bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational scanning ofCRXclassifies clinical variants and reveals biochemical properties of the transcriptional effector domain
Authors: Shepherdson James L. , Granas David M. , Li Jie , Shariff Zara , Plassmeyer Stephen P. , Holehouse Alex S. , White Michael A. , Cohen Barak A. 
Published: March 2024

AbstractCone-Rod Homeobox, encoded byCRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants inCRXhave been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observedCRXgenetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of theCRXDMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
Sub-cone visual resolution by active, adaptive sampling in the human foveola
Authors: Witten Jenny L. , Lukyanova Veronika , Harmening Wolf M. 
Published: March 2024

AbstractThe foveated architecture of the human retina and the eye’s mobility enable prime spatial vision, yet the interplay between photoreceptor cell topography and the constant motion of the eye during fixation remains unexplored. Within vivofoveal cone-resolved imaging and simultaneous microscopic photo stimulation, we examined visual acuity in both eyes of 16 participants while precisely recording the stimulus path on the retina. We find that resolution thresholds were correlated with the individual retina’s sampling capacity, and exceeded what static sampling limits would predict by 18 %, on average. The length and direction of fixational drift motion, previously thought to be primarily random, played a key role in achieving this sub-cone diameter resolution. The oculomotor system finely adjusts drift behavior towards retinal areas with higher cone densities within only a few hundred milliseconds to enhance retinal sampling.
Homeotic and non-homeotic patterns in the tetrapod vertebral formula
Authors: Cerbus Rory T. , Hiratani Ichiro , Kawaguchi Kyogo 
Published: March 2024

AbstractVertebrae can be differentiated into five categories along the body axis in tetrapods, with its numerical distribution known as the vertebral formula. The vertebral formula is a principal tool for connecting development and phylogeny [1]. This is largely due to its robust relationship with the conserved clusters ofHoxgenes [2], which exhibit expression boundaries coincident with vertebral divisions [3–11]. One avenue for variations in the vertebral formula is thus throughHox-mediated homeotic transformations, which manifest as a relatively fixed sum of adjacent vertebral counts. This expectation is borne out in the mammalian thoracolumbar count [12], but to date, no similar vertebral patterns have been found. Here we conduct a systematic search by generating a large dataset of complete vertebral formulae in a diverse range of tetrapod species and probing the variance of linear combinations of vertebrae. We uncover additional mammalian homeotic patterns, but also unexpected balances between distal vertebrae not comprehensible withHox-mediated regionalization. One distal pattern appears during the progression from theropods to birds, demonstrating its phylogenetic importance. We further show that several vertebral counts correlate with posterior intergenic distances in theHoxBgene cluster. By creating a vertebral formula database and mathematically defining patterns, our work establishes a quantitative approach for comparative genomics in morphology.
Traumatic injury causes selective degeneration and TDP-43 mislocalization in human iPSC-derivedC9orf72-associated ALS/FTD motor neurons
Authors: Martin Eric J. , Santacruz Citlally , Mitevska Angela , Jones Ian E. , Krishnan Gopinath , Gao Fen-Biao , Finan John D. , Kiskinis Evangelos 
Published: March 2024

ABSTRACTA hexanucleotide repeat expansion (HRE) inC9orf72is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). However, patients with the HRE exhibit a wide disparity in clinical presentation and age of symptom onset suggesting an interplay between genetic background and environmental stressors. Neurotrauma as a result of traumatic brain or spinal cord injury has been shown to increase the risk of ALS/FTD in epidemiological studies. Here, we combine patient-specific induced pluripotent stem cells (iPSCs) with a custom-built device to deliver biofidelic stretch trauma toC9orf72patient and isogenic control motor neurons (MNs)in vitro. We find that mutant but not control MNs exhibit selective degeneration after a single incident of severe trauma, which can be partially rescued by pretreatment with aC9orf72antisense oligonucleotide. A single incident of mild trauma does not cause degeneration but leads to cytoplasmic accumulation of TDP-43 inC9orf72MNs. This mislocalization, which only occurs briefly in isogenic controls, is eventually restored inC9orf72MNs after 6 days. Lastly, repeated mild trauma ablates the ability of patient MNs to recover. These findings highlight alterations in TDP-43 dynamics inC9orf72ALS/FTD patient MNs following traumatic injury and demonstrate that neurotrauma compounds neuropathology inC9orf72ALS/FTD. More broadly, our work establishes anin vitroplatform that can be used to interrogate the mechanistic interactions between ALS/FTD and neurotrauma.
A multi-tissuede novotranscriptome assembly and relative gene expression of the vulnerable freshwater salmonidThymallus ligericus
Authors: Secci-Petretto Giulia , Weiss Steven , Gomes-dos-Santos André , Persat Henri , Machado André M. , Vasconcelos Inês , C. Castro L. Filipe , Froufe Elsa 
Published: March 2024

AbstractFreshwater ecosystems are among the most endangered worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources are a key tool to comprehend species’ adaptability and serve as the foundation for conservation initiatives. The Loire grayling,Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. It comprises fragmented populations dispersed over a small area and has been identified as a vulnerable species. Here, we provide a multi-tissuede novotranscriptome assembly ofT. ligericus. The final assembly, with a contig N50 of 1,221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible, along with structural and functional annotations and relative gene expression of five tissues. This is the first transcriptomic resource for this species, and it will serve as the foundation for future research on a species that is increasingly exposed to environmental stressors.
Investigation of the Fasciola Cinereum, Absent in BTBR mice, and Comparison with the Hippocampal Area CA2
Authors: Lee Su Hyun , Cooke Michaela E , Duan Kai Zheng , Williams Avram Sarah K , Song June , Elkahloun Abdel G , McGrady George ,   NISC Comparative Sequencing Program, Howley Austin , Samal Babru , Young W. Scott 
Published: March 2024

AbstractThe arginine vasopressin 1b receptor (Avpr1b) plays an important role in social behaviors including social learning, memory, and aggression, and is known to be a specific marker for the cornu ammonis area 2 (CA2) regions of the hippocampus. The fasciola cinereum (FC) is an anatomical region in which Avpr1b expressing neurons are prominent, but the functional roles of the FC have yet to be investigated. Surprisingly, the FC is absent in the inbred BTBR T+tf/J (BTBR) mouse strain used to study core behavioral deficits of autism. Here, we characterized and compared transcriptomic expression profiles using single nucleus RNA sequencing and identified 7 different subpopulations and heterogeneity within the dorsal CA2 (dCA2) and FC.Mef2c,involved in autism spectrum disorder, is more highly expressed in the FC. Using Hiplexin situhybridization, we examined the neuroanatomical locations of these subpopulations in the proximal and distal regions of the hippocampus. Anterograde tracing of Avpr1b neurons specific for the FC showed projections to the IG, dCA2, lacunosum molecular layer of CA1, dorsal fornix, septofibrial nuclei, and intermediate lateral septum (iLS). In contrast to the dCA2, inhibition of Avpr1b neurons in the FC by the inhibitory DREADD system during behavioral testing did not impair social memory. We performed single nucleus RNA sequencing in the dCA2 region and compared between wildtype (WT) and BTBR mice. We found that transcriptomic profiles of dCA2 neurons between BTBR and WT mice are very similar as they did not form any unique clusters; yet, we found there were differentially expressed genes between the dCA2s of BTBR and WT mice. Overall, this is a comprehensive study of the comparison of Avpr1b neuronal subpopulations between the FC and dCA2. The fact that FC is absent in BTBR mice, a mouse model for autism spectrum disorder, suggests that the FC may play a role in understanding neuropsychiatric disease.
Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy
Authors: Lichauco Carmina , Foss Eric J. , Gatbonton-Schwager Tonibelle , Athow Nelson F. , Lofts Brandon , Acob Robin , Taylor Erin , Marquez James J. , Lao Uyen , Miles Shawna , Bedalov Antonio 
Published: March 2024

AbstractThe association between late replication timing and low transcription rates in eukaryotic heterochromatin is well-known, yet the specific mechanisms underlying this link remain uncertain. InSaccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). We have previously reported that in the absence ofSIR2, a derepressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the nondisplaced MCMs. Furthermore, we found that both, activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity ofFUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication originin vivorelies on the nucleosome context shaped by a single chromatin remodeler.
Operation regimes of spinal circuits controlling locomotion and role of supraspinal drives and sensory feedback
Authors: Rybak Ilya A. , Shevtsova Natalia A. , Markin Sergey N. , Prilutsky Boris I. , Frigon Alain 
Published: March 2024

AbstractLocomotion in mammals is directly controlled by the spinal neuronal network, operating under the control of supraspinal signals and somatosensory feedback that interact with each other. However, the functional architecture of the spinal locomotor network, its operation regimes, and the role of supraspinal and sensory feedback in different locomotor behaviors, including at different speeds, remain unclear. We developed a computational model of spinal locomotor circuits receiving supraspinal drives and limb sensory feedback that could reproduce multiple experimental data obtained in intact and spinal-transected cats during tied-belt and split-belt treadmill locomotion. We provide evidence that the spinal locomotor network operates in different regimes depending on locomotor speed. In an intact system, at slow speeds (< 0.4 m/s), the spinal network operates in a non-oscillating state-machine regime and requires sensory feedback or external inputs for phase transitions. Removing sensory feedback related to limb extension prevents locomotor oscillations at slow speeds. With increasing speed and supraspinal drives, the spinal network switches to a flexor-driven oscillatory regime and then to a classical half-center regime. Following spinal transection, the model predicts that the spinal network can only operate in the state-machine regime. Our results suggest that the spinal network operates in different regimes for slow exploratory and fast escape locomotor behaviors, making use of different control mechanisms.
Engineered Flt3L Drives Tolerogenic State to Attenuate Anti-drug Antibody Responses
Authors: Alpar Aaron T. , Wallace Rachel P. , Refvik Kirsten C. , Gomes Suzana , Solanki Ani , Gray Laura T. , Slezak Anna J. , Lauterbach Abigail L. , Hesser Lauren A. , Cao Shijie , Medellín J. Emiliano Gómez , Robinson Lauren G. , Hubbell Jeffrey A. 
Published: March 2024

AbstractImmune reactions to protein drugs present substantial challenges to protein replacement for treating congenital diseases and metabolic deficiencies, due to the lack of endogenous tolerance or the protein drug’s partial or total non-human origin. We sought to transiently modify the immune environment when the adaptive response to the drug antigen is mounted to lessen future reactions upon continued therapeutic treatment, without modifying the drug itself. Herein, we characterize a recombinant fusion of the cytokine Flt3L to serum albumin and describe a novel pathway of Flt3L-mediated immune regulation. We highlight reduced activation of dendritic cells (DC) as well as an increased frequency of DCs expressing LAP, a TGF-β precursor. These effects in combination with low doses of the exogenous antigen led to less TH2 differentiation. This enabled a tolerance-biasing induction regimen to significantly decrease anti-drug antibodies upon repeated exposure to a clinically used, immunogenic fungal enzyme, rasburicase. This induction regimen reduced the Tfh compartment and increased Tfh cells expressing Foxp3 and PD-L1, suggesting a regulatory response. Overall, we introduce the use of a Flt3L variant as an induction therapeutic to modulate the innate immune response, thereby attenuating the adaptive reaction to antigenic protein drugs and addressing an unmet clinical need.
Modeling of chemo-radiotherapy targeting growing vascular tumors: a continuum-level approach
Authors: Lampropoulos Ioannis , Koutsi Marina , Kavousanakis Michail 
Published: March 2024

AbstractThe aim of this study is to demonstrate the enhanced efficiency of combined therapeutic strategies for the treatment of growing tumors, based on computational experiments of a continuous-level modeling framework. In particular, the tumor growth is simulated within a contaminated tissue and treated as a multiphase fluid of high viscosity, with each cellular species considered as a distinct fluid phase. Our model integrates the impact of chemical species on tumor dynamics, and we model –through reaction-diffusion equations– the spatio-temporal evolution of oxygen, vascular endothelial growth factor (VEGF) and chemotherapeutic agents. Simulations of a growing tumor exposed to external radiation showcase the rapid impact of radiotherapy on tumor suppression, however this effect diminishes over time. To enhance the therapeutic efficiency of radiotherapy, we investigate the combination of external radiation with the anti-VEGF drug bevacizumab and the cytotoxic drug docetaxel. Our simulations demonstrate that this synergistic approach integrates the immediate effectiveness of radiation therapy with the enduring tumor-suppressive capabilities of chemotherapy.
The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism
Authors: Fan Yani , Du Minghao , Zhang Weiwei , Deng Wei , Yang Ence , Wang Shunxian , Yan Luwen , Zhang Liao , Kang Seogchan , Steenwyk Jacob L , An Zhiqiang , Liu Xingzhong , Xiang Meichun 
Published: March 2024

AbstractNematode-trapping fungi (NTF), most of which belong to a monophyletic lineage in Ascomycota, cannibalize nematodes and other microscopic animals, raising questions regarding the types and mechanisms of genomic changes that enabled carnivorism and adaptation to the carbon-rich and nitrogen-poor environment created by the Permian-Triassic extinction event. Here, we conducted comparative genomic analyses of 21 NTF and 21 non-NTF to address these questions. Carnivorism-associated changes include expanded genes for nematode capture, infection, and consumption (e.g., adhesive proteins, CAP superfamily, eukaryotic aspartyl proteases, and serine-type peptidases). Although the link between secondary metabolite (SM) production and carnivorism remains unclear, we found that the numbers of SM gene clusters among NTF are significantly lower than those among non-NTF. Significantly expanded cellulose degradation gene families (GH5, GH7, AA9, and CBM1) and contracted genes for carbon-nitrogen hydrolases (enzymes that degrade organic nitrogen to ammonia) are likely associated with adaptation to the carbon-rich and nitrogen-poor environment. Through horizontal gene transfer events from bacteria, NTF acquired theMurgene cluster (participating in synthesizing peptidoglycan of the bacterial cell wall) andHyl(a virulence factor in animals). Disruption ofMurEreduced NTF’s ability to attract nematodes, supporting its role in carnivorism. This study provides new insights into how NTF evolved and diversified after the Permian-Triassic mass extinction event.
Role of Weight Loss Induced Prediabetes Remission in the Prevention of Type 2 Diabetes – Time to Improve Diabetes Prevention
Authors: von Schwartzenberg Reiner Jumpertz , Arreola Elsa Vazquez , Sandforth Arvid , Hanson Robert L. , Birkenfeld Andreas L. 
Published: March 2024

AbstractAims/hypothesisFor individuals with prediabetes, the current American Diabetes Association (ADA) guidelines recommend a body weight loss >7% to prevent the development of type 2 diabetes (T2D) without any glycemic target goals. However, we have recently shown that weight loss induced prediabetes remission reduces relative T2D risk by 73% within the following two years. Therefore, we investigated relative T2D risk reduction in people with weight loss vs those with weight loss and prediabetes remission in an independent cohort: the randomized controlled Diabetes Prevention Program (DPP).MethodsIndividuals who lost >7% of their body weight over the first year were included in this analysis. Of these, 416 were assigned to intensive lifestyle intervention and 64 received placebo. Remission of prediabetes was defined by normalization of fasting and 2h glucose during an oral glucose tolerance test and a normalized HbA1c according to ADA criteria. Non-remission was given when at least one of these criteria was not met. We computed Kaplan-Meier curves and compared them using log-rank tests and future T2D risk was assessed by computing the relative risk between groups.ResultsIn DPP, 480 individuals achieved a weight loss of >7% and of these 114 additionally achieved prediabetes remission. Over the period of 6 years, those who achieved weight loss and remission had a 66% lower relative risk to develop T2D compared to those who only met the 7% weight loss goal [RR=0.34, 95% CI (0.15, 0.76)]. Similarly, weight loss responders had a lower relative future T2D risk compared to weight loss non-responders [RR=0.28, 95% CI (0.13, 0.64)]. Importantly, there was only a single T2D case in weight loss responders for up to 4 years after the intervention.Conclusions/interpretationThe combination of achieving weight loss goals and prediabetes remission is most effective in reducing future T2D risk. Thus, beside weight loss goals, interventions in individuals with prediabetes should be continued until prediabetes remission is achieved and this ought to be adapted in current clinical praxis guidelines.
Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders
Authors: Jurgens Julie A. , Barry Brenda J. , Chan Wai-Man , MacKinnon Sarah , Whitman Mary C. , Matos Ruiz Paola M. , Pratt Brandon M. , England Eleina M. , Pais Lynn , Lemire Gabrielle , Groopman Emily , Glaze Carmen , Russell Kathryn A. , Singer-Berk Moriel , Di Gioia Silvio Alessandro , Lee Arthur S. , Andrews Caroline , Shaaban Sherin , Wirth Megan M. , Bekele Sarah , Toffoloni Melissa , Bradford Victoria R. , Foster Emma E. , Berube Lindsay , Rivera-Quiles Cristina , Mensching Fiona M. , Sanchis-Juan Alba , Fu Jack M. , Wong Isaac , Zhao Xuefang , Wilson Michael W. , Weisburd Ben , Lek Monkol ,   Ocular CCDD Phenotyping Consortium, Brand Harrison , Talkowski Michael E. , MacArthur Daniel G. , O’Donnell-Luria Anne , Robson Caroline D. , Hunter David G. , Engle Elizabeth C. 
Published: March 2024

ABSTRACTPurposeTo identify genetic etiologies and genotype/phenotype associations for unsolved ocular congenital cranial dysinnervation disorders (oCCDDs).MethodsWe coupled phenotyping with exome or genome sequencing of 467 pedigrees with genetically unsolved oCCDDs, integrating analyses of pedigrees, human and animal model phenotypes, andde novovariants to identify rare candidate single nucleotide variants, insertion/deletions, and structural variants disrupting protein-coding regions. Prioritized variants were classified for pathogenicity and evaluated for genotype/phenotype correlations.ResultsAnalyses elucidated phenotypic subgroups, identified pathogenic/likely pathogenic variant(s) in 43/467 probands (9.2%), and prioritized variants of uncertain significance in 70/467 additional probands (15.0%). These included known and novel variants in established oCCDD genes, genes associated with syndromes that sometimes include oCCDDs (e.g.,MYH10, KIF21B, TGFBR2, TUBB6),genes that fit the syndromic component of the phenotype but had no prior oCCDD association (e.g.,CDK13, TGFB2), genes with no reported association with oCCDDs or the syndromic phenotypes (e.g.,TUBA4A, KIF5C, CTNNA1, KLB, FGF21), and genes associated with oCCDD phenocopies that had resulted in misdiagnoses.ConclusionThis study suggests that unsolved oCCDDs are clinically and genetically heterogeneous disorders often overlapping other Mendelian conditions and nominates many candidates for future replication and functional studies.