bluuebunny/crossref_metadata_2025 huggingface dataset:
A metabolic-dysfunction associated steatotic liver acinus biomimetic induces pancreatic islet dysfunction in a coupled microphysiology system
Authors: Aleman Julio , Ravikumar K , Wiegand Connor , Schurdak Mark E. , Vernetti Lawrence , Gavlock Dillon , Reese Celeste , DeBiasio Richard , LaRocca Greg , Angarita Yulder Daniel , Gough Albert , Soto-Gutierrez Alejandro , Behari Jaideep , Yechoor Vijay , Miedel Mark T. , Stern Andrew M. , Banerjee Ipsita , Taylor D. Lansing
Published: April 2024

Preclinical and clinical studies suggest that lipid-induced hepatic insulin resistance is a primary defect that predisposes to dysfunction in pancreatic islets, implicating a perturbed liver-pancreas axis underlying the comorbidity of T2DM and MASLD. To investigate this hypothesis, we developed a human biomimetic microphysiological system (MPS) coupling our vascularized liver acinus MPS (vLAMPS) with primary islets on a chip (PANIS) enabling MASLD progression and islet dysfunction to be quantitatively assessed. The modular design of this system (vLAMPS-PANIS) allows intra-organ and inter-organ dysregulation to be deconvoluted. When compared to normal fasting (NF) conditions, under early metabolic syndrome (EMS) conditions, the standalone vLAMPS exhibited characteristics of early stage MASLD, while no significant differences were observed in the standalone PANIS. In contrast, with EMS, the coupled vLAMPS-PANIS exhibited a perturbed islet-specific secretome and a significantly dysregulated glucose stimulated insulin secretion (GSIS) response implicating direct signaling from the dysregulated liver acinus to the islets. Correlations between several pairs of a vLAMPS-derived and a PANIS-derived secreted factors were significantly altered under EMS, as compared to NF conditions, mechanistically connecting MASLD and T2DM associated hepatic factors with islet-derived GLP-1 synthesis and regulation. Since vLAMPS-PANIS is compatible with patient–specific iPSCs, this platform represents an important step towards addressing patient heterogeneity, identifying complex disease mechanisms, and advancing precision medicine.
FREDDIE: A comprehensive tool for detecting exonization of retrotransposable elements in short and long RNA sequencing data
Authors: Mercuri Rafael L. V. , Miller Thiago L. A. , dos Santos Filipe F. , de Lima Matheus F. , Rangel-Pozzo Aline , Galante Pedro A. F.
Published: April 2024

Background

Transposable elements (TEs) constitute a significant portion of mammalian genomes, accounting for about 50% of the total DNA. Intragenic TEs are of particular interest as they are co-transcribed with their host genes in pre-mRNA, potentially leading to the formation of novel chimeric transcripts and the exonization of TEs. The abundance of RNA sequencing data currently available offers a unique opportunity to explore transcriptomic variations. However, a significant limitation is the capability of existing computational tools. Here, we introduce FREDDIE, an innovative algorithm designed to detect the exonization of retrotransposable elements using RNA-seq data. FREDDIE can process short and long RNA sequencing data, assemble and quantify transcripts, evaluate coding potential, and identify protein domains in chimeric transcripts involving exonized TEs and retrocopies.

Results

To demonstrate the efficacy of FREDDIE, we analyzed and validated TE exonization in two human cancer cell lines, K562 and U251. We have identified 322 chimeric transcripts, of which 126 were from K562, and 196 were from U251. Among these chimeric transcripts, there were 35 that showed similar exonization patterns and host genes. These transcripts involve protein-coding genes of the host and exonization of LINE-1 (L1), Alu elements, and retrocopies of coding genes. We have selected some candidates and validated them experimentally through RT-PCR. The validation rate for these candidates was 70%, later confirmed by long-read sequencing.

Additionally, we applied FREDDIE to analyze TE exonization across 157 glioblastoma samples, identifying 1,010 chimeric transcripts. The majority of these transcripts involved the exonization of Alu elements (69.8%), followed by L1 (20.6%) and retrocopies (9.6%). Notably, we discovered a highly expressed L1 exonization within the ROS gene, resulting in a truncated open reading frame (ORF) with the deletion of two protein domains.

Conclusions

FREDDIE is an efficient and user-friendly tool for identifying chimeric transcripts that involve exonization of intragenic TEs. Overall, FREDDIE enables comprehensive investigations into the contributions of TEs to transcriptome evolution, variation, and disease-associated abnormalities, and it operates effectively on standard computing systems.

FREDDIE is publicly available:https://github.com/galantelab/freddie
A flexible intracortical brain-computer interface for typing using finger movements
Authors: Shah Nishal P. , Willsey Matthew S. , Hahn Nick , Kamdar Foram , Avansino Donald T. , Fan Chaofei , Hochberg Leigh R. , Willett Francis R. , Henderson Jaimie M.
Published: April 2024

Keyboard typing with finger movements is a versatile digital interface for users with diverse skills, needs, and preferences. Currently, such an interface does not exist for people with paralysis. We developed an intracortical brain-computer interface (BCI) for typing with attempted flexion/extension movements of three finger groups on the right hand, or both hands, and demonstrated its flexibility in two dominant typing paradigms. The first paradigm is “point-and-click” typing, where a BCI user selects one key at a time using continuous real-time control, allowing selection of arbitrary sequences of symbols. During cued character selection with this paradigm, a human research participant with paralysis achieved 30-40 selections per minute with nearly 90% accuracy. The second paradigm is “keystroke” typing, where the BCI user selects each character by a discrete movement without real-time feedback, often giving a faster speed for natural language sentences. With 90 cued characters per minute, decoding attempted finger movements and correcting errors using a language model resulted in more than 90% accuracy. Notably, both paradigms matched the state-of-the-art for BCI performance and enabled further flexibility by the simultaneous selection of multiple characters as well as efficient decoder estimation across paradigms. Overall, the high-performance interface is a step towards the wider accessibility of BCI technology by addressing unmet user needs for flexibility.
Epigenetic cross-talk between Sirt1 and Dnmt1 promotes axonal regeneration after spinal cord injury in zebrafish
Authors: Gupta Samudra , Hui Subhra Prakash
Published: April 2024

Though spinal cord injury (SCI) causes irreversible sensory and motor impairments in human, adult zebrafish retain the potent regenerative capacity by injury-induced proliferation of central nervous system (CNS)-resident progenitor cells to develop new functional neurons at the lesion site. The hallmark of SCI in zebrafish lies in a series of changes in the epigenetic landscape, specifically DNA methylation and histone modifications. Decoding the post-SCI epigenetic modifications is therefore critical for the development of therapeutic remedies that boost SCI recovery process. Here, we have studied on Sirtuin1 (Sirt1), a non-classical histone deacetylase that potentially play a critical role in neural progenitor cells (NPCs) proliferation and axonal regrowth following SCI in zebrafish. We investigated the role of Sirt1 in NPC proliferation and axonal regrowth in response to injury in the regenerating spinal cord and found that Sirt1 is involved in the induction of NPC proliferation along with glial bridging during spinal cord regeneration. We also demonstrate that Sirt1 plays a pivotal role in regulating the HIPPO pathway through deacetylation-mediated inactivation of Dnmt1 and subsequent hypomethylation ofyap1promoter, leading to the induction ofctgfaexpression, which drives the NPC proliferation and axonal regrowth to complete the regenerative process. In conclusion, our study reveals a novel cross-talk between two important epigenetic effectors, Sirt1 and Dnmt1, in the context of spinal cord regeneration, establishing a previously undisclosed relation between Sirt1 and Yap1 which provides a deeper understanding of the underlying mechanisms governing injury-induced NPC proliferation and axonal regrowth. Therefore, we have identified Sirt1 as a novel, major epigenetic regulator of spinal cord regeneration by modulating the HIPPO pathway in zebrafish.
Comparative Analysis of Machine Learning Algorithms for Breast Cancer Classification: SVM Outperforms XGBoost, CNN, RNN, and Others
Authors: Ghosh Prithwish , Chatterjee Debashis
Published: April 2024

This study evaluates ten machine learning algorithms for classifying breast cancer cases as malignant or benign based on physical attributes. Algorithms tested include XGBoost, CNN, RNN, AdaBoost, Adaptive Decision Learner, fLSTM, GRU, Random Forest, SVM, and Logistic Regression. Using a robust dataset from UCI machine learning Breast Cancer, SVM emerged as the most accurate, achieving 98.2456% accuracy. While AdaBoost, Logistic Regression, Neural Networks, and Random Forest showed promise, none matched SVM’s accuracy. These findings underscore the potential of machine learning, particularly SVMs, in cancer diagnosis and treatment by analyzing physical attributes for improved diagnostics and targeted therapies.
Autophosphorylation of the Tousled-like kinases TLK1 and TLK2 regulates recruitment to damaged chromatin via PCNA interaction
Authors: West Kirk L. , Kreiling Natasha , Raney Kevin D. , Ghosal Gargi , Leung Justin W
Published: April 2024

Tousled-like kinases 1 and 2 (TLK1 and 2) are cell cycle-regulated serine/threonine kinases that are involved in multiple biological processes. Mutation of TLK1 and 2 confer neurodegenerative diseases. Recent studies demonstrate that TLK1 and 2 are involved in DNA repair. However, there is no direct evidence that TLK1 and 2 function at DNA damage sites. Here, we show that both TLK1 and TLK2 are hyper-autophosphorylated at their N-termini, at least in part, mediated by their homo-or hetero-dimerization. We found that TLK1 and 2 hyper-autophosphorylation suppresses their recruitment to damaged chromatin. Furthermore, both TLK1 and 2 associate with PCNA specifically through their evolutionarily conserved non-canonical PCNA-interacting protein (PIP) box at the N-terminus, and mutation of the PIP-box abolishes their recruitment to DNA damage sites. Mechanistically, the TLK1 and 2 hyper-autophosphorylation masks the PIP-box and negatively regulates their recruitment to the DNA damage site. Overall, our study dissects the detailed genetic regulation of TLK1 and 2 at damaged chromatin, which provides important insights into their emerging roles in DNA repair.
Radiation resistance in cervical cancer: An insight on mitochondrial associated membranes and its related proteins
Authors: Lakshminarasimhan Harini , Santhoshkumar Rashmi , Srivastava Sweta
Published: April 2024

Radiation therapy proves ineffective against radiation-resistant cancers, exacerbating the disease. The Mitochondrial Associated Membrane (MAM) forms through the tethering of the endoplasmic reticulum to the mitochondrial membrane. Under stress conditions such as radiation, mitochondrial function becomes impaired, prompting the recruitment of endoplasmic reticulum proteins for cell survival. Therefore, understanding the role of ER and mitochondria interactions is crucial for the development of inhibitors or drugs to sensitize cancer cells to radiation. In this study, we focused on ultrastructural alterations in radiation-resistant cells. The main structural changes observed included mitochondrial elongation, mitophagy, the presence of lipid droplets, and shortened ER segments. While MAM formation (the interaction between the ER and mitochondria) was observed in SiHa cells not exposed to radiation, it was disrupted in radiation-resistant cells. We analysed genes associated with mitochondrial elongation, mitophagy, lipid droplet formation, short ER fragments, and ER stress using a dataset from cervical cancer patients in The Cancer Genome Atlas (TCGA). Our analyses suggest that BNIP3L is implicated in therapy failure and tumour recurrence. In future, inhibiting BNIP3L could potentially sensitize resistant cells to radiation therapy.
Neural circuit basis of adolescent THC-induced potentiation of opioid responses later in life
Authors: Hubbard Elizabeth , Galinato Vivienne Mae , Derdeyn Pieter , Bartas Katrina , Mahler Stephen V. , Beier Kevin T.
Published: April 2024

Use of one drug of abuse typically influences the behavioral response to other drugs, either administered at the same time or a subsequent time point. The nature of the drugs being used, as well as the timing and dosing, also influence how these drugs interact. Here, we tested the effects of adolescent THC exposure on the development of morphine-induced behavioral adaptations following repeated morphine exposure during adulthood. We found that adolescent THC administration potentiated reward, and paradoxically impaired the development of morphine reward. Following a forced abstinence period, we then mapped the whole-brain response to a moderate dose of morphine, and found that adolescent THC administration led to increased morphine-induced activity in the basal ganglia and increased functional connectivity between frontal cortical regions and the ventral tegmental area. Last, we show using rabies virus-based circuit mapping that adolescent THC exposure triggers a long-lasting elevation in connectivity from the frontal cortex regions onto ventral tegmental dopamine cells. Our study adds to the rich literature on the interaction between drugs of abuse, including THC and opioids, and provides potential circuit substates by which adolescent THC exposure influences responses to morphine later in life.
Heme allocation in eukaryotic cells relies on mitochondrial heme export through FLVCR1b to cytosolic GAPDH
Authors: Jayaram Dhanya Thamaraparambil , Sivaram Pranav , Biswas Pranjal , Dai Yue , Sweeny Elizabeth A. , Stuehr Dennis J.
Published: April 2024

Heme is an iron-containing cofactor essential for life. In eukaryotes heme is generated in the mitochondria and must leave this organelle to reach protein targets in other cell compartments. Mitochondrial heme binding by cytosolic GAPDH was recently found essential for heme distribution in eukaryotic cells. Here, we sought to uncover how mitochondrial heme reaches GAPDH. Experiments involving a human cell line and a novel GAPDH reporter construct whose heme binding in live cells can be followed by fluorescence revealed that the mitochondrial transmembrane protein FLVCR1b exclusively transfers mitochondrial heme to GAPDH through a direct protein-protein interaction that rises and falls as heme transfers. In the absence of FLVCR1b, neither GAPDH nor downstream hemeproteins received any mitochondrial heme. Cell expression of TANGO2 was also required, and we found it interacts with FLVCR1b to likely support its heme exporting function. Finally, we show that purified GAPDH interacts with FLVCR1b in isolated mitochondria and triggers heme transfer to GAPDH and its downstream delivery to two client proteins. Identifying FLVCR1b as the sole heme source for GAPDH completes the path by which heme is exported from mitochondria, transported, and delivered into protein targets within eukaryotic cells.
Bridging verbal coordination and neural dynamics
Authors: Schwab-Mohamed Isaïh , Mercier Manuel R. , Trébuchon Agnès , Morillon Benjamin , Lancia Leonardo , Schön Daniele
Published: April 2024

Our use of language, which is profoundly social in nature, essentially takes place in interactive contexts and is shaped by precise coordination dynamics that interlocutors must observe. Thus, language interaction is highly demanding on fast adjustment of speech production. Here, we developed a real-time coupled-oscillators virtual partner that allows - by changing the coupling strength parameters - to modulate the ability to synchronise speech with a virtual speaker. Then, we recorded the intracranial brain activity of 16 patients with drug-resistant epilepsy while they performed a verbal coordination task with the virtual partner (VP). More precisely, patients had to repeat short sentences synchronously with the VP. This synchronous speech task is efficient to highlight both the dorsal and ventral language pathways. Importantly, combining time-resolved verbal coordination and neural activity shows more spatially differentiated patterns and different types of neural sensitivity along the dorsal pathway. More precisely, high-frequency activity in left secondary auditory regions is highly sensitive to verbal coordinative dynamics, while primary regions are not. Finally, the high-frequency activity of the IFG BA44 (bilaterally) seems to specifically index the online coordinative adjustments that are continuously required to compensate deviation from synchronisation. These findings illustrate the possibility and value of using a fully dynamic, adaptive and interactive language task to gather deeper understanding of the subtending neural dynamics involved in speech perception, production as well as their interaction.
Economic Evaluation of Hypertension screening in Iran using Markov model
Authors: Daroudi Rajabali , Akbari Sari Ali , Zamandi Mahmoud , Yousefi Elham
Published: April 2024

Introduction and purpose

Hypertension is one of the most common non-communicable diseases in the world. However, in LMCs, there is not enough evidence-based information about the cost-effectiveness of preventive interventions for hypertension. Therefore, the purpose of this study is to conduct an economic evaluation of high blood pressure screening strategies in Iran in 2020.

Method

We did an economic evaluation of 9 blood pressure screening strategies, including screening annually or every two or three years from the ages of 30, 40, or 50, using the Markov model. The Markov model was designed and implemented based on the natural history of cardiovascular disease in the 2020 TreeAge Pro software. The quality-adjusted life years and the average cost of high blood pressure screening and treatment per person were estimated from society’s perspective for the lifetime. Input data of the model were derived from published literature, expert opinion, and available data sources

Findings

All screening interventions were more costly and more effective compared to no screening. Five strategies, including screening every three years from the age of 50, 40, and 30 years and screening every two years and annually from the age of 30, were undominated. Incremental cost-effectiveness ratios for these strategies ranged from $90.5 to $38,289.57. Probabilistic sensitivity analysis indicated that, at a cost-effectiveness threshold close to one times the GDP per capita, screening every two or three years from age 30 had the highest cost-effectiveness, with probabilities of 0.589 and 0.361, respectively.

Conclusion

Based on the findings of the economic evaluation, all screening strategies are more cost-effective compared to no screening, and among the screening strategies, considering about one times the GDP per capita as the cost-effectiveness threshold, a screening strategy every two years, starting at the age of 30, is the most cost-effective strategy.
Molecular differences between neonatal and adult stria vascularis from organotypic explants and transcriptomics
Authors: Thulasiram Matsya Ruppari , Yamamoto Ryosuke , Olszewski Rafal T. , Gu Shoujun , Morell Robert J. , Hoa Michael , Dabdoub Alain
Published: April 2024

The stria vascularis (SV), part of the blood-labyrinth barrier, is an essential component of the inner ear that regulates the ionic environment required for hearing. SV degeneration disrupts cochlear homeostasis, leading to irreversible hearing loss, yet a comprehensive understanding of the SV, and consequently therapeutic availability for SV degeneration, is lacking. We developed a whole-tissue explant model from neonatal and adult mice to create a robust platform for SV research. We validated our model by demonstrating that the proliferative behaviour of the SVin vitromimics SVin vivo,providing a representative model and advancing high-throughput SV research. We also provided evidence for pharmacological intervention in our system by investigating the role of Wnt/β-catenin signaling in SV proliferation. Finally, we performed single-cell RNA sequencing fromin vivoneonatal and adult mouse SV and revealed key genes and pathways that may play a role in SV proliferation and maintenance. Together, our results contribute new insights into investigating biological solutions for SV-associated hearing loss.

Significance

Hearing loss impairs our ability to communicate with people and interact with our environment. This can lead to social isolation, depression, cognitive deficits, and dementia. Inner ear degeneration is a primary cause of hearing loss, and our study provides an in depth look at one of the major sites of inner ear degeneration: the stria vascularis. The stria vascularis and associated blood-labyrinth barrier maintain the functional integrity of the auditory system, yet it is relatively understudied. By developing a newin vitromodel for the young and adult stria vascularis and using single cell RNA sequencing, our study provides a novel approach to studying this tissue, contributing new insights and widespread implications for auditory neuroscience and regenerative medicine.

Highlights

- We established an organotypic explant system of the neonatal and adult stria vascularis with an intact blood-labyrinth barrier.

- Proliferation of the stria vascularis decreases with agein vitro, modelling its proliferative behaviourin vivo.

- Pharmacological studies using ourin vitroSV model open possibilities for testing injury paradigms and therapeutic interventions.

- Inhibition of Wnt signalling decreases proliferation in neonatal stria vascularis.

- We identified key genes and transcription factors unique to developing and mature SV cell types using single cell RNA sequencing.
Expansion ofin vitro Toxoplasma gondiicysts using enzymatically enhanced ultrastructure expansion microscopy
Authors: Bondarenko Kseniia , Limoge Floriane , Pedram Kayvon , Gissot Mathieu , Young Joanna C.
Published: April 2024

Expansion microscopy (ExM) is an innovative approach to achieve super-resolution images without using super-resolution microscopes, based on the physical expansion of the sample. The advent of ExM has unlocked super-resolution imaging for a broader scientific circle, lowering the cost and entry skill requirements to the field. One of its branches, ultrastructure ExM (U-ExM), has become popular among research groups studying Apicomplexan parasites, including the acute stage ofToxoplasma gondiiinfection. The chronic cyst-forming stage ofToxoplasma, however, resists U-ExM expansion, impeding precise protein localisation. Here, we solve thein vitrocyst’s resistance to denaturation required for successful U-ExM of the encapsulated parasites. As the cyst’s main structural protein CST1 contains a mucin domain, we added an enzymatic digestion step using the pan-mucinase StcE prior to the expansion protocol. This allowed full expansion of the cysts in fibroblasts and primary neuronal cell culture without interference with the epitopes of the cyst-wall associated proteins. Using StcE-enhanced U-ExM, we clarified the shape and location of the GRA2 protein important for establishing a normal cyst. Expanded cysts revealed GRA2 granules spanning across the cyst wall, with a notable presence observed outside on both sides of the CST1-positive layer.

Importance

Toxoplasma gondiiis an intracellular parasite capable of establishing long-term chronic infection in nearly all warm-blooded animals. During the chronic stage, parasites encapsulate into cysts in a wide range of tissues but particularly in neurons of the central nervous system and in skeletal muscle. Current anti-Toxoplasma drugs do not eradicate chronic parasites and leave behind a reservoir of infection. As the cyst is critical for both transmission and pathology of the disease, we need to understand more fully the biology of the cyst and its vulnerabilities.

The advent of a new super-resolution approach called ultrastructure expansion microscopy allowed in-depth studies of the acute stage ofToxoplasmainfection but not the cyst-forming stage, which resists protocol-specific denaturation. Here, we show that an additional step of enzymatic digestion using mucinase StcE allows full expansion of theToxoplasmacysts, offering a new avenue for a comprehensive examination of the chronic stage of infection using an accessible super-resolution technique.
Improved mouse models of the small intestine microbiota using region-specific sampling from humans
Authors: Culver Rebecca N. , Spencer Sean Paul , Violette Arvie , Lemus Silva Evelyn Giselle , Takeuchi Tadashi , Nafarzadegan Ceena , Higginbottom Steven K. , Shalon Dari , Sonnenburg Justin , Huang Kerwyn Casey
Published: April 2024

Our understanding of region-specific microbial function within the gut is limited due to reliance on stool. Using a recently developed capsule device, we exploit regional sampling from the human intestines to develop models for interrogating small intestine (SI) microbiota composition and function.In vitroculturing of human intestinal contents produced stable, representative communities that robustly colonize the SI of germ-free mice. During mouse colonization, the combination of SI and stool microbes altered gut microbiota composition, functional capacity, and response to diet, resulting in increased diversity and reproducibility of SI colonization relative to stool microbes alone. Using a diverse strain library representative of the human SI microbiota, we constructed defined communities with taxa that largely exhibited the expected regional preferences. Response to a fiber-deficient diet was region-specific and reflected strain-specific fiber-processing and host mucus-degrading capabilities, suggesting that dietary fiber is critical for maintaining SI microbiota homeostasis. These tools should advance mechanistic modeling of the human SI microbiota and its role in disease and dietary responses.
Cryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2
Authors: Solorio-Kirpichyan Kristina , Fan Xiao , Golovenko Dmitrij , Korostelev Andrei A. , Yan Nieng , Korennykh Alexei
Published: April 2024

GCN2 is a conserved receptor kinase activating the Integrated Stress Response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of ahistidyl tRNAsynthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain. How HRSL contributes to GCN2 signaling remains unknown. Here we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeastKluyveromyces marxianus. This structure shows a constitutive symmetrical homodimer featuring a compact helical-bundle structure at the junction between HRSL and kinase domains, in the core of the receptor. Mutagenesis demonstrates that this junction structure activates GCN2 and indicates that our cryo-EM structure captures the active signaling state of HRSL. Based on these results, we put forward a GCN2 regulation mechanism, where HRSL drives the formation of activated kinase dimers. Remaining domains of GCN2 have the opposite role and in the absence of stress they help keep GCN2 basally inactive. This autoinhibitory activity is relieved upon stress ligand binding. We propose that the opposing action of HRSL and additional GCN2 domains thus yields a regulated ISR receptor.

Significance statement

Regulation of protein synthesis (translation) is a central mechanism by which eukaryotic cells adapt to stressful conditions. In starving cells, this translational adaptation is achieved via the receptor kinase GCN2, which stays inactive under normal conditions, but is switched on under stress. The molecular mechanism of GCN2 switching is not well understood due to the presence of a structurally and biochemically uncharacterizedhistidyl tRNAsynthetase-like domain (HRSL) at the core of GCN2. Here we use single-particle cryo-EM and biochemistry to elucidate the structure and function of HRSL. We identify a structure at the kinase/HRSL interface, which forms crossed helices and helps position GCN2 kinase domains for activation. These data clarify the molecular mechanism of GCN2 regulation.
Reliability of self-reported risk factors for age-related brain disease
Authors: Tack Reinier W.P. , Senff Jasper R. , Kimball Tamara N. , Prapiadou Savvina , Yechoor Nirupama , Rosand Jonathan , Singh Sanjula D. , Anderson Christopher D.
Published: April 2024

Importance

modifiable risk factors, including hypertension, hypercholesterolemia, diabetes, kidney disease, hearing impairment, and being overweight, increase risk of stroke, dementia, and late life depression (LLD), but may be poorly understood by patients.

Objective

To aid in the design of brain health risk stratification tools, we aimed to determine whether self-reported modifiable risk factors can identify at-risk patients on a population level.

Design

cohort study using cross-sectional data of ten iterations of the National Health and Examination Surveys (NHANES) from 1999 to 2018. Analyses were conducted between February and April of 2024.

Setting

US population-based cohorts

Participants

all participants who had both questionnaire data and objective measurements available.

Exposure

we collected data on answers to common questions and compared these to objectively measured risk factors for age-related brain disease.

Main outcomes and measures

we compared answers to simple questions to objectively measured risk factors. We reported means and 95% confidence intervals of objective measurements, created confusion matrices to determine common metrics, and compared performance of individual questions. We defined a question reliable if performance, measured through F1 scores, was > 0.7, as moderately reliable if F1 score was 0.5-0.7 and as unreliable if F1 score was < 0.5.

Results

Participants with both objective measurements and questionnaire data ranged from 16,966 (median age 32, 9,113 [20%] black, 19,993 [45%] white) in hearing impairment to 63,834 (median age 39, 14,156 [22%] black, 25,754 [40%] white) in diabetes. Mean values of objective measurements were significantly increased across all risk factors in patients that responded “Yes” to common questions on their presence compared to those who answered “No”. Performance of questions in identifying at-risk patients measured by F1 score was 0.25 in kidney disease, 0.44 in hypercholesterolemia, 0.56 in hypertension, 0.59 in hearing impairment, 0.71 in diabetes and 0.81 in being overweight.

Conclusion and relevance

in this study of multiple cohorts of up to 63,834 Americans, self-reported awareness of meeting clinical criteria for diabetes or being overweight were reliable, hypertension or hearing impairment were moderately reliable, and hypercholesterolemia or kidney disease were unreliable. These results could be used to guide construction of risk factor screening tools.
Plasmodium knowlesiinfection is associated with elevated circulating biomarkers of brain injury and endothelial activation
Authors: Bertran-Cobo Cesc , Dumont Elin , Noordin Naqib Rafieqin , Lai Meng-Yee , Stone William , Tetteh Kevin KA , Drakeley Chris , Krishna Sanjeev , Lau Yee-Ling , Wassmer Samuel C
Published: April 2024

Introduction

Malaria remains a major public health concern with substantial morbidity and mortality worldwide. In Malaysia, the emergence ofPlasmodium knowlesihas led to a surge in zoonotic malaria cases and deaths in recent years. Signs of cerebral involvement have been observed in a non-comatose, fatal case of severe knowlesi infection, but the potential impact of this malaria species on the brain remains underexplored. To address this gap, we investigated circulating levels of brain injury, inflammation, and vascular biomarkers in a cohort of knowlesi-infected patients and controls.

Methods

Archived plasma samples from 19 patients with confirmed symptomatic knowlesi infection and 19 healthy, age-matched controls from Peninsular Malaysia were analysed. A total of 52 plasma biomarkers of brain injury, inflammation, and vascular activation were measured using Luminex and SIMOA assays. Wilcoxon tests were used to examine group differences, and biomarker profiles were explored through hierarchical clustering heatmap analysis.

Results

Bonferroni-corrected analyses revealed significantly elevated brain injury biomarker levels in knowlesi-infected patients, including S100B (p<0.0001), Tau (p=0.0007), UCH-L1 (p<0.0001), αSyn (p<0.0001), Park7 (p=0.0006), NRGN (p=0.0022), and TDP-43 (p=0.005). Compared to controls, levels were lower in the infected group for BDNF (p<0.0001), CaBD (p<0.0001), CNTN1 (p<0.0001), NCAM-1 (p<0.0001), GFAP (p=0.0013), and KLK6 (p=0.0126). Hierarchical clustering revealed distinct group profiles for circulating levels of brain injury and vascular activation biomarkers.

Conclusions

Our findings highlight for the first time the impact ofPlasmodium knowlesiinfection on the brain, with distinct alterations in cerebral injury and endothelial activation biomarker profiles compared to healthy controls. Further studies are warranted to investigate the pathophysiology and clinical significance of these altered surrogate markers, through both neuroimaging and long-term neurocognitive assessments.
Unveiling the threat: Characterization ofClostridioides difficileInfection in the Northwest Region of Buenos Aires between 2019-2023 and Associated Risk Factors redefined through a Meta-Analysis
Authors: Barbero Angela María , Moriconi Nicolás Diego , Palma Sabina , Celano Josefina , Balbi María Gracia , Morro Lorenzo Sebastián , Calvo Zarlenga María Martina , Suárez Jorgelina , Martínez María Guadalupe , Machain Mónica Graciela , Altamiranda Carlos Gabriel , Erbiti Gabriel , Hernández Del Pino Rodrigo Emanuel , Pasquinelli Virginia
Published: April 2024

Clostridioides difficilestands as the leading cause of hospital acquired enteric infection in developed countries. In Argentina, the epidemiology ofClostridioides difficileinfection (CDI) is currently poorly characterized. Therefore, we conducted a retrospective case-control study evaluating the prevalence of CDI in 249 stool samples collected between 2019 and 2023 in the Northwest region of Buenos Aires. The presence ofC. difficilewas detected by combining three techniques (EIA, PCR and toxigenic culture) in a diagnostic algorithm. Clinical and demographic data from patients was also analyzed to identify CDI-associated risk factors. 1 in 5 patients presentedC. difficileas the etiological agent of diarrhea and the 80% of CDI+ cases carried toxigenic strains, with a third of cases acquired in the community. Age ≥69 years, previous use of antibiotics, previous hospitalization and previous episodes of CDI emerged as predisposing factors for CDI in our study cohort. Blood parameters such as an elevated number of leukocytes and platelets, a decreased basophil count, and an increased urea concentration were identified as indicators of CDI. We also carried out a systematic review and a meta-analysis where we contrasted our results with 39 studies selected from different countries around the world. At the global level, the meta-analysis highlighted advanced age, previous consumption of antibiotics and previous hospitalization as CDI risk factors and the leukocyte count as an indicator of CDI. These results emphasize the importance of epidemiological studies and reveal crucial information for healthcare decision-making regarding CDI.
Membrane curvature catalyzes actin nucleation through nano-scale condensation of N-WASP-FBP17
Authors: Zhu Kexin , Guo Xiangfu , Chandrasekaran Aravind , Miao Xinwen , Rangamani Padmini , Zhao Wenting , Miao Yansong
Published: April 2024

Actin remodeling is spatiotemporally regulated by surface topographical cues on the membrane for signaling across diverse biological processes. Yet, the mechanism dynamic membrane curvature prompts quick actin cytoskeletal changes in signaling remain elusive. Leveraging the precision of nanolithography to control membrane curvature, we reconstructed catalytic reactions from the detection of nano-scale curvature by sensing molecules to the initiation of actin polymerization, which is challenging to study quantitatively in living cells. We show that this process occurs via topographical signal-triggered condensation and activation of the actin nucleation-promoting factor (NPF), Neuronal Wiskott-Aldrich Syndrome protein (N-WASP), which is orchestrated by curvature-sensing BAR-domain protein FBP17. Such N-WASP activation is fine-tuned by optimizing FBP17 to N-WASP stoichiometry over different curvature radii, allowing a curvature-guided macromolecular assembly pattern for polymerizing actin network locally. Our findings shed light on the intricate relationship between changes in curvature and actin remodeling via spatiotemporal regulation of NPF/BAR complex condensation.
PSMAx-Guided PROTAC Degraders for Tumor-Specific Protein Degradation in Prostate Cancer
Authors: Meng Xiaolei , Hu Xiaolin , Zhang Siqi , Zhang Sai , Wang Xiao , Ma Shumin , Qin Chong
Published: April 2024

PROTACs, degrading target protein to treat diseases, represent a highly promising drug design strategy. However, the degradation of target proteins by PROTACs in non-disease tissues may lead to systemic toxicity. Herein, capitalizing on the characteristic overexpression of PSMA in prostate cancer tumor tissues, we devised a PSMA-guided PROTACs specific targeting to prostate cancer. By conjugating AR degraders and BET degraders separately with PSMA ligands via cleavable linkers, two classes of PSMA-guided PROTACs were obtained.In vitroexperiments demonstrated that PSMA-guided PROTAC molecules selectively degraded target proteins in PSMA-overexpressing prostate cancer cells, without affecting target proteins in non-PSMA-overexpressing cells.In vivostudies revealed that compared to conventional PROTACs, PSMA-guided PROTACs enhanced drug exposure in prostate cancer tumor tissues, prolonged half-life, and consequently achieved stronger and more sustained therapeutic effects. The PSMA-guided PROTAC strategy provides a novel avenue for disease tissue-specific PROTAC research, holding significant implications for targeted therapy in prostate cancer.
A human forebrain organoid model reveals the essential function of GTF2IRD1-TTR-ERK axis for the neurodevelopmental deficits of Williams Syndrome
Authors: Zhao Xingsen , Sun Qihang , Shou Yikai , Chen Weijun , Wang Mengxuan , Qu Wenzheng , Huang Xiaoli , Li Ying , Wang Chao , Gu Yan , Ji Chai , Shu Qiang , Li Xuekun
Published: April 2024

Williams Syndrome (WS; OMIM#194050) is a rare disorder, which is caused by the microdeletion of one copy of 25-27 genes, and WS patients display diverse neuronal deficits. Although remarkable progresses have been achieved, the mechanisms for these distinct deficits are still largely unknown. Here, we have shown that neural progenitor cells (NPCs) in WS forebrain organoids display abnormal proliferation and differentiation capabilities, and synapse formation. Genes with altered expression are related to neuronal development and neurogenesis. Single cell RNA-seq (scRNA-seq) data analysis revealed 13 clusters in healthy control and WS organoids. WS organoids show an aberrant generation of excitatory neurons. Mechanistically, the expression of transthyretin (TTR) are remarkably decreased in WS forebrain organoids. We have found that GTF2IRD1 encoded by one WS associated geneGTF2IRD1binds toTTRpromoter regions and regulates the expression ofTTR. In addition, exogenous TTR can activate ERK signaling and rescue neurogenic deficits of WS forebrain organoids.Gtf2ird1deficient mice display similar neurodevelopmental deficits as observed in WS organoids. Collectively, our study reveals critical function of GTF2IRD1 in regulating neurodevelopment of WS forebrain organoids and mice through regulating TTR-ERK pathway.
Multiple direct and indirect roles of Paf1C in elongation, splicing, and histone post-translational modifications
Authors: Francette Alex M. , Arndt Karen M.
Published: April 2024

Paf1C is a highly conserved protein complex with critical functions during eukaryotic transcription. Previous studies have shown that Paf1C is multi-functional, controlling specific aspects of transcription, ranging from RNAPII processivity to histone modifications. However, it is unclear how specific Paf1C subunits directly impact transcription and coupled processes. We have compared conditional depletion to steady-state deletion for each Paf1C subunit to determine the direct and indirect contributions to gene expression inSaccharomyces cerevisiae. Using nascent transcript sequencing, RNAPII profiling, and modeling of transcription elongation dynamics, we have demonstrated direct effects of Paf1C subunits on RNAPII processivity and elongation rate and indirect effects on transcript splicing and repression of antisense transcripts. Further, our results suggest that the direct transcriptional effects of Paf1C cannot be readily assigned to any particular histone modification. This work comprehensively analyzes both the immediate and extended roles of each Paf1C subunit in transcription elongation and transcript regulation.
Molecular basis for the interactions of eIF2β with eIF5, eIF2B, and 5MP1 and their regulation by CK2
Authors: Wagner Paul A. , Song Meimei , Ficner Ralf , Kuhle Bernhard , Marintchev Assen
Published: April 2024

The heterotrimeric GTPase eukaryotic translation initiation factor 2 (eIF2) delivers the initiator Met-tRNAito the ribosomal translation preinitiation complex (PIC). eIF2β has three lysine-rich repeats (K-boxes), important for binding to the GTPase-activating protein eIF5, the guanine nucleotide exchange factor eIF2B, and the regulator eIF5-mimic protein (5MP). Here, we combine X-ray crystallography with NMR to understand the molecular basis and dynamics of these interactions. The crystal structure of yeast eIF5-CTD in complex with eIF2β K-box 3 reveals an extended binding site on eIF2β, far beyond the K-box. We show that eIF2β contains three distinct binding sites, centered on each of the K-boxes, and human eIF5, eIF2Bε, and 5MP1 can bind to all three sites, while reducing each other’s affinities. Our results reveal how eIF2B speeds up the dissociation of eIF5 from eIF2-GDP to promote nucleotide exchange; and how 5MP1 can destabilize eIF5 binding to eIF2 and the PIC, to promote stringent start codon selection. All these affinities are increased by CK2 phosphomimetic mutations, highlighting the role of CK2 in both remodeling and stabilizing the translation apparatus.
Structural basis for bispecific antibody design: arrangement of domain linkage produces activity enhancement
Authors: Sato Kyohei , Uehara Shiro , Tsugita Atsushi , Ishiyama Shieru , Maejima Atsushi , Nakahara Ishin , Nazuka Misae , Matsui Takashi , Gatsogiannis Christos , Yokoyama Takeshi , Kumagai Izumi , Makabe Koki , Asano Ryutaro , Tanaka Yoshikazu
Published: April 2024

A bispecific antibody (BsAb) is a protein genetically engineered from two different antibodies, allowing simultaneous binding to two kinds of antigen to bring them into close proximity. BsAbs have been developed as anti-cancer drugs that accumulate lymphocytes onto cancer cells by bridging antigens present on each. Ex3 is a bispecific diabody composed of the two fused variable regions (Fvs) of an anti-epidermal growth factor receptor (EGFR) antibody and an anti-CD3 antibody with potent cancer cytotoxic activity. In Ex3, the LH-type, in which the variable regions of the light chain (VLs) are located at the N-terminus of those of the heavy chain (VHs), exerted 1000-fold greater anticancer activity than the HL-type, in which the VHs are located at the N-terminus of the VLs. This effect (termed ‘activity enhancement’), in which the activity is greatly enhanced by domain rearrangement, has been reported not only for Ex3 but also for several other BsAbs. However, the molecular details of this activity enhancement have yet to be elucidated. In this study, we determined the cryo-EM structures of Ex3 LH- and HL-types in complex with CD3 and EGFR. Structural comparison of the LH- and HL-types showed that rearrangement of the domain linkage produces drastic structural differences in the overall shape of these complexes, and dynamics attributed to the flexibility between the two Fvs. These findings provide valuable insights into the molecular mechanism for the activity enhancement of BsAbs. This study will be a stepping stone towards establishing a design foundation for BsAb development.
Analyzing interviews on computational thinking for introductory physics students: Toward a generalized assessment
Authors: Gambrell Justin , Brewe Eric
Published: April 2024

Computational thinking in physics has many different forms, definitions, and implementations depending on the level of physics or the institution it is presented in. To better integrate computational thinking in introductory physics, we need to understand what physicists find important about computational thinking in introductory physics. We present a qualitative analysis of 26 interviews asking academic (N_a=18) and industrial (N_i=8) physicists about the teaching and learning of computational thinking in introductory physics courses. These interviews are part of a long-term project toward developing an assessment protocol for computational thinking in introductory physics. We find that academic and industrial physicists value students’ ability to read code and that (or ) and spreadsheets were the preferred computational language or environment used. Additionally, the interviewees mentioned that identifying the core physics concepts within a program, explaining code to others, and good program hygiene (i.e., commenting and using meaningful variable names) are important skills for introductory students to acquire. We also find that while a handful of interviewees note that the experience and skills gained from computation are quite useful for student’s future careers, they also describe multiple limiting factors of teaching computation in introductory physics, such as curricular overhaul, not having “space” for computation’, and student rejection. The interviews show that while adding computational thinking to physics students’ repertoire is important, the importance really comes from using computational thinking to learn and understand physics better. This informs us that the assessment we develop should only include the basics of computational thinking needed to assess introductory physics knowledge.

Published by the American Physical Society
2024