bluuebunny/crossref_metadata_2025 huggingface dataset:
Acupuncture triggers earlier recovery from ischemic stroke than sham needling in a rat model
Authors: He Wuxian , Tang Hongtu , Li Jia , Shen Xiaoyan , Li Chenrui , Liu Huafeng , Yu Weichuan
Published: July 2024

Summary paragraph

Acupuncture, a traditional Chinese medical treatment that has been practiced for over 2,000 years, is widely used around the world [1]. However, its efficacy and distinction from random stimulation are still being questioned [2, 3]. Over the years, many studies have reported either favorable, neutral or even skeptical outcomes regarding the treatment effect of acupuncture on diverse ailments [4–7]. The major question behind this controversy is whether acupuncture is different from random needle insertion and whether its efficacy can be attributed to the placebo effect [8, 9]. Here, we use micro-positron emission tomography (microPET) imaging in a randomized controlled animal study to show that acupuncture facilitates faster recuperation in comparison to sham acupuncture and blank control. Based on the microPET imaging of subjects undergoing daily acupuncture over two weeks’ duration, we dynamically monitored the metabolic activity levels in different brain regions and found that both acupoint and non-acupoint stimulation could improve ischemic stroke recovery. This finding is consistent with previous reports that both acupuncture and sham needling show a positive effect in the treatment of diseases [4, 5, 8]. More importantly, we further found that rats receiving acupuncture at Baihui (GV20) and Shuigou (GV26), two commonly used acupoints for stroke rehabilitation based on the concept of the meridian system, showed earlier recovery effects than rats receiving sham needling treatment. This difference mainly appeared in regions involved in motor control and was validated by a balance beam walking test. Our findings, in conjunction with a recent electroacupuncture study that revealed a neuroanatomical pathway to mediate the vagal-adrenal anti-inflammatory axis [10], provide quantitative evidence supporting the specificity of acupoints in acupuncture therapy.
Alternative splicing controls pan-neuronal homeobox gene expression
Authors: Leyva-Díaz Eduardo , Cesar Michael , Pe Karinna , Jordá-Llorens Jose Ignacio , Valdivia Jessica , Hobert Oliver
Published: July 2024

The pan-neuronally expressed and phylogenetically conserved CUT homeobox geneceh-44/CUXorchestrates pan-neuronal gene expression throughout the nervous system ofC. elegans.As in many other species, including humans,ceh-44/CUXis encoded by a complex locus that also codes for a Golgi-localized protein. How gene expression from this complex locus is controlled and, inC. elegans, directed to all cells of the nervous system has not been investigated. We show here that pan-neuronal expression of CEH-44/CUX is controlled by a pan-neuronal RNA splicing factor, UNC-75/CELF, theC. eleganshomolog of vertebrate CELF proteins. UNC-75/CELF temporally and spatially specifies the production of an alternative, CEH-44/CUX homeobox gene-encoding transcript from a ubiquitously expressed gene locus, which also produces a Golgi apparatus-localized golgin protein, CONE-1 (“CASPofnematodes”). During embryogenesis thecone-1/ceh-44locus exclusively produces the Golgi-localized CONE-1/CASP protein in all tissues, but upon the onset of postmitotic terminal differentiation of neurons, UNC-75/CELF induces the production of the alternative CEH-44/CUX CUT homeobox gene-encoding transcript, exclusively in the nervous system. Hence, UNC-75/CELF-mediated alternative splicing not only directs pan-neuronal gene expression, but also excludes a phylogenetically deeply conserved golgin from the nervous system, paralleling surprising spatial specificities of another golgin that we describe here as well. In summary, our findings provide novel insights into how all cells in a nervous system acquire pan-neuronal identity features.
Loss of PINK1 causes age-dependent mitochondrial trafficking deficits in nigrostriatal dopaminergic neurons through aberrant activation of p38 MAPK
Authors: Zhao Jingyu , Chen Yuanxin , Zhi Lianteng , Xu Qing , Zhang Hui , Li Chenjian
Published: July 2024

Mutations inPTEN-induced putative kinase 1(PINK1) gene cause early-onset, autosomal-recessive familial inherited Parkinson’s disease (PD). Previous studies have shown age-related declines in dopamine release and ATP levels in the striatum ofPink1-/-mice, but the underlying mechanisms remain unclear. While the role of PINK1 in mitochondrial transport has been studied in cell culture andDrosophila, its impacts on axonal transport in dopaminergic neurons and the consequent synaptic and axonal degenerationin vivoremain critical questions that warrant further investigation. In this study, we developed a TH-Mito-Dendra2 transgenic mouse model to label mitochondria in dopaminergic neurons with Dendra2 protein. Using this model, we found that loss of PINK1 causes age-dependent deficits in mitochondrial axonal trafficking, with reduced anterograde movement and increased static mitochondria in acute brain slices. Pharmacological induction of reactive oxygen species (ROS) and calcium release hindered mitochondrial mobility. Additionally,Pink1knockout mice showed increased levels of mitochondrial calcium and ROS. Furthermore,Pink1-/-mice showed p38 MAPK hyperactivation. Treatment with the p38 inhibitor SB202190 restored mitochondrial motility and increased anterograde transport. Taken together, our findings suggest that loss of PINK1 disrupts mitochondrial trafficking by disturbing calcium homeostasis and ROS production via the p38 pathway for PD pathogenesis.
Super-enhancer-drivenCACNA2D2is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)
Authors: Geyer Florian H. , Ritter Alina , Kinn-Gurzo Seneca , Faehling Tobias , Li Jing , Jarosch Armin , Ngo Carine , Vinca Endrit , Aljakouch Karim , Orynbek Azhar , Ohmura Shunya , Kirchner Thomas , Imle Roland , Romero-Pérez Laura , Bertram Stefanie , de Álava Enrique , Postel-Vilnay Sophie , Banito Ana , Sill Martin , Versleijen-Jonkers Yvonne M.H. , Mayer Benjamin F.B. , Ebinger Martin , Sparber-Sauer Monika , Stegmaier Sabine , Baumhoer Daniel , Hartmann Wolfgang , Krijgsveld Jeroen , Horst David , Delattre Olivier , Grohar Patrick J. , Grünewald Thomas G. P. , Cidre-Aranaz Florencia
Published: July 2024

Desmoplastic small round cell tumor (DSRCT) is a highly aggressive cancer predominantly occurring in male adolescents and young adults. The lack of a comprehensive understanding on the biology of the disease is paralleled by its dismal survival rates (5–20%). To overcome this challenge, we first identified and prioritized urgently needed resources for clinicians and researchers. Thus, we established genome-wide single-cell RNA-sequencing and bulk proteomic data of in vitro and in vivo-generated knockdown models of the pathognomonic DSRCT fusion oncoprotein (EWSR1::WT1) and combined them with an original systems-biology-based pipeline including patient data and the largest histology collection of DSRCTs and morphological mimics available to date. These novel tools were enriched with curated public datasets including patient- and cell line-derived ChIP-seq, bulk and single-cell RNA-seq studies resulting in a multi-model and multi-omic toolbox for discovery analyses. As a proof of concept, our approach revealed the alpha-2/delta subunit of the voltage-dependent calcium channel complex, CACNA2D2, as a highly overexpressed, super-enhancer driven, direct target of EWSR1::WT1. Single-cell and bulk-level analyses of patient samples and xenografted cell lines highlighted CACNA2D2 as a critical component of our newly established EWSR1::WT1 oncogenic signature, that can be employed to robustly identify DSRCT in reference sets. Finally, we show that CACNA2D2 is a highly sensitive and specific single biomarker for fast, simple, and cost-efficient diagnosis of DSRCT. Collectively, we establish a large-scale multi-omics dataset for this devastating disease and provide a blueprint of how such toolbox can be used to identify new and clinically relevant diagnostic markers, which may significantly reduce misdiagnoses, and thus improve patient care.
MONOPTEROSisoformMP11irrole during somatic embryogenesis inArabidopsis thaliana
Authors: Wójcikowska Barbara , Belaidi Samia , Mironova Victoria , Boisivon Helene Robert
Published: July 2024

Auxin is crucial for plant morphogenesis, includingin vivoandin vitroembryo development. Exogenous auxin application is necessary for inducing embryogenic responses inin vitrocultured explants of Arabidopsis and other plants. Thus, components of auxin transport, signaling, and metabolism are key to somatic embryo formation. AUXIN RESPONSE FACTOR (ARF) transcription factors, which bind to auxin response elements to control the auxin-responsive gene expression, are vital in somatic embryo regeneration. ARFs are often repressed by AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs). MONOPTEROS (MP)/ARF5 is especially important in the embryogenic transition, being highly expressed during somatic embryogenesis; its mutant cannot develop somatic embryos. TheMP11irtranscript, an alternatively spliced variant ofMP/ARF5, produces a truncated protein missing the Phox and Bem1p (PB1) domain, crucial for ARF-Aux/IAA dimerization. This makes the MP11ir isoform insensitive to Aux/IAA repression, suggesting auxin-independent regulation. High levels ofMP11irtranscript are observed during auxin- and trichostatin A-dependent induction of somatic embryogenesis. Both MP/ARF5 and MP11ir are essential for embryo regeneration in thempS319mutant. However, overexpressing truncated MP/ARF5 protein (ΔARF5) lacking the PB1 domain inhibits somatic embryogenesis, leading to callus formation instead of somatic embryos. OverexpressingΔARF5, lacking MP/ARF5 protein (mp/arf5mutant), and blocking of MP/ARF5 action with auxin-resistant BODENLOS (BDL) protein affect the expression of genes involved in auxin biosynthesis, likeTRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1(TAA1),TAA1-RELATED 1(TAR1),YUCCA3(YUC3),YUC5andYUC8, which may be potential targets of MP11ir and/or MP/ARF5. Consequently,ΔARF5overexpression alters auxin homeostasis and endogenous auxin levels, hindering embryogenic transition.
Genome-wide Identification of the Laccase Gene Family in White Jute (Corchorus capsularis): Potential Targets for Lignin Engineering in Bast Fiber
Authors: Parida Subhadarshini , Jha Deepak Kumar , Kumari Khushbu , Pradhan Seema , Dey Nrisingha , Majumder Shuvobrata
Published: July 2024

The industrial bast fibre crop jute (Corchorussp.) is known for its long lignocellulosic multi-utility fibres. Information on jute fibre lignification is limited, and many enzymes in the jute lignin pathway are not well documented. One such enzyme is laccase (EC 1.10.3.2), involved in the final polymerization step of lignification. A whole-genome search of white jute (Corchorus capsularis) revealed 34 putative laccase (CcaLAC) genes. Phylogenetic analysis categorized these genes into six groups, with 17 predominantly expressed in phloem tissue, 9 in leaf, and 4 in xylem and roots. A steady increase in gene expression, from plantlets to crop harvest, was observed for severalCcaLACs. Some were selected for further analysis based on homology withArabidopsislignin pathway-modifying laccases (AtLACs). Transcriptomics data confirmed their expression in phloem tissues, with some showing significantly lower expression indlpf, a low-lignin fibre-containing white jute mutant. Changes inCcaLACexpression were observed under abiotic stresses like ABA hormone and copper heavy metal. Target sites for Ath-miR397a and Ath-miR397b were predicted in 11 and 9CcaLACs, respectively, suggesting possible post-transcriptional modification via microRNA. Subcellular localization showedCcaLACs in multiple plant cell compartments. Protein structure predictions revealed up to 10 motifs in CcaLACs, with 18 containing transmembrane helices. Overall,CcaLAC28andCcaLAC32are likely involved in the lignification process of phloem (bast) in white jute. Modifying these genes could enhance our understanding of lignification and potentially lead to the development of low-lignin jute fibres, meeting high industrial demands globally.

Highlights

Jute is known for its long lignocellulosic fibres.

34 putative laccase genes were identified in white jute.

17 laccase genes are mainly expressed in phloem tissue.

CcaLAC28andCcaLAC32are key candidates for lignification.

Laccase genes showed changes under abiotic stresses.

Key Message

Identified 34 laccase genes in white jute, key for understanding and engineering lignification in fibres.
Ablation of B cell-derived IL-10 increases tuberculosis resistance
Authors: Hertz David , Marwitz Sebastian , Eggers Lars , von Borstel Linda , Parvathy Gishnu Harikumar , Behrends Jochen , Jonigk Danny D. , Manz Rudolf A. , Goldmann Torsten , Schneider Bianca E.
Published: July 2024

Due to the historical dogma, that host defense against intracellular pathogens is mediated by cell-mediated immunity, B cells have been considered unimportant in providing protection againstMycobacterium tuberculosis(Mtb) and remained understudied for decades. However, emerging evidence suggests a more complex and multifaceted role for B cells in tuberculosis (TB) immunity. They accumulate at the side of infection in both animal models and human TB patients, suggesting a potential link to protective immunity. Still, the diverse roles of B cells in TB immunity continue to be unraveled. Apart from antibodies, B cells produce a wide range of cytokines, which can influence the local immune response. Here we addressed the relevance of interleukin 10 (IL-10) secreting B cells in long-term control of theMtbBeijing strain HN878. Our research highlights the previously unknown role of B cell-derived IL-10 as a negative regulator of protective immunity in TB. For the first time, we demonstrate that mice lacking B cell-derived IL-10 show increased resistance to aerosolMtbinfection, as evidenced by a delayed onset of clinical symptoms and prolonged survival. Notably, this effect was significantly more pronounced in males compared to females, and was accompanied by male-specific immune alterations, indicating a previously unknown sex-specific regulatory role of B cell-derived IL-10 duringMtbinfection.
Immersive exposure to simulated visual hallucinations modulates high-level human cognition
Authors: Greco Antonino , Rastelli Clara , Ubaldi Andrea , Riva Giuseppe
Published: July 2024

Understanding altered states of consciousness induced by psychedelic drugs is crucial for advancing our knowledge of conscious perception and developing clinical applications for psychiatric conditions. Recently, technological advances in virtual reality (VR) headsets and deep neural network for generative computer vision have enabled the controlled, immersive simulation of visual hallucinations. Although there is some evidence that simulated visual hallucinations increase cognitive flexibility, comprehensive experimental data on how this artificially altered perceptual phenomenology affects high-level human cognition is lacking. We addressed this gap by measuring a wide range of behavioral tasks in human participants after the exposure to VR immersive panoramic (360°) videos and their psychedelic counterparts generated by the DeepDream algorithm. Participants exhibited reduced task-switching costs after simulated psychedelic exposure compared to naturalistic exposure when instructed to invert the stimulus-response mapping, consistent with increased cognitive flexibility. No significant differences were observed between naturalistic and simulated psychedelic exposure in linguistic association tasks at word and sentence levels. Crucially, we found that visually grounded high-level cognitive processes were modulated by exposure to simulated hallucinations, as evidenced by participants’ drawing performance. These findings reveal how altering perceptual phenomenology through simulated visual hallucinations significantly modulates high-level human cognition. Our results provide insights into the interdependence of bottom-up and top-down cognitive processes and encourage further investigation into the effects of artificial psychedelic experiences on human cognition. This research may offer valuable insights into altered states of consciousness without pharmacological intervention, potentially informing both basic neuroscience and clinical applications.
The Three Stages of Learning to Master a Sensory Augmentation Device: Activation - Acquisition - Integration
Authors: Mühlinghaus Sascha , Schmidt Vincent , König Peter
Published: July 2024

By augmenting sensory perception through technology, researchers study how humans use and perceive the novel sensory input provided. Nevertheless, little is known about how learning unfolds over time. To this end, 27 participants trained with an augmentation device (feelSpace belt), which provides tactile feedback about the direction of the cardinal north, over the course of six weeks. During the training phase, we tracked participants’ progress using two different self-report questionnaires containing Likert-scale and open questions. Experts quantified responses to open questions using a previously established category system. As human raters are known to be susceptible to biases, we later reproduced the expert categorization using ChatGPT-4, finding a high congruence between the two classification approaches. The results suggest a three-stage model that best describes the process of acquiring an augmented sense. During the early activation stage, processing the augmented signal requires effort, induces fatigue, and a heightened awareness of the environment. In the knowledge acquisition phase, participants develop a more detailed cognitive spatial representation containing information about objects and places in relation to their current location. The deep integration stage is marked by participants seamlessly integrating the augmented information into existing perceptual processes and automatic use. The results support the supervised use of large language models (LLMs) for the analysis of qualitative data.
Pre-stimulus Activity Mediates Event-Related Theta Synchronization and Alpha Desynchronization During Memory Formation in Healthy Aging
Authors: Strzelczyk Dawid , Langer Nicolas
Published: July 2024

The capacity to learn is a key determinant for the quality of life but is known to decline to varying degrees with age. However, despite mounting evidence of memory deficits in older age, the neural mechanisms contributing to successful or impeded memory remain unclear. Previous research has primarily focused on memory formation through remembered versus forgotten comparisons, lacking the ability to capture the incremental nature of learning. Moreover, previous EEG studies have primarily examined oscillatory brain activity during the encoding phase, such as event-related synchronization (ERS) of mid-frontal theta and desynchronisation (ERD) of parietal alpha, while neglecting the potential influence of pre-stimulus activity. To address these limitations, we employed a sequence learning paradigm, where 113 young and 117 older participants learned a fixed sequence of visual locations through repeated observations (6423 sequence repetitions, 55 ’944 stimuli). This paradigm enabled us to investigate mid-frontal theta ERS, parietal alpha ERD, and how they are affected by pre-stimulus activity during the incremental learning process. Behavioral results revealed that young subjects learned significantly faster than older subjects, in line with expected age-related cognitive decline. Successful incremental learning was directly linked to decreases of mid-frontal theta ERS and increases of parietal alpha ERD. Notably, these neurophysiological changes were less pronounced in older individuals, reflecting a slower rate of learning. Importantly, the mediation analysis revealed that in both age groups, mid-frontal pre-stimulus theta partially mediated the relationship between learning and mid-frontal theta ERS. Furthermore, the overall impact of learning on parietal alpha ERD was primarily driven by its positive influence on pre-stimulus alpha activity. Our findings offer new insights into the age-related differences in memory formation and highlight the importance of pre-stimulus activity in explaining post-stimulus responses during learning.
Evolution of intrinsic transcriptional terminators in their genomic context
Authors: Toledo-Aparicio David , Denisov Stepan , Bernard Charles , Redondo Rodrigo AF , Carter Caroline C , Khomarbaghi Zahra , Pittrich Dorothea A , Nagy-Staron Anna , Guet Cali C , Lagator Mato
Published: July 2024

Transcriptional gene expression relies on two fundamental processes - transcription initiation and termination. Transcriptional termination is essential for the coordinated control of gene expression. Intrinsic termination, the major mechanism of transcriptional termination in bacteria, relies on the sequence-dependent folding of nascent mRNA into a hairpin structure that enables RNA polymerase to dissociate from DNA. Despite their central role in regulating expression in prokaryotic genomes, the conservation of intrinsic terminators and the factors that shape their evolution remain poorly understood. Here, we combine comparative genomics with experimental measurements of terminator function, to study the conservation of intrinsic terminators between Escherichia coli and Salmonella enterica subsp. pullorum. While the two species are closely related, the sequence and function of most terminators are not conserved, with less than 20% of all terminators having an identifiable ortholog - in stark contrast to 60% for coding sequences. Terminators with higher sequence conservation also had more conserved function, indicative of stabilizing selection. The local genomic context shapes the evolution of intrinsic terminators, as their sequence conservation is dependent on the conservation of the upstream gene, while their function is affected by the distance to the downstream gene. Ultimately, any theory of gene regulatory network evolution ought to account for how transcriptional terminators evolve.
In-SilicoAnalyses of Molecular Force Sensors for Mechanical Characterization of Biological Systems
Authors: Lopez Diana M. , Castro Carlos E. , Sotomayor Marcos
Published: July 2024

Mechanical forces play key roles in biological processes such as cell migration and sensory perception. In recent years molecular force sensors have been developed as tools forin situforce measurements. Here we use all-atom steered molecular dynamics simulations to predict and study the relationship between design parameters and mechanical properties for three types of molecular force sensors commonly used in cellular biological research: two peptide-and one DNA-based. The peptide-based sensors consist of a pair of fluorescent proteins, which can undergo Förster resonance energy transfer (FRET), linked by spider silk (GPGGA)nor synthetic (GGSGGS)ndisordered regions. The DNA-based sensor consists of two fluorophore-labeled strands of DNA that can be unzipped or sheared upon force application with a FRET signal as readout of dissociation. We simulated nine sensors, three of each kind. After equilibration, flexible peptide linkers of three different lengths were stretched by applying forces to their N-and C-terminal Cα atoms in opposite directions. Similarly, we equilibrated a DNA-based sensor and pulled on the phosphate atom of the terminal guanine of one strand and a selected phosphate atom on the other strand in the opposite direction. These simulations were performed at constant velocity (0.01 nm/ns – 10 nm/ns) and constant force (10 pN – 500 pN) for all versions of the sensors. Our results show how the force response of these sensors depends on their length, sequence, configuration and loading rate. Mechanistic insights gained from simulations analyses indicate that interpretation of experimental results should consider the influence of transient formation of secondary structure in peptide-based sensors and of overstretching in DNA-based sensors. These predictions can guide optimal fluorophore choice and facilitate the rational design of new sensors for use in protein, DNA, hybrid systems, and molecular devices.

STATEMENT OF SIGNIFICANCE

Biomolecular structures involved in various biological processes, including muscle function and sensory perception, generate, convey, and respond to mechanical forces.In-vivoaccurate measurement of these forces is challenging but needed to understand biological function. Here we present a comprehensive computational analysis of three different types of molecular force sensors used to report pico-Newton level forces in biomolecular systems. Our atom-level simulation predictions provide mechanistic insight that can facilitate experimental data interpretation, selection of sensor design parameters, and the development of new force sensors tailored to specific applications and environments.
An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes
Authors: Furlanis Elisabetta , Dai Min , Leyva Garcia Brenda , Vergara Josselyn , Pereira Ana , Pelkey Kenneth , Tran Thien , Gorissen Bram L. , Vlachos Anna , Hairston Ariel , Huang Shuhan , Dwivedi Deepanjali , Du Sarah , Wills Sara , McMahon Justin , Lee Anthony T. , Chang Edward F. , Razzaq Taha , Qazi Ahmed , Vargish Geoffrey , Yuan Xiaoqing , Caccavano Adam , Hunt Steven , Chittajallu Ramesh , McLean Nadiya , Hewit Lauren , Paranzino Emily , Rice Haley , Cummins Alex C. , Plotnikova Anya , Mohanty Arya , Tangen Anne Claire , Shin Jung Hoon , Azadi Reza , Eldridge Mark A.G. , Alvarez Veronica A. , Averbeck Bruno B. , Alyahyay Mansour , Reyes Vallejo Tania , Soheib Mohammed , Vattino Lucas G. , MacGregor Cathryn P. , Banks Emmie , Olah Viktor Janos , Naskar Shovan , Hill Sophie , Liebergall Sophie , Badiani Rohan , Hyde Lili , Xu Qing , Allaway Kathryn C. , Goldberg Ethan M. , Nowakowski Tomasz J. , Lee Soohyun , Takesian Anne E. , Ibrahim Leena A. , Iqbal Asim , McBain Chris J. , Dimidschstein Jordane , Fishell Gord , Wang Yating
Published: July 2024

In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate fine neuronal subtypes are still limited. Here, we performed systematic analysis of single cell genomic data to identify enhancer candidates for each of the cortical interneuron subtypes. We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic neurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (GCaMP) and manipulate (opto- or chemo-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.
Synergistic Biophysics and Machine Learning Modeling to Rapidly Predict Cardiac Growth Probability
Authors: Jones Clara E. , Oomen Pim J.A.
Published: July 2024

Abstract

Computational models that can predict growth and remodeling of the heart could have important clinical applications. However, the time it takes to calibrate and run current models while considering data uncertainty and variability makes them impractical for routine clinical use. This study aims to address this need by creating a computational framework to efficiently predict cardiac growth probability. We utilized a biophysics model to rapidly simulate cardiac growth following mitral valve regurgitation (MVR). Here we developed a two-tiered Bayesian History Matching approach augmented with Gaussian process emulators for efficient calibration of model parameters to align with growth outcomes within a 95%confidence interval. We first generated a synthetic data set to assess the accuracy of our framework, and the effect of changes in data uncertainty on growth predictions. We then calibrated our model to match baseline and chronic canine MVR data and used an independent data set to successfully validate the ability of our calibrated model to accurately predict cardiac growth probability. The combined biophysics and machine learning modeling framework we proposed in this study can be easily translated to predict patient-specific cardiac growth.
Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression
Authors: Venu Vrinda , Small Eric M. , Roth Cullen , Adikari Samantha H. , Cornelia Vlot Anna Hendrika , Sullivan Kyle A. , Abeyratne Chanaka Roshan , Jacobson Daniel , Starkenburg Shawn R. , Sanbonmatsu Karissa Y. , Steadman Christina R.
Published: July 2024

Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells). Treatment induced substantial (13%) genomic rearrangement that rebounds despite persistent gene expression changes and spreading of acetylation. The chromatin functional landscape (accessibility, active transcription modification, and gene expression) is controlled and locus-specific, while chromatin contacts are globally altered resulting in a moderate weakening of topologically associating domains. Chromatin states are more dynamic at transcriptionally active loci while genes with reduced expression are epigenetically stable suggesting chromatin architectural turnover and nucleosome remodeling is locus-specific and underlies the bidirectional expression changes. Thus, local 3D chromatin and genome structural dynamics is integral for loci regulation in response to epigenomic perturbation. The partial persistence of these altered features may have larger implications for efficacy of epigenetic drugs in amelioration of disease states.
Advancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences inBos indicus
Authors: Azam Sarwar , Sahu Abhisek , Pandey Naveen Kumar , Neupane Mahesh , Van Tassel Curtis P , Rosen Benjamin D , Gandham Ravi Kumar , Rath Subha Narayan , Majumdar Subeer S
Published: July 2024

Background

India, with the world’s largest cattle population and more than 50 registered breeds ofBos indicus, stands as a vital reservoir of genetic diversity. However, the abundant diversity among Indian cattle breeds highlights the inadequacy of a single reference sequence to represent the entire genomic content of desi cattle. We recognize the need to capture the genomic differences within theBos indicuspopulation as a whole, and specifically within the dairy cattle subset by identifying non-reference sequences and constructing a pangenome.

Finding

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ’Linked-Read’ technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to theBos indicusBrahman reference genome. A pangenome ofBos indicuscattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-Reference Unique Insertions (NUIs) spanning 7.57 Mbs was identified through both methods, representing the pangenome of IndianBos indicusbreeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with theBos tauruspangenome. Among these, 2,312 NUIs - encompassing ∼2 Mb, were commonly found in 98 samples of the 5 breeds and designated asBos indicusCommon Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (LncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis. The protein-coding genes were found in various prominent Quantitative Trait Loci (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly LINEs. Additionally,70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

Conclusion

This is the first report unveiling a robust set of NUIs defining the pangenome ofBos indicusbreeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.
Prediction of inhibitory peptides againstE. coliwith desired MIC value
Authors: Bajiya Nisha , Kumar Nishant , Raghava Gajendra P. S.
Published: July 2024

In the past, several methods have been developed for predicting antibacterial and antimicrobial peptides, but only limited attempts have been made to predict their minimum inhibitory concentration (MIC) values. In this study, we trained our models on 3,143 peptides and validated them on 786 peptides whose MIC values have been determined experimentally againstEscherichia coli(E. coli). The correlational analysis reveals that the Composition Enhanced Transition and Distribution (CeTD) attributes strongly correlate with MIC values. We initially employed the similarity search strategy utilizing BLAST to estimate MIC values of peptides but found it inadequate for prediction. Next, we developed machine learning techniques-based regression models using a wide range of features, including peptide composition, binary profile, and embeddings of large language models. We implemented feature selection techniques like minimum Redundancy Maximum Relevance (mRMR) to select the best relevant features for developing prediction models. Our Random forest-based regressor, based on selected features, achieved a correlation coefficient (R) of 0.78, R-squared (R²) of 0.59, and a root mean squared error (RMSE) of 0.53 on the validation dataset. Our best model outperforms the existing methods when benchmarked on an independent dataset of 498 inhibitory peptides ofE. coli. One of the major features of the web-based platform EIPpred developed in this study is that it allows users to identify or design peptides that can inhibitE. coliwith the desired MIC value (https://webs.iiitd.edu.in/raghava/eippred).

Highlights

Prediction of MIC value of peptides againstE.coli.

An independent dataset was generated for comparison.

Feature selection using the mRMR method.

A regressor method for designing novel inhibitory peptides.

A web server and standalone package for predicting the inhibitory activity of peptides.
CODARFE: Unlocking the prediction of continuous environmental variables based on microbiome
Authors: Barbosa Murilo Caminotto , da Silva João Fernando Marques , Alves Leonardo Cardoso , Finn Robert D , Paschoal Alexandre Rossi
Published: July 2024

Despite the surge in data acquisition, there is a limited availability of tools capable of effectively analyzing microbiome data that identify correlations between taxonomic compositions and continuous environmental factors. Furthermore, existing tools also do not predict the environmental factors in new samples, underscoring the pressing need for innovative solutions to enhance our understanding of microbiome dynamics and fulfill the prediction gap. Here, we introduce CODARFE, a novel tool for sparse compositional microbiome-predictors selection and prediction of continuous environmental factors. We tested CODARFE against four state-of-the-art tools in two experiments. First, CODARFE outperformed predictor selection in 21 out of 24 databases in terms of correlation. Second, among all the tools, CODARFE achieved the highest number of previously identified bacteria linked to environmental factors for human data—that is, at least 7% more. We also tested CODARFE in a cross-study, using the same biome but under different external effects (e.g., ginseng field and cattle for arable soil, and HIV and crohn’s disease for human gut), using a model trained on one dataset to predict environmental factors on another dataset, achieving 11% of mean absolute percentage error. Finally, CODARFE is available in five formats, including a Windows version with a graphical interface, to installable source code for Linux servers and an embedded Jupyter notebook available at MGnify -https://github.com/alerpaschoal/CODARFE.
The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth
Authors: Lyu Munan , Iida Hiroyuki , Eekhout Thomas , Mäkelä Meeri , Muranen Sampo , Ye Lingling , Vatén Anne , Wybouw Brecht , Wang Xin , De Rybel Bert , Mähönen Ari Pekka
Published: July 2024

During the process of secondary growth, the vascular cambium produces the conductive xylem and phloem cells, while the phellogen (cork cambium) deposit phellem (cork) as the outermost protective barrier. Although most of the secondary tissues is made up by parenchyma cells which are also produced by both cambia, their diversity and function are poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories of the cell types in theArabidopsisroot undergoing secondary growth. By analysing 93 reporter lines, we were able to identify 20 different cell types or cell states, many of which have not been described before. We additionally observed distinct transcriptome signatures of parenchyma cells depending on their maturation state and proximity to the conductive cell types. Our data shows that both xylem and phloem parenchyma tissues are required for normal formation of conductive tissue cell types. Furthermore, we showed that mature phloem parenchyma gradually obtains periderm identity, and this transition can be accelerated by jasmonate or wounding. Thus, our study reveals the remarkable dynamic and diverse nature of parenchyma cells during secondary growth.
Embryo movement is required for limb tendon maturation
Authors: Rolfe Rebecca A. , Talak Busturkmen Ebru , Sliney Lauren , Hayden Grace , Dunne Nicholas , Buckley Niamh , McCarthy Helen , Szczesny Spencer E. , Murphy Paula
Published: July 2024

Following early cell specification and tenocyte differentiation at the sites of future tendons, very little is known about how tendon maturation into robust load-bearing tissue is regulated. Between embryonic day (E)16 and E18 in the chick, there is a rapid change in mechanical properties which is dependent on normal embryo movement. However, the tissue, cellular and molecular changes that contribute to this transition are not well defined. Here we profiled aspects of late tendon development (collagen fibre alignment, cell organisation and Yap pathway activity), describing changes that coincide with tissue maturation. We compared effects of rigid (constant static loading) and flaccid (no loading) immobilisation to gain insight into developmental steps influenced by mechanical cues. We show that YAP signalling is active and responsive to movement in late tendon. Collagen fibre alignment increased over time and under static loading. Cells organise into end-to-end stacked columns with increased distance between adjacent columns, where collagen fibres are deposited; this organisation was lost following both types of immobilisation. We conclude that specific aspects of tendon maturation requires controlled levels of dynamic muscle-generated stimulation. Such a developmental approach to understanding how tendons are constructed will inform future work to engineer improved tensile load-bearing tissues.
Discrimination of Jamaican fruit bat lymphocytes by flow cytometry
Authors: Burke Bradly E. , Rocha Savannah M. , Campbell Corey , Creissen Elizabeth , Tjalkens Ronald B. , Ma Wenjun , Henao-Tamayo Marcela , Schountz Tony
Published: July 2024

Bats are natural reservoir hosts of many important zoonotic viruses but because there are few immunological reagents and breeding colonies available for infectious disease research, little is known about their immune responses to infection. We established a breeding colony Jamaican fruit bats (Artibeus jamaicensis) to study bat virology and immunology. The species is used as a natural reservoir model for H18N11 influenza A virus, and as a surrogate model for SARS-CoV-2, MERS-CoV and Tacaribe virus. As part of our ongoing efforts to develop this model organism, we sought to identify commercially available monoclonal antibodies (mAb) for profiling Jamaican fruit bat lymphocytes. We identified several cross-reactive mAb that can be used to identify T and B cells; however, we were unable to identify mAb for three informative T cell markers, CD3γ, CD4 and CD8α. We targeted these markers for the generation of hybridomas, and identified several clones to each that can be used with flow cytometry and fluorescence microscopy. Specificity of the monoclonal antibodies was validated by sorting lymphocytes, followed by PCR identification of confirmatory transcripts. Spleens of Jamaican fruit bats possess about half the number of T cells than do human or mouse spleens, and we identified an unusual population of cells that expressed the B cell marker CD19 and the T cell marker CD3. The availability of these monoclonal antibodies will permit a more thorough examination of adaptive immune responses in Jamaican fruit bats that should help clarify how the bats control viral infections and without disease.

Importance

Bats naturally host a number of viruses without disease, but which can cause significant disease in humans. Virtually nothing is known about adaptive immune responses in bats because of a lack of immunological tools to examine such responses. We have begun to address this deficiency by identifying several commercially available monoclonal antibodies to human and mouse antigens that are cross-reactive to Jamaican fruit bat lymphocyte orthologs. We also generated monoclonal antibodies to Jamaican fruit bat CD3γ, CD4 and CD8α that are suitable for identifying T cell subsets by flow cytometry and immunofluorescent staining of fixed tissues. Together, these reagents will allow a more detailed examination of lymphocyte populations in Jamaican fruit bats.
Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration
Authors: Lv Guohua , Sayles Nicole M. , Huang Yun , Mancinelli Chiara D. , McAvoy Kevin , Shneider Neil A. , Manfredi Giovanni , Kawamata Hibiki , Eliezer David
Published: July 2024

CHCHD10 is mutated in rare cases of FTD and ALS and aggregates in mouse models of disease. Here we show that the disordered N-terminal domain of CHCHD10 forms amyloid fibrils and report their cryoEM structure. Disease-associated mutations cannot be accommodated by the WT fibril structure, while sequence differences between CHCHD10 and CHCHD2 are tolerated, explaining the co-aggregation of the two proteins and linking CHCHD10 and CHCHD2 amyloid fibrils to neurodegeneration.
Preventing escape and malfunction of recoded cells due to tRNA base changes
Authors: Chiappino-Pepe Anush , Radford Felix , Budnik Bogdan , Taş Hüseyin , Augustin Teresa L , Burgess Hana M , Moret Michaël , Dharani Azim M , Zheng Qinmei , Fan Weicheng , Africawala Maksud M , Thapa Shova , Kuru Erkin , Narasimhan Kamesh , Marchand Jorge A , Perrotta Ramiro M , Stokes Jonathan M , Lunshof Jeantine E , Aach John D , Tam Jenny M , Church George M
Published: July 2024

Engineering the genetic code restricts DNA transfer (cellular bioisolation) and enables new chemistries via non-standard amino acid incorporation. These distinct properties make recoded cells state-of-the-art safe technologies. However, evolutionary pressures may endanger the longevity of the recoding. Here, we reveal that recodedEscherichia colilacking 18,214 serine codons and two tRNASercan express wild-type antibiotic resistance genes and escape up to seven orders of magnitude faster than expected. We show a two-step escape process whereby recoded cells mistranslate antibiotic resistance genes to survive until modified or mutated tRNAs reintroduce serine into unassigned codons. We developed genetic-code-sensitive kill switches that sense serine incorporation and prevent cellular escape while preserving encoding of three distinct non-standard amino acids. This work lays the foundation for the long-term controlled function of cells that incorporate new chemistries, with implications for the design, use, and biosafety of synthetic genomes in clinical and environmental applications where physical containment is insufficient.
Early evolution of BA.2.86 sheds light on the origins of highly divergent SARS-CoV-2 lineages
Authors: Escalera-Zamudio Marina , Tan Cedric C S , van Dorp Lucy , Balloux François
Published: July 2024

Since the emergence of SARS-CoV-2 in late 2019, highly divergent variants with novel constellations of mutations have periodically emerged to displace previously co-circulating virus lineages. The evolutionary mechanisms behind this process remain unclear, but the prevailing hypothesis supports emergence through single events followed by a rapid accumulation of mutations in individual long-term infections. In July 2023, the Omicron-descending BA.2.86 Variant of Interest (VOI) emerged to outcompete other virus lineages, with descending sublineages still dominating as of December 2024. We use BA.2.86 as a case study to test the hypothesis that highly divergent variants emerge during a single chronic infection. By applying a comprehensive suite of evolutionary analyses to independent high-resolution datasets, we identify a cluster of approximately 100 BA.2 genomes that fall directly ancestral and shorten the branch leading to BA.2.86, carrying some BA.2.86-specific lineage defining mutations. These genomes, sampled from multiple countries and at different timepoints, share a single ancestor dating back to December 2021. Additionally, we detect over 2600 earlier BA.2, BA.2.75, and XBB.1.5 genomes with multiple mutations later associated with BA.2.86. These genomes represent a standing genetic variation that likely facilitated a gradual evolution in the direct ancestry of this variant. We further uncover a complex evolutionary process involving recombination between the BA.2.75 and XBB.1.5 parental lineages. Together, our results challenge the notion of a single emergence event, and instead support a more complex scenario, with BA.2.86 likely having evolved over multiple transmission chains.
Rapid Detection of Active Coronavirus Infection by Lateral Flow Test Strips: A New Approach to Distinguish Replicating Viruses from Non-Replicating Viruses
Authors: Davis Darnell , Lamb Caitlin H. , Myhrvold Cameron , Ullah Hemayet
Published: July 2024

This manuscript describes the development of an alternative method to detect active coronavirus infection, which targets negative-sense RNA, a product of active viral replication. Few diagnostic methods are capable of discriminating between replicating and non-replicating viruses, complicating decisions related to quarantine and therapeutic interventions. We propose strand-specific nucleic acid diagnostics as a means of distinguishing between active and inactive RNA virus infections and prototype a CRISPR-based lateral flow assay that specifically detects replicating coronaviruses. Such a paradigm in diagnostics could guide more effective public health measures to curb the spread of SARS-CoV-2 and other single-stranded viruses.