bluuebunny/crossref_metadata_2025 huggingface dataset:
The Influence of Knee Varus Deformity on the Kinematic and Dynamic Characteristics of Musculoskeletal Models During Gait
Authors: Tabeiy Sina , Karimpour Morad , Shirvani Azizollah , Vaziri Arash Sherafat
Published: November 2023

Background

Musculoskeletal modeling has paved the way of measuring kinematic and kinetic variables during motions. Nonetheless, since the commonly-used generic models are created based on averaged data; thus, they cannot accurately mimic subjects with skeletal deformities. To overcome this obstacle, one can build personalized models based on subject’s MRI or CT scan data, which is both time and money consuming. The other promising way is to manipulate generic models and create semi-personalized models to match with the individual’s skeletal system at the joint of interest.

Research Question

Can a semi-personalized model reduce marker error in gait analysis? How a semi-personalized model differentiates the ROM of the lower limb joints and muscle activation pattern while having varus deformity?

Method

We developed the varus-valgus tool (freely available on:https://simtk.org/projects/var-val-tool) in MATLAB using OpenSim Application Programming Interface (API) to incorporate varus-valgus deformity in the generic OpenSim models. A 36-year-old female subject with a complaint of knee pain participated in our study. The subject had 6.5 and 11.9 degrees of varus in the right and left leg, respectively. A semi-personalized model of the subject was first created using generic OpenSim models. Then, markers’ error during Inverse Kinematic (IK), joints Range of Motion (ROM) and the activation of Tensor Fasciae Latae (TFL), a knee adductor, and Gracilis, a knee abductor, were calculated and compared between a semi-personalized model and a generic model.

Results

Significant difference was observed in markers’ error during IK between generic and semipersonalized models (p<0.05). Substantial alterations were found in the ROM of the hip, knee and ankle joints while using semi-personalized model. Moreover, the activation pattern of TFL experienced a dramatic rise whereas Gracilis saw a fall during each gait cycle in semi-personalized models.

Significance

Implementing varus-valgus deformity in the generic models substantially reduces markers’ error which leads to more accurate results. It was observed that semi-personalized models showed different ROM compared to generic ones.
DeepSipred: A deep-learning-based approach on siRNA inhibition prediction
Authors: Liu Bin , Huang Huiya , Liao Weixi , Pan Xiaoyong , Jin Cheng , Yuan Ye
Published: November 2023

Motivation

The use of exogenous small interfering RNAs (siRNAs) for gene silencing has become a widespread molecular tool for gene function study and new drug identification. Although the pathway of RNAi to mediate gene expression has been widely investigated, the selection of hyperfunctional siRNA with high inhibition remains challenging.

Results

In this study, we build a deep-learning-based approach on siRNA inhibition prediction, named DeepSipred. It combines features from sequence context, thermodynamic property, and other expert knowledge together to predict the inhibition more accurately than existing methods. The sequence features from siRNA and local target mRNA are generated via one-hot encoding and pretrained RNA-FM encoding. The convolution layers with multiple kernels in DeepSipred can detect various decisive motifs, which will determine the actual inhibition of siRNA. The thermodynamic features are calculated from Gibbs Free Energy. In addition, the expert knowledge includes those design criteria from previous studies. Benchmarked on large available public datasets, the 10-fold cross-validation results indicate that our predictor achieving the state-of-the-art performance.

Contact

yuanye_auto@sjtu.edu.cnorchengjin520@sjtu.edu.cn.
Cultural use of tropane alkaloids ofBrugmansiaspecies and cultivars in Colombia depends on local plant growth environment rather than genetic diversity
Authors: Rojas Sofia , Madriñan Santiago , Stahl Mark , Harter Klaus
Published: November 2023

Borracheros or Angel Trumpets (Brugmansiaspp.) of theSolanaceaeplant family are known for producing scopolamine and other tropane alkaloids and are widely used by indigenous communities in the Andes for medicinal and ritual purposes. Growing different varieties has increased the popularity ofBrugmansiaspecies in recent years, leading to the promotion of hybridization to get new morphotypes. However, so far no medical or cultural use of plant extracts could be linked to selectedBrugmansiaspecies or cultivars. Moreover, until now there is only limited knowledge about the effect of hybridization on tropane alkaloid contents and/or diversity ofBrugmansiaspecies or cultivars. Here, a liquid chromatography-mass spectrometry (LC-MS) approach was applied to identify and characterize secondary metabolite contents in variousBrugmansiaspecies and hybrids from different geographic origins in Colombia. The analysis of the metabolic data sets revealed that tropane alkaloids and other secondary metabolites accumulate in a leaf and flower specific manner. Although some minor differences were found betweenBrugmansiasubgroups, the only significant difference exists between plants collected in the Sibundoy Valley, where they have been domesticated by indigenous communities since a long time and those, which so far have not been used by humans at all. The different genetic constitutions ofBrugmanciaspecies and cultivars are not the dominating reason for their differences in tropane alkaloid contents and medical and cultural usages, as there is no clear taxonomical signature based on the metabolite properties for species segregation. Instead, their use by indigenous communities during ceremonies and for medical treatment such as wound healing, infection control, rheumatism and arthritis is rather caused by the plasticity of the individual plants to react to the local abiotic and biotic environments by the variation of secondary metabolite composition and by the differences in the bioavailability of the active compounds as result of the extraction method.
Epigenetic predictors of species maximum lifespan and other life history traits in mammals
Authors: Li Caesar Z. , Haghani Amin , Yan Qi , Lu Ake T. , Zhang Joshua , Fei Zhe , Ernst Jason , Yang X. William , Gladyshev Vadim N. , Raj Ken , Seluanov Andrei , Gorbunova Vera , Horvath Steve
Published: November 2023

Maximum lifespan is an intrinsic characteristic of a biological species and is defined as the longest time an individual of a species has been reported to survive. By analyzing 15K samples derived from 348 mammalian species representing 25 taxonomic orders we previously identified CpG methylation sites associated with maximum lifespan. Here we present accurate DNA methylation-based (DNAm) predictors of maximum lifespan (r=0.89), average gestation time (r=0.96), and age at sexual maturity (r=0.85). Our DNAm maximum lifespan predictor indicates a potential innate longevity advantage for females over males in 17 mammalian species such as humans, red deer, and cattle. The DNAm maximum lifespan predictions do not vary significantly by caloric restriction and partial reprogramming. Genetic disruptions in the somatotropic axis, which includes growth hormone, IGF-1, and their related receptors, have an impact on DNAm maximum lifespan only in select mouse tissues. Cancer mortality rates in major mammalian orders show no correlation with our epigenetic estimates of life history traits. The DNAm maximum lifespan predictor does not detect variation in lifespan between individuals of the same species, such as between the breeds of dogs. We also present the first prototypes of accurate pan mammalian DNAm predictors of sex and tissue type.

Collectively, our findings indicate that maximum lifespan is determined, at least in part, by an epigenetic signature that is an intrinsic property of each species and is distinct from the signatures that relate to individual lifespan, which is unaffected by interventions influencing the mortality risk of individuals.
The proteome of agroinfiltratedNicotiana benthamianais shaped by extensive protein processing
Authors: Zheng Kaijie , Lyu Joy C. , Thomas Emma L. , Schuster Mariana , Sanguankiattichai Nattapong , Ninck Sabrina , Kaschani Farnusch , Kaiser Markus , van der Hoorn Renier A. L.
Published: November 2023

Processing by proteases irreversibly regulates the fate of plant proteins and hampers the production of recombinant protein in plants, yet only few processing events have been described in agroinfiltratedNicotiana benthamiana, which has emerged as a favorite transient protein expression platform in plant science and molecular pharming. Here, we used in-gel digests and mass spectrometry to monitor the migration and topography of 5,040 plant proteins of agroinfiltratedN. benthamianawithin a protein gel. By plotting the peptides over the gel slices, we generated peptographs that reveal where which part of each protein was detected within the protein gel. These data uncovered that 60% of the detected proteins have proteoforms that migrate at lower than predicted molecular weights, implicating extensive proteolytic processing. For instance, this analysis confirms the proteolytic removal and degradation of autoinhibitory prodomains of most but not all proteases, and revealed differential processing within pectinemethylesterase and lipase families. This analysis also uncovered intricate processing of glycosidases and uncovered that ectodomain shedding might be common for a diverse range of receptor-like kinases. Transient expression of double-tagged candidate proteins confirmed various processing eventsin vivo. This extensive proteomic dataset can be investigated further and demonstrates that most plant proteins are proteolytically processed and implicates an extensive proteolytic machinery shaping the proteome of agroinfiltratedN. benthamiana.
Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538
Authors: Bay Yasmin , Fransen Stine M. , Pickering Darryl S. , Frydenvang Karla , Francotte Pierre , Pirotte Bernard , Kristensen Anders Skov , Kastrup Jette Sandholm
Published: November 2023

Kainate receptors play an important role in the central nervous system by mediating postsynaptic excitatory neurotransmission and modulating the release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. To date, only three structures of the ligand-binding domain (LBD) of the kainate receptor subunit GluK1 in complex with positive allosteric modulators have been determined by X-ray crystallography, all belonging to class II modulators. Here, we report a high-resolution structure of GluK1-LBD in complex with kainate and BPAM538, which belongs to the full-spanning class III. One BPAM538 molecule binds at the GluK1 dimer interface, thereby occupying two allosteric binding sites simultaneously. BPAM538 stabilizes the active receptor conformation with only minor conformational changes being introduced to the receptor. Using a calcium-sensitive fluorescence-based assay, a 5-fold potentiation of the kainate response (100 μM) was observed in the presence of 100 μM BPAM538, whereas no potentiation was observed at GluK2.

Highlights

1.9 Å structure of the kainate receptor GluK1-LBD in complex with kainate and BPAM538

The positive allosteric modulator BPAM538 occupies two binding sites

The binding mode is similar to class III modulators described for AMPA receptors

BPAM538 prefers GluK1 over GluK2
Active-like structure of the ligand-binding domain of GluK2 with L-glutamate and the positive allosteric modulator BPAM344
Authors: Bay Yasmin , Jeppesen Mie Egeberg , Frydenvang Karla , Francotte Pierre , Pirotte Bernard , Pickering Darryl S. , Kristensen Anders Skov , Kastrup Jette Sandholm
Published: November 2023

Kainate receptors belong to the family of ionotropic glutamate receptors and contribute to the majority of fast excitatory neurotransmission. Consequently, they also play a role in brain diseases. Therefore, understanding how these receptors can be modulated is of importance. Our study provides a dimeric crystal structure of the ligand-binding domain of the kainate receptor GluK2 in complex with L-glutamate and the small molecule positive allosteric modulator, BPAM344, in an active-like conformation. The role of Thr535 and Gln786 for modulation of GluK2 by BPAM344 was investigated using a calcium-sensitive fluorescence-based assay on transiently transfected cells expressing GluK2 and mutants hereof. This study may aid design of tool compounds targeting kainate receptors, elucidating their potential as targets for treatment of brain diseases.
High temporal frequency light response in mouse retina requires FAT3 signaling in bipolar cells
Authors: Avilés Evelyn C. , Wang Sean K. , Patel Sarina , Shi Shuxiang , Lin Lucas , Kefalov Vladimir J. , Goodrich Lisa V. , Cepko Constance L. , Xue Yunlu
Published: November 2023

Vision is initiated by the reception of light by photoreceptors and subsequent processing via downstream retinal neurons. Proper cellular organization depends on the multi-functional tissue polarity protein FAT3, which is required for amacrine cell connectivity and retinal lamination. Here we investigated the retinal function ofFat3mutant mice and found decreases in physiological and perceptual responses to high frequency flashes. These defects did not correlate with abnormal amacrine cell wiring, pointing instead to a role in bipolar cell subtypes that also express FAT3. The role of FAT3 in the response to high temporal frequency flashes depends upon its ability to transduce an intracellular signal. Mechanistically, FAT3 binds to the synaptic protein PTPσ, intracellularly, and is required to localize GRIK1 to OFF-cone bipolar cell synapses with cone photoreceptors. These findings expand the repertoire of FAT3’s functions and reveal its importance in bipolar cells for high frequency light response.
Cannabinoid receptor type 2 expression in mouse brain: from mapping to regulation in microglia under inflammatory conditions
Authors: Grabon Wanda , Ruiz Anne , Gasmi Nadia , Degletagne Cyril , Georges Béatrice , Belmeguenai Amor , Bodennec Jacques , Rheims Sylvain , Marcy Guillaume , Bezin Laurent
Published: November 2023

Since its detection in the brain, the cannabinoid receptor type 2 (CB2) has been deemed a promising therapeutic target for various neurological and psychiatric disorders. However, precise brain mapping of CB2 expression is currently lacking. Using magnetic cell sorting, calibrated reverse transcription-quantitative PCR, and single-nucleus RNA-seq, we revealed the low level of CB2 expression in all brain regions examined, mainly by a few microglial cells and by neurons in an even lower proportion. Upon lipopolysaccharide stimulation to simulate non-sterile neuroinflammatory conditions, we demonstrated that the inflammatory response was associated with a transient reduction in CB2 mRNA levels in the brain tissue, particularly in microglia. This result, confirmed in the BV2 microglial cells, contrasts with the positive correlation observed between CB2 mRNA levels and the inflammatory response upon stimulation by interferon-gamma, which models sterile inflammatory conditions. Thus, discrete brain CB2 expression may be upregulated or downregulated depending on the inflammatory context.
Effect of Schizophrenia linkedDRD2gene mutations and correlation of social behavior with biochemical changes in a post-weaning isolated mouse model
Authors: Mukesh Nivedhitha , Divi Pavan Kumar , Maikap Shimantika , Mohapatra Saswati , Rajan Muskaan , Kanthimath Sanjana , Mishra Nishant , Kar Karunakar , Anand Bibin G , Annamneedi Anil
Published: November 2023

Neurological disorders encompass a diverse range of conditions that affect individuals cognitive, emotional, and social functioning. Though these disorders are multifactorial, genetic factors play a significant role in the pathogenesis. Especially, synaptic gene mutations or synaptic protein dysfunction are shown to be closely associated with neuropathology. This study aims at understanding the critical role of synaptic compartment by conducting comprehensive analysis of existing synaptic gene mutations responsible for the development of three significant disorders in the Indian population: autism spectrum disorder (ASD), epilepsy and schizophrenia (SZ). Ourin-silicoanalysis predicts that mutations in synaptic genesRPL10(rs387906727),GABRA1(rs121434579) andDRD2(rs1801028) corresponding to ASD, epilepsy and SZ respectively, are deleterious. Of these, SZ-related mutations inDRD2(D(2) dopamine receptor) are deleterious and due to its genetic association also with ASD as well sociosexual behavior, this study focuses on DRD2.In silicoanalysis using molecular docking revealed an abnormal interaction between D(2) dopamine receptor and neuronal calcium sensor 1, which may hamper neurotransmitter regulation. We further employed a post-weaning social isolation mice model of SZ to investigate the D(2) dopamine receptor expression levels in hippocampus and social behavioral changes. We observed a reduced immunofluorescent intensities of D(2) dopamine receptor and NCS1 compared to group-housed controls in hippocampus and a trend towards an impaired sociosexual behavior characterized by anogenital sniffing in a male-female social interaction test. Altogether, our study helps to further our understanding of synaptic signaling in the context of SZ and decode the probable mechanism by which disrupted synaptic signaling and protein-protein interaction may lead to the disease pathology and further aid in identifying novel therapeutic targets.
HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression
Authors: Keikhosravi Adib , Almansour Faisal , Bohrer Christopher H. , Fursova Nadezda A. , Guin Krishnendu , Sood Varun , Misteli Tom , Larson Daniel R. , Pegoraro Gianluca
Published: November 2023

High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software for image analysis workflows does not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new algorithms for existing analysis pipelines and to adding new analysis pipelines through separate plugins. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI analysis platform for a variety of cell biology applications.
Three-dimensional chromatin landscapes in MLLr AML
Authors: Sui Pinpin , Zhang Peng , Pan Feng
Published: November 2023

Rearrangements of the mixed lineage leukemia (MLLr) gene are frequently associated with aggressive acute myeloid leukemia (AML). However, the treatment options are limited due to the genomic complexity and dynamics of 3D structure, which regulate oncogene transcription and leukemia development. Here, we carried out an integrative analysis of 3D genome structure, chromatin accessibility, and gene expression in gene-edited MLL-AF9 AML samples. Our data revealed profound MLLr-specific alterations of chromatin accessibility, A/B compartments, topologically associating domains (TAD), and chromatin loops in AML. The local 3D configuration of the AML genome was rewired specifically at loci associated with AML-specific gene expression. Together, our results show that the 3D chromatin undergoes extensive reorganization at multiple architectural levels, which underpins the remodeling of the transcriptome in MLLr AML.
Experimental evidence of nocturnal pollination services for berry crops
Authors: Blareau Elsa , Requier Fabrice
Published: November 2023

Insect-mediated pollination is essential for crop production but is mainly studied considering diurnal pollinators only. Using pollinator exclusion techniques to prevent either diurnal or nocturnal insect visits we estimate the contribution of day-active and night-active pollinators to fruit set, seed set, fruit weight and fruit volume in three berry crops. We find that nocturnal pollination improves seed set compared to exclusion of all insect visits for one crop (raspberry), confirming the existence and importance of a nocturnal pollination service. Moreover, we found a general pattern where best crop pollination resulted from combined services of diurnal and nocturnal insect visits. These results call for urgent consideration of nocturnal pollination in crop production and management, towards inclusive pollinator-friendly schemes including night-active pollinators.
Auxetic patch material exhibits systolic thickening and restores pump function in a finite element model of acute myocardial infarction repair
Authors: Borrello Joseph , Zheng Zirui , Estrada Ana Cristina , Costa Kevin D.
Published: November 2023

Passive mechanical reinforcement of the infarcted heart has been shown to counteract infarct expansion and left ventricular (LV) functional degradation. However, traditional patch plasty of the ischemic region also restricts diastolic filling, reducing cardiac output. These negative side-effects can be minimized with strategic modification of the standard patch, suggesting further functional improvements could be possible through a broader exploration of patch materials. This study examines the potential advantages of a patch graft with auxetic properties, having a negative Poisson’s ratio (ν < 0). For preliminary evaluation, an established finite element model of LV biomechanics pre- and post-acute infarction, originally developed for modeling patch plasty with non-auxetic, or meiotic, materials, was modified to simulate epicardial implantation of auxetic patch materials. A homogeneous auxetic patch graft (ν = -0.2) exhibited radial thickening during systole, driven by tension on the patch from the neighboring contracting myocardium; but the patch thickness expanded away from the LV cavity and therefore did not improve ventricular mechanics compared to a standard meiotic patch graft (ν = 0.4). Alternatively, a heterogeneous auxetic patch design with an outer reinforcement layer caused inwardly-directed systolic thickening that restored the LV pressure-volume relationship toward baseline function, without adversely affecting fiber stress in the border zone or remote myocardium compared to the meiotic patch. This computational modeling study demonstrates the potential to harness auxetic mechanical properties for improving LV pump function in the setting of acute myocardial infarction, motivating further experimental validation of auxetic metamaterial patch devices for surgical repair of injured myocardium.
TRAFICA: An Open Chromatin Language Model to Improve Transcription Factor Binding Affinity Prediction
Authors: Xu Yu , Wang Chonghao , Xu Ke , Ding Yi , Lyu Aiping , Zhang Lu
Published: November 2023

Abstract

In silico transcription factor and DNA (TF-DNA) binding affinity prediction plays a vital role in examining TF binding preferences and understanding gene regulation. The existing tools employ TF-DNA binding profiles fromin vitrohigh-throughput technologies to predict TF-DNA binding affinity. However, TFs tend to bind to sequences in open chromatin regionsin vivo, such TF binding preference is seldomly considered by these existing tools. In this study, we developed TRAFICA, an open chromatin language model to predict TF-DNA binding affinity by integrating the characteristics of sequences from open chromatin regions in ATAC-seq experiments andin vitroTF-DNA binding profiles from high-throughput technologies. We applied self-supervised learning to pre-train TRAFICA on over 13 million nucleotide sequences from the peaks in ATAC-seq experiments to learn the TF binding preferencein vivo. TRAFICA was further fine-tuned using the TF-DNA binding profiles from PBM and HT-SELEX technologies to learn the association between TFs and their target DNA sequences. We observed that TRAFICA significantly outperformed both machine learning-based and deep learning-based tools in predictingin vitroandin vivoTF-DNA binding affinity. These findings indicate that considering the characteristics of sequences from open chromatin regions could significantly improve TF-DNA binding affinity prediction, particularly when limited TF-DNA binding profiles from high-throughput technologies are available for specific TFs.
Electrophysiological analyses of human dorsal root ganglia and human induced pluripotent stem cell-derived sensory neurons from male and female donors
Authors: Zurek Nesia A. , Ehsanian Reza , Goins Aleyah E. , Adams Ian M. , Petersen Timothy , Goyal Sachin , Shilling Mark , Westlund Karin N. , Alles Sascha R.A.
Published: November 2023

Human induced pluripotent stem cell-derived sensory neurons (hiPSC-SNs) and human dorsal root ganglia (hDRG) neurons are popular tools in the field of pain research; however, few groups make use of both approaches. For screening and analgesic validation purposes, important characterizations can be determined of the similarities and differences between hDRG and hiPSC-SNs. This study focuses specifically on electrophysiology properties of hDRG in comparison to hiPSC-SNs. We also compared hDRG and hiPSC-SNs from both male and female donors to evaluate potential sex differences. We recorded neuronal size, rheobase, resting membrane potential, input resistance, and action potential waveform properties from 83 hiPSCs-SNs (2 donors) and 108 hDRG neurons (9 donors). We observed several statistically significant electrophysiological differences between hDRG and hiPSC-SNs, such as size, rheobase, input resistance, and several actional potential (AP) waveform properties. Correlation analysis also revealed many properties that were positively or negatively correlated, some of which were differentially correlated between hDRG and hiPSC-SNs. This study shows several differences between hDRG and hiPSC-SNs and allows better understanding of the advantages and disadvantages of both for use in pain research. We hope this study will be a valuable resource for pain researchers considering the use of these humanin vitrosystems for mechanistic studies and/or drug development projects.
Limitations of line-scan MRI for directly measuring neural activity
Authors: Wilson Joshua M. , Wu Hua , Kerr Adam B. , Wandell Brian A. , Gardner Justin L.
Published: November 2023

Several groups have reported using 2D line-scan MRI sequences in humans and mice to directly measure neural responses to stimuli (the “DIANA response”). Other groups have been unable to replicate the DIANA response, even with higher field strength and more repetitions. Part of this discrepancy is likely due to a limited understanding of the noise profile of the line-scan MRI sequence: specifically, the consequences of deviations from the assumption of stationarity between each line acquisition. Here, we collected data using an MRI line-scan method while human subjects viewed a blank screen with the purpose of studying noise unique to the acquisition sequence. We found temporal fluctuations in the reconstructed time series from localized groups of voxels that could easily be confused with neural responses to stimuli. These fluctuations were present both in the head and in the surrounding empty volume along the span of the phase-encoding direction from the head. The timing of these fluctuations varied systematically and smoothly along the phase-encoding direction. These features can be explained by a model that accounts for the acquisition sequence and incorporates time-varying contrast fluctuations in the imaging substrate. Using the model, we quantify the amount of cortical- and scan-averaging one might need to reliably distinguish a DIANA response from noise.
PAH DEFICIENT PATHOLOGY IN HUMANIZED c.1066-11G>A PHENYLKETONURIA MICE
Authors: Martínez-Pizarro Ainhoa , Picó Sara , López-Márquez Arístides , Rodriguez-López Claudia , Montalvo Elena , Alvarez Mar , Castro Margarita , Ramón-Maiques Santiago , Pérez Belén , Lucas José J , Richard Eva , Desviat Lourdes R
Published: November 2023

We have generated using CRISPR/Cas9 technology a partially humanized mouse model of the neurometabolic disease phenylketonuria (PKU), carrying the highly prevalentPAHvariant c.1066-11G>A. This variant creates an alternative 3’ splice site, leading to the inclusion of 9 nucleotides coding for 3 extra amino acids between Q355 and Y356 of the protein. HomozygousPahc.1066-11A mice, with a partially humanized intron 10 sequence with the variant, accurately recapitulate the splicing defect and present almost undetectable hepatic PAH activity. They exhibit fur hypopigmentation, lower brain and body weight and reduced survival. Blood and brain phenylalanine levels are elevated, along with decreased tyrosine, tryptophan and monoamine neurotransmitter levels. They present behavioral deficits, mainly hypoactivity and diminished social interaction, locomotor deficiencies and an abnormal hind-limb clasping reflex. Changes in the morphology of glial cells, increased GFAP and Iba1 staining signals and decreased myelinization are observed. Hepatic tissue exhibits nearly absent PAH protein, reduced levels of chaperones DNAJC12 and HSP70 and increased autophagy markers LAMP1 and LC3BII, suggesting possible coaggregation of mutant PAH with chaperones and subsequent autophagy processing. This PKU mouse model with a prevalent human variant represents a useful tool for pathophysiology research and for novel therapies development.
Using compartmental models to understand excitation-inhibition imbalance in epilepsy
Authors: Kamaraj Aravind Kumar , Szuromi Matthew Parker , Galvis Daniel , Stacey William , Skeldon Anne C , Terry John
Published: November 2023

Epileptic seizures are characterized by abnormal synchronous bursting of neurons. This is commonly attributed to an imbalance between excitatory and inhibitory neurotransmission. We introduce compartmental models from epidemiology to study this interaction between excitatory and inhibitory populations of neurons in the context of epilepsy. Neurons could either be bursting or susceptible, and the propagation of action potentials within the brain through the bursting of neurons is considered as an infection spreading through a population. We model the recruitment of neurons into bursting and their subsequent decay to susceptibility to be influenced by the proportion of excitatory and inhibitory neurons bursting, resulting in a two population Susceptible – Infected - Susceptible (SIS) model. This approach provides a tractable framework to inspect the mechanisms behind seizure generation and termination. Considering the excitatory neurotransmission as an epidemic spreading through the neuronal population and the inhibitory neurotransmission as a competing epidemic that stops the spread of excitation, we establish the conditions for a seizure-like state to be stable. Subsequently, we show how an activity-dependent dysfunction of inhibitory mechanisms such as impaired GABAergic inhibition or inhibitory–inhibitory interactions could result in a seizure even when the above conditions are not satisfied.
Pseudomonas syringaeinfectivity correlates to altered transcript and metabolite levels ofArabidopsisMediator mutants
Authors: Blomberg Jeanette , Tasselius Viktor , Vergara Alexander , Karamat Fazeelat , Imran Qari Muhammad , Strand Åsa , Rosvall Martin , Björklund Stefan
Published: November 2023

Rapid metabolic responses to pathogens are essential for plant survival and depend on numerous transcription factors. Mediator is the major transcriptional co-regulator for integration and transmission of signals from transcriptional regulators to RNA polymerase II. Using four Arabidopsis Mediator mutants,med16,med18,med25andcdk8, we studied how differences in regulation of their transcript and metabolite levels correlate to their responses toPseudomonas syringaeinfection. We found thatmed16andcdk8were susceptible, whilemed25showed increased resistance. Glucosinolate, phytoalexin and carbohydrate levels were reduced already before infection inmed16andcdk8, but increased inmed25, which also displayed increased benzenoids levels. Early after infection, wild type plants showed reduced glucosinolate and nucleoside levels, but increases in amino acids, benzenoids, oxylipins and the phytoalexin Camalexin. The Mediator mutants showed altered levels of these metabolites and in regulation of genes encoding key enzymes for their metabolism. At later stage, mutants displayed defective levels of specific amino acids, carbohydrates, lipids and jasmonates which correlated to their infection response phenotypes. Our results reveal thatMED16,MED25andCDK8are required for a proper, coordinated transcriptional response of genes which encode enzymes involved in important metabolic pathways for Arabidopsis responses toPseudomonas syringaeinfections.

HIGHLIGHT

Plants need to defend themselves against different types of infections. We show that subunits of the Mediator transcriptional coactivator coordinate metabolic responses ofArabidopsis thalianato infections byPseudomonas syringae.
Chromosome-scale genome assembly ofPoa trivialisand population genomics reveals widespread gene flow in a cool-season grass seed production system
Authors: Brunharo Caio A. C. G. , Benson Christopher W. , Huff David R. , Lasky Jesse R.
Published: November 2023

Poa trivialis(L.) is a cool-season grass species found in various environments worldwide. In addition to being a desired turfgrass species, it is a common weed of agricultural systems and natural areas. As a weed, it is an important contaminant of commercial cool-season grass seed lots, resulting in widespread gene flow facilitated by human activities and causing significant economic losses to farmers. To better understand and manage infestations, we assembled and annotated a haploid genome ofP. trivialisand studied troublesome field populations from Oregon, the largest cool-season grass seed producing region in the United States. The genome assembly resulted in 1.35 Gb of DNA sequence distributed among seven chromosome-scale scaffolds, revealing a high content of transposable elements, conserved synteny withP. annua, and a close relationship with other C3grasses. A reduced-representation sequencing analysis of field populations revealed limited genetic diversity and suggested potential gene flow and human-assisted dispersal in the region. The genetic resources and insights intoP. trivialisprovided by this study will improve weed management strategies and enable the development of molecular detection tests for contaminated seed lots to limit seed-mediated gene flow. These resources should also be beneficial for turfgrass breeders seeking to improve desirable traits of commercialP. trivialisvarieties and help to guide breeding efforts in other crops to enhance the resiliency of agricultural ecosystems under climate change.

Significance statement

The chromosome-scale assembly ofPoa trivialisand population genomic analyses provide crucial insights into the gene flow of weedy populations and contribute a valuable genomic resource for the plant science community.
Traitor-virus-guided discovery of novel antiviral factors
Authors: Prelli Bozzo Caterina , Laliberté Alexandre , De Luna Aurora , Pastorio Chiara , Regensburger Kerstin , Krebs Stefan , Graf Alexander , Blum Helmut , Volcic Meta , Sparrer Konstantin M.J. , Kirchhoff Frank
Published: November 2023

Complex pathogen-host interactions govern the outcome of viral exposures but remain poorly understood because current methods to elucidate antiviral mechanisms are prone to artefacts and lack sensitivity. Here, we developed a virus-guided technology platform where the pathogen itself reveals its cellular opponents. To accomplish this, we engineered replication-competent HIV-1 expressing sgRNAs targeting potential antiviral genes in Cas9-expressing CD4+T cells. Simultaneous analysis of HIV-1 constructs targeting >500 candidate genes revealed that sgRNAs againstGRN,CIITA,EHMT2,CEACAM3,CC2D1B,RHOAandHMOX1are strongly enriched over several rounds of replication. Overexpression and knock-out studies confirmed the antiretroviral activity of most factors but failed for some. Finally, we show that lack of the accessorynefgene increased enrichment of sgRNAs targeting SERINC5 and IFI16 demonstrating that this method allows identification of targets of accessory proteins. The versatile and effective HIV-guided CRISPR technology offers numerous possibilities for clarification of virus-host interactions and innate defense mechanisms.
Flood-irrigated agriculture mediates climate-induced wetland scarcity for summering sandhill cranes in western North America
Authors: Donnelly J. Patrick , Collins Daniel P. , Knetter Jeffrey M. , Gammonley James H. , Boggie Matthew A. , Grisham Blake A. , Cathy Nowak M. , Naugle David E.
Published: November 2023

Documenting a species’ extent is often the first step in understanding its ecology and is critical to informing conservation planning. Basic information about species distributions is lacking in many regions of the world, forcing natural resource managers to answer complex ecological questions with incomplete data. Information gaps are compounded by climate change, driving resource bottlenecks that can act as new and powerful demographic constraints on fauna. Here, we reconstructed greater sandhill crane (Antigone canadensis tabida) summering range in western North America using movement data from 120 GPS-tagged individuals to determine how landscape composition shaped their distributions. Landscape variables developed from remotely sensed data were combined with bird locations using cloud computing and machine learning to model distribution probabilities. Additionally, land-use practices and land ownership were summarized within summer range as a measure of use dependence. Wetland variables identified as important predictors of bird distributions were also evaluated in a post hoc analysis using satellite imagery to measure the long-term (1984–2022) effects of climate-driven surface water drying. Wetlands and associated agricultural practices accounted for 1.2% of the summer range but were key predictors of greater sandhill crane occurrence. Bird distributions were patterned primarily by riparian floodplains that concentrated water, wetlands, and flood-irrigated agriculture in otherwise arid and semi-arid landscapes. Findings highlighted the critical role of private lands in greater sandhill crane ecology as they accounted for 78% of predicted distributions. Wetland drying observed in portions of the range from 1984 to 2022 represented an emerging ecological bottleneck that could limit future greater sandhill crane summer range. Study outcomes provide novel insight into the significance of ecosystem services provided by flood-irrigated agriculture that supported nearly 60% of the wetland resources used by birds. Findings suggest greater sandhill cranes function as an umbrella species for agroecology and climate change adaptation strategies seeking to reduce agricultural water use through improved efficiency while also maintaining distinct flood-irrigation practices supporting greater sandhill cranes and other wetland-dependent wildlife. To inform conservation design, we make our wetland and sandhill crane summering distributions publicly available as interactiveweb-basedmapping tools.
Habitat remediation followed by managed connectivity reduces unwanted changes in evolutionary trajectory of high extirpation risk populations
Authors: Lamka Gina F. , Willoughby Janna R.
Published: November 2023

As we continue to convert green spaces into roadways and buildings, connectivity between populations and biodiversity will continue to decline. In threatened and endangered species, this trend is particularly concerning because the cessation of immigration can cause increased inbreeding and loss of genetic diversity, leading to lower adaptability and higher extirpation probabilities in these populations. Unfortunately, monitoring changes in genetic diversity from management actions such as assisted migration and predicting the extent of introduced genetic variation that is needed to prevent extirpation is difficult and costly in situ. Therefore, we designed an agent-based model to link population-wide genetic variability and the influx of unique alleles via immigration to population stability and extirpation outcomes. These models showed that management of connectivity can be critical in restoring at-risk populations and reducing the effects of inbreeding depression; increased connectivity prevented extirpation for the majority of scenarios we considered (71.5% of critically endangered populations and 100% of endangered and vulnerable populations). However, the rescued populations were more similar to the migrant source population (average FSTrange 0.05 – 0.10) compared to the historical recipient population (average FSTrange 0.23 – 0.37). This means that these management actions not only recovered the populations from the effects of inbreeding depression, but they did so in a way that changed the evolutionary trajectory that was predicted and expected for these populations prior to the population crash. This change was most extreme in populations with the smallest population sizes, which are representative of critically endangered species that could reasonably be considered candidates for restored connectivity or translocation strategies. Understanding how these at-risk populations change in response to varying management interventions has broad implications for the long-term adaptability of these populations and can improve future efforts for protecting locally adapted allele complexes when connectivity is restored.
Structural Insights into Dopamine Receptor-Ligand Interactions: From Agonists to Antagonists
Authors: Barbosa Emmanuel , Clift Heather , Olson Linda , Zhu Lan , Liu Wei
Published: November 2023

This study explores the intricacies of dopamine receptor-ligand interactions, focusing on the D1R and D5R subtypes. Using molecular modeling techniques, we investigate the binding of the pan-agonist rotigotine, revealing a universal binding mode at the orthosteric binding pocket (OBP). Additionally, we analyze the stability of antagonist-receptor complexes with SKF83566 and SCH23390. By examining the impact of specific mutations on ligand-receptor interactions through computational simulations and thermostability assays, we gain insights into binding stability. Our research also delves into the structural and energetic aspects of antagonist binding to D1R and D5R in their inactive states. These findings enhance our understanding of dopamine receptor pharmacology and hold promise for drug development in central nervous system disorders, opening doors to future research and innovation in this field.
Height loss in adulthood is associated with health outcomes in later life in men and women enrolled in the 1946 UK Birth Cohort (NSHD)
Authors: Matthes Katarina L. , Staub Kaspar
Published: November 2023

Objective

To investigate the relationship between height in childhood and relative height loss in adult-hood, and to examine the association between height loss and health at age 69.

Design

Cohort study.

Setting

Data from one of the oldest ongoing cohort studies, the National Survey of Health and Development (NSHD, 1946 UK birth cohort)

Participants

2,119 study participants who completed the nurse home visit during the 24thand most recent available follow-up examination at age 69.

Main outcome measures

Linear regression models to estimate the association between measured height in childhood years relative height loss between ages 36 and 69. Logistic regression models using generalized additive models to estimate the probability of worse health at age 69 (chronic disease score, general health status, osteoarthritis, and pain while walking) in association with height loss.

Results

Between the ages of 36 and 69, men lost an average of 2.03 cm and women 2.44 cm. Women lost significantly more height than men (p<0.001). The taller the participants were at a young age, the more height they lost in adulthood. There was a significant association between height loss in adulthood on the one hand and general health, chronic disease score (in men), osteoarthritis (in men), and walking pain at age 69. These findings largely persisted after adjusting the models for overweight, sociodemo-graphic information, and lifestyle factors earlier in life.

Conclusions

Height loss seems to mirror deteriorating health as people age. Height measurement and assessment of height loss should be part of regular examinations after the age of 40 to monitor general health status, especially in the case of severe height loss.
TMS-induced plasticity improving cognitive control in OCD I: Clinical and neuroimaging outcomes from a randomised trial of rTMS for OCD
Authors: Fitzsimmons Sophie M.D.D. , Postma Tjardo , van Campen A. Dilene , Vriend Chris , Batelaan Neeltje M. , van Oppen Patricia , Hoogendoorn Adriaan W. , van der Werf Ysbrand D. , van den Heuvel Odile A.
Published: November 2023

Background

Repetitive transcranial magnetic stimulation (rTMS) is an emerging treatment option for obsessive-compulsive disorder (OCD). The neurobiological mechanisms of rTMS in OCD have, however, been incompletely characterized. We compared clinical outcomes and changes in task-based brain activation following three different rTMS stimulation protocols, all combined with exposure and response prevention (ERP).

Methods

In this three-arm proof-of-concept randomized controlled clinical trial, 61 treatment-refractory adult OCD patients received 16 sessions of rTMS immediately prior to ERP over 8 weeks, with task-based functional MRI (tb-fMRI) scans and clinical assessments pre- and post-treatment. Patients received either: high frequency (HF) rTMS to the left dorsolateral prefrontal cortex (DLPFC) (n=19 (6M/13F)); HF rTMS to the left pre-supplementary motor area (preSMA) (n=23 (10M/13F)); or control rTMS to the vertex (n=19 (6M/13F)). Changes in tb-fMRI activation pre-post treatment were compared using both a Bayesian region-of-interest and a general linear model whole-brain approach.

Results

Mean OCD symptom severity decreased significantly in all treatment groups (delta=- 10.836, p<0.001, 95% CI [-12.504, -9.168]), with no differences between groups. Response rate in the entire sample was 57.4%. Groups receiving DLPFC or preSMA rTMS showed, respectively, a decrease in planning and error processing task-related activation after treatment that was associated with symptom improvement, while individuals in the vertex rTMS group with greater symptom improvement showed an increase in inhibition-related activation.

Conclusions

PreSMA and DLPFC rTMS combined with ERP led to significant symptom improvement related to activation decreases in targeted task networks, although we observed no differences in symptom reduction between groups.

This trial was registered at clinicaltrials.gov (NCT03667807)