bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic and functional diversity of β-N-acetylgalactosamine residue-targeting glycosidases expanded by deep-sea metagenome
Authors: Sumida Tomomi , Hiraoka Satoshi , Usui Keiko , Ishiwata Akihiro , Sengoku Toru , Stubbs Keith A , Tanaka Katsunori , Deguchi Shigeru , Fushinobu Shinya , Nunoura Takuro
Published: July 2023

β-N-Acetylgalactosamine-containing glycans play essential roles in several biological processes, including cell adhesion, signal transduction, and immune responses. β-N-Acetylgalactosaminidases hydrolyze β-N-acetylgalactosamine linkages of various glycoconjugates. However, their biological significance remains ambiguous, primarily because only one type of enzyme, exo-β-N-acetylgalactosaminidases that specifically act on β-N-acetylgalactosamine residues, has been documented so far. In this study, we identified three novel glycoside hydrolase families distributed among all three domains of life and characterized eight novel β-N-acetylgalactosaminidases and β-N-acetylhexosaminidase through sequence-based screening of deep-sea metagenomes and subsequent searching of public protein databases. Despite low sequence similarity, the crystal structures of these enzymes demonstrate that all enzymes share a prototype structure and diversify their substrate specificities (endo-, dual-endo/exo-, and exo-) through the accumulation of mutations and insertional amino acid sequences. The diverse β-N-acetylgalactosaminidases reported in this study could facilitate the comprehension of their structures and functions and present novel evolutionary pathways for expanding their substrate specificity.
Functional and topological analysis of PSENEN, the fourth subunit of the γ-secretase complex
Authors: Serneels Lutgarde , Bammens Leen , Zwijsen An , Tolia Alexandra , Chávez-Gutiérrez Lucía , De Strooper Bart
Published: July 2023

The γ-secretase complexes are intramembrane cleaving proteases involved in the generation of the Aβ peptides in Alzheimer’s Disease. The complex consists of four subunits, with Presenilin, harboring the catalytic site. Here, we study the role of the smallest subunit, PSENEN or Presenilin enhancer 2 (PEN-2), encoded by the genePsenen,in vivoandin vitro. We find a profound Notch-deficiency phenotype inPsenen−/−embryos confirming the essential role of PSENEN in the γ-secretase complex. We usedPsenen−/−fibroblasts to explore the structure-function of PSENEN by the Scanning Cysteine Accessibility Method. Glycine22 and Proline27 which border the membrane domains 1 and 2 of PSENEN are involved in complex formation and stabilization of γ-secretase. The hairpin structured hydrophobic membrane domains 1 and 2 are exposed to a water-containing cavity in the complex, while transmembrane domain 3 is not water exposed. We finally demonstrate the essential role of PSENEN for the cleavage activity of the complex. PSENEN is more than a structural component of the γ-secretase complex and might contribute to the catalytic mechanism of the enzyme.
Unbiased method for spectral analysis of cells with great diversity of autofluorescence spectra
Authors: Roet Janna E.G. , Mikula Aleksandra M. , de Kok Michael , Chadick Cora H. , Vallejo Juan J. Garcia , Roest Henk P. , van der Laan Luc J.W. , de Winde Charlotte M. , Mebius Reina E.
Published: July 2023

Autofluorescence is an intrinsic feature of cells, caused by the natural emission of light by its cellular content, that can complicate analysis of flow cytometry data. Different cell types have different autofluorescence spectra and even within one cell type heterogeneity of autofluorescence spectra can be present, for example as a consequence of activation status or metabolic changes. By using full spectrum flow cytometry, the emission spectrum of a fluorochrome is captured by a set of detectors across a range of wavelengths, creating an unique spectrum for this fluorochrome, that is used to unmix the signal of a full stained sample into the signals of the different fluorochromes. Importantly, this technology can also be used to identify the aut-ofluorescence signal of an unstained sample, which can be used for unmixing purposes and to separate the autofluorescence signal from the fluorophore signals. However, this only works if the sample has one homogeneous autofluorescence spectrum. To analyze samples with a heterogeneous autofluorescence spectral profile, we here setup an unbiased workflow to detect all different autofluorescence spectra present in a sample to take them along as ‘autofluorescence signatures’ during the unmixing of the full stained samples. First, clusters of cells with similar autofluorescence spectra are identified by unbiased dimensional reduction and clustering. Then, unique autofluorescence clusters are determined and are used to improve the unmixing accuracy of the full stained sample. This unbiased method allows for the identification of all autofluorescence spectra present in a sample, independent of cell types and intensity of the autofluorescence spectra. Furthermore, this method is equally useful for spectral analysis of different biological samples, including tissue cell suspensions, peripheral blood mononuclear cells andin vitrocultures of (primary) cells.
Inference of infectious disease transmission using multiple genomes per host
Authors: Carson Jake , Keeling Matt , Wyllie David , Ribeca Paolo , Didelot Xavier
Published: July 2023

In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak ofPseudomonas aeruginosaamongst cystic fibrosis patients and a nosocomial outbreak ofKlebsiella pneumoniae.
Epidermal IL-33 drives inflammation in necroptosis-induced skin inflammation by recruiting TNF-producing immune cells
Authors: Fernandez-Nasarre Africa , Srivastava Vikas , Bennett Ffion , Michel Laurence , Bensussan Armand , Choy Ernest H. , Bagot Martine , Bonnet Marion C.
Published: July 2023

Caspase-8 deficiency in the epidermis (caspase-8EKO) results in cutaneous inflammation resembling pustular psoriasis, triggered by necroptotic cell death of keratinocytes. Necroptosis is a highly proinflammatory form of programmed necrosis due to the release of intracellular molecules called alarmins, which can act as inflammatory mediators. However, their role in necroptosis-induced skin inflammation remains unexplored. Here, we demonstrate that alarmin IL-33 and its receptor ST2 are essential early mediators of necroptosis-induced skin inflammation. Genetic ablation ofIl-33orSt2dramatically delays lesion development and improves survival of caspase-8EKOanimals. IL-33 is highly expressed in necroptotic epidermis of caspase-8EKOmice and induces immune cell recruitment in the skin upon keratinocyte necroptosis. Impairment of the IL33-ST2 axis does not affect epidermal necroptosis but reduces the recruitment of TNF-producing infiltrating immune cells and subsequent amplification of cutaneous inflammation. Collectively, our findings highlight a pivotal role for IL-33 and ST2 in necroptosis-induced skin inflammation.

Teaser

Inhibition of IL-33/ST2 axis alleviates necroptosis-induced skin inflammation by reducing TNF production in the dermis.
Rho-associated kinase regulates Langerhans cell morphology and responsiveness to tissue damage
Authors: Peterman Eric , Quitevis Elgene J.A. , Goo Camille E.A. , Rasmussen Jeffrey P.
Published: July 2023

Skin is often the first physical barrier to encounter invading pathogens and physical damage. Damage to the skin must be resolved quickly and efficiently to maintain organ homeostasis. Epidermal-resident immune cells known as Langerhans cells use dendritic protrusions to dynamically surveil the skin microenvironment, which contains epithelial keratinocytes and somatosensory peripheral axons. The mechanisms governing Langerhans cell dendrite dynamics and responses to tissue damage are not well understood. Using skin explants from adult zebrafish, we show that Langerhans cells maintain normal surveillance activity following axonal degeneration and use their dynamic dendrites to engulf small axonal debris. By contrast, a ramified-to-rounded shape transition accommodates the engulfment of larger keratinocyte debris. We find that Langerhans cell dendrites are richly populated with actin and sensitive to a broad spectrum actin inhibitor. We further show that Rho-associated kinase (ROCK) inhibition leads to elongated dendrites, perturbed clearance of large debris, and reduced Langerhans cell migration to tissue-scale wounds. Altogether, our work describes the unique dynamics of Langerhans cells and involvement of the ROCK pathway in immune cell responses to damage of varying magnitude.
A genetic screen to uncover molecular mechanisms underlying lipid transfer protein function at membrane contact sites and neurodegeneration
Authors: Mishra Shirish , Manohar Vaishnavi , Chandel Shabnam , Manoj Tejaswini , Bhattacharya Subhodeep , Hegde Nidhi , Nath Vaisaly R , Krishnan Harini , Wendling Corinne , Di Mattia Thomas , Martinet Arthur , Chimata Prasanth , Alpy Fabien , Raghu Padinjat
Published: July 2023

Lipid transfer proteins mediate the transfer of lipids between organelle membranes in eukaryotes and loss of function in these has been linked to neurodegenerative disorders. However, the mechanism by which loss of lipid transfer protein function leads to neurodegeneration is not understood. InDrosophilaphotoreceptors, depletion of Retinal Degeneration B (RDGB), a phosphatidylinositol transfer protein localized to endoplasmic reticulum-plasma membrane contact sites leads to defective phototransduction and retinal degeneration but the mechanism by which RDGB function is regulated and the process by which loss of this activity leads to retinal degeneration is not understood. RDGB is localized to membrane contact sites (MCS) and this depends in the interaction of its FFAT motif with the ER integral protein VAP. To identify regulators of RDGB functionin vivo, we depleted more than 300 VAP interacting proteins and identified a set of 52 suppressors ofrdgB. The molecular identity of these suppressors indicates a role for novel lipids in regulating RDGB function and for transcriptional and ubiquitination processes in mediating retinal degeneration inrdgB. The human homologs of several of these molecules have been implicated in neurodevelopmental diseases underscoring the importance of VAP mediated processes in these disorders.
Apically localized PANX1 impacts neuroepithelial expansion in human cerebral organoids
Authors: Noort Rebecca J. , Flemmer Robert T. , Moore Craig S. , Belbin Thomas J. , Esseltine Jessica L.
Published: July 2023

Dysfunctional paracrine signaling through Pannexin 1 (PANX1) channels is linked to several adult neurological pathologies and emerging evidence suggests that PANX1 plays an important role in human brain development. It remains unclear how early PANX1 influences brain development, or how loss of PANX1 alters the developing human brain. Using a cerebral organoid model of early human brain development, we find that PANX1 is expressed at all stages of organoid development from neural induction through to neuroepithelial expansion and maturation. Interestingly, PANX1 cellular distribution and subcellular localization changes dramatically throughout cerebral organoid development. During neural induction, PANX1 becomes concentrated at the apical membrane domain of neural rosettes where it co-localizes with several apical membrane adhesion molecules. During neuroepithelial expansion,PANX1-/- organoids are significantly smaller than control and exhibit significant gene expression changes related to cell adhesion, Wnt signaling and non-coding RNAs. As cerebral organoids mature, PANX1 expression is significantly upregulated and is primarily localized to neuronal populations outside of the ventricular-like zones. Ultimately, PANX1 protein can be detected in all layers of a 21-22 post conception week human fetal cerebral cortex. Together, these results show that PANX1 is dynamically expressed by numerous cell types throughout embryonic and early fetal stages of human corticogenesis and loss of PANX1 compromises neuroepithelial expansion due to dysregulation of cell-cell and cell-matrix adhesion, perturbed intracellular signaling, and changes to gene regulation.
Identification of state-specific proteomic and transcriptomic signatures of microglia-derived extracellular vesicles
Authors: Santiago Juliet V. , Natu Aditya , Ramelow Christina C. , Rayaprolu Sruti , Xiao Hailian , Kumar Vishnu , Seyfried Nicholas T. , Rangaraju Srikant
Published: July 2023

Microglia are resident immune cells of the brain that play important roles in mediating inflammatory responses in several neurological diseases via direct and indirect mechanisms. One indirect mechanism may involve extracellular vesicle (EV) release, so that the molecular cargo transported by microglia-derived EVs can have functional effects by facilitating intercellular communication. The molecular composition of microglia-derived EVs, and how microglial activation states impacts EV composition and EV-mediated effects in neuroinflammation, remain poorly understood. We hypothesize that microglia-derived EVs have unique molecular profiles that are determined by microglial activation state. Using size-exclusion chromatography to purify EVs from BV2 microglia, combined with proteomic (label-free quantitative mass spectrometry or LFQ-MS) and transcriptomic (mRNA and non-coding RNA seq) methods, we obtained comprehensive molecular profiles of microglia-derived EVs. LFQ-MS identified several classic EV proteins (tetraspanins, ESCRT machinery, and heat shock proteins), in addition to over 200 proteins not previously reported in the literature. Unique mRNA and microRNA signatures of microglia-derived EVs were also identified. After treating BV2 microglia with lipopolysaccharide (LPS), interleukin-10, or transforming growth factor beta, to mimic pro-inflammatory, anti-inflammatory, or homeostatic states, respectively, LFQ-MS and RNA seq revealed novel state-specific proteomic and transcriptomic signatures of microglia-derived EVs. Particularly, LPS treatment had the most profound impact on proteomic and transcriptomic compositions of microglia-derived EVs. Furthermore, we found that EVs derived from LPS-activated microglia were able to induce pro-inflammatory transcriptomic changes in resting responder microglia, confirming the ability of microglia-derived EVs to relay functionally-relevant inflammatory signals. These comprehensive microglia-EV molecular datasets represent important resources for the neuroscience and glial communities, and provide novel insights into the role of microglia-derived EVs in neuroinflammation.
Method for Depletion of Mitochondria DNA in Human Bronchial Epithelial Cells
Authors: Novotny Michael V. , Xu Weiling , Mulya Anny , Janocha Allison J. , Erzurum Serpil C.
Published: July 2023

Introduction

Mitochondria are increasingly recognized to play a role in the airway inflammation of asthma. Model systems to study the role of mitochondrial gene expression in bronchial epithelium are lacking. Here, we create custom bronchial epithelial cell lines derived from primary airway epithelium that are depleted of mitochondrial DNA.

Methods

We treated BET-1A and BEAS-2B cells with ethidium bromide (EtBr) with or without 2’,3’-dideoxycytidine (ddC) to create cells lacking mitochondrial DNA (mtDNA). Cells’ mtDNA copy number were verified by quantitative polymerase chain reaction (qPCR) in comparison to nuclear DNA (nDNA). Cells were also assessed for oxidative phosphorylation by measures of oxygen consumption using the Seahorse analyzer.

Results

One week of EtBr treatment led to ∼95% reduction of mtDNA copy number (mtDNA-CN) in cells (mtDNA-CN, mean±SE, baseline vs. treatment: BEAS-2B, 820 ± 62 vs. 56 ± 9; BET-1A, 957 ± 52 vs. 73 ± 2), which was further reduced by addition of 25 μM ddC (mtDNA-CN: BEAS-2B, 2.8; BET-1A, 47.9). Treatment for up to three weeks with EtBr and ddC led to near complete loss of mtDNA (mtDNA-CN: BEAS-2B, 0.1; BET-1A, 0.3). The basal oxygen consumption rate (OCR) of mtDNA-depleted BET-1A and BEAS-2B cells dropped to near zero. Glycolysis measured by extracellular acidification rate (ECAR) increased ∼two-fold in cells when mtDNA was eliminated [ECAR (mpH/min/103cells), baseline vs. treatment: BEAS-2B, 0.50 ± 0.03 vs. 0.94 ± 0.10P=0.005; BET-1A, 0.80 ± 0.04 vs. 1.14 ± 0.06P=0.001].

Conclusion

Mitochondrial DNA–depleted BET-1A ρ0 and BEAS-2B ρ0 cell lines are viable, lack the capacity for aerobic respiration, and increase glycolysis. This cell model system can be used to further test mitochondrial mechanisms of inflammation in bronchial epithelial cells.
Impact of sickle cell trait hemoglobin inPlasmodium falciparum-infected erythrocytes
Authors: Seidu Zakaria , Ofori Michael F. , Hviid Lars , Lopez-Perez Mary
Published: July 2023

Sickle cell trait (HbAS) confers protection against severePlasmodium falciparummalaria but has little effect on infection ratesper se. The reason for this is not fully understood. However, it appears to involve impaired parasite survival at the low oxygen tensions prevailing in the postcapillary venules whereP. falciparum-infected erythrocytes (IEs) often accumulate. This IE sequestration is mediated by parasite-encoded IE surface ligands, primarily PfEMP1. Different variants of this family of proteins bind to host receptors with different tissue distributions. We hypothesized thatP. falciparumparasites modulate PfEMP1 expression to enhance their survival by altering IE tissue distribution in HbAS hosts. To test this, we studied PfEMP1 expression in parasites maintained in vitro in HbAS and HbAA erythrocytes. We found that parasite survival and PfEMP1 expression were reduced in HbAS IEs, particularly at low oxygen tensions, without obvious qualitative differences in PfEMP1 expression between HbAA and HbAS IEs. In contrast, parasites growing in HbAS erythrocytes increased their transcription ofpfsa2, a parasite gene hypothesized to be under HbS-dependent selection. Taken together, our findings support the hypothesis of quantitative but not qualitative modulation of PfEMP1 expression as a parasite strategy for coping with HbAS-related host resistance. Moreover, it provides a hint at the role ofPfsa2in parasite adaptation to HbAS and highlights the importance of further research.
Genetic Evidence for Geographic Structure within the Neanderthal Population
Authors: Rogers Alan R.
Published: July 2023

PSMC estimates of Neanderthal effective population size (Ne) exhibit a roughly 5-fold decline across the most recent 20 ky before the death of each fossil. To explain this pattern, this article develops new theory relating genetic variation to geographic population structure and local extinction. It argues that the observed pattern results from subdivision and gene flow. If two haploid genomes are sampled from the same subpopulation, their recent ancestors are likely to be geographic neighbors and therefore coalesce rapidly. By contrast, remote ancestors are likely to be far apart, and their coalescent rate is lower. Consequently,Neis larger in the distant past than in the recent past.

New theoretical results show that modest rates of extinction cause substantial reductions in heterozygosity, Wright’sFST, andNe.
Neural Correlates of High-Level Visual Saliency Models
Authors: Kroner Alexander , Senden Mario , Goebel Rainer
Published: July 2023

Visual saliency highlights regions in a scene that are most relevant to an observer. The process by which a saliency map is formed has been a crucial subject of investigation in both machine vision and neuroscience. Deep learning-based approaches incorporate high-level information and have achieved accurate predictions of eye movement patterns, the overt behavioral analogue of a saliency map. As such, they may constitute a suitable surrogate of cortical saliency computations. In this study, we leveraged recent advances in computational saliency modeling and the Natural Scenes Dataset (NSD) to examine the relationship between model-based representations and the brain. Our aim was to uncover the neural correlates of high-level saliency and compare them with low-level saliency as well as emergent features from neural networks trained on different tasks. The results identified hV4 as a key region for saliency computations, informed by semantic processing in ventral visual areas. During natural scene viewing, hV4 appears to serve a transformative role linking low- and high-level features to attentional selection. Moreover, we observed spatial biases in ventral and parietal areas for saliency-based receptive fields, shedding light on the interplay between attention and oculomotor behavior.
Incremental Self-Organization of Spatio-Temporal Spike Pattern Detection
Authors: Dehghani-Habibabadi Mohammad , Müller Lenny , Pawelzik Klaus
Published: July 2023

Brains learn new information while retaining already acquired contents. It is not known by what mechanisms synapses preserve previously stored memories while they are plastic and contribute to further learning. To understand how this notorious stability-plasticity dilemma might be resolved, we investigate a one layer self-supervised neural network that incrementally learns to detect new spatio-temporal spike patterns without loosing existing selectivities. A plausible combination of Hebbian mechanisms, hetero-synaptic plasticity, and synaptic scaling enables unsupervised learning of spatio-temporal input patterns by single neurons. In networks acquisition of different patterns one after the other is achieved by including pre-synaptic hetero-synaptic plasticity which enforces differentiation of the neurons’ selectivities. We found, however, that only when additionally the training spikes are both, jittered and stochastic past memories persist despite ongoing learning. This input variability selects a subset of weights and drives them into a regime where synaptic scaling induces self-stabilization. Thereby our model provides a novel explanation for the stability of synapses related to preexisting contents despite ongoing plasticity, and suggests how nervous systems could incrementally learn and exploit temporally precise Poisson rate codes.

Significance Statement

Activity-dependent changes in synaptic efficacy are thought to underlie learning. While ongoing synaptic plasticity is necessary for learning new content, it is detrimental to the traces of previously acquired memories. Here, we show how memories for spatio-temporal patterns can be protected from overwriting. A combination of biologically plausible synaptic plasticity mechanisms turns single neurons into robust detectors of statistically dominant input patterns. For networks, we find that memory stability is achieved when the patterns to be learned are temporally sloppy and noisy, as opposed to being frozen. This variability drives the relevant synaptic weights to large efficacies, where they become self-reinforcing and continue to support the initially learned patterns. As a result, such a network can incrementally learn one pattern after another.
Motor Improvement in Neurological Conditions (MINC): Multiple Sclerosis Design and methods of a single-arm feasibility study
Authors: van der Groen Onno , Learmonth Yvonne , van Rijn Kirsten , Smith James , Edwards Dylan
Published: August 2023

Introduction

Multiple sclerosis (MS) is a chronic progressive neurological disease. There is ample evidence that exercise can be beneficial. The advancement of modern technology led to improvements in the way therapy can be offered and can make it more motivating, thereby increasing adherence. The primary objective of this two site single blinded randomized control trial (RCT) is to explore the feasibility of conducting a multicentre definite RCT trial with a neuroanimation intervention of high-dose practice in people with mild-to-moderate MS. The secondary objective is to collect data on the variability of outcome measures to inform sample size calculations for a RCT. The tertiary outcome is to assess if this intervention changes exercise behaviour.

Methods and analysis

This study is in preparation for a future definitive randomised control trial (RCT) where the efficacy compared to a dose matched control therapy will be assessed. The setting for this study is a research laboratory at Edith Cowan University (ECU) and a neurological service provider, Multiple Sclerosis Society of Western Australia (MSWA). This feasibility study will recruit people with MS who have mild to moderate disability. Subjects will participate in 24 session, 2 times a week, of 60 minutes time-on-task intense arm training, using an exergaming system. Participants will undergo a follow up within 3 days and at 6 months after the final study visit.

Ethics and dissemination

This study was approved by the local Ethics Committee of Edith Cowan University. Subjects will be included after signing informed consent. Study outcomes will be disseminated through presentations at scientific conferences and through peer-reviewed journals.

Trial registration

ACTRN12622000281796

Strengths and limitations of this study

The study intervention is a newly developed exercise intervention protocol designed to be engaging and motivating

Next to investigating primary efficacy in order to determine sample size for a larger trial, the study also uses implementation science to assess future obstacles in a follow up randomized control trial

The feasibility of conducting a larger trial will be based on standardised criteria regarding process, resource, and management metrics

This study without a control group demonstrates feasibility rather than efficacy
Early Sport Specialization Impact on Rates of Injury in Collegiate and Professional Sport Participation: A Systematic Review and Meta-analysis
Authors: Adlou Bahman , Weimar Wendi , Wilburn Christopher , Wilson Alan
Published: August 2023

Early sport specialization (ESS) is common among adolescent athletes due to desire of reaching elite status; however, the long-term impact of ESS on sports injury (SI) rates is not fully understood. We performed a systematic review and meta-analysis of the literature to evaluate the effect of ESS on SI rates during elite sport participation. Search included PubMed, Web of Science, SPORTDiscus, EMBASE, Cochrane, CINAHL, ERIC, and Medline databases. Preferred Reporting Items for Systematic Reviews and MetaAnalyses (PRISMA) guidelines were followed to identify published peer-reviewed articles from inception to 23 March 2023. Eligible studies reported numbers of elite athletes in collegiate, national, and professional teams in ESS and their counterpart category, as well as the portion of each group with at least one SI. Studies on concussion or non-contact injuries, or without explicit injury reports during elite sprot participation were excluded. Five articles were included in the review; 3 reported SIs on collegiate and 2 reported on professional athletes. A total of 3087 athletes were included (ESS = 45%). The overall effect was not significant and demonstrated that ESS athletes had a lower odd (OR=0.7) of a SI during elite sport participation. Articles with clear reports are scarce, and thus limit the impact of the findings in this study. High heterogeneity was evident in this analysis, largely due to lack of standardized terminology, evaluation, and data representation. Prospective studies that consider diverse athlete population of the same sport are warranted.
ZNF512B binds RBBP4 via a variant NuRD interaction motif and aggregates chromatin in a NuRD complex-independent manner
Authors: Wunderlich Tim Marius , Deshpande Chandrika , Paasche Lena W. , Friedrich Tobias , Diegmüller Felix , Daus Nadine , Naseer Haniya , Stebel Sophie E. , Leers Jörg , Lan Jie , Trinh Van Tuan , Vázquez Olalla , Butter Falk , Bartkuhn Marek , Mackay Joel P. , Hake Sandra B.
Published: August 2023

The evolutionarily conserved histone variant H2A.Z plays a crucial role in various DNA-based processes but the underlying mechanisms by which it acts are not completely understood.

Recently, we identified the zinc finger protein ZNF512B as an H2A.Z-, HMG20A- and PWWP2A-associated protein. Here, we report that ZNF512B binds the nucleosome remodeling and deacetylase (NuRD) complex. We discover a conserved amino acid sequence within ZNF512B that resembles the NuRD-interaction motif (NIM) previously identified in FOG-1 and other transcriptional regulators. By solving the crystal structure of this motif bound to the NuRD component RBBP4 and by applying several biochemical assays we demonstrate that this internal NIM is both necessary and sufficient for robust NuRD binding. Transcriptome analyses and reporter assays identify ZNF512B as a repressor of gene expression that can act in both NuRD-dependent and -independent ways. Surprisingly, high levels of ZNF512B expression lead to nuclear protein and chromatin aggregation foci that form independent of the interaction with the NuRD complex but depend on the zinc finger domains of ZNF512B. Our study has implications for diseases in which ZNF512B expression is deregulated, such as cancer and neurodegenerative diseases, and hint at the existence of more proteins as potential NuRD interactors.
Reactive nitrogen species inhibit branched chain alpha-ketoacid dehydrogenase complex and impact muscle cell metabolism
Authors: Arp Nicholas L. , Seim Gretchen , Josephson Jordyn , Fan Jing
Published: August 2023

Branched chain α-ketoacid dehydrogenase complex (BCKDC) is the rate limiting enzyme in branched chain amino acid (BCAA) catabolism, a metabolic pathway with great importance for human health. BCKDC belongs to the mitochondrial α-ketoacid dehydrogenase complex family, which also includes pyruvate dehydrogenase complex (PDHC) and oxoglutarate dehydrogenase complex (OGDC). Here we revealed that BCKDC can be substantially inhibited by reactive nitrogen species (RNS) via a mechanism similar to what we recently discovered with PDHC and OGDC — modifying the lipoic arm on its E2 subunit. In addition, we showed that such reaction between RNS and the lipoic arm of the E2 subunit can further promote inhibition of the E3 subunits of α-ketoacid dehydrogenase complexes. We examined the impacts of this RNS-mediated BCKDC inhibition in muscle cells, an important site of BCAA metabolism, and demonstrated that the nitric oxide production induced by cytokine stimulation leads to a strong inhibition of BCKDC activity and BCAA oxidation in myotubes and myoblasts. More broadly, nitric oxide production reduced the level of functional lipoic arms across the multiple α-ketoacid dehydrogenases and led to intracellular accumulation of their substrates (α-ketoacids), reduction of their products (acyl-CoAs), and a lower cellular energy charge. This work revealed a new mechanism for BCKDC regulation, demonstrated its biological significance, and elucidated the mechanistic connection between RNS-driven inhibitory modifications on the E2 and E3 subunits of α-ketoacid dehydrogenases. Together with previous work, we revealed a general mechanism for RNS to inhibit all α-ketoacid dehydrogenases, which has numerous physiological implications across multiple cell types.
Rapid Genotyping ofNothobranchius furzeriEmbryos, Larvae, and Adult Fish via High-Resolution Melt Analysis (HRMA)
Authors: Krug Johannes , Richter Annekatrin , Englert Christoph
Published: August 2023

CRISPR–Cas9 has eased the induction of sequence-specific mutations and has therefore become a powerful tool to generate mutant lines for studying the role of specific genes. The cellular repair of Cas9-induced double-stranded DNA breaks by the error-prone nonhomologous end-joining pathway can result in various indel mutations. Having identified and chosen a specific mutation in a target gene, the establishment of a respective mutant line requires a feasible and precise method to differentiate the genotypes of the offspring. Here, we provide a protocol that allows genotyping of large numbers ofNothobranchius furzeriembryos, larvae, and adults harboring a previously identified indel or point mutation in a short time via high-resolution melt analysis (HRMA).
Points to Consider When Establishing and RearingCulexMosquitoes in the Laboratory
Authors: Meuti Megan E. , Siperstein Alden , Wolkoff Matthew
Published: August 2023

Culexmosquitoes transmit several pathogens to humans and animals, including viruses that cause West Nile fever and St. Louis encephalitis and filarial nematodes that cause canine heartworm and elephantiasis. Additionally, these mosquitoes have a cosmopolitan distribution and provide interesting models for understanding population genetics, overwintering dormancy, disease transmission, and other important and ecological questions. However, unlikeAedesmosquitoes that produce eggs that can be stored for weeks at a time, no obvious “stopping” point exists in the development ofCulexmosquitoes. Therefore, these mosquitoes require nearly continuous care and attention. Here, we describe some general considerations when rearing laboratory colonies ofCulexmosquitoes. We highlight different methods so that readers may choose what works best for their experimental needs and laboratory infrastructure. We hope that this information will enable additional scientists to conduct laboratory research on these important disease vectors.
TheAXEAP2program forKβ X-ray emission spectra analysis using artificial intelligence
Authors: Hwang In-Hui , Kelly Shelly D. , Chan Maria K. Y. , Stavitski Eli , Heald Steve M. , Han Sang-Wook , Schwarz Nicholas , Sun Cheng-Jun
Published: August 2023

The processing and analysis of synchrotron data can be a complex task, requiring specialized expertise and knowledge. Our previous work addressed the challenge of X-ray emission spectrum (XES) data processing by developing a standalone application using unsupervised machine learning. However, the task of analyzing the processed spectra remains another challenge. Although the non-resonantKβ XES of 3dtransition metals are known to provide electronic structure information such as oxidation and spin state, finding appropriate parameters to match experimental data is a time-consuming and labor-intensive process. Here, a new XES data analysis method based on the genetic algorithm is demonstrated, applying it to Mn, Co and Ni oxides. This approach is also implemented as a standalone application,Argonne X-ray Emission Analysis 2(AXEAP2), which finds a set of parameters that result in a high-quality fit of the experimental spectrum with minimal intervention.AXEAP2is able to find a set of parameters that reproduce the experimental spectrum, and provide insights into the 3delectron spin state, 3d–3pelectron exchange force andKβ emission core-hole lifetime.
Architecture of the rings of 5-arylidenerhodanine derivatives versus P-gp inhibition
Authors: Nitek Wojciech , Szymańska Ewa , Tejchman Waldemar , Żesławska Ewa
Published: July 2023

5-Arylidene derivatives of rhodanine show various biological activities. The new crystal structures of five derivatives investigated towards ABCB1 efflux pump modulation are reported, namely, 2-[5-([1,1′-biphenyl]-4-ylmethylidene]-4-oxo-2-thioxothiazolidin-3-yl)acetic acid dimethyl sulfoxide monosolvate, C18H13NO3S2·C2H6OS (1), 4-[5-([1,1′-biphenyl]-4-ylmethylidene]-4-oxo-2-thioxothiazolidin-3-yl)butanoic acid, C20H17NO3S2 (2), 5-[4-(benzyloxy)benzylidene]-2-thioxothiazolidin-4-one, C17H13NO2S2 (3), 4-{5-[4-(benzyloxy)benzylidene]-4-oxo-2-thioxothiazolidin-3-yl}butanoic acid, C21H19NO4S2 (4), and 5-[4-(diphenylamino)benzylidene]-2-thioxothiazolidin-4-one, C22H16N2OS2 (5). Compounds 1 and 3–5 crystallize in the triclinic space group P-1, while 2 crystallizes in the monoclinic space group P21/n, where the biphenyl moiety is observed in two positions (A and B). Two molecules are present in the asymmetric unit of 5 and, for the other four compounds, there is only one molecule; moreover, 1 crystallizes with one dimethyl sulfoxide molecule. The packing of the molecules containing a carboxyl group (1, 2 and 4) is determined by O—H...O hydrogen bonds, while in the other two compounds (3 and 5), the packing is determined by N—H...O hydrogen bonds. Additionally, induced-fit docking studies have been performed for the active compounds to investigate their putative binding mode inside the human glycoprotein P (P-gp) binding pocket.
Crystal structures of human and mouse ketohexokinase provide a structural basis for species- and isoform-selective inhibitor design
Authors: Ebenhoch Rebecca , Bauer Margit , Romig Helmut , Gottschling Dirk , Kley Jörg Thomas , Heine Niklas , Weber Alexander , Uphues Ingo , Nar Herbert , Pautsch Alexander
Published: August 2023

A molecular understanding of the proteins involved in fructose metabolism is essential for controlling the current spread of fructose-related obesity, diabetes and related adverse metabolic states in Western populations. Fructose catabolism starts with the phosphorylation of D-fructose to fructose 1-phosphate by ketohexokinase (KHK). KHK exists in two alternatively spliced isoforms: the hepatic and intestinal isoform KHK-C and the peripheral isoform KHK-A. Here, the structure of apo murine KHK (mKHK), which differs from structures of human KHK in overall conformation, is reported. An isoform-selective ligand, which offers a 50-fold higher potency on mKHK and human KHK-A compared with KHK-C, is further characterized. In mKHK, large-scale conformational changes are observed upon ligand binding. The structures suggest a combined strategy for the design of species- and isoform-selective KHK inhibitors.
Are humanitarian supply chains sustainable? A systematic review and future research themes
Authors: Nawazish Mohammed , Nandakumar M.K. , Mateen Arqum
Published: July 2023

Purpose

To address the challenges encountered in disaster responses, optimize resource utilization, minimize environmental and social impact, and ensure transparency and accountability, it is essential to review humanitarian supply chains and incorporate sustainability considerations. Humanitarian organizations can enhance their ability to deliver timely and effective assistance to those in need by continuously improving supply chain practices. Consequently, this work explores the convergence of two fast-growing domains: sustainability and humanitarian supply chain management (HSCM).

Design/methodology/approach

The authors conducted a systematic literature review of peer-reviewed articles to identify the prominent research trends and themes from the two domains' interactions. The extant literature is represented under the theory, context, characteristics, and research method (TCCM) framework. The authors have utilized a stakeholder theory perspective to identify coordination and collaboration among the various stakeholders.

Findings

This study's review findings reveal five future research directions formulating this study's central themes: the role of environmental sustainability, coordination, and collaboration in building effective HSCs; the role of humanitarian aid for the responsive HSC; the influence of big data predictive analytics on the HSC performance; development and empirical validation of sustainable HSC performance framework; the role of HSC stakeholders in building effective and efficient HSCs.

Originality/value

There is no existing academic literature review available on sustainable HSCM. This review fills this void by fostering discussion about sustainable humanitarian supply chains where the authors notably propose the TCCM framework in the context of sustainable HSCM, followed by a stakeholder network.
Recognising a signature pedagogy for public relations teaching and learning in the last twenty years
Authors: Kinnear Susan Lilico , Bowman Sarah
Published: July 2023

Purpose

This study attempts to identify the drivers for change in Public Relations education and what assumptions are made about professional practice. The authors suggest signature pedagogy has the potential to deepen our understanding of the teaching and learning of Public Relations and what this means as the Public Relations curriculum adapts. The paper has theoretical and practical value. It forefronts the concept of signature pedagogy as a fresh way to look at Public Relations teaching and learning that can be developed.

Design/methodology/approach

This paper aims to explore the historical and contemporary context of teaching Public Relations within a university setting, how it has evolved and the assumptions that underpin it both nationally and internationally. Using a mixed methods approach, the paper investigates how the curriculum has changed since 2000, how it interacts with industry and how it reflects educational historical and contemporary frameworks. It also explores the assumptions on which Public Relations education was and is based and whether signature pedagogy is evidenced.

Findings

This study concludes that, from a signature pedagogy perspective, many current Public Relations curricula emphasise surface structures of learning. Deep structures, focusing on critical engagement and conceptual approaches to problem solving, are more variable, disconnected and contested. The data indicate the existence of an Anglo-American, skills-based approach to Public Relations knowledge, alongside international nuances around multi-culturalism. From a practical viewpoint, the paper contributes to how Public Relations programmes can be designed, taught and adapted in the future.

Originality/value

The paper evidences fully unique, primary research.
Football (soccer?) on campus. Examining the historical development and promotion of the world’s most popular sport through transatlantic university comparisons
Authors: Isaacson Tom , Theofilou Anastasios
Published: July 2023

Purpose

Football is the world's most popular sport and the role of football on campus is of interest to university public relations (PR) and management professionals tasked with operations, promotions and reputation management. The purpose of the study is to explore similarities and differences in the structure and promotion of football on campus in the USA and the UK.

Design/methodology/approach

The authors completed this case study research by focusing on two related cases using cross-case pattern identification. Consistent with case study research, data collection methods were combined. Depth interviews with PR and management professionals at USA and UK universities were supported by archived documents, published media and social media accounts.

Findings

Football maintains a high level of popularity among students on campus, but each country's approach reveals different models and competitive market forces. In the USA, varsity football faces competition from popular revenue-producing sports (e.g. American football and men's basketball), but growth in the overall game, which is assisted by international influences, indicates future advancement opportunities. In the UK, football is the dominant campus sport with unique ties to professional football and high growth potential for the women's game. The lack of a fan-based model indicates the possibility for structural change, but stiff competition exists with the historically popular and well-developed professional game.

Research limitations/implications

A well-known limitation of case study research is the absence of generalizability, and each case has aspects that are unique to the research (Lucas et al., 2018). That applies in this instance as well. Variance is expected to exist between, and among universities and, based on this data, this is not possible to generalize to other universities. However, future survey research could use these results to help with the development of research questions using quantitative methods.

Originality/value

Sports PR research using the case model with professional teams has been conducted, but the authors found no published PR research comparing the structure and promotion of football at USA and UK universities. The outcomes can help with future research inquiries and theory development and are instructive for professionals working in the field.
Managing the high capital cost of prefabricated construction through stakeholder collaboration: a two-mode network analysis
Authors: Zhang Youxi , Liu Yu , Yu Rui , Zuo Jian , Dong Na
Published: July 2023

Purpose

Prefabricated construction (PC) can benefit construction industry due to its high efficiency, energy saving, consumption reduction and safety. However, the high capital cost is a critical challenge hindering its development in China. The collaboration of PC stakeholders is conducive to improving cost management efficiency and optimizing resource allocation which has been ignored in previous studies. Therefore, this study aims to explore the collaboration paths of stakeholders in the process of solving critical cost influencing factors (CIFs) of PC to reduce costs.

Design/methodology/approach

Firstly, 25 CIFs and five main stakeholders that affect PC capital cost were identified through literature research and expert interviews. Then, questionnaires were used to investigate the relationship between stakeholders and CIFs from the perspectives of three stakeholder attributes of proximity, attitude and power, respectively. Finally, based on the survey data, three stakeholder-CIF networks from three attributes perspective and a comprehensive network were constructed and used for subsequent social network analysis.

Findings

(1) Stakeholders mainly show willingness and potential to collaborate on organization and management factors; (2) More stakeholders pay attention to incentive policies and the setting of prefabrication rates and assembly rates, while all stakeholders have the right to facilitate information and resource sharing in the PC supply chain; (3) The comprehensive network shows a core-periphery structure. As core stakeholders, contractor, designer and manufacturer are more likely to actively manage the 14 core CIFs.

Originality/value

This paper innovatively combined stakeholder and cost management in PC, and used two-mode network based on three stakeholder perspectives to reveal the collaboration potential and motivation of stakeholders in PC cost management. The findings not only provide guidance for stakeholders to find potential partners and optimize resource allocation in solving specific cost issues, but also facilitate stakeholders' sustainable collaboration to achieve PC's cost performance.