication in monocytes
Authors: Mahmud Jamil , Geiler Brittany W. , Biswas Juthi , Miller Michael J. , Myers Julia E. , Matthews Stephen M. , Wass Amanda B. , O’Connor Christine M. , Chan Gary C.
Published: September 2023

Establishing a non-productive quiescent/silent infection within monocytes is essential for spread of human cytomegalovirus (HCMV). Yet, how HCMV establishes a quiescent infection in monocytes remains unclear. US28 is a viral G protein-coupled receptor (GPCR) essential for silent infections within cells of the myeloid lineage. We found virion-associated US28 was rapidly delivered to monocytes, whilede novosynthesized US28 was delayed for several days. A recombinant mutant virus lacking US28 (US28Δ) was unable to establish a quiescent infection, resulting in a fully productive lytic replication cycle. Mechanistically, viral entry of US28Δ phosphorylated Akt at both serine 473 (S473) and threonine 308 (T308), which contrasted with the site-specific phosphorylation of Akt at S473 following WT infection. Preventing Akt bi-phosphorylation prevented lytic replication of US28Δ, and ectopic expression of a constitutively phosphorylated Akt variant triggered lytic replication of WT infection. Our data demonstrate that virion-delivered US28 fine-tunes Akt activity to permit HCMV infection to enter a quiescent state following primary infection of monocytes.
Rosetta Energy Analysis of AlphaFold2 models: Point Mutations and Conformational Ensembles
Authors: Stein Richard A. , Mchaourab Hassane S.
Published: September 2023

There has been an explosive growth in the applications of AlphaFold2, and other structure prediction platforms, to accurately predict protein structures from a multiple sequence alignment (MSA) for downstream structural analysis. However, two outstanding questions persist in the field regarding the robustness of AlphaFold2 predictions of the consequences of point mutations and the completeness of its prediction of protein conformational ensembles. We combined our previously developed method SPEACH_AF with model relaxation and energetic analysis with Rosetta to address these questions. SPEACH_AF introduces residue substitutions across the MSA and not just within the input sequence. With respect to conformational ensembles, we combined SPEACH_AF and a new MSA subsampling method, AF_cluster, and for a benchmarked set of proteins, we found that the energetics of the conformational ensembles generated by AlphaFold2 correspond to those of experimental structures and explored by standard molecular dynamic methods. With respect to point mutations, we compared the structural and energetic consequences of having the mutation(s) in the input sequence versus in the whole MSA (SPEACH_AF). Both methods yielded models different from the wild-type sequence, with more robust changes when the mutation(s) were in the whole MSA. While our findings demonstrate the robustness of AlphaFold2 in analyzing point mutations and exploring conformational ensembles, they highlight the need for multi parameter structural and energetic analyses of these models to generate experimentally testable hypotheses.
Pervasive mislocalization of pathogenic coding variants underlying human disorders
Authors: Lacoste Jessica , Haghighi Marzieh , Haider Shahan , Lin Zhen-Yuan , Segal Dmitri , Reno Chloe , Qian Wesley Wei , Xiong Xueting , Shafqat-Abbasi Hamdah , Ryder Pearl. V. , Senft Rebecca , Cimini Beth A. , Roth Frederick P. , Calderwood Michael , Hill David , Vidal Marc , Yi S. Stephen , Sahni Nidhi , Peng Jian , Gingras Anne-Claude , Singh Shantanu , Carpenter Anne E. , Taipale Mikko
Published: September 2023

Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease-causing. This creates a new bottleneck: determining the functional impact of each variant – largely a painstaking, customized process undertaken one or a few genes or variants at a time. Here, we established a high-throughput imaging platform to assay the impact of coding variation on protein localization, evaluating 3,547 missense variants of over 1,000 genes and phenotypes. We discovered that mislocalization is a common consequence of coding variation, affecting about one-sixth of all pathogenic missense variants, all cellular compartments, and recessive and dominant disorders alike. Mislocalization is primarily driven by effects on protein stability and membrane insertion rather than disruptions of trafficking signals or specific interactions. Furthermore, mislocalization patterns help explain pleiotropy and disease severity and provide insights on variants of unknown significance. Our publicly available resource will likely accelerate the understanding of coding variation in human diseases.
Backmapping with Mapping and Isomeric Information
Authors: Kim Siyoung
Published: September 2023

I present a powerful and flexible backmapping tool named Multiscale Simulation Tool (mstool) that converts a coarse-grained (CG) system into all-atom (AA) resolution and only requires AA to CG mapping and isomeric information (cis/trans/dihedral/chiral). The backmapping procedure includes two simple steps: a) AA atoms are randomly placed near the corresponding CG beads according to the provided mapping scheme. b) Energy minimization is performed with two modifications in the AA force field (FF). First, nonbonded interactions are replaced with cosine functions to ensure numerical stability. Second, additional torsions are imposed to maintain molecules’ isomeric properties. To test the simplicity and robustness of the tool, I backmapped multiple membrane and protein CG structures into AA resolution, including a four-bead CG lipid model (resolution increased by a factor of 34) without using intermediate resolution. The tool is freely available atgithub.com/ksy141/mstool.

TABLE OF CONTENTS (TOC)
Host cell glycosylation selects for infection with CCR5- versus CXCR4-tropic HIV-1
Authors: Itell Hannah L. , Humes Daryl , Baumgarten Nell E. , Overbaugh Julie
Published: September 2023

HIV-1 infection involves a selection bottleneck that leads to transmission of one or a few HIV variants, which nearly always use CCR5 as the coreceptor (R5 viruses) for viral entry as opposed to CXCR4 (X4 viruses). The host properties that drive this selection are not well understood and may hold keys to factors that govern HIV susceptibility. In this report, we identified SLC35A2, a transporter of UDP-galactose, as a candidate X4-specific restriction factor in CRISPR-knockout screens in primary target CD4+T cells. SLC35A2 inactivation in CD4+T cells, which resulted in truncation of glycans due to the absence of galactose, not only increased X4 infection levels, but also consistently decreased infection levels of R5 HIV strains. Single cycle infections demonstrated that the effect is host cell dependent. SLC35A2 is expressed in CD4+T cells at different tissue sites, with high levels in the genital tract – the site of most HIV infections. These data support a role for a host cell protein that regulates glycan structure on HIV infection, with enhanced R5 infection but reduced X4 infection associated with SLC35A2-mediated glycosylation. Host cell glycosylation may therefore contribute to R5 selection and host susceptibility during HIV transmission.
Simple Adjustment of Intra-nucleotide Base-phosphate Interaction in OL3 AMBER Force Field Improves RNA Simulations
Authors: Mlýnský Vojtěch , Kührová Petra , Stadlbauer Petr , Krepl Miroslav , Otyepka Michal , Banáš Pavel , Šponer Jiří
Published: September 2023

Molecular dynamics (MD) simulations represent an established tool to study RNA molecules. Outcome of MD studies depends, however, on the quality of the used force field (ff). Here we suggest a correction for the widely used AMBER OL3ffby adding a simple adjustment of nonbonded parameters. The reparameterization of Lennard-Jones potential for the –H8…O5’– and –H6…O5’– atom pairs addresses an intra-nucleotide steric clash occurring in the type 0 base-phosphate interaction (0BPh). The non-bonded fix (NBfix) modification of 0BPh interactions (the NBfix0BPhmodification) was tuned via reweighting approach and, subsequently, tested using extensive set of standard and enhanced sampling simulations of both unstructured and folded RNA motifs. The modification corrects minor but visible intra-nucleotide clash for theantinucleobase conformation. We observed that structural ensembles of small RNA benchmark motifs simulated with the NBfix0BPhmodification provide better agreement with experiments. No side-effects of the modification were observed in standard simulations of larger structured RNA motifs. We suggest that the combination of OL3 RNAffand NBfix0BPhmodification is a viable option to improve RNA MD simulations.
Conserved nucleocytoplasmic density homeostasis drives cellular organization across eukaryotes
Authors: Biswas Abin , Muñoz Omar , Kim Kyoohyun , Hoege Carsten , Lorton Benjamin M. , Shechter David , Guck Jochen , Zaburdaev Vasily , Reber Simone
Published: September 2023

The packing and confinement of macromolecules in the cytoplasm and nucleoplasm has profound implications for cellular biochemistry. How intracellular density distributions vary and affect cellular physiology remains largely unknown. Here, we show that the nucleus is less dense than the cytoplasm and that living systems establish and maintain a constant density ratio between these compartments. Using label-free biophotonics and theory, we show that nuclear density is set by a pressure balance across the nuclear envelopein vitro,in vivoand during early development. Nuclear transport establishes a specific nuclear proteome that exerts a colloid osmotic pressure, which, assisted by entropic chromatin pressure, draws water into the nucleus. UsingC. elegans, we show that while nuclear-to-cytoplasmic (N/C)volumeratios change during early development, the N/Cdensityratio is robustly maintained. We propose that the maintenance of a constant N/Cdensityratio is the biophysical driver of one of the oldest tenets of cell biology: the N/Cvolumeratio. In summary, this study reveals a previously unidentified homeostatic coupling of macromolecular densities that drives cellular organization with implications for pathophysiologies such as senescence and cancer.
Robust nuclease-dead S. aureus dCas9-mediated alpha-synuclein knockdown in substantia nigra in a humanized mouse model of Parkinson’s disease
Authors: Torres C. Alejandra Morato , Zafar Faria , Sastre Danuta , Hermesky De’Angelo , Chen Max Y. , Vazquez Jocelyn Palafox , Qi Lei Stanley , Kirik Deniz , Schüle Birgitt
Published: September 2023

Parkinson’s disease (PD) is becoming increasingly prevalent due to an aging society, which places a substantial disease burden on patients and their families and an annual cost estimated at 52 billion dollars. However, no approved disease modulatory therapies that halt disease progression are available. Alpha-synuclein is a critical therapeutic target found in aggregated form in Lewy bodies which is the diagnostic hallmark of PD. Familial autosomal dominant forms of PD can present with causative exonic point mutations, copy number multiplications, and non-coding risk variants in the alpha-synuclein gene. The disease onset, severity, and progression depend on the gene expression levels of the alpha-synuclein. Here, we demonstrate thatStreptococcus aureusdCas9 (sadCas9)-mediated CRISPR interference (CRISPRi) reduces alpha-synuclein mRNA and protein levels in a humanized mouse model. The mechanism of action is based on the principle that a complementary single guide RNA (sgRNA) recruits the sadCas9 protein to the promoter region of alpha-synuclein and modulates target gene transcription, leading to reduced gene expression. We show robust downregulation of alpha-synuclein in neurons after unilateral stereotactic injection into the substantia nigra of adult mice 1 and 6 months after surgery. This work shows proof of concept that viral-mediated sadCas9 CRISPR interference can be a promising therapeutic strategy to reduce alpha-synucleinin vivo.

Graphical abstract

eTOC synopsis

This study focuses on the development of an AAV9 nuclease-dead S. aureus CRISPR/Cas9 expression system designed to target the humanSNCApromoter. The objective is to achieve downregulation of α-synuclein (a-syn) expression. After performing surgery and introducing the expression system, the levels of a-syn were measured at 1 month and 6 months post-surgery. The results indicate a significant downregulation of a-syn at both time points. Furthermore, it was observed that the initial immune response to the system attenuated over time, reaching control levels at the 6-month mark. These findings suggest the potential of this expression system for long-term downregulation of a-syn and provide insights into the immune response dynamics associated with its use.
Characterization of Turkish Pine Honey and Differentiation from Floral Honeys by NMR Spectroscopy and Chemometric Analysis
Authors: Kahraman Kerem , Göcenler Oktay , Dağ Çağdaş
Published: September 2023

Honey is a viscous, supersaturated sugar solution produced by bees through the enzymatic transformation of nectar from flowers, containing a complex mixture of carbohydrates, organic acids, enzymes, and other minor constituents. Although honey has been used for thousands of years for its nutritional and medicinal properties, it has been the subject of increasing attention in recent years due to increasing adulterated honey production. Consequently, assessment of honey quality and authenticity has become essential to ensure consumer confidence of regional honey and to perverse the practice of authentic honey production. In this study, we employed nuclear magnetic resonance (NMR) spectroscopy and chemometric analysis to characterize Turkish Pine honey and compare it to flower honey originating from the Oceania, Aegean, and West Coast of North America regions. Utilizing1H NMR spectroscopy, the chemical profile of Turkish Pine honey was characterized, and unique peaks were found. Additionally, PLS-DA statistical analysis was employed to further investigate the distinction of Turkish Pine honey among other floral and regional honeys. Upon completion of our statistical analysis, we were able to effectively distinguish Turkish Pine honey from other regional honey types, allowing us to formulate a universal test for authenticity of Turkish Pine Honey.
Germ cells do not progress through spermatogenesis in the infertile zebrafish testis
Authors: Sposato Andrea L. , Llewellyn Darren R. , Weber Jenna M. , Hollins Hailey L. , Schrock Madison N. , Farrell Jeffrey A. , Gagnon James A.
Published: September 2023

Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have greatly informed our understanding of typical spermatogenesis, the molecular and cellular mechanisms underlying spermatogenesis are not yet understood, particularly with respect to the onset of fertility. We used single-cell RNA sequencing to generate a developmental atlas of the zebrafish testis. Using 5 timepoints across the adult life of a zebrafish, we described cellular profiles in the testis during and after fertility. While all germ cell stages of spermatogenesis are detected in testes from fertile adult zebrafish, testes from older infertile males only contained spermatogonia and a reduced population of spermatocytes. These remaining germ cells are transcriptionally distinct from fertile spermatogonia. Immune cells including macrophages and lymphocytes drastically increase in abundance in infertile testes. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of male fertility.
Temporal dynamics of hippocampal activity predict stable patterns of sensitization or habituation to noxious stimulation across sessions
Authors: Harrison Richard , van Reekum Carien M. , Adams Greig , Gandhi W. , Salomons Tim V.
Published: September 2023

Acute pain serves to warn an organism of potential damage. When nociceptive stimulation persists, two possible responses emerge: If no risk of harm is anticipated, habituation may occur. If harm is considered possible, pain sensitization is likely. An individual’s adaptation to prolonged pain may provide insight into their ability to manage resources, and possibly their likelihood of developing chronic pain. Yet, little is known about the stability of these individual differences or their underlying neural mechanisms. Eighty-five participants undertook a repetitive noxious stimulation task and a resting-state scan in an MRI scanner, in a first session. They then completed the same task outside the scanner on three separate days. Pain adaptation was operationalized as the slope of change in pain ratings within session. Intraclass correlations were calculated between slopes across the four sessions, which demonstrated high stability and association with emotional disposition. Individuals who habituated to repeated stimuli showed increasing activity in the anterior hippocampus and amygdala, while individuals who sensitized showed increasing activity in the sensorimotor cortices. These clusters were then used as seeds in resting state analysis, with habituation associated with higher functional connectivity between hippocampus/amygdala and ventromedial prefrontal cortex(vmPFC), and higher connectivity between sensorimotor regions and the hippocampus, amygdala and insula cortex. Our findings suggest that pain adaptation is a stable phenotypic trait, which may have implications for the prediction of chronic pain.

This study implicates neural sensory and appraisal systems in these stable responses, offering insight into the mechanisms underlying trait-like responses to prolonged nociceptive input.
Phosphoproteomics implicates glutamatergic and dopaminergic signalling in the antidepressant-like properties of the iron chelator deferiprone
Authors: Uzungil Volkan , Luza Sandra , Opazo Carlos M , Mees Isaline , Li Shanshan , Ang Ching-Seng , Williamson Nicholas A , Bush Ashley I , Hannan Anthony J , Renoir Thibault
Published: September 2023

Current antidepressants have limitations due to insufficient efficacy and delay before improvement in symptoms. Polymorphisms of the serotonin transporter (5-HTT) gene have been linked to depression (when combined with stressful life events) and to altered response to selective serotonergic reuptake inhibitors. We have previously revealed the antidepressant-like properties of the iron chelator deferiprone in the 5-HTT knock-out (KO) mouse model of depression. Furthermore, deferiprone was found to alter neural activity in the prefrontal cortex of both wild-type (WT) and 5-HTT KO mice. In the current study, we examined the molecular effects of acute deferiprone treatment in the prefrontal cortex of both genotypes via phosphoproteomics. In WT mice treated with deferiprone, there were 22 differentially expressed phosphosites, with gene ontology analysis implicating cytoskeletal proteins. In 5-HTT KO mice treated with deferiprone, we found 33 differentially expressed phosphosites. Gene ontology analyses revealed phosphoproteins that were predominantly involved in synaptic and glutamatergic signalling. In a drug naive cohort, the analysis revealed 21 differentially expressed phosphosites in 5-HTT KO compared to WT mice. We confirmed the deferiprone-induced increase in Tyrosine hydroxylase serine 40 residue phosphorylation (pTH-Ser40) (initially revealed in our phosphoproteomics study) by western blots, with deferiprone increasing pTH-Ser40 expression in WT and 5-HTT KO mice. As glutamatergic and synaptic signalling are dysfunctional in 5-HTT KO mice (and are the target of fast-acting antidepressant drugs such as ketamine), these molecular effects may underpin deferiprone’s antidepressant-like properties. Furthermore, dopaminergic signalling may also be involved in deferiprone’s antidepressant-like properties.
Transcription factor networks link B-lymphocyte development and malignant transformation in leukemia
Authors: Sigvardsson Mikael
Published: September 2023

Rapid advances in genomics have opened unprecedented possibilities to explore the mutational landscapes in malignant diseases, such as B-cell acute lymphoblastic leukemia (B-ALL). This disease is manifested as a severe defect in the production of normal blood cells due to the uncontrolled expansion of transformed B-lymphocyte progenitors in the bone marrow. Even though classical genetics identified translocations of transcription factor-coding genes in B-ALL, the extent of the targeting of regulatory networks in malignant transformation was not evident until the emergence of large-scale genomic analyses. There is now evidence that many B-ALL cases present with mutations in genes that encode transcription factors with critical roles in normal B-lymphocyte development. These includePAX5,IKZF1,EBF1, andTCF3, all of which are targeted by translocations or, more commonly, partial inactivation in cases of B-ALL. Even though there is support for the notion that germline polymorphisms in thePAX5andIKZF1genes predispose for B-ALL, the majority of leukemias present with somatic mutations in transcription factor-encoding genes. These genetic aberrations are often found in combination with mutations in genes that encode components of the pre-B-cell receptor or the IL-7/TSLP signaling pathways, all of which are important for early B-cell development. This review provides an overview of our current understanding of the molecular interplay that occurs between transcription factors and signaling events during normal and malignant B-lymphocyte development.
Explainable machine learning for diffraction patterns
Authors: Nawaz Shah , Rahmani Vahid , Pennicard David , Setty Shabarish Pala Ramakantha , Klaudel Barbara , Graafsma Heinz
Published: September 2023

Serial crystallography experiments at X-ray free-electron laser facilities produce massive amounts of data but only a fraction of these data are useful for downstream analysis. Thus, it is essential to differentiate between acceptable and unacceptable data, generally known as `hit' and `miss', respectively. Image classification methods from artificial intelligence, or more specifically convolutional neural networks (CNNs), classify the data into hit and miss categories in order to achieve data reduction. The quantitative performance established in previous work indicates that CNNs successfully classify serial crystallography data into desired categories [Ke, Brewster, Yu, Ushizima, Yang & Sauter (2018). J. Synchrotron Rad.
25, 655–670], but no qualitative evidence on the internal workings of these networks has been provided. For example, there are no visualization methods that highlight the features contributing to a specific prediction while classifying data in serial crystallography experiments. Therefore, existing deep learning methods, including CNNs classifying serial crystallography data, are like a `black box'. To this end, presented here is a qualitative study to unpack the internal workings of CNNs with the aim of visualizing information in the fundamental blocks of a standard network with serial crystallography data. The region(s) or part(s) of an image that mostly contribute to a hit or miss prediction are visualized.
catena-Poly[[diaquabis(1,3-dihydro-3-oxoisobenzofuran-1-acetato)copper(II)]-μ-N,N′-(ethane-1,2-diyl)dinicotinamide]
Authors: Pumford Sean R. , LaDuca Robert L.
Published: September 2023

The title compound, {[Cu(C10H7O4)2(C14H14N4O2)(H2O)2]
n
, contains octahedrally coordinated CuII ions ligated by two bis(1,3-dihydro-3-oxo-1-isobenzofuranacetate (dibf) ligands and two trans water molecules, linked by N,N′-(ethane-1,2-diyl)dinicotinamide (edn) ligands into mono-periodic coordination polymer chains. The dibf ligands exhibit a pseudo-mirror positional disorder over two positions in a 89.2 (3)/10.8 (3) ratio; the central amide groups of the edn ligands are disordered pseudo-rotationally in the same ratio. These mono-periodic chain motifs are held into supramolecular di-periodic supramolecular layers by means of N—H...O hydrogen bonding between edn amide groups and unligated dibf carboxylate O atoms. In turn, the supramolecular layers are held by crystal packing forces into the full crystal structure of the title compound.
The 18th FINA world masters championships and destination loyalty
Authors: Kim Euisoo , Kim Sukkyu , Jeong Yunduk
Published: September 2023

Purpose

Based on a stimulus–organism–response theory, the purpose of this study is to empirically examine structural equation model linking personal involvement, positive emotions, tourist satisfaction and destination loyalty among sport tourists to a mega sport event. Moreover, moderating effects of place attachment on the relation between the aforementioned variables were investigated.

Design/methodology/approach

The validities and reliabilities of the measures were investigated through confirmatory factor analysis, Cronbach's alpha and correlation analysis. A structural equation modelling with maximum likelihood estimation was tested to analyze the relationships among the research variables using 383 participants.

Findings

The results revealed positive associations among stimulus (personal involvement), organism (positive emotions) and response (tourist satisfaction and destination loyalty). Moreover, the authors found moderating effect of place attachment on the relationships between personal involvement and positive emotions, personal involvement and tourist satisfaction and tourist satisfaction and destination loyalty.

Research limitations/implications

This study holds the potential to aid destination managers in acquiring a more profound comprehension of how personal involvement contributes to elicit positive emotions, keep tourists satisfied and build destination loyalty as well as demonstrating the moderating roles of place attachment. However, generalizing the findings to alternative contexts presents a formidable challenge. Enhancing the applicability of these findings could be achieved through prospective research endeavors that explore visitors in diverse cities spanning various continents.

Originality/value

The study contributed to the literature by providing empirical evidence that personal involvement evokes positive emotions while also plays significant role in improving satisfaction and loyalty. Given the importance of experiences in sport tourism, this study also confirmed the role of positive emotions on tourist satisfaction and destination loyalty. Additionally, this study examined the moderating effect of place attachment, which has not been investigated in sport tourism context.
The effect of perceived quality and customer engagement on the loyalty of users of Spanish fitness centres
Authors: Gálvez-Ruiz Pablo , Calabuig Ferran , Grimaldi-Puyana Moisés , González-Serrano María Huertas , García-Fernández Jerónimo
Published: September 2023

Purpose

The purpose of this paper is to analyse the influence of perceived quality and customer engagement on perceived value and satisfaction in a model to evaluate loyalty in users of fitness centres.

Design/methodology/approach

Through an online questionnaire, the study uses a large sample of 6,584 users from 44 low-cost fitness centres from different cities in Spain. After validating the measurement model, the hypotheses were tested through structural equation (SEM) modelling technique, noting the existence of significant relationships.

Findings

The results showed that two dimensions of perceived quality have a positive influence on perceived value (employees) and satisfaction (facilities). However, the enthused participation dimension of customer engagement also indicated an important impact on perceived value and satisfaction, thus confirming the influence of this dimension in the context of sports services for users' loyalty.

Originality/value

With a large sample, the importance of this study lies in the use of strategies to achieve a greater influence on perceived value and satisfaction, with the aim of increasing customer loyalty in fitness centres. This is why, in addition to the service quality, the influence of the customer engagement dimensions is included, which have not been previously analysed in this emerging business model.
What does expatriate success mean? Developing a comprehensive definition through a systematic literature review
Authors: El Amine Nour R. , Cascón-Pereira Rosalía
Published: September 2023

Purpose

Despite being one of the most used dependent variables in expatriate management research, no clear-cut understanding exists of what expatriate success means. Thus, this study aims to propose an integrative definition of expatriate success by providing an overview of expatriate success's dimensions, antecedents, and their interplay.

Design/methodology/approach

A systematic literature review (SLR) was conducted to achieve the purpose. A total of 249 empirical studies (quantitative 111, qualitative 50, mixed-methods 17), literature reviews (67) and meta-analyses (4) on expatriate success were reviewed from Web of Science and Scopus databases published from 1990 until December 2021. The study selection criteria followed the PRISMA flowchart steps, and then descriptive and network analyses were performed to identify expatriates' success dimensions, antecedents and their interplay.

Findings

The findings show the interplay among antecedents and dimensions of expatriate success across three levels (individual, interpersonal and organisational) to clarify the concept of expatriate success. Also, the study offers a comprehensive definition of expatriate success based on the dimensions identified.

Research limitations/implications

The suggested definition of expatriate success elucidates the “atheoretical”, multidimensional and socially constructed nature of the construct and hence, calls for more “theoretical”, multidimensional and subjective considerations of the term to ground human resource management practices addressed to attain expatriates' success.

Originality/value

This paper provides an integrative definition of expatriate success, giving greater insight into the construct, in addition to critically reflecting on it.