bluuebunny/crossref_metadata_2025_split huggingface dataset:
Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase
Authors: Zeinert Rilee , Zhou Fei , Franco Pedro , Zöller Jonathan , Lessen Henry J. , Aravind L. , Langer Julian D. , Sodt Alexander J. , Storz Gisela , Matthies Doreen 
Published: March 2024

AbstractMagnesium (Mg2+) uptake systems are present in all domains of life given the vital role of this ion. Bacteria acquire Mg2+via conserved Mg2+channels and transporters. The transporters are required for growth when Mg2+is limiting or during bacterial pathogenesis, but, despite their significance, there are no known structures for these transporters. Here we report the first structure of the Mg2+transporter MgtA solved by single particle cryo-electron microscopy (cryo-EM). Using mild membrane extraction, we obtained high resolution structures of both a homodimeric form (2.9 Å), the first for a P-type ATPase, and a monomeric form (3.6 Å). Each monomer unit of MgtA displays a structural architecture that is similar to other P-type ATPases with a transmembrane domain and two soluble domains. The dimer interface consists of contacts between residues in adjacent soluble nucleotide binding and phosphotransfer regions of the haloacid dehalogenase (HAD) domain. We suggest oligomerization is a conserved structural feature of the diverse family of P-type ATPase transporters. The ATP binding site and conformational dynamics upon nucleotide binding to MgtA were characterized using a combination of cryo-EM, molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and mutagenesis. Our structure also revealed a Mg2+ion in the transmembrane segments, which, when combined with sequence conservation and mutagenesis studies, allowed us to propose a model for Mg2+transport across the lipid bilayer. Finally, our work revealed the N-terminal domain structure and cytoplasmic Mg2+binding sites, which have implications for related P-type ATPases defective in human disease.
Effect of translation enhancing nascent SKIK peptide on the arrest peptides containing consecutive Proline
Authors: Nishikawa Yuma , Fujikawa Riko , Nakano Hideo , Kanamori Takashi , Ojima-Kato Teruyo 
Published: March 2024

AbstractRibosome arrest peptides (RAPs) such as SecM arrest peptide (SecM AP) and WPPP with consecutive Pro residues, are known to induce translational stalling inEscherichia coli. We demonstrate that the translation enhancing SKIK peptide tag, which consisted of four amino acid residues Ser-Lys-Ile-Lys, effectively alleviate translational arrest caused by WPPP. Moreover, the proximity between SKIK and WPPP significantly influences the extent of this alleviation, observed in both PURE cell-free protein synthesis and in vivo protein production systems, resulting in a substantial increase in the yield of proteins containing such RAPs. Furthermore, we unveil that nascent SKIK peptide tag and translation elongation factor P (EF-P) which alleviate ribosome stalling in consecutive-Pro rich protein, synergistically promote translation. A kinetic analysis based on the generation of super folder green fluorescent protein under in vitro translation reaction reveals that the ribosome turnover is enhanced by more than 10-fold when the SKIK peptide tag is positioned immediately upstream of the SecM AP sequence. Our findings provide valuable insights into optimizing protein production processes, which are essential for advancing synthetic biology applications.Abstract Figure
A general strategy to engineer high-performance mammalian Whole-Cell Biosensors
Authors: Mallozzi Alessio , Fusco Virginia , Ragazzini Francesco , Praznik Arne , Jerala Roman , di Bernardo Diego 
Published: March 2024

AbstractTranscription-based whole-cell biosensors (WCBs) are cells engineered with an analyte-responsive promoter driving the transcription of a reporter gene. WCBs can sense and report on bioactive molecules (analytes) relevant to human health. Designing an analyte-sensitive promoter requires a cumbersome trial-and-error approach and usually results in biosensors with poor performance. Here, we integrated Synthetic Biology with Control Engineering to design, computationally model, and experimentally implement high-performance biosensors in mammalian cells. Our approach, unlike traditional methods, does not rely on optimizing individual components such as promoters and transcription factors. Instead, it uses biomolecular circuits to enhance the biosensor’s performance despite inherent component flaws. We experimentally implemented eight different biosensors by employing CRISPR-Cas systems, then quantitatively compared their performance and identified one configuration, which we named CASense, that overcomes the limitations of current biosensors. Our approach is generalisable and can be adapted to sense any analyte of interest for which there is an analyte-sensitive promoter, making it a versatile tool for multiple applications. As a proof of concept, we engineered a high-performance biosensor of intracellular copper due to the critical role that copper plays in human health and disease, and to the lack of techniques able to measure intracellular copper levels in living cells. The significance of our work lies in its potential to impact the monitoring of bioactive molecules and chemicals both in vitro and in vivo, which is crucial in areas such as toxicology, drug discovery, disease diagnosis and therapy.
Arf family GTPases are present in Asgard archaea
Authors: Vargová Romana , Chevreau Roxanne , Alves Marine , Courbin Camille , Terry Kara , Legrand Pierre , Eliáš Marek , Ménétrey Julie , Dacks Joel B. , Jackson Catherine L. 
Published: March 2024

SummaryThe emergence of eukaryotes from their prokaryotic ancestors is one of the most fundamental evolutionary events in the history of life. Little is robustly known about how eukaryogenesis occurred, but a major breakthrough came with the identification of the Asgardarchaeota, the closest prokaryotic lineage to eukaryotes yet discovered. Endomembrane organelles, and the capacity to transport material between them, are major hallmarks of eukaryotic cells. The Arf family GTPases are crucial regulators of organelle dynamics in eukaryotes, functioning in vesicle budding, membrane tethering and membrane-cytoskeleton interactions. Although an expanded GTPase complement has been reported in the Asgardarchaeota, the specific origins of the Arf family remain elusive. Here we report a new group of prokaryotic GTPases, the ArfRs. Widely present in Asgardarchaeota and almost exclusive to them, it is the clade from which all eukaryotic Arf family proteins are derived. Heterologous expression of representative Asgardarchaeota ArfR proteins in the model eukaryoteSaccharomyces cerevisiaeand X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results show that Arf family GTPases are present in Asgardarchaeota, and strongly suggest that they originated in the archaeal contributor to eukaryogenesis, providing support for nascent endomembrane system capacity evolving early in eukaryogenesis.
Domain coupling in activation of a family C GPCR
Authors: Latorraca Naomi R. , Sabaat Sam , Habrian Chris , Bleier Julia , Stanley Cherise , Marqusee Susan , Isacoff Ehud Y. 
Published: March 2024

AbstractThe G protein–coupled metabotropic glutamate receptors form homodimers and heterodimers with highly diverse responses to glutamate and varying physiological function. The molecular basis for this diversity remains poorly delineated. We employ molecular dynamics, single-molecule spectroscopy, and hydrogen–deuterium exchange to dissect the pathway of activation triggered by glutamate. We find that activation entails multiple loosely coupled steps and identify a novel pre-active intermediate whose transition to the active state forms dimer interactions that set signaling efficacy. Such subunit interactions generate functional diversity that differs across homodimers and heterodimers. The agonist-bound receptor is remarkably dynamic, with low occupancy of G protein–coupling conformations, providing considerable headroom for modulation of the landscape by allosteric ligands. Sites of sequence diversity within the dimerization interface and diverse coupling between activation rearrangements may contribute to precise decoding of glutamate signals and transients over broad spatial and temporal scales.
Doublecortin reinforces microtubules to promote growth cone advance in soft environments
Authors: Dema Alessandro , Charafeddine Rabab A. , van Haren Jeffrey , Rahgozar Shima , Viola Giulia , Jacobs Kyle A. , Kutys Matthew L. , Wittmann Torsten 
Published: March 2024

AbstractDoublecortin (DCX) is a microtubule-associated protein critical for brain development. Although most highly expressed in the developing central nervous system, the molecular function of DCX in neuron morphogenesis remains unknown and controversial. We demonstrate that DCX function is intimately linked to its microtubule-binding activity. By using human induced pluripotent stem cell (hiPSC)- derived cortical i3Neurons genome engineered to express mEmerald-tagged DCX from the endogenous locus, we find that DCX-MT interactions become highly polarized very early during neuron morphogenesis. DCX becomes enriched only on straight microtubules in advancing growth cones with approximately 120 DCX molecules bound per micrometer of growth cone microtubule. At a similar saturation, microtubule-bound DCX molecules begin to impede lysosome transport, and thus can potentially control growth cone organelle entry. In addition, by comparing control, DCX-mEmerald and knockout DCX -/Y i3Neurons, we find that DCX stabilizes microtubules in the growth cone peripheral domain by reducing the microtubule catastrophe frequency and the depolymerization rate. DCX -/Y i3Neuron morphogenesis was inhibited in soft microenvironments that mimic the viscoelasticity of brain tissue and DCX -/Y neurites failed to grow toward brain-derived neurotrophic factor (BDNF) gradients. Together with high resolution traction force microscopy data, we propose a model in which DCX-decorated, rigid growth cone microtubules provide intracellular mechanical resistance to actomyosin generated contractile forces in soft physiological environments in which weak and transient adhesion-mediated forces in the growth cone periphery may be insufficient for productive growth cone advance. These data provide a new mechanistic understanding of how DCX mutations cause lissencephaly-spectrum brain malformations by impacting growth cone dynamics during neuron morphogenesis in physiological environments.
Lipidomic analysis of human TANGO2-deficient cells suggests a lipid imbalance as a cause of TANGO2 deficiency disease
Authors: Mehranfar Mahsa , Asadi Paria , Shokohi Rozmehr , Milev Miroslav P. , Gamberi Chiara , Sacher Michael 
Published: March 2024

ABSTRACTTANGO2 deficiency disease (TDD) is a multisystem disease caused by variants in theTANGO2gene. Symptoms include neurodevelopmental delays, seizures and potentially lethal metabolic crises and cardiac arrhythmias. While the function of TANGO2 remains elusive, vitamin B5/pantothenic acid supplementation has been shown to alleviate symptoms in a fruit fly model and has also been used to treat individuals suffering from TDD with success. Since vitamin B5 is the precursor to the lipid activator coenzyme A (CoA), we hypothesized that TANGO2-deficient cells would display changes in the lipid profile compared to control and that these changes would be rescued by vitamin B5 supplementation. In addition, the specific changes seen might point to a pathway in which TANGO2 functions. Indeed, we found profound changes in the lipid profile of human TANGO2-deficient cells as well as an increased pool of free fatty acids in both human cells devoid of TANGO2 andDrosophilaharboring a previously described TANGO2 loss of function allele. All these changes were reversed upon vitamin B5 supplementation. Pathway analysis showed significant increases in triglyceride as well as in lysophospholipid levels as the top enriched pathways in the absence of TANGO2. Consistent with a defect in triglyceride metabolism, we found changes in lipid droplet numbers and sizes in the absence of TANGO2 compared to control. Our data will allow for comparison between other model systems of TDD and the homing in on critical lipid imbalances that lead to the disease state.
Genome sequences of fourIxodesspecies expands understanding of tick evolution
Authors: de Araujo Alexandra Cerqueira , Noël Benjamin , Bretaudeau Anthony , Labadie Karine , Boudet Matéo , Tadrent Nachida , Istace Benjamin , Kritli Salima , Cruaud Corinne , Olaso Robert , Deleuze Jean-François , Voordouw Maarten , Hervet Caroline , Plantard Olivier , Zamoto-Niikura Aya , Chertemps Thomas , Maïbèche Martine , Hilliou Frédérique , Goff Gaëlle Le , Chmelar Jindrich , Mazák Vilém , Jmel Mohammed Amine , Kotsyfakis Michalis , Medina José María , Hackenberg Michael , Šimo Ladislav , Koutroumpa Fotini A. , Wincker Patrick , Kopacek Petr , Perner Jan , Aury Jean-Marc , Rispe Claude 
Published: March 2024

AbstractTicks, hematophagous acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genusIxodes, which includes the main vectors of Lyme disease. Here, we present the complete genome sequences of four tick species, derived from a single female individual, with a particular focus on the European speciesIxodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three otherIxodesspecies,I. persulcatus, I. pacificusandI. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genusIxodesand of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained forI. ricinusreveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes. The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.
The Interplay of Resource Availability and Parent Foraging Strategies on Juvenile Sparrow Individual Specialization
Authors: Ricote Natalia , Weinberger Constanza , Ramírez-Otarola Natalia , Bustamante Sara , Málaga María Lucía , Barceló Gonzalo , Sabat Pablo , Newsome Seth D. , Maldonado Karin 
Published: March 2024

AbstractTemporal variation in resource availability, amplified by global change, may have strong impacts on species breeding at temperate and high latitudes that cue their reproduction to exploit seasonal resource pulses. This study examines how resource availability and parental care influence niche partitioning between and within age classes in the rufous-collared sparrow, which provides extensive parental care. We hypothesized juveniles would exhibit narrower niches focused on high-quality resources compared to adults, regardless of resource availability. We used stable isotope analysis to quantify individual and population niches in juveniles and adults across the breeding season in two cohorts experiencing contrasting resource landscapes. Contrary to our initial hypothesis, juveniles exhibited greater among individual diet variation and smaller total niche widths (i.e., higher levels of individual specialization) during periods of high food availability in comparison to periods of food scarcity. Interestingly, total niche width and individual specialization of adults remained stable across seasons despite a shift in trophic level, highlighting their potential role in providing a consistent diet for their young. These findings reveal a dynamic interplay between resource availability, parental care, and individual specialization, with important implications for understanding population resilience under variable resource scenarios. The study also suggests that adult sparrows modify their provisioning strategies based on resources, potentially buffering offspring from environmental fluctuations. Understanding age-specific responses to resource variation is crucial for predicting species responses to ecological conditions, particularly in regions like central Chile where seasonal resource limitation is expected to become more variable in response to climate change.
Neuronal ARHGAP8 controls synapse structure and AMPA receptor-mediated synaptic transmission
Authors: Schmidt Jeannette , Inácio Ângela , Ferreira Joana S , Serrenho Débora , Socodato Renato , Beltrão Nuno , Ribeiro Luís F , Pinheiro Paulo , Relvas João B , Carvalho Ana Luisa 
Published: March 2024

AbstractThe aberrant formation and function of neuronal synapses are recognized as major phenotypes in many cases of neurodevelopmental (NDDs) and -psychiatric disorders (NPDs). A growing body of research has identified an expanding number of susceptibility genes encoding proteins with synaptic function. Here, we present the first brain-focused characterization of a potential new susceptibility gene,ARHAGP8, which encodes a Rho GTPase activating protein (RhoGAP). Accumulating evidence suggests that ARHGAP8 plays a pivotal role in the pathogenesis of NPDs/NDDs. We provide the first evidence for ARHGAP8 as a novel player at excitatory synapses, with its synaptic localisation linked to the presence of the developmentally important NMDA receptor subunit GluN2B. By increasing ARHGAP8 levels in hippocampal neurons to mimic the copy number variant found in a subset of patients, we observed reductions in dendritic complexity and spine volume, accompanied by a significant decrease in synaptic AMPA receptor-mediated transmission. These results suggest that ARHGAP8 plays a role in shaping the morphology and function of excitatory synapses, and prompt further investigation of ARHGAP8 as a candidate gene in NDDs/NPDs.
Rational structure-guided design of a blood stage malaria vaccine immunogen presenting a single epitope from PfRH5
Authors: Harrison Thomas E. , Alam Nawsad , Farrell Brendan , Quinkert Doris , Lias Amelia M. , King Lloyd D.W. , Draper Simon J. , Campeotto Ivan , Higgins Matthew K. 
Published: March 2024

AbstractDespite recent success in licencing of two malaria vaccines, there continues to be an urgent need for improved vaccine immunogens as the world aims for malaria eradication. The invasion of erythrocytes byPlasmodium falciparumis an essential step in the life cycle of the parasite, preceding symptoms of disease and parasite transmission. Antibodies which target the PfRH5 protein are highly effective at preventing erythrocyte invasion and the most effective growth-inhibitory antibodies bind to a single epitope. Here we used Rosetta-based protein design to produce a focused synthetic immunogen on which this epitope is presented on a small scaffold. Structural biology and biophysics were used to demonstrate that the immunogen is correctly folded and binds neutralising monoclonal antibodies with at least nanomolar affinity. In immunised rats, the immunogen induced PfRH5-targeting antibodies that inhibit parasite growth at a thousand-fold lower concentration that those induced through immunisation with PfRH5. Finally, we show that priming with the focused immunogen and boosting with PfRH5 achieves the best balance between antibody quality and quantity and induces the most effective growth-inhibitory response. This rationally designed vaccine immunogen is now available for use as part of future malaria vaccines, alone or in combination with other immunogens.One Sentence SummaryRational, structure-guided design has been used to produce a vaccine immunogen in which the epitope for the most growth-inhibitory monoclonal antibody targeting PfRH5 has been correctly presented on a synthetic scaffold for use in a vaccine to protect from blood-stage malaria.
Could financialisation explain why developers are building more expensive houses? Evidence for Malaysia
Authors: Hui Hon Chung 
Published: February 2024

Purpose
The purpose of this paper is to examine the effects of financialisation on the changing structure of housing supply in Malaysia. The share of newly launched sub-MYR250,000 houses has been decreasing continuously in the past decade. This implies that housing developers are launching more expensive houses. The greater focus on higher cost housing could be attributed to inflation. But while input cost is rising, the housing sector has also become increasingly financialised. This claim can be supported by the rising share of mortgage and real estate loans in gross domestic product. Financialisation is a process in which the financial sector becomes more dominant relative to the real sector. The extent to which this process is responsible for the changing structure of housing supply in Malaysia is investigated.

Design/methodology/approach
A survey of the literature suggested that the decreasing the proportion of newly launched sub-MYR250,000 housing could be result of rising input cost, greater degree of financialisation and changing market concentration. Thus, long-run cointegrating equations were formulated and estimated. These equations linked housing share with financialisation, market structure and input cost. The quantitative and qualitative impact of financialisation on the structure of housing supply is of interest.

Findings
The analyses of secondary data suggested that financialisation and input cost did indeed contribute to the decrease in proportion of newly launched sub-MYR250,000 housing. However, the impact of market concentration on housing share was ambiguous. This conclusion survived several robustness checks.

Practical implications
The financialisation of the housing sector implies that developers are increasingly building for profits instead of accommodating the social objective of providing shelter. This result is unsettling because access to adequate housing is a human right. The transformation of housing from the concept of a shelter to a tradable, money-making asset could be a major contributor to the declining housing affordability in the country. Thus, efforts to improve affordability must take account of the effects of financialisation.

Originality/value
An empirical framework for assessing the changes in the structure of housing supply was developed. Existing studies tended to focus only on the volume of housing supply. It is a comprehensive study on changes in the structure of housing supply. Second, while existing studies on the financialisation of housing are mostly qualitative in methodology, this paper offers a quantitative assessment of the financialisation in the housing sector.
Asking MultiCrit Questions: A Reflexive and Critical Framework to Promote Health Data Equity for the Multiracial Population
Authors: LAM‐HINE TRACY , FORTHAL SARAH , JOHNSON CANDICE Y. , CHIN HELEN B. 
Published: March 2024

Policy Points
Health equity work primarily centers monoracial populations; however, the rapid growth of the Multiracial population and increasingly clear health disparities affecting the people in that population complicate our understanding of racial health equity.
Limited resources exist for health researchers and professionals grappling with this complexity, likely contributing to the relative dearth of health literature describing the Multiracial population.
We introduce a question‐based framework built on core principles from Critical Multiracial Theory (MultiCrit) and Critical Race Public Health Praxis, designed for researchers, clinicians, and policymakers to encourage health data equity for the Multiracial population.