bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convergence of direction, location and theta in the rat anteroventral thalamic nucleus
Authors: Lomi Eleonora , Jeffery Kate J. , Mitchell Anna S. 
Published: January 2023

SummaryRetrosplenial cortex (RSC) is a cortical region that computes heading direction from landmark information, but how it does this remains unknown. Recently we found that its two major subregions receive differential projections from two anteroventral thalamic (AV) subfields; dorsomedial (AVDM) and ventrolateral (AVVL). To probe the respective contributions of these inputs we recorded single neurons and local field potentials from AV in rats during foraging. We observed and characterized neurons modulated by theta oscillations, heading direction, and a conjunction of these. Unexpectedly, we also discovered place cells (neurons modulated by location). Consistent with the notion that AV contains two parallel subcircuits, there was a prevalence of non-conjunctive cells in AVDM, and of conjunctive and place neurons in AVVL. This integration of spatial and movement signals in AV is consistent with a thalamic role in multimodal integration and may be important for supplying the spatial information that modulates RSC directional responding.
Selection of Extended CRISPR RNAs with Enhanced Targeting and Specificity
Authors: Herring-Nicholas Ashley , Dimig Hillary , Roesing Miranda , Josephs Eric A. 
Published: January 2023

ABSTRACTFor a CRISPR guide RNA (gRNA) with a specific target but activity at known “off-target” sequences, we present a method to screen hundreds of thousands of gRNA variants with short, randomized 5’ nucleotide extensions near its DNA-targeting segment—a modification that can increase Cas9 gene editing specificity by orders of magnitude with certain 5’- extension sequences,viasome as-yet-unknown mechanism that makesde novodesign of the extension sequence difficult to perform manually—to robustly identify extended gRNAs (x-gRNAs) that have been counter-selected against activity at those off-target sites and that exhibit significantly enhanced Cas9 specificity for their intended targets.
Chloroquine induces eryptosis inP. falciparum-infectedred blood cells and the release of extracellular vesicles with a unique protein profile
Authors: Carrera-Bravo Claudia , Zhou Tianchi , Hang Jing Wen , Modh Harshvardhan , Huang Fred , Malleret Benoit , Wacker Matthias G , Wang Jiong-Wei , Renia Laurent , Tan Kevin SW 
Published: January 2023

ABSTRACTMalaria is a vector-borne parasitic disease that affects millions worldwide. In order to reach the objective, set by the World Health Organization to decrease the cases by 2030, antimalarial drugs with novel modes of action are required. Previously, a novel mechanism of action of chloroquine (CQ) was reported involving features of programmed cell death in the parasite, mainly characterized by calcium efflux from the digestive vacuole (DV) permeabilization. Increased intracellular calcium induces the suicidal death of erythrocytes also known as eryptosis. This study aimed to identify the hallmarks of eryptosis due to calcium redistribution and the downstream cellular effects during CQ treatment in iRBCs.Plasmodium falciparum3D7 at mid-late trophozoites were used for the antimalarial drug treatment. Our results revealed increased phosphatidylserine (PS) exposure, cell shrinkage and membrane blebbing, delineating an eryptotic phenotype in the host RBC. Interestingly, the blebs on the surface of the iRBCs released to the extracellular milieu become extracellular vesicles (EVs) which are essential for intercellular communication due to their cargo of proteins, nucleic acids, lipids and metabolites. The proteomic characterization displayed 2 highly enriched protein clusters in EVs from CQ-treated iRBCs, the proteasome and ribosome. We demonstrated that this unique protein cargo is not associated with the parasite growth rate. Additionally, we found that these particular EVs might activate IFN signaling pathways mediated by IL-6 in THP-1-derived macrophages. Our findings shed new insights into a novel drug-induced cell death mechanism that targets the parasite and specific components of the infected host RBC.IMPORTANCEOur previous studies have shown that chloroquine (CQ) treatment in iRBCs triggersPlasmodium falciparumdigestive vacuole (DV) membrane permeabilization leading to calcium redistribution. Interestingly, increased intracellular calcium concentration is the main inducer of the suicidal death of red blood cells (RBCs) called eryptosis. The present study shed new insights into a novel CQ-induced cell death mechanism that targets the parasite and the infected host RBC by inducing key phenotypic hallmarks of eryptosis: PS exposure, cell shrinkage and membrane blebbing. Moreover, the proteomic characterization of the blebs released to the extracellular milieu also known as extracellular vesicles (EVs) revealed a cargo highly enriched in ribosomal proteins and proteasome subunits relevant for host-parasite interactions. These findings highlight CQ’s effect on calcium homeostasis disruption in infected red blood cells (iRBCs) with cellular and immunological consequences of great significance for malaria pathogenesis and potential clinical implications.
A hepatitis B virus (HBV) sequence variation graph improves sequence alignment and sample-specific consensus sequence construction for genetic analysis of HBV
Authors: Duchen Dylan , Clipman Steven , Vergara Candelaria , Thio Chloe L. , Thomas David L. , Duggal Priya , Wojcik Genevieve L. 
Published: January 2023

ABSTRACTHepatitis B virus (HBV) remains a global public health concern, with over 250 million individuals living with chronic HBV infection (CHB) and no curative therapy currently available. Viral diversity is associated with CHB pathogenesis and immunological control of infection. Improved methods to characterize the viral genome at both the population and intra-host level could aid drug development efforts. Conventionally, HBV sequencing data are aligned to a linear reference genome and only sequences capable of aligning to the reference are captured for analysis. Reference selection has additional consequences, including sample-specific ‘consensus’ sequence construction. It remains unclear how to select a reference from available sequences and whether a single reference is sufficient for genetic analyses. Using simulated short-read sequencing data generated from full-length publicly available HBV genome sequences and HBV sequencing data from a longitudinally sampled individual with CHB, we investigate alternative graph-based alignment approaches. We demonstrate that using a phylogenetically representative ‘genome graph’ for alignment, rather than linear reference sequences, avoids issues of reference ambiguity, improves alignment, and facilitates the construction of sample-specific consensus sequences genetically similar to an individual’s infection. Graph-based methods can therefore improve efforts to characterize the genetics of viral pathogens, including HBV, and may have broad implications in host pathogen research.
The ‘phruta’ R package and ‘salphycon’ shiny app: increasing access, reproducibility, and transparency in phylogenetic analyses
Authors: Román-Palacios Cristian 
Published: January 2023

AbstractCurrent practices for assembling phylogenetic trees often recur to sequence data stored in GenBank. However, the molecular and taxonomic make up of sequences deposited in GenBank is generally not very clear.‘phruta’, a newly developed ‘R’ package, is designed to primarily improve access to genetic data stored in GenBank. Functions in ‘phruta’ further enable users to assemble single- and multi-gene molecular datasets, and run basic phylogenetic tasks, all within ‘R’.The structure of the functions implemented in ‘phruta’, designed as a workflow, aim to allow users to assemble simple workflows for particular tasks, which are in turn expected to increase reproducibility of relatively simple phylogenies.To support the use of ‘phruta’ by researchers in different fields with variable levels of coding expertise, this paper presents ‘salphycon’, a shiny web app that is expected to increase access to the fundamental functions in the ‘phruta’ ‘R’ package.
A novel role of USP7 in imparting partial EMT state in colorectal cancer through the DDX3X-β-catenin axis
Authors: Basu Bhaskar , Karmakar Subhajit , Basu Malini , Ghosh Mrinal K. 
Published: January 2023

AbstractEpithelial mesenchymal transition (EMT) is a fundamental and highly regulated process that is normally observed during embryonic development and tissue repair but is deregulated during advanced cancer. Classically, through the process of EMT, cancer cells gradually transition from a predominantly epithelial phenotype to a more invasive mesenchymal phenotype. Increasing studies have, however, brought into light the existence of unique intermediary states in EMT, often referred to as partial EMT states. Through our studies we have found the deubiquitinase USP7 to be strongly associated with the development of such a partial EMT state in colon cancer cells, characterized by the acquisition of mesenchymal characteristics but without the reduction in epithelial markers. We found USP7 to be overexpressed in colon adenocarcinomas and to be closely associated with advancing tumor stage. We found that functional inhibition or knockdown of USP7 is associated with a marked reduction in mesenchymal markers and in overall migration potential of cancer cells. Starting off with a proteomics-based approach we were able to identify and later on verify the DEAD box RNA helicase DDX3X to be an interacting partner of USP7. We then went on to show that USP7, through the stabilization of DDX3X, augments Wnt/β-catenin signaling, which has previously been shown to be greatly associated with colorectal cancer cell invasiveness. Our results strongly suggest a positive role of USP7 in the development of a partial mesenchymal phenotype in colorectal cancer.
A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5
Authors: Ives Callum M. , Şahin Alp Tegin , Thomson Neil J. , Zachariae Ulrich 
Published: January 2023

AbstractA key capability of ion channels is the facilitation of selective permeation of certain ionic species across cellular membranes at high rates. Due to their physiological significance, ion channels are of great pharmaceutical interest as drug targets. The polymodal signal-detecting Transient Receptor Potential (TRP) superfamily of ion channels form a particularly promising group of drug targets. While most members of this family permeate a broad range of cations including Ca2+, TRPM4 and TRPM5 are unique due to their strong monovalent-selectivity and impermeability for divalent cations. Here, we investigated the mechanistic basis for their unique monovalent-selectivity byin silicoelectrophysiology simulations of TRPM5. Our simulations reveal an unusual mechanism of cation selectivity, which is underpinned by the function of the central channel cavity rather than the selectivity filter. Our results suggest that a subtle hydrophobic barrier at the cavity entrance ("hydrophobic funnel") enables monovalent, but not divalent cations to pass and occupy the cavity at physiologically relevant membrane voltages. Monovalent cations then permeate efficiently by a co-operative, distant knock-on mechanism between two binding regions in the extracellular pore vestibule and the central cavity. By contrast, divalent cations do not enter or interact favourably with the channel cavity due to its raised hydrophobicity. Hydrophilic mutations in the transition zone between the selectivity filter and the central channel cavity abolish the barrier for divalent cations, enabling both monovalent and divalent cations to traverse TRPM5.
Homeodomain-interacting protein kinase maintains neuronal homeostasis during normalCaenorhabditis elegansaging and systemically regulates longevity from serotonergic and GABAergic neurons
Authors: Lazaro-Pena Maria I. , Cornwell Adam B. , Diaz-Balzac Carlos A. , Das Ritika , Ward Zachary C. , Macoretta Nicholas , Thakar Juilee , Samuelson Andrew V. 
Published: January 2023

AbstractAging and the age-associated decline of the proteome is determined in part through neuronal control of evolutionarily conserved transcriptional effectors, which safeguard homeostasis under fluctuating metabolic and stress conditions by regulating an expansive proteostatic network. We have discovered theCaenorhabditis eleganshomeodomain-interactingproteinkinase (HPK-1) acts as a key transcriptional effector to preserve neuronal integrity, function, and proteostasis during aging. Loss ofhpk-1results in drastic dysregulation in expression of neuronal genes, including genes associated with neuronal aging. During normal aginghpk-1expression increases throughout the nervous system more broadly than any other kinase. Within the aging nervous system,hpk-1induction overlaps with key longevity transcription factors, which suggestshpk-1expression mitigates natural age-associated physiological decline. Consistently, pan-neuronal overexpression ofhpk-1extends longevity, preserves proteostasis both within and outside of the nervous system, and improves stress resistance. Neuronal HPK-1 improves proteostasis through kinase activity. HPK-1 functions cell non-autonomously within serotonergic and GABAergic neurons to improve proteostasis in distal tissues by specifically regulating distinct components of the proteostatic network. Increased serotonergic HPK-1 enhances the heat shock response and survival to acute stress. In contrast, GABAergic HPK-1 induces basal autophagy and extends longevity, which requiresmxl-2(MLX),hlh-30(TFEB), anddaf-16(FOXO). Our work establisheshpk-1as a key neuronal transcriptional regulator critical for preservation of neuronal function during aging. Further, these data provide novel insight as to how the nervous system partitions acute and chronic adaptive response pathways to delay aging by maintaining organismal homeostasis.
Glycine homeostasis requires reverse SHMT flux
Authors: McBride Matthew J. , Hunter Craig J. , Rabinowitz Joshua D. 
Published: January 2023

SUMMARYThe folate-dependent enzyme serine hydroxymethyltransferase (SHMT) reversibly converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Such one-carbon unit production plays a critical role in development, the immune system, and cancer. Here we show that the whole-body SHMT flux acts to net consume rather than produce glycine. Pharmacological inhibition of whole-body SHMT1/2 and genetic knockout of liver SHMT2 elevated circulating glycine levels up to eight-fold. Stable isotope tracing revealed that the liver converts glycine to serine, which is then converted by serine dehydratase into pyruvate and burned in the tricarboxylic acid cycle. In response to diets deficient in serine and glycine, de novo biosynthetic flux was unaltered but SHMT2- and serine dehydratase-mediated catabolic flux was lower. Thus, glucose-derived serine synthesis does not respond to systemic demand. Instead, circulating serine and glycine homeostasis is maintained through variable consumption, with liver SHMT2 as a major glycine-consuming enzyme.
Plasmodium falciparumGCN5 plays a key role in regulating artemisinin resistance–related stress responses
Authors: Lucky Amuza Byaruhanga , Wang Chengqi , Shakri Ahmad Rushdi , Kalamuddin Mohammad , Chim-Ong Anongruk , Li Xiaolian , Miao Jun 
Published: January 2023

ABSTRACTPlasmodium falciparumcauses the most severe malaria and is exposed to various environmental and physiological stresses in the human host. Given that GCN5 plays a critical role in regulating stress responses in model organisms, we aimed to elucidate PfGCN5’s function in stress responses inP. falciparum. The protein level of PfGCN5 was substantially induced under three stress conditions (heat shock, low glucose starvation, and dihydroartemisinin, the active metabolite of artemisinin (ART)). With a TetR-DOZI conditional knockdown (KD) system, we successfully down-regulated PfGCN5 to ∼50% and found that KD parasites became more sensitive to all three stress conditions. Transcriptomic analysis via RNA-seq identified ∼1,000 up-and down-regulated genes in the wildtype (WT) and KD parasites under these stress conditions. Importantly, DHA induced transcriptional alteration of many genes involved in many aspects of stress responses, which were heavily shared among the altered genes under heat shock and low glucose conditions, including ART-resistance-related genes such asK13andcoronin. Based on the expression pattern between WT and KD parasites under three stress conditions, ∼300-400 genes were identified to be involved in PfGCN5-dependent, general and stress-condition-specific responses with high levels of overlaps among three stress conditions. Notably, using ring-stage survival assay (RSA), we found that KD or inhibition of PfGCN5 could sensitize the ART-resistant parasites to the DHA treatment. All these indicate that PfGCN5 is pivotal in regulating general and ART-resistance-related stress responses in malaria parasites, implicating PfGCN5 as a potential target for malaria intervention.IMPORTANCEMalaria leads to about half a million deaths annually and these casualties were majorly caused by the infection ofPlasmodium falciparum. This parasite strives to survive by defending against a variety of stress conditions, such as malaria cyclical fever (heat shock), starvation due to low blood sugar (glucose) levels (hypoglycemia), and drug treatment. Previous studies have revealed thatP. falciparumhas developed unique stress responses to different stresses including ART treatment, and ART-resistant parasites harbor elevated stress responses. In this study, we provide critical evidence on the role of PfGCN5, a histone modifier, and a chromatin coactivator, in regulating general and stress-specific responses in malaria parasites, indicating that PfGCN5 can be used as a potential target for anti-malaria intervention.
Data-driven Targeting of COVID-19 Vaccination Programs: An Analysis of the Evidence on Impact, Implementation, Ethics and Equity
Authors: McLaren Zoë M. 
Published: January 2023

AbstractThe data-driven targeting of COVID-19 vaccination programs is a major determinant of the ongoing toll of COVID-19. Targeting of access to, outreach about and incentives for vaccination can reduce total deaths by 20-50 percent relative to a first-come-first-served allocation. This piece performs a systematic review of the modeling literature on the relative benefits of targeting different groups for vaccination and evaluates the broader scholarly evidence – including analyses of real-world challenges around implementation, equity, and other ethical considerations – to guide vaccination targeting strategies. Three-quarters of the modeling studies reviewed concluded that the most effective way to save lives, reduce hospitalizations and mitigate the ongoing toll of COVID-19 is to target vaccination program resources to high-risk people directly rather than reducing transmission by targeting low-risk people. There is compelling evidence that defining vulnerability based on a combination of age, occupation, underlying medical conditions and geographic location is more effective than targeting based on age alone. Incorporating measures of economic vulnerability into the prioritization scheme not only reduces mortality but also improves equity. The data-driven targeting of COVID-19 vaccination program resources benefits everyone by efficiently mitigating the worst effects of the pandemic until the threat of COVID-19 has passed.
Crosslinking by ZapD drives the assembly of short FtsZ filaments into toroidal structures in solution
Authors: Merino-Salomón Adrián , Schneider Jonathan , Babl Leon , Krohn Jan-Hagen , Sobrinos-Sanguino Marta , Schäfer Tillman , Luque-Ortega Juan R. , Alfonso Carlos , Jiménez Mercedes , Jasnin Marion , Schwille Petra , Rivas Germán 
Published: January 2023

AbstractBacterial cell division relies on the Z ring, a cytoskeletal structure that acts as a scaffold for the assembly of the divisome. To date, the detailed mechanisms underlying the assembly and stabilization of the Z ring remain elusive. This study highlights the role of the FtsZ-associated protein (Zap) ZapD in the assembly and stabilization of Z-ring-like structures via filament crosslinking. Using cryo-electron tomography and biochemical analysis, we show that, at equimolar concentrations of ZapD and FtsZ, ZapD induces the formation of toroidal structures composed of short, curved FtsZ filaments that are crosslinked vertically, but also laterally and diagonally. At higher concentrations of ZapD, regularly spaced ZapD dimers crosslink FtsZ filaments from above, resulting in the formation of straight bundles. Despite the simplicity of this reconstituted system, these findings provide valuable insights into the structural organization and stabilization of the Z ring by Zap proteins in bacterial cells, revealing the key role of optimal crosslinking density and geometry in enabling filament curvature and ring formation.
Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley
Authors: Cosenza Francesco , Shrestha Asis , Van Inghelandt Delphine , Casale Federico A. , Wu Po-Ya , Weisweiler Marius , Li Jinquan , Wespel Franziska , Stich Benjamin 
Published: January 2023

ABSTRACTFlowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Although their role as key traits, a comprehensive understanding of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Through a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as identify new genetic variants by single and multi-population quantitative trait loci (QTL) analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected one new QTL for flowering time and two new QTL for plant height. Finally, we identified a new functional allelic variant of the main regulatory genePpd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect or low frequency, genetic variants underlie the control of these two traits.
Leftward transfer of a chemosensory polycystin initiates left-dominant calcium signaling for lateralized embryonic development
Authors: Tanaka Yosuke , Morozumi Ai , Hirokawa Nobutaka 
Published: January 2023

SummaryLeft-dominant [Ca2+]ielevation on the margin of ventral node furnishes the initial laterality signaling in mouse embryos. It depends on nodal flow, FGFR signaling, and PKD1L1-containing polycystin channels, of which interrelationship is still missing. Here we show that PKD1L1 protein is predominantly accumulated on the left margin of the nodal pit and serves as a chemosensory channel for Nodal-mediated [Ca2+]ielevation. PKD1L1/PKD2 overexpression augmented the Nodal sensitivity of fibroblasts. We detected PKD1L1-containing fragile meshwork of fibrous strands using KikGR-PKD1L1 knockin mice, especially when the extraembryonic membrane was preserved. The portion of meshwork bridging over nodal crown cells significantly lateralized to the left. This bridge was formed by a leftward flow of PKD1L1-containing fibrous strands, which can be suppressed by the FGFR inhibitor SU5402 that antagonized the [Ca2+]ielevation as well. These data provide evidence for a leftward transfer of chemosensory PKD1L1 polycystin channel, as a readout mechanism of nodal flow.