bluuebunny/crossref_metadata_2025 huggingface dataset:
Sequential Effects in Reaching Reveal Efficient Coding in Motor Planning
Authors: Wang Tianhe , Fang Yifan , Whitney David
Published: October 2024

The nervous system utilizes prior information to enhance the accuracy of perception and action. Prevailing models of motor control emphasize Bayesian models, which suggest that the system adjusts the current motor plan by integrating information from previous observations. While Bayesian integration has been extensively examined, those studies usually applied a highly stable and predictable environment. In contrast, in many real-life situations, motor goals change rapidly over time in a relatively unpredictable way, leaving it unclear whether Bayesian integration is useful in those natural environments. An alternative model that leverages prior information to improve performance is efficient coding, which suggests that the motor system maximizes the accuracy by dynamically tuning the allocation of the encoding resources based on environmental statistics. To investigate whether this adaptive mechanism operates in motor planning, we employed center-out reaching tasks with motor goals changing in a relatively unpredictable way, where Bayesian and efficient coding models predict opposite sequential effects. Consistent with the efficient coding model, we found that current movements were biased in the opposite direction of previous movements. These repulsive biases were amplified by intrinsic motor variability. Moreover, movement variability decreased when successive reaches were similar to each other. Together, these effects support the presence of efficient coding in motor planning, a novel mechanism with which the motor system maintains flexibility and high accuracy in dynamic environments.
Analyzing the Molecular Mechanism of Eucalyptol, Limonene and Pinene Enteric Capsules (QIENUO) in the Treatment of Pulmonary cystic fibrosis with Network Pharmacology and Verifying Molecular Docking
Authors: Tu Tiantaixi , Zhu Xinjie , Wang Congyin , Chen Wei , Zheng Yihu
Published: October 2024

Objective

To explore the mechanism of Eucalyptol, Limonene and Pinene Enteric Capsules (QIENUO) in the treatment of pulmonary cystic fibrosis (CPF), analyze the common targets of QIENUO and CPF, and verify the molecular docking of core proteins and small molecules.

Methods

The main active compounds and their corresponding targets were obtained from PubChem, SwissTargetprediction, GeneCards, PharmMapper and TCMSP databases. Targets related to CPF were screened from GeneCards, OMIM, DisGeNET and TTD databases. The common “QIENUO-CPF” targets were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) through the website of Weishengxin. Protein-protein interaction (PPI) network and compound-target-pathway network were constructed by Cytoscape, and the network parameters were systematically analyzed. The interaction between core protein and monomer components was evaluated and verified by molecular docking method.

Results

228 active compounds target and 1354 CPF-related targets were screened out, and 92 common targets were analyzed by GO and KEGG. The results showed that the therapeutic effect of QIENUO on CPF was mainly through AMPK signaling pathway, cGMP-PKG signaling pathway and TGF-β signaling pathway. The results of molecular docking show that the binding energy of 9 of 15 pairs of ligand-receptor pairs is lower than-6 kjmol-1.

Conclusion

QIENUO exhibits huge potential as a therapeutic agent for the treatment of pulmonary cystic fibrosis. The specific molecular mechanism and effective active components of QIENUO treat CPF were studied and demonstrated, which provided theoretical basis for better clinical application of QIENUO.
Remote activation of place codes by gaze in a highly visual animal
Authors: Payne Hannah L. , Aronov Dmitriy
Published: October 2024

Vision enables many animals to perform spatial reasoning from remote locations. By viewing distant landmarks, animals recall spatial memories and plan future trajectories. Although these spatial functions depend on hippocampal place cells, the relationship between place cells and active visual behavior is unknown. Here, we studied a highly visual animal, the chickadee, in a behavior that required alternating between remote visual search and spatial navigation. We leveraged the unique head-directed nature of avian vision to track gaze in freely moving animals. We discovered a profound link between place coding and gaze. Place cells activated not only when the chickadee was in a specific location, but also when it simply gazed at that location from a distance. Gaze coding was precisely timed by fast, ballistic head movements called “head saccades”. On each saccadic cycle, the hippocampus switched between encoding a prediction of what the bird was about to see and a reaction to what it actually saw. The temporal structure of these responses was coordinated by subclasses of interneurons that fired at different phases of the saccade. We suggest that place and gaze coding are components of a unified process by which the hippocampus represents the location that an animal is currently attending to. This process allows the hippocampus to implement both local and remote spatial functions.
Heartbeat related activity in the anterior thalamus differs between phasic and tonic REM sleep periods
Authors: Simor Péter , Lilla Róka Zita , Szalárdy Orsolya , Jordán Zsófia , Halász László , Erőss Loránd , Fabó Dániel , Bódizs Róbert
Published: October 2024

Rapid eye movement (REM) sleep is a fundamental sleep state associated with diverse functions from elemental physiological processes to higher order neurocognitive functions. A growing body of research indicates that REM sleep with eye movements (phasic REM) differs from REM periods without ocular activity (tonic) in terms of spontaneous and evoked neural responses. Studies using auditory stimulation consistently observed enhanced evoked responses in tonic versus phasic REM, indicating that the external processing is largely diminished when the eyes move during REM sleep. Whereas exteroceptive processing during sleep is widely studies, investigation on interoception (the processing of bodily signals) during sleep is scarce, and limited to scalp electroencephalographic recordings. Here we studied interoceptive processing in a group of epileptic patients (N = 11) by measuring their heartbeat-related neural activity in the anterior nucleus of the thalamus (ANT) during phasic and tonic REM sleep and resting wakefulness. Evoked potentials and beta–low gamma spectral power locked to the heartbeat were significantly different in phasic REM compared to tonic REM and wakefulness. Heartbeat-related neural signals exhibited pronounced inter-trial phase synchronization at lower (7–20 Hz) oscillatory activity in all vigilance states, but reduced gamma synchronization at later time points in phasic REM only. Tonic REM and wakefulness did not show significant differences in heartbeat-related activity in the ANT. Our findings indicate that heartbeat-related neural activity is detectable at the level of the ANT, showing distinct signatures of interoceptive processing in phasic REM compared to tonic REM and wakefulness.
Cenozoic evolutionary history obscures the Mesozoic origins of acanthopterygian fishes
Authors: Brownstein Chase D. , Dornburg Alex , Near Thomas J.
Published: October 2024

Sister lineage comparisons provide a valuable tool for understanding evolutionary origins of species-rich clades.Percomorpha, comprising over 18,900 species, represents one of the most species-rich vertebrate clades. However, the phylogenetic resolution of its sister lineage remains unclear, obscuring whether contrasts in histories of diversification provide insights into the factors that gave rise to this clade’s diversity. Using 887 ultraconserved element loci and Sanger-sequenced nuclear genes, we resolve the phylogenetic relationships of the three closest relatives ofPercomorpha-the roughies, flashlightfishes, porcupinefishes and fangtooths (Trachichthyiformes), the squirrelfishes and soldierfishes (Holocentridae), and the whalefishes, bigscales, and alfonsinos (Berycoidei)-and the placement of percomorphs among them. Contrary to expectations from the fossil record, we demonstrate that living lineages ofBerycoidei,Holocentridae, andTrachichthyiformesall diversified after the Cretaceous-Paleogene mass extinction. Our findings show that multiple clades inTrachichthyiformesandBerycoideiindependently colonized deep ocean habitats during the climatically unstable Eocene and Oligocene and shallow-water reefs during the extensive hotspot migration and faunal turnover of the Early Miocene. Due to their complex evolutionary history, the closest relatives ofPercomorphaare not ideal for understanding the origins of this exceptionally species-rich clade.
Genetic Association of Glutathione S-Transferase Omega 2(GSTO2)Gene Variant (rs156697) with Chronic Kidney Disease Patients of Pakistani Origin
Authors: Afzal Abeer , Saif Rashid , Atta Asia , Jafri Saghir Ahmad , Naqvi Syeda Komal Abbas
Published: October 2024

Chronic Kidney Disease (CKD) poses a significant global health challenge. The kidneys can be compromised by internal diseases, environmental influences and various genetic factors. Among the genetic factors, particularly,GSTO2gene plays a crucial role in cellular processes and enzyme performance, which can lead to interstitial kidney damage and contribute to CKD. The current study investigates the genetic association between theGSTO2gene variation (rs156697) and CKD in the Punjabi community. This study examined the association between theGSTO2gene locus (c.424A>T) and CKD in a Punjabi population using ARMS-PCR genotyping. A total of 50 samples were analyzed, revealing 19 homozygous wild-type, 25 heterozygous and 6 homozygous mutants. PLINK data analysis toolset indicated an insignificant genotypic association with CKD phenotype with observedp-valueof 0.7177 and an odds ratio of 0.85. Similarly, the alternative allele frequency of 0.34 and 0.375 was also observed in CKD and normal controls respectively. In the future, further studies with more genetic markers along with functional studies with large sample data may be performed for robust statistical evidence of the association of subject gene with CKD patients in Pakistan.
Prevalence of dementia risk factors in a memory clinic setting: The Oxford Brain Health Clinic
Authors: Blane J. , Gillis G. , Griffanti L. , Mitchell R. , Pretorius P.M. , Forster S. , Shabir S. , Maffei L. , O’Donoghue M.C. , Fossey J. , Raymont V. , Martos L. , Mackay C.E .
Published: October 2024

With promising disease-modifying therapies (DMTs) emerging and good evidence to support risk reduction in the delay of dementia onset and progression, it is important to understand the profile of patients attending memory assessment services to estimate what proportion of patients might benefit from different types of interventions. The Oxford Brain Health Clinic (OBHC) is a psychiatry-led, clinical-research service that offers memory clinic patients detailed clinical assessments and equal access to research opportunities as part of their secondary care pathway. In this work, we describe the characteristics of OBHC patients in terms of demographics, diagnoses and prevalence of potentially modifiable risk factors compared with a cohort of healthy volunteers and the average memory clinic population. Our results suggest that high research consent rates (91.5%) in the OBHC resulted in a highly representative cohort of the clinical population. Based on Lecanemab trial inclusion criteria, 24.6% of the OBHC population may be suitable for further investigation into DMTs. Furthermore, 67.4% of OBHC patients have at least one potentially modifiable risk factor that may benefit from lifestyle interventions, particularly those focused on depression, sleep and physical activity.
Mendelian randomization, lipids and coronary artery disease: trade-offs between study designs and assumptions
Authors: Shi Joy , Swanson Sonja A , Diemer Elizabeth W , Gerlovin Hanna , Posner Daniel C , Wilson Peter WF , Gaziano J Michael , Cho Kelly , Hernán Miguel A ,   on behalf of the VA Million Veteran Program
Published: October 2024

Background. Mendelian randomization (MR) studies have been described as naturally occurring randomized controlled trials (RCTs). However, MR often deviates from appropriate RCT design principles and relies heavily on two-sample approaches. We used data from the Million Veteran Program (MVP) to empirically evaluate the impact of study design choices and use of one- versus two-sample MR in a study of lipids and coronary artery disease. Methods. Our MR study included MVP participants of European descent with no history of coronary artery disease or contraindications to low-density lipoprotein cholesterol (LDL-C)-related therapies. We sequentially modified the eligibility criteria, study duration and follow-up to reflect common study design decisions for MR. In all designs, we used one- and two-sample approaches to estimate 10-year risks of coronary artery disease per 39 mg/dL increase in LDL-C or 15.6 mg/dL increase in high-density lipoprotein cholesterol (HDL-C). Results. For LDL-C, one-sample estimates varied across designs (odds ratios from 1.50 [95% CI: 1.34,1.68] to 2.23 [95% CI: 1.93,2.59]) and were most sensitive to the inclusion of prevalent outcome events in the analysis. Odds ratios obtained via two-sample MR were attenuated (1.13 [95% CI: 1.01,1.26] to 1.30 [95% CI: 1.15,1.46]). For HDL-C, we observed inverse or null relationships and estimates were qualitatively similar across all designs (odds ratios from 0.76 [95% CI: 0.68,0.86] to 0.93 [95% CI: 0.65,1.34]). Conclusions. MR estimates can, in practice, be impacted by decisions in study design due to trade-offs between different biases, and investigators should evaluate the sensitivity of their estimates to different design decisions.
Longitudinal co-development of mental and cardio-metabolic health from childhood to young adulthood
Authors: Defina Serena , Cecil Charlotte A.M. , Felix Janine , Walton Esther , Tiemeier Henning
Published: October 2024

Objective: Depressive symptoms and cardio-metabolic risk factors often co-occur. However, our understanding of the potential mechanisms and temporal dynamics underlying their co-development remains elusive. Method: This population-based cohort study examined bidirectional longitudinal associations between depressive symptoms and cardio-metabolic risk factors from age 10 to 25 years, using prospective data from the ALSPAC Study. Participants with at least one (of six) follow-up measurement for each outcome were included in the analyses. We measured depressive symptoms through self- as well as parent-reports, and assessed several cardio-metabolic risk factors (including adiposity measures, lipid profiles and inflammation). Results: Among our 7970 (47% male) participants, we found bidirectional, within-person associations between self-reported depressive symptoms and adiposity (i.e., fat/lean mass index, but not body mass index), across the study period. Adiposity was more stable over time (β [range] = 0.75 [0.54; 0.84]), compared to depressive symptoms (0.26 [0.12; 0.38]), and it had a stronger prospective (i.e., cross-lagged) association with future depressive symptoms (0.07 [0.03, 0.13]) compared to that between depressive symptom and future adiposity (0.04 [0.03, 0.06]). The magnitude of these associations reached its peak between 14 and 16 years. We did not find evidence of cross-lagged associations in either direction between depressive symptoms and waist circumference, insulin, triglycerides, LDL cholesterol or C-reactive protein. Conclusions: These findings suggest a bidirectional relationship between depressive symptoms and cardio-metabolic risk factors, particularly adiposity (i.e., fat/lean mass). Adiposity showed a stronger prospective association with future depressive symptoms, than vice versa, however their relationship revealed more reciprocal than previously thought.
Quantifying the Trainability of Peripheral Nerve Function in Young and Older Adults
Authors: Shields JoCarol E. , Smith Claire M. , Reese Shawn M. , Santos Marcel L. Dos , Parodi Maria , DeFreitas Jason M.
Published: October 2024

It is well known that the natural progression of age can result in motor neuron degeneration. Consequently, this leads to slowing of nerve conduction, denervation, and reduced motor function. Slower neural conduction can negatively alter an individual’s response time, which could increase the risk of falls. Further investigation is needed to determine the potential role exercise interventions may afford in mitigating age-related nerve deterioration. The purpose was two-fold: first, to determine the effects of resistance training on nerve conduction velocity (NCV), and second, to determine if changes in NCV are dependent on age. We hypothesized that training would result in faster nerves in both young and older adults, albeit to a lesser extent in older adults. Forty-eight subjects (18-84 yrs) completed this study (n = 26 younger, 22 older). Motor NCV and maximal strength were recorded before and after 4-weeks of handgrip training in both limbs. Training was conducted 3×/week with the use of a grip training kit. Mixed-factorial ANOVAs revealed significant increases in NCV for both the young (p< 0.001) and older training groups (p< 0.001), but neither control groups (p > 0.05). The young training group showed increased handgrip strength after four weeks (p= 0.004), while the other groups did not. The results of this study suggest that resistance training may be a viable method to counteract age-related nerve deterioration. These outcomes have the potential to improve quality of life and generate greater independence for our older populations.

NEW & NOTEWORTHY

Aging is characterized by a slowing in nerve conduction speed, which could potentially affect how quickly an individual responds to unexpected incidents. Consequently, this slowing could increase the risk of falls and injuries. This study utilized resistance training as an intervention to mitigate age-related nerve deterioration. We show that motor nerve conduction velocity significantly increases in both young and older adults after 4-weeks of training.
A novel modelling framework to simulate the effects of HIV stigma on HIV transmission dynamics
Authors: Bisanzio Donal , Roberts Sarah T. , Stelmach Rachel D. , McClellan Kendall N. , Bobashev Georgiy , Adams Joella , Karriker-Jaffe Katherine , Endres-Dighe Stacy M. , Saalim Khalida , Blackburn Natalie , Nyblade Laura
Published: October 2024

Introduction

HIV remains a global public health challenge, with social determinants such as stigma influencing transmission dynamics, access to testing, and treatment. HIV stigma shapes both individual behaviour and community responses to HIV. However, modelling approaches have rarely represented the complex role of stigma in HIV epidemics. Our study introduces an innovative modelling framework designed to capture the interplay between stigma and HIV transmission dynamics.

Methods

We modelled effects of anticipated, internalised, and experienced HIV stigma on HIV testing, antiretroviral treatment initiation, and treatment adherence. We built an individual-based model representing the HIV epidemic (HIV-IBM) in a USA-like population of 3 million individuals that accounts for community demography, behaviour, and healthcare access. Stigma parameters were based on a scoping review focused on the prevalence and effects of stigma in people living with and without HIV. HIV-IBM was used to assess effects of interventions targeting different types of stigma. We tested reductions of stigma by 50% and 100% across the simulated population and performed a sensitivity analysis to identify effects of each type of stigma on the simulated HIV epidemic.

Results

Without reduced stigma, the HIV-IBM had an annual incidence rate of 12.6 (95% credible interval [CI]: 11.4-13.5) new cases per 100,000 people. Reducing the overall level of stigma in the population by 50% resulted in an annual incidence rate of 9.6 (95% CI: 8.6-10.3) per 100,000, and a 100% reduction in stigma resulted in an annual incidence rate of just 6.8 (95% CI: 6.1-7.3) per 100,000. In addition to reducing HIV incidence, reducing stigma resulted in a substantial increase of viral suppression among people living with HIV (50% stigma reduction: +10.5%; 100% stigma reduction: +16.4%). Sensitivity analysis showed that outcomes resulting from interventions targeting each type of stigma were highly heterogeneous.

Conclusion

Simulation results suggest that reducing HIV stigma could have a large effect on HIV incidence and viral suppression. Our model framework provides a dynamic approach to understanding the role of stigma in HIV outcomes that facilitates exploration of stigma reduction strategies and offers insights to inform evidence-based policies and interventions for reducing stigma and curtailing HIV.
Identification of novel associations of candidate loci with Alzheimer’s disease by leveraging the shared genetic basis with hippocampal volume
Authors: Jiang Chenyang , van der Lee Sven J. , Tesi Niccolo , van der Flier Wiesje M. , Tijms Betty M. , Reus Lianne M.
Published: October 2024

Objective

Alzheimer’s disease (AD) is a complex neurodegenerative disorder with a considerable genetic contribution that remains not fully understood. The hippocampus plays a critical role in learning and memory, with its volume loss being a core hallmark of AD. Hippocampal volume also has a strong heritable component and its genetic underpinnings may help us to understand the complex biological mechanism underlying AD.

Methods

We performed cross-trait analysis of exisiting GWAS data on late-onset AD and Hippocampal volumes using the conjunctional false discovery rate (conjFDR) framework to identify the specific shared genetic basis.For identified SNPs, we performed functional annotation and phenome-wide association studies (PheWAS).

Results

Our cross-trait analyses identified 11 non-APOE lead genetic loci, of which 7 loci showed discordant directional effects (loci associated with decreased risk for AD and smaller hippocampal volumes, and vice versa). We found thatSHARPINandTNIP1genes play a role in AD by affecting the hippocampal volumes. In addition, we observed 9 novel AD-hippocampus loci in genes previously implicated in AD (IGIPandACE) and novel AD-genes (KCTD13, HINT1, SH3TC2, FAM53B, TPM1, IL34andSSH2). Phenome-wide association study highlighted varying degrees of pleiotropy, including brain imaging measurements, white blood cell markers, red blood cell markers, and lipids in multiple shared loci.

Conclusions

Our integrating GWAS study reveals a shared genetic basis between AD and hippocampal volumes. By integrating GWAS summary statistics for these two traits, we identified both novel and previously reported AD-hippocampus loci. Functional analysis highlights the roles of immune cells and lipid markers in the shared loci and traits, suggesting a shared neurobiological basis for both traits.
PHLOWER - Single cell trajectory analysis using Decomposition of the Hodge Laplacian
Authors: Cheng Mingbo , Jansen Jitske , Reimer Katharina , Nagai James Shiniti , Li Zhijian , Kießling Paul , Grasshoff Martin , Kuppe Christoph , Schaub Michael T. , Kramann Rafael , Costa Ivan G.
Published: October 2024

Multi-modal single-cell sequencing, which captures changes in chromatin and gene expression in the same cells, is a game changer in the study of gene regulation in cellular differentiation processes. Computational trajectory analysis is a key computational task for inferring differentiation trees from this single-cell data, though current methods struggle with complex, multi-branching trees and multi-modal data. To address this, PHLOWER leverages simplicial complexes and Hodge Laplacian decomposition to infer trajectory embeddings. These natural representations of cell differentiation facilitate the estimation of their underlying differentiation trees. We evaluate PHLOWER through benchmarking with multi-branching differentiation trees and using novel kidney organoid multi-modal and spatial single-cell data. These demonstrate the power of PHLOWER in both the inference of complex trees and the identification of transcription factors regulating off-target cells in kidney organoids.
Controllability and cause in human collaboration
Authors: Spiering Lisa , Trier Hailey A , O’Reilly Jill , Kolling Nils , Wittmann Marco K , Rushworth Matthew F S , Scholl Jacqueline
Published: October 2024

There has been considerable interest in how we ascertain whether an environment is controllable and the neural mechanisms mediating this process. An especially acute version of this problem occurs when multiple people collaborate towards a joint outcome. Here we demonstrate that in such ambiguous social contexts, people engage in specific patterns of behaviour that we refer to as active disambiguation. This process helps individuals establish what they themselves, as opposed to others, control and what consequence they themselves cause or that another person causes. People identify when active disambiguation is needed and engage in it at that time. A pattern of activity in the supramarginal gyrus that emerges during and after active disambiguation is linked to establishing controllability and tracking the outcomes from which control is inferred. Activity in this brain region also signals a second learning mechanism, by which individuals attribute outcomes to themselves versus others, in proportion to their perceived control.
A previously reported bottleneck in human ancestry 900 kya is likely a statistical artifact
Authors: Deng Yun , Nielsen Rasmus , Song Yun S.
Published: October 2024

It was recently reported that a severe ancient bottleneck occurred around 900 thousand years ago in the ancestry of African populations, while this signal is absent in non-African populations. Here, we present evidence to show that this finding is likely a statistical artifact.
Mitigation of Reproductive Function in Sodium Fluoride-administered Wistar Rats byTamarindus indicaFruit Pulp Ethanol Extract
Authors: Usman Lutfat A. , Ajani Emmanuel O. , Ishiaku Muhammed A. , Bankole Taofeeq A. , Ibrahim Rasheed B. , Saka Dauda K.
Published: October 2024

Infertility is a stigmatized and emotionally challenging issue for affected individuals, often compounded by the high costs of conventional fertility treatments. This study investigated the prophylactic and therapeutic effects of an ethanolic extract of Tamarindus indica fruit pulp on sodium fluoride-induced sexual and reproductive dysfunction in Wistar rats. The extract was prepared via ethanol maceration, followed by filtration and drying. Seventy Wistar rats were used, with an initial acute toxicity study indicating no adverse effects at 5000 mg/kg of the extract.

Following toxicity assessment, rats were divided into seven groups, with varying treatments involving Tamarindus indica extract, sodium fluoride, and clomid. After the treatment period, biochemical analyses revealed that rats treated with 400 mg/kg of Tamarindus indica extract showed significant improvements (p < 0.05) in sperm count, luteinizing hormone (in males), testosterone, estrogen, along with reduced levels of follicle-stimulating hormone (in males), and luteinizing hormone (in females). Histopathological examination revealed normal histomorphology in certain groups treated with the extract. Phytochemical analysis identified the presence of tannins and steroids in the extract.

The study concluded that Tamarindus indica fruit pulp extract exhibits both prophylactic and therapeutic effects on sodium fluoride-induced sexual and reproductive dysfunction in rats, with the most significant effects observed at a 400 mg/kg dosage. These findings suggest that Tamarindus indica extract could serve as an alternative to conventional treatments for infertility.
Exploring the effect of Hydrocarbon Cross-linkers on the Structure and Binding of Stapled p53 Peptides
Authors: Choudhury Asha Rani , Gaikwad Vikram , Maity Atanu , Chakrabarti Rajarshi
Published: October 2024

Short-length peptides are used as therapeutics due to their high target specificity and low toxicity, for example, peptides designed for targeting the interaction between oncogenic protein p53 and E3 ubiquitin ligase MDM2. These peptide therapeutics form a class of successful inhibitors. To design such peptide-based inhibitors, stapling is one of the methods in which amino acid side chains are stitched together to get conformationally rigid peptides, ensuring effective binding to their partners. In the current work, we use computer simulations to investigate p53 peptides stapled with hydrocarbon chains of different lengths and positions of attachment to the peptide. We subsequently analyze their binding efficiency with MDM2. The introduction of stapling agents restricts the conformational dynamics of peptides, resulting in higher persistence of helicity. The efficiency of the stapling agents has also been verified imposing these stapled peptides to adverse conditions viz. thermal and chemical denaturation. In addition, the conformational exploration of peptides has been investigated using Temperature replica exchange molecular dynamics (T-REMD) simulations. From both the unbiased and T-REMD simulations, p53 with a long hydrocarbon cross-linker shows a more conformationally rigid structure having high helicity compared to other stapled peptides. The rigidity gained due to cross-linking reduces the entropy of the peptide in the free state and thereby facilitates the complexation process. From the binding studies, we have shown that the peptide having multiple short staples has shown a larger enthalpy change during binding free energy, resulting from its orientation and interactions of residues in the binding interface. On the other hand, a peptide with a single long stapling agent shows less entropic penalty than other systems. Our studies suggest a plausible rationale for the relation between the length and the position of attachment of cross-linkers to peptides and the binding free energies between the peptides and their target partners.
Rho-dependent termination and RNase E-mediated cleavage: Dual pathways for RNA 3’ end processing in polycistronic mRNA
Authors: Jeon Heung Jin , N Monford Paul Abishek , Wang Xun , Lim Heon M.
Published: October 2024

“Pre-full-length” transcripts are produced at the end of the polycistronic galactose (gal)operon, 5’galE-galT-galK-galM3’, via Rho-dependent (RDT) and -independent transcription termination (RIT). The full-lengthgalETKMmRNA’s 3’ end is acquired by exo-nucleolytic processing of the 3’-OH ends of the pre-full-length transcripts. However, thegaloperon produces an mRNA namedgalEwhose 3’ end forms at ∼120 nucleotides from thegalEstop codon, thus in the following gene,galT, establishing polarity in gene expression. In this study, we investigated the molecular processes that generate the 3’ end ofgalEmRNA. We discovered that the 3’ ends of pre-galE mRNA are produced in the middle of thegalTgene as a result of the combination of two separate molecular processes - one previously reported as RDT and the other as unreported RNase E-mediated transcript cleavage. The 3’ ends of the pre-galEmRNA are exo-nucleolytically processed to the current 3’ end of thegalEmRNA. A hairpin structure of 8 base-pair stems and 4 nucleotide-loop formed 5-10 nucleotides upstream of the 3’ ends of thegalEmRNA blocks the exoribonuclease digestion and renders stability. These findings showed that RNase E produces RNA 3’end establishing polarity in gene expression, in contrast to the general role of mRNA degradation.

Significance statement

Here, we show the findings of two molecular mechanisms that generate the pre-galEmRNA 3’ends in thegaloperon: Rho-dependent termination (RDT) and RNase E-mediated cleavage. These 3’ ends are subsequently processed to produce stablegalEmRNA with a hairpin structure that prevents exoribonuclease degradation. This mechanism establishes gene expression polarity by generating the 3’ end ofgalEmRNA within thegalTgene, contrasting with the usual mRNA degradation role of RNase E. The study reveals a unique role of RNase E in mRNA processing and stability.
FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells
Authors: Ado Sakina , Dong Chuang , Attaf Noudjoud , Moussa Myriam , Carrier Agathe , Milpied Pierre , Navarro Jean-Marc
Published: October 2024

Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. However, in most cases, the specificity and affinity of the B cell antigen receptor cannot be inferred from its sequence. Antibody cloning and expression from single B cells is then required for functional assays. Here we propose a method that integrates FACS-based 5’-end single-cell RNA sequencing (FB5P-seq) and monoclonal antibody cloning for integrative analysis of single B cells. Starting from a cell suspension, single B cells are FACS-sorted into 96-well plates for reverse transcription, cDNA barcoding and amplification. A fraction of the single-cell cDNA is used for preparing 5’-end RNA-seq libraries that are sequenced for retrieving transcriptome-wide gene expression and paired BCR sequences. The archived cDNA of selected cells of interest is used as input for cloning heavy and light chain variable regions into antibody expression plasmid vectors. The corresponding monoclonal antibodies are produced by transient transfection of a eukaryotic producing cell line and purified for functional assays. We provide detailed step-by-step instructions and describe results obtained on ovalbumin-specific murine germinal center B cells after immunization. Our method is robust, flexible, cost-effective, and applicable to different B cell types and species. We anticipate it will be useful for mapping antigen specificity and affinity of rare B cell subsets characterized by defined gene expression and/or antigen receptor sequence.
Cell extract-based in vitro DNA replication enables sustainable cell-free gene expression
Authors: Zheng Xiao , Gao Wenli , Liu Wan-Qiu , Zhang Yufei , Lu Yicong , Huang Shuhui , Ji Xiangyang , Liu Yifan , Ling Shengjie , Li Jian
Published: October 2024

Cell extract-based cell-free gene expression (CFE) systems break cellular boundaries and create emerging platforms for synthetic biology applications. However, these systems lack intrinsic DNA replication capability, thereby limiting sustained transcription and translation in a cell-free environment. Here, we introduce a LoopReX system based on E. coli CFE by integration of the DNA replication machinery, enabling iterative in vitro DNA replication and sustainable cell-free gene expression. We establish LoopReX by integrating phi29 DNA polymerase into the crude lysate-based E. coli CFE system, allowing for coupled DNA replication and protein expression. We elucidate the synergetic mechanisms between T7 RNA polymerase and phi29 DNA polymerase in facilitating in vitro DNA replication. Additionally, we optimize LoopReX reaction conditions by machine learning strategies. Finally, we demonstrate that the enhanced LoopReX system achieves highly efficient DNA replication and protein production in an iterative, scalable, and sustainable manner. We anticipate that LoopReX will significantly advance the application of CFE in synthetic biology.
Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii
Authors: Van de Vloet Antoine , Prost-Boxoen Lucas , Bafort Quinten , Paing Yunn Thet , Casteleyn Griet , Jomat Lucile , Lemaire Stéphane , De Clerck Olivier , Van de Peer Yves
Published: October 2024

Whole genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. Chlamydomonas reinhardtii, a haploid green alga, is a valuable model organism with profound potential to study the impact of ploidy increase on the longer-term in a laboratory environment. This is partly due to the ability to successfully increase the ploidy level. We developed a strategy to engineer ploidy in Chlamydomonas reinhardtii using a collection of non-interfering antibiotic selectable markers. This approach allows to induce higher ploidy levels in Chlamydomonas reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy. We demonstrate the creation of diploids, triploids and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in Chlamydomonas reinhardtii. Our study greatly facilitates the application of Chlamydomonas reinhardtii to study polyploidy, both in fundamental and applied settings.
A novel recombinant PHB production platform in filamentous cyanobacteria avoiding nitrogen starvation while preserving cell viability
Authors: Fink Phillipp , Menzel Claudia , Kwon Jong-Hee , Forchhammer Karl
Published: October 2024

During the past decades, the importance of developing sustainable, carbon dioxide (CO2)-neutral and biodegradable alternatives to conventional plastic has become evident in the context of global pollution issues. Therefore, heterotrophic bacteria such asCupriavidussp. have been intensively explored for the synthesis of the biodegradable polymer polyhydroxybutyrate (PHB). PHB is also naturally produced by a variety of phototrophic cyanobacteria, which only need sunlight and CO2,thereby allowing a CO2negative, eco-friendly synthesis of this polymer. However, a major drawback of the use of cyanobacteria is the need of a two-stage production process, since relevant amount of PHB synthesis only occurs after transferring the cultures to conditions of nitrogen starvation, which hinders continuous, large-scale production.

This study aimed at generating, by means of genetic engineering, a cyanobacterium that continuously produces PHB in large amounts. We choose a genetically amenable filamentous cyanobacterium of the genusNostocsp., which is a diazotrophic cyanobacterium, capable of atmospheric nitrogen (N2) fixation but naturally does not produce PHB. We transformed thisNostocstrain with various constructs containing the PHB synthesis operon fromCupriavidus necatorH16. In fact, while the transformants initially produced PHB, the PHB-producing strains rapidly lost cell viability. Therefore, we next attempted further optimization of the biosynthetic gene cluster. Finally, we succeeded in stabilized PHB production, whilst simultaneously avoiding decreasing cell viability. In conclusion, the recombinantNostocstrain constructed in the present work constitutes the first example of a continuous and stable PHB production platform in cyanobacteria, which has been decoupled from nitrogen starvation and, hence, harbours great potential for sustainable, industrial PHB production.
The pneumococcal bacteriocin streptococcin B is produced as part of the early competence cascade and promotes intraspecies competition
Authors: Richardson JD , Guo Emily , Wyllie Ryan M , Jensen Paul , Dawid Suzanne
Published: October 2024

Streptococcus pneumoniaeis an important human pathogen that normally resides in the human nasopharynx. Competence mediated bacteriocin expression byS pneumoniaeplays a major role in both the establishment and persistence of colonization on this polymicrobial surface. Over 20 distinct bacteriocin loci have been identified in pneumococcal genomes, but only a small number have been characterized phenotypically. In this work, we demonstrate that 3/4th ofS. pneumoniaestrains contain a highly conservedscblocus that encodes an active lactococcin 972-like bacteriocin called Streptococcin B. In these backgrounds, thescbABClocus is part of the early competence cascade due to a ComE binding site in the promoter region. Streptococcin B producing strains target both members of the population that have failed to activate competence and the 25% of the population that carry a naturally occurring deletion of the ComE binding site and the functional bacteriocin gene. The ComR-type regulator found directly upstream of thescblocus inS. pneumoniaestrains can activatescbexpression independent of the presence of the ComE binding site but only when stimulated by a peptide that is encoded in thescblocus ofS. pseudopneumoniae, a closely related bacterium which also inhabits the human nasopharynx. Given the co-regulation with competence and the phenotypic confirmation of activity, Streptococcin B represents a previously unrecognized fratricide effector that gives producing strains an additional advantage over the naturally occurring deleted strains during colonization.

Importance

Streptococcus pneumoniaeis a common cause of pneumonia, meningitis, sinusitis and otitis media. In order to successfully colonize humans, a pre-requisite to the development of invasive disease,S. pneumoniaemust compete with other bacterial inhabitants of the nasal surface for space and nutrients. Bacteriocins are small antimicrobial peptides produced by bacteria that typically target neighboring bacteria by disruption of the cell surface.S. pnuemoniaeencodes a large number of potential bacteriocin, but, for most, their role in competitive interactions has not been defined. This work demonstrates that isolates that produce the bacteriocin Streptococcin B have an advantage over non producers. These observations contribute to our understanding of the competitive interactions that precede development ofS. pneumoniaedisease.
Structure and stabilization of the antigenic glycoprotein building blocks of the New World mammarenavirus spike complex
Authors: Paesen Guido C. , Ng Weng M. , Sutton Geoff , Doores Katie J. , Bowden Thomas A.
Published: October 2024

The spillover of New World (NW) arenaviruses from rodent reservoirs into human populations poses a continued risk to human health. NW arenaviruses present a glycoprotein (GP) complex on the envelope surface of the virion, which orchestrates host-cell entry and is a key target of the immune response arising from infection and immunization. Each protomer of the trimeric GP is composed of a stable signal peptide (SSP), a GP1 attachment glycoprotein, and a GP2 fusion glycoprotein. To glean insights into the architecture of this key therapeutic target, we determined the crystal structures of NW GP1–GP2 heterodimeric complexes from Junín virus (JUNV) and Machupo virus (MACV). Due to the metastability of the interaction between GP1 and GP2, structural elucidation required the introduction of a disulfide bond at the GP1–GP2 complex interface, but no other stabilizing modifications were required. While the overall assembly of NW GP1–GP2 is conserved with that presented by Old World (OW) arenaviruses, including Lassa virus (LASV) and lymphocytic choriomeningitis virus (LCMV), NW GP1–GP2 complexes are structurally distinct. Indeed, we note that when compared to the OW GP1–GP2 complex, the globular portion of NW GP1 undergoes limited structural alterations upon detachment from its cognate GP2. We further demonstrate that our engineered GP1–GP2 heterodimers are antigenically relevant and recognized by neutralizing antibodies. These data provide insights into the distinct assemblies presented by NW and OW arenaviruses, as well as provide molecular-level blueprints that may guide vaccine development.

Importance

Although the emergence of New World (NW) hemorrhagic fever mammarenaviruses poses an unceasing threat to human health, there is a paucity of reagents capable of protecting against the transmission of these pathogens from their natural rodent reservoirs. This is, in part, attributed to our limited understanding of structure and function of the NW glycoprotein spike complex presented on the NW arenavirus surface. Here, we provide a detailed molecular-level description of how the two major components of this key therapeutic target assemble to form a key building block of the NW arenaviral spike complex. The insights gleaned from this work provide a framework for guiding the structure-based development of NW arenaviral vaccines.
Expression Profiles of FABP4 and FABP5 in Breast Cancer: Clinical Implications and Perspectives
Authors: Jiang Xingshan , Xiong Yiqin , Yu Jianyu , Avellino Anthony , Liu Shanshan , Han Xiaochun , Wang Zhaohua , Shilyansky Jonathan S. , Curry Melissa A. , Hao Jiaqing , Sauter Edward R. , Sugg Sonia L. , Li Bing
Published: October 2024

The incidence of breast cancer continues to rise each year despite significant advances in diagnosis and treatment. Obesity-associated dysregulated lipid metabolism is believed to contribute to the increasing risk of breast cancer. However, the mechanisms linking lipid dysregulation to breast cancer risk and progression remain to be determined. The family of fatty acid binding proteins (FABPs) evolves to facilitate lipid transport and metabolism. As the predominant isoforms of FABP members expressed in breast tissue, adipose FABP (A-FABP, also known as FABP4) and epithelial FABP (E-FABP, FABP5) have been shown to play critical roles in breast carcinogenesis. In this study, we collected surgical breast tissue samples from 96 women with different subtypes of breast cancer and comprehensively analyzed the expression pattens of FABP4 and FABP5. We found that distinct expression profiles of FABP4 and FABP5 were associated with their unique roles in breast cancer development. FABP4, mainly expressed in breast stroma, especially in adipose tissue, supported neighboring tumor cell lymphvascular invasion through secretion from adipocytes. In contrast, FABP5, primarily expressed in epithelial-derived tumor cells, promoted tumor metastasis by enhancing lipid metabolism. Thus, elevated levels of FABP4 and FABP5 could serve as poor prognostic markers for breast cancer. Inhibiting the activity of FABP4 and/or FABP5 may offer a novel strategy for breast cancer treatment.
CK1α, FAM83H, and FAM83B contribute to bundling of neurofilaments and are sequestered in cellular and mice models of ARSACS
Authors: Atkinson Caitlin S. , Cheng-Boivin Zacharie , Larochelle Nancy , Minotti Sandra , Gentil Benoit J.
Published: October 2024

Autosomal recessive spastic ataxia of the Charlevoix-Saguenay (ARSACS) is a rare neurodegenerative disorder characterized by mutations in theSACSgene that encodes for the sacsin protein. Sacsin dysfunction in ARSACS results in neurofilament bundling, a phenotype observed in various cellular models of ARSACS. The mechanisms underlying bundling in ARSACS remain unclear. With neurofilament phosphorylation controlling several processes of intermediate filament dynamics, its dysregulation may play a role in ARSACS. Accordingly, we investigated the interaction between CK1α (Casein Kinase 1α) and its adaptor proteins FAM83H or FAM83B (FAMily with sequence similarity 83). Here, we report that these target proteins are upregulated in ARSACS patient fibroblasts and co-localize at the sites of intermediate filament bundling. In theSacs-/-cerebellum, FAM83B compensated for the lack of FAM83H expression, suggesting a cell-type specific activity of CK1α that depends on the relative expression of its adaptor proteins. Further, CK1α inhibition with D4475 or knockdown of the target proteins with the CRISPR system caused neurofilament bundling, a phenotype that was only partially remedied by CK1α activation with SSTC3. Our findings suggest that CK1α, FAM83H, and FAM83B contribute to neurofilament bundling in ARSACS; however, the inability of CK1α to resolve neurofilament bundling may reflect an error in a priming phosphorylation event in ARSACS. Future research is needed to understand the hierarchical phosphorylation cascade to CK1α activity and its contribution to ARSACS pathology.

Highlights

CK1α and its cell-specific adaptors are upregulated in ARSACS and targeted to the sites of bundles

Knockdown of CK1α, FAM83H, and FAM83B cause neurofilament bundling

Activation of CK1α partially remediates bundling