bluuebunny/crossref_metadata_2025 huggingface dataset:
Designing a hybrid in silico/in-cell controller robust to process–model mismatch associated with dynamically regulated enzyme overexpression
Authors: Ohkubo Tomoki , Sakumura Yuichi , Zhang Fuzhong , Kunida Katsuyuki
Published: March 2024

Discrepancy between model predictions and actual processes, known as process–model mismatch (PMM), remains a serious challenge in bioprocess optimization. Previously, we proposed the hybrid in silico/in-cell controller (HISICC) concept combining model-based optimization with cell-based feedback to address the PMM problem. Herein, this approach was advanced to regulate intracellular concentrations of rate-limiting enzymes. Advanced HISICC was demonstrated using an engineeredEscherichia colistrain for fatty acid production (FA3). This strain harbors an in-cell feedback controller, which decelerates acetyl-CoA carboxylase (ACC) overexpression in response to sensing the concentration of malonyl-CoA formed by this enzyme. A mathematical model for FA3 was constructed and validated using experimental data. Simulations assuming various PMM revealed that the HISICC using FA3 effectively mitigates toxicity from excessive ACC by robustly adapting braking its overexpression, minimizing yield loss. This study confirmed HISICC as a viable strategy for enhancing bioprocess efficiency, especially in balancing the bottleneck enzyme levels.
High-accuracy crRNA array assembly strategy for multiplex CRISPR
Authors: Zhao Xiangtong , Yang Lixian , Li Peng , Cheng Zijing , Jia Yongshi , Luo Limin , Bi Aihong , Xiong Hanchu , Zhang Haibo , Zhang Jinrui , Zhang Yaodong
Published: March 2024

Simultaneous targeting of multiple loci with CRISPR system, a tool known as multiplex CRISPR, offers us more feasibility to manipulate and elucidate the intricate and redundant endogenous networks underlying complex cellular functions. Owing to the versatility of the continuously emerging Cas nucleases and the utilization of CRISPR arrays, multiplex CRISPR has been implemented by numerous in vitro and in vivo studies. However, a streamlined practical strategy for CRISPR array assembly with both convenience and accuracy is still lacking. Here, we present a novel high-accuracy, cost- and time-saving strategy for CRISPR array assembly. Using this strategy, we efficiently accomplished the assembly of up to twelve crRNAs (for AsCas12a) or fifteen crRNAs (for RfxCas13d) in a single reaction. Moreover, we reveal that CRISPR arrays driven by Pol II promoters exhibit a distinct targeting pattern compared to Pol III promoters, which could be exploited for specific distributions of CRISPR intensity. For long CRISPR arrays, we designed a better approach than simply selecting one from U6 or EF1a. Collectively, our study provides a flexible and powerful tool for the convenient implementation of multiplex CRISPR across DNA to RNA, facilitating the dissection of sophisticated cellular networks and the future realization of multi-target gene therapy.
‘You are too much in this modern world, that’s why you are like this’: Understanding perceptions of mental health among Somali people in London
Authors: Gonzalez Caitlin , Humberstone Elizabeth , Willott Chris
Published: March 2024

This is a qualitative study exploring the perceptions of mental health among Somali people living in London. Participants, over the age of 18 and identifying as Somali, were recruited from a community centre in West London. Seven participants were recruited, and semi-structured interviews were conducted to better understand perceptions of mental health, care-seeking, treatment and different understandings of these issues within their community. Interview transcripts were imported into NVIVO version 14 to be coded, and description-focussed thematic analysis was used to interpret key themes.

Concerns around judgement, shame and stigma are key issues affecting attitudes towards mental health in this group. Other important issues affecting conceptualisations and attitudes towards mental health were intergenerational differences, isolation from the community, stigma and secrecy. Participants also reported the importance of protective factors, particularly faith and family in their lives. This research adds to existing literature in exploring perceptions of mental health in Somali communities in the UK, and such research is helpful in identifying cultural barriers to recognition and treatment of mental health within this community.
Anticoagulation-related complications and their outcomes in hemodialysis patients with acute kidney injury at selected hospitals in Ethiopia
Authors: Kedir Hanan Muzeyin , Yabeyu Abdella Birhan , Ejigu Addisu Melkie , Tadesse Tamrat Assefa , Sisay Eskinder Ayalew
Published: March 2024

Introduction

During hemodialysis (HD), the presence of clots in the dialyzer can diminish the effective surface area of the device. In severe cases, clot formation in the circuit can halt treatment and lead to blood loss in the system. Thus, ensuring proper anticoagulation during HD is crucial to prevent clotting in the circuit while safeguarding the patient from bleeding risks. This study aimed to evaluate anticoagulation outcomes and related factors in HD patients with acute kidney injury (AKI) at selected hospitals in Ethiopia.

Method

A prospective, multicenter observational study was carried out between October 1, 2021, and March 31, 2022. The study encompassed all AKI patients undergoing HD at least once during the study period. Descriptive statistics were utilized to summarize the data, and multinomial logistic regression analysis was employed to identify factors associated to clotting and bleeding.

Results

Data were gathered from 1010 HD procedures conducted on 175 patients. Extracorporeal circuit clotting was detected in 34 patients during 39 (3.9%) dialysis sessions, while bleeding incidents occurred in 27 patients across 29 (2.9%) sessions. A statistically significant association was found between both the total number of HD treatments and blood flow rate with incidents of clotting. Factors such as length of hospitalization, serum creatinine levels at admission, signs and symptoms associated with uremia, along with utilization of anticoagulants or antiplatelet medications demonstrated an association with bleeding events.

Conclusion

Clotting affected 19.4% of participants, while bleeding occurred in 15.4%, underscoring the importance of close monitoring. The frequency of HD sessions and blood flow rate are correlated with clotting, while hospitalization duration, serum creatinine levels, uremic symptoms, and anticoagulant use are associated with bleeding events.
Graph Structured Neural Networks for Perturbation Biology
Authors: Evans Nathaniel J. , Mills Gordon B. , Wu Guanming , Song Xubo , McWeeney Shannon
Published: March 2024

Computational modeling of perturbation biology identifies relationships between molecular elements and cellular response, and an accurate understanding of these systems will support the full realization of precision medicine. Traditional deep learning, while often accurate in predicting response, is unlikely to capture the true sequence of involved molecular interactions. Our work is motivated by two assumptions: 1) Methods that encourage mechanistic prediction logic are likely to be more trustworthy, and 2) problem-specific algorithms are likely to outperform generic algorithms. We present an alternative to Graph Neural Networks (GNNs) termed Graph Structured Neural Networks (GSNN), which uses cell signaling knowledge, encoded as a graph data structure, to add inductive biases to deep learning. We apply our method to perturbation biology using the LINCS L1000 dataset and literature-curated molecular interactions. We demonstrate that GSNNs outperform baseline algorithms in several prediction tasks, including 1) perturbed expression, 2) cell viability of drug combinations, and 3) disease-specific drug prioritization. We also present a method called GSNNExplainer to explain GSNN predictions in a biologically interpretable form. This work has broad application in basic biological research and pre-clincal drug repurposing. Further refinement of these methods may produce trustworthy models of drug response suitable for use as clinical decision aids.
Comparison of monomeric variants of StayGold
Authors: Shimozono Satoshi , Ando Ryoko , Sugiyama Mayu , Hirano Masahiko , Niino Yusuke , Miyawaki Atsushi
Published: March 2024

StayGold is a bright and highly photostable fluorescent protein (FP) that forms an obligate dimer, thereby limiting its application as a soluble marker. On the basis of the structural information of this FP, we disrupted the dimerization to generate a monomeric variant, mStayGold, which inherits both the extremely high photostability and the high practical brightness of StayGold, for molecular fusion and membrane-targeting applications. Meanwhile, two other research groups have independently monomerized StayGold using different strategies. As a result, multiple StayGold monomers are currently available, creating confusion in the research community. In the present study, we investigated the three basic properties—photostability, brightness, and dispersibility—of these monomers by performing detailed side-by-side comparisons. This study highlights the difficulties of StayGold monomerization with emphasis on the tradeoff between photostability and brightness in FP technology.
mulea - an R package for enrichment analysis using multiple ontologies and empirical FDR correction
Authors: Turek Cezary , Ölbei Márton , Stirling Tamás , Fekete Gergely , Tasnádi Ervin , Gul Leila , Bohár Balázs , Papp Balázs , Jurkowski Wiktor , Ari Eszter
Published: March 2024

Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrectedp-values. To address these challenges, we introducemulea, an R package offering comprehensive overrepresentation and functional enrichment analysis.muleaemploys an innovativeempirical false discovery rate (eFDR) correction method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies.muleaexpands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis,muleaprovides gene sets (in standardised GMT format) for 27 model organisms, covering 16 databases and various identifiers resulting in almost 900 files. Additionally, themuleaDataExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally,mulea’s architecture allows for easy integration of user-defined ontologies, expanding its applicability across diverse research areas.

Availability and Implementation

Software for the tools demonstrated in this article is available as anRpackage on GitHub:https://github.com/ELTEbioinformatics/mulea.
Heat Shock alters the distribution andin vivointeraction of major nuclear structural proteins – Lamin B with DNA Topoisomerase II, and with nucleic acids
Authors: Rowińska Marta , Tomczak Aleksandra , Jabłońska Jadwiga , Piekarowicz Katarzyna , Machowska Magdalena , Rzepecki Ryszard
Published: March 2024

Lamins and topoisomerases have been studied as major karyoskeletal proteins since early 80-ties. Today, lamins are thought to be responsible not only for maintenance and structural support of cell nuclei but also involved, directly or indirectly, in regulation of chromatin structure, chromatin distribution, gene expression, splicing, transcription and transport. Topoisomerases are involved in maintenance of chromosomal scaffold and structural functions in cell nuclei and topology of chromatin and DNA, and play an important role in regulation of transcription. They are also necessary in mitosis. For studying lamins and topoisomerase II,Drosophila melanogastermodel has been used for many years since flies genome contains only single gene coding for B-type lamins (lamin Dm) and single gene coding for A-type lamins (lamin C). Flies have only single gene coding for topoisomerase II (Top2).

We previously reported that lamin Dm (Lam Dm) and topoisomerase II (Top2) bindin vivoboth DNA and RNA and the properties of both proteins have been modulated by specific phosphorylation on particular sites. Here we report the first part of results of the project focused on the demonstration of the role of lamins and Top2 in the regulation of gene expression and chromatin organization upon heat shock (HS) induction and recovery (R). We demonstrated that heat shock significantly induced specific phosphorylation of lamin Dm at least on S25, which affects lamin properties and distribution. Lam Dm and Top2 were relocated and changed properties including solubility. Both proteins interact with each other directly and indirectly and binding was significantly increased under HS. The relocation of Lam Dm and Top2 was associated with the relocation of chromatin as detected in polyploid third instar larvae nuclei.In vivophotocrosslinking and IP (immunoprecipitation) studies indicated a significant increase in binding to chromatin and nucleic acids upon HS induction. The highest binding affinity showed a soluble fraction of lamin Dm and topoisomerase II while the lowest was the insoluble fraction (“nuclear matrix” fraction). All the detected changes in properties and location of proteins returned to “normal” after recovery from heat shock. Based on thi s data and our preliminary interactome data for lamin Dm and Top2 we believe that both proteins play essential roles in the proper response of fly cells to HS by participation in the rearrangement of protein complexes, also associated with DNA and RNA, chromatin remodelling and proper gene expression regulation.
Defining the most potent osteoinductive culture conditions for MC3T3-E1 cells reveals no implication of oxidative stress or energy metabolism
Authors: Semicheva Alexandra , Ersoy Ufuk , Vasilaki Aphrodite , Myrtziou Ioanna , Kanakis Ioannis
Published: March 2024

MC3T3-E1 preosteoblastic cell line is widely utilised as a reliablein vitrosystem to assess bone formation. However, the experimental growth conditions for these cells hugely diverge and, particularly, the osteogenic medium (OSM) composition varies in research studies. Therefore, we aimed to define the ideal culture conditions for MC3T3-E1 subclone 4 cells with regards to mineralization capacity and explore if oxidative stress or cellular metabolism processes are implicated. Cells were treated with 9 different combinations of long-lasting ascorbate (Asc) and β-glycerophosphate (βGP) and osteogenesis/calcification were evaluated at 3 different time-points by qPCR, Western blotting and bone nodule staining. Key molecules of oxidative and metabolic pathways were also assessed. It was found that sufficient mineral deposition was achieved only in 150μg.mL-1/2mM Asc/βGP combination at 21d in OSM and this was supported byRunx2, Alpl, BglapandCol1a1expression levels increase. NOX2 and SOD2 as well as PGC1α and Tfam were also monitored as indicators of redox and metabolic processes, respectively, where no differences were observed. Elevation in OCN protein levels and ALP activity showed that mineralisation comes as a result of these differences. This work defines the most appropriate culture conditions for MC3T3-E1 cells and could be used by other research laboratories in this field.
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

Magnesium (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

Ribosome 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

Transcription-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

The 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

The 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.
Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification
Authors: Jousheghani Zahra Zare , Patro Rob
Published: March 2024

Motivation: Long read sequencing technology is becoming an increasingly indispensable tool in genomic and transcriptomic analysis. In transcriptomics in particular, long reads offer the possibility of sequencing full-length isoforms, which can vastly simplify the identification of novel transcripts and transcript quantification. However, despite this promise, the focus of much long read method development to date has been on transcript identification, with comparatively little attention paid to quantification. Yet, due to differences in the underlying protocols and technologies, lower throughput (i.e. fewer reads sequenced per sample compared to short read technologies), as well as technical artifacts, long read quantification remains a challenge, motivating the continued development and assessment of quantification methods tailored to this increasingly prevalent type of data. Results: We introduce a new method and software tool for long read transcript quantification called oarfish. Our model incorporates a novel and innovative coverage score, which affects the conditional probability of fragment assignment in the underlying probabilistic model. We demonstrate that by accounting for this coverage information, oarfish is able to produce more accurate quantification estimates than existing long read quantification methods, particularly when one considers the primary isoforms present in a particular cell line or tissue type. Availability and Implementation: Oarfish is implemented in the Rust programming language, and is made available as free and open-source software under the BSD 3-clause license. The source code is available at https://www.github.com/COMBINE-lab/oarfish.
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

Doublecortin (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

TANGO2 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

Ticks, 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.
Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency
Authors: Wu Jinjun , Xiao Yu , Liu Yunzheng , Wen Li , Jin Chuanyang , Liu Shun , Paul Sneha , He Chuan , Regev Oded , Fei Jingyi
Published: March 2024

Nuclear speckles, a type of membraneless nuclear organelle in higher eukaryotic cells, play a vital role in gene expression regulation. Using the reverse transcription-based RNA-binding protein binding sites sequencing (ARTR-seq) method, we study human transcripts associated with nuclear speckles. We identify three gene groups whose transcripts demonstrate different speckle localization properties and dynamics: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-mRNA stage, and not enriched in speckles. Specifically, we find that stably-enriched transcripts contain inefficiently spliced introns. We show that nuclear speckles specifically facilitate splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, underscoring a tight interplay between genome organization, RNA cis-elements, and transcript speckle enrichment, and connecting transcript speckle localization with splicing efficiency. Finally, we show that speckles can act as hubs for the regulated retention of introns during cellular stress. Collectively, our data highlight a role of nuclear speckles in both co- and post-transcriptional splicing regulation.
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

Temporal 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

The 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.
Structural basis of the allosteric regulation of cyanobacterial glucose-6-phosphate dehydrogenase by the redox sensor OpcA
Authors: Doello Sofía , Shvarev Dmitry , Theune Marius , Sauerwein Jakob , Klon Alexander , Keskin Erva , Boehm Marko , Gutekunst Kirstin , Forchhammer Karl
Published: March 2024

The oxidative pentose phosphate (OPP) pathway is a fundamental carbon catabolic route for generating reducing power and metabolic intermediates for biosynthetic processes. In addition, its first two reactions form the OPP shunt, which replenishes the Calvin-Bassham cycle under certain conditions. Glucose-6-phosphate dehydrogenase (G6PDH) catalyzes the first and rate-limiting reaction of this metabolic route. In photosynthetic organisms, G6PDH is redox-regulated to allow fine-tuning and to prevent futile cycles while carbon is being fixed. In cyanobacteria, regulation of G6PDH requires the redox protein OpcA, but the underlying molecular mechanisms behind this allosteric activation remain elusive. Here, we used enzymatic assays andin vivointeraction analyses to show that OpcA binds G6PDH under different environmental conditions. However, complex formation enhances G6PDH activity when OpcA is oxidized and inhibits it when OpcA is reduced. To understand the molecular basis of this regulation, we used cryogenic electron microscopy to determine the structure of cyanobacterial G6PDH and the G6PDH-OpcA complex. OpcA binds the G6PDH tetramer and induces conformational changes in the active site of G6PDH. The redox sensitivity of OpcA is achieved by intramolecular disulfide bridge formation, which influences the allosteric regulation of G6PDH.In vitroassays reveal that the level of G6PDH activation depends on the number of bound OpcA molecules, which implies that this mechanism allows delicate fine-tuning. Our findings unveil a novel and unique molecular mechanism governing the regulation of the OPP pathway in cyanobacteria.
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

Despite 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 Summary

Rational, 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.
AnophelesEgg Collection, Disinfection, and Hatching
Authors: Leite Laura N. , Bascuñán Priscila , Dotson Ellen M. , Benedict Mark Q.
Published: March 2024

Gravid (i.e., with fully developed eggs), matedAnophelesfemales typically lay their eggs directly on water ∼48–72 h after a blood meal. Unlike some other mosquito species,Anopheleseggs cannot be desiccated and stored for long durations, and, hence, colonies must be reared continuously. In this protocol, we discuss methods for egg collection, including individual anden masseoviposition; egg disinfection to avoid the transmission of infectious agents to the next generation; and egg hatching for colony maintenance or experimentation. We also include optional methods for estimating life history traits such as fecundity, fertility, and larval mortality rates from egg counts.
AnophelesAdult Anesthesia, Feeding, and Sex Separation
Authors: Leite Laura N. , Bascuñán Priscila , Dotson Ellen M. , Benedict Mark Q.
Published: March 2024

The adult stage is the only nonaquatic stage of theAnophelesmosquito. Both male and femaleAnophelesmosquitoes require access to a source of sugar to survive. In the insectary, a temperature of ∼27°C and 80% relative humidity and a cycle of 12 h light:12 h dark light, ideally with a sunrise and sunset period, are necessary minimum conditions to mimic their natural environment. Laboratory-rearedAnophelescan survive for over a month; however, decreased activity and increased mortality may be observed ∼2 wk postemergence depending on the species and health of the colony. Details on how to maintain adultsAnophelesare discussed here. Information and considerations on blood and sugar feeding are described. This protocol also provides instructions on how to differentiate male and female adult mosquitoes.
AnophelesPupa Collection and Sex Identification
Authors: Leite Laura N. , Bascuñán Priscila , Dotson Ellen M. , Benedict Mark Q.
Published: March 2024

For mostAnophelesspecies, larval–pupal metamorphosis commences ∼1 wk after egg hatching. However, depending on the amount of food provided, H2O temperature, and larval density, the pupation process can be accelerated or delayed. Synchronous pupation is difficult to accomplish consistently, and, thus, pupae need to be separated from larvae daily. Adult emergence will take place 24–48 h after pupation. Most adults will eclose before the next morning (light cycle) in many species. Here, we provide information on some methods available to collect pupae and to sort pupae by sex. Notably, pupa collection and sorting are some of the most time-consuming procedures of the overall mosquito rearing process. Some methods mentioned here attempt to help reduce work effort and time required.
Color-octet nonrelativistic QCD matrix elements for heavy quarkonium decays in the refined Gribov-Zwanziger theory
Authors: Chung Hee Sok
Published: March 2024

We determine color-octet nonrelativistic QCD matrix elements for quarkonium decays from moments of the two-point correlation function of the QCD field-strength tensor computed in the refined Gribov-Zwanziger theory. We find that a tree-level calculation in the refined Gribov-Zwanziger theory can give a suitable description of the QCD field-strength correlation function at both short and long distances, which leads to moments that are infrared finite and can be properly renormalized. By using the color-octet matrix elements we obtain, we quantitatively improve the nonrelativistic effective field theory description of quarkonium decay rates, especially for the χQJ and ηQ states, where Q=c or b.

Published by the American Physical Society
2024
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.