bluuebunny/crossref_metadata_2025 huggingface dataset:
A Flat Protein Complex Shapes Rough ER Membrane Sheets
Authors: Sawyer Eric M. , Jensen Liv E. , Meehl Janet B. , Larsen Kevin P. , Petito Daniel A. , Hurley James H. , Voeltz Gia K.
Published: October 2023

Rough ER sheets are a fundamental domain of the ER and the gateway into the secretory pathway. While reticulon proteins stabilize high-curvature ER tubules, it is unclear if other proteins scaffold the flat membranes of rough ER sheets. Through a proteomics screen using ER sheet localized RNA-binding proteins as bait, we identify the Sigma-1 receptor (SigmaR1) as an ER sheet shaping factor. High-resolution live cell imaging and electron tomography assign SigmaR1 as an ER sheet-localized factor whose levels determine the amount of rough ER sheets in cells. Structure-guided mutagenesis and in vitro reconstitution on giant unilamellar vesicles further support a mechanism whereby SigmaR1 oligomers use their extended arrays of amphipathic helices to bind and flatten the lumenal leaflet of ER membranes. Our results demonstrate an unexpected way for proteins to sense and propagate flat membrane sheets.
Intrinsic disorder specifies discreet functions of nucleoplasmin-like histone chaperones
Authors: Gauthier Courtney M. , LeGallais Josey , Savic Neda , Moradi-Fard Sarah , Grew Arden , Loe Martin , Kirlikaya Baran , Cobb Jennifer , Nelson Christopher J.
Published: October 2023

Nucleoplasmin (NPM) histone chaperones regulate distinct processes in the nucleus and nucleolus. While intrinsically disordered regions (IDRs) are hallmarks of NPMs, it is not clear if all NPM functions require these unstructured features. We assessed the importance of IDRs in yeast NPM-like proteins and found that regulation of rDNA copy number, and genetic interactions with the nucleolar RNA surveillance machinery require the highly conserved FKBP prolyl isomerase domain, but not the NPM domain or IDRs. By contrast, transcriptional silencing in the nucleus requires IDRs. We demonstrate that multiple lysines in poly-acidic serine/lysine motifs of IDRs are required for both lysine polyphosphorylation and NPM-mediated transcriptional silencing. These results demonstrate that NPM-like proteins do not rely on IDRs for all chromatin-related functions.
Traumatic brain injury disrupts state-dependent functional cortical connectivity in a mouse model
Authors: Bottom-Tanzer Samantha , Corella Sofia , Meyer Jochen , Sommer Mary , Bolaños Luis , Murphy Timothy , Quiñones Sadi , Heiney Shane , Shtrahman Matthew , Whalen Michael , Oren Rachel , Higley Michael J. , Cardin Jessica A. , Noubary Farzad , Armbruster Moritz , Dulla Chris
Published: October 2023

Traumatic brain injury (TBI) is the leading cause of death in young people and can cause cognitive and motor dysfunction and disruptions in functional connectivity between brain regions. In human TBI patients and rodent models of TBI, functional connectivity is decreased after injury. Recovery of connectivity after TBI is associated with improved cognition and memory, suggesting an important link between connectivity and functional outcome. We examined widespread alterations in functional connectivity following TBI using simultaneous widefield mesoscale GCaMP7c calcium imaging and electrocorticography (ECoG) in mice injured using the controlled cortical impact (CCI) model of TBI. Combining CCI with widefield cortical imaging provides us with unprecedented access to characterize network connectivity changes throughout the entire injured cortex over time. Our data demonstrate that CCI profoundly disrupts functional connectivity immediately after injury, followed by partial recovery over 3 weeks. Examining discrete periods of locomotion and stillness reveals that CCI alters functional connectivity and reduces theta power only during periods of behavioral stillness. Together, these findings demonstrate that TBI causes dynamic, behavioral state-dependent changes in functional connectivity and ECoG activity across the cortex.
The Structure and Statistics of Language Jointly Shape Cross-frequency Neural Dynamics During Spoken Language Comprehension
Authors: Weissbart Hugo , Martin Andrea E.
Published: October 2023

Humans excel at extracting structurally-determined meaning from speech despite inherent physical variability. This study explores the brain's ability to predict and understand spoken language robustly. It investigates the relationship between structural and statistical language knowledge in brain dynamics, focusing on phase and amplitude modulation. Using syntactic features from constituent hierarchies and surface statistics from a transformer model as predictors of forward encoding models, we reconstructed cross-frequency neural dynamics from MEG data during audiobook listening. Our findings challenge a strict separation of linguistic structure and statistics in the brain, with both aiding neural signal reconstruction. Syntactic features had a more temporally spread impact, and both word entropy and the number of closing syntactic constituents were linked to the phase-amplitude coupling of neural dynamics, implying a role in temporal prediction and cortical oscillation alignment during speech processing. Our results indicate that structured and statistical information jointly shape neural dynamics during spoken language comprehension and suggest an integration process via a cross-frequency coupling mechanism.
AleRax: A tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss
Authors: Morel Benoit , Williams Tom A. , Stamatakis Alexandros , Szöllősi Gergely J.
Published: October 2023

Motivation

Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics. Ideally, phylogenetic methods should not only model substitutions along gene trees, which explain differences between homologous gene sequences, but also the processes that generate the gene trees themselves along a shared species tree. To conduct accurate inferences, one needs to account for uncertainty at both levels, that is, in gene trees estimated from inherently short sequences and in their diverse evolutionary histories along a shared species tree.

Results

We present AleRax, a software that can infer reconciled gene trees together with a shared species tree using a simple, yet powerful, probabilistic model of gene duplication, transfer, and loss. A key feature of AleRax is its ability to account for uncertainty in the gene tree and its reconciliation by using an efficient approximation to calculate the joint phylogenetic-reconciliation likelihood and sample reconciled gene trees accordingly. Simulations and analyses of empirical data show that AleRax is one order of magnitude faster than competing gene tree inference tools while attaining the same accuracy. It is consistently more robust than species tree inference methods such as SpeciesRax and ASTRAL-Pro 2 under gene tree uncertainty. Finally, AleRax can process multiple gene families in parallel thereby allowing users to compare competing phylogenetic hypotheses and estimate model parameters, such as DTL probabilities for genome-scale datasets with hundreds of taxa

Availability and Implementation

GNU GPL athttps://github.com/BenoitMorel/AleRaxand data are made available athttps://cme.h-its.org/exelixis/material/alerax_data.tar.gz.

Contact

Benoit.Morel@h-its.org

Supplementary information

Supplementary material is available.
Cue-specific neuronal ensembles span intermittent rate coding of working memory
Authors: Panichello Matthew F , Jonikaitis Donatas , Oh Jin , Zhu Shude , Trepka Ethan B , Moore Tirin
Published: October 2023

Persistent, memorandum-specific neuronal spiking activity has long been hypothesized to underlie working memory. However, emerging evidence suggests a possible role for ‘activity-silent’ synaptic mechanisms. This issue remains controversial because evidence for either view has largely depended on datasets that fail to capture single-trial population dynamics or on indirect measures of neuronal spiking. We addressed this by examining the dynamics of mnemonic information on single trials obtained from large, local populations of prefrontal neurons recorded simultaneously in monkeys performing a working memory task. We show that mnemonic information does not persist in the spiking activity of prefrontal neurons, but instead alternates between ‘On’ and ‘Off’ periods during memory delays. At the level of single neurons, Off periods are driven by a coordinated loss of selectivity for memoranda and a return of firing rates to baseline levels. Further exploiting the large-scale recordings, we asked whether the functional connectivity among large neuronal ensembles depended on information held in working memory. We show that mnemonic information is available in the pattern of ensemble connectivity during the memory delay in both On and Off periods of neuronal activity. Intermittent epochs of memoranda-specific spiking therefore coexist with activity-silent mechanisms to span memory delays.
The landscape of ancient human pathogens in Eurasia from the Stone Age to historical times
Authors: Sikora Martin , Canteri Elisabetta , Fernandez-Guerra Antonio , Oskolkov Nikolay , Ågren Rasmus , Hansson Lena , Irving-Pease Evan K. , Mühlemann Barbara , Nielsen Sofie Holtsmark , Scorrano Gabriele , Allentoft Morten E. , Seersholm Frederik Valeur , Schroeder Hannes , Gaunitz Charleen , Stenderup Jesper , Vinner Lasse , Jones Terry C. , Nystedt Bjørn , Parkhill Julian , Fugger Lars , Racimo Fernando , Kristiansen Kristian , Iversen Astrid K. N. , Willerslev Eske
Published: October 2023

Infectious diseases have had devastating impacts on human populations throughout history. Still, the origins and past dynamics of human pathogens remain poorly understood1. To create the first spatiotemporal map of diverse ancient human microorganisms and parasites, we screened shotgun sequencing data from 1,313 ancient human remains covering 35,000 years of Eurasian history for ancient DNA deriving from bacteria, viruses, and parasites. We demonstrate the widespread presence of ancient microbial DNA in human remains, identifying over 2,400 individual species hits in 896 samples. We report a wide range of pathogens detected for the first time in ancient human remains, including the food-borne pathogensYersinia enterocoliticaandShigellaspp., the animal-borneLeptospira interrogans, and the malaria-causing parasitePlasmodium vivax. Our findings extend the spatiotemporal range of previously described ancient pathogens such asYersinia pestis, the causative agent of plague,Hepatitis B virus, andBorrelia recurrentis, the cause of louse-borne relapsing fever (LBRF). For LRBF we increase the known distribution from a single medieval genome to 31 cases across Eurasia covering 5,000 years. Grouping the ancient microbial species according to their type of transmission (zoonotic, anthroponotic, sapronotic, opportunistic, and other), we find that most categories are identified throughout the entire sample period, while zoonotic pathogens, which are transmitted from living animals to humans or which have made a host jump into humans from animals in the timeframe of this study, are only detected from ∼6,500 years ago. The incidence of zoonotic pathogens increased in our samples some 1,000 years later before reaching the highest detection rates ∼5,000 years ago, and was associated with a human genetic ancestry component characteristic of pastoralist populations from the Eurasian Steppe. Our results provide the first direct evidence for an epidemiological transition to an increased burden of zoonotic infectious diseases following the domestication of animals2. However, they also reveal that the spread of these pathogens first becomes frequent thousands of years after increased animal-human contact, likely coinciding with the pastoralist migrations from the Eurasian Steppe3,4. This study provides the first spatiotemporal map of past human pathogens using genomic paleoepidemiology, and the first direct evidence for an epidemiological transition of increased zoonotic infectious disease burden after the onset of agriculture, through historical times.
Concurrent encoding of sequence predictability and event-evoked prediction error in unfolding auditory patterns
Authors: Hu Mingyue , Bianco Roberta , Rodriguez Hidalgo Antonio , Chait Maria
Published: October 2023

Human listeners possess an innate capacity to discern patterns within rapidly evolving auditory sequences. Core questions, at the forefront of ongoing research, focus on the mechanisms through which these representations are acquired and whether the brain prioritizes or suppresses predictable sensory signals.

Previous work, using fast sequences (tone-pips presented at a rate of 20Hz), revealed sustained response effects that appear to track the dynamic predictability of the sequence. Here we extend the investigation to slower sequences (4Hz), permitting the isolation of responses to individual tones. Stimuli were 50ms tone-pips, ordered into random (RND) and regular (REG; a repeating pattern of 10 frequencies) sequences; Two timing profiles were created: in ‘fast’ sequences tone-pips were presented in direct succession (20 Hz); in ‘slow’ sequences tone-pips were separated by a 200ms silent gap (4 Hz).

Naive participants (N=22; both sexes) passively listened to these sequences, while brain responses were recorded using magnetoencephalography (MEG). Results unveiled a heightened magnitude of sustained brain responses in REG when compared to RND patterns. This manifested from three tones after the onset of the pattern repetition, even in the context of slower sequences characterized by extended pattern durations (2500ms). This observation underscores the remarkable implicit sensitivity of the auditory brain to acoustic regularities. Importantly, brain responses evoked by single tones exhibited the opposite pattern - stronger responses to tones in RND compared to REG sequences. The demonstration of simultaneous but opposing sustained and evoked response effects reveals concurrent processes that shape the representation of unfolding auditory patterns.

Significance Statement

Humans excel at detecting predictable patterns within sound sequences, a process crucial for listening, language processing, and music appreciation. However, questions persist about the underlying neural mechanisms and the specific information monitored by the brain.

Our study addresses these questions by analysing magnetoencephalography (MEG) signals from participants exposed to predictable and unpredictable tone-pip patterns. We found that the MEG signal simultaneously captures two crucial aspects of predictability tracking.

Firstly, sustained MEG activity, tracking the sequence’s evolution, dynamically assesses pattern predictability, shedding light on how the brain evaluates reliability. Secondly, phasic MEG activity, reflecting responses to individual events, shows reduced activity to predictable tones, aligning with the idea that the brain efficiently encodes and anticipates upcoming events in predictable contexts.
PKCδ is an activator of neuronal mitochondrial metabolism that mediates the spacing effect on memory consolidation
Authors: Comyn Typhaine , Preat Thomas , Pavlowsky Alice , Plaçais Pierre-Yves
Published: October 2023

Relevance-based selectivity and high energy cost are two distinct features of long-term memory (LTM) formation that warrant its default inhibition. Spaced repetition of learning is a highly conserved cognitive mechanism that can lift this inhibition. Here, we questioned how the spacing effect integrates experience selection and energy efficiency at the cellular and molecular levels. We showed inDrosophilathat spaced training triggers LTM formation by extending over several hours an increased mitochondrial metabolic activity in neurons of the associative memory center, the mushroom bodies (MBs). We found that this effect is mediated by PKCδ, a member of the so-called ‘novel PKC’ family of enzymes, which uncovers the critical function of PKCδ in neurons as a regulator of mitochondrial metabolism for LTM. Additionally, PKCδ activation and translocation to mitochondria result from LTM-specific dopamine signaling on MB neurons. By bridging experience-dependent neuronal circuit activity with metabolic modulation of memory-encoding neurons, PKCδ signaling binds the cognitive and metabolic constraints underlying LTM formation into a unified gating mechanism.
From head to tail - Atomistic mechanism of long-range coupling from the cytosolic sensor domain to the selectivity filter in TREK K2Pchannels
Authors: Türkaydin Berke , Schewe Marcus , Riel Elena , Schulz Friederike , Biedermann Johann , Baukrowitz Thomas , Sun Han
Published: October 2023

The two-pore domain potassium (K2P) channels TREK-1 and TREK-2 link neuronal excitability to a variety of stimuli including mechanical force, lipids, temperature and phosphorylation. This regulation involves the C-terminus as a polymodal stimulus sensor and the selectivity filter (SF) as channel gate. Using crystallographic up- and down-state structures of TREK-2 as a template for full atomistic molecular dynamics simulations, we reveal that the SF in down-state undergoes inactivation via conformational changes at the S1 ion coordination site, while the up-state structure maintains a stable and conductive SF. This provides an atomistic understanding of the low channel activity previously assigned to the down state, but not evident from the crystal structure. Furthermore, by using (de-)phosphorylation mimics and chemically attaching lipid tethers to the proximal C-terminus (pCt), we confirm the hypothesis that moving the pCt towards the membrane induces the up-state. We also uncover two gating pathways by which movement of the pCt controls the stability (i.e. conductivity) of the filter gate. Together, these findings provide atomistic insights into the SF gating mechanism and the physiological regulation of TREK channels by phosphorylation.
METTL3/MYCN cooperation drives neural crest differentiation and provides therapeutic vulnerability in neuroblastoma
Authors: Thombare Ketan , Vaid Roshan , Pucci Perla , Mendez Akram , Burgos-Panadero Rebeca , Ayyalusamy Ritish , Rehan Aqsa Ali , Baig Mohammad Hassan , Nale Sagar Dattatraya , Bartenhagen Christoph , Dong Jae-June , Fischer Matthias , Turner Suzanne D. , Mondal Tanmoy
Published: October 2023

Neuroblastoma (NB) is the most common extracranial childhood cancer, caused by the improper differentiation of developing trunk neural crest cells (tNCC) in the sympathetic nervous system. TheN6-methyladenosine (m6A) epitranscriptomic modification controls post-transcriptional gene expression but the mechanism by which the m6A methyltransferase complex METTL3/METTL14/WTAP is recruited to specific loci remains to be fully characterized. We explored whether the m6A epitranscriptome could fine-tune gene regulation in migrating/differentiating tNCC. We demonstrate that the m6A modification regulates the expression ofHOXgenes in tNCC, thereby contributing to their timely differentiation into sympathetic neurons. Furthermore, we show that posteriorHOXgenes are m6A modified in MYCN-amplified NB with reduced expression. In addition, we provide evidence that sustained overexpression of the MYCN oncogene in tNCC drives METTL3 recruitment to a specific subset of genes including posteriorHOXgenes creating an undifferentiated state. Moreover, METTL3 depletion/inhibition induces DNA damage and differentiation of MYCN overexpressing cells and increases vulnerability to chemotherapeutic drugs in MYCN-amplified patient-derived xenografts (PDX) cells, suggesting METTL3 inhibition could be a potential therapeutic approach for NB.
Spatial transcriptomics in the adultDrosophilabrain and body
Authors: Janssens Jasper , Mangeol Pierre , Hecker Nikolai , Partel Gabriele , Spanier Katina , Ismail Joy , Hulselmans Gert , Aerts Stein , Schnorrer Frank
Published: October 2023

Recently, we have achieved a significant milestone with the creation of the Fly Cell Atlas. This single-nuclei atlas encompasses the entire fly, covering the entire head and body, in addition to all major organs. This atlas catalogs many hundreds of cell types, of which we annotated 250. Thus, a large number of clusters remain to be fully characterized, in particular in the brain. Furthermore, by applying single-nuclei sequencing, all information about the spatial location of the cells in the body and of about possible subcellular localization of the mRNAs within these cells is lost. Spatial transcriptomics promises to tackle these issues. In a proof-of-concept study, we have here applied spatial transcriptomics using a selected gene panel to pinpoint the locations of 150 mRNA species in the adult fly. This enabled us to map unknown clusters identified in the Fly Cell Atlas to their spatial locations in the fly brain. Additionally, spatial transcriptomics discovered interesting principles of mRNA localization and transcriptional diversity within the large and crowded muscle cells that may spark future mechanistic investigations. Furthermore, we present a set of computational tools that will allow for easier integration of spatial transcriptomics and single-cell datasets.
NEDD4-binding protein 1 suppresses HBV replication by degrading HBV RNAs
Authors: Kobayashi Nobuhiro , Suzuki Saori , Sakamoto Yuki , Suzuki Rigel , Mori Kento , Kosugi Yume , Liang Lihan , Saito Tomoya , Izumi Takuma , Noda Kisho , Okuzaki Daisuke , Kanegae Yumi , Hayashi Sanae , Tanaka Yasuhito , Matsuura Yoshiharu , Takeuchi Osamu , Tamura Tomokazu , Taketomi Akinobu , Fukuhara Takasuke
Published: October 2023

Chronic infection with hepatitis B virus (HBV) places patients at increased risk for liver cirrhosis and hepatocellular carcinoma. Although nucleos(t)ide analogs are mainly used for the treatment of HBV, they require long-term administration and may lead to the emergence of drug resistant mutants. Therefore, to identify targets for the development of novel anti-HBV drugs, we screened for HBV-suppressive host factors using a plasmid expression library of RNA-binding proteins (RBPs). We screened 132 RBPs using an expression plasmid library by measuring HBV relaxed circular DNA (rcDNA) levels in hepatocellular carcinoma. Our screen identified NEDD4-binding protein 1 (N4BP1) as having an anti-HBV effect. In hepatocellular carcinoma cell lines transfected or infected with HBV, overexpression of N4BP1 decreased rcDNA levels while knockdown or knockout of the gene encoding N4BP1 rescued rcDNA levels. N4BP1 possesses the KH-like and RNase domains and both were required for the anti-HBV effect of N4BP1. Additionally, we measured levels of HBV pregenomic RNA (pgRNA) and covalently closed circular DNA (cccDNA) in the RBP-transfected cells and confirmed that N4BP1 binds pgRNA directly and degraded both the 3.5 kb and 2.4/2.1 kb HBV RNA. In summary, N4BP1 is a newly identified host factor able to counteract HBV production by promoting the degradation of 3.5 kb and 2.1/2.4 kb HBV RNA.

Importance

There is still a large number of HBV-infected people in the world today because of no curative treatment for HBV infection. In this study, we focused on and screened RNA-binding proteins to identify new host factors which inhibit HBV replication. As a result, we found that NEDD4-binding protein 1 (N4BP1) expression suppresses rcDNA production by promoting the degradation of pregenomic RNA, 2.4kb and 2.1kb HBV RNA. Furthermore, KH-like domain or RNase domain of N4BP1 were involved in this anti-HBV effect. In addition, the N4BP1 levels were lower in HCC resection samples of exacerbated patients, suggesting that individual N4BP1 levels might be related to HCC progression. This novel factor can potentially become a key to new HBV treatments.
Structural insights into the FtsEX-EnvC complex regulation on septal peptidoglycan hydrolysis in Vibrio cholerae
Authors: Hao Aili , Suo Yang , Lee Seok-Yong
Published: October 2023

During bacterial cell division, hydrolysis of septal peptidoglycan (sPG) is crucial for cell separation. This sPG hydrolysis is performed by the enzyme amidases whose activity is regulated by the integral membrane protein complex FtsEX-EnvC. FtsEX is an ATP-binding cassette transporter and EnvC is a long coiled-coiled protein that interacts with and activates the amidases. The molecular mechanism by which the FtsEX-EnvC complex activates amidases remains largely unclear. We present the cryo-electron microscopy structure of the FtsEX-EnvC complex from the pathogenic bacteriaV. cholerae(FtsEX-EnvCVC). FtsEX-EnvCVCin the presence of ADP adopts a distinct conformation where EnvC is “horizontally extended” rather than “vertically extended”. Subsequent structural studies suggest that EnvC can swing between these conformations in space in a nucleotide-dependent manner. Our structural analysis and functional studies suggest that FtsEX-EnvCvc may employ spatial control of EnvC for amidase activation, suggesting species-specific diversity in the FtsEX-EnvC regulation on septal peptidoglycan hydrolysis.
METI: Deep profiling of tumor ecosystems by integrating cell morphology and spatial transcriptomics
Authors: Jiang Jiahui , Liu Yunhe , Qin Jiangjiang , Wu Jingjing , Chen Jianfeng , Pizzi Melissa P. , Segura Rossana L. , Yamashita Kohei , Xu Zhiyuan , Pei Guangsheng , Cho Kyung Serk , Chu Yanshuo , Sinjab Ansam F. , Peng Fuduan , Han Guangchun , Wang Ruiping , Yan Xinmiao , Dai Enyu , Dai Yibo , Li Mingyao , Futreal Andrew , Maitra Anirban , Lazar Alexander , Cheng Xiangdong , Kadara Humam , Ajani Jaffer , Jazaeri Amir A. , Gao Jianjun , Hu Jian , Wang Linghua
Published: October 2023

The recent advance of spatial transcriptomics (ST) technique provides valuable insights into the organization and interactions of cells within the tumor microenvironment (TME). While various analytical tools have been developed for tasks such as spatial clustering, spatially variable gene identification, and cell type deconvolution, most of them are general methods lacking consideration of histological features in spatial data analysis. This limitation results in reduced performance and interpretability of their results when studying the TME. Here, we present a computational framework named,Morphology-Enhanced SpatialTranscriptome Analysis Integrator (METI) to address this gap. METI is an end-to-end framework capable of spatial mapping of both cancer cells and various TME cell components, robust stratification of cell type and transcriptional states, and cell co-localization analysis. By integrating both spatial transcriptomics, cell morphology and curated gene signatures, METI enhances our understanding of the molecular landscape and cellular interactions within the tissue, facilitating detailed investigations of the TME and its functional implications. The performance of METI has been evaluated on ST data generated from various tumor tissues, including gastric, lung, and bladder cancers, as well as premalignant tissues. Across all these tissues and conditions, METI has demonstrated robust performance with consistency.
Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational controlin vivo
Authors: Gaikwad Swati , Ghobakhlou Fardin , Zhang Hongen , Hinnebusch Alan G.
Published: October 2023

Initiating translation of most eukaryotic mRNAs depends on recruitment of methionyl initiator tRNA (Met-tRNAi) in a ternary complex (TC) with GTP-bound eukaryotic initiation factor 2 (eIF2) to the small (40S) ribosomal subunit, forming a 43S preinitiation complex (PIC) that attaches to the mRNA and scans the 5’-untranslated region (5’ UTR) for an AUG start codon. Previous studies have implicated mammalian eIF2A in GTP-independent binding of Met-tRNAi to the 40S subunit and its recruitment to specialized mRNAs that do not require scanning, and in initiation at non-AUG start codons, when eIF2 function is attenuated by phosphorylation of its α-subunit during stress. The role of eIF2A in translationin vivois poorly understood however, and it was unknown whether the conserved ortholog in budding yeast can functionally substitute for eIF2. We performed ribosome profiling of a yeast deletion mutant lacking eIF2A and isogenic wild-type (WT) cells in the presence or absence of eIF2α phosphorylation induced by starvation for amino acids isoleucine and valine. Whereas starvation of WT confers changes in translational efficiencies (TEs) of hundreds of mRNAs, theeIF2AΔmutation conferred no significant TE reductions for any mRNAs in non-starved cells, and it reduced the TEs of only a small number of transcripts in starved cells containing phosphorylated eIF2α. We found no evidence that eliminating eIF2A altered the translation of mRNAs containing putative IRES elements, or harboring uORFs initiated by AUG or near-cognate start codons, in non-starved or starved cells. Thus, very few mRNAs (possibly only one) appear to employ eIF2A for Met-tRNAi recruitment in yeast cells, even when eIF2 function is attenuated by stress.
LRP1 Triggers Pro-inflammatory Cell-signaling in Response to Extracellular Tau Independently of the NMDA Receptor
Authors: Azmoon Pardis , Mantuano Elisabetta , Poudel Binita , Zampieri Carlotta , Gonias Steven L.
Published: October 2023

In Alzheimer’s Disease (AD) and other neurodegenerative diseases, microtubule-associated protein Tau forms abnormal intracellular aggregates. The mechanisms by which Tau may promote AD progression remain incompletely understood. Injured and dying neurons release Tau into the extracellular spaces in the CNS. The released Tau may be taken up by receptors in the LDL Receptor gene family, including Low Density Lipoprotein Receptor-related Protein-1 (LRP1), which is expressed by microglia, astrocytes, and neurons. This process may be important for clearing Tau from extracellular spaces but may also promote the seeding of Tau aggregates in new cells. Our laboratory has shown that endocytosis of LRP1 ligands is coupled to the activation of cell-signaling and regulation of inflammation. Notably, different LRP1 ligands can induce either pro-inflammatory or anti-inflammatory responses, depending on the co-receptors that function with LRP1. Here, we demonstrate that in cultured macrophages, microglia, and astrocytes, extracellular Tau induces an LRP1-dependent pro-inflammatory response, characterized by NFκB activation and expression of pro-inflammatory cytokines. Unlike other LRP1 ligands that elicit anti-inflammatory responses, the response to Tau occurs independently of the NMDA receptor. When LRP1 is deleted or silenced, macrophages, microglia, and astrocytes do not respond to Tau, whereas whenGrin1is deleted or the NMDA-R is pharmacologically inhibited, the responses remain unchanged. Because we have evidence that LRP1 in microglia expresses anti-inflammatory activity in response to ligands other than Tau, understanding the role of LRP1 in microglia and astrocytesin vivoin Alzheimer’s Disease and other neuroinflammatory processes is an important future goal.

SIGNIFICANCE STATEMENT

In Alzheimer’s Disease and other neurodegenerative diseases, microtubule-associated protein Tau forms abnormal intracellular aggregates that contribute to disease progression. When released extracellularly, Tau binds to the transmembrane receptor LRP1, expressed by diverse cells in the CNS. LRP1 has the unique ability to couple ligand uptake with activation of cell-signaling. We demonstrated that Tau binding to LRP1 activates pro-inflammatory responses in macrophages, microglia, and astrocytes, characterized by NFκB activation and cytokine release. This signaling occurs independently of the NMDA receptor, which distinguishes Tau from other LRP1 ligands. These results define a novel pathway by which extracellular Tau regulates neuroinflammation in Alzheimer’s Disease, providing new therapeutic opportunities that target LRP1 without interfering with NMDA-R functions.
A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism inSaccharomyces cerevisiae
Authors: Bowles Isobel E. , Jackman Jane E.
Published: October 2023

InSaccharomyces cerevisiaea single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed byS. cerevisiaeTrm10 plays a biologically important role for one of these tRNA substrates, tRNATrp. Overexpression of tRNATrp(and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of thetrm10Δstrain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrpis depleted intrm10Δcells, and its levels are further decreased upon growth in 5FU, while another Trm10 substrate (tRNAGly) is not affected under these conditions. Thus, m1G9 inS. cerevisiaeis another example of a tRNA modification that is present on multiple tRNAs but is only essential for the biological function of one of those species. In addition to the effects of m1G9 on mature tRNATrp, precursor tRNATrpspecies accumulate in the same strains, an effect that is due to at least two distinct mechanisms. The levels of mature tRNATrpare rescued in thetrm10Δmet22Δstrain, consistent with the known role of Met22 in tRNA quality control, where deletion ofmet22causes inhibition of 5’-3’ exonucleases that catalyze tRNA decay. However, none of the known Met22-associated exonucleases appear to be responsible for decay of hypomodified tRNATrp, based on inability of mutants of each enzyme to rescue growth of thetrm10Δstrain in the presence of 5FU. Thus, the surveillance of tRNATrpappears to constitute a distinct tRNA quality control pathway inS. cerevisiae.
Clinical Decision Support Systems implementation in Africa: a systemic review
Authors: Nortey Jacob Nii Noye , Takyi Kate , Adabo Andrew , Suleiman Rashida
Published: October 2023

The healthcare system in Africa is characterized by the lack of trained clinicians, resources, brain drain and quality care processes. To mitigate these challenges, some African countries have resorted to the use of health information technologies such as the Clinical Decision Support System (CDSS). Globally, CDSS implementations in the health sector have been reported to have reduced medical error, increased hospital accessibility and standard of care. Studies on the number of implemented CDSS in Africa were found to be limited since only a few are available. Despite this setback, the few implemented CDSSs are effective, efficient, and reliable in the diagnosis of diseases. In order to fully ascertain the impact of CDSS implementation in African counties, we evaluated the documented CDSS programs that are in operation. An extensive search was performed on Google Scholar, PubMed, and SCOPUS. About 38 (thirty-eight) publications were identified, of which some met the inclusion criteria. Limited implementation of CDSS was observed in the African countries. The review showed promising impacts of CDSS in African healthcare centers especially in the diagnose and treatment of pediatric and maternal related disease.
An axonemal intron splicing program sustainsPlasmodiummale development
Authors: Guan Jiepeng , Wu Peijia , Mo Xiaoli , Zhang Xiaolong , Liang Wenqi , Zhang Xiaoming , Jiang Lubing , Li Jian , Cui Huiting , Yuan Jing
Published: October 2023

Differentiation of male gametocyte into flagellated fertile male gamete relies on the axoneme assembly, a major component of male development for mosquito transmission of malaria parasite. RNA-binding protein (RBP)-mediated post-transcription regulation plays important roles in eukaryotic sexual development, including thePlasmodiumfemale development. However, the role of RBP in defining thePlasmodiummale transcriptome and its function in the male gametogenesis remain elusive. Here, we screened the gender expression of the genome-wide RBPs and identified an undescribed male-specific RBP geneRbpm1in thePlasmodium. RBPm1 is localized in the nucleus of male gametocytes. RBPm1-deficient parasites fail to assemble the axoneme for male gametogenesis and thus mosquito transmission. RBPm1 interacts with spliceosome E complex and regulates splicing initiation of certain introns in a group of 26 axonemal genes. RBPm1 deficiency results in intron retention and protein loss of these axonemal genes. Intron deletion restores axonemal proteins expression and partially rectifies axonemal defects in RBPm1-null gametocytes. Further splicing assays in both reporter and endogenous genes exhibit stringent recognition of the axonemal introns by RBPm1. Therefore, the splicing activator RBPm1 and its target introns constitute an axonemal intron splicing program in the post-transcription regulation essential forPlasmodiummale development.
Biomolecular condensates form spatially inhomogeneous network fluids
Authors: Dar Furqan , Cohen Samuel R. , Mitrea Diana M. , Phillips Aaron H. , Nagy Gergely , Leite Wellington C. , Stanley Christopher B. , Choi Jeong-Mo , Kriwacki Richard W. , Pappu Rohit V.
Published: October 2023

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.
The cytoplasmic phosphate level has a central regulatory role in the phosphate starvation response ofCaulobacter crescentus
Authors: Billini Maria , Hoffmann Tamara , Kühn Juliane , Bremer Erhard , Thanbichler Martin
Published: October 2023

In bacteria, the availability of environmental inorganic phosphate is typically sensed by the conserved PhoR-PhoB two-component signal transduction pathway, which is thought to use the flux through the PstSCAB phosphate transporter as a readout of the extracellular phosphate level to control phosphate-responsive genes. While the sensing of environmental phosphate is well-investigated, the regulatory effects of cytoplasmic phosphate are unclear. Here, we disentangle the physiological and transcriptional responses ofCaulobacter crescentusto changes in the environmental and cytoplasmic phosphate levels by uncoupling phosphate uptake from the activity of the PstSCAB system, using an additional, heterologously produced phosphate transporter. This approach reveals a two-pronged response ofC. crescentusto phosphate limitation, in which PhoR-PhoB signaling mostly facilitates the utilization of alternative phosphate sources, whereas the cytoplasmic phosphate level controls the morphological and physiological adaptation of cells to growth under global phosphate limitation. These findings open the door to a comprehensive understanding of phosphate signaling in bacteria.
The serine/threonine kinase CcAkt regulates the fertility ofCoridius chinensis
Authors: Feng Jinyu , Du Juan , Li Shangwei , Chen Xingxing
Published: October 2023

Akt (also known as protein kinase B) belongs to the multifunctional serine/threonine kinase family and is an important component of the insulin signaling pathway that plays a key role in many biological processes such as cell growth, proliferation, and survival. However, few studies have reported the effect of Akt on reproduction in Hemiptera. In this study, we cloned and characterized theAktgene fromCoridius chinensis(CcAkt). The open reading frame ofCcAkthas a length of 1,563 bp and encodes 520 amino acids. It has a conserved pleckstrin homology domain, a serine/threonine protein kinase catalytic domain, and a serine/threonine protein kinase domain. Phylogenetic analysis showed thatCcAktandHhAktofHalyomorpha halyshad the highest similarity. Analysis of temporal and spatial expression patterns revealed thatCcAktis expressed throughout development and in various tissues ofC. chinensisadults.CcAktexpression was high in female adult and the fourth instar nymph stage ofC. chinensis. InC. chinensisadult,CcAktexpression was highest in the testis and ovary. Injection of bovine insulin inducedCcAktexpression, whereas that of 20-hydroxyecdysone significantly reducedCcAktexpression. Both hormones, however, induced the expression ofvitellogenin(Vg) andvitellogenin receptor(VgR). In unmated females,CcAktknockout resulted in decreased expression ofCcVgandCcVgR, stunted the development of the ovarioles, decreased the number of eggs and hatching rate. These findings suggest that CcAkt may be involved in regulating the reproduction ofC. chinensis.
Optimizing Cryo-EM Structural Analysis of Gi-coupling Receptors via Engineered Gtand Nb35 Application
Authors: Oshima Hidetaka S. , Sano Fumiya K. , Akasaka Hiroaki , Iwama Aika , Shihoya Wataru , Nureki Osamu
Published: October 2023

Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in the case of GPCR-Gicomplexes, scFv16, an antibody that recognizes the intricate interface of the complex, has been mainly implemented to stabilize the complex. However, owing to their flexibility and heterogeneity, structural determinations of GPCR-Gicomplexes remain both challenging and resource-intensive. By employing eGαt, which exhibits binding affinity to modified nanobody Nb35, the cryo-EM structure of Rhodopsin-eGαtcomplex was previously reported. Using this modified G protein, we determined the structure of the ETB-eGtcomplex bound to the modified Nb35. The determined structure of ETBreceptor was the same as the previously reported ETB-Gicomplex, and the resulting dataset demonstrated significantly improved anisotropy. This modified G protein will be utilized for the structural determination of other GPCR-Gicomplexes.

Highlights

The study introduces the engineered G protein subunit eGαT, which enhances the resolution of GPCR-G protein structures by suppressing G protein conformational fluctuations and is particularly beneficial for Gi-coupled receptors.

The cryo-EM structure of the ETBreceptor complexed with eGt-Nb35 reveals improved map quality, reduced anisotropy, and isotropic density distribution, increasing the accuracy of structural analysis.

Structural comparison between ETB-Giand ETB-eGtreveals similar receptor-G protein interactions, demonstrating the utility of eGt-Nb35 for studying GPCR-Gicomplexes and the potential for broader applications within the Gifamily.
Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription
Authors: Lu Feiyue , Park Brandon J. , Fujiwara Rina , Wilusz Jeremy E. , Gilmour David S. , Lehmann Ruth , Lionnet Timothée
Published: October 2023

Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in regions of high local concentration known as clusters, which are thought to facilitate transcription. Using the histone locus ofDrosophilanurse cells as a model, we find that Pol II forms long-lived, transcriptionally poised clusters distinct from liquid droplets, which contain unbound and paused Pol II. Depletion of the Integrator complex endonuclease module, but not its phosphatase module or Pol II pausing factors disperses these Pol II clusters. Consequently, histone transcription fails to reach peak levels during S-phase and aberrantly continues throughout the cell cycle. We propose that Pol II clustering is a regulatory step occurring near promoters that limits rapid gene activation to defined times.

One Sentence Summary

Using theDrosophilahistone locus as a model, we show that clustered RNA polymerase II is poised for synchronous activation.
Digital gait measures capture 1-year progression in early-stage spinocerebellar ataxia type 2
Authors: Seemann Jens , Daghsen Lina , Cazier Mathieu , Lamy Jean-Charles , Welter Marie-Laure , Giese Martin A. , Synofzik Matthis , Durr Alexandra , Ilg Winfried , Coarelli Giulia
Published: October 2023

BACKGROUND

With disease-modifying drugs in reach for cerebellar ataxias, fine-grained digital health measures are highly warranted to complement clinical and patient-reported outcome measures in upcoming treatment trials and treatment monitoring. These measures need to demonstrate sensitivity to capture change, in particular in the early stages of the disease.

OBJECTIVE

To unravel gait measures sensitive to longitudinal change in the - particularly trial-relevant- early stage of spinocerebellar ataxia type 2 (SCA2).

METHODS

Multi-center longitudinal study with combined cross-sectional and 1-year interval longitudinal analysis in early-stage SCA2 participants (n=23, including 9 pre-ataxic expansion carriers; medianATXN2CAG repeat expansion 38±2; median SARA [Scale for the Assessment and Rating of Ataxia] score 4.83±4.31). Gait was assessed using three wearable motion sensors during a 2-minute walk, with analyses focusing on gait measures of spatiotemporal variability shown sensitive to ataxia severity, e.g. lateral step deviation.

RESULTS

We found significant changes for gait measures between baseline and 1-year follow-up with large effect sizes (lateral step deviation p=0.0001, effect size rprb=0.78), whereas the SARA score showed no change (p=0.67). Sample size estimation indicates a required cohort size of n=43 to detect a 50% reduction in natural progression. Test-retest reliability and Minimal Detectable Change analysis confirm the accuracy of detecting 50% of the identified 1-year change.

CONCLUSIONS

Gait measures assessed by wearable sensors can capture natural progression in early-stage SCA2 within just one year – in contrast to a clinical ataxia outcome. Lateral step deviation thus represents a promising outcome measure for upcoming multi-centre interventional trials, particularly in the early stages of cerebellar ataxia.
Identifying representational structure in CA1 to benchmark theoretical models of cognitive mapping
Authors: Lee J. Quinn , Keinath Alexandra T. , Cianfarano Erica , Brandon Mark P.
Published: October 2023

Decades of theoretical and empirical work have suggested the hippocampus instantiates some form of a cognitive map. Yet, tests of competing theories have been limited in scope and largely qualitative in nature. Here, we develop a novel framework to benchmark model predictions against observed neuronal population dynamics as animals navigate a series of geometrically distinct environments. In this task space, we show a representational structure in the dynamics of hippocampal remapping that generalizes across brains, discriminates between competing theoretical models, and effectively constrains biologically viable model parameters. With this approach, we find that accurate models capture the correspondence in spatial coding of a changing environment. The present dataset and framework thus serve to empirically evaluate and advance theories of cognitive mapping in the brain.