bluuebunny/crossref_metadata_2025 huggingface dataset:
Universal pretreatment development for low-input proteomics using Lauryl Maltose Neopentyl Glycol
Authors: Konno Ryo , Ishikawa Masaki , Nakajima Daisuke , Endo Yusuke , Ohara Osamu , Kawashima Yusuke
Published: August 2023

In recent years, the demand for low-input proteomics, most notably single-cell proteomics (SCP), has increased. In this study, we developed a Lauryl Maltose Neopentyl Glycol (LMNG)-assisted sample preparation (LASP) method that suppresses the loss of proteins and peptides in samples by adding LMNG, a surfactant, to the digested solution and removing the LMNG simply via reversed phase solid-phase extraction. The advantage of removing LMNG during sample preparation for general proteomic analysis is that it prevents mass spectrometry (MS) contamination. When the LASP method was applied to the low-input SP3 method and on-bead digestion in immunoprecipitation-MS, the recovery of the digested peptides was greatly improved. Furthermore, we established a simple and operationally easy sample preparation method for SCP based on the LASP method (scpLASP) and identified a median of 1,175 proteins from a single HEK239F cell using liquid chromatography (LC)-MS/MS with a throughput of 80 samples per day.
Transthyretin has conformation-selective proteolytic activity against α-synuclein
Authors: Sárkány Zsuzsa , Gião Tiago , Liz Márcia Almeida , Planas Antoni , Macedo-Ribeiro Sandra , Cardoso Isabel , Arsequell Gemma , Martins Pedro M.
Published: August 2023

Transthyretin (TTR) is a plasma protein known as a transporter of thyroxine and retinol but also can inhibit the formation of amyloid β-peptide (Aβ) fibrils and catalyze the proteolysis of apolipoprotein A-I and Aβ. Here, recombinant TTR is shown to have proteolytic activity against specific conformations of α-synuclein (aSyn), a protein that accumulates in intraneuronal inclusions characteristic of Parkinson’s disease (PD). Our discovery stemmed from the observation of a marked decrease in aSyn aggregation in the presence of submicromolar concentrations of TTR. Using integrated biophysical techniques, including advanced microscopy and mass spectrometry, we found that aSyn aggregation is prevented due to the proteolytic cleavage of free aSyn by TTR, in a reaction that is slower for S-glutathionylated TTR and faster for TTR preparations containing vestigial amounts of ∼70 kDa TTR oligomers (oTTR). Interestingly, this proteolysis-trigger effect is not unique to oTTR since it can also be induced by Teflon and glass surfaces independently of which TTR preparation is tested. Our results indicate that a change in aSyn conformation must precede the proteolysis step. The proteolysis of misfolded aSyn emerges as a possible TTR function with implications for the understanding of different neurodegenerative disorders.
Biophysical analysis reveals autophosphorylation as an important negative regulator of LRRK2 dimerization
Authors: Guaitoli Giambattista , Zhang Xiaojuan , Saitta Francesca , Miglionico Pasquale , Silbermann Laura M. , Ho Franz Y. , von Zweydorf Felix , Signorelli Marco , Tych Kasia , Fessas Dimitrios , Raimondi Francesco , Kortholt Arjan , Gloeckner Christian Johannes
Published: August 2023

Leucine-rich repeat kinase 2 (LRRK2) is a large, multi-domain protein which is associated with Parkinson’s disease. Although high-resolution structures of LRRK2 are available, little is known about the complex dynamics behind the inter-domain regulation of LRRK2 and its perturbation by pathogenic variants. Previous studies have demonstrated that LRRK2 goes through an oligomerization cycle at the membrane, however it remains unclear in which form it exerts its kinase activity. Moreover, the LRRK2 monomer-dimer equilibrium and associated functional implications at a molecular level also need further investigation. In the present work, we used a multi-faceted approach to better understand LRRK2 oligomerization and suggest a functional model of how LRRK2 interacts with its substrates. To this end, we combined nano differential scanning calorimetry and mass photometry with molecular modelling. The thermal analysis resulted in a multistep denaturation profile, elucidating novel insights into the composite structural organization of the multi-domain protein LRRK2. Furthermore, LRRK2 shows a remarkable thermal stability, confirming its oligomeric nature. By using mass photometry, we could observe a monomer-dimer equilibrium which is altered by R1441G, a pathogenic variant within the Roc-COR interface. Most importantly, we could demonstrate that autophosphorylation induces LRRK2 monomerization, indicating a novel intramolecular feedback mechanism. Finally, we investigated the interaction of LRRK2 with its substrate, RAB10 by integrative computational modelling. The resulting models suggest that the monomeric form of LRRK2 is the favored protein conformation for the interaction with its substrate, leading to an increasing interest in the monomer-dimer equilibrium as a possible intervention point for the pathology.
Heterogeneity of radial spokes structural components and associated enzymes inTetrahymenacilia
Authors: Bicka Marta , Black Corbin , Ghanaeian Avrin , Joachimiak Ewa , Osinka Anna , Majhi Sumita , Konopka Anna , Bulska Ewa , Bui Khanh Huy , Wloga Dorota
Published: August 2023

Radial spokes (RS), the T-shaped, multiprotein complexes of motile cilia, transmit regulatory signals from the central apparatus to the outer doublet complexes, including inner dynein arms. In the vast majority of ciliated species, RSs assemble as repeats of triplets (RS1-RS2-RS3), and each spoke is associated with a different subset of inner dynein arms. Studies inChlamydomonasand mice sperm flagella led to the identification of RS proteins (RSPs) and revealed that some structural components are either RS1- or RS2-specific. In contrast, the protein composition of RS3 remains largely unknown. We used the ciliateTetrahymena thermophilato investigate the protein composition of individual RSs, including the poorly characterized RS3. TheTetrahymenagenome encodes three RSP3 paralogs. Using engineeredRSP3knock-out mutants and previously studied RS mutants withCFAP61,CFAP91, orCFAP206deletion and complementary approaches, including bioinformatics, total ciliome comparisons, and cryo-electron tomography with subtomogram averaging, we identifiedTetrahymenaRSP orthologs and solved the composition of individual RSs, showing their subunit heterogeneity. We found that RSP3 proteins are components of RS1 and RS2 but not RS3. Based on the presence of the RSP3 paralog, we distinguished sub-types of RS1 (RSP3A- or RSP3B-containing) and RS2 spokes (RSP3B- or RSP3C-containing). We identified novel RS-associated proteins, including several enzymes that may locally regulate ADP/ATP levels, GMP-recycling-related enzymes, and enzymes regulating phosphorylation levels. These discoveries will help to better understand the molecular mechanism(s) that regulate cilia beating and overall cilia metabolism.

Impact Statement

Identification of the subtypes of RS1 and RS2 spokes and RS1-3-specific RSPs. Discovery of the novel radial spoke structural components and RS-associated enzymes regulating ADP/ATP ratio and protein phosphorylation.
Decoding host-microbiome interactions through co-expression network analysis within the non-human primate intestine
Authors: Uehara Mika , Inoue Takashi , Hase Sumitaka , Sasaki Erika , Toyoda Atsushi , Sakakibara Yasubumi
Published: August 2023

The gut microbiome affects the health status of the host through complex interactions with the host’s intestinal wall. These host-microbiome interactions may spatially vary along the physical and chemical environment of the intestine, but these changes remain unknown. This study investigated these intricate relationships through a gene co-expression network analysis based on dual transcriptome profiling of different intestinal sites—cecum, transverse colon, and rectum— of the primate common marmoset. We proposed a gene module extraction algorithm based on graph theory to find tightly interacting gene modules of the host and the microbiome from a vast co-expression network. The 27 gene modules identified by this method, which include both host and microbiome genes, not only produced results consistent with previous studies regarding the host-microbiome relationships, but also provided new insights into microbiome genes acting as potential mediators in host-microbiome interplays. Specifically, we discovered associations between the host geneFBP1, a cancer marker, and polysaccharide degradation-related genes (pfkAandfucI) coded byBacteroides vulgatus, as well as relationships between host B-cell specific genes (CD19,CD22,CD79B,PTPN6) and a tryptophan synthesis gene (trpB) coded byParabacteroides distasonis. Furthermore, our proposed module extraction algorithm surpassed existing approaches by successfully defining more functionally related gene modules, providing insights for understanding the complex relationship between the host and the microbiome.

IMPORTANCE

We unveiled the intricate dynamics of the host-microbiome interactions along the colon by identifying closely interacting gene modules from a vast gene co-expression network, constructed based on simultaneous profiling of both host and microbiome transcriptomes. Our proposed gene module extraction algorithm, designed to interpret inter-species interactions, enabled the identification of functionally related gene modules encompassing both host and microbiome genes, which was challenging with conventional modularity maximization algorithms. Through these identified gene modules, we discerned previously unrecognized bacterial genes that potentially mediate in known relationships between host genes and specific bacterial species. Our findings underscore the spatial variations in host-microbiome interactions along the colon, rather than displaying a uniform pattern throughout the colon.
Molecular basis for short-chain thioester hydrolysis by acyl hydrolase domains intrans-acyltransferase polyketide synthases
Authors: Fage Christopher D. , Passmore Munro , Tatman Ben P. , Smith Helen G. , Jian Xinyun , Dissanayake Upeksha C. , Andrés Cisneros G. , Challis Gregory L. , Lewandowski Józef R. , Jenner Matthew
Published: August 2023

Polyketide synthases (PKSs) are multi-domain enzymatic assembly lines that biosynthesise a wide selection of bioactive natural products from simple building blocks. In contrast to theircis-acyltransferase (AT) counterparts,trans-AT PKSs rely on stand-alone AT domains to load extender units onto acyl carrier protein (ACP) domains embedded in the core PKS machinery.Trans-AT PKS gene clusters also encode acyl hydrolase (AH) domains, which are predicted to share the overall fold of AT domains, but hydrolyse aberrant acyl chains from ACP domains, thus ensuring efficient polyketide biosynthesis. How such domains specifically target short acyl chains, in particular acetyl groups, tethered as thioesters to the substrate-shuttling ACP domains, with hydrolytic rather than acyl transfer activity, has remained unclear. To answer these questions, we solved the first structure of an AH domain and performed structure-guided activity assays on active site variants. Our results offer key insights into chain length control and selection against coenzyme A-tethered substrates, and clarify how the interaction interface between AH and ACP domains contributes to recognition of cognate and non-cognate ACP domains. Combining our experimental findings with molecular dynamics simulations allowed for the production of a data-driven model of an AH:ACP domain complex. Our results advance the currently incomplete understanding of polyketide biosynthesis bytrans-AT PKSs, and provide foundations for future bioengineering efforts.
Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents: Implications for deep-sea carbon cycling
Authors: Hu Sarah K. , Anderson Rika E. , Pachiadaki Maria G. , Edgcomb Virginia P. , Serres Margrethe H. , Sylva Sean P. , German Christopher R. , Seewald Jeffrey S. , Lang Susan Q. , Huber Julie A.
Published: August 2023

Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers, hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured cell abundances and predation pressures of vent-associated microbial eukaryotes in low temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed underin situpressure that show higher cell abundances and grazing rates compared to those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between protistan grazing rate, prey cell abundance, and temperature of end member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. The quantification of protistan biomass and grazing pressure shows that hydrothermally-fueled microbial food webs play a significant role in the broader deep-sea carbon budget by contributing to local carbon export and supply of nutrient resources to the deep ocean.
An adult clock component links circadian rhythms to pancreatic β-cell maturation
Authors: Montalvo Ana P. , Gruskin Zoe L. , Leduc Andrew , Liu Mai , Gao Zihan , Ahn June H. , Straubhaar Juerg R. , Slavov Nikolai , Alvarez-Dominguez Juan R.
Published: August 2023

How ubiquitous circadian clocks orchestrate tissue-specific outputs is not well understood. Pancreatic β cell-autonomous clocks attune insulin secretion to daily energy cycles, and desynchrony from genetic or behavioral disruptions raises type 2 diabetes risk. We show that the transcription factor DEC1, a clock component induced in adult β cells, coordinates their glucose responsiveness by synchronizing energy metabolism and secretory gene oscillations.Dec1-ablated mice develop lifelong hypo-insulinemic diabetes, despite normal islet formation and intact circadianClockandBmal1activators. DEC1, but not CLOCK/BMAL1, binds maturity-linked genes that mediate respiratory metabolism and insulin exocytosis, andDec1loss disrupts their transcription synchrony. Accordingly, β-cellDec1ablation causes hypo-insulinemia due to immature glucose responsiveness, dampening insulin rhythms. Thus, Dec1 links circadian clockwork to the β-cell maturation process, aligning metabolism to diurnal energy cycles.
Bifunctional Monosaccharides Preferentially Localize to Nuclear Subcompartments
Authors: Barahtjan Pavel , Iglesias-Artola Juan M. , Böhlig Kristin , Lohmann Annett , Nadler André
Published: August 2023

Recent progress in glycan research has been driven by widespread implementations of metabolic oligosaccharide engineering. Complementing existing approaches, we here introduce bifunctional, UV-crosslinkable and clickable N-acetylglucosamine and N-acetylgalactosamine analogues, which enable direct visualization of the intracellular probe distribution as well as distinguishing monomeric and macromolecule-bound fractions. Using this feature, we find that monomeric N-acetylmonosaccharides partition into RNA-rich nuclear compartments such as nuclear speckles and nucleoli. This suggests the existence of spatially separated N-acetylmonosccharide pools within the nucleoplasm. Taken together, bifunctional N-acetylmonosaccharide probes are a powerful discovery tool for probing intracellular localization of monosaccharides and glycosylated macromolecules.
Uncovering convergence and divergence between autism and schizophrenia using genomic tools and patients’ neurons
Authors: Romanovsky Eva , Choudhary Ashwani , Peles David , Akel Ahmad Abu , Stern Shani
Published: August 2023

Autism spectrum disorders (ASDs) are highly heritable and result in abnormal repetitive behaviors and impairment in communication and cognitive skills. Previous studies have focused on the genetic correlation between ASDs and other neuropsychiatric disorders, but an in-depth understanding of the correlation to other disorders is required. We conducted an extensive meta-analysis of common variants identified in ASDs by genome-wide association studies (GWAS) and compared it to the consensus genes and single nucleotide polymorphisms (SNPs) of Schizophrenia (SCZ). We found approximately 75% of the SNPs that are associated with ASD are also associated with SCZ. We have also probed cellular phenotypes reported in ASD neurons compared to SCZ neurons from induced pluripotent stem cell (iPSC) models. Interestingly, Autism neurons start with an early maturation and schizophrenia neurons start with a late maturation, but both end up with deficits in synaptic activity when compared to control neurons as they mature.
Cryopreservation effect on DNA methylation profile in rainbow trout spermatozoa
Authors: El Kamouh Marina , Brionne Aurélien , Laurent Audrey , Labbé Catherine
Published: August 2023

Spermatozoa are the cells the most commonly used for cryopreservation of valuable genetic resources in aquaculture. It is known that fish spermatozoa transmit to the embryo not only their genetic but also their epigenetic profile, particularly DNA methylation. Therefore, any alteration of the DNA methylation profile in spermatozoa induces the risk of transmitting epigenetic alterations to the offspring. The aim of this study was to assess the effect of cryopreservation on DNA methylation in rainbow trout spermatozoa. To trigger variable cellular response after freezing-thawing, spermatozoa from mature males were cryopreserved with dimethyl sulfoxide, methanol or glycerol as cryoprotectant. We observed that dimethyl sulfoxide was the best to preserve thawed spermatozoa functions. Methanol preserved only slightly all the cellular parameters, while glycerol failed to protect motility and fertilization ability. The consequences on DNA methylation were assessed using Reduced Representation Bisulfite Sequencing (RRBS). Sperm cryopreservation did not thoroughly impact DNA methylation, although 335 to 564 differentially methylated cytosines were characterized depending on the cryoprotectant. Very few of them were shared between cryoprotectants, and no correlation with the extent of cellular damage was found. Our study showed that DNA methylation was only slightly altered after sperm cryopreservation, and this may render further analysis of the risk for the progeny very challenging.
Hepatitis B virus x (HBx) protein increases cellular OCT3/4 and MYC and facilitates cellular reprogramming
Authors: Sanal Madhusudana Girija , Gupta Sarita , Saha Rahul , Vats Nisha , Sarin Shiv Kumar
Published: August 2023

HBx is a multifunctional protein coded by the Hepatitis B virus which is involved in various cellular processes such as proliferation, cell survival/apoptosis, and histone methylation. HBx was reported to be associated with liver ‘cancer stem cells’. The stemness inducing properties of HBx could also facilitate the generation of pluripotent stem cells from somatic cells. It is well established that somatic cells can be reprogrammed to induced pluripotent stem cells (iPSC) using a cocktail of transcription factors called Yamanaka’s factors (OCT4, SOX2, KLF4, and MYC). The reprogramming process proceeds step-by-step with reprogramming factor chromatin interactions, transcription and chromatin states changing during transitions. HBx is a ‘broad spectrum trans-activator’ and therefore could facilitate these transitions. We electroporated low passage and high passage (difficult to reprogram) fibroblasts using Yamanaka’s factors (YF) with and without HBx and evaluated the reprogramming efficiency. We also investigated the tri-lineage and terminal differentiation potential of iPSC derived using HBx. We found, addition of HBx to YF, improves iPSC derivation, and increases the efficiency of iPSC generation from ‘difficult or hard-to-reprogram samples’ such as high passage/senescent fibroblasts. Furthermore, we show that HBx can substitute the key transcription factor MYC in the YF cocktail to generate iPSC. Our results have practical value in improving the efficiency of pluripotent stem cell derivation from ‘difficult to reprogram’ somatic cells in addition to providing some insights into the mechanisms of liver carcinogenesis in chronic hepatitis B. To conclude, HBx improves the reprogramming efficiency of YFs. HBx increases the cellular levels of OCT3/4 and MYC.

Lay summary

HBx is a protein made by hepatitis B virus. Yamanaka’s Factors (YF) are a mixture of ‘master-proteins’ which are used to convert adult cells to embryonic stem cells. We found that HBx protein can augment the efficiency of YF in generating these stem cells (concept summary figure).
The unconventional Myosin-1C augments endothelial secretion of von Willebrand factor by linking contractile actomyosin machinery to the plasma membrane
Authors: El-Mansi Sammy , Mitchell Tom P. , Miklavc Pika , Frick Manfred , Nightingale Thomas D.
Published: August 2023

Blood endothelial cells control the hemostatic and inflammatory response by secreting von Willebrand factor (VWF) and P-selectin from storage organelles called Weibel-Palade bodies (WPB). Actin-associated motor proteins regulate this secretory pathway at multiple points. Prior to fusion, myosin Va forms a complex that anchors WPBs to peripheral actin structures allowing maturation of content. Post-fusion, an actomyosin ring/coat is recruited and compresses to forcibly expel the largest VWF multimers. Here we provide the first evidence for the involvement of class I myosins during regulated VWF secretion. We show that unconventional myosin-1C (Myo1c) is recruited post fusion via its pleckstrin homology domain in an actin-independent process providing a link between the actin ring and phosphatidylinositol 4,5-bisphosphate (PIP2) at the membrane of the fused organelle. This is necessary to ensure maximal VWF secretion in response to secretagogue stimulation. Inhibition of class I myosins using the inhibitor Pentachloropseudilin alters the kinetics of the exocytic actin ring. These data offer new insight into the control of an essential physiological process and provide a new potential way in which it might be therapeutically controlled.

SIGNFICANCE STATEMENT

Myosin motors play diverse roles in regulated secretion. In endothelial cells, the role of conventional myosins (e.g. non-muscle myosin II) are well described however little is known about the requirement of unconventional myosins. Our data identify an important function of the class 1 myosin, Myosin-1C, in the actomyosin mediated expulsion of an essential blood clotting factor (von Willebrand factor) from endothelial cells. This is the first description of how class 1 myosins contribute to primary hemostasis and is therefore greatly improves our understanding of a fundamental physiological process.
Fundamental steps in Minichromosome Maintenance complex assembly are conserved from archaea to eukaryotes
Authors: Noble Oliver W , Degut Clement , Hodgkinson Michael R , Chong James P J , Plevin Michael J
Published: August 2023

Minichromosome maintenance (MCM) proteins are the replicative helicase in both archaea and eukaryotes. Recent cryo-EM studies have defined key steps in the assembly pathway of the eukaryotic MCM2-7 complex and determined roles for each subunit. While archaeal MCMs are simpler in composition, we know little about how these homohexameric MCMs assemble. Investigation of archaeal MCMs has largely focussed on proteins from thermophilic organisms, which typically form robust oligomers under ambient experimental conditions, preventing dissection of their assembly pathway. Here, we describe an uncharacterised MCM from the mesophilic archaeonMancarchaeum acidophilum(MacMCM). A 3D structure ofMacMCM reveals subunit-subunit interfaces that are more similar to yeast MCM2-7 than previously studied MCMs from thermophilic archaea. We show that assembly of aMacMCM homohexamer on DNA proceeds via comparable steps to MCM2-7. These results reveal an ancient mechanism underlies assembly of the MCM complex, which is conserved from archaea to eukaryotes.
Aurora A mediated new phosphorylation of RAD51 is observed in Nuclear Speckles
Authors: Alaouid Mohamad , Ymbe Parfait Kenfack , Philippot-Ménil Vanessa , Cueff Gwennina , Demeyer Alexandre , Marquis Damien , Ayadi Nizar , Fleury Fabrice , Benhelli-Mokrani Houda
Published: August 2023

To maintain its genome integrity, the cell uses complementary and orchestrated processes, among which is the DNA Damage Response. Pre mRNA maturation is an essential step of the DNA damage response that provides an adapted proteome in order to face genotoxic stress. We describe here a new phosphorylation of the RAD51 recombinase, on its Ser97 residue. This new Aurora A mediated RAD51 phosphorylation modulates itsin vitroactivity evaluated by D-loop and polymerization assays. Using recombinant proteins, we show that RAD51 is an RNA binding protein and that the Ser97 phosphorylation modulates its RNA binding affinityin vitro. Using a specifically generated antibody we revealed that this Ser97 phosphorylation is correlated with RAD51 localization into the RNA maturation membrane less organelles, Nuclear Speckles. We describe here for the first time the presence of RAD51 DNA repair factor within the Nuclear Speckles, raising the hypothesis of a possible role for RAD51 in splicing modulation. This point is of particular interest in the context of splicing profiles modulations associated with radio and/or chemoresistance.
Atlas ofDES(desmin) variants: Impact of variants located within the head domain on filament assembly
Authors: Voß Sabrina , Walhorn Volker , Holler Stephanie , Gärtner Anna , Pohl Greta , Gummert Jan , Anselmetti Dario , Milting Hendrik , Brodehl Andreas
Published: August 2023

Desmin is a muscle-specific intermediate filament protein, which plays a significant role in providing structural integrity of cardiomyocytes by connecting different cell organelles and multi-protein complexes.DESmutations cause cardiomyopathies and skeletal myopathies. Most of these pathogenic mutations are localized in the highly conserved rod domain and affect the filament assembly.

However, the impact ofDESvariants within the N-terminal head domain on the filament assembly process is widely unknown. Therefore, we inserted a set of 85 different head domain variants with unknown significance from human genetic databases in expression constructs and investigated their impact on filament formation in cell culture in combination with confocal microscopy. The majority of these desmin variants do not affect the filament assembly. However, the desmin variants -p.S13P, -p.N107D, -p.E108G and -p.K109E significantly inhibit the filament assembly. Additionally, we expressed and purified recombinant desmin and investigated the filament assembly defects by atomic force microscopy verifying these findings at the single molecular level. Furthermore, we truncated systematically the head domain to investigate which general parts of this domain are necessary for filament assembly.

In summary, our functional investigations might be relevant for the classification of novelDESvariants and the genetic counselling of patients carrying desmin head variants.
Zinc-Induced Fluorescence Turn-on in Native and Mutant Phycoerythrobilin-Binding Orange Fluorescent Proteins
Authors: Jensen Gary C. , Janis Makena K. , Jara Jazzmin , Abbasi Nasir , Zastrow Melissa L.
Published: August 2023

Cyanobacteriochrome (CBCR)-derived fluorescent proteins are a class of reporters that can bind bilin cofactors and fluoresce across the ultraviolet to near-infrared spectrum. Derived from phytochrome-related photoreceptor proteins in cyanobacteria, many of these proteins use a single small GAF domain to autocatalytically bind a bilin and fluoresce. The second GAF domain of All1280 fromNostocsp. PCC7120 is a DXCF motif-containing protein that exhibits blue light-responsive photochemistry when bound to its native cofactor, phycocyanobilin. GAF2 can also bind non-photoswitching phycoerythrobilin (PEB), resulting in a highly fluorescent protein. Given the small size, high quantum yield, and that, unlike green fluorescent proteins, bilin-binding proteins can be used in anaerobic organisms, the orange fluorescent GAF2-PEB protein is a promising platform for designing new genetically encoded metal ion sensors. Here we show that GAF2-PEB undergoes a ∼5-fold reversible zinc-induced fluorescence enhancement with blue-shifted emission maximum (572 to 517 nm), which is not observed for a related PEB-bound GAF fromSynechocystissp. PCC6803 (Slr1393g3). Zn2+significantly enhances GAF2-PEB fluorescence across a biologically relevant pH range from 6.0–9.0 and with pH-dependent µM to nM dissociation constants. Site-directed mutants aiming to sterically decrease and increase access to PEB show a decreased and similar amount of zinc-induced fluorescence enhancement, respectively. Mutation of the cysteine residue within the DXCF motif to alanine abolishes zinc-induced fluorescence enhancement. Collectively, these results support the presence of a fluorescence enhancing Zn2+binding site in GAF2-PEB likely involving coordination to the bilin cofactor and requiring a nearby cysteine residue.
The cerebellum acts as the analog to the medial temporal lobe for sensorimotor memory
Authors: Hadjiosif Alkis M. , Gibo Tricia L. , Smith Maurice A.
Published: August 2023

The cerebellum is critical for sensorimotor learning. The specific contribution that it makes, however, remains unclear. Inspired by the classic finding that, for declarative memories, medial temporal lobe structures provide a gateway to the formation of long-term memory but are not required for short-term memory, we hypothesized that, for sensorimotor memories, the cerebellum may play an analogous role. Here we studied the sensorimotor learning of individuals with severe ataxia from cerebellar degeneration. We dissected the memories they formed during sensorimotor learning into a short-term temporally-volatile component, that decays rapidly with a time constant of just 15-20sec and thus cannot lead to long-term retention, and a longer-term temporally-persistent component that is stable for 60 sec or more and leads to long-term retention. Remarkably, we find that these individuals display dramatically reduced levels of temporally-persistent sensorimotor memory, despite spared and even elevated levels of temporally-volatile sensorimotor memory. In particular, we find both impairment that systematically increases with memory window duration over shorter memory windows (<12 sec) and near-complete impairment of memory maintenance over longer memory windows (>25 sec). This dissociation uncovers a new role for the cerebellum as a gateway for the formation of long-term but not short-term sensorimotor memories, mirroring the role of the medial temporal lobe for declarative memories. It thus reveals the existence of distinct neural substrates for short-term and long-term sensorimotor memory, and it explains both newly-identified trial-to-trial differences and long-standing study-to-study differences in the effects of cerebellar damage on sensorimotor learning ability.

Significance Statement

A key discovery about the neural underpinnings of memory, made more than half a century ago, is that long-term, but not short-term, memory formation depends on neural structures in the brain’s medial temporal lobe (MTL). However, this dichotomy holds only for declarative memories – memories for explicit facts such as names and dates – as long-term procedural memories – memories for implicit knowledge such as sensorimotor skills – are largely unaffected even with substantial MTL damage. Here we demonstrate that the formation of long-term, but not short-term, sensorimotor memory depends on a neural structure known as the cerebellum, and we show that this finding explains the variability previously reported in the extent to which cerebellar damage affects sensorimotor learning.
Cyclin B3 is a dominant fast-acting cyclin that drives rapid early embryonic mitoses
Authors: Lara-Gonzalez Pablo , Variyar Smriti , Budrewicz Jacqueline , Schlientz Aleesa , Varshney Neha , Bellaart Andrew , Moghareh Shabnam , Nguyen Anh Cao Ngoc , Oegema Karen , Desai Arshad
Published: August 2023

In many species, early embryonic mitoses proceed at a very rapid pace, but how this pace is achieved is not understood. Here we show that in the earlyC. elegansembryo, cyclin B3 is the dominant driver of rapid embryonic mitoses. Metazoans typically have three cyclin B isoforms that associate with and activate Cdk1 kinase to orchestrate mitotic events: the related cyclins B1 and B2 and the more divergent cyclin B3. We show that whereas embryos expressing cyclins B1 and B2 support slow mitosis (NEBD to Anaphase ∼ 600s), the presence of cyclin B3 dominantly drives the ∼3-fold faster mitosis observed in wildtype embryos. CYB-1/2-driven mitosis is longer than CYB-3-driven mitosis primarily because the progression of mitotic events itself is slower, rather than delayed anaphase onset due to activation of the spindle checkpoint or inhibitory phosphorylation of the anaphase activator CDC-20. Addition of cyclin B1 to cyclin B3-only mitosis introduces an ∼60s delay between the completion of chromosome alignment and anaphase onset, which likely ensures segregation fidelity; this delay is mediated by inhibitory phosphorylation on CDC-20. Thus, the dominance of cyclin B3 in driving mitotic events, coupled to introduction of a short cyclin B1-dependent delay in anaphase onset, sets the rapid pace and ensures fidelity of mitoses in the earlyC. elegansembryo.
The mTOR pathway genesmTOR,Rheb,Depdc5,Pten, andTsc1have convergent and divergent impacts on cortical neuron development and function
Authors: Nguyen Lena H. , Xu Youfen , Nair Maanasi , Bordey Angelique
Published: August 2023

Brain somatic mutations in various components of the mTOR complex 1 (mTORC1) pathway have emerged as major causes of focal malformations of cortical development and intractable epilepsy. While these distinct gene mutations converge on excessive mTORC1 signaling and lead to common clinical manifestations, it remains unclear whether they cause similar cellular and synaptic disruptions underlying cortical network hyperexcitability. Here, we show thatin uteroactivation of the mTORC1 activators,RhebormTOR, or biallelic inactivation of the mTORC1 repressors,Depdc5,Tsc1, orPtenin mouse medial prefrontal cortex leads to shared alterations in pyramidal neuron morphology, positioning, and membrane excitability but different changes in excitatory synaptic transmission. Our findings suggest that, despite converging on mTORC1 signaling, mutations in different mTORC1 pathway genes differentially impact cortical excitatory synaptic activity, which may confer gene-specific mechanisms of hyperexcitability and responses to therapeutic intervention.
The evaluation on the protection performance of high temperature sacrificial anode for ABS A steels in H2S-containing environment
Authors: Zhao Yongtao , Li Weili , Xuan Xiaoyang , Gao Jianbang , Wang Jue , Dong Liang , Zang Dawei , Wang Mingjian , Zhong Xiankang
Published: August 2023

Purpose

This study aims to evaluate the protection performance of zinc as sacrificial anode for ABS A steel in the presence of H2S under different temperatures, pH and salinities.

Design/methodology/approach

In this paper, weight loss measurements and electrochemical measurements are used to evaluate the corrosion degree of zinc and ABS A steel.

Findings

Under the conditions involved in this work, it is shown that zinc is a nice sacrificial anode with the reason of its stable potential and excellent anode current efficiency according to the relevant standard. And it is also found that the hydrogen evolution does not occur on ABS A steel specimens. The potential difference between cathode and anode is suitable; thus, it can be concluded that each steel is well protected.

Originality/value

To the best of the authors’ knowledge, no other study has analyzed the protection mechanism and effect of zinc as sacrificial anode in H2S-containing environments under high temperature at present.
Keeping the ball rolling: using the S-O-R framework to investigate the determinants of football fan loyalty
Authors: Rahman Mohammad M. , Rosenberger Philip J. , Yun Jin Ho , de Oliveira Mauro José , Köcher Sören
Published: August 2023

Purpose

Insights into how fan experience can be used to cultivate football (soccer) fan loyalty are limited. Based on the stimulus–organism–response (S-O-R) paradigm, this study develops and tests a theoretical model investigating the effects of football-game socialisation, team interest, football interest and transaction satisfaction (stimuli) on fanship and cumulative satisfaction (organism), and subsequently, attitudinal loyalty and behavioural loyalty (response). National culture was a moderator.

Design/methodology/approach

A self-administered online survey collected data from a convenience sample of 762 football fans from Brazil, China and Germany.

Findings

The PLS-SEM results support the S-O-R based model, indicating that football fan-loyalty behaviours are determined by fanship and cumulative satisfaction with the team. Fan experiences, in turn, are also found to be influenced by fan perceptions relating to socialisation, team interest, football interest and transaction satisfaction—elements over which the football team's management may exert some degree of control. Some national cultural differences were found, with three of the model's 12 structural paths significantly different for Germany vis-à-vis Brazil.

Originality/value

This study advances the authors’ understanding of the significance of socialisation and fan-interest factors for football, providing evidence supporting the role of the fan experience and service-consumption stimuli related to those game experiences as significant drivers (stimuli) of the fan's affective (fanship) and cognitive states (cumulative satisfaction). This study enriches the limited body of evidence on fanship's role as a driver of attitudinal and behavioural loyalty. Finally, the multi-country study partially supports the moderation effect of national culture.
Risk-taking by banks: evidence from European Union countries
Authors: Garcia Maria Teresa Medeiros , Ye Ana Jin
Published: August 2023

Purpose

The aim of this paper is to study the relationship between banks' ownership structure and their risk-taking behavior as well as the impact of banking regulation on banks' approach to taking risk, after the 2008 financial crisis.

Design/methodology/approach

The empirical analysis considers a sample of listed banks from European Union (EU) countries, over the period of 2011–2016 and uses the generalized least squared (GLS) random effect (RE) method, following Baltagi and Wu (1999) and Pathan (2009).

Findings

The authors find that the structure of the board of directors can influence bank risk behavior but not the ownership concentration. No significant relation was found between the influence of the regulatory environment and bank risk, i.e., stricter regulation has no effect on risk taking by banks.

Originality/value

The paper contributes to the literature in risk measures and banks' corporate governance. It also considers the impact of regulatory framework on banks' risk-taking behavior. The aim of this empirical analysis was to examine in greater detail these subjects and the dynamics between them after the significant structural changes in the macroeconomic environment and in the financial system, particularly with regards the regulatory and supervisory framework following the 2008 financial crisis, using data from European Union countries.
Advanced intelligent health advice with informative summaries to facilitate treatment decision-making
Authors: Liu Yi-Hung , Chen Sheng-Fong
Published: August 2023

Purpose

Whether automatically generated summaries of health social media can assist users in appropriately managing their diseases and ensuring better communication with health professionals becomes an important issue. This paper aims to develop a novel deep learning-based summarization approach for obtaining the most informative summaries from online patient reviews accurately and effectively.

Design/methodology/approach

This paper proposes a framework to generate summaries that integrates a domain-specific pre-trained embedding model and a deep neural extractive summary approach by considering content features, text sentiment, review influence and readability features. Representative health-related summaries were identified, and user judgements were analysed.

Findings

Experimental results on the three real-world health forum data sets indicate that awarding sentences without incorporating all the adopted features leads to declining summarization performance. The proposed summarizer significantly outperformed the comparison baseline. User judgement through the questionnaire provides realistic and concrete evidence of crucial features that remarkably influence patient forum review summaries.

Originality/value

This study contributes to health analytics and management literature by exploring users’ expressions and opinions through the health deep learning summarization model. The research also developed an innovative mindset to design summarization weighting methods from user-created content on health topics.
Reducing forced labour in supply chains: what could traditional companies learn from social enterprises?
Authors: Vanpoucke Evelyne , Klassen Robert D.
Published: August 2023

Purpose

Forced labour is one of the most exploitative practices in supply chains, generating serious human right abuses. The authors seek to understand how relationships for reducing forced labour are influenced by institutional logics. The emerging supply chain efforts of social enterprises offer particularly intriguing approaches, as their social mission can spur creative new approaches and reshape widely adopted management practices.

Design/methodology/approach

The authors study supplier relationships in the smartphone industry and compare the evolving practices of two cases: the first, a growing novel social enterprise; and the second, a high-profile commercial firm that has adopted a progressive role in combating forced labour.

Findings

The underlying institutional logic influenced each firm's willingness to act beyond its direct suppliers and to collaborate in flexible ways that create systematic change. Moreover, while both focal firms had clear, well-documented procedures related to forced labour, the integration, rather than decoupling, of forced labour and general supply chain policies provided a more effective way to reduce the risks of forced labour in social enterprises.

Research limitations/implications

As authors’ comparative case study approach may lack generalizability, future research is needed to broadly test their propositions.

Practical implications

The paper identifies preconditions in terms of institutional logics to successfully reduce the risk of forced labour in supply chains.

Originality/value

This paper discusses how social enterprises can provide a learning laboratory that enables commercial firms to identify options for supplier relationship improvement.
Recognizing the impact of value-belief-norm theory on pro-environmental behaviors of higher education students: considering aspects for social-marketing applications
Authors: Negm Eiman
Published: August 2023

Purpose

This study aims to examine how higher education can mold pro-environmental actions among students with educational social-marketing leads; it probes into the direct influence of four value orientations toward pro-environmental beliefs, norms and behaviors.

Design/methodology/approach

This quantitative research sought deductive reasoning. Data gathering took place in January 2023, following a cross-sectional framework. The researcher visited various private universities in Egypt, which used effort to change the practices among students toward sustainable developments, distributing digitally administrated questionnaires to students on campus. Through convenience nonprobability sampling, 581 questionnaires were collected and statistically analyzed, using SPSS.

Findings

This study shows that altruistic and biospheric value impact students’ personal beliefs toward pro-environmental behaviors; students’ personal beliefs significantly impact the norms that are present on campus; the norms found on campus impact significantly students to behave as green passengers, recyclers and utility-savers.

Practical implications

Higher education institutions play a significant role in promoting the manifestations of rationality and objectivity among students about environmental challenges and sustainable development. Eco-friendly behaviors are rooted in values; thus, understanding the initial values among students is critical in developing coping strategies and social marketing initiatives that inspire the needed conservational behaviors.

Originality/value

By aligning the value-belief-norm theory with two disciplines (higher education on sustainability and social marketing), this study builds upon the theory, identifying the underlying value-structures that inspire students’ necessary environmental and sustainable behaviors to improve societies for future generation rightness. This study provides more nuanced insights into a better educational intervention for shaping students’ manners toward environmentalism to improve communities worldwide.
Does external debt drive inflation in Sudan: evidence from symmetric and asymmetric ARDL approaches
Authors: Sharaf Mesbah Fathy , Shahen Abdelhalem Mahmoud
Published: August 2023

Purpose

This study aims to examine the symmetric and asymmetric impact of external debt on inflation in Sudan from 1970 to 2020 within a multivariate framework by including money supply and the nominal effective exchange rate as additional inflation determinants.

Design/methodology/approach

The authors utilize an Auto Regressive Distributed Lag (ARDL) model to examine the symmetric impact of external debt on inflation, while the asymmetric impact is examined using a Nonlinear ARDL (NARDL) model. The existence of a long-run relationship between inflation and external debt is tested using the bounds-testing approach to cointegration, and a vector error-correction model is estimated to determine the short parameters of equilibrium dynamics.

Findings

The linear ARDL model results show that external debt has no statistically significant impact on inflation in the long run. On the contrary, the results of the NARDL model show that positive and negative external debt shocks statistically affect inflation in the long run. The estimated long-run elasticity coefficients of the linear and nonlinear ARDL models reveal that the domestic money supply has a statistically significant positive impact on inflation. In contrast, the nominal effective exchange rate has a statistically significant negative impact on inflation.

Practical implications

The reliance on symmetric analysis may not be sufficient to uncover the existence of a linkage between external debt and inflation. Proper external debt management is crucial to control inflation rates in Sudan.

Originality/value

To date, no empirical study has assessed the external debt-inflation nexus and its potential asymmetry in Sudan, and the current study aims to fill this gap in the literature.